An in-silico glimpse into the pH dependent structural changes of T7 RNA polymerase: a protein with simplicity

• Published in: Scientific reports 2017-07, Vol.7 (1), p.6290-12, Article 6290
• Main Authors: Borkotoky, Subhomoi, Kumar Meena, Chetan, Bhalerao, Gopalkrishna M., Murali, Ayaluru
• Format: Article
• Language: English
• Subjects: 101/28; 631/114/2411; 631/1647/328/2082; 631/1647/48; 631/45/535/1267; Adenosine Triphosphate - metabolism; Computational Biology - methods; Computer Simulation; DNA-directed RNA polymerase; DNA-Directed RNA Polymerases - chemistry; DNA-Directed RNA Polymerases - metabolism; Electron microscopy; Guanosine triphosphate; Heparin; Heparin - metabolism; Humanities and Social Sciences; Hydrogen-Ion Concentration; Molecular Docking Simulation; Molecular Dynamics Simulation; multidisciplinary; pH effects; Protein Conformation; Protein structure; RNA polymerase; Science; Science (multidisciplinary); Subunit structure; Transmission electron microscopy; Viral Proteins - chemistry; Viral Proteins - metabolism
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-017-06586-1

The capability of performing an array of functions with its single subunit structure makes T7 RNA polymerase (T7RNAP) as one of the simplest yet attractive target for various investigations ranging from structure determinations to several biological tests. In this study, with the help of molecular dynamics (MD) calculations and molecular docking, we investigated the effect of varying pH conditions on conformational flexibility of T7RNAP. We also studied its effect on the interactions with a well established inhibitor (heparin), substrate GTP and T7 promoter of T7RNAP. The simulation studies were validated with the help of three dimensional reconstructions of the polymerase at different pH environments using transmission electron microscopy and single particle analysis. On comparing the simulated structures, it was observed that the structure of T7RNAP changes considerably and interactions with its binding partners also changes as the pH shifts from basic to acidic. Further, it was observed that the C-terminal end plays a vital role in the inefficiency of the polymerase at low pH. Thus, this in-silico study may provide a significant insight into the structural investigations on T7RNAP as well as in designing potent inhibitors against it in varying pH environments.