Nonequilibrium molecular dynamics simulation of the energy transport through a peptide helix

Abstract

Recent progress in transient infrared spectroscopy has made it possible to monitor the transient flow of vibrational energy along a peptide helix [V. Botan et al., Proc. Natl. Acad. Sci. U.S.A. 104, 12749 (2007)]. To provide a theoretical description of these experiments, extensive nonequilibrium molecular dynamics simulations of the photoinduced energy transport in a photoswitchable Aib peptide are performed. By calculating the response of the molecule caused by its excitation via optical and infrared pulses as well as temperature jump and stationary heating, it is shown that these methods are equivalent in that they provide approximately the same molecular energy transfer times. The resulting thermal diffusivity of 10 A(2) ps(-1) qualitatively agrees with the results of previous normal mode calculations for proteins and with experimental bulk values (e.g., 14 A(2) ps(-1) for water). To compare to experiment, a new way of approximating the measured signals is suggested which leads to an improved agreement with the experimental results and explains previous discrepancies. To elucidate the mechanism of energy transfer, modifications to the molecular dynamics force field are introduced, which reveal that the energy transfer occurs mainly through the peptide backbone and depends surprisingly little on the force field parametrization. Employing a harmonic model, quantum-mechanical effects are estimated to moderately (about a factor of 2) speed up the energy transport along the peptide.

Transition from IVR limited vibrational energy transport to bulk heat transport

“…the transient red-shift, does not reflect the overall residue energy, which, however, was the basis for all MD simulations. Based on these ideas, Stock and coworkers modified and reran their MD simulations of energy transport through the peptide [43]. Instead of simulating the total residue energy of the amino acid sites, they calculated the time evolution of the energy of the localized C=O modes.…”

Reactive molecular dynamics simulations of switching processes of azobenzene-based monolayer on surface

“…[42][43][44][45][46][47][48][49] Nguyen et al employed nonequilibrium MD to simulate the rearrangement of a photoswitchable bicyclic azobenzene octapeptide in the solution. [42][43][44][45] Heinz et al employed a similar method to model the azobenzene in the interlayer and liquid crystal. 47,48 They altered the formalism of the N=N torsion potential in the force field and got a qualitatively reasonable picture.…”

A method for analyzing the vibrational energy flow in biomolecules in solution

“…From a theoretical point of view, the intramolecular vibrational energy flow in biomolecules has also received a great deal of attention 2, 28 through different approaches including harmonic theories, 8,26,[29][30][31][32][33] molecular dynamics (MD) simulations, 28,[34][35][36][37][38][39][40][41][42][43][44][45][46] coarse-grained models, 33,47 and quantum methods. 21,[48][49][50][51][52][53] Despite this diversity of theoretical treatments, comparison between experimental and theoretical studies is still unsatisfactory because it faces the major difficulty that whereas experiments provide information on the energy transport spectroscopically from the vibrational modes which are active in the technique employed, most of the theoretical treatments discuss the energy flow in terms of residuebased models which, although shown to be quite useful in describing the spatial evolution of the energy, 38,39,41,44 are not well suited for direct comparison with observed data since the residues are not the experimentally active units.…”

“…21,[48][49][50][51][52][53] Despite this diversity of theoretical treatments, comparison between experimental and theoretical studies is still unsatisfactory because it faces the major difficulty that whereas experiments provide information on the energy transport spectroscopically from the vibrational modes which are active in the technique employed, most of the theoretical treatments discuss the energy flow in terms of residuebased models which, although shown to be quite useful in describing the spatial evolution of the energy, 38,39,41,44 are not well suited for direct comparison with observed data since the residues are not the experimentally active units. In addition, the total content of vibrational energy of a biomolecule cannot be expressed as a sum of the individual contributions of the residues due to the potential energy couplings existing among them, which preclude a detailed and accurate quantification of the vibrational energy flow.…”