Give me a resin

What is it?

Is there a more evocative Christmas smell than the fragrance of a fresh pine tree? Mulled wine with cinnamon spices or a roasting turkey are close contenders for the prize, but for literary purposes let’s opt for the heady scent of a Christmas Fir. That rich winter wonderland terpentine-like citrus aroma is the product of several molecules (read more here http://www.compoundchem.com/2014/12/19/christmastrees/), the most significant of which is pinene.

Pinene is a terpene found in the resin of pine trees, and as well as generating the distinctive coniferous scent, it is also a potent inhibitor of the human Cytochrome P450 2B enzyme. CYP450 proteins are a superfamily of enzymes essential for hormone, cholesterol and vitamin D synthesis and metabolism. They also assist in the clearance of toxins from the body via the liver. So, if you ever you needed a “resin” not to eat your Christmas tree…

What does it look like?

Pinene

Researchers determined the crystal structure of (+)–α-pinene bound to CYP450 2B6 to better understand how this pine tree molecule can bind, inhibit, and alter the enzyme1. This is important to learn about how the enzymes generally interact with a diverse range of substrates.

(+)-α-pinene binds tightly at the CYP450 2B6 active site. The CYP450 2B6 active site is remarkably flexible and moves and shifts to mould around the pinene molecule as it binds.

Where did the structure come from?

This structure is of human CYP450 2B6 and is PDB ID 4I91.

References

  1. Wilderman et al., Journal of the American Chemical Society 2013: 135: (10433-10440)

Why does a lobster change colour on cooking?

Prof John Helliwell answers one of those Australian Christmas conundrums – why do lobsters change colour when you cook them?  Crystallography has the answer:

lobster

This posting, Helen Maynard-Casely tells me, has a Christmas aspect. At Christmas time colleagues ‘down under’ are tucking into cooked lobster whilst the rest of us ‘up north’ are having Christmas turkey!

What is it?

Crystal grown by the microbatch method in a 2µl drop under oil. The photograph shows the natural blue colour of the crystal. Crystal size: 100  ×  100  ×  500  µm. Courtesy of Prof Naomi Chayen.

Crystal grown by the microbatch method in a 2µl drop under oil. The photograph shows the natural blue colour of the crystal. Crystal size: 100  ×  100  ×  500  µm. Courtesy of Prof Naomi Chayen.

The active coloration molecule in the lobster shell is astaxanthin (AXT). When it is bound to the lobster protein complex crustacyanin it is blue-black and when not bound to the protein crustacyanin AXT is orange-red (at equivalent dilutions). The molecular geometric and electronic factors which cause this colour change (a bathochromic shift) have been identified from the X-ray crystal structure of beta-crustacyanin (Cianci et al 2002). The protein releases its grip on the AXT when the protein would be denatured – such as by boiling. The AXT causes the crustacyanin to adopt a quite different arrangement of protein subunits compared with the apocrustacyanin (Cianci et al 2001).

dimer_2

Apocrustacyanin A1 dimer (Cianci et al 2001 Acta Cryst D)

 

The whole project of studying beta-crustacyanin and of apocrustacyanin by X-ray crystallography was made possible through the expert research on macromolecular crystallisation, and also the growth of these particular crystals, by Prof Naomi Chayen and her coworkers at Imperial College in London.

Apocrustacyanin A1 crystals; different crystal habits, identical unit cell dimensions (Naomi Chayen, Imperial College, London).

Apocrustacyanin A1 crystals; different crystal habits, identical unit cell dimensions (Naomi Chayen, Imperial College, London).

Intriguingly other lobster crustacyanins such as the Australian Western Rock Lobster has ‘red’ and ‘white’ phases of its life cycle but not blue-black along with an interesting genetic make up in this respect (Wade et al (2009)).

Other lobster crustacyanins; the Australian Western Rock Lobster (which has ‘red’ and ‘white’ phases); also only one gene (type 2)

Other lobster crustacyanins; the Australian Western Rock Lobster (which has ‘red’ and ‘white’ phases); also only one gene (type 2)

Cianci, P.J. Rizkallah, A. Olczak, J. Raftery, N.E. Chayen, P.F. Zagalsky and J.R. Helliwell “Structure of apocrustacyanin A1 using softer X-rays” (2001) Acta Crystallographica Section D-Biological Crystallography D57, 1219-1229.

Cianci, P.J. Rizkallah, A. Olczak, J. Raftery, N.E. Chayen, P.F. Zagalsky and J.R. Helliwell “The molecular basis of the coloration mechanism in lobster shell: β-crustacyanin at 3.2 A resolution” (2002) PNAS USA 99, 9795-9800.

