monodon) ( Table 1) A phylogenetic analysis of the penaeidin fam

monodon) ( Table 1). A phylogenetic analysis of the penaeidin family was performed at the amino acid level using MAFFT version 6 by the Neighbor Joining (NJ) method. The phylogenetic

tree of Fein-Penaeidin showed that the penaeidin family was divided into five groups: Penaeidin of P. monodon is the first group, Penaeidin 2 of L. vannamei, Litopenaeus schmitti, Litopenaeus stylirostris, Farfantepenaeus paulensis is the second group. Penaeidin 3 of L. vannamei, F. paulensis, L. schmitti, L. stylirostris and Fenneropenaeus chinensis is the third group. Penaeidin 4 of L. vannamei and penaeidin 5 of F. chinensis is the fourth group. Penaeidin like antimicrobial peptide in F. indicus reported by Antony et al. [44] is the fifth group where in the present study Fein-Penaeidin found highly homologous with P. monodon penaeidins and originates from the same branches of P. monodon ( Fig.

3). The secondary structure analysis using GOR CX 5461 4 showed that the percentage of coil and helix is maximum in Fein-Penaeidin (Fig. 4a). Among 77 amino acids, 59 amino acids (76.62 %) were found to have random coil structure and about 10 amino acids (12.99 %) were found to have an alpha helix structure. The protein also had extended strands. The final over all model energy was as low as −3037.183 kJ/mol. Quality assessment of the modeled protein was done in SAVS. The stereochemical quality of a protein, stereochemical parameters of the residues and the statistical Z-score deviation of the modeled protein Cell Cycle inhibitor was verified using SAVS version 1. The score given to the modeled protein was greater than 0.2, suggesting that the modeled protein has a refined structure. The overall click here quality factor as shown by the errat option of the SAVS metaserver, was 83.871. The Ramachandran plot provided by the procheck option showed that 91.5% of the amino

acids residues are present in the more favoured region, 8.5% of the amino acid residues are in the additionally allowed region (Fig. 4b). Only 0.5% of the residues were present in the disallowed region. A good quality model would be expected to have over 90% of the amino acid residues in the most favoured region, and during homology modeling 98% of the amino acid residues must be present in the allowed region. This shows that the target protein as a good quality model. The distribution of Fein-Penaeidin mRNA in different tissues was examined and the mRNA expression level of Fein-Penaeidin varied among the samples tested in the haemocytes, heart, hepatopancreas, gills, muscles, intestine and eye of non-challenged shrimp. Total RNA from different tissues of Fein-Penaeidin were extracted, transcribed into cDNAs then used as the template for PCR amplification. Beta-actin served as control. qRT-PCR analysis showed that interestingly Fein-Penaeidin were expressed in all parts of the tissues tested.

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