The normal modes of a protein: Native bovine pancreatic trypsin inhibitor

Abstract

A completely general treatment of normal mode analysis is developed that can be used with any potential energy function and any set of generalized coordinates. The method is applied to the calculation of the normal modes of the small protein bovine pancreatic trypsin inhibitor that has been the subject of many previous theoretical studies. The potential energy function used comprises a torsion angle potential, a van der Waals potential between nonbonded pairs of atoms, and a hydrogen bond potential. Therefore, the generalized coordinates used are the 208 Φ, ϕ, and χ torsion angles about single bonds. This eliminates the difficulties inherent in using internal or Cartesian coordinates for a large molecule. Many dynamic properties of the protein may now be calculated in the normal mode description. In particular, the rms magnitudes and pair correlations of the fluctuations in positions and velocities of the α-carbon atoms and various classes of torsion angles, such as backbone, side chain, β-sheet, and α-helix, are calculated and analyzed to identify the most correlated modes. In addition, the ir intensities are calculated.