Language：English   Publishing type：Research paper (international conference proceedings)  

DOI： 10.11517/pjsai.JSAI2024.0_4Q3IS2d05

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Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jcim.4c00172

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Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

Nanohoops, an exciting class of fluorophores with supramolecular binding abilities, have the potential to become innovative tools within biological imaging and sensing. Given the biological importance of cell membranes, incorporation...

DOI： 10.1039/d4sc03408b

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Language：English   Publishing type：Research paper (scientific journal)  

Hydroxycarboxylic acid receptors (HCAR1, HCAR2, and HCAR3) transduce Gi/o signaling upon biding to molecules such as lactic acid, butyric acid and 3-hydroxyoctanoic acid, which are associated with lipolytic and atherogenic activity, and neuroinflammation. Although many reports have elucidated the function of HCAR2 and its potential as a therapeutic target for treating not only dyslipidemia but also neuroimmune disorders such as multiple sclerosis and Parkinson's disease, the structural basis of ligand recognition and ligand-induced Gi-coupling remains unclear. Here we report three cryo-EM structures of the human HCAR2-Gi signaling complex, each bound with different ligands: niacin, acipimox or GSK256073. All three agonists are held in a deep pocket lined by residues that are not conserved in HCAR1 and HCAR3. A distinct hairpin loop at the HCAR2 N-terminus and extra-cellular loop 2 (ECL2) completely enclose the ligand. These structures also reveal the agonist-induced conformational changes propagated to the G-protein-coupling interface during activation. Collectively, the structures presented here are expected to help in the design of ligands specific for HCAR2, leading to new drugs for the treatment of various diseases such as dyslipidemia and inflammation.

DOI： 10.1038/s41467-023-42764-8

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Publishing type：Research paper (scientific journal)   Publisher：MDPI AG  

Tubulin has been recently reported to form a large family consisting of various gene isoforms; however, the differences in the molecular features of tubulin dimers composed of a combination of these isoforms remain unknown. Therefore, we attempted to elucidate the physical differences in the molecular motility of these tubulin dimers using the method of measurable pico-meter-scale molecular motility, diffracted X-ray tracking (DXT) analysis, regarding characteristic tubulin dimers, including neuronal TUBB3 and ubiquitous TUBB5. We first conducted a DXT analysis of neuronal (TUBB3-TUBA1A) and ubiquitous (TUBB5-TUBA1B) tubulin dimers and found that the molecular motility around the vertical axis of the neuronal tubulin dimer was lower than that of the ubiquitous tubulin dimer. The results of molecular dynamics (MD) simulation suggest that the difference in motility between the neuronal and ubiquitous tubulin dimers was probably caused by a change in the major contact of Gln245 in the T7 loop of TUBB from Glu11 in TUBA to Val353 in TUBB. The present study is the first report of a novel phenomenon in which the pico-meter-scale molecular motility between neuronal and ubiquitous tubulin dimers is different.

DOI： 10.3390/ijms242015423

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.jmb.2023.168189

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Language：English   Publishing type：Research paper (scientific journal)  

Mutations of G protein-coupled receptors (GPCRs) cause various human diseases, but the mechanistic details are limited. Here, we establish p.E303K in the gene encoding the endothelin receptor type A (ETAR/EDNRA) as a recurrent mutation causing mandibulofacial dysostosis with alopecia (MFDA), with craniofacial changes similar to those caused by p.Y129F. Mouse models carrying either of these missense mutations exhibited a partial maxillary-to-mandibular transformation, which was rescued by deleting the ligand endothelin 3 (ET3/EDN3). Pharmacological experiments confirmed the causative ETAR mutations as gain of function, dependent on ET3. To elucidate how an amino acid substitution far from the ligand binding site can increase ligand affinity, we used molecular dynamics (MD) simulations. E303 is located at the intracellular end of transmembrane domain 6, and its replacement by a lysine increased flexibility of this portion of the helix, thus favoring G protein binding and leading to G protein-mediated enhancement of agonist affinity. The Y129F mutation located under the ligand binding pocket reduced the sodium-water network, thereby affecting the extracellular portion of helices in favor of ET3 binding. These findings provide insight into the pathogenesis of MFDA and into allosteric mechanisms regulating GPCR function, which may provide the basis for drug design targeting GPCRs.

DOI： 10.1172/JCI151536

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Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

Abstract

Toll-like receptor 3 (TLR3) is a member of the TLR family, which plays an important role in the innate immune system and is responsible for recognizing viral double-stranded RNA (dsRNA). Previous biochemical and structural studies have revealed that a minimum length of approximately 40–50 base pairs of dsRNA is necessary for TLR3 binding and dimerization. However, efficient TLR3 activation requires longer dsRNA and the molecular mechanism underlying its dsRNA length-dependent activation remains unknown. Here, we report cryo-electron microscopy analyses of TLR3 complexed with longer dsRNA. TLR3 dimers laterally form a higher multimeric complex along dsRNA, providing the basis for cooperative binding and efficient signal transduction.

DOI： 10.1038/s41467-023-35844-2

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Other Link： https://www.nature.com/articles/s41467-023-35844-2

Language：English   Publishing type：Research paper (scientific journal)  

Based on many crystal structures of ligand complexes, much study has been devoted to understanding the molecular recognition of SARS-CoV-2 3C-like protease (3CLpro), a potent drug target for COVID-19. In this research, to extend this present static view, we examined the kinetic process of binding/unbinding of an eight-residue substrate peptide to/from 3CLpro by evaluating the path ensemble with the weighted ensemble simulation. The path ensemble showed the mechanism of how a highly flexible peptide folded into the bound form. At the early stage, the dominant motion was the diffusion on the protein surface showing a broad distribution, whose center was led into the cleft of the chymotrypsin fold. We observed a definite sequential formation of the hydrogen bonds at the later stage occurring in the cleft, initiated between Glu166 (3CLpro) and P3_Val (peptide), followed by binding to the oxyanion hole and completed by the sequence-specific recognition at P1_Gln.

DOI： 10.1021/acs.jcim.2c00946

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Language：English   Publishing type：Research paper (scientific journal)  

UNLABELLED: SARS-CoV-2 3C-like protease (3CLpro), a potential therapeutic target for COVID-19, consists of a chymotrypsin fold and a C-terminal α-helical domain (domain III), the latter of which mediates dimerization required for catalytic activation. To gain further understanding of the functional dynamics of SARS-CoV-2 3CLpro, this review extends the scope to the comparative study of many crystal structures of proteases having the chymotrypsin fold (clan PA of the MEROPS database). First, the close correspondence between the zymogen-enzyme transformation in chymotrypsin and the allosteric dimerization activation in SARS-CoV-2 3CLpro is illustrated. Then, it is shown that the 3C-like proteases of family Coronaviridae (the protease family C30), which are closely related to SARS-CoV-2 3CLpro, have the same homodimeric structure and common activation mechanism via domain III mediated dimerization. The survey extended to order Nidovirales reveals that all 3C-like proteases belonging to Nidovirales have domain III, but with various chain lengths, and 3CLpro of family Mesoniviridae (family C107) has the same homodimeric structure as that of C30, even though they have no sequence similarity. As a reference, monomeric 3C proteases belonging to the more distant family Picornaviridae (family C3) lacking domain III are compared with C30, and it is shown that the 3C proteases are rigid enough to maintain their structures in the active state. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12551-022-01020-x.

DOI： 10.1007/s12551-022-01020-x

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Language：English   Publishing type：Research paper (scientific journal)  

Semaphorins constitute a large family of secreted and membrane-bound proteins that signal through cell-surface receptors, plexins. Semaphorins generally use low-affinity protein-protein interactions to bind with their specific plexin(s) and regulate distinct cellular processes such as neurogenesis, immune response, and organogenesis. Sema6D is a membrane-bound semaphorin that interacts with class A plexins. Sema6D exhibited differential binding affinities to class A plexins in prior cell-based assays, but the molecular mechanism underlying this selectivity is not well understood. Therefore, we performed hybrid in vitro/in silico analysis to examine the binding mode of Sema6D to class A plexins and to identify residues that give rise to the differential affinities and thus contribute to the selectivity within the same class of semaphorins. Our biophysical binding analysis indeed confirmed that Sema6D has a higher affinity for Plexin-A1 than for other class A plexins, consistent with the binding selectivity observed in the previous cell-based assays. Unexpectedly, our present crystallographic analysis of the Sema6D-Plexin-A1 complex showed that the pattern of polar interactions is not interaction-specific because it matches the pattern in the prior structure of the Sema6A-Plexin-A2 complex. Thus, we performed in silico alanine scanning analysis and discovered hotspot residues that selectively stabilized the Sema6D-Plexin-A1 pair via Van der Waals interactions. We then validated the contribution of these hotspot residues to the variation in binding affinity with biophysical binding analysis and molecular dynamics simulations on the mutants. Ultimately, our present results suggest that shape complementarity in the binding interfaces is a determinant for binding selectivity.

DOI： 10.1002/pro.4452

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jcim.2c00987

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Language：English   Publishing type：Research paper (scientific journal)  

Hydration free energy (HFE) is a key factor in improving protein-ligand binding free energy (BFE) prediction accuracy. The HFE itself can be calculated using the three-dimensional reference interaction model (3D-RISM); however, the BFE predictions solely evaluated using 3D-RISM are not correlated to the experimental BFE for abundant protein-ligand pairs. In this study, to predict the BFE for multiple sets of protein-ligand pairs, we propose a machine learning approach incorporating the HFEs obtained using 3D-RISM, termed 3D-RISM-AI. In the learning process, structural metrics, intra-/intermolecular energies, and HFEs obtained via 3D-RISM of ∼4000 complexes in the PDBbind database (ver. 2018) were used. The BFEs predicted using 3D-RISM-AI were well correlated to the experimental data (Pearson's correlation coefficient of 0.80 and root-mean-square error of 1.91 kcal/mol). As important factors for the prediction, the difference in the solvent accessible surface area between the bound and unbound structures and the hydration properties of the ligands were detected during the learning process.

DOI： 10.1021/acs.jpcb.2c03384

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Language：English   Publishing type：Research paper (scientific journal)  

The coronavirus membrane protein (M) is the most abundant viral structural protein and plays a central role in virus assembly and morphogenesis. However, the process of M protein-driven virus assembly are largely unknown. Here, we report the cryo-electron microscopy structure of the SARS-CoV-2 M protein in two different conformations. M protein forms a mushroom-shaped dimer, composed of two transmembrane domain-swapped three-helix bundles and two intravirion domains. M protein further assembles into higher-order oligomers. A highly conserved hinge region is key for conformational changes. The M protein dimer is unexpectedly similar to SARS-CoV-2 ORF3a, a viral ion channel. Moreover, the interaction analyses of M protein with nucleocapsid protein (N) and RNA suggest that the M protein mediates the concerted recruitment of these components through the positively charged intravirion domain. Our data shed light on the M protein-driven virus assembly mechanism and provide a structural basis for therapeutic intervention targeting M protein.

DOI： 10.1038/s41467-022-32019-3

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Language：English  

DOI： 10.1021/jacs.2c07339

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Language：English   Publishing type：Research paper (scientific journal)  

Inspired by mechanosensitive potassium channels found in nature, we developed a fluorinated amphiphilic cyclophane composed of fluorinated rigid aromatic units connected via flexible hydrophilic octa(ethylene glycol) chains. Microscopic and emission spectroscopic studies revealed that the cyclophane could be incorporated into the hydrophobic layer of the lipid bilayer membranes and self-assembled to form a supramolecular transmembrane ion channel. Current recording measurements using cyclophane-containing planer lipid bilayer membranes successfully demonstrated an efficient transmembrane ion transport. We also demonstrated that the ion transport property was sensitive to the mechanical forces applied to the membranes. In addition, ion transport assays using pH-sensitive fluorescence dye revealed that the supramolecular channel possesses potassium ion selectivity. We also performed all-atom hybrid quantum-mechanical/molecular mechanical simulations to assess the channel structures at atomic resolution and the mechanism of selective potassium ion transport. This research demonstrated the first example of a synthetic mechanosensitive potassium channel, which would open a new door to sensing and manipulating biologically important processes and purification of key materials in industries.

DOI： 10.1021/jacs.2c04118

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Language：English   Publishing type：Research paper (scientific journal)  

Membrane permeability of cyclic peptides is an important factor in drug design. To investigate the membrane permeability of cyclic peptides using molecular dynamics (MD) simulations, the accurate force fields for unnatural amino acids present in the cyclic peptides are required. Therefore, we developed the CHARMM force fields of the unnatural amino acids present in cyclosporin A (CsA), a cyclic peptide used as an immune suppressor. Especially for N-methyl amino acids, which contribute to the membrane permeability of cyclic peptides, we developed a grid correction map (CMAP) of the energy surface using the φ and ψ dihedral angles in the main chain of CsA. To validate the developed force field, we performed MD simulations, including the generalized replica exchange with solute tempering method, of CsA in water and chloroform solvents. The conformations of CsA in water and chloroform sampled using the developed force field were consistent with those of the experimental results of the solution nuclear magnetic resonance spectroscopy.

DOI： 10.2142/biophysico.bppb-v19.0045

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Language：English   Publishing type：Research paper (scientific journal)  

The 3C-like protease (3CLpro) of SARS-CoV-2 is a potential therapeutic target for COVID-19. Importantly, it has an abundance of structural information solved as a complex with various drug candidate compounds. Collecting these crystal structures (83 Protein Data Bank (PDB) entries) together with those of the highly homologous 3CLpro of SARS-CoV (101 PDB entries), we constructed the crystal structure ensemble of 3CLpro to analyze the dynamic regulation of its catalytic function. The structural dynamics of the 3CLpro dimer observed in the ensemble were characterized by the motions of four separate loops (the C-loop, E-loop, H-loop, and Linker) and the C-terminal domain III on the rigid core of the chymotrypsin fold. Among the four moving loops, the C-loop (also known as the oxyanion binding loop) causes the order (active)-disorder (collapsed) transition, which is regulated cooperatively by five hydrogen bonds made with the surrounding residues. The C-loop, E-loop, and Linker constitute the major ligand binding sites, which consist of a limited variety of binding residues including the substrate binding subsites. Ligand binding causes a ligand size dependent conformational change to the E-loop and Linker, which further stabilize the C-loop via the hydrogen bond between the C-loop and E-loop. The T285A mutation from SARS-CoV 3CLpro to SARS-CoV-2 3CLpro significantly closes the interface of the domain III dimer and allosterically stabilizes the active conformation of the C-loop via hydrogen bonds with Ser1 and Gly2; thus, SARS-CoV-2 3CLpro seems to have increased activity relative to that of SARS-CoV 3CLpro.

