Agarwal Nipanshu, Jaiswal Nancy, Gulati Khushboo, Gangele Krishnakant, Nagar Nupur, Kumar Dinesh, Poluri Krishna Mohan
Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India.
Centre of Biomedical Research, SGPGIMS Campus, Lucknow 226014, India.
Biochemistry. 2021 Nov 2;60(43):3236-3252. doi: 10.1021/acs.biochem.1c00395. Epub 2021 Oct 19.
The summarized amalgam of internal relaxation modulations and external forces like pH, temperature, and solvent conditions determine the protein structure, stability, and function. In a free-energy landscape, although conformers are arranged in vertical hierarchy, there exist several adjacent parallel sets with conformers occupying equivalent energy cleft. Such conformational states are pre-requisites for the functioning of proteins that have oscillating environmental conditions. As these conformational changes have utterly small re-arrangements, nuclear magnetic resonance (NMR) spectroscopy is unique in elucidating the structure-dynamics-stability-function relationships for such conformations. survives and causes gastric cancer at extremely low pH also. However, least is known as to how the genome of the pathogen is protected from reactive oxygen species (ROS) scavenging in the gut at low pH under acidic stress. In the current study, biophysical characteristics of DNA binding protein (Hup) have been elucidated at pH 2 using a combination of circular dichroism, fluorescence, NMR spectroscopy, and molecular dynamics simulations. Interestingly, the protein was found to have conserved structural features, differential backbone dynamics, enhanced stability, and DNA binding ability at low pH as well. In summary, the study suggests the partaking of Hup protein even at low pH in DNA protection for maintaining the genome integrity.
内部松弛调节与诸如pH值、温度和溶剂条件等外力的综合作用决定了蛋白质的结构、稳定性和功能。在自由能景观中，尽管构象异构体按垂直层次排列，但存在几个相邻的平行集合，其中构象异构体占据等效的能量裂隙。这种构象状态是具有振荡环境条件的蛋白质发挥功能的先决条件。由于这些构象变化的重排极其微小，核磁共振（NMR）光谱在阐明此类构象的结构-动力学-稳定性-功能关系方面具有独特性。在极低的pH值下也能存活并引发胃癌。然而，关于病原体的基因组如何在酸性应激下低pH值的肠道环境中免受活性氧（ROS）清除的影响，人们了解得最少。在当前的研究中，通过圆二色性、荧光、NMR光谱和分子动力学模拟相结合的方法，阐明了pH值为2时DNA结合蛋白（Hup）的生物物理特性。有趣的是，该蛋白在低pH值下也具有保守的结构特征、不同的主链动力学、增强的稳定性和DNA结合能力。总之，该研究表明即使在低pH值下，Hup蛋白也参与DNA保护以维持基因组完整性。
