Monday, June 30, 2014

Phycocyanin against Alzheimer’s?

Could a light-harvesting protein phycocyanin be used as a novel drug against Alzheimer’s diesase (AD) [1, 2]?

In the present study, intact hexameric phycocyanin was isolated and crystallized from the cyanobacterium Leptolyngbya sp. N62DM, and the structure was solved to a resolution of 2.6 Å. Molecular docking studies show that the phycocyanin αβ-dimer interacts with the enzyme β-secretase, which catalyzes the proteolysis of the amyloid precursor protein to form plaques. The molecular docking studies suggest that the interaction between phycocyanin and β-secretase is energetically more favorable than previously reported inhibitor-β-secretase interactions. Transgenic Caenorhabditis elegans worms, with a genotype to serve as an AD-model, were significantly protected by phycocyanin. Therefore, the present study provides a novel structure-based molecular mechanism of phycocyanin-mediated therapy against AD.
  1. Singh, N.K., Hasan, S.S., Kumar, J., Raj, I., Pathan, A.A., Parmar, A., Shakil, S., Gourinath, S. and Madamwar D. (2014) Crystal structure and interaction of phycocyanin with β-secretase: A putative therapy for Alzheimer's disease. CNS Neurol. Disord. Drug Targets, in press.
  2. PDB:4L1E

Saturday, May 24, 2014

[Fe3S4] ferredoxin from Rhodopseudomonas palustris

The crystal structure of a novel [Fe3S4] ferredoxin associated with CYP194A4 from Rhodopseudomonas palustris has been solved at 2.15 Å resolution [1—3]. The ferredoxin, HaPuxC, contains an atypical CXXHXXC(X)nCP iron-sulphur cluster-binding motif. HaPuxC is the first P450 electron-transfer partner of this type to be structurally characterised.

  1. Zhang, T., Zhang, A., Bell, S.G., Wong, L.-L. and Zhou, W. (2014) The structure of a novel electron-transfer ferredoxin from Rhodopseudomonas palustris HaA2 which contains a histidine residue in its iron-sulfur cluster-binding motif. Acta Crystallographica D70, 1453—1464.
  2. PDB:4ID8
  3. PDB:4OV1

Thursday, May 01, 2014

Tetracalcium octachromium(3+) strontium octacarbonate hexadecahydroxide sulfate pentaicosahydrate

The Polar Bear peninsula in Western Australia is one of the many places on this planet I never heard before. The reason I mention it now is that a new mineral named putnisite was discovered there, and this mineral caused a bit of a stir recently, for being “completely unique and unrelated to anything”. In fact, if you Google “Polar Bear peninsula”, all you find is putnisite.

In 2007, specimens of an unknown mineral forming purple crystals (a) were collected at the Polar Bear peninsula while prospecting for nickel and gold. The specimens were eventually forwarded to Peter Elliott, a research associate with the South Australian Museum, for examination.


Elliott et al. [2] report the composition and crystal structure of this unique mineral, named in honour of mineralogists Christine and Andrew Putnis of the Institut für Mineralogie, Universtität Münster, Germany. The compositional name for putnisite I come up with is “tetracalcium octachromium(3+) strontium octacarbonate hexadecahydroxide sulfate pentaicosahydrate”. Curiously, Mindat and Mineralienatlas give the molecular formula containing only 23 molecules of water.


The crystal structure (b) was determined from single-crystal X-ray diffraction data. Cr(OH)4O2 octahedra (red) link by edge-sharing to form an eight-membered ring. At the centre of each ring lies a decacoordinated Sr2+ cation (purple). The rings are decorated by carbonate triangles (green), each of which links by corner-sharing to two Cr(OH)4O2 octahedra. Rings are linked by Ca(H2O)4O4 polyhedra (blue) to form a sheet parallel to the (100) plane. Adjacent sheets are joined along the [100] direction by corner-sharing sulfate tetrahedra (yellow).

  1. Mills, R. (2014) New mineral shows nature’s infinite variability.
  2. Elliott, P., Giester, G., Rowe, R. and Pring, A. (2014) Putnisite, SrCa4Cr3+8(CO3)8SO4(OH)16·25H2O, a new mineral from Western Australia: description and crystal structure. Mineralogical Magazine 78, 131—144.

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