A simple and reliable approach to docking protein-protein complexes from very sparse NOE-derived intermolecular distance restraints

J Biomol NMR. 2006 Sep;36(1):37-44. doi: 10.1007/s10858-006-9065-2. Epub 2006 Sep 12.


A simple and reliable approach for docking protein-protein complexes from very sparse NOE-derived intermolecular distance restraints (as few as three from a single point) in combination with a novel representation for an attractive potential between mapped interaction surfaces is described. Unambiguous assignments of very sparse intermolecular NOEs are obtained using a reverse labeling strategy in which one the components is fully deuterated with the exception of selective protonation of the delta-methyl groups of isoleucine, while the other component is uniformly (13)C-labeled. This labeling strategy can be readily extended to selective protonation of Ala, Leu, Val or Met. The attractive potential is described by a 'reduced' radius of gyration potential applied specifically to a subset of interfacial residues (those with an accessible surface area > or = 50% in the free proteins) that have been delineated by chemical shift perturbation. Docking is achieved by rigid body minimization on the basis of a target function comprising the sparse NOE distance restraints, a van der Waals repulsion potential and the 'reduced' radius of gyration potential. The method is demonstrated for two protein-protein complexes (EIN-HPr and IIA(Glc)-HPr) from the bacterial phosphotransferase system. In both cases, starting from 100 different random orientations of the X-ray structures of the free proteins, 100% convergence is achieved to a single cluster (with near identical atomic positions) with an overall backbone accuracy of approximately 2 A. The approach described is not limited to NMR, since interfaces can also be mapped by alanine scanning mutagenesis, and sparse intermolecular distance restraints can be derived from double cycle mutagenesis, cross-linking combined with mass spectrometry, or fluorescence energy transfer.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Intramural

MeSH terms

  • Bacterial Proteins / chemistry
  • Bacterial Proteins / isolation & purification
  • Bacterial Proteins / metabolism*
  • Buffers
  • Carbon Isotopes
  • Crystallography, X-Ray
  • Deuterium / metabolism
  • Hydrogen-Ion Concentration
  • Isoleucine / chemistry
  • Models, Molecular
  • Molecular Weight
  • Nuclear Magnetic Resonance, Biomolecular*
  • Phosphates / chemistry
  • Phosphoenolpyruvate Sugar Phosphotransferase System / chemistry
  • Phosphoenolpyruvate Sugar Phosphotransferase System / isolation & purification
  • Phosphoenolpyruvate Sugar Phosphotransferase System / metabolism*
  • Phosphotransferases (Nitrogenous Group Acceptor) / chemistry
  • Phosphotransferases (Nitrogenous Group Acceptor) / isolation & purification
  • Phosphotransferases (Nitrogenous Group Acceptor) / metabolism*
  • Protein Binding
  • Protein Structure, Tertiary
  • Protons
  • Solvents / chemistry


  • Bacterial Proteins
  • Buffers
  • Carbon Isotopes
  • Phosphates
  • Protons
  • Solvents
  • Isoleucine
  • Deuterium
  • Phosphoenolpyruvate Sugar Phosphotransferase System
  • phosphocarrier protein HPr
  • Phosphotransferases (Nitrogenous Group Acceptor)
  • phosphoenolpyruvate-protein phosphotransferase
  • sodium phosphate