MECHANISM OF FOLDING OF THE SH3 DOMAIN

SH3结构域的折叠机制

• 批准号: 6519996
• 负责人: DAVID BAKER
• 金额: $ 25.86万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-05-01 至 2004-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6519996
• 关键词: chemical kinetics; computer simulation; conformation; evolution; hydropathy; model design /development; molecular dynamics; nuclear magnetic resonance spectroscopy; physical model; protein denaturation; protein folding; protein sequence; protein structure; structural biology; thermodynamics

The objective of this proposal is to use a combination of experimental and computational approaches to develop a physically plausible model for the folding of the src SH3 domain capable of accurately predicting the results of further experimental measurements. The rate limiting step in folding will be probed by analyzing the kinetic consequences of both single and multiple amino acid substitutions in combination with both all atom and simplified computational models. The starting point of the folding reaction, the denatured state, will be probed by studying peptide models, the kinetics of exchange from the native state, and by direct NMR characterization. The importance of hydrophobic-hydrophyllic patterning and the relationship between sequence conservation and kinetics will be investigated using phage display selection methods. The experimental data will be compared with the results of computational methods including a recently developed ab initio folding simulation method, a simple model which computes the rate and transition state structure from the sequence and native state using simple physical principles, and all atom MD simulations. The ultimate goal is a therapy for beta sheet proteins capable for predicting the folding rate, the structure in the transition state ensemble, and the residual structure in the denatured state from the sequence and structure of the native protein.

本提案的目的是使用实验和计算方法的结合来开发一个物理上合理的模型，用于src SH3结构域的折叠，能够准确预测进一步实验测量的结果。结合全原子和简化计算模型，通过分析单个和多个氨基酸取代的动力学后果，探讨折叠中的限速步骤。折叠反应的起始点，即变性状态，将通过研究肽模型、从天然状态交换的动力学以及直接的核磁共振表征来探索。利用噬菌体展示选择方法，研究疏水-亲水模式的重要性以及序列保存与动力学之间的关系。实验数据将与计算方法的结果进行比较，包括最近开发的从头算折叠模拟方法，一个简单的模型，从序列和原生态计算速率和过渡态结构，使用简单的物理原理，以及所有原子MD模拟。最终目标是一种能够从天然蛋白的序列和结构中预测折叠速率、过渡态集合结构和变性态残余结构的β片蛋白疗法。