IS BURST HYDROPHOBIC COLLAPSE NECESSARY FOR PROTEIN-FOLDING

Folding of the lattice model of proteins is studied using Monte Carlo simulation. The amino acid sequence is designed to have a pronounced e nergy minimum for a given target (native) conformation. Our simulation s reveal two possible scenarios. When the overall attraction between r esidues dominates, we find that folding to the native conformation is preceded by a rapid collapse into a burst intermediate which is a comp act but structureless globule. Then, after a much longer time, an all- or-none transition from the globule to the native conformation occurs. In contrast, when the overall attraction is not strong, we do not obs erve a burst collapse stage. Instead, we find an all-or-none transitio n directly from the coil to the native conformation. Both scenarios yi eld comparable rates of folding. On the basis of these findings we dis cuss the role of intermediates in thermodynamics and kinetics of prote in folding.