Prediction of polyelectrolyte polypeptide structures using Monte Carlo conformational search methods with implicit solvation modeling.
Many interesting proteins possess defined sequence stretches containing negatively charged amino acids. At present, experimental methods (X-ray crystallography, NMR) have failed to provide structural data for many of these sequence domains. We have applied the dihedral probability grid-Monte Carlo (DPG-MC) conformational search algorithm to a series of N- and C-capped polyelectrolyte peptides, (Glu)20, (Asp)20, (PSer)20, and (PSer-Asp)10, that represent polyanionic regions in a number of important proteins, such as parathymosin, calsequestrin, the sodium channel protein, and the acidic biomineralization proteins. The atomic charges were estimated from charge equilibration and the valence and van der Waals parameters are from DREIDING. Solvation of the carboxylate and phosphate groups was treated using sodium counterions for each charged side chain (one Na+ for COO-; two Na for CO(PO3)-2) plus a distance-dependent (shielded) dielectric constant, epsilon = epsilon 0 R, to simulate solvent water. The structures of these polyelectrolyte polypeptides were obtained by the DPG-MC conformational search with epsilon 0 = 10, followed by calculation of solvation energies for the lowest energy conformers using the protein dipole-Langevin dipole method of Warshel. These calculations predict a correlation between amino acid sequence and global folded conformational minima: 1. Poly-L-Glu20, our structural benchmark, exhibited a preference for right-handed alpha-helix (47% helicity), which approximates experimental observations of 55-60% helicity in solution. 2. For Asp- and PSer-containing sequences, all conformers exhibited a low preference for right-handed alpha-helix formation (< or = 10%), but a significant percentage (approximately 20% or greater) of beta-strand and beta-turn dihedrals were found in all three sequence cases: (1) Aspn forms supercoil conformers, with a 2:1:1 ratio of beta-turn:beta-strand:alpha-helix dihedral angles; (2) PSer20 features a nearly 1:1 ratio of beta-turn:beta-sheet dihedral preferences, with very little preference for alpha-helical structure, and possesses short regions of strand and turn combinations that give rise to a collapsed bend or hairpin structure; (3) (PSer-Asp)10 features a 3:2:1 ratio of beta-sheet:beta-turn:alpha-helix and gives rise to a superturn or C-shaped structure.
Arthur Amos Noyes Laboratory for Chemical Physics, California Institute of Technology, Pasadena 91125, USA.
J S
JS
Evans
S I
SI
Chan
W A
WA
Goddard
D000465:Algorithms; D000595:Amino Acid Sequence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D011099:Polyglutamic Acid / Q000737:chemistry; D011336:Probability; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012984:Software; D012996:Solutions; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D010455:Peptides; D011506:Proteins; D012996:Solutions; D011099:Polyglutamic Acid; C027794:polyserine; C017645:polyaspartate