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Multiscale Modeling and Simulation Approaches to Lipid–Protein Interactions

Multiscale Modeling and Simulation Approaches to Lipid–Protein Interactions
Multiscale Modeling and Simulation Approaches to Lipid–Protein Interactions

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.

Coarse-grained (CG) models, Lipid-binding protein, Membrane peptides, Membrane proteins, Molecular dynamics (MD) simulation, Molecular modeling, Multiscale, Protein–lipid interactions
1064-3745
1-30
Humana Press Inc.
Huber, Roland G.
114d3558-3288-4a57-87cf-c712953a803a
Carpenter, Timothy S.
f46feb20-3a47-49e8-8d21-9f24b69c9d0a
Dube, Namita
3399432a-9a12-465a-8444-6f6cdcab7bbc
Holdbrook, Daniel A.
d114c018-fb42-4a49-9b50-f7739feb75f5
Ingólfsson, Helgi I.
44ad13ab-bff2-4dd3-8530-b2243f229bfb
Irvine, William A.
6a53c0f8-2a5b-4a6d-b87b-7762847ce709
Marzinek, Jan K.
64e75d21-98b8-44d8-96f7-5076859e13ec
Samsudin, Firdaus
b01e87a0-af50-44d6-bca4-f511c40165f9
Allison, Jane R.
94e01c3f-714f-48cd-a61d-5e888a1afe82
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Bond, Peter J.
08f46940-85e8-44c4-a368-d94342a10fd6
Kleinschmidt, J.
Huber, Roland G.
114d3558-3288-4a57-87cf-c712953a803a
Carpenter, Timothy S.
f46feb20-3a47-49e8-8d21-9f24b69c9d0a
Dube, Namita
3399432a-9a12-465a-8444-6f6cdcab7bbc
Holdbrook, Daniel A.
d114c018-fb42-4a49-9b50-f7739feb75f5
Ingólfsson, Helgi I.
44ad13ab-bff2-4dd3-8530-b2243f229bfb
Irvine, William A.
6a53c0f8-2a5b-4a6d-b87b-7762847ce709
Marzinek, Jan K.
64e75d21-98b8-44d8-96f7-5076859e13ec
Samsudin, Firdaus
b01e87a0-af50-44d6-bca4-f511c40165f9
Allison, Jane R.
94e01c3f-714f-48cd-a61d-5e888a1afe82
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Bond, Peter J.
08f46940-85e8-44c4-a368-d94342a10fd6
Kleinschmidt, J.

Huber, Roland G., Carpenter, Timothy S., Dube, Namita, Holdbrook, Daniel A., Ingólfsson, Helgi I., Irvine, William A., Marzinek, Jan K., Samsudin, Firdaus, Allison, Jane R., Khalid, Syma and Bond, Peter J. (2019) Multiscale Modeling and Simulation Approaches to Lipid–Protein Interactions. In, Kleinschmidt, J. (ed.) Methods in Molecular Biology. (Methods in Molecular Biology, , (doi:10.1007/978-1-4939-9512-7_1), 2003) New York, NY. Humana Press Inc., pp. 1-30. (doi:10.1007/978-1-4939-9512-7_1).

Record type: Book Section

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.

Full text not available from this repository.

More information

e-pub ahead of print date: 20 June 2019
Keywords: Coarse-grained (CG) models, Lipid-binding protein, Membrane peptides, Membrane proteins, Molecular dynamics (MD) simulation, Molecular modeling, Multiscale, Protein–lipid interactions

Identifiers

Local EPrints ID: 434369
URI: http://eprints.soton.ac.uk/id/eprint/434369
ISSN: 1064-3745
PURE UUID: 605703ff-7bb9-457f-8ae7-f970e5cd8ded
ORCID for Firdaus Samsudin: ORCID iD orcid.org/0000-0003-2766-4459
ORCID for Syma Khalid: ORCID iD orcid.org/0000-0002-3694-5044

Catalogue record

Date deposited: 20 Sep 2019 16:30
Last modified: 07 Oct 2020 02:09

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