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

描述(申请人提供)：人类基因组的完整性依赖于许多过程来确保DNA复制的保真度。这些过程的效率至关重要，因为DNA错误往往是疾病发病的关键。确保基因组完整性的一个重要过程是修复受损的DNA。DNA损伤有几种类型，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：切除受损的碱基和激活碱基切除修复(BER)过程，或直接脱烷基化。前一种途径涉及几种参与误码率级联的酶。后一种途径可以由AlkB家族的酶来执行。AlkB家族酶是非血红素铁和酮戊二酸依赖的酶，执行DNA的氧化脱烷基化。一些癌症治疗涉及烷化剂，人们试图通过抑制烷化损伤修复来加强这些治疗。通过详细了解AlkB家族蛋白的结构和反应机理，可以为开发过渡态类似物抑制剂提供有用的信息，从而有助于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实现使用的力场可能不能准确地描述近距离的MM环境，并且是不可极化的，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，本方案的目标是：i)用量子力学/分子力学(QM/MM)、分子动力学(MD)和同源模型研究AlkB酶家族的结构/功能/反应活性。Ii)开发第一个QM/MM程序，将QM程序与两个高级力场(GEM和阿米巴)接口，以准确描述MM环境；并开发一种在QM/MM模拟中引入远程静电效应的新方法。对AlkB及其人类同系物的结构、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。我们的合作者罗伯特·豪辛格教授和托马斯·霍利斯教授将根据我们的计算结果进行实验研究。教授们。任鹏宇和David Case将在琥珀计划套件中协助QM/MM的实施。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，并产生对可用于提高癌症治疗疗效的重要酶家族的结构和机制方面的见解。

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.