Protein recognition of adenylate: an example of a fuzzy recognition template

Abstract

The interaction between protein and adenylate in a non-homologous dataset of 18 high-resolution protein/nucleotide crystal structures is analysed. We find that each constituent of adenylate, adenine, ribose and phosphate, is substantially buried. Adenine has a largely hydrophobic protein interface, while phosphate interacts primarily with hydrophilic residues; ribose is intermediate. A detailed study of hydrogen bonding in these complexes shows hydrogen bonds between protein and adenine to be surprisingly scarce. There does not seem to be a conserved hydrogen-bonding pattern for adenine recognition. The hydrogen bonds that are seen have geometries close to energy minima found in our Distributed Multipole Analysis based model calculations. The experimental hydrogen-bonded geometries have a characteristic signature in our model energy calculations, with a dominant attractive electrostatic term. For stacked interactions, however, the dispersion energy dominates. Finally, we present the concept of a fuzzy recognition template, as a useful means of describing the protein/adenylate interactions presented here, which will also be a valuable concept for characterising other protein/ligand interactions.