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For: Yasuda S, Yoshidome T, Harano Y, Roth R, Oshima H, Oda K, Sugita Y, Ikeguchi M, Kinoshita M. Free-energy function for discriminating the native fold of a protein from misfolded decoys. Proteins 2011;79:2161-71. [PMID: 21557318 DOI: 10.1002/prot.23036] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2010] [Revised: 02/24/2011] [Accepted: 03/13/2011] [Indexed: 11/08/2022]
Number Cited by Other Article(s)
1
Yasuda S, Hayashi T, Kajiwara Y, Murata T, Kinoshita M. Analyses based on statistical thermodynamics for large difference between thermophilic rhodopsin and xanthorhodopsin in terms of thermostability. J Chem Phys 2019;150:055101. [DOI: 10.1063/1.5082217] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
2
Hayashi T, Inoue M, Yasuda S, Petretto E, Škrbić T, Giacometti A, Kinoshita M. Universal effects of solvent species on the stabilized structure of a protein. J Chem Phys 2018;149:045105. [PMID: 30068177 DOI: 10.1063/1.5042111] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
3
Hayashi T, Yasuda S, Škrbić T, Giacometti A, Kinoshita M. Unraveling protein folding mechanism by analyzing the hierarchy of models with increasing level of detail. J Chem Phys 2017;147:125102. [DOI: 10.1063/1.4999376] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
4
Yasuda S, Kajiwara Y, Toyoda Y, Morimoto K, Suno R, Iwata S, Kobayashi T, Murata T, Kinoshita M. Hot-Spot Residues to be Mutated Common in G Protein-Coupled Receptors of Class A: Identification of Thermostabilizing Mutations Followed by Determination of Three-Dimensional Structures for Two Example Receptors. J Phys Chem B 2017. [DOI: 10.1021/acs.jpcb.7b02997] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
5
Kajiwara Y, Yasuda S, Takamuku Y, Murata T, Kinoshita M. Identification of thermostabilizing mutations for a membrane protein whose three-dimensional structure is unknown. J Comput Chem 2016;38:211-223. [DOI: 10.1002/jcc.24673] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 10/24/2016] [Accepted: 10/30/2016] [Indexed: 01/15/2023]
6
Suzuki M, Imao A, Mogami G, Chishima R, Watanabe T, Yamaguchi T, Morimoto N, Wazawa T. Strong Dependence of Hydration State of F-Actin on the Bound Mg(2+)/Ca(2+) Ions. J Phys Chem B 2016;120:6917-28. [PMID: 27332748 DOI: 10.1021/acs.jpcb.6b02584] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
7
Urquiza-Carvalho GA, Fragoso WD, Rocha GB. Assessment of semiempirical enthalpy of formation in solution as an effective energy function to discriminate native-like structures in protein decoy sets. J Comput Chem 2016;37:1962-72. [DOI: 10.1002/jcc.24415] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/29/2016] [Accepted: 05/11/2016] [Indexed: 11/09/2022]
8
Yasuda S, Kajiwara Y, Takamuku Y, Suzuki N, Murata T, Kinoshita M. Identification of Thermostabilizing Mutations for Membrane Proteins: Rapid Method Based on Statistical Thermodynamics. J Phys Chem B 2016;120:3833-43. [DOI: 10.1021/acs.jpcb.6b01405] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
9
Ikebe J, Umezawa K, Higo J. Enhanced sampling simulations to construct free-energy landscape of protein-partner substrate interaction. Biophys Rev 2016;8:45-62. [PMID: 28510144 PMCID: PMC5425738 DOI: 10.1007/s12551-015-0189-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 12/07/2015] [Indexed: 01/08/2023]  Open
10
Murakami S, Oshima H, Hayashi T, Kinoshita M. On the physics of thermal-stability changes upon mutations of a protein. J Chem Phys 2015;143:125102. [DOI: 10.1063/1.4931814] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
11
Kamo F, Ishizuka R, Matubayasi N. Correlation analysis for heat denaturation of Trp-cage miniprotein with explicit solvent. Protein Sci 2015;25:56-66. [PMID: 26189564 DOI: 10.1002/pro.2754] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/15/2015] [Indexed: 11/10/2022]
12
