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For: Karanicolas J, Brooks CL. The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci 2002;11:2351-61. [PMID: 12237457 PMCID: PMC2373711 DOI: 10.1110/ps.0205402] [Citation(s) in RCA: 317] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Number Cited by Other Article(s)
1
Mazzaferro N, Sasmal S, Cossio P, Hocky GM. Good Rates From Bad Coordinates: The Exponential Average Time-dependent Rate Approach. J Chem Theory Comput 2024;20:5901-5912. [PMID: 38954555 PMCID: PMC11270837 DOI: 10.1021/acs.jctc.4c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024]
2
Sternke-Hoffmann R, Sun X, Menzel A, Pinto MDS, Venclovaite U, Wördehoff M, Hoyer W, Zheng W, Luo J. Phase Separation and Aggregation of α-Synuclein Diverge at Different Salt Conditions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2308279. [PMID: 38973194 DOI: 10.1002/advs.202308279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 05/27/2024] [Indexed: 07/09/2024]
3
Jung J, Yagi K, Tan C, Oshima H, Mori T, Yu I, Matsunaga Y, Kobayashi C, Ito S, Ugarte La Torre D, Sugita Y. GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. J Phys Chem B 2024;128:6028-6048. [PMID: 38876465 PMCID: PMC11215777 DOI: 10.1021/acs.jpcb.4c02096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/16/2024]
4
Sternke-Hoffmann R, Sun X, Menzel A, Pinto MDS, Venclovaitė U, Wördehoff M, Hoyer W, Zheng W, Luo J. Phase Separation and Aggregation of α-Synuclein Diverge at Different Salt Conditions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582895. [PMID: 38464093 PMCID: PMC10925286 DOI: 10.1101/2024.03.01.582895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
5
Bjarnason S, McIvor JAP, Prestel A, Demény KS, Bullerjahn JT, Kragelund BB, Mercadante D, Heidarsson PO. DNA binding redistributes activation domain ensemble and accessibility in pioneer factor Sox2. Nat Commun 2024;15:1445. [PMID: 38365983 PMCID: PMC10873366 DOI: 10.1038/s41467-024-45847-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/01/2024] [Indexed: 02/18/2024]  Open
6
Barati F, Hosseini F, Vafaee R, Sabouri Z, Ghadam P, Arab SS, Shadfar N, Piroozmand F. In silico approaches to investigate enzyme immobilization: a comprehensive systematic review. Phys Chem Chem Phys 2024;26:5744-5761. [PMID: 38294035 DOI: 10.1039/d3cp03989g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
7
Lan PD, Nissley DA, O’Brien EP, Nguyen TT, Li MS. Deciphering the free energy landscapes of SARS-CoV-2 wild type and Omicron variant interacting with human ACE2. J Chem Phys 2024;160:055101. [PMID: 38310477 PMCID: PMC11223169 DOI: 10.1063/5.0188053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 01/08/2024] [Indexed: 02/05/2024]  Open
8
Bačić Toplek F, Scalone E, Stegani B, Paissoni C, Capelli R, Camilloni C. Multi-eGO: Model Improvements toward the Study of Complex Self-Assembly Processes. J Chem Theory Comput 2024;20:459-468. [PMID: 38153340 PMCID: PMC10782439 DOI: 10.1021/acs.jctc.3c01182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 12/29/2023]
9
Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023;52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
10
Galvanetto N, Ivanović MT, Chowdhury A, Sottini A, Nüesch MF, Nettels D, Best RB, Schuler B. Extreme dynamics in a biomolecular condensate. Nature 2023:10.1038/s41586-023-06329-5. [PMID: 37468629 DOI: 10.1038/s41586-023-06329-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/14/2023] [Indexed: 07/21/2023]
11
Halder R, Nissley DA, Sitarik I, Jiang Y, Rao Y, Vu QV, Li MS, Pritchard J, O'Brien EP. How soluble misfolded proteins bypass chaperones at the molecular level. Nat Commun 2023;14:3689. [PMID: 37344452 DOI: 10.1038/s41467-023-38962-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/24/2023] [Indexed: 06/23/2023]  Open
