The nonplanarity of the peptide group: Molecular dynamics simulations with a polarizable two-state model for the peptide bond

The general properties of the peptide bond can be described from a linear combination of two states: a single bond neutral form and a double bond zwitterionic form. However, environmental effects can shift the balance of the linear combination. This would cause the rigidity of torsional rotations of the peptide bond to be environmentally dependent and, in fact, an analysis of protein structures in the protein data bank reveals a different degree of nonplanarity for different secondary structure elements. A potential is presented in which the peptide bond is treated as a linear combination of two states; the coefficients of the two states are updated as the simulation progresses using an extended Lagrangian formalism. The model is applied to the helix/coil transition of polyalanine. Fluctuations in the planarity of the peptide dihedral angle are found to increase the rate constant for the coil to helix transition by a factor of two. (C) 2000 American Institute of Physics. [S0021-9606(00)50411-5].