Journal of Physical Chemistry, Vol.100, No.38, 15588-15598, 1996
Intrinsic Torsional Potential Parameters for Conformational-Analysis of Peptides and Proteins
New sets of intrinsic torsional parameters, obtained by fitting to experimental and/or theoretical values of torsional barriers and relative conformational energies of various uncharged model organic compounds, are presented, They are intended for use in conformational energy computations on peptides and proteins. A three-term Fourier series expansion is used to represent the intrinsic torsional energy. Each set of intrinsic torsional parameters, obtained from a single model compound, reproduces experimental torsional barriers, relative conformational energies, and torsion angles of related molecules not used for the parametrization. The sets of parameters of a new potential function, including electrostatic interactions based on partial atomic charges, and nonbonded, hydrogen-bond, and intrinsic torsional energies, are tested in conformational energy calculations on a model peptide N-acetyl-N’-methylalanineamide. The electrostatic energy component plays a significant role in the total conformational energy and leads to a high relative energy of the alpha(R) (A) conformation compared to the C-7(eq) (C) conformation, although the latter is still the global minimum. These results differ from those with ECEPP/3, CHARMM, and AMBER, but are reasonably consistent with those from recent ab initio studies.
Keywords:ORBITAL ELECTRONEGATIVITY METHOD;MODIFIED PARTIAL EQUALIZATION;SULFUR STRETCHING FREQUENCIES;PHASE ELECTRON-DIFFRACTION;HYDROGEN-BOND INTERACTIONS;OCCURRING AMINO-ACIDS;LOW-ENERGY CONFORMERS;MICROWAVE-SPECTRUM;INTERNAL-ROTATION;MOLECULAR-STRUCTURE