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

Katrin Adamczyk, Niall Simpson, Gregory M. Greetham, Andrea Gumiero, Martin A. Walsh, Michael Towrie, Anthony W. Parker, Neil Hunt

Research output: Contribution to journalArticle

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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.

Original languageEnglish
Pages (from-to)505-516
Number of pages12
JournalChemical Science
Volume6
Issue number1
Early online date22 Oct 2014
DOIs
Publication statusPublished - 1 Jan 2015

Fingerprint

Catalase
Infrared spectroscopy
Heme
Water
Enzymes
Ligands
Peroxidase
Stretching
Peroxidases
Molecules
Proton transfer
Structural dynamics
Vibrational spectra
Hydrogen bonds
Pumps
Proteins
Experiments

Keywords

  • chemical processing
  • fast dynamics
  • ultrafast multidimensional infrared spectroscopy

Cite this

Adamczyk, K., Simpson, N., Greetham, G. M., Gumiero, A., Walsh, M. A., Towrie, M., ... Hunt, N. (2015). Ultrafast infrared spectroscopy reveals water-mediated coherent dynamics in an enzyme active site. Chemical Science, 6(1), 505-516. https://doi.org/10.1039/c4sc02752c
Adamczyk, Katrin ; Simpson, Niall ; Greetham, Gregory M. ; Gumiero, Andrea ; Walsh, Martin A. ; Towrie, Michael ; Parker, Anthony W. ; Hunt, Neil. / Ultrafast infrared spectroscopy reveals water-mediated coherent dynamics in an enzyme active site. In: Chemical Science. 2015 ; Vol. 6, No. 1. pp. 505-516.
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Adamczyk, K, Simpson, N, Greetham, GM, Gumiero, A, Walsh, MA, Towrie, M, Parker, AW & Hunt, N 2015, 'Ultrafast infrared spectroscopy reveals water-mediated coherent dynamics in an enzyme active site', Chemical Science, vol. 6, no. 1, pp. 505-516. https://doi.org/10.1039/c4sc02752c

Ultrafast infrared spectroscopy reveals water-mediated coherent dynamics in an enzyme active site. / Adamczyk, Katrin; Simpson, Niall; Greetham, Gregory M.; Gumiero, Andrea; Walsh, Martin A.; Towrie, Michael; Parker, Anthony W.; Hunt, Neil.

In: Chemical Science, Vol. 6, No. 1, 01.01.2015, p. 505-516.

Research output: Contribution to journalArticle

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Adamczyk K, Simpson N, Greetham GM, Gumiero A, Walsh MA, Towrie M et al. Ultrafast infrared spectroscopy reveals water-mediated coherent dynamics in an enzyme active site. Chemical Science. 2015 Jan 1;6(1):505-516. https://doi.org/10.1039/c4sc02752c