Journal Article

Deciphering the ATP-binding mechanism(s) in NLRP-NACHT 3D models using structural bioinformatics approaches

De, Sachinandan, Maharana, Jitendra, Panda, Debashis

2018

Overview

Nucleotide-binding and oligomerization domain (NOD)-like receptors (NLRs), the first line of defense, are the cytosolic pattern recognition receptors (PRRs) that regulate the inflammatory activity in response to invading pathogens. NLRs are the members of AAA+ ATPase superfamily that comprises of N-terminal EBD(s), a centrally positioned NOD/NACHT and varying range of LRRs towards the C-terminal end. Due to the lack of structural data, the functional aspects of NLRP-signaling mechanism, which includes pathogen recognition, nucleotide-binding, and sensor-adaptor-effector interactions, are not fully understood. In this study, we implemented structural bioinformatics approaches including protein modeling, docking, and molecular dynamics simulations to explore the structural-dynamic features of ADP-/ATP-Mg2+ binding in NLRPNACHT models. Our results indicate a similar mode of ATP-Mg2+ binding in all NLRPNACHT models and the interacting residues are found consistent with reported mutagenesis data. Accompanied by the key amino acids (proposed to be crucial for ATP-Mg2+ coordination), we further have noticed that some additional conserved residues (including 'Trp' of the PhhCW motif, and 'Phe' and 'Tyr' of the GFxxxxRxxYF motif) are potentially interacting with ATP during dynamics; which require further experimentation for legitimacy. Overall, this study will help in understanding the ADP-/ATP-Mg2+ binding mechanisms in NLRPs in a broader perspective and the proposed ATP-binding pocket will aid in designing novel inhibitors for the regulation of inflammasome activity.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Adenosine diphosphate / Adenosine triphosphatase / Adenosine triphosphate / Adenosine Triphosphate - metabolism / Agricultural biotechnology / Amino Acid Sequence - genetics / Amino acids / Apoptosis / ATP / ATP (Adenosine triphosphate) / Binding / Binding sites / Bioinformatics / Biology and Life Sciences / Computational biology / Computational Biology - methods / Computer simulation / Defense mechanisms / Diabetes / Dynamic structural analysis / Experimentation / Immunity, Innate / Inflammasomes / Inflammasomes - immunology / Inflammasomes - metabolism / Inflammation / Kinases / Magnesium / Medicine and Health Sciences / Molecular docking / Molecular Docking Simulation / Molecular dynamics / Molecular Dynamics Simulation / Mutagenesis / Mutation / Oligomerization / Pathogens / Pattern recognition / Pattern recognition receptors / Physical Sciences / Protein Binding - immunology / Protein Domains - genetics / Protein Domains - immunology / Proteins / Receptors / Receptors, Pattern Recognition - metabolism / Research and Analysis Methods / Residues / Sequence Alignment / Signal transduction / Signal Transduction - immunology / Structure-function relationships / Three dimensional models / Zebrafish