Sw. Rick et Re. Cachau, The nonplanarity of the peptide group: Molecular dynamics simulations witha polarizable two-state model for the peptide bond, J CHEM PHYS, 112(11), 2000, pp. 5230-5241
The general properties of the peptide bond can be described from a linear c
ombination of two states: a single bond neutral form and a double bond zwit
terionic 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 t
wo 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 o
f Physics. [S0021-9606(00)50411-5].