Carbonic anhydrase binding site parameterization in OPLS-AA force field.

Guillaume Bernadat, Claudiu T Supuran, Bogdan I Iorga

Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Labex LERMIT, Centre de Recherche de Gif, 1 Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France.

Bioorganic & medicinal chemistry 2013 Mar 15

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The parameterization of carbonic anhydrase binding site in OPLS-AA force field was performed using quantum chemistry calculations. Both OH2 and OH(-) forms of the binding site were considered, showing important differences in terms of atomic partial charges. Three different parameterization protocols were used, and the results obtained highlighted the importance of including an extended binding site in the charge calculation. The force field parameters were subsequently validated using standard molecular dynamics simulations. The results presented in this work should greatly facilitate the use of molecular dynamics simulations for studying the carbonic anhydrase, and more generally, the metallo-enzymes. Copyright © 2012 Elsevier Ltd. All rights reserved.

Citation

Guillaume Bernadat, Claudiu T Supuran, Bogdan I Iorga. Carbonic anhydrase binding site parameterization in OPLS-AA force field. Bioorganic & medicinal chemistry. 2013 Mar 15;21(6):1427-30