Infrared signatures of the peptide dynamical transition: a molecular dynamics simulation study

The Journal of Chemical Physics
Maja KobusGerhard Stock

Abstract

Recent two-dimensional infrared (2D-IR) experiments on a short peptide 3(10)-helix in chloroform solvent [E. H. G. Backus et al., J. Phys. Chem. B 113, 13405 (2009)] revealed an intriguing temperature dependence of the homogeneous line width, which was interpreted in terms of a dynamical transition of the peptide. To explain these findings, extensive molecular dynamics simulations at various temperatures were performed in order to construct the free energy landscape of the system. The study recovers the familiar picture of a glass-forming system, which below the glass transition temperature T(g) is trapped in various energy basins, while it diffuses freely between these basins above T(g). In fact, one finds at T(g) approximately 270 K a sharp rise of the fluctuations of the backbone dihedral angles, which reflects conformational transitions of the peptide. The corresponding C=O frequency fluctuations are found to be a sensitive probe of the peptide conformational dynamics from femtosecond to nanosecond time scales and lead to 2D-IR spectra that qualitatively match the experiment. The calculated homogeneous line width, however, does not show the biphasic temperature dependence observed in experiment.

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Citations

Dec 12, 2012·The Journal of Physical Chemistry. a·A R LamS Mukamel
Apr 5, 2011·The Journal of Chemical Physics·Maja KobusGerhard Stock
Jan 3, 2015·The Journal of Chemical Physics·Andrzej J RzepielaGerhard Stock
Oct 13, 2019·Nature Communications·Justin E ElenewskiMichael Zwolak
Jul 25, 2018·The Journal of Chemical Physics·Justin E ElenewskiMichael Zwolak
Jan 21, 2011·The Journal of Physical Chemistry. a·Atsunori Sakurai, Yoshitaka Tanimura
Jan 7, 2011·The Journal of Physical Chemistry. B·Arend G DijkstraJasper Knoester
Mar 9, 2019·Journal of Chemical Theory and Computation·Arup Kumar Pathak, Tusar Bandyopadhyay
Nov 19, 2015·Journal of Chemical Theory and Computation·Sebastian Buchenberg Gerhard Stock

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