Wade, N.M.; Tollenaere, A.; Hall, M.R.; Degnan, B.M. Evolution of a Novel Carotenoid–Binding Protein Responsible for Crustacean Shell Color. Mol. Biol. Evol. 2009, 26(8), 1851–1864.

Oh deer…

Roisin McMahon gets us into the jollity of the season….

Did Rudolph go to school?

No. He was Elf-taught.

What do reindeers hang on their Christmas trees?

Horn-aments!

How come you never head about the tenth reindeer, Olive?

Because Olive, the other reindeer, used to laugh and call him names

What is it?

Today’s festive crystal structure is of reindeer β-lactoglobulin. β-lactoglobulin is a whey protein present in the milk of many but not all mammals. It is not found in human milk. Despite extensive investigation, the function of β-lactroglobulin is not yet known. It may be a food source, or it may function as a carrier protein as it is known to bind hydrophobic molecules.

UntitledWhat does it look like?

β-lactoglobulins are part of the lipocalin superfamily. They have a 8 stranded β-barrel fold with one α-helix. Hydrophobic molecules such as retinol or palmitic acid can bind within the centre of the barrel.

Where did the structure come from?

This structure is of reindeer β-lactoglobulin. The protein was purified from reindeer milk. (Q. How do you milk a reindeer? Answers on a post card please as I really wish I had a punch line for this one.) It is PDB ID 1YUP1.

References

  1. Oksanen et al., Acta Crystallographica Section D 2006. 62:1369-1375

Jokes from here http://www.whychristmas.com/fun/cracker_jokes.shtml and here http://www.bjentertainments.co.uk/dan/xmas%20jokes.htm

Factor IX: Christmas Factor

What does it look like?

Porcine Factor IXa

Porcine Factor IXa

What is it?

Christmas factor, despite its name, is not named after the festive season during the month of December. The scientific name is Factor IX and is named after Stephen Christmas, whose blood sample lacking Factor IX lead to a new form of haemophilia being discovered.

As a child in the 1950’s Stephen Christmas was diagnosed haemophilia. It was known by then that people suffering from haemophilia were deficient in a protein called Factor VIII. Factor VIII is one of the many proteins that are involved with forming blood clots when one suffers a cut, and a lack of Factor VIII leads to an inability to form blood clots upon injury. However, when doctors tested Stephen Christmas’ blood they found that he had perfectly normal levels of Factor VIII but yet still suffered from haemophilia. It was later discovered that Stephen was lacking a different blood clotting factor, Factor IX, which is also known as Christmas Factor. There is now known to be two different types of haemophilia. Those who are lacking Factor VIII (haemophilia A), and those who are lacking in Factor IX (haemophilia B) accounting for approximately 20 % of people who suffer from haemophilia. Sadly, Stephen Christmas passed away on the 20th December 1993 from HIV/AIDS contracted from a contaminated blood transfusion. Modern treatments for haemophilia are transfusions of the purified forms of the missing factors, and this, in combination with modern screening of blood products greatly reduces the chance of any contaminants.

Factor IX is a serine protease and is cleaved into two polypeptide chains to become active. The structure shown here is the activated form termed Factor IXa. In the presence of membrane phospholipids, calcium, and Factor VIII, the activated Factor IXa will cleave the next protein in the blood clotting pathway known as Factor X. Factor IXa consists of four different domains: a Gla domain (red) for binding phospholipids and calcium ions, two EGF-like domains (cyan and magenta) for binding other proteins, and a protease domain (green) which cleaves Factor X.

Where does it come from?

The structure shown here is porcine Factor IXa and was solved by Hans Brandstetter and colleagues in 1995 [1]. The structure was taken from the Protein Data Bank with PDB code 1PFX.

[1] H. Brandstetter, M. Bauer, R. Huber, P. Lollar and W. Bode: X-ray structure of clotting factor IXa: active site and module structure related to Xase activity and hemophilia B. Proc. Natl. Acad. Sci. USA. (1995) 92: 9796-9800.

A tree bark suspension and a Nobel Prize later…. We wonder less about the structural basis of the action of aspirin

Today we have another guest post from Lawrence Norris of @BlackPhysicists.  A super read that charts how the every day drug aspirin went from being ancient medicine to how modern crystallography could explain how it works.  Enjoy!

