Determinants of Folding Mechanism in Small Proteins

描述（由申请人提供）：大多数蛋白质在功能上是进化优化的，但在折叠上不是。因此，了解蛋白质折叠机制将有助于我们设计出在不改变其功能的情况下进行折叠优化的蛋白质。此外，错误折叠和聚集是致命疾病的基础，如囊性纤维化、阿尔茨海默病和其他淀粉样病变，以及ii型糖尿病。蛋白质折叠的预测框架，特别是在非原生状态及其序列的确定，将极大地影响折叠相关疾病的生物医学研究。我们将通过对一些快速折叠蛋白质的动力学和热力学研究，开发和验证这样一个蛋白质折叠的预测框架。我们打算了解这些蛋白质折叠机制的决定因素，并通过与实验的广泛比较来验证我们的理解。在显式溶剂和隐式溶剂中的全原子分子力学力场将用于表征非原生态和折叠路径。

DESCRIPTION (provided by applicant): Most proteins are evolutionarily optimized for function, but not for folding. Thus, understanding protein folding mechanisms will help us design proteins that are optimized for folding without altering their functions. In addition, misfolding and aggregation underlie fatal diseases such as cystic fibrosis, Alzheimer's disease and other amyloidoses, and type-II diabetes. A predictive framework for protein folding, particularly in the nonnative states and its sequence determination, will greatly impact biomedical research of folding-related diseases. We will develop and validate such a predictive framework for protein folding through the studies of kinetics and thermodynamics of a few fast-folding proteins. We intend to understand the determinants of folding mechanisms for these proteins at all-atom details and validate our understanding by comparing with experiment extensively. An all-atom molecular mechanics force field in both explicit solvent and in implicit solvent will be used to characterize the nonnative states and the folding pathways. 1) We plan to: (a) investigate the interplay of sequence and topology in the determination of the folding rates and pathways for two engineered proteins with Zn-finger motif: FSD1 and PDA8D; (b) perturb their folding pathways by mutation to achieve sub-microsecond folding rates in this family. 2) We will investigate: (a) what makes the predicted rate of protein A based on topology correct, but the predicted rate of Engrailed Homeodomain off by a factor of 40; (b) what makes protein A so sensitive to mutation -- a single mutation can change its rate by a factor of 10 or higher; (c) what makes Engrailed Homeodomain tolerate drastic changes in sequence with little change in folding rates. We will computationally probe many aspects of their folding processes, the denatured states, the transition states, the intermediate states if any, and the pathways towards native states to understand the differences.