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For: Wang Y, Gan L, Wang E, Wang J. Exploring the Dynamic Functional Landscape of Adenylate Kinase Modulated by Substrates. J Chem Theory Comput 2012;9:84-95. [PMID: 26589012 DOI: 10.1021/ct300720s] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
1
Nam K, Arattu Thodika AR, Grundström C, Sauer UH, Wolf-Watz M. Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. J Chem Inf Model 2024;64:150-163. [PMID: 38117131 PMCID: PMC10778088 DOI: 10.1021/acs.jcim.3c01618] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
2
Lichtinger SM, Biggin PC. Tackling Hysteresis in Conformational Sampling: How to Be Forgetful with MEMENTO. J Chem Theory Comput 2023;19:3705-3720. [PMID: 37285481 PMCID: PMC10308841 DOI: 10.1021/acs.jctc.3c00140] [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: 02/03/2023] [Indexed: 06/09/2023]
3
Lu J, Scheerer D, Haran G, Li W, Wang W. Role of Repeated Conformational Transitions in Substrate Binding of Adenylate Kinase. J Phys Chem B 2022;126:8188-8201. [PMID: 36222098 PMCID: PMC9589722 DOI: 10.1021/acs.jpcb.2c05497] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
4
Chu WT, Yan Z, Chu X, Zheng X, Liu Z, Xu L, Zhang K, Wang J. Physics of biomolecular recognition and conformational dynamics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2021;84:126601. [PMID: 34753115 DOI: 10.1088/1361-6633/ac3800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
5
Orädd F, Ravishankar H, Goodman J, Rogne P, Backman L, Duelli A, Nors Pedersen M, Levantino M, Wulff M, Wolf-Watz M, Andersson M. Tracking the ATP-binding response in adenylate kinase in real time. SCIENCE ADVANCES 2021;7:eabi5514. [PMID: 34788091 PMCID: PMC8597995 DOI: 10.1126/sciadv.abi5514] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/27/2021] [Indexed: 05/25/2023]
6
Lee BH, Park SW, Jo S, Kim MK. Protein conformational transitions explored by a morphing approach based on normal mode analysis in internal coordinates. PLoS One 2021;16:e0258818. [PMID: 34735476 PMCID: PMC8568156 DOI: 10.1371/journal.pone.0258818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/05/2021] [Indexed: 11/19/2022]  Open
7
Chu X, Wang J. Deciphering the molecular mechanism of the cancer formation by chromosome structural dynamics. PLoS Comput Biol 2021;17:e1009596. [PMID: 34752443 PMCID: PMC8631624 DOI: 10.1371/journal.pcbi.1009596] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/30/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022]  Open
8
Ojeda-May P, Mushtaq AU, Rogne P, Verma A, Ovchinnikov V, Grundström C, Dulko-Smith B, Sauer UH, Wolf-Watz M, Nam K. Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions. Biochemistry 2021;60:2246-2258. [PMID: 34250801 PMCID: PMC8297476 DOI: 10.1021/acs.biochem.1c00221] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
9
Wang S, Xu Y, Yu XW. Micro-Aqueous Organic System: A Neglected Model in Computational Lipase Design? Biomolecules 2021;11:848. [PMID: 34200257 PMCID: PMC8226779 DOI: 10.3390/biom11060848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022]  Open
10
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]
11
Miller MD, Phillips GN. Moving beyond static snapshots: Protein dynamics and the Protein Data Bank. J Biol Chem 2021;296:100749. [PMID: 33961840 PMCID: PMC8164045 DOI: 10.1016/j.jbc.2021.100749] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 01/02/2023]  Open
12
Chu WT, Wang J. Thermodynamic and sequential characteristics of phase separation and droplet formation for an intrinsically disordered region/protein ensemble. PLoS Comput Biol 2021;17:e1008672. [PMID: 33684117 PMCID: PMC7939360 DOI: 10.1371/journal.pcbi.1008672] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/04/2021] [Indexed: 11/21/2022]  Open