Today’s post spans the bridge between ancient pharmacognosy and modern biophysics. The history of aspirin and its medical use can be traced back to the second millennium BC.  Medicines from willow and other salicylate-rich plants appear in the Egyptian pharmacology papyri.  Hippocrates, the father or modern medicine, administered willow tree bark to women to help relieve pain associated with childbirth.  Later the tree bark was used to alleviate general pain and fevers.

In 1763 Oxford University chemist, Edward Stone, isolated the active compound from Hippocrates preparation, which turned out to be salicylic acid.  In 1853 French chemist Charles Frédéric Gerhardt synthesized acetylsalicylic acid, albeit in an unstable and impure form.  In 1897 German chemist Felix Hoffman, working for Bayer, first synthesize pure acetyl salicylic acid, which later became known as aspirin.  Bayer took aspirin to market almost immediately, and established a complete market association of Bayer AG with the drug.  “Bayer Aspirin” had been on the market for nearly 50 years when Wheatly determined the crystal structure of aspirin in 1964 [1].  There have been several reports of an elusive second crystal polymorphs of aspirin. (See 7 Feb 2014 post on this blog.)

Aspirin-3D-balls.png
Aspirin-3D-balls“. Licensed under Public domain via Wikimedia Commons.

Aspirin took on the moniker of “wonder drug” as it worked wonders against the miseries of aches, pains, fever and inflammation, and scientists wondered why.   Here is where the story of aspirin merges with the Nobel Prize winning work of Bergstrom, Samuelsson and Vane [2] .   This trio and their co-workers elucidated the structure [3] and function of prostaglandins, which are paracrine hormones that mediate many physiological functions having to do with platelet aggregation and smooth muscle tone.   They identified prostaglandin H synthase (PGHS),  as being the key control point enzyme in the “prostaglandin cascade”.   Vane in particular showed that it was possible to block the synthesis and thus the action of prostaglandins with aspirin [4].

Still it was not known exactly how aspirin works.  Enter the work of Picot, Loll and Garavito who solved the crystal structure of PGHS (aka COX)  in 1994 [5].  It bears mentioning here that the crystallization of PGHS, being a membrane protein,  was a tour de force in protein crystallography.  When its structure was published in 1994, there were less than a dozen other membrane proteins in the PDB database.

COX-2 inhibited by Aspirin.png
COX-2 inhibited by Aspirin” by Jeff Dahl – self-made, release to public domain. Licensed under Public domain via Wikimedia Commons.

Following their initial work, Loll, et. al., were able to solve the structure of the enzyme with aspirin bound [6], and also with other drugs that compete with aspirin in the marketplace, e.g., ibuprofen [7].   Others showed how Naproxen (Alleve) binds to the enzyme [8].   Aspirin, it turns out, is an irreversible inhibitor of PGHS.  It acetylates a key serine residue in the enzyme’s active site, and that prevents the natural substrate from situating itself for productive enzyme activity.

Alas though, this is not the whole story of how this wonder drug works physiologically.  Recent results indicate that aspirin is an antiporter partner to protons in mitochondria.  Also aspirin apparently induces formation of inflammation-reducing NO radicals, and signaling through NF-κB.

References
[1]  Wheatley, P. J. “The crystal and molecular structure of aspirin.” J. Chem. Soc., 1163 (1964), 6036-6048, 10.1039/JR9640006036

[2] “The Nobel Prize in Physiology or Medicine 1982”. Nobelprize.org. Nobel Media AB 2014. Web. 25 Nov 2014. <http://www.nobelprize.org/nobel_prizes/medicine/laureates/1982/>

[3]   Abrahamsson, S. “A direct determination of the molecular structure of prostaglandin F2-1.” Acta Crystallographica 16.5 (1963), 409-418, 10.1107/S0365110X63001079

[4]  Vane, J. R. “Inhibition of prostaglandin synthesis as a mechanism of action for aspirin-like drugs.” Nature 231.25 (1971): 232-235, 10.1038/newbio231232a0

[5]  Picot, D, P. J. Loll, and R. M. Garavito. “The X-ray crystal structure of the membrane protein prostaglandin H2 synthase-1.” Nature 367.6460 (1994), 243-249, 10.1038/367243a0

[6]  Loll, P. J., D. Picot, and R. M. Garavito. “The structural basis of aspirin activity inferred from the crystal structure of inactivated prostaglandin H2 synthase.” Nature Structural & Molecular Biology 2.8 (1995), 637-643, 10.1038/nsb0895-637

[7]  Selinsky, Barry S., et al. “Structural analysis of NSAID binding by prostaglandin H2 synthase: time-dependent and time-independent inhibitors elicit identical enzyme conformations.” Biochemistry 40.17,  5172-5180, (2001), 10.1021/bi010045s

[8]  Duggan, Kelsey C., et al. “Molecular basis for cyclooxygenase inhibition by the non-steroidal anti-inflammatory drug naproxen.”  Journal of Biological Chemistry 285.45 (2010), 34950-34959, 10.1074/jbc.M110.162982

 

DNA Polymerase in Celebration of Evolution Day

Today’s Anton tells us about a structure behind one aspect of evolution.

