Modeling dimerizations of transmembrane proteins using Brownian dynamics simulations.
The dimerizations of membrane proteins, Outer Membrane Phospholipase A (OMPLA) and glycophorin A (GPA), have been simulated by an adapted Brownian Dynamics program. To mimic the membrane protein environment, we introduced a hybrid electrostatic potential map of membrane and water for electrostatic interaction calculations. We added a van der Waals potential term to the force field of the current version of the BD program to simulate the short-range interactions of the two monomers. We reduced the BD sampling space from three dimensions to two dimensions to improve the efficiency of BD simulations for membrane proteins. The OMPLA and GPA dimers predicted by our 2D-BD simulation and structural refinement is in good agreement with the experimental structures. The adapted 2D-BD method could be used for prediction of dimerization of other membrane proteins, such as G protein-coupled receptors, to help better understanding of the structures and functions of membrane proteins.
Cui
Meng
M
Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York University, Box 1218, New York, NY 10029, USA. meng.cui@mssm.edu
Mezei
Mihaly
M
Osman
Roman
R
D000465:Algorithms; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry; D002462:Cell Membrane / Q000737:chemistry; D016000:Cluster Analysis; D003198:Computer Simulation; D030562:Databases, Protein; D004058:Diffusion; D019281:Dimerization; D006021:Glycophorins / Q000737:chemistry; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D054466:Phospholipases A1 / Q000737:chemistry; D055672:Static Electricity; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D001425:Bacterial Outer Membrane Proteins; D006021:Glycophorins; D008565:Membrane Proteins; D014867:Water; D054466:Phospholipases A1; C412876:outer membrane phospholipase A