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/RestrictedAccess |
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 |
|