What does it look like?

The Klenow fragment of DNA polymerase I from E. coli (in blue) with template and new DNA strands (green and magenta respectively).

The Klenow fragment of DNA polymerase I from E. coli (in blue) with template and new DNA strands (green and magenta respectively).

What is it?

Today is evolution day, the day where the publication of Charles Darwin’s seminal work On the Origin of Species in 1859 is celebrated. DNA and its specific sequence of bases: A, T, C, and G, have a lot to do with evolution but since we’ve already blogged about the structure of DNA for Rosalind Franklin’s birthday, I thought I’d write about the protein that replicates the DNA when a cell divides: DNA polymerase.

DNA replication is semi-conservative: that is, each strand of DNA acts as the template for the new copy and one of copy each goes to the two new daughter cells. There are billions of A, T, C, and G’s that make up a genome thus it is of the utmost importance that DNA polymerase is extremely accurate in its job. Typically DNA polymerase will make one mistake for every billon bases copied. There are a number of reasons why DNA polymerase is so accurate. 1. DNA polymerase can select the correct bases for the correct pairing (i.e. A pairs with T and G pairs with C); 2. There is a proof reading mechanism and 3. Repair systems if a mistake is spotted.

Many those one in a billion mistakes will never show as a unique characteristic but some could result in a random mutation that is seen as observable characteristics (the phenotype) in an organism. If that mutation is in the reproductive cells then the mutation could be passed onto the next generation and with the favour of natural selection propagate for many generations.

As a mistake in copying DNA can prove to be disastrous as well a beneficial there is a lot of redundancy in DNA replication with many organisms having more than one DNA polymerase. E. coli for instance has five DNA polymerases. The structure shown today is the Klenow fragment of E. coli DNA polymerase I. The Klenow fragment is the part of the polymerase where replication and proof reading occur but other domains have been removed. The structure resembles the shape of a hand with the DNA being held between a finger and thumb.

Where did it come from?

DNA polymerase I from E. coli was discovered by Arthur Kornberg in 1956 (and later won the Nobel Prize for Physiology and Medicine in 1959 for the discovery). The structure shown here was solved in 1993 [1] by Lorena Beese, Victoria Derbyshire, and Thomas Steitz (who won the Noble prize for Chemistry in 2009 with Venkatraman Ramakrishnan and Ada Yonath for their work on the ribosome). The structure was taken from the Protein Data Bank (PDB number: 1KLN).

[1] L.S. Beese, V. Derbyshire, T.A. Steitz (1993) Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science 260: 352-355.

From crystal to structure in 84 years

What is it?

In 1926 Jack Bean urease was the first protein to be crystallised 1, earning a place in the history books for this humble plant protein and a Nobel Prize for James B. Sumner (see yesterday’s post for more). Besides establishing that proteins could be crystallised, Sumner’s work was remarkable for demonstrating that proteins could be isolated and purified whilst retaining enzymatic activity. Despite this landmark advance in protein biochemistry and crystallography, it was a further 84 years before the crystal structure of Jack Bean Urease was determined, in what must surely be the longest running crystallography endeavour in history2.

Where did the structure come from?

Urease is an enzyme in plants, bacteria and fungi that helps to break urea into ammonia and carbon dioxide. Whilst other urease structures were known – for example Helicobacter pylori urease, the structure of which helped to explain how this bacterium can survive in the acid environment of the human stomach3 – the structure of Jack Bean urease was only determined in 2010.

What does it look like?

Urease

Plant ureases are single chain proteins. Jack Bean urease is a T-shaped molecule of four domains (coloured here in red, blue, yellow and pink.) In common with other ureases, Jack Bean Ureases binds two nickel ions (blue spheres) in its active site; these are required for enzymatic breakdown of urea.

This structure is Protein Data Bank ID 3LA4

References

  1. Sumner, 1926: J. Biol. Chem. 69:435-441
  2. Balasubramanian & Ponnuraj. 2010 J. Mol. Biol. 400:274-283
  3. Ha et al., 2001. Nature Structural Biology 8: 505-509