Research Interests

Structural Virology: Protein-RNA interactions

In eukaryotic cells, the initiation of translation begins with the formation of a complex of proteins (eukaryotic initiation factors - eIFs) around the cap at the 5' end of the mRNA. This eIF complex helps to regulate the interaction of the mRNA with the small ribosomal subunit. A number of RNA viruses (e.g. picornaviruses, flaviviruses) adopt an alternative mechanism of translation initiation in which an extended and structured segment of RNA at the 5' end of the genome - the Internal Ribosome Entry Site (IRES) - permits interaction with the ribosome without the cap-binding complex being formed. (In recent years IRES elements have been identified in eukaryotic genes, indicating that they have a wider role in translation initiation than was first thought).

We are applying structural methods to elucidate the function of the IRES at the molecular level. One of the unusual features of IRESes is that, in addition to some of the normal eIFs, they recruit host-cell proteins which are not normally implicated in translation.Such proteins included the polypyrimidine tract binding protein (PTB), a splicing regulator, the La protein, a factor involved in pre-tRNA maturation and Ebp1 (ErbB3 binding protein 1), a transcriptional regulator. We are currently working on the structures of all these proteins. These projects, which are being done in collaboration with Steve Matthews (Imperial) and Maria Conte (King's College London), are providing new insights into molecular mechanisms of all three proteins. Click on the Publications link on the left to see our publications in this area.

Structural Virology: Viral enzymes

Foot-and-mouth disease virus (FMDV) is a highly contagious RNA virus that poses a severe threat to livestock around the world. In 2001 the UK was hit by an epidemic that cost over £20 billion to control. Although vaccines are available, they were not used in this instance due to technical and political problems. The ongoing threat of renewed outbreaks has stimulated the search for alternative means of disease control.

The virus contains a single-strand positive-sense RNA genome that is translated to yield a long polyprotein precursor. The 3C protease serves to cleave this into the functional proteins required for replication and is therefore an attractive target for antiviral drug design. We have recently determined the high-resolution crystal structure of FMDV 3C protease, confirming that it is a chymotrypsin-like cysteine protease. Our structure not only provides new insights into the catalytic mechanism for this class of enzyme (which has been the subject of some debate for over 10 years) but also lays down a detailed molecular template for the design of enzyme inhibitors that may ultimately be developed as anti-FMDV drugs. Such drugs might be used to control future outbreaks.

Sept 08: Check out our short film on YouTube about the work on FMDV 3C.

Human serum albumin (HSA) is an extremely abundant protein in the bloodstream. Its primary function is to transport fatty acid molecules, but it also binds a wide variety of drugs and may distort their pharmacokinetics. Although a great deal of biochemical work on albumin in the past 40 years has sought to investigate the way that the protein binds to its various ligands, there was relatively little structural information on ligand binding sites.

We use X-ray crystallography to analyse the interactions of HSA with endogenous and exogenous ligands at high resolution. We published the first structure of HSA complexed with a fatty acid (myristic acid). This work and follow-up studies with other fatty acids have revealed the locations of seven fatty acid binding sites on the protein that are common to medium and long-chain fatty acids. We also found that fatty acid binding induces a significant conformational change in HSA (see animation link on right). Our results stimulated the development (in collaboration with Prof Jim Hamilton, Boston University, USA) of new NMR-based approaches to measuring the binding affinity of the different fatty acid sites on the protein.

We have also investigated how other endogenous compounds such as thyroxine, hemin, renal toxins and bilirubin bind to the protein and how it absorbs such a wide variety of drugs. This work has begun to provide a much fuller structural description of the way the ligand binding capacity of HSA and yields new clues about the interactions between ligands. It has also fostered an exciting collaboration with Profs Tsuchida and Komatsu (Waseda University, Japan) who are engineering HSA-hemin complexes to create artificial blood molecules.