One of the ultimate goals of structural biology is the de novo design and rational engineering of peptide and protein structure. Significant progress toward this goal has been made in several areas however the membrane proteins, particularly beta-sheet membrane proteins, have been studied only infrequently. Membrane beta-structures are abundant and have been implicated in a number of important biological processes and yet little is known about the principles of beta-sheet folding and structure in membranes. In previous studies we found several families of short hydrophobic peptides that fold cooperatively into oligomeric beta-sheets in membranes, suggesting that beta-sheet formation in any part of a membrane is stabilized mainly by strong hydrogen-bonding interactions. Based on this idea, we hypothesize that three conditions are necessary for a polypeptide to form beta-sheets in a lipid bilayer membrane: 1) the peptide must be hydrophobic enough to stably partition into the membrane; 2) it must be able to form a beta-sheet with hydrophobic membrane-interacting surfaces; and 3) It must have a sequence that disfavors alpha-helix formation. In particular, we hypothesize that a membrane-spanning beta-barrel can only be formed by a peptide with an alternating sequence of hydrophobic and hydrophilic residues, or dyad repeat sequence motif. The research proposed here is designed to test the various parts of this hypothesis in several complimentary ways: through iterative peptide design, through fundamental thermodynamic measurements and through genomic approaches to detection and structure prediction. The long term objectives of the studies proposed here are to better understand the fundamental principles of beta-sheet folding in membranes and to use that information for the de novo design of membrane-spanning beta-barrels using peptide systems.
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