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Intrinsic dynamics of an enzyme underlies catalysis


A unique feature of chemical catalysis mediated by enzymes is that the catalytically reactive atoms are embedded within a folded protein. Although current understanding of enzyme function has been focused on the chemical reactions and static three-dimensional structures, the dynamic nature of proteins has been proposed to have a function in catalysis1,2,3,4,5. The concept of conformational substates has been described6; however, the challenge is to unravel the intimate linkage between protein flexibility and enzymatic function. Here we show that the intrinsic plasticity of the protein is a key characteristic of catalysis. The dynamics of the prolyl cistrans isomerase cyclophilin A (CypA) in its substrate-free state and during catalysis were characterized with NMR relaxation experiments. The characteristic enzyme motions detected during catalysis are already present in the free enzyme with frequencies corresponding to the catalytic turnover rates. This correlation suggests that the protein motions necessary for catalysis are an intrinsic property of the enzyme and may even limit the overall turnover rate. Motion is localized not only to the active site but also to a wider dynamic network. Whereas coupled networks in proteins have been proposed previously3,7,8,9,10, we experimentally measured the collective nature of motions with the use of mutant forms of CypA. We propose that the pre-existence of collective dynamics in enzymes before catalysis is a common feature of biocatalysts and that proteins have evolved under synergistic pressure between structure and dynamics.

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Figure 1: Protein dynamics necessary for catalysis is an intrinsic property of the enzyme.
Figure 2: Identification of residues that build a common dynamic network in CypA.
Figure 3: Probing correlated motions of CypA by point mutations.


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We thank K. H. Wildman for discussions. This work was supported by NIH grants to D.K., by a grant from the Canadian Institutes of Health Research to L.E.K., and by a grant from the Swedish Research Council to M.W.W. Part of the NMR studies was performed at the NHMFL at Florida with support from the NSF.

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Corresponding author

Correspondence to Dorothee Kern.

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Reprints and permissions information is available at The authors declare no competing financial interests.

Supplementary information

Supplementary Figure 1

Concentration dependence of relaxation dispersion data for CypA. (PDF 216 kb)

Supplementary Figure 2

Quantitative analysis of protein dynamics of free CypA at 25°C. (PDF 197 kb)

Supplementary Figure 3

Pre-existing motions within the active site of CypA. (PDF 210 kb)

Supplementary Figure 4

Backbone amide chemical shift differences of CypA mutants. (PDF 258 kb)

Supplementary Figure Legends

Text to accompany the above Supplementary Figures. (DOC 30 kb)

Supplementary Tables

Supplementary Tables 1–4. (DOC 157 kb)

Supplementary Methods

Additional descriptions of methods used in this study. (DOC 29 kb)

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Eisenmesser, E., Millet, O., Labeikovsky, W. et al. Intrinsic dynamics of an enzyme underlies catalysis. Nature 438, 117–121 (2005).

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