Aldosterone synthase structures

Earlier this year [1], the crystal structures of human aldosterone synthase (CYP11B2) were solved in complex with a substrate 11-deoxycorticosterone [2] and an inhibitor fadrozole [3].

1. Strushkevich, N., Gilep, A.A., Shen, L., Arrowsmith, C.H., Edwards, A.M., Usanov, S.A. and Park, H.-W. (2013) Structural insights into aldosterone synthase substrate specificity and targeted inhibition. Molecular Endocrinology 27, 315—324.
2. PDB:4DVQ
3. PDB:4FDH

Supercool

Once again, Summer is upon us. And what could be more satisfying on a hot Summer day than cold beer? I’ll tell you what: really cold beer.

In any good Spanish bar, they will serve you beer in a frozen glass, or copa fría. Here’s a pair of well-chilled beer tankards:

When you pour cold beer in copa fría, it will form ice crystals:

How much ice is formed, depends on temperature and beer strength. In general, the stronger the drink, the lower the freezing point.

On a number of occasions, I was chilling beer in the freezer. Then taking it out, opening the bottle and pouring it into the glass. There are four experimentally observed outcomes.

1. Beer is liquid both in a bottle and in a glass
2. Beer is liquid in a bottle but gets frozen as poured in a glass
3. Beer gets solid in a bottle so no way to pour it in a glass
4. Beer bottle explodes in the freezer

Scenario B is the most interesting one. (Scenario D is also interesting, but I won’t recommend it.) This is how the resulting beer slush looks like:

Now I saw a number of articles on the web where they explain this phenomenon with supercooling. I should say that I am not satisfied with this explanation. Why “supercooled” beer is not getting frozen in the bottle, even if I shake it, but forms slush once outside? When I put a bottle of (non-fizzy) rosé in a freezer, it either stays liquid (and remains liquid upon opening and pouring) or develops fine crystals of ice (which stay as they are upon opening both in a bottle and in a glass). On one occasion, a forgotten in a freezer bottle of rosé got frozen solid. (According to The Academic Wino, “the freezing point of table wine is –5 °C”, and my freezer goes down to –18 °C.)

To explain what happens, we don’t need to bring supercooling in. We just have to keep in mind that our drink is an aqueous solution. And that alcohol is only one of many solutes there. Of them, the most important are sugars and carbon monoxide. (Some beers, such as Guinness, contain dissolved dinitrogen as well as CO₂.)

For dissolution to take place, the overall change of free energy should be negative, but the heat may be either absorbed or released. The dissolving of sugar in water is an endothermic process. The increase in temperature results in an increase in solubility. The reverse process, precipitation (often in form of crystallisation), is exothermic.

On the contrary, the dissolving of gases in water is exothermic. The increase in temperature results in an decrease in gas solubility. The reverse process, gas evolution, is endothermic. So as soon as the bottle is opened, the gas starts to escape and the temperature drops — in our example, below the freezing temperature. Sometimes, it drops so rapidly that beer freezes in the bottleneck. And while I am on it: as this video shows, dissolving of alcohol in water is also exothermic. Not that it changes much in our beer glass experiments.

¡Salud!

More photos of beer @ Shutterstock.

You’re in CD spectroscopy

One day, idly browsing the web (as usual), I came across this:

I disagree with an unknown (to me) co-author of Antoine de Saint-Exupéry. For one thing, you don’t have to be “in organic chemistry” to recognise a reaction coordinate diagram. For another, 25 or so years ago my first reaction (that is, if I never read Le Petit Prince) would be: “Hey dude, your CD spectrum is upside down”. The fact is, I am still alive, so my life then was far from being over.

Isn’t the Web great? Nowadays I don’t have to venture to the library and sift through the J. Biol. Chem.’s and J. Mol. Biol.’s. (Even if I wanted, there is no library like that in Fuerteventura.) I can get the CD spectra online and for free in the Protein Circular Dichroism Data Bank [1]. Better still, using DichroMatch I can find spectra that are similar to my query [2]. (I just checked: it works!) Here’s how the CD spectrum of a typical α-helical protein (such as haemoglobin) looks like (a):

(a)

So... where’s a hat? Back in 1990s, our lab had a decommissioned Jobin Yvon Mark IV dichrograph, which, as I understand now, was an excellent machine. The haemoglobin spectrum would look more or less like this (b):

(b)

Neither equipment nor our samples allowed us to collect spectra below 200 nm, therefore most of the spectrum was in the negative ellipticity region. We did not really need to go below 200 nm: we were mostly monitoring ellipticity at 222 nm as a function of temperature or concentration of guanidinium chloride or other denaturing agents.

