Dynamics of Polypeptide Diffusion and Collapse

University Of Florida, Gainesville FL

Investigators

Abstract

Hagen MCB 0077907 This 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 different configurations; 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 early in 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.