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Title: Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory

Abstract

It is fundamental for the flourishing biological cells that membrane proteins mediate the process. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requires knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment. Here, we present here current studies in computational and experimental membrane protein biophysics, and show how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins.

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [7];  [3];  [8];  [9];  [10];  [1];  [5];  [11];  [12];  [13];  [8];  [14];  [15];  [5] more »;  [3];  [16];  [17];  [7];  [18];  [19];  [20];  [21];  [22] « less
+ Show Author Affiliations
  1. Academy of Athens (Greece)
  2. Univ. of California, Davis, CA (United States); RMIT Univ., Melbourne (Australia)
  3. Univ. of California, Irvine, CA (United States)
  4. Univ. of Nice Sophia Antipolis and French National Center for Scientific Research (France)
  5. Zuse Inst. of Berlin (Germany)
  6. Rutgers Univ., Camden, NJ (United States)
  7. Univ. College, Dublin (Ireland)
  8. Temple Univ., Philadelphia, PA (United States)
  9. Univ. of Granada (Spain)
  10. Linnaeus Univ., Kalmar (Sweden)
  11. IBPC and CNRS, Paris (France)
  12. Univ. of Lorraine, Nancy (France); Lomonosov Moscow State Univ. (Russia)
  13. Univ. of Athens (Greece)
  14. Univ. of Southampton (United Kingdom)
  15. Univ. of Alberta, Edmonton, AB (Canada)
  16. Pompeu Fabra Univ., Barcelona (Spain)
  17. Univ. of Lorraine and CNRS, Nancy (France)
  18. Univ. of Nice Sophia Antipolis and French National Center for Scientific Research (France)
  19. Johns Hopkins Univ., Baltimore, MD (United States)
  20. Univ. of Cambridge (United Kingdom)
  21. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  22. Free Univ. of Berlin (Germany)
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE; National Science Foundation (NSF)
OSTI Identifier:
1265906
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Membrane Biology
Additional Journal Information:
Journal Volume: 248; Journal Issue: 4; Journal ID: ISSN 0022-2631
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Cournia, Zoe, Allen, Toby W., Andricioaei, Ioan, Antonny, Bruno, Baum, Daniel, Brannigan, Grace, Buchete, Nicolae-Viorel, Deckman, Jason T., Delemotte, Lucie, del Val, Coral, Friedman, Ran, Gkeka, Paraskevi, Hege, Hans-Christian, Hénin, Jérôme, Kasimova, Marina A., Kolocouris, Antonios, Klein, Michael L., Khalid, Syma, Lemieux, M. Joanne, Lindow, Norbert, Roy, Mahua, Selent, Jana, Tarek, Mounir, Tofoleanu, Florentina, Vanni, Stefano, Urban, Sinisa, Wales, David J., Smith, Jeremy C., and Bondar, Ana-Nicoleta. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. United States: N. p., 2015. Web. doi:10.1007/s00232-015-9802-0.
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Cournia, Zoe, Allen, Toby W., Andricioaei, Ioan, Antonny, Bruno, Baum, Daniel, Brannigan, Grace, Buchete, Nicolae-Viorel, Deckman, Jason T., Delemotte, Lucie, del Val, Coral, Friedman, Ran, Gkeka, Paraskevi, Hege, Hans-Christian, Hénin, Jérôme, Kasimova, Marina A., Kolocouris, Antonios, Klein, Michael L., Khalid, Syma, Lemieux, M. Joanne, Lindow, Norbert, Roy, Mahua, Selent, Jana, Tarek, Mounir, Tofoleanu, Florentina, Vanni, Stefano, Urban, Sinisa, Wales, David J., Smith, Jeremy C., & Bondar, Ana-Nicoleta. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. United States. https://doi.org/10.1007/s00232-015-9802-0
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Cournia, Zoe, Allen, Toby W., Andricioaei, Ioan, Antonny, Bruno, Baum, Daniel, Brannigan, Grace, Buchete, Nicolae-Viorel, Deckman, Jason T., Delemotte, Lucie, del Val, Coral, Friedman, Ran, Gkeka, Paraskevi, Hege, Hans-Christian, Hénin, Jérôme, Kasimova, Marina A., Kolocouris, Antonios, Klein, Michael L., Khalid, Syma, Lemieux, M. Joanne, Lindow, Norbert, Roy, Mahua, Selent, Jana, Tarek, Mounir, Tofoleanu, Florentina, Vanni, Stefano, Urban, Sinisa, Wales, David J., Smith, Jeremy C., and Bondar, Ana-Nicoleta. Thu . "Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory". United States. https://doi.org/10.1007/s00232-015-9802-0. https://www.osti.gov/servlets/purl/1265906.
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@article{osti_1265906,
title = {Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory},
author = {Cournia, Zoe and Allen, Toby W. and Andricioaei, Ioan and Antonny, Bruno and Baum, Daniel and Brannigan, Grace and Buchete, Nicolae-Viorel and Deckman, Jason T. and Delemotte, Lucie and del Val, Coral and Friedman, Ran and Gkeka, Paraskevi and Hege, Hans-Christian and Hénin, Jérôme and Kasimova, Marina A. and Kolocouris, Antonios and Klein, Michael L. and Khalid, Syma and Lemieux, M. Joanne and Lindow, Norbert and Roy, Mahua and Selent, Jana and Tarek, Mounir and Tofoleanu, Florentina and Vanni, Stefano and Urban, Sinisa and Wales, David J. and Smith, Jeremy C. and Bondar, Ana-Nicoleta},
abstractNote = {It is fundamental for the flourishing biological cells that membrane proteins mediate the process. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requires knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment. Here, we present here current studies in computational and experimental membrane protein biophysics, and show how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins.},
doi = {10.1007/s00232-015-9802-0},
journal = {Journal of Membrane Biology},
number = 4,
volume = 248,
place = {United States},
year = {Thu Jun 11 00:00:00 EDT 2015},
month = {Thu Jun 11 00:00:00 EDT 2015}
}
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  • Xue, Yi; Chowdhury, Somenath; Liu, Xuying
  • Biochemistry, Vol. 51, Issue 18
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Molecular Dynamics Simulations of Voltage-Gated Cation Channels: Insights on Voltage-Sensor Domain Function and Modulation
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Enzymatic activation of voltage-gated potassium channels
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Neurosteroid binding sites on GABAA receptors
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Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: A molecular dynamics simulation study
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  • Piggot, Thomas J.; Holdbrook, Daniel A.; Khalid, Syma
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1828, Issue 2
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Nanopore Analysis of a Small 86-Residue Protein
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Regulation of voltage-gated potassium channels by PI(4,5)P2
journal, July 2012

