Publications

  1. D. Gurvic, A.G. Leach, U. Zachariae (2022).
    Data-driven derivation of molecular substructures that enhance drug activity in Gram-negative bacteria.
    J. Med. Chem., in press.

  2. C.M. Ives, N.J. Thomson, U. Zachariae (2022).
    A co-operative knock-on mechanism underpins Ca2+-selective cation permeation in TRPV channels.
    bioRxiv, 486690.

  3. G. Williamson, A.S. Brito, A. Bizior, G. Tamburrino, G. Dias Mirandela, T. Harris, P.A. Hoskisson, U. Zachariae, A.M. Marini*, M. Boeckstaens*, A. Javelle* (2022).
    (*joint corresponding/last authors.)
    Coexistence of Ammonium Transporter and Channel Mechanisms in Amt-Mep-Rh Twin-His Variants Impairs the Filamentation Signaling Capacity of Fungal Mep2 Transceptors.
    mBio, e02913-21.

  4. A. Mironenko, U. Zachariae, B.L. de Groot, W. Kopec (2021).
    The persistent question of potassium channel permeation mechanisms.
    J. Mol. Biol. 433, 167002.

  5. N.J. Thomson, O.N. Vickery, C.M. Ives, U. Zachariae (2021).
    Ion-water coupling controls class A GPCR signal transduction.
    bioRxiv, 271510.

  6. A. Bartsch†, C.M. Ives†, C. Kattner, F. Pein, M. Diehn, M. Tanabe, A. Munk, U. Zachariae*, C. Steinem*, S. Llabrés* (2021). (†joint first authors, *joint corresponding/last authors.)
    An antibiotic-resistance conferring mutation in a neisserial porin: Structure, ion flux, and ampicillin binding.
    BBA Biomembranes, 183601.

  7. A.H. Alghamdi, J.C. Munday, G.D. Campagnaro, D. Gurvic, F. Svensson, C.E. Okpara, A. Kumar, M.E.M. Abril, P. Milic, L. Watson, D.l Paape, L. Settimo, A. Dimitriou, J. Wielinska, G. Smart, L.F. Anderson, C.M. Woodley, S.P.Y. Kelley, H.M.S. Ibrahim, F. Hulpia , M.I. Al-Salabi, A.A. Eze, I.A. Teka, S. Gudin, C. Dardonville, R.R. Tidwell, M. Carrington, P.M. O'Neill, D.W. Boykin, U. Zachariae, H.P. De Koning (2020).
    Positively selected modifications in the pore of TbAQP2 allow pentamidine to enter Trypanosoma brucei.
    eLife 9, e56416.

  8. I. Rodriguez-Espigares, M. Torrens-Fontanals, J.K.S. Tiemann, D. Aranda-Garcia, J.M. Ramirez-Anguita, T.M. Stepniewski, N. Worp, A. Varela-Rial, A. Morales-Pastor, B.M. Lacruz, G. Pandy-Szekeres, E. Mayol, T. Giorgino, J. Carlsson, X. Deupi, S. Filipek, M. Filizola, J.C. Gomez-Tamayo, A Gonzalez, H Gutierrez-de-Teran, M Jimenez, W Jespers, J. Kapla, G. Khelashvili, P. Kolb, D. Latek, M. Marti-Solano, P. Matricon, M.T. Matsoukas, P. Miszta, M. Olivella, L. Perez-Benito, D. Provasi, S. Rios, I. Rodriguez-Torrecillas, J. Sallander, A. Sztyler, N. Vaidehi, S. Vasile, H. Weinstein, U. Zachariae, P.W. Hildebrand, G. De Fabritiis, F. Sanz, D.E. Gloriam, A. Cordomi, R. Guixa-Gonzalez, J. Selent (2020).
    GPCRmd uncovers the dynamics of the 3D-GPCRome.
    Nature Methods 17, 777-787.

  9. G. Williamson†, G. Tamburrino†, G. Dias Mirandela†, M. Boeckstaens†, M. Bage, A.V. Pisliakov, C.M. Ives, E. Terras, A. Bizior, P.A. Hoskisson, A.M. Marini, U. Zachariae*, A. Javelle* (2020). (†joint first authors, *joint corresponding/last authors.)
    A two-lane mechanism for selective biological ammonium transport.
    eLife 9, e57183.

      See also commentary article: Ammonium Transporters: A molecular dual carriageway, eLife 9, e61148.

  10. A. Krah, R.G. Huber, U. Zachariae, P.J. Bond (2020).
    On the ion coupling mechanism of the MATE transporter ClbM.
    BBA Biomembranes 1862, 183137.

  11. S. Llabrés, M.I. Tsenkov, S.A. MacGowan, G.J. Barton, U. Zachariae (2020).
    Disease-related single-point mutations alter the global dynamics of a tetratricopeptide (TPR) alpha-solenoid domain.
    J. Struct. Biol. 209, 107405.

  12. A. Bartsch†, S. Llabrés†, F. Pein, C. Kattner, M. Schön, M. Diehn, M. Tanabe, A. Munk, U. Zachariae*, C. Steinem* (2019). (†joint first authors, *joint corresponding/last authors.)
    High-resolution experimental and computational electrophysiology reveals weak beta-lactam binding events in the porin PorB.
    Scientific Reports 9, 1264.

  13. G. Dias Mirandela, G. Tamburrino, P.A. Hoskisson, U. Zachariae, A. Javelle (2019).
    The lipid environment determines the activity of the E. coli ammonium transporter, AmtB.
    FASEB Journal 33, 1989-1999.

  14. W. Kopec, D.A. Köpfer, O.N. Vickery, A.S. Bondarenko, T.L.C. Jansen, B.L. de Groot*, U. Zachariae* (2018).
    Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels. (*joint corresponding/last authors.)
    Nature Chemistry 10, 813-820.

      See also News & Views: The naked truth about K+ selectivity.

  15. G. Dias Mirandela, G. Tamburrino, M.T. Ivanovic, F.N. Strnad, O. Byron, T. Rasmussen, P.A. Hoskisson, J.S. Hub*, U. Zachariae*, F. Gabel*, A. Javelle (2018).
    (*equal contribution.)
    Merging in-solution X-ray and neutron scattering data allows fine structural analysis of membrane-protein detergent complexes.
    J. Phys. Chem. Lett. 9, 3410-3414.

  16. M. Gundogdu, S. Llabrés, A. Gorelik, A.T. Ferenbach, U. Zachariae, D.M.F. van Aalten (2018).
    The O-GlcNAc Transferase Intellectual Disability Mutation L254F Distorts the TPR Helix.
    Cell Chemical Biology 5, 513-518.

      See also press reports, e.g. in Drug Discovery Today.

  17. K. Zeth, U. Zachariae (2018).
    Ten years of high resolution structural research on the voltage dependent anion channel (VDAC) - recent developments and future directions.
    Front. Physiol. 9, 108.

  18. O.N. Vickery, C.A. Carvalheda, S.A. Zaidi, A.V. Pisliakov, V. Katritch, U. Zachariae (2018).
    Intracellular Transfer Of Na+ In An Active State G Protein Coupled Receptor.
    Structure 26, 171-180.

  19. G. Tamburrino, S. Llabrés, O.N. Vickery, S.J. Pitt, U. Zachariae (2017).
    Modulation of the Neisseria gonorrhoeae drug efflux conduit MtrE.
    Scientific Reports 7, 17091.

  20. A.W.P. Fitzpatrick, S. Llabrés, A. Neuberger, D. Brook, X.C. Bai, S. Murakami, U. Okada, H. van Veen, U. Zachariae, S.H.W. Scheres*, B.F. Luisi*, D. Du* (2017).
    Structure of the MacAB-TolC ABC type tripartite multidrug efflux pump.
    Nature Microbiology 2, 17070.

  21. A. Krah, U. Zachariae (2017).
    Insights into the ion-coupling mechanism in the MATE transporter NorM-VC.
    Physical Biology 14, 045009.

  22. O.N. Vickery, J.-P. Machtens, U. Zachariae (2016).
    Membrane potentials regulating GPCRs: Insights from experiments and molecular dynamics simulations.
    Curr. Opin. Pharmacol. 30, 44-50.