DOI： 10.1016/j.jmb.2021.167324

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.bmc.2021.116500

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Language：English   Publishing type：Research paper (scientific journal)  

Ubiquitin-specific protease 8 (USP8) is a deubiquitinating enzyme involved in multiple membrane trafficking pathways. The enzyme activity is inhibited by binding to 14-3-3 proteins. Mutations in the 14-3-3-binding motif in USP8 are related to Cushing's disease. However, the molecular basis of USP8 activity regulation remains unclear. This study identified amino acids 645-684 of USP8 as an autoinhibitory region, which might interact with the catalytic USP domain, as per the results of pull-down and single-molecule FRET assays performed in this study. In silico modelling indicated that the region forms a WW-like domain structure, plugs the catalytic cleft, and narrows the entrance to the ubiquitin-binding pocket. Furthermore, 14-3-3 inhibited USP8 activity partly by enhancing the interaction between the WW-like and USP domains. These findings provide the molecular basis of USP8 autoinhibition via the WW-like domain. Moreover, they suggest that the release of autoinhibition may underlie Cushing's disease due to USP8 mutations.

DOI： 10.1038/s42003-021-02802-x

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Language：English   Publishing type：Research paper (scientific journal)  

The mineralocorticoid receptor (MR) is a nuclear receptor whose endogenous ligands are mineralocorticoids, a type of steroid hormone. The activating S810L mutation is known to cause severe early-onset and pregnancy-related hypertension. Progesterone binds to the wild-type (WT) MR as a passive antagonist with fast dissociation; however, it binds to the S810L mutant as a full agonist with slow dissociation. The switch in the biological activity of progesterone is considered to be one of the causes of the disease. First, we used steered molecular dynamics simulations to analyze the dissociation process of progesterone for the WT and the S810L mutant. Progesterone in the WT dissociated from the ligand-binding pocket with a weak force in comparison with progesterone in the S810L mutant due to the large inflow of water molecules into the pocket. Therefore, we used conventional molecular dynamics simulations for the ligand-free structures of the WT and the S810L mutant to investigate the effect of the mutation on the inflow of water. In the WT, water molecules enter the ligand-binding pocket in two ways: in the vicinity of (i) Arg817 and (ii) Ser810. In contrast, few water molecules enter the pocket in the S810L mutant because of the large size and hydrophobic nature of the Leu810 side chain. Fast dissociation is a common feature among passive antagonists of MR; therefore, we inferred that the water inflow could be responsible for the dissociation kinetics of progesterone in the WT and the S810L mutant.

DOI： 10.1021/acs.jcim.1c00389

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Language：English   Publishing type：Research paper (scientific journal)  

The vitamin D receptor ligand-binding domain (VDR-LBD) undergoes conformational changes upon ligand binding. In this nuclear receptor family, agonistic or antagonistic activities are controlled by the conformation of the helix (H)12. However, all crystal structures of VDR-LBD reported to date correspond to the active H12 conformation, regardless of agonist/antagonist binding. To understand the mechanism of VDR-LBD regulation structurally, conformational samplings of agonist- and antagonist-bound rat VDR-LBD were performed using the generalized replica exchange with solute tempering (gREST) method. The gREST simulations demonstrated different structural responses of rat VDR-LBD to agonist or antagonist binding, whereas in conventional molecular dynamics simulations, the conformation was the same as that of the crystal structures, regardless of agonist/antagonist binding. In the gREST simulations, a spontaneous conformational change of H12 was observed only for the antagonist complex. The different responses to agonist/antagonist binding were attributed to hydrophobic core formation at the ligand-binding pocket and cooperative rearrangements of H11. The gREST method can be applied to the examination of structure-activity relationships for multiple VDR-LBD ligands.

DOI： 10.1021/acs.jcim.1c00534

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Publisher：Research Square Platform LLC  

Abstract

Low-resolution electron density maps can pose a major obstacle in the determination and use of protein structures. Herein, we describe a novel method, quality assessment based on an electron density map (QAEmap), that evaluates local protein structures determined by X-ray crystallography and corrects structural errors using low-resolution maps. QAEmap uses a three-dimensional deep convolutional neural network with electron density maps and their corresponding coordinates as input and predicts the correlation between the local structure and the putative high-resolution experimental electron density map. This estimates how well the structure fits the high-resolution map. Further, we propose that this method may be applied to evaluate ligand binding, which can be difficult to determine at low resolution.

DOI： 10.21203/rs.3.rs-687363/v1

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Other Link： https://www.researchsquare.com/article/rs-687363/v1.html

Language：English   Publishing type：Research paper (scientific journal)  

Antibody labeling has been conducted extensively for structure determination using both X-ray crystallography and electron microscopy (EM). However, establishing target-specific antibodies is a prerequisite for applying antibody-assisted structural analysis. To expand the applicability of this strategy, an alternative method has been developed to prepare an antibody complex by inserting an exogenous epitope into the target. It has already been demonstrated that the Fab of the NZ-1 monoclonal antibody can form a stable complex with a target containing a PA12 tag as an inserted epitope. Nevertheless, it was also found that complex formation through the inserted PA12 tag inevitably caused structural changes around the insertion site on the target. Here, an attempt was made to improve the tag-insertion method, and it was consequently discovered that an alternate tag (PA14) could replace various loops on the target without inducing large structural changes. Crystallographic analysis demonstrated that the inserted PA14 tag adopts a loop-like conformation with closed ends in the antigen-binding pocket of the NZ-1 Fab. Due to proximity of the termini in the bound conformation, the more optimal PA14 tag had only a minor impact on the target structure. In fact, the PA14 tag could also be inserted into a sterically hindered loop for labeling. Molecular-dynamics simulations also showed a rigid structure for the target regardless of PA14 insertion and complex formation with the NZ-1 Fab. Using this improved labeling technique, negative-stain EM was performed on a bacterial site-2 protease, which enabled an approximation of the domain arrangement based on the docking mode of the NZ-1 Fab.

DOI： 10.1107/S2059798321002527

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TFIIH is a crucial transcription and DNA repair factor consisting of the seven-subunit core. The core subunit p62 contains a pleckstrin homology domain (PH-D), which is essential for locating TFIIH at transcription initiation and DNA damage sites, and two BSD (BTF2-like transcription factors, synapse-associated proteins and DOS2-like proteins) domains. A recent cryo-electron microscopy (cryo-EM) structure of human TFIIH visualized most parts of core, except for the PH-D. Here, by nuclear magnetic resonance spectroscopy we have established the solution structure of human p62 PH-D connected to the BSD1 domain by a highly flexible linker, suggesting the flexibility of PH-D in TFIIH. Based on this dynamic character, the PH-D was modeled in the cryo-EM structure to obtain the whole human TFIIH core structure, which indicates that the PH-D moves around the surface of core with a specific but limited spatial distribution; these dynamic structures were refined by molecular dynamics (MD) simulations. Furthermore, we built models, also refined by MD simulations, of TFIIH in complex with five p62-binding partners, including transcription factors TFIIEα, p53 and DP1, and nucleotide excision repair factors XPC and UVSSA. The models explain why the PH-D is crucially targeted by these factors, which use their intrinsically disordered acidic regions for TFIIH recruitment.

DOI： 10.1093/nar/gkaa1045

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Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/asia.202001415

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Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/asia.202001106

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Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/asia.202001106

Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

<title>Abstract</title>
Toll-like receptor 7 (TLR7) recognizes both microbial and endogenous RNAs and nucleosides. Aberrant activation of TLR7 has been implicated in several autoimmune diseases including systemic lupus erythematosus (SLE). Here, by modifying potent TLR7 agonists, we develop a series of TLR7-specific antagonists as promising therapeutic agents for SLE. These compounds protect mice against lethal autoimmunity. Combining crystallography and cryo-electron microscopy, we identify the open conformation of the receptor and reveal the structural equilibrium between open and closed conformations that underlies TLR7 antagonism, as well as the detailed mechanism by which TLR7-specific antagonists bind to their binding pocket in TLR7. Our work provides small-molecule TLR7-specific antagonists and suggests the TLR7-targeting strategy for treating autoimmune diseases.

DOI： 10.1038/s41467-020-19025-z

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Other Link： http://www.nature.com/articles/s41467-020-19025-z

Language：English   Publishing type：Research paper (scientific journal)   Publisher：John Wiley and Sons Inc.  

Hydration is a critical factor in the ligand binding process. Herein, to examine the hydration states of ligand binding sites, the three-dimensional distribution function for the water oxygen site, gO(r), is computed for 3,706 ligand-free protein structures based on the corresponding small molecule–protein complexes using the 3D-RISM theory. For crystallographic waters (CWs) close to the ligand, gO(r) reveals that several CWs are stabilized by interaction networks formed between the ligand, CW, and protein. Based on the gO(r) for the crystallographic binding pose of the ligand, hydrogen bond interactions are dominant in the highly hydrated regions while weak interactions such as CH-O are dominant in the moderately hydrated regions. The polar heteroatoms of the ligand occupy the highly hydrated and moderately hydrated regions in the crystallographic (correct) and wrongly docked (incorrect) poses, respectively. Thus, the gO(r) of polar heteroatoms may be used to distinguish the correct binding poses.

DOI： 10.1002/jcc.26406

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.molliq.2020.114129

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Here, we have constructed neural network-based models that predict atomic partial charges with high accuracy at low computational cost. The models were trained using high-quality data acquired from quantum mechanics calculations using the fragment molecular orbital method. We have succeeded in obtaining highly accurate atomic partial charges for three representative molecular systems of proteins, including one large biomolecule (approx. 2000 atoms). The novelty of our approach is the ability to take into account the electronic polarization in the system, which is a system-dependent phenomenon, being important in the field of drug design. Our high-precision models are useful for the prediction of atomic partial charges and expected to be widely applicable in structure-based drug designs such as structural optimization, high-speed and high-precision docking, and molecular dynamics calculations.

DOI： 10.1021/acs.jcim.0c00273

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During homologous recombination, Rad51 forms a nucleoprotein filament on single-stranded DNA to promote DNA strand exchange. This filament binds to double-stranded DNA (dsDNA), searches for homology, and promotes transfer of the complementary strand, producing a new heteroduplex. Strand exchange proceeds via two distinct three-strand intermediates, C1 and C2. C1 contains the intact donor dsDNA whereas C2 contains newly formed heteroduplex DNA. Here, we show that the conserved DNA binding motifs, loop 1 (L1) and loop 2 (L2) in site I of Rad51, play distinct roles in this process. L1 is involved in formation of the C1 complex whereas L2 mediates the C1-C2 transition, producing the heteroduplex. Another DNA binding motif, site II, serves as the DNA entry position for initial Rad51 filament formation, as well as for donor dsDNA incorporation. Our study provides a comprehensive molecular model for the catalytic process of strand exchange mediated by eukaryotic RecA-family recombinases.

DOI： 10.1038/s41467-020-16750-3

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Biological membranes play pivotal roles in the cellular activities. Transmembrane proteins are the central molecules that conduct membrane-mediated biochemical functions such as signal transduction and substance transportation. Not only the molecular functions but also the supramolecular properties of the transmembrane proteins such as self-assembly, delocalization, orientation and signal response are essential for controlling cellular activities. Here we report anisotropic ligand responses of a synthetic multipass transmembrane ion channel. An unsymmetrical molecular structure allows for oriented insertion of the synthetic amphiphile to a bilayer by addition to a pre-formed membrane. Complexation with a ligand prompts ion transportation by forming a supramolecular channel, and removal of the ligand deactivates the transportation function. Biomimetic regulation of the synthetic channel by agonistic and antagonistic ligands is also demonstrated not only in an artificial membrane but also in a biological membrane of a living cell.

DOI： 10.1038/s41467-020-16770-z

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.jmb.2020.05.006

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Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

DOI： 10.1063/1.5140499

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Publisher：Cold Spring Harbor Laboratory  

Abstract

During homologous recombination, Rad51 forms a nucleoprotein filament on single-stranded DNA to promote DNA strand exchange. This filament binds to double-stranded DNA (dsDNA), searches for homology, and promotes transfer of the complementary strand, producing a new heteroduplex. Strand exchange proceeds via two distinct three-strand intermediates, C1 and C2. C1 contains the intact donor dsDNA whereas C2 contains newly formed heteroduplex DNA. Here, we show that conserved DNA binding motifs, loop 1 (L1) and loop 2 (L2) in site I of Rad51, play distinct roles in this process. L1 is involved in formation of the C1 complex whereas L2 mediates the C1-C2 transition, producing the heteroduplex. Another DNA binding motif, site II, serves as the DNA entry position for initial Rad51 filament formation, as well as for second donor dsDNA incorporation. Our study provides a comprehensive molecular model for the catalytic process of strand exchange mediated by eukaryotic RecA family recombinases.

DOI： 10.1101/839324

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© 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc. We propose a novel force-field-parametrization procedure that fits the parameters of potential functions in a manner that the pair distribution function (DF) of molecules derived from candidate parameters can reproduce the given target DF. Conventionally, approaches to minimize the difference between the candidate and target DFs employ radial DFs (RDF). RDF itself has been reported to be insufficient for uniquely identifying the parameters of a molecule. To overcome the weakness, we introduce energy DF (EDF) as a target DF, which describes the distribution of the pairwise energy of molecules. We found that the EDF responds more sensitively to a small perturbation in the pairwise potential parameters and provides better fitting accuracy compared to that of RDF. These findings provide valuable insights into a wide range of coarse graining methods, which determine parameters using information obtained from a higher-level calculation than that of the developed force field. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

DOI： 10.1002/jcc.26035

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.molliq.2019.111374

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Language：English   Publishing type：Research paper (scientific journal)  

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Language：English  

The combination of molecular dynamics (MD) simulations and small-angle X-ray scattering (SAXS), called the MD-SAXS method, is efficient for investigating protein dynamics. To overcome the time-scale limitation of all-atom MD simulations, coarse-grained (CG) representations are often utilized for biomolecular simulations. In this study, we propose a method to combine CG MD simulations with SAXS, termed the CG-MD-SAXS method. In the CG-MD-SAXS method, the scattering factors of CG particles for proteins and nucleic acids are evaluated using high-resolution structural data in the Protein Data Bank, and the excluded volume and the hydration shell are modeled using two adjustable parameters to incorporate solvent effects. To avoid overfitting, only the two parameters are adjusted for an entire structure ensemble. To verify the developed method, theoretical SAXS profiles for various proteins, DNA/RNA, and a protein-RNA complex are compared with both experimental profiles and theoretical profiles obtained by the all-atom representation. In the present study, we applied the CG-MD-SAXS method to the Swi5-Sfr1 complex and three types of nucleosomes to obtain reliable ensemble models consistent with the experimental SAXS data.

