COMPUTER SIMULATION OF CORRELATED DYNAMICS DURING LIGAND BINDING & CATALYSIS

该项目将使用先进的计算机模拟技术来 研究DFHR中与催化事件相关的动力学和波动 和β-内酰胺酶，与实验小组密切合作解释 核磁共振和诱变数据。该分析将扩展传统的分子 以新的方式研究长轴相关运动的动力学模拟 距离标度和开发催化途径的详细模型， 使用以下技术。 (A)关键动力学中间态的分子动力学模拟 通过实验表征了DHFR的催化循环，提供了 研究这些分子的涨落和动力学的基础 系统之间的耦合以及这些系统之间的催化作用。类似 将对进化上不太成熟的酶进行模拟 金属β-内酰胺酶系统。 (B)在DHFR中生成的催化路径的模型 轨迹技术寻找过渡态的生成技术 以及连接催化中间体(或 它们的类似物通过核磁共振、结晶学和突变分析得到。 (C)dhfr和beta的调和和拟调和分析- 基于建议结构的游离型和配基结合型内酰胺酶 催化中间态和脱辅酶模型的研究 长波长、低频率的相关运动可以影响 这些制度的整体刚性。从这些衍生出来的运动模型 将创建研究，使用可调整的参数来适应核磁共振松弛 数据。 (D)与项目3合作，完善解决方案结构 不含或与抑制剂复合的β-内酰胺酶。这一目标 将首先涉及基于量子力学的模型的发展 对于双金属活性中心，随后进行结构建模。

This project will use developed computer simulation techniques to study dynamics and fluctuations associated with catalytic events in DFHR and beta-lactamase, working closely with experimental groups to interpret NMR and mutagenesis data. The analysis will extend conventional molecular dynamics simulations in novel ways to study correlated motions at long distance scales and to develop detailed models of catalytic pathways, using the following techniques. (a) Molecular dynamics simulations on key kinetic intermediate states characterized experimentally for the catalytic cycle of DHFR, providing a basis for the study of fluctuations and dynamics of these molecular systems and the coupling between these to catalytic function. Similar simulations will be performed for the evolutionally less mature enzyme system of metallo beta-lactamase. (b) Models for catalytic pathways in DHFR generated by novel trajectory techniques generation techniques that find transition states and reaction paths to connect structures of catalytic intermediates (or their analogues generated by NMR, crystallography and mutational analysis. (c) Harmonic and quasiharmonic analyses of both DHFR and beta- lactamase in free and ligand-bound forms, based on proposed structural models of catalytic intermediate states and the apo-enzymes, to study long-wavelength, low-frequency correlated motions that can affect the overall rigidity of these system. Motional models derived from these studies will be created, with adjustable parameters to fit NMR relaxation data. (d) Collaboration with Project 3 to refine a solution structure of beta-lactamase both free and in complex with inhibitors. This objective will involve first the development of quantum mechanically based models for the bimetallic active site followed by structural modeling.