Publikationen

52.

Zeitschriftenartikel

Yee, A. W.; Aldeghi, M.; Blakeley, M. P.; Ostermann, A.; Mas, P. J.; Moulin, M.; de Sanctis, D.; Bowler, M. W.; Mueller-Dieckmann, C.; Mitchell, E. P. et al.; Haertlein, M.; de Groot, B. L.; Boeri Erba, E.; Forsyth, V. T.: A molecular mechanism for transthyretin amyloidogenesis. Nature Communications 10 (1), 925 (2019)

MPG.PuRe

53.

Zeitschriftenartikel

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. et al.; 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.; Baukrowitz, T.: A pharmacological master key mechanism that unlocks the selectivity filter gate in K⁺ channels. Science 363 (6429), S. 875 - 880 (2019)

MPG.PuRe

54.

Zeitschriftenartikel

Awasthi, N.; Kopec, W.; Wilkosz, N.; Jamroz, D.; Hub, J. S.; Zatorska, M.; Petka, R.; Nowakowska, M.; Kepczynski, M.: Molecular mechanism of polycation-induced pore formation in biomembranes. ACS Biomaterials Science and Engineering 5 (2), S. 780 - 794 (2019)

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ZIP

55.

Zeitschriftenartikel

Cordeiro, S.; Finol-Urdaneta, R. K.; Köpfer, D.; Markushina, A.; Song, J.; French, R. J.; Kopec, W.; de Groot, B. L.; Giacobassi, M. J.; Leavitt, L. S. et al.; Raghuraman, S.; Teichert, R. W.; Olivera, B. M.; Terlau, H.: Conotoxin κM-RIIIJ, a tool targeting asymmetric heteromeric K_v1 channels. Proceedings of the National Academy of Sciences of the United States of America 116 (3), S. 1059 - 1064 (2019)

MPG.PuRe

56.

Zeitschriftenartikel

Briones, R.; Blau, C.; Kutzner, C.; de Groot, B. L.; Aponte-Santamaría, C.: GROmaρs: A GROMACS-based toolset to analyze density maps derived from molecular dynamics simulations. Biophysical Journal 116 (1), S. 4 - 11 (2019)

MPG.PuRe

57.

Zeitschriftenartikel

Lutz, H.; Jaeger, V.; Weidner, T.; de Groot, B. L.: Interpretation of interfacial protein spectra with enhanced molecular simulation ensembles. Journal of Chemical Theory and Computation 15 (1), S. 698 - 707 (2019)

MPG.PuRe

58.

Zeitschriftenartikel

Gu, R. X.; Baoukina, S.; Tieleman, D. P.: Cholesterol flip-flop in heterogeneous membranes. Journal of Chemical Theory and Computation 15 (3), S. 2064 - 2070 (2019)

MPG.PuRe

59.

Zeitschriftenartikel

Paul, F.; Wu, H.; Vossel, M.; de Groot, B. L.; Noé, F.: Identification of kinetic order parameters for non-equilibrium dynamics. The Journal of Chemical Physics 150 (16), 164120 (2019)

MPG.PuRe

60.

Zeitschriftenartikel

Rovo, P.; Smith, C. A.; Gauto, D.; de Groot, B. L.; Schanda, P.; Linser, R.: Mechanistic insights into microsecond time-scale motion of solid proteins using complementary ¹⁵N and ¹H relaxation dispersion techniques. Journal of the American Chemical Society 141 (2), S. 858 - 869 (2019)

MPG.PuRe

61.

Zeitschriftenartikel

Aldeghi, M.; Gapsys, V.; de Groot, B. L.: Accurate estimation of ligand binding affinity changes upon protein mutation. ACS Central Science 4 (12), S. 1708 - 1718 (2018)

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ZIP

62.

Zeitschriftenartikel

Brennecke, J. T.; de Groot, B. L.: Quantifying asymmetry of multimeric proteins. The Journal of Physical Chemistry A 122 (39), S. 7924 - 7930 (2018)

MPG.PuRe

63.

Zeitschriftenartikel

Kopec, W.; Köpfer, D.; Vickery, O. N.; Bondarenko, A. S.; Jansen, T. L. C.; de Groot, B. L.; Zachariae, U.: Direct knock-on of desolvated ions governs strict ion selectivity in K⁺ channels. Nature Chemistry 10 (8), S. 813 - 820 (2018)

MPG.PuRe

64.

