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For: Hammes-Schiffer S, Benkovic SJ. Relating Protein Motion to Catalysis. Annu Rev Biochem 2006;75:519-41. [PMID: 16756501 DOI: 10.1146/annurev.biochem.75.103004.142800] [Citation(s) in RCA: 466] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Number Cited by Other Article(s)
101
Li Y, Wang Y, Huang G, Gao J. Cooperativity Principles in Self-Assembled Nanomedicine. Chem Rev 2018;118:5359-5391. [PMID: 29693377 DOI: 10.1021/acs.chemrev.8b00195] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
102
Direct observation of ultrafast large-scale dynamics of an enzyme under turnover conditions. Proc Natl Acad Sci U S A 2018. [PMID: 29531052 PMCID: PMC5879700 DOI: 10.1073/pnas.1720448115] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]  Open
103
Reyes AC, Amyes TL, Richard JP. A reevaluation of the origin of the rate acceleration for enzyme-catalyzed hydride transfer. Org Biomol Chem 2018;15:8856-8866. [PMID: 28956050 DOI: 10.1039/c7ob01652b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
104
Schlee S, Klein T, Schumacher M, Nazet J, Merkl R, Steinhoff HJ, Sterner R. Relationship of Catalysis and Active Site Loop Dynamics in the (βα)8-Barrel Enzyme Indole-3-glycerol Phosphate Synthase. Biochemistry 2018;57:3265-3277. [DOI: 10.1021/acs.biochem.8b00167] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
105
Genetically Fused T4L Acts as a Shield in Covalent Enzyme Immobilisation Enhancing the Rescued Activity. Catalysts 2018. [DOI: 10.3390/catal8010040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
106
Arai M. Unified understanding of folding and binding mechanisms of globular and intrinsically disordered proteins. Biophys Rev 2018;10:163-181. [PMID: 29307002 PMCID: PMC5899706 DOI: 10.1007/s12551-017-0346-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/13/2017] [Indexed: 12/18/2022]  Open
107
Slow domain reconfiguration causes power-law kinetics in a two-state enzyme. Proc Natl Acad Sci U S A 2018;115:513-518. [PMID: 29298911 DOI: 10.1073/pnas.1714401115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
108
DeGregorio N, Iyengar SS. Efficient and Adaptive Methods for Computing Accurate Potential Surfaces for Quantum Nuclear Effects: Applications to Hydrogen-Transfer Reactions. J Chem Theory Comput 2017;14:30-47. [DOI: 10.1021/acs.jctc.7b00927] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
109
Ranasinghe C, Guo Q, Sapienza PJ, Lee AL, Quinn DM, Cheatum CM, Kohen A. Protein Mass Effects on Formate Dehydrogenase. J Am Chem Soc 2017;139:17405-17413. [PMID: 29083897 PMCID: PMC5800309 DOI: 10.1021/jacs.7b08359] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
110
Patterns of coevolving amino acids unveil structural and dynamical domains. Proc Natl Acad Sci U S A 2017;114:E10612-E10621. [PMID: 29183970 DOI: 10.1073/pnas.1712021114] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
111
Li J, Xie Y, Wang R, Fang Z, Fang W, Zhang X, Xiao Y. Mechanism of salt-induced activity enhancement of a marine-derived laccase, Lac15. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017;47:225-236. [PMID: 28875401 DOI: 10.1007/s00249-017-1251-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/07/2017] [Accepted: 08/23/2017] [Indexed: 10/18/2022]
112
Ghosh A, Ostrander JS, Zanni MT. Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy. Chem Rev 2017;117:10726-10759. [PMID: 28060489 PMCID: PMC5500453 DOI: 10.1021/acs.chemrev.6b00582] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
113
Sang P, Hu W, Ye YJ, Li LH, Zhang C, Xie YH, Meng ZH. In silico screening, molecular docking, and molecular dynamics studies of SNP-derived human P5CR mutants. J Biomol Struct Dyn 2017;35:2441-2453. [PMID: 27677826 DOI: 10.1080/07391102.2016.1222967] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 08/07/2016] [Indexed: 01/13/2023]
114
Kohne M, Zhu C, Warncke K. Two Dynamical Regimes of the Substrate Radical Rearrangement Reaction in B12-Dependent Ethanolamine Ammonia-Lyase Resolve Contributions of Native Protein Configurations and Collective Configurational Fluctuations to Catalysis. Biochemistry 2017;56:3257-3264. [PMID: 28548844 DOI: 10.1021/acs.biochem.7b00294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
115
Better than Membranes at the Origin of Life? Life (Basel) 2017. [PMID: 28632159 PMCID: PMC5492150 DOI: 10.3390/life7020028] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
116
Miller SR. An appraisal of the enzyme stability‐activity trade‐off. Evolution 2017;71:1876-1887. [DOI: 10.1111/evo.13275] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 05/09/2017] [Indexed: 12/23/2022]
117
