BIOCOMPUTATIONAL ANALYSIS AND CHARACTERIZATION OF SOME ANTIFREEZE PROTEINS
| Autor: | Subramanian Balaji, Krishnamoorthy Sivakumar, Ganga Radhakrishnan |
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| Rok vydání: | 2007 |
| Předmět: | |
| Zdroj: | Journal of Theoretical and Computational Chemistry. :127-140 |
| ISSN: | 1793-6888 0219-6336 |
| Popis: | Novel bioinformatic procedures and computational methods have been used to analyze, characterize and provide more detailed description of some selected fish antifreeze proteins (AFPs) retrieved from Swiss–Prot database. Analysis shows that AFPs are rich in non-polar residues and that the AFPs Q01758 and P05140 contain SS bonds. The aliphatic index computed by ExPasy's ProtParam infers that AFPs may be stable for a wide range of temperatures and the AFP P80961 is classified as an unstable protein. The very low GRAVY index of AFP P80961 infers its higher hydrosolubility. Secondary structure analysis shows that the flounder and sculpin fish AFPs are found to be of predominant ∝–helical structures and the rest of them are with mixed secondary structures. The average molecular weight of AFPs computed is 9584 Da. SOSUI server predicts one transmembrane region in P04002 (winter flounder fish) and two regions in P09031 (yellowtail flounder fish). The predicted transmembrane regions were visualized and analyzed using helical wheel plots generated by EMBOSS pepwheel tool. The residues A, L, G and N are identified as the antigenic sites by EMBOSS antigenic program. The presence of 11 Cys residues in AFPs Q01758 (rainbow smelt fish) and P05140 (sea raven fish) indicates the presence of disulfide bridges (SS bonds) in these AFPs, and it is also recognized by CYS_REC tool and well documented from the three dimensional structure using Rasmol tool. |
| Databáze: | OpenAIRE |
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