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Biotech Science

Easier Way to Convert Proteins into Crystals 92

Posted by ScuttleMonkey from the crystal-clear-science dept.
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."
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Easier Way to Convert Proteins into Crystals More

Easier Way to Convert Proteins into Crystals

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  • This is Big (Score:5, Informative)

    by eldavojohn ( 898314 ) * <eldavojohn@noSpAM.gmail.com> on Wednesday January 18, 2006 @02:04PM (#14501492) Journal
    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 [davidson.edu] whereby we better understand its function [faseb.org].

    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.).
    • I always thought that DNA contains proteins , and not proteins contain DNA, ATGTTA....
    • Yes, but attacking prions will allow us to eat raw cannibalistic cow brain with impunity!
    • Also, by converting proteins to crystals, it enables us to arrange them into superstructures which can be rapidly oxidized in a fused silicate tube and subsequently internally analyzed by lung tissue.
      • Also, by converting proteins to crystals, it enables us to arrange them into superstructures which can be rapidly oxidized in a fused silicate tube and subsequently internally analyzed by lung tissue.
        My god, with this technology, we could manufacture the purest Methamphetamine known to man.

        Party at Imperial College London tonight! Thank meth Doctor Stephenson!

    • Re:This is Big (Score:5, Informative)

      by ruckerz2k ( 653900 ) on Wednesday January 18, 2006 @02:20PM (#14501706)
      Though the parent is correct, this technology greatly reduces the time and effort involved in 'crystallizing' proteins. Most common approach is to use the hanging drop method [davidson.edu], where a drop of the sample is suspended over a highly concentrated solution. The sample concentrates due to the negative osmotic pressure and the protein 'crystallizes'. The crystallization process can be hastened by using a 'nucleant', usually a small crystal of the sample that you have previously crystallized. Also, the exact identity and composition of the concentrated solution is varied in order to find the right crystallization conditions. This is a very tedious process (imagine setting up 96 different concentrated solutions, each differing in about 1% concentration of the solutes) and time intensive.

      The discovery of a 'universal' nucleant (close to the one suggested by the authors of this study) and the development of a matrix to encourage crystallization would greatly speed the screening process, and ultimately, crystallization of proteins.

    • By speeding up the (currently extremely tedious) process of crystallization and hopefully making inroads into the ~70% of all protein which currently can't be crystallized, this will rapidly improve our understanding of the structures of whole classes of proteins.
    • Getting a protein in solution to precipitate as a well-formed crystal is the first step in using X-ray crystallography to determine its structure. This first step, at least until now, has been more art and magic than science. This breakthrough doesn't do anything to speed up the structure determination, which will still take a long time for each protein being studied.

    • Re:This is Big (Score:4, Informative)

      by SIGFPE ( 97527 ) on Wednesday January 18, 2006 @02:31PM (#14501827) Homepage
      Talk about Karma whoring! A bunch of sentences culled from a variety of sources from someone who really doesn't know what they are talking about. Now that's dangerous.



      Viruses are obviously first on the chopping block...

      Non "obviously" at all. There are countless medical applications for X-ray crystallography. Any time you want to study the structure of a protein it comes in handy. Many diseases are attacked by researchers from the point of view of receptor binding - the binding together of proteins to other compounds like a lock and key. Such receptors act like switches activating or controlling biological processes. These are ubiquitous in nature and understanding the shape of these 'locks' and 'keys' can be useful in trying to understand the mechanisms of all kinds of diseases whether or not they are caused by pathogens.

    • Re:This is Not so Big (Score:5, Informative)

      by sam_handelman ( 519767 ) <samuel...handelman@@@gmail...com> on Wednesday January 18, 2006 @02:32PM (#14501837) Journal
      This is an improvement on a known technique. The abstract [pnas.org] 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. [pnas.org]), 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.
      • Crystalization is difficult and, frankly, rather unscientific
        You're not kidding. My favorite example is the fact that many crystallographers add diet coke to aid in crystallization.

    • Re:This is Big (Score:1, Interesting)

      by DerCed ( 155038 )
      Yeah, you've got it mostly right.
      In structural biology, the x-ray crystallographers try to find out the exact 3-dimensional structure of a single protein. Since almost everything in the biochemistry of the human body works with proteins, they are a common target for drugs!

