Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements
Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements
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DOI：
10.1073/pnas.1514240113
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发表时间：
2016-03-22
影响因子：
11.1
通讯作者：
Milo, Ron
中科院分区：
文献类型：
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作者：
Davidi, Dan;Noor, Elad;Milo, Ron
周转数，也称为k(CAT)值，是酶的基本性质。然而，k(CAT)数据很少，而且是在体外测量的，因此可能不能真实地反映体内的情况。一个有待阐明的基本问题是：对于活体中酶的最大催化速率，k(CAT)值有多大的代表性？在这里，我们利用组学数据来计算k(Max)(Vivo)，即观察到的酶在细胞内的最大催化速率。与大肠杆菌的k(Cat)值比较，对数标度(p<；10(-10))的相关系数r(2)=0.62，均方根差0.54(线性标度的3.5倍)，表明体内和体外的最大速率基本一致。通过考虑酶的饱和度和热力学决定的反向通量，我们进一步细化了k(Max)(Vivo)和k(Cat)值之间的对应关系。我们提出的方法描述了体外和体内酶催化之间的定量关系，并提供了一种从组学数据中提取酶动力学常数的高通量方法。
Turnover numbers, also known as k(cat) values, are fundamental properties of enzymes. However, k(cat) data are scarce and measured in vitro, thus may not faithfully represent the in vivo situation. A basic question that awaits elucidation is: how representative are k(cat) values for the maximal catalytic rates of enzymes in vivo? Here, we harness omics data to calculate k(max)(vivo), the observed maximal catalytic rate of an enzyme inside cells. Comparison with k(cat) values from Escherichia coli, yields a correlation of r(2) = 0.62 in log scale (p < 10(-10)), with a root mean square difference of 0.54 (3.5-fold in linear scale), indicating that in vivo and in vitro maximal rates generally concur. By accounting for the degree of saturation of enzymes and the backward flux dictated by thermodynamics, we further refine the correspondence between k(max)(vivo) and k(cat) values. The approach we present here characterizes the quantitative relationship between enzymatic catalysis in vitro and in vivo and offers a high-throughput method for extracting enzyme kinetic constants from omics data.