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

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Abstract

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.

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Data Availability

All data generated and studies are available within this manuscriptand its supplementary article.

Code Availability

Not applicable.

Abbreviations

CSP:

Cold shock proteins

ssDNA:

Single-stranded DNA

D1:

(DNA-binding site: residue symbol and position in the sequence)

RMSD:

Root Mean Square Deviation

RMSF:

Root Mean Square Fluctuation

SASA:

Solvent-Accessible Surface Area

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Acknowledgements

The authors would like to thank, Amity Institute of Biotechnology, Amity University, Kolkata, India, for their cooperation.

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  1. Amity Institute of Biotechnology, Amity University, Kolkata, India

    Alankar Roy & Sujay Ray

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  1. Alankar Roy
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  2. Sujay Ray
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Contributions

AR and SR conceived of the presented idea. AR, did the calculation part. SR helped to select databases, softwares and webservers required for this study. Main backbone manuscript was written by AR. Tables, Figures were constructed by AR with the help of SR. Some portion of the result and discussion portion was specifically oriented by AR and SR. Overall Guidance and design were given by SR.

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Correspondence to Sujay Ray.

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Roy, A., Ray, S. Traversing DNA-Protein Interactions Between Mesophilic and Thermophilic Bacteria: Implications from Their Cold Shock Response. Mol Biotechnol 66, 824–844 (2024). https://doi.org/10.1007/s12033-023-00711-4

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