Protein folding by domain V of Escherichia coli 23S rRNA: Specificity of RNA-protein interactions

Dibyendu Samanta, Debashis Mukhopadhyay, Saheli Chowdhury, Jaydip Ghosh, Saumen Pal, Arunima Basu, Arpita Bhattacharya, Anindita Das, Debasis Das, Chanchal DasGupta

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

The peptidyl transferase center, present in domain V of 23S rRNA of eubacteria and large rRNA of plants and animals, can act as a general protein folding modulator. Here we show that a few specific nucleotides in Escherichia coli domain V RNA bind to unfolded proteins and, as shown previously, bring the trapped proteins to a folding-competent state before releasing them. These nucleotides are the same for the proteins studied so far: bovine carbonic anhydrase, lactate dehydrogenase, malate dehydrogenase, and chicken egg white lysozyme. The amino acids that interact with these nucleotides are also found to be specific in the two cases tested: bovine carbonic anhydrase and lysozyme. They are either neutral or positively charged and are present in random coils on the surface of the crystal structure of both the proteins. In fact, two of these amino acid-nucleotide pairs are identical in the two cases. How these features might help the process of protein folding is discussed.

Original languageEnglish (US)
Pages (from-to)3344-3352
Number of pages9
JournalJournal of Bacteriology
Volume190
Issue number9
DOIs
StatePublished - May 2008
Externally publishedYes

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Protein Folding
Nucleotides
RNA
Escherichia coli
Carbonic Anhydrases
Muramidase
Proteins
Peptidyl Transferases
Amino Acids
Protein Unfolding
Egg White
Malate Dehydrogenase
L-Lactate Dehydrogenase
Chickens
Bacteria
Protein Domains

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Immunology

Cite this

Samanta, D., Mukhopadhyay, D., Chowdhury, S., Ghosh, J., Pal, S., Basu, A., ... DasGupta, C. (2008). Protein folding by domain V of Escherichia coli 23S rRNA: Specificity of RNA-protein interactions. Journal of Bacteriology, 190(9), 3344-3352. https://doi.org/10.1128/JB.01800-07

Protein folding by domain V of Escherichia coli 23S rRNA : Specificity of RNA-protein interactions. / Samanta, Dibyendu; Mukhopadhyay, Debashis; Chowdhury, Saheli; Ghosh, Jaydip; Pal, Saumen; Basu, Arunima; Bhattacharya, Arpita; Das, Anindita; Das, Debasis; DasGupta, Chanchal.

In: Journal of Bacteriology, Vol. 190, No. 9, 05.2008, p. 3344-3352.

Research output: Contribution to journalArticle

Samanta, D, Mukhopadhyay, D, Chowdhury, S, Ghosh, J, Pal, S, Basu, A, Bhattacharya, A, Das, A, Das, D & DasGupta, C 2008, 'Protein folding by domain V of Escherichia coli 23S rRNA: Specificity of RNA-protein interactions', Journal of Bacteriology, vol. 190, no. 9, pp. 3344-3352. https://doi.org/10.1128/JB.01800-07
Samanta, Dibyendu ; Mukhopadhyay, Debashis ; Chowdhury, Saheli ; Ghosh, Jaydip ; Pal, Saumen ; Basu, Arunima ; Bhattacharya, Arpita ; Das, Anindita ; Das, Debasis ; DasGupta, Chanchal. / Protein folding by domain V of Escherichia coli 23S rRNA : Specificity of RNA-protein interactions. In: Journal of Bacteriology. 2008 ; Vol. 190, No. 9. pp. 3344-3352.
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