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Feedback- 1.
Croce, R. & van Amerongen, H. Natural strategies for photosynthetic light-harvesting. Nat. Chem. Biol. 10, 492–501 (2014).
- 2.
Reimers, J. R. et al. Challenges facing an understanding of the nature of low-energy excited states in photosynthesis. Biochim. Biophys. Acta 1857, 1627–1640 (2016).
- 3.
Mirkovic, T. et al. Light absorption and energy transfer in the antenna complexes of photosynthetic organisms. Chem. Rev. 117, 249–293 (2017).
- 4.
Madigan, M. T. A novel photosynthetic bacterium isolated from a Yellowstone hot spring. Science 225, 313–315 (1984).
- 5.
Glaeser, J. & Overmann, J. Selective enrichment and characterization of Roseospirillum parvum, gen. nov. and sp. nov., a new purple nonsulfur bacterium with unusual light absorption properties. Arch. Microbiol. 171, 405–416 (1999).
- 6.
Permentier, H. P., Neerken, S., Overmann, J. & Amesz, J. A bacteriochlorophyll a antenna complex from purple bacteria absorbing at 963 nm. Biochemistry 40, 5573–5578 (2001).
- 7.
Kimura, Y. et al. Effects of calcium ions on the thermostability and spectroscopic properties of the LH1-RC complex from a new thermophilic purple bacterium Allochromatium tepidum. J. Phys. Chem. B 121, 5025–5032 (2017).
- 8.
Suzuki, H. et al. Purification, characterization and crystallization of the core complex from thermophilic purple sulfur bacterium Thermochromatium tepidum. Biochim. Biophys. Acta 1767, 1057–1063 (2007).
- 9.
Kimura, Y. et al. Calcium ions are involved in the unusual red shift of the light-harvesting 1 Qy transition of the core complex in thermophilic purple sulfur bacterium Thermochromatium tepidum. J. Biol. Chem. 283, 13867–13873 (2008).
- 10.
Kimura, Y., Yu, L.-J., Hirano, Y., Suzuki, H. & Wang, Z.-Y. Calcium ions are required for the enhanced thermal stability of the light-harvesting-reaction center core complex from thermophilic purple sulfur bacterium Thermochromatium tepidum. J. Biol. Chem. 284, 93–99 (2009).
- 11.
Yu, L.-J., Kato, S. & Wang, Z.-Y. Examination of the putative Ca2+-binding site in the light-harvesting complex 1 of thermophilic purple sulfur bacterium Thermochromatium tepidum. Photosynth. Res. 106, 215–220 (2010).
- 12.
Niwa, S. et al. Structure of the LH1-RC complex from Thermochromatium tepidum at 3.0 Å. Nature 508, 228–232 (2014).
- 13.
Yu, L.-J., Suga, M., Wang-Otomo, Z.-Y. & Shen, J.-R. Structure of photosynthetic LH1-RC supercomplex at 1.9 Å resolution. Nature 556, 209–213 (2018).
- 14.
Ma, F., Yu, L.-J., Wang-Otomo, Z.-Y. & van Grondelle, R. The origin of the unusual Qy red shift in LH1-RC complexes from purple bacteria Thermochromatium tepidum as revealed by Stark absorption spectroscopy. Biochim. Biophys. Acta 1847, 1479–1486 (2015).
- 15.
Ma, F., Yu, L.-J., Hendrikx, R., Wang-Otomo, Z.-Y. & van Grondelle, R. Direct observation of energy detrapping in LH1-RC complex by two-dimensional electronic spectroscopy. J. Am. Chem. Soc. 139, 591–594 (2017).
- 16.
Imanishi, M. et al. A dual role for Ca2+ in expanding the spectral diversity and stability of light-harvesting 1 reaction center photocomplexes of purple phototrophic bacteria. Biochemistry 58, 2844–2852 (2019).
- 17.
Tan, L.-M. et al. New insights into the mechanism of uphill excitation energy transfer from core antenna to reaction center in purple photosynthetic bacteria. J. Phys. Chem. Lett. 9, 3278–3284 (2018).
- 18.
Kimura, Y. et al. Metal cations modulate the bacteriochlorophyll-protein interaction in the light-harvesting 1 core complex from Thermochromatium tepidum. Biochim. Biophys. Acta 1817, 1022–1029 (2012).
- 19.
Yu, L.-J., Kawakami, T., Kimura, Y. & Wang-Otomo, Z.-Y. Structural basis for the unusual Qy red-shift and enhanced thermostability of the LH1 complex from Thermochromatium tepidum. Biochemistry 55, 6495–6504 (2016).
