Calculation of protein conformation by the build-up procedure. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data.
Low-energy conformations of a set of tetrapeptides derived from the small protein bovine pancreatic trypsin inhibitor (BPTI) were generated by a build-up procedure from the low-energy conformations of single amino acid residues. At each stage, various-size fragments were built up from all combinations of smaller ones, the total energies were then minimized, and the low-energy conformations were retained for the next stage. The energies of the tetrapeptides were re-ordered by including the effects of hydration. No information other than the amino acid sequence was used to obtain the low-energy conformations of the hydrated tetrapeptides. The latter were then supplemented with a limited set of simulated NMR distance information, derived from the X-ray structure of BPTI, to provide a basis for building the rest of the whole protein molecule by the same procedure. A total of 189 upper bounds, plus 12 pairs of upper and lower bounds pertaining to the location of the three disulfide bonds in this molecule, were used. Four sets of conformations of the entire molecule were generated by utilizing different combinations of smaller fragments. It was possible to obtain low-energy conformations with small rms deviations, 1.1 to 1.4 A for the alpha-carbons, from the structure derived by X-ray diffraction. The average deviations of the backbone dihedral angles were also low, viz. 23 degrees to 26 degrees.
Vásquez
M
M
Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853-1301.
Scheraga
H A
HA
D000595:Amino Acid Sequence; D007611:Aprotinin; D009682:Magnetic Resonance Spectroscopy; D008433:Mathematics; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009842:Oligopeptides; D011487:Protein Conformation; D013816:Thermodynamics; D014961:X-Ray Diffraction
D009842:Oligopeptides; D007611:Aprotinin