A different type of donut – beta-sliding clamp

What does it look like?

Beta has a striking resemblance to a donut, but isn’t as tasty. The protein is actually a dimer, with the arrows showing the dimeric interface. Each dimer has three domains comprised of two beta-sheets and two a-helices.

Image generated by VMD (Visual Molecular Dynamics) using the coordinates from the Protein Data Bank (PDB code: 3Q4J)

Image generated by VMD (Visual Molecular Dynamics) using the coordinates from the Protein Data Bank (PDB code: 3Q4J)

What is it?

The Escherichia coli beta-sliding clamp (beta) is an aptly named DNA replication protein. It is clamped onto and slides along DNA, recruiting other replication proteins to the DNA during the different stages of replication. What makes this an interesting protein is the nature of these interactions, as every protein that interacts with b binds in the same pocket by very similar amino acid motifs. On the structure, the consensus amino acid motif (QLDLF) is bound into the pocket. This conserved binding has made the E. coli beta protein a target for novel antibiotics, and many potential antibacterial small molecules have been published.

Where does it come from?

The first crystal structure was solved by X.P. Kong and colleagues in 1992 [1] and since then, many structures of E. coli beta in complex with protein binding partner consensus motifs [2] and small molecule inhibitors [3] have been solved.

 

[1] Kong, X.P., Onrust, R., O’Donnell, M., and Kuriyan, J. (1992). Three-dimensional structure of the b subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp. Cell 69(3): 425-437

[2] Wolff, P., Olieric, V., Briand, J.P., Chaloin, O., Dejeagere, A., Dumas, P., Ennifar, E., Guichard, G., Wagner, J., and Burnouf, D.Y. (2011). Structure-based design of short peptide ligands binding onto the E. coli processivity ring. Journal of Medicinal Chemistry 54(13): 4627-4637

[3] Yin, Z., Whittell, L.R., Wang, Y., Jergic, S., Lui, M., Harry, E.J., Dixon, N.E., Beck, J.L., Kelso, M.J., and Oakley, A.J. (2014). Discovery of lead compounds targeting the bacterial sliding clamp using a fragment-based approach. Journal of Medicinal Chemistry 57: 2799-2806

A ring of progress – Benzene

What does it look like?

Image generated by the Mercury crystal structure visualisation software http://www.ccdc.cam.ac.uk/Solutions/CSDSystem/Pages/Mercury.aspx

Image generated by the Mercury crystal structure visualisation software http://www.ccdc.cam.ac.uk/Solutions/CSDSystem/Pages/Mercury.aspx

What is it?

Benzene is the simplest aromatic hydrocarbon and also quite the crystallographic puzzle for many years. Though it had been known for a long time that benzene was made up of a ring of carbon atoms, in the early years of the crystallography one question that was sought by a number of researchers was to determine the shape of the ring of benzene. There was a lot of debate, for instance WL Bragg (one of the founders of the field of crystallography) thought the molecule itself was bent.

The work of Cox in 1932 that showed that the molecule within solid benzene was not bent and in fact a flat ring. However, it was Kathleen Lonsdale who had paved the way for the understanding of the shape of the benzene molecule, with her structure of hexamethylbenzene in 1929. Together this work paved the way for the wide field of molecular crystallography that has many impacts on our way of life.

Where did the structure come from?

Cox first published the structure of benzene in the Proceedings of the Royal Society A in 1932, but refined his structure with a number of other investigations at different temperatures.

 

An extra-terrestrial hydrocarbon – Ethane

What does it look like?

Image generated by the Mercury crystal structure visualisation software http://www.ccdc.cam.ac.uk/Solutions/CSDSystem/Pages/Mercury.aspx

Image generated by the Mercury crystal structure visualisation software http://www.ccdc.cam.ac.uk/Solutions/CSDSystem/Pages/Mercury.aspx

What is it?

Ethane is one of the simple hydrocarbons, with and has a number of uses and nuisances in wider life and industry. Like methane it’s one of those materials that people only think of as a gas. But, like methane (and indeed every other gas) given cold enough conditions ethane will freeze to a solid. Ethane in particular does this at 90 K, where it becomes a plastic crystal – meaning that the molecules within the structure are rotating. This means that the structures is very simple, a pack of spheres in a body centred arrangement (like Roentgenium).

