SPECIFIC NUCLEUS AS THE TRANSITION-STATE FOR PROTEIN-FOLDING - EVIDENCE FROM THE LATTICE MODEL

We have studied the folding mechanism of lattice model 36-mer proteins . Using a simulated annealing procedure in sequence space, we have des igned sequences to have sufficiently low energy in a given target conf ormation, which plays the role of the native structure in our study. T he sequence design algorithm generated sequences for which the native structures is a pronounced global energy minimum. Then, designed seque nces were subjected to lattice Monte Carlo simulations of folding. In each run, starting from a random coil conformation, the chain reached its native structure, which is indicative that the model proteins solv e the Levinthal paradox. The folding mechanism involved nucleation gro wth. Formation of a specific nucleus, which is a particular pattern of contacts, is shown to be a necessary and sufficient condition for sub sequent rapid folding to the native state. The nucleus represents a tr ansition state of folding to the molten globule conformation. The sear ch for the nucleus is a rate-limiting step of folding and corresponds to overcoming the major free energy barrier. We also observed a foldin g pathway that is the approach to the native state after nucleus forma tion; this stage takes about 1% of the simulation time. The nucleus is a spatially localized substructure of the native state having 8 out o f 40 native contacts. However, monomers belonging to the nucleus are s cattered along the sequence, so that several nucleus contacts are long -range while other are short-range. A folding nucleus was also found i n a longer chain 80-mer, where it also constituted 20% of the native s tructure. The possible mechanism of folding of designed proteins, as w ell as the experimental implications of this study is discussed.