DOI： 10.2142/biophysico.16.0_377

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DOI： 10.3389/fphys.2019.00046

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Nature Publishing Group  

Metabolites generated via oxygenation of the omega-3 double bond (omega-3 oxygenation) in eicosapentaenoic acid (EPA) have recently been identified as novel anti-inflammatory lipid mediators. Therefore, oxygenase(s) responsible for this metabolic pathway are of particular interest. We performed genome-wide screening of mouse cytochrome P450 (CYP) isoforms to explore enzymes involved in omega-3 oxygenation of EPA. As a result, 5 CYP isoforms (mouse Cyp1a2, 2c50, 4a12a, 4a12b, and 4f18) were selected and identified to confer omega-3 epoxidation of EPA to yield 17,18-epoxyeicosatetraenoic acid (17,18-EpETE). Stereoselective production of 17,18-EpETE by each CYP isoform was confirmed, and molecular modeling indicated that chiral differences stem from different EPA binding conformations in the catalytic domains of respective CYP enzymes.

DOI： 10.1038/s41598-018-26325-4

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DOI： 10.1021/acs.jctc.8b00280

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpcb.8b00443

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Language：English   Publisher：Springer Verlag  

Protein functions require specific structures frequently coupled with conformational changes. The scale of the structural dynamics of proteins spans from the atomic to the molecular level. Theoretically, all-atom molecular dynamics (MD) simulation is a powerful tool to investigate protein dynamics because the MD simulation is capable of capturing conformational changes obeying the intrinsically structural features. However, to study long-timescale dynamics, efficient sampling techniques and coarse-grained (CG) approaches coupled with all-atom MD simulations, termed multiscale MD simulations, are required to overcome the timescale limitation in all-atom MD simulations. Here, we review two examples of rotary motor proteins examined using free energy landscape (FEL) analysis and CG-MD simulations. In the FEL analysis, FEL is calculated as a function of reaction coordinates, and the long-timescale dynamics corresponding to conformational changes is described as transitions on the FEL surface. Another approach is the utilization of the CG model, in which the CG parameters are tuned using the fluctuation matching methodology with all-atom MD simulations. The long-timespan dynamics is then elucidated straightforwardly by using CG-MD simulations.

DOI： 10.1007/s12551-017-0373-4

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：eLife Sciences Publications Ltd  

The multidrug transporter AcrB transports a broad range of drugs out of the cell by means of the proton-motive force. The asymmetric crystal structure of trimeric AcrB suggests a functionally rotating mechanism for drug transport. Despite various supportive forms of evidence from biochemical and simulation studies for this mechanism, the link between the functional rotation and proton translocation across the membrane remains elusive. Here, calculating the minimum free energy pathway of the functional rotation for the complete AcrB trimer, we describe the structural and energetic basis behind the coupling between the functional rotation and the proton translocation at atomic resolution. Free energy calculations show that protonation of Asp408 in the transmembrane portion of the drug-bound protomer drives the functional rotation. The conformational pathway identifies vertical shear motions among several transmembrane helices, which regulate alternate access of water in the transmembrane as well as peristaltic motions that pump drugs in the periplasm.

DOI： 10.7554/eLife.31715

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：International Union of Crystallography  

Ionic scattering factors of atoms that compose biological molecules have been computed by the multi-configuration Dirac-Fock method. These ions are chemically unstable and their scattering factors had not been reported except for O-. Yet these factors are required for the estimation of partial charges in protein molecules and nucleic acids. The electron scattering factors of these ions are particularly important as the electron scattering curves vary considerably between neutral and charged atoms in the spatial-resolution range explored in structural biology. The calculated X-ray and electron scattering factors have then been parameterized for the major scattering curve models used in X-ray and electron protein crystallography and single-particle cryo-EM. The X-ray and electron scattering factors and the fitting parameters are presented for future reference.

DOI： 10.1107/S2052252518005237

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Language：Japanese   Publisher：THE VITAMIN SOCIETY OF JAPAN  

DOI： 10.20632/vso.92.1_18

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Other Link： https://ndlsearch.ndl.go.jp/books/R000000004-I028798270

DOI： 10.1007/978-981-13-2200-6_15

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Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

<p>We unravel the physical origins of the large difference between cellobiose and maltose, which consist of two β-1,4 and α-1,4 linked <sc>d</sc>-glucose units, respectively, in terms of the solubility in water.</p>

DOI： 10.1039/c8cp04377a

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：CELL PRESS  

The proper location and timing of Dnmt1 activation are essential for DNA methylation maintenance. We demonstrate here that Dnmt1 utilizes two-monoubiquitylated histone H3 as a unique ubiquitin mark for its recruitment to and activation at DNA methylation sites. The crystal structure of the replication foci targeting sequence (RFTS) of Dnmt1 in complex with H3-K18Ub/23Ub reveals striking differences to the known ubiquitin-recognition structures. The two ubiquitins are simultaneously bound to the RFTS with a combination of canonical hydrophobic and atypical hydrophilic interactions. The C-lobe of RFTS, together with the K23Ub surface, also recognizes the N-terminal tail of H3. The binding of H3K18Ub/23Ub results in spatial rearrangement of two lobes in the RFTS, suggesting the opening of its active site. Actually, incubation of Dnmt1 with H3K18Ub/23Ub increases its catalytic activity in vitro. Our results therefore shed light on the essential role of a unique ubiquitin-binding module in DNA methylation maintenance.

DOI： 10.1016/j.molcel.2017.09.037

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ACADEMIC PRESS INC ELSEVIER SCIENCE  

Direct dissection of the angles of single fluorophores under an optical microscope has been a challenging approach to study the dynamics of proteins in an aqueous solution. For angle quantifications of single substrates, however, there was only one report (Nishizaka et al., 2014) because of difficulties of construction of experimental systems with active proteins working at the single-molecule level. We here show precise estimation of orientation of single fluorescent nucleotides bound to single tubulins that comprise microtubule. When single -headed kinesins immobilized on a glass surface drive the sliding of microtubules, microtubules show corkscrewing with regular pitches (Yajima et al., 2005 & 2008). We found, by using a three-dimensional tracking microscope, that S8A mutant kinesin also showed precise corkscrewing with a 330-m pitch, which is 13% longer than that of the wild type. The assay with the mutant was combined with a defocused imaging technique to visualize the rotational behavior of fluorescent nucleotide bound to corkscrewing microtubule. Notably, the defocused pattern of single TAMRA-GTP periodically changed, precisely correlating to its precession movement. The time course of the change in the fluorophore angle projected to the xy-plane enabled to estimate both the fluorophore orientation against microtubule axis and the precision of angle-determination of analyses system. The orientation showed main distribution with peaks at -40, 50 and 60. To identify their molecular conformations, the rigorous docking simulations were performed using an atomic-level structure modeled by fitting x-ray crystal structures to the cryo-electron microscopy map. Among isomers, 2'-O-EDA-GDP labeled with 5- or 6-TAMRA were mainly specified as possible candidates as a substrate, which suggested the hydrolysis of TAMRA-GTP by tubulins. (C) 2017 Elsevier Inc. All rights reserved.

DOI： 10.1016/j.bbrc.2017.01.165

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：CELL PRESS  

Enterococcus hirae V-1-ATPase is a molecular motor composed of the A(3)B(3) hexamer ring and the central stalk. In association with ATP hydrolysis, three catalytic AB pairs in the A(3)B(3) ring undergo conformational changes, which lead to a 120 degrees rotation of the central stalk. To understand how the conformational changes of three catalytic pairs induce the 120 degrees rotation of the central stalk, we performed multiscale molecular dynamics (MD) simulations in which coarse-grained and all-atom MD simulations were combined using a fluctuation matching methodology. During the rotation, a catalytic AB pair spontaneously adopted an intermediate conformation, which was not included in the initial inputs of the simulations and was essentially close to the "bindable-like'' structure observed in a recently solved crystal structure. Furthermore, the creation of a space between the bindable-like and tight pairs was required for the central stalk to rotate without steric hindrance. These cooperative rearrangements of the three catalytic pairs are crucial for the rotation of the central stalk.

DOI： 10.1016/j.bpj.2017.01.029

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Language：Japanese   Publisher：(公社)日本薬学会  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The configurational entropy of solute molecules is a crucially important quantity to study various biophysical processes. Consequently, it is necessary to establish an efficient quantitative computational method to calculate configurational entropy as accurately as possible. In the present paper, we investigate the quantitative performance of the quasi-harmonic and related computational methods, including widely used methods implemented in popular molecular dynamics (MD) software packages, compared with the Clausius method, which is capable of accurately computing the change of the configurational entropy upon temperature change. Notably, we focused on the choice of the coordinate systems (i.e., internal or Cartesian coordinates). The Boltzmann-quasi-harmonic (BQH) method using internal coordinates outperformed all the six methods examined here. The introduction of improper torsions in the BQH method improves its performance, and anharmonicity of proper torsions in proteins is identified to be the origin of the superior performance of the BQH method. In contrast, widely used methods implemented in MD packages show rather poor performance. In addition, the enhanced sampling of replica-exchange MD simulations was found to be efficient for the convergent behavior of entropy calculations. Also in folding/unfolding transitions of a small protein, Chignolin, the BQH method was reasonably accurate. However, the independent term without the correlation term in the BQH method was most accurate for the folding entropy among the methods considered in this study, because the QH approximation of the correlation term in the BQH method was no longer valid for the divergent unfolded structures.

DOI： 10.1021/acs.jctc.6b00563

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Vitamin D receptor (VDR) controls the expression of numerous genes through the conformational change caused by binding 1 alpha,25-dihydroxyvitamin D-3. Helix 12 in the ligand-lpinding domain (LBD) is key to regulating VDR activation. The structures of apo VDR-LBD and the VDR-LBD antagonist complex are unclear. Here, we reveal their unprecedented structures in solution using a hybrid method combining small-angle X-ray scattering and molecular dynamics simulations. In apo rat VDR-LBD, helix 12 is partially unraveled, and it is positioned around the canonical active position and fluctuates. Helix 11 greatly bends toward the outside at Q396, creating a kink In the rat VDR-LBD/antagonist complex, helix 12 does not generate the activation function 2 surface, arid loop 1112 is remarkably flexible compared to that in the apo rat VDR-LBD. On the basis of these structural insights, we propose a "folding-door model" to deseribe the mechanism of agonism/antagonism of VDR-LBD,

DOI： 10.1021/acs.jmedchem.6b00682

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL ACAD SCIENCES  

The dystrophin glycoprotein complex, which connects the cell membrane to the basement membrane, is essential for a variety of biological events, including maintenance of muscle integrity. An O-mannose-type GalNAc-beta 1,3-GlcNAc-beta 1,4-(phosphate-6)-Man structure of alpha-dystroglycan (alpha-DG), a subunit of the complex that is anchored to the cell membrane, interacts directly with laminin in the basement membrane. Reduced glycosylation of alpha-DG is linked to some types of inherited muscular dystrophy; consistent with this relationship, many disease-related mutations have been detected in genes involved in O-mannosyl glycan synthesis. Defects in protein O-linked mannose beta 1,2-N-acetylglucosaminyltransferase 1 (POMGnT1), a glycosyltransferase that participates in the formation of GlcNAc-beta 1,2-Man glycan, are causally related to muscle-eye-brain disease (MEB), a congenital muscular dystrophy, although the role of POMGnT1 in postphosphoryl modification of GalNAc-beta 1,3-GlcNAc-beta 1,4-(phosphate-6)- Man glycan remains elusive. Our crystal structures of POMGnT1 agreed with our previous results showing that the catalytic domain recognizes substrate O-mannosylated proteins via hydrophobic interactions with little sequence specificity. Unexpectedly, we found that the stem domain recognizes the beta-linked GlcNAc of O-mannosyl glycan, an enzymatic product of POMGnT1. This interaction may recruit POMGnT1 to a specific site of alpha-DG to promote GlcNAc-beta 1,2-Man clustering and also may recruit other enzymes that interact with POMGnT1, e.g., fukutin, which is required for further modification of the GalNAc-beta 1,3-GlcNAc-beta 1,4-(phosphate-6)-Man glycan. On the basis of our findings, we propose a mechanism for the deficiency in postphosphoryl modification of the glycan observed in POMGnT1-KO mice and MEB patients.

DOI： 10.1073/pnas.1525545113

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATURE PUBLISHING GROUP  

During chromatin-regulated processes, the histone H2A-H2B heterodimer functions dynamically in and out of the nucleosome. Although detailed crystal structures of nucleosomes have been established, that of the isolated full-length H2A-H2B heterodimer has remained elusive. Here, we have determined the solution structure of human H2A-H2B by NMR coupled with CS-Rosetta. H2A and H2B each contain a histone fold, comprising four alpha-helices and two beta-strands (alpha(1)-beta(1)-alpha(2)-beta 2-alpha(3)-alpha(C)), together with the long disordered N- and C-terminal H2A tails and the long N-terminal H2B tail. The N-terminal alpha(N) helix, C-terminal beta(3) strand, and 3(10) helix of H2A observed in the H2A-H2B nucleosome structure are disordered in isolated H2A-H2B. In addition, the H2A alpha(1) and H2B alpha(C) helices are not well fixed in the heterodimer, and the H2A and H2B tails are not completely random coils. Comparison of hydrogen-deuterium exchange, fast hydrogen exchange, and {H-1}-N-15 hetero-nuclear NOE data with the CS-Rosetta structure indicates that there is some conformation in the H2A 3(10) helical and H2B Lys11 regions, while the repression domain of H2B (residues 27-34) exhibits an extended string-like structure. This first structure of the isolated H2A-H2B heterodimer provides insight into its dynamic functions in chromatin.