12
Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images. PLoS Comput Biol 2022;18:e1010384. [PMID: 36580448 PMCID: PMC9833559 DOI: 10.1371/journal.pcbi.1010384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/11/2023] [Accepted: 12/20/2022] [Indexed: 12/30/2022]  Open
13
Multivariate effects of pH, salt, and Zn2+ ions on Aβ40 fibrillation. Commun Chem 2022;5:171. [PMID: 36697708 PMCID: PMC9814776 DOI: 10.1038/s42004-022-00786-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022]  Open
14
Rizuan A, Jovic N, Phan TM, Kim YC, Mittal J. Developing Bonded Potentials for a Coarse-Grained Model of Intrinsically Disordered Proteins. J Chem Inf Model 2022;62:4474-4485. [PMID: 36066390 PMCID: PMC10165611 DOI: 10.1021/acs.jcim.2c00450] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
15
Chang L, Perez A. Deciphering the Folding Mechanism of Proteins G and L and Their Mutants. J Am Chem Soc 2022;144:14668-14677. [PMID: 35930769 DOI: 10.1021/jacs.2c04488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
16
Oide M, Sugita Y. Protein Folding Intermediates on the Dimensionality Reduced Landscape with UMAP and Native Contact Likelihood. J Chem Phys 2022;157:075101. [DOI: 10.1063/5.0099094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
17
Ooka K, Liu R, Arai M. The Wako-Saitô-Muñoz-Eaton Model for Predicting Protein Folding and Dynamics. Molecules 2022;27:molecules27144460. [PMID: 35889332 PMCID: PMC9319528 DOI: 10.3390/molecules27144460] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022]  Open
18
Sahoo A, Lee PY, Matysiak S. Transferable and Polarizable Coarse Grained Model for Proteins─ProMPT. J Chem Theory Comput 2022;18:5046-5055. [PMID: 35793442 DOI: 10.1021/acs.jctc.2c00269] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
19
Multi-eGO: An in silico lens to look into protein aggregation kinetics at atomic resolution. Proc Natl Acad Sci U S A 2022;119:e2203181119. [PMID: 35737839 PMCID: PMC9245614 DOI: 10.1073/pnas.2203181119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
20
Tan C, Jung J, Kobayashi C, Torre DUL, Takada S, Sugita Y. Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations. PLoS Comput Biol 2022;18:e1009578. [PMID: 35381009 PMCID: PMC9012402 DOI: 10.1371/journal.pcbi.1009578] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/15/2022] [Accepted: 03/26/2022] [Indexed: 12/28/2022]  Open
21
Effects of ionic strength on the folding and stability of SAMP1, a ubiquitin-like halophilic protein. Biophys J 2022;121:552-564. [PMID: 35063455 PMCID: PMC8874027 DOI: 10.1016/j.bpj.2022.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/13/2021] [Accepted: 01/13/2022] [Indexed: 11/21/2022]  Open
22
Release of linker histone from the nucleosome driven by polyelectrolyte competition with a disordered protein. Nat Chem 2022;14:224-231. [PMID: 34992286 DOI: 10.1038/s41557-021-00839-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 10/19/2021] [Indexed: 12/13/2022]
23
Santhakumar V, Manuel Mascarenhas N. The role of C-terminal helix in the conformational transition of an arginine binding protein. J Struct Biol X 2022;6:100071. [PMID: 36035778 PMCID: PMC9402392 DOI: 10.1016/j.yjsbx.2022.100071] [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: 04/04/2022] [Accepted: 08/06/2022] [Indexed: 11/27/2022]  Open
24
Nguyen H, Lan PD, Nissley DA, O’Brien EP, Li MS. Electrostatic Interactions Explain the Higher Binding Affinity of the CR3022 Antibody for SARS-CoV-2 than the 4A8 Antibody. J Phys Chem B 2021;125:7368-7379. [PMID: 34228472 PMCID: PMC8276604 DOI: 10.1021/acs.jpcb.1c03639] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/30/2021] [Indexed: 12/23/2022]
25
