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For: Boehr DD, Dyson HJ, Wright PE. An NMR perspective on enzyme dynamics. Chem Rev 2007;106:3055-79. [PMID: 16895318 DOI: 10.1021/cr050312q] [Citation(s) in RCA: 355] [Impact Index Per Article: 19.7] [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
Das N, Khan T, Halder B, Ghosh S, Sen P. Macromolecular crowding effects on protein dynamics. Int J Biol Macromol 2024;281:136248. [PMID: 39374718 DOI: 10.1016/j.ijbiomac.2024.136248] [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: 06/29/2024] [Revised: 09/30/2024] [Accepted: 09/30/2024] [Indexed: 10/09/2024]
2
Chao FA, Byrd RA. Existence of Singularities in NMR Relaxation Dispersion Profiles: Implications for Hidden Dynamics. J Am Chem Soc 2024;146:24467-24475. [PMID: 39172084 DOI: 10.1021/jacs.4c06720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
3
Lorenz UJ. Microsecond time-resolved cryo-electron microscopy. Curr Opin Struct Biol 2024;87:102840. [PMID: 38810313 DOI: 10.1016/j.sbi.2024.102840] [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: 02/13/2024] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024]
4
Mondal S, Sauer MA, Heyden M. Exploring Conformational Landscapes Along Anharmonic Low-Frequency Vibrations. J Phys Chem B 2024;128:7112-7120. [PMID: 38986052 PMCID: PMC11584282 DOI: 10.1021/acs.jpcb.4c02743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
5
Banayan NE, Hsu A, Hunt JF, Palmer AG, Friesner RA. Parsing Dynamics of Protein Backbone NH and Side-Chain Methyl Groups using Molecular Dynamics Simulations. J Chem Theory Comput 2024;20:6316-6327. [PMID: 38957960 PMCID: PMC11528701 DOI: 10.1021/acs.jctc.4c00378] [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] [Indexed: 07/04/2024]
6
Stroet M, Setz M, Lee T, Malde AK, van den Bergen G, Sykacek P, Oostenbrink C, Mark AE. On the Validation of Protein Force Fields Based on Structural Criteria. J Phys Chem B 2024;128:4602-4620. [PMID: 38711373 PMCID: PMC11103706 DOI: 10.1021/acs.jpcb.3c08469] [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: 12/29/2023] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/08/2024]
7
Tan H, Duan M, Xie H, Zhao Y, Liu H, Yang M, Liu M, Yang J. Fast collective motions of backbone in transmembrane α helices are critical to water transfer of aquaporin. SCIENCE ADVANCES 2024;10:eade9520. [PMID: 38718112 PMCID: PMC11078191 DOI: 10.1126/sciadv.ade9520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/04/2024] [Indexed: 05/12/2024]
8
Rahman MH, Hegazy L. Mechanism of antagonist ligand binding to REV-ERBα. Sci Rep 2024;14:8401. [PMID: 38600172 PMCID: PMC11006950 DOI: 10.1038/s41598-024-58945-4] [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: 01/11/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]  Open
9
Sun X, Alfermann J, Li H, Watkins MB, Chen YT, Morrell TE, Mayerthaler F, Wang CY, Komatsuzaki T, Chu JW, Ando N, Mootz HD, Yang H. Subdomain dynamics enable chemical chain reactions in non-ribosomal peptide synthetases. Nat Chem 2024;16:259-268. [PMID: 38049653 PMCID: PMC11227371 DOI: 10.1038/s41557-023-01361-4] [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: 06/06/2022] [Accepted: 10/03/2023] [Indexed: 12/06/2023]
10
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]
11
Ding Q, Sun Z, Ma W. Probing conformational kinetics of catalase with and without magnetic field by single-entity collision electrochemistry. Sci Bull (Beijing) 2023;68:2564-2573. [PMID: 37718236 DOI: 10.1016/j.scib.2023.08.056] [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: 05/29/2023] [Revised: 07/12/2023] [Accepted: 08/23/2023] [Indexed: 09/19/2023]
12
Shukla VK, Heller GT, Hansen DF. Biomolecular NMR spectroscopy in the era of artificial intelligence. Structure 2023;31:1360-1374. [PMID: 37848030 DOI: 10.1016/j.str.2023.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/19/2023]
13
