A New Set of Molecular Mechanics Parameters for Hydroxyproline and Its Use in Molecular Dynamics Simulations of Collagen-Like Peptides.

Sanghyun Park, Randall J. Radmer, Teri E. Klein, and Vijay S. Pande.
Journal of Computational Chemistry (2005)

SUMMARY: Simulation of the collagen triple helix has been given less attention than more common protein “folds.” Here we present newly derived parameters for such simulations to gain better agreement with experimental data, and thereby offering insight into the stability of the triple helix structure.

TECHNICAL ABSTRACT: Recently, the importance of proline ring pucker conformations in collagen has been suggested in the context of hydroxylation of prolines. The previous molecular mechanics parameters for hydroxyproline, however, do not reproduce the correct pucker preference. We have developed a new set of parameters that reproduces the correct pucker preference. Our molecular dynamics simulations of proline and hydroxyproline monomers as well as collagen-like peptides, using the new parameters, support the theory that the role of hydroxylation in collagen is to stabilize the triple helix by adjusting to the right pucker conformation (and thus the right f angle) in the Y position.