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Modeling dimerizations of transmembrane proteins using Brownian dynamics simulations

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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.

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Acknowledgements

We thank Professor S. H. Northrup for his permission to adapt the MacroDox3.2.2 Program, and for his helpful discussions. We gratefully acknowledge financial support from National Institute Health Grant DC007721 (M.C.), and DC006696 (Marianna Max). The computations were made possible by grants of the National Center for Supercomputing Applications under MCB060020P and MCB070095T (MC).

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Authors and Affiliations

  1. Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York University, Box 1218, New York, NY, 10029, USA

    Meng Cui, Mihaly Mezei & Roman Osman

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  1. Meng Cui
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  2. Mihaly Mezei
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  3. Roman Osman
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Correspondence to Meng Cui or Roman Osman.

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Cui, M., Mezei, M. & Osman, R. Modeling dimerizations of transmembrane proteins using Brownian dynamics simulations. J Comput Aided Mol Des 22, 553–561 (2008). https://doi.org/10.1007/s10822-008-9198-3

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