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For: Jagielska A, Scheraga HA. Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: All-atom molecular dynamics in implicit solvent. J Comput Chem 2007;28:1068-82. [PMID: 17279497 DOI: 10.1002/jcc.20631] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Number Cited by Other Article(s)
1
Rahmatullah R, Marquis CP. Evaluation of alternate hosts for recombinant expression of a reductive dehalogenase. Enzyme Microb Technol 2024;174:110390. [PMID: 38147780 DOI: 10.1016/j.enzmictec.2023.110390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 12/28/2023]
2
Folescu DE, Onufriev AV. A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules. ACS OMEGA 2022;7:26123-26136. [PMID: 35936397 PMCID: PMC9352323 DOI: 10.1021/acsomega.2c01484] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
3
Onufriev AV, Izadi S. Water models for biomolecular simulations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1347] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
4
Otosu T, Ishii K, Oikawa H, Arai M, Takahashi S, Tahara T. Highly Heterogeneous Nature of the Native and Unfolded States of the B Domain of Protein A Revealed by Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy. J Phys Chem B 2017;121:5463-5473. [DOI: 10.1021/acs.jpcb.7b00546] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
5
Izadi S, Anandakrishnan R, Onufriev AV. Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber. J Chem Theory Comput 2016;12:5946-5959. [PMID: 27748599 PMCID: PMC5649046 DOI: 10.1021/acs.jctc.6b00712] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
6
Protein remains stable at unusually high temperatures when solvated in aqueous mixtures of amino acid based ionic liquids. J Mol Model 2016;22:258. [DOI: 10.1007/s00894-016-3123-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 09/08/2016] [Indexed: 10/20/2022]
7
Anandakrishnan R, Drozdetski A, Walker RC, Onufriev AV. Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations. Biophys J 2016;108:1153-64. [PMID: 25762327 DOI: 10.1016/j.bpj.2014.12.047] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 12/23/2014] [Accepted: 12/29/2014] [Indexed: 11/24/2022]  Open
8
Radic S, Nedumpully-Govindan P, Chen R, Salonen E, Brown JM, Ke PC, Ding F. Effect of fullerenol surface chemistry on nanoparticle binding-induced protein misfolding. NANOSCALE 2014;6:8340-8349. [PMID: 24934397 DOI: 10.1039/c4nr01544d] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
9
Moritsugu K, Kidera A, Smith JC. Solvent Friction Effects Propagate over the Entire Protein Molecule through Low-Frequency Collective Modes. J Phys Chem B 2014;118:8559-65. [DOI: 10.1021/jp503956m] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
10
Mukhopadhyay A, Aguilar BH, Tolokh IS, Onufriev AV. Introducing Charge Hydration Asymmetry into the Generalized Born Model. J Chem Theory Comput 2014;10:1788-1794. [PMID: 24803871 PMCID: PMC3985468 DOI: 10.1021/ct4010917] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Indexed: 12/15/2022]
11
Yin Y, Maisuradze GG, Liwo A, Scheraga HA. Hidden protein folding pathways in free-energy landscapes uncovered by network analysis. J Chem Theory Comput 2012;8:1176-1189. [PMID: 22715321 DOI: 10.1021/ct200806n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
12
Onufriev AV, Sigalov G. A strategy for reducing gross errors in the generalized Born models of implicit solvation. J Chem Phys 2011;134:164104. [PMID: 21528947 DOI: 10.1063/1.3578686] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]  Open
13
Tian XH, Zheng YH, Jiao X, Liu CX, Chang S. Computational model for protein unfolding simulation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011;83:061910. [PMID: 21797406 DOI: 10.1103/physreve.83.061910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 03/11/2011] [Indexed: 05/31/2023]
14
Maisuradze GG, Liwo A, Ołdziej S, Scheraga HA. Evidence, from simulations, of a single state with residual native structure at the thermal denaturation midpoint of a small globular protein. J Am Chem Soc 2010;132:9444-52. [PMID: 20568747 DOI: 10.1021/ja1031503] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
15
Qi Y, Huang Y, Liang H, Liu Z, Lai L. Folding simulations of a de novo designed protein with a betaalphabeta fold. Biophys J 2010;98:321-9. [PMID: 20338854 DOI: 10.1016/j.bpj.2009.10.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2009] [Revised: 10/08/2009] [Accepted: 10/13/2009] [Indexed: 01/06/2023]  Open
16
Maupetit J, Derreumaux P, Tufféry P. A fast method for large-scale de novo peptide and miniprotein structure prediction. J Comput Chem 2010;31:726-38. [PMID: 19569182 DOI: 10.1002/jcc.21365] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
17
Maisuradze GG, Senet P, Czaplewski C, Liwo A, Scheraga HA. Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field. J Phys Chem A 2010;114:4471-85. [PMID: 20166738 PMCID: PMC2849147 DOI: 10.1021/jp9117776] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
18
Maisuradze GG, Liwo A, Scheraga HA. Relation between free energy landscapes of proteins and dynamics. J Chem Theory Comput 2010;6:583-595. [PMID: 23620713 DOI: 10.1021/ct9005745] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
19
Frembgen-Kesner T, Elcock AH. Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins. J Chem Theory Comput 2009;5:242-56. [DOI: 10.1021/ct800499p] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
20
Baxa MC, Freed KF, Sosnick TR. Quantifying the structural requirements of the folding transition state of protein A and other systems. J Mol Biol 2008;381:1362-81. [PMID: 18625237 PMCID: PMC2742318 DOI: 10.1016/j.jmb.2008.06.067] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Revised: 06/18/2008] [Accepted: 06/23/2008] [Indexed: 11/22/2022]
21
Lei H, Wu C, Wang ZX, Zhou Y, Duan Y. Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations. J Chem Phys 2008;128:235105. [PMID: 18570534 DOI: 10.1063/1.2937135] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]  Open
22
Scheraga HA. From helix-coil transitions to protein folding. Biopolymers 2008;89:479-85. [PMID: 18008324 DOI: 10.1002/bip.20890] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
23
Strodel B, Fitzpatrick AW, Vendruscolo M, Dobson CM, Wales DJ. Characterizing the First Steps of Amyloid Formation for the ccβ Peptide. J Phys Chem B 2008;112:9998-10004. [DOI: 10.1021/jp801222x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
24
Chen J, Brooks CL, Khandogin J. Recent advances in implicit solvent-based methods for biomolecular simulations. Curr Opin Struct Biol 2008;18:140-8. [PMID: 18304802 DOI: 10.1016/j.sbi.2008.01.003] [Citation(s) in RCA: 254] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 12/22/2007] [Accepted: 01/09/2008] [Indexed: 11/29/2022]
25
Chen J, Brooks CL. Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. Phys Chem Chem Phys 2007;10:471-81. [PMID: 18183310 DOI: 10.1039/b714141f] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
26
Murarka RK, Liwo A, Scheraga HA. Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone. J Chem Phys 2007;127:155103. [DOI: 10.1063/1.2784200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]  Open
27
Chen J, Brooks CL, Scheraga HA. Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy. J Phys Chem B 2007;112:242-9. [PMID: 17880128 PMCID: PMC2561919 DOI: 10.1021/jp074355h] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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