MECHANISM OF FOLDING OF THE SH3 DOMAIN

这项建议的目的是使用实验和计算方法的组合来开发一个物理上可信的src SH3结构域折叠模型，能够准确地预测进一步实验测量的结果。通过分析单个和多个氨基酸取代的动力学结果，结合所有原子和简化的计算模型，探讨折叠中的限速步骤。折叠反应的起点，变性状态，将通过研究多肽模型、从天然状态交换的动力学和直接的核磁共振表征来探索。将利用噬菌体展示选择方法研究疏水-水叶模式的重要性以及序列保守性和动力学之间的关系。实验数据将与计算方法的结果进行比较，这些方法包括最近开发的从头计算折叠模拟方法，使用简单的物理原理从序列和本征状态计算速率和过渡态结构的简单模型，以及所有的原子MD模拟。最终的目标是治疗β折叠蛋白，能够根据天然蛋白的序列和结构预测折叠速度、过渡态整体结构和变性状态的残基结构。

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.