CONTACT INTERACTIONS METHOD - A NEW ALGORITHM FOR PROTEIN-FOLDING SIMULATIONS

Computer simulations of simple exact lattice models are an aid in the study of protein folding process; they have sometimes resulted in pred ictions experimentally proved. The contact interactions (CI) method is here proposed as a new algorithm for the conformational search in the low-energy regions of protein chains modeled as copolymers of hydroph obic and polar monomers configured as self-avoiding walks on square or cubic lattices. It may be regarded as an extension of the standard Mo nte Carlo method improved by the concept of cooperativity deriving fro m nonlocal contact interactions. A major difference with respect to ot her algorithms is that criteria for the acceptance of new conformation s generated during the simulations are not based on the energy of the entire molecule, but cooling factors associated with each residue defi ne regions of the model protein with higher or lower mobility. Nine se quences of length ranging from 20 to 64 residues were used on the squa re lattice and 15 sequences of length ranging from 46 to 136 residues were used on the cubic lattice. The CI algorithm proved very efficient both in two and three dimensions, and allowed us to localize energy m inima nor localized by other searching algorithms described in the lit erature. Use of this algorithm is not limited to the conformational se arch, because it allows the exploration of thermodynamic and kinetic b ehavior of model protein chains.