Peptide Secondary Structure: Folding, Mechanisms, Rates and Optimization

University Of Washington, Seattle WA

Investigators

Abstract

Protein folding and design continue to be extremely active areas of research and both rely to a significant extent on understanding the factors that control the stability and folding rates of secondary structure elements (particularly alpha-helices and beta-hairpins). The increasing evidence for secondary (and other local) structure in the unfolded states of proteins and for the biological significance of poorly folded proteins makes an understanding of secondary structuring more important than it earlier appeared. Furthermore, determining the time constants for the formation of different elements of local and secondary structure will indicate whether these structuring transitions are pre-equilibrium processes relative to collapse in Diffusion-Collision models of protein folding. This proposal experimentally addresses the factors that control the stability and folding rates of protein secondary structure elements (particularly alpha-helices and beta-hairpins). The major goals of the proposed research are: 1) to define the timescales of helix nucleation (and possibly helix propagation), beta-turn/beta-hairpin formation, and loop searches that produce local hydrophobic clusters, 2) to establish the individual contributions of local sequence strings to secondary structure formation and folding cooperativity, and 3) the quantitation of free energy contributions from specific interactions that lead to stable isolated secondary structure elements. Results from the last two research topics will be used to parameterize an algorithm for predicting the structural features of unfolded protein states. New systems and methods will be used to answer important questions in helix/coil transition theory - 1) Is alanine uniquely favorable for helix stabilization; and if so, why and in which contexts? 2) How is the heterogeneity of helical ensembles effected by: a) hydrophobic, backbone-desolvating residues, and b) end-capping interactions. With the support of the Organic and Macromolecular Chemistry Program, Professor Niels H. Andersen, of the Department of Chemistry at the University of Washington, is carrying out fundamental studies designed to elucidate the details of protein folding. The prediction of protein structure and function purely from the amino acid sequence has gained a practical significance with the availability of protein sequences from the numerous genome projects that have been completed. An atomic level understanding of folding mechanisms will greatly facilitate both protein structure prediction and design, essential for both the a priori design of artificial systems with protein-like folding or functional properties and for re-engineering natural systems. The insight gained from a better understanding of protein structural stability could also prove useful in stabilizing the native state or improving the folding efficiency of proteins which in their excited or misfolded states are likely to be amyloidogenic.