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For: Lemak AS, Lepock JR, Chen JZY. Molecular dynamics simulations of a protein model in uniform and elongational flows. Proteins 2003;51:224-35. [PMID: 12660991 DOI: 10.1002/prot.10273] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Number Cited by Other Article(s)
1
Herrera-Rodríguez AM, Dasanna AK, Daday C, Cruz-Chú ER, Aponte-Santamaría C, Schwarz US, Gräter F. The role of flow in the self-assembly of dragline spider silk proteins. Biophys J 2023;122:4241-4253. [PMID: 37803828 PMCID: PMC10645567 DOI: 10.1016/j.bpj.2023.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 07/14/2023] [Accepted: 09/29/2023] [Indexed: 10/08/2023]  Open
2
Papež P, Merzel F, Praprotnik M. Rotational Dynamics of a Protein under Shear Flow Studied by the Eckart Frame Formalism. J Phys Chem B 2023;127:7231-7243. [PMID: 37556834 PMCID: PMC10461304 DOI: 10.1021/acs.jpcb.3c02324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/20/2023] [Indexed: 08/11/2023]
3
Lamura A. Self-Attractive Semiflexible Polymers under an External Force Field. Polymers (Basel) 2022;14:polym14214762. [PMID: 36365755 PMCID: PMC9658670 DOI: 10.3390/polym14214762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]  Open
4
Hakala T, Yates EV, Challa PK, Toprakcioglu Z, Nadendla K, Matak-Vinkovic D, Dobson CM, Martínez R, Corzana F, Knowles TPJ, Bernardes GJL. Accelerating Reaction Rates of Biomolecules by Using Shear Stress in Artificial Capillary Systems. J Am Chem Soc 2021;143:16401-16410. [PMID: 34606279 PMCID: PMC8517977 DOI: 10.1021/jacs.1c03681] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Indexed: 12/15/2022]
5
Walinda E, Morimoto D, Shirakawa M, Scheler U, Sugase K. Visualizing protein motion in Couette flow by all-atom molecular dynamics. Biochim Biophys Acta Gen Subj 2020;1864:129383. [DOI: 10.1016/j.bbagen.2019.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 06/06/2019] [Accepted: 06/06/2019] [Indexed: 12/29/2022]
6
Szymczak P, Cieplak M. Hydrodynamic effects in proteins. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2011;23:033102. [PMID: 21406855 DOI: 10.1088/0953-8984/23/3/033102] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
7
Singh AR, Giri D, Kumar S. Force induced unfolding of biopolymers in a cellular environment: a model study. J Chem Phys 2009;131:065103. [PMID: 19691413 DOI: 10.1063/1.3197010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
8
Ge H, Jin F, Li J, Wu C. How Much Force Is Needed To Stretch a Coiled Chain in Solution? Macromolecules 2009. [DOI: 10.1021/ma9005523] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
9
Singh AR, Giri D, Kumar S. Effects of molecular crowding on stretching of polymers in poor solvent. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009;79:051801. [PMID: 19518472 DOI: 10.1103/physreve.79.051801] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 01/28/2009] [Indexed: 05/27/2023]
10
Rajesh R, Giri D, Jensen I, Kumar S. Role of pulling direction in understanding the energy landscape of proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008;78:021905. [PMID: 18850863 DOI: 10.1103/physreve.78.021905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Indexed: 05/26/2023]
11
Szymczak P, Cieplak M. Stretching of proteins in a uniform flow. J Chem Phys 2007;125:164903. [PMID: 17092135 DOI: 10.1063/1.2358346] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
12
Kumar S, Jensen I, Jacobsen JL, Guttmann AJ. Role of conformational entropy in force-induced biopolymer unfolding. PHYSICAL REVIEW LETTERS 2007;98:128101. [PMID: 17501157 DOI: 10.1103/physrevlett.98.128101] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Indexed: 05/15/2023]
13
Kumar S, Giri D. Does changing the pulling direction give better insight into biomolecules? PHYSICAL REVIEW LETTERS 2007;98:048101. [PMID: 17358815 DOI: 10.1103/physrevlett.98.048101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Indexed: 05/14/2023]
14
Jaspe J, Hagen SJ. Do protein molecules unfold in a simple shear flow? Biophys J 2006;91:3415-24. [PMID: 16891374 PMCID: PMC1614479 DOI: 10.1529/biophysj.106.089367] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
15
Kumar S, Giri D. Force-induced conformational transition in a system of interacting stiff polymers: application to unfolding. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005;72:052901. [PMID: 16383670 DOI: 10.1103/physreve.72.052901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2005] [Indexed: 05/05/2023]
16
Ji S, Ding J. Nonequilibrium Monte Carlo simulation of lattice block copolymer chains subject to oscillatory shear flow. J Chem Phys 2005;122:164901. [PMID: 15945701 DOI: 10.1063/1.1884595] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
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