Computer Simulation of Enzymatic Reactions

获得酶作用的定量描述是分子生物学最重要的挑战之一。因此，我们建议继续我们的研究项目，旨在开发、改进和实施酶促反应模拟的计算模型。在以前的资助期间，我们已经证明了我们的经验价电子键（EVB）方法的一般适用性。近年来，我们开始开发更严格的从头算方法，利用日益增加的计算机能力。我们的新策略包括：(a)量子力学（从头算）/朗格万偶极子（QM(ai)/LD）模型，该模型提供了溶液中反应潜在表面的关键信息。这使我们能够校准EVB表面用于酶的研究；(b)从头算自由能摄动（QM(ai)/FEP），它使用EVB表面作为参考电位，从而使我们能够开始从头算酶促反应的自由能；(c)约束密度泛函理论（CDFT）方法，它允许我们在从头算水平上表示蛋白质的大部分。虽然这些方法还需要进一步的验证，但我们已经准备好将它们用于酶催化的研究。除了方法开发项目外，我们在研究不同类型的酶促反应和探索不同催化机制的可行性方面取得了重大进展。为了利用我们的先进技术，我们建议在以下三个方向上取得进展：(a)我们将进行方法开发研究，其中包括：(i)改进构建参考溶液反应的从头算方法。我们将特别关注溶液反应的过渡态搜索和熵修正的评估；（ii）在EVB表面的自动精炼中使用溶液表面；（iii）使用EVB表面作为自动细化EVB表面的参考电位；（iii）利用EVB表面作为酶的QM(ai)/FEP研究的参考电位；（iv）金属酶的CDFT研究。(b)我们将对几类重要的酶促反应进行系统研究，包括：(i)丝氨酸和半胱氨酸蛋白酶；（ii） DNA聚合酶；（三）核糖核酸酶。(c)我们将研究不同催化建议的相对重要性，包括(i)熵效应；（ii）低势垒氢键；（iii）近攻型外形；(4)酶活性位点的预组织。

Gaining a quantitative description of enzyme action is one of the most important challenges of molecular biology. Thus, we propose a continuation of our research projects aimed at the development, refinement, and implementation of computational models for simulations of enzymatic reactions. During previous grant periods we have demonstrated the general applicability of our empirical valence bond (EVB) approach. In recent years we started to develop more rigorous ab initio approaches that exploit the increasing availability of computer power. Our new strategies include: (a) quantum mechanical (ab initio)/Langevin dipole (QM(ai)/LD) model which provide crucial information about potential surfaces of reactions in solution. This allows us to calibrate EVB surfaces for studies of enzymes; (b) an ab initio free energy perturbation (QM(ai)/FEP) which uses EVB surfaces as reference potentials and thus allows us to start evaluating ab initio free energies of enzymatic reactions; and (c) a constrain density functional theory (CDFT) approach, which allows us to represent large parts of the protein at the ab initio level. Although these approaches still require further validation, we are ready to use them in studies of enzymatic catalysis. In addition to the method development projects, we have made significant progress in studying different classes of enzymatic reactions and in exploring the feasibility of different catalytic mechanisms. In order to exploit our advanced we propose to advance in the following three directions: (a) we will conduct method development studies that will include: (i) improving our ab initio approaches for constructing reference solution reactions. In particular, we will focus on transition state search and evaluation of entropic corrections for solution reactions; (ii) using solution surfaces in automated refined of EVB surfaces; (iii) using the EVB surfaces as reference potentials in automated refinement of EVB surfaces; (iii) using the EVB surfaces as reference potentials for QM(ai)/FEP studies of enzymes; (iv) CDFT studies of metalloenzyme. (b) We will conduct systematic studies of several important classes of enzymatic reactions including: (i) serine and cysteine proteases; (ii) DNA polymerase; and (iii) ribonuclease. (c) We will conduct studies of the relative importance of different catalytic proposals, including (i) entropic effects; (ii) low barrier hydrogen bond; (iii) near attack conformers; and (iv) pre-organization of enzyme active sites.