  23. D.T. Baptista-Hon, A. Krah, U. Zachariae, T.G. Hales (2016).
    A role for loop G in the beta-1 strand in GABAA receptor activation
    J. Physiol. 594, 5555-5571.

  24. O.N. Vickery, J.-P. Machtens, G. Tamburrino, D. Seeliger, U. Zachariae (2016).
    Structural mechanisms of voltage-sensing in G-protein coupled receptors.
    Structure 24, 997-1007.

  25. C. Kutzner, D.A. Köpfer, J.-P. Machtens, B.L. de Groot, C. Song, U. Zachariae (2016).
    Insights into the function of ion channels by computational electrophysiology simulations.
    BBA Biomembranes 1858, 1741-1752.

  26. G.B. Brandani, M. Schor, R. Morris, N. Stanley-Wall, C.E. MacPhee, D. Marenduzzo*, U. Zachariae* (2015).
    (*joint corresponding/last authors.)
    The bacterial hydrophobin BslA is a switchable ellipsoidal Janus colloid.
    Langmuir 31, 11558-11563.

  27. A.S. Rose, U. Zachariae, H. Grubmüller, K.P. Hofmann, P. Scherer, P.W. Hildebrandt (2015).
    Role of Structural Dynamics at the Receptor G Protein Interface for Signal Transduction
    Plos One 10, e0143399.

  28. K.M. Bromley, R.J. Morris, L. Hobley, G.B. Brandani, R.M.C. Gillespie, M. McCluskey, U. Zachariae, D. Marenduzzo, N.R. Stanley-Wall, C.E. MacPhee (2015).
    Interfacial self-assembly of a bacterial hydrophobin.
    Proc. Nat. Acad. Sci. USA 112, 5419-5424.

  29. J.P. Machtens, D. Kortzak, C. Lansche, A. Leinenweber, P. Kilian, B. Begemann, U. Zachariae, D. Ewers, B.L. de Groot, R. Briones, C. Fahlke (2015).
    Mechanisms of Anion Conduction by Coupled Glutamate Transporters.
    Cell 160, 542-553.

  30. R.A. Pumroy, S. Ke, D.J. Hart, U. Zachariae, G. Cingolani (2015).
    Molecular determinants for nuclear import of influenza A PB2 by importin alpha isoforms 3 and 7.
    Structure 23, 374-384.

  31. D.A. Köpfer, C. Song, T. Gruene, G.M. Sheldrick, U. Zachariae*, B.L. de Groot* (2014).
    (*joint corresponding/last authors.)
    Ion permeation in K+ channels occurs by direct Coulomb knock-on.
    Science 346, 352-355.

  32. A.S. Rose, M. Elgeti, U. Zachariae, H. Grubmüller, K.P. Hofmann, P. Scherer, P.W. Hildebrandt (2014).
    Position of transmembrane helix 6 determines receptor-G protein coupling specificity.
    J. Am. Chem. Soc. 136, 11244-11247.

  33. E.L. Compton, K. Page, H.E. Findlay, M. Haertlein, M. Moulin, U. Zachariae, D.G. Norman, F. Gabel, A. Javelle (2014).
    Conserved structure and domain organisation amongst bacterial Slc26 transporters.
    Biochem. J. 463, 297-307.

  34. C. Kattner, D. Toussi, J. Zaucha, L.M. Wetzler, N. Rüppel, U. Zachariae, P. Massari, M. Tanabe (2014).
    Crystallographic analysis of Neisseria meningitidis extracellular loops potentially implicated in TLR2 recognition.
    J. Struct. Biol. 185, 440-447.

  35. N. Dölker, C.E. Blanchet, B. Voß, D. Haselbach, C. Kappel, T. Monecke, D. Svergun, H. Stark, R. Ficner, U. Zachariae, H. Grubmüller, A. Dickmanns (2013).
    Structural determinants and mechanism of mammalian CRM1 allostery.
    Structure 21, 1350-1360.

  36. G.B. Brandani, M. Schor, C.E. MacPhee, H. Grubmüller, U. Zachariae*, D. Marenduzzo* (2013).
    (*joint corresponding/last authors.)
    Quantifying disorder through conditional entropy: An application to fluid mixing.
    Plos One 8, e65617.

