THEORETICAL AND EXPERIMENTAL STUDY OF PROTEIN FOLDING

我们建议发展下一代蛋白质折叠理论，它将是定量的，直到单个残基的分辨水平。该理论将提供主要蛋白质折叠的动力学和热力学“指纹”，勾勒出哪些残基对热力学稳定最重要，哪些残基是动力学“加速器踏板”。这将有助于从天然蛋白质的多个序列比对中获得的新的进化数据合理化。在追求这一目标的过程中，我们将发展一系列重要的技术和理论方法，如高效的蒙特卡罗蛋白质设计、蛋白质序列选择的分析理论和折叠可设计性，这是一种选择真实蛋白质折叠动态能力最强的序列的进化算法。此外，我们将发展分析理论和模拟来为折叠的成核机制提供充分的理论基础，包括最重要的问题，即蛋白质折叠核的决定因素是什么。作为这项工作的必然结果，我们将进行蛋白质“手术”和“正畸”的实验研究，我们将把快速折叠蛋白质ADA2H的折叠核移植到其慢折叠结构同系物ACP中，以显著提高后者的折叠率。此外，我们还将通过对绒毛蛋白的实验研究来检验成核理论，合理地将折叠核重新设计为芳香核，并研究核移动的功能、动力学和热力学后果。

We propose to develop next generation of theory of protein folding that will be quantitative up to single residue resolution level. The theory will provide kinetic and thermodynamic "fingerprints" of major protein folds outlining which residues are most important for thermodynamic stabilization and which ones are kinetic "accelerator pedals". This will help to rationalize the emerging evolutionary data from multiple sequence alignments of natural proteins. In pursuing this goal we will develop a series of important techniques and theoretical approaches such as efficient Monte-Carlo protein design, analytical theory of sequence selection in proteins and fold designability, an evolutionary algorithm for selection of most kinetically competent sequences of real protein folds. Further, we will develop analytical theory and simulations to provide full rationale to the nucleation mechanism of folding, including the most important issue of what are the determinants of protein folding nucleus. As a corollary to this effort we will carry out experimental studies of protein "surgery" and "orthodontics" whereby we will transplant folding nucleus of a fast-folding protein ADA2h into its slow-folding structural homolog AcP in order to dramatically raise the folding rate of the latter. Furthermore we will test the theory of nucleation by experimental studies of villin where we will rationally redesign folding nucleus into aromatic core and will study functional, kinetic and thermodynamic consequences of nucleus shifts.