Human Apaf-1 apoptosome at 3.8 Å

The apoptotic protease-activating factor 1 (Apaf-1) exists in normal cells as an autoinhibited monomer. Upon binding to cytochrome c and dATP, Apaf-1 forms a heptameric complex known as the apoptosome. Zhou et al. report an atomic structure of an intact human Apaf-1 apoptosome at 3.8 Å resolution determined by single-particle, cryo-electron microscopy [1, 2].

1. Zhou, M., Li, Y., Hu, Q., Bai, X.-c., Huang, W., Yan, C., Scheres, S.H.W. and Shi, Y. (2015) Atomic structure of the apoptosome: mechanism of cytochrome c- and dATP-mediated activation of Apaf-1. Genes & Development 29, 2349—2361.
2. PDB:3JBT

A magnetic protein biocompass?

A team of scientists from Peking University report a putative magnetic receptor (MagR) protein in Drosophila, CG8198 [1]. MagR binds an iron—sulphur cluster and interacts with photoreceptor cryptochrome (Cry) proteins to form a multimeric magnetosensing rod-like complex. Assemblies of these rods were observed orienting themselves in a weak magnetic field. Qin et al. speculate that these structures may function like compasses in living organisms, although the mechanism of magnetoreception in vivo remains a mystery [2].

A complete Cry/MagR magnetosensor protein complex structure model with 10 Crys helically binding to the rod-like MagR polymer consisting of 20 MagRs.

1. Qin, S., Yin, H., Yang, C., Dou, Y., Liu, Z., Zhang, P., Yu, H., Huang, Y., Feng, J., Hao, J., Hao, J., Deng, L., Yan, X., Dong, X., Zhao, Z., Jiang, T., Wang, H.-W., Luo, S.-J. and Xie, C. (2016) A magnetic protein biocompass. Nature Materials 15, 217–226.
2. Cyranoski, D. (2015) Long-sought biological compass discovered: Protein complex offers explanation for how animals sense Earth’s magnetic pull. Nature 527, 283–284.

Nitrite binding modes in CuNIR

Fukuda and Inoue [1] have determined the crystal structure of the C135A mutant of thermostable copper nitrite reductase (CuNIR) from Geobacillus thermodenitrificans in complex with nitrite to 1.55 Å resolution. Interestingly, this high-temperature (320 K) structure [2] displays a near-bidentate binding mode of nitrite distinct from a monodentate mode in a cryogenic structure [3]:

To our knowledge, this is the first case in which the difference in substrate binding modes between cryogenic and high-temperature structures has been visualized by crystallography.

The copper site geometries are given in Table 1.

Table 1 (adapted from [4])

Cu—Ligand Distances (Å)	3X1N (320 K)	3WKP (100 K)
I. Type 1 Cu—residue distances
T1Cu—H95Nδ1	2.08	2.14
T1Cu—H143Nδ1	2.01	1.96
T1Cu—M148Sδ	2.13	2.07
II. Type 2 Cu—residue distances
T2Cu—H100Nε2	2.07	1.96
T2Cu—H134Nε2	2.00	1.95
T2Cu—H294Nε2	1.98	2.01
T2Cu—water	2.02	n/a
III. Type 2 Cu—nitrite distances
T2Cu—Oproximal	2.13	1.97
T2Cu—N	2.21	2.85
T2Cu—Odistal	2.52	3.41

1. Fukuda, Y. and Inoue, T. (2015) High-temperature and high-resolution crystallography of thermostable copper nitrite reductase. Chemical Communications 51, 6532—6535.
2. PDB:3X1N
3. PDB:3WKP
4. Fukuda, Y. and Inoue, T. (2015) High-temperature and high-resolution crystallography of thermostable copper nitrite reductase. Electronic Supplementary Material.

Colourful Compound Interest

I discovered Andy Brunning’s Compound Interest last year and got absolutely hooked on it – and I don’t even teach chemistry! If, perchance, you do teach chemistry and don’t yet know what CI is all about, then you probably should check it out. (And if you want to use the material in the classroom, you can download the high-resolution PDF files.) The topics range from general chemistry to material science, chemical warfare and everyday compounds. You’ve got answers to many questions you always wanted to ask but never had time to find out for yourself, like, “is it worth (not) to refrigerate tomatoes?”. The Undeserved Reputations section is a perfect antidote to the “oh my God, our food is still full of chemicals” stream of rubbish published by your Facebook friends.

Here are ten the top ten some of my CI favourites.

Metal Ion Flame Test Colours Chart

1. This is how (I’d like to think) I’ve got interested in chemistry. We used to have a gas hob in our kitchen. I loved the fact that the flame was blue. One day, my brother told me that you can make the flame bright orangey-yellow if you sprinkle it with table salt or bicarbonate of soda. “Why?”, I asked. “Sodium”, was the answer. Unsatisfactory as it was, it stayed in my memory. Yes, chemistry won’t be of any interest to me if not for flame and colours.



Colours of Transition Metal Ions in Aqueous Solution

2. When they are not busy burning or, better still, exploding stuff, your archetypal chemists are often imagined (and therefore portrayed; or is it the other way round?) as hiding behind the test tubes filled with colourful solutions. Which is just as well. The test tubes filled with colourless solutions would be really boring.



