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, SCVTLYQSWRYSQADNGCA, corresponding to the first beta-hairpin (residues 10 to 28) of the alpha-amylase inhibitor tendamistat (PDB entry 3AIT) has been studied by molecular dynamics simulations in explicit water under periodic boundary conditions at several temperatures (300 K, 360 K and 400 K), starting from various conformations for simulation lengths, ranging from 10 to 30 ns. Comparison of trajectories of the reduced and oxidized native peptides reveals the importance of the disulphide bridge closing the beta-hairpin in maintaining a proper turn conformation, thereby insuring a proper side-chain arrangement of the conserved turn residues. This allows rationalization of the conservation of those cysteine residues among the family of alpha-amylase inhibitors. High temperature simulations starting from widely different initial configurations (native beta-hairpin, alpha and left-handed helical and extended conformations) begin sampling similar regions of the conformational space within tens of nanoseconds, and both native and non-native beta-hairpin conformations are recovered. Transitions between conformational clusters are accompanied 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 beta-hairpin formation in which the turn is formed first, followed by hydrogen bond formation closing the hairpin, and subsequent stabilization by side-chain hydrophobic interactions.
Bonvin
A M
AM
Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, 3584-CH, The Netherlands. abonvin@nmr.chem.uu.nl
van Gunsteren
W F
WF
D000595:Amino Acid Sequence; D003198:Computer Simulation; D017124:Conserved Sequence; D004220:Disulfides / Q000737:chemistry / Q000378:metabolism; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000378:metabolism*; D006860:Hydrogen Bonding; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012997:Solvents; D013696:Temperature; D013816:Thermodynamics; D014867:Water / Q000378:metabolism; D000516:alpha-Amylases / Q000037:antagonists & inhibitors
D004220:Disulfides; D004791:Enzyme Inhibitors; D010455:Peptides; D012997:Solvents; D014867:Water; D000516:alpha-Amylases; C030526:tendamistate