Seminar Colour Guide:              
Hamburg Speaker
Monday, 26 February 2018, 13:00Add to calendarThe structure of F-form actin at atomic
resolutions: mutual switching between
polymorphic transition and ATPase
Yuichiro Maeda, Nagoya Univ Graduate School of Science, Structural Biology Research Center, Japan, JapanHost: Matthias WilmannsSeminar Room 48e, EMBL Hamburg
Abstract: Upon polymerization, actin changes its conformation from
G-form to F-form (Oda et al, 2009, Nature)(Fig.1), which triggers
the ATPase.
(1) A 3.8 Å resolution cryo-EM structure of cofilin-actin
co-filament indicates that cofilin binding brings the actin
molecule into C-form, another conformation. The cofilin-actin
filament structure account for the selective and cooperative
binding of cofilin to ADP-F-actin, formation of cofilin-clusters on
F-actin, severing F-actin at the cluster ends, and accelerated
depolymerization at B- and P-ends.
(2) Crystal structures (at 2.3 Å resolutions) have been
obtained from F2A4 complex (2:4 complex of an actin-binding
protein fragmin (full length) with actin)(Fig.2). Within this
complex, 4 molecules of actin are assembled in the same manner
as in F-actin; two subunits at the B-end are in F-form, two
longitudinal actin-actin contacts as well as one diagonal contact
are canonical. This structure, the first crystal structure of F-form
actin, reveals distinct nature of actin-actin contacts, longitudinal
vs. diagonal contacts.
(3) To our surprise, monomeric F-form actin has been found
in the crystal structure (at 1.15-1.2 Å resolutions) of 1:1 complex
of N-terminal domain-1 of fragmin (F1) with actin (F1A), either
with bound MgAMPPNP (a structural analog of MgATP),
MgADPPi, or MgADP (Fig.3). These structures have allowed us
to investigate plausible reaction paths of actin ATPase by
QM/MM simulations. The reaction path of ATP hydrolysis is very
much similar to those in other ATPase, like myosin. Remarkably,
the main chain configuration is identical between F-ATP and
F-ADP form. However, MD simulations reveal that F-ADP is less
stable, with a pronounced tendency of transition towards G-form.
(4) The monomeric F-form actin is identical to the F-form
actin within F-actin. This means that the G-to-F transition is
induced not only by polymerization but also by a transition
inducer like F1. F1 does not dictate, but selects an actin
conformation. Similarly, we believe that the identical
conformation of F-ATP and F-ADP must be the property of actin itself, not due to F1-binding
hindering in a conformational transition.
Analysis of these recently obtained structures together with all the PDB-deposited actin
structures at atomic resolutions has revealed that actin molecule can take G-, F-, C- (in
cofilin-actin complex) and O-form (in profiling-actin complex) , depending on spatial
relationship between the two rigid bodies , the inner domain (ID) and the outer domain (OD)
excluding the D-loop (Fig.4). Remarkably, MD/PCA analysis reveals that structural
fluctuations of actin monomer are dominated by tendencies of G/F, G/O and F/C transitions,
and that this is shared between monomeric G-form actin and monomeric F-form actin with
bound F1, irrespective of bound nucleotides. (18.1.2018)
Hamburg Speaker
Friday, 9 March 2018, 13:00Add to calendarProtein-ligand interaction energy for crystallographic model building and validationDaria Beshnova, EMBL, Hamburg Unit, GermanyHost: Victor LamzinSeminar Room 48e, EMBL Hamburg
Hamburg Speaker
Friday, 16 March 2018, 13:00Add to calendar"Beyond standard bioSAXS"Martin Schroer, EMBL, Hamburg Unit, GermanyHost: Dmitri SvergunSeminar Room 48e, EMBL Hamburg
Hamburg Speaker
Friday, 23 March 2018, 13:00Add to calendarCollagen fibril under stress: insight from molecular dynamics simulationsAgnieszka Obarska, EMBL, Hamburg Unit, GermanyHost: Matthias WilmannsSeminar Room 48e, EMBL Hamburg
Hamburg Speaker
Friday, 6 April 2018, 13:00Add to calendarNew developments on our High-thoughput Crystallization and Molecular Biophysics FacilityMaria Garcia, EMBL Hamburg Unit, GermanyHost: tdbSeminar Room 48e, EMBL Hamburg
Hamburg Speaker
Friday, 13 April 2018, 13:00Add to calendarZipping and unzipping transcriptional regulation Vivian Pogenberg, EMBL Hamburg Unit, GermanyHost: Matthias WilmannsSeminar Room 48e, EMBL Hamburg
Hamburg Speaker
Friday, 20 April 2018, 13:00Add to calendartbdAndrey Gruzinov, EMBL Hamburg Unit, GermanyHost: Dmitri SvergunSeminar Room 48e, EMBL Hamburg
Hamburg Speaker
Friday, 27 April 2018, 13:00Add to calendarTo be announcedEgor Sobolev, EMBL Hamburg Unit, GermanyHost: Victor LamzinSeminar Room 48e, EMBL Hamburg
Hamburg Speaker
Friday, 4 May 2018, 13:00Add to calendarStructure of the Mycobacterial Type VII Secretion SystemKatherine Beckham, EMBL Hamburg Unit, GermanyHost: Matthias WilmannsSeminar Room 48e, EMBL Hamburg
