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.

Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR

Nature volume 449, pages 1078–1082 (2007)Cite this article

Abstract

Large-scale domain rearrangements in proteins have long been recognized to have a critical function in ligand binding and recognition, catalysis and regulation1,2,3,4,5. Crystal structures have provided a static picture of the apo (usually open) and holo usually closed) states. The general question arises as to whether the apo state exists as a single species in which the closed state is energetically inaccessible and interdomain rearrangement is induced by ligand or substrate binding, or whether the predominantly open form already coexists in rapid equilibrium with a minor closed species. The maltose-binding protein (MBP), a member of the bacterial periplasmic binding protein family6, provides a model system for investigating this problem because it has been the subject of extensive studies by crystallography7,8, NMR9,10,11 and other biophysical techniques11,12,13. Here we show that although paramagnetic relaxation enhancement (PRE) data for the sugar-bound form are consistent with the crystal structure of holo MBP, the PRE data for the apo state are indicative of a rapidly exchanging mixture (ns to μs regime) of a predominantly (∼95%) open form (represented by the apo crystal structure) and a minor (∼5%) partially closed species. Using ensemble simulated annealing refinement against the PRE data we are able to determine a 〈r-6〉 ensemble average structure of the minor apo species and show that it is distinct from the sugar-bound state.

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

Get just this article for as long as you need it

$39.95

Learn more

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

Figure 1: Domain reorientation of MBP on binding maltotriose.
Figure 2: PRE measurements on apo and holo MBP.
Figure 3: Simulated annealing refinement of the minor species of apo MBP.
Figure 4: Structure of the minor partly closed form of apo MBP.

References

  1. Anderson, C. M. & Zucker, F. H. Steitz, T. Space-filling models of kinase clefts and conformational change. Science 204, 375–380 (1979)

    Article  ADS  CAS  Google Scholar 

  2. Gerstein, M., Lesk, A. M. & Chothia, C. Structural mechanisms for domain movements in proteins. Biochemistry 33, 6739–6749 (1994)

    Article  CAS  Google Scholar 

  3. Gerstein, M. & Krebs, W. A. A database of macromolecular motions. Nucleic Acids Res. 26, 4280–4290 (1998)

    Article  CAS  Google Scholar 

  4. Hayward, S. & Berendsen, H. J. C. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins Struct. Funct. Genet. 30, 144–154 (1998)

    Article  CAS  Google Scholar 

  5. Wolf-Watz, M. et al. Linkage between dynamics and catalysis in a thermophilic–mesophilic enzyme pair. Nat. Struct. Mol. Biol. 11, 945–949 (2004)

    Article  CAS  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Sharff, A. J., Rodseth, L. E., Spurlino, J. C. & Quiocho, F. A. Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of maltodextrin binding protein involved in active transport and chemotaxis. Biochemistry 31, 10657–10663 (1992)

    Article  CAS  Google Scholar 

  8. Quiocho, F. A. & Spurlino, J. C. &. Rodseth, L. E. Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport/chemosensory receptor. Structure 5, 997–1015 (1997)

    Article  CAS  Google Scholar 

  9. Skynnikov, N. R. et al. Orienting domains in proteins using dipolar couplings measured by liquid-state NMR: differences in solution and crystal forms of maltodextrin binding protein loaded with β-cyclodextrin. J. Mol. Biol. 295, 1265–1273 (2000)

    Article  Google Scholar 

  10. Evenäs, J. et al. Ligand-induced structural changes to maltodextrin-binding protein as studied by solution NMR spectroscopy. J. Mol. Biol. 309, 961–974 (2001)

    Article  Google Scholar 

  11. Millet, O., Hudson, R. P. & Kay, L. E. The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy. Proc. Natl Acad. Sci. USA 100, 12700–12705 (2003)

    Article  ADS  CAS  Google Scholar 

  12. Hall, J. A., Thorgeirsson, T. E., Liu, J., Shin, Y. K. & Nikaido, H. Two modes of ligand binding in maltose-binding protein of Escherichia coli: electron paramagnetic resonance study of ligand-induced global conformational changes by site-directed spin labeling. J. Biol. Chem. 272, 17615–17622 (1997)

