Bioinformatics Analysis of Evolution of Secondary Structures of Protein Trypsin Beta

Authors(1) :-Mahin Ghorbani

Impact of divergence of amino acid sequences of protein during evolution on the secondary structures of polypeptide and phylogenetic significance of different secondary structures such as alpha helix, beta sheet and random coil in evolution are not known . Due to conservation of conformationally identifiable regions through evolution, in closely related species, the amino acid sequence will show close similarity, thereby giving rise to similar structural motifs after folding the proteins. To understand the most conserved secondary structure element of a protein, we have conducted a bioinformatics work for molecular evolution of protein trypsin beta as a sample in order to analysis the phylogeny of secondary strucutres (alpha helix, beta sheet and random coil) of proteins Trypsin Beta among 25 species. In this method we retrieved amino acid sequences of these proteins from 25 species from protein data bank then folded each individually into 3-D structure using the software J-Pred. From the folded sequence it was possible to identify sequences in regions forming alpha helix, Beta sheet, random coil, which we retrieved and individually ligated end-end to obtain peptides made up of sequence in the random coil, alpha helix and beta sheet conformations ( final functional shape).Then examined the phylogentic trees built after aligning the sequence using four different multiple alignment protocols. The result has assumed that random coil of Trypisn beta was phylogentically most conserved .This project plays significant role in understanding the role of molecular evolution of proteins and their phylogenic significance.

Authors and Affiliations

Mahin Ghorbani
Department of Biotechnology, Fergusson College, F. C. Road, Pune, Maharashtra, India

Bioinformatics, Molecular Evolution, Secondary Structures ,Trypsin Beta, Multiple Sequence Alignment , Phylogeny.

  1. Drenth, J.: Principles of Protein X-Ray Crystallography 2nd ed. (Springer-Verlag,New York, 1999).
  2. Evans, J.N.S.: Biomolecular NMR Spectroscopy (Oxford University Press,Oxford, 1995).
  3. Schmidt, A. and Lamzin, V.S.: Veni, vidi, vici—atomic resolution unravelling the mysteries of protein function. Curr.Opin. Struct. Biol. 2002,12:698–703.
  4. Brooks DJ, Fresco JR, Lesk AM, Singh M.Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code. Mol Biol Evol. 2002 Oct;19(10):1645-55.
  5. Cole C, Barber JD & Barton GJ. Nucleic Acids Res. 2008. 35 (suppl. 2) W197-W201 link]
  6. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J. and Higgins D.G. (2007)ClustalW and ClustalX version 2.Bioinformatics 23(21): 2947-2948
  7. Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res. 2005 Feb;15(2):330-40.
  8. Magis C, Taly JF, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Notredame C. T-Coffee: Tree-based consistency objective function for alignment evaluation. Methods Mol Biol. 2014;1079:117-29. doi: 10.1007/978-1-62703-646-7_7.
  9. Katoh, Standley, MAFFT multiple sequence alignment software version 7: improvements in performance and usability. (Outlines version 7) 2013 (Molecular Biology and Evolution 30:772-780
  10. Felsenstein, J. 1989. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166
  11. Wheeler, T.J. 2009. Large-scale neighbor-joining with NINJA. In S.L. Salzberg and T. Warnow (Eds.), Proceedings of the 9th Workshop on Algorithms in Bioinformatics. WABI 2009, pp. 375-389. Springer, Berlin.
  12. Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei (2001) MEGA2 : Molecular Evolutionary Genetics Analysis. Ver. 2.0, Bioinformatics 17:1244-1245
  13. Poland D. Contribution of secondary structure to the heat capacity and enthalpy distribution of the unfolded state in proteins, Biopolymers. 2002 Jan;63(1):59-65.
  14. Sathyanarayana N. Gummadi.What Is the Role of Thermodynamics on Protein Stability, Biotechnology and Bioprocess Engineering 2003, 8: 9-18
  15. Ghorbani M and Karimi H. Cyclin-Dependent Kinases as valid targets for cancer treatment. Journal of Pharmacy Research 2015,9(6),377-382
  16. Ghorbani M, Karimi H, 'Ion Channels Association with Diseases and their Role as Therapeutic Targets in Drug Discovery', International Journal of Scientific Research in Science and Technology(IJSRST), 1(3):65-69,July-August 2015.
  17. Ghorbani M, Karimi H, 'Role of Aquaporins in Diseases and Drug Discovery', International Journal of Scientific Research in Science and Technology(IJSRST),1(3):60-64, July-August 2015
  18. Mahin Ghorbani, Hamed Karimi, 'Role of G-Protein Coupled Receptors in Cancer Research and Drug Discovery', International Journal of Scientific Research in Science and Technology (IJSRST),1(3), pp.122-126, July-August 2015.
  19. Mahin Ghorbani, Hamed karimi, 'Role of Biomarkers in Cancer Research and Drug Development', International Journal of Scientific Research in Science and Technology(IJSRST),1(3), pp.127-132, July- August 2015
  20. Mahin Ghorbani, Hamed Karimi, 'Bioinformatics Methods for Biochemical Pathways and System Biology Analysis', International Journal of Scientific Research in Science and Technology (IJSRST),1(4),75-79, September-October 2015.

Publication Details

Published in : Volume 2 | Issue 4 | July-August 2016
Date of Publication : 2016-08-30
License:  This work is licensed under a Creative Commons Attribution 4.0 International License.
Page(s) : 112-115
Manuscript Number : IJSRST162419
Publisher : Technoscience Academy

Print ISSN : 2395-6011, Online ISSN : 2395-602X

Cite This Article :

Mahin Ghorbani, " Bioinformatics Analysis of Evolution of Secondary Structures of Protein Trypsin Beta, International Journal of Scientific Research in Science and Technology(IJSRST), Print ISSN : 2395-6011, Online ISSN : 2395-602X, Volume 2, Issue 4, pp.112-115 , July-August-2016. Available at doi : 10.32628/IJSRST162419
Journal URL :

Article Preview

Contact Us