Journal of Molecular Modeling

, Volume 19, Issue 4, pp 1891–1900 | Cite as

Comparative modeling of Rab6 proteins: identification of key residues and their interactions with guanine nucleotides

  • Sandeep Kumar Mulukala Narasimha
  • Shravan Kumar Gunda
  • Mahmood Shaik
Original Paper
First Online:
Received:
Accepted:

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.

Keywords

GDP GMP-PNP GTP FlexX Modeller9.10 Rab6 Sybyl Vesicle trafficking 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Sandeep Kumar Mulukala Narasimha
    • 1
  • Shravan Kumar Gunda
    • 1
  • Mahmood Shaik
    • 1
  1. 1.Bioinformatics DivisionOsmania UniversityHyderabadIndia

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