Slashdot Mirror
Easier Way to Convert Proteins into Crystals
Roland Piquepaille writes "As you might know, proteins need to be transformed into 3-D crystals before their atomic structures and their properties can be analyzed. And production of high quality crystals from proteins has been a difficult task until now. But scientists in the U.K. have successfully used a porous medium, or 'nucleant,' a material that encourages protein molecules to crystallize. Their first step towards 'holy grail' of crystallography could help speed up the development of new medicines and treatments."
Ok, so I don't know a ton about nuclear medicine, I know just enough to be dangerous. Protein crystallization allows us to see it's structure whereby we better understand its function.
The reason this bit of news is so big is that it will (hopefully) allow researchers a way to quickly look at the structures of proteins in such as (in the second link) infectious diseases transmitted by prions, or protein particles. Prions seem to be pure protein; they contain neither DNA nor RNA.
If we can understand the shape and formation of proteins, we can understand how viruses and cells work because proteins are the building blocks. Viruses are obviously first on the chopping block as they are the smallest and infect millions of people world wide (AIDS, influenza, the common cold, etc.).
My work here is dung.
To find the three-d structure by x-ray crystallography, you have to crystallize the protein. Actually doing so, with different proteins, is an astoundingly difficult task, so much so that something like five Nobel prizes have been given for research into crystallization and x-ray crystallography development, and another ten or so Nobels given for determination of three-d structure of various proteins were, in essence, awarded for getting the protein to crystallize.
Side story: there was a famous German chemist named Emil Fischer, who originally determined the structures of a bunch of sugars. That was, again, largely a crystallization problem. He had, as Germans did in the 1890's, an enormous beard, and was playing with chemicals all day long, which tended to condense in his beard. It was said that if you could not get something to crystallize out of solution, no matter what you did, you asked Fischer to come to your lab and fluff his beard over your beaker, and the seed crystals falling from it were of such variety that one was almost guaranteed to be correct for your particular situation and get it to crystallize. So this isn't exactly NEW technology.
Nostalgia's not what it used to be.
Hopefully this will encourage more individuals to pursue advanced degrees in protein crystallography. I was recently at a talk where a soon-to-be PhD was discussing her crystallography work. She said that many people choose to pursue other areas in biochemistry/structural biology because protein crystallography is very unpredictable. Some proteins will crystallize in months while others can take YEARS! Waiting years before you can really dive into your PhD research is very discouraging.
This is an improvement on a known technique. The abstract is as over-reaching as the press release (the linked article).
I'm not a crystallographer, but I work in a lab group that has many crystalographers in it.
It's been known for some time that you can use a variety of materials - including things with porous surfaces, which is what is used here - to assist the process of crystallization. Crystalization is difficult and, frankly, rather unscientific - you take the protein you want to crystallize, and you try different techniques and tricks (of which porous nucleants are an example) until you can get it to work.
So, okay, it would be a "holy grail" if you could find one technique that would let you crystallize most things without going through all that trouble.
However, based on only seven examples (Subscribers only, I'm afraid.), you absolutely cannot conclude that this is a universal nucleant - based on the similarity among the seven examples, I'd be very surprised if it were; even if it were a universal nucleant, nucleation does not always guarantee usable crystals.
Those caveats aside, it does look like a useful advance.
The good and new comes from no quarter where it is looked for, and is always something different from what is expected.
NMR diesn't rquire crystallization, but it does require transfer of the protein to a non-native solution (which may affect tert structure). Not that crystallization doesn't do this also...
Plus, NMR results or more vague than X-Ray crystallography, and can only be used with small proteins, whereas crystallography works for even very large proteins (provided you can get them crystallized).
"Trolls they were, but filled with the evil will of their master: a fell race..." -- J.R.R. Tolkien on Olog-hai
While I agree that this is a major advance, I think calling this the "holy grail" is going too far. Currently there a several ways of doing large screens for crystallization conditions which utilize robots and nanoliter volumes of protein/condition to screen thousands of precipitant mixtures. The two real major stumbling blocks in crystallography are purification of monodisperse, nearly homogeneous protein (with respect to post-translational modifications as well as identity of the protein species) and the real "holy grail" problem, which is ab initio phase determination.
Since X-rays cannot be lensed, the Fourier transform of the diffraction pattern (which is the Fourier synthesis of the ordered electrons in the crystal) requires knowing not only the intensities, a trivial task, but also the relative phase angle of each reflection. This is a problem with possible solutions on the order of 6^n, where n is the total number of unique reflections, or about 5-10,000 for an average macromolecular structure at 3 angstrom Bragg spacing, allowing for a +/- accuracy of 30 degrees for each phase angle. Current solutions rely on searching reciprocal space with similar known structures (Molecular Replacement) or several ab initio methods that require one or more heavy element derivatives of native crystals. The first approach only works for crystals where a very similar structure is already known and available to the investigator. The second approach requires further screening for heavy metals that bind in ordered sites in the crystal without significant alteration of the native lattice, then usually a trip to a tunable X-ray source at a synchrotron. This second approach can burn through an astounding number of crystals and investigator time. There are shortcuts such as making the protein with Seleno-methionine instead of methionine (selenium has a usable X-ray edge for phasing, unlike sulfur),but this is normally done after initial purification and crystallization have been optimized. For more reading on the phase problem, I'd recommend either Alexander McPherson or Jan Drenth's excellent introductory textbooks on macromolecular crystallography.