Analysis of binding site hot spots on the surface of Ras GTPase

J Mol Biol. 2011 Nov 4;413(4):773-89. doi: 10.1016/j.jmb.2011.09.011. Epub 2011 Sep 16.


We have recently discovered an allosteric switch in Ras, bringing an additional level of complexity to this GTPase whose mutants are involved in nearly 30% of cancers. Upon activation of the allosteric switch, there is a shift in helix 3/loop 7 associated with a disorder to order transition in the active site. Here, we use a combination of multiple solvent crystal structures and computational solvent mapping (FTMap) to determine binding site hot spots in the "off" and "on" allosteric states of the GTP-bound form of H-Ras. Thirteen sites are revealed, expanding possible target sites for ligand binding well beyond the active site. Comparison of FTMaps for the H and K isoforms reveals essentially identical hot spots. Furthermore, using NMR measurements of spin relaxation, we determined that K-Ras exhibits global conformational dynamics very similar to those we previously reported for H-Ras. We thus hypothesize that the global conformational rearrangement serves as a mechanism for allosteric coupling between the effector interface and remote hot spots in all Ras isoforms. At least with respect to the binding sites involving the G domain, H-Ras is an excellent model for K-Ras and probably N-Ras as well. Ras has so far been elusive as a target for drug design. The present work identifies various unexplored hot spots throughout the entire surface of Ras, extending the focus from the disordered active site to well-ordered locations that should be easier to target.

Publication types

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

MeSH terms

  • Allosteric Site
  • Binding Sites
  • Crystallography, X-Ray
  • Guanosine Triphosphate / chemistry
  • Guanosine Triphosphate / metabolism*
  • Humans
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Protein Binding
  • Protein Conformation
  • ras Proteins / chemistry*
  • ras Proteins / metabolism*


  • Guanosine Triphosphate
  • ras Proteins

Associated data

  • PDB/17785
  • PDB/3RRY
  • PDB/3RRZ
  • PDB/3RS0
  • PDB/3RS2
  • PDB/3RS3
  • PDB/3RS4
  • PDB/3RS5
  • PDB/3RS7
  • PDB/3RSL
  • PDB/3RSO