Protein Crystallization Hits

A while ago Luc posted this useful comment to as a response to the blog post "Stability not required to grow protein crystals and: Ala, Gly & Phe are your friends":

There is already a very useful webserver to help you design mutants with better chances of crystallization, The Surface Entropy reduction Prediction Server. 

 http://nihserver.mbi.ucla.edu/SER/ 

 Reference: Lukasz Goldschmidt, David Cooper, Zygmunt Derewenda, David Eisenberg. (2007).

Toward rational protein crystallization: A Web server for the design of crystallizable protein variants

Protein Science. 16:1569-1576 (2007 Aug). 

There is also a nice review by Derewenda about protein engineering to enhance crystallizability and improve crystal properties. 

Derewenda ZS.

Application of protein engineering to enhance crystallizability and improve crystal properties.

Acta Crystallogr D Biol Crystallogr. 2010 May;66(Pt 5):604-15.

Thanks for this feedback, Luc!

Peter

Let's assume for a minute you're dealing with a protein of a certain sequence and you're wondering if the protein is crystallizable. The tool to assess crystallizability is: XtalPred. This is an online server that accepts amino acid sequences and provides you with:
• a comparison of protein features with corresponding distribution from the TargetDB 
• summary features with crystallization problem areas  
• prediction of ligands and
• lists close homologs that are more likely to crystallize.
The algorithms used are described in this paper. There's also a related blog post about the biggest Secret in crystallography here.

How about taking XtalPred for a test drive? Let's make it simple and use Lysozyme as an example. There are many conditions under which Hen Egg white Lysozyme crystallizes - it's a great workhorse for test-crystallizations. The PDB gives you 1151 'Structure Hits' when searching for Lysozyme.

OK, let's take the amino acid sequence of Hen Egg white Lysozyme (P00698), remove the leader sequence and submit it to XtalPred. 

XtalPred input page with Lysozyme sequence inserted.

Here's what you get: 

XtalPred output page with results displayed in tabular form

OK - Xtal pred finds the target ID and lots of other info - even that there are 516 homologs available in the PDB. But it classifies Lysozyme into the red crystallization class: "Difficult"??? A poor grade of five on a scale of 1 (optimal) to 6 (very difficult).
Come on guys - Lysozyme, difficult?

Lysozyme cystallizes easily! Check out this paper from 1946, reporting on Lysozyme crystallization from egg white (check out the nice historical photographs of Lysozyme crystals).
Lysozyme crystals even grow when triggered with a flash of light. Lysozyme crystallization is indeed fool proof - I've successfully taught a physicist how to crystallize Lysozyme (a theoretical physisists who'd never touched a pipettor).

I guess that if you get an XtalPred result in the green = 'optimal' zone you've got crystals in your vial once you go back to the bench.

Peter

As a trained biochemist I've always had a hard time finding information on small molecules. There are just too many different names and I hadn't been dealing with small molecule compounds often enough to get comfortable with their use. Parlez-vous smiles string?

It is easy to get confused in the jungle of systematic names, trade names, smiles strings, names with spelling mistakes, synonymous designations, CAS numbers etc. Nonetheless, small molecule compounds are a key component in protein crystallography-based drug discovery and, in membrane protein crystallization you're dealing with small molecule detergents and additives all the time. Need to co-crystallize or soak your protein crystals with small molecules - how do I find relevant data to construct a comound library? At the top of my frustration I had identified that there are >10 different names just for one single compound: Triton X-100. How can you make sense in this babylonian mess? Initially I got by with crutches: The sheer weight of the printed Merck index takes the fun out of finding any compound information. So Sigma had always been my friend and their online catalog does an OK job to aggregate data for particular compounds. And of course I have used popular online search engines only to become stuck with possibly dubious information. But none of that worked to my satisfaction.

So what a relief when I found the Google for small molecule compounds: ChemSpider. 

Finding small molecule information is a blast with the chemistry search engine ChemSpider.

Simply search by name, MW, chemical elements or chemical properties and find exact matches or expand your search to identify similar compounds. All nicely tied in with literature data bases and commercial sources in case you want to get the materials in the real world.

ChemSpider is actually better than Google because you're not restricted to search with typed words only, you can search starting from structures that you draw in a Java pop-up window.

ChemSpider tool to draw small molecule structures. Submit what you have in mind to a search and receive information about the small molecule compound from a variety of sources.

Designing small molecule compound libraries has never been easier.

Thanks to the folks at ChemSpider!
Peter

A while ago I lost a bet to Mark here at Emerald: in my foolishness I had predicted that structure determination programs (molecular replacement, SAD phasing and so forth) could be done on a cell phone within a year. I lost the bet, but Mark was a good sport and shared the bottle with the team here at Emerald (wondering though whether anybody has done the feat in the meantime).

The topic of hand held computing in crystallography is still fascinating, nevertheless. Cell phones are used for so many different things now but I'm still waiting a bona fide crystallography application, though. Anything out there?

The closest to what I have seen in this regard was recently at the 2009 ACA meeting in Toronto, Canada. Mark Warren from the University of Bath had cut a rectangular hole in his poster and managed to stick his iPhone right behind it, showing a "Crystallograhic Movie". 

Well done, Mark!
Peter