Folding proteins by first-passage-times-optimized replica exchange.
Replica exchange simulations have become the method of choice in computational protein science, but they still often do not allow an efficient sampling of low-energy protein configurations. Here, we reconstruct replica flow in the temperature ladder from first passage times and use it for temperature optimization, thereby maximizing sampling. The method is applied in simulations of folding thermodynamics for a number of proteins starting from the pentapeptide Met-enkephalin, through the 36-residue HP-36, up to the 67-residue protein GS-alpha3W.
Nadler
Walter
W
John-von-Neumann Institute for Computing, Forschungszentrum Jülich, D-52425 Jülich, Germany. w.nadler@fz-juelich.de
Meinke
Jan H
JH
Hansmann
Ulrich H E
UH
D055592:Biophysical Phenomena; D004744:Enkephalin, Methionine / Q000737:chemistry; D019205:GTP-Binding Protein alpha Subunits, Gs / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D009010:Monte Carlo Method; D016900:Neurofilament Proteins / Q000737:chemistry; D010446:Peptide Fragments / Q000737:chemistry; D017510:Protein Folding; D013816:Thermodynamics
D016900:Neurofilament Proteins; D010446:Peptide Fragments; C115223:villin headpiece subdomain peptide; D004744:Enkephalin, Methionine; D019205:GTP-Binding Protein alpha Subunits, Gs