What Causes the Colour of Gemstones?

3. Who didn’t dream of finding a treasure, that is, a pirate’s chest filled with gold and jewels? Wait. I still dream of that. I remember how surprised I was when, back in elementary school, I read in some book that ruby and sapphire are basically the same mineral corundum, the only difference is in a type of impurity. Well it’s quite an important difference then. Without impurities, most gemstones would be colourless.



The Chemistry of The Colours of Blood

4. My interest in bioinorganic chemistry (even though at the time I didn’t know at it was called that) was also awakened in school, when I learned that some animals have blue blood. I also discovered that, contrary to what anatomy textbooks show, veins do not carry blue blood in humans. I am not sure if I was relieved or disappointed. Later, already in the university, I read about a Soviet-developed fluorocarbon-based blood substitute nicknamed “Blue Blood”. Fascinating stuff.



The Chemicals Behind the Colours of Autumn Leaves

5. I remember, as a child, reading, or rather browsing, an illustrated book about plants (translated from English), with many beautiful colour photographs. “This apple is yellow because of anthocyanin”. Next page: “This apple is yellow because of carotene”. Next page: “This apple is green because of chlorophyll”. The realisation dawned that, apple-wise, being green is not only necessary but sometimes sufficient.

   But what about leaves? When autumn comes, chlorophyll starts to break down and we get to see other pigments in them. Apart from caroteinoids and flavonoids, there are also coloured chlorophyll degradation products, termed “rusty pigments”.



The Chemistry of Stain Removal

6. Sometimes, however, we want to get rid of all these beautiful colours. The infographic shows the chemical methods of achieving that, although I am not sure that “enzymatic stains” is a correct name for stains caused by blood or grass (yes, haem and chlorophyll again!).



The Atmospheres of the Solar System

7. Alchemists associated seven metals with seven planets (which included the sun and the moon). At the time, it seemed to be quite reasonable. Now that nobody expects Mercury to be made of mercury (and, for that matter, Pluto to be made of plutonium), precious little is known about composition of these planets. About their atmospheres, we’ve learned a bit more. Hey, isn’t it amazing that Mercury’s atmosphere has by far highest percentage of molecular oxygen (42%) compared to any other atmosphere in Solar system? We still won’t be able to breathe there though, because its atmosphere is way too thin (its surface pressure is less than 10⁻¹⁴ bar).



The Metals in UK Coins

8. Compared to gemstones, coins are so much duller, especially now that we don’t come across either gold or silver coins any longer. Continuing the alchemical tradition, we can say that modern British coins of 20 pence and higher are mostly from Venus (that is, copper), while 1 p, 2 p, 5 p and 10 p coins are mostly from Mars (i.e. iron). Of course, you can find much more metal variety in commemorative coins.



The Metal Reactivity Series

9. In contrast to their salts, aqueous complexes and gemstones, pure metals do not offer a great variety of colours. Copper is red, gold is yellow and caesium is yellowish; the rest are coming in many shades of grey. But their chemical behaviour is wildly different, as this infographics shows. You don’t need a sophisticated lab equipment or fancy reagents, just water and some (diluted) acids. If there’s no reaction whatsoever, you’ve got a precious metal. Easy!



Analytical Chemistry – Infrared (IR) Spectroscopy

10. Did I tell you that my first love, as far as the world of analytical chemistry is concerned, was vibrational spectroscopy? If not, I’m telling you now. I’ve never got to do any experiment worthy of a publication, because if I did, believe me, it would have been awesome. This infographics reminded me of happy days of my studenthood when I knew and cared more about amide bands (bless them) than about money or my future career.

There is no perfect language

From The Information: A History, A Theory, A Flood by James Gleick:

It was once thought that a perfect language should have an exact one-to-one correspondence between words and their meanings. There should be no ambiguity, no vagueness, no confusion. Our earthly Babel is a falling off from the lost speech of Eden: a catastrophe and a punishment. “I imagine,” writes the novelist Dexter Palmer, “that the entries of the dictionary that lies on the desk in God’s study must have one-to-one correspondences between the words and their definitions, so that when God sends directives to his angels, they are completely free from ambiguity. Each sentence that He speaks or writes must be perfect, and therefore a miracle.” We know better now. With or without God, there is no perfect language.

Leibniz thought that if natural language could not be perfect, at least the calculus could: a language of symbols rigorously assigned. “All human thoughts might be entirely resolvable into a small number of thoughts considered as primitive.” These could then be combined and dissected mechanically, as it were. “Once this had been done, whoever uses such characters would either never make an error, or, at least, would have the possibility of immediately recognizing his mistakes, by using the simplest of tests.” Gödel ended that dream.

On the contrary, the idea of perfection is contrary to the nature of language. Information theory has helped us understand that — or, if you are a pessimist, forced us to understand it.

Periodic Videos

It’s been a while since I posted anything on this blog, but now I’m back.

This is a very cool collection of videos, “a lesson about every single element on the periodic table”. Featuring Professor and a really awesome reaction, here’s one about one of my favourite elements. Yes, iron is in my blood! (In yours too.)