Protein Crystallization Hits

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

Enjoy,

Peter

Earlier this month I received an email from John Wiley & Sons, confirming that 'The supplement file is now available at http://onlinelibrary.wiley.com/doi/10.1110/ps.073263108/suppinfo'. More than half a year ago I had pointed out that the 'supplementary material' to a paper was not available online. Now it is. Took a while, but  THANKS A LOT for following through, John Wiley & Sons!

When you go to this page, you can download Simon Newstead's alpha-MP-database.xls.

Although somewhat outdated, this spreadsheet contains a concise summary of crystallization conditions from 121 alpha helical membrane protein structures that are listed in the PDB. The extensive analysis of crystallization conditions is described in the accompanying paper:

Newstead S, Ferrandon S, & Iwata S (2008).

Rationalizing alpha-helical membrane protein crystallization.

Protein science, 17 (3), 466-72

PMID: 18218713

While this accounting exercise is not the sexiest of all science, it is of great interest to all of us membrane protein crystallizers . The database is a handy tool that can be consulted when only small quantities of membrane protein sample is available and one is forced to focus on 'what's worked in the past'.  And of course, this data summary is incredibly for the design of new (although highly biased) crystallization matrices. This is exactly what Simon has done: based on his own analysis, a new sparse matrix crystallization screen, called MemGold  is described.

Great work!

Peter

Over the past two years I've systematically reduced the amount of printed paper in my office as well as in my private life. The idea behind this effort is that 'going digital' with all my documents will make it simpler to store and quickly find information that I need. This is work in progress where the crucial software elements that stuck are Sync Toy (general file housekeeping), PICASA (automatic archiving of images) and Google Desktop (searches everything I have on my PC; yes - I'm a PC).

The most recent addition to this toolset is Mendeley. This is a PDF file organization tool that's devised specifically for researchers to archive, annotate and share their PDF articles. To say the least, I'm very impressed with Mendeley's utility. Within a short period of time Mendeley has helped me to aggregate and organize all of my (currently 642 and growing library of) PDF documents. The functionality goes well beyond a traditional Reference Manager. Features are here, the ones that I like particularly are:

• making notes within PDFs,
• sharing libraries over the web,
• backing up my own collection of articles,
• cross-talk with Zotero (a Firefox-based reference manager),
• cross-platform compatibility (I have Mendeley installed on Windows 7 and on iPhone/iPod touch, and use it via the web browser interface - works seamlessly so far) and
• search functionality.

Here's a quick primer to Mendeley:

Mendeley Teaching Presentation

Mendeley : the best research tool since streak-seeding?

There's even a social media facette too; here's my Mendeley profile - friend me if you'd like: 

Oh - and did I mention that Mendeley is available for free?

Cheers,

Peter

I've said it more than once: "5 min surfing the web can save you a week in the lab".  Here's my most recent online favourite:

BRENDA, the Comprehensive Enzyme Information System. 

BRENDA stands for Braunschweig Enzyme Database and its utility as a starting point for expression, purification and crystallization may be enormous if you're working on enzymes. The search function of this online database is simple to use, yet allows simple identification according to EC number, common/recommended names, systematic names and synonymous names.

Let's say you're interested in 'phosphatases'. Use this keyword to search under 'crystallization' and you'll be treated with a well-organized table that lists 16 different phosphatases with crystallization notes and references to the corresponding primary literature (see below).  This works best for enzymes that have been crystallized already but you may be able to spot trends if your crystallization target belongs to a similar-behaving protein family. 

The real strength of BRENDA though is additional information that is provided, such as stability information (pH, temperature, organic solvent, oxidation, storage) and functional parameters and binding partners (small molecule ligands, metals, substrates). This knowledge can be key to preparing the protein sample upstream of the crystallization process.

My take: if you're working on an enzyme and have not checked out BRENDA yet, go there today.

Cheers,

Peter

There seems to be a live webcast from the ICCBM13, the 13th International Conference on the Crystallization of Biological Macromolecules at Trinity College in Dublin, Ireland. Stay tuned from 12th to the 16th September 2010 to learn what's new in protein crystallization science.

I'm not planning on staying up late over here on the west coast of the US. But the talks should be avalable for download at a later time, wouldn't you think so?

Cheers,

Peter