DOI： 10.1038/srep24999

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DOI： 10.1016/j.bpj.2015.11.1767

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Language：Japanese   Publisher：The Physical Society of Japan (JPS)  

DOI： 10.11316/jpsgaiyo.71.1.0_3180

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DOI： 10.1016/j.bpj.2015.11.915

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Language：English   Publisher：The Biophysical Society of Japan  

<p>Understanding how proteins fold through a vast number of unfolded states is a major subject in the study of protein folding. Herein, we present itinerary profiling as a simple method to analyze molecular dynamics trajectories, and apply this method to Trp-cage. In itinerary profiling, structural clusters included in a trajectory are represented by a bit sequence, and a number of trajectories, as well as the structural clusters, can be compared and classified. As a consequence, the structural clusters that characterize the foldability of trajectories were able to be identified. The connections between the clusters were then illustrated as a network and the structural features of the clusters were examined. We found that in the true folding funnel, Trp-cage formed a left-handed main-chain topology and the Trp6 side-chain was located at the front of the main-chain ring, even in the initial unfolded states. In contrast, in the false folding funnel of the pseudo-native states, in which the Trp6 side-chain is upside down in the protein core, Trp-cage had a right-handed main-chain topology and the Trp side-chain was at the back. The initial topological partition, as determined by the main-chain handedness and the location of the Trp residue, predetermines Trp-cage foldability and the destination of the trajectory to the native state or the pseudo-native states.</p>

DOI： 10.2142/biophysico.13.0_295

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Physical Society  

Coherent x-ray diffraction imaging (CXDI) enables us to visualize noncrystalline sample particles with micrometer to submicrometer dimensions. Using x-ray free-electron laser (XFEL) sources, two-dimensional diffraction patterns are collected from fresh samples supplied to the irradiation area in the "diffraction-before-destruction" scheme. A recent significant increase in the intensity of the XFEL pulse is promising and will allow us to visualize the three-dimensional structures of proteins using XFEL-CXDI in the future. For the protocol proposed for molecular structure determination using future XFEL-CXDI [T. Oroguchi and M. Nakasako, Phys. Rev. E 87, 022712 (2013)10.1103/PhysRevE.87.022712], we require an algorithm that can classify the data in accordance with the structural polymorphism of proteins arising from their conformational dynamics. However, most of the algorithms proposed primarily require the numbers of conformational classes, and then the results are biased by the numbers. To improve this point, here we examine whether a method based on the manifold concept can classify simulated XFEL-CXDI data with respect to the structural polymorphism of a protein that predominantly adopts two states. After random sampling of the conformations of the two states and in-between states from the trajectories of molecular dynamics simulations, a diffraction pattern is calculated from each conformation. Classification was performed by using our custom-made program suite named enma, in which the diffusion map (DM) method developed based on the manifold concept was implemented. We successfully classify most of the projection electron density maps phase retrieved from diffraction patterns into each of the two states and in-between conformations without the knowledge of the number of conformational classes. We also examined the classification of the projection electron density maps of each of the three states with respect to the Euler angle. The present results suggest that the DM method is imperative for future applications of XFEL-CXDI experiments for proteins, and clarify issues to be taken care of in the future application.

DOI： 10.1103/PhysRevE.92.032710

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

The hydration free energy (HFE) is a crucially important physical quantity to discuss various chemical processes in aqueous solutions. Although an explicit-solvent computation with molecular dynamics (MD) simulations is a preferable treatment of the HFE, huge computational load has been inevitable for large, complex solutes like proteins. In the present paper, we propose an efficient computation method for the HFE. In our method, the HFE is computed as a sum of. &lt; U-UV &gt;/2 (&lt; U-UV &gt; is the ensemble average of the sum of pair interaction energy between solute and water molecule) and the water reorganization term mainly reflecting the excluded volume effect. Since &lt; U-UV &gt; can readily be computed through a MD of the system composed of solute and water, an efficient computation of the latter term leads to a reduction of computational load. We demonstrate that the water reorganization term can quantitatively be calculated using the morphometric approach (MA) which expresses the term as the linear combinations of the four geometric measures of a solute and the corresponding coefficients determined with the energy representation (ER) method. Since the MA enables us to finish the computation of the solvent reorganization term in less than 0.1 s once the coefficients are determined, the use of the MA enables us to provide an efficient computation of the HFE even for large, complex solutes. Through the applications, we find that our method has almost the same quantitative performance as the ER method with substantial reduction of the computational load. (C) 2015 AIP Publishing LLC.

DOI： 10.1063/1.4919636

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DOI： 10.2142/biophys.55.023

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Biophysical Society  

One of the motive forces for F1-ATPase rotation is the conformational change of the catalytically active β subunit due to closing and opening motions caused by ATP binding and hydrolysis, respectively. The closing motion is accomplished in two steps: the hydrogen-bond network around ATP changes and then the entire structure changes via B-helix sliding, as shown in our previous study. Here, we investigated the opening motion induced by ATP hydrolysis using all-atom free-energy simulations, combining the nudged elastic band method and umbrella sampling molecular-dynamics simulations. Because hydrolysis requires residues in the α subunit, the simulations were performed with the αβ dimer. The results indicate that the large-scale opening motion is also achieved by the B-helix sliding (in the reverse direction). However, the sliding mechanism is different from that of ATP binding because sliding is triggered by separation of the hydrolysis products ADP and Pi. We also addressed several important issues: 1), the timing of the product Pi release
2), the unresolved half-closed β structure
and 3), the ADP release mechanism. These issues are fundamental for motor function
thus, the rotational mechanism of the entire F1-ATPase is also elucidated through this αβ study. During the conformational change, conserved residues among the ATPase proteins play important roles, suggesting that the obtained mechanism may be shared with other ATPase proteins. When combined with our previous studies, these results provide a comprehensive view of the β-subunit conformational change that drives the ATPase.

DOI： 10.1016/j.bpj.2014.11.1853

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The finite-size effect in periodic system is examined for the charging free energy of protein in explicit solvent over a variety of charged states. The key to the finite-size correction is the self-energy, which is defined as the interaction energy of the solute with its own periodic images and the neutralizing background. By employing the thermodynamic-integration method with systematically varied sizes of the unit cell of molecular dynamics (MD) simulations, we show for ubiquitin that the self-energy corrects the finite-size effect on the charging free energy within 1 kcal/mol at total charges of -5e, -1e, neutral, and +1e and within 5 kcal/mol even for a highly charged state with +8e. We then sought the additional correction from the solvation effect using the numerical solution to the Poisson equation of the protein with implicit solvent. This correction reduces the cell-size dependence of the charging free energy at +8e to 3 kcal/mol and is well expressed as the self-energy divided by the dielectric constant of solvent water.

DOI： 10.1021/ct5008394

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Language：Japanese   Publisher：The Physical Society of Japan (JPS)  

DOI： 10.11316/jpsgaiyo.70.2.0_3019

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER-VERLAG BERLIN  

F-1-ATPase is a rotary motor enzyme. Despite many theoretical and experimental studies, the molecular mechanism of the motor rotation is still not fully understood. However, plenty of available data provide a clue as to how this molecular motor rotates: with nucleotide perturbations, the catalytically active beta subunit propagates its structural changes to the entire alpha(3)beta(3) complex via both sides of the subunits, resulting that asymmetry is created in the alpha(3)beta(3) hexamer ring. In the sequential reaction step, the structure of the asymmetrical alpha(3)beta(3) complex changes from one state to the other due to the nucleotide perturbations, and the gamma subunit axis follows the sequentially changing alpha(3)beta(3) structure. Therefore, there are mainly two essential elements for motor rotation: the conformational change of the beta subunit and the asymmetrical structure of the alpha(3)beta(3) subunit complex. Therefore, this chapter reports a series of studies focused on these two elements via combinational approaches of molecular dynamics (MD) simulations and experimental or other theoretical studies. In addition to the motor rotation factors, the combined study also revealed other important elements of F-1-ATPase, such as torque transmission and the chemical reaction pathway, which is described in the later part of this chapter. All of these results provide insight into the rotational mechanism and deepen the understanding of this molecular motor.

DOI： 10.1007/978-3-319-02970-2_17

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.54.S136_6

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.54.S273_5

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.54.S203_4

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.54.S189_6

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.54.S214_6

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DOI： 10.1016/j.bpj.2013.11.3382

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The multidrug transporter AcrB actively exports a wide variety of noxious compounds using proton-motive force as an energy source in Gram-negative bacteria. AcrB adopts an asymmetric structure comprising three protomers with different conformations that are sequentially converted during drug export; these cyclic conformational changes during drug export are referred to as functional rotation. To investigate functional rotation driven by proton-motive force, all-atom molecular dynamics simulations were performed. Using different protonation states for the titratable residues in the middle of the transmembrane domain, our simulations revealed the correlation between the specific protonation states and the side-chain configurations. Changing the protonation state for Asp408 induced a spontaneous structural transition, which suggests that the proton translocation stoichiometry may be one proton per functional rotation cycle. Furthermore, our simulations demonstrate that alternating the protonation states in the transmembrane domain induces functional rotation in the porter domain, which is primarily responsible for drug transport.

DOI： 10.1021/bi400119v

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The Rad51 ATPase plays central roles in DNA homologous recombination. Yeast Rad51 dimer structure in the active form of the filament was constructed using homology modeling techniques, and all-atom molecular dynamics (MD) simulations were performed using the modeled structure. We found two crucial interaction networks involving ATP: one is among the γ-phosphate of ATP, K+ ions, H352, and D374
the other is among the adenine ring of ATP, R228, and P379. Multiple MD simulations were performed in which the number of bound K + ions was changed. The simulated structures suggested that K + ions are indispensable for the stabilization of the active dimer and resemble the arginine and lysine fingers of other P-loop containing ATPases and GTPases. MD simulations also showed that the adenine ring of ATP mediates interactions between adjacent protomers. Furthermore, in MD simulations starting from a structure just after ATP hydrolysis, the opening motion corresponding to dissociation from DNA was observed. These results support the hypothesis that ATP and K+ ions function as glue between protomers. © 2013 Biophysical Society.

DOI： 10.1016/j.bpj.2013.02.014

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The minimum structural unit of chromatin is the nucleosome core particle (NCP), consisting of 146 bp of DNA wrapped around a histone octamer, which itself contains two H2A/H2B dimers and one (H3/H4)(2) tetramer. These multimers possess functionally important tail regions that are intrinsically disordered. In order to elucidate the mechanisms behind NCP assembly and disassembly processes, which are highly related to gene expression, structural characterization of the H2A/H2B dimer and (H3/H4)(2) tetramer will be of importance. In the present study, human histone multimers with disordered tail regions were characterized by electrospray ionization (ESI) ion mobility-mass spectrometry (IM-MS) and molecular dynamics (MD) simulation. Experimentally obtained arrival times of these histone multimer ions showed rather wide distributions, implying that multiple conformers exist for each histone multimer in the gas phase. To examine their structures, MD simulations of the histone multimers were performed first in solution and then in vacuo at four temperatures, resulting in a variety of histone multimer structures. Theoretical collision cross-section (CCS) values calculated for the simulated structures revealed that structural models with smaller CCS values had more compact tail regions than those with larger CCS values. This implied that variation of the CCS values of the histone multimers were primarily due to the random behaviors of the tail regions in the gas phase. The combination of IM-MS and MD simulation enabled clear and comprehensive characterization of the gas-phase structures of histone multimers containing disordered tails.

DOI： 10.1021/ac400395j

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

We have recently proposed the "packing exchange mechanism" for F-1-ATPase, wherein the perturbation by a substrate binding/release or an ATP hydrolysis is followed by the reorganization of the asymmetric packing structure of the alpha(3)beta(3) complex, accompanying the gamma subunit rotation. As part of a further investigation of this rotational mechanism, we performed all-atom molecular dynamics simulations for yeast F-1-ATPase both before and after a 16 degrees rotation of the gamma subunit triggered by a Pi release. We analyzed the structural fluctuations, the subunit interface interactions, and the dynamics of the relative subunit arrangements before and after the rotation. We found that with the Pi release the alpha(E)beta(E) subunit interface becomes looser, which also allosterically makes the alpha(DP)beta(DP) subunit interface looser. This structural communication between these interfaces takes place through a tightening of the alpha(TP)beta(TP) subunit interface. The gamma subunit interacts less strongly with alpha(DP) and beta(DP) and more strongly with alpha(TP) and beta(TP). After the Pi release, the tightly packed interfaces are reorganized from the interfaces around beta(DP) to those around beta(TP), inducing the 16 degrees rotation. These results, which are consistent with the packing exchange mechanism, allow us to deduce a view of the structural change during the 40 degrees rotation.

DOI： 10.1021/jp312499u

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DOI： 10.1016/j.bpj.2012.11.1846

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.53.S239_2

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DOI： 10.2142/biophys.53.S239_1

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

It is now recognized that intrinsically disordered proteins (IDPs) play important roles as hubs in intracellular networks, and their structural characterisation is of significance. However, due to their highly dynamic features, it is challenging to investigate the structures of IDPs solely by conventional methods. In the present study, we demonstrate a novel method to characterise protein complexes using electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) in combination with small-angle X-ray scattering (SAXS). This method enables structural characterisation even of proteins that have difficulties in crystallisation. With this method, we have characterised the Schizosaccharomyces pombe Swi5-Sfr1 complex, which is expected to have a long disordered region at the N-terminal portion of Sfr1. ESI-IM-MS analysis of the Swi5-Sfr1 complex revealed that its experimental collision cross-section (CCS) had a wide distribution, and the CCS values of the most dominant ions were similar to 56% of the theoretically calculated value based on the SAXS low-resolution model, suggesting a significant size reduction in the gas phase. The present study demonstrates that the newly developed method for calculation of the theoretical CCSs of the SAXS low-resolution models of proteins allows accurate evaluation of the experimental CCS values of IDPs provided by ESI-IM-MS by comparing with the low-resolution solution structures. Furthermore, it was revealed that the combination of ESI-IM-MS and SAXS is a promising method for structural characterisation of protein complexes that are unable to crystallise.

