酶促反应动力学
Dynamics of enzymatic reactions.
作者信息
Warshel A
出版信息
Proc Natl Acad Sci U S A. 1984 Jan;81(2):444-8. doi: 10.1073/pnas.81.2.444.
Abstract
The detailed molecular dynamics of an actual bond-breaking event in a fluctuating enzyme substrate complex is simulated. The method developed allows one to explore what type of fluctuations are involved in enzymatic reactions and to evaluate entropic contributions to enzyme catalysis. The fluctuations of the enzyme electrostatic potential are found to be a key dynamical factor in reactions that involve a large change in the polarity of the reacting bonds.
摘要
模拟了波动的酶-底物复合物中实际键断裂事件的详细分子动力学。所开发的方法使人们能够探索酶促反应中涉及何种类型的波动，并评估熵对酶催化的贡献。发现酶静电势的波动是涉及反应键极性发生重大变化的反应中的关键动力学因素。
相似文献
1
Dynamics of enzymatic reactions.酶促反应动力学
Proc Natl Acad Sci U S A. 1984 Jan;81(2):444-8. doi: 10.1073/pnas.81.2.444.
2
Calculations of enzymatic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes.酶促反应的计算：酶中pKa、质子转移反应和一般酸催化反应的计算。
Biochemistry. 1981 May 26;20(11):3167-77. doi: 10.1021/bi00514a028.
3
Hydrogen tunneling links protein dynamics to enzyme catalysis.氢隧穿将蛋白质动力学与酶催化联系起来。
Annu Rev Biochem. 2013;82:471-96. doi: 10.1146/annurev-biochem-051710-133623.
4
The dynamical nature of enzymatic catalysis.酶催化的动态本质。
Acc Chem Res. 2015 Feb 17;48(2):407-13. doi: 10.1021/ar5002928. Epub 2014 Dec 24.
5
Mechanical catalysis on the centimetre scale.厘米尺度上的机械催化。
J R Soc Interface. 2015 Mar 6;12(104):20141271. doi: 10.1098/rsif.2014.1271.
6
Correlated conformational fluctuations during enzymatic catalysis: Implications for catalytic rate enhancement.酶催化过程中的相关构象波动：对催化速率提高的影响。
Protein Sci. 2001 Jul;10(7):1319-30. doi: 10.1110/ps.220101.
7
Energetics of enzyme catalysis.酶催化的能量学
Proc Natl Acad Sci U S A. 1978 Nov;75(11):5250-4. doi: 10.1073/pnas.75.11.5250.
8
The entropic contributions in vitamin B12 enzymes still reflect the electrostatic paradigm.维生素B12酶中的熵贡献仍然反映了静电范式。
Proc Natl Acad Sci U S A. 2015 Apr 7;112(14):4328-33. doi: 10.1073/pnas.1503828112. Epub 2015 Mar 24.
9
Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis.对酶催化的动力学贡献：一个流行假说的关键检验
Chem Rev. 2006 May;106(5):1737-56. doi: 10.1021/cr040427e.
10
Empirical valence bond calculations of enzyme catalysis.
Ann N Y Acad Sci. 1981;367:370-82. doi: 10.1111/j.1749-6632.1981.tb50579.x.
引用本文的文献
1
A multi-layered computational structural genomics approach enhances domain-specific interpretation of Kleefstra syndrome variants in EHMT1.一种多层计算结构基因组学方法增强了对EHMT1中克莱夫斯特拉综合征变体的结构域特异性解读。
Comput Struct Biotechnol J. 2023 Oct 13;21:5249-5258. doi: 10.1016/j.csbj.2023.10.022. eCollection 2023.
2
Study of the Sensing Kinetics of G Protein-Coupled Estrogen Receptor Sensors for Common Estrogens and Estrogen Analogs.常见雌激素和雌激素类似物的 G 蛋白偶联雌激素受体传感器的传感动力学研究。
Molecules. 2023 Apr 7;28(8):3286. doi: 10.3390/molecules28083286.
3
Evolution Conserves the Network of Coupled Residues in Dihydrofolate Reductase.进化保存二氢叶酸还原酶中偶联残基的网络。
Biochemistry. 2019 Sep 17;58(37):3861-3868. doi: 10.1021/acs.biochem.9b00460. Epub 2019 Aug 30.
