THE EARLY-STAGE OF FOLDING OF VILLIN HEADPIECE SUBDOMAIN OBSERVED IN A 200-NANOSECOND FULLY SOLVATED MOLECULAR-DYNAMICS SIMULATION

A new approach in implementing classical molecular dynamics simulation for parallel computers has enabled a simulation to be carried out on a protein with explicit representation of water an order of magnitude longer than previously reported and will soon enable such simulations to be carried into the microsecond time range, We have used this appro ach to study the folding of the villin headpiece subdomain, a 36-resid ue small protein consisting of three helices, from an unfolded structu re to a molten globule state, which has a number of features of the na tive structure. The time development of the solvation free energy, the radius of gyration, and the mainchain rms difference from the native NR IR structure showed that the process can be seen as a 60-nsec ''bur st'' phase followed by a slow ''conformational readjustment'' phase. W e found that the burial of the hydrophobic surface dominated the early phase of the folding process and appeared to be the primary driving f orce of the reduction in the radius of gyration in that phase.