March 7, 2013 21:48
It's getting time again to do some spring-cleaning in the protein crystallization lab.
A well-organized lab is more productive, is fun to work in, produces better results and costs less money. That's why I'd recommend spring cleaning to everyone running a protein crystallization lab. Depending on how your particular lab is set up you may want to do some or all of the following:
- Toss out all old crystallization plates for those crystallization projects that have been completed to make room for new crystallization trials.
- Replace all opened crystallization reagent containers ('crystallization screens'). Using evaporated formulations can produce more annoying salt crystals and fewer crystallization hits due to lower organic solvent concentration; contaminated formulations proteolyze your protein solution and light sensitive reagents such as MES or PEG can react with protein molecules, rendering them uncrystallizable. And of course: replace these crystallization screens with new Emerald Bio Wizard kits! and stock solutions. Buying in bundles makes sense! Ask us for your reagent kit combination or stock solution libraries.
- Clean working surfaces to minimize contamination of crystallization experiments with dust.
- Organize: Put tools, such as pipettors, tip boxes, pins, wands, tongs, razor blades and fresh crystallization screens in labeled boxes or on shelves. You may be surprised by the amount of work space you can gain.
- Check your tools, and if necessary earmark them for cleaning or calibration : microscopes, robotic instrumentation, liquid dispensing instruments, dewars.
- Computer: Archive old files, check backup routine and clean up desktops (Disk Cleanup)
- Safety-check the protein crystallization work area: do you have appropriate gloves, lab goggles, coats, clean-up kits, containers and cabinets available? Lab safety matters!
- Pick up the trash. Empty out disposables containers for sharps, various liquids (heavy metal, organics, halides, hazardous liquids) and plastics.
So, show some of your inner Martha Stewart and spring-clean your protein crystallization lab!
P.S. Now that I think of it- maybe you want to keep some of these old formulations for use as a 'last resort'. These moldy, evaporated and reactive formulations may be of use in some special cases. More about that at another time.
March 1, 2013 00:54
Darren Begley recently put up an interesting post about "Grooming your fragment library: Checking the quality of commercially-sourced fragments".
The point he's making is that tight QC measures are key to the success of fragment screening:
"These results highlight the importance of implementing tight quality control measures for preliminary vetting of commercially-sourced materials, as well as maintaining and curating a fragment screening library. It also puts forth a statistical likelihood of around 10-15% failure, regardless of vendor. Most importantly, we have seen our methods reduce risks while accelerating drug discovery. "
This is certainly true for NMR-based experiments and of course also applies to crystallography-based fragment screening.
I was glad to see Derek Lowe pick up the discussion in this blog post: Not What It Says On the Label, Though
Several of the comments to this post support Darren's findings and drive this message home: Buyer beware!
November 15, 2012 18:29
Genetic Engineering & Biotechnology News has a separate Expert Tips section. If you are looking for start-up advice for growing membrane protein crystals, you may want to have a look at this recent post:
8 Often-Overlooked Tips for Membrane Protein Crystallization
June 16, 2012 01:06
If only we would not have to ‘waste’ so much protein sample for mind-numbing trial and error crystallization experiments. Aside from clever pre-crystallization screening approaches, there are now several reports that indicate that we may start to get a handle to more rational approaches. This is the first short review of such a report towards shortening the path from protein sample to crystals.
The observation is that ‘Immobilized metal-affinity chromatography protein-recovery screening is predictive of crystallographic structure success’. A post-mortem analysis of purification and crystallization data has revealed quantitatively what many of us have picked up at the bench: proteins that purify well are easy to crystallize.
Choi R, Kelley A, Leibly D, Hewitt SN, Napuli A, & Van Voorhis W (2011). Immobilized metal-affinity chromatography protein-recovery screening is predictive of crystallographic structure success. Acta crystallographica. Section F, Structural biology and crystallization communications, 67 (Pt 9), 998-1005 PMID: 21904040
The authors of this paper however have taken this observation as a starting point and have devised a low cost IMAC high-throughput protocol (using multichannel pipettors, affinity beads and filter plates; the procedure is described in exquisite detail; thank you very much!). They applied this protocol to more than 4330 proteins (SSGCID effort) to mine IMAC recovery data for rules and find that they determined more than twice as many structures of those proteins that showed a high IMAC recovery, as compared to those with a low IMAC recovery.
March 17, 2012 06:50
In a protein crystallization laboratory you typically see a lot of stock solutions on the shelf. These are used to create optimization screens to improve the quality of protein crystals. Grid-screening is a tried-and-proven way to identify better crystal growth conditions. How many do you really need?
Depends - of course. Generally, the number and type of stock solutions that you should maintain in the wet lab is directly correlated to the type of primary protein crystallization screens that are typically applied used. For instance if all your first pass crystallizations are carried out with JCSG+, it would make sense to have the 84 stock solutions on the shelf, ready to be dispensed into a protein crystallization tray. From my own experience I can tell that if these stock solutions are not handy, researchers tend to use shortcut. No Tricine buffer on the shelf? - what the heck, let's go with Tris. This may work for some crystallizations, but you're out of luck if the buffer molecule is required for providing crystal contacts. The issue is that taking such shortcuts has the potential to derail your entire structure determination project.
Clearly, having these stock solutions on the shelf improves the speed and success rate of crystallographic protein structure determination. Have you ever counted and made a list with the stock solutions that you should have handy? If not, the list below may be a good starting point for you. I'm listing number of different stock solutions that go into the production of protein crystallization screens from Hampton Research, Jena BioScience, Fluidigm, Molecular Dimensions, Qiagen, and of course from Emerald Bio.
Supplier, name and the associated number of stock solutions that are required for the production and optimization of protein crystallization hits. How this data was generated: Here at Emerald Bio we produce a lot of sparse matrix screens and we accomplish this with our fleet of Matrix Maker instruments that are instructed from a database of screen definitions. Since we keep track of many crystallization screens we can identify the number of stock solutions that are used in a number of commercial protein crystallization screens.
In average there are 40 different stocks (+- 22) that are required for these protein crystallization screens.
That's a lot of stock solutions.