Chen M, Kálai T, Cascio D, Bridges MD, Whitelegge JP, Elgeti M, Hubbell WL. A Highly Ordered Nitroxide Side Chain for Distance Mapping and Monitoring Slow Structural Fluctuations in Proteins. APPLIED MAGNETIC RESONANCE 2023;55:251-277. [PMID: 38357006 PMCID: PMC10861403 DOI: 10.1007/s00723-023-01618-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/06/2023] [Accepted: 09/09/2023] [Indexed: 02/16/2024]
14
Shukla VK, Siemons L, Hansen DF. Intrinsic structural dynamics dictate enzymatic activity and inhibition. Proc Natl Acad Sci U S A 2023;120:e2310910120. [PMID: 37782780 PMCID: PMC10576142 DOI: 10.1073/pnas.2310910120] [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: 06/28/2023] [Accepted: 08/14/2023] [Indexed: 10/04/2023]  Open
15
Hansen AL, Xiang X, Yuan C, Bruschweiler-Li L, Brüschweiler R. Excited-state observation of active K-Ras reveals differential structural dynamics of wild-type versus oncogenic G12D and G12C mutants. Nat Struct Mol Biol 2023;30:1446-1455. [PMID: 37640864 PMCID: PMC10584678 DOI: 10.1038/s41594-023-01070-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/17/2023] [Indexed: 08/31/2023]
16
Chen KW, Sun TY, Wu YD. New Insights into the Cooperativity and Dynamics of Dimeric Enzymes. Chem Rev 2023;123:9940-9981. [PMID: 37561162 DOI: 10.1021/acs.chemrev.3c00042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
17
Li W, Kohne M, Warncke K. Reactivity Tracking of an Enzyme Progress Coordinate. J Phys Chem Lett 2023;14:7157-7164. [PMID: 37540029 PMCID: PMC10440813 DOI: 10.1021/acs.jpclett.3c01464] [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: 05/28/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023]
18
Lee E, McLeod MJ, Redzic JS, Marcolin B, Thorne RE, Agarwal P, Eisenmesser EZ. Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle. Front Mol Biosci 2023;10:1244587. [PMID: 37645217 PMCID: PMC10461185 DOI: 10.3389/fmolb.2023.1244587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023]  Open
19
Lee E, Redzic JS, Zohar Eisenmesser E. Relaxation and single site multiple mutations to identify and control allosteric networks. Methods 2023;216:51-57. [PMID: 37302521 PMCID: PMC11066977 DOI: 10.1016/j.ymeth.2023.06.002] [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: 05/04/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]  Open
20
De Biasi F, Hope MA, Avalos CE, Karthikeyan G, Casano G, Mishra A, Badoni S, Stevanato G, Kubicki DJ, Milani J, Ansermet JP, Rossini AJ, Lelli M, Ouari O, Emsley L. Optically Enhanced Solid-State 1H NMR Spectroscopy. J Am Chem Soc 2023. [PMID: 37366803 DOI: 10.1021/jacs.3c03937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
21
Ray KK, Kinz-Thompson CD, Fei J, Wang B, Lin Q, Gonzalez RL. Entropic control of the free-energy landscape of an archetypal biomolecular machine. Proc Natl Acad Sci U S A 2023;120:e2220591120. [PMID: 37186858 PMCID: PMC10214133 DOI: 10.1073/pnas.2220591120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 04/17/2023] [Indexed: 05/17/2023]  Open
22
Yin G, Huang J, Petela J, Jiang H, Zhang Y, Gong S, Wu J, Liu B, Shi J, Gao Y. Targeting small GTPases: emerging grasps on previously untamable targets, pioneered by KRAS. Signal Transduct Target Ther 2023;8:212. [PMID: 37221195 DOI: 10.1038/s41392-023-01441-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/28/2023] [Accepted: 04/14/2023] [Indexed: 05/25/2023]  Open
23
Olivieri C, Walker C, Manu V, Porcelli F, Taylor SS, Bernlohr DA, Veglia G. An NMR portrait of functional and dysfunctional allosteric cooperativity in cAMP-dependent protein kinase A. FEBS Lett 2023;597:1055-1072. [PMID: 36892429 PMCID: PMC11334100 DOI: 10.1002/1873-3468.14610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 03/10/2023]
24
A Comparison of Bonded and Nonbonded Zinc(II) Force Fields with NMR Data. Int J Mol Sci 2023;24:ijms24065440. [PMID: 36982515 PMCID: PMC10055966 DOI: 10.3390/ijms24065440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023]  Open
25
Akke M, Weininger U. NMR Studies of Aromatic Ring Flips to Probe Conformational Fluctuations in Proteins. J Phys Chem B 2023;127:591-599. [PMID: 36640108 PMCID: PMC9884080 DOI: 10.1021/acs.jpcb.2c07258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/25/2022] [Indexed: 01/15/2023]
26
Muduli S, Mishra S. Ligands-induced open-close conformational change during DapE catalysis: Insights from molecular dynamics simulations. Proteins 2023;91:781-797. [PMID: 36633566 DOI: 10.1002/prot.26466] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/20/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023]
27
Amann SJ, Keihsler D, Bodrug T, Brown NG, Haselbach D. Frozen in time: analyzing molecular dynamics with time-resolved cryo-EM. Structure 2023;31:4-19. [PMID: 36584678 PMCID: PMC9825670 DOI: 10.1016/j.str.2022.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/10/2022] [Accepted: 11/25/2022] [Indexed: 12/30/2022]
28
Bongiovanni G, Harder OF, Drabbels M, Lorenz UJ. Microsecond melting and revitrification of cryo samples with a correlative light-electron microscopy approach. Front Mol Biosci 2022;9:1044509. [PMID: 36438663 PMCID: PMC9685559 DOI: 10.3389/fmolb.2022.1044509] [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: 09/14/2022] [Accepted: 10/28/2022] [Indexed: 08/25/2023]  Open
29
Li H, Wu S, Ma A. Origin of Protein Quake: Energy Waves Conducted by a Precise Mechanical Machine. J Chem Theory Comput 2022;18:5692-5702. [PMID: 35951409 DOI: 10.1021/acs.jctc.2c00514] [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] [Indexed: 11/28/2022]
30
Fusco G, Bemporad F, Chiti F, Dobson CM, De Simone A. The role of structural dynamics in the thermal adaptation of hyperthermophilic enzymes. Front Mol Biosci 2022;9:981312. [PMID: 36158582 PMCID: PMC9490001 DOI: 10.3389/fmolb.2022.981312] [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: 06/29/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022]  Open
31
Shenoy A, Davis AR, Roberts ET, Amster IJ, Barb AW. Metabolic15N labeling of the N-glycosylated immunoglobulin G1 Fc with an engineered Saccharomyces cerevisiae strain. JOURNAL OF BIOMOLECULAR NMR 2022;76:95-105. [PMID: 35802275 DOI: 10.1007/s10858-022-00397-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
32
Mori T, Saito S. Molecular Insights into the Intrinsic Dynamics and Their Roles During Catalysis in Pin1 Peptidyl-prolyl Isomerase. J Phys Chem B 2022;126:5185-5193. [PMID: 35795989 DOI: 10.1021/acs.jpcb.2c02095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
33
An NMR look at an engineered PET depolymerase. Biophys J 2022;121:2882-2894. [PMID: 35794828 PMCID: PMC9388554 DOI: 10.1016/j.bpj.2022.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/15/2022] [Accepted: 06/30/2022] [Indexed: 12/30/2022]  Open
34
Singewald K, Wilkinson JA, Hasanbasri Z, Saxena S. Beyond structure: Deciphering site-specific dynamics in proteins from double histidine-based EPR measurements. Protein Sci 2022;31:e4359. [PMID: 35762707 PMCID: PMC9202549 DOI: 10.1002/pro.4359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 12/27/2022]
35
A litmus test for classifying recognition mechanisms of transiently binding proteins. Nat Commun 2022;13:3792. [PMID: 35778416 PMCID: PMC9249894 DOI: 10.1038/s41467-022-31374-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 06/15/2022] [Indexed: 11/17/2022]  Open
36
Harder OF, Voss JM, Olshin PK, Drabbels M, Lorenz UJ. Microsecond melting and revitrification of cryo samples: protein structure and beam-induced motion. Acta Crystallogr D Struct Biol 2022;78:883-889. [PMID: 35775987 PMCID: PMC9248841 DOI: 10.1107/s205979832200554x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/21/2022] [Indexed: 11/10/2022]  Open
37
Clore GM. NMR spectroscopy, excited states and relevance to problems in cell biology - transient pre-nucleation tetramerization of huntingtin and insights into Huntington's disease. J Cell Sci 2022;135:jcs258695. [PMID: 35703323 PMCID: PMC9270955 DOI: 10.1242/jcs.258695] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
38
Karunanithy G, Yuwen T, Kay LE, Hansen DF. Towards autonomous analysis of chemical exchange saturation transfer experiments using deep neural networks. JOURNAL OF BIOMOLECULAR NMR 2022;76:75-86. [PMID: 35622310 PMCID: PMC9246985 DOI: 10.1007/s10858-022-00395-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/05/2022] [Indexed: 06/12/2023]
