Thermodynamics of protein-RNA recognition in a highly conserved region of the large-subunit ribosomal RNA

Publisher Website
Google Scholar
Abstract
Ribosomal protein L11 from Escherichia coli specifically binds to 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 103-104-fold more tightly than tRNA. Binding constants are on the order of 10 .mu.M-1 and are only weakly dependent on K+ concentration (.vdelta. log K/.vdelta. log [K+] = -1.4) or temperature. Binding requires multivalent cations; Mg2+ is taken up into the complex with an affinity of .apprx. 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 curves is shifted to higher pH for the smaller of two RNA fragments tested. This result sugests that the smaller fragment favors a conformational 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.