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生物磷酸盐水解计算建模中的挑战与进展

Challenges and advances in the computational modeling of biological phosphate hydrolysis.

作者信息

Petrović Dušan, Szeler Klaudia, Kamerlin Shina Caroline Lynn

机构信息

Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.

出版信息

Chem Commun (Camb). 2018 Mar 28;54(25):3077-3089. doi: 10.1039/c7cc09504j. Epub 2018 Feb 7.

Abstract

Phosphate ester hydrolysis is fundamental to many life processes, and has been the topic of substantial experimental and computational research effort. However, even the simplest of phosphate esters can be hydrolyzed through multiple possible pathways that can be difficult to distinguish between, either experimentally, or computationally. Therefore, the mechanisms of both the enzymatic and non-enzymatic reactions have been historically controversial. In the present contribution, we highlight a number of technical issues involved in reliably modeling these computationally challenging reactions, as well as proposing potential solutions. We also showcase examples of our own work in this area, discussing both the non-enzymatic reaction in aqueous solution, as well as insights obtained from the computational modeling of organophosphate hydrolysis and catalytic promiscuity amongst enzymes that catalyze phosphoryl transfer.

摘要

磷酸酯水解是许多生命过程的基础,一直是大量实验和计算研究工作的主题。然而,即使是最简单的磷酸酯也可以通过多种可能的途径水解,这些途径无论是在实验上还是计算上都很难区分。因此,酶促反应和非酶促反应的机制在历史上一直存在争议。在本论文中,我们强调了可靠地模拟这些计算上具有挑战性的反应所涉及的一些技术问题,并提出了潜在的解决方案。我们还展示了我们在这一领域的工作实例,讨论了水溶液中的非酶促反应,以及从有机磷酸酯水解的计算模型和催化磷酰基转移的酶之间的催化混杂性中获得的见解。

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