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Molecular dynamics study of human carbonic anhydrase II in complex with Zn2+ and acetazolamide on the basis of all-atom force field simulations.
- Source :
-
Biophysical Chemistry . Jul2016, Vol. 214, p54-60. 7p. - Publication Year :
- 2016
-
Abstract
- Human carbonic anhydrase II (hCAII) represents an ultimate example of the perfectly efficient metalloenzymes, which is capable of catalyzing the hydration of carbon dioxide with a rate approaching the diffusion controlled limit. Extensive experimental studies of this physiologically important metalloprotein have been done to elucidate the fundamentals of its enzymatic actions: what residues anchor the Zn 2+ (or another divalent cation) at the bottom of the binding pocket; how the relevant residues work concertedly with the divalent cation in the reversible conversions between CO 2 and HCO 3 – ; what are the protonation states of the relevant residues and acetazolamide, an inhibitor complexed with hCAII, etc. In this article, we present a detailed computational study on the basis of the all-atom CHARMM force field where Zn 2+ is represented with a simple model of divalent cation using the transferrable parameters available from the current literature. We compute the hydration free energy of Zn 2+ , the characteristics of hCAII-Zn 2+ complexation, and the absolute free energy of binding acetazolamide to the hCAII-Zn 2+ complex. In each of these three problems, our computed results agree with the experimental data within the known margin of error without making any case-by-case adjustments to the parameters. The quantitatively accurate insights we gain in this all-atom molecular dynamics study should be helpful in the search and design of more specific inhibitors of this and other carbonic anhydrases. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 03014622
- Volume :
- 214
- Database :
- Academic Search Index
- Journal :
- Biophysical Chemistry
- Publication Type :
- Academic Journal
- Accession number :
- 115884301
- Full Text :
- https://doi.org/10.1016/j.bpc.2016.05.006