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

S L Moodie, John Blayney Owen Mitchell, J M Thornton

Research output: Contribution to journalArticlepeer-review

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. (C) 1996 Academic Press Limited

Original languageEnglish
Pages (from-to)486-500
Number of pages15
JournalJournal of Molecular Biology
Volume263
Issue number3
Publication statusPublished - 1 Nov 1996

Keywords

  • protein-ligand recognition
  • nucleotides
  • Distributed Multipole Analysis
  • hydrogen bonding
  • INTERMOLECULAR PERTURBATION-THEORY
  • CRYSTAL-STRUCTURE
  • CHARGE-DISTRIBUTION
  • ATOMIC-STRUCTURE
  • BINDING-SITES
  • HYDROGEN-BOND
  • COMPLEX
  • AMP
  • RESOLUTION
  • KINASE

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