Publications
2021
Navarro-Retamal, C., Schott-Verdugo, S., Gohlke, H., and Dreyer, I. (2021)
Computational Analyses of the AtTPC1 (Arabidopsis Two-Pore Channel 1) Permeation Pathway
Int. J. Mol. Sci. 22, 10345
Moe-Lange, J., Gappel, N.M., Machado, M., Wudick, M.M., Sies, C.S.A, Schott-Verdugo, S.N., Bonus, M., Mishra, S., Hartwig, T., Bezrutczyk, M., Basu, D., Farmer, E.E., Gohlke, H., Malkovskiy, A., Haswell, E.S., Lercher, M.J., Ehrhardt, D.W., Frommer, W.B., and Kleist, T.J. (2021)
Interdependence of a mechanosensitive anion channel and glutamate receptors in distal wound signalling
Sci. Adv. 7, eabg4298
Mironenko, A., Zachariae, U., de Groot, B.L., and Kopec, W. (2021)
The Persistent Question of Potassium Channel Permeation Mechanisms
J. Mol. Biol. 433, 167002
Roy, R.N., Hendriks, K., Kopec, W., Abdolvand, S., Weiss, K.L., de Groot, B.L., Lange, A., Sun, H., and Coates, L. (2021)
IUCrJ 8, 421-430
Chiariello, M.G., Alfonso-Prieto, M., Ippoliti, E., Fahlke, C., and Carloni, P. (2021)
Mechanisms Underlying Proton Release in CLC-type F–/H+ Antiporters
J. Phys. Chem. Lett. 12, 4415-4420
Kostritskii, A.Y., Alleva, C., Cönen, S., and Machtens, J.P. (2021)
g_elpot: A Tool for Quantifying Biomolecular Electrostatics from Molecular Dynamics Trajectories
J. Chem. Theory Comput. 17, 3157-3167
Kostritskii, A.Y., and Machtens, J.P. (2021)
Nat. Commun. 12, 2826
Hendriks, K., Öster, C., Shi, C., Sun, H., and Lange, A. (2021)
Sodium Ions Do Not Stabilize the Selectivity Filter of a Potassium Channel
J. Mol. Biol. 433, 167091
Proks, P., Schewe,, Conrad, L.J., Rao, S., Rathje, K., Rödström, K.E.J., Carpenter, E.P., Baukrowitz, T., and Tucker, S.J. (2021)
J. Gen. Physiol. 153, e202012812
Chang, W.W., Matt, A.-S., Schewe, M., Musinszki, M., Grüssel, S., Brandenburg, J., Garfield, D., Bleich, M., Baukrowitz, T., and Hu, M.Y. (2021)
Proc. Natl. Acad. Sci. USA 118, e2101378118
Schirmeyer,, Hummert, S., Eick, T., Schulz, E., Schwabe, T., Ehrlich, G., Kukaj, T., Wiegand, M., Sattler, C., Schmauder, R., Zimmer, T., Kosmalla, N., Münch, J., Bonus, M., Gohlke, H., and Benndorf, K. (2021)
Proc. Natl. Acad. Sci. USA 118, e2100469118
Pfleger, C., Kusch, J., Kondapuram, M., Schwabe, T., Sattler, C., Benndorf, K, and Gohlke, H. (2021)
Allosteric signaling in C-linker and cyclic nucleotide-binding domain of HCN2 channels
Biophys. J. 120, 950-963
Biedermann, J., Braunbeck, S., Plested, A.J.R., and Sun, H. (2021)Nonselective cation permeation in an AMPA-type glutamate receptor
Proc. Nat. Acad. Sci. USA 118, e2012843118
Alleva, C., Machtens, J.-P., Kortzak, D., Weyand, I., and Fahlke, C. (2021)Molecular basis of coupled transport and anion conduction in excitatory amino acid transporters
Neurochem. Res., https://doi.org/10.1007/s11064-021-03252-x
Winterstein, L.M., Kukovetz, K., Hansen, U.P., Schroeder, I., Van Etten, J.L., Moroni, A., Thiel, G., and Rauh, O. (2021)
Distinct lipid bilayer compositions have general and protein-specific effects on K+ channel function
J. Gen. Physiol. 153, e202012731
2020
Alleva, C., Kovalev, K., Astashkin, R., Berndt, M.I., Baeken, C., Balandin, T., Gordeliy, V., Fahlke, C., and Machtens, J.P. (2020)
Sci. Adv. 6, eaba9854
Sattler, C., Eick, T., Hummert, S., Schulz, E., Schmauder, R., Schweinitz, A., Unzeitig, C., Schwede, F., and Benndorf, K. (2020)
Sci. Rep. 10, 21751
Kolen, B., Kortzak, D., Franzen, A., and Fahlke, C. (2020)
An amino-terminal point mutation increases EAAT2 anion currents without affecting glutamarte transport rates
J. Biol. Chem. 295, 14936-14947
Rühlmann, A.H., Körner, J., Hausmann, R., Bebrivenski, N., Neuhof, C., Detro-Dassen, S., Hautvast, P., Benasolo, C.A., Meents, J., Machtens, J.P., Schmalzing, G., and Lampert, A. (2020)Uncoupling sodium channel dimers restores the phenotype of a pain-linked Nav1.7 channel mutation
Br. J. Pharmacol. 177, 4481-4496
Kopec, W., Żak, A., Jamróz, D., Nakahata, R., Yusa, S.I., Gapsys, V., and Kepczynski, M. (2020)Polycation-anionic lipid membrane interactions
Langmuir 36, 12435-12450
Langan, P.S., Vandavasi, V.G., Kopec, W., Sullivan, B., Afonne, P.V., Weiss, K.L., de Groot, B.L. and Coates, L. (2020)
The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation
IUCrJ 7, 835-843
Schubeis, T., Le Marchand, T., Daday, C., Kopec, W., Movellan, K.T., Stanek, J., Schwarzer, T.S., Castiglione, K., de Groot, B.L., Pintacuda, G., and Andreas, L.B. (2020)A β-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkL
Proc. Nat. Acad. Sci. USA 117, 21014-2102
Bolnykh, V., Rothlisberger, U., and Carloni, P. (2020)
Isr. J. Chem. 60, 694-704
Lelle, M., Otte, M., Bonus, M., Gohlke, H., and Benndorf, K. (2020)
Fluorophore‐Labeled Cyclic Nucleotides as Potent Agonists of Cyclic Nucleotide‐Regulated Ion Channels
ChemBioChem 21, 1-11
Alberione, M.A., Moeller, R., Kirui, J., Ginkel, C., Doepke, M., Ströh, L.J., Machtens, J.P., Pietschmann, T., and Gerold, G. (2020)Single-nucleotide variants in human CD81 influence hepatitis C virus infection of hepatoma cells
Med. Microbiol. Immunol. 22, 1-16
Bolnykh, V., Olsen, J.M.H., Meloni, S., Bircher, M.P., Ippoliti, E., Carloni, P., and Rothlisberger, U. (2020)MiMiC: Multiscale Modeling in Computational Chemistry
Front. Mol. Biosci. 7, 45
Chiariello, M.G., Bolnykh, V., Ippoliti, E., Meloni, S., Olsen, J.M.H, Beck, T., Rothlisberger, U., Fahlke, C., and Carloni, P. (2020)
J. Am. Chem. Soc., doi: 10.1021/jacs.9b13588
Nematian-Ardestani, E., Abd-Wahab, F., Chatelain, F.C., Sun, H., Schewe, M., Baukrowitz, T., and Tucker, S.J. (2020)
J. Biol. Chem. 295, 610-618
2019
