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Title: Vibrational energy flow in the villin headpiece subdomain: Master equation simulations

Abstract

We examine vibrational energy flow in dehydrated and hydrated villin headpiece subdomain HP36 by master equation simulations. Transition rates used in the simulations are obtained from communication maps calculated for HP36. In addition to energy flow along the main chain, we identify pathways for energy transport in HP36 via hydrogen bonding between residues quite far in sequence space. The results of the master equation simulations compare well with all-atom non-equilibrium simulations to about 1 ps following initial excitation of the protein, and quite well at long times, though for some residues we observe deviations between the master equation and all-atom simulations at intermediate times from about 1–10 ps. Those deviations are less noticeable for hydrated than dehydrated HP36 due to energy flow into the water.

Authors:
 [1];  [2]; ;  [3];  [4];  [5]
  1. Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557 (United States)
  2. (FRIAS), University of Freiburg, Freiburg (Germany)
  3. Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg (Germany)
  4. Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg (Germany)
  5. (Germany)
Publication Date:
OSTI Identifier:
22416159
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 142; Journal Issue: 7; Other Information: (c) 2015 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; ATOMS; CHEMICAL BONDS; COMPARATIVE EVALUATIONS; COMPUTERIZED SIMULATION; DEHYDRATION; EQUATIONS; EQUILIBRIUM; EXCITATION; POWER TRANSMISSION; PROTEINS; RESIDUES; WATER

Citation Formats

Leitner, David M., E-mail: dml@unr.edu, E-mail: stock@physik.uni-freiburg.de, Freiburg Institute for Advanced Studies, Buchenberg, Sebastian, Brettel, Paul, Stock, Gerhard, E-mail: dml@unr.edu, E-mail: stock@physik.uni-freiburg.de, and Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg. Vibrational energy flow in the villin headpiece subdomain: Master equation simulations. United States: N. p., 2015. Web. doi:10.1063/1.4907881.
Leitner, David M., E-mail: dml@unr.edu, E-mail: stock@physik.uni-freiburg.de, Freiburg Institute for Advanced Studies, Buchenberg, Sebastian, Brettel, Paul, Stock, Gerhard, E-mail: dml@unr.edu, E-mail: stock@physik.uni-freiburg.de, & Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg. Vibrational energy flow in the villin headpiece subdomain: Master equation simulations. United States. doi:10.1063/1.4907881.
Leitner, David M., E-mail: dml@unr.edu, E-mail: stock@physik.uni-freiburg.de, Freiburg Institute for Advanced Studies, Buchenberg, Sebastian, Brettel, Paul, Stock, Gerhard, E-mail: dml@unr.edu, E-mail: stock@physik.uni-freiburg.de, and Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg. Sat . "Vibrational energy flow in the villin headpiece subdomain: Master equation simulations". United States. doi:10.1063/1.4907881.
@article{osti_22416159,
title = {Vibrational energy flow in the villin headpiece subdomain: Master equation simulations},
author = {Leitner, David M., E-mail: dml@unr.edu, E-mail: stock@physik.uni-freiburg.de and Freiburg Institute for Advanced Studies and Buchenberg, Sebastian and Brettel, Paul and Stock, Gerhard, E-mail: dml@unr.edu, E-mail: stock@physik.uni-freiburg.de and Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg},
abstractNote = {We examine vibrational energy flow in dehydrated and hydrated villin headpiece subdomain HP36 by master equation simulations. Transition rates used in the simulations are obtained from communication maps calculated for HP36. In addition to energy flow along the main chain, we identify pathways for energy transport in HP36 via hydrogen bonding between residues quite far in sequence space. The results of the master equation simulations compare well with all-atom non-equilibrium simulations to about 1 ps following initial excitation of the protein, and quite well at long times, though for some residues we observe deviations between the master equation and all-atom simulations at intermediate times from about 1–10 ps. Those deviations are less noticeable for hydrated than dehydrated HP36 due to energy flow into the water.},
doi = {10.1063/1.4907881},
journal = {Journal of Chemical Physics},
number = 7,
volume = 142,
place = {United States},
year = {Sat Feb 21 00:00:00 EST 2015},
month = {Sat Feb 21 00:00:00 EST 2015}
}