Ultrafast infrared spectroscopy reveals water-mediated coherent dynamics in an enzyme active site

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Adamczyk, Katrin and Simpson, Niall and Greetham, Gregory M. and Gumiero, Andrea and Walsh, Martin A. and Towrie, Michael and Parker, Anthony W. and Hunt, Neil (2015) Ultrafast infrared spectroscopy reveals water-mediated coherent dynamics in an enzyme active site. Chemical Science, 6 (1). pp. 505-516. ISSN 2041-6539 (https://doi.org/10.1039/c4sc02752c)

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Abstract

Understanding the impact of fast dynamics upon the chemical processes occurring within the active sites of proteins and enzymes is a key challenge that continues to attract significant interest, though direct experimental insight in the solution phase remains sparse. Similar gaps in our knowledge exist in understanding the role played by water, either as a solvent or as a structural/dynamic component of the active site. In order to investigate further the potential biological roles of water, we have employed ultrafast multidimensional infrared spectroscopy experiments that directly probe the structural and vibrational dynamics of NO bound to the ferric haem of the catalase enzyme from Corynebacterium glutamicum in both H2O and D2O. Despite catalases having what is believed to be a solvent-inaccessible active site, an isotopic dependence of the spectral diffusion and vibrational lifetime parameters of the NO stretching vibration are observed, indicating that water molecules interact directly with the haem ligand. Furthermore, IR pump-probe data feature oscillations originating from the preparation of a coherent superposition of low-frequency vibrational modes in the active site of catalase that are coupled to the haem ligand stretching vibration. Comparisons with an exemplar of the closely-related peroxidase enzyme family shows that they too exhibit solvent-dependent active-site dynamics, supporting the presence of interactions between the haem ligand and water molecules in the active sites of both catalases and peroxidases that may be linked to proton transfer events leading to the formation of the ferryl intermediate Compound I. In addition, a strong, water-mediated, hydrogen bonding structure is suggested to occur in catalase that is not replicated in peroxidase; an observation that may shed light on the origins of the different functions of the two enzymes.

ORCID iDs

Adamczyk, Katrin, Simpson, Niall ORCID logoORCID: https://orcid.org/0000-0003-3139-472X, Greetham, Gregory M., Gumiero, Andrea, Walsh, Martin A., Towrie, Michael, Parker, Anthony W. and Hunt, Neil ORCID logoORCID: https://orcid.org/0000-0001-7400-5152;
CORE (COnnecting REpositories)