Malik, S. I. | Search bioRxiv

bioRxiv2020

Serpins: Purification and characterization of potent protease inhibitors from Clostridium thermocellum

Clostridium thermocellum produces an extracellular cellulosome (a multiprotein complex produced by firmicutes bacteria), which, owing to its extracellular location, is open to protease attack. Serine protease inhibitors (serpins) protect bacteria against protease attack. However, their structure and function are poorly characterized. This study identified and amplified the serpin 1270 gene from the C. thermocellum genome. Purified serpins were cloned into the pTXB1 vector using the one-step sequence and ligation-independent cloning reaction and transformed into Escherichia coli BL21 DE3 cells. Enzyme overexpression and purification and enzyme inhibitory assays were performed. The results showed that serpin 1270 has 89% inhibition against Bacillus subtilisin and 64% inhibition against trypsin, chymotrypsin, and papain.

biochemistry↗

bioRxiv2018

Computational Analysis of Dynamical Fluctuations of Oncoprotein E7 (HPV) for the Hot Spot Residue Identification Using Elastic Network Model

Virus proteins after invading human body alter host protein-protein interaction networks, resulting in the creation of new interactions, along with destroying or modifying other interactions or proteins. Topological features of new or modified networks compromise the host system causing increased production of viral particles. The molecular basis for this alteration of proteins interactivity is short linear peptide motifs similar in both virus and humans. These motifs are identified by modular domains, which are the subunits of a protein, in the human body, resulting in stabilization or moderation of these protein interactions Protein molecules can be modeled by elastic network models showing the fluctuations of residues when they are biologically active. We focused our computational study on the binding and competing interactions of the E7 protein of HPV with Rb protein. Our study was based on analysis of dynamic fluctuations of E7 in host cell and correlation analysis of specific residue found in motif of LxCxE, that is the key region in stabilizing interaction between E7 and Rb. Hot spot residue of E7 were also identified which could provide platform for drug prediction in future. Nevertheless, our study validates the role of linear binding motifs LxCxE of E7 of HPV in interacting with Rb as an important event in propagation of HPV in human cells and transformation of infection into cervical cancer.

bioinformatics↗