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Viewing upcoming talks containing the keyword: 3
Stand-alone and hybrid structural characterization of proteins using EPR spectroscopy on spin labels (EaStCHEM/BSRC joint colloquium)
Speaker: Gunnar Jeschke (ETHZ)
Proteins and their complexes are not always accessible to established approaches for determination of atomistic structures, and even if they are, a single structure with atomistic resolution may not be representative of the whole conformational space that is required for their function. Alternative information on this conformational space can be obtained by electron paramagnetic resonance (EPR spectroscopy), usually after spin labels have been introduced via site-directed mutations. Since paramagnetic centres are rare in proteins and in their native environment, no assignment or resolution problems arise even in large proteins or complexes and in physiologically relevant environments. If two labels are introduced, the distance distribution between them rather than only a mean distance can be measured, so that direct information on conformational distributions is obtained, which is hard to come by with other approaches.
These potential advantages come at a price. Site-directed mutations and spin labelling are elaborate. Thus, EPR restraints on structure are usually sparse and need to be combined in hybrid approaches with information from other techniques. The labels themselves are flexible side groups with their own conformational distribution, a property that limits precision of the restraints and requires extension of existing approaches for modelling structure.
In this talk I will explain how information on label accessibility by oxygen and water and on label-to-label distance distribution can be obtained. Modelling of the conformational distribution of the spin label and its accuracy limits will be shortly discussed. Based on this, I will explain how a label at a structurally unresolved site can be located by an approach similar to the global position system,1 how conformational ensembles can be generated from distance distribution restraints,2 and how relative orientation and translation of structurally resolved domains can be determined.3 Hybrid approaches will be illustrated using NMR and EPR on a protein-RNA complex,4 x-ray crystallography, SAXS, and EPR on the FnIII-3,4 domains of integrin a6b4,5 and x-ray crystallography, NMR, and EPR on the active form of the pro-apoptotic protein Bax.1
1S. Bleicken, G. Jeschke, C. Stegmüller, R. Salvador-Gallego, A.J. García-Sáez, E. Bordignon, Mol. Cell 2014, 56, 496-505. Structural Model of Active Bax at the Membrane
2G. Jeschke, Proteins, 2016, in press, DOI: 10.1002/prot.25000 Ensemble models of proteins and protein domains based on distance distribution restraints
3 D. Hilger, Ye. Polyhach, E. Padan, H. Jung, G. Jeschke, Biophys. J., 2007, 93, 3675-3683. High-resolution structure of a Na+/H+ antiporter dimer obtained by pulsed EPR distance measurements
4 O. Duss, E. Michel, M. Yulikov, M. Schubert, G. Jeschke, F. H.-T. Allain, Nature, 2014, 509, 588-592. Structural basis of the non-coding RNA RsmZ acting as protein sponge
5N. Alonso-García, I. García-Rubio, J. A. Manso, R. M. Buey, H. Urien, A. Sonnenberg, G. Jeschke, J. M. de Pereda, Acta Cryst. D, 2015 71, 969-985. Combination of X-ray crystallography, SAXS and DEER to obtain the structure of the FnIII-3,4 domains of integrin a6b4
On: June 1, 2016 From: 15h30 To: 16h30View talk
Physics and Astronomy Colloquia
Speaker: Professor J.C. SÃ©amus Davis (School of Physics and Astronomy, University of St Andrews)
Everything around us, everything each of us has ever experienced, and virtually everything underpinning our technological society and economy is governed by quantum mechanics. Yet this most fundamental physical theory of nature often feels as if it is a set of somewhat eerie and counterintuitive ideas of no direct relevance to our lives. Why is this? One reason is that we cannot perceive the strangeness (and astonishing beauty) of the quantum mechanical phenomena all around us by using our own senses.
In this lecture I will describe the recent development of techniques that allow us to image electronic quantum phenomena directly at the atomic scale. As examples, we will visually explore the previously unseen and very beautiful forms of quantum matter making up electronic liquid crystals and high temperature superconductors and find that they are closely related. I will discuss the implications for fundamental physics research and also for advanced materials and new technologies, arising from quantum matter visualization.
On: June 8, 2016 From: 18h00 To: 19h00View talk
Cond Mat Seminars
Speaker: Hannah Price (Trento Univ)
Synthetic dimensions have recently emerged as a powerful way to implement artificial gauge fields and create topological energy bands for neutral particles. In this approach, discrete internal degrees of freedom are externally coupled and reinterpreted as lattice sites along an additional synthetic dimension, where an artificial magnetic field can be imprinted via the applied coupling. In the first half of my talk, I will present our new generic proposal for how to realise a synthetic dimension in ultracold atoms that relies only on a harmonic potential and a time-dependent modulation . This simple scheme is able to overcome many limitations of previous implementations, extending these ideas to a much wider range of experimental set-ups and providing an intriguing route towards quantum Hall physics and strongly-correlated states. In the second half of my talk, I will focus on how synthetic dimensions may allow us to probe higher-dimensional topological physics for the first time. In particular, I will motivate the 4D quantum Hall effect through a semiclassical analysis and discuss how this physics could be explored in the center-of-mass drift of an ultracold atomic cloud [2,3]. H. M. Price, T. Ozawa and N. Goldman, in preparation. H. M. Price, O. Zilberberg, T. Ozawa, I. Carusotto, N. Goldman, Phys. Rev. Lett. 115, 195303 (2015). H. M. Price, O. Zilberberg, T. Ozawa, I. Carusotto and N. Goldman, arXiv:1602.01696.
On: June 13, 2016 From: 10h00 To: 11h00View talk
Speaker: Anne Osbourn (John Innes Center)
Plants produce a wealth of natural products that are valuable as industrial or pharmaceutical products. For example, plant-derived drugs represent >5% of the total pharmaceutical industry with sales revenues of £18 billion. The growing reliance on chemicals from plants is driving demand for green, environmentally friendly and sustainable feedstocks across industrial sectors in order to enable us to reduce our dependence on products derived from chemical refineries. Importantly, many of the natural products that are produced by plants are structurally complex and beyond the reach of chemical synthesis. These compounds are commonly extracted from plant material either growing in the wild or in cultivation. Availability is limited by difficulties in accessing and cultivating source species, low yield and problems of purification. The scale of the economic opportunity for improving the supply of high value products from plants is therefore enormous.
The vast majority of the natural product diversity encoded by plant genomes remains as yet untapped. The explosion in available plant genome sequence data coupled with affordable DNA synthesis and new DNA assembly technologies now offer unprecedented opportunities to harness the full breadth of plant natural product diversity and generate novel molecules in foreign hosts using synthetic biology approaches. The recent discovery that genes for the synthesis of different kinds of natural products are organised in biosynthetic gene clusters in plant genomes is now opening up opportunities for systematic mining for new pathways and chemistries. The production of plant and plant-inspired molecules in heterologous plant and microbial expression systems will enable the development of rational strategies to produce known and new-to-nature chemicals that are tailored for particular applications. This presentation will focus on our work on triterpene engineering using synthetic biology approaches.
On: June 15, 2016 From: 15h30 To: 16h30View talk