Tuesday, April 22, 2014

Thermochromatium tepidum LH1—RC complex at 3.0 Å

The light-harvesting core antenna (LH1) and the reaction centre (RC) of purple photosynthetic bacteria form a supramolecular complex (LH1—RC) to use sunlight energy in a highly efficient manner. Niwa et al. [1—4] report the first near-atomic structure of a LH1—RC complex, namely that of a Ca2+-bound complex from Thermochromatium tepidum. The RC is surrounded by 16 heterodimers of the LH1 αβ-subunit that form a completely closed structure. The Ca2+ ions are located at the periplasmic side of LH1. Thirty-two bacteriochlorophyll a and sixteen spirilloxanthin molecules in the LH1 ring form an elliptical assembly.

  1. Niwa, S., Yu, L.-J., Takeda, K., Hirano, Y., Kawakami, T., Wang-Otomo, Z.-Y. and Miki, K. (2014) Structure of the LH1—RC complex from Thermochromatium tepidum at 3.0 Å. Nature 508, 228—232.
  2. PDB:3WMM.
  3. PDB:3WMN.
  4. PDB:3WMO.

Thursday, February 27, 2014

Smell of pine vs climate change

That’s right: the smell of pine trees from boreal forests could mitigate the global warming — provided that the global warming doesn’t kill the forests first [1]. The volatile organic compounds (VOCs), responsible for the smell of pine, react with atmospheric oxygen to form aerosols. These aerosols scatter solar radiation and also act as cloud condensation nuclei, thereby affecting the Earth’s radiation balance. An international group including researchers from Finland, Germany, Denmark and USA has discovered a direct pathway leading from several biogenic VOCs, such as monoterpenes, to the formation of extremely low-volatility vapours (ELVOCs) [2].

These vapours form at significant mass yield in the gas phase and condense irreversibly onto aerosol surfaces to produce secondary organic aerosol, helping to explain the discrepancy between the observed atmospheric burden of secondary organic aerosol and that reported by many model studies. We further demonstrate how these low-volatility vapours can enhance, or even dominate, the formation and growth of aerosol particles over forested regions, providing a missing link between biogenic VOCs and their conversion to aerosol particles.

Structures of the main VOCs studied by Ehn et al. [2]

The air was sampled in Hyytiälä, Finland and the chamber experiments were conducted at the Jülich Research Centre in Germany.

  1. McGrath, M. Smell of forest pine can limit climate change. BBC News, 26 February 2014.
  2. Ehn, M., Thornton, J.A., Kleist, E., Sipilä, M., Junninen, J., Pullinen, I., Springer, M., Rubach, F., Tillmann, R., Lee, B., Lopez-Hilfiker, F., Andres, S., Acir, I.-H., Rissanen, M., Jokinen, T., Schobesberger, S., Kangasluoma, J., Kontkanen, J., Nieminen, T., Kurtén, T., Nielsen, L.B., Jørgensen, S., Kjaergaard, H.G., Canagaratna, M., Dal Maso, M.D., Berndt, T., Petäjä, T., Wahner, A., Veli-Matti Kerminen, V.-M., Kulmala, M., Worsnop, D.R., Wildt, J. and Mentel, T.F. (2014) A large source of low-volatility secondary organic aerosol. Nature 506, 476—479.

Saturday, January 18, 2014

Sodium chloride revisited

Everybody knows that the formula of sodium chloride is NaCl. Right? Right. But recently, the team of Artem Oganov at Stony Brook University have shown that there are other stable types of crystalline sodium chloride. They have predicted several thermodynamically stable compounds: Na3Cl, Na2Cl, Na3Cl2, NaCl3, and NaCl7. Moreover, by utilising high-pressure techniques, they synthesised cubic and orthorhombic NaCl3 and two-dimensional tetragonal Na3Cl [1, 2].

NaCl3 (space group Pm3n)
Na3Cl (space group P4/mmm)

“One of these materials — Na3Cl — has a fascinating structure”, says Oganov. “It is comprised of layers of NaCl and layers of pure sodium. The NaCl layers act as insulators; the pure sodium layers conduct electricity” [3].

  1. Zhang, W., Oganov, A.R., Goncharov, A.F., Zhu, Q., Boulfelfel, S.E., Lyakhov, A.O., Stavrou, E., Somayazulu, M., Prakapenka, V.B. and Konôpková, Z. (2013) Unexpected stable stoichiometries of sodium chlorides. Science 342, 1502—1505; arXiv:1310.7674v1
  2. Ibáñez Insa, J. (2013) Reformulating table salt under pressure. Science 342, 1459—1460.
  3. SBU team discovers new compounds that challenge the foundation of chemistry. Stony Brook University Newsroom, December 19, 2013.

Tuesday, November 26, 2013

Magnetochrome-containing iron oxidase MamP

Magnetotactic bacteria (MTB) are a diverse group of prokaryotes that have a singular ability to align with geomagnetic field lines. This ability is due to special organelles called magnetosomes. Magnetosomes are composed of single-magnetic-domain nanocrystals of magnetite [Fe(II)Fe(III)2O4] or greigite [Fe(II)Fe(III)2S4] embedded in biological membrane.

“Magnetochrome” is a name proposed in 2012 by Marina Siponen and co-authors for a cytochrome domain conserved within all known MTB and not found in any other species to date [1]. Recently, the crystal structure of the magnetosome-associated protein MamP has been solved at 1.8 Å resolution [2—4]. The minimal unit of MamP is a dimer. Each monomer consists of a PDZ domain fused to two magnetochrome domains. It was also shown in an in vitro mineralisation experiment that MamP functions as an iron oxidase mediating the iron(III) ferrihydrite production from iron(II) [2]:

4Fe2+ + 7H2O → 2Fe2O3·H2O + 12H+ + 4e
  1. Siponen, M.I., Adryanczyk, G., Ginet, N., Arnoux, P. and Pignol, D. (2012) Magnetochrome: a c-type cytochrome domain specific to magnetotatic bacteria. Biochemical Society Transactions 40, 1319—1323.
  2. Siponen, M.I., Legrand, P., Widdrat, M., Jones, S.R., Zhang, W.-J., Chang, M.C.Y., Faivre, D., Arnoux, P. and Pignol, D. (2013) Structural insight into magnetochrome-mediated magnetite biomineralization. Nature 502, 681—684.
  3. PDB:4JJ0
  4. PDB:4JJ3

Saturday, October 26, 2013

The first viral cytochrome b5

A unicellular green alga Ostreococcus tauri is the smallest (less than 1 μm in diameter) free-living eukaryote yet described. Viruses that can infect high-light and low-light adapted strains of O. tauri have been isolated and their genomes sequenced. Interestingly, low-light-strain infecting virus (OtV-2) differ from the high-light-strain infecting viruses by encoding a potential cytochrome b5 [1]. This protein was cloned, biochemically characterised and its three-dimensional structure resolved [2, 3].

The absorption spectra of oxidised and reduced recombinant OtV-2 haemoprotein are almost identical to those of purified human cytochrome b5.

It was also shown that the protein can substitute for yeast cytochrome b5 in the CYP51-mediated sterol 14α-demethylation. Structurally, the viral protein is similar to other known cytochromes b5 but lacks a hydrophobic C-terminal anchor. Thus, the first virally encoded cytochrome b5 is also the first cytosolic cytochrome b5 characterised. However, the physiological role of viral cytochrome b5 remains unknown.

  1. UniProt:E4WM77
  2. Reid, E.L., Weynberg, K.D., Love, J., Isupov, M.N., Littlechild, J.A., Wilson, W.H., Kelly, S.L., Lamb, D.C. and Allen, M.J. (2013) Functional and structural characterisation of a viral cytochrome b5. FEBS Letters, 587, 3633—3639.
  3. PDB:4B8N

Thursday, September 26, 2013

Ochre, a great universal

From Architecture of First Societies: A Global Perspective by Mark Jarzombek:

Known scientifically as hematite, ochre is a reddish iron-containing rock that was used as a coloring substance made by grinding the stone into a powder that when mixed with fat or water formed a paste. Homo erectus had already begun to work with ochre, thus securing it as a key, nonfunctional element in human life.
Ochre was a great universal of all First Societies. The Blackfeet of the American Plains referred to it as nitsisaan or “real paint” and profusely daubed it on their ceremonial garments. Its color was thought to represent the sun and the energy that permeates all things, making a person rubbed with it appear holy and powerful. Its redness and brilliance signaled supernatural potency overlapping with a range of cosmological concepts revolving around rain, fertility, hunting, and death. The nineteen-century painter George Catlin painted the Sioux worshipping at a red boulder in the open grasslands of the Great Plains.
Sioux Worshiping at the Red Boulders
George Catlin, Sioux Worshiping at the Red Boulders, 1837—1839
Ceremonial uses of ochre still exist today, such as among the Maasai in Kenya during certain initiation rituals, by Amazon tribes and by Aboriginal people in Australia.
The !Kung, who live in the Kalahari desert of Botswana and who are among the oldest of the surviving First Society people in the world, use the pigment in rituals dealing with a woman’s first menstruation. A female initiate, on emergence from seclusion, would present the women of her kin group with lumps of ochre for decorating their faces and cloaks and also for adorning the young men to protect them when out hunting.

Saturday, August 31, 2013

Metallomics and the Cell

This volume, edited by Lucia Banci, is probably the first real book on metallomics. The table of contents looks very promising, and judging from those bits that I am able to access, I’d love to say that is is a great book... But honestly I can’t. The days when I could persuade the library to purchase (for me) a book, however expensive, are long gone. At the Springer website, eBook is priced at €142.79 and hardcover costs €181.85. You can buy them slightly cheaper from Amazon ($175.82 and $227.05, respectively.)

The book is dedicated to Ivano Bertini, who sadly passed away last year. I was lucky enough to meet the man himself on a few occasions. Ivano was a formidable scientist and one of the most colourful figures of bioinorganic chemistry and structural biology.

Metallomics and the Cell
Metal Ions in Life Sciences, vol. 12
Lucia Banci, Editor
  1. Banci, L. and Bertini, I. Metallomics and the cell: some definitions and general comments, pp. 1—13.
  2. Penner-Hahn, J.E. Technologies for detecting metals in single cells, pp. 15—40.
  3. Clausen, M.J.V. and Poulsen, H. Sodium/potassium homeostasis in the cell, pp. 41—67.
  4. Romani, A.M.P. Magnesium homeostasis in mammalian cells, pp. 69—118.
  5. Brini, M., Calì, T., Ottolini, D. and Carafoli, E. Intracellular calcium homeostasis and signaling, pp. 119—168.
  6. Roth, J., Ponzoni, S. and Aschner, M. Manganese homeostasis and transport, pp. 169—201.
  7. Andrews, S., Norton, I., Salunkhe, A.S., Goodluck, H., Aly, W.S.M., Mourad-Agha, H. and Cornelis, P. Control of iron metabolism in bacteria, pp. 203—239.
  8. Dlouhy, A.C. and Outten, C.E. The iron metallome in eukaryotic organisms, pp. 241—278.
  9. Benson, D.R. and Rivera, M. Heme uptake and metabolism in bacteria, pp. 279—332.
  10. Cracan, V. and Banerjee, R. Cobalt and corrinoid transport and biochemistry, pp. 333—374.
  11. Sydor, A.M. and Zamble, D.B. Nickel metallomics: general themes guiding nickel homeostasis, pp. 375—416.
  12. Rensing, C. and McDevitt, S.F. The copper metallome in prokaryotic cells, 417—450.
  13. Vest, K.E., Hashemi, H.F. and Cobine, P.A. The copper metallome in eukaryotic cells, pp. 451—478.
  14. Maret, W. Zinc and the zinc proteome, pp. 479—501.
  15. Mendel, R.R. Metabolism of molybdenum, pp. 503—528.
  16. Gladyshev, V.N. and Zhang, Y. Comparative genomics analysis of the metallomes, pp. 529—580.