Protein Crystallization Hits

Some of you may know that Emerald BioStructures, as part of the Seattle Structural Genomics Center for Infectious Disease (SSGCID) has contributed to submitting more than 444 protein structures to the PDB in the past 4 years. That's quite an achievement and my congratulations go out to the project teams that are behind these structures, most of them determined via X-ray crystallography. Some of this output, including methods used to achieve this level of productivity, are described in the  September 2011 issue of Acta Cryst F.

One of the protein production methods that has been key for several of my own 2011 protein crystallization projects: lysis scouting with the Protein Maker instrument (described in this open access article "The Protein Maker: an automated system for high-throughput parallel purification". 

Smith, E., Begley, D., Anderson, V., Raymond, A., Haffner, T., Robinson, J., Edwards, T., Duncan, N., Gerdts, C., Mixon, M., Nollert, P., Staker, B., & Stewart, L. (2011). The Protein Maker: an automated system for high-throughput parallel purification Acta Crystallographica Section F Structural Biology and Crystallization Communications, 67 (9), 1015-1021 DOI: 10.1107/S1744309111028776

What is lysis scouting?

Stated simply, lysis scouting combines the testing of a set of cell-lysis buffer conditions with IMAC (ion metal affinity chromatography) . This is done to increase the yield of proteins that appear partially soluble or insoluble under standard lysis buffer conditions.  This procedure results in a clear path forward for scaled-up production of purified protein samples for protein crystallization trials.

How is lysis scouting done?

A single batch of protein expressing E.coli cells is split into 12 pools and lysed by sonication in 12 different buffer conditions. The paper shows as an example P450 51 A1 (CYP51A1) with a 6xHis-Smt tag. This is the outline of the lysis scouting protocol:

1. Prepare 12 aliquots, each corresponding to 3 g of wet cell paste
2. Resuspend in 30 mL lysis buffer (one out of an array of 12) - see table below.

Cell lysis buffers for testing lysis conditions of recombinantly expressed fungal cytochrome P450

3. Sonicate to lyse and spin to remove cell debris

4. Clarify lysates and load on 12 x 1 mL Ni-affinity matrix column

5. Wash, elute and analyze fractions

SDS-PAGE showing that buffers 1C and 1D extract much more of the target protein CYP51A1 (red boxes). L(load), W(wash) and E(elution) fractions are shown next to MW standards.

While well expressed, CYP51A seemed insoluble using standard cell-lysis methods. The lysis-scouting procedure yielded a buffer system with a detergent (CHAPS or octyl glucoside)  in the presence of high salt concentrations (500 mM NaCl).

The utility of the Protein Maker instrument in this process is the short time it takes to run a lysis scouting experiment. Total run time is approximately 1.5 hours (excluding sample analysis). I.e. many proteins can be tested for optimal lysis conditions in a single day - and since the instrument carries out the experiment for you and in parallel, there is plenty of time to strategize the next steps of mg-scale production of the protein sample for crystallization. 

There are many protein structures that we have produced in 2011 that would not exist without Protein Maker supported lysis optimization.

A true work horse.

Peter

This week I flew down to San Diego to attend the protein purification sessions at PepTalk . The part I was most interested in was an inaugural session, called 'Higher Throughput Protein Purification" (not going to contemplate the 'higher than what?' issue). There were contributions from the fields of automation, particularly challenging targets, sample management and process development.  Interestingly, there were several common threads that the presenters discussed:

• Importance of using multiple constructs in purification and crystallization
• The one-size-fits-all approach is failing more often now with targets becoming more challenging
• Protein purification requires scouting on the level of lysis, purification and scale-up.

Portion of my 2012 PepTalk program on 'higher throughput protein purification'.

Clearly, our game is becoming more difficult on the side of protein purification, requiring new techniques and methods for attacking complex targets. 

Cheers,

Peter

Sorting through my past years' crystallization reports I'm particularly glad about the fact that all of the crystal images are associated with a description of the crystallization precipitation cocktail. In the same image. Of course one can always go back to the original notebook and dig out the particular crystallization condition used, but time tends to cast doubts and having the well solutions directly associated with the crystals shown in  an image is very practical. Here's a simple way to pull out primary screen parameters for association with a particular crystallization experiment:

Let's say the crystallization was done with the JCSG+ screen, formulation from well E4

• Go to E-Screen Builder 
• Select Vendor (Emerald BioSystems),  pick screen: JCSG+
• Click on E4 - et voila, E4 contains 1260 mM Ammonium sulfate, 200 mM Lithium sulfate and 100 mM Tris at pH 8.5.
• From here you can take a screenshot, or use the 'Snipping Tool' to copy and paste this image right next to the image of the crystal in your report.

Finding a particular protein crystallization screen condition is simple: 1. select vendor, 2. select screen, 3. select hit. The crystallization formulation is displayed for you to (4) cut and paste into a crystallization report.

Easy, isn't it?

Peter