Wednesday, 22 December 2010

Metals in Proteins: A British Crystallographic Association Meeting

The British Crystallographic Association (BCA) is the UK's national society for crystallography- the study of molecular structure using X-rays - applied in physical sciences and in engineering. It has four discipline-specific special interest groups and a further group for young scientists. Protein crystallography is, obviously enough, the main concern of the Biological Structures Group. That group always holds a one-day scientific meeting in mid-December, just before the Christmas break. The 2010 Winter Meeting was held on 15 December in Reading University, hosted by Dr Kim Watson and her colleagues at the School of Biological Sciences there. Its main theme was the role that metals play in protein structure and function, particularly in signalling and transport proteins.

Before the main business could begin, however, the delegates heard two interesting short talks. The first was by Martin Welsh, coordinator of life sciences research at Diamond, the UK's synchrotron facility (located in the Oxfordshire countryside). This provides the most intense radiation sources for X-ray crystallography (and other analytical techniques) in the country, and although it has been open since 2007 it is still complete. The UK scientific community is still deciding the range of problems to be addressed by the last set of beam lines, which in turn will determine how they are constructed. He called for the structural biology community to become fully involved in this process, as it risks losing out to the physical scientists.

The second introductory talk was by the BCA's President, Professor Elspeth Garman from the University of Oxford: first structural biologist to hold this position for many years. She explained how the relationship between technological developments in X-ray crystallography and the biological insights that it provides is as strong now as it was when Dorothy Hodgkin (Nobel Laureate in Chemistry 1964) was solving the structures of penicillin, vitamin B12 and (in 1969) the peptide hormone, insulin.

Highlights of structural biology research were then presented in three main sessions. The first of these featured three keynote lectures by distinguished structural biologists. The only common feature of the biological systems described was the fact that metal ions formed a crucial part of their mechanism of action.

First, Chris Schofield from the University of Oxford described his group's work elucidating how mammals sense and respond to changes in the concentration of oxygen. This work can be said to date back to the nineteenth century, when climbers, and people living at high altitude where oxygen concentrations are lower, were first observed to have increased numbers of red blood cells. It is now known, in part thanks to Schofield's work, that cells respond to low oxygen levels through a transcription factor called Hypoxia Inducible Factor 1 (HIF-1), which in turn regulates the production of another protein, erythropoietin, which is involved in the production of red blood cells. HIF-1 is upregulated if oxygen concentrations are low and broken down by the proteasome when concentrations are high. Schofield has used crystallography to determine the structural basis of the "switch" between the stable (low oxygen) and unstable (high oxygen) forms of this enzyme. The stable form contains two key proline residues (link is to section 2) and these are oxidised to hydroxyproline to give the unstable, high oxygen form. The enzyme that catalyses this oxidation reaction, HIF prolyl hydrolase (PHD) binds an iron ion in its active site unusually tightly, which causes it to react unusually slowly; it is this slow reaction that enables it to react to long-term changes in oxygen concentration.

Ben Bax, from GlaxoSmithKline (GSK) in Stevenage (and formerly a Birkbeck postdoc), then described how X-ray crystallography is being used to design novel inhibitors of bacterial proteins called DNA topoisomerases. These are enzymes that catalyse the winding and unwinding of DNA molecules, a process that is different enough in bacteria for inhibitors of these enzymes to be specific and effective antibacterial drugs. Bacteria have two forms of this enzyme, topoisomerase II (or DNA gyrase) and topoisomerase IV. Both these, confusingly, are known as type II topoisomerases; these are the target of the fluoroquinolone antibiotics, which have been in clinical use since 1962 and had sales of over $7Bn in 2009. Bax's group at GSK has solved the structure of a complex between the antibiotic moxifloxacin and topoisomerase IV from Acinetobacter baumannii, revealing that the enzyme-inhibitor interaction involves a magnesium ion that is not involved in the catalytic reaction (PDB entry 2XKK). They have also solved the structure of DNA gyrase from Staphylococcus aureus in complex with a novel bacterial topoisomerase inhibitor (PDB entry 2XCS), which sheds new insight into the enzyme's mechanism and the role of manganese ions in it.

The final talk in this session was given by Wyatt Yue, from the Structural Genomics Consortium in Oxford, and concerned the structure and function of an enzyme, methylmalonyl-CoA mutase (but known, thankfully enough, as MUT) which is involved in the metabolism of vitamin B12 (also known as cobalamin). This vitamin is essential for life; bacteria can synthesise it, but mammals need to take it in through their diets. Its structure was solved by Dorothy Hodgkin in 1954. It can bind cobalt in any of its oxidation states: Co(I), Co(II) and Co(III). Although only two enzymes including MUT require vitamin B12 as a co-factor, its deficiency can cause severe disease. Yue and his group have solved the structure of MUT bound to vitamin B12 (PDB entry 2XIJ) and that of an associated protein, a GTP-binding protein known as MMAA (PDB entry 2WWW). This protein is believed to act as a "gatekeeper", necessary for binding MUT to the appropriate, adenosyl form of vitamin B12. Two copies of the same MMAA mutation, which abolishes its interaction with MUT, have recently been identified in a patient with the metabolic disorder methylmalonic aciduria.

There were two further sessions at the conference, which I don't have room to blog about: one covered metal ion transport and catalysis, and the other metals in proteins that function as transporters, receptors and chaperones. There is some more information on the conference website.

Merry Christmas!