Poster Presentation 2014 International Biophysics Congress

Molecular dnamics simulation of membrane phase diagram (#692)

Ivan Ortega-Blake 1 , Fernando Favela-Rosales 2 , César Millan-Pacheco 1 , Humberto Saint-Martin 1 , Armando Antillón 1 , Jorge Hernández-Cobos 1 , Mauricio D. Carbajal-Tinoco 2
  1. Instituto de Ciencias Físicas , Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
  2. Departamento de Física, Cinvestav, Mexico DF, Mexico
Molecular Dynamics simulations are a powerful tool for the understanding at the molecular level the mechanisms behind biological processes. In particular the simulations of lipid bilayers are now a current practice, leading to information on the molecular processes of such complex systems. However, as with any other numerical simulation, the need of validation with respect to the phenomenon of interest is required. In this work we looked into the possible reproduction, via MD, of behaviors along the phase diagram of a mixture of POPC and cholesterol (1). We compare the results obtained with different size of membrane patches and different force fields, both, in GROMACS and CHARMM simulations. We found that the force field is determinant in order to reproduce the experimental behavior of lipid diffusion along the phase diagram(2). There is a change of slope on the cholesterol dependence at a given temperature when changing from one phase to another. Only an ab-initio refined potential was able to do this(3). Moreover the radial distribution functions corresponding to the different force fields present quite distinct behavior.
  1. Silva L, Coutinho A, Fedorov A, Prieto M (2006a) Competitive binding of cholesterol and ergosterol to the polyene antibiotic nystatin: a fluorescence study. Biophys J 90:3625–3631
  2. de Almeida, R. F. M., A. Fedorov, and M. Prieto (2003) Sphingomyelin/phosphatidylcholine/cholesterol phase diagram: boundaries and composition of lipid rafts. Biophys J 85:2406–2416.
  3. Joakim P. M. Jämbeck, Alexander P. Lyubartsev, Derivation and Systematic Validation of a Refined All- Atom Force Field for Phosphatidylcholine Lipids, J. Phys. Chem. B, 2012, 116 (10), 3164-3179