Zeitschriftenartikel

Bastys, T.; Gapsys, V.; Doncheva, N. T.; Kaiser, R.; de Groot, B. L.; Kalinina, O. V.: Consistent prediction of mutation effect on drug binding in HIV-1 protease using alchemical calculations. Journal of Chemical Theory and Computation 14 (7), S. 3397 - 3408 (2018)

MPG.PuRe

65.

Zeitschriftenartikel

Heinz, L. P.; Kopec, W.; de Groot, B. L.; Fink, R. H. A.: In silico assessment of the conduction mechanism of the ryanodine receptor 1 reveals previously unknown exit pathways. Scientific Reports 8, 6886 (2018)

MPG.PuRe

66.

Zeitschriftenartikel

Sabo, T. M.; Gapsys, V.; Walter, K. F. A.; Fenwick, R. B.; Becker, S.; Salvatella, X.; de Groot, B. L.; Lee, D.; Griesinger, C.: Utilizing dipole-dipole cross-correlated relaxation for the measurement of angles between pairs of opposing CαHα-CαHα bonds in anti-parallel β-sheets. Methods 138-139, S. 85 - 92 (2018)

MPG.PuRe

67.

Zeitschriftenartikel

Brennecke, J. T.; de Groot, B. L.: Mechanism of mechanosensitive gating of the TREK-2 potassium channel. Biophysical Journal 114 (6), S. 1336 - 1343 (2018)

MPG.PuRe

68.

Zeitschriftenartikel

Shi, C.; He, Y.; Hendriks, K.; de Groot, B. L.; 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 (2018)

MPG.PuRe

69.

Zeitschriftenartikel

Matthes, D.; Gapsys, V.; Griesinger, C.; de Groot, B. L.: Resolving the atomistic modes of anle138b inhibitory action on peptide oligomer formation. ACS Chemical Neuroscience 8 (12), S. 2791 - 2808 (2017)

MPG.PuRe

70.

Zeitschriftenartikel

Gapsys, V.; de Groot, B. L.: Alchemical free energy calculations for nucleotide mutations in protein-DNA complexes. Journal of Chemical Theory and Computation 13 (12), S. 6275 - 6289 (2017)

MPG.PuRe

71.

Zeitschriftenartikel

Ban, D.; Smith, C. A.; de Groot, B. L.; Griesinger, C.; Lee, D.: Recent advances in measuring the kinetics of biomolecules by NMR relaxation dispersion spectroscopy. Archives of Biochemistry and Biophysics 628, S. 81 - 91 (2017)

MPG.PuRe

72.

Zeitschriftenartikel

Aponte-Santamaria, C.; Fischer, G.; Bath, P.; Neutze, R.; de Groot, B. L.: Temperature dependence of protein-water interactions in a gated yeast aquaporin. Scientific Reports 7, 4016 (2017)

MPG.PuRe

73.

Zeitschriftenartikel

Machtens, J. P.; Briones, R.; Alleva, C.; de Groot, B. L.; Fahlke, C.: Gating charge calculations by computational electrophysiology simulations. Biophysical Journal 112 (7), S. 1396 - 1405 (2017)

MPG.PuRe

74.

Zeitschriftenartikel

Saboe, P. O.; Rapisarda, C.; Kaptan, S.; Hsiao, Y. S.; Summers, .. R.; De Zorzi, R.; Dukovski, D.; Yu, J.; de Groot, B. L.; Kumar, M. et al.; Walz, T.: Role of pore-lining residues in defining the rate of water conduction by Aquaporin-0. Biophysical Journal 112 (5), S. 953 - 965 (2017)

MPG.PuRe

75.

Zeitschriftenartikel

Briones, R.; Aponte-Santamaria, C.; de Groot, B. L.: Localization and ordering of lipids around Aquaporin-0: Proteinand lipid mobility effects. Frontiers in Physiology 8, 124 (2017)

MPG.PuRe

76.

Zeitschriftenartikel

Gapsys, V.; de Groot, B. L.: pmx Webserver: A user friendly interface for alchemistry. Journal of Chemical Information and Modeling 57 (2), S. 109 - 114 (2017)

MPG.PuRe

77.

