Research Article Open Access

Homology Modeling of Buffalo (Bubalus bubalis) Interferon-Tau Protein

Indu Joshi1, Sunil Kumar2, Arminder Kaur3, C.S. Mukhopadhyay4 and Dinesh Kumar5
  • 1 Maharishi Markandeshwar Engineering College, India
  • 2 Institute of Life Sciences, India
  • 3 NC College of Engineering Israna, India
  • 4 Guru Angad Dev Veterinary and Animal Sciences University, India
  • 5 Indian Agricultural Statistics Research Institute, India

Abstract

Interferon-Tau (IFNt) contributes towards maternal recognition of pregnancy in ruminants (like, cattle, buffalo, goat, giraffe). IFNt has been extensively studied in most of the ruminants except for buffalo Bubalus bubalis). The present study has been undertaken to predict the secondary structure of Interferon-tau in buffalo. The available amino acid sequence of bubaline IFNt (sequence database of SwissProt) was subjected to protein-BLAST to find similar sequences with high scores and low e-values. The ovine IFNt sequence (PDB code: 1B5L) was selected for further computational analysis of the bubaline IFNt sequence to predict the secondary and tertiary structure. The secondary structure of the modeled bubaline IFNt was predicted using STRIDE. The 3D structure was generated using academic version of MODELER9v6. The probability density functions (pdf) were used to restrain Cα-Cα distances, main chain N-O distances as well as main-chain and side-chain dihedral angles. The energy minimization and van der waal contacts were taken care of using ACCELRYS DS Modeling 2.0. The residue profiles of the obtained three-dimensional models were checked by VERIFY3D. The energetic architecture and the correctness of the generated model revealed that the predicted secondary model was correct and acceptable. The predicted structure of the bubaline IFNt constructed through homology modeling from ovine IFNt, could be used for further profiling the species specific difference in IFNt activity.

Current Research in Bioinformatics
Volume 2 No. 1, 2013, 8-14

DOI: https://doi.org/10.3844/ajbsp.2013.8.14

Submitted On: 1 November 2012 Published On: 2 January 2018

How to Cite: Joshi, I., Kumar, S., Kaur, A., Mukhopadhyay, C. & Kumar, D. (2013). Homology Modeling of Buffalo (Bubalus bubalis) Interferon-Tau Protein. Current Research in Bioinformatics, 2(1), 8-14. https://doi.org/10.3844/ajbsp.2013.8.14

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Keywords

  • Interferon-tau
  • Buffalo
  • Homology Modeling
  • Bioinformatics