Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

The spatial architecture of protein function and adaptation

Nature volume 491, pages 138–142 (2012)Cite this article

Subjects

Abstract

Statistical analysis of protein evolution suggests a design for natural proteins in which sparse networks of coevolving amino acids (termed sectors) comprise the essence of three-dimensional structure and function1,2,3,4,5. However, proteins are also subject to pressures deriving from the dynamics of the evolutionary process itself—the ability to tolerate mutation and to be adaptive to changing selection pressures6,7,8,9,10. To understand the relationship of the sector architecture to these properties, we developed a high-throughput quantitative method for a comprehensive single-mutation study in which every position is substituted individually to every other amino acid. Using a PDZ domain (PSD95pdz3) model system, we show that sector positions are functionally sensitive to mutation, whereas non-sector positions are more tolerant to substitution. In addition, we find that adaptation to a new binding specificity initiates exclusively through variation within sector residues. A combination of just two sector mutations located near and away from the ligand-binding site suffices to switch the binding specificity of PSD95pdz3 quantitatively towards a class-switching ligand. The localization of functional constraint and adaptive variation within the sector has important implications for understanding and engineering proteins.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Sector architecture in the PDZ domain family.
Figure 2: Complete single mutagenesis in PSD95pdz3.
Figure 3: The relationship of mutational sensitivity of positions to the protein sector.
Figure 4: Adaptation through sector variation.

References

  1. Halabi, N., Rivoire, O., Leibler, S. & Ranganathan, R. Protein sectors: evolutionary units of three-dimensional structure. Cell 138, 774–786 (2009)

    Article  CAS  Google Scholar 

  2. Lockless, S. W. & Ranganathan, R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286, 295–299 (1999)

    Article  CAS  Google Scholar 

  3. Russ, W. P., Lowery, D. M., Mishra, P., Yaffe, M. B. & Ranganathan, R. Natural-like function in artificial WW domains. Nature 437, 579–583 (2005)

    Article  ADS  CAS  Google Scholar 

  4. Socolich, M. et al. Evolutionary information for specifying a protein fold. Nature 437, 512–518 (2005)

    Article  ADS  CAS  Google Scholar 

  5. Süel, G. M., Lockless, S. W., Wall, M. A. & Ranganathan, R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nature Struct. Mol. Biol. 10, 59–69 (2003)

    Article  Google Scholar 

  6. Bershtein, S., Segal, M., Bekerman, R., Tokuriki, N. & Tawfik, D. S. Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein. Nature 444, 929–932 (2006)

    Article  ADS  CAS  Google Scholar 

  7. Bloom, J. D., Labthavikul, S. T., Otey, C. R. & Arnold, F. H. Protein stability promotes evolvability. Proc. Natl Acad. Sci. USA 103, 5869–5874 (2006)

    Article  ADS  CAS  Google Scholar 

  8. Draghi, J. A., Parsons, T. L., Wagner, G. P. & Plotkin, J. B. Mutational robustness can facilitate adaptation. Nature 463, 353–355 (2010)

    Article  ADS  CAS  Google Scholar 

  9. Tiana, G., Shakhnovich, B. E., Dokholyan, N. V. & Shakhnovich, E. I. Imprint of evolution on protein structures. Proc. Natl Acad. Sci. USA 101, 2846–2851 (2004)

    Article  ADS  CAS  Google Scholar 

  10. Voigt, C. A., Kauffman, S. & Wang, Z. G. Rational evolutionary design: the theory of in vitro protein evolution. Adv. Protein Chem. 55, 79–160 (2000)

    Article  CAS  Google Scholar 

  11. Anfinsen, C. B. Principles that govern the folding of protein chains. Science 181, 223–230 (1973)

    Article  ADS  CAS  Google Scholar 

  12. Reynolds, K. A., McLaughlin, R. N. & Ranganathan, R. Hot spots for allosteric regulation on protein surfaces. Cell 147, 1564–1575 (2011)

    Article  CAS  Google Scholar 

  13. Peterson, F. C., Penkert, R. R., Volkman, B. F. & Prehoda, K. E. Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transition. Mol. Cell 13, 665–676 (2004)

    Article  CAS  Google Scholar 

  14. Hatley, M. E., Lockless, S. W., Gibson, S. K., Gilman, A. G. & Ranganathan, R. Allosteric determinants in guanine nucleotide-binding proteins. Proc. Natl Acad. Sci. USA 100, 14445–14450 (2003)

    Article  ADS  CAS  Google Scholar 

  15. Shulman, A. I., Larson, C., Mangelsdorf, D. J. & Ranganathan, R. Structural determinants of allosteric ligand activation in RXR heterodimers. Cell 116, 417–429 (2004)

    Article  CAS  Google Scholar 

  16. Smock, R. R. O., Russ, W. P., Swain, J. F., Leibler, S., Ranganathan, R. & Gierasch, L. M. An interdomain sector mediating allostery in Hsp70 molecular chaperones. Mol. Syst. Biol. 6, 414 (2010)

    Article  Google Scholar 

  17. Bradley, P., Misura, K. M. S. & Baker, D. Toward high-resolution de novo structure prediction for small proteins. Science 309, 1868–1871 (2005)

