Dr. Robert Daniels, Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University
Monday 10th March, 4.00 p.m., Marlowe Lecture Theatre 1
Transmembrane domains (TMDs) from single-spanning membrane proteins are commonly viewed as hydrophobic membrane anchors for functional domains. Influenza neuraminidase (NA) exemplifies this concept as it retains enzymatic function upon proteolytic release from the membrane. However, we recently showed that the TMD is required for the proper folding of the NA head domain (1), and that the NA TMDs in human H1N1 viruses have become increasingly less hydrophobic, which has altered their assembly by enhancing the TMD association (2). These results suggested that the TMD from NA is changing to maintain compatibility with the distal enzymatic head domain. The seminar will cover our current work on the investigation of this relationship where we analyzed influenza A viruses encoding NA chimeras where the amphipathic TMDs from an old and modern NA (N1) were exchanged, or replaced by an engineered hydrophobic TMD (3). The results from this work provide a likely explanation for why the NA TMDs became more polar, show how modifying the intrinsic TMD folding properties can adapt a distal domain to its environment, and how the virus exploits the co-translation insertion process to support the membrane insertion of these marginally hydrophobic TMDs.
- da Silva, D. V., Nordholm, J., Madjo, U., Pfeiffer, A., and Daniels, R. (2013) Assembly of subtype 1 influenza neuraminidase is driven by both the transmembrane and head domains. J Biol Chem 288, 644-653
- Nordholm, J., da Silva, D. V., Damjanovic, J., Dou, D., and Daniels, R. (2013) Polar residues and their positional context dictate the transmembrane domain interactions of influenza a neuraminidases. J Biol Chem 288, 10652-10660
- da Silva, D. V., Nordholm, J., Dou, D., and Daniels, R. (2014) Temperature adaptation of influenza A viruses through the NA transmembrane domain. Submitted
Dr. Paul Bowyer, London School of Hygiene and Tropical Medicine, London
Monday 3rd March 2014, 4.00 p.m., Marlowe Lecture Theatre 1
The asexual bloodstages of the malaria parasite, Plasmodium falciparum, are responsible for the majority of the clinical symptoms of disease and are therefore attractive targets for chemical and vaccine based therapies. This talk will focus on just a few minutes of the 48-hour asexual cycle as the parasite first exits the red blood cell and, after a brief extracellular phase, then enters a new one.
The first portion of the talk will focus on the c-GMP dependent protein kinase (PKG) as a target for small molecule inhibitors. This protein is known to be essential for escape of the parasite from the host cell and I will describe the chemical genetic screens used to develop improved, selective inhibitors of PKG.
The second part of the talk will describe on-going work investigating the diversity of routes by which the extracellular merozoite (parasite) gains access to a new red blood cell. Many proteins exposed on the surface of the merozoite have been the subject of vaccine discovery programmes but the extent of allelic variation within the exposed proteins and the ability of the parasite to tolerate different ligand : receptor combinations during invasion complicates the process of antigen selection. Work investigating the diversity of ligand-receptor interactions involved in invasion pathways of fresh P. falciparum isolates, across a gradient of transmission intensity in West Africa, will be described.
Professor Judith Armitage FRS, Department of Biochemistry, University of Oxford
Monday 24th February, 4.00 p.m., Marlowe Lecture Theatre 1
Most bacteria swim. Swimming motility is driven by a helical flagellum rotated at up to 1300rev/sec at its base by a transmembrane ion driven rotary motor. The motor can rotate clockwise or counter-clockwise and changes in switching frequency biases the overall swimming pattern of the bacterium towards an optimum environment for growth.
Structural and cryo electron microscopy studies suggested the motor resembles a tiny electric motor, but our in vivo studies have shown that the motor is a dynamic nanomachine, with protein subunits exchanging with pools of protein as the rotor spins. In the bacterium R. sphaeroides motor switching is controlled by two chemosensory pathways. The proteins of one pathway localise with transmembrane chemoreceptors into membrane patches, while the other pathway localises in the cytoplasm to midcell with soluble chemoreceptors. On division each daughter cell must inherit a membrane and a soluble complex to allow chemotaxis. Using a combination of molecular genetics, biochemistry and fluorescent imaging we have developed a spatio-temporal model for protein localisation and segregation through the cell cycle and enroute identified a novel mechanism for proteins to piggy-back on segregating chromosomes.