However, this plastic phase has only a very narrow range of stability, when you cool from 90 K by only 0.5 K, the rotation of the molecules stop and the structures becomes monoclinic (ie much less symmetric than when it first freezes.).

There are lots of reasons that this is interesting from a fundamental point of view, but when you think about the lakes of Titan the freezing of solid ethane becomes a process that could sculpt this icy moon. Titan is the only other body in our solar system known to have liquid on the surface, great seas and lakes that are thought to be made up of methane and ethane. But the surface temperature of Titan is about 90 K, so as the temperature skirts about this parts of the ocean could freeze and then melt when things got a little warmer. Could it explain the mystery ‘island’ observed by the Cassini spacecraft recently?

Where did the structure come from?

The structure of ethane, both the plastic and monoclinic phases, were discovered in 1978 by van Nes and Vos. This work was published in Acta Cryst, and the structures can be found in the Cambridge Structure Database (CSD) (refcode ETHANE for the plastic phase and ETHATE 01 for the monoclinic phase).

June birthstone – Pearl

June is a lucky month; it has two possible birthstones, both crystalline. We have already talked about one of the possible birthstones – moonstone. The other option is a Pearl. Made up of a variant of CaCO3 – Aragonite.

What does it look like?

The aragonite structure, CaCO3. Ca is yellow, C is green and oxygen is grey. This picture was made using the diamond crystal structure visualisation software package.

The aragonite structure, CaCO3. Ca is yellow, C is green and oxygen is grey. This picture was made using the diamond crystal structure visualisation software package.

What is it?

Pearls are produced naturally by Molluscs as a way of removing irritants from their shells. This irritant is usually a parasite rather than a particulate irritant such as sand. In theory any mollusc can produce a pearl but the best quality pearls with the best iridescence are produced by oysters.

Pearl

Diagram comparing a cross-section of a cultured pearl, upper, with a natural pearl, lower. Taken from http://en.wikipedia.org/wiki/Pearl

Cultured pearls are grown by introducing a tiny piece of foreign tissue from another shell. This then starts the growth of a pearl sac and ultimately the precipitation of aragonite and a pearl. Cultured pearls are distinguished from their natural counterparts by an X-ray. The figure below shows the internal structure of a cultured vs natural pearl. Both are built up of layers but the layers are oriented differently.

Where did the structure come from?

This structure is from: Antao S M and I Hassan (2009) The orthorhombic structure of CaCO3, SrCO3, PbCO3 and BaCO3: Linear structural trends The Canadian Mineralogist 47 1245 and is available on the AMCSD.

“Roll out the Barrel” Structure of the LptD-LptE translocon complex from bacteria

What is it?

Lipopolysaccharide (LPS) is an essential component of the bacterial cell wall and protects bacteria against antibiotics. The LPS translocon complex, consisting of two proteins (LptD:LptE ) is critical for transport and insertion of these protective LPS molecules in the outer wall. Thus, targeting these essential proteins in the bacterial cell membrane may be novel mechanism for developing antibiotics against multi-drug resistant bacteria.

What does it look like?

LptD (pink) forms a novel 26-stranded β-barrel, which is reportedly the largest β-barrel protein structure known to date. LptE (aqua) adopts a roll-like structure located inside the barrel of LptD. Together these proteins form a unique two-protein ‘barrel and plug’ architecture. LPS is passed sequentially from LptC to LptA and then to the LptD:LptE complex, and is finally inserted into the outer membrane of the bacterium.

For more information about this structure, and a movie showing the LptD:LptE complex, see http://www.diamond.ac.uk/Home/News/LatestNews/18-06-14.html

Image generated by Pymol (http://www.pymol.org/) using the coordinates from the protein data bank (accession code: 4N4R)

Image generated by Pymol (http://www.pymol.org/) using the coordinates from the protein data bank (accession code: 4N4R)

Where did the structure come from?        

This structure of LptD:LptE complex from Salmonella typhimurium was determined using the Diamond Synchrotron Light Source and published in Nature in June 2014. Understanding the mechanism of LPS insertion into the outer membrane of bacteria may help develop novel antibiotics.

Bi George, it’s bismuth!

What does it look like?

Image generated by the VESTA (Visualisation for Electronic and STructual Analysis) software http://jp-minerals.org/vesta/en/

Image generated by the VESTA (Visualisation for Electronic and STructual Analysis) software http://jp-minerals.org/vesta/en/

 

Why is bismuth our next crystal structure? Because bismuth crystals are just plain cool looking!