Mind you, not all proteins have this inverted hat region in their CD spectra. For example, ferredoxin (c), rubredoxin (d) or immunoglobulin G (e):

(c)

(d)

(e)

In the 21st century, protein X-ray crystallography became very much a routine technique. Once you solve the structure, there’s no mystery left. On the contrary, the CD spectra are as beautiful and enigmatic as star spectra. They still need an intelligent interpreter. They tell the story and in the same time keep the secret. I think the little prince would appreciate them.

1. Whitmore, L., Woollett, B., Miles, A.J., Klose, D.P., Janes, R.W. and Wallace, B.A. (2011) PCDDB: the protein circular dichroism data bank, a repository for circular dichroism spectral and metadata. Nucleic Acids Research 39, D480—D486.
2. Klose, D.P., Wallace, B.A. and Janes, R.W. (2012) DichroMatch: a website for similarity searching of circular dichroism spectra. Nucleic Acids Research 40, W547—W552.

The first CYP1A1 structure

CYP1A1 was one of the first P450 enzymes to be characterised and, as its name indicates, holds the first place in the systematic nomenclature of P450s [1]. However, it was not until last year that the first crystal structure of human CYP1A1 in complex with α-naphthoflavone has been determined at 2.6 Å resolution [2]. The structure [3] is released this week.

1. Nebert, D.W., Nelson, D.R., Coon, M.J., Estabrook, R.W., Feyereisen, R., Fujii-Kuriyama, Y., Gonzalez, F.J., Guengerich, F.P., Gunsalus, I.C., Johnson, E.F., Loper, J.C., Sato, R., Waterman, M.R. and Waxman, D.J. (1991) The P450 superfamily: update on new sequences, gene mapping, and recommended nomenclature. DNA Cell Biol. 10, 1—14.
2. Walsh, A.A., Szklarz, G.D. and Scott, E.E. (2012) Cytochrome P450 1A1 structure and utility in predicting drug and xenobiotic metabolism. Proceedings of the 19th International Symposium on Microsomes and Drug Oxidations and 12th European ISSX Meeting, Noordwijk, The Netherlands, 17—21 June 2012.
3. PDB:4I8V

Binary pnictogen halides

Here’s a tricky (trick?) question from the final exam of MITx course Introduction to Solid State Chemistry:

Which compound has the higher boiling point, phosphorus trifluoride (PF₃) or phosphorus pentafluoride (PF₅)?

Naturally, you are supposed to figure this out from the first principles, or rather, from some principles taught in this course, not from Wikipedia (or “by googling”, as some put it).

(a)	(b)

The problem is, the “right” answer, PF₃, is actually, factually wrong. Even though this question cost only two points (of 150), a rather animated debate followed the exam.

Those who defended the “right” but factually wrong answer (a) were proposing that what the problem was testing our thinking rather than actual knowledge, and our thinking should have been along the lines of VSEPR model. VSEPR rules correctly predict PF₃ to be trigonal pyramidal and PF₅ to be trigonal bipyramidal. The dipole moment of a polar molecule PF₃ should make it less volatile than apolar PF₅. Those who chose the “wrong” but factually correct answer (b) were arguing that polarisability of larger PF₅ is higher than that of PF₃ and therefore the London dispersion forces in PF₅ would beat dipole-dipole interactions in PF₃. The (a) party were saying that making the answer you’d get by applying principles different to the one you’d get by “googling” is a good protection against cheating. The (b) party were retorting that this is a silly way of protection, that the question asked was what has the higher boiling point, not what could be expected to have the higher boiling point, and that expecting students to come up with the factually wrong answer is not exactly pedagogical.

Truth to be told, the methods of estimating boiling or melting points of materials were simply not a part of this course. The only thing one could do was to determine whether the molecule has a non-zero dipole moment. But there is no way to figure out which effect will be stronger, the increase in dispersion forces or dipole-dipole interactions.

One would think that the physical properties of such simple compounds as binary halides of Group 15 elements (pnictogens) are studied well and long ago. Not really. I tried to compile a table of dipole moments and melting/boiling points for pnictogen tri- and pentahalides, MX₃ and MX₅, using various resources [1—5]. As you can see, there are still many gaps.

Trihalide	μ (D)	mp (°C)	bp (°C)	Pentahalide	mp (°C)	bp (°C)
NF3	0.234	–207	–129	—
PF3	1.03	–151.5	–101.8	PF5	–93.7	–84.5
AsF3	2.59	–6.0	62.8	AsF5	–79.8	–52.8
SbF3	?	290	345	SbF5	8.3	141
BiF3	?	649	900	BiF5	154.4	230
NCl3	0.6	–40	71	—
PCl3	0.97	–93.6	76.1	PCl5	167	160s
AsCl3	2.15	–16.0	130.8	AsCl5	–50	?
SbCl3	2.75	73.4	223	SbCl5	4	140
BiCl3	4.6	233.5	441	BiCl5	?	?
NBr3	?	?	?	—
PBr3	?	–41.5	173.2	PBr5	<100d	106d
AsBr3	1.66	31	221	AsBr5	?	?
SbBr3	2.47	96	288	SbBr5	?	?
BiBr3	3.6	219	462	BiBr5	?	?
NI3	?	–20s	?	—
PI3	~0	61.1	227	PI5	41	?
AsI3	?	141	400	AsI5	?	?
SbI3	1.58	170.5	401	SbI5	79	401
BiI3	?	408.6	~542	BiI5	?	?

d, decomposition
s, sublimation

What, if any, trends can we see?