  37. M. Porrini, U. Zachariae, P.E. Barran, C.E. MacPhee (2013).
    The Effect of Protonation State on the Stability of Amyloid Oligomers Assembled From TTR(105-115).
    J. Phys. Chem. Lett. 4, 1233-1238.

  38. C. Song, C. Weichbrodt, E.S. Salnikov, M. Dynowski, B.O. Forsberg, B. Bechinger, C. Steinem, B.L. de Groot, U. Zachariae*, K. Zeth* (2013).
    (*joint corresponding/last authors.)
    Crystal structure and functional mechanism of a human antimicrobial membrane channel.
    Proc. Nat. Acad. Sci. USA 110, 4586-4591.

      Commentary article: AMPs in Action, Science 339, 1127.
      PDB: 2YMK; PDB molecule of the month, June 2013.

  39. C. Kattner†, J. Zaucha†, F. Jaenecke, U. Zachariae*, M. Tanabe* (2013).
    (†joint first authors, *joint corresponding/last authors.)
    Identification of a cation transport pathway in Neisseria meningitidis PorB.
    Proteins 81, 830-840.

      PDB: 3VY8
      Cover article of Proteins.

  40. T. Monecke, D. Haselbach, B. Voß, A. Russek, P. Neumann, E. Thomson, E. Hurt, U. Zachariae, H. Stark, H. Grubmüller, A. Dickmanns, and R. Ficner (2013).
    Structural basis for cooperativity of CRM1 export complex formation.
    Proc. Nat. Acad. Sci. USA 110, 960-965.

      PDB: 4FGV and 4HZK.

  41. A.E. Howery, S. Elvington, S.J. Abraham, K.H. Choi, S. Phillips, C.M. Ryan, R.L. Sanford, S. Simpson-Dworschak, J. Almqvist, K. Tran, T.A. Chew, U. Zachariae, O.S. Andersen, J. Whitelegge, K. Matulef, J. Du Bois, and M.C. Maduke (2012).
    A designed inhibitor of a CLC antiporter blocks function through a unique binding mode.
    Chem. Biol. 19, 1460-1470.

      Commentary article: G. Zifarelli, M. Pusch: A kick-start for CLC antiporters
      pharmacology, Chem. Biol., 19, 1358 (2012).

  42. C. Kappel, N. Dölker, R. Kumar, M. Zink, U. Zachariae, and H. Grubmüller (2012).
    Universal relaxation governs non-equilibrium elasticity of biomolecules.
    Phys. Rev. Lett. 109, 118304.

  43. D.A. Köpfer, U. Hahn, I. Ohmert, G. Vriend, O. Pongs, B.L. de Groot, and U. Zachariae (2012).
    A molecular switch driving inactivation in the cardiac K+ channel hERG.
    PLOS ONE 7, e41023.

  44. U. Zachariae*, R. Schneider*, R. Briones, Z. Gattin, J.P. Demers, E. Maier, M. Zweckstetter, C. Griesinger, S. Becker, R. Benz, B.L. de Groot, and A. Lange (2012).
    (*joint first authors.)
    Beta-barrel mobility underlies closure of the voltage-dependent anion channel.
    Structure 20, 1540-1549.

  45. C. Kutzner, H. Grubmüller, B.L. de Groot, and U. Zachariae (2011).
    Computational electrophysiology: The molecular dynamics of ion channel permeation and selectivity in atomistic detail.
    Biophys. J. 101, 809-817.

      Commentary article: Benoit Roux: New & Notable, Biophys. J., 101, 755-756.

  46. S. Villinger, R. Briones, K. Giller, U. Zachariae, A. Lange, B.L. de Groot, C. Griesinger, S. Becker, and M. Zweckstetter (2010).
    Functional dynamics in the voltage-dependent anion channel.
    Proc. Nat. Acad. Sci. USA 107, 22546-22551.

  47. C. Kappel, U. Zachariae, N. Dölker, and H. Grubmüller (2010).
    An unusual hydrophobic core confers extreme flexibility to HEAT repeat proteins.
    Biophys. J. 99, 1596-1603.

