Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, 605014, India.
UGC-DAE Consortium for Scientific Research Kalpakkam Node, Kokilamedu, Tamilnadu, 603104, India.
Sci Rep. 2017 Jul 24;7(1):6290. 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.
T7 RNA 聚合酶（T7RNAP）的单一亚基结构使其具备执行多种功能的能力，成为从结构测定到多种生物学测试等各种研究的理想目标之一。在这项研究中，借助分子动力学（MD）计算和分子对接，我们研究了不同 pH 值条件对 T7RNAP 构象灵活性的影响。我们还研究了它对与一种成熟抑制剂（肝素）、底物 GTP 和 T7RNAP 的 T7 启动子相互作用的影响。借助透射电子显微镜和单颗粒分析，在不同 pH 环境下对聚合酶进行三维重建，对模拟研究进行了验证。通过比较模拟结构，我们观察到 T7RNAP 的结构发生了很大变化，并且随着 pH 值从碱性向酸性变化，其与结合伙伴的相互作用也发生了变化。此外，我们观察到 C 末端在聚合酶在低 pH 值时效率低下方面起着至关重要的作用。因此，这项计算机研究可能为 T7RNAP 的结构研究以及在不同 pH 值环境下设计针对它的有效抑制剂提供重要的见解。
