Friday, 6 January 2012

BCA Winter Meeting: Structures of Supramolecular Assemblies

The British Crystallographic Association (BCA) is a national organisation set up to support all types of crystallography in the UK. It is affiliated to the International Union of Crystallography and has five special interest groups, one of which, the Biological Structures Group, is devoted to the study, by crystallography, of proteins and other biological macromolecules. One of the Biological Structure Group's main activities is its annual Winter Meeting, which conventionally takes place just before the Christmas break. This is always well attended by students and post-docs; the speakers, however, are generally senior scientists presenting some of their most exciting recent research in protein structure.

The 2011 BCA Winter Meeting was held at the Diamond Light Source, the country's national synchroton facility (which is located at Harwell, near Didcot in Oxfordshire. When it opened in 1997 it was the largest scientific facility to be built in the UK for over thirty years. Synchrotons like Diamond generate highly intense, monochromatic (single-wavelength) beams of electromagnetic radiation that are used for many types of scientific experiment, including X-rays for crystallography. The theory behind how X-ray diffraction is used to solve the structuresof proteins is not covered in PPS, but it is in both the courses that can be taken for the second year of the MSc: fairly briefly in the general Techniques for Structural Molecular Biology course and very extensively in a specialist course.

This meeting took "Structures of Supramolecular Assemblies" as its theme and featured nine distinguished speakers, discussing complex structures, biological mechanisms and protein-protein interactions. And the first speaker was none other than the head of the Department of Biological Sciences at Birkbeck, Professor Gabriel Waksman. His ground-breaking work on the structure and mechanism of fibres that form at the outer membrane of bacteria such as E. coli to attach to the host cells has been discussed previously on this blog (e.g. in June 2011) and so will not be described in more detail here.

Waksman's talk was followed by two more describing proteins and protein complexes that are embedded in the membranes of bacterial cells. The first of these was given by Colin Kleanthous from the University of York, who described proteins involved in signalling through porins, proteins that form pores in the outer membranes of Gram negative bacteria. Porins were the first transmembrane proteins to be discovered where the membrane-spanning region forms a beta barrel rather than a bundle of alpha helices. Very many alpha-helical membrane proteins pass signals into cells from their environment, with the signal arising when ligand binding triggers the receptor to either dimerise or make a subtle change in its structure (conformation). Colicins are protein antibiotics that are synthesised by bacteria, often to kill very similar bacteria that occupy the same ecological niche. They do this by "parasitizing" the porins through which nutrients enter the target bacteria, a particularly difficult task as porins act as filters that generally allow only "nutrient-sized" molecules (less than about 600Da) to enter cells. Kleanthous described the structures and mechanisms of the "outer membrane translocation" domains of several colicins bound to porins; his group is now trying to solve the structures of intact colicin-porin complexes using both crystallography and electron microscopy.

Leo Sazanov from the MRC Laboratory of Molecular Biology in Cambridge then described the structure of respiratory complex I, which is embedded in the bacterial inner membrane.. This is the first enzyme in the respiratory chain, and it is found in mitochondria as well as bacteria: the respiratory complex I in human mitochondria has been implicated in the pathology of Parkinson's disease.  The bacterial enzyme complex is smaller and simpler than the human one and is often used as a model system. Sazanov and his group crystallised the complete complex from Thermus thermophilus, a "thermophilic" bacterium that can live in extremely hot conditions. Proteins from thermophilic bacteria are often more stable and easier to crystallise than their equivalents in other species. The complete structure was found to contain no fewer than 63 transmembrane helices, 14 in each of three similar subunits. Sazanov discovered that this protein's mechanism involves a quite substantial conformational change between its oxidised and reduced form; an analogy with coupling rods has led the protein to be described as the "steam engine of the cell". It featured, in similar terms on the front cover of the issue of Nature in which the structure was described (Efremov et al. (2010), Nature 465, 441-5).

Nature cover illustrating the structure of respiratory complex I
About 5% of all proteins in an "average" bacterium are synthesised in response to heat or other stress signals. Stresssosomes are large multi-protein complexes found in bacteria and that control this stress response through the release of another protein, known as the sigma factor. Rick Lewis from the University of Newcastle described how the overall structure of a stressosome from Bacillus subtilis has been solved by electron microscopy and structures of some of the individual components by crystallography.  He is using these structures to explore the mechanism through which the stressosome senses the presence of stress conditions. Although several pieces of the stress response pathway still remain to be discovered, his group has shown how the system could respond to differences in levels of light and oxygen (the latter through the presence of a globin domain in one of the stressome proteins), how it could regulate the production of diguanylate cyclase, and how the system is re-set through the action of a serine/threonine phosphatase (the structure of which was solved at Diamond).

Helen Walden of Cancer Research UK described how her group's structural studies are shedding light on the mechanism of a DNA repair pathway that is damaged in Fanconi anaemia, a rare genetic disorder that causes, among other things, a greatly increased susceptibility to one form of leukaemia. This repair pathway, which fixes cross-links in DNA, is triggered by the single ubiquitinylation of a DNA repair protein. (This is the fusion of a small protein known as ubiquitin with a target protein.) The process is triggered when cross-links cause DNA to stop replicating; the first step is the assembly, in the nucleus, of eight proteins into a "core complex" in the nucleus. The core complex then activates another protein, known as FANCL, and this catalyses the fusion of ubiquitin with the DNA repair protein, activating it. The structure of FANCL was recently solved in Walden's group by Ambrose Cole, who is now a post-doc at Birkbeck (PDB 3ZQS). Interestingly, the structure of this protein is not the beta-propellor that was predicted by sequence analysis; instead, it contains two domains similar to the ubiquitin conjugating enzyme UBC. Mutations that abolish ubiquitin binding are known to cause disease.
These are only a few highlights of  a fascinating day's science. Other, no less interesting, structures presented there included several viral proteins: the HIV integrase bound to some of its inhibitors, presented by Peter Cherepanov (Imperial College London); the nucleoprotein from the virus that causes Lassa fever, described by Chang-jing Dong (University of St. Andrew's); and the NS1 protein from the influenza virus, described by Phil Kerry, also from St. Andrew's

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