Automated identification of functional dynamic contact networks from X-ray crystallography

Nat Methods. 2013 Sep;10(9):896-902. doi: 10.1038/nmeth.2592. Epub 2013 Aug 4.


Protein function often depends on the exchange between conformational substates. Allosteric ligand binding or distal mutations can stabilize specific active-site conformations and consequently alter protein function. Observing alternative conformations at low levels of electron density, in addition to comparison of independently determined X-ray crystal structures, can provide mechanistic insights into conformational dynamics. Here we report a new algorithm, CONTACT, that identifies contact networks of conformationally heterogeneous residues directly from high-resolution X-ray crystallography data. Contact networks determined for Escherichia coli dihydrofolate reductase (ecDHFR) predict the observed long-range pattern of NMR chemical shift perturbations of an allosteric mutation. A comparison of contact networks in wild-type and mutant ecDHFR suggests that mutations that alter optimized contact networks of coordinated motions can impair catalytic function. CONTACT-guided mutagenesis can exploit the structure-dynamics-function relationship in protein engineering and design.

Publication types

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

MeSH terms

  • Algorithms*
  • Binding Sites
  • Crystallography, X-Ray*
  • Cyclophilin A / chemistry
  • Cyclophilin A / metabolism
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / metabolism
  • Humans
  • Models, Molecular*
  • Mutagenesis
  • Mutation
  • Nuclear Magnetic Resonance, Biomolecular
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / metabolism*
  • Structure-Activity Relationship
  • Tetrahydrofolate Dehydrogenase / chemistry*
  • Tetrahydrofolate Dehydrogenase / genetics
  • Tetrahydrofolate Dehydrogenase / metabolism*


  • Escherichia coli Proteins
  • Proteins
  • Tetrahydrofolate Dehydrogenase
  • Cyclophilin A

Associated data

  • PDB/4KJJ
  • PDB/4KJK
  • PDB/4KJL