Structural basis for catalytically restrictive dynamics of a high-energy enzyme state.

Michael Kovermann,A Elisabeth Sauer-Eriksson,Uwe H Sauer,Jörgen Ådén,Magnus Wolf-Watz,Christin Grundström

doi:10.1038/ncomms8644

Michael Kovermann, A Elisabeth Sauer-Eriksson + Show 4 more

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https://doi.org/10.1038/ncomms8644

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Journal: Nature Communications	Publication Date: Jul 3, 2015
Citations: 39	License type: CC BY 4.0

Affiliation: Umeå University

Abstract

An emerging paradigm in enzymology is that transient high-energy structural states play crucial roles in enzymatic reaction cycles. Generally, these high-energy or ‘invisible' states cannot be studied directly at atomic resolution using existing structural and spectroscopic techniques owing to their low populations or short residence times. Here we report the direct NMR-based detection of the molecular topology and conformational dynamics of a catalytically indispensable high-energy state of an adenylate kinase variant. On the basis of matching energy barriers for conformational dynamics and catalytic turnover, it was found that the enzyme's catalytic activity is governed by its dynamic interconversion between the high-energy state and a ground state structure that was determined by X-ray crystallography. Our results show that it is possible to rationally tune enzymes' conformational dynamics and hence their catalytic power—a key aspect in rational design of enzymes catalysing novel reactions.

Highlights

An emerging paradigm in enzymology is that transient high-energy structural states play crucial roles in enzymatic reaction cycles
The dynamic interconversions of enzymes’ ground and high-energy states have mainly been characterized indirectly via nuclear magnetic resonance (NMR) relaxation dispersion experiments[1,2], which have been used to unravel the catalytic cycles of cyclophilin A (CypA)[3,4], adenylate kinase (AdK)[5], dihydrofolate reductase (DHFR)[6] and RNase A7, and to explore the structures of sparsely populated folding intermediates[8]
The high-energy AdK state corresponds to an open substrate-bound conformation that is in equilibrium with a stable substrate-bound ground state populating a closed structure

Summary

Introduction

An emerging paradigm in enzymology is that transient high-energy structural states play crucial roles in enzymatic reaction cycles. An enzyme’s capacity to enhance the rate of its catalysed reaction depends on its ability to reduce the free energy of transition state compound(s) (that is, formation of Michaelis’ complexes), activate functional groups, dehydrate active sites and align substrates in an optimal geometry for reaction These functionalities are linked to the enzymes’ conformational dynamics, which are defined in terms of the timedependent displacement of atomic coordinates. In an enzymatic reaction cycle, it is possible to identify stable ground states that can be characterized experimentally using techniques such as X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. Such ground states include substrate-free and substrate-bound states, but high-resolution ground state structures alone cannot fully explain enzymes’ catalytic power. Our results show that it is possible to tune catalytically relevant enzyme dynamics, which is essential for the de novo design of enzymes[15]

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