Predicting functions of cytochrome c oxidase subunit 1 from Spinycheek crayfish using computational methods

Author Affiliations

  • 1University of Rwanda, College of Science and Technology, Department of Biology, Avenue de l’Armée, Po. Box 3900, Kigali-Rwanda
  • 2University of Rwanda, College of Science and Technology, Department of Biology, Avenue de l’Armée, Po. Box 3900, Kigali-Rwanda
  • 3University of Rwanda, College of Science and Technology, Department of Biology, Avenue de l’Armée, Po. Box 3900, Kigali-Rwanda

Int. Res. J. Biological Sci., Volume 6, Issue (1), Pages 6-14, January,10 (2017)

Abstract

Understanding the cell functioning at molecular level is the goal of most of molecular biology researchers. Molecular biology involves macromolecules which are block of life, on research scene. Among others, proteins have a big range of functions and can only be clear if their structures are available. Assigning functions to all known sequences that are being generated in the public domain by different genomic projects, constitutes a big challenge. It is for that very reason the functions of cytochrome c oxidase subunit 1 from Spinycheek crayfish (Uniprot id: G3GHF6) were predicted using computational methods. Local sequence alignment was conducted to retrieve potential structural homologs having structures determined using experimental methods. Multiple sequence alignment has shown conserved motifs which could be of biological interest. Prediction of three-dimensional structure of cytochrome c oxidase subunit 1 through homology modeling followed by structure assessment and validation using ERRAT and PROCHECK, suggested the predicted model was of acceptable quality. Docking studies using HEX software demonstrated that this protein has affinity with heme ligand with eleven residues involved in these interactions. These interactions are similar to those observed when the heme ligand was docked onto the x-ray structure of the protein used as template for homology modeling exercise. This research shades lights on the function of cytochrome c oxidase subunit 1from Spinycheek crayfish.

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