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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

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Title 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
Not Available
 
Creator Maharana J.
Sahoo B.R.
Bej A.
Jena I.
Parida A.
Sahoo J.R.
Dehury B.
Patra M.C.
Martha S.R.
Balabantray S.
Pradhan S.K.
Behera B.K.
 
Subject Models of Zebrafish
Molecular Dynamics Simulations
ATP Binding Orientations
 
Description Not Available
Nucleotide-binding oligomerization domain-containing protein 1 (NOD1) and NOD2 are cytosolic pattern recognition receptors playing pivotal roles in innate immune signaling. NOD1 and NOD2 recognize bacterial peptidoglycan derivatives iE-DAP and MDP, respectively and undergoes conformational alternation and ATP-dependent self-oligomerization of NACHT domain followed by downstream signaling. Lack of structural adequacy of NACHT 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 organism zebrafish (Danio rerio) using computational methods. Our study highlighted the differential ATP binding modes in NOD1 and NOD2. In NOD1, γ-phosphate of ATP faced toward the central nucleotide binding cavity like NLRC4, whereas in NOD2 the cavity was occupied by adenine moiety. The conserved ‘Lysine’ at Walker A formed hydrogen bonds (H-bonds) and Aspartic acid (Walker B) formed electrostatic interaction with ATP. At Sensor 1, Arg328 of NOD1 exhibited an H-bond with ATP, whereas corresponding Arg404 of NOD2 did not. ‘Proline’ of GxP motif (Pro386 of NOD1 and Pro464 of NOD2) interacted with adenine moiety and His511 at Sensor 2 of NOD1 interacted with γ-phosphate group of ATP. In contrast, His579 of NOD2 interacted with the adenine moiety having a relatively inverted orientation. Our findings are well supplemented with the molecular interaction of ATP with NLRC4, and consistent with mutagenesis data reported for human, which indicates evolutionary shared NOD signaling mechanism. Together, this study provides novel insights into ATP binding mechanism, and highlights the differential ATP binding modes in zebrafish NOD1 and NOD2.
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Date 2019-08-30T11:51:18Z
2019-08-30T11:51:18Z
2015-03-26
 
Type Research Paper
 
Identifier Maharana J., Sahoo B.R., Bej A., Jena I., Parida A., Sahoo J.R., Dehury B., Patra M.C., Martha S.R., Balabantray S., Pradhan S.K., Behera B.K. 2015. 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. Plos One. DOI:10.1371/journal.pone.0121415.
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http://krishi.icar.gov.in/jspui/handle/123456789/22774
 
Language English
 
Relation Not Available;
 
Publisher Not Available