- 20.
Kimura, Y. et al. Spectroscopic and thermodynamic characterization of the metal-binding sites in the LH1-RC complex from thermophilic photosynthetic bacterium Thermochromatium tepidum. J. Phys. Chem. B 120, 12466–12473 (2016).
- 21.
Rücker, O., Köhler, A., Behammer, B., Sichau, K. & Overmann, J. Puf operon sequences and inferred structures of light-harvesting complexes of three closely related Chromatiaceae exhibiting different absorption characteristics. Arch. Microbiol. 194, 123–134 (2012).
- 22.
Koepke, J. et al. pH Modulates the quinone position in the photosynthetic reaction center from Rhodobacter sphaeroides in the neutral and charge separated states. J. Mol. Biol. 371, 396–409 (2007).
- 23.
Qian, P., Siebert, C. A., Wang, P., Canniffe, D. P. & Hunter, C. N. Cryo-EM structure of the Blastochloris viridis LH1-RC complex at 2.9 Å. Nature 556, 203–208 (2018).
- 24.
Williams, J. C. et al. Effects of mutations near the bacteriochlorophylls in reaction centers from Rhodobacter sphaeroides. Biochemistry 31, 11029–11037 (1992).
- 25.
Murchison, H. A. et al. Mutations designed to modify the environment of the primary electron donor of the reaction center from Rhodobacter sphaeroides: phenylalanine to leucine at L167 and histidine to phenylalanine at L168. Biochemistry 32, 3498–3505 (1993).
- 26.
Mattioli, T. A., Lin, X., Allen, J. P. & Williams, J. C. Correlation between multiple hydrogen bonding and alteration of the oxidation potential of the bacteriochlorophyll dimer of reaction centers from Rhodobacter sphaeroides. Biochemistry 34, 6142–6152 (1995).
- 27.
Nagatsuma, S. et al. Phospholipid distributions in purple phototrophic bacteria and LH1-RC core complexes. Biochim. Biophys. Acta Bioenerg. 1860, 461–468 (2019).
- 28.
Jakob-Grun, S., Radeck, J. & Braun, P. Ca2+-binding reduces conformational flexibility of RC-LH1 core complex from thermophilic Thermochromatium tepidum. Photosynth. Res. 111, 139–147 (2012).
- 29.
Ma, F., Yu, L.-J., Hendrikx, R., Wang-Otomo, Z.-Y. & van Grondelle, R. Excitonic and vibrational coherence in the excitation relaxation process of two LH1 complexes as revealed by two-dimensional electronic spectroscopy. J. Phys. Chem. Lett. 8, 2751–2756 (2017).
- 30.
Ma, F. et al. Metal cations induced ab-BChl a heterogeneity in LH1 as revealed by temperature-dependent fluorescence splitting. ChemPhysChem 18, 2295–2301 (2017).
- 31.
Cogdell, R. J., Howard, T. D., Isaac, N. W., McLuskey, K. & Gardiner, A. T. Structural factors which control the position of the Qy absorption band of bacteriochlorophyll a in purple bacterial antenna complexes. Photosynth. Res. 74, 135–141 (2002).
- 32.
Cogdell, R. J., Gall, A. & Köhler, J. The architecture and function of the light-harvesting apparatus of purple bacterial: from single molecules to in vivo membranes. Quart. Rev. Biophys. 39, 227–324 (2006).
- 33.
Robert, B. In The purple phototrophic bacteria (eds Hunter, C. N., Daldal, F. & Beatty, J. T.) 199–212 (Springer, 2009).
- 34.
Sturgis, J. N. & Robert, B. Pigment binding-site and electronic properties in light-harvesting proteins of purple bacteria. J. Phys. Chem. 101, 7227–7231 (1997).
- 35.
Uyeda, U., Williams, J. C., Roman, M., Mattioli, T. A. & Allen, J. P. The influence of hydrogen bonds on the electronic structure of light-harvesting complexes from photosynthetic bacteria. Biochemistry 49, 1146–1159 (2010).
- 36.
Zerlauskiene, O. et al. Static and dynamic protein impact on electronic properties of light-harvesting complex LH2. J. Phys. Chem. B 112, 15883–15892 (2008).
- 37.
Mascle-Allemand, C., Duquesne, K., Lebrun, R., Scheuring, S. & Sturgis, J. N. Antenna mixing in photosynthetic membranes from Phaeospirillum molischianum. Proc. Natl Acad. Sci. USA 107, 5357–5362 (2010).