Giulini M, Rigoli M, Mattiotti G, Menichetti R, Tarenzi T, Fiorentini R, Potestio R. From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules. Front Mol Biosci 2021;8:676976. [PMID: 34164432 PMCID: PMC8215203 DOI: 10.3389/fmolb.2021.676976] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/06/2021] [Indexed: 12/18/2022]  Open
26
Shinobu A, Kobayashi C, Matsunaga Y, Sugita Y. Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins. J Chem Inf Model 2021;61:2427-2443. [PMID: 33956432 DOI: 10.1021/acs.jcim.1c00286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
27
Bedford JT, Poutsma J, Diawara N, Greene LH. The nature of persistent interactions in two model β-grasp proteins reveals the advantage of symmetry in stability. J Comput Chem 2021;42:600-607. [PMID: 33534913 DOI: 10.1002/jcc.26477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/27/2020] [Accepted: 11/22/2020] [Indexed: 01/25/2023]
28
Mahmood MI, Poma AB, Okazaki KI. Optimizing Gō-MARTINI Coarse-Grained Model for F-BAR Protein on Lipid Membrane. Front Mol Biosci 2021;8:619381. [PMID: 33693028 PMCID: PMC7937874 DOI: 10.3389/fmolb.2021.619381] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/14/2021] [Indexed: 12/31/2022]  Open
29
Smith AK, Soltani M, Wilkerson JW, Timmerman BD, Zhao EL, Bundy BC, Knotts TA. Coarse-grained simulation of PEGylated and tethered protein devices at all experimentally accessible surface residues on β-lactamase for stability analysis and comparison. J Chem Phys 2021;154:075102. [PMID: 33607875 DOI: 10.1063/5.0032019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
30
Brotzakis ZF, Vendruscolo M, Bolhuis PG. A method of incorporating rate constants as kinetic constraints in molecular dynamics simulations. Proc Natl Acad Sci U S A 2021;118:e2012423118. [PMID: 33376207 PMCID: PMC7812743 DOI: 10.1073/pnas.2012423118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
31
Ugarte La Torre D, Takada S. Coarse-grained implicit solvent lipid force field with a compatible resolution to the Cα protein representation. J Chem Phys 2020;153:205101. [PMID: 33261497 DOI: 10.1063/5.0026342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
32
Subramanian S, Golla H, Divakar K, Kannan A, de Sancho D, Naganathan AN. Slow Folding of a Helical Protein: Large Barriers, Strong Internal Friction, or a Shallow, Bumpy Landscape? J Phys Chem B 2020;124:8973-8983. [PMID: 32955882 PMCID: PMC7659034 DOI: 10.1021/acs.jpcb.0c05976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
33
Avestan MS, Javidi A, Ganote LP, Brown JM, Stan G. Kinetic effects in directional proteasomal degradation of the green fluorescent protein. J Chem Phys 2020;153:105101. [DOI: 10.1063/5.0015191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
34
Nguyen HL, Lan PD, Thai NQ, Nissley DA, O'Brien EP, Li MS. Does SARS-CoV-2 Bind to Human ACE2 More Strongly Than Does SARS-CoV? J Phys Chem B 2020;124:7336-7347. [PMID: 32790406 PMCID: PMC7433338 DOI: 10.1021/acs.jpcb.0c04511] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
35
Protein mechanics probed using simple molecular models. Biochim Biophys Acta Gen Subj 2020;1864:129613. [DOI: 10.1016/j.bbagen.2020.129613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/06/2020] [Accepted: 04/08/2020] [Indexed: 01/14/2023]
36
Mioduszewski Ł, Różycki B, Cieplak M. Pseudo-Improper-Dihedral Model for Intrinsically Disordered Proteins. J Chem Theory Comput 2020;16:4726-4733. [PMID: 32436706 PMCID: PMC7588027 DOI: 10.1021/acs.jctc.0c00338] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
37
Lafita A, Tian P, Best RB, Bateman A. TADOSS: computational estimation of tandem domain swap stability. Bioinformatics 2020;35:2507-2508. [PMID: 30500878 PMCID: PMC6612889 DOI: 10.1093/bioinformatics/bty974] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 10/13/2018] [Accepted: 11/28/2018] [Indexed: 11/17/2022]  Open