Wifling, D., Pfleger, C., Kaindl, J., Ibrahim, P, Kling, R.C., Buschauer, A., Gohlke, H., and Clark, T. (2019)
Basal histamine H4 receptor activation: Agonist mimicry by the diphenylalanine motif
Chem. Eur. J. 25, 14613-14624
Leypold, T., Bonus, M., Spiegelhalter, F., Schwede, f., Schwabe, T., Gohlke, H., and Kusch, J. (2019)
N6-modified cAMP derivatives that activate protein kinase A also act as full agonists of murine HCN2 channels
J. Biol. Chem. 294, 17978-17987
Bratanov, D., Kovalev, K., Machtens, J. P., Astashkin, R., Chizhov, I., Soloviov, D., Volkov, D., Polovinkin, V., Zabelskii, D., Mager, T., Gushchin, I., Rokitskaya, T., Antonenko, Y., Alekseev, A., Shevchenko, V., Yutin, N., Rosselli, R., Baeken, C., Borshchevskiy, V., Bourenkov, G., Popov, A., Balandin, T., Büldt, G., Manstein, D. J., Rodriguez-Valera, F., Fahlke, C., Bamberg, E., Koonin, E., and Gordeliy, V. (2019)
Unique structure and function of viral rhodopsins
Nat. Commun. 10, 4939
Kopec, W., Rothberg, B.S., and de groot, B.L. (2019)
Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling
Nat. Commun. 10, 5366
Kortzak, D., Alleva, C., Weyand, I., Ewers, D., Zimmermann, M. I., Franzen, A., Machtens, J. P., and Fahlke, C. (2019)
Allosteric gate modulation confers K+ coupling in glutamate transporters
EMBO J. 38, e101468
Bonomi, M., Bussi, G., Camilloni, C., Tribello, G. A., Banáš, P., Barducci, A., Bernetti, M., Bolhuis, P. G., Bottaro, S., Branduardi, D., Capelli, R., Carloni, P., Ceriotti, M., Cesari, A., Chen, H., Chen, W., Colizzi, F., De, S., De La Pierre, M., Donadio, D., Drobot, V., Ensing, B., Ferguson, A. L., Filizola, M., Fraser, J. S., Fu, H., Gasparotto, P., Gervasio, F. L., Giberti, F., Gil-Ley, A., Giorgino, T., Heller, G. T., Hocky, G. M., Iannuzzi, M., Invernizzi, M., Jelfs, K. E., Jussupow, A., Kirilin, E., Laio, A., Limongelli, V., Lindorff-Larsen, K., Löhr, T., Marinelli, F., Martin-Samos, L., Masetti, M., Meyer, R., Michaelides, A., Molteni, C., Morishita, T., Nava, M., Paissoni, C., Papaleo, E., Parrinello, M., Pfaendtner, J., Piaggi, P., Piccini, G.M., Pietropaolo, A., Pietrucci, F., Pipolo, S., Provasi, D., Quigley, D., Raiteri, P., Raniolo, S., Rydzewski, J., Salvalaglio, M., Sosso, G. C., Spiwok, V., Šponer, J., Swenson, D. W. H., Tiwary, P., Valsson, O., Vendruscolo, M., Voth, G. A., and White, A. (2019)
Promote Transparency and Reproducibility in Enhanced Molecular Simulations
Nat. Methods 16, 670–673
Öster, C., Hendriks, K., Kopec, W., Chevelkov, V., Shi, C., Michl, D., Lange, S., Sun, H., de Groot, B. L., and Lange, A. (2019)
The conduction pathway of potassium channels is water free under physiological conditions
Sci. Adv. 5, eaaw6756
Otte, M., Schweinitz, A., Lelle, M., Thon, S., Enke, U., Yüksel, S., Schmauder, R., Bonus, M., Gohlke, H., and Benndorf, K. (2019) Novel fluorescent cyclic nucleotide derivatives to study CNG and HCN channel function
