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Deinococcus radiodurans

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    1. Takala, H., Niebling, S., Berntsson, O., Björling, A., Lehtivuori, H., Häkkänen, H., Panman, M., Gustavsson, E., Hoernke, M., Newby, G. and Zontone, F., 2016. Light-induced structural changes in a monomeric bacteriophytochrome.Structural Dynamics, 3(5), p.054701. pdf
    2. Feliks, M., Lafaye, C., Shu, X., Royant, A. and Field, M., 2016. Structural Determinants of Improved Fluorescence in a Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins: Insights from Continuum Electrostatic Calculations and Molecular Dynamics Simulations. Biochemistry, 55(31), pp.4263-4274. pdf
    3. Shcherbakova, D.M., Baloban, M., Pletnev, S., Malashkevich, V.N., Xiao, H., Dauter, Z. and Verkhusha, V.V., 2015. Molecular basis of spectral diversity in near-infrared phytochrome-based fluorescent proteins. Chemistry & biology,22(11), pp.1540-1551. pdf
    4. Takala, H., Björling, A., Linna, M., Westenhoff, S. and Ihalainen, J.A., 2015. Light-induced changes in the dimerization interface of bacteriophytochromes.Journal of Biological Chemistry, 290(26), pp.16383-16392. pdf
    5. Li, F., Burgie, E.S., Yu, T., Héroux, A., Schatz, G.C., Vierstra, R.D. and Orville, A.M., 2015. X-ray radiation induces deprotonation of the bilin chromophore in crystalline D. radiodurans phytochrome. Journal of the American Chemical Society, 137(8), pp.2792-2795. pdf
    6. Takala, H., Lehtivuori, H., Hammarén, H., Hytönen, V.P. and Ihalainen, J.A., 2014. Connection between absorption properties and conformational changes in Deinococcus radiodurans phytochrome. Biochemistry, 53(45), pp.7076-7085. pdf
    7. Burgie, E.S., Wang, T., Bussell, A.N., Walker, J.M., Li, H. and Vierstra, R.D., 2014. Crystallographic and electron microscopic analyses of a bacterial phytochrome reveal local and global rearrangements during photoconversion.Journal of Biological Chemistry, 289(35), pp.24573-24587. pdf
    8. Takala, H., Björling, A., Berntsson, O., Lehtivuori, H., Niebling, S., Hoernke, M., Kosheleva, I., Henning, R., Menzel, A., Ihalainen, J.A. and Westenhoff, S., 2014. Signal amplification and transduction in phytochrome photosensors.Nature, 509(7499), p.245. pdf
    9. Nieder, J.B., Stojković, E.A., Moffat, K., Forest, K.T., Lamparter, T., Bittl, R. and Kennis, J.T., 2013. Pigment–Protein Interactions in Phytochromes Probed by Fluorescence Line Narrowing Spectroscopy. The Journal of Physical Chemistry B, 117(48), pp.14940-14950. pdf
    10. Lehtivuori, H., Rissanen, I., Takala, H., Bamford, J., Tkachenko, N.V. and Ihalainen, J.A., 2013. Fluorescence properties of the chromophore-binding domain of bacteriophytochrome from Deinococcus radiodurans. The Journal of Physical Chemistry B, 117(38), pp.11049-11057. pdf
    11. Falklöf, O. and Durbeej, B., 2013. Modeling of phytochrome absorption spectra. Journal of computational chemistry, 34(16), pp.1363-1374. pdf
    12. Auldridge, M.Epdf., Satyshur, K.A., Anstrom, D.M. and Forest, K.T., 2012. Structure-guided engineering enhances a phytochrome-based infrared fluorescent protein. Journal of Biological Chemistry, 287(10), pp.7000-7009. pdf
    13. Li H, Zhang J, Vierstra RD, Li H. Quaternary organization of a phytochrome dimer as revealed by cryoelectron microscopy. Proceedings of the National Academy of Sciences. 2010 Jun 15;107(24):10872-7. pdf
    14. Matute, R.A., Contreras, R. and González, L., 2010. Time-Dependent DFT on Phytochrome Chromophores: A Way to the Right Conformer. The Journal of Physical Chemistry Letters, 1(4), pp.796-801. pdf
    15. Bornschlögl, T., Anstrom, D.M., Mey, E., Dzubiella, J., Rief, M. and Forest, K.T., 2009. Tightening the knot in phytochrome by single-molecule atomic force microscopy. Biophysical journal, 96(4), pp.1508-1514. pdf
    16. Kaminski, S., Daminelli, G. and Mroginski, M.A., 2009. Molecular dynamics simulations of the chromophore binding site of Deinococcus radiodurans bacteriophytochrome using new force field parameters for the phytochromobilin chromophore. The Journal of Physical Chemistry B, 113(4), pp.945-958. pdf
    17. von Stetten, D., Günther, M., Scheerer, P., Murgida, D.H., Mroginski, M.A., Krauß, N., Lamparter, T., Zhang, J., Anstrom, D.M., Vierstra, R.D. and Forest, K.T., 2008. Chromophore heterogeneity and photoconversion in phytochrome crystals and solution studied by resonance Raman spectroscopy.Angewandte Chemie International Edition, 47(25), pp.4753-4755. pdf
    18. Wagner, J.R., Zhang, J., von Stetten, D., Günther, M., Murgida, D.H., Mroginski, M.A., Walker, J.M., Forest, K.T., Hildebrandt, P. and Vierstra, R.D., 2008. Mutational analysis of Deinococcus radiodurans bacteriophytochrome reveals key amino acids necessary for the photochromicity and proton exchange cycle of phytochromes. Journal of Biological Chemistry, 283(18), pp.12212-12226. pdf
    19. Yoon, J.M., Hahn, T.R., Cho, M.H., Jeon, J.S., Bhoo, S.H. and Kwon, Y.K., 2008. The PHY domain is required for conformational stability and spectral integrity of the bacteriophytochrome from Deinococcus radiodurans.Biochemical and biophysical research communications, 369(4), pp.1120-1124. pdf
    20. Wagner, J.R., Zhang, J., Brunzelle, J.S., Vierstra, R.D. and Forest, K.T., 2007. High resolution structure of Deinococcus bacteriophytochrome yields new insights into phytochrome architecture and evolution. Journal of Biological Chemistry, 282(16), pp.12298-12309. pdf
    21. Wagner, J.R., Brunzelle, J.S., Forest, K.T. and Vierstra, R.D., 2005. A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome. Nature, 438(7066), pp.325-331. pdf
    22. Bhoo, S.H., Davis, S.J., Walker, J., Karniol, B. and Vierstra, R.D., 2001. Bacteriophytochromes are photochromic histidine kinases using a biliverdin chromophore. Nature, 414(6865), pp.776-779. pdf
    23. Takala, H., Niebling, S., Berntsson, O., Björling, A., Lehtivuori, H., Häkkänen, H., Panman, M., Gustavsson, E., Hoernke, M., Newby, G. and Zontone, F., 2016. Light-induced structural changes in a monomeric bacteriophytochrome.Structural Dynamics, 3(5), p.054701. pdf
    24. Björling, A., Berntsson, O., Lehtivuori, H., Takala, H., Hughes, A.J., Panman, M., Hoernke, M., Niebling, S., Henry, L., Henning, R. and Kosheleva, I., 2016. Structural photoactivation of a full-length bacterial phytochrome. Science Advances, 2(8), p.e1600920. pdf
    25. Lamparter, T., 2006. A computational approach to discovering the functions of bacterial phytochromes by analysis of homolog distributions. BMC bioinformatics, 7(1), p.1. pdf


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