Paper Citing NAMD - Abstract
Librando, Vito; Pappalardo, Matteo
Computational study on the interaction of a ring-hydroxylating dioxygenase from Sphingomonas CHY-1 with PAHs
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:915-919, JUN 2011
The massive computational resources available in the framework of a grid paradigm approach represent an emerging tool in the bioinformatics field. In this paper, we used the above approach in the rapid determination of the interactions between the ring-hydroxylating dioxygenase, comprised six enzymatic subunits, and polycyclic aromatic hydrocarbons (PAHs) in their optimal positions. The results were obtained by simulating enzyme dynamics at 300K through molecular dynamics calculations. For the first time, the equilibrated structure of the dioxygenase revealed a network of channels throughout the enzyme that were sufficiently large to allow a flow of small ions or molecules from the inner core of the complex to its exterior surface. The ring-hydroxylating dioxygenase was able to interact with some of the studied PAHs. Additionally, not only the number of aromatic rings but also the PAH shape were critical in predicting the ability of the dioxygenase to interact with these types of molecules. Docking calculations shed light on a new possible binding site that is far from the enzymatic one, which is potentially interesting in considering the stability of the enzyme itself. (C) 2011 Elsevier Inc. All rights reserved.