      The problem in crystallization lies in the properties of the proteins themselves. They are flexible, dynamic, fragile little machines which SHOULD NOT crystallize in your cells (exactly this happens in diseases linked to prions). So they a
    • Sure being able to find suitable crystallization conditions for proteins is a bottleneck at the moment and this will aid in the process and add to the 20,000 plus know Protein structures, however, this is limited to certain types of proteins. A lot of really interesting proteins however are more flexible, and its this flexibility thats the key to understanding a lot of protein function. Structures derived from crystals don't give so much information about protein dynamics and molten globule like states of p
    • Prion disease kills less people than lightning.

      It's important to fix for a number of reasons, but way less important than the many other areas of medicine in which this development could be useful.

      In my even less informed opinion.
    • Quibble #1: This is not "nuclear medicine", it is "structural biochemistry."
      The field of nuclear medicine is concerned with things like radiation therapy and PET scanning.

      http://science.howstuffworks.com/nuclear-medicine. htm [howstuffworks.com]
      http://jnm.snmjournals.org/ [snmjournals.org]
      http://www.biomedcentral.com/bmcnuclmed/ [biomedcentral.com]

      Quibble #2: Your second link is very outdated. Structures for several prion proteins were determined several
    • I observe this phenomenon all the time on top of my uncleaned plates in the kitchen sink :)
  • Drink lots of beer and then pee in the snow.
  • CURSES!

    They've beaten me to the protein-to-crystal technology that was to be the core of my patent-pending Doomsday Device!

    I wonder what the DeathLegion's union rep will say when I announce 10,000 layoffs...
  • 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.
    Ever hear of using NMR to determine tertiary structure in solution? Just for the record, it doesn't require cystals.

    • Re:Ever hear of NMR structure determination? (Score:4, Informative)

      by Red Flayer ( 890720 ) on Wednesday January 18, 2006 @02:33PM (#14501848) Journal
      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).
      • I understand what you're saying.

        I just don't like the use of absolutes by the person who submitted the article.

        Both tehcniques have pros and cons and the best approach (given infinite time and money) would be to employ both in parallel. In fact, I believe that with the adavnces in NMR technology, it will one day replace the use of X-ray crystallography.

        Also a scientist, you'd even be more marketable with both skillsets at the end :)

        • I thnk you're right on all counts, except maybe your last point (generalization may preclude being 'tops' in either method).

          I suspect that the submitter:
          (1) Isn't up on the subject, and
          (2) Didn't bother to do some background research before submitting.

          Still, I'm glad the article was submitted and posted :)
      • The molecular weight limit of NMR has been increasing quite a bit and now proteins on the order of 100 kDa are possible, although technically challenging. Lewis Kay's group at the University of Toronto has done a solution structure of an 80 kDa protein, for instance.
      • I take exception to the "NMR results [are] more vague than X-Ray crystallography". If you do NMR structure determination, you would know that it doesn't have to be that way. It depends on how much information you can get from the NMR NOESY spectra, which is basically a map that tells you which hydrogen atoms are close to other hydrogen atoms. The "vague" statement may refer to the simulations that are required to transform the NMR spectrum into a structure. However, X-ray crystallography also requires c
      • Not sure what you mean by "non-native" solution. The protein will (hopefully) be in a native conformation in the buffer. But NMR does suffer from size limitations and is only possible for rather small proteins, at the moment. Advances in pulse sequences may improve the performance. (Nuclear magnetic resonance relies on radio pulses in a very strong magnetic field (>10 Tesla) to observe "relaxation" in the aligned molecules. It is the same as MRI, but no one wants a medical procedure with "Nuclear" i
      • Plus, NMR results or more vague than X-Ray crystallography, and can only be used with small proteins,

        This is a common misconception, and while Xray structures are often more *precise*, they are not always more *accurate*. It is also somewhat like comparing apples and oranges, since one is in a crystal, the other is more free to move without distortion in solution

        Protein structures determined by NMR are typically represented as an ensemble of possible 'best fits' to the observed NMR data, and so often
    • NMR is great, because it's fast, relatively easy to run, and tolerant of substrate. But it isn't absolutely accurate. Techniques such as nOesy and cosey allow for determination of stereochemistry via two-dimensionaly NMR, showing contact through bonding and through-space interactions. However the data from a nOe experiment can be inconclusive, especially in cyclic systems. Only X-ray data can actually confirm the true structure then.
      A friend, also doing a Ph. D in chemistry, has just binned half his thesis
    • NMR has an inherit weight limit. Relatively few protein structures are found using it, most are done by XRAY-C. Currently, of all proteins structured, 5000 are by NMR 28,000 by XRAY. See http://www.pdb.org/pdb/static.do?p=general_informa tion/pdb_statistics/index.html&tb=false [pdb.org]

  • Understanding protein structure.. (Score:3, Informative)

    by jonasmit ( 560153 ) on Wednesday January 18, 2006 @02:27PM (#14501785)
    is critical to translating the information obtained in, for example, the Human Genome Project. The DNA gives us the blueprint but the protein does the work. Currently, there is no way to predict protein structure from DNA. Therefore, you must see the structure to understand how the protein works. Also it is important to note that in Protein-Protein interactions. Protein-Protein interactions are important in normal cell singalling events as well as in how virii infect cells (like HIV1 binding to gp120/gp41).

