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Dynamically driven protein allostery

Nature Structural & Molecular Biology volume 13, pages 831–838 (2006)Cite this article

Abstract

Allosteric interactions are typically considered to proceed through a series of discrete changes in bonding interactions that alter the protein conformation. Here we show that allostery can be mediated exclusively by transmitted changes in protein motions. We have characterized the negatively cooperative binding of cAMP to the dimeric catabolite activator protein (CAP) at discrete conformational states. Binding of the first cAMP to one subunit of a CAP dimer has no effect on the conformation of the other subunit. The dynamics of the system, however, are modulated in a distinct way by the sequential ligand binding process, with the first cAMP partially enhancing and the second cAMP completely quenching protein motions. As a result, the second cAMP binding incurs a pronounced conformational entropic penalty that is entirely responsible for the observed cooperativity. The results provide strong support for the existence of purely dynamics-driven allostery.

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Figure 1: Distinct conformational states of CAPN.
Figure 2: Effect of sequential cAMP binding on the structure of CAPN, assessed by chemical shift mapping.
Figure 3: Effect of sequential cAMP binding on the slow motions of CAPN.
Figure 4: CPMG relaxation dispersion data of 15N backbone amides of CAPN.
Figure 5: Effect of sequential cAMP binding on the fast motions of CAPN.
Figure 6: Effect of sequential binding of cAMP to CAPN on amide exchange rates, shown as the kex1/kex2 ratio for binding of each cAMP molecule (where kex1 and kex2 are exchange rates before and after cAMP binding, respectively).
Figure 7: Energetics of cooperative sequential binding of cAMP to CAPN.
Figure 8: Effect of sequential binding of cAMP on order parameters of CAPN.
Figure 9: Overall effect of sequential cAMP binding on conformation and dynamics of CAPN.

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Acknowledgements

We thank P. Loria (Yale) and P. Huskey (Rutgers) for providing us with scripts for the analysis of some of the relaxation data. This work was supported by US National Science Foundation grant MCB-0618259 to C.G.K. and by US National Institutes of Health grant GM41376 and a Howard Hughes Medical Institute investigatorship to R.H.E.

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Authors and Affiliations

  1. Department of Chemistry, Rutgers University, Newark, 07102, New Jersey, USA

    Nataliya Popovych, Shangjin Sun & Charalampos G Kalodimos

  2. Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry, Rutgers University, Piscataway, 08854, New Jersey, USA

    Richard H Ebright

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Correspondence to Charalampos G Kalodimos.

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Supplementary information

Supplementary Fig. 1

Molecular drawing of CAPN. (PDF 412 kb)

Supplementary Fig. 2

Classes of chemical shift behavior of CAPN during its sequential interaction with cAMP. (PDF 214 kb)

Supplementary Fig. 3

Relaxation rates of CAPN as a function of the ligation state. (PDF 350 kb)

Supplementary Fig. 4

Overlaid HSQC spectra of CAPN as a function of the ligation state. (PDF 347 kb)

Supplementary Figure 5

Rex values of cAMP1-CAPN at two cAMP concentrations. (PDF 305 kb)

Supplementary Figure 6

Changes in order parameters upon sequential cAMP binding. (PDF 305 kb)

Supplementary Discussion

Contribution to Rex from cAMP binding and dissociation is negligible. (PDF 303 kb)

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Popovych, N., Sun, S., Ebright, R. et al. Dynamically driven protein allostery. Nat Struct Mol Biol 13, 831–838 (2006). https://doi.org/10.1038/nsmb1132

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