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Deinococcus radiodurans

  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 Dynamics3(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. Biochemistry55(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 Chemistry290(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 Society137(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. Biochemistry53(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 Chemistry289(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.Nature509(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 B117(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 B117(38), pp.11049-11057. pdf
  11. Falklöf, O. and Durbeej, B., 2013. Modeling of phytochrome absorption spectra. Journal of computational chemistry34(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 Chemistry287(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 Letters1(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 journal96(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 B113(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 Edition47(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 Chemistry283(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 communications369(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 Chemistry282(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. Nature438(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. Nature414(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 Dynamics3(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 Advances2(8), p.e1600920. pdf
  25. Lamparter, T., 2006. A computational approach to discovering the functions of bacterial phytochromes by analysis of homolog distributions. BMC bioinformatics7(1), p.1. pdf