Zeitschriftenartikel

Huang, J.; Rauscher, S.; Nawrocki, G.; Ran, T.; Feig, M.; de Groot, B. L.; Grubmüller, H.; MacKerell, A. D.: CHARMM36m: An improved force field for folded and intrinsically disordered proteins. Nature Methods 14 (1), S. 71 - 73 (2017)

MPG.PuRe

78.

Zeitschriftenartikel

Briones, R.; Weichbrodt, C.; Paltrinieri, L.; Mey, I.; Villinger, S.; Giller, K.; Lange, A.; Zweckstetter, M.; Griesinger, C.; Becker, S. et al.; Steinem, C.; de Groot, B. L.: Voltage dependence of conformational dynamics and subconducting states of VDAC-1. Biophysical Journal 111 (6), S. 1223 - 1234 (2016)

MPG.PuRe

79.

Zeitschriftenartikel

Ilgü, H.; Jeckelmann, J. M.; Gapsys, V.; Ucurum, Z.; de Groot, B. L.; Fotiadis, D.: Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC. Proceedings of the National Academy of Sciences of the United States of America 113 (37), S. 10358 - 10363 (2016)

MPG.PuRe

80.

Zeitschriftenartikel

Matthes, D.; Gapsys, V.; Brennecke, J. T.; de Groot, B. L.: An atomistic view of amyloidogenic self-assembly: Structure and dynamics of heterogeneous conformational states in the pre-nucleation phase. Scientific Reports 6, 33156 (2016)

MPG.PuRe

81.

Zeitschriftenartikel

Assentoft, M.; Kaptan, S.; Schneider, H. P.; Deitmer, J. W.; de Groot, B. L.; MacAulay, N.: Aquaporin 4 as a NH3 channel. Journal of Biological Chemistry 291 (36), S. 19184 - 19195 (2016)

MPG.PuRe

82.

Zeitschriftenartikel

Kutzner, C.; Köpfer, D.; Machtens, J. P.; de Groot, B. L.; Song, C.; Zachariae, U.: Insights into the function of ion channels by computational electrophysiology simulations. Biochimica et Biophysica Acta - Biomembranes 1858 (7, B), S. 1741 - 1752 (2016)

MPG.PuRe

83.

Zeitschriftenartikel

Gapsys, V.; Michielssens, S.; Seeliger, D.; de Groot, B. L.: Accurate and rigorous prediction of the changes in protein free energies in a large-scale mutation scan. Angewandte Chemie-International Edition 55 (26), S. 7364 - 7368 (2016)

MPG.PuRe

84.

Zeitschriftenartikel

Singer, M.; Krivobokova, T.; Munk, A.; De Groot, B. L.: Partial least squares for dependent data. Biometrika 103 (2), S. 351 - 362 (2016)

MPG.PuRe

85.

Zeitschriftenartikel

Kirscht, A.; Kaptan, S. S.; Bienert, G. P.; Chaumont, F.; Nissen, P.; de Groot, B. L.; Kjellbom, P.; Gourdon, P.; Johanson, U.: Crystal structure of an ammonia-permeable aquaporin. PLOS Biology 14 (3), e1002411 (2016)

MPG.PuRe

86.

Zeitschriftenartikel

Smith, C. A.; Ban, D.; Pratihar, S.; Giller, K.; Paulat, M.; Becker, S.; Griesinger, C.; Lee, D.; de Groot, B. L.: Allosteric switch regulates protein–protein binding through collective motion. Proceedings of the National Academy of Sciences of the United States of America 113 (12), S. 3269 - 3274 (2016)

MPG.PuRe

87.

Zeitschriftenartikel

Schewe, M.; Nematian-Ardestani, E.; Sun, H.; Musinszki, M.; Cordeiro, S.; Bucci, G.; de Groot, B. L.; Tucker, S. J.; Rapedius, M.; Baukrowitz, T.: A non-canonical voltage sensor controls gating in K2P K2 channels. Cell 164 (5), S. 937 - 949 (2016)

MPG.PuRe

88.

