BEGIN:VCALENDAR VERSION:2.0 PRODID:-//CERN//INDICO//EN BEGIN:VEVENT SUMMARY:Short Talk 2\, Sergei Grudinin - Novel algorithms for integrative structural biology. DTSTART;VALUE=DATE-TIME:20191009T121500Z DTEND;VALUE=DATE-TIME:20191009T123500Z DTSTAMP;VALUE=DATE-TIME:20260525T152648Z UID:indico-contribution-134-754@lindico453.srv.lu.se DESCRIPTION:Speakers: Sergei Grudinin (Inria / CNRS)\nIn my talk I will pr esent our approach for modeling macromolecular\nflexibility of large molec ular assemblies and how it can be combined with\nsparse experimental data obtained with small-angle and cross-linking\nexperiments.\nLarge macromole cular machines\, such as proteins and their complexes\, are\ntypically ver y flexible at physiological conditions\, and this flexibility is\nimportan t for their structure and function. Computationally\, it can be often\napp roximated with just a few collective coordinates\, which can be computed\n e.g. using the Normal Mode Analysis (NMA). NMA determines low-frequency\nm otions at a very low computational cost and these are particularly\nintere sting to the structural biology community because they are commonly\nassum ed to give insight into protein function and dynamics [1].\nOne of the cha llenges in the community is the explanation of solution smallangle\nscatte ring profiles. Very recently\, we designed a computational scheme\nthat us es the nonlinear normal modes [2] as a low-dimensional representation\nof the protein motion subspace and optimizes protein structures guided by the \nSAXS and SANS profiles [3\,4]. For example\, in the CASP12 and CASP13\ne xercises\, this scheme obtained best models for some (3 out of 9 in CASP12 )\nSAXS-assisted targets [5\,6]. Overall\, the flexible fitting scheme typ ically allows\na significant improvement of the goodness of fit to experim ental profiles in a\nvery reasonable computational time. The NMA analysis also allows to\nautomatically split macromolecules into rigid domains\, or to be used together\nwith the cross-linking data\, as we demonstrated in the recent CASP13\nchallenge [7].\n\nReferences:\n[1] Grudinin\, S.\, Lain e\, E.\, & Hoffmann\, A. (2019). Predicting protein functional\nmotions: a n old recipe with a new twist. bioRxiv\, 703652.\n[2] Hoffmann\, A. & Grud inin\, S. (2017). J. Chem. Theory Comput. 13\, 2123 –\n2134. For more in formation https://team.inria.fr/nano-d/software/nolbnormal-\nmodes/\n[3] G rudinin\, S. et al. (2017). Acta Cryst. D\, D73\, 449 – 464. For more\ni nformation https://team.inria.fr/nano-d/software/pepsi-saxs/\n[4] https:// team.inria.fr/nano-d/software/pepsi-sans/\n[5] http://predictioncenter.org /casp13/zscores_final_assisted.cgi?target_flag=S\n[6] Tamò\, G. E.\, Abri ata\, L. A.\, Fonti\, G.\, & Dal Peraro\, M. (2018). Proteins:\nStructure\ , Function\, and Bioinformatics\, 86\, 215-227.\n[7] http://predictioncent er.org/casp13/zscores_final_assisted.cgi?target_flag=X\n\nhttps://lindico4 53.srv.lu.se/event/125/contributions/754/ LOCATION:Kulturen Auditorium URL:https://lindico453.srv.lu.se/event/125/contributions/754/ END:VEVENT BEGIN:VEVENT SUMMARY:Keynote 1\, Prof. Poul Nissen: Structure and Dynamics of Membrane Transport Proteins DTSTART;VALUE=DATE-TIME:20191009T111500Z DTEND;VALUE=DATE-TIME:20191009T115500Z DTSTAMP;VALUE=DATE-TIME:20260525T152648Z UID:indico-contribution-134-752@lindico453.srv.lu.se DESCRIPTION:Speakers: Poul Nissen (Aarhus University)\nUsing membrane prot ein crystallography\, small-angle scattering techniques\, and cryo-EM\, an d also a range of biochemical and biophysical methods such as electrophysi ology\, single-molecule FRET\, and molecular dynamics simulations\, we hav e obtained deep insight into the functional cycle of primary active transp orters of the P-type ATPase family. These transport ATPases are fundamenta l to physiology\, and malfunctions are linked to diseases such as neurolog ical and cardiovascular disorders. \nThe transmembrane gradients for the k ey cations Na+\, K+\, and Ca2+ are generated by Na+\,K+-ATPase and Ca2+-AT Pases. In brain\, Na+\,K+-ATPase activity accounts for an estimated 40-70% of total ATP hydrolysis and potentiates e.g. Na+ and K+ channels for thei r activity in action potentials\, membrane potential\, and Na+ coupled tra nsport of e.g. glucose\, metabolite\, neurotransmitters\, Ca2+ efflux\, pH and Cl- control. Ca2+-ATPases maintain steep calcium gradients\, internal Ca2+ stores\, and cytoplasmic free calcium at accurate levels that define and potentiate calcium signalling pathways. \nLipid flippases\, also of t he P-type ATPase family (P4-ATPases) maintain asymmetric lipid distributio ns in biomembranes. Their activity potentiates membrane dynamics\, but the structure and function of lipid flippases remained enigmatic until recent ly. We determined the first structures of lipid flippases using cryo-EM an d revealed at the same time a detailed insight into lipid recognition and autoregulation.