- 38.
Brotosudarmo, T. H. P. et al. Single-molecule spectroscopy reveals that individual low-light LH2 complexes from Rhodopseudomonas palustris 2.1.6. have a heterogeneous polypeptide composition. Biophys. J. 97, 1491–1500 (2009).
- 39.
Dutton, P. L., Kaufmann, K. J., Chance, B. & Rentzepis, P. M. Picosecond kinetics of the 1250 nm band of the Rps. sphaeroides reaction center: the nature of the primary photochemical intermediary state. FEBS Lett. 60, 275–280 (1975).
- 40.
Kobayashi, M. et al. Reconstitution and replacement of bacteriochlorophyll a molecules in photosynthetic reaction centers. J. Biochem. 136, 363–369 (2004).
- 41.
Philipson, K. D. & Sauer, K. Comparative study of the circular dichroism spectra of reaction centers from several photosynthetic bacteria. Biochemistry 12, 535–539 (1973).
- 42.
Sekine, F. et al. Gene sequencing and characterization of the light-harvesting complex 2 from thermophilic purple sulfur bacterium Thermochromatium tepidum. Photosynth. Res. 111, 9–18 (2012).
- 43.
Kimura, Y. et al. Characterization of the quinones in purple sulfur bacterium Thermochromatium tepidum. FEBS Lett. 589, 1761–1765 (2015).
- 44.
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
- 45.
Rohou, A. & Grigorieff, N. Fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
- 46.
Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007).
- 47.
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).
- 48.
Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003).
- 49.
Kucukelbir, A., Sigworth, F. J. & Tagare, H. D. Quantifying the local resolution of cryo-EM density maps. Nat. Methods 11, 63–65 (2014).
- 50.
Pettersen, E. F. et al. UCSF Chimera–a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
- 51.
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D66, 486–501 (2010).
- 52.
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).
- 53.
Nicholls, R. A., Tykac, M., Kovalevskiy, O. & Murshudov, G. N. Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM. Acta Crystallogr. D Struct. Biol. 74, 492–505 (2018).
- 54.
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010).
- 55.
DeLano, W. L. The PyMOL Molecular Graphics System (DeLano Scientific, LCC, San Carlos, CA USA, 2004).
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Source: https://www.nature.com/articles/s41467-020-18748-3
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Original Text (This is the original text for your reference.)
- 1.
Croce, R. & van Amerongen, H. Natural strategies for photosynthetic light-harvesting. Nat. Chem. Biol. 10, 492–501 (2014).
- 2.
Reimers, J. R. et al. Challenges facing an understanding of the nature of low-energy excited states in photosynthesis. Biochim. Biophys. Acta 1857, 1627–1640 (2016).
- 3.
Mirkovic, T. et al. Light absorption and energy transfer in the antenna complexes of photosynthetic organisms. Chem. Rev. 117, 249–293 (2017).
- 4.
Madigan, M. T. A novel photosynthetic bacterium isolated from a Yellowstone hot spring. Science 225, 313–315 (1984).
- 5.
Glaeser, J. & Overmann, J. Selective enrichment and characterization of Roseospirillum parvum, gen. nov. and sp. nov., a new purple nonsulfur bacterium with unusual light absorption properties. Arch. Microbiol. 171, 405–416 (1999).
- 6.
Permentier, H. P., Neerken, S., Overmann, J. & Amesz, J. A bacteriochlorophyll a antenna complex from purple bacteria absorbing at 963 nm. Biochemistry 40, 5573–5578 (2001).
- 7.
Kimura, Y. et al. Effects of calcium ions on the thermostability and spectroscopic properties of the LH1-RC complex from a new thermophilic purple bacterium Allochromatium tepidum. J. Phys. Chem. B 121, 5025–5032 (2017).
- 8.
Suzuki, H. et al. Purification, characterization and crystallization of the core complex from thermophilic purple sulfur bacterium Thermochromatium tepidum. Biochim. Biophys. Acta 1767, 1057–1063 (2007).
- 9.
Kimura, Y. et al. Calcium ions are involved in the unusual red shift of the light-harvesting 1 Qy transition of the core complex in thermophilic purple sulfur bacterium Thermochromatium tepidum. J. Biol. Chem. 283, 13867–13873 (2008).
- 10.
Kimura, Y., Yu, L.-J., Hirano, Y., Suzuki, H. & Wang, Z.-Y. Calcium ions are required for the enhanced thermal stability of the light-harvesting-reaction center core complex from thermophilic purple sulfur bacterium Thermochromatium tepidum. J. Biol. Chem. 284, 93–99 (2009).
