title: Conformational preferences of substituted prolines in the collagen triple helix.
abstract: Researchers have recently questioned the role hydroxylated prolines play in stabilizing the collagen triple helix. To address these issues, we have developed new molecular mechanics parameters for the simulation of peptides containing 4(R)-fluoroproline (Flp), 4(R)-hydroxyproline (Hyp), and 4(R)-aminoproline (Amp). Simulations of peptides based on these parameters can be used to determine the components that stabilize hydroxyproline over proline in the triple helix. The dihedrals F-C-C-N, O-C-C-N, and N-C-C-N were built using a N-beta-ethyl amide model. One nanosecond simulations were performed on the trimers [(Pro-Pro-Gly)(10)](3), [(Pro-Hyp-Gly)(10)](3), [(Pro-Amp-Gly)(10)](3), [(Pro-Amp(1+)-Gly)(10)](3), and [(Pro-Flp-Gly)(10)](3) in explicit solvent. The results of our simulations suggest that pyrrolidine ring conformation is mediated by the strength of the gauche effect and classical electrostatic interactions.
authors.affiliation: Stanford Medical Informatics, 251 Campus Drive, MSOB X-215, Stanford University, Stanford, CA 94305-5479, USA.
authors.forename: Sean D
authors.initials: SD
authors.lastname: Mooney
authors.forename: Peter A
authors.initials: PA
authors.lastname: Kollman
authors.forename: Teri E
authors.initials: TE
authors.lastname: Klein
mesh_terms: D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003094:Collagen / Q000737:chemistry*; D006860:Hydrogen Bonding; D006900:Hydroxylation; D008958:Models, Molecular; D011392:Proline / Q000737:chemistry*; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry
chemical_list: D012997:Solvents; D003094:Collagen; D011392:Proline