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Bert L. de Groot - Publications

Affiliations: 
Computational Biomolecular Dynamics group Max Planck Institute for Biophysical Chemistry, Göttingen, Niedersachsen, Germany 
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49 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Kopec W, Thomson AS, de Groot BL, Rothberg BS. Interactions between selectivity filter and pore helix control filter gating in the MthK channel. The Journal of General Physiology. 155. PMID 37318452 DOI: 10.1085/jgp.202213166  0.367
2023 Gu RX, de Groot BL. Central cavity dehydration as a gating mechanism of potassium channels. Nature Communications. 14: 2178. PMID 37069187 DOI: 10.1038/s41467-023-37531-8  0.491
2023 Lam CK, de Groot BL. Ion Conduction Mechanisms in Potassium Channels Revealed by Permeation Cycles. Journal of Chemical Theory and Computation. PMID 37040262 DOI: 10.1021/acs.jctc.3c00061  0.515
2022 Öster C, Tekwani Movellan K, Goold B, Hendriks K, Lange S, Becker S, de Groot BL, Kopec W, Andreas LB, Lange A. Direct Detection of Bound Ammonium Ions in the Selectivity Filter of Ion Channels by Solid-State NMR. Journal of the American Chemical Society. 144: 4147-4157. PMID 35200002 DOI: 10.1021/jacs.1c13247  0.377
2021 Roy RN, Hendriks K, Kopec W, Abdolvand S, Weiss KL, de Groot BL, Lange A, Sun H, Coates L. Structural plasticity of the selectivity filter in a nonselective ion channel. Iucrj. 8: 421-430. PMID 33953928 DOI: 10.1107/S205225252100213X  0.446
2021 Mironenko A, Zachariae U, de Groot BL, Kopec W. The Persistent Question of Potassium Channel Permeation Mechanisms. Journal of Molecular Biology. 433: 167002. PMID 33891905 DOI: 10.1016/j.jmb.2021.167002  0.455
2021 Najbauer EE, Becker S, Giller K, Zweckstetter M, Lange A, Steinem C, de Groot BL, Griesinger C, Andreas LB. Structure, gating and interactions of the voltage-dependent anion channel. European Biophysics Journal : Ebj. PMID 33782728 DOI: 10.1007/s00249-021-01515-7  0.415
2021 Zhang Y, Daday C, Gu RX, Cox CD, Martinac B, de Groot BL, Walz T. Visualization of the mechanosensitive ion channel MscS under membrane tension. Nature. PMID 33568813 DOI: 10.1038/s41586-021-03196-w  0.415
2021 Daday C, de Groot BL. Lipid-protein forces predict conformational changes in a mechanosensitive channel. European Biophysics Journal : Ebj. 50: 181-186. PMID 33355710 DOI: 10.1007/s00249-020-01488-z  0.304
2020 Langan PS, Vandavasi VG, Kopec W, Sullivan B, Afonne PV, Weiss KL, de Groot BL, Coates L. The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation. Iucrj. 7: 835-843. PMID 32939275 DOI: 10.1107/S2052252520008271  0.436
2020 Schubeis T, Le Marchand T, Daday C, Kopec W, Tekwani Movellan K, Stanek J, Schwarzer TS, Castiglione K, de Groot BL, Pintacuda G, Andreas LB. A β-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkL. Proceedings of the National Academy of Sciences of the United States of America. 117: 21014-21021. PMID 32817429 DOI: 10.1073/pnas.2002598117  0.301
2020 Gu RX, de Groot BL. Lipid-protein interactions modulate the conformational equilibrium of a potassium channel. Nature Communications. 11: 2162. PMID 32358584 DOI: 10.1038/s41467-020-15741-8  0.518
