title: Comparative modeling of Rab6 proteins: identification of key residues and their interactions with guanine nucleotides.
abstract: The cytoplasm of a eukaryotic cell consists of a wide variety of membrane bound cell organelles and continuous flow of proteins amongst these organelles is a major challenge and must be stringently maintained in order to continue the correct biochemical functioning inside a cell. The transportation of various proteins amongst these organelles is facilitated by a vast Tubulo-vesicular network mediated by carrier proteins. The Rabs belong to small G proteins super family involved in the regulation and vesicle transport in between the organelles by shuttling between the active GTP and inactive GDP bound states. In this paper we put forth the homology modeling and docking studies of Rab6A proteins (Mus musculus, Gallus gallus and Caenorhabditis elegans) with GTP, GMP-PNP and GDP molecules and a comparative study between these proteins is done to identify key residues out of which serine of the phosphate binding loop (P - loop) and aspartic acid showed prominent interactions with the GTP, GDP and GMP-PNP nucleotides and cogitate that aspartic acid might also help in the stabilization of the switch I region of the Rab proteins besides serine.
authors: Bioinformatics Division, Osmania University, Hyderabad 500007 Andhra Pradesh, India. sandeep2k9@yahoo.com
authors: Sandeep Kumar
authors: SK
authors: Mulukala Narasimha
authors: Shravan Kumar
authors: SK
authors: Gunda
authors: Mahmood
authors: M
authors: Shaik
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001224:Aspartic Acid / Q000737:chemistry*; D017173:Caenorhabditis elegans; D002645:Chickens; D006153:Guanosine Diphosphate / Q000737:chemistry*; D006160:Guanosine Triphosphate / Q000737:chemistry*; D006165:Guanylyl Imidodiphosphate / Q000737:chemistry*; D051379:Mice; D062105:Molecular Docking Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding; D016415:Sequence Alignment; D012694:Serine / Q000737:chemistry*; D040681:Structural Homology, Protein; D020691:rab GTP-Binding Proteins / Q000737:chemistry*
chemical_list: C094135:Rab6 protein; D006153:Guanosine Diphosphate; D001224:Aspartic Acid; D006165:Guanylyl Imidodiphosphate; D012694:Serine; D006160:Guanosine Triphosphate; D020691:rab GTP-Binding Proteins