Mixed quantum mechanical/molecular mechanical (QM/MM) study of the deacylation reaction in a penicillin binding protein (PBP) versus in a class C β-lactamase
Mixed quantum mechanical/molecular mechanical (QM/MM) study of the deacylation reaction in a penicillin binding protein (PBP) versus in a class C β-lactamase
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DOI：
10.1021/ja036879a
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发表时间：
2004-06-23
影响因子：
15
通讯作者：
Friesner, RA
中科院分区：
文献类型：
--
作者：
Gherman, BF;Goldberg, SD;Friesner, RA
青霉素结合蛋白 (PBP) 和 β-内酰胺酶中酰基酶中间体的脱酰率存在显着差异的根源仍然是一个未解之谜，其解决方案对于了解细菌抗生素耐药性非常重要。在这项工作中，使用精确、大规模的混合从头算量子力学/分子力学 (QM/MM) 计算来研究头孢噻吩和链霉菌 DD-肽酶之间形成的酰基酶中间体的水解。 R61（一种 PBP）和阴沟肠杆菌 P99 头孢菌素酶（一种 C 类 β-内酰胺酶）。 P99 的定性和定量与实验动力学一致。 β-内酰胺酶更快的脱酰化速率归因于 P99 中 Tyr150 周围更有利的静电环境（与 R61 中的 Tyr159 相比），这有利于该残基作为通用碱基的功能。发现这在很大程度上是通过 P99 共价结合配体而不同时消除与 Tyr150 的氢键的能力来实现的，事实证明 R61 中的 Tyr159 的情况并非如此。这项工作为该领域的进一步工作提供了重要的基础，例如选择能够将 PBP 转化为 β-内酰胺酶的突变。
The origin of the substantial difference in deacylation rates for acyl-enzyme intermediates in penicillin-binding proteins (PBPs) and beta-lactamases has remained an unsolved puzzle whose solution is of great importance to understanding bacterial antibiotic resistance. In this work, accurate, large-scale mixed ab initio quantum mechanical/molecular mechanical (QM/MM) calculations have been used to study the hydrolysis of acyl-enzyme intermediates formed between cephalothin and the DD-peptidase of Streptomyces sp. R61, a PBP, and the Enterobacter cloacae P99 cephalosporinase, a class C beta-lactamase. Qualitative and, in the case of P99, quantitative agreement was achieved with experimental kinetics. The faster rate of deacylation in the beta-lactamase is attributed to a more favorable electrostatic environment around Tyr150 in P99 (as compared to that for Tyr159 in R61) which facilitates this residue's function as the general base. This is found to be in large part accomplished by the ability of P99 to covalently bind the ligand without concurrent elimination of hydrogen bonds to Tyr150, which proves not to be the case with Tyr159 in R61. This work provides an essential foundation for further work in this area, such as selecting mutations capable of converting the PBP into a beta-lactamase.