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 catalysis^{1, 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 cis–trans 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 previously^{3, 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.

1. Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
2. Departments of Medical Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
3. National High Magnetic Field Laboratory at Florida State University, Tallahassee, Florida 32310, USA
4. †Present addresses: Plataforma de Biomolecules, Parc Cientific de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Catalonia, Spain (O.M.); The Scripps Research Institute, Department of Chemistry, La Jolla, California 92037, USA (D.A.B.); University of Utah School of Medicine, Department of Biochemistry, Salt Lake City, Utah 84132, USA (J.J.S.); University of Umeå, Department of Biochemistry, Umeå SE-901 87, Sweden (M.W.W.)

Correspondence to: Dorothee Kern¹ Correspondence and requests for materials should be addressed to D.K. (Email: dkern@brandeis.edu).

Received 27 June 2005; Accepted 3 August 2005

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