39
Mames A, Jopa S, Pietrzak M, Ratajczyk T. Deactivation of catalysts in simultaneous reversible and irreversible parahydrogen NMR signal enhancement, and the role of co-ligands in the stabilization of the reversible method. RSC Adv 2022;12:15986-15991. [PMID: 35733673 PMCID: PMC9136854 DOI: 10.1039/d2ra02872g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/23/2022] [Indexed: 11/21/2022]  Open
40
Construction of L-Asparaginase Stable Mutation for the Application in Food Acrylamide Mitigation. FERMENTATION 2022. [DOI: 10.3390/fermentation8050218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
41
A single-molecule stochastic theory of protein-ligand binding in the presence of multiple unfolding/folding and ligand binding pathways. Biophys Chem 2022;285:106803. [DOI: 10.1016/j.bpc.2022.106803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 11/19/2022]
42
Tugarinov V, Ceccon A, Clore GM. NMR methods for exploring 'dark' states in ligand binding and protein-protein interactions. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022;128:1-24. [PMID: 35282867 PMCID: PMC8921508 DOI: 10.1016/j.pnmrs.2021.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 05/24/2023]
43
Kohne M, Li W, Ionescu A, Zhu C, Warncke K. Resolution and characterization of contributions of select protein and coupled solvent configurational fluctuations to radical rearrangement catalysis in coenzyme B12-dependent ethanolamine ammonia-lyase. Methods Enzymol 2022;669:229-259. [PMID: 35644173 PMCID: PMC9270175 DOI: 10.1016/bs.mie.2021.12.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Galenkamp NS, Maglia G. Single-Molecule Sampling of Dihydrofolate Reductase Shows Kinetic Pauses and an Endosteric Effect Linked to Catalysis. ACS Catal 2022;12:1228-1236. [PMID: 35096468 PMCID: PMC8787752 DOI: 10.1021/acscatal.1c04388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/13/2021] [Indexed: 12/21/2022]
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Das N, Yadav S, Negi KS, Tariff E, Sen P. Microsecond Active-Site Dynamics Primarily control Proteolytic Activity of Bromelain: A Single Molecular Level Study with a Denaturant, a Stabilizer and a Macromolecular Crowder. BBA ADVANCES 2022;2:100041. [PMID: 37082607 PMCID: PMC10074955 DOI: 10.1016/j.bbadva.2022.100041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/13/2021] [Accepted: 01/10/2022] [Indexed: 10/19/2022]  Open
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Das N, Sen P. Macromolecular Crowding Effect on the Structure, Function, Conformational Dynamics and Relative Domain Movement of a Multi-Domain Protein as a function of Crowder Shape and Interaction. Phys Chem Chem Phys 2022;24:14242-14256. [DOI: 10.1039/d1cp04842b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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The native state conformational heterogeneity in the energy landscape of protein folding. Biophys Chem 2022;283:106761. [DOI: 10.1016/j.bpc.2022.106761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 11/18/2022]
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T RR, Saharay M, Smith JC, Krishnan M. Correlated Response of Protein Side-Chain Fluctuations and Conformational Entropy to Ligand Binding. J Phys Chem B 2021;125:9641-9651. [PMID: 34423989 DOI: 10.1021/acs.jpcb.1c01227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Voss JM, Harder OF, Olshin PK, Drabbels M, Lorenz UJ. Rapid melting and revitrification as an approach to microsecond time-resolved cryo-electron microscopy. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Voss JM, Harder OF, Olshin PK, Drabbels M, Lorenz UJ. Microsecond melting and revitrification of cryo samples. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2021;8:054302. [PMID: 34734102 PMCID: PMC8550802 DOI: 10.1063/4.0000129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/06/2021] [Indexed: 05/29/2023]
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