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In Silico Charecterization of Keratitis Causing Herpes Simplex Virus (HSV 1) Membrane Proteins using Computational Tools and Servers

Author Affiliations

  • 1Center for Advanced Computing and Bioinformatics, CRD PRIST University, Thanjavur, Tamilnadu, INDIA
  • 2 Department of Biotechnology, FASC, MITS, Laxmangarh, Rajasthan, INDIA

Res. J. Recent Sci., Volume 1, Issue (11), Pages 27-31, November,2 (2012)

Abstract

Herpes viruses plays important role in the viral keratitis ocular infection almost all the HSV’s carrying the same virion morphology; icosahedral capsids containing the viral genome are surrounded by an amorphous layer of tegument, and this is encased in a lipid bilayer containing about a dozen different viral glycoprotein’s, 3D structure of proteins makes a pathways towards a drug designing and studies of drug interaction, they may have similar in sequences but differently in biological functions specially in case of the diseases. Present study focused on the characterization viral envelope proteins such as P04290, P06477, P04486 which having a great importance in the keratitis disease caused by HSV. Primary structure analysis shows that proteins are having high leucine residues with some cystein residues; Expasy Protparam studies inferred that all are unstable in nature; Secondary structure shows that some are predominate alpha helices with random coils. Transmembrane region prediction by SOSUI server predicted that P04290 and contain only one transmembrane region while P06477 soluble protein. Four transmembrane regions found in P04486 protein all predicted regions were analyzed by the helical plots using EMBOSS pepwheel 6.1, 3D structure identification done by using Swiss Model and structure validation has been done by PROCHECK and WHAT IF, such a modelled structures provides basic knowledge and good functional analysis for experimentally derived structures.

References

  1. Akhtar J. And Shukla D., Viral entry mechanism, cellular and viral mediators of herpes simplex virus entry, FEBS J, 276(24), 7228-7236 (2009)
  2. Connoliy S.A., Jackson J.O., et. al, Fusing structure and function a structural view of herpes machinery, Nat rev Microbiol, 9(5), 369-381 (2011)
  3. Akhtar M.J. et. al, A role hepain sulphate in viral surfing, Biochem Biophys Res Commun, 391(1), 176-81, (2010)
  4. Raquel Naldinho-Souto, Helena Browneand Tony Minson Herpes Simplex Virus Tegument Protein VP16 Is a Component of Primary Enveloped Virions, ncbi.nih.nic.gov.pmc(2009)
  5. Gupta Manish and Sharma Vimukta, Targeted drug delivery system: A Review, Res.J.Chem.Sci, 1(2) (2011)
  6. Donnelly M. and Elliott G., Fluorescent tagging of herpes simplex virus tegument protein VP13/14 in virus infection, J. Virol., 75, 2575-2583 (2001)
  7. Mishra Subhra, Characterization of Protein Interfaces to Infer Protein-Protein Interaction, Res.J.Chem.Sci.,(7),36-40 (2012)
  8. CLC bio., CLC free Workbench. http://www.clcbio.com/index.php?id=28, 27/10/2006 (2006)
  9. Gill S.C. and Von Hippel P.H., Calculation of protein extinction coefficients from amino acids sequences data, Anal. Biochem., 182-319 (1989)
  10. Bachmair A., Finley D. and Varshavsky A., In vivo half-life of aprotein is a function of its amino-terminal residue. Science, 234(4773) 179-186 (1986)
  11. Gonda D.K. and Bachmair A., et.al., Universality and structure of the N-end rule, J.Biol Chem, 264(28), 16700-16712 (1989)
  12. Tobias J.W., Shrader T.E., Rocap G. and Varshavsky A., The N-end rule in bacteria, Science, (254), 1374 (1991)
  13. Ciechanover A., Schwartz A.L., How are substrates recognized by the ubiquitin-mediated proteolytic system?Trends Biochem Sci.,(12), 483–488 (1989)
  14. Guruprasad K., Reddy B.V.B. and Pandit M.W., Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence, Prot. Eng., (4) 155 (1990)
  15. Ikai A., Thermostability and Aliphatic Index of Globular Proteins, J. Biochem., (88), 1895 (1980)
  16. Kyte J. and Doolittle R.F., A simple method for displaying the hydropathic character of a protein, J. Mol. Biol., (157),105 (1982)
  17. Blanchet C., Combet C., Geourjon C. and Deléage G., MPSA: integrated system for multiple protein sequence analysis with client/server capabilities, TIBS, 25(291), 147 (2000)
  18. Eisenhaber F., Imperiale F., Argos P. and Froemmel C., Prediction of Secondary Structural Content of Proteins from Their Amino Acid Composition Alone, Proteins Struct. Funct. Design, 25, 157 (1996)
  19. Takatsugu Hirokawa, Seah Boon-Chieng and Shigeki Mitaku, SOSUI: classification and secondary structure prediction system for membrane proteins, Bioinform. Appl, Note (14), 378 (1998)
  20. Ramachandran G.N. and Sasiskharan V., Conformation of polypeptides and proteins, Adv.Prot. Chem., (23) 283, (1968)
  21. Laskowski R.A., Rullmannn J.A., MacArthur M.W., Kaptein R. and Thornton J.M., AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR, Biomol NMR,, 477-486(1996)