Paper Citing NAMD - Abstract
Prasad, Nirmal K.; Vindal, Vaibhav; Narayana, Siva Lakshmi; Ramakrishna, V.; Kunal, Swaraj Priyaranjan; Srinivas, M.
In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes
JOURNAL OF MOLECULAR MODELING, 18:2013-2019, MAY 2012
Laccases belong to multicopper oxidases, a widespread class of enzymes implicated in many oxidative functions in various industrial oxidative processes like production of fine chemicals to bioremediation of contaminated soil and water. In order to understand the mechanisms of substrate binding and interaction between substrates and Pycnoporus cinnabarinus laccase, a homology model was generated. The resulted model was further validated and used for docking studies with toxic industrial dyes- acid blue 74, reactive black 5 and reactive blue 19. Interactions of chemical mediators with the laccase was also examined. The docking analysis showed that the active site always cannot accommodate the dye molecules, due to constricted nature of the active site pocket and steric hindrance of the residues whereas mediators are relatively small and can easily be accommodated into the active site pocket, which, thereafter leads to the productive binding. The binding properties of these compounds along with identification of critical active site residues can be used for further site-directed mutagenesis experiments in order to identify their role in activity and substrate specificity, ultimately leading to improved mutants for degradation of these toxic compounds.