    Article  ADS  CAS  Google Scholar 

  18. Kuhlman, B. et al. Design of a novel globular protein fold with atomic-level accuracy. Science 302, 1364–1368 (2003)

    Article  ADS  CAS  Google Scholar 

  19. Hilser, V. J. & Thompson, E. B. Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins. Proc. Natl Acad. Sci. USA 104, 8311–8315 (2007)

    Article  ADS  CAS  Google Scholar 

  20. Chi, C. N. et al. Reassessing a sparse energetic network within a single protein domain. Proc. Natl Acad. Sci. USA 105, 4679–4684 (2008)

    Article  ADS  CAS  Google Scholar 

  21. Dove, S. L., Joung J. K & Hochschild, A. Activation of prokaryotic transcription through arbitrary protein-protein contacts. Nature 386, 627–630 (1997)

    Article  ADS  CAS  Google Scholar 

  22. Niethammer, M. et al. CRIPT, a novel postsynaptic protein that binds to the third PDZ domain of PSD-95/SAP90. Neuron 20, 693–707 (1998)

    Article  CAS  Google Scholar 

  23. Adkar, B. V. et al. Protein model discrimination using mutational sensitivity derived from deep sequencing. Structure 20, 371–381 (2012)

    Article  CAS  Google Scholar 

  24. Fowler, D. M. et al. High-resolution mapping of protein sequence-function relationships. Nature Methods 7, 741–746 (2010)

    Article  CAS  Google Scholar 

  25. Kinney, J. B., Murugan, A., Callan, C. G. & Cox, E. C. Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc. Natl Acad. Sci. USA 107, 9158–9163 (2010)

    Article  ADS  CAS  Google Scholar 

  26. van Opijnen, T., Bodi, K. L. & Camilli, A. Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nature Methods 6, 767–772 (2009)

    Article  CAS  Google Scholar 

  27. Whipple, F. W., Ptashne, M. & Hochschild, A. The activation defect of a λ-cI positive control mutant. J. Mol. Biol. 265, 261–265 (1997)

    Article  CAS  Google Scholar 

  28. Clackson, T. & Wells J. A A hot spot of binding energy in a hormone-receptor interface. Science 267, 383–386 (1995)

    Article  ADS  CAS  Google Scholar 

  29. Songyang, Z. et al. Recognition of unique carboxyl-terminal motifs by distinct PDZ domains. Science 275, 73–77 (1997)

    Article  CAS  Google Scholar 

  30. Kussell, E. & Leibler, S. Phenotypic diversity, population growth, and information in fluctuating environments. Science 309, 2075–2078 (2005)

    Article  ADS  CAS  Google Scholar 

  31. Studier, F. W. Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif. 41, 207–234 (2005)

    Article  CAS  Google Scholar 

  32. Lutz, R. & Bujard, H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. 25, 1203–1210 (1997)

    Article  CAS  Google Scholar 

  33. Elowitz, M. B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335–338 (2000)

    Article  ADS  CAS  Google Scholar 

  34. Bushman, F. D., Shang, C. & Ptashne, M. A single glutamic acid residue plays a key role in the transcriptional activation function of lambda repressor. Cell 58, 1163–1171 (1989)

    Article  CAS  Google Scholar 

  35. Jain, D., Nickels, B. E., Sun, L., Hochschild, A. & Darst, S. A. Structure of a ternary transcription activation complex. Mol. Cell 13, 45–53 (2004)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank W. Russ, P. Mishra and other members of the Ranganathan laboratory for contributions to this work, W. Wakeland and C. Liang for assistance with Solexa sequencing, E. Curry and A. Mobley for assistance with flow cytometry, and M. Elowitz for providing the pZ plasmids. We acknowledge support from the University of Texas Southwestern Graduate School and Pharmacology Training Grant (R. N. M.), the Helen Hay Whitney Fellowship program (F.J.P.) and support from the National Institutes of Health (R01EY018720-05, R.R.), The Robert A. Welch Foundation (I-1366, R.R.) and the Green Center for Systems Biology (R.R.).

Author information

Author notes

  1. Richard N. McLaughlin Jr

    Present address: Present address: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109-1024, USA.,

Authors and Affiliations

  1. Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, 75390-9050, Texas, USA

    Richard N. McLaughlin Jr, Frank J. Poelwijk, Arjun Raman, Walraj S. Gosal & Rama Ranganathan

  2. Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, 75390-9050, Texas, USA

    Richard N. McLaughlin Jr, Frank J. Poelwijk, Arjun Raman, Walraj S. Gosal & Rama Ranganathan

Authors
  1. Richard N. McLaughlin Jr
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Frank J. Poelwijk
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Arjun Raman
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Walraj S. Gosal
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Rama Ranganathan
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

R.N.M. and R.R. developed the research plan and experimental strategy. R.N.M. built the B2H assay, collected the data and wrote and executed the code for analysis of the B2H and sequencing data. F.J.P. and W.S.G. improved the dynamic range of the B2H assay. A.R. carried out the mutational analysis in Fig. 4 e, f. R.N.M. and R.R. analysed the data and wrote the paper.

Corresponding author

Correspondence to Rama Ranganathan.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-7, Supplementary Data and Supplementary References. (PDF 2404 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

McLaughlin Jr, R., Poelwijk, F., Raman, A. et al. The spatial architecture of protein function and adaptation. Nature 491, 138–142 (2012). https://doi.org/10.1038/nature11500

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature11500

This article is cited by

Comments

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.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing