beta-Hairpin stability and folding: Molecular dynamics studies of the first beta-hairpin of tendamistat

The stability and (un)folding of the 19-residue peptide, SCVTLYQSWRYSQADNGC A, corresponding to the first P-hairpin (residues 10 to 28) of the alpha-am ylase inhibitor tendamistat (PDB entry 3AIT) has been studied by molecular dynamics simulations in explicit water under periodic boundary conditions a t several temperatures (300 K, 360 K and 400 K), starting from various conf ormations for simulation lengths, ranging from 10 to 30 ns. Comparison of t rajectories of the reduced and oxidized native peptides reveals the importa nce of the disulphide bridge closing the beta-hairpin in maintaining a prop er turn conformation, thereby insuring a proper side-chain arrangement of t he conserved turn residues. This allows rationalization of the conservation of those cysteine residues among the family of alpha-amylase inhibitors. H igh temperature simulations starting from widely different initial configur ations (native beta-hairpin, alpha and left-handed helical and extended con formations) begin sampling similar regions of the conformational space with in tens of nanoseconds, and both native and non-native beta-hairpin conform ations are recovered. Transitions between conformational clusters are accom panied by an increase in energy fluctuations, which is consistent with the increase in heat capacity measured experimentally upon protein folding. The folding events observed in the various simulations support a model for bet a-hairpin formation in which the turn is formed first, followed by hydrogen bond formation closing the hairpin, and subsequent stabilization by side-c hain hydrophobic interactions. (C) 2000 Academic Press.