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.

Relative investments

In a commentary in Science (1 Feb 2008), Adrian Cho wrote that the amount of money awarded in research grants increases much less than investment in construction and facilities operation - a graph neatly illustrates this.

A similar trend may be in operation in Spain - the Government reduced the budget for the Ministry of Science and Innovation, but increases spending in the "planE" - which mainly funds buildings, and lends more money to industry.

What about basic science (knowledge), being the new motor of the economy?

Protein evolution is irreversible

In their paper "An epistatic ratchet constrains the direction of glucocorticoid receptor evolution", Bridgham, Ortlund and Thornton show that sequence evolution of glucocorticoid receptor is irreversible. Although they only show it for one protein, it may be a general principle. This means that even if evolution was repeated in exactly the same conditions, a completely different world would result, by chance.

La Ciencia Española no necesita tijeras

Or, translated: Spanish Science does not need scissors.

This week the Spanish 2010 budget was presented by the Government - the main conclusion is a deep cut in the budget. For instance, the Spanish National Research Council, will have to make do with 15% less than in 2009.

At the same time, more more is lent to enterprises - yes, lent, not given - to mask the cuts. These loans are presented in the budget on equal terms as the "gifts" to universities, to research institutes (but also companies), and to individual researchers as specific research grants.

This is something the president, Zapatero, had promised not to do when coming to power.

To follow the suggestion in this blog, I post a specific reason for not cutting science funds here:

- Funds for science in Spain should not be cut (or converted into loans for companies as the minister Garmendia is doing), because spending, and output, is still well below average for developed countries.

Paul Kammerer

Although I am not a genetics expert, the Science news article "The Case of the Midwife Toad: Fraud or Epigenetics? piqued my interest. It would be interesting to see if someone finally manages to repeat Paul Kammerer's experiment.

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.

Bacterial cultures that can count up to three

In a recent issue of Science, Friedland et al. report bacterial cultures that can count up to 3 - albeit without knowing it themselves. What they count are pulses of arabinose, a sugar - and they report via fluorescence signal.

Journal club 15/6/2009

In their paper "Chaperonin overexpression promotes genetic variation and enzyme evolution", Tokuriki and Tawfik show protein stability is a major constraint in protein evolution. Chaperonin over-expression can, at least partially, mitigate it, see Nature 459, 668-673. In the same issue of Nature, Mueller et al. present the structure of an alpha-helical toxin pore and propose a detailed mechanism for pore-formation, see pages 726-730.

Modern humans come from East Africa, near de Red Sea

As reported in the issue of Science of 1 May 2009, p. 575

by Ann Gibbons in "Africans' Deep Genetic Roots Reveal Their Evolutionary Story":

The data also confirm earlier research indicating that the source population for the out-of-Africa migration of modern humans came from east Africa near the Red Sea.

Dangers in the lab

It is always good to read about dangers in the lab, and Nature in it's issue of 2 April has a nice feature about it on page 664-665 (subscription necessary). Note the following passage about the dangers of a mercury compound:
Chemist Karen Wetterhahn spilt a drop of dimethylmercury on her gloved hand in 1996 at Dartmouth College in New Hampshire. At the time, it was not known that the chemical passes through latex, so she did not realize it had reached her skin. She fell ill five months later and died within the year.

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!

p321

P321 is probably my favourite crystallographic spacegroup, as viral fibre proteins also seem to like to crystallise "in it".

The name may be seen as a blatant almost-copy of the much more professional protein crystallography blog www.p212121.com and it perhaps is. In any case, this is going to be much more low-key and probably have much more infrequent entries...

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.