Molecular Dynamics Simulation of Small Molecules Interacting with Biological Membranes.

Martinotti, C; Ruiz-Perez, L; Deplazes, E; Mancera, RL

Molecular Dynamics Simulation of Small Molecules Interacting with Biological Membranes.

Martinotti, C Ruiz-Perez, L Deplazes, E

Mancera, RL

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Publisher:: WILEY-V C H VERLAG GMBH
Publication Type:: Journal Article
Citation:: Chemphyschem : a European journal of chemical physics and physical chemistry, 2020, 21, (14), pp. 1486-1514
Issue Date:: 2020-07

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Field	Value	Language
dc.contributor.author	Martinotti, C
dc.contributor.author	Ruiz-Perez, L
dc.contributor.author	Deplazes, E https://orcid.org/0000-0003-2052-5536
dc.contributor.author	Mancera, RL
dc.date.accessioned	2020-11-03T00:55:12Z
dc.date.available	2021-08-12T19:00:59Z
dc.date.issued	2020-07
dc.identifier.citation	Chemphyschem : a European journal of chemical physics and physical chemistry, 2020, 21, (14), pp. 1486-1514
dc.identifier.issn	1439-4235
dc.identifier.issn	1439-7641
dc.identifier.uri	http://hdl.handle.net/10453/143704
dc.description.abstract	Cell membranes protect and compartmentalise cells and their organelles. The semi-permeable nature of these membranes controls the exchange of solutes across their structure. Characterising the interaction of small molecules with biological membranes is critical to understanding of physiological processes, drug action and permeation, and many biotechnological applications. This review provides an overview of how molecular simulations are used to study the interaction of small molecules with biological membranes, with a particular focus on the interactions of water, organic compounds, drugs and short peptides with models of plasma cell membrane and stratum corneum lipid bilayers. This review will not delve on other types of membranes which might have different composition and arrangement, such as thylakoid or mitochondrial membranes. The application of unbiased molecular dynamics simulations and enhanced sampling methods such as umbrella sampling, metadynamics and replica exchange are described using key examples. This review demonstrates how state-of-the-art molecular simulations have been used successfully to describe the mechanism of binding and permeation of small molecules with biological membranes, as well as associated changes to the structure and dynamics of these membranes. The review concludes with an outlook on future directions in this field.
dc.format	Print-Electronic
dc.language	eng
dc.publisher	WILEY-V C H VERLAG GMBH
dc.relation.ispartof	Chemphyschem : a European journal of chemical physics and physical chemistry
dc.relation.isbasedon	10.1002/cphc.202000219
dc.rights	info:eu-repo/semantics/embargoedAccess
dc.subject	0202 Atomic, Molecular, Nuclear, Particle and Plasma Physics, 0306 Physical Chemistry (incl. Structural), 0307 Theoretical and Computational Chemistry
dc.subject.classification	Chemical Physics
dc.title	Molecular Dynamics Simulation of Small Molecules Interacting with Biological Membranes.
dc.type	Journal Article
utslib.citation.volume	21
utslib.location.activity	Germany
utslib.for	0202 Atomic, Molecular, Nuclear, Particle and Plasma Physics
utslib.for	0306 Physical Chemistry (incl. Structural)
utslib.for	0307 Theoretical and Computational Chemistry
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Life Sciences
pubs.organisational-group	/University of Technology Sydney
utslib.copyright.status	open_access	*
dc.date.updated	2020-11-03T00:55:04Z
pubs.issue	14
pubs.publication-status	Published
pubs.volume	21
utslib.citation.issue	14

Abstract:

Cell membranes protect and compartmentalise cells and their organelles. The semi-permeable nature of these membranes controls the exchange of solutes across their structure. Characterising the interaction of small molecules with biological membranes is critical to understanding of physiological processes, drug action and permeation, and many biotechnological applications. This review provides an overview of how molecular simulations are used to study the interaction of small molecules with biological membranes, with a particular focus on the interactions of water, organic compounds, drugs and short peptides with models of plasma cell membrane and stratum corneum lipid bilayers. This review will not delve on other types of membranes which might have different composition and arrangement, such as thylakoid or mitochondrial membranes. The application of unbiased molecular dynamics simulations and enhanced sampling methods such as umbrella sampling, metadynamics and replica exchange are described using key examples. This review demonstrates how state-of-the-art molecular simulations have been used successfully to describe the mechanism of binding and permeation of small molecules with biological membranes, as well as associated changes to the structure and dynamics of these membranes. The review concludes with an outlook on future directions in this field.

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http://hdl.handle.net/10453/143704