Molecular dynamics of hydrogen bonds in bovine pancreatic trypsin inhibitor protein

Molecular dynamics simulations starting from the X-ray structure(1) of bovine pancreatic trypsin inhibitor protein (BPTI) reveal that the different hydrogen bonds observed in the X-ray coordinates have different stabilities as indicated by the mean lengths and length fluctuations. The most stable hydrogen bonds involve the hydrogen atoms observed to exchange most slowly with solvent in NMR experiments(2), and to have the shortest lengths in the X-ray structure. This agreement between calculation and experiment suggests that molecular dynamics simulations can complement X-ray studies by providing reliable information about the rates and pathways of conformational changes about the mean positions observed in protein crystals.