Thermodynamics of protein-RNA recognition in a highly conserved region of the large-subunit ribosomal RNA.
Ribosomal protein L11 from Escherichia coli specifically binds to a highly conserved region of 23S ribosomal RNA. The thermodynamics of forming a complex between this protein and several different rRNA fragments have been investigated, by use of a nitrocellulose filter binding assay. A 57-nucleotide region of the RNA (C1052-U1108) contains all the protein recognition features, and an RNA fragment containing this region binds L11 10(3)-10(4)-fold more tightly than tRNA. Binding constants are on the order of 10 microM-1 and are only weakly dependent on K+ concentration (delta log K/delta log [K+] = -1.4) or temperature. Binding requires multivalent cations; Mg2+ is taken up into the complex with an affinity of approximately 3 mM-1. Other multivalent cations tested, Ca2+ and Co(NH3)63+, promote binding nearly as well. The pH dependence of binding is a bell-shaped curve with a maximum near neutral pH, but the entire curve is shifted to higher pH for the smaller of two RNA fragments tested. This result suggests that the smaller fragment favors a conformation stabilizing protonated forms of the RNA recognition site and is potentially relevant to a hypothesis that this rRNA region undergoes an ordered series of conformational changes during the ribosome cycle.
Ryan
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Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218.
Draper
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D001483:Base Sequence; D001665:Binding Sites; D006863:Hydrogen-Ion Concentration; D008969:Molecular Sequence Data; D009994:Osmolar Concentration; D011188:Potassium / Q000494:pharmacology; D012335:RNA, Ribosomal / Q000502:physiology*; D012338:RNA, Ribosomal, 23S / Q000502:physiology*; D012269:Ribosomal Proteins / Q000502:physiology*; D013816:Thermodynamics
D012335:RNA, Ribosomal; D012338:RNA, Ribosomal, 23S; D012269:Ribosomal Proteins; C027624:ribosomal protein L11; D011188:Potassium