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Mesoscale Computational Modeling of Protein-Membrane Interactions Based on Continuum Mean-Field Theory

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SNAREs

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1860))

Abstract

Quantitative computational modeling of protein-membrane interactions is of great importance as it aids in the interpretation of experimental results and enables design and exploration of new experimental systems. This review describes one such computational approach conceived specifically to treat electrostatically driven interactions between a lipid membrane and a protein (or protein domains) adsorbing onto the membrane. The methodology is based on self-consistent minimization of the governing free energy functional which is expressed in the mean-field approximation and has contributions from electrostatic interactions as well as from mixing entropy of lipids in the membrane and ions in the solution. The method enables calculation of the free energy of the binding process and quantification of the steady-state lipid distribution around the adsorbing protein. The extension of the method to include membrane deformation degrees of freedom further allows calculation of the equilibrium bilayer shape upon the protein binding.

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Acknowledgments

GK is grateful to Profs. Harel Weinstein and Daniel Harries for their guidance and support during the development of the computational methodology described in this work. GK is also thankful to Nathan Baker for his advice on modifying APBS and his valuable feedback on the mean-field model. GK is supported by the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute of Computational Biomedicine at Weill Cornell Medical College through gratefully acknowledged support from the 1923 Fund. 

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Authors and Affiliations

  1. Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA

    George Khelashvili

  2. Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, NY, USA

    George Khelashvili

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  1. George Khelashvili
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Correspondence to George Khelashvili .

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Editors and Affiliations

  1. Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA

    Rutilio Fratti

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Khelashvili, G. (2019). Mesoscale Computational Modeling of Protein-Membrane Interactions Based on Continuum Mean-Field Theory. In: Fratti, R. (eds) SNAREs. Methods in Molecular Biology, vol 1860. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8760-3_2

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  • DOI: https://doi.org/10.1007/978-1-4939-8760-3_2

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8759-7

  • Online ISBN: 978-1-4939-8760-3

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