A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides.
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 phi angle) in the Y position.
Park
Sanghyun
S
Department of Chemistry and Structural Biology, Stanford University, Stanford, California 94305, USA.
Radmer
Randall J
RJ
Klein
Teri E
TE
Pande
Vijay S
VS
D003094:Collagen / Q000737:chemistry*; D003198:Computer Simulation; D006909:Hydroxyproline / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D011789:Quantum Theory
D010455:Peptides; D003094:Collagen; D006909:Hydroxyproline