COMPUTATIONAL STUDIES OF GART

甘氨酸酰胺核糖核苷酸转化酶（GART）是生物合成DNA嘌呤碱基的重要酶。它也是抗肿瘤或抗菌药物靶向的有吸引力的候选者。了解GART的结构-功能关系是合理设计药物的第一步。高分辨率晶体结构数据的可用性和描述酶促反应的详细动力学机制使GART成为研究对结构形成和催化重要的重要域-域相互作用的理想模型系统。我们提出了一种基于求解线性化泊松-玻尔兹曼方程的计算方法，从理论上计算所有可电离基团的pKa值。我们期望描述单体-二聚体转变中可电离基团的作用，并了解His54， His7, Glu70, Tyr67, Tyr78， Tyr115和其他可滴定残基在转变机制中的作用。由于这个计算将利用GART的x射线结构，我们期望阐明二聚化时构象变化的意义。我们建议结合蒙特卡罗和随机动力学方法（MC/SD）来模拟Glu70Ala GART突变体110-131残基中ph依赖的无序环-有序环/螺旋转变，以及蛋白质整体局部构象转变的影响及其催化活性。

Glycinamide Ribonucleotide Transformylase (GART) is an important enzyme for the biosynthesis of purine bases for DNA. It is also an attractive candidate for targeting with antineoplastic or antimicrobial agents. Understanding of structure-function relations in GART is a first step for rational drug design. The availability of high resolution crystal structure data and detailed kinetic mechanisms describing the enzymatic reaction make GART an ideal model system to investigate significant domain-domain interactions that are important for structure formation and catalysis. We propose to theoretically calculate the pKa values of all ionizable groups of GART using a novel computational approach which is based on solving the linearized Poisson-Boltzmann equation. We expect to delineate the role of the ionizable groups that are responsible for the monomer-dimer transition and to understand the role His54, His7, Glu70, Tyr67, Tyr78, Tyr115 and other titratable residues in the mechanism of the transition. Since this calculation will utilize the X-ray structures of GART we expect to elucidate the significance of the conformational changes upon dimerization. We propose to apply a combination of Monte Carlo and Stochastic dynamics methods (MC/SD) to model the pH-dependent disordered loop-ordered loop/helix transition in residues 110-131 of the Glu70Ala GART mutant and the effect of the local conformational transition in the protein overall and its catalytic activity.