Abstract
AbstractMolecular dynamics (MD) simulations of biomolecules are performed at various levels of atomic detail from all-atom models to coarse grained models. United-atom models are at an intermediate level, in which non-polar hydrogen atoms are subsumed into their adjacent carbon-atom reducing the number of particles for a DPPC lipid molecule by 60%. United-atom models of the lipids DPPC, DMPC, POPC and POPG in the GROMOS96 53a6 force field were developed, that reproduced experimental properties of lipid bilayers without assumption of a constant surface area or inclusion of surface pressure. In the absence of experimental data a surface per lipid area for the negatively charged POPG of 0.700±0.007 nm2 was obtained that is higher than 0.53 to 0.56 nm2 reported in previous simulation studies in the literature. It is argued that MD simulations of anionic bilayers may have underestimated the steric requirements of sodium counter ions entering the head group region in order to compensate the negative charge. The use of the DMPC GROMOS96 53a6 model was evaluated in an MD simulation of the ErbB2 transmembrane peptide and showed closer agreement with the NMR-derived structure than the GROMOS87 force field that was most commonly used for membrane protein simulations previously. Lipid topologies and coordinates are available via LipidBook (http://lipidbook.bioch.ox.ac.uk/).
Highlights
United-atom force fields for molecular dynamics (MD) simulations provide a higher computational efficiency especially in lipid membrane simulations with little sacrifice in accuracy, when compared to allatom forcefields
Molecular dynamics simulations calculate the thermal motions of molecules subjected to the physics-based interaction forces:
The time evolution of the system is calculated from Newton’s equations of motions: 2m dri dt vi r(t t) r(t) v(t t ) t 2
Summary
United-atom force fields for molecular dynamics (MD) simulations provide a higher computational efficiency especially in lipid membrane simulations with little sacrifice in accuracy, when compared to allatom forcefields. Excellent united-atom lipid models are available, but in combination with the depreciated GROMOS87 protein force field. The aims of this research were to develop unitedatom models of the lipid 1,2-dipalmitoyl-sn-glycero-3phosphocholine (DPPC), 1,2-dimyristoyl-sn-glycero3-phosphocholine (DMPC), 1-palmitoyl-2-oleoyl-snglycero-3-phosphocholine (POPC) and 1-palmitoyl-2oleoyl-sn-glycero-3-phosphoglycerol (POPG) for the modern GROMOS96 53a6 force field
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