MECHANISM OF FOLDING OF THE SH3 DOMAIN

这个建议的目的是使用实验和计算方法的组合，以开发一个物理上合理的模型，能够准确地预测进一步的实验测量的结果的src SH 3域的折叠。 在折叠的限速步骤将探讨通过分析动力学的后果，结合所有原子和简化的计算模型的单个和多个氨基酸取代。 折叠反应的起始点，变性状态，将通过研究肽模型，从天然状态交换的动力学，并通过直接NMR表征来探索。 将使用噬菌体展示选择方法研究疏水-疏水基图案化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，包括最近开发的从头折叠模拟方法，一个简单的模型，该模型使用简单的物理原理从序列和自然状态计算速率和过渡态结构，以及所有原子的MD模拟。 最终目标是能够从天然蛋白质的序列和结构预测折叠速率、过渡态系综中的结构和变性状态下的残余结构的β折叠蛋白质的疗法。

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.