The tertiary structures of proteins are determined by both local geometric preferences and noncovalent interactions between amino acid residues distant from one another in primary structure. In proteins composed of beta-sheets, the mutual recognition of neighboring strands must be guided by the correct pairing of amino acid side chains. Our goal is to discover the rules for strand pairing in beta-sheet proteins using a variety of experimental and computational methods. We will apply these rules towards the development of new protein structure prediction algorithms. A better understanding of beta-sheet formation should lead to improved protein engineering and design. It is also becoming clear that protein aggregation is often driven by intermolecular sheet formation, and as such, understanding the forces that drive sheet formation could therefore have direct implications towards the design of therapies that inhibit pathological aggregation. The experimental model system for our studies is CspA, the major cold shock protein in E. coli. The goals of this proposal are: 1) Derive residue pairing propensities for beta-sheet residues. The database of three-dimensional protein structures will be surveyed for correlations between residue identity, location and neighbors among amino acids in a beta conformation. Interactions will be sorted into categories based on structure and environment. We will also study residue pairing using a combinatorial mutagenesis/genetic screening approach in order to 2) determine to what extent allowed combinations of amino acids on neighboring strands depend upon the local environment. 3) Study the thermodynamic and kinetic consequences of altering beta sheets. A subset of the-mutant proteins generated above will be purified and studied spectroscopically to correlate residue neighbor identity with protein stability and folding/unfolding rates. From these studies we hope to propose a general mechanism for strand pairing. 4) Develop an algorithm for scoring strand pairing in model-built proteins and for predicting beta-sheet structure. Using the information obtained on residue pairing, we will develop a potential function for evaluating predicted protein structures. We will extend the evaluation procedure to a new combinatorial prediction scheme. 5) Study strand pairing strength through the generation of permuted proteins.
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