Theory and Simulation of DNA Repair Enzymes; Mechanism, Structure and Function

描述（由申请人提供）：人类基因组的完整性取决于许多过程，以确保DNA复制的保真度。这些过程的效率至关重要，因为DNA中的错误往往是疾病发作的关键。确保基因组完整性的一个重要过程是修复受损的DNA。存在几种类型的DNA损伤，包括（但不限于）：烷基化、氧化、水解、加合物形成、碱基错配， 还有其他的烷基化的DNA碱基可以通过两种主要途径去除：切除受损碱基和激活碱基切除修复（BER）过程，或直接脱烷基化。前一种途径涉及BER级联中涉及的几种酶。后一种途径可以通过AlkB家族的酶进行。AlkB家族酶是非血红素铁和？酮戊二酸依赖性酶，其进行DNA的氧化脱烷基化。一些癌症治疗涉及烷化剂，并且已经尝试通过抑制烷化剂损伤修复来增强这些疗法。从AlkB家族蛋白的结构和反应机制的详细理解中获得的信息可以通过提供有用的信息来开发过渡态类似物抑制剂来帮助开发这些酶的抑制剂。一种方法是通过计算方法，包括量子力学/分子力学（QM/MM）方法。目前，大多数QM/MM实现采用的力场可能无法准确描述近距离的MM环境，不可极化，并且缺乏包括远程静电效应的方法。我们的长期目标是通过计算机模拟来了解参与DNA修复的酶的机制，结构和功能。为此，本提案的目标是：i）通过量子力学/分子力学（QM/MM）、分子动力学（MD）和同源模建来研究AlkB家族酶的结构/功能/反应性。ii）开发第一个QM/MM程序，将QM程序与两个先进力场（GEM和AMOEBA）连接起来，以准确描述MM环境;并开发一种新方法，在QM/MM模拟中引入远程静电效应。对AlkB及其人类同源物的结构、功能和反应机制的详细了解将为抑制这些酶的可能方法提供见解。我们的合作者Robert Housinger教授和托马斯霍利斯教授将根据我们的计算结果进行实验研究。教授Pengyu Ren和大卫案例将提供协助与QM/MM的实施在AMBER套件的计划。拟议项目的成功完成将为酶反应的计算提供准确的计算工具，并对可用于提高癌症治疗疗效的重要酶家族产生结构和机制见解。

DESCRIPTION (provided by applicant): Human genome integrity depends on many processes to ensure the fidelity of the duplication of DNA. The efficiency of these processes is crucial since errors in DNA can often be key to disease onset. An important process to insure genome integrity is the repair of damaged DNA. There are several types of DNA damage including (but not limited to): alkylation, oxidation, hydrolysis, adduct formation, base mismatch, among others. Alkylated DNA bases may be removed by two main routes: excision of the damaged base and activation of the base excision repair (BER) process, or direct dealkylation. The former route involves several enzymes involved in the BER cascade. The latter route may be performed by the AlkB family of enzymes. AlkB family enzymes are non-heme iron and ?-ketoglutarate dependent enzymes that perform an oxidative dealkylation of DNA. Some cancer treatments involve alkylating agents, and attempts have been made to enhance these therapies by inhibiting alkylating damage repair. Information gained from a detailed understanding of the structure and reaction mechanism of AlkB family proteins can aid in the development of inhibitors for these enzymes by providing useful information to develop transition state analogue inhibitors. One approach for this is via computational methods, including quantum mechanical/molecular mechanical (QM/MM) methods. Currently, most QM/MM implementations employ force fields that may not accurately describe the MM environment at close range, are not polarizable and lack methods to include long-range electrostatic effects. Our long-term goal is to understand the mechanism, structure and function of enzymes involved in DNA repair by means of computational simulations. To this end, the goals of the present proposal are: i) To study the structure/function/reactivity of AlkB family of enzymes by quantum mechanical/molecular mechanical (QM/MM), molecular dynamics (MD) and homology modeling. ii) To develop the first QM/MM program that interfaces a QM program with a two advanced force fields (GEM and AMOEBA) to accurately describe the MM environment; and to develop a novel method to introduce long-range electrostatic effects in QM/MM simulations. The detailed understanding of the structure, function and reaction mechanism of AlkB and its human homologues will provide insights into possible methods to inhibit these enzymes. Our collaborators, Prof. Robert Housinger and Prof. Thomas Hollis, will perform experimental studies based on our computational results. Profs. Pengyu Ren and David Case will provide assistance with the QM/MM implementation in the AMBER suite of programs. The successful completion of the proposed project will provide an accurate computational tool for the calculation of enzyme reactions, and the generation of structural and mechanistic insights on an important family of enzymes that may be used to enhance the efficacy of cancer treatments.