Ligand-RNA complex

The Kd values are determined by plotting the fraction of RNA bound by the hgand (traction bound) versus the total hgand concentration. The frac-hon bound is determined by dividing the abundances of the ligand-RNA complexes (1 1 and 2 1 ligand-RNA complexes) by the total abundance of the RNA. The traction bound is related to the Kd with the following equahon ... 

Kostjukov VV, Evstigneev MP (2012) Energy of ligand-RNA complex formation. Biophysics 57(4) 450 63... 

McGregor, A., Murray, J.B., Adams, C.J., Stoddey, P.G. and Connolly, B. A. (1999) Secondary structure mapping of an RNA ligand that has high affinity for tire MeLT repressor protein and interference modification analysis of tlie protein-RNA complex, J. Biol. Chem. 274, 2255-2562. 

Energy analysis of ligand-NA interactions, sketched out above for typical DNA in-tercalators, DNA minor groove binders and RNA binders, enables us to answer the key question, viz. What physical factors stabilize/destabilize the ligand-NA complexes in solution and what are their relative importance The follow-up question now is How one can use the results of the energy analysis, say, in rational design of new drags ... 

Photoprocesses of RNA-bound copper complexes with macroheterocyclic ligands 98CRV1201. 

Fluorescence polarization anisotropy of a ligand and its complexes with DNA or RNA can be given by the following expression ... 

The general types of protein-protein interactions that occur in cells include receptor-ligand, enzyme-substrate, multimeric complex formations, structural scaffolds, and chaperones. However, proteins interact with more targets than just other proteins. Protein interactions can include protein-protein or protein-peptide, protein-DNA/RNA or protein-nucleic acid, protein-glycan or protein-carbohydrate, protein-lipid or protein-membrane, and protein-small molecule or protein-ligand. It is likely that every molecule within a cell has some kind of specific interaction with a protein. 

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