DOI： 10.1039/c2an35878f

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.53.S115_5

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.53.S239_3

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：CELL PRESS  

F-1-ATPase is an ATP-driven rotary motor that generates torque at the interface between the catalytic beta-subunits and the rotor gamma-subunit. The beta-subunit inwardly rotates the C-terminal domain upon nucleotide binding/dissociation; hence, the region of the C-terminal domain that is in direct contact with gamma-termed the DELSEED loop-is thought to play a critical role in torque transmission. We substituted all the DELSEED loop residues with alanine to diminish specific DELSEED loop-gamma interactions and with glycine to disrupt the loop structure. All the mutants rotated unidirectionally with kinetic parameters comparable to those of the wild-type F-1, suggesting that the specific interactions between DELSEED loop and gamma is not involved in cooperative interplays between the catalytic beta-subunits. Glycine substitution mutants generated half the torque of the wild-type F-1, whereas the alanine mutant generated comparable torque. Fluctuation analyses of the glycine/alanine. mutants revealed that the gamma-subunit was less tightly held in the alpha(3)beta(3)-stator ring of the glycine mutant than in the wild-type F-1 and the alanine mutant. Molecular dynamics simulation showed that the DELSEED loop was disordered by the glycine substitution, whereas it formed an alpha-helix in the alanine mutant. Our results emphasize the importance of loop rigidity for efficient torque transmissions.

DOI： 10.1016/j.bpj.2012.06.054

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

We show how to characterize the native-structure models of a protein using our free-energy function F which is based on hydration thermodynamics. Ubiquitin is adopted as an example protein. We consider models determined by the X-ray crystallography and two types of NMR model sets. A model set of type 1 comprises candidate models for a fixed native structure, and that of type 2 forms an ensemble of structures representing the structural variability of the native state. In general, the X-ray models give lower F than the NMR models. There is a trend that, as a model deviates more from the model with the lowest F among the X-ray models, its F becomes higher. Model sets of type 1 and those of type 2, respectively, exhibit two different characteristics with respect to the correlation between the deviation and F. It is argued that the total amount of constraints such as NOEs effectively taken into account in constructing the NMR models can be examined by analyzing the behavior of F. We investigate structural characteristics of the models in terms of the energetic and entropic components of F which are relevant to intramolecular hydrogen bonding and to backbone and side-chain packing, respectively.

DOI： 10.1021/jp301541z

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The complex of sensory rhodopsin II (SRII) and its cognate transducer HtrII (2:2 SRII-HtrII complex) consists of a photoreceptor and its signal transducer, respectively, associated with negative phototaxis in extreme halophiles. In this study to investigate how photoexcitation in SRII affects the structures of the complex, we conducted two series of molecular dynamics simulations of the complex of SRII and truncated HtrII (residues 1-136) of Natronomonas pharaonis linked with a modeled HAMP domain in the lipid bilayer using the two crystal structures of the ground state and the M-intermediate state as the starting structures. The simulation results showed significant enhancements of the structural differences observed between the two crystal structures. Helix F of SRII showed an outward motion, and the C-terminal end of transmembrane domain 2 (TM2) in HtrII rotated by similar to 10 degrees. The most significant structural changes were observed in the overall orientations of the two SRII molecules, closed in the ground state and open in the M-state. This change was attributed to substantial differences in the structure of the four-helix bundle of the HtrII dimer causing the apparent rotation of TM2. These simulation results established the structural basis for the various experimental observations explaining the structural differences between the ground state and the M-intermediate state.

DOI： 10.1021/bi300696b

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Enzymatic hydrolysis of nucleotide triphosphate (NTP) plays a pivotal role in protein functions. In spite of its biological significance, however, the chemistry of the hydrolysis catalysis remains obscure because of the complex nature of the reaction. Here we report a study of the molecular mechanism of hydrolysis of adenosine triphosphate (ATP) in F-1-ATPase, an ATP-driven rotary motor protein. Molecular simulations predicted and single-molecule observation experiments verified that the rate-determining step (RDS) is proton transfer (PT) from the lytic water molecule, which is strongly activated by a metaphosphate generated by a preceding P-gamma-O-beta bond dissociation (POD). Catalysis of the POD that triggers the chain activation of the PT is fulfilled by hydrogen bonds between Walker motif A and an arginine finger, which commonly exist in many NTPases. The reaction mechanism unveiled here indicates that the protein can regulate the enzymatic activity for the function in both the POD and PT steps despite the fact that the RDS is the PT step.

DOI： 10.1021/ja211027m

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Rad51 forms a helical filament on single-stranded DNA and promotes strand exchange between two homologous DNA molecules during homologous recombination. The Swi5-Sfr1 complex interacts directly with Rad51 and stimulates strand exchange. Here we describe structural and functional aspects of the complex. Swi5 and the C-terminal core domain of Sfr1 form an essential activator complex with a parallel coiled-coil heterodimer joined firmly together via two previously uncharacterized leucine-zipper motifs and a bundle. The resultant coiled coil is sharply kinked, generating an elongated crescent-shaped structure suitable for transient binding within the helical groove of the Rad51 filament. The N-terminal region of Sfr1, meanwhile, has an interface for binding of Rad51. Our data suggest that the snug fit resulting from the complementary geometry of the heterodimer activates the Rad51 filament and that the N-terminal domain of Sfr1 plays a role in the efficient recruitment of the Swi5-Sfr1 complex to the Rad51 filaments.

DOI： 10.1016/j.str.2012.01.005

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.52.S80_1

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.52.S101_4

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DOI： 10.1063/1.4734298

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DOI： 10.1016/j.bpj.2011.11.3862

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DOI： 10.2142/biophys.52.S127_5

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC  

In eukaryotes, DNA strand exchange is the central reaction of homologous recombination, which is promoted by Rad51 recombinases forming a right-handed nucleoprotein filament on single-stranded DNA, also known as a presynaptic filament. Accessory proteins known as recombination mediators are required for the formation of the active presynaptic filament. One such mediator in the fission yeast Schizosaccharomyces pombe is the Swi5-Sfr1 complex, which has been identified as an activator of Rad51 that assists in presynaptic filament formation and stimulates its strand exchange reaction. Here, we determined the 1: 1 binding stoichiometry between the two subunits of the Swi5-Sfr1 complex using analytical ultracentrifugation and electrospray ionization mass spectrometry. Small-angle x-ray scattering experiments revealed that the Swi5-Sfr1 complex displays an extremely elongated dogleg-shaped structure in solution, which is consistent with its exceptionally high frictional ratio (f/f(0)) of 2.0 +/- 0.2 obtained by analytical ultracentrifugation. Furthermore, we determined a rough topology of the complex by comparing the small-angle x-ray scattering-based structures of the Swi5-Sfr1 complex and four Swi5-Sfr1-Fab complexes, in which the Fab fragments of monoclonal antibodies were specifically bound to experimentally determined sites of Sfr1. We propose a model for how the Swi5-Sfr1 complex binds to the Rad51 filament, in which the Swi5-Sfr1 complex fits into the groove of the Rad51 filament, leading to an active and stable presynaptic filament.

DOI： 10.1074/jbc.M111.303339

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Equine beta-lactoglobulin (ELG) assumes non-native helices during refolding and in partially folded states. Previously, circular dichroism (CD) combined with site-directed mutagenesis identified helical regions in the acid- and cold-denatured states of ELG. It is also known that a fragment of ELG, CHIBL (residues 88-142), has a structure similar to that of the cold-denatured state. For the study reported herein, the structure of a shorter fragment, CHIBL Delta F (residues 97-142), was investigated by CD and nuclear magnetic resonance spectroscopy. The secondary chemical shifts clearly showed that non-native alpha-helices are present in two different regions, residues 98-107 and 114-135, and are connected by a native disulfide bond. The CD spectra of two peptides that correspond to the helical regions are characterized by weak helical signatures, and the sum of their CD spectra is nearly the same as the spectrum of disulfide-reduced CHIBL Delta F. Therefore, the non-native helices are stabilized by the disulfide, and non-native helix formation may occur only during the refolding of the disulfide-intact protein. Supporting this conclusion is the observation that tear lipocalin, a homologue of ELG that lacks the disulfide, does not form non-native helices during folding.

DOI： 10.1021/bi2013239

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

Ion mobility MS was employed to study the structure of the beta B2B3-crystallin heterodimer following its detection by ESI-TOF MS. The results demonstrate that the heterodimer has a similar cross-section (3 165 angstrom(2)) and structure to the beta B2B2-crystallin homodimer. Several homology-modelled structures for the beta B2B3 heterodimer were constructed and assessed in terms of their calculated collision cross-sections and whether the solvent accessibilities of reactive amino acid side chains throughout the beta B3 subunit are in accord with measured oxidation levels in radical probe MS protein footprinting experiments. The beta B2B3 heterodimer AD model provides the best representation of the heterodimer&apos;s structure overall following a consideration of both the ion mobility and radical probe MS data.

DOI： 10.1111/j.1742-4658.2011.08309.x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

In this study, free-energy function (FEF) for discriminating the native fold of a protein from misfolded decoys was investigated. It is a physics-based function using an all-atom model, which comprises the hydration entropy (HE) and the total dehydration penalty (TDP). The HE is calculated using a hybrid of a statistical-mechanical theory applied to a molecular model for water and the morphometric approach. The energetic component is suitably taken into account in a simple manner as the TDP. On the basis of the results from a careful test of the FEF, which have been performed for 118 proteins in representative decoy sets, we show that its performance is distinctly superior to that of any other function. The FEF varies largely from model to model for the candidate models for the native structure (NS) obtained from nuclear magnetic resonance experiments, but we can find models or a model for which the FEF becomes lower than for any of the decoy structures. A decoy set is not suited to the test of a free-energy or potential function in cases where a protein isolated from a protein complex is considered and the structure in the complex is used as the model NS of the isolated protein without any change or where portions of the terminus sides of a protein are removed and the percentage of the secondary structures lost due to the removal is significantly high. As these findings are made possible, we can assume that our FEF precisely captures the features of the true NS.

DOI： 10.1002/prot.23036

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD  

The causal relationship between protein structural change and ligand binding was classified and annotated for 839 nonredundant pairs of crystal structures in the Protein Data Bank-one with and the other without a bound low-molecular-weight ligand molecule. Protein structural changes were first classified into either domain or local motions depending on the size of the moving protein segments. Whether the protein motion was coupled with ligand binding was then evaluated based on the location of the ligand binding site and by application of the linear response theory of protein structural change. Protein motions coupled with ligand binding were further classified into either closure or opening motions. This classification revealed the following: (i) domain motions coupled with ligand binding are dominated by closure motions, which can be described by the linear response theory; (ii) local motions frequently accompany order-disorder or alpha-helix-coil conformational transitions; and (iii) transferase activity (Enzyme Commission number 2) is the predominant function among coupled domain closure motions. This could be explained by the closure motion acting to insulate the reaction site of these enzymes from environmental water. (c) 2011 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.jmb.2011.02.058

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F-1-ATPase is an ATP-driven rotary motor enzyme. The beta subunit changes its conformation from an open to a closed form upon ATP binding. The motion in the beta subunit is regarded as a major driving force for rotation of the central stalk. In this Article, we explore the conformational change of the beta subunit using all-atom free energy simulations with explicit solvent and propose a detailed mechanism for the conformational change. The beta subunit conformational change is accomplished roughly in two characteristic steps: changing of the hydrogen-bond network around ATP and the dynamic movement of the C-terminal domain via sliding of the B-helix. The details of the former step agree well with experimental data. In the latter step, sliding of the B-helix enhances the hydrophobic stabilization due to the exclusion of water molecules from the interface and improved packing in the hydrophobic core. This step contributes to a decrease in free energy, leading to the generation of torque in the F-1-ATPase upon ATP binding.

DOI： 10.1021/ja1070152

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We propose a novel picture of the rotation mechanism of F-1-ATPase, a rotary-motor protein complex. Entropy, which originates from the translational displacement of water molecules, is treated as the key factor in the proposal. We calculate the water entropy gains upon formation of the alpha-beta, alpha-gamma, and beta-gamma subunit pairs. The gain is given as the difference between the hydration entropy of a subunit pair and the sum of the hydration entropies of the separate subunits forming the pair. The calculation is made using a hybrid of a statistical-mechanical theory for molecular liquids and morphometric approach. The water entropy gain is considered as a measure of tightness of the packing at each subunit interface. The results are highly correlated with the numbers of stable contacts at the subunit interfaces estimated by a molecular dynamics simulation. We also calculate the hydration entropies of three different subcomplexes comprising the gamma subunit, one of the beta subunits, and two a. subunits adjacent to them. The major finding is that the packing in F-1-ATPase is highly asymmetrical, and this asymmetry is ascribed to the water entropy effect. We discuss how the rotation of the gamma subunit is induced by such chemical processes as ATP binding, ATP hydrolysis, and release of the products. In our picture, the asymmetrical packing plays crucially important roles, and the rotation is driven by the water entropy effect.

DOI： 10.1021/ja109594y

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The combination of small-angle X-ray solution scattering (SAXS) experiments and molecular dynamics (MD) simulations is now becoming a powerful tool to study protein conformations in solution at an atomic resolution. In this study, we investigated effects of ionic strength on SAXS data theoretically by using MD simulations of hen egg white lysozyme at various NaCl concentrations from 0 to 1 M. The calculated SAXS excess intensities showed a significant dependence on ion concentration, which originates from the different solvent density distributions in the presence and absence of ions. The addition of ions induced a slow convergence of the SAXS data, and a similar to 20 ns simulation is required to obtain convergence of the SAXS data with the presence of ions whereas only a 0.2 ns simulation is sufficient in the absence of ions. To circumvent the problem of the slow convergence in the presence of ions, we developed a novel method that reproduces the SAXS excess intensities with the presence of ions from short MD trajectories in pure water. By applying this method to SAXS data for the open and closed forms of transferrin at 1 M ion concentration, the correct form could be identified by simply using short MD simulations of the protein in pure water for 0.2 ns. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3526488]

DOI： 10.1063/1.3526488

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

"Hot spots'' are residues accounting for the majority of the protein-protein binding free energy (BFE) despite that they comprise only a small fraction of the protein-protein interface. A hot spot can be found experimentally by measuring the BFE change upon mutating it to alanine: the mutation gives rise to a significantly large increase in the BFE. Theoretical prediction of hot spots is an enthusiastic subject in biophysics, biochemistry, and bioinformatics. For the development of a reliable prediction method, it is essential to understand the physical origin of hot spots. To this end, we calculate the water-entropy gains upon binding both for a wild-type complex and for its mutant complex using a hybrid method of the angle-dependent integral equation theory applied to a molecular model for water and the morphometric approach. We note that this type of calculation has never been employed in the previously reported methods. The BFE change due to alanine mutation is evaluated only from the change in the water-entropy gain with no parameters fitted to the experimental data. It is shown that the overall performance of predicting hot spots in our method is higher than that in Robetta, a standard free-energy-based method using fitting parameters, when the most widely used criterion for defining an actual hot spot is adopted. This result strongly suggests that the water-entropy effect we calculate is the key factor governing basic physics of hot spots.