Professor Kevin Sinclair, School of Biosciences, University of Nottingham
Monday 17th February, 4.00 p.m. Stacey Lecture Theatre 1
Overview: Compelling evidence exists, both from epidemiological studies in humans and direct interventionist studies in animals, to indicate that impaired reproductive fitness and many non-communicable diseases of adulthood originate from aberrant developmental events that occur in utero. Studies at Nottingham focus on the periconceptional period and consider the effects of parental nutrition and the composition of gamete/embryo culture media employed in assisted reproduction (ART), with an emphasis on one-carbon metabolism and epigenetic programming of offspring health. Studies in each of these three areas extend from rodents to large animals, and utilise embryonic and somatic cells and tissues of human origin.
Dr Mark Shepherd comments on a recent article featuring his group’s work that was selected as cover image in the scientific journal “Antioxidants and Redox Signalling”.
“Many bacterial pathogens overcome the biocidal action of copper during infection. We demonstrate that the ScsC protein of Salmonella contributes to survival during conditions of copper stress, and report the crystal structure and biochemical properties of this soluble, periplasmically-located thioredoxin-like protein. Our findings have implications on the mechanism by which Salmonella circumvents the toxic effects of redox-active copper (II) ions. ScsC is encoded by several species of pathogenic bacteria, highlighting the significance of this newly characterised protective mechanism.”
Dr. Shepherd teaches metabolism to student in the second year, and is the Programme Director of our new MSc in Infectious Diseases.
Shepherd, M., Heras, B., Achard, M., King, G. J., Argente, M. P., Kurth, F., Taylor, S. L., Howard, M. J., King, N. P., Schembri, M. A. and McEwan, A. G. (2013). “Structural and functional characterisation of ScsC, a periplasmic thioredoxin-like protein from Salmonella enterica serovar Typhimurium.” Antiox. Redox Sign. 19(13): 1494-1506.
Dr. Anthony P. Davenport, Clinical Pharmacology Unit, University of Cambridge
Monday 10th February, 4.00 p.m., Marlowe Lecture Theatre 1
Our research focuses on understanding the role of novel G-protein-coupled receptors(GPCRs), together with their transmitters in the human cardiovascular system and how these are altered with disease. We concentrate on Class A GPCRs as these are the targets of about half of currently available medicines with ~90 genes encoding ‘orphan’ receptors remaining in the human genome. Each orphan GPCR is a potential drug target. A number of orphan receptors have been paired with their cognate endogenous ligands, that can be targeted using established computational modelling as well as medicinal chemistry strategies, to identify selective agonists and antagonists. Our approach will be illustrated with the apelin peptides which have an emerging role in the cardiovascular system. Down-regulation of the apelin signalling pathway is associated with cardiovascular disease including heart failure and a synthetic agonist would be of benefit. A limitation of many agonists acting at GPCRs is that after stimulating G-protein pathways to elicit a physiological response. The target receptor is internalized and ‘silenced’ via the β-arrestin pathway. Our solution is to design an agonist that shows G-protein pathway bias with reduced loss of efficacy owing to receptor down-regulation that are currently being tested in first in human, proof of principle studies.
Professor Jannette Carey, Department of Chemistry, Princeton University, USA
Monday 3rd February 2014, 4.00 p.m., Marlowe Lecture Theatre 1
The binding of one ligand to a protein can alter the affinity of another ligand; this is the basic definition of allostery. Mechanisms of allosteric signal transmission have been elusive. Results will be presented from a synergistic approach that combines measurements of ligand binding affinity using complementary
experimental methods and molecular dynamics simulations of ligand occupancy and conformational states.
