Sunden Fanny, Peck Ariana, Salzman Julia, Ressl Susanne, Herschlag Daniel
Department of Biochemistry, Beckman Center, Stanford University, Stanford, United States.
Molecular and Cellular Biochemistry Department, Indiana University Bloomington, Bloomington, United States.
Elife. 2015 Apr 22;4:e06181. doi: 10.7554/eLife.06181.
Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes.
酶通过将反应速率加速至生物时间尺度来维持生命。传统研究聚焦于识别直接参与酶促反应的残基，但这些所谓的“催化残基”嵌入在广泛的相互作用网络中。尽管这些网络的特性对于我们理解酶的功能、进化和工程至关重要，但尚未得到定量和系统的探索。我们剖析了大肠杆菌碱性磷酸酶活性位点中五个残基的相互作用网络。对特定残基复杂催化相互依赖性的分析确定了三个能量上独立但结构上相互连接的功能单元，它们具有不同的协同模式。从进化的角度来看，这个网络出现的可能性比完全协同的网络高出几个数量级。从功能的角度来看，则产生了新的催化见解。此外，这种全面的能量表征对于评估合理设计高效酶所需的算法将是必要的。
