Roy Alankar, Ray Sujay
Amity Institute of Biotechnology, Amity University, Kolkata, India.
3 Biotech. 2023 Jul;13(7):236. doi: 10.1007/s13205-023-03656-2. Epub 2023 Jun 15.
Cold shock proteins (CSPs) are small, cytoplasmic, ubiquitous and acidic proteins. They have a single nucleic acid-binding domain and pose as "RNA chaperones" by binding to ssRNA in a low sequence specificity and cooperative manner. They are found in a family of nine homologous CSPs in . CspA, CspB, CspG and CspI are immensely cold inducible, CspE and CspC are consistently released at usual physiological temperatures and CspD is also induced under nutrient stress. The paralogous protein pairs CSPA/CSPB, CSPC/CSPE, CSPG/CSPI and CSPF/CSPH were first identified. The eight proteins were subjected to molecular modelling and simulation to obtain the most stable conformation in correspondence to their equilibrated RMSD and RMSF graph. The results were compared and it was observed that CSPB, CSPE, CSPF and CSPI were more stable than their paralogous partner conforming to their near equilibrated RMSD curve and low fluctuating RMSF graph. The paralogous proteins were docked with ssRNA and simultaneously binding affinity, interaction types, electrostatic surface potential, hydrophobicity, conformational analysis and SASA were calculated to minutely study and understand the molecular mechanism initiated by these proteins. It was found that CSPB, CSPC, CSPH and CSPI displayed higher affinity towards ssRNA than their paralogous partner. The results further corroborated with ΔGmmgbsa and ΔGfold energy. Between the paralogous pairs CSPC, CSPH and CSPI exhibited higher binding free energy than their partner. Further, CSPB, CSPC and CSPI exhibited higher folding free energy than their paralogous pair. CSPH exhibited highest ΔGmmgbsa of - 522.2 kcal/mol and lowest was displayed by CSPG of around - 309.3 kcal/mol. Highest number of mutations were recognised in CSPF/CSPH and CSPG/CSPI pair. Difference in interaction pattern was maximum in CSPF/CSPH owing to their high number of non-synonymous substitutions. Maximum difference in surface electrostatic potential was observed in case of CSPA, CSPG and CSPF. This research work emphasizes on discerning the molecular mechanism initiated by these proteins with a structural, mutational and functional approach.
The online version contains supplementary material available at 10.1007/s13205-023-03656-2.
冷休克蛋白（CSPs）是一类小的、存在于细胞质中的、普遍存在的酸性蛋白。它们具有单一的核酸结合结构域，通过以低序列特异性和协同方式与单链RNA结合，充当“RNA伴侣”。在[具体物种]中发现了一个由九个同源CSP组成的家族。CspA、CspB、CspG和CspI在低温下高度可诱导，CspE和CspC在正常生理温度下持续释放，CspD在营养胁迫下也会被诱导。首次鉴定出同源蛋白对CSPA/CSPB、CSPC/CSPE、CSPG/CSPI和CSPF/CSPH。对这八种蛋白质进行分子建模和模拟，以获得与其平衡的均方根偏差（RMSD）和均方根波动（RMSF）图相对应的最稳定构象。对结果进行比较后发现，根据其接近平衡的RMSD曲线和低波动的RMSF图，CSPB、CSPE、CSPF和CSPI比其同源伴侣更稳定。将同源蛋白与单链RNA对接，并同时计算结合亲和力、相互作用类型、静电表面电位、疏水性、构象分析和溶剂可及表面积（SASA），以详细研究和理解这些蛋白质引发的分子机制。发现CSPB、CSPC、CSPH和CSPI对单链RNA的亲和力高于其同源伴侣。结果通过ΔGmmgbsa和ΔGfold能量进一步得到证实。在同源对中，CSPC、CSPH和CSPI表现出比其伴侣更高的结合自由能。此外，CSPB、CSPC和CSPI表现出比其同源对更高的折叠自由能。CSPH表现出最高的ΔGmmgbsa为 - 522.2 kcal/mol，最低的是CSPG，约为 - 309.3 kcal/mol。在CSPF/CSPH和CSPG/CSPI对中识别出的突变数量最多。由于其大量的非同义替换，CSPF/CSPH的相互作用模式差异最大。在CSPA、CSPG和CSPF的情况下观察到表面静电电位的最大差异。这项研究工作强调通过结构、突变和功能方法来识别这些蛋白质引发的分子机制。
在线版本包含可在10.1007/s13205-023-03656-2获取的补充材料。
