Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids.

The Journal of Physical Chemistry. B
Joakim P M Jämbeck, Alexander P Lyubartsev

Abstract

An all-atomistic force field (FF) has been developed for fully saturated phospholipids. The parametrization has been largely based on high-level ab initio calculations in order to keep the empirical input to a minimum. Parameters for the lipid chains have been developed based on knowledge about bulk alkane liquids, for which thermodynamic and dynamic data are excellently reproduced. The FFs ability to simulate lipid bilayers in the liquid crystalline phase in a tensionless ensemble was tested in simulations of three lipids: 1,2-diauroyl-sn-glycero-3-phospocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 1,2-dipalmitoyl-sn-glycero-3-phospcholine (DPPC). Computed areas and volumes per lipid, and three different kinds of bilayer thicknesses, have been investigated. Most importantly NMR order parameters and scattering form factors agree in an excellent manner with experimental data under a range of temperatures. Further, the compatibility with the AMBER FF for biomolecules as well as the ability to simulate bilayers in gel phase was demonstrated. Overall, the FF presented here provides the important balance between the hydrophilic and hydrophobic forces present in lipid bilayers and therefore can be used for ...Continue Reading

References

Aug 1, 1978·Biophysical Journal·J F Nagle, D A Wilkinson
Mar 1, 1991·Chemistry and Physics of Lipids·D Marsh
Jan 1, 1986·Methods in Enzymology·S A Simon, T J McIntosh
Aug 1, 1974·Proceedings of the National Academy of Sciences of the United States of America·P B HitchcockG G Shipley
Feb 17, 1981·Biochemistry·R WolfendenC C Southgate
Apr 1, 1993·Biophysical Journal·S Tristram-NagleJ F Nagle
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Sep 1, 1996·Biophysical Journal·F Jähnig
Mar 26, 1998·Biochimica Et Biophysica Acta·D P TielemanH J Berendsen
Nov 10, 1998·Chemistry and Physics of Lipids·H I PetracheJ F Nagle
Mar 1, 1985·Physical Review A: General Physics·W G Hoover
May 1, 1994·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·W SunJ F Nagle
Mar 22, 2000·Magnetic Resonance in Medicine : Official Journal of the Society of Magnetic Resonance in Medicine·P S ToftsJ M Pope
Jun 27, 2000·Biophysical Journal·W RawiczE Evans
Sep 12, 2000·Current Opinion in Structural Biology·J F Nagle, S Tristram-Nagle
Oct 6, 2000·Biochimica Et Biophysica Acta·S C CostiganR H Templer
Nov 7, 2000·Biochimica Et Biophysica Acta·J F Nagle, S Tristram-Nagle
Jun 19, 2002·Accounts of Chemical Research·Richard W PastorScott E Feller
Dec 24, 2002·Biophysical Journal·Stephanie Tristram-NagleJohn F Nagle
May 29, 2003·Biophysical Journal·Sagar A PanditMax L Berkowitz
Nov 19, 2003·Chemistry and Physics of Lipids·Jonathan N SachsThomas B Woolf
Apr 30, 2004·Journal of Computational Chemistry·Junmei WangDavid A Case
Jun 11, 2004·Biophysical Journal·Justin Gullingsrud, Klaus Schulten
Jul 21, 2004·Journal of Computational Chemistry·Chris OostenbrinkWilfred F van Gunsteren
Jul 23, 2004·The Journal of Chemical Physics·Donald HamelbergJ Andrew McCammon
Sep 30, 2004·Biophysical Journal·Jakob Wohlert, Olle Edholm
Nov 3, 2004·Biochimica Et Biophysica Acta·Anthony G Lee

