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

Abstract

Membrane proteins mediate processes that are fundamental for the flourishing of biological cells. 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. 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.

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Acknowledgments

ZC, ANB, and JCS would like to acknowledge funding from Centre Européen de Calcul Atomique et Moléculaire (CECAM) to host the Workshop “Coupling between protein, water, and lipid dynamics in complex biological systems: Theory and Experiments” that took place in September 2013, Lausanne, Switzerland. JTD, IA, and MR used the computational resources of the Modeling Facility of the Department of Chemistry, University of California Irvine funded by NSF Grant CHE-0840513 for this work. A-NB was supported in part by the Marie Curie International Rein-tegration Award IRG-26920 and used computing time from the North-German Supercomputing Alliance, HLRN. TWA was supported by ARC DP120103548, NSF MCB1052477, DE Shaw Anton (PSCA00061P; NRBSC, through NIH RC2GM093307), VLSCI (VR0200), and NCI (dd7). BA and SV acknowledge the support by ERC advanced Grant No. 268888. ZC and PG would like to acknowledge Reference Framework (NSRF) 2011–2013, National Action “Cooperation,” under grant entitled “Magnetic Nanoparticles for targeted MRI therapy (NANOTHER),” with code “11ΣYΝ-1-1799.” The program is cofunded by the European Regional Development Fund and national resources. Part of the calculations presented herein were performed using resources of the LinkSCEEM-2 project, funded by the EC under FP7 through Capacities Research Infrastructure, INFRA-2010-1.2.3 Virtual Research Communities, Combination of Collaborative Project and Coordination and Support Actions (CP-CSA) under Grant agreement no. RI-261600. GB was supported in part by NSF grant MCB1330728 from the National Science Foundation and Grant PO1GM55876-14A1 from the National Institutes of Health. LD received funding from EU FP7 (PIOF-GA-2012-329534). LD, and MLK used the computational resources of Temple University, supported by the National Science Foundation through major research instrumentation grant number CNS-09-58854. FT and NVB are grateful for financial support from the Irish Research Council, and for using the computational facilities of the Biowulf Linux cluster at the National Institutes of Health, USA and the Irish Centre for High-End Computing (ICHEC). JS acknowledges support from the Instituto de Salud Carlos III FEDER (CP12/03139) and the GLISTEN European Research Network.

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Correspondence to Zoe Cournia, Jeremy C. Smith or Ana-Nicoleta Bondar.

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Cournia, Z., Allen, T.W., Andricioaei, I. et al. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. J Membrane Biol 248, 611–640 (2015). https://doi.org/10.1007/s00232-015-9802-0

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Keywords

  • Membrane proteins
  • Lipids
  • Protein structure
  • Protein function
  • Protein dynamics
  • Membrane-mediated interactions