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For: Oyen D, Fenwick RB, Aoto PC, Stanfield RL, Wilson IA, Dyson HJ, Wright PE. Defining the Structural Basis for Allosteric Product Release from E. coli Dihydrofolate Reductase Using NMR Relaxation Dispersion. J Am Chem Soc 2017;139:11233-11240. [PMID: 28737940 PMCID: PMC5562155 DOI: 10.1021/jacs.7b05958] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Indexed: 12/12/2022]
Number Cited by Other Article(s)
1
Rao H, Yang T, Wang Y, Fei J, Bie LH, Gao J. Molecular dynamics simulation on the role of CL5D in accelerating the product dissociation of SIRT6. Phys Chem Chem Phys 2025;27:4298-4306. [PMID: 39925168 DOI: 10.1039/d4cp03870c] [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: 02/11/2025]
2
Chong W, Zhang Z, Li Z, Meng S, Nian B, Hu Y. Hook loop dynamics engineering transcended the barrier of activity-stability trade-off and boosted the thermostability of enzymes. Int J Biol Macromol 2024;278:134953. [PMID: 39181358 DOI: 10.1016/j.ijbiomac.2024.134953] [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: 07/04/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024]
3
Hou XN, Song B, Zhao C, Chu WT, Ruan MX, Dong X, Meng LS, Gong Z, Weng YX, Zheng J, Wang J, Tang C. Connecting Protein Millisecond Conformational Dynamics to Protein Thermal Stability. JACS AU 2024;4:3310-3320. [PMID: 39211624 PMCID: PMC11350723 DOI: 10.1021/jacsau.4c00649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
4
McCullagh M, Zeczycki TN, Kariyawasam CS, Durie CL, Halkidis K, Fitzkee NC, Holt JM, Fenton AW. What is allosteric regulation? Exploring the exceptions that prove the rule! J Biol Chem 2024;300:105672. [PMID: 38272229 PMCID: PMC10897898 DOI: 10.1016/j.jbc.2024.105672] [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: 06/21/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024]  Open
5
Krempl C, Wurm JP, Beck Erlach M, Kremer W, Sprangers R. Insights into the Structure of Invisible Conformations of Large Methyl Group Labeled Molecular Machines from High Pressure NMR. J Mol Biol 2023;435:167922. [PMID: 37330282 DOI: 10.1016/j.jmb.2022.167922] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 06/19/2023]
6
Cetin E, Atilgan AR, Atilgan C. DHFR Mutants Modulate Their Synchronized Dynamics with the Substrate by Shifting Hydrogen Bond Occupancies. J Chem Inf Model 2022;62:6715-6726. [PMID: 35984987 PMCID: PMC9795552 DOI: 10.1021/acs.jcim.2c00507] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
7
Torgeson KR, Clarkson MW, Granata D, Lindorff-Larsen K, Page R, Peti W. Conserved conformational dynamics determine enzyme activity. SCIENCE ADVANCES 2022;8:eabo5546. [PMID: 35921420 PMCID: PMC9348788 DOI: 10.1126/sciadv.abo5546] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/16/2022] [Indexed: 05/31/2023]
8
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]
9
Nierzwicki L, East KW, Morzan UN, Arantes PR, Batista VS, Lisi GP, Palermo G. Enhanced specificity mutations perturb allosteric signaling in CRISPR-Cas9. eLife 2021;10:e73601. [PMID: 34908530 PMCID: PMC8741213 DOI: 10.7554/elife.73601] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/14/2021] [Indexed: 11/13/2022]  Open
10
Singh A, Fenwick RB, Dyson HJ, Wright PE. Role of Active Site Loop Dynamics in Mediating Ligand Release from E. coli Dihydrofolate Reductase. Biochemistry 2021;60:2663-2671. [PMID: 34428034 DOI: 10.1021/acs.biochem.1c00461] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
11
Elings W, Chikunova A, van Zanten DB, Drenth R, Ahmad MUD, Blok AJ, Timmer M, Perrakis A, Ubbink M. Two β-Lactamase Variants with Reduced Clavulanic Acid Inhibition Display Different Millisecond Dynamics. Antimicrob Agents Chemother 2021;65:e0262820. [PMID: 34031049 PMCID: PMC8284444 DOI: 10.1128/aac.02628-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 05/07/2021] [Indexed: 11/20/2022]  Open
