Volume 2, Number 1/2, p. 12-18
Ariel Fernández
Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA, and
Instituto de Matemática, Universidad Nacional del Sur, CONICET, Bahía Blanca 8000, Argentina.
Folding proteins in an environment-sensitive lattice
As it folds onto itself, a protein creates local solvent environments which affect its pairwise intramolecular interactions. Thus, in the absence of cosolvents, backbone hydrogen bonds are not stable unless they are protected from water attack by the chain itself. This sensitivity to conformation-dependent environments is modelled by introducing self-avoiding walks in a cubic lattice subject to three-body correlations. These correlations arise due to the proximity of solvent-organizing units to pairs of interacting units. The correlations are shown to account for the nonadditivity of clustering forces and the cooperativity of the folding process.
Keywords: cooperativity, correlations, cubic lattice, protein folding.