Models photoactive yellow protein

Vengris, M. Larsen, D. S. Van der Horst, M. A. Larsen, O. F. A. HeUingwerf, K. J. Van Grondelle, R. Ultrafast dynamics of isolated model photoactive yellow protein chromophores "Chemical perturbation theory" in the laboratory. J. Phys. Chem. B 2005,109,4197-4208. 

Hybrid multiscale models enable us to focus on the relevant part of a system. For example, Leenders et al. studied the proton transfer process in the photoactive yellow protein (Figure 6.3) [9], They used Car-Parrinello molecular dynamics [10], a QM method for dynamics simulations, to describe the chromophore and its hydrogen-bonded network in the protein pocket (middle and right-hand circles). This was combined with a traditional MD force field of 28 600 atoms, simulating the entire protein in water (left-hand circle). 

To begin to elucidate such issues and to create a theoretical framework for them, we have focused [4-9] on a model of a protonated Schiff base (PSB) in a nonequilibrium dielectric continuum solvent. A key feature for the Sj-Sq Cl in PSBs such as retinal which plays a key role in the chromophore s cis-trans isomerization is that a charge transfer is involved, implying a strong electrostatic coupling to a polar and polarizable environment. In particular, there is translocation of a positive charge [92], discussed further below. Charge transfer also characterizes the earliest events in the photoactive yellow protein photocycle, for example [93],... 

Photoactive yellow protein (PYP) was discovered 20 year ago in Halorhodospira halophila, then known as Ectothiorhodospira halophila [1,2]. In several halophilic purple bacteria it has a vital role in the avoidance response to blue light (phototaxis). It has been thoroughly studied as a model photoreceptor system and as the structural prototype for the PAS class of signal transduction proteins. PYP has 125 amino acid residues in an a// -fold with six antiparallel /1-sheets and several helices (see Fig. 5.1). The covalently bound p-coumaric acid chromophore is linked to the only cysteine in the protein (Cys69) (see Fig. 5.1). Hellingwerf has published an excellent review of the photophysical behavior of PYP [1],... 

Figure 34 CIS calculations, in a sequence of increasingly diffuse basis sets, for the phe-nolate isomer of p-coumaric acid, a chemical model of the chromophore in photoactive yellow protein. (The energy level structure of this molecule is depicted in Figure 16.) Dashed lines connect the n n transition(s) obtained in each basis, which mix with the continuum states in the more diffuse basis sets. The lowest-energy level in each basis set represents —e oMO which is the threshold energy for the onset of the continuum in the hasis-set limit. The other levels denote CIS excitation energies, most of which correspond to discretized continuum states. Adapted with permission from Ref. 187 copyright 2013 American Institute of Physics.

Through the years, PYP has become popular as a model system. This is easily demonstrated by a literature search with the key words Photoactive Yellow Protein. Where only a few years ago, the search result would contain mostly papers on PYP itself, nowadays, studies on many other proteins are included, for which PYP is seen as a model or reference system. Three areas of research in particular are relevant for this role-model function ... 

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