The role of dynamic conformational ensembles in biomolecular recognition

Nat Chem Biol. 2009 Nov;5(11):789-96. doi: 10.1038/nchembio.232.


Molecular recognition is central to all biological processes. For the past 50 years, Koshland's 'induced fit' hypothesis has been the textbook explanation for molecular recognition events. However, recent experimental evidence supports an alternative mechanism. 'Conformational selection' postulates that all protein conformations pre-exist, and the ligand selects the most favored conformation. Following binding the ensemble undergoes a population shift, redistributing the conformational states. Both conformational selection and induced fit appear to play roles. Following binding by a primary conformational selection event, optimization of side chain and backbone interactions is likely to proceed by an induced fit mechanism. Conformational selection has been observed for protein-ligand, protein-protein, protein-DNA, protein-RNA and RNA-ligand interactions. These data support a new molecular recognition paradigm for processes as diverse as signaling, catalysis, gene regulation and protein aggregation in disease, which has the potential to significantly impact our views and strategies in drug design, biomolecular engineering and molecular evolution.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Binding Sites
  • DNA / chemistry
  • DNA / genetics
  • Databases, Protein
  • Disease
  • Drug Design
  • Enzymes / chemistry
  • Enzymes / metabolism
  • Evolution, Molecular
  • Gene Expression Regulation
  • Genetic Engineering / methods
  • Genetic Engineering / trends
  • Humans
  • Ligands
  • Models, Molecular
  • Molecular Conformation*
  • Pattern Recognition, Visual / physiology
  • Protein Conformation
  • Proteins / chemistry
  • Proteins / genetics
  • RNA / chemistry
  • RNA / genetics
  • Repressor Proteins / chemistry
  • Repressor Proteins / metabolism
  • Thermodynamics


  • Enzymes
  • Ligands
  • Proteins
  • Repressor Proteins
  • RNA
  • DNA