Pohorille A, Wilson MA, Shannon G. Flexible Proteins at the Origin of Life. Life (Basel) 2017;7:E23. [PMID: 28587235 PMCID: PMC5492145 DOI: 10.3390/life7020023] [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: 03/13/2017] [Revised: 05/10/2017] [Accepted: 05/24/2017] [Indexed: 11/17/2022]  Open
118
Ruzsányi V, Péter Kalapos M. Breath acetone as a potential marker in clinical practice. J Breath Res 2017;11:024002. [DOI: 10.1088/1752-7163/aa66d3] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
119
Paladino A, Marchetti F, Rinaldi S, Colombo G. Protein design: from computer models to artificial intelligence. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1318] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
120
Narayanan C, Bafna K, Roux LD, Agarwal PK, Doucet N. Applications of NMR and computational methodologies to study protein dynamics. Arch Biochem Biophys 2017;628:71-80. [PMID: 28483383 DOI: 10.1016/j.abb.2017.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 02/07/2023]
121
Hayashi S, Uchida Y, Hasegawa T, Higashi M, Kosugi T, Kamiya M. QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins. Annu Rev Phys Chem 2017;68:135-154. [DOI: 10.1146/annurev-physchem-052516-050827] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
122
Norris V, Krylov SN, Agarwal PK, White GJ. Synthetic, Switchable Enzymes. J Mol Microbiol Biotechnol 2017;27:117-127. [PMID: 28448969 DOI: 10.1159/000464443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
123
Warshel A, Bora RP. Perspective: Defining and quantifying the role of dynamics in enzyme catalysis. J Chem Phys 2017;144:180901. [PMID: 27179464 DOI: 10.1063/1.4947037] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
124
Pica A, Graziano G. Shedding light on the extra thermal stability of thermophilic proteins. Biopolymers 2017;105:856-63. [PMID: 27449333 DOI: 10.1002/bip.22923] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 07/12/2016] [Accepted: 07/20/2016] [Indexed: 11/08/2022]
125
On the indirect relationship between protein dynamics and enzyme activity. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017;125:52-60. [PMID: 28163054 DOI: 10.1016/j.pbiomolbio.2017.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 02/01/2017] [Indexed: 11/22/2022]
126
Alotaibi M, Reyes BD, Le T, Luong P, Valafar F, Metzger RP, Fogel GB, Hecht D. Structure-based analysis of Bacilli and plasmid dihydrofolate reductase evolution. J Mol Graph Model 2017;71:135-153. [PMID: 27914300 PMCID: PMC5203806 DOI: 10.1016/j.jmgm.2016.10.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 10/04/2016] [Accepted: 10/10/2016] [Indexed: 12/15/2022]
127
Zelleke T, Marx D. Free-Energy Landscape and Proton Transfer Pathways in Oxidative Deamination by Methylamine Dehydrogenase. Chemphyschem 2016;18:208-222. [DOI: 10.1002/cphc.201601113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Indexed: 12/26/2022]
128
Modestova Y, Ugarova NN. Color-shifting mutations in the C-domain of L. mingrelica firefly luciferase provide new information about the domain alternation mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016;1864:1818-1826. [DOI: 10.1016/j.bbapap.2016.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 09/09/2016] [Accepted: 09/14/2016] [Indexed: 02/07/2023]
129
Gating role of His 72 in TmPurL enzyme uncovered by structural analyses and molecular dynamics simulations. Bioorg Med Chem Lett 2016;26:5644-5649. [DOI: 10.1016/j.bmcl.2016.10.070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 10/03/2016] [Accepted: 10/24/2016] [Indexed: 11/18/2022]
130
Alawieh H, Wicker N, Al Ayoubi B, Moulinier L. Penalized multidimensional fitting for protein movement detection. J Appl Stat 2016. [DOI: 10.1080/02664763.2016.1261811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
131
Kinematic molecular manufacturing machines. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
132
Rohlman CE, Blanco MR, Walter NG. Putting Humpty-Dumpty Together: Clustering the Functional Dynamics of Single Biomolecular Machines Such as the Spliceosome. Methods Enzymol 2016;581:257-283. [PMID: 27793282 DOI: 10.1016/bs.mie.2016.08.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
133
Albesa-Jové D, Guerin ME. The conformational plasticity of glycosyltransferases. Curr Opin Struct Biol 2016;40:23-32. [DOI: 10.1016/j.sbi.2016.07.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/23/2016] [Accepted: 07/08/2016] [Indexed: 12/22/2022]
134
Duine JA, Strampraad MJF, Hagen WR, de Vries S. The cooperativity effect in the reaction of soluble quinoprotein (PQQ-containing) glucose dehydrogenase is not due to subunit interaction but to substrate-assisted catalysis. FEBS J 2016;283:3604-3612. [PMID: 27491947 DOI: 10.1111/febs.13829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/12/2016] [Accepted: 08/02/2016] [Indexed: 11/29/2022]
