Biophysical Society Thematic Meeting - October 25-30, 2015

Polymers and Self Assembly: From Biology to Nanomaterials Poster Session II

31-POS Board 31 Prediction of Cleavage Specificity in Proteases by Biased Sequence Search Threading Gonca Ozdemir Isik, Nevra Ozer . Marmara University, Istanbul, Turkey. The assessment of substrate specificity in proteases is crucial in drug development studies, where interpreting the adaptability of residue positions can be useful in understanding how inhibitors might best fit within the substrate binding sites. In this work, the substrate variability and substrate specificity of the Hepatitis C virus (HCV) NS3/4A serine protease and the Adenovirus 2 (AdV2) cysteine protease was investigated by the computational biased sequence search threading (BSST) methodology. Using available crystal structures, the template structures for the substrate-bound proteases were created in silico by performing various peptide building and docking procedures followed by energy minimization and molecular dynamics simulations. BSST was performed starting with known binding, nonbinding and random peptide sequences that were threaded onto the template complex structures, and low energy sequences were searched using low-resolution knowledge-based potentials. Then, target sequences of yet unidentified potential substrates were predicted by statistical probability approaches applied on the low energy sequences. The results show that the majority of the predicted substrate positions correspond to the natural substrate sequences with conserved amino acid preferences. For NS3/4A serine protease cleavage, significant selection for Pro at P2 and Cys at P1 positions is observed, where these positions are correlated with increased cleavage efficiency hence are probably less tolerant to change. For AdV2 cysteine protease, BSST produces similar significant results for both type 1 (XGX-G) and type 2 (XGG-X) consensus cleavage sites, where P2 and P1’ positions have Gly with highest percentage in type 1 (XGX-G) while P2 and P1 positions have Gly in type 2 (XGG-X). Overall, supported by the successful outcomes with the case studies of HCV NS3/4A serine protease and AdV2 cysteine protease here, BSST seems to be a powerful methodology for prediction of substrate specificity in protease systems.

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