Leap-dynamics: efficient sampling of conformational space of proteins and peptides in solution.
A molecular simulation scheme, called Leap-dynamics, that provides efficient sampling of protein conformational space in solution is presented. The scheme is a combined approach using a fast sampling method, imposing conformational 'leaps' to force the system over energy barriers, and molecular dynamics (MD) for refinement. The presence of solvent is approximated by a potential of mean force depending on the solvent accessible surface area. The method has been successfully applied to N-acetyl-L-alanine-N-methylamide (alanine dipeptide), sampling experimentally observed conformations inaccessible to MD alone under the chosen conditions. The method predicts correctly the increased partial flexibility of the mutant Y35G compared to native bovine pancreatic trypsin inhibitor. In particular, the improvement over MD consists of the detection of conformational flexibility that corresponds closely to slow motions identified by nuclear magnetic resonance techniques.
Kleinjung
J
J
Physical Biochemistry Division, National Institute for Medical Research, Mill Hill, London, UK. jkleinj@nimr.mrc.ac.uk
Bayley
P
P
Fraternali
F
F
D000409:Alanine / Q000737:chemistry / Q000378:metabolism; D019943:Amino Acid Substitution / Q000235:genetics; D000818:Animals; D007611:Aprotinin / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D002417:Cattle; D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D009038:Motion; D018583:Pliability; D011487:Protein Conformation; D012996:Solutions; D012997:Solvents; D013816:Thermodynamics; D014867:Water / Q000378:metabolism
D004151:Dipeptides; D012996:Solutions; D012997:Solvents; D014867:Water; D007611:Aprotinin; D000409:Alanine