• The dipole moment of MX₃ grows larger down the group of the central atom M, e.g. μ(NF₃) < μ(PF₃) < μ(AsF₃), and grows smaller down the group of ligand atom X, e.g. μ(SbCl₃) > μ(SbBr₃) > μ(SbI₃).
• As the sizes of both central atom and ligands go up, so do the melting and boiling points.
• As dipole moments go up, so do the melting and boiling points.

Something curious happens, though, when one crosses the phosphorus—arsenic borderline. AsF₃ has a dipole moment of 2.59 debye. As expected, both mp and bp of AsF₃ are, respectively, higher than those of AsF₅. PF₃, however, has much lower moment of 1.03 D. Both mp and bp of PF₃ are, respectively, lower than those of PF₅. Similarly, mp of AsCl₃ is higher than mp of AsCl₅, whereas mp of PCl₃ is lower than mp of PCl₅. Similarly... but no, there are too many gaps in the table “down there”.

Which shows, by the way, that “googling” does not help if the data is not available. For the future, the course authors may consider asking a very similar question about a pair of compounds from “down there”. Thus the whole conflict between the (as yet unknown) “truth” and “expected answer” could be easily avoided.

Since the electronegativities decrease down the group for both M and L, the most polar M—L bond must be Bi—F bond and BiF₃ should have the largest dipole moment. Well I couldn’t find its value. But it is known that bismuth trifluoride has ionic structure, and has the highest melting (649 °C) and boiling (900 °C) points of all binary pnictogen halides. On the other side of the spectrum, we have extremely sensitive nitrogen triiodide. A feather tickle, a loud noise and, I suppose, any attempt to measure its dipole moment will set off an explosive decomposition (see the video below):

2 NI₃ → N₂ + 3 I₂

References

1. Earnshaw, A. and Greenwood, N (1997) Chemistry of the Elements, 2nd Edition. Butterworth-Heinemann, Oxford.
2. Nelson, R.D., Jr., Lide, D.R., Jr. and Maryott, A.A. (1967) Selected values of electric dipole moments for molecules in the gas phase. National Standard Reference Data Series — National Bureau of Standards 10, Washington, DC.
3. Cotton, S. (2001) Nitrogen triiodide. Molecule of the Month collection, University of Bristol.
4. WebElements
5. atomistry.com

Macromolecular Xmas decorations

This year I don’t have a Christmas tree. (There aren’t many in Fuerteventura.) But I’ve got some models from this week’s new PDB structures [1—5] which look Christmassy enough to decorate my blog. Merry Christmas and a happy New Year everybody!

1. Hui, F., Scheib, U., Hu, Y., Sommer, R.J., Aroian, R.V. and Ghosh, P. (2012) Structure and glycolipid binding properties of the nematicidal protein Cry5B. Biochemistry 51, 9911—9921.
2. Lence, E., Tizón, L., Otero, J.M., Peón, A., Prazeres, V.F.V., Llamas-Saiz, A.L., Fox, G.C., van Raaij, M.J., Lamb, H., Hawkins, A.R. and González-Bello, C. (2012) Mechanistic basis of the inhibition of type II dehydroquinase by (2S)- and (2R)-2-benzyl-3-dehydroquinic acids. ACS Chem. Biol., in press.
3. Strugatsky, D., McNulty, R., Munson, K., Chen, C.-K., Soltis, S.M., Sachs, G. and Luecke, H. (2012) Structure of the proton-gated urea channel from the gastric pathogen Helicobacter pylori. Nature, in press.
4. Tang, Q., Gao, P., Liu, Y.-P., Gao, A., An, X.-M., Liu, S., Yan, X.-X. and Liang, D.-C. (2012) RecOR complex including RecR N-N dimer and RecO monomer displays a high affinity for ssDNA. Nucleic Acids Res. 40, 11115—11125.
5. Ziervogel, B.K. and Roux, B. (2012) The binding of antibiotics in OmpF porin. Structure, in press.

The discovery of the quantum dot

Louis Brus talks about his discovery of colloidal quantum dots in 1980s.

One of the truisms of science is that the basic research scientists who invent something are not the best judges of where it’s useful.