title: Insight into structural organization and protein-protein interaction of non structural 3 (NS3) proteins from dengue serotypes.
abstract: Dengue infections produce a distinct character of virus-induced intracellular membrane alterations which are associated with the viral replication machinery. Currently, the NS3 protein is being targeted for antiviral therapy against dengue. NS3 protein of dengue virus interacts with nuclear receptor binding protein (NRBP) of human causing cell trafficking between the Endoplasmic Reticulum (ER) and Golgi, which interacts with Rac3, a member of the Rho-GTPase family. No crystal structure of the NRBP is available for any species, thus limiting the complete understanding of structure- function relationships of this protein. The present study deals with the molecular modeling of the viral protein (NS3 of DENV1-4), the host protein (NRBP) and their interactions through protein-protein docking study. Theoretical threedimensional structures of the NRBP and NS3 were modeled using the Modeller 9v8, and the evaluated models were docked using GRAMM-X to study the mode of protein-protein interaction (NRBP as receptor and NS3 as ligand). The docked docking complexes were further evaluated for interaction analysis by the RosettaDock Server. Suface and interface residues were observed along with hydrogen and hydrophobic interaction. The conserved residues forming hydrogen interaction of NRBP with DENV1-4 serotypes were found to be GLN 305, SER 363 and GLN 379.
authors.forename: Pratap
authors.initials: P
authors.lastname: Parida
authors.forename: R N S
authors.initials: RN
authors.lastname: Yadav
authors.affiliation: Centre for Studies in Biotechnology, Dibrugarh University, Assam-786004, India. pratapparida2007yahoo.com@gmail.com.
authors.forename: Kishore
authors.initials: K
authors.lastname: Sarma
mesh_terms: D000595:Amino Acid Sequence; D003716:Dengue Virus / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D025941:Protein Interaction Mapping; D017433:Protein Structure, Secondary; D020365:RNA Helicases / Q000737:chemistry; D018160:Receptors, Cytoplasmic and Nuclear / Q000737:chemistry*; D016415:Sequence Alignment; D012697:Serine Endopeptidases / Q000737:chemistry; D065288:Serogroup; D033921:Vesicular Transport Proteins / Q000737:chemistry*; D017361:Viral Nonstructural Proteins / Q000737:chemistry*; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D020365:RNA Helicases; D018160:Receptors, Cytoplasmic and Nuclear; D012697:Serine Endopeptidases; D033921:Vesicular Transport Proteins; D017361:Viral Nonstructural Proteins; C410809:NRBP1 protein, human; C060028:NS3 protein, flavivirus; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases