MULTIRESOLUTION SAMPLING METHODS FOR PROTEIN & PEPTIDE CONFORMATIONAL SPACE

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Within this component of our core research project on long timescale/length scale sampling for protein and peptide folding, we have developed "minimalist" representations of protein topologies and sequences based on simplified Ca-based interaction models. The development of these models has been automated allowing one to construct such a representation of a protein structure and carry out folding studies on this representation given a PDB file. We are in the process of providing an automated means of producing these models for scientists over the WWW, thus allowing scientists within the broad community to investigate the folding aspects of their particular protein sequences/topologies. Our protocol produces CHARMM topology and parameter files appropriate for studies of the thermodynamics and kinetics of folding of these models. We have used such minimalist models together with theoretical developments to explore the "optimization" of such minimalist models for protein folding. Our studies have demonstrated that we can explore a rather large range of the underlying energy function space using these methods and hence significantly reduce the computational cost of developing representative minimalist models for protein folding. We anticipate these ideas will be transferable to studies of DNA and RNA models as well as questions involving virus assembly. Our first paper on this topic has been recently accepted for publication in the Journal of Chemical Physics. The full title and references are: Exploring the Space of Protein Folding Hamiltonians: The Balance of Forces in a Minimalist b-Barrel Model. J.-E. Shea, Y. D. Nochomovitz, Z. Guo and C. L. Brooks III, J. Chem. Phys., accepted for publication (1998). Frontiers of Science 1997 - Chemical Physics of Protein Folding. C. L. Brooks III, M. Gruebele, J. N. Onuchic and P. G. Wolynes PNAS, in press (1998).