Intramolecular allosteric communication in dopamine D2 receptor revealed by evolutionary amino acid covariation

Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3539-44. doi: 10.1073/pnas.1516579113. Epub 2016 Mar 15.


The structural basis of allosteric signaling in G protein-coupled receptors (GPCRs) is important in guiding design of therapeutics and understanding phenotypic consequences of genetic variation. The Evolutionary Trace (ET) algorithm previously proved effective in redesigning receptors to mimic the ligand specificities of functionally distinct homologs. We now expand ET to consider mutual information, with validation in GPCR structure and dopamine D2 receptor (D2R) function. The new algorithm, called ET-MIp, identifies evolutionarily relevant patterns of amino acid covariations. The improved predictions of structural proximity and D2R mutagenesis demonstrate that ET-MIp predicts functional interactions between residue pairs, particularly potency and efficacy of activation by dopamine. Remarkably, although most of the residue pairs chosen for mutagenesis are neither in the binding pocket nor in contact with each other, many exhibited functional interactions, implying at-a-distance coupling. The functional interaction between the coupled pairs correlated best with the evolutionary coupling potential derived from dopamine receptor sequences rather than with broader sets of GPCR sequences. These data suggest that the allosteric communication responsible for dopamine responses is resolved by ET-MIp and best discerned within a short evolutionary distance. Most double mutants restored dopamine response to wild-type levels, also suggesting that tight regulation of the response to dopamine drove the coevolution and intramolecular communications between coupled residues. Our approach provides a general tool to identify evolutionary covariation patterns in small sets of close sequence homologs and to translate them into functional linkages between residues.

Keywords: Evolutionary Trace; G protein-coupled receptors; allostery; residue covariation.

Publication types

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

MeSH terms

  • Algorithms
  • Amino Acid Substitution
  • Amino Acids / chemistry
  • Amino Acids / genetics
  • Binding Sites / genetics
  • Dopamine / metabolism
  • Evolution, Molecular*
  • GTP-Binding Proteins / metabolism
  • Genetic Variation
  • HEK293 Cells
  • Humans
  • Ligands
  • Models, Molecular
  • Mutagenesis, Site-Directed
  • Protein Interaction Domains and Motifs
  • Receptors, Dopamine D2 / chemistry*
  • Receptors, Dopamine D2 / genetics*
  • Receptors, Dopamine D2 / metabolism
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Serotonin / metabolism
  • Thermodynamics


  • Amino Acids
  • Ligands
  • Receptors, Dopamine D2
  • Recombinant Proteins
  • Serotonin
  • GTP-Binding Proteins
  • Dopamine