- 11.
Yu, L.-J., Kato, S. & Wang, Z.-Y. Examination of the putative Ca2+-binding site in the light-harvesting complex 1 of thermophilic purple sulfur bacterium Thermochromatium tepidum. Photosynth. Res. 106, 215–220 (2010).
- 12.
Niwa, S. et al. Structure of the LH1-RC complex from Thermochromatium tepidum at 3.0 Å. Nature 508, 228–232 (2014).
- 13.
Yu, L.-J., Suga, M., Wang-Otomo, Z.-Y. & Shen, J.-R. Structure of photosynthetic LH1-RC supercomplex at 1.9 Å resolution. Nature 556, 209–213 (2018).
- 14.
Ma, F., Yu, L.-J., Wang-Otomo, Z.-Y. & van Grondelle, R. The origin of the unusual Qy red shift in LH1-RC complexes from purple bacteria Thermochromatium tepidum as revealed by Stark absorption spectroscopy. Biochim. Biophys. Acta 1847, 1479–1486 (2015).
- 15.
Ma, F., Yu, L.-J., Hendrikx, R., Wang-Otomo, Z.-Y. & van Grondelle, R. Direct observation of energy detrapping in LH1-RC complex by two-dimensional electronic spectroscopy. J. Am. Chem. Soc. 139, 591–594 (2017).
- 16.
Imanishi, M. et al. A dual role for Ca2+ in expanding the spectral diversity and stability of light-harvesting 1 reaction center photocomplexes of purple phototrophic bacteria. Biochemistry 58, 2844–2852 (2019).
- 17.
Tan, L.-M. et al. New insights into the mechanism of uphill excitation energy transfer from core antenna to reaction center in purple photosynthetic bacteria. J. Phys. Chem. Lett. 9, 3278–3284 (2018).
- 18.
Kimura, Y. et al. Metal cations modulate the bacteriochlorophyll-protein interaction in the light-harvesting 1 core complex from Thermochromatium tepidum. Biochim. Biophys. Acta 1817, 1022–1029 (2012).
- 19.
Yu, L.-J., Kawakami, T., Kimura, Y. & Wang-Otomo, Z.-Y. Structural basis for the unusual Qy red-shift and enhanced thermostability of the LH1 complex from Thermochromatium tepidum. Biochemistry 55, 6495–6504 (2016).
- 20.
Kimura, Y. et al. Spectroscopic and thermodynamic characterization of the metal-binding sites in the LH1-RC complex from thermophilic photosynthetic bacterium Thermochromatium tepidum. J. Phys. Chem. B 120, 12466–12473 (2016).
- 21.
Rücker, O., Köhler, A., Behammer, B., Sichau, K. & Overmann, J. Puf operon sequences and inferred structures of light-harvesting complexes of three closely related Chromatiaceae exhibiting different absorption characteristics. Arch. Microbiol. 194, 123–134 (2012).
- 22.
Koepke, J. et al. pH Modulates the quinone position in the photosynthetic reaction center from Rhodobacter sphaeroides in the neutral and charge separated states. J. Mol. Biol. 371, 396–409 (2007).
- 23.
Qian, P., Siebert, C. A., Wang, P., Canniffe, D. P. & Hunter, C. N. Cryo-EM structure of the Blastochloris viridis LH1-RC complex at 2.9 Å. Nature 556, 203–208 (2018).
- 24.
Williams, J. C. et al. Effects of mutations near the bacteriochlorophylls in reaction centers from Rhodobacter sphaeroides. Biochemistry 31, 11029–11037 (1992).
- 25.
Murchison, H. A. et al. Mutations designed to modify the environment of the primary electron donor of the reaction center from Rhodobacter sphaeroides: phenylalanine to leucine at L167 and histidine to phenylalanine at L168. Biochemistry 32, 3498–3505 (1993).
- 26.
Mattioli, T. A., Lin, X., Allen, J. P. & Williams, J. C. Correlation between multiple hydrogen bonding and alteration of the oxidation potential of the bacteriochlorophyll dimer of reaction centers from Rhodobacter sphaeroides. Biochemistry 34, 6142–6152 (1995).
- 27.
Nagatsuma, S. et al. Phospholipid distributions in purple phototrophic bacteria and LH1-RC core complexes. Biochim. Biophys. Acta Bioenerg. 1860, 461–468 (2019).
- 28.
Jakob-Grun, S., Radeck, J. & Braun, P. Ca2+-binding reduces conformational flexibility of RC-LH1 core complex from thermophilic Thermochromatium tepidum. Photosynth. Res. 111, 139–147 (2012).
