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Molecular modeling and phylogenetic analysis of Esx homeobox-1 protein of Bubalus bubalis

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Abstract

ESX-1 is an X-linked gene, which encodes for a homeobox protein. The ESX-1 expressed specifically in extra-embryonic tissues during development and in the adult testis as well. In the present study, we have predicted the three-dimensional structure of ESX-1 homeobox protein of Bubalus bubalis using homology modeling. The predicted model further explored for identification of ligand binding sites, which may be useful for understanding specific role in functional site residues during catalysis. This study also demonstrated the phylogenetic analysis of ESX-1 homeobox protein of B. bubalis with different similar species. The ESX-1 homeobox protein of B. bubalis has shown similarity with Bos taurus, Ovis aries and Capra hircus species.

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References

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nuclei Acids Res 25:3389–3402

    Article  Google Scholar 

  • Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22:195–201

    Article  Google Scholar 

  • Bellve AR, Cavicchia JC, Millette CF, O’Brien DA, Bhatnagar YM, Dym M (1977) Spermatogenesis cells of the prepuberal mouse: isolation and morphological characterization. J Cell Biol 74:64–85

    Article  Google Scholar 

  • Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242

  • Eddy EM (2002) Male germ cell gene expression. Recent Prog Horm Res 57:103–128

    Article  Google Scholar 

  • Eisenberg D, Schwarz E, Komaromy M, Wall R (1984) Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol 179(1):125–142

    Article  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nuclei Acids Symp Ser 41:95–98

    Google Scholar 

  • Heinig M, Frishman M (2004) STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res 32:500–502

    Article  Google Scholar 

  • Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89:10915–10919

    Article  Google Scholar 

  • Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105

    Article  Google Scholar 

  • Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291

    Article  Google Scholar 

  • Laskowski RA, Watson JD, Thornton JM (2005) ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 33:89–93

    Article  Google Scholar 

  • Li Y, Behringer RR (1998) Esx1 is an X-chromosome-imprinted regulator of placental development and fetal growth. Nat Genet 20:309–311

    Article  Google Scholar 

  • Li Y, Lemaire P, Behringer RR (1997) Esx1, a novel X chromosome-linked homeobox gene expressed in mouse extra-embryonic tissues and male germ cells. Dev Biol 188:85–95

    Article  Google Scholar 

  • Lia Y, Lemaireb P, Behringera RR (1997) Esx1, a novel X chromosome-linked homeobox gene expressed in mouse extraembryonic tissues and male germ cells. Dev Biol 188(1):85–95

    Article  Google Scholar 

  • Lüthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356:83–85

    Article  Google Scholar 

  • Martí-Renom MA, Stuart AC, Fiser A, Sánchez R, Melo F, Sali A (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29:291–325

    Article  Google Scholar 

  • Nakamuta N, Kobayashi S (2004) Developmental expression of p63 in the mouse testis. J Vet Med Sci 66:681–687

    Article  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    Google Scholar 

  • Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779–815

    Article  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673–4680

    Article  Google Scholar 

  • Vijay N, Harikrishna P, Bhure SK (2011) Characterization of buffalo Esx-1 gene: an X-linked homeobox protein (Submitted)

  • Wang H, San Agustin Jj, Witman GB, Kilpartrick DL (2004) Novel role for a sterol response element binding protein in directing spermatogenesis cell-specific gene expression. Mol Cell Boil 24:10681–10688

    Article  Google Scholar 

  • Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35:407–410

    Article  Google Scholar 

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Acknowledgments

We appreciate reviewers valuable suggestions and comments.

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Authors and Affiliations

  1. Center of Bioinformatics, University of Allahabad, Allahabad, India

    Pooja Tripathi & Vijay Tripathi

  2. Department of Biochemistry, Indian Veterinary Research Institute, Bareilly, India

    Brijesh Singh Yadav

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  1. Pooja Tripathi
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  2. Brijesh Singh Yadav
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  3. Vijay Tripathi
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Correspondence to Vijay Tripathi.

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Tripathi, P., Yadav, B.S. & Tripathi, V. Molecular modeling and phylogenetic analysis of Esx homeobox-1 protein of Bubalus bubalis . Netw Model Anal Health Inform Bioinforma 3, 57 (2014). https://doi.org/10.1007/s13721-014-0057-y

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  • DOI: https://doi.org/10.1007/s13721-014-0057-y

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