DOI： 10.1039/c1cp21597c

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.51.S118_6

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DOI： 10.2142/biophys.51.S49_4

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DOI： 10.2142/biophys.51.S133_4

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The sarcoplasmic reticulum Ca2+-ATPase transports two Ca2+ per ATP hydrolyzed from the cytoplasm to the lumen against a large concentration gradient. During transport, the pump alters the affinity and accessibility for Ca2+ by rearrangements of transmembrane helices. In this study, all-atom molecular dynamics simulations were performed for wild-type Ca2+-ATPase in the Ca2+-bound form and the Gln mutants of Glu771 and Glu908. Both of them contribute only one carboxyl oxygen to site I Ca2+, but only Glu771Gln completely looses the Ca2+-binding ability. The simulations show that: (i) For Glu771Gln, but not Glu908Gln, coordination of Ca2+ was critically disrupted. (ii) Coordination broke at site II first, although Glu771 and Glu908 only contribute to site I. (iii) A water molecule bound to site I Ca2+ and hydrogen bonded to Glu771 in wild-type, drastically changed the coordination of Ca2+ in the mutant. (iv) Water molecules flooded the binding sites from the lumenal side. (v) The side chain conformation of Ile775, located at the head of a hydrophobic cluster near the lumenal surface, appears critical for keeping out bulk water. Thus the simulations highlight the importance of the water molecule bound to site I Ca2+ and point to a strong relationship between Ca2+-coordination and shielding of bulk water, providing insights into the mechanism of gating of ion pathways in cation pumps.

DOI： 10.1073/pnas.1015819107

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL PUBLISHING, INC  

The assembly of the presynaptic filament of recombinases represents the most important step in homologous recombination. The formation of the filament requires assistance from mediator proteins. Swi5 and Sfr1 have been identified as mediators in fission yeast and these proteins form a complex that stimulates strand exchange. Here, the expression, purification and crystallization of Swi5 and its complex with an N-terminally truncated form of Sfr1 (delta N180Sfr1) are presented. Analytical ultracentrifugation of the purified samples showed that Swi5 and the protein complex exist as tetramers and heterodimers in solution, respectively. Swi5 was crystallized in two forms belonging to space groups C2 and R3 and the crystals diffracted to 2.7 A resolution. Swi5-delta N180Sfr1 was crystallized in space group P2(1)2(1)2 and the crystals diffracted to 2.3 A resolution. The crystals of Swi5 and Swi5-delta N180Sfr1 are likely to contain one tetramer and two heterodimers in the asymmetric unit, respectively.

DOI： 10.1107/S1744309110032239

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Using molecular dynamics (MD) simulations and analyses of NMR relaxation order parameters, we investigated conformational changes of side chains in hydrophobic cores upon DNA binding for the DNA binding/transactivation domain of the transcription factor PhoB, in which backbone conformational changes upon DNA binding are small. The simulation results correlated well with experimental order parameters for the backbone and side-chain methyl groups, showing that the order parameters generally represent positional fluctuations of the backbone and side-chain methyl groups. However, topological effects of the side chains on the order parameters were also found and could be eliminated using normalized order parameters for each amino acid type. Consistent with the NMR experiments, the normalized order parameters from the MD simulations showed that the side chains in one of the two hydrophobic cores (the soft core) were highly flexible in comparison with those in the other hydrophobic core (the hard core) before DNA binding and that the flexibility of the hydrophobic cores, particularly of the soft core, was reduced upon DNA binding. Principal component analysis of methyl group configurations revealed strikingly different side-chain dynamics for the soft and hard cores. In the hard core, side-chain configurations were simply distributed around one or two average configurations. In contrast, the side chains in the soft core dynamically varied their configurations in an equilibrium ensemble that included binding configurations as minor components before DNA binding. DNA binding led to a restriction of the side-chain dynamics and a shift in the equilibrium toward binding configurations, in clear correspondence with a population-shift model.

DOI： 10.1021/ja103218x

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F1-ATPase is an adenosine tri-phosphate (ATP)-driven rotary motor enzyme. We investigated the structural fluctuations and concerted motions of subunits in F1-ATPase using molecular dynamics (MD) simulations. An MD simulation for the α3β3γ complex was carried out for 30 ns. Although large fluctuations of the N-terminal domain observed in simulations of the isolated βE subunit were suppressed in the complex simulation, the magnitude of fluctuations in the C-terminal domain was clearly different among the three β subunits (βE, βTPand. βDP). Despite fairly similar conformations of the βTP and βDP subunits, the βDP subunit exhibits smaller fluctuations in the C-terminal domain than the βTP subunit due to their dissimilar interface configurations. Compared with the βTP subunit, the βDP subunit stably interacts with both the adjacent αDP and αE subunits. This sandwiched configuration in the βDP subunit leads to strongly correlated motions between, the βDP and adjacent α subunits. The βDP exhibits an extensive network of highly correlated motions with bound ATP and the γ subunit, as well as with the adjacent α subunits, suggesting that the structural changes occurring in the catalytically active βDP subunit can effectively induce movements of the γ subunit. © 2010 Wiley Periodicals, Inc.

DOI： 10.1002/jcc.21508

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC  

Thermostable direct hemolysin (TDH) is a major virulence factor of Vibrio parahaemolyticus that causes pandemic foodborne enterocolitis mediated by seafood. TDH exists as a tetramer in solution, and it possesses extreme hemolytic activity. Here, we present the crystal structure of the TDH tetramer at 1.5 angstrom resolution. The TDH tetramer forms a central pore with dimensions of 23 angstrom in diameter and similar to 50 angstrom in depth. pi-Cation interactions between protomers comprising the tetramer were indispensable for hemolytic activity of TDH. The N-terminal region was intrinsically disordered outside of the pore. Molecular dynamic simulations suggested that water molecules permeate freely through the central and side channel pores. Electron micrographs showed that tetrameric TDH attached to liposomes, and some of the tetramer associated with liposome via one protomer. These findings imply a novel membrane attachment mechanism by a soluble tetrameric pore-forming toxin.

DOI： 10.1074/jbc.M109.074526

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Normal mode analysis, with the all-atom or coarse-grained elastic network model, represents the equilibrium fluctuation of protein molecule in the Eckart frame, where contributions from external motions (translation and rotation) of the entire protein molecule are eliminated. On the other hand, domain motion is frequently exhibited by the relative motion of one domain to the other. Such a representation of fluctuations in the non-Eckart frame cannot be achieved by conventional normal mode analysis. Here, we propose normal mode analysis in a non-Eckart frame, where the external degrees of freedom are fixed for any portion of the system. In this analysis, the covariance matrix in the Eckart frame is transformed into one in the non-Eckart frame. Using a molecular dynamics simulation, we have confirmed the validity of the transformation formula and discussed the physical implication of the formula.

DOI： 10.1063/1.3352566

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Dihedral angles are alternative set of variables to Cartesian coordinates for representing protein dynamics. The two sets of variables exhibit extremely different behavior. Motions in dihedral angle space are characterized by latent dynamics, in which motion induced in each dihedral angle is always compensated for by motions of many other dihedral angles, in order to maintain a rigid globular shape. Using molecular dynamics simulations, we propose a molecular mechanism for the latent dynamics in dihedral angle space. It was found that, due to the unique structure of dihedral principal components originating in the globular shape of the protein, the dihedral principal components with large (small) amplitudes are highly correlated with the eigenvectors of the metric matrix with small (large) eigenvalues. Such an anticorrelation in the eigenmode structures minimizes the mean square displacement of Cartesian coordinates upon rotation of dihedral angles. In contrast, a short peptide, deca-alanine in this study, does not show such behavior of the latent dynamics in the dihedral principal components, but shows similar behaviors to those of the Cartesian principal components, due to the absence of constraints to maintain a rigid globular shape.

DOI： 10.1063/1.3360144

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The epsilon subunit, a small subunit located in the F-1 domain of ATP synthase and comprising two distinct domains, all N-terminal beta w-sandwich structure and C-terminal alpha-helical region, serves as an intrinsic inhibitor of ATP hydrolysis activity. This inhibitory function is especially important in photosynthetic organisms as the enzyme cannot synthesize ATP in the dark, but may catalyse futile ATP hydrolysis reactions. To understand the structure-function relationship of this subunit in F-1 from photosynthetic organisms, we solved the NMR structure of the epsilon subunit of ATP synthase obtained from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1, and examined the flexibility of the C-terminal domains using molecular dynamics Simulations. In addition, we revealed the significance of the C-terminal alpha-helical region of the epsilon Subunit in determining the binding affinity to the complex based oil the assessment of the inhibition of ATPase activity by the cyanobacterial epsilon subunit and the chimaeric subunits composed of the N-terminal domain from the cyanobacterium and the C-terminal domain from spinach. The differences observed in the structural and biochemical properties of chloroplast and bacterial epsilon subunits explains the distinctive characteristics of the epsilon subunits in the ATPase complex of the photosynthetic organism.

DOI： 10.1042/BJ20091247

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F-1-ATPase (F-1) is the water-soluble portion of ATP synthase and a rotary molecular motor in which the rotary shaft, the gamma subunit, rotates with 120 degrees steps against the alpha(3)beta(3) stator ring upon ATP hydrolysis. While the crystal structures of F-1 exhibit essentially one stable conformational state of F-1, single-molecule rotation studies revealed that there are two stable conformations of F-1 in each 120 degrees step: the ATP-binding dwell state and the catalytic dwell state. This chapter provides the experimental procedure for the determination of which catalytic state the crystal structures of F-1 represent, by the use of a cross-linking technique in the single-molecule rotation assay. The beta and gamma subunits are crosslinked through a disulfide bond between two cysteine residues genetically introduced at the positions where the beta and gamma subunits have a specific contact in the crystal structures of the ADP-bound form. In the single-molecule rotation assay, the cross-linked F-1 shows a pause at the catalytic dwell state that corresponds to the dwell angle in one turn where the beta subunit undergoes ATP hydrolysis. Thus, this experiment reveals not only that the crystal structure represents the catalytic dwell state but also that the ADP-bound beta subunit represents the catalytically active state. A protocol for inhibition of the wildtype F-1 with chemical inhibitors such as adenosine-5'-(beta,gamma-imino)-triphosphate (AMP-PNP) or/and N-3(-) under crystallization conditions is also provided.

DOI： 10.1016/S0076-6879(10)75012-6

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DOI： 10.2142/biophys.50.S21_2

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DOI： 10.2142/biophys.50.S30_1

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DOI： 10.2142/biophys.50.S116_5

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.50.S146_5

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.50.S152_5

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.50.S52_2

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Language：English   Publishing type：Research paper (scientific journal)  

The halobacterial transducer of sensory rhodopsin II (HtrII) is a photosignal transducer associated with phototaxis in extreme halophiles. The HAMP domain, a linker domain in HtrII, is considered to play an important role in transferring the signal from the membrane to the cytoplasmic region, although its structure in the complex remains undetermined. To establish the structural basis for understanding the mechanism of signal transduction, we present an atomic model of the structure of the N-terminal HAMP domain from Natronomonas pharaonis (HtrII: 84-136), based on molecular dynamics (MD) simulations. The model was built by homology modeling using the NMR structure of Af1503 from Archaeoglobus fulgidus as a template. The HAMP domains of Af1503 and HtrII were stable during MD simulations over 100 ns. Quantitative analyses of inter-helical packing indicated that the Af1503 HAMP domain stably maintained unusual knobs-to-knobs packing, as observed in the NMR structure, while the bulky side-chains of HtrII shifted the packing state to canonical knobs-into-holes. The role of the connector loop in maintaining structural stability was also discussed using MD simulations of loop deletion mutants. ©2010 THE BIOPHYSICAL SOCIETY OF JAPAN.

DOI： 10.2142/biophysics.6.27

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.50.S32_1

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DOI： 10.1016/j.cplett.2010.03.015

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JOHN WILEY & SONS INC  

Coupling between proteins motion and ligand binding can be well explained by the linear response theory (Ikeauchi, M.; Ueno, J.; Sato, M.; Kidera, A. Phys Rev Lett 2005, 94, 078102.), in which the structural change is treated as a response to ligand binding. The prediction accuracy of structural change upon ligand binding has been improved by replacing the variables in the linear response theory from Cartesian coordinates to dihedral angles. The dihedral angle theory can more accurately describe the rotational motions of protein domains compared with the Cartesian theory, which tends to shift the coordinate to the tangential direction of the domain rotation. In this study, the ligand-bound form of Ferric-binding protein was predicted from its ligand-free form using the dihedral linear response theory. When the variance-covariance matrix, the key component in the linear response theory, was derived by linear conversion from Cartesian coordinates to dihedral angles, the dihedral linear response theory gave an improvement in the prediction. Therefore, the description of the rotational motion by dihedral angles is crucial for accurate prediction of protein structural chance. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 30: 2602-2608, 2009

DOI： 10.1002/jcc.21269

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-LISS  

We have developed a free-energy function based on an all-atom model for proteins. It comprises two components, the hydration entropy (HE) and the total dehydration penalty (TDP). Upon a transition to a more compact structure, the number of accessible configurations arising from the translational displacement of water molecules in the system increases, leading to a water-entropy gain. To fully account for this effect, the HE is calculated using a statistical-mechanical theory applied to a molecular model for water. The TDP corresponds to the sum of the hydration energy and the protein intramolecular energy when a fully extended structure, which possesses the maximum number of hydrogen bonds wit water molecules and no intramolecular hydrogen bonds, is chosen as the standard one. When a donor an an acceptor (e.g., N and O, respectively) are buried in the interior after the break of hydrogen bonds with water molecules, if they form an intramolecular hydrogen bond, no penalty is imposed. When a donor or an acceptor is buried with no intramolecular hydrogen bond formed, an energetic penalty is imposed. We examine all the donors and acceptors for backbone-backbone, backbone-side chain, and side chain-side chain intramolecular hydrogen bonds and calculate the TDP. Our free-energy function has been tested for three different decoy sets. It is better than any other physics-based or knowledge-based potential function in terms of the accuracy in discriminating the native fold from misfolded decoys and the achievement of high Z-scores. Proteins 2009; 77:950-961. (C) 2009 Wiley-Liss, Inc.

