title: Side-chain torsional potentials: effect of dipeptide, protein, and solvent environment.
abstract: Side-chain torsional potentials in the bovine pancreatic trypsin inhibitor are calculated from empirical energy functions by use of the known X-ray structure of the protein and the rigid-geometry mapping technique. The potentials are analyzed to determine the roles and relative importance of contributions from the dipeptide backbone, the protein, and the crystalline environment of solvent and other protein molecules. The structural characteristics of the side chains determine two major patterns of energy surfaces, E(X1,X2): a gamma-branched pattern and a pattern for longer, straight side chains (Arg, Lys, Glu, and Met). Most of the dipeptide potential curves and surfaces have a local minimum corresponding to the side-chain torsional angles in the X-ray structure. Addition of the protein forces sharpens and/or selects from these minima, providing very good agreement with the experimental conformation for most side chains at the surface or in the core of the protein. Inclusion of the crystalline environment produces still better results, especially for the side chains extending away from the protein. The results are discussed in terms of the details of the interactions due to the surrounding, calculated solvent-accessibility figures and the temperature factors derived from the crystallographic refinement of the pancreatic trypsin inhibitor.
mesh_terms: D000818:Animals; D002417:Cattle; D004151:Dipeptides; D004735:Energy Transfer; D008433:Mathematics; D011487:Protein Conformation; D011506:Proteins; D012997:Solvents; D014359:Trypsin Inhibitor, Kazal Pancreatic; D014361:Trypsin Inhibitors; D014961:X-Ray Diffraction
chemical_list: D004151:Dipeptides; D011506:Proteins; D012997:Solvents; D014361:Trypsin Inhibitors; D014359:Trypsin Inhibitor, Kazal Pancreatic