Elucidating photoinduced structural changes in phytochromes by the combined application of resonance Raman spectroscopy and theoretical methods

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Phytochromes constitute a family of red-light sensing photoreceptors in plants and microorganisms. The photoactive cofactor is an open-chain methine-bridged tetrapyrrole that, upon light absorption, undergoes a double bond isomerisation followed by series thermal relaxation processes which eventually lead to the functional structural change of the protein. Resonance Raman spectroscopy has contributed significantly to the understanding of the molecular functioning of these proteins although both the experiments and the interpretation of the spectra represent a considerable challenge. This account is dedicated to describe achievements, potential and limitations of combined resonance Raman spectroscopic and theoretical approaches for elucidating cofactor structures in phytochromes. Experimental approaches are discussed paying specific attention on strategies to overcome unwanted photochemical and photophysical processes when probing the various states of the photoinduced reaction cycle of phytochromes. The most comprehensive set of experimental data on phytochromes, including engineered protein variants and adducts formed with isotopically labelled tetrapyrroles, has been obtained by resonance Raman spectroscopy with near-infrared excitation that also allows probing phytochrome crystals without photo-induced destruction. Quantum mechanical calculations of Raman spectra of model compounds represent a first approximation for determining the methine bridge geometry of the protein-bound tetrapyrroles and constitute the basis for the identification of marker bands for specific structural properties such as the protonation state of the cofactor. Drawbacks of this theoretical method that inevitably neglects the protein environment have become evident with the first determinations of three-dimensional structures of phytochromes. These structural models can now be used for employing hybrid methods that combine quantum mechanical and molecular mechanics calculations of the cofactor and the protein matrix, respectively. Although further developments are required for a more accurate description of the protein force field, this methodology promises to become a powerful tool for a comprehensive extraction of structural information from the Raman spectra such it may allow refining structural models of the cofactor site derived by protein crystallography.