Institute of Biological and Biomedical Sciences
A major focus of our research is on the structure of proteins and understanding the molecular basis of their interactions with nucleic acids (DNA and RNA), as well as protein-protein interactions, protein-ligand interactions and enzyme structure and mechanisms. Such interactions are fundamental to understanding both basic biological mechanisms and the development of new therapies. The applications of our research range from the development of novel antibiotic targets to structure-based drug design for amyloid diseases.
Current and recent projects in molecular biophysics include the structural and biochemical investigation of DNA methyltransferases and endonucleases (Kneale, Gowers), transcription factors and repressors (Kneale, McGeehan), ribonucleases and RNA chaperones (Callaghan, Gowers), metalloproteinases (Pickford), serum amyloid P component (Kolstoe) and the structure and biotechnological applications of novel cellulase enzymes (McGeehan).
We also collaborate with IBBS colleagues (Clark et al.) and with NREL in the USA on theoretical approaches e.g. molecular dynamics. We are engaged in biomedical research involving the structural biology underpinning prion diseases (e.g. CJD), Alzheimer’s disease and mitochondrial diseases, much of it involving collaboration with partners in biomedical and clinical centres in the UK and USA. Our future plans include collaborating on further structural biology projects with other IBBS groups (e.g. Thorne, Lewis, Hafizi), plus a number of external collaborations recently instigated in the UK and elsewhere.
OUR CURRENT RESEARCH
Nucleic Acid Structure and Gene Regulation
We now know that only 2% of the human genome codes for proteins, while the remaining 98% of the genome plays an important regulatory role. This includes coding sequences for over 10,000 RNA molecules involved in gene regulation, together with numerous genomic control sites that are regulated by protein-DNA interactions. It is also becoming evident that many of the mutations that give rise to cancer and a wide variety of genetic diseases are found in these regulatory regions, rather than in the gene itself. In bacteria, the relevant protein-nucleic acid interactions involved in the control of gene expression represent novel drug targets for combating microbial infection. Our interests are in investigating the molecular interactions that mediate gene regulation, the detailed 3D structure of regulatory regions of DNA and RNA, together with the 3D structure (and thermodynamics) of the relevant protein-nucleic acid complexes. We are applying structural and biophysical techniques to a wide variety of prokaryotic and eukaryotic systems: These include bacterial restriction-modification controller proteins and sRNAs, RNA chaperones, HMG box proteins involved in cell differentiation, and transcription factors involved in embryonic development.
Enzyme Structure and Function
Enzymes play a vital role in all biological cells and, in addition, can often be exploited through biotechnology. We are investigating a wide variety of enzymes, many of biomedical significance, such as matrix metalloproteinases (MMPs) that are involved in degradation of the extracellular matrix, restriction enzymes that are involved the horizontal transfer of genes in bacterial populations, DNA methyltransferases that protect specific DNA sequences from degradation, and ribonucleases that are crucial for degradation of bacterial RNA and the regulation of bacterial genes.
Others enzymes we study have important applications in biotechnology – for example glycoside hydrolases for the degradation of cellulose and molecular motor proteins that use the energy of ATP to translocate along DNA at high speed. We are studying the structure/function of these enzymes, and their interaction with substrates, ligands and inhibitors, using the full gamut of techniques available within in the group, including access to synchrotron radiation facilities at Diamond.
Protein Structure and Biomedical Science
Many other proteins play vital roles in the cell that have great pathological significance, such as those involved in the membrane protein complexes that make up the mitochondrial respiratory chain. We are using molecular modeling methods to analyse the 3D location of the amino acids in these multi-subunit complexes that are altered in a wide variety of diseases – currently with an emphasis of brain cancer – to understand the significance of the mutations observed in the clinic. We also study the structure and interactions of proteins such as serum amyloid P component (SAP), involved in pathologies such as amyloidosis (and related acute phase proteins) and structure-based drug design and biophysical methods are being used to investigate potential inhibitors. Our research includes the structure of the nucleosome assembly protein (NAP) and its interaction with histones, important players in both DNA replication and chromatin remodeling in eukaryotes. We also have a long standing research interest in the single stranded DNA binding protein g5p, and we have shown it also interacts with tetraplex DNA. This has led to very fruitful collaboration with the USA National Prion Surveillance Unit (Case Western Medical School), and we have shown in a number of clinical studies that g5p can be used for the identification and analysis of prion-related diseases such as CJD.
All our biological and biomedical research is underpinned by state-of-the-art biophysical approaches, backed up by protein purification and expression, site-directed mutagenesis, EMSAs and other methods to characterize biomolecules and their interactions. We have expertise (and instrumentation) for a wide range of methodologies, and are developing both the techniques and the analysis methods that we require (for example, new computational procedures to solve the 3-D structures of proteins by NMR, new technologies for SPR analysis of RNA interactions, and an on-line spectrophotometer on the synchrotron beam). We have extensive in-house facilities for X-ray crystallography, NMR, circular dichroism (CD), analytical ultracentrifugation (AUC), light scattering (DLS and MALLS), SPR and calorimetry (both ITC and DSC). We have allocations of beam time at the Diamond synchrotron not only for X-ray crystallography, but also small angle x-ray scattering (SAXS) and synchrotron radiation CD (SRCD). In addition, we have regular allocations of beam time at Institute Laue-Langevin (Grenoble) for SANS and at ESRF (Grenoble) for crystallography and SAXS. In addition we make use of Electron Microscopy (EM) and Atomic Force Microscopy (AFM) facilities that are available within IBBS.