Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein.

Department of Biophysical Chemistry, University of Groningen, Nijenborg 4, 9747 AG Groningen, The Netherlands.
Journal of the American Chemical Society (Impact Factor: 10.68). 05/2004; 126(13):4228-33. DOI: 10.1021/ja039557f
Source: PubMed

ABSTRACT Atomistic QM/MM simulations have been carried out on the complete photocycle of Photoactive Yellow Protein, a bacterial photoreceptor, in which blue light triggers isomerization of a covalently bound chromophore. The "chemical role" of the protein cavity in the control of the photoisomerization step has been elucidated. Isomerization is facilitated due to preferential electrostatic stabilization of the chromophore's excited state by the guanidium group of Arg52, located just above the negatively charged chromophore ring. In vacuo isomerization does not occur. Isomerization of the double bond is enhanced relative to isomerization of a single bond due to the steric interactions between the phenyl ring of the chromophore and the side chains of Arg52 and Phe62. In the isomerized configuration (ground-state cis), a proton transfer from Glu46 to the chromophore is far more probable than in the initial configuration (ground-state trans). It is this proton transfer that initiates the conformational changes within the protein, which are believed to lead to signaling.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The Newton-X program is a general-purpose program package for excited-state molecular dynamics, including nonadiabatic methods. Its modular design allows Newton-X to be easily linked to any quantum-chemistry package that can provide excited-state energy gradients. At the current version, Newton-X can perform nonadiabatic dynamics using Columbus, Turbomole, Gaussian, and Gamess program packages with multireference configuration interaction, multiconfigurational self-consistent field, time-dependent density functional theory, and other methods. Nonadiabatic dynamics simulations with a hybrid combination of methods, such as Quantum-Mechanics/Molecular-Mechanics, are also possible. Moreover, Newton-X can be used for the simulation of absorption and emission spectra. The code is distributed free of charge for noncommercial and nonprofit uses at WIREs Comput Mol Sci 2014, 4:26–33. doi: 10.1002/wcms.1158 The authors have declared no conflicts of interest in relation to this article. For further resources related to this article, please visit the WIREs website.
    Wiley Interdisciplinary Reviews: Computational Molecular Science. 01/2014; 4(1).
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Free-energy landscapes decisively determine the progress of enzymatically catalyzed reactions [Cornish-Bowden (2012), Fundamentals of Enzyme Kinetics, 4th ed.]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [Moffat (2001), Chem. Rev. 101, 1569-1581; Schmidt et al. (2005), Methods Mol. Biol. 305, 115-154; Schmidt (2008), Ultrashort Laser Pulses in Medicine and Biology] because both can be determined from the same set of X-ray data. Here, it is demonstrated how barriers of activation can be determined solely from five-dimensional crystallography, where in addition to space and time, temperature is a variable as well [Schmidt et al. (2010), Acta Cryst. A66, 198-206]. Directly linking molecular structures with barriers of activation between them allows insight into the structural nature of the barrier to be gained. Comprehensive time series of crystallographic data at 14 different temperature settings were analyzed and the entropy and enthalpy contributions to the barriers of activation were determined. One hundred years after the discovery of X-ray scattering, these results advance X-ray structure determination to a new frontier: the determination of energy landscapes.
    Acta Crystallographica Section D Biological Crystallography 12/2013; 69(Pt 12):2534-42. · 12.67 Impact Factor
  • Source
    Nature Chemistry 03/2014; 6(4):258-9. · 21.76 Impact Factor


1 Download
Available from