38
Taylor PA, Jayaraman A. Molecular Modeling and Simulations of Peptide–Polymer Conjugates. Annu Rev Chem Biomol Eng 2020;11:257-276. [DOI: 10.1146/annurev-chembioeng-092319-083243] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
39
Kimura R, Aumpuchin P, Hamaue S, Shimomura T, Kikuchi T. Analyses of the folding sites of irregular β-trefoil fold proteins through sequence-based techniques and Gō-model simulations. BMC Mol Cell Biol 2020;21:28. [PMID: 32295515 PMCID: PMC7477875 DOI: 10.1186/s12860-020-00271-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/31/2020] [Indexed: 02/07/2023]  Open
40
Nissley DA, Vu QV, Trovato F, Ahmed N, Jiang Y, Li MS, O'Brien EP. Electrostatic Interactions Govern Extreme Nascent Protein Ejection Times from Ribosomes and Can Delay Ribosome Recycling. J Am Chem Soc 2020;142:6103-6110. [PMID: 32138505 DOI: 10.1021/jacs.9b12264] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
41
Arsiccio A, McCarty J, Pisano R, Shea JE. Heightened Cold-Denaturation of Proteins at the Ice–Water Interface. J Am Chem Soc 2020;142:5722-5730. [DOI: 10.1021/jacs.9b13454] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
42
Hussain S, Haji-Akbari A. Studying rare events using forward-flux sampling: Recent breakthroughs and future outlook. J Chem Phys 2020;152:060901. [DOI: 10.1063/1.5127780] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
43
Wang Y, Brooks Iii CL. Electrostatic Forces Control the Negative Allosteric Regulation in a Disordered Protein Switch. J Phys Chem Lett 2020;11:864-868. [PMID: 31940206 DOI: 10.1021/acs.jpclett.9b03618] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
44
Theoretical and computational advances in protein misfolding. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020;118:1-31. [PMID: 31928722 DOI: 10.1016/bs.apcsb.2019.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
45
Ruiz-Ortiz I, De Sancho D. Competitive binding of HIF-1α and CITED2 to the TAZ1 domain of CBP from molecular simulations. Phys Chem Chem Phys 2020;22:8118-8127. [DOI: 10.1039/d0cp00328j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
46
Dima RI, Stan G. Computational Studies of Mechanical Remodeling of Substrate Proteins by AAA+ Biological Nanomachines. ACS SYMPOSIUM SERIES 2020. [DOI: 10.1021/bk-2020-1356.ch008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
47
Wei S, Zou X, Tian J, Huang H, Guo W, Chen Z. Control of Protein Conformation and Orientation on Graphene. J Am Chem Soc 2019;141:20335-20343. [PMID: 31774666 DOI: 10.1021/jacs.9b10705] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Schuler B, Borgia A, Borgia MB, Heidarsson PO, Holmstrom ED, Nettels D, Sottini A. Binding without folding - the biomolecular function of disordered polyelectrolyte complexes. Curr Opin Struct Biol 2019;60:66-76. [PMID: 31874413 DOI: 10.1016/j.sbi.2019.12.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/29/2019] [Accepted: 12/05/2019] [Indexed: 12/16/2022]
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Shinobu A, Kobayashi C, Matsunaga Y, Sugita Y. Building a macro-mixing dual-basin Gō model using the Multistate Bennett Acceptance Ratio. Biophys Physicobiol 2019;16:310-321. [PMID: 31984186 PMCID: PMC6975896 DOI: 10.2142/biophysico.16.0_310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/02/2019] [Indexed: 12/01/2022]  Open
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Takada S. Gō model revisited. Biophys Physicobiol 2019;16:248-255. [PMID: 31984178 PMCID: PMC6976017 DOI: 10.2142/biophysico.16.0_248] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 07/16/2019] [Indexed: 12/14/2022]  Open
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