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For: Khavrutskii IV, Price DJ, Lee J, Brooks CL. Conformational change of the methionine 20 loop of Escherichia coli dihydrofolate reductase modulates pKa of the bound dihydrofolate. Protein Sci 2007;16:1087-100. [PMID: 17473015 PMCID: PMC2206655 DOI: 10.1110/ps.062724307] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Revised: 03/05/2007] [Accepted: 03/06/2007] [Indexed: 10/23/2022]
Number Cited by Other Article(s)
1
Wan Q, Bennett BC, Wymore T, Li Z, Wilson MA, Brooks CL, Langan P, Kovalevsky A, Dealwis CG. Capturing the Catalytic Proton of Dihydrofolate Reductase: Implications for General Acid-Base Catalysis. ACS Catal 2021;11:5873-5884. [PMID: 34055457 PMCID: PMC8154319 DOI: 10.1021/acscatal.1c00417] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/19/2021] [Indexed: 02/04/2023]
2
Mhashal AR, Major DT. Temperature-Dependent Kinetic Isotope Effects in R67 Dihydrofolate Reductase from Path-Integral Simulations. J Phys Chem B 2021;125:1369-1377. [PMID: 33522797 PMCID: PMC7883348 DOI: 10.1021/acs.jpcb.0c10318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/05/2021] [Indexed: 11/28/2022]
3
Adesina AS, Świderek K, Luk LYP, Moliner V, Allemann RK. Electric Field Measurements Reveal the Pivotal Role of Cofactor-Substrate Interaction in Dihydrofolate Reductase Catalysis. ACS Catal 2020;10:7907-7914. [PMID: 32905264 PMCID: PMC7467645 DOI: 10.1021/acscatal.0c01856] [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] [Received: 04/26/2020] [Revised: 06/18/2020] [Indexed: 12/31/2022]
4
DHFR Inhibitors: Reading the Past for Discovering Novel Anticancer Agents. Molecules 2019;24:molecules24061140. [PMID: 30909399 PMCID: PMC6471984 DOI: 10.3390/molecules24061140] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/18/2019] [Accepted: 03/20/2019] [Indexed: 11/17/2022]  Open
5
Abbat S, Jaladanki CK, Bharatam PV. Exploring PfDHFR reaction surface: A combined molecular dynamics and QM/MM analysis. J Mol Graph Model 2018;87:76-88. [PMID: 30508692 DOI: 10.1016/j.jmgm.2018.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/16/2018] [Accepted: 11/19/2018] [Indexed: 11/18/2022]
6
Mhashal AR, Pshetitsky Y, Cheatum CM, Kohen A, Major DT. Evolutionary Effects on Bound Substrate pKa in Dihydrofolate Reductase. J Am Chem Soc 2018;140:16650-16660. [DOI: 10.1021/jacs.8b09089] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
7
Mhashal AR, Pshetitsky Y, Eitan R, Cheatum CM, Kohen A, Major DT. Effect of Asp122 Mutation on the Hydride Transfer in E. coli DHFR Demonstrates the Goldilocks of Enzyme Flexibility. J Phys Chem B 2018;122:8006-8017. [PMID: 30040418 DOI: 10.1021/acs.jpcb.8b05556] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
8
Duff MR, Borreguero JM, Cuneo MJ, Ramanathan A, He J, Kamath G, Chennubhotla SC, Meilleur F, Howell EE, Herwig KW, Myles DAA, Agarwal PK. Modulating Enzyme Activity by Altering Protein Dynamics with Solvent. Biochemistry 2018;57:4263-4275. [PMID: 29901984 DOI: 10.1021/acs.biochem.8b00424] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
9
Paukovich N, Xue M, Elder JR, Redzic JS, Blue A, Pike H, Miller BG, Pitts TM, Pollock DD, Hansen K, D'Alessandro A, Eisenmesser EZ. Biliverdin Reductase B Dynamics Are Coupled to Coenzyme Binding. J Mol Biol 2018;430:3234-3250. [PMID: 29932944 DOI: 10.1016/j.jmb.2018.06.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/05/2018] [Accepted: 06/06/2018] [Indexed: 12/28/2022]
10
