In silico 3-D structure prediction of cytochrome b protein of sisorid catfish Glyptothorax ngapang

Abstract

Samples of cold water catfish Glyptothorax ngapang were collected from Iril River at Serou, Manipur. Full length cytochrome b (cyt b) was amplified with primer pair L14724 and H15915 in 14 samples. PCR products were sequenced using automated ABI 3730 sequencer and submitted to NCBI. The nucleotide sequences were converted to amino acid sequences by defining the reading frame. Before prediction, it was confirmed that no 3-D structure was available for this protein in fish. A comparative modeling method was used for the prediction of the structure of cyt b protein. For the modeling, template protein 1BCC chain C, having identity 88%, E value 6e-175 and alignment score 1571, was obtained by Geno3D server. By comparing the template protein, a rough model was constructed for the target protein using MODELLER, a program for comparative modeling. The structure of cyt b protein of G. ngapang was found to resemble to a high resolution structure of 1BCC chain C of cytochrome bc1 complex from chicken. From Ramachandran plot analysis, it was observed that the percentage of residues falling into the most favoured regions was 93.1%.