❮ Previous
Next ❯

Citations

Aug 25, 2012·The Journal of Physical Chemistry. B·Åge A SkjevikKnut Teigen
Apr 9, 2013·The Journal of Physical Chemistry. B·Anthony R BraunJohn F Nagle
Feb 20, 2014·Journal of Molecular Modeling·Alexei M NikitinAlexander P Lyubartsev
Jan 11, 2014·Biochimica Et Biophysica Acta·Moutusi MannaIlpo Vattulainen
Feb 26, 2016·Frontiers in Bioengineering and Biotechnology·Liping SunRainer A Böckmann
Feb 7, 2016·Biochimica Et Biophysica Acta·David PogerAlan E Mark
Jan 26, 2016·Biochimica Et Biophysica Acta·O H Samuli Ollila, Georg Pabst
Nov 19, 2015·Journal of Biomolecular Structure & Dynamics·Zhenyan JiangRainer A Böckmann
Jan 15, 2016·Journal of Chemical Theory and Computation·Pavel BuslaevIvan Gushchin
Nov 27, 2015·The Journal of Physical Chemistry. B·Alexey A Dmitriev, Nikolay Vladimirovich Surovtsev
Jan 15, 2016·Biochimica Et Biophysica Acta·Alexander P Lyubartsev, Alexander L Rabinovich
Jan 10, 2016·Biochimica Et Biophysica Acta·Sonja A Kirsch, Rainer A Böckmann
Apr 11, 2015·The Journal of Physical Chemistry. B·Paul StevensonAlipasha Vaziri
Jan 3, 2016·Journal of Molecular Graphics & Modelling·Brad Van Oosten, Thad A Harroun
Mar 8, 2016·Biochimica Et Biophysica Acta·Mariusz Kepczynski, Tomasz Róg
Nov 18, 2015·Journal of Chemical Theory and Computation·Jaakko J UusitaloSiewert J Marrink
Oct 28, 2014·The Journal of Physical Chemistry. B·Cayla M MillerJeetain Mittal
Nov 18, 2015·Journal of Chemical Theory and Computation·Iwona Siuda, D Peter Tieleman
Oct 29, 2015·The Journal of Physical Chemistry. B·Alexandru BotanJoona Petteri Tynkkynen
May 15, 2013·The Journal of Physical Chemistry. B·Jon KaplaArnold Maliniak
May 8, 2014·Journal of Chemical Theory and Computation·Callum J DicksonRoss C Walker
Mar 8, 2016·Biochimica Et Biophysica Acta·Matti Javanainen, Hector Martinez-Seara
Oct 18, 2015·Biochimica Et Biophysica Acta·Virginia MiguelAdriana B Pierini
Jan 3, 2016·The Journal of Chemical Physics·Christopher M MacDermaidGiacomo Fiorin
Nov 21, 2015·Journal of Chemical Theory and Computation·Christian L WennbergErik Lindahl
Aug 17, 2014·Biochimica Et Biophysica Acta·Dennis C KochChristian Kandt
Aug 26, 2014·Biochimica Et Biophysica Acta·Kiyotaka AkaboriStephanie Tristram-Nagle
Apr 30, 2014·Journal of Computational Chemistry·Alexander Mirzoev, Alexander P Lyubartsev
Mar 17, 2016·Langmuir : the ACS Journal of Surfaces and Colloids·João Victor Narducci FerreiraLuciano Caseli
Nov 18, 2015·Journal of Chemical Theory and Computation·Samuel Genheden, Jonathan W Essex
Feb 11, 2016·Journal of Chemical Information and Modeling·Damian BartuziDariusz Matosiuk
Oct 31, 2015·Journal of Chemical Information and Modeling·Damian BartuziDariusz Matosiuk
Apr 2, 2016·Physical Chemistry Chemical Physics : PCCP·Åge A SkjevikIan R Gould
Sep 4, 2015·Journal of Chemical Information and Modeling·Andrea BortolatoJonathan S Mason

❮ Previous
Next ❯

Methods Mentioned

BETA
X-ray
NMR
the
neutron
neutron scattering

Software Mentioned

Gromacs
Gaussian09
AMBER03
UA
NPAT
MDynaMix
GAFF
Red
GROMOS
- GUI

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.