12
Thompson S, Zhang Y, Ingle C, Reynolds KA, Kortemme T. Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme. eLife 2020;9:53476. [PMID: 32701056 PMCID: PMC7377907 DOI: 10.7554/elife.53476] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 07/09/2020] [Indexed: 12/03/2022]  Open
13
Pritišanac I, Alderson TR, Güntert P. Automated assignment of methyl NMR spectra from large proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020;118-119:54-73. [PMID: 32883449 DOI: 10.1016/j.pnmrs.2020.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 05/05/2023]
14
Cao YP, Xia YP, Gu XF, Han L, Chen Q, Zhi GY, Zhang DH. PEI-crosslinked lipase on the surface of magnetic microspheres and its characteristics. Colloids Surf B Biointerfaces 2020;189:110874. [DOI: 10.1016/j.colsurfb.2020.110874] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 01/19/2020] [Accepted: 02/12/2020] [Indexed: 12/23/2022]
15
Protein Dynamics revealed by NMR Relaxation Methods. Emerg Top Life Sci 2020;2:93-105. [PMID: 33241122 DOI: 10.1042/etls20170139] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
16
Directional conformer exchange in dihydrofolate reductase revealed by single-molecule nanopore recordings. Nat Chem 2020;12:481-488. [DOI: 10.1038/s41557-020-0437-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/10/2020] [Indexed: 12/18/2022]
17
Babu CS, Lim C. Sensitivity of Functional Loop Conformations on Long-Range Electrostatics: Implications for M20 Loop Dynamics in E. coli Dihydrofolate Reductase. J Chem Theory Comput 2020;16:2028-2033. [PMID: 32192329 DOI: 10.1021/acs.jctc.9b01285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
18
Aoto PC, Stanfield RL, Wilson IA, Dyson HJ, Wright PE. A Dynamic Switch in Inactive p38γ Leads to an Excited State on the Pathway to an Active Kinase. Biochemistry 2019;58:5160-5172. [PMID: 31794659 DOI: 10.1021/acs.biochem.9b00932] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
19
Plangger R, Juen MA, Hoernes TP, Nußbaumer F, Kremser J, Strebitzer E, Klingler D, Erharter K, Tollinger M, Erlacher MD, Kreutz C. Branch site bulge conformations in domain 6 determine functional sugar puckers in group II intron splicing. Nucleic Acids Res 2019;47:11430-11440. [PMID: 31665419 PMCID: PMC6868427 DOI: 10.1093/nar/gkz965] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/07/2019] [Accepted: 10/10/2019] [Indexed: 12/29/2022]  Open
20
The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release. Commun Biol 2018;1:226. [PMID: 30564747 PMCID: PMC6290769 DOI: 10.1038/s42003-018-0236-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/15/2018] [Indexed: 12/02/2022]  Open
21
Palmer AG, Koss H. Chemical Exchange. Methods Enzymol 2018;615:177-236. [PMID: 30638530 DOI: 10.1016/bs.mie.2018.09.028] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
22
Nagae T, Yamada H, Watanabe N. High-pressure protein crystal structure analysis of Escherichia coli dihydrofolate reductase complexed with folate and NADP. Acta Crystallogr D Struct Biol 2018;74:895-905. [PMID: 30198899 PMCID: PMC6130465 DOI: 10.1107/s2059798318009397] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/29/2018] [Indexed: 11/10/2022]  Open
23
Nerli S, McShan AC, Sgourakis NG. Chemical shift-based methods in NMR structure determination. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018;106-107:1-25. [PMID: 31047599 PMCID: PMC6788782 DOI: 10.1016/j.pnmrs.2018.03.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 05/08/2023]
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