Biophys. J. 116, 2411-2422
Preising, M. N., Görg, B., Friedburg, C., Qvartskhava, N., Budde, B. S., Bonus, M., Toliat, M. R., Pfleger, C., Altmüller, J., Herebian, D., Beyer, M., Zöllner, H. J., Wittsack, H. J., Schaper, J., Klee, D., Zechner, U., Nürnberg, P., Schipper, J., Schnitzler, A., Gohlke, H., Lorenz, B., Häussinger, D., and Bolz, H. J. (2019)
FASEB J. 25, fj201900914RR
Schott-Verdugo, S., and Gohlke, H. (2019)
J. Chem. Inf. Model. 59, 2522-2528
Paul, F., Wu, H., Vossel, M., de Groot, B. L., and Noé, F. (2019)
J. Chem. Phys. 150, 164120
Bolnykh, V., Olsen, J.M.H., Meloni, S., Bircher, M. P., Ippoliti, E., Carloni, P., and Rothlisberger, U. (2019)
J. Chem. Theory Comput. 15, 5601-5613
Capelli, R., Carloni, P., and Parrinello, M. (2019)
J. Phys. Chem. Letters 10, 3495-3499
Olsen, J.M.H., Bolnykh V., Meloni, S., Ippoliti, E., Bircher, M. P., Carloni, P., and Rothlisberger, U. (2019)
MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry
J. Chem. Theory Comput. 15, 3810-3823
Schewe, M., Sun, H., Mert, Ü., Mackenzie, A., Pike, A. C. W., Schulz, F., Constantin, C., Vowinkel, K. S., Conrad, L. J., Kiper, A. K., Gonzalez, W., Musinszki, M., Tegtmeier, M., Pryde, D. C., Belabed, H., Nazare, M., de Groot, B. L., Decher, N., Fakler, B., Carpenter, E. P., Tucker, S. J., and Baukrowitz, T. (2019)
Science 363, 875-880
2018
Körner, J., Meents, J., Machtens, J.-P., and Lampert, A. (2018)
J. Physiol. 596, 2433-2445
Otte, M., Schweinitz, A., Bonus, M., Enke, U., Schumann, C., Gohlke, H., and Benndorf, K. (2018)
Hydrophobic alkyl chains substituted to the 8-position of cyclic nucleotides enhance activation of CNG and HCN channels by an intricate enthalpy - entropy compensation
Sci. Rep. 8, 14960
Sunkara, M. R., Schwabe, T., Ehrlich, G., Kusch, J., and Benndorf, K. (2018)
J. Gen. Physiol. 150, 1261
Kopec, W., Köpfer, D.A., Vickery, O.N., Bondarenko, A.S., Jansen, T.L.C., de Groot, B.L. and Zachariae, U. (2018)
Nat. Chem. 10, 813
Heinz, L.P., Kopec, W., de Groot, B.L., and Fink, R.A.H. (2018)
Sci. Rep. 8, 6886
Hummert, S., Thon, S., Eick, T., Schmauder, R., Schulz, E., and Benndorf, K. (2018)
PLOS Comput. Biol. 14, e1006045
Shi, C., He, Y., Hendriks, K., de Groot, B.L., Cai, X., Tian, C., Lange, A., and Sun, H. (2018)
Nat. Commun. 9,717
Mardt, A., Pasquali, L., Wu, H., and Noé, F. (2018)
Nat. Commun. 9, 5
2017
Pfleger, C., Minges, A., Boehm, M., McClendon, C. L., Torella, R., and Gohlke, H. (2017)
J. Chem. Theory Comput. 13, 6343
Riva, I., Eibl, C., Volkmer, R., Carbone, A. L., and Plested, A. J. R. (2017)
eLIFE 6, e28680
Zhang, W., Eibl, C., Weeks, A. M., Riva, I., li, Y., Plested, A. J. R. Plested, and Howe, J. R. (2017)
Biophysical. J. 113, 1