    Article  CAS  Google Scholar 

  13. Zhang, Y. et al. Model of maltose-binding protein/chemoreceptor complex supports intrasubunit signaling mechanism. Proc. Natl Acad. Sci. USA 96, 939–944 (1999)

    Article  ADS  CAS  Google Scholar 

  14. Iwahara, J. & Clore, G. M. Detecting transient intermediates in macromolecular binding by paramagnetic NMR. Nature 440, 1227–1230 (2006)

    Article  ADS  CAS  Google Scholar 

  15. Tang, C., Iwahara, J. & Clore, G. M. Visualization of transient encounter complexes in protein-protein association. Nature 444, 383–386 (2006)

    Article  ADS  CAS  Google Scholar 

  16. Clore, G. M. & Garrett, D. S. R-factor, free R and complete cross-validation for dipolar coupling refinement of NMR structures. J. Am. Chem. Soc. 121, 9008–9012 (1999)

    Article  CAS  Google Scholar 

  17. Iwahara, J., Schwieters, C. D. & Clore, G. M. Ensemble approach for NMR structure refinement against 1H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecules. J. Am. Chem. Soc. 126, 5879–5896 (2004)

    Article  CAS  Google Scholar 

  18. Clore, G. M. & Bewley, C. A. Using conjoined rigid body/torsion angle simulated annealing to determine the relative orientation of covalently linked protein domains from dipolar couplings. J. Magn. Reson. 154, 329–335 (2002)

    Article  ADS  CAS  Google Scholar 

  19. Zweckstetter, M., Hummer, G. & Bax, A. Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phases. Biophys. J. 86, 3444–3460 (1994)

    Article  Google Scholar 

  20. Palmer, A. G. NMR characterization of the dynamics of biomacromolecules. Chem. Rev. 104, 3623–3640 (2004)

    Article  CAS  Google Scholar 

  21. Duan, X. & Quiocho, F. A. Structural evidence for a dominant role of nonpolar interactions in the binding of a transport/chemosensory receptor to its highly polar ligands. Biochemistry 41, 706–712 (2002)

    Article  CAS  Google Scholar 

  22. Iwahara, J., Tang, C. & Clore, G. M. Practical aspects of 1H transverse paramagnetic relaxation enhancement measurements on macromolecules. J. Magn. Reson. 184, 185–195 (2007)

    Article  ADS  CAS  Google Scholar 

  23. Clore, G. M., Starich, M. R. & Gronenborn, A. M. Measurement of residual dipolar couplings of macromolecules aligned in a nematic phase of a colloidal suspension of rod-shaped viruses. J. Am. Chem. Soc. 120, 10571–10572 (1998)

    Article  CAS  Google Scholar 

  24. Schwieters, C. D., Kuszewski, J. & Clore, G. M. Using Xplor-NIH for NMR molecular structure determination. Progr. NMR Spectrosc. 48, 47–62 (2006)

    Article  CAS  Google Scholar 

  25. Schwieters, C. D. & Clore, G. M. Reweighted atomic densities to represent ensembles of NMR structures. J. Biomol. NMR 23, 221–225 (2002)

    Article  CAS  Google Scholar 

  26. Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA 98, 10037–10041 (2001)

    Article  ADS  CAS  Google Scholar 

  27. Ganesh, C., Shah, A. N., Swaminathan, C. P., Surolia, A. & Varadarajan, R. Thermodynamic characterization of the reversible, two-state unfolding of maltose binding protein, a large two-domain protein. Biochemistry 36, 5020–5028 (1997)

    Article  CAS  Google Scholar 

  28. Peruvshin, K., Riek, R., Wider, G. & Wüthrich, K. Attenuated T2 relaxation by mutual cancellation of dipole–dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biologial macromolecules in solution. Proc. Natl Acad. Sci. USA 94, 12366–12371 (1997)

