Skip to main content
SpringerLink
Log in

In silico characterization of antifreeze proteins using computational tools and servers

  • Published:
Journal of Chemical Sciences Aims and scope Submit manuscript

Abstract

In this paper, seventeen different fish Antifreeze Proteins (AFPs) retrieved from Swiss-Prot database are analysed and characterized using in silico tools. Primary structure analysis shows that most of the AFPs are hydrophobic in nature due to the high content of non-polar residues. The presence of 11 cysteines in the rainbow smelt fish and sea raven fish AFPs infer that these proteins may form disulphide (SS) bonds, which are regarded as a positive factor for stability. The aliphatic index computed by Ex-Pasy’s ProtParam infers that AFPs may be stable for a wide range of temperature. Secondary structure analysis shows that most of the fish AFPs have predominant α-helical structures and rest of the AFPs have mixed secondary structure. The very high coil structural content of rainbow smelt fish and sea raven fish AFPs are due to the rich content of more flexible glycine and hydrophobic proline amino acids. Proline has a special property of creating kinks in polypetide chains and disrupting ordered secondary structure. SOSUI server predicts one transmembrane region in winter flounder fish and atlantic cod and two transmembrane regions in yellowtail flounder fish AFP. The predicted transmembrane regions were visualized and analysed using helical wheel plots generated by EMBOSS pepwheel tool. The presence of disulphide (SS) bonds in the AFPs Q01758 and P05140 are predicted by CYS_REC tool and also identified from the three-dimensional structure using Rasmol tool. The disulphide bonds identified from the three-dimensional structure using the Rasmol tool might be correct as the evaluation parameters are within the acceptable limits for the modelled 3D structures.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Sivakumar K 2005 Adv. BioTech. IV 27

    Google Scholar 

  2. Sivakumar K, Balaji S and Gangaradhakrishnan BioChemistry: An Indian Journal (in press)

  3. Sivakumar K 2006 Adv. BioTech. IV 18

    Google Scholar 

  4. King-Hwa Ling, Shu-San Loo, Rozita Rosli, Mariana Nor Shamsudin, Rahmah Mohamed and Kiew-Lian Wan 2007 Silico Biol. 7 0011

  5. Chitta Suresh Kumar, Anuradha C M, Venkata Rao K and Venkateswara Swamy K 2005 Int. J. Genomics Proteomics 2 1

    Google Scholar 

  6. Yuri F, Bogdanov, Sergei Y, Dadashev and Tatiana M Grishaeva 2003 Silico Biol. 3 0015

  7. Courtney E Garry and Robert F Garry 2004 Theor. Biol. Med. Model. 1 10

    Article  CAS  Google Scholar 

  8. Rachel E Bell and Nir Ben-Tal 2003 Comp. Funct. Genom. 4 420

    Article  CAS  Google Scholar 

  9. Raymond J A and DeVries A L 1977 Proc. Natl. Acad. Sci. USA 74 2589

    Article  CAS  Google Scholar 

  10. Peter L Davies and Choy L Hew 1990 The FASEB J. 4 2460

    CAS  Google Scholar 

  11. Knight C A, DeVries A L and Oolman L D 1984 Nature (London) 308 295

    Article  CAS  Google Scholar 

  12. Garth L, Fetcher, Sally V Goddard and Yaling Wu 1999 Chemtech. 30 17

    Google Scholar 

  13. Chao H, Davies P L and Carpenter J F 1996 J. Exp. Biol. Sep. 199 2071

    CAS  Google Scholar 

  14. Parody-Morreale A, Murphy K P, Di Cera E, Fall R, DeVries A L and Gill S J 1988 Nature (London) 333 782

    Article  CAS  Google Scholar 

  15. Steffen P, Graether Carolyn M Slupsky Peter L, Davies and Brian D Sykes 2001 Biophys. J. 81 1677

    Article  Google Scholar 

  16. Pranav Dalal and Frank D Sonnichsen 2000 J. Chem. Inf. Comput. Sci. 40 1276

    Article  CAS  Google Scholar 

  17. Li Tong, Qingsong Lin, Raymond Wong. W K, Asma Ali, Daniel Lim, Wing L Sung, Choy L Hew and Danie S C Yang 2000 Protein expression and purification 18 175