DOI： 10.1002/prot.22520

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：CELL PRESS  

EcoO109I is a type II restriction endonuclease that functions as a dimer in solution. Upon DNA binding to the enzyme, the two subunits rotate counterclockwise relative to each other, as the two catalytic domains undergo structural changes to capture the cognate DNA. Using a 150-ns molecular dynamics simulation, we investigated the intrinsic dynamics of the DNA-free enzyme in solution to elucidate the relationship between enzyme dynamics and structural changes. The simulation revealed that the enzyme is considerably flexible, and thus exhibits large fluctuations in the radius of gyration. The small-angle x-ray scattering profile calculated from the simulation, including scattering from explicit hydration water, was in agreement with the experimentally observed profile. Principal component analysis revealed that the major dynamics were represented by the open-close and counterclockwise motions: the former is required for the enzyme to access DNA, whereas the latter corresponds to structural changes upon DNA binding. Furthermore, the intrinsic dynamics in the catalytic domains were consistent with motions capturing the cognate DNA. These results indicate that the structure of EcoO109I is intrinsically flexible in the direction of its functional movement, to facilitate effective structural changes for sequence-specific DNA recognition and processing.

DOI： 10.1016/j.bpj.2008.12.3914

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Aquaporins and aquaglyceroporins are membrane channel proteins that selectively transport water and small molecules such as glycerol across biological membranes. Molecular dynamics simulations have made substantial contributions toward understanding the permeation mechanisms of aquaporins in atomic detail. Osmotic pressure is the driving force of the transport by aquaporins. The osmotic water permeability of aquaporins can be estimated from equilibrium molecular dynamics simulations by using linear response theory. The relationship between osmotic permeability and channel structure was investigated by the recently proposed pf-matrix method. In addition to the water transport, other functions of aquaporins and aquaglyceroporins, i.e., glycerol permeation, proton blockage, and gating, have also been extensively studied by molecular dynamics simulations.

DOI： 10.2741/3308

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.49.S106_4

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.49.S67_1

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.49.S82_4

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Post-translational modification by small ubiquitin-like modifier (SUMO) proteins has been implicated in the regulation of a variety of cellular events. The functions of sumoylation are often mediated by downstream effector proteins harboring SUMO-interacting motifs (SIMs) that are composed of a hydrophobic core and a stretch of acidic residues. MBD1-containing chromatin-associated factor 1 (MCAF1), a transcription repressor, interacts with SUMO-2/3 and SUMO-1, with a preference for SUMO-2/3. We used NMR spectroscopy to solve the solution structure of the SIM of MCAF1 bound to SUMO-3. The hydrophobic core of the SIM forms a parallel beta-sheet pairing with strand beta2 of SUMO-3, whereas its C-terminal acidic stretch seems to mediate electrostatic interactions with a surface area formed by basic residues of SUMO-3. The significance of these electrostatic interactions was shown by mutations of both SUMO-3 and MCAF1. The present structural and biochemical data suggest that the acidic stretch of the SIM of MCAF1 plays an important role in the binding to SUMO-3.

DOI： 10.1074/jbc.M802528200

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-LISS  

The solution structure of the complex between the transcription factor PhoB DNA-binding/transactivation domain and DNA was determined by NMR spectroscopy and simulated annealing in a periodic boundary box of explicit water with the particle mesh Ewald method. The refined structures provided better convergence and better local geometry compared with the structures determined in vacuum. The hydrogen bond interactions between the PhoB domain and DNA in the aqueous environment were fully formed. The complex structure was found to be very similar to the crystal structure, particularly at the PhoB-DNA interface, much more so than expected from the vacuum structure. These results indicate the importance of the proper treatment of electrostatic and hydration influences in describing protein-DNA interactions. The hydration structures observed for the refined structures contained most of the crystal waters as a subset. We observed that various water-mediated PhoB-DNA interactions contributed to the molecular recognition between PhoB and DNA.

DOI： 10.1002/prot.21874

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.48.S83_2

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.48.S76_4

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.48.S63_1

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.48.S24_6

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD  

Molecular dynamics simulations of protein unfolding were performed at an elevated temperature for the authentic and recombinant forms of goat (x-lactalbumin. Despite very similar three-dimensional structures, the two forms have significantly different unfolding rates due to an extra N-terminal methionine in the recombinant protein. To identify subtle differences between the two forms in the highly stochastic kinetics of unfolding, we classified the unfolding trajectories using the multiple alignment method based on the analogy between the biological sequences and the molecular dynamics trajectories. A dendrogram derived from the multiple trajectory alignment revealed a clear difference in the unfolding pathways of the authentic and recombinant proteins, i.e. the former reached the transition state in an all-or-none manner while the latter unfolded less cooperatively. It was also found in the classification that the two forms of the protein shared a common transition state structure, which was in excellent agreement with the transition state structure observed experimentally in the Phi-value analysis. (c) 2007 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.jmb.2007.06.023

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：CELL PRESS  

Single-channel osmotic water permeability (p(f)) is a key quantity for investigating the transport capability of the water channel protein, aquaporin. However, the direct connection between the single scalar quantity pf and the channel structure remains unclear. In this study, based on molecular dynamics simulations, we propose a p(f)-matrix method, in which pf is decomposed into contributions from each local region of the channel. Diagonal elements of the pf matrix are equivalent to the local permeability at each region of the channel, and off-diagonal elements represent correlated motions of water molecules in different regions. Averaging both diagonal and off-diagonal elements of the pf matrix recovers pf for the entire channel; this implies that correlated motions between distantly-separated water molecules, as well as adjacent water molecules, influence the osmotic permeability. The pf matrices from molecular dynamics simulations of five aquaporins (AQP0, AQP1, AQP4, AqpZ, and GlpF) indicated that the reduction in the water correlation across the Asn-Pro-Ala region, and the small local permeability around the ar/R region, characterize the transport effciency of water. These structural determinants in water permeation were confirmed in molecular dynamics simulations of three mutants of AqpZ, which mimic AQP1.

DOI： 10.1529/biophysj.107.101170

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DOI： 10.1016/j.cplett.2007.01.087

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Other Link： http://orcid.org/0000-0001-9738-9216

Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY  

Several accessory proteins referred to as mediators are required for the full activity of the Rad51 (Rhp51 in fission yeast) recombinase. In this study, we analyzed in vivo functions of the recently discovered Swi5/Sfr1 complex from fission yeast. In normally growing cells, the Swi5-GFP protein localizes to the nucleus, where it forms a diffuse nuclear staining pattern with a few distinct foci. These spontaneous foci do not form in swi2 Delta mutants. Upon UV irradiation, Swi5 focus formation is induced in swi2D mutants, a response that depends on Sfr1 function, and Sfr1 also forms foci that colocalize with damage-induced Rhp51 foci. The number of UV-induced Rhp51 foci is partially reduced in swi5 Delta and rhp57 Delta mutants and completely abolished in an swi5D rhp57D double mutant. An assay for products generated by HO endonuclease-induced DNA double-strand breaks (DSBs) reveals that Rhp51 and Rhp57, but not Swi5/Sfr1, are essential for crossover production. These results suggest that Swi5/Sfr1 functions as an Rhp51 mediator but processes DSBs in a manner different from that of the Rhp55/57 mediator.

DOI： 10.1038/sj.emboj.7601582

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Language：English   Publishing type：Research paper (scientific journal)  

Intracellular nickel is required by Escherichia coli as a cofactor for a number of enzymes and is necessary for anaerobic respiration. However, high concentrations of nickel are toxic, so both import and export systems have evolved to control the cellular level of the metal. The nik operon in E. coli encodes a nickel-uptake system that includes the periplasmic nickel-binding protein NikA. The crystal structures of wild-type NikA both bound to nickel and in the apo form have been solved previously. The liganded structure appeared to show an unusual interaction between the nickel and the protein in which no direct bonds are formed. The highly unusual nickel coordination suggested by the crystal structure contrasted strongly with earlier X-ray spectroscopic studies. The known nickel-binding site has been probed by extensive mutagenesis and isothermal titration calorimetry and it has been found that even large numbers of disruptive mutations appear to have little effect on the nickel affinity. The crystal structure of a binding-site mutant with nickel bound has been solved and it is found that nickel is bound to two histidine residues at a position distant from the previously characterized binding site. This novel site immediately resolves the conflict between the crystal structures and other biophysical analyses. The physiological relevance of the two binding sites is discussed. © International Union of Crystallography, 2007.

DOI： 10.1107/S0907444906048712

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

Intracellular nickel is required by Escherichia coli as a cofactor for a number of enzymes and is necessary for anaerobic respiration. However, high concentrations of nickel are toxic, so both import and export systems have evolved to control the cellular level of the metal. The nik operon in E. coli encodes a nickel-uptake system that includes the periplasmic nickel-binding protein NikA. The crystal structures of wildtype NikA both bound to nickel and in the apo form have been solved previously. The liganded structure appeared to show an unusual interaction between the nickel and the protein in which no direct bonds are formed. The highly unusual nickel coordination suggested by the crystal structure contrasted strongly with earlier X-ray spectroscopic studies. The known nickel-binding site has been probed by extensive mutagenesis and isothermal titration calorimetry and it has been found that even large numbers of disruptive mutations appear to have little effect on the nickel affinity. The crystal structure of a binding-site mutant with nickel bound has been solved and it is found that nickel is bound to two histidine residues at a position distant from the previously characterized binding site. This novel site immediately resolves the conflict between the crystal structures and other biophysical analyses. The physiological relevance of the two binding sites is discussed.

DOI： 10.1107/S0907444906048712

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.47.S245_1

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.47.S262_4

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.47.S85_2

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.47.S25_1

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.47.S113_4

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.47.S42_1

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.47.S222_4

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.47.S127_1

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.47.S24_2

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Phospholamban is a 52-residue integral membrane protein that regulates the activity of the sarcoplasmic reticulum calcium pump in cardiac muscle. Its inhibitory action is relieved when phospholamban is phosphorylated at Ser16 by cAMP-dependent protein kinase. To computationally explore all possible conformations of the phosphorylated form, and thereby to understand the structural effects of phosphorylation, replica-exchange molecular dynamics (REMD) was applied to the cytoplasmic domain that includes Ser16. The simulations showed that (i) without phosphorylation, the region from Lys3 to Ser16 takes all alpha-helical conformations; (ii) when phosphorylated, the alpha-helix is partially unwound in the C-terminal part ( from Ser10 to Ala15) resulting in less extended conformations; (iii) the phosphate at Ser16 forms salt bridges with Arg9, Arg13, and/or Arg14; and (iv) the salt bridges with Arg13 and Arg14 distort the alpha-helix and induce unwinding of the C-terminal part. We then applied conventional all-atom molecular dynamics simulations to the full-length phospholamban in the phospholipid bilayer. The results were consistent with those obtained with REMD simulations, suggesting that the transmembrane part of phospholamban and the lipid bilayer itself have only minor effects on the conformational changes in the cytoplasmic domain. The distortions caused by the salt bridges involving the phosphate at Ser16 readily explain the relief of the inhibitory effect of phospholamban by phosphorylation, as they will substantially reduce the population of all helical conformations, which are presumably required for the binding to the calcium pump. This will also be the mechanism for releasing the phosphorylated phospholamban from kinase.

DOI： 10.1021/bi061071z

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.46.275

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Other Link： https://jlc.jst.go.jp/DN/JALC/00284355193?from=CiNii

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.46.S378_1

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：OXFORD UNIV PRESS  

In unicellular and multicellular eukaryotes, elaborate gene regulatory mechanisms facilitate a broad range of biological processes from cell division to morphological differentiation. In order to fully understand the gene regulatory networks involved in these biological processes, the spatial and temporal patterns of expression of many thousands of genes will need to be determined in real time in living organisms. Currently available techniques are not sufficient to achieve this goal; however, novel methods based on magnetic resonance (MR) imaging may be particularly useful for sensitive detection of gene expression in opaque tissues. This report describes a novel reporter gene system that monitors gene expression dynamically and quantitatively, in yeast cells, by measuring the accumulation of inorganic polyphosphate (polyP) using MR spectroscopy (MRS) or MR spectroscopic imaging (MRI). Because this system is completely non-invasive and does not require exogenous substrates, it is a powerful tool for studying gene expression in multicellular organisms, as well.

DOI： 10.1093/nar/gkl135

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.46.S308_3

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.46.S157_4

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.46.S171_3

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.46.S287_4

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.46.S408_3

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.46.S316_4

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.46.S335_1

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD  

The recombinant form of goat alpha-lactalbumin has a significantly faster unfolding rate compared to the authentic form, although the two molecules differ only in an extra methionine at the N terminus of the recombinant. The mechanism of the destabilization caused by this residue was investigated through the combined use of kinetic experiments and molecular dynamics simulations. Unfolding simulations for the authentic and recombinant forms at 398 K (ten trajectories of 5 ns for each form, 100 ns total) precisely reproduced the experimentally observed differences in unfolding behavior. In addition, experiments reproduced the destabilization of a mutant protein, T38A, faithfully as predicted by the simulations. This bidirectional verification between experiments and simulations enabled the atomically detailed description of the role of the extra methionine residue in the unfolding process. (c) 2005 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.jmb.2005.09.061

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

Molecular dynamics simulations were performed for four members of the aquaporin family (AQP1, AQPZ, AQP0, and GlpF) in the explicit membrane environment. The single-channel water permeability, p(f), was evaluated to be GlpF similar to AQPZ &gt; AQP1 &gt;&gt; AQP0, while their relative pore sizes were GlpF &gt;&gt; AQP1 &gt; AQPZ &gt; AQP0. This relation between pf and pore size indicates that water permeability was determined not only by the channel radius, but also another competing factor. Analysis of water dynamics revealed that this factor was the single-file nature of water transport. (c) 2005 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.

DOI： 10.1016/j.febslet.2005.09.018

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

DOI： 10.1021/ja0427505

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMERICAN PHYSICAL SOC  

A simple formula based on linear response theory is proposed to explain and predict the structural change of proteins upon ligand binding. By regarding ligand binding as an external perturbation, the structural change as a response is described by atomic fluctuations in the ligand-free form and the protein-ligand interactions. The results for three protein systems of various sizes are consistent with the observations in the crystal structures, confirming the validity of the linear relationship between the equilibrium fluctuations and the structural change upon ligand binding.

