Conformational changes: How small is big enough? (original) (raw)

Nature Medicine volume 4, pages 1112–1114 (1998)Cite this article

The finding that small conformational changes are important in protein function is the ending of an old controversy and the beginning of new applications. The induced-fit theory proposed1,2,3,4,5 that protein flexibility is an essential characteristic of enzymes, in contrast to the rather rigid key-lock or template theory of Emil Fischer — that is, a hand-in-glove type of flexible fit versus the jig-saw puzzle type of rigid fit. The induced-fit theory was stated in the following terms: the precise orientation of catalytic groups is required for enzyme action; the substrate causes an appreciable change in the three-dimensional relationship of the amino acids of the protein; and the changes in the protein structure caused by the substrate will bring the catalytic groups into the proper alignment, whereas the non-substrate will not. The induced fit theory explained many anomalies–such as the ability of enzymes to exclude omnipresent water, regulation outside the active site and non-competitive inhibition–but it was at first greeted with skepticism, as are all theories that confront long-established concepts.

When the first two structures of enzymes (lysozyme and ribonuclease) were solved by x-ray crystallography6,7, small conformational changes were found between the structures of the enzyme in the absence and in the presence of substrate. I was surprised that these small changes were discarded as unimportant, rather than being cited as a confirmation of the new theory. Later, large changes in conformation of the enzyme carboxypeptidase (Lipscomb and co-workers8) and of hexokinase (Steitz and colleagues9) were observed, and the induced-fit theory is in all biochemistry textbooks today. However, the question I set out to answer in the beginning (which is still relevant today) was: „How small of a conformational change is big enough?” Because the induced-fit theory was proposed before crystallography had been successfully applied to proteins, the size of the conformational change was defined in functional terms; that is, a change big enough to produce the desired catalysis. With many X-ray structures of enzymes today, almost all of which show conformational changes10, the question has become: „Are all of the changes important? And if not, which ones are?” Fortunately, the tools are now available to answer that question, as it has become even more relevant as we explore ways to apply enzymology to solve medical problems of therapy and chemical problems of new materials.

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

Relevant articles

Open Access articles citing this article.

Access options

Subscribe to this journal

Receive 12 print issues and online access

$209.00 per year

only $17.42 per issue

Buy this article

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

Additional access options:

Figure 1: Superpositions of various isocitrate dehydrogenase complexes, including isocitrate-Mg2+-NHDP (green) and isocitrate-Ca2+-NADP (pink), Y160F-IDH-isocitrate-Mg2+-NADP (blue) solved by time-resolved Laue crystallography, and IDH-NADP (yellow).

