Role of N-Terminal Helix in Interaction of Ribosomal Protein S15 with 16S rRNA

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S. V. Revtovich, A. D. Nikulin^*, and S. V. Nikonov

Institute of Protein Research, Russian Academy of Sciences, Institutskaya ul. 4, 142290 Pushchino, Moscow Region, Russia; fax: (7-095) 924-0493; E-mail: nikulin@vega.protres.ru

^* To whom correspondence should be addressed.

Received March 19, 2004; Revision received April 20, 2004

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The position and conformation of the N-terminal helix of free ribosomal protein S15 was earlier found to be modified under various conditions. This variability was supposed to provide the recognition by the protein of its specific site on 16S rRNA. To test this hypothesis, we substituted some amino acid residues in this helix and assessed effects of these substitutions on the affinity of the protein for 16S rRNA. The crystal structure of the complex of one of these mutants (Thr3Cys S15) with the 16S rRNA fragment was determined, and a computer model of the complex containing another mutant (Gln8Met S15) was designed. The available and new information was analyzed in detail, and the N-terminal helix was concluded to play no significant role in the specific binding of the S15 protein to its target on 16S rRNA.

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KEY WORDS: RNA-protein interactions, ribosomal proteins, crystal structure, S15 protein, 16S ribosomal RNA

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