Oda K, Kinoshita M. Physicochemical origin of high correlation between thermal stability of a protein and its packing efficiency: a theoretical study for staphylococcal nuclease mutants. Biophys Physicobiol 2015;12:1-12. [PMID: 27493849 PMCID: PMC4736840 DOI: 10.2142/biophysico.12.0_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 06/18/2015] [Indexed: 12/01/2022]  Open
13
Yoshidome T, Ekimoto T, Matubayasi N, Harano Y, Kinoshita M, Ikeguchi M. An accurate and efficient computation method of the hydration free energy of a large, complex molecule. J Chem Phys 2015;142:175101. [DOI: 10.1063/1.4919636] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
14
Yasuda S, Hayashi T, Kinoshita M. Physical origins of the high structural stability of CLN025 with only ten residues. J Chem Phys 2014;141:105103. [DOI: 10.1063/1.4894753] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
15
Oshima H, Kinoshita M. Effects of sugars on the thermal stability of a protein. J Chem Phys 2014;138:245101. [PMID: 23822280 DOI: 10.1063/1.4811287] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
16
Yasuda S, Oshima H, Kinoshita M. Structural stability of proteins in aqueous and nonpolar environments. J Chem Phys 2013;137:135103. [PMID: 23039615 DOI: 10.1063/1.4755755] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
17
Kinoshita M. A new theoretical approach to biological self-assembly. Biophys Rev 2013;5:283-293. [PMID: 28510109 DOI: 10.1007/s12551-013-0100-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 01/02/2013] [Indexed: 11/25/2022]  Open
18
Yoshidome T, Ito Y, Matubayasi N, Ikeguchi M, Kinoshita M. Structural characteristics of yeast F1-ATPase before and after 16-degree rotation of the γ subunit: theoretical analysis focused on the water-entropy effect. J Chem Phys 2012;137:035102. [PMID: 22830731 DOI: 10.1063/1.4734298] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
19
Yoshidome T, Kinoshita M. Physical origin of hydrophobicity studied in terms of cold denaturation of proteins: comparison between water and simple fluids. Phys Chem Chem Phys 2012;14:14554-66. [PMID: 23014986 DOI: 10.1039/c2cp41738c] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
20
Application of Hydration Thermodynamics to the Evaluation of Protein Structures and Protein-Ligand Binding. ENTROPY 2012. [DOI: 10.3390/e14081443] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
21
Mishima H, Yasuda S, Yoshidome T, Oshima H, Harano Y, Ikeguchi M, Kinoshita M. Characterization of experimentally determined native-structure models of a protein using energetic and entropic components of free-energy function. J Phys Chem B 2012;116:7776-86. [PMID: 22697465 DOI: 10.1021/jp301541z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
22
Koppole S, Schaefer M. A discriminative Ramachandran potential of mean force aimed at minimizing secondary structure bias. J Comput Chem 2012;33:791-9. [DOI: 10.1002/jcc.22908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 10/24/2011] [Accepted: 11/20/2011] [Indexed: 11/12/2022]
23
Du S, Harano Y, Kinoshita M, Sakurai M. A scoring function based on solvation thermodynamics for protein structure prediction. Biophysics (Nagoya-shi) 2012;8:127-38. [PMID: 27493529 PMCID: PMC4629643 DOI: 10.2142/biophysics.8.127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 07/31/2012] [Indexed: 12/01/2022]  Open
24
Kodama R, Roth R, Harano Y, Kinoshita M. Morphometric approach to thermodynamic quantities of solvation of complex molecules: Extension to multicomponent solvent. J Chem Phys 2011;135:045103. [DOI: 10.1063/1.3617247] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
25
Oshima H, Yasuda S, Yoshidome T, Ikeguchi M, Kinoshita M. Crucial importance of the water-entropy effect in predicting hot spots in protein–protein complexes. Phys Chem Chem Phys 2011;13:16236-46. [DOI: 10.1039/c1cp21597c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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