一个世纪的酶动力学分析，1913 年至 2013 年。
A century of enzyme kinetic analysis, 1913 to 2013.
机构信息
Institute for Cell and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, 2500 Speedway, MBB 3.122, Austin, TX 78735, USA.
出版信息
FEBS Lett. 2013 Sep 2;587(17):2753-66. doi: 10.1016/j.febslet.2013.07.012. Epub 2013 Jul 12.
Abstract
This review traces the history and logical progression of methods for quantitative analysis of enzyme kinetics from the 1913 Michaelis and Menten paper to the application of modern computational methods today. Following a brief review of methods for fitting steady state kinetic data, modern methods are highlighted for fitting full progress curve kinetics based upon numerical integration of rate equations, including a re-analysis of the original Michaelis-Menten full time course kinetic data. Finally, several illustrations of modern transient state kinetic methods of analysis are shown which enable the elucidation of reactions occurring at the active sites of enzymes in order to relate structure and function.
摘要
本文追溯了从 1913 年迈克利斯和门坦论文到当今现代计算方法定量分析酶动力学的历史和逻辑发展过程。简要回顾了拟合稳态动力学数据的方法之后，重点介绍了基于速率方程数值积分拟合完整过程曲线动力学的现代方法，包括对原始迈克尔逊门坦完整时间过程动力学数据的重新分析。最后，展示了几种现代瞬态动力学分析方法的实例，这些方法可用于阐明酶活性部位的反应，以关联结构与功能。
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2
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J Enzyme Inhib Med Chem. 2013 Aug;28(4):879-93. doi: 10.3109/14756366.2012.688039. Epub 2012 May 28.
3
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Structure. 2012 Apr 4;20(4):618-27. doi: 10.1016/j.str.2012.02.018. Epub 2012 Apr 3.
4
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J Am Chem Soc. 2012 Jan 11;134(1):293-304. doi: 10.1021/ja206873f. Epub 2011 Dec 19.
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