Measuring and modelling dynamical changes in the structure of photoactive yellow protein

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Biological photoreceptors are very suitable for studies of the structure–function relationship in proteins. Of the many possible candidates, from at least six different families, we discuss here photoactive yellow protein (PYP, a member of the Xanthopsin family). The excellent physical and photochemical stability of PYP has allowed recording of a large amount of data relevant for this characteristic. The timescales relevant for functional transitions in PYP are most easily studied with transient spectroscopy. Application of the combination of UV/Vis and FTIR spectroscopy has revealed (besides multiple electronically excited states) the subsequent involvement of the following transient intermediates: I0, pR1, pR2, pB′, pB and pBdeprot. The structures of these transient intermediates have been characterized with general structural techniques like X-ray diffraction and NMR spectroscopy. Most extensive results have been obtained with X-ray diffraction, applied both in a time-resolved mode and by making use of low-temperature trapping. This has led to a detailed description of the reversible spatial changes in PYP that follow light activation. The structure of the transient intermediates, however, is exquisitely sensitive to constraints from the molecular environment of the protein, like the absence/presence of a crystalline lattice. Extrapolating these results to the signalling state of PYP in vivo is extremely complicated but also very challenging. Rather than measure, one can also simulate and/or calculate the spatial structures of transient intermediates of PYP. This challenge is most straightforwardly tackled with a detailed analysis of the intrinsic dynamics of the stable receptor state of PYP. Such studies have revealed striking similarities in the dynamics of all PAS domain proteins of which a spatial structure has been determined. The next challenge is to properly describe the change in configuration of the chromophore, induced by light, and to expand such simulations to the timescale relevant for completion of this photocycle.