THEORETICAL AND EXPERIMENTAL STUDY OF PROTEIN FOLDING

我们建议开发下一代的蛋白质折叠理论，这将是定量的单残基分辨率水平。 该理论将提供主要蛋白质折叠的动力学和热力学“指纹”，概述哪些残基对热力学稳定性最重要，哪些是动力学“加速踏板”。 这将有助于合理化从天然蛋白质的多序列比对中出现的进化数据。 在追求这一目标，我们将开发一系列重要的技术和理论方法，如有效的蒙特-卡罗蛋白质设计，分析理论的序列选择的蛋白质和折叠的可设计性，进化算法选择的最具动力学能力的序列的真实的蛋白质折叠。 此外，我们将发展分析理论和模拟，为折叠的成核机制提供充分的理论基础，包括蛋白质折叠核的决定因素是什么这一最重要的问题。 作为这一努力的必然结果，我们将进行蛋白质“手术”和“移植”的实验研究，我们将移植折叠核的快速折叠蛋白ADA 2h到其缓慢折叠的结构同源物AcP，以显着提高后者的折叠速率。此外，我们将测试成核理论的实验研究绒毛，我们将合理地重新设计折叠成芳核核，并将研究功能，动力学和热力学后果的核位移。

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.