Validation of all-atom phosphatidylcholine lipid force fields in the tensionless NPT ensemble
A recently defined charge set, to be used in conjunction with the all-atom CHARMM27r force field, has been validated for a series of phosphatidylcholine lipids. The work of Sonne et al. successfully replicated experimental bulk membrane behaviour for dipalmitoylphosphatidylcholine (DPPC) under the i...
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| Published in | Biochimica et biophysica acta Vol. 1788; no. 3; pp. 638 - 649 |
|---|---|
| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
Netherlands
Elsevier B.V
01.03.2009
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| Abstract | A recently defined charge set, to be used in conjunction with the all-atom CHARMM27r force field, has been validated for a series of phosphatidylcholine lipids. The work of Sonne et al. successfully replicated experimental bulk membrane behaviour for dipalmitoylphosphatidylcholine (DPPC) under the isothermal-isobaric (NPT) ensemble. Previous studies using the defined CHARMM27r charge set have resulted in lateral membrane contraction when used in the tensionless NPT ensemble, forcing the lipids to adopt a more ordered conformation than predicted experimentally. The current study has extended the newly defined charge set to 1-palmitoyl-2-oleoyl-
sn-glycero-3-phosphatidylcholine (POPC) and 1-palmitoyl-2-docosahexaenoyl-
sn-glycero-3-phosphatidylcholine (PDPC). Molecular dynamics simulations were run for each of the lipids (including DPPC) using both the CHARMM27r charge set and the newly defined modified charge set. In all three cases a significant improvement was seen in both bulk membrane properties and individual atomistic effects. Membrane width, area per lipid and the depth of water penetration were all seen to converge to experimental values. Deuterium order parameters generated with the new charge set showed increased disorder across the width of the bilayer and reflected both results from experiment and similar simulations run with united atom models. These newly validated models can now find use in mixed biological simulations under the tensionless ensemble without concern for lateral contraction. |
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| AbstractList | A recently defined charge set, to be used in conjunction with the all-atom CHARMM27r force field, has been validated for a series of phosphatidylcholine lipids. The work of Sonne et al. successfully replicated experimental bulk membrane behaviour for dipalmitoylphosphatidylcholine (DPPC) under the isothermal-isobaric (NPT) ensemble. Previous studies using the defined CHARMM27r charge set have resulted in lateral membrane contraction when used in the tensionless NPT ensemble, forcing the lipids to adopt a more ordered conformation than predicted experimentally. The current study has extended the newly defined charge set to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) and 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphatidylcholine (PDPC). Molecular dynamics simulations were run for each of the lipids (including DPPC) using both the CHARMM27r charge set and the newly defined modified charge set. In all three cases a significant improvement was seen in both bulk membrane properties and individual atomistic effects. Membrane width, area per lipid and the depth of water penetration were all seen to converge to experimental values. Deuterium order parameters generated with the new charge set showed increased disorder across the width of the bilayer and reflected both results from experiment and similar simulations run with united atom models. These newly validated models can now find use in mixed biological simulations under the tensionless ensemble without concern for lateral contraction. A recently defined charge set, to be used in conjunction with the all-atom CHARMM27r force field, has been validated for a series of phosphatidylcholine lipids. The work of Sonne et al. successfully replicated experimental bulk membrane behaviour for dipalmitoylphosphatidylcholine (DPPC) under the isothermal-isobaric (NPT) ensemble. Previous studies using the defined CHARMM27r charge set have resulted in lateral membrane contraction when used in the tensionless NPT ensemble, forcing the lipids to adopt a more ordered conformation than predicted experimentally. The current study has extended the newly defined charge set to 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphatidylcholine (POPC) and 1-palmitoyl-2-docosahexaenoyl- sn-glycero-3-phosphatidylcholine (PDPC). Molecular dynamics simulations were run for each of the lipids (including DPPC) using both the CHARMM27r charge set and the newly defined modified charge set. In all three cases a significant improvement was seen in both bulk membrane properties and individual atomistic effects. Membrane width, area per lipid and the depth of water penetration were all seen to converge to experimental values. Deuterium order parameters generated with the new charge set showed increased disorder across the width of the bilayer and reflected both results from experiment and similar simulations run with united atom models. These newly validated models can now find use in mixed biological simulations under the tensionless ensemble without concern for lateral contraction. |
| Author | Taylor, Justine Watson, Graeme W. Whiteford, Nava E. Bradley, Geoff |
| Author_xml | – sequence: 1 givenname: Justine surname: Taylor fullname: Taylor, Justine organization: School of Chemistry, University of Dublin, Trinity College, Dublin 2, Ireland – sequence: 2 givenname: Nava E. surname: Whiteford fullname: Whiteford, Nava E. organization: School of Chemistry, University of Dublin, Trinity College, Dublin 2, Ireland – sequence: 3 givenname: Geoff surname: Bradley fullname: Bradley, Geoff organization: Trinity Centre for High Performance Computing, University of Dublin, Trinity College, Dublin 2, Ireland – sequence: 4 givenname: Graeme W. surname: Watson fullname: Watson, Graeme W. email: watsong@tcd.ie organization: School of Chemistry, University of Dublin, Trinity College, Dublin 2, Ireland |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/19014902$$D View this record in MEDLINE/PubMed |
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| Snippet | A recently defined charge set, to be used in conjunction with the all-atom CHARMM27r force field, has been validated for a series of phosphatidylcholine... |
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| SubjectTerms | 1,2-Dipalmitoylphosphatidylcholine - chemistry Computer Simulation Membranes, Artificial Models, Molecular Molecular dynamics Phosphatidylcholines - chemistry Phospholipid bilayer Simulation |
| Title | Validation of all-atom phosphatidylcholine lipid force fields in the tensionless NPT ensemble |
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