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For: Jones HBL, Wells SA, Prentice EJ, Kwok A, Liang LL, Arcus VL, Pudney CR. A complete thermodynamic analysis of enzyme turnover links the free energy landscape to enzyme catalysis. FEBS J 2017. [PMID: 28650586 DOI: 10.1111/febs.14152] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Number Cited by Other Article(s)
1
Walker EJ, Hamill CJ, Crean R, Connolly MS, Warrender AK, Kraakman KL, Prentice EJ, Steyn-Ross A, Steyn-Ross M, Pudney CR, van der Kamp MW, Schipper LA, Mulholland AJ, Arcus VL. Cooperative Conformational Transitions Underpin the Activation Heat Capacity in the Temperature Dependence of Enzyme Catalysis. ACS Catal 2024;14:4379-4394. [PMID: 38633402 PMCID: PMC11020164 DOI: 10.1021/acscatal.3c05584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/16/2024] [Accepted: 02/16/2024] [Indexed: 04/19/2024]
2
Warrender AK, Pan J, Pudney C, Arcus VL, Kelton W. Red edge excitation shift spectroscopy is highly sensitive to tryptophan composition. J R Soc Interface 2023;20:20230337. [PMID: 37935360 PMCID: PMC10645072 DOI: 10.1098/rsif.2023.0337] [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: 06/12/2023] [Accepted: 10/16/2023] [Indexed: 11/09/2023]  Open
3
Ramakrishnan K, Johnson RL, Winter SD, Worthy HL, Thomas C, Humer DC, Spadiut O, Hindson SH, Wells S, Barratt AH, Menzies GE, Pudney CR, Jones DD. Glycosylation increases active site rigidity leading to improved enzyme stability and turnover. FEBS J 2023;290:3812-3827. [PMID: 37004154 PMCID: PMC10952495 DOI: 10.1111/febs.16783] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/14/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
4
Warrender AK, Pan J, Pudney CR, Arcus VL, Kelton W. Constant domain polymorphisms influence monoclonal antibody stability and dynamics. Protein Sci 2023;32:e4589. [PMID: 36759959 PMCID: PMC9951194 DOI: 10.1002/pro.4589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
5
Gao S, Zhang W, Barrow SL, Iavarone AT, Klinman JP. Temperature-dependent hydrogen deuterium exchange shows impact of analog binding on adenosine deaminase flexibility but not embedded thermal networks. J Biol Chem 2022;298:102350. [PMID: 35933011 PMCID: PMC9483566 DOI: 10.1016/j.jbc.2022.102350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/29/2022]  Open
6
Kwok A, Camacho IS, Winter S, Knight M, Meade RM, Van der Kamp MW, Turner A, O'Hara J, Mason JM, Jones AR, Arcus VL, Pudney CR. A Thermodynamic Model for Interpreting Tryptophan Excitation-Energy-Dependent Fluorescence Spectra Provides Insight Into Protein Conformational Sampling and Stability. Front Mol Biosci 2021;8:778244. [PMID: 34926581 PMCID: PMC8681860 DOI: 10.3389/fmolb.2021.778244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022]  Open
7
Wilson MA. Mapping Enzyme Landscapes by Time-Resolved Crystallography with Synchrotron and X-Ray Free Electron Laser Light. Annu Rev Biophys 2021;51:79-98. [PMID: 34932909 PMCID: PMC9132212 DOI: 10.1146/annurev-biophys-100421-110959] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
8
Winter SD, Jones HBL, Răsădean DM, Crean RM, Danson MJ, Pantoş GD, Katona G, Prentice E, Arcus VL, van der Kamp MW, Pudney CR. Chemical Mapping Exposes the Importance of Active Site Interactions in Governing the Temperature Dependence of Enzyme Turnover. ACS Catal 2021;11:14854-14863. [PMID: 34956689 PMCID: PMC8689651 DOI: 10.1021/acscatal.1c04679] [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: 10/11/2021] [Revised: 11/16/2021] [Indexed: 12/26/2022]
9
Evolution of dynamical networks enhances catalysis in a designer enzyme. Nat Chem 2021;13:1017-1022. [PMID: 34413499 DOI: 10.1038/s41557-021-00763-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 06/30/2021] [Indexed: 02/08/2023]
10
Hindson SA, Bunzel HA, Frank B, Svistunenko DA, Williams C, van der Kamp MW, Mulholland AJ, Pudney CR, Anderson JLR. Rigidifying a De Novo Enzyme Increases Activity and Induces a Negative Activation Heat Capacity. ACS Catal 2021;11:11532-11541. [PMID: 34557328 PMCID: PMC8453482 DOI: 10.1021/acscatal.1c01776] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/29/2021] [Indexed: 12/22/2022]
11
Lund BA, Thomassen AM, Carlsen TJW, Leiros HKS. Biochemical and biophysical characterization of the OXA-48-like carbapenemase OXA-436. Acta Crystallogr F Struct Biol Commun 2021;77:312-318. [PMID: 34473108 PMCID: PMC8411929 DOI: 10.1107/s2053230x21008645] [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: 04/29/2021] [Accepted: 08/18/2021] [Indexed: 11/08/2023]  Open
12
Xu Y, Huang J. Validating the CHARMM36m protein force field with LJ-PME reveals altered hydrogen bonding dynamics under elevated pressures. Commun Chem 2021;4:99. [PMID: 36697521 PMCID: PMC9814493 DOI: 10.1038/s42004-021-00537-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/08/2021] [Indexed: 01/28/2023]  Open
13