13
Chu WT, Wang J. Influence of sequence length and charged residues on Swc5 binding with histone H2A-H2B. Proteins 2020;89:512-520. [PMID: 33320380 DOI: 10.1002/prot.26035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/25/2020] [Accepted: 12/12/2020] [Indexed: 01/23/2023]
14
Zhang Y, Cao Z, Zhang JZ, Xia F. Double-Well Ultra-Coarse-Grained Model to Describe Protein Conformational Transitions. J Chem Theory Comput 2020;16:6678-6689. [PMID: 32926616 DOI: 10.1021/acs.jctc.0c00551] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
15
Chu X, Wang J. Conformational state switching and pathways of chromosome dynamics in cell cycle. APPLIED PHYSICS REVIEWS 2020;7:031403. [PMID: 32884608 PMCID: PMC7376616 DOI: 10.1063/5.0007316] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/11/2020] [Indexed: 05/02/2023]
16
Kong J, Li J, Lu J, Li W, Wang W. Role of substrate-product frustration on enzyme functional dynamics. Phys Rev E 2020;100:052409. [PMID: 31869999 DOI: 10.1103/physreve.100.052409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Indexed: 01/19/2023]
17
Yuan Y, Zhu Q, Song R, Ma J, Dong H. A Two-Ended Data-Driven Accelerated Sampling Method for Exploring the Transition Pathways between Two Known States of Protein. J Chem Theory Comput 2020;16:4631-4640. [PMID: 32320614 DOI: 10.1021/acs.jctc.9b01184] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
18
Chu WT, Shammas SL, Wang J. Charge Interactions Modulate the Encounter Complex Ensemble of Two Differently Charged Disordered Protein Partners of KIX. J Chem Theory Comput 2020;16:3856-3868. [PMID: 32325001 DOI: 10.1021/acs.jctc.9b01264] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
19
Yu C, Liu Q, Chen C, Wang J. Quantification of the Underlying Mechanisms and Relationships Among Cancer, Metastasis, and Differentiation and Development. Front Genet 2020;10:1388. [PMID: 32194614 PMCID: PMC7061528 DOI: 10.3389/fgene.2019.01388] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/19/2019] [Indexed: 12/28/2022]  Open
20
Liu F, Yang N. Multiscale landscape of molecular mechanism of SIRT1 activation by STACs. Phys Chem Chem Phys 2020;22:826-837. [PMID: 31840716 DOI: 10.1039/c9cp04931b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
21
Stiller JB, Kerns SJ, Hoemberger M, Cho YJ, Otten R, Hagan MF, Kern D. Probing the Transition State in Enzyme Catalysis by High-Pressure NMR Dynamics. Nat Catal 2019;2:726-734. [PMID: 32159076 DOI: 10.1038/s41929-019-0307-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
22
Li W, Wang J, Zhang J, Takada S, Wang W. Overcoming the Bottleneck of the Enzymatic Cycle by Steric Frustration. PHYSICAL REVIEW LETTERS 2019;122:238102. [PMID: 31298900 DOI: 10.1103/physrevlett.122.238102] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/10/2019] [Indexed: 06/10/2023]
23
Ye C, Ding C, Ma R, Wang J, Zhang Z. Electrostatic interactions determine entrance/release order of substrates in the catalytic cycle of adenylate kinase. Proteins 2019;87:337-347. [PMID: 30615212 DOI: 10.1002/prot.25655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 01/01/2019] [Accepted: 01/02/2019] [Indexed: 12/29/2022]
24
Weinhäupl K, Lindau C, Hessel A, Wang Y, Schütze C, Jores T, Melchionda L, Schönfisch B, Kalbacher H, Bersch B, Rapaport D, Brennich M, Lindorff-Larsen K, Wiedemann N, Schanda P. Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space. Cell 2018;175:1365-1379.e25. [PMID: 30445040 PMCID: PMC6242696 DOI: 10.1016/j.cell.2018.10.039] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 08/16/2018] [Accepted: 10/15/2018] [Indexed: 12/04/2022]
25
