COMPUTATIONAL STUDIES OF GART

GART 的计算研究

• 批准号: 6178878
• 负责人: DIMITRIOS MORIKIS
• 金额: $ 4.63万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-06-01 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/6178878
• 关键词: acidity /alkalinity; computer simulation; conformation; dimer; hydroxymethyltransferases; ionic bond; ionization; ionization constant; protein structure function; ribose phosphate

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.

甘氨酰胺核糖核苷酸转化酶 (GART) 是 DNA 嘌呤碱基生物合成的重要酶。 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 中的结构-功能关系是合理药物设计的第一步。 高分辨率晶体结构数据和描述酶反应的详细动力学机制的可用性使 GART 成为研究对结构形成和催化非常重要的重要域-域相互作用的理想模型系统。 我们建议使用一种基于求解线性泊松-玻尔兹曼方程的新颖计算方法从理论上计算 GART 所有可电离基团的 pKa 值。 我们期望描述负责单体-二聚体转变的可电离基团的作用，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。 由于该计算将利用 GART 的 X 射线结构，我们希望阐明二聚化时构象变化的重要性。 我们建议应用蒙特卡罗和随机动力学方法 (MC/SD) 的组合来模拟 Glu70Ala GART 突变体残基 110-131 中 pH 依赖性无序环有序环/螺旋转变以及整体蛋白质中局部构象转变及其催化活性的影响。