Studies of the Activation Steps Concurrent to Ligand Binding in δOR and κOR Opioid Receptors Based on Molecular Dynamics Simulations

ABSTRACT

Regulating gene expression directly at the mRNA level represents a novel approach in the control of cellular processes in all organisms. In this respect, RNA-binding proteins, while in the presence of their cognate ligands, play a key role by targeting the mRNA to regulate its expression through attenuation or anti-termination mechanisms. Although many proteins are known to use these mechanisms in the regulation of gene expression, no structural insights have been revealed, to date, to explain how these proteins trigger the conformation for the recognition of RNA. This review describes the HutP mediated anti-termination mechanism by combining the in vivo, in vitro and X-ray analyses of the activated conformation of HutP, initiated by the coordination of L-histidine and Mg²⁺ ions, based on our previous and recently solved crystal structures (uncomplexed HutP, HutP-Mg²⁺, HutP-L-histidine, HutP-Mg²⁺-L-histidine, HutP-Mg2+-Lhistidine-RNA (21-mer and 55-mer)). In this anti-termination process, HutP initiates destabilization at the 5’-end of its mRNA by binding to the first UAG-rich region and then accesses the second UAG-rich region, located downstream of the stable G-C-rich segment of the terminator stem. By this mode of action, HutP appears to disrupt the G-C rich terminator stem loop, and allow the RNA polymerase to pass through the destabilized terminator, thus it prevents premature termination of transcription in the RNA segment preceding the regions encoding for the genes responsible for histidine degradation

Keywords:

Anti-termination, homology modeling, attenuation, RNA-binding proteins, metal ions, allosteric activation.