References

  1. Koshland, D.E. Application of a Theory of Enzyme Specificity to Protein Synthesis. Proc. Natl. Acad. Sci. USA 44, 98– 104 (1958).
    Article CAS Google Scholar
  2. Koshland, D.E. Correlation of Structure and Function in Enzyme Action. Science 142, 1533–1541 ( 1963).
    Article CAS Google Scholar
  3. Koshland, D.E. The Role of Flexibility in Enzyme Action. Cold Spring Harbor Symp. Quant. Biol. 28, 473–482 (1963).
    Article Google Scholar
  4. Thoma, J.A. & Koshland, D.E. Competitive Inhibition by Substrate During Enzyme Action Evidence for the Induced-Fit Theory. J. Am. Chem. Soc. 82, 3329–3333 (1960).
    Article CAS Google Scholar
  5. Yankeelov, J.A. & Koshland, D.E. Evidence for Conformation Changes Induced by Substrates of Phosphoglucomutase. J. Biol. Chem. 240, 1593–1602 (1965).
    CAS PubMed Google Scholar
  6. Blake, C.C.F. et al. Structure of hen egg white lysozyme. Nature 206, 757–761 (1965).
    Article CAS Google Scholar
  7. Wyckoff, H.W. et al. Structure of ribonuclease-S at 6Å Resolution,. J. Biol. Chem. 242, 3749–3753 (1967).
    CAS PubMed Google Scholar
  8. Steitz, T.A., Ludwig, M.L., Quiocho, F.A. & Lipscomb, W.N. The Structure of Carboxypepidase A. V. Studies of Enzyme-Substrate and Enzyme-Inhibitor Complexes at 6Å Resolution. J. Biol. Chem. 242 , 4662–4668 (1967).
    CAS PubMed Google Scholar
  9. Anderson, C.M., Zucker, F.H. & Steitz, T.A. Space-Filling Models of Kinase Clefts and Conformation Changes. Science 204, 375– 380 (1979).
    Article CAS Google Scholar
  10. Gerstein, M., Lesk, A.M. & Chothia, C. Structural Mechanisms for Domain Movements in Proteins. Biochem. 33, 6739–6749 (1994).
    Article CAS Google Scholar
  11. Mesecar, A.D., Stoddard, B.L. & Koshland, D.E.. Orbital Steering in the Catalytic Power of Enzymes: Small Structural Changes with Large Catalytic Consequences. Science 277, 202–206 ( 1997).
    Article CAS Google Scholar
  12. Milburn, M.V. et al. Three-Dimensional Structures of the Ligand-Binding Domain of the Bacterial Aspartate Receptor With and Without a Ligand. Science 254, 1342–1347 ( 1991).
    Article CAS Google Scholar
  13. Adler, J. Chemotaxis in Bacteria. Science 153, 708 –716 (1966).
    Article CAS Google Scholar
  14. Koshland, D.E. in Bacterial Chemotaxis as a Model Behavioral System (Raven, New York, 1980)
    Google Scholar
  15. Ottemann, K.M., Thorgeirsson, T.E., Kolodziej, A.F., Shin, Y.K. & Koshland, D.E. Direct measurement of small ligand-induced conformational changes in the aspartate receptor using EPR. Biochem. 37, 7062–7069 ( 1998).
    Article CAS Google Scholar
  16. Chen, X. & Koshland, D.E. Probing the Structure of the Cytoplasmic Domain of the Aspartate Receptor by Targeted Disulfide Cross-Linking. Biochem. 39, 11858–11864 (1997).
    Article Google Scholar
  17. Kolodziej, A.F., Tan, T. & Koshland, D.E. Producing Positive, Negative, and No Cooperativity by Mutations at a Single Residue Located at the Subunit Interface in the Aspartate Receptor of Salmonella typhimurium. Biochem. 35, 14782–14792 (1996).
    Article CAS Google Scholar
  18. Milligan, D.L. & Koshland, D.E. Purification and Characterization of the Periplasmic Domain of the Aspartate Chemoreceptor. J. Biol. Chem. 268, 19991– 19997 (1993).
    CAS PubMed Google Scholar
  19. Biemann, H.-P. & Koshland, D.E. Aspartate Receptors of Escherichia coli and Salmonella typhimurium Bind Ligand with Negative and Half-of-Sites Cooperativity. Biochem. 33, 629–634 (1994).
    Article CAS Google Scholar
  20. Berg, H., Segal, J.E. & Block, S.M.. Temporal Comparisons on Bacterial Chemotaxis. Proc. Natl. Acad. Sci. USA 83, 8989– 8991 (1986).
    Article Google Scholar
  21. Baylor, D.A., Lamb, T.D. & Yaw, K.W. The Membrane Current of Single Rod Outer Segments. J. Physiol. 288, 107–127 (1979).
    CAS PubMed PubMed Central Google Scholar
  22. Hecht, S., Shlaer, S. & Perenne, M.H. Energy, quanta & vision. J. Gen. Physiol. 25, 819 (1942).
    Article CAS Google Scholar
  23. Koshland, D.E. Evolution of Catalytic Function. Cold Spring Harbor Symp. Quant. Biol. 52, 1 (1987).
    Article CAS Google Scholar
  24. Koshland, D.E. The Evolution of Function in Enzymes. Fed. Proc. 35 , 2104–2111 (1976).
    CAS PubMed Google Scholar
  25. Stemmer, W.P. . Rapid Evolution of a Protein in vitro by DNA Shuffling. Nature 370, 389–391 ( 1994).
    Article CAS Google Scholar

Download references

Acknowledgements

This author acknowledges funding from the National Science Foundation, the National Institutes of Health and the W.M. Keck Foundation.

Author information

Authors and Affiliations

  1. Department of Molecular & Cell Biology, University of California, 229 Stanley Hall, Berkley, 94720-3206, CA
    Daniel E. Koshland Jr.

Authors

  1. Daniel E. Koshland Jr.
    You can also search for this author inPubMed Google Scholar

Rights and permissions

About this article

Cite this article

Koshland , D. Conformational changes: How small is big enough? .Nat Med 4, 1112–1114 (1998). https://doi.org/10.1038/2605

Download citation

This article is cited by