title: Completely geometrically optimized DFT/ONIOM triple-helical collagen-like structures containing the ProProGly, ProProAla, ProProDAla, and ProProDSer triads.
abstract: We report completely optimized ONIOM DFT/AM1 molecular orbital calculations on several collagen-like triple helices based upon the repeating triad, ProProGly. The requirement of Gly as every third amino acid in collagen can be attributed to its enantiomorphic nature, as it behaves as a Damino acid in collagen. We, therefore, explored related collagen-like triple helices with one of the central Gly's mutated to either L or DAla; l-Ala appreciably destabilizes, while d-Ala slightly stabilizes the triple helical structure. Mutation of the same Gly to DSer, which is simply DAla with an OH in place of one of the methyl H's, induces a much greater stabilization due to an additional H-bond formed between this OH and a C=O on an adjacent peptide strand. Energies are presented for the triple helices and their component strands (both optimized and distorted to their triple helical geometries) relative to the component amino acids. The variation of relative energies with the chosen reference is delineated.
authors.affiliation: Department of Chemistry, City University of New York-Hunter College and The Graduate School, 695 Park Avenue, New York, NY 10021, USA.
authors.forename: Midas I-Hsien
authors.initials: MI
authors.lastname: Tsai
authors.forename: Yujia
authors.initials: Y
authors.lastname: Xu
authors.forename: J J
authors.initials: JJ
authors.lastname: Dannenberg
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D003094:Collagen / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D009842:Oligopeptides; D010455:Peptides; C507182:Pro-Pro-D-Ser; C044555:prolyl-prolyl-glycine; C027789:prolyl-prolyl-alanine; D003094:Collagen