  48. J. K. Forwood, A. Lange, U. Zachariae, M. Marfori, C. Preast, H. Grubmuller, M. Stewart, A. H. Corbett, and B. Kobe (2010).
    Quantitative structural analysis of importin-beta flexibility:
    Paradigm for solenoid protein structures.
    Structure 18, 1171-1183.

  49. N. Dölker, U. Zachariae, and H. Grubmüller (2010).
    Hydrophilic linkers and polar contacts affect aggregation of FG repeat peptides.
    Biophys. J. 98, 2653-2661.

  50. A. Stary, S. J. Wacker, L. Boukharta, U. Zachariae, Y. Karimi-Nejad, J. Aqvist, G. Vriend, and B.L. de Groot (2010).
    Toward a consensus model of the hERG potassium channel.
    ChemMedChem 5, 455-467.

  51. U. Zachariae*, F. Giordanetto, and A.G. Leach (2009).
    (*corresponding author.)
    Side chain flexibilities in the human Ether-a-go-go Related Gene potassium channel (hERG) together with matched-pair binding studies suggest a new binding mode for channel blockers.
    J. Med. Chem. 952, 4266-4276.

      Faculty of 1000 Evaluation:
      - Zelda R Wasserman (2010):
      http://f1000biology.com/article/id/1366966/evaluation

  52. U. Zachariae, R. Schneider, P. Velisetty, A. Lange, D. Seeliger, S.J. Wacker, Y. Karimi-Nejad, G. Vriend, S. Becker, O. Pongs, M. Baldus, and B.L. de Groot (2008).
    The molecular mechanism of toxin-induced conformational changes in a potassium channel: relation to C-type inactivation.
    Structure 16, 747-754.

  53. C. Hartmann, M. Chami, U. Zachariae, B.L. de Groot, A. Engel, and M.G. Grütter (2008).
    Vacuolar protein sorting: two different functional states of the AAA-ATPase Vps4p.
    J. Mol. Biol. 377, 352-363.

  54. U. Zachariae* and H. Grubmüller (2008).
    (*corresponding author.)
    Importin-beta: Structural and dynamic determinants of a molecular spring.
    Structure 16, 906-915.

  55. U. Zachariae and H. Grubmüller (2006).
    A highly strained nuclear conformation of the exportin Cse1p revealed by molecular dynamics simulations.
    Structure 14, 1469-1478.

  56. U. Zachariae, T. Klühspies, S. De, H. Engelhardt, and K. Zeth (2006).
    High resolution crystal structures and molecular dynamics simulations reveal substrate binding in the porin Omp32.
    J. Biol. Chem. 281, 7413-7420.

      PDB: 2FGQ and 2FGR.

  57. M. Grigorov, P. van Bladeren, U. Zachariae, S. Kochhar, L.B. Fay, I. Corthesy, M.A. Juillerat, M. Affolter (2005).
    Methods of producing bioactive compositions.
    European Patent EP1799838B1, granted 2010.

  58. A. Koumanov, U. Zachariae, H. Engelhardt, and A. Karshikoff (2003).
    Improved 3D continuum calculations of ion flux through membrane channels.
    Eur. Biophys. J. 32, 689-702.

  59. U. Zachariae, V. Helms, and H. Engelhardt (2003).
    Multi-step mechanism of chloride translocation in a strongly anion selective porin channel.
    Biophys. J. 85, 954-962.

  60. U. Zachariae, A. Koumanov, H. Engelhardt, and A. Karshikoff (2002).
    Electrostatic properties of the anion-selective porin Omp32 from Delftia acidovorans and of the arginine cluster of bacterial porins.
    Protein Sci. 11, 1309-1319.

  61. U. Zachariae*, T.A. Schuttrigkeit*, T. von Feilitzsch, J. Wiehler, J. von Hummel, B. Steipe, and M.E. Michel-Beyerle (2001).
    (*joint first authors.)
    Picosecond time-resolved FRET in the fluorescent protein from Discosoma Red (wt-dsRed).
    ChemPhysChem, 2, 325-328.

  62. U. Zachariae and C.R.D. Lancaster (2001).
    Proton uptake associated with the reduction of the primary quinone QA influences the binding site of the secondary quinone QB in Rhodopseudomonas viridis photosynthetic reaction centres.
    Biochim. Biophys. Acta Bioenergetics 1505, 280-290.