Structural Biology
Our research concentrates on the use of biophysical tools to investigate the three dimensional structure of macromolecules and their complexes. X-ray crystallography is one of the primary techniques used, together with Atomic Force Microscopy. These techniques are all available in the Centre for Biomolecular Sciences and the School of Pharmacy. Our main focus of interest is on biological macromolecules involved in important aspects of physiology and disease states together with macromolecular complexes and small molecule ligand/drug complexes. Crystal structures can be used as templates for structure based drug design.
Coagulation Factor XI & Von Willebrand Factor
It is well understood that circulating plasma proteins and platelets play a pivotal role in blood clotting. These coagulation factors are also involved in pathological thrombus formation and associated heart disease. A recent development includes the determination of the full length factor XI zymogen crystal structure revealing a novel transactivation mechanism for a serine proteinase ( Nature Structural and Molecular Biology 13(6), 557-558). This research is funded by a British Heart Foundation programme grant.
Other collaborative grants within the School of Pharmacy in this area include studies on protein folding of the plasma protein von Willebrand factor with Phil Williams and Stephanie Allen (LBSA, BBSRC funded).
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Integrin Receptors & Collagen
Integrins are the principal family of cellular receptors that mediate interactions with the extracellular matrix (ECM) and are involved in a wide variety of physiological processes including cell proliferation, the suppression of apoptosis and cell migration. JE�s lab has determined a number of key structures from the integrin field. These include the structure of the alpha2-I domain collagen peptide ligand complex (illustrated below, CELL 101: 47-56), the unliganded alpha2-I domain and the GFOGER cognate collagen peptide. Development of this research is funded by Cancer Research UK and aims to determine further complex crystal structures which ultimately will provide a scaffold for structure based drug design (Collaboration with Dr Weng Chan and Prof Peter Fischer within the School of Pharmacy). We have also studied the cytoplasmic side of integrin signalling by determining structures of talin which was carried out in collaboration with David Critchley and Gordon Roberts, Univ of Leicester. (EMBO Journal , 23(15), 2942-2951)
Alpha2-I Domain Collagen Peptide Ligand Complex
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DNA Binding Proteins
The DNA-binding protein, RdgC, is associated with recombination and replication fork repair in Escherichia coli and with the virulence-associated, pilin antigenic variation mediated by RecA and other recombination proteins in Neisseria species. We solved the structure of the E. coli protein and refined it to 2.4A. RdgC crystallizes as a dimer with a head-to-head, tail-to-tail organization forming a ring with a 30Å diameter hole at the center. The central hole is lined with positively charged residues and provides a highly plausible DNA binding channel This work was carried out in collaboration with Robert Lloyd’s group from the Institute of Genetics UoN (J Biol Chem. 282(17):12353-7)
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Binding of the Anti-Cancer Prodrug CB1954 to the Activating Enzyme NQO2 Revealed by the Crystal Structure of their Complex
The bifunctional alkylating agent CB1954 has been the focus of Directed Enzyme Prodrug Therapy (DEPT) for over a decade now, although endogenous human activating enzymes such as NQO2 have also been studied. We have determined the structure of NQO2 in complex with CB1954. The data now provide a frame of reference for the rationalization of past SAR studies with a repertoire of CB1954 analogues and opens the door to structure-guided redesign of the prodrug. (M.AbuKhader, J.Heap, C.D.Matteis, B.Kellam, S.W.Doughty, N.Minton, M.Paoli, 2005, Journal Medicinal Chemistry 48, 7714-9).
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Macromolecular Complexes in the Ubiquitin System
p97 is an essential, abundant and highly conserved ATPase that is directed to different functions within cells by using different adaptor proteins and has been associated with neurodegenerative diseases and cancer.
We were the first to show how p97 interacts with an adaptor protein (p47) and predicted that UBX domains in general are p97 binding domains, by demonstrating that a conserved loop region in UBX domains is essential for p97 binding. Based on the characteristics of this loop region we suggested a classification of ubiquitin-like domains. We identified the domain structure of the adaptor protein p47 including a novel domain and characterised the full-length p97-p47 complex in different nucleotide states that led to the first model for protein-protein disassembly by p97. (EMBO Journal, 25(9):1967-76; EMBO Journal, 23(5):1030-9; J. Struct. Biol., 156(1):12-28). Leading on from these studies conducted at Imperial College London, ID’s lab is now studying proteases in the ubiquitin pathway.
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Biocatalysts for Pharmaceutical Applications
Several industrial processes use enzymes from different organisms to act as proficient biocatalysts. We solved the structure of a glycosylated flavoprotein where the cofactor does not have a redox role in catalysis and established the mechanism by solving structures with substrates and inhibitors. We were also able to explain why this flavoprotein does not act as an oxidase. Our research enabled the targeted modification of the active site to design a better biocatalyst for substrates of pharmaceutical significance (building blocks for ACE inhibitors, anticoagulants. (Protein Science, 11, 292-300; Structure (Camb), 9, 803-815.). This research was carried out in collaboration with Karl Gruber and Christoph Kratky from the University of Graz. Following on from this research ID’s lab is currently exploring other enzymes of pharmaceutical and industrial relevance.
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Academic Staff
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Dr J Emsley - Associate Professor & Reader in Macromolecular Crystallography
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Dr C De Matteis - Reader in Pharmaceutical Chemistry & Science
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Dr I Dreveny - Lecturer in Macromolecular Crystallography
Protein Expression Labs