135
Rahnama S, Saffar B, Kahrani ZF, Nazari M, Emamzadeh R. Super RLuc8: A novel engineered Renilla luciferase with a red-shifted spectrum and stable light emission. Enzyme Microb Technol 2016;96:60-66. [PMID: 27871386 DOI: 10.1016/j.enzmictec.2016.09.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/18/2016] [Accepted: 09/19/2016] [Indexed: 11/17/2022]
136
Sacquin-Mora S. Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus? J R Soc Interface 2016;12:rsif.2015.0876. [PMID: 26577596 DOI: 10.1098/rsif.2015.0876] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]  Open
137
Godsey MH, Davulcu O, Nix JC, Skalicky JJ, Brüschweiler RP, Chapman MS. The Sampling of Conformational Dynamics in Ambient-Temperature Crystal Structures of Arginine Kinase. Structure 2016;24:1658-1667. [PMID: 27594681 DOI: 10.1016/j.str.2016.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 07/01/2016] [Accepted: 07/06/2016] [Indexed: 01/26/2023]
138
Hu S, Cattin‐Ortolá J, Munos JW, Klinman JP. Hydrostatic Pressure Studies Distinguish Global from Local Protein Motions in C−H Activation by Soybean Lipoxygenase‐1. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
139
Hu S, Cattin-Ortolá J, Munos JW, Klinman JP. Hydrostatic Pressure Studies Distinguish Global from Local Protein Motions in C-H Activation by Soybean Lipoxygenase-1. Angew Chem Int Ed Engl 2016;55:9361-4. [PMID: 27348724 PMCID: PMC5040518 DOI: 10.1002/anie.201603592] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Indexed: 01/28/2023]
140
Cunha AV, Bondarenko AS, Jansen TLC. Assessing Spectral Simulation Protocols for the Amide I Band of Proteins. J Chem Theory Comput 2016;12:3982-92. [PMID: 27348022 DOI: 10.1021/acs.jctc.6b00420] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
141
Singh P, Islam Z, Kohen A. Examinations of the Chemical Step in Enzyme Catalysis. Methods Enzymol 2016;577:287-318. [PMID: 27498642 DOI: 10.1016/bs.mie.2016.05.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
142
Conformational flexibility related to enzyme activity: evidence for a dynamic active-site gatekeeper function of Tyr(215) in Aerococcus viridans lactate oxidase. Sci Rep 2016;6:27892. [PMID: 27302031 PMCID: PMC4908395 DOI: 10.1038/srep27892] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/26/2016] [Indexed: 01/15/2023]  Open
143
Lisi GP, Loria JP. Solution NMR Spectroscopy for the Study of Enzyme Allostery. Chem Rev 2016;116:6323-69. [PMID: 26734986 PMCID: PMC4937494 DOI: 10.1021/acs.chemrev.5b00541] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
144
Deo C, Bogliotti N, Métivier R, Retailleau P, Xie J. A Visible-Light-Triggered Conformational Diastereomer Photoswitch in a Bridged Azobenzene. Chemistry 2016;22:9092-6. [DOI: 10.1002/chem.201601400] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Indexed: 11/07/2022]
145
Moree B, Connell K, Mortensen RB, Liu CT, Benkovic SJ, Salafsky J. Protein Conformational Changes Are Detected and Resolved Site Specifically by Second-Harmonic Generation. Biophys J 2016;109:806-15. [PMID: 26287632 PMCID: PMC4547196 DOI: 10.1016/j.bpj.2015.07.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/29/2015] [Accepted: 07/02/2015] [Indexed: 12/21/2022]  Open
146
Zhao ZW, Xie XS, Ge H. Nonequilibrium Relaxation of Conformational Dynamics Facilitates Catalytic Reaction in an Elastic Network Model of T7 DNA Polymerase. J Phys Chem B 2016;120:2869-77. [PMID: 26918464 DOI: 10.1021/acs.jpcb.5b11002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
147
Saldaño TE, Monzon AM, Parisi G, Fernandez-Alberti S. Evolutionary Conserved Positions Define Protein Conformational Diversity. PLoS Comput Biol 2016;12:e1004775. [PMID: 27008419 PMCID: PMC4805271 DOI: 10.1371/journal.pcbi.1004775] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 01/27/2016] [Indexed: 12/18/2022]  Open
148
Paloncýová M, Navrátilová V, Berka K, Laio A, Otyepka M. Role of Enzyme Flexibility in Ligand Access and Egress to Active Site: Bias-Exchange Metadynamics Study of 1,3,7-Trimethyluric Acid in Cytochrome P450 3A4. J Chem Theory Comput 2016;12:2101-9. [DOI: 10.1021/acs.jctc.6b00075] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
149
Reddish MJ, Vaughn MB, Fu R, Dyer RB. Ligand-Dependent Conformational Dynamics of Dihydrofolate Reductase. Biochemistry 2016;55:1485-93. [PMID: 26901612 DOI: 10.1021/acs.biochem.5b01364] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
150
Colombo M, Girard E, Franzetti B. Tuned by metals: the TET peptidase activity is controlled by 3 metal binding sites. Sci Rep 2016;6:20876. [PMID: 26853450 PMCID: PMC4745047 DOI: 10.1038/srep20876] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 01/11/2016] [Indexed: 11/09/2022]  Open
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