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Theoretical approach to the innovative mutation of naphthalene 1,2-dioxygenase: a molecular dynamics and docking study

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Abstract

Polycyclic aromatic hydrocarbons are a family of ubiquitous pollutants whose environmental behavior has been widely studied. Different bacterial species are able to decompose hydrocarbons by using them as a food source. One of the best-studied enzymes is naphthalene 1,2-dioxygenase (NDO). A practical way to optimize the degradation process is by mutating the protein involved, increasing both the degradation capacity of the enzyme and its ability to work under extreme environmental conditions of high temperature and low pH. Herein, we describe the study of NDO using molecular dynamics and docking calculations to discover new mutants with high degrading capabilities. We modeled eleven new mutants of NDO. The results indicate that increasing the size of the active site cavity in the mutants allowed for the insertion of high molecular weight PAHs. Additionally, the physicochemical properties of the NDO active sites make the sites well suited to interactions with PAHs, so most amino-acid modifications should not result in significantly altered behavior of NDO.

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Acknowledgments

This work was funded by the Italian Ministry of Education, University and Research (MIUR), PRIN 2009, and the COMETA Consortium.

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Authors and Affiliations

  1. Dipaparrtimento di Scienze Chimiche, Università di Catania, Viale A. Doria 6, 95125, Catania, Italy

    Vito Librando & Matteo Pappalardo

  2. Research Center for Analysis, Monitoring and Minimization Methods of Environmental Risk, Chemical Science Building, Viale A. Doria 6, 95125, Catania, Italy

    Vito Librando & Matteo Pappalardo

Authors
  1. Vito Librando
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  2. Matteo Pappalardo
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Correspondence to Vito Librando.

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Librando, V., Pappalardo, M. Theoretical approach to the innovative mutation of naphthalene 1,2-dioxygenase: a molecular dynamics and docking study. J Mol Model 20, 2354 (2014). https://doi.org/10.1007/s00894-014-2354-x

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