RESEARCH ARTICLE Structural Models of Zebrafish (Danio rerio) NOD1 and NOD2 NACHT Domains Suggest Differential ATP Binding Orientations: Insights from Computational Modeling, Docking and Molecular Dynamics Simulations Jitendra Maharana1,2*, Bikash Ranjan Sahoo1, Aritra Bej1, Itishree Jena1☯, Arunima Parida1☯, Jyoti Ranjan Sahoo1, Budheswar Dehury3, Mahesh Chandra Patra1, Sushma Rani Martha1, Sucharita Balabantray1, Sukanta Kumar Pradhan1, Bijay Kumar Behera2* 1 Department of Bioinformatics, Orissa University of Agriculture and Technology,Bhubaneswar, Odisha, India, 2 Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India, 3 Biomedical Informatics Centre, Regional Medical Research Institute (ICMR), Bhubaneswar, Odisha, India OPEN ACCESS ☯ These authors contributed equally to this work. Citation: Maharana J, Sahoo BR, Bej A, Jena I, *
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[email protected] (BKB) Parida A, Sahoo JR, et al. (2015) Structural Models of Zebrafish (Danio rerio) NOD1 and NOD2 NACHT Domains Suggest Differential ATP Binding Orientations: Insights from Computational Modeling, Abstract Docking and Molecular Dynamics Simulations. PLoS ONE 10(3): e0121415. doi:10.1371/journal. Nucleotide-binding oligomerization domain-containing protein 1 (NOD1) and NOD2 are cy- pone.0121415 tosolic pattern recognition receptors playing pivotal roles in innate immune signaling. NOD1 Academic Editor: Ivo G. Boneca, Institut Pasteur and NOD2 recognize bacterial peptidoglycan derivatives iE-DAP and MDP, respectively Paris, FRANCE and undergoes conformational alternation and ATP-dependent self-oligomerization of Received: September 23, 2014 NACHT domain followed by downstream signaling. Lack of structural adequacy of NACHT Accepted: February 1, 2015 domain confines our understanding about the NOD-mediated signaling mechanism. Here, we predicted the structure of NACHT domain of both NOD1 and NOD2 from model organ- Published: March 26, 2015 ism zebrafish (Danio rerio) using computational methods.