Biasing a Monte Carlo chain growth method with Ramachandran's plot: application to twenty-L-alanine.
In this paper, we explore the possibility of using experimental observations in the Monte Carlo chain growth method that we have previously developed. In this method, the macromolecule (peptide, protein, nuclei acid, etc.) is grown atom-by-atom (or residue-by-residue, etc.) and partial chains are replicated according to their Boltzmann weights. Once the molecule completed, we are left with a Boltzmann-distributed ensemble of configurations. For long molecules, an efficient sampling of the (extremely large) phase space is difficult for obvious reasons (existence of many local minima, limited computer memory, etc.). In the case in which one is mainly interested in the low energy conformations, we have incorporated in the growth scheme experimental observations taken from the Protein Data Banks. More precisely, we have considered the case of twenty-L-alanine and we have used the (experimental) Ramachandran's plot for this residue. The biased growth procedure goes as follows: (a) each time one adds along the main backbone chain, either a carbon atom belonging to a carbonyl group, or a nitrogen atom, its dihedral angle (theta) or (psi) is drawn with a probability law that reflects the experimental Ramachandran (theta, psi) plot; (b) the bias introduced in this way is canceled through an extra term in the energy (replication energy = true energy + bias energy); (c) the configurations, generated at T = 1000 K, are then energy minimized.(ABSTRACT TRUNCATED AT 250 WORDS)
Bascle
J
J
Service de Physique Théorique, CE-Saclay, Gif-sur-Yvette, France.
Garel
T
T
Orland
H
H
Velikson
B
B
D000409:Alanine / Q000737:chemistry*; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D013816:Thermodynamics
D010455:Peptides; D000409:Alanine