On the Calculation of Acyl Chain Order Parameters from Lipid Simulations.

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dc.contributor.author Piggot, Thomas J
dc.contributor.author Allison, Jane R
dc.contributor.author Sessions, Richard B
dc.contributor.author Essex, Jonathan W
dc.coverage.spatial United States
dc.date.accessioned 2022-05-24T22:43:33Z
dc.date.available 2022-05-24T22:43:33Z
dc.date.issued 2017-11
dc.identifier.citation (2017). Journal of Chemical Theory and Computation, 13(11), 5683-5696.
dc.identifier.issn 1549-9618
dc.identifier.uri https://hdl.handle.net/2292/59491
dc.description.abstract For molecular dynamics simulations of biological membrane systems to live up to the potential of providing accurate atomic level detail into membrane properties and functions, it is essential that the force fields used to model such systems are as accurate as possible. One membrane property that is often used to assess force field accuracy is the carbon-hydrogen (or carbon-deuterium) order parameters of the lipid tails, which can be accurately measured using experimental NMR techniques. There are a variety of analysis tools available to calculate these order parameters from simulations and it is essential that these computational tools work correctly to ensure the accurate assessment of the simulation force fields. In this work we compare many of these computational tools for calculating the order parameters of POPC membranes. While tools that work on all-atom systems and tools that work on saturated lipid tails in general work extremely well, we demonstrate that the majority of the tested tools that calculate the order parameters for unsaturated united-atom lipid tails do so incorrectly. We identify tools that do perform accurate calculations and include one such program with this work, enabling rapid and accurate calculation of united-atom lipid order parameters. Furthermore, we discuss cases in which it is nontrivial to appropriately predict the unsaturated carbon order parameters in united-atom systems. Finally, we examine order parameter splitting for carbon 2 in sn-2 lipid chains, demonstrating substantial deviations from experimental values in several all-atom and united-atom lipid force fields.
dc.format.medium Print-Electronic
dc.language eng
dc.publisher American Chemical Society (ACS)
dc.relation.ispartofseries Journal of chemical theory and computation
dc.rights Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher.
dc.rights.uri https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm
dc.subject Lipid Bilayers
dc.subject Models, Biological
dc.subject Molecular Dynamics Simulation
dc.subject 1.1 Normal biological development and functioning
dc.subject Science & Technology
dc.subject Physical Sciences
dc.subject Chemistry, Physical
dc.subject Physics, Atomic, Molecular & Chemical
dc.subject Chemistry
dc.subject Physics
dc.subject MOLECULAR-DYNAMICS SIMULATIONS
dc.subject COARSE-GRAINED MODEL
dc.subject ATOM FORCE-FIELD
dc.subject PHOSPHATIDYLCHOLINE BILAYERS
dc.subject BIOLOGICAL-MEMBRANES
dc.subject PHOSPHOLIPID-BILAYERS
dc.subject MAGNETIC-RESONANCE
dc.subject CONSTANT-PRESSURE
dc.subject SEGMENTAL ORDER
dc.subject FULL HYDRATION
dc.subject 0307 Theoretical and Computational Chemistry
dc.subject 0601 Biochemistry and Cell Biology
dc.subject 0803 Computer Software
dc.title On the Calculation of Acyl Chain Order Parameters from Lipid Simulations.
dc.type Journal Article
dc.identifier.doi 10.1021/acs.jctc.7b00643
pubs.issue 11
pubs.begin-page 5683
pubs.volume 13
dc.date.updated 2022-04-27T23:13:39Z
dc.rights.holder Copyright: The author en
dc.identifier.pmid 28876925 (pubmed)
pubs.author-url https://www.ncbi.nlm.nih.gov/pubmed/28876925
pubs.end-page 5696
pubs.publication-status Published
dc.rights.accessrights http://purl.org/eprint/accessRights/RetrictedAccess en
pubs.subtype Journal Article
pubs.elements-id 739562
pubs.org-id Science
pubs.org-id Biological Sciences
dc.identifier.eissn 1549-9626
pubs.record-created-at-source-date 2022-04-28
pubs.online-publication-date 2017-10-16


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