Liu F, Ji Q, Wang H, Wang J. Mechanochemical Model of the Power Stroke of the Single-Headed Motor Protein KIF1A. J Phys Chem B 2018;122:11002-11013. [PMID: 30179486 DOI: 10.1021/acs.jpcb.8b04433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
26
Wang Y, Tian P, Boomsma W, Lindorff-Larsen K. Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias. J Phys Chem B 2018;122:11174-11185. [DOI: 10.1021/acs.jpcb.8b06335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
27
Chu WT, Wang J. Quantifying the Intrinsic Conformation Energy Landscape Topography of Proteins with Large-Scale Open-Closed Transition. ACS CENTRAL SCIENCE 2018;4:1015-1022. [PMID: 30159398 PMCID: PMC6107866 DOI: 10.1021/acscentsci.8b00274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Indexed: 06/08/2023]
28
Gadkari VV, Harvey SR, Raper AT, Chu WT, Wang J, Wysocki VH, Suo Z. Investigation of sliding DNA clamp dynamics by single-molecule fluorescence, mass spectrometry and structure-based modeling. Nucleic Acids Res 2018;46:3103-3118. [PMID: 29529283 PMCID: PMC5888646 DOI: 10.1093/nar/gky125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/23/2018] [Accepted: 02/12/2018] [Indexed: 12/20/2022]  Open
29
Yadav R, Lu HP. Revealing dynamically-organized receptor ion channel clusters in live cells by a correlated electric recording and super-resolution single-molecule imaging approach. Phys Chem Chem Phys 2018. [PMID: 29517089 DOI: 10.1039/c7cp08030a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
30
Zheng Y, Cui Q. Multiple Pathways and Time Scales for Conformational Transitions in apo-Adenylate Kinase. J Chem Theory Comput 2018;14:1716-1726. [PMID: 29378407 DOI: 10.1021/acs.jctc.7b01064] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
31
Zhao L, Lu HP, Wang J. Exploration of Multistate Conformational Dynamics upon Ligand Binding of a Monomeric Enzyme Involved in Pyrophosphoryl Transfer. J Phys Chem B 2018;122:1885-1897. [PMID: 29385349 DOI: 10.1021/acs.jpcb.7b12562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
32
Wang Y, Makowski L. Fine structure of conformational ensembles in adenylate kinase. Proteins 2017;86:332-343. [DOI: 10.1002/prot.25443] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 10/12/2017] [Accepted: 11/03/2017] [Indexed: 11/07/2022]
33
Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways. Proc Natl Acad Sci U S A 2017;114:E7959-E7968. [PMID: 28855336 DOI: 10.1073/pnas.1702599114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
34
Molecular dynamics simulation reveals how phosphorylation of tyrosine 26 of phosphoglycerate mutase 1 upregulates glycolysis and promotes tumor growth. Oncotarget 2017;8:12093-12107. [PMID: 28076845 PMCID: PMC5355328 DOI: 10.18632/oncotarget.14517] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 12/16/2016] [Indexed: 12/19/2022]  Open
35
Molecular mechanism of multispecific recognition of Calmodulin through conformational changes. Proc Natl Acad Sci U S A 2017;114:E3927-E3934. [PMID: 28461506 DOI: 10.1073/pnas.1615949114] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
36
Chu WT, Clarke J, Shammas SL, Wang J. Role of non-native electrostatic interactions in the coupled folding and binding of PUMA with Mcl-1. PLoS Comput Biol 2017;13:e1005468. [PMID: 28369057 PMCID: PMC5400261 DOI: 10.1371/journal.pcbi.1005468] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/21/2017] [Accepted: 03/20/2017] [Indexed: 11/23/2022]  Open
37
Chu JW, Yang H. Identifying the structural and kinetic elements in protein large-amplitude conformational motions. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1283885] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
38