2019 de Maré SW, Venskutonytė R, Eltschkner S, de Groot BL, Lindkvist-Petersson K. Structural Basis for Glycerol Efflux and Selectivity of Human Aquaporin 7. Structure (London, England : 1993). 28: 215-222.e3. PMID 31831212 DOI: 10.1016/j.str.2019.11.011  0.386
2019 Kopec W, Rothberg BS, de Groot BL. Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling. Nature Communications. 10: 5366. PMID 31772184 DOI: 10.1038/S41467-019-13227-W  0.414
2019 Öster C, Hendriks K, Kopec W, Chevelkov V, Shi C, Michl D, Lange S, Sun H, de Groot BL, Lange A. The conduction pathway of potassium channels is water free under physiological conditions. Science Advances. 5: eaaw6756. PMID 31392272 DOI: 10.1126/sciadv.aaw6756  0.412
2019 Paul F, Wu H, Vossel M, de Groot BL, Noé F. Identification of kinetic order parameters for non-equilibrium dynamics. The Journal of Chemical Physics. 150: 164120. PMID 31042914 DOI: 10.1063/1.5083627  0.312
2019 Song C, de Groot BL, Sansom MSP. Lipid Bilayer Composition Influences the Activity of the Antimicrobial Peptide Dermcidin Channel. Biophysical Journal. PMID 31010668 DOI: 10.1016/J.Bpj.2019.03.033  0.407
2019 Schewe M, Sun H, Mert Ü, Mackenzie A, Pike ACW, Schulz F, Constantin C, Vowinkel KS, Conrad LJ, Kiper AK, Gonzalez W, Musinszki M, Tegtmeier M, Pryde DC, Belabed H, ... ... de Groot BL, et al. A pharmacological master key mechanism that unlocks the selectivity filter gate in K channels. Science (New York, N.Y.). 363: 875-880. PMID 30792303 DOI: 10.1126/Science.Aav0569  0.376
2019 Brennecke JT, de Groot BL. Mechanism of Mechanosensitive Gating of the TREK-2 Potassium Channel. Biophysical Journal. 114: 1336-1343. PMID 29590591 DOI: 10.1016/j.bpj.2018.01.030  0.46
2018 Cordeiro S, Finol-Urdaneta RK, Köpfer D, Markushina A, Song J, French RJ, Kopec W, de Groot BL, Giacobassi MJ, Leavitt LS, Raghuraman S, Teichert RW, Olivera BM, Terlau H. Conotoxin κM-RIIIJ, a tool targeting asymmetric heteromeric K1 channels. Proceedings of the National Academy of Sciences of the United States of America. PMID 30593566 DOI: 10.1073/Pnas.1813161116  0.326
2018 Kopec W, Köpfer DA, Vickery ON, Bondarenko AS, Jansen TLC, de Groot BL, Zachariae U. Direct knock-on of desolvated ions governs strict ion selectivity in K channels. Nature Chemistry. 10: 813-820. PMID 30030538 DOI: 10.1038/S41557-018-0105-9  0.386
2018 Heinz LP, Kopec W, de Groot BL, Fink RHA. In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathways. Scientific Reports. 8: 6886. PMID 29720700 DOI: 10.1038/s41598-018-25061-z  0.439
2018 Shi C, He Y, Hendriks K, de Groot BL, Cai X, Tian C, Lange A, Sun H. A single NaK channel conformation is not enough for non-selective ion conduction. Nature Communications. 9: 717. PMID 29459730 DOI: 10.1038/s41467-018-03179-y  0.479
2017 Aponte-Santamaría C, Fischer G, Båth P, Neutze R, de Groot BL. Temperature dependence of protein-water interactions in a gated yeast aquaporin. Scientific Reports. 7: 4016. PMID 28638135 DOI: 10.1038/s41598-017-04180-z  0.301
2017 Machtens JP, Briones R, Alleva C, de Groot BL, Fahlke C. Gating Charge Calculations by Computational Electrophysiology Simulations. Biophysical Journal. 112: 1396-1405. PMID 28402882 DOI: 10.1016/J.Bpj.2017.02.016  0.592