Subramanian S, Jones HB, Frustaci S, Winter S, van der Kamp MW, Arcus VL, Pudney CR, Vollmer F. Sensing Enzyme Activation Heat Capacity at the Single-Molecule Level Using Gold-Nanorod-Based Optical Whispering Gallery Modes. ACS APPLIED NANO MATERIALS 2021;4:4576-4583. [PMID: 34085031 PMCID: PMC8165693 DOI: 10.1021/acsanm.1c00176] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
14
Directed evolution of glycosyltransferase for enhanced efficiency of avermectin glucosylation. Appl Microbiol Biotechnol 2021;105:4599-4607. [PMID: 34043077 DOI: 10.1007/s00253-021-11279-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 03/15/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
15
Kaspar F, Wolff DS, Neubauer P, Kurreck A, Arcus VL. pH-Independent Heat Capacity Changes during Phosphorolysis Catalyzed by the Pyrimidine Nucleoside Phosphorylase from Geobacillus thermoglucosidasius. Biochemistry 2021;60:1573-1577. [PMID: 33955225 DOI: 10.1021/acs.biochem.1c00156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
16
Red-Edge Excitation Shift Spectroscopy (REES): Application to Hidden Bound States of Ligands in Protein-Ligand Complexes. Int J Mol Sci 2021;22:ijms22052582. [PMID: 33806656 PMCID: PMC7961384 DOI: 10.3390/ijms22052582] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 01/13/2023]  Open
17
He Z, Paul F, Roux B. A critical perspective on Markov state model treatments of protein-protein association using coarse-grained simulations. J Chem Phys 2021;154:084101. [PMID: 33639768 PMCID: PMC7902085 DOI: 10.1063/5.0039144] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
18
Monoclonal antibody stability can be usefully monitored using the excitation-energy-dependent fluorescence edge-shift. Biochem J 2021;477:3599-3612. [PMID: 32869839 PMCID: PMC7527260 DOI: 10.1042/bcj20200580] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 11/17/2022]
19
Duff MR, Redzic JS, Ryan LP, Paukovich N, Zhao R, Nix JC, Pitts TM, Agarwal P, Eisenmesser EZ. Structure, dynamics and function of the evolutionarily changing biliverdin reductase B family. J Biochem 2021;168:191-202. [PMID: 32246827 DOI: 10.1093/jb/mvaa039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/19/2020] [Indexed: 11/14/2022]  Open
20
Novel insights in linking solvent relaxation dynamics and protein conformations utilizing red edge excitation shift approach. Emerg Top Life Sci 2021;5:89-101. [PMID: 33416893 DOI: 10.1042/etls20200256] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/14/2020] [Accepted: 12/18/2020] [Indexed: 01/01/2023]
21
Kramers’ Theory and the Dependence of Enzyme Dynamics on Trehalose-Mediated Viscosity. Catalysts 2020. [DOI: 10.3390/catal10060659] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
22
Phillips RS, Craig S, Kovalevsky A, Gerlits O, Weiss K, Iorgu AI, Heyes DJ, Hay S. Pressure and Temperature Effects on the Formation of Aminoacrylate Intermediates of Tyrosine Phenol-lyase Demonstrate Reaction Dynamics. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03967] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
23
Droplet-based optofluidic systems for measuring enzyme kinetics. Anal Bioanal Chem 2019;412:3265-3283. [PMID: 31853606 DOI: 10.1007/s00216-019-02294-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/15/2019] [Accepted: 11/19/2019] [Indexed: 01/05/2023]
24
Jones HBL, Crean RM, Mullen A, Kendrick EG, Bull SD, Wells SA, Carbery DR, MacMillan F, van der Kamp MW, Pudney CR. Exposing the Interplay Between Enzyme Turnover, Protein Dynamics, and the Membrane Environment in Monoamine Oxidase B. Biochemistry 2019;58:2362-2372. [PMID: 30964996 DOI: 10.1021/acs.biochem.9b00213] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
25
Dušeková E, Garajová K, Yavaşer R, Varhač R, Sedlák E. Hofmeister effect on catalytic properties of chymotrypsin is substrate-dependent. Biophys Chem 2018;243:8-16. [DOI: 10.1016/j.bpc.2018.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/30/2018] [Accepted: 10/09/2018] [Indexed: 12/26/2022]
26
Matyushov DV. Fluctuation relations, effective temperature, and ageing of enzymes: The case of protein electron transfer. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.06.087] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
27
Jones HBL, Crean RM, Matthews C, Troya AB, Danson MJ, Bull SD, Arcus VL, van der Kamp MW, Pudney CR. Uncovering the Relationship between the Change in Heat Capacity for Enzyme Catalysis and Vibrational Frequency through Isotope Effect Studies. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
28
Buß O, Rudat J, Ochsenreither K. FoldX as Protein Engineering Tool: Better Than Random Based Approaches? Comput Struct Biotechnol J 2018;16:25-33. [PMID: 30275935 PMCID: PMC6158775 DOI: 10.1016/j.csbj.2018.01.002] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/21/2017] [Accepted: 01/20/2018] [Indexed: 02/04/2023]  Open
29
Ren W, Fei X, Tian J, Li Y, Jing M, Fang H, Xu L, Wang Y. Multiscale immobilized lipase for rapid separation and continuous catalysis. NEW J CHEM 2018. [DOI: 10.1039/c8nj01950a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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