AG Theoretische Biophysik, Max-Delbrueck-Centrum fuer Molekulare Medizin, Robert-Roessle-Str.10, D-13122 Berlin-Buch, Germany
Membrane proteins serve important biological functions e.g. transport of metabolites and ions, cell recognition and association. An understanding of the structure and dynamics of membrane proteins is an important prerequisite to gain insight into their function.
A computer simulation model of a protein immersed in a membrane has been developed to study protein and membrane dynamics.
In order to keep the study of longtime (nano- microseconds) dynamics feasible a reduced bead representation of the protein and the membrane lipids was used. The membrane was assumed to be planar and particle motion was restricted to the x-y plane.
Lipid and protein interactions are described by a Lennard Jones type potential and no explicit ions or water are included in the simulation. Instead a continuum representation for the membrane environment was chosen. Here, a recently developed approach representing polarization charges by virtual dipoles to approximately solve Poisson's equation was used.
The energy is calculated as a sum of van der Waals interactions and electro- static contributions (real and virtual charges and dipoles). Preliminary results on a helical membrane protein will be presented.
References:
1. H.Sklenar, F.Eisenhaber, M.Poncin, R.Lavery (1991) in: Theoretical
Biochemistry and Molecular Biophysics (D.L.Ceveridge and R.Lavery, Eds.),
Vol.2, pp.317-335, Adenine Press New York
2. M.Baldwin (1993), EMBO Journal Vol. 12 No.4, pp. 1693-1703
3. Donelly (1993), Protein Science, 2, pp. 55-70
4. M.Flower (1995), EMBO Journal Vol.14 No.5, pp. 884-893