Open Access Open Access  Restricted Access Subscription Access

Physicochemical Properties of Insect and Plant Antifreeze Proteins:A Computational Study


Affiliations
1 Centre for Nanotechnology and Advanced Biomaterials, SASTRA University, Thirumalaisamudram, Thanjavur 613 401, India
 

Antifreeze proteins are found in cold-surviving organisms. These proteins have greater structural diversity among same and different species. In this study, a total of 14 antifreeze proteins from both insects and plants were selected randomly and their physicochemical characteristics along with their structural features were analysed using computational tools. The results indicate that plant antifreeze proteins are mostly hydrophilic, which can interact with ice/water effectively. The study shows that the thermal stability of plant antifreeze proteins is greater than insect antifreeze proteins. Among the chosen sequences, insect antifreeze proteins were mostly β-sheet and plant antifreeze proteins were α-helix.

Keywords

Antifreeze Proteins, Disulphide Bonds, Homology Modelling, Hydrophobicity, Thermal Stability.
User
Notifications
Font Size

  • Jia, Z. and Davies, P. L., Antifreeze proteins: an unusual receptor– ligand interaction. Trends Biochem. Sci., 2002, 27, 101–106.
  • Venketesh, S. and Dayananda, C., Properties, potentials, and prospects of antifreeze proteins. Crit. Rev. Biotechnol., 2008, 28, 57–82.
  • Sivakumar, K., Balaji, S. and Gangaradhakrishnan, In silico characterization of antifreeze proteins using computational tools and servers. J. Chem. Sci., 2007, 119, 571–579.
  • Md. Hossain, M., Fish antifreeze proteins: computational analysis and physicochemical characterization. Int. Curr. Pharm. J., 2012, 1, 18–26.
  • Liou, Y. C., Tocilj, A., Davies, P. L. and Jia, Z., Mimicry of ice structure by surface hydroxyls and water of a beta-helix antifreeze protein. Nature, 2000, 406, 322–324.
  • Kristiansen, E., Ramlov, H., Hagen, L., Pedersen, S. A., Andersen, R. A. and Zachariassen, K. E., Isolation and characterization of hemolymph antifreeze proteins from larvae of the longhorn beetle Rhagium inquisitor (L.). Comp. Biochem. Physiol. B Biochem. Mol. Biol., 2005, 142, 90–97.
  • Andorfer, C. A. and Duman, J. G., Isolation and characterization of cDNA clones encoding antifreeze protein of the pyrochorid beetle Dendrodies canadensis. J. Insect Physiol., 2000, 46, 365–372.
  • Tyshenko, M. G., Doucet, D., Davies, P. L. and Walker, V. K., The antifreeze potential of the spruce budworm thermal hysteresis protein. Nat. Biotechnol., 1997, 15, 887–890.
  • Hon, W. C., Griffith, M., Mlynarz, A., Kwok, Y. C. and Yang, D. S. C., Antifreeze proteins in winter rye are similar to pathogenesisrelated proteins. Plant Physiol., 1995, 109, 879–889.
  • Sidebottom, C. et al., Heat-stable antifreeze protein from grass. Nature, 2000, 406, 256–256.
  • Worrall, D. et al., A carrot leucine-rich repeat protein that inhibits ice recrystallization. Science, 1998, 282, 115–117.
  • Davies, P. L. and Sykes, B. D., Antifreeze proteins. Curr. Opin. Struct. Biol., 1997, 7, 828–834.
  • Ewart, K. V., Lin, Q. and Hew, C. L., Structure, function and evolution of antifreeze proteins. Cell Mol. Life. Sci., 1999, 55, 271–283.
  • Ben, R. N., Antifreeze glycoproteins – preventing the growth of ice. Chem. Bio. Chem., 2001, 2, 161–166.
  • Tachibana, Y., Fletcher, G. L., Fujitani, N., Tsuda, S., Monde, K. and Nishimura, S. I., Antifreeze glycoproteins: Elucidation of the structural motifs that is essential for antifreeze activity. Angew. Chem. Int., 2004, 43, 856–862.
  • Duman, J. G., Antifreeze and ice nucleator proteins in terrestrial arthropods. Annu. Rev. Physiol., 2001, 63, 327–357.
  • Hiilovaara-Teijo, M., Hannukkala, A., Griffith, M., Yu, X.-M., and Pihakaski-Maunsbach, K., Snow-mold-induced apoplastic proteins in winter rye leaves lack antifreeze activity. Plant Physiol., 1999, 121, 665–673.
