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On the calculation of acyl chain order parameters from lipid simulations

On the calculation of acyl chain order parameters from lipid simulations
On the calculation of acyl chain order parameters from lipid simulations
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 non-trivial 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.
1549-9618
Piggot, Thomas J.
d91247c8-1c4d-4cdb-a398-47546dfbe64a
Allison, Jane R.
94e01c3f-714f-48cd-a61d-5e888a1afe82
Sessions, Richard B.
d0b37bc6-44a8-4ac9-806c-666885865af1
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Piggot, Thomas J.
d91247c8-1c4d-4cdb-a398-47546dfbe64a
Allison, Jane R.
94e01c3f-714f-48cd-a61d-5e888a1afe82
Sessions, Richard B.
d0b37bc6-44a8-4ac9-806c-666885865af1
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5

Piggot, Thomas J., Allison, Jane R., Sessions, Richard B. and Essex, Jonathan W. (2017) On the calculation of acyl chain order parameters from lipid simulations. Journal of Chemical Theory and Computation. (doi:10.1021/acs.jctc.7b00643).

Record type: Article

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 non-trivial 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.

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Accepted/In Press date: 6 September 2017
e-pub ahead of print date: 6 September 2017

Identifiers

Local EPrints ID: 415146
URI: https://eprints.soton.ac.uk/id/eprint/415146
ISSN: 1549-9618
PURE UUID: 3b74b8c8-70d2-4ee8-837c-128c280f6c73
ORCID for Jonathan W. Essex: ORCID iD orcid.org/0000-0003-2639-2746

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Date deposited: 01 Nov 2017 17:30
Last modified: 14 Mar 2019 05:33

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