title: Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline.
abstract: We present a mixed quantum-classical model for studying the amide I vibrational dynamics (predominantly CO stretching) in peptides and proteins containing proline. There are existing models developed for determining frequencies of and couplings between the secondary amide units. However, these are not applicable to proline because this amino acid has a tertiary amide unit. Therefore, a new parametrization is required for infrared-spectroscopic studies of proteins that contain proline, such as collagen, the most abundant protein in humans and animals. Here, we construct the electrostatic and dihedral maps accounting for solvent and conformation effects on frequency and coupling for the proline unit. We examine the quality and the applicability of these maps by carrying out spectral simulations of a number of peptides with proline in D(2)O and compare with experimental observations.
authors.affiliation: Center for Theoretical Physics and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
authors.forename: Santanu
authors.initials: S
authors.lastname: Roy
authors.forename: Joshua
authors.initials: J
authors.lastname: Lessing
authors.forename: Georg
authors.initials: G
authors.lastname: Meisl
authors.forename: Ziad
authors.initials: Z
authors.lastname: Ganim
authors.forename: Andrei
authors.initials: A
authors.lastname: Tokmakoff
authors.forename: Jasper
authors.initials: J
authors.lastname: Knoester
authors.forename: Thomas L C
authors.initials: TL
authors.lastname: Jansen
mesh_terms: D000465:Algorithms; D000577:Amides / Q000737:chemistry*; D000818:Animals; D003903:Deuterium / Q000737:chemistry; D006801:Humans; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry; D011392:Proline / Q000737:chemistry*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013055:Spectrophotometry, Infrared; D014732:Vibration; D014867:Water / Q000737:chemistry
chemical_list: D000577:Amides; D010455:Peptides; D011506:Proteins; D012997:Solvents; D014867:Water; D011392:Proline; D003903:Deuterium