Mhashal AR, Vardi-Kilshtain A, Kohen A, Major DT. The role of the Met20 loop in the hydride transfer in Escherichia coli dihydrofolate reductase. J Biol Chem 2017;292:14229-14239. [PMID: 28620051 DOI: 10.1074/jbc.m117.777136] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/24/2017] [Indexed: 11/06/2022]  Open
11
Luk LYP, Loveridge EJ, Allemann RK. Protein motions and dynamic effects in enzyme catalysis. Phys Chem Chem Phys 2016;17:30817-27. [PMID: 25854702 DOI: 10.1039/c5cp00794a] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
12
Pshetitsky Y, Eitan R, Verner G, Kohen A, Major DT. Improved Sugar Puckering Profiles for Nicotinamide Ribonucleoside for Hybrid QM/MM Simulations. J Chem Theory Comput 2016;12:5179-5189. [PMID: 27490188 DOI: 10.1021/acs.jctc.6b00401] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
13
Rabelo VW, Sampaio TF, Duarte LD, Lopes DHB, Abreu PA. Structure–activity relationship of a series of 1,2-dihydroquinoline analogues and binding mode with Vibrio cholerae dihydrofolate reductase. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1583-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
14
Hanoian P, Liu CT, Hammes-Schiffer S, Benkovic S. Perspectives on electrostatics and conformational motions in enzyme catalysis. Acc Chem Res 2015;48:482-9. [PMID: 25565178 PMCID: PMC4334233 DOI: 10.1021/ar500390e] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
15
Liu CT, Francis K, Layfield JP, Huang X, Hammes-Schiffer S, Kohen A, Benkovic SJ. Escherichia coli dihydrofolate reductase catalyzed proton and hydride transfers: temporal order and the roles of Asp27 and Tyr100. Proc Natl Acad Sci U S A 2014;111:18231-6. [PMID: 25453098 PMCID: PMC4280594 DOI: 10.1073/pnas.1415940111] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
16
Toward resolving the catalytic mechanism of dihydrofolate reductase using neutron and ultrahigh-resolution X-ray crystallography. Proc Natl Acad Sci U S A 2014;111:18225-30. [PMID: 25453083 DOI: 10.1073/pnas.1415856111] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]  Open
17
Doron D, Stojković V, Gakhar L, Vardi-Kilshtain A, Kohen A, Major DT. Free energy simulations of active-site mutants of dihydrofolate reductase. J Phys Chem B 2014;119:906-16. [PMID: 25382260 DOI: 10.1021/jp5059963] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
18
Wan Q, Kovalevsky AY, Wilson MA, Bennett BC, Langan P, Dealwis C. Preliminary joint X-ray and neutron protein crystallographic studies of ecDHFR complexed with folate and NADP+. Acta Crystallogr F Struct Biol Commun 2014;70:814-8. [PMID: 24915100 PMCID: PMC4051544 DOI: 10.1107/s2053230x1400942x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 04/26/2014] [Indexed: 11/10/2022]  Open
19
Ruiz-Pernia JJ, Luk LYP, García-Meseguer R, Martí S, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Increased dynamic effects in a catalytically compromised variant of Escherichia coli dihydrofolate reductase. J Am Chem Soc 2013;135:18689-96. [PMID: 24252106 PMCID: PMC3949409 DOI: 10.1021/ja410519h] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Indexed: 01/19/2023]
20
Guo J, Loveridge EJ, Luk LYP, Allemann RK. Effect of Dimerization on Dihydrofolate Reductase Catalysis. Biochemistry 2013;52:3881-7. [DOI: 10.1021/bi4005073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
21
Fan Y, Cembran A, Ma S, Gao J. Connecting protein conformational dynamics with catalytic function as illustrated in dihydrofolate reductase. Biochemistry 2013;52:2036-49. [PMID: 23297871 DOI: 10.1021/bi301559q] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
22
