Theoretical studies of environmental effects on protein conformation. 1. Flexibility of the peptide bond
Journal of the American Chemical Society
American Chemical Society
The effects of hydrogen bonding on peptide bonds are studied by quantum mechanical methods. The peptide unit is modeled by trans-N-methylacetamide (NMA) which is allowed to interact with various hydrogen bonding species that are similar to those typically found in the environment of a peptide within a protein molecule. These species include waters of hydration, other peptide units, and the side chains of amino acid residues. The effects of these species on the flexibility and electronic charge distribution of NMA can be interpreted in terms of resonance structures and atomic orbital overlap. All species are found to have a restricting influence on the conformation of a peptide bond. Nonplanar deformations of the peptide unit require more energy in the presence of these species. The effects of partial as well as full hydration of the peptide are considered. It is found that many of the effects of a full hydration shell can be simulated by the interaction with two water molecules. A correlation is found between the increased rigidity of the peptide and several parameters of charge redistribution. Interpeptide hydrogen bonding is found to have much the same effects as hydration. Interaction of a peptide unit with the electrically charged side chains of several residues is also predicted to result in a significantly more rigid peptide.
Theoretical Studies of Environmental Effects on Protein Conformation: Flexibility of the Peptide Bond S. Scheiner and C. W. Kern J. Am. Chem. Soc., 1977 99 (21), 7042-7050.