Homology Modeling of Buffalo (Bubalus bubalis) Interferon-Tau Protein
Indu Joshi, Sunil Kumar, Arminder Kaur, C. S. Mukhopadhyay and Dinesh Kumar
DOI : 10.3844/ajbsp.2012.79.86
Current Research in Bioinformatics
Volume 1, Issue 2
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) was 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, can be used for functional characterization of bubaline IFNt.
© 2012 Indu Joshi, Sunil Kumar, Arminder Kaur, C. S. Mukhopadhyay and Dinesh Kumar. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.