2016 Briones R, Weichbrodt C, Paltrinieri L, Mey I, Villinger S, Giller K, Lange A, Zweckstetter M, Griesinger C, Becker S, Steinem C, de Groot BL. Voltage Dependence of Conformational Dynamics and Subconducting States of VDAC-1. Biophysical Journal. 111: 1223-34. PMID 27653481 DOI: 10.1016/J.Bpj.2016.08.007  0.473
2016 Assentoft M, Kaptan S, Schneider HP, Deitmer JW, de Groot BL, MacAulay N. Aquaporin 4 as a NH3 Channel. The Journal of Biological Chemistry. PMID 27435677 DOI: 10.1074/jbc.M116.740217  0.349
2016 Kirscht A, Kaptan SS, Bienert GP, Chaumont F, Nissen P, de Groot BL, Kjellbom P, Gourdon P, Johanson U. Crystal Structure of an Ammonia-Permeable Aquaporin. Plos Biology. 14: e1002411. PMID 27028365 DOI: 10.1371/Journal.Pbio.1002411  0.312
2016 Schewe M, Nematian-Ardestani E, Sun H, Musinszki M, Cordeiro S, Bucci G, de Groot BL, Tucker SJ, Rapedius M, Baukrowitz T. A Non-canonical Voltage-Sensing Mechanism Controls Gating in K2P K(+) Channels. Cell. 164: 937-49. PMID 26919430 DOI: 10.1016/J.Cell.2016.02.002  0.449
2016 Kutzner C, Köpfer DA, Machtens JP, de Groot BL, Song C, Zachariae U. Insights into the function of ion channels by computational electrophysiology simulations. Biochimica Et Biophysica Acta. PMID 26874204 DOI: 10.1016/j.bbamem.2016.02.006  0.621
2015 Machtens JP, Kortzak D, Lansche C, Leinenweber A, Kilian P, Begemann B, Zachariae U, Ewers D, de Groot BL, Briones R, Fahlke C. Mechanisms of anion conduction by coupled glutamate transporters. Cell. 160: 542-53. PMID 25635461 DOI: 10.1016/J.Cell.2014.12.035  0.584
2014 Köpfer DA, Song C, Gruene T, Sheldrick GM, Zachariae U, de Groot BL. Ion permeation in K⁺ channels occurs by direct Coulomb knock-on. Science (New York, N.Y.). 346: 352-5. PMID 25324389 DOI: 10.1126/Science.1254840  0.466
2013 Gapsys V, de Groot BL, Briones R. Computational analysis of local membrane properties. Journal of Computer-Aided Molecular Design. 27: 845-58. PMID 24150904 DOI: 10.1007/s10822-013-9684-0  0.367
2013 Linder T, de Groot BL, Stary-Weinzinger A. Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA Plos Computational Biology. 9. PMID 23658510 DOI: 10.1371/journal.pcbi.1003058  0.408
2013 Song C, Weichbrodt C, Salnikov ES, Dynowski M, Forsberg BO, Bechinger B, Steinem C, de Groot BL, Zachariae U, Zeth K. Crystal structure and functional mechanism of a human antimicrobial membrane channel. Proceedings of the National Academy of Sciences of the United States of America. 110: 4586-91. PMID 23426625 DOI: 10.1073/pnas.1214739110  0.304
2012 Köpfer DA, Hahn U, Ohmert I, Vriend G, Pongs O, de Groot BL, Zachariae U. A molecular switch driving inactivation in the cardiac K+ channel HERG. Plos One. 7: e41023. PMID 22848423 DOI: 10.1371/Journal.Pone.0041023  0.334
2012 Zachariae U, Schneider R, Briones R, Gattin Z, Demers JP, Giller K, Maier E, Zweckstetter M, Griesinger C, Becker S, Benz R, De Groot BL, Lange A. β-Barrel mobility underlies closure of the voltage-dependent anion channel Structure. 20: 1540-1549. PMID 22841291 DOI: 10.1016/J.Str.2012.06.015  0.372
