Amity Institute of Biotechnology, Amity University, Kolkata, India.
Mol Biotechnol. 2024 Apr;66(4):824-844. doi: 10.1007/s12033-023-00711-4. Epub 2023 Mar 11.
Cold shock proteins (CSPs) are small, acidic proteins which contain a conserved nucleic acid-binding domain. These perform mRNA translation acting as "RNA chaperones" when triggered by low temperatures initiating their cold shock response. CSP- RNA interactions have been predominantly studied. Our focus will be CSP-DNA interaction examination, to analyse the diverse interaction patterns such as electrostatic, hydrogen and hydrophobic bonding in both thermophilic and mesophilic bacteria. The differences in the molecular mechanism of these contrasting bacterial proteins are studied. Computational techniques such as modelling, energy refinement, simulation and docking were operated to obtain data for comparative analysis. The thermostability factors which stabilise a thermophilic bacterium and their effect on their molecular regulation is investigated. Conformational deviation, atomic residual fluctuations, binding affinity, Electrostatic energy and Solvent Accessibility energy were determined during stimulation along with their conformational study. The study revealed that mesophilic bacteria E. coli CSP have higher binding affinity to DNA than thermophilic G. stearothermophilus. This was further evident by low conformation deviation and atomic fluctuations during simulation.
冷休克蛋白（CSPs）是一种小型酸性蛋白，含有保守的核酸结合结构域。这些蛋白在低温触发时充当“RNA 伴侣”，从而启动冷休克反应，进行 mRNA 翻译。目前主要研究 CSP 与 RNA 的相互作用。我们将重点研究 CSP 与 DNA 的相互作用，以分析嗜热菌和中温菌中各种相互作用模式，如静电、氢键和疏水键。研究这些对比鲜明的细菌蛋白的分子机制差异。通过建模、能量细化、模拟和对接等计算技术来获取数据，进行比较分析。我们还研究了稳定嗜热菌的热稳定性因素及其对分子调控的影响。在刺激过程中，我们确定了构象偏差、原子残差波动、结合亲和力、静电能和溶剂可及能，并进行了构象研究。研究表明，与嗜热菌 G. stearothermophilus 相比，中温菌 E. coli CSP 对 DNA 的结合亲和力更高。这一点在模拟过程中较低的构象偏差和原子波动中得到了进一步证实。
