Traversing DNA-Protein Interactions Between Mesophilic and Thermophilic Bacteria: Implications from Their Cold Shock Response

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. [Graphics] .

Automated summary

Cold shock proteins (CSPs), small acidic proteins with a conserved nucleic acid-binding domain, act as RNA chaperones in mRNA translation upon low temperature-induced cold shock response. While CSP-RNA interactions have been extensively studied, this research focuses on examining CSP-DNA interactions in both thermophilic and mesophilic bacteria, analyzing their diverse interaction patterns. Computational techniques including modeling, energy refinement, simulation, and docking were employed to obtain data for comparative analysis. The study investigates the molecular mechanisms and factors affecting thermostability in thermophilic bacteria, revealing that the mesophilic bacteria E. coli CSP exhibits a higher binding affinity to DNA compared to the thermophilic G. stearothermophilus, supported by lower conformational deviation and atomic fluctuations during simulation.