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Journal of Bacteriology, May 2008, p. 3344-3352, Vol. 190, No. 9
0021-9193/08/$08.00+0     doi:10.1128/JB.01800-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Protein Folding by Domain V of Escherichia coli 23S rRNA: Specificity of RNA-Protein Interactions ^,

Department of Biophysics, Molecular Biology and Genetics, University College of Science, Kolkata-700009, India,¹ Structural Genomics Section, Saha Institute of Nuclear Physics, Kolkata-700064, India²

Received 14 November 2007/ Accepted 24 February 2008

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.

Published ahead of print on 29 February 2008.

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