Chu WT, Nesbitt NM, Gnatenko DV, Li Z, Zhang B, Seeliger MA, Browne S, Mantle TJ, Bahou WF, Wang J. Enzymatic Activity and Thermodynamic Stability of Biliverdin IXβ Reductase Are Maintained by an Active Site Serine. Chemistry 2017;23:1891-1900. [PMID: 27897348 DOI: 10.1002/chem.201604517] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Indexed: 11/10/2022]
39
Gong Z, Gu XH, Guo DC, Wang J, Tang C. Protein Structural Ensembles Visualized by Solvent Paramagnetic Relaxation Enhancement. Angew Chem Int Ed Engl 2016;56:1002-1006. [DOI: 10.1002/anie.201609830] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/09/2016] [Indexed: 12/25/2022]
40
Gong Z, Gu XH, Guo DC, Wang J, Tang C. Protein Structural Ensembles Visualized by Solvent Paramagnetic Relaxation Enhancement. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609830] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
41
Probing conformational dynamics of an enzymatic active site by an in situ single fluorogenic probe under piconewton force manipulation. Proc Natl Acad Sci U S A 2016;113:15006-15011. [PMID: 27940917 DOI: 10.1073/pnas.1613404114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
42
Sasmal DK, Yadav R, Lu HP. Single-Molecule Patch-Clamp FRET Anisotropy Microscopy Studies of NMDA Receptor Ion Channel Activation and Deactivation under Agonist Ligand Binding in Living Cells. J Am Chem Soc 2016;138:8789-801. [DOI: 10.1021/jacs.6b03496] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
43
Kurkcuoglu Z, Doruker P. Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins. PLoS One 2016;11:e0158063. [PMID: 27348230 PMCID: PMC4922591 DOI: 10.1371/journal.pone.0158063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/09/2016] [Indexed: 01/03/2023]  Open
44
Li D, Liu MS, Ji B. Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case. Biophys J 2016;109:647-60. [PMID: 26244746 DOI: 10.1016/j.bpj.2015.06.059] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 06/19/2015] [Accepted: 06/29/2015] [Indexed: 12/22/2022]  Open
45
Cui D, Ren W, Li W, Wang W. Molecular simulations of substrate release and coupled conformational motions in adenylate kinase. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1142/s0219633616500048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
46
Papaleo E, Saladino G, Lambrughi M, Lindorff-Larsen K, Gervasio FL, Nussinov R. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem Rev 2016;116:6391-423. [DOI: 10.1021/acs.chemrev.5b00623] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
47
Kobayashi C, Matsunaga Y, Koike R, Ota M, Sugita Y. Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins. J Phys Chem B 2015;119:14584-93. [PMID: 26536148 DOI: 10.1021/acs.jpcb.5b07668] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
48
Lee J, Joo K, Brooks BR, Lee J. The Atomistic Mechanism of Conformational Transition of Adenylate Kinase Investigated by Lorentzian Structure-Based Potential. J Chem Theory Comput 2015;11:3211-24. [PMID: 26575758 DOI: 10.1021/acs.jctc.5b00268] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ono J, Takada S, Saito S. Couplings between hierarchical conformational dynamics from multi-time correlation functions and two-dimensional lifetime spectra: Application to adenylate kinase. J Chem Phys 2015;142:212404. [DOI: 10.1063/1.4914328] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
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Formoso E, Limongelli V, Parrinello M. Energetics and structural characterization of the large-scale functional motion of adenylate kinase. Sci Rep 2015;5:8425. [PMID: 25672826 PMCID: PMC4325324 DOI: 10.1038/srep08425] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 01/08/2015] [Indexed: 12/22/2022]  Open
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