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For: Ishida H. Essential function of the N-termini tails of the proteasome for the gating mechanism revealed by molecular dynamics simulations: Essential Function of the N-termini Tails of the Proteasome. Proteins 2014;82:1985-99. [DOI: 10.1002/prot.24553] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 02/24/2014] [Accepted: 03/04/2014] [Indexed: 11/07/2022]
Number Cited by Other Article(s)
1
Ishida H, Kono H. Free Energy Landscape of H2A-H2B Displacement From Nucleosome. J Mol Biol 2022;434:167707. [PMID: 35777463 DOI: 10.1016/j.jmb.2022.167707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/11/2022] [Accepted: 06/23/2022] [Indexed: 12/14/2022]
2
Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA. Proc Natl Acad Sci U S A 2021;118:2020452118. [PMID: 33558240 DOI: 10.1073/pnas.2020452118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
3
Kono H, Sakuraba S, Ishida H. Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome. Biophys Physicobiol 2019;16:337-343. [PMID: 31984189 PMCID: PMC6975924 DOI: 10.2142/biophysico.16.0_337] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/05/2019] [Indexed: 01/19/2023]  Open
4
Kawabata T. Detection of cave pockets in large molecules: Spaces into which internal probes can enter, but external probes from outside cannot. Biophys Physicobiol 2019;16:391-406. [PMID: 31984193 PMCID: PMC6975925 DOI: 10.2142/biophysico.16.0_391] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/27/2019] [Indexed: 12/01/2022]  Open
5
Insight into Inhibitor Binding in the Eukaryotic Proteasome: Computations of the 20S CP. Int J Mol Sci 2018;19:ijms19123858. [PMID: 30514002 PMCID: PMC6321098 DOI: 10.3390/ijms19123858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/21/2018] [Accepted: 11/28/2018] [Indexed: 11/16/2022]  Open
6
Elghobashi-Meinhardt N. Exploring Peptide⁻Solvent Interactions: A Computational Study. Molecules 2018;23:E2355. [PMID: 30223458 PMCID: PMC6225229 DOI: 10.3390/molecules23092355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 09/06/2018] [Accepted: 09/10/2018] [Indexed: 11/17/2022]  Open
7
Kono H, Sakuraba S, Ishida H. Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA. PLoS Comput Biol 2018;14:e1006024. [PMID: 29505570 PMCID: PMC5854429 DOI: 10.1371/journal.pcbi.1006024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 03/15/2018] [Accepted: 02/01/2018] [Indexed: 11/19/2022]  Open
8
Ishida H, Kono H. H4 Tails Potentially Produce the Diversity in the Orientation of Two Nucleosomes. Biophys J 2017;113:978-990. [PMID: 28877499 DOI: 10.1016/j.bpj.2017.07.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/29/2017] [Accepted: 07/20/2017] [Indexed: 11/17/2022]  Open
9
Gunnoo M, Cazade PA, Galera-Prat A, Nash MA, Czjzek M, Cieplak M, Alvarez B, Aguilar M, Karpol A, Gaub H, Carrión-Vázquez M, Bayer EA, Thompson D. Nanoscale Engineering of Designer Cellulosomes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016;28:5619-47. [PMID: 26748482 DOI: 10.1002/adma.201503948] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/01/2015] [Indexed: 05/27/2023]
10
Ishida H, Matsumoto A. Mechanism for verification of mismatched and homoduplex DNAs by nucleotides-bound MutS analyzed by molecular dynamics simulations. Proteins 2016;84:1287-303. [PMID: 27238299 DOI: 10.1002/prot.25077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/13/2016] [Accepted: 05/24/2016] [Indexed: 11/10/2022]
11
Ishida H, Matsumoto A. Free-energy landscape of reverse tRNA translocation through the ribosome analyzed by electron microscopy density maps and molecular dynamics simulations. PLoS One 2014;9:e101951. [PMID: 24999999 PMCID: PMC4084982 DOI: 10.1371/journal.pone.0101951] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 06/12/2014] [Indexed: 01/11/2023]  Open
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