Dynamics of Polypeptide Diffusion and Collapse

这个项目将阐明在折叠模型和模拟中探索的景观和参数制度之间的关系，以及真实蛋白质分子的特性。它将使用时间分辨激光光谱来探测未展开和部分折叠的蛋白质分子的构象动力学，目的是提取对折叠的景观描述重要的基本参数。对未折叠的细胞色素c和其他分子进行激光光解实验，可以测量未折叠多肽的构象扩散速率，残基间相互作用对扩散的影响，以及这种扩散对整体折叠速度的限制。它们还将允许直接测量紧凑变性蛋白质在不同构型之间相互转换的时间尺度；这个时间尺度直接表明了景观描述中的“粗糙”程度。利用纳秒分辨率的激光温度跳变光谱，这项工作还将研究蛋白质分子的特性，这些特性决定了蛋白质分子的崩溃动力学——从膨胀到致密变性结构的快速转变。这些实验将增强对蛋白质折叠早期发生的动力学事件的理解，它们也将为蛋白质折叠理论和实验之间更详细的比较提供依据。蛋白质是如何折叠的——一个随机缠绕的多肽链是如何获得合适的紧凑结构的——仍然是生物学、化学和物理学领域最重要和最有趣的问题之一。近年来，折叠研究在理论和实验技术方面取得了一些非常重大的进展。理论家们已经发展出一种描述蛋白质折叠的“新观点”或“能量景观”，它使用凝聚态物理学的统计思想来识别和探索那些直接控制折叠过程的速度和动力学的蛋白质特征。与此同时，实验方面的进展包括开发新的光学方法来触发和观察折叠的快速阶段，这些阶段发生在纳秒或微秒的时间尺度上。因为这些新技术允许实验家探索和解决折叠中最早的事件，现在有可能研究真正的蛋白质分子和理论家研究的简化模型蛋白质之间的联系。利用新的光学技术，本研究旨在通过表征实际分子的能量景观的形状和统计特性，以及这些景观上的扩散动力学，加强理论与实验之间的联系。

HagenMCB 0077907This project will clarify the relationship between landscape and parameter regimes that have been explored in models and simulations of folding, and the properties of real protein molecules. It will use time-resolved laser spectroscopy to probe the conformational dynamics of unfolded and partially folded protein molecules, with the aim of extracting basic parameters of importance to landscape descriptions of folding. Laser photolysis experiments on unfolded cytochrome-c and other molecules will allow measurement of the rate of conformational diffusion of an unfolded polypeptide, the effect of inter-residue interactions on that diffusion, and the limitations that this diffusion places on overall folding speed. They will also allow direct measurement of the time scales on which compact denatured proteins interconvert between differentconfigurations; this time scale directly indicates the degree of 'roughness' in landscape descriptions. Using nanosecond-resolved laser temperature jump spectroscopy, this work will also examine the properties of a protein molecule that determine the dynamics of its collapse - the rapid transition from expanded to compact denatured configurations. These experiments will enhance understanding of dynamical events that occur earlyin protein folding, and they should also provide grounds for more detailed comparisons between protein folding theory and experiment.The question of how proteins fold - how a randomly coiled polypeptide chain attains its proper compact structure - remains one of the most important and interesting problems at the interface of biology, chemistry, and physics. The study of folding has benefited in recent years from several very significant advances in both theory and experimental technique. Theoreticians have developed a "new view", or "energy landscape" description of protein folding, which uses statistical ideas from condensed matter physics to identify and explore those characteristics of proteins that directly control the speed and dynamics of the folding process. At the same time, experimental advances have included the development of new optical methods for triggering and observing the rapid phases of folding, which occur on nanosecond or microsecond time scales. Because these new techniques allow experimentalists to explore and resolve the very earliest events in folding, it is now possible to investigate the connection between real protein molecules and the simplified model proteins studied by theoreticians. Applying new optical techniques, this work aims to strengthen the connection between theory and experiment by characterizing the shapes and statistical properties of energy landscapes of actual molecules, and the dynamics of diffusion on those landscapes.