- 29.
Ma, F., Yu, L.-J., Hendrikx, R., Wang-Otomo, Z.-Y. & van Grondelle, R. Excitonic and vibrational coherence in the excitation relaxation process of two LH1 complexes as revealed by two-dimensional electronic spectroscopy. J. Phys. Chem. Lett. 8, 2751–2756 (2017).
- 30.
Ma, F. et al. Metal cations induced ab-BChl a heterogeneity in LH1 as revealed by temperature-dependent fluorescence splitting. ChemPhysChem 18, 2295–2301 (2017).
- 31.
Cogdell, R. J., Howard, T. D., Isaac, N. W., McLuskey, K. & Gardiner, A. T. Structural factors which control the position of the Qy absorption band of bacteriochlorophyll a in purple bacterial antenna complexes. Photosynth. Res. 74, 135–141 (2002).
- 32.
Cogdell, R. J., Gall, A. & Köhler, J. The architecture and function of the light-harvesting apparatus of purple bacterial: from single molecules to in vivo membranes. Quart. Rev. Biophys. 39, 227–324 (2006).
- 33.
Robert, B. In The purple phototrophic bacteria (eds Hunter, C. N., Daldal, F. & Beatty, J. T.) 199–212 (Springer, 2009).
- 34.
Sturgis, J. N. & Robert, B. Pigment binding-site and electronic properties in light-harvesting proteins of purple bacteria. J. Phys. Chem. 101, 7227–7231 (1997).
- 35.
Uyeda, U., Williams, J. C., Roman, M., Mattioli, T. A. & Allen, J. P. The influence of hydrogen bonds on the electronic structure of light-harvesting complexes from photosynthetic bacteria. Biochemistry 49, 1146–1159 (2010).
- 36.
Zerlauskiene, O. et al. Static and dynamic protein impact on electronic properties of light-harvesting complex LH2. J. Phys. Chem. B 112, 15883–15892 (2008).
- 37.
Mascle-Allemand, C., Duquesne, K., Lebrun, R., Scheuring, S. & Sturgis, J. N. Antenna mixing in photosynthetic membranes from Phaeospirillum molischianum. Proc. Natl Acad. Sci. USA 107, 5357–5362 (2010).
- 38.
Brotosudarmo, T. H. P. et al. Single-molecule spectroscopy reveals that individual low-light LH2 complexes from Rhodopseudomonas palustris 2.1.6. have a heterogeneous polypeptide composition. Biophys. J. 97, 1491–1500 (2009).
- 39.
Dutton, P. L., Kaufmann, K. J., Chance, B. & Rentzepis, P. M. Picosecond kinetics of the 1250 nm band of the Rps. sphaeroides reaction center: the nature of the primary photochemical intermediary state. FEBS Lett. 60, 275–280 (1975).
- 40.
Kobayashi, M. et al. Reconstitution and replacement of bacteriochlorophyll a molecules in photosynthetic reaction centers. J. Biochem. 136, 363–369 (2004).
- 41.
Philipson, K. D. & Sauer, K. Comparative study of the circular dichroism spectra of reaction centers from several photosynthetic bacteria. Biochemistry 12, 535–539 (1973).
- 42.
Sekine, F. et al. Gene sequencing and characterization of the light-harvesting complex 2 from thermophilic purple sulfur bacterium Thermochromatium tepidum. Photosynth. Res. 111, 9–18 (2012).
- 43.
Kimura, Y. et al. Characterization of the quinones in purple sulfur bacterium Thermochromatium tepidum. FEBS Lett. 589, 1761–1765 (2015).
- 44.
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
- 45.
Rohou, A. & Grigorieff, N. Fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
- 46.
Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007).
- 47.
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).
- 48.
Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003).
- 49.
Kucukelbir, A., Sigworth, F. J. & Tagare, H. D. Quantifying the local resolution of cryo-EM density maps. Nat. Methods 11, 63–65 (2014).
- 50.
Pettersen, E. F. et al. UCSF Chimera–a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
- 51.
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D66, 486–501 (2010).
- 52.
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).
- 53.
Nicholls, R. A., Tykac, M., Kovalevskiy, O. & Murshudov, G. N. Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM. Acta Crystallogr. D Struct. Biol. 74, 492–505 (2018).
- 54.
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010).
- 55.
DeLano, W. L. The PyMOL Molecular Graphics System (DeLano Scientific, LCC, San Carlos, CA USA, 2004).
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