    Article  ADS  Google Scholar 

  29. Yang, D. & Kay, L. E. TROSY triple-resonance four-dimensional NMR spectroscopy of a 46 ns tumbling protein. J. Am. Chem. Soc. 121, 2571–2575 (1999)

    Article  CAS  Google Scholar 

  30. Bax, A., Kontaxis, G. & Tjandra, N. Dipolar couplings in macromolecular structure determination. Methods Enzymol. 339, 127–174 (2001)

    Article  CAS  Google Scholar 

  31. Kontaxis, G., Clore, G. M. & Bax, A. Evaluation of cross-relaxation effects and measurement of one-bond couplings in proteins with short transverse relaxation times. J. Magn. Reson. 143, 184–196 (2000)

    Article  ADS  CAS  Google Scholar 

  32. Hwang, P. M., Skrynnikov, N. R. & Kay, L. E. Domain orientation in β-cyclodextrin-loaded maltose binding protein: diffusion anisotropy measurements confirm the results of a dipolar coupling study. J. Biomol. NMR 20, 83–88 (2001)

    Article  CAS  Google Scholar 

  33. Schwieters, C. D. & Clore, G. M. Internal coordinates for molecular dynamics and minimization in structure determination and refinement. J. Magn. Reson. 152, 288–302 (2001)

    Article  ADS  CAS  Google Scholar 

  34. Nilges, M., Gronenborn, A. M., Brünger, A. T. & Clore, G. M. Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints: application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng. 2, 27–38 (1988)

    Article  CAS  Google Scholar 

  35. Clore, G. M. & Kuszewski, J. χ1 rotamer populations and angles of mobile surface side chains are accurately predicted by a torsion angle database potential of mean force. J. Am. Chem. Soc. 124, 2866–2867 (2002)

    Article  CAS  Google Scholar 

  36. Suh, J.-Y., Iwahara, J. & Clore, G. M. Intramolecular domain–domain association/dissociation and phosphoryl transfer in the mannitol transporter of Escherichia coli are not coupled. Proc. Natl Acad. Sci. USA 104, 3153–3158 (2007)

    Article  ADS  CAS  Google Scholar 

  37. Svergun, D., Barberato, C. & Koch, M. H. J. CRYSOL: a program to evaluate X-ray scattering of biological macromolecules from atomic coordinates. J. Appl. Cryst. 28, 768–773 (1995)

    Article  CAS  Google Scholar 

  38. DeLano, W. L. The PyMol Molecular Graphics System, 〈http://www.pymol.org〉 (DeLano Scientific, San Carlos, CA, 2002)

    Google Scholar 

Download references

Acknowledgements

We thank J. Iwahara, A. Grishaev and A. Szabo for helpful discussions; and A. Grishaev and L. Guo for assistance with SAXS data collection and processing. Use of the Advanced Photon Source was supported by the US Department of Energy, Basic Energy Sciences, Office of Science. BioCAT is a National Institutes of Health-supported Research Center. This work was supported by funds from the Intramural Program of the NIH, the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) and the AIDS Targeted Antiviral program of the Office of the Director of the NIH (to G.M.C.).

An ensemble of 50 sets of coordinates for the equilibrium mixture of major (95%) open and minor (5%) partly closed species of MBP, together with the PRE experimental restraints, are deposited in the Protein Data Bank with accession codes 2V93 and R2V93MR, respectively.

Author information

Authors and Affiliations

  1. Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA ,

    Chun Tang & G. Marius Clore

  2. Division of Computational Bioscience, Building 12A, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892-5624, USA,

    Charles D. Schwieters

Authors
  1. Chun Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Charles D. Schwieters
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. G. Marius Clore
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to G. Marius Clore.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains Supplementary Figures S1-S17 and Supplementary Table S1 with Legends, Supplementary Notes and additional references. (PDF 2358 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Tang, C., Schwieters, C. & Clore, G. Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR. Nature 449, 1078–1082 (2007). https://doi.org/10.1038/nature06232

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature06232

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