  • Duman, J. G., Purification and characterization of a thermal hysteresis protein from a plant, the bittersweet nightshade Solanum dulcamara. Biochim. Biophys. Acta, 1994, 1206, 129–135.
  • Griffith, M. and Yaish, W. F., Antifreeze proteins in overwintering plants: a tale of two activities. Trends Plant. Sci., 2004, 9, 399–405.
  • Bansal, H., Narang, D. and Jabalia, N., Computational characterization of antifreeze proteins of typhula ishikariensis – gray snow mould. J. Proteins Proteomics, 2014, 5, 169–176.
  • Boeckmann, B. et al., The SWISS-PROT protein knowledgebase and its supplement TrEMBL. Nucleic Acids Res., 2003, 31, 365–370.
  • Gasteiger, E., Protein identification and analysis tools on the ExPASy Server. In The Proteomics Protocols Handbook (ed. Walker, J. M.), Humana Press, 2005, pp. 571–607.
  • Gill, S. C. and Von Hippel, P. H., Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem., 1989, 182, 319–328.
  • Guruprasad, K., Reddy, B. V. P. 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. Protein Eng. Des. Sel., 1990, 4, 155–164.
  • Ikai, A. J., Thermo stability and aliphatic index of globular proteins. J. Biochem., 1980, 88, 1895–1898.
  • Kyte, J. and Doolittle, R. F., A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 1982, 157, 105–132.
  • Geourjon, C. and Deléage, G., SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput. Appl. Biosci., 1995, 11, 681–684.
  • Hirokawa, T., Boon-Chieng, S. and Mitaku, S., SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics, 1998, 14, 378–379.
  • Ferre, F. and Clote, P., DiANNA: a web server for disulfide connectivity prediction. Nucleic Acids Res., 2005, 33 (web server issue), W230–W232.
  • Arnold, K., Bordoli, L., Kopp, J. and Schwede, T., The Swiss– Model workspace: a web-based environment for protein structure homology modelling. Bioinformatics, 2006, 22, 195–201.
  • Haymet, A. D. J., Ward, L. G. and Harding, M. M., Winter Flounder ‘Antifreeze’ proteins: Synthesis and ice growth inhibition of analogues that probe the relative importance of hydrophobic and hydrogen bonding interactions. J. Am. Chem. Soc., 1999, 121, 941–948.
  • Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D. J., Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res., 1997, 25, 3389–3402.
  • Remmert, M., Biegert, A., Hauser, A. and Soding, J., HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods, 2012, 9, 173–175.
  • Lovell, S. C. et al., Structure validation by Cα geometry: φ, ψ and Cβ deviation. Proteins: Struct, Funct, Bioinf., 2003, 50, 437–450.
  • Laskowski, R. A., MacArthur, M. W., Moss, D. S. and Thornton, J. M., PROCHECK – a program to check the stereochemical quality of protein structures. J. Appl. Cryst., 1993, 26, 283–291.
  • Urrutia, M. E., Duman, J. G. and Knight, C. A., Plant thermal hysteresis proteins. Biochim. Biophys. Acta, 1992, 1121, 199–206.

Abstract Views: 191

PDF Views: 74




  • Physicochemical Properties of Insect and Plant Antifreeze Proteins:A Computational Study

Abstract Views: 191  |  PDF Views: 74

Authors

L. Ramya
Centre for Nanotechnology and Advanced Biomaterials, SASTRA University, Thirumalaisamudram, Thanjavur 613 401, India

Abstract


Antifreeze proteins are found in cold-surviving organisms. These proteins have greater structural diversity among same and different species. In this study, a total of 14 antifreeze proteins from both insects and plants were selected randomly and their physicochemical characteristics along with their structural features were analysed using computational tools. The results indicate that plant antifreeze proteins are mostly hydrophilic, which can interact with ice/water effectively. The study shows that the thermal stability of plant antifreeze proteins is greater than insect antifreeze proteins. Among the chosen sequences, insect antifreeze proteins were mostly β-sheet and plant antifreeze proteins were α-helix.

Keywords


Antifreeze Proteins, Disulphide Bonds, Homology Modelling, Hydrophobicity, Thermal Stability.

References





DOI: https://doi.org/10.18520/cs%2Fv112%2Fi07%2F1512-1520