A framework for stochastic simulations and visualization of biological electron-transfer dynamics

Nakano, C. Masato; Byun, Hye Suk; Ma, Heng; Wei, Tao; El-Naggar, Mohamed Y.

doi:10.1016/j.cpc.2015.03.009

Title: A framework for stochastic simulations and visualization of biological electron-transfer dynamics

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Abstract

Electron transfer (ET) dictates a wide variety of energy-conversion processes in biological systems. Visualizing ET dynamics could provide key insight into understanding and possibly controlling these processes. We present a computational framework named VizBET to visualize biological ET dynamics, using an outer-membrane Mtr–Omc cytochrome complex in Shewanella oneidensis MR-1 as an example. Starting from X-ray crystal structures of the constituent cytochromes, molecular dynamics simulations are combined with homology modeling, protein docking, and binding free energy computations to sample the configuration of the complex as well as the change of the free energy associated with ET. This information, along with quantum-mechanical calculations of the electronic coupling, provides inputs to kinetic Monte Carlo (KMC) simulations of ET dynamics in a network of heme groups within the complex. Visualization of the KMC simulation results has been implemented as a plugin to the Visual Molecular Dynamics (VMD) software. Finally, VizBET has been used to reveal the nature of ET dynamics associated with novel nonequilibrium phase transitions in a candidate configuration of the Mtr–Omc complex due to electron–electron interactions.

Authors:

Nakano, C. Masato ^[1]; Byun, Hye Suk ^[2]; Ma, Heng ^[3]; Wei, Tao ^[3]; El-Naggar, Mohamed Y. ^[4]

Flintridge Preparatory School, La Canada Flintridge, CA (United States)
Univ. of Southern California, Los Angeles, CA (United States). Dept. of Physics & Astronomy
Lamar Univ., Beaumont, TX (United States). Dan F. Smith Dept. of Chemical Engineering
Univ. of Southern California, Los Angeles, CA (United States). Dept. of Physics & Astronomy, Dept. of Biological Sciences, and Dept. of Chemistry

Publication Date:: Tue Mar 31 00:00:00 EDT 2015

Research Org.:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Univ. of Southern California, Los Angeles, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

OSTI Identifier:: 1565295

Alternate Identifier(s):: OSTI ID: 1246977

Grant/Contract Number:: SC0010609; FG02-13ER16415

Resource Type:: Accepted Manuscript

Journal Name:: Computer Physics Communications

Additional Journal Information:: Journal Volume: 193; Journal Issue: C; Journal ID: ISSN 0010-4655

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

Subject:: 74 ATOMIC AND MOLECULAR PHYSICS; 97 MATHEMATICS AND COMPUTING; computer science; physics; visualization; biological electron transfer; molecular dynamics simulation; MM/PBSA; Kinetic Monte Carlo simulation

Citation Formats


                    Nakano, C. Masato, Byun, Hye Suk, Ma, Heng, Wei, Tao, and El-Naggar, Mohamed Y. A framework for stochastic simulations and visualization of biological electron-transfer dynamics.  United States: N. p., 2015. 
Web.  doi:10.1016/j.cpc.2015.03.009.

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                    Nakano, C. Masato, Byun, Hye Suk, Ma, Heng, Wei, Tao, & El-Naggar, Mohamed Y. A framework for stochastic simulations and visualization of biological electron-transfer dynamics.  United States.  https://doi.org/10.1016/j.cpc.2015.03.009

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                    Nakano, C. Masato, Byun, Hye Suk, Ma, Heng, Wei, Tao, and El-Naggar, Mohamed Y. Tue .  
"A framework for stochastic simulations and visualization of biological electron-transfer dynamics".  United States.  https://doi.org/10.1016/j.cpc.2015.03.009.  https://www.osti.gov/servlets/purl/1565295.

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@article{osti_1565295,

  title        = {A framework for stochastic simulations and visualization of biological electron-transfer dynamics},

  author       = {Nakano, C. Masato and Byun, Hye Suk and Ma, Heng and Wei, Tao and El-Naggar, Mohamed Y.},

  abstractNote = {Electron transfer (ET) dictates a wide variety of energy-conversion processes in biological systems. Visualizing ET dynamics could provide key insight into understanding and possibly controlling these processes. We present a computational framework named VizBET to visualize biological ET dynamics, using an outer-membrane Mtr–Omc cytochrome complex in Shewanella oneidensis MR-1 as an example. Starting from X-ray crystal structures of the constituent cytochromes, molecular dynamics simulations are combined with homology modeling, protein docking, and binding free energy computations to sample the configuration of the complex as well as the change of the free energy associated with ET. This information, along with quantum-mechanical calculations of the electronic coupling, provides inputs to kinetic Monte Carlo (KMC) simulations of ET dynamics in a network of heme groups within the complex. Visualization of the KMC simulation results has been implemented as a plugin to the Visual Molecular Dynamics (VMD) software. Finally, VizBET has been used to reveal the nature of ET dynamics associated with novel nonequilibrium phase transitions in a candidate configuration of the Mtr–Omc complex due to electron–electron interactions.},

  doi          = {10.1016/j.cpc.2015.03.009},

  journal      = {Computer Physics Communications},

  number       = C,

  volume       = 193,

  place        = {United States},

  year         = {Tue Mar 31 00:00:00 EDT 2015},

  month        = {Tue Mar 31 00:00:00 EDT 2015}

}

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