Determinants of Folding Mechanism in Small Proteins

小蛋白质折叠机制的决定因素

• 批准号: 6822504
• 负责人: RAY LUO
• 金额: $ 26.54万
• 依托单位: UNIVERSITY OF CALIFORNIA-IRVINE
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-08-01 至 2009-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6822504
• 关键词: DNA binding protein; chemical kinetics; chemical models; computational biology; computer simulation; model design /development; protein engineering; protein folding; protein sequence; protein structure function; thermodynamics; DNA binding protein; chemical kinetics; chemical models; computational biology; computer simulation; model design /development; protein engineering; protein folding; protein sequence; protein structure function; thermodynamics

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.

描述（由申请人提供）：大多数蛋白质在功能方面进行了进化优化，但不能用于折叠。因此，了解蛋白质折叠机制将有助于我们设计用于折叠的蛋白质，而无需更改其功能。此外，错误折叠和聚集是致命疾病的基础，例如囊性纤维化，阿尔茨海默氏病和其他淀粉样蛋白以及II型糖尿病。蛋白质折叠的预测框架，尤其是在非本地状态及其序列确定，将极大地影响与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的动力学和热力学的研究来开发和验证蛋白质折叠的预测框架。我们打算在所有原子细节上了解这些蛋白质的折叠机制的决定因素，并通过广泛的实验进行比较来验证我们的理解。明确溶剂和隐式溶剂中的全原子分子力学力场将用于表征非本地状态和折叠途径。 1）我们计划：（a）研究序列和拓扑的相互作用，以确定具有Zn手指基序的两个工程蛋白的折叠速率和途径：FSD1和PDA8D； （b）通过突变扰动其折叠途径，以实现该家族的亚微秒折叠率。 2）我们将调查：（a）是什么使基于拓扑的蛋白质A的预测速率正确，但是预测的同源域的预测率为40倍； （b）使蛋白质对突变如此敏感的原因 - 单个突变可以将其速率提高10倍或更高； （c）是什么使插入的同源域可耐受序列的急剧变化，而折叠率几乎没有变化。我们将在计算其折叠过程的许多方面，变性状态，过渡状态，中间状态（如果有）以及通往本地状态的途径以了解差异的许多方面。