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)
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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.

A little helper – Elf3

What is it?

E74-like factor-3 (Elf3) is a transcription factor. This means that it is a protein involved in the expression of genes. Elf3 works with other proteins to regulate genes involved in inflammation and cancer; it is has been found to be abnormally expressed in some lung and breast cancers.

In order to ensure proper gene expression, transcription factor activity is highly regulated. Accordingly Elf3 is held in an “off” state and must be specifically turned on before it can bind to DNA to start gene expression. The interaction of Elf3 with DNA is also highly specific, again to avoid abnormal gene expression that may lead to disease.

In order to learn how Elf3 recognises, binds and activates gene expression, researchers solved the crystal structure of the Elf3 bound to DNA from one of its target genes.

What does it look like?

ELF3This structure is of a specific part of mouse Elf3, the so-called E-twenty-six (Ets) domain, bound to DNA from mouse Type II TGF-b receptor promoter. Promoter DNA sequences provide a “start to read me from here” instruction to transcription factors so this structure provides lots of information about how the two molecules talk to each other.

Elf3 (green) is shown bound to DNA (red double helix)

Where did the structure come from?

This structure is PDB ID 3JTH1.

References

  1. Agarkar et al., Journal of Molecular Biology, 2010. 397, 278-289

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.

Munc18: No Munc-eying around with our molecular transport machinery!

What is it?

The transport of chemicals or proteins across the membranes of cells is a vital part of life. Chemicals may need to be released in order to send a signal to the cell next door, or sometimes, a protein must be relocate from inside the cell to sit on the cell membrane so it can do its job.

For this reason, the Sec/Munc18 (SM) family of proteins—involved in fusion between two membranes—are an essential for this molecular transport and play a key part of healthy cell function. These SM proteins are involved in neurotransmitter release in the brain and in the maintenance of glucose levels (i.e. by relocating the glucose transporter to the cell surface so it can pump glucose into the cell).

Within our cells, chemicals or molecules can be isolated from the rest of the cell contents by containing them within small membrane encapsulated vesicles. But the molecular mechanisms behind how proteins, including SM, coordinate the fusion of these vesicle membrane to the outer membrane of the cell, so that neurotransmitters or the glucose transporter can do their thing, is not understood.

Crystal structures of SM proteins alone, and in complex with their partner proteins are helping us to decode the complex mechanisms of the membrane fusion event. And the importance of research in this area is essential for the development of new treatments for neurological diseases or diabetes. Indeed, Randy W. Schekman, Thomas C. Südhof, and James E. Rothman were awarded the 2013 Nobel Prize in Physiology or Medicine for their discoveries on the protein machinery that regulates vesicle traffic, including the SM proteins! You can read more about their Nobel Prize and their research here.

What does it look like?

SM proteins, such as Munc18-1 (or Munc18a) shown below, consist of three separate domains that fold into a U-shaped or arch-shaped architecture. Image generated by Pymol (using the coordinates from the protein data bank (accession code: 3PUJ).

SM proteins, such as Munc18-1 (or Munc18a) shown below, consist of three separate domains that fold into a U-shaped or arch-shaped architecture. Image generated by Pymol (using the coordinates from the protein data bank (accession code: 3PUJ).

Where did the structure come from?

This is the structure of rat Munc18-1 that was solved in complex with a portion of its partner protein, syntaxin (Sx). The structure was published in 2011 PNAS by a team of researchers from the Institute for Molecular Bioscience, UQ, Australia.

A total of 12 SM structures have been determined, either alone or complexed to a truncated protein partner or short peptide sequence. Click here for a review on the current structural information of SM proteins.

I’m pretty, but don’t touch me as I’m deadly

What does it look like?

Batrachotoxin A from the poison dart frog Phyllobates aurotaenia. Carbon atoms in brown, oxygen atoms in red and nitrogen atoms in blue.

Batrachotoxin A from the poison dart frog Phyllobates aurotaenia. Carbon atoms in brown, oxygen atoms in red and nitrogen atoms in blue.

What is it?

Today is Isabella Karle’s birthday. A leading crystallographer who in her early career worked on the Manhattan project to synthesise plutonium compounds, but became famous for solving the structure of the toxin found in the skin secretions of South American poison dart frogs. Isabella worked with her husband Jerome Karle at the United States Naval Research Laboratory. Jerome Karle won the Nobel Prize for chemistry in 1985 with Herbert Hauptman for their work in X-ray crystallography. Although Isabella didn’t win the Nobel Prize she scored a huge number of awards and prizes in her own right including the US National Medal of Science.

Colombian poison dart frog, Phyllobates aurotaenia. Image from: http://en.wikipedia.org/wiki/Phyllobates_aurotaenia#

Colombian poison dart frog, Phyllobates aurotaenia. Image from: http://en.wikipedia.org/wiki/Phyllobates_aurotaenia#

The toxin shown here is batrachotoxin from the glands of the Dendrobatidae family of frogs found in South and Central America. Native South American tribesmen coat the tips of their hunting darts with the skin secretions of the frogs to give the darts added lethality. The batrachotoxin is extremely lethal requiring only 100 micrograms (or 0.0001 grams) to kill an average sized adult. Batrachotoxin is a neurotoxin and works by binding to the sodium ion channels found in neurons. When batrachotoxin binds to the sodium ion channels the pumps remain permanently open stopping the messages from travelling along neurons and leading to paralysis and heart failure.

Batrachotoxin from frogs consists of three molecules: batrachotoxin A, isobatrachotoxin and pseudobatrachotoxin. The structure shown here is batrachotoxin A that has an additional p-bromobenzoate. The toxin consists of a steroidal structure with its three 6 carbon rings and one 5 carbon ring linked together, and is also an alkaloid due to the presence of the basic nitrogen.

Where did it come from?

The structure was solved by T. Tokuyama and colleagues in 1968 [1] and the structure shown is from the Cambridge Structural Database and published by Isabella Karle in 1969 [2].

[1] Takashi Tokuyama , John Daly , B. Witkop , Isabella L. Karle , J. Karle: The structure of batrachotoxinin A, a novel steroidal alkaloid from the Columbian arrow poison frog, Phyllobates aurotaenia. J. Am. Chem. Soc. (1968) 90, 1917–1918

[2] I.L.Karle, J.Karle: The structural formula and crystal structure of the O-p-bromobenzoate derivative of batrachotoxinin A, C31H38NO6Br, a frog venom and steroidal alkaloid. Acta Cryst. (1969). B25, 428-434