K Geethika, Thomas Angel Rose, Vyjayanthi T Srividya, Mandal Soumit S
Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India.
Center for Atomic, Molecular and Optical Sciences & Technologies, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India.
Phys Chem Chem Phys. 2022 Aug 17;24(32):19401-19413. doi: 10.1039/d2cp02190k.
Archaea have histone homologues and chromatin proteins to organize their DNA into a compact form. This allows them to survive in extreme climates. Cren7 is one such chromatin protein conserved in Crenarchaeota. When Cren7 binds to model natural DNA, calf thymus DNA (CTD, 58% AT content) and polynucleotides under adverse solution conditions (high temperature, ionic strength), CD bands at 275-290 nm shift to higher wavelengths indicating structural changes in DNA. It formed a strong complex with CTD and poly(dA-dT)·poly(dA-dT), a combination of electrostatic and non-electrostatic interactions. A low binding enthalpy indicated that the process was driven by entropy. The interaction was independent of the nature of the anions present in the solution. On studying the variation in protein affinity with salt concentration, it was estimated that the electrostatic interaction at the interface involves 3 pairs of ions at the protein-DNA interface. The affinity and binding site size decreased on changing the pH of the solution (between pH 6 and 8), but temperature did not result in such effects. Cren7 bound to 10 bp of DNA, increasing its flexibility and thermal stability by more than 30 C. Increasing the amount of Cren7 produces cooperative structural transitions in DNAs without any similar transition in the protein. These crucial binding parameters, energetics, and structural changes decipher the mystery of Cren7 mediated DNA organization in Crenarchaeota.
古菌具有组蛋白同源物和染色质蛋白，可将其DNA组织成紧密的形式。这使它们能够在极端气候中生存。Cren7就是嗜泉古菌门中保守的一种这样的染色质蛋白。当Cren7在不利的溶液条件（高温、离子强度）下与模型天然DNA、小牛胸腺DNA（CTD，58%的AT含量）和多核苷酸结合时，275 - 290 nm处的圆二色性（CD）带向更高波长移动，表明DNA的结构发生了变化。它与CTD和聚（dA - dT）·聚（dA - dT）形成了强复合物，这是静电和非静电相互作用的组合。低结合焓表明该过程由熵驱动。这种相互作用与溶液中存在的阴离子的性质无关。在研究蛋白质亲和力随盐浓度的变化时，据估计蛋白质 - DNA界面处的静电相互作用涉及3对离子。改变溶液的pH值（pH 6至8之间）时，亲和力和结合位点大小会降低，但温度不会产生这种影响。Cren7与10 bp的DNA结合，使其柔韧性和热稳定性提高了30多摄氏度。增加Cren7的量会在DNA中产生协同结构转变，而蛋白质中不会有任何类似的转变。这些关键的结合参数、能量学和结构变化解开了嗜泉古菌门中Cren7介导的DNA组织之谜。
