title: Modeling the thermal unfolding 2DIR spectra of a β-hairpin peptide based on the implicit solvent MD simulation.
abstract: We simulated the equilibrium isotope-edited FTIR and 2DIR spectra of a β-hairpin peptide trpzip2 at a series of temperatures. The simulation was based on the configuration distributions generated using the GB(OBC) implicit solvent model and the integrated tempering sampling (ITS) technique. A soaking procedure was adapted to generate the peptide in explicit solvent configurations for the spectroscopy calculations. The nonlinear exciton propagation (NEP) method was then used to calculate the spectra. Agreeing with the experiments, the intensities and ellipticities of the isotope-shifted peaks in our simulated signals have the site-specific temperature dependences, which suggest the inhomogeneous local thermal stabilities along the peptide chain. Our simulation thus proposes a cost-effective means to understand a peptide's conformational change and related IR spectra across its thermal unfolding transition.
authors.affiliation: Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China.
authors.forename: Tianmin
authors.initials: T
authors.lastname: Wu
authors.forename: Lijiang
authors.initials: L
authors.lastname: Yang
authors.forename: Ruiting
authors.initials: R
authors.lastname: Zhang
authors.forename: Qiang
authors.initials: Q
authors.lastname: Shao
authors.forename: Wei
authors.initials: W
authors.lastname: Zhuang
mesh_terms: D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D058767:Protein Unfolding; D012997:Solvents / Q000737:chemistry*; D013055:Spectrophotometry, Infrared; D013696:Temperature
chemical_list: D010455:Peptides; D012997:Solvents