2012 Wacker SJ, Jurkowski W, Simmons KJ, Fishwick CW, Johnson AP, Madge D, Lindahl E, Rolland JF, de Groot BL. Identification of selective inhibitors of the potassium channel Kv1.1-1.2((3)) by high-throughput virtual screening and automated patch clamp. Chemmedchem. 7: 1775-83. PMID 22473914 DOI: 10.1002/Cmdc.201100600  0.357
2011 Kutzner C, Grubmüller H, de Groot BL, Zachariae U. Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail. Biophysical Journal. 101: 809-17. PMID 21843471 DOI: 10.1016/j.bpj.2011.06.010  0.528
2011 Boukharta L, Keränen H, Stary-Weinzinger A, Wallin G, de Groot BL, Aqvist J. Computer simulations of structure-activity relationships for HERG channel blockers. Biochemistry. 50: 6146-56. PMID 21657256 DOI: 10.1021/Bi200173N  0.34
2011 de Groot BL, Hub JS. A decade of debate: significance of CO2 permeation through membrane channels still controversial. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 12: 1021-2. PMID 21442707 DOI: 10.1002/cphc.201000974  0.371
2010 Villinger S, Briones R, Giller K, Zachariae U, Lange A, De Groot BL, Griesinger C, Becker S, Zweckstetter M. Functional dynamics in the voltage-dependent anion channel Proceedings of the National Academy of Sciences of the United States of America. 107: 22546-22551. PMID 21148773 DOI: 10.1073/Pnas.1012310108  0.397
2010 Hub JS, Winkler FK, Merrick M, de Groot BL. Potentials of mean force and permeabilities for carbon dioxide, ammonia, and water flux across a Rhesus protein channel and lipid membranes. Journal of the American Chemical Society. 132: 13251-63. PMID 20815391 DOI: 10.1021/ja102133x  0.405
2009 Fischer G, Kosinska-Eriksson U, Aponte-Santamaría C, Palmgren M, Geijer C, Hedfalk K, Hohmann S, de Groot BL, Neutze R, Lindkvist-Petersson K. Crystal structure of a yeast aquaporin at 1.15 angstrom reveals a novel gating mechanism. Plos Biology. 7: e1000130. PMID 19529756 DOI: 10.1371/Journal.Pbio.1000130  0.365
2009 Portella G, de Groot BL. Determinants of water permeability through nanoscopic hydrophilic channels. Biophysical Journal. 96: 925-38. PMID 19186131 DOI: 10.1016/j.bpj.2008.09.059  0.319
2008 Portella G, Hub JS, Vesper MD, de Groot BL. Not only enthalpy: large entropy contribution to ion permeation barriers in single-file channels. Biophysical Journal. 95: 2275-82. PMID 18515367 DOI: 10.1529/biophysj.108.130609  0.428
2008 Zachariae U, Schneider R, Velisetty P, Lange A, Seeliger D, Wacker SJ, Karimi-Nejad Y, Vriend G, Becker S, Pongs O, Baldus M, de Groot BL. The molecular mechanism of toxin-induced conformational changes in a potassium channel: relation to C-type inactivation. Structure (London, England : 1993). 16: 747-54. PMID 18462679 DOI: 10.1016/J.Str.2008.01.018  0.329
2008 Hub JS, de Groot BL. Mechanism of selectivity in aquaporins and aquaglyceroporins. Proceedings of the National Academy of Sciences of the United States of America. 105: 1198-203. PMID 18202181 DOI: 10.1073/pnas.0707662104  0.326
2002 Fujiyoshi Y, Mitsuoka K, de Groot BL, Philippsen A, Grubmüller H, Agre P, Engel A. Structure and function of water channels. Current Opinion in Structural Biology. 12: 509-15. PMID 12163075 DOI: 10.1016/S0959-440X(02)00355-X  0.432
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