Hamburg Speaker
Friday, 18 May 2018, 13:00Add to calendarModel-building challenges for crystallographic maps at low-resolution
Grzegorz Chojnowski, EMBL Hamburg Unit, GermanyHost: Victor LamzinSeminar Room 48e, EMBL Hamburg
Hamburg Speaker
Friday, 25 May 2018, 13:00Add to calendarVariations of subunit α, γ and ε of the Mycobacterium tuberculosis F-ATP synthase cause structural, mechanistic and enzymatic alterations, leading to the design of novel TB compoundsGerhard Grueber, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 639798 Singapore, SingaporeHost: Dmitri SvergunSeminar Room 48e, EMBL Hamburg
Abstract: With one-third of mankind infected subclinically, an incidence of nine million new cases of active tuberculosis disease (TB) and two million deaths per year, Mycobacterium tuberculosis, remains the most important bacterial pathogen in the world [1]. This enzyme complex is composed of nine subunits in the stoichiometry of α3:β3:γ:δ:ε:a:b:b :c9, and organized in a membrane-embedded FO domain (a:b:b :c9-12) and a water soluble F1 part (α3:β3:γ:δ:ε:). Mycobacterial F-ATP synthase has been shown to be essential for growth and survival, which is different from other prokaryotes, where the enzyme is dispensable for growth on fermentable carbon sources and where increased glycolytic flux can compensate for the loss of oxidative phosphorylation [2]. Another special feature of the mycobacterial F-ATP synthase is its inability to establish a significant proton gradient during ATP hydrolysis, and its low or latent ATPase activity in the fast- or slow-growing form [3-4].
The presentation reveals that at least the three subunits α, γ and ε contribute to the important enzymatic differences of mycobacterial F-ATP synthases in suppression of proton pumping and proton motive force (PMF) formation [4-6], which is essential because dissipating the PMF is lethal to mycobacteria, as well as in ATP formation, employing them as potential drug targets. Our novel atomic structure of the rotating subunit ε in solution provides insights into a new mechanism of coupling proton-conduction with ATP synthesis and identifies a second binding site of the TB drug bedaquiline (BDQ, Sirturo®) [6].
Using a combination of recombineering, ensemble and single molecule assays, solution X-ray scattering, NMR spectroscopy and electron microscopy it will be shown that unique mycobacterial stretches inside the nucleotide-binding subunit α and γ influence cell growth, ATPase activity and ATP synthesis of the pathogen [4-5].
These data formed a platform to identify and synthesize new compounds, which effectively inhibit ATPase and ATP synthesis of mycrobacterial F-ATP synthase and inhibit growth of Mycobacterium smegmatis, M. bovis as well as M. tuberculosis.
References
1. World Health Organization (2014) Global Tuberculosis Report 2014, 1-171
2. Cook, G.M., Hards, K., Vilcheze, C., Hartman, T. & Berney, M. (2014) Energetics of Respiration and Oxidative Phosphorylation in Mycobacteria. Microbiol. Spectr. 2, doi:10.1128/microbiolspec.MGM2-0015-2013.
3. Haagsma, A.C., Driessen, N.N., Hahn, M.M., Lill, H. & Bald, D. (2010) ATP synthase in slow- and fast-growing mycobacteria is active in ATP synthesis and blocked in ATP hydrolysis direction. FEMS Microbiol. Lett. 313, 68-74.
4. Hotra, A., Suter, M., Biuković, G., Ragunathan, P., Kundu, S. Dick, T. & Grüber, G. (2016) Deletion of a unique loop in the mycobacterial F-ATP synthase gamma subunit sheds light on its inhibitory role in ATP hydrolysis-driven H(+) pumping. FEBS J. 283, 1947-1961.
5. Ragunathan, P., Sielaff, H., Sundararaman, L., Biuković, G., Manimekalai, M.S.S., Singh, D., Kundu, S., Wohland, T., Frasch, W., Dick, T. & Grüber, G. (2017) The uniqueness of subunit α of mycobacterial F-ATP synthases: An evolutionary variant for niche adaptation. J. Biol. Chem. 292, 11262-11279.
6. Shin, J., Ragunathan, P., Sundararaman, L., Nartey, W., Kundu, S., Manimekalai, M.S.S., Bogdanović, N., Dick, T. & Grüber, G. (2018) The NMR solution structure of Mycob
External Faculty Speaker
Friday, 1 June 2018, 13:00Add to calendartbdErvin Fodor, University of Oxford, United KingdomHost: Jan KosinskiSeminar Room 48e, EMBL Hamburg
Abstract: tbd
Hamburg Speaker
Friday, 8 June 2018, 13:00Add to calendarStructural characterisation of the von Willebrand factorEmma Ruoqi Xu, EMBL, Hamburg Unit, GermanyHost: Matthias WilmannsSeminar Room 48e, EMBL Hamburg
Hamburg Speaker
Friday, 15 June 2018, 13:00Add to calendar"Substrate promiscuity and drug uptake in proton dependent oligo-peptide transporters"
Christian Loew, EMBL, Hamburg Unit, GermanyHost: Christian LoewSeminar Room 48e, EMBL Hamburg