Letter | Published:

Computational design of receptor and sensor proteins with novel functions


The formation of complexes between proteins and ligands is fundamental to biological processes at the molecular level. Manipulation of molecular recognition between ligands and proteins is therefore important for basic biological studies1 and has many biotechnological applications, including the construction of enzymes2,3,4, biosensors5,6, genetic circuits7, signal transduction pathways8 and chiral separations9. The systematic manipulation of binding sites remains a major challenge. Computational design offers enormous generality for engineering protein structure and function10. Here we present a structure-based computational method that can drastically redesign protein ligand-binding specificities. This method was used to construct soluble receptors that bind trinitrotoluene, l-lactate or serotonin with high selectivity and affinity. These engineered receptors can function as biosensors for their new ligands; we also incorporated them into synthetic bacterial signal transduction pathways, regulating gene expression in response to extracellular trinitrotoluene or l-lactate. The use of various ligands and proteins shows that a high degree of control over biomolecular recognition has been established computationally. The biological and biosensing activities of the designed receptors illustrate potential applications of computational design.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


  1. 1

    Bishop, A. et al. Unnatural ligands for engineered proteins: new tools for chemical genetics. Annu. Rev. Biophys. Biomol. Struct. 29, 577–606 (2000)

  2. 2

    Harris, J. L. & Craik, C. S. Engineering enzyme specificity. Curr. Opin. Chem. Biol. 2, 127–132 (1998)

  3. 3

    Bolon, D. N. & Mayo, S. L. Enzyme-like proteins by computational design. Proc. Natl Acad. Sci. USA 98, 14274–14279 (2001)

  4. 4

    Benson, D. E., Haddy, A. E. & Hellinga, H. W. Converting a maltose receptor into a nascent binuclear oxygenase by computational design. Biochemistry 41, 3262–3267 (2002)

  5. 5

    Hellinga, H. W. & Marvin, J. S. Protein engineering and the development of generic biosensors. Trends Biotechnol. 16, 183–189 (1998)

  6. 6

    de Lorimier, R. M. et al. Design, construction and analysis of a family of fluorescent biosensors. Protein Sci. 11, 2655–2675 (2002)

  7. 7

    Hasty, J., McMillen, D. & Collins, J. J. Engineered gene circuits. Nature 420, 224–230 (2002)

  8. 8

    Koh, J. T. Engineering selectivity and discrimination into ligand–receptor interfaces. Chem. Biol. 9, 17–23 (2002)

  9. 9

    Maier, N. M., Franco, P. & Lindner, W. Separation of enantiomers: needs, challenges, perspectives. J. Chromatogr. A 906, 3–33 (2001)

  10. 10

    Arnold, F. H. Combinatorial and computational challenges for biocatalyst design. Nature 409, 253–257 (2001)

  11. 11

    Fersht, A. R. Structure and Mechanism in Protein Science (Freeman, New York, 1999)

  12. 12

    Dahiyat, B. I. & Mayo, S. L. De novo protein design: Fully automated sequence selection. Science 278, 82–87 (1997)

  13. 13

    Looger, L. L. & Hellinga, H. W. Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics. J. Mol. Biol. 307, 429–445 (2001)

  14. 14

    Reina, J. et al. Computer-aided design of a PDZ domain to recognize new target sequences. Nature Struct. Biol. 9, 621–627 (2002)

  15. 15

    Tam, R. & Saier, M. H. Jr. Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. Microbiol. Rev. 57, 320–346 (1993)

  16. 16

    Vyas, M. N., Vyas, N. K. & Quiocho, F. A. Crystallographic analysis of the epimeric and anomeric specificity of the periplasmic transport/chemosensory protein receptor for d-glucose and d-galactose. Biochemistry 33, 4762–4768 (1994)

  17. 17

    Mowbray, S. L. & Cole, L. B. 1.7 Å X-ray structure of the periplasmic ribose receptor from Escherichia coli. J. Mol. Biol. 225, 155–175 (1992)

  18. 18

    Quiocho, F. A. & Vyas, N. K. Novel stereospecificity of the l-arabinose-binding protein. Nature 310, 381–386 (1984)

  19. 19

    Sun, Y. J., Rose, J., Wang, B. C. & Hsiao, C. D. The structure of glutamine-binding protein complexed with glutamine at 1.94 Å resolution: comparisons with other amino acid binding proteins. J. Mol. Biol. 278, 219–229 (1998)

  20. 20

    Yao, N., Trakhanov, S. & Quiocho, F. A. Refined 1.89 Å structure of the histidine-binding protein complexed with histidine and its relationship with many other active transport/chemosensory proteins. Biochemistry 33, 4769–4779 (1994)

  21. 21

    Kuntz, I. D., Chen, K., Sharp, K. A. & Kollman, P. A. The maximal affinity of ligands. Proc. Natl Acad. Sci. USA 96, 9997–10002 (1999)

  22. 22

    Dahiyat, B. I. & Mayo, S. L. Protein design automation. Protein Sci. 5, 895–903 (1996)

  23. 23

    Stock, A. M., Robinson, V. L. & Goudreau, P. N. Two-component signal transduction. Annu. Rev. Biochem. 69, 183–215 (2000)

  24. 24

    Baumgartner, J. W. et al. Transmembrane signalling by a hybrid receptor: communication from the domain of chemoreceptor Trg that recognizes sugar-binding proteins to the kinase/phosphatase domain of osmosensor. EnvZ. J. Bacteriol. 176, 1157–1163 (1994)

  25. 25

    Daunert, S. et al. Genetically engineered whole-cell sensing systems: coupling biological recognition with reporter genes. Chem. Rev. 100, 2705–2738 (2000)

  26. 26

    Yinon, Y. Field detection and monitoring of explosives. Trends Anal. Chem. 21, 292–301 (2002)

  27. 27

    Mead, K. S. Using lobster noses to inspire robot sensor design. Trends Biotechnol. 20, 276–277 (2002)

  28. 28

    Cumming, C. L. et al. Using novel fluorescent polymers as sensory materials for above-ground sensing of chemical signature compounds emanating from buried land mines. IEEE Trans. Geosci. Remote Sens. 39, 1119–1128 (2001)

  29. 29

    Burlage, R. S., Patek, D. R. & Everman, K. R. Method for detection of buried explosives using a biosensor. US patent 5,972,638 (1999).

  30. 30

    Burtis, C. A. & Ashwood, E. R. Tietz Textbook of Clinical Chemistry (Saunders, London, 1999)

Download references


We thank M. Inouye for the gift of the RU1012 strain, L. Loew for the gift of styryl dyes, S. Conrad and G. Shirman for assistance with mutagenesis and protein chemistry, and M. G. Prisant for construction of the computer cluster. This work was supported by grants from the Office of Naval Research, the Defense Advanced Research Project Agency and the National Institutes of Health.

Author information

Correspondence to Homme W. Hellinga.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Materials (DOC 1863 kb)

Rights and permissions

Reprints and Permissions

About this article

Further reading

Figure 1: Structures of a representative receptor and all target ligands.
Figure 2: Stereo views of representative designed ligand-binding sites: a, TNT.R3; b, Lac.R1; c, Lac.H1; d, Stn.A1 (dashed lines indicate hydrogen bonds between protein and ligand; numbers identify side chains close to the ligand).
Figure 3: Synthetic two-component signal transduction pathway24.


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.