Following chemical reactions in special crystals

In their paper "X-ray observation of a transient hemiaminal trapped in a porous network" (plus commentary), Kawamichi et al. show how a chemical reaction can be followed in a crystal. Well, strictly, taking three snapshot - of the starting compound, of a kinetically trapped intermediate, an then, after heating, of the product. Impressive, nonetheless.

Constraints and Restraints

In the paper "A short history of SHELX" by George Sheldrick (Acta Crystallographica A, 2008, 64, 112-122) is explained very clearly something I did not completely realise:

- CONstraints lower the number of variables to refine, while

- REstraints augment the number of observations.

What follows from this is that for low resolution structures introducing extra constraints (for instance strict NCS) is more efficient than introducing extra restraints, the reason being that you need more than one observation per refined variable.

This is not actually implemented in all crystallographic protein structure refinement programs, which I think is a shame.

NMR and crystallography, or rather, crystallography and NMR.

I like the ultimate paragraph of the Highlight written by Burkhard Luy in Angewandte Chemie Int. Ed. (2007, volume 46, pages 4214-4216), it illustrates the complementarity of X-ray crystallography and NMR spectroscopy very well:

"With the NMR techniques developed over the past decade and the availability of corresponding crystal structures, molecular complexes of nearly unlimited size seem to be amenable to liquid-state dynamics measurements. These results are an important step in understanding the modes of operation of complicated molecular machines in biological systems."

Note that the crystal structure of the 20S proteasome complex was necessary in order to be able to interpret the NMR signals of the particle, and that the NMR results shed light on dynamic properties which crystallography had not measured.
Also note the NMR work was expensive, requiring extensive labeling, mutation to make a monomeric version - so it would presumably be only worth doing this for very important macromolecular complexes.

Tracing a protein at 5.5 Å resolution

In a paper published in Nature 26 March 2009 (p. 475), Pomeranz Krummel et al. describe the structure of human spliceosomal U1 snRNP at 5.5 Å resolution. what struck me is how they traced the structure of one of the component proteins: via mutating individually all methionine residues of the Se-Met versions of the protein, crystallising and collecting data of all variant complexes and locating the said methionines in anomalous difference maps. A real tour-de-force!

Crystallography dead and buried? I think not!

For those who think crystallography is dead and buried, the issue of Nature of 19/3/2009 has three (interesting!) papers with X-ray crystallography results.

On page 305 Koder et al. describe the design and engineering of an O2 transport proteins, mimicking haemoglobin in many aspects. The design was guided by structure determination through NMR spectroscopy and X-ray crystallography. Although their protein was small enough to be studied by NMR (which has the advantage of not having to crystallise the protein and of being able to study dynamic properties of proteins in solution), they still chose to also determine several structures by crystallography. Probably because it provides an even more accurate view...

On page 315, Lee et al. have produced hybrid organic-inorganic rotaxanes and molecular shuttles - and managed to crystallise and solve the structures of these dynamic molecules.

Finally, on page 367, Hearn et al. present studies of a bacterial membrane transport protein that transports hydrophobic compounds. They show, via mutational and structural analyses, that the compounds leave the transporter through a "side door", into the membrane. Presumably, they then access the periplasmic space by diffusion. As membrane proteins are impossible (or at least very difficult) to study at high resolution by any other technique, X-ray crystallography was the method of choice here.

My conclusion for today, X-ray crystallography is alive and well and has provided essential information for three important papers. What IS clearly a trend, is that high-impact papers contains structural information more and more as a part, not as the main "show" like before.