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纤维素酶 I 糖基化反应的计算反应动力学的分子细节。

Molecular details from computational reaction dynamics for the cellobiohydrolase I glycosylation reaction.

机构信息

Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.

出版信息

J Am Chem Soc. 2011 Dec 7;133(48):19474-82. doi: 10.1021/ja206842j. Epub 2011 Nov 9.

Abstract

Glycosylation of cellobiose hydrolase I (CBHI), is a key step in the processing and degradation of cellulose. Here the pathways and barriers of the reaction are explored using the free energy from adaptive reaction coordinate forces (FEARCF) reaction dynamics method coupled with SCC-DFTB/MM. In many respects CBHI follows the expected general GH7 family mechanism that involves the Glu-X-Asp-X-X-Glu motif. However, critical electronic and conformational details, previously not known, were discovered through our computations. The central feature that ensures the success of the glycosylation reaction are the Glu212 nucleophile's hydrogen bond to the hydroxyl on C2, of the glucose in the -1 position of the cellulosic strand. This Glu212 function restricts the C2 hydroxyl in such a way as to favor the formation of the (4)E ring pucker of the -1 position glucose. A frontier molecular orbital analysis of the structures along the reaction surface proves the existence of an oxocarbenium ion, which has both transition state and intermediate character. The transition state structure is able to descend down the glycosylation pathway through the critical combination of Asp214 (HOMO), ring oxygen (LUMO), and Glu212 (HOMO), anomeric carbon (LUMO) interactions. Using the fully converged FEARCF SCC-DFTB/MM reaction surface, we find a barrier of 17.48 kcal/mol separating bound cellulose chain from the glycosylated CBHI. Taking recrossing into account gives k(cat) = 0.415 s(-1) for cellobiohydrolase glycosylation.

摘要

纤维二糖水解酶 I(CBHI)的糖基化是纤维素加工和降解的关键步骤。在此,使用自适应反应坐标力(FEARCF)反应动力学方法与 SCC-DFTB/MM 耦合,探索了反应的途径和障碍。在许多方面,CBHI 遵循预期的 GH7 家族机制,该机制涉及 Glu-X-Asp-X-X-Glu 基序。然而,通过我们的计算发现了以前未知的关键电子和构象细节。确保糖基化反应成功的核心特征是Glu212亲核试剂与纤维素链上-1 位葡萄糖的 C2 羟基之间的氢键。这种 Glu212 功能以限制 C2 羟基的方式限制 C2 羟基,有利于-1 位葡萄糖的(4)E 环构象的形成。反应表面结构的前沿分子轨道分析证明了存在一个氧杂环丁烷离子,它具有过渡态和中间特征。过渡态结构能够通过 Asp214(HOMO)、环氧(LUMO)和 Glu212(HOMO)、糖苷键碳原子(LUMO)相互作用的关键组合,沿着糖基化途径下降。使用完全收敛的 FEARCF SCC-DFTB/MM 反应表面,我们发现从结合的纤维素链到糖基化 CBHI 的分离有 17.48 kcal/mol 的能垒。考虑重交叉,纤维素二糖水解酶的糖基化的 k(cat) = 0.415 s(-1)。

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