    Article  CAS  Google Scholar 

  18. Wilkins S P, Bluma A J, Burkepilea D E, Rutland T J Wierzbicki A, Kelly M and Hamanna M T 2002 CMLS, Cell. Mol. Life Sci. 59 2210

    Article  CAS  Google Scholar 

  19. Boeckmann B, Bairoch A, Apweiler R, Blatter M-C, Estreicher A, Gasteiger E, Martin M J, Michoud K, O’Donovan C, Phan I, Pilbout S and Schneider M 2003 Nucl. Acids Res. 31 365

    Article  CAS  Google Scholar 

  20. CLC bio., 2006. CLC free Workbench. http://www.clcbio.com/index.php?id=28, (27/10/2006)

  21. Gill S C and Von Hippel P H 1989 Anal. Biochem. 182 319

    Article  CAS  Google Scholar 

  22. Bachmair A, Finley D and Varshavsky A 1986 Science 234 179

    Article  CAS  Google Scholar 

  23. Gonda D K, Bachmair A, Wunning I, Tobias J W, Lane W S and Varshavsky A 1989 J. Biol. Chem. 264 16700

  24. Tobias J W, Shrader T E, Rocap G and Varshavsky A 1991 Science 254 1374

    Article  CAS  Google Scholar 

  25. Ciechanover A and Schwartz A L 1989 Trends Biochem. Sci. 14 483

    Article  CAS  Google Scholar 

  26. Guruprasad K, Reddy B V B and Pandit M W 1990 Prot. Eng. 4 155

    Article  CAS  Google Scholar 

  27. Ikai A 1980 J. Biochem. 88 1895

    CAS  Google Scholar 

  28. Kyte J and Doolittle R F 1982 J. Mol. Biol. 157 105

    Article  CAS  Google Scholar 

  29. Combet C, Blanchet C, Geourjon C and Deléage G 2000 TIBS 25 291, 147

    Google Scholar 

  30. Eisenhaber F, Imperiale F, Argos P and Froemmel C 1996 Proteins: Struct. Funct. Design 25 157

    Article  CAS  Google Scholar 

  31. Takatsugu Hirokawa, Seah Boon-Chieng and Shigeki Mitaku 1998 Bioinform. Appl. Note 14 378

    Article  CAS  Google Scholar 

  32. Ramachandran G N and Sasiskharan V 1968 Adv. Prot. Chem. 23 283

    CAS  Google Scholar 

  33. CYS_REC. http://sun1.softberry.com/berry.phtml?topic=cys_rec&group=help & subgroup=propt. (27/10/2006)

  34. Lambert C, Leonard N, De Bolle X and Depiereux E 2002 Bioinformatics 18 1250

    Article  CAS  Google Scholar 

  35. Lovell S C, Davis I W, Arendall III W B, de Bakker P I W, Word J M, Prisant M G, Richardson J S and Richardson D C 2002 Proteins: Structure, Function & Genetics 50 437

    Article  CAS  Google Scholar 

  36. Cristobal S, Zemla A, Fischer D, Rychlewski L and Elofsson A 2001 BMC Bioinformatics 2 5

    Article  CAS  Google Scholar 

  37. Ilya N Shindyalov and Philip E Bourne 2001 Nucl. Acids Res. 29 228

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Chemistry, Sri Chandrasekharendra Saraswathi Viswa Maha Vidyalaya (Deemed University), Enathur, Kanchipuram, 631 561, India

    K. Sivakumar & S. Balaji

  2. EXCEL and Polymer Science Labs, Central Leather Research Institute, Adyar, Chennai, 600 020, India

    Gangaradhakrishnan

Authors
  1. K. Sivakumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. S. Balaji
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gangaradhakrishnan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to K. Sivakumar.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sivakumar, K., Balaji, S. & Gangaradhakrishnan In silico characterization of antifreeze proteins using computational tools and servers. J Chem Sci 119, 571–579 (2007). https://doi.org/10.1007/s12039-007-0072-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12039-007-0072-y

Keywords

Search

Navigation