Zeitschriftenartikel

Kaptan, S.; Assentoft, M.; Schneider, H. P.; Fenton, R. A.; Deitmer, J. W.; MacAulay, N.; de Groot, B. L.: H95 is a pH-dependent gate in Aquaporin 4. Structure 23 (12), S. 2309 - 2318 (2015)

MPG.PuRe

89.

Zeitschriftenartikel

Rose, A. S.; Zachariae, U.; Grubmüller, H.; Hofmann, K. P.; Scheerer, P.; Hildebrand, W.: Role of structural dynamics at the receptor G protein interface for signal transduction. PLOS One 10 (11), e0143399 (2015)

MPG.PuRe

90.

Zeitschriftenartikel

Rauscher, S.; Gapsys, V.; Gajda, M. J.; Zweckstetter, M.; de Groot, B. L.; Grubmüller, H.: Structural ensembles of intrinsically disordered proteins depend strongly on force field: A comparison to experiment. Journal of Chemical Theory and Computation 11 (11), S. 5513 - 5524 (2015)

MPG.PuRe

91.

Zeitschriftenartikel

Gapsys, V.; Narayanan, R. L.; Xiang, S.; de Groot, B. L.; Zweckstetter, M.: Improved validation of IDP ensembles by one-bond Cα-Hα scalar couplings. Journal of Biomolecular NMR 63 (3), S. 299 - 307 (2015)

MPG.PuRe

92.

Zeitschriftenartikel

Kutzner, C.; Páll, S.; Fechner, M.; Esztermann, A.; de Groot, B.; Grubmüller, H.: Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. Journal of Computational Chemistry 36 (26), S. 1990 - 2008 (2015)

MPG.PuRe

93.

Zeitschriftenartikel

Linser, R.; Salvi, N.; Briones, R.; Rovo, P.; de Groot, B. L.; Wagner, G.: The membrane anchor of the transcriptional activator SREBP is characterized by intrinsic conformational flexibility. Proceedings of the National Academy of Sciences of the United States of America 112 (40), S. 12390 - 12395 (2015)

MPG.PuRe

94.

Zeitschriftenartikel

Kutzner, C.; Páll, S.; Fechner, M.; Esztermann, A.; De Groot, B.; Grubmueller, H.: Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. arXiv, 1507.00898v1 (2015)

MPG.PuRe

pre-print

95.

Zeitschriftenartikel

Andrini, O.; Keck, M.; Briones, R.; Lourdel, S.; Vargas-Poussou, R.; Teulon, J.: ClC-K chloride channels: Emerging pathophysiology of Bartter syndrome type 3. American Journal of Physiology-Renal Physiology 308 (12), S. F1324 - F1334 (2015)

MPG.PuRe

96.

Zeitschriftenartikel

Michielssens, S.; de Groot, B. L.; Grubmüller, H.: Binding affinities controlled by shifting conformational equilibria: Opportunities and limitations. Biophysical Journal 108 (10), S. 2585 - 2590 (2015)

MPG.PuRe

97.

Zeitschriftenartikel

Gapsys, V.; Michielssens, S.; Seeliger, D.; de Groot, B. L.: Pmx: Automated protein structure and topology generation for alchemical perturbations. Journal of Computational Chemistry 36 (5), S. 348 - 354 (2015)

MPG.PuRe

98.

Zeitschriftenartikel

Machtens, J. P.; Kortzak, D.; Lansche, C.; Leinenweber, A.; Kilian, P.; Begemann, B.; Zachariae, U.; Ewers, D.; de Groot, B. L.; Briones, R. et al.; Fahlke, C.: Mechanisms of anion conduction by coupled glutamate transporters. Cell 160 (3), S. 542 - 553 (2015)

MPG.PuRe

99.

Zeitschriftenartikel

Smith, C. A.; Ban, D.; Pratihar, S.; Giller, K.; Schwiegk, C.; de Groot, B. L.; Becker, S.; Griesinger, C.; Lee, D.: Population shuffling of protein conformations. Angewandte Chemie International Edition 54 (1), S. 207 - 210 (2015)

MPG.PuRe

100.

Zeitschriftenartikel

Köpfer, D.; Song, C.; Gruene, T.; Sheldrick, G. M.; Zachariae, U.; de Groot, B. L.: Ion permeation in K+ channels occurs by direct Coulomb knock-on. Science 345 (6207), S. 352 - 355 (2014)

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