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An Assay for Quantifying Protein-RNA Binding in Bacteria
Published on: June 12, 2019
Cold shock domain protein from Philosamia ricini prefers single-stranded nucleic acids binding
Ashutosh Mani1, P K Yadava, Dwijendra K Gupta
1Center of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Allahabad 211002, India.
Journal of Biomolecular Structure & Dynamics
|June 28, 2012
Summary
Cold shock domain (CSD) proteins preferentially bind single-stranded RNA and DNA. Further research suggests flanking domains enhance binding to double-stranded DNA in the silkworm Philosamia ricini.
Area of Science:
- Molecular Biology
- Genomics
- Biochemistry
Background:
- Cold shock proteins are conserved nucleic acid-binding proteins.
- Eukaryotic homologs contain cold shock domains (CSDs) in Y-box proteins.
- CSDs exhibit conserved structures and nucleic acid binding capabilities across species.
Purpose of the Study:
- Investigate the nucleic acid binding preferences of the cold shock domain (CSD) protein from Philosamia ricini.
- Characterize the binding affinity of P. ricini CSD for various nucleic acid structures.
Main Methods:
- Cloning and sequencing of the P. ricini Y-box protein cDNA.
- Comparative genomics and phylogenetic analysis to confirm protein family.
- Molecular docking simulations comparing P. ricini CSD, human CSD, and bacterial cold shock protein.
Main Results:
- The deduced amino acid sequence confirmed P. ricini protein belongs to the CSD family.
- CSD proteins demonstrate a preferential binding affinity for single-stranded RNA and DNA.
- Molecular docking revealed potential roles for N- and C-terminal domains in dsDNA interaction and binding stability.
Conclusions:
- Cold shock domain proteins exhibit inherent specificity for single-stranded nucleic acids.
- Accessory domains may modulate binding to double-stranded DNA and enhance overall protein stability.
- This study provides insights into the functional roles of CSD proteins in Philosamia ricini.
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