HOMOLOGY MODELING OF BUFFALO (&lt;i&gt;BUBALUS BUBALIS&lt;/i&gt;) INTERFERON-TAU PROTEIN

Joshi Joshi

doi:10.3844/ajbsp.2012.79.86

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.

Highlights

Interferons (IFN), the glycoproteins belonging to the larger class of cytokines, are released in response to the invading microbial pathogens or tumor cells to exercise anti-luteolytic, antiviral and anti-proliferative effects (Cooke et al, 2009)
BLASTP search was performed against Protein Data Bank (PDB) with default parameters to find suitable templates for homology modeling
Based on the maximum identity with high score and lower e-value 1B5L was used as the template for homology modeling

Summary

Introduction

Interferons (IFN), the glycoproteins belonging to the larger class of cytokines, are released in response to the invading microbial pathogens or tumor cells to exercise anti-luteolytic, antiviral and anti-proliferative effects (Cooke et al, 2009). Interferon-tau (IFNt) constitutes a novel type-I of interferon, which is not virus-inducible, unlike IFN-alpha and IFN-beta. The successful establishment of pregnancy is a result of the protection of the conceptus by the maternal recognition of the fetus, mediated via interferon-tau. It displays high antiviral and anti-proliferative activities across ruminants with a prominent lack of cytotoxicity. It inhibits the endometrial oxytocin receptors in order to mute the pulsatile release of prostaglandin-F2-alpha that induces luteolysis and increases protein synthesis in uterine glands to promote implantation of embryo. The effect of IFNt on Corresponding Author: Dinesh Kumar, Centre for Agricultural Bioinformatics (CABIN), Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi-110012, India Tel: +91-9416111753 Fax: +91-11 25841564

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Results

Conclusion