4
Modulating Enzyme Activity by Altering Protein Dynamics with Solvent.通过溶剂改变蛋白质动力学来调节酶活性
Biochemistry. 2018 Jul 24;57(29):4263-4275. doi: 10.1021/acs.biochem.8b00424. Epub 2018 Jul 6.
5
Molecular Basis for K63-Linked Ubiquitination Processes in Double-Strand DNA Break Repair: A Focus on Kinetics and Dynamics.双链DNA断裂修复中K63连接的泛素化过程的分子基础：聚焦动力学与动态变化
J Mol Biol. 2017 Nov 10;429(22):3409-3429. doi: 10.1016/j.jmb.2017.05.029. Epub 2017 Jun 3.
6
Perspective: Defining and quantifying the role of dynamics in enzyme catalysis.观点：定义并量化动力学在酶催化中的作用。
J Chem Phys. 2016 May 14;144(18):180901. doi: 10.1063/1.4947037.
7
Tales of Dihydrofolate Binding to R67 Dihydrofolate Reductase.二氢叶酸与R67二氢叶酸还原酶结合的故事
Biochemistry. 2016 Jan 12;55(1):133-45. doi: 10.1021/acs.biochem.5b00981. Epub 2015 Dec 21.
8
Histidine Orientation Modulates the Structure and Dynamics of a de Novo Metalloenzyme Active Site.组氨酸取向调节从头设计金属酶活性位点的结构与动力学
J Am Chem Soc. 2015 Aug 19;137(32):10164-76. doi: 10.1021/jacs.5b02840. Epub 2015 Aug 6.
9
Measuring electric fields and noncovalent interactions using the vibrational stark effect.利用振动斯塔克效应测量电场和非共价相互作用。
Acc Chem Res. 2015 Apr 21;48(4):998-1006. doi: 10.1021/ar500464j. Epub 2015 Mar 23.
10
Probing protein multidimensional conformational fluctuations by single-molecule multiparameter photon stamping spectroscopy.通过单分子多参数光子标记光谱法探测蛋白质多维构象波动
J Phys Chem B. 2014 Oct 16;118(41):11943-55. doi: 10.1021/jp5081498. Epub 2014 Oct 3.
本文引用的文献
1
Molecular dynamics of hydrogen bonds in bovine pancreatic trypsin inhibitor protein.牛胰蛋白酶抑制剂蛋白中氢键的分子动力学
Nature. 1981 Nov 26;294(5839):379-80. doi: 10.1038/294379a0.
2
Calculations of enzymatic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes.酶促反应的计算：酶中pKa、质子转移反应和一般酸催化反应的计算。
Biochemistry. 1981 May 26;20(11):3167-77. doi: 10.1021/bi00514a028.
3
The internal dynamics of globular proteins.球状蛋白质的内部动力学。
CRC Crit Rev Biochem. 1981;9(4):293-349. doi: 10.3109/10409238109105437.
4
The three-dimensional structure of an enzyme molecule.酶分子的三维结构。
Sci Am. 1966 Nov;215(5):78-90. doi: 10.1038/scientificamerican1166-78.
5
Bicycle-pedal model for the first step in the vision process.视觉过程第一步的自行车踏板模型。
Nature. 1976 Apr 22;260(5553):679-83. doi: 10.1038/260679a0.
6
Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme.酶促反应的理论研究：溶菌酶反应中碳正离子的介电、静电和空间稳定作用
J Mol Biol. 1976 May 15;103(2):227-49. doi: 10.1016/0022-2836(76)90311-9.
7
Temperature-dependent X-ray diffraction as a probe of protein structural dynamics.温度依赖型X射线衍射作为蛋白质结构动力学的一种探测手段
Nature. 1979 Aug 16;280(5723):558-63. doi: 10.1038/280558a0.
8
Viscosity-dependent structural fluctuations in enzyme catalysis.酶催化中与粘度相关的结构波动
Biochemistry. 1979 Apr 3;18(7):1269-75. doi: 10.1021/bi00574a023.
9
Enzyme dynamics: the statistical physics approach.酶动力学：统计物理学方法
Annu Rev Biophys Bioeng. 1979;8:69-97. doi: 10.1146/annurev.bb.08.060179.000441.
10
Dynamics of activated processes in globular proteins.球状蛋白质中活化过程的动力学
Proc Natl Acad Sci U S A. 1979 Aug;76(8):3585-9. doi: 10.1073/pnas.76.8.3585.
Zotero 插件