OFF LATTICE APPROACH TO PROTEIN STRUCTURE PREDICTION

Cornell University Ithaca, Ithaca NY

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Abstract

One approach to the prediction of protein structure from sequence defines the native structure as the global energy minimum. Because the search for the global energy minimum of even a relatively small protein is impractical in an all-atom approach, during the past few years we have developed a simplified united-residue representation of the polypeptide chain. Once the global energy minimum of the simplified chain has been found, the chain can be converted to an all-atom chain and the search completed with an all-atom force field, such as ECEPP/3 used in this work. During this year, we focused our attention on the final development of the force field to include multibody or correlation terms that are necessary for the stabilization of regular secondary structures and developing and implementing the methods of global optimization to search the conformational space of the simplified chain. Based on the distance-scaling method of global optimization, we developed an efficient and reliable procedure for global optimization that we call the Basin-to-Deformed-Basin-Coupling method that is based on locating the regions of significantly low energy by gradually deforming the energy surface and locating the minima corresponding to the original potential in these regions by reversing the deformation. At present, the method is capable of locating the global energy minima of model polyalanine chains of up to 30 residues in length.