Dynamic modelling of a helical peptide in solution using NMR data: multiple conformations and multi-spin effects.
Nuclear Overhauser effect (NOE) measurements on molecules in solution provide information about only the ensemble-averaged properties of these molecules. An algorithm is presented that uses a list of NOEs to produce an ensemble of molecules that on average agrees with these NOEs, taking into account the effect of surrounding spins on the buildup of each NOE ('spin diffusion'). A simplified molecular dynamics simulation on several copies of the molecule in parallel is restrained by forces that are derived directly from differences between calculated and measured NOEs. The algorithm is tested on experimental NOE data of a helical peptide derived from bovine pancreatic trypsin inhibitor.
Kemmink
J
J
European Molecular Biology Laboratory, Heidelberg, Germany.
Scheek
R M
RM
D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D007611:Aprotinin / Q000737:chemistry / Q000235:genetics; D002417:Cattle; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry / Q000235:genetics; D010455:Peptides / Q000737:chemistry* / Q000235:genetics; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012996:Solutions; D013816:Thermodynamics
D010446:Peptide Fragments; D010455:Peptides; D012996:Solutions; D007611:Aprotinin