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Solvent-Free, Highly Coarse-Grained Models for Charged Lipid Systems.

Srivastava A, Voth GA - J Chem Theory Comput (2014)

Bottom Line: We present a methodology to develop coarse-grained lipid models such that electrostatic interactions between the coarse-grained sites can be derived accurately from an all-atom molecular dynamics trajectory and expressed as an effective pairwise electrostatic potential with appropriate screening functions.The resulting electrostatic interactions are fitted to screened electrostatics functions, with a special treatment for distance-dependent dielectrics and screened dipole-dipole interactions.The vdW interactions are derived separately.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, The University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States.

ABSTRACT
We present a methodology to develop coarse-grained lipid models such that electrostatic interactions between the coarse-grained sites can be derived accurately from an all-atom molecular dynamics trajectory and expressed as an effective pairwise electrostatic potential with appropriate screening functions. The reference nonbonded forces from the all-atom trajectory are decomposed into separate electrostatic and van der Waals (vdW) forces, based on the multiscale coarse-graining method. The coarse-grained electrostatic potential is assumed to be a general function of unknown variables and the final site-site interactions are obtained variationally, where the residual of the electrostatic forces from the assumed field is minimized. The resulting electrostatic interactions are fitted to screened electrostatics functions, with a special treatment for distance-dependent dielectrics and screened dipole-dipole interactions. The vdW interactions are derived separately. The resulting charged hybrid coarse-graining method is applied to various solvent-free three-site models of anionic lipid systems.

No MeSH data available.


MSD of DOPC:DOPS bilayersystem with 5000 lipids calculated usingcenter of mass diffusion. The MSD for 1:1 DOPC:DOPS is denoted inblack, and the MSD for 3:1 DOPC:DOPS is shown in red.
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fig6: MSD of DOPC:DOPS bilayersystem with 5000 lipids calculated usingcenter of mass diffusion. The MSD for 1:1 DOPC:DOPS is denoted inblack, and the MSD for 3:1 DOPC:DOPS is shown in red.

Mentions: The two-dimensionalMSD is calculated to estimate the lipid diffusion constant and thusevaluate the fluidity of the bilayer model. As expected, the MSD ofboth CG lipid systems is linear with time (see Figure 6) and indicates the long-time-scale liquid-like behavior inthe lateral plane. The diffusionconstant of lipids in both 1:1 and 3:1 DOPC:DOPS mixture is 2.5 ×10–7 cm2/s. The diffusion constant isan order of magnitude higher than experimental measurements (∼10–8 cm2/s), indicating that the model effectivelysimulates much larger time scales than predicted from AA MD. Suchbehavior is consistent with all CG models, considering that the reduceddegrees of freedom, no friction terms in the dynamics,64 and the softer free-energy profile facilitatefaster dynamics. It seems that the diffusion constant does not dependon the relative ratios of the two lipids, confirming the expectedhigh miscibility of the simulated composition.


Solvent-Free, Highly Coarse-Grained Models for Charged Lipid Systems.

Srivastava A, Voth GA - J Chem Theory Comput (2014)

MSD of DOPC:DOPS bilayersystem with 5000 lipids calculated usingcenter of mass diffusion. The MSD for 1:1 DOPC:DOPS is denoted inblack, and the MSD for 3:1 DOPC:DOPS is shown in red.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4196741&req=5

fig6: MSD of DOPC:DOPS bilayersystem with 5000 lipids calculated usingcenter of mass diffusion. The MSD for 1:1 DOPC:DOPS is denoted inblack, and the MSD for 3:1 DOPC:DOPS is shown in red.
Mentions: The two-dimensionalMSD is calculated to estimate the lipid diffusion constant and thusevaluate the fluidity of the bilayer model. As expected, the MSD ofboth CG lipid systems is linear with time (see Figure 6) and indicates the long-time-scale liquid-like behavior inthe lateral plane. The diffusionconstant of lipids in both 1:1 and 3:1 DOPC:DOPS mixture is 2.5 ×10–7 cm2/s. The diffusion constant isan order of magnitude higher than experimental measurements (∼10–8 cm2/s), indicating that the model effectivelysimulates much larger time scales than predicted from AA MD. Suchbehavior is consistent with all CG models, considering that the reduceddegrees of freedom, no friction terms in the dynamics,64 and the softer free-energy profile facilitatefaster dynamics. It seems that the diffusion constant does not dependon the relative ratios of the two lipids, confirming the expectedhigh miscibility of the simulated composition.

Bottom Line: We present a methodology to develop coarse-grained lipid models such that electrostatic interactions between the coarse-grained sites can be derived accurately from an all-atom molecular dynamics trajectory and expressed as an effective pairwise electrostatic potential with appropriate screening functions.The resulting electrostatic interactions are fitted to screened electrostatics functions, with a special treatment for distance-dependent dielectrics and screened dipole-dipole interactions.The vdW interactions are derived separately.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, The University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States.

ABSTRACT
We present a methodology to develop coarse-grained lipid models such that electrostatic interactions between the coarse-grained sites can be derived accurately from an all-atom molecular dynamics trajectory and expressed as an effective pairwise electrostatic potential with appropriate screening functions. The reference nonbonded forces from the all-atom trajectory are decomposed into separate electrostatic and van der Waals (vdW) forces, based on the multiscale coarse-graining method. The coarse-grained electrostatic potential is assumed to be a general function of unknown variables and the final site-site interactions are obtained variationally, where the residual of the electrostatic forces from the assumed field is minimized. The resulting electrostatic interactions are fitted to screened electrostatics functions, with a special treatment for distance-dependent dielectrics and screened dipole-dipole interactions. The vdW interactions are derived separately. The resulting charged hybrid coarse-graining method is applied to various solvent-free three-site models of anionic lipid systems.

No MeSH data available.