  • Kruse, Martin; Hammond, Gerald R. V.; Hille, Bertil
  • The Journal of General Physiology, Vol. 140, Issue 2
  • DOI: 10.1085/jgp.201210806

E. coli Outer Membrane and Interactions with OmpLA
journal, June 2014

  • Wu, Emilia L.; Fleming, Patrick J.; Yeom, Min Sun
  • Biophysical Journal, Vol. 106, Issue 11
  • DOI: 10.1016/j.bpj.2014.04.024

Evaluations of the Absolute and Relative Free Energies for Antidepressant Binding to the Amino Acid Membrane Transporter LeuT with Free Energy Simulations
journal, April 2010

  • Zhao, Chunfeng; Caplan, David A.; Noskov, Sergei Yu.
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 6
  • DOI: 10.1021/ct9006597

Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms
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  • Wales, David J.; Doye, Jonathan P. K.
  • The Journal of Physical Chemistry A, Vol. 101, Issue 28
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Cholesterol depletion activates rapid internalization of submicron-sized acetylcholine receptor domains at the cell membrane
journal, January 2007

Structure and Dynamics of Parallel β-Sheets, Hydrophobic Core, and Loops in Alzheimer’s Aβ Fibrils
journal, May 2007

How Does a Voltage Sensor Interact with a Lipid Bilayer? Simulations of a Potassium Channel Domain
journal, February 2007

Investigation of Single-Molecule Kinetics Mediated by Weak Hydrogen Bonds within a Biological Nanopore
journal, January 2011

  • Asandei, Alina; Apetrei, Aurelia; Park, Yoonkyung
  • Langmuir, Vol. 27, Issue 1
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Protein Translocation Across the Bacterial Cytoplasmic Membrane
journal, June 2008

Immobilized lipid in acetylcholine receptor-rich membranes from Torpedo marmorata.
journal, September 1978

  • Marsh, D.; Barrantes, F. J.
  • Proceedings of the National Academy of Sciences, Vol. 75, Issue 9
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Interpreting the Aggregation Kinetics of Amyloid Peptides
journal, July 2006

Predictions for Cholesterol Interaction Sites on the A 2A Adenosine Receptor
journal, September 2012

  • Lee, Ji Young; Lyman, Edward
  • Journal of the American Chemical Society, Vol. 134, Issue 40
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Forcing independent velocity distributions in an experimental granular fluid
journal, May 2007

Molecular Modeling and Simulation of Membrane Lipid-Mediated Effects on GPCRs
journal, December 2012

Metastability and Markov State Models in Molecular Dynamics
book, January 2013

Effect of salt bridges on the energy landscape of a model protein
journal, November 2004

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Stationary points and dynamics in high-dimensional systems
journal, December 2003

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  • The Journal of Chemical Physics, Vol. 119, Issue 23, p. 12409-12416
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Visualization of Molecules with Positional Uncertainty
book, January 1999

Jamming of frictional spheres and random loose packing
journal, January 2010

Potential Energy and Free Energy Landscapes
journal, October 2006

  • Wales, David J.; Bogdan, Tetyana V.
  • The Journal of Physical Chemistry B, Vol. 110, Issue 42
  • DOI: 10.1021/jp0680544

Interaction of the Acetylcholine (Nicotinic) Receptor Protein from Torpedo marmorata Electric Organ with Monolayers of Pure Lipids
journal, April 1978

Reconstitution of intramembrane proteolysis in vitro reveals that pure rhomboid is sufficient for catalysis and specificity
journal, January 2005

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  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 6
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Naturally secreted oligomers of amyloid β protein potently inhibit hippocampal long-term potentiation in vivo
journal, April 2002

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Globular amyloid beta-peptide1-42 oligomer - a homogenous and stable neuropathological protein in Alzheimer's disease
journal, November 2005

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