  • Nobel Prize material (Score:5, Funny)

    by smellsofbikes ( 890263 ) on Wednesday January 18, 2006 @02:28PM (#14501786) Journal
    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.

  • This should impact future graduate students (Score:5, Insightful)

    by radiashun ( 220050 ) on Wednesday January 18, 2006 @02:28PM (#14501788)
    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.
    • It is also a fairly lucrative field, and you need people with advanced degrees.

      Did you ever see the prices that a crystallographic lab charges (even for academia)?

      I don't think that NMR people get paid as well...

    • It is true that we need more people in the field, but we need people to improve on current techniques, such as the researchers mentioned in the article. We don't just need more people using the same old methods. Currently protein crystallization is almost all trial and error, which obviously isn't most efficient way to do much of anything. I currently work in a crystallography lab myself, and I can tell you from expereince that it is an extremely painful process. While the human genome project was a hu

  • Roland Piquepaille knows nothing. (Score:1, Informative)

    by Anonymous Coward
    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.

    Simply NOT TRUE.

    Proteins must be crystalized before they can be analyzed by X-ray crystallography. They can be analyzed by many, many other methods even if they aren't crystals. And frankly, given that proteins aren't in crystalline form in the body, knowing the crystalline form isn't always useful.

    NMR (nuclear magnetic resonance) spectroscopy wi
    • For high-resolution structures of large molecules, X-Ray crystallography is still the way to go.
    • I'm afraid not. Nothing beats having an accurate structure from Px. I spent several years as a postdoc attempting to grow large crystals of a membrane protein (at the time one of the first three or four membrane proteins to be crystallized). As we really were interested in knowing the structure rather than how we got it as light relief from purifying the protein on a near industrial scale and seeding thousands of crystallization trials we tried every other structural analysis method we could get our ha
    • Indeed, there are techniques on the horizon to study atomic resolution without crystals, and the ability to observe a single molecule may be someday routine. But for atomic resolution (~1 angstrom or so) at ths time, nothing beats Roentgen's x-ray, equations of Laue and the Bragg, Bernal and Crowfoot's crystallization techniques, and an obscenely powerful digital computer (even though proteins were crystallized in 1918, the first structure coincides with digital computers 40 years later, as 3-D fourier tra

  • Of course (Score:1, Offtopic)

    by Tumbleweed ( 3706 ) *
    As you might know, proteins need to be transformed into 3-D crystals before their atomic structures and their properties can be analyzed.

    I knew that.

  • Or don't crystallize at all(!) (Score:3, Interesting)

    by infolib ( 618234 ) on Wednesday January 18, 2006 @02:46PM (#14502015)
    It might be possible to determine protein structure with just a single molecule, no need for crystallization at all, e.g. with free electron lasers [nih.gov]

    The brilliance of x-ray sources are right now undergoing a revolution much faster than Moore's law.

  • crystallization is tough stuff (Score:3, Interesting)

    by !splut ( 512711 ) <sputNO@SPAMalum.rpi.edu> on Wednesday January 18, 2006 @03:03PM (#14502249) Journal
    IAASB (structural biologist), and while I can't verify their findings, I can back up the premise in the article that generating diffraction-quality protein crystals is one of the two major bottlenecks to X-ray crystallography (the other being purification).

    It's pretty easy to understand why. Not only do you need pure protein, but one must find conditions under which that protein forms relatively large, single crystals. The chief variables, aside from the homogeneity of the protein you're starting off with, include temperature, pH, protein concentration, choice of and concentration of precipitant (generally a chemical that drives the protein out of solution), choice of and concentration of additive compounds, in some cases detergents... The researcher must traverse this multidemensional search space by trial and error, with a limited quantity of protein, looking for the optimal conditions. On top of that, the conditions that confer the ideal level of nucleation may not be ideal for crystal growth...

