Article

Journal of Computer-Aided Molecular Design

, Volume 22, Issue 8, pp 553-561

Modeling dimerizations of transmembrane proteins using Brownian dynamics simulations

  • Meng CuiAffiliated withDepartment of Structural and Chemical Biology, Mount Sinai School of Medicine, New York University Email author 
  • , Mihaly MezeiAffiliated withDepartment of Structural and Chemical Biology, Mount Sinai School of Medicine, New York University
  • , Roman OsmanAffiliated withDepartment of Structural and Chemical Biology, Mount Sinai School of Medicine, New York University Email author 

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Abstract

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.

Keywords

Molecular modeling Brownian dynamics Molecular recognition Transmembrane protein Dimerization