Modeling the Thermal Unfolding 2DIR Spectra of a β‑Hairpin Peptide Based on the Implicit Solvent MD Simulation

• Published in: The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory Vol. 117; no. 29; pp. 6256 - 6263
• Main Authors: Wu, Tianmin, Yang, Lijiang, Zhang, Ruiting, Shao, Qiang, Zhuang, Wei
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 25.07.2013
• Subjects: Atomic and molecular physics; Calculations and mathematical techniques in atomic and molecular physics (excluding electron correlation calculations); Computer simulation; Electronic structure of atoms, molecules and their ions: theory; Exact sciences and technology; Hydrogen Bonding; Mathematical models; Molecular dynamics and other numerical methods; Molecular Dynamics Simulation; Peptides; Peptides - chemistry; Physics; Protein Structure, Secondary; Protein Unfolding; Sampling; Simulation; Solvents; Solvents - chemistry; Spectra; Spectrophotometry, Infrared; Spectroscopy; Temperature; Temperature dependence; Fourier transform spectroscopy; Peptides; Isotope shifts; Thermal stability; Molecular dynamics method
• ISSN: 1089-5639; 1520-5215
• DOI: 10.1021/jp400625a

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 GBOBC 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.