Biological recognition patterns implicated by the formation and stability of ternary metal ion complexes of low-molecular-weight formed with amino acid/peptides and nucleobases/nucleosides

Metal-peptide or metal-nucleoside complexes may be used as models to identify recognition patterns for nucleic acids and peptides. Zinc fingers or mer and fur proteins are also examples of ternary systems with non-direct covalent bonds towards DNA. In low-molecular-weight ternary complexes some recognition patterns are repeatedly observed. This recognition tackles with the complexity of the systems and is responsible for the extra stabilization of such complexes. Some of these recognition patterns are: (a) long bonds between metal ions and nucleobases; (b) hydrogen bonds between the amino group of amino acids and a carbonyl group of the nucleobases and vice versa; (c) hydrogen bonds between a coordinated water molecule and one of the ligands; (d) stacking between nucleobases and aromatic ring or hydrophobic residues of amino acids; (e) possible direct d-pi interactions between metal ions and aromatic rings, as well as CH center dot center dot center dot pi interactions and other odd recognition patterns that can still be rationalized. (C) 2007 Elsevier B.V. All rights reserved.