Substrate specificity of the DnaK chaperone determined by screening cellulose-bound peptide libraries

EMBO J. 1997 Apr 1;16(7):1501-7. doi: 10.1093/emboj/16.7.1501.


Hsp70 chaperones assist protein folding by ATP-dependent association with linear peptide segments of a large variety of folding intermediates. The molecular basis for this ability to differentiate between native and non-native conformers was investigated for the DnaK homolog of Escherichia coli. We identified binding sites and the recognition motif in substrates by screening 4360 cellulose-bound peptides scanning the sequences of 37 biologically relevant proteins. DnaK binding sites in protein sequences occurred statistically every 36 residues. In the folded proteins these sites are mostly buried and in the majority found in beta-sheet elements. The binding motif consists of a hydrophobic core of four to five residues enriched particularly in Leu, but also in Ile, Val, Phe and Tyr, and two flanking regions enriched in basic residues. Acidic residues are excluded from the core and disfavored in flanking regions. The energetic contribution of all 20 amino acids for DnaK binding was determined. On the basis of these data an algorithm was established that predicts DnaK binding sites in protein sequences with high accuracy.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Binding Sites
  • Cellulose*
  • Computer Simulation
  • Escherichia coli / metabolism*
  • Escherichia coli Proteins*
  • HSP70 Heat-Shock Proteins / chemistry*
  • HSP70 Heat-Shock Proteins / metabolism*
  • Information Systems
  • Models, Molecular
  • Molecular Chaperones / chemistry*
  • Molecular Chaperones / metabolism*
  • Molecular Sequence Data
  • Peptide Fragments / chemistry
  • Peptides / chemistry*
  • Peptides / metabolism
  • Protein Folding
  • Protein Structure, Secondary*
  • Reproducibility of Results
  • Substrate Specificity
  • Thermodynamics


  • Escherichia coli Proteins
  • HSP70 Heat-Shock Proteins
  • Molecular Chaperones
  • Peptide Fragments
  • Peptides
  • Cellulose
  • dnaK protein, E coli