Ghosh Soma, Chandra Nagasuma, Vishveshwara Saraswathi
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India.
I.I.Sc. Mathematics Initiative, Indian Institute of Science, Bangalore, Karnataka, India.
PLoS Comput Biol. 2015 Dec 23;11(12):e1004500. doi: 10.1371/journal.pcbi.1004500. eCollection 2015 Dec.
Metalloproteins form a major class of enzymes in the living system that are involved in crucial biological functions such as catalysis, redox reactions and as 'switches' in signal transductions. Iron dependent repressor (IdeR) is a metal-sensing transcription factor that regulates free iron concentration in Mycobacterium tuberculosis. IdeR is also known to promote bacterial virulence, making it an important target in the field of therapeutics. Mechanistic details of how iron ions modulate IdeR such that it dimerizes and binds to DNA is not understood clearly. In this study, we have performed molecular dynamic simulations and integrated it with protein structure networks to study the influence of iron on IdeR structure and function. A significant structural variation between the metallated and the non-metallated system is observed. Our simulations clearly indicate the importance of iron in stabilizing its monomeric subunit, which in turn promotes dimerization. However, the most striking results are obtained from the simulations of IdeR-DNA complex in the absence of metals, where at the end of 100ns simulations, the protein subunits are seen to rapidly dissociate away from the DNA, thereby forming an excellent resource to investigate the mechanism of DNA binding. We have also investigated the role of iron as an allosteric regulator of IdeR that positively induces IdeR-DNA complex formation. Based on this study, a mechanistic model of IdeR activation and DNA binding has been proposed.
金属蛋白是生物系统中一类主要的酶，参与催化、氧化还原反应等关键生物学功能，并在信号转导中充当“开关”。铁依赖性阻遏物（IdeR）是一种金属感应转录因子，可调节结核分枝杆菌中的游离铁浓度。已知IdeR还能促进细菌毒力，使其成为治疗领域的一个重要靶点。铁离子如何调节IdeR使其二聚化并与DNA结合的机制细节尚不清楚。在本研究中，我们进行了分子动力学模拟，并将其与蛋白质结构网络相结合，以研究铁对IdeR结构和功能的影响。观察到金属化和未金属化系统之间存在显著的结构差异。我们的模拟清楚地表明了铁在稳定其单体亚基方面的重要性，这反过来又促进了二聚化。然而，最引人注目的结果来自于在没有金属的情况下对IdeR-DNA复合物的模拟，在100纳秒模拟结束时，可以看到蛋白质亚基迅速从DNA上解离，从而形成了一个研究DNA结合机制的绝佳资源。我们还研究了铁作为IdeR的变构调节剂的作用，它能正向诱导IdeR-DNA复合物的形成，并基于本研究提出了IdeR激活和DNA结合的机制模型。