    We have developed shortcuts over the past 20 years, or so. Kits are available that allow one to screen through frequently successful crystallization conditions. The number of conditions one can test in one go is gradually increasing, as things miniturize somewhat.

    The ease-of-crystallization varies amazingly from one protein to another, and tricks that improve one do not necessarily work for another, but anything that simplifies the process will be greatly appreciated by the field.
    • 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 th
  • between burial, cremation, or crystilization?

    cool..
  • In a related story, the university has built a town for residents to move into and a modest price.

    Yep. Three and four bedroom homes that do not have transmutation circles covered up with wallpaper. Oh, and pay no attention to the symmetry of the town map or the position of the homes and businesses being positioned where they are. It's not a giant alchemy transmutation circle! You're silly and watch too much anime! It's a Rorschach test. Yeah! And from what I see I see two philosopher sto--stoner poder

  • Probably gonna start a flamewar, but... (Score:3, Interesting)

    by cr0sh ( 43134 ) on Wednesday January 18, 2006 @04:34PM (#14503381) Homepage
    If proteins can be crystalized (albeit with some difficulty), in order to study structure and makeup, then is the reverse true? That is, could some proteins be created from a crystal matrix?

    I know this isn't a new idea. I don't have references handy to prove it isn't, I just know that I have read arguments about it. This theory is used to explain the origins of life (distinct from the theory of evolution). Basically, you have the whole "early earth molecular soup mix with electrical activity providing the spark-o-life" (Miller-Urey Experiment [wikipedia.org]), forming organic compounds, which are then (in some manner) "processed" by crystal structures forming later (?).

    It makes me wonder if it wouldn't be possible to study crystals in a similar manner to see whether they could (in some manner) aid the formation of the organic compounds formed by the Miller-Urey (and other similar) experiments into early proteins or protein-like structures? Does anyone know if such a study has already been undertaken? Or, is this idea nothing more than baseless speculation with no foundation in reality? I am sincerely curious...

    • Re:Probably gonna start a flamewar, but... (Score:1, Interesting)

      by Anonymous Coward
      There are theories of the origins of life that invoke highly ordered matricies like montmorillonite clays that have been shown to catalyze some biologically relevant reactions, as well as induce the formation of lipid bilayer micelles, which would have been important for the formation of primordial cells. But for the most part, biologists agree that RNA probably came along before proteins, so looking for a template that could create RNA would probably be a better target.

      But whatever the method, the way to
  • Wow, structure, function... everyone has posted good comments. But isn't the real problem understanding how proteins FOLD! We know the make-up of many proteins, but do not understand HOW they work because it is tied up in exactly how they fold. This new method does not address this issue. Scientist are trying to understand how proteins work based on their shape AFTER they have folded. If we could figure out HOW they fold, we wouldn't have to examine each one individually. We could predict the final sha
    • Thats why I am a member of Team 11108 for FAH!

      When I build a machine for a client, I try to encourage them to run the FAH core whenever their computer is on, and install it by default.
    • "If we could figure out HOW they fold, we wouldn't have to examine each one individually. We could predict the final shape and function based on the knowledge of we have of the protein making intstructions and HOW THEY FOLD." On the right track but knowing the shape a protein will fold to is not enough. We still need to know the structure-function relationship. Knowing how it will fold is a little closer, but it's not the holy grail either. The holy grail is knowing directly from the sequence what the fu
      • How they fold is necessary knowledge to modify a protein. You don't need to know a modified protein's ultimate function BEFORE you make and test it. The testing would tell you that. But the structure IS the function when it comes to proteins, based on how they work. By coupling with complementary receptors, the proteins express themselves many different ways. This is thought to happen with some proteins in the middle of completely folding, thus expressing two separate functions.
    • I've thought about this plenty, but to have some benchmarks for the shapes different proteins make, we need lots of evidence that a folding model matches the true output of the mRNA. So yeah, I look forward to the day when we can truly predict how they fold, but it's going to take a lot of work to determine the ways that different amino acids interact and how the conformational shape changes due to different interactions throughout the process of elongation. Then if that wasn't enough, we'll need to also
  • I hope this isn't the first step on the way to creating Ice-Nine [technovelgy.com]!
  • Given that the Sanger institute has over a billion gene sequence on file, and (according to Wikipedia) the Protein Data Bank has about 30-odd thousand structures, and assuming that structure and sequence are of roughly equal scientific interest, can we conclude that determining a protein structure is 30,000 times harder than determining a gene sequence?

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