Gaussian model of protein folding

Abstract

The thermodynamics and kinetics of protein folding depend on the sequence of monomer units along the chain. To explore the sequence dependence, current modeling—all-atom simulations and lattice models, for example—require time-consuming computer simulations. There are currently no analytical models by which folding properties can be computed directly from the monomer sequence. Here we introduce a simple analytical model of folding, based on assuming springlike forces for covalent and noncovalent interactions. Thermodynamic and kinetic properties of folding can be obtained directly for specific sequences in Go-like models. Remarkably, although it is a continuum model, some choices of parameters give the same stable conformations as in the corresponding lattice model. The main point of elasticity-based folding models is that their properties can be understood in complete detail, and with little computational investment. This may be useful for understanding how the shapes of energy landscapes, including stable states and kinetic barriers, depend on amino acid sequence.