If you don’t believe me, then check this one out:

(image courtesy of Wikipedia)

(image courtesy of Wikipedia)

Bismuth is a commonly used metal, in part because of its low toxicity, and can be found in lots of everyday products like makeup and medications, including the aptly named Pepto-Bismol. Naturally, however, bismuth isn’t bright pink, but light gray, like in the cube above. The rainbow sheen on the large crystal actually comes from a surface oxide layer that forms on the bismuth during crystal growth.

The crystal structure of bismuth is relatively simple, as is shown above. Bismuth has a rhombohedal unit cell, which means that here only two of the lattice parameters are the same and two of the angles in the unit cell are 90° while the third is 120°. But this crystal structure isn’t what causes such a distinct type of crystal to form. This type of “staircase” like growth is called a hopper crystal. These types of crystals form because the outside of the crystal grows faster than the inside, so the large crystals never get “filled in”. However, the growth of the inside portion of the crystal is still dictated by the crystal structure, which is how the “step” features form.

Since bismuth is a relatively safe and easy to obtain metal, you can actually make bismuth crystals at home in your kitchen (or garage if you happen to have a gas torch around). You can check out a video of stove-top bismuth crystals here.

Where did this structure come from?

The first determination of the structure of bismuth was reported in 1962 by P. Cucka and C.S. Barrnett. (http://onlinelibrary.wiley.com/doi/10.1107/S0365110X62002297/abstract) You can also find the structure at #5000215 in the Crystallography Open Database. (http://www.crystallography.net/5000215.html)

A bit of a mouthful – sodium vanadium fluorophosphates: Na3V2O2x(PO4)2F3-2x

What does it look like?

Image generated by the VESTA (Visualisation for Electronic and STructual Analysis) software http://jp-minerals.org/vesta/en/

Image generated by the VESTA (Visualisation for Electronic and STructual Analysis) software http://jp-minerals.org/vesta/en/

What is it?

Compounds in the Na3V2O2x(PO4)2F3-2x family have shown promise to be used in the next generation of batteries, as positive electrodes in rechargeable sodium-ion batteries. Yes, this is correct, researchers are feverishly trying to find out whether we can replace lithium-ion batteries with sodium-ion batteries. Why? The major reason is that sodium is much cheaper than lithium. However, a number of challenges in moving from lithium to sodium exist, one of the biggest is size – for a bigger charge carrier like sodium one needs a bigger tunnel, channel or hole. This is where the sodium vanadium fluorophosphates come into play. They have two sites which can host sodium and they have been shown to provide similar energy storage capabilities to lithium-ion battery positive electrodes in idealised systems. The challenges are to make a real system and test these materials for extended periods of time.

Although, the sodium vanadium fluorophosphates may have a fancy application, these materials are actually synthetically and crystallographically fascinating! Synthetically because there are difficult to make and it is often the carbon content in the reagent mix that promotes formation with minimal impurities and some semblance of vanadium oxidation state control. Wait what? Carbon, there is no carbon in the formula? Well carbon appears to influence the hydrothermal reaction to an extent and its role is still unclear. What is more interesting is the vanadium oxidation state and the ratio of F:O in the structure… F and O are very hard to differentiate using X-ray or neutron diffraction, a crystallographers nightmare, but one can use bond length analysis, 23Na & 19F NMR, double titration, and XANESto figure out the ratio of F:O and then model this in diffraction data. Additionally, the ratio of F:O2- tells us about the oxidation state of vanadium which is often mixed valent ranging from 3+ to 4+. To add further complexity to the situation there are four known polymorphs of this material and two of them can be present under ambient (room temperature and pressure) conditions. It is a challenging material to work with but if it can be used to realise sodium-ion batteries, the challenges are worth overcoming.

Where did the structure come from?

The original work on this system is likely to be the work of Le Meins et al. in 1999 (J.-M. Le Meins et al., J. Solid State Chem., 1999, 148, 260.), but the work of Tsirlin et al. in 2011 (A.A. Tsirlin et al., Phys. Rev. B 2011, 84, 014429.) and our work in Serras et al in 2014 (DOI: 10.1039/c4ta00773e) address a number of pertinent issues that were concerning in the literature. We use in situ synchrotron X-ray diffraction to illustrate the structural evolution of this positive electrode in a sodium-ion cell.