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Number Cited by Other Article(s)
1
Hayashi T, Matsuda T, Nagata T, Katahira M, Kinoshita M. Mechanism of protein-RNA recognition: analysis based on the statistical mechanics of hydration. Phys Chem Chem Phys 2019;20:9167-9180. [PMID: 29560998 DOI: 10.1039/c8cp00155c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
2
Oshima H, Hayashi T, Kinoshita M. Statistical Thermodynamics for Actin-Myosin Binding: The Crucial Importance of Hydration Effects. Biophys J 2017;110:2496-2506. [PMID: 27276267 DOI: 10.1016/j.bpj.2016.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 01/01/2023]  Open
3
Melo R, Fieldhouse R, Melo A, Correia JDG, Cordeiro MNDS, Gümüş ZH, Costa J, Bonvin AMJJ, Moreira IS. A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces. Int J Mol Sci 2016;17:E1215. [PMID: 27472327 PMCID: PMC5000613 DOI: 10.3390/ijms17081215] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/11/2016] [Accepted: 07/18/2016] [Indexed: 12/17/2022]  Open
4
Hayashi T, Oshima H, Yasuda S, Kinoshita M. Mechanism of One-to-Many Molecular Recognition Accompanying Target-Dependent Structure Formation: For the Tumor Suppressor p53 Protein as an Example. J Phys Chem B 2015;119:14120-9. [PMID: 26421917 DOI: 10.1021/acs.jpcb.5b08513] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
5
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: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
6
Franck JM, Ding Y, Stone K, Qin PZ, Han S. Anomalously Rapid Hydration Water Diffusion Dynamics Near DNA Surfaces. J Am Chem Soc 2015;137:12013-23. [PMID: 26256693 PMCID: PMC4656248 DOI: 10.1021/jacs.5b05813] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
7
Hayashi T, Chiba S, Kaneta Y, Furuta T, Sakurai M. ATP-induced conformational changes of nucleotide-binding domains in an ABC transporter. Importance of the water-mediated entropic force. J Phys Chem B 2014;118:12612-20. [PMID: 25302667 DOI: 10.1021/jp507930e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
8
Hayashi T, Oshima H, Mashima T, Nagata T, Katahira M, Kinoshita M. Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition. Nucleic Acids Res 2014;42:6861-75. [PMID: 24803670 PMCID: PMC4066790 DOI: 10.1093/nar/gku382] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
9
Martin DR, Fioretto D, Matyushov DV. Depolarized light scattering and dielectric response of a peptide dissolved in water. J Chem Phys 2014;140:035101. [DOI: 10.1063/1.4861965] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
10
Ahmed MH, Habtemariam M, Safo MK, Scarsdale JN, Spyrakis F, Cozzini P, Mozzarelli A, Kellogg GE. Unintended consequences? Water molecules at biological and crystallographic protein–protein interfaces. Comput Biol Chem 2013;47:126-41. [DOI: 10.1016/j.compbiolchem.2013.08.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/27/2013] [Accepted: 08/27/2013] [Indexed: 01/31/2023]
11
Mishima H, Oshima H, Yasuda S, Amano KI, Kinoshita M. On the physics of multidrug efflux through a biomolecular complex. J Chem Phys 2013;139:205102. [DOI: 10.1063/1.4832896] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
12
May A, Pool R, van Dijk E, Bijlard J, Abeln S, Heringa J, Feenstra KA. Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins. ACTA ACUST UNITED AC 2013;30:326-34. [PMID: 24273239 DOI: 10.1093/bioinformatics/btt675] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
13
Valid entropy–enthalpy compensation: Fine mechanisms at microscopic level. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.02.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
14
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: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
15
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: 5.2] [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
16
Doyle CM, Rumfeldt JA, Broom HR, Broom A, Stathopulos PB, Vassall KA, Almey JJ, Meiering EM. Energetics of oligomeric protein folding and association. Arch Biochem Biophys 2012;531:44-64. [PMID: 23246784 DOI: 10.1016/j.abb.2012.12.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/29/2012] [Accepted: 12/05/2012] [Indexed: 12/11/2022]
17
Wojdyla JA, Fleishman SJ, Baker D, Kleanthous C. Structure of the ultra-high-affinity colicin E2 DNase--Im2 complex. J Mol Biol 2012;417:79-94. [PMID: 22306467 DOI: 10.1016/j.jmb.2012.01.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 01/10/2012] [Accepted: 01/13/2012] [Indexed: 11/18/2022]
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