Suppr超能文献

冷冻残基对酶反应机制的 PES 探索的影响。

Influence of Frozen Residues on the Exploration of the PES of Enzyme Reaction Mechanisms.

机构信息

UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto , Rua do Campo Alegre s/n, 4169-007 Porto, Portugal.

出版信息

J Chem Theory Comput. 2017 Nov 14;13(11):5486-5495. doi: 10.1021/acs.jctc.7b00768. Epub 2017 Oct 25.

Abstract

In this work, we studied one of the very widely used approximations in the prediction of an enzyme reaction mechanism with computational methods, that is, fixing residues outside a given radius surrounding the active site. This avoids the unfolding of truncated models during MD calculations, avoids the expansion of the active site in cluster model calculations (albeit here only specific atoms are frozen), and prevents drifting between local minima when adiabatic mapping with large QM/MM models is used. To test this, we have used the first step of the reaction catalyzed by HIV-1 protease, as the detrimental effects of this approximation are expected to be large here. We calculated the PES with shells of frozen residues of different radii. Models with free regions under a 6.00 Å radius showed signs of being overconstrained. The QM/MM energy barrier for the remaining models was only slightly sensitive to this approximation (average of 0.8 kcal·mol, maximum of 1.6 kcal·mol-1). The influence over the energy of reaction was almost negligible. This widely used approximation seems safe and robust. The resulting error is on average below 1.6 kcal·mol, which is small when compared with others deriving from, for example, the choice of the density functional or semiempirical MO/SCC-DFTB method, the basis set used, or even the lack of sampling or incomplete sampling.

摘要

在这项工作中,我们研究了在使用计算方法预测酶反应机制时非常广泛使用的一种近似方法,即固定活性位点周围给定半径范围内的残基。这避免了在 MD 计算中展开截断模型,避免了在簇模型计算中扩展活性位点(尽管这里仅冻结了特定原子),并防止了在使用具有大 QM/MM 模型的绝热映射时在局部最小值之间漂移。为了测试这一点,我们使用了 HIV-1 蛋白酶催化的反应的第一步,因为预计在这里这种近似的有害影响会很大。我们使用不同半径的冻结残基壳计算 PES。半径为 6.00Å 以下有自由区域的模型显示出过度约束的迹象。剩余模型的 QM/MM 能垒对此近似值的敏感性仅略有不同(平均为 0.8 kcal·mol,最大为 1.6 kcal·mol-1)。对反应能的影响几乎可以忽略不计。这种广泛使用的近似方法似乎是安全和稳健的。平均误差低于 1.6 kcal·mol,与其他因素(例如,密度泛函或半经验 MO/SCC-DFTB 方法的选择、使用的基组,甚至采样不足或不完全采样)相比,这个误差很小。

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验