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

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• 作者：Tianmin Wu ; Lijiang Yang ; Ruiting Zhang ; Qiang Shao ; Wei Zhuang
• 刊名：The Journal of Physical Chemistry A
• 出版年：2013
• 出版时间：July 25, 2013
• 年：2013
• 卷：117
• 期：29
• 页码：6256-6263
• 全文大小：474K
• 年卷期：v.117,no.29(July 25, 2013)
• ISSN：1520-5215

文摘

We simulated the equilibrium isotope-edited FTIR and 2DIR spectra of a 尾-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鈥檚 conformational change and related IR spectra across its thermal unfolding transition.