A structural perspective on the temperature dependent activity of enzymes

被引:1
作者
McLeod, Matthew J. [1 ,2 ]
Barwell, Sarah A. E. [2 ]
Holyoak, Todd [2 ]
Thorne, Robert E. [1 ]
机构
[1] Cornell Univ, Dept Phys, Ithaca, NY 14850 USA
[2] Univ Waterloo, Dept Biol, Waterloo, ON N2L 3G1, Canada
基金
美国国家卫生研究院; 加拿大自然科学与工程研究理事会; 美国国家科学基金会;
关键词
LOOP LID DOMAIN; PHOSPHOENOLPYRUVATE CARBOXYKINASE; ARRHENIUS PLOTS; CYTOSOLIC PEPCK; MECHANISM; DYNAMICS; INHIBITION; TRANSITION; ENSEMBLES; CATALYSIS;
D O I
10.1016/j.str.2025.02.013
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Enzyme activity varies with temperature. Unlike small-molecule catalysts, the structural ensembles of enzymes can change substantially with temperature, but it is unclear how this modulates temperature dependent activity. Here, multi-temperature X-ray crystallography was used to record structural changes from-20 degrees C to 40 degrees C for a mesophilic enzyme in complex with inhibitors mimicking substrate-, intermediate-, and product-bound states, representative of major complexes on the reaction coordinate. Inhibitors, substrates and active site loops increasingly populated catalytically competent conformations as temperature increased. These changes occurred even in temperature ranges where kinetic measurements showed roughly linear Arrhenius/Eyring behavior, where parameters characterizing the system are assumed to be temperature independent. Simple analysis shows that linear Arrhenius/Eyring behavior can still be observed when the underlying activation energy/enthalpy values vary with temperature. Our results indicate a critical role for temperature dependent atomic-resolution structural data in interpreting temperature dependent kinetic data from enzymatic systems.
引用
收藏
页码:924 / 934.e2
页数:14
相关论文
共 69 条
[1]   Towards automated crystallographic structure refinement with phenix.refine [J].
Afonine, Pavel V. ;
Grosse-Kunstleve, Ralf W. ;
Echols, Nathaniel ;
Headd, Jeffrey J. ;
Moriarty, Nigel W. ;
Mustyakimov, Marat ;
Terwilliger, Thomas C. ;
Urzhumtsev, Alexandre ;
Zwart, Peter H. ;
Adams, Paul D. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2012, 68 :352-367
[2]   Calculation of Heat Capacity Changes in Enzyme Catalysis and Ligand Binding [J].
Aqvist, Johan ;
van der Ent, Florian .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2022, 18 (10) :6345-6353
[3]   Temperature, Dynamics, and Enzyme-Catalyzed Reaction Rates [J].
Arcus, Vickery L. ;
Mulholland, Adrian J. .
ANNUAL REVIEW OF BIOPHYSICS, VOL 49, 2020, 2020, 49 :163-180
[4]   On the Temperature Dependence of Enzyme-Catalyzed Rates [J].
Arcus, Vickery L. ;
Prentice, Erica J. ;
Hobbs, Joanne K. ;
Mulholland, Adrian J. ;
Van der Kamp, Marc W. ;
Pudney, Christopher R. ;
Parker, Emily J. ;
Schipper, Louis A. .
BIOCHEMISTRY, 2016, 55 (12) :1681-1688
[5]  
Arrhenius S.A., 1889, Z. Phys. Chem, V4, P96, DOI [DOI 10.1515/ZPCH-1889-0408, 10.1515/zpch-1889-0408]
[6]   THE CCP4 SUITE - PROGRAMS FOR PROTEIN CRYSTALLOGRAPHY [J].
BAILEY, S .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1994, 50 :760-763
[7]   Inhibition and Allosteric Regulation of Monomeric Phosphoenolpyruvate Carboxykinase by 3-Mercaptopicolinic Acid [J].
Balan, Marc D. ;
Mcleod, Matthew J. ;
Lotosky, William R. ;
Ghaly, Mark ;
Holyoak, Todd .
BIOCHEMISTRY, 2015, 54 (38) :5878-5887
[8]   Directional regulation of cytosolic PEPCK catalysis is mediated by competitive binding of anions [J].
Barwell, Sarah A. E. ;
Duman, Ramona ;
Wagner, Armin ;
Holyoak, Todd .
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2022, 637 :218-223
[9]   Temperature artifacts in protein structures bias ligand-binding predictions [J].
Bradford, Shanshan Y. C. ;
El Khoury, Lea ;
Ge, Yunhui ;
Osato, Meghan ;
Mobley, David L. ;
Fischer, Marcus .
CHEMICAL SCIENCE, 2021, 12 (34) :11275-11293
[10]   Structural Insights into the Mechanism of Phosphoenolpyruvate Carboxykinase Catalysis [J].
Carlson, Gerald M. ;
Holyoak, Todd .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2009, 284 (40) :27037-27041