Life requires information transfer from nucleic acids to proteins. This involves the physical movement of decoding machines (ribosomes) along linear nucleic acid templates (mRNAs). In a recent collaboration between the Schools of Biosciences and Computing, Kent researchers have deciphered the principles by which sophisticated ribosomal traffic control mechanisms enable cellular protein synthesis to proceed with optimal efficiency.
Dr Tobias von der Haar, the PI of this study, teaches Biochemistry and Molecular Biology at both undergraduate and postgraduate levels.
Chu D, Kazana E, Bellanger N, Singh T, Tuite MF and von der Haar T (2014) Translation elongation can control translation initiation on eukaryotic mRNAs. EMBO Journal 33: 21-34.
Prof. Dr. Vitor A.P. Martins dos Santos, Systems and Synthetic Biology, Wageningen University Germany
Monday 27th January 2014, 4.00 p.m., Marlowe Lecture Theatre 1
I will report on the construction of a genome-streamlined bacterium cell endowed with assembled genetic circuits for the production of high added-value aromatics and bioplastics. We developed and validated experimentally a genome-scale, model framework of the metabolism and transport of the biocatalytic chassis, Pseudomonas putida. Predictions pin-pointed interventions that, once implemented in-vivo through combinations of mutants and feeding strategies, enabled re-programming of carbon metabolism for a stark increase in the production of high-value precursors of bioplastics and fine-chemicals. To simplify and stabilize the chassis, we streamlined the 6-megabase genome through a newly developed excision method based on the combination of customized mini-transposons and the FLP-FRT site-specific recombination system. After 4 cycles, we shed 8% of the genome, thereby simplifying cellular wiring with no negative impact on the fitness. Genome-wide analyses of the streamlined chassis – through combined mathematical modelling and experiments – yielded new insights into the metabolism and regulation of this industrial bacterium. In parallel, we developed and experimentally validated a detailed dynamic model of the circuit coded by the pWW0 plasmid (a plug-and-play circuit for the biotransformation of aromatics). The model revealed that the architecture of the key regulatory node of the promoter system Ps/Pr can discriminate between alternative and competing carbon sources, which is of utmost relevance for biocatalyis of aromatic-derived fine chemicals. The study of the interplay between the biocatalytic circuit and the metabolic wiring of the chassis revealed unexpected mechanisms that control the expression of the “plugged-in” circuit. This workflow generated a streamlined bacterial factory, devoid of unnecessary gene complements and undesired cross-talk, thereby enabling a higher degree of control and, hence re-programming, by plugging-and-playing at will.
Vítor Martins dos Santos holds the Chair for Systems and Synthetic Biology at the Wageningen University, The Netherlands, is the Director of the Wageningen Centre for Systems Biology and President of the Dutch Society of Biotechnology. He received a doctorate on environmental bioprocess engineering at Wageningen University. He did a post-doc in the Dept. of Molecular Biology of the Spanish Research Council (CSIC) in Granada, Spain and moved subsequently to the German National Centre for Biotechnology where he built the Systems and Synthetic Biology research group.
He has coordinated and participated in numerous national and international projects in Systems and Synthetic Biology and has been involved in advising science and governance policies, and has carried out intense research in the field. A major thrust of his research is the streamlining of microbial chassis and (computer-assisted) re-programming of cellular behaviour for medical, industrial and environmental applications.
Dr. Renier van der Hoorn, Head of Plant Chemetics Lab, University of Oxford
Monday 20th January 2014, 4.00 p.m., Marlowe Lecture Theatre 1
Activity-based protein profiling (ABPP) is a powerful functional proteomics approach to display the active proteome using small molecule probes that covalently and irreversibly react with the active site residue of proteins. Labeled proteins can be displayed on protein gels and purified and identified by mass spectrometry. This approach displays the availability and reactivity of active site residues of proteins, which is a hallmark for protein activities. I will give examples of specific probes, broad-range probes and probes that have unexpected labeling sites that are still informative on the activity of proteins. Using examples from plant science, I will show that ABPP can be broadly applied on different organisms, both on extracted proteomes and on living cells or whole organisms.