In silico analysis of novel peptides from the drosophila melanogaster non-coding DNA

Master of Science in Computational Science 2013-2015 EXT T.K Manoj Kumar Pawan K Dhar ( Director ) " Centre for Systems and Synthetic Biology, University of Kerala, Thiruvananthapuram "

Noncoding DNA, the DNA that do not encode protein sequences. All organisms have noncoding DNA, but the amount is greatly varies among species. However the functions and stability of ncDNA are yet to be discovered. To study about the functions, stability and therapeutic values of noncoding DNA, 62 intergenic sequences of Drosophila melanogaster were selected. The selected intergenic sequences were refined by removing similar sequences after doing a similarity search against all known protein sequences. Thus we got completely novel intergenic sequences which were then converted into peptide sequences and these resultant sequences are considered for further study. The structures of the novel protein were predicted using ab initio method. We tried to predict the functions of peptides in two methods. In the first method, the functions of peptides were predicted according to the nature of domains present in them. In the second method, comparing the structure of novel peptides with the PDB structures. From the structure comparison results, a peptide ID_26 which is highly similar with PDB structure Gp41, a viral trans-membrane protein. Enfuvirtide (also known as T-20) is a fusion inhibitor drug that binds to Gp41 and prevent HIV-1 entry. Interaction based studies were done in order to check if our peptide possess similar function also as of Gp41. The stability of novel peptides were determined by calculating the interatomic interactions in the 3D structure. We hope that the predicted therapeutic values of novel peptides could generate information for designing the peptide drugs.