DOI： 10.1103/PhysRevLett.94.078102

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.45.S135_2

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.45.S128_3

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DOI： 10.2142/biophys.45.S41_4

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.45.S38_2

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.45.S6_1

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DOI： 10.2142/biophys.45.S243_4

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DOI： 10.2142/biophys.45.S233_1

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DOI： 10.2142/biophys.45.S233_2

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL ACAD SCIENCES  

To scrutinize how a protein folds at atomic resolution, we performed 200 molecular dynamics simulations (each of 50 ns) of the miniprotein Trp-cage on the computational grid. Within the trajectories, 58 folding and 31 unfolding events were identified and subjected to extensive comparison and classification. Based on an analogy with biological sequences, the folding and unfolding trajectories (arrays of sequential snapshots of structures) were aligned by dynamic programming allowing gaps. A phylogenetic tree derived from the alignments revealed four distinct groups of the trajectories, characterized by the Trp side-chain motions and the main-chain motions. It was found that only one group attained the native structure and that the other three led to pseudonative structures having the correct main-chain trace but different nonnative Trp side-chain rotamers, indicating that those four folded structures were each attained through a unique folding pathway.

DOI： 10.1073/pnas.0407015102

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：BLACKWELL PUBLISHING LTD  

The structure of the tryptophan synthase beta(2) subunit (Pfbeta(2)) from the hyperthermophile, Pyrococcus furiosus, was determined by X-ray crystallographic analysis at 2.2 Angstrom resolution, and its stability was examined by DSC. This is the first report of the X-ray structure of the tryptophan synthase beta(2) subunit alone, although the structure of the tryptophan synthase alpha(2)beta(2) complex from Salmonella typhimurium has already been reported. The structure of Pfbeta(2) was essentially similar to that of the beta(2) subunit (Stbeta(2)) in the alpha(2)beta(2) complex from S. typhimurium. The sequence alignment with secondary structures of Pfbeta and Stbeta in monomeric form showed that six residues in the N-terminal region and three residues in the C-terminal region were deleted in Pfbeta, and one residue at Pro366 of Stbeta and at Ile63 of Pfbeta was inserted. The denaturation temperature of Pfbeta(2) was higher by 35 degreesC than the reported values from mesophiles at approximate to pH 8. On the basis of structural information on both proteins, the analyses of the contributions of each stabilization factor indicate that: (a) the higher stability of Pfbeta(2) is not caused by either a hydrophobic interaction or an increase in ion pairs; (b) the number of hydrogen bonds involved in the main chains of Pfbeta is greater by about 10% than that of Stbeta, indicating that the secondary structures of Pfbeta are more stabilized than those of Stbeta and (c) the sequence of Pfbeta seems to be better fitted to an ideally stable structure than that of Stbeta, as assessed from X-ray structure data.

DOI： 10.1111/j.1432-1033.2004.04191.x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JOHN WILEY & SONS INC  

A partial rigid-body method of molecular dynamics simulations for proteins and membranes is presented. In this method, the symplectic integrator for rigid bodies is combined with the equations of motion for the NPT ensemble. The standard NPT ensemble is extended to the membrane-specific ensembles, the NPAT (constant normal pressure and lateral surface area of membranes and constant temperature) and NPgammaT (constant normal pressure and lateral surface tension of membranes and constant temperature) ensembles. By more than 30-ns simulations of aqueous proteins and hydrated lipid bilayers, the results of the partial rigid-body method demonstrated excellent conservation of total energy and consistent behavior with the traditional constraint method in terms of structural distribution and fluctuation of proteins and lipids. The efficient implementation of the partial rigid-body method in parallel computation is presented, which is shown to work well in large-scale molecular dynamics simulations. (C) 2004 Wiley Periodicals, Inc.

DOI： 10.1002/jcc.10402

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.44.S56_1

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DOI： 10.2142/biophys.44.S63_3

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DOI： 10.2142/biophys.44.S213_1

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DOI： 10.2142/biophys.44.S212_3

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DOI： 10.2142/biophys.44.S113_3

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL ACAD SCIENCES  

Homologous recombination is an important biological process that occurs in all organisms and facilitates genome rearrangements and repair of DNA double-strand breaks. Eukaryotic Rad51 proteins (Rad51(sp) or Rhp51 in fission yeast) are functional and structural homologs of bacterial RecA protein, an evolutionarily conserved protein that plays a key role in homologous pairing and strand exchange between homologous DNA molecules in vitro. Here we show that the fission yeast swi5(+) gene, which was originally identified as a gene required for normal mating-type switching, encodes a protein conserved among eukaryotes and is involved in a previously uncharacterized Rhp51 (Rad51(sp))-dependent recombination repair pathway that does not require the Rhp55/57 (Rad55/57(sp)) function. Protein interactions with both Swi5 and Rhp51 were found to be mediated by a domain common to Swi2 and Sfr1 (Swi five-dependent recombination repair protein 1, a previously uncharacterized protein with sequence similarity to the C-terminal part of Swi2). Genetic epistasis analyses suggest that the Swi5-Sfr1-Rhp51 interactions function specifically in DNA recombination repair, whereas the Swi5-Swi2-Rhp5l interactions may function, together with chromodomain protein Swi6 (HP1 homolog), in mating-type switching.

DOI： 10.1073/pnas.2632890100

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.43.S62_2

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DOI： 10.1016/S0009-2614(03)00425-1

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.43.S90_2

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

A new algorithm for parallel calculation of the second derivatives (Hessian) of the conformational energy function of biomolecules in internal coordinates is proposed. The basic scheme of this algorithm is the division of the entire calculation of the Hessian matrix (called "task") into subtasks and the optimization of the assignment of processors to each subtask by considering both the load balancing and reduction of the communication cost. A genetic algorithm is used for this optimization considering the dependencies between subtasks. We applied this method to a glutaminyl transfer RNA (Gln-tRNA) molecule for which the scalability of our previously developed parallel algorithm was significantly decreased when the large number of processors was used. The speedup for the calculation was 32.6 times with 60 processors, which is considerably better than the speedup for our previously reported parallel algorithm. The elapsed time for the calculation of subtasks, data sending, and data receiving was analyzed, and the effect of the optimization using the genetic algorithm is discussed. (C) 2002 John Wiley Sons, Inc.

DOI： 10.1002/jcc.10039

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC  

Growing evidence suggests that horizontal gene transfer plays an integral role in the evolution of bacterial genomes. One of the debated examples of horizontal gene transfer from animal to prokaryote is the fibronectin type III domain (FnIIID). Certain extracellular proteins of soil bacteria contain an unusual cluster of FnHIDs, which show sequence similarity to those of animals and are likely to have been acquired horizontally from animals. Here we report the solution structure of the FnIIID of chitinase A1 from Bacillus circulans WL-12. To the best of our knowledge, this is the first tertiary structure to be reported for an FnIIID from a bacterial protein. The structure of the domain shows significant similarity to FnIIIDs from animal proteins. Sequence comparisons with FnIIIDs from other soil bacteria proteins show that the core-forming residues are highly conserved and, thus, are under strong evolutionary pressure. Striking similarities in the tertiary structures of bacterial FnIlIDs and their mammalian counterparts may support the hypothesis that the evolution of the FnIIID in bacterial carbohydrases occurred horizontally. The total lack of surface-exposed aromatic residues also suggests that the role of this FnIIID is different from those of other bacterial beta-sandwich domains, which function as carbohydrate-binding modules.

DOI： 10.1074/jbc.M109726200

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.41.S38_4

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.41.S105_1

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.40.S92_2

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Language：English   Publishing type：Research paper (international conference proceedings)  

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.40.S171_1

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.39.S163_4

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DOI： 10.1002/(SICI)1520-684X(19991130)30:13<13::AID-SCJ2>3.0.CO;2-7

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：ELSEVIER SCIENCE BV  

On hydrophobic effects, roles of water and the influence of denaturants are analyzed using molecular simulations. Roles of the hydrogen bonding and the hard core of water on hydrophobic effects are clarified by comparison of simulation results of water and the simple fluid whose size and density are the same as those of water.
As analysis of the influence of urea on hydrophobic effects, two methane association in urea solution is calculated. Our results support the hypothesis that urea stabilizes association of two methane. and we found out that it is due to smallness of a methane molecule. For larger hydrocarbons (with more than two carbon atoms), urea weakens hydrophobic effects, and we found out that it is due to the attractive interaction between solute and solvent.

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.39.S178_2

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The roles of hydrogen bonding and the hard core of water on hydrophobic hydration are clarified using Monte Carlo simulation and the test particle method to compare the cavity formation in water with that in a Lennard-Jones (LJ) fluid with the same molecular size and density. Similarities and differences in the cavity formation in the two fluids are examined in terms of the free energy, the energy change, and the change in the coordination number upon cavity formation. The free energy of cavity formation at a given density and the decrease in the coordination number around cavities in water are similar to those in the LJ fluid. These similarities are due to geometrical restriction of the hard core of molecules. The effect of the hydrogen bonding of water can be seen in the coordination-number dependence of the average energy of one molecule, regardless of whether water is in bulk or in the hydration shell. The temperature dependence of the correlation between the coordination number and energy can explain both the temperature dependence of hydrophobic enthalpy in the thermodynamic level and that of molecular energy changes near cavities in the molecular level. We conclude that combining the water-specific coordination-number dependence of energy (the hydrogen-bonding effect) with the decreased coordination number around hydrophobic groups (the hard-core effect) explains the special characteristics of hydrophobic hydration, such as iceberg formation, the entropy decrease at room temperature, and the large positive heat capacity change.

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

The off-lattice theory of solvation presented here is a generalization of the Flory-Huggins lattice theory of solvation using the fused hard-sphere system as a reference. The contact free energy, a generalization of the Flory chi, is formulated by a perturbation approach. The perturbation term contains the bulk-compression contribution in addition to the contact foe energy, and the bulk-compression is shown to compensate with the hard-sphere pressure of the reference system. The contact free energy is shown to be a local thermodynamical quantity and is related to the solvent accessible surface area. (C) 1998 Elsevier Science B.V.

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DOI： 10.1002/(SICI)1096-987X(19981130)19:15<1716::AID-JCC4>3.0.CO;2-Q

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Language：English   Publisher：Japanese Society for Bioinformatics  

DOI： 10.11234/gi1990.9.395

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Language：English   Publisher：Japanese Society for Bioinformatics  

DOI： 10.11234/gi1990.9.353

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Language：English   Publisher：Japanese Society for Bioinformatics  

We developed a computational method to detect identities in tRNA genes. The method uses the multidimensional scaling method to classify the sequences of tRNA genes into multiple groups of similar sequences, and also to extract characteristic bases that are conserved within a group but differ from other groups. This procedure was applied recursively to classify the sequences into hierarchical groups so that characteristic sites can be detected more precisely. We were able to detect many characteristic sites in T and D domains of tRNAs as well as the characteristic sites that have been detected experimentally. This suggests that the preservation of L-shape structure in tRNAs is important to the tRNA-ARS recognition.

DOI： 10.11234/gi1990.8.330

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：INTERNATIONAL SOCIETY COMPUTER S & THEIR APPLICATIONS (ISCA)  

This paper describes the design and implementation of a parallel programming environment, called PVMx, which provides dynamic resource management services. The PVMx has a flexible structure that allows users to specify a variety of polities for resource allocation, according to the application and hardware configuration. II also provides a scalable mechanism for resource management and provides a programming interface compatible with PVM. We have developed a general load distribution service as one of the resource allocation policies in PVMx and have applied it to a molecular dynamics simulation. This paper also describes the implementation and performance for the service.

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DOI： 10.1021/j100020a074

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：CELL PRESS  

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：CELL PRESS  

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Language：Japanese   Publisher：The Physical Society of Japan (JPS)  

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：CELL PRESS  

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：CELL PRESS  

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Language：Japanese   Publishing type：Article, review, commentary, editorial, etc. (other)  

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：GENETICS SOC JAPAN  

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：CELL PRESS  

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：CELL PRESS  

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：CELL PRESS  

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：CELL PRESS  

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：AMER CHEMICAL SOC  

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：BIOPHYSICAL SOCIETY  

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Language：English  

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Language：Japanese   Publisher：共立出版  

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：BIOPHYSICAL SOCIETY  

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：BIOPHYSICAL SOCIETY  

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DOI： 10.1021/ja002064f

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Other Link： http://id.ndl.go.jp/bib/5700590

Language：English   Publisher：INTERNATIONAL SOCIETY COMPUTER S & THEIR APPLICATIONS (ISCA)  

We have designed and implemented a new parallel programming environment called Parsley, which provides fine-grained scheduling services based on the structure of application programs. In Parsley, application programs are divided into subtasks which may run serially or in parallel. Parsley provides a programming interface that allows a user to define subtasks and to specify precedence constraints among them. According to this specification, Parsley schedules subtasks and allocates processors, thus, the subtasks are executed in a dependence-driven manner. We developed a parallel molecular dynamics simulation program based on the Parsley mechanism and executed it on three scalable multiprocessor systems, HITACHI SR2201, IBM SP/2, COMPAQ DS20 cluster. We found that Parsley is efficient for large-scale molecular dynamics simulation and that load balancing and automatic improvement of scheduling policies can be adopted to the scalable multiprocessor systems of different architecture.

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DOI： 10.1063/1.477940

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DOI： 10.1016/S0009-2614(99)00574-6

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DOI： 10.1093/nar/26.8.1974

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DOI： 10.1016/S0009-2614(98)00282-6

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DOI： 10.1021/jp980210m

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DOI： 10.1016/S0009-2614(97)01381-X

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

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Language：English   Publisher：ELSEVIER SCIENCE BV  

We present a general thermodynamical theory that can be used to extract contact free energies from solubility data. The physical pictures of the long-disputed Flory-Huggins and Sharp's theories of solvation were clarified by introducing a novel decomposition of the unitary process. It is shown that the Flory-Huggins theory takes insufficient account of excluded volume effects. We propose a theory of solvation using the fused hard-sphere theory, and the ''packing entropy'' introduced in this theory enables us to extend the accessible surface-area formalism to the case of chain solvents. (C) 1997 Elsevier Science B.V.

DOI： 10.1016/S0009-2614(97)00165-6

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：OXFORD UNIV PRESS  

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：OXFORD UNIV PRESS  

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