\nThe talk will cover methodological approaches supporting the functional and mechanistic insight we have gained.\n\nhttps://lindico4 53.srv.lu.se/event/125/contributions/752/ LOCATION:Kulturen Auditorium URL:https://lindico453.srv.lu.se/event/125/contributions/752/ END:VEVENT BEGIN:VEVENT SUMMARY:Keynote 2\, Prof. Yifan Cheng: Single particle cryo-EM of membrane proteins DTSTART;VALUE=DATE-TIME:20191009T123500Z DTEND;VALUE=DATE-TIME:20191009T131500Z DTSTAMP;VALUE=DATE-TIME:20260525T152648Z UID:indico-contribution-134-755@lindico453.srv.lu.se DESCRIPTION:Speakers: Yifan Cheng (UC San Francisco)\nWith the technologic al breakthroughs in the past few years\, single particle cryo-electron mic roscopy (cryo-EM) has enabled rapid progresses in structure determination of integral membrane proteins\, particularly ion channels. The pace of str ucture determination of integral membrane proteins by single particle cryo -EM is unprecedented in structural biology. With such a rapid progress\, i t is also very critical to interpretation of cryo-EM density maps carefull y to ensure that interpretation is data-driven. I will discuss some practi cal examples to demonstrate the significance of careful interpretations of single particle cryo-EM density maps. \n\nFurthermore\, as a prominent ex ample in structural biology of membrane proteins\, structural studies of t ransient receptor potential (TRP) channel superfamily demonstrated nicely how technological breakthroughs impacts scientific discoveries. As an exam ple of our recent studies of TRP channels by single particle cryo-EM\, TRP V5 (transient receptor potential vanilloid 5) represents a unique calcium- selective TRP channel essential for calcium homeostasis. Unlike other TRPV channels\, TRPV5 and its close homolog\, TRPV6\, do not exhibit thermosen sitivity or ligand-dependent activation but are constitutively open at phy siological membrane potentials and modulated by calmodulin (CaM) in a calc ium-dependent manner. Structural studies of truncated and full-length TRPV 5 in lipid nanodiscs\, as well as of a TRPV5 W583A mutant and TRPV5 in com plex with CaM provide novel insights to the mechanism of calcium regulatio n and reveal a flexible stoichiometry of CaM binding to TRPV5.\n\nhttps:// lindico453.srv.lu.se/event/125/contributions/755/ LOCATION:Kulturen Auditorium URL:https://lindico453.srv.lu.se/event/125/contributions/755/ END:VEVENT BEGIN:VEVENT SUMMARY:Short Talk 1\, Veronika Nesverova - Structural insights into AQP2 targeting to multivesicular bodies DTSTART;VALUE=DATE-TIME:20191009T115500Z DTEND;VALUE=DATE-TIME:20191009T121500Z DTSTAMP;VALUE=DATE-TIME:20260525T152648Z UID:indico-contribution-134-753@lindico453.srv.lu.se DESCRIPTION:Speakers: Veronika Nesverova (Lund University)\nThe multivesic ular sorting machinery is a crucial mechanism for targeting membrane prote ins\nfor recycling or degradation. The lysosomal trafficking regulator-int eracting protein 5 (LIP5)\nwhich coordinates the action of this machinery is also known to bind directly to the membrane\nprotein cargo. In case of aquaporin 2 (AQP2) the binding of LIP5 during the endocytic pathway\nin ki dney collecting duct cells ensures an effective regulation of urine volume [1].\nIn our group\, we have previously studied the role of AQP2 phosphor ylation in AQP2-LIP5\ninteraction [2]. Currently we are focusing on elucid ating the structural details of the complex\nin order to better understand how membrane proteins are delivered to the multivesicular\nbodies. We hav e constructed alanine mutants of single residues in the proposed binding s ites\nof both AQP2 and LIP5. Studying the binding affinity of these mutant s using fluorescence\nquenching helps us understand which residues are dir ectly involved in the binding.\nFurther\, AQP2 was successfully incorporat ed into MSP-based nanodiscs and negative stain\nelectron microscopy confir med homogeneous state of the particles. We have collected high\nresolution images on Titan Krios and are currently processing the data.\n\n[1] B. W. M. Van Balkom\, M. Boone\, G. Hendriks\, E. Kamsteeg\, J. H. Robben\, H. C. Stronks\, A.\nVan Der Voorde\, and F. Van Herp\, “LIP5 Interacts with Aquaporin 2 and Facilitates Its\nLysosomal Degradation\,” pp. 990–100 1\, 2009.\n[2] J. V. Roche\, S. Survery\, S. Kreida\, V. Nesverova\, H. Am pah-Korsah\, M. Gourdon\, P. M. T.\nDeen\, and S. Törnroth-Horsefield\, “Phosphorylation of human aquaporin 2 (AQP2)\nallosterically controls it s interaction with the lysosomal trafficking protein LIP5\,” J. Biol.\nC hem.\, vol. 292\, no. 35\, pp. 14636–14648\, 2017.\n\nhttps://lindico453 .srv.lu.se/event/125/contributions/753/ LOCATION:Kulturen Auditorium URL:https://lindico453.srv.lu.se/event/125/contributions/753/ END:VEVENT END:VCALENDAR