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Lipid-Protein Interactions pp 1–30Cite as

Multiscale Modeling and Simulation Approaches to Lipid–Protein Interactions

Part of the Methods in Molecular Biology book series (MIMB,volume 2003)

Abstract

Lipid membranes play a crucial role in living systems by compartmentalizing biological processes and forming a barrier between these processes and the environment. Naturally, a large apparatus of biomolecules is responsible for construction, maintenance, transport, and degradation of these lipid barriers. Additional classes of biomolecules are tasked with transport of specific substances or transduction of signals from the environment across lipid membranes. In this article, we intend to describe a set of techniques that enable one to build accurate models of lipid systems and their associated proteins, and to simulate their dynamics over a variety of time and length scales. We discuss the methods and challenges that allow us to derive structural, mechanistic, and thermodynamic information from these models. We also show how these models have recently been applied in research to study some of the most complex lipid–protein systems to date, including bacterial and viral envelopes, neuronal membranes, and mammalian signaling systems.

Key words

  • Molecular dynamics (MD) simulation
  • Molecular modeling
  • Protein–lipid interactions
  • Lipid-binding protein
  • Membrane proteins
  • Membrane peptides
  • Multiscale
  • Coarse-grained (CG) models

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Acknowledgments

T.S.C. and H.I.I. acknowledge that this work has been supported in part by the Joint Design of Advanced Computing Solutions for Cancer (JDACS4C) program established by the U.S. Department of Energy (DOE) and the National Cancer Institute (NCI) of the National Institutes of Health. T.S.C. and H.I.I. note that this work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-JRNL-752805. J.R.A. acknowledges the following sources of funding: Rutherford Discovery Fellowship (15-MAU-001); Marsden grant (15-UOA-105); New Zealand Ministry of Business, Innovation and Employment (MBIE) Endeavour Smart Ideas grant (UOCX1706); Maurice Wilkins Centre for Molecular Biodiscovery Flagship Project grant (MWC 3716850). W.A.I. was supported by the following sources of funding: Massey University Doctoral Scholarship; Massey University Doctoral Dissemination grant. N.D. thanks the Nehru trust for Cambridge University and Rajiv Gandhi (UK) foundation for funding. P.J.B. and J.K.M. acknowledge funding from the Ministry of Education in Singapore (MOE AcRF Tier 3 Grant Number MOE2012-T3-1-008).

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  1. Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore

    Roland G. Huber, Daniel A. Holdbrook, Jan K. Marzinek & Peter J. Bond

  2. Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA

    Timothy S. Carpenter & Helgi I. Ingólfsson

  3. Department of Chemistry, University of Cambridge, Cambridge, UK

    Namita Dube

  4. Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand

    William A. Irvine

  5. School of Chemistry, University of Southampton, Southampton, UK

    Firdaus Samsudin & Syma Khalid

  6. School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand

    Jane R. Allison

  7. Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand

    Jane R. Allison

  8. Department of Biological Sciences, National University of Singapore, Singapore, Singapore

    Peter J. Bond

Authors
  1. Roland G. Huber
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  2. Timothy S. Carpenter
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  3. Namita Dube
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  4. Daniel A. Holdbrook
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  5. Helgi I. Ingólfsson
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  6. William A. Irvine
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  7. Jan K. Marzinek
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  8. Firdaus Samsudin
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  9. Jane R. Allison
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  10. Syma Khalid
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  11. Peter J. Bond
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Corresponding author

Correspondence to Peter J. Bond .

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Editors and Affiliations

  1. Department of Biophysics, Institute of Biology, FB10 and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany

    Prof. Dr. Jörg H. Kleinschmidt

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Huber, R.G. et al. (2019). Multiscale Modeling and Simulation Approaches to Lipid–Protein Interactions. In: Kleinschmidt, J. (eds) Lipid-Protein Interactions. Methods in Molecular Biology, vol 2003. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9512-7_1

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  • DOI: https://doi.org/10.1007/978-1-4939-9512-7_1

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