Arora K, Brooks CL. Multiple intermediates, diverse conformations, and cooperative conformational changes underlie the catalytic hydride transfer reaction of dihydrofolate reductase. Top Curr Chem (Cham) 2013;337:165-87. [PMID: 23420416 PMCID: PMC4394636 DOI: 10.1007/128_2012_408] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
23
Hu X, Legler PM, Khavrutskii I, Scorpio A, Compton JR, Robertson KL, Friedlander AM, Wallqvist A. Probing the donor and acceptor substrate specificity of the γ-glutamyl transpeptidase. Biochemistry 2012;51:1199-212. [PMID: 22257032 DOI: 10.1021/bi200987b] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
24
Stojković V, Perissinotti LL, Willmer D, Benkovic SJ, Kohen A. Effects of the donor-acceptor distance and dynamics on hydride tunneling in the dihydrofolate reductase catalyzed reaction. J Am Chem Soc 2012;134:1738-45. [PMID: 22171795 DOI: 10.1021/ja209425w] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
25
Goh GB, Knight JL, Brooks CL. Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent. J Chem Theory Comput 2011;8:36-46. [PMID: 22337595 DOI: 10.1021/ct2006314] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
26
Doron D, Major DT, Kohen A, Thiel W, Wu X. Hybrid Quantum and Classical Simulations of the Dihydrofolate Reductase Catalyzed Hydride Transfer Reaction on an Accurate Semi-Empirical Potential Energy Surface. J Chem Theory Comput 2011;7:3420-37. [PMID: 26598171 DOI: 10.1021/ct2004808] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
27
Bhabha G, Lee J, Ekiert DC, Gam J, Wilson IA, Dyson HJ, Benkovic SJ, Wright PE. A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science 2011;332:234-8. [PMID: 21474759 DOI: 10.1126/science.1198542] [Citation(s) in RCA: 365] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
28
Arora K, Brooks Iii CL. Functionally important conformations of the Met20 loop in dihydrofolate reductase are populated by rapid thermal fluctuations. J Am Chem Soc 2010;131:5642-7. [PMID: 19323547 DOI: 10.1021/ja9000135] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
29
Butterfoss GL, DeRose EF, Gabel SA, Perera L, Krahn JM, Mueller GA, Zheng X, London RE. Conformational dependence of 13C shielding and coupling constants for methionine methyl groups. JOURNAL OF BIOMOLECULAR NMR 2010;48:31-47. [PMID: 20734113 PMCID: PMC5598763 DOI: 10.1007/s10858-010-9436-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Accepted: 07/13/2010] [Indexed: 05/12/2023]
30
Evans RM, Behiry EM, Tey LH, Guo J, Loveridge EJ, Allemann RK. Catalysis by Dihydrofolate Reductase from the Psychropiezophile Moritella profunda. Chembiochem 2010;11:2010-7. [DOI: 10.1002/cbic.201000341] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
31
Loveridge EJ, Maglia G, Allemann RK. The role of arginine 28 in catalysis by dihydrofolate reductase from the hyperthermophile Thermotoga maritima. Chembiochem 2010;10:2624-7. [PMID: 19816891 DOI: 10.1002/cbic.200900465] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
32
Loveridge EJ, Behiry EM, Swanwick RS, Allemann RK. Different Reaction Mechanisms for Mesophilic and Thermophilic Dihydrofolate Reductases. J Am Chem Soc 2009;131:6926-7. [DOI: 10.1021/ja901441k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
33
Bas DC, Rogers DM, Jensen JH. Very fast prediction and rationalization of pKa values for protein-ligand complexes. Proteins 2008;73:765-83. [PMID: 18498103 DOI: 10.1002/prot.22102] [Citation(s) in RCA: 892] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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