Journal of
Bioinformatics and Sequence Analysis

  • Abbreviation: J. Bioinform. Seq. Anal.
  • Language: English
  • ISSN: 2141-2464
  • DOI: 10.5897/JBSA
  • Start Year: 2009
  • Published Articles: 46

Full Length Research Paper

A framework for classification of antifreeze proteins in over wintering plants based on their sequence and structural features

J. Muthukumaran1, P. Manivel1, M. Kannan1, J. Jeyakanthan2 and R. Krishna1*
1Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry – 605 014, India. 2Department of Bioinformatics, Alagappa University, Karaikudi, 630 003, India.
Email: [email protected], [email protected]

  •  Accepted: 11 April 2011
  •  Published: 31 May 2011

Abstract

 

Overwintering plants produce antifreeze proteins (AFPs) which permits the plant survival in cold condition. Analysis of sequence and structural features of these proteins would help in better understanding of their functions. In this study, we report the analysis of 40 plant AFPs on the basis of sequence and structural based classification scheme (CS). Sequence based CS segregates the AFPs into various categories such as physicochemical properties, transmembrane regions, glycosylation sites, and sub cellular localization. Phylogeny based CS separate the chosen proteins into several groups, in which, the AFP from Festuca pratensis,Pinus monticolaRicinus communis and Populus suaveolens are newly identified leucine rich repeat (LRR), pathogenesis related (PR), hemagglutinin related (HR) and pleckstrin homology (PH) family, respectively. The secondary and 3D structures of 27 AFPs were predicted, whereas the remaining 13 protein structures were reported in different studies. Selected proteins are found to have mixed secondary structural elements and the more coil like content were observed in few of the proteins. The proposed classification scheme in over wintering plants can be useful in searching the newly sequenced plant genome for putative AFPs or designing an engineered construct helpful for several industrial and biomedical applications.

 

Key words: Antifreeze protein, ice-structuring protein, ice-binding protein, thermal hysteresis proteins, over wintering plants.