Publications of the Department (MPG.PuRe list)

Jelen, S.; Wacker, S.; Aponte-Santamaria, C. A.; Skott, M.; Rojek, A.; Johanson, U.; Kjellbom, P.; Nielsen, S.; de Groot, B. L.; Ruetzler, M.: Aquaporin-9 protein is the primary route of hepatocyte glycerol uptake for glycerol gluconeogenesis in mice. Journal of Biological Chemistry 286 (52), pp. 44319 - 44325 (2011)

Godec, A.; Smith, J. C.; Merzel, F.: Increase of both order and disorder in the first hydration shell with increasing solute polarity. Physical Review Letters 107 (26), 267801 (2011)

Ban, D.; Funk, M.; Gulich, R.; Egger, D.; Sabo, T. M.; Walter, K. F. A.; Fenwick, R. B.; Giller, K.; Pichierri, F.; de Groot, B. L. et al.; Lange, O. F.; Grubmüller, H.; Salvatella, X.; Wolf, M.; Loidl, A.; Kree, R.; Becker, S.; Lakomek, N. A.; Lee, D.; Lunkenheimer, P.; Griesinger, C.: Kinetics of conformational sampling in ubiquitin. Angewandte Chemie-International Edition 50 (48), pp. 11437 - 11440 (2011)

Lopez, M.; Vu, H.; Wang, C. K.; Wolf, M. G.; Groenhof, G.; Innocenti, A.; Supuran, C. T.; Poulsen, S. A.: Promiscuity of carbonic anhydrase II. Unexpected ester hydrolysis of carbohydrate-based sulfamate inhibitors. Journal of the American Chemical Society 133 (45), pp. 18452 - 18462 (2011)

Ukmar, T.; Maver, U.; Planinsek, O.; Kaucic, V.; Gaberscek, M.; Godec, A.: Understanding controlled drug release from mesoporous silicates: Theory and experiment. Journal of Controlled Release 155 (3), pp. 409 - 417 (2011)

Seeliger, D.; Buelens, F. P.; Götte, M.; de Groot, B. L.; Grubmüller, H.: Towards computional specificity screening of DNA-binding proteins. Nucleic Acids Research 39 (19), pp. 8281 - 8290 (2011)

Kutzner, C.; Grubmüller, H.; de Groot, B. L.; Zachariae, U.: Computational Electrophysiology: The molecular dynamics of ion channel Permeation and selectivity in atomistic detail. Biophysical Journal 101 (4), pp. 809 - 817 (2011)

de Jong, D. H.; Schaefer, L. V.; de Vries, A. H.; Marrink, S. J.; Berendsen, H. J. C.; Grubmüller, H.: Determining equilibrium constants for dimerization reactions from molecular dynamics simulations. Journal of Computational Chemistry 32 (9), pp. 1919 - 1928 (2011)

Boukharta, L.; Keranen, H.; Stary-Weinzinger, A.; Wallin, G.; de Groot, B. L.; Aqvist, J.: Computer simulations of structure-activity relationships for hERG channel blockers. Biochemistry 50 (27), pp. 6146 - 6156 (2011)

Hub, J. S.; de Groot, B. L.: Comment on “Molecular selectivity in aquaporin channels studied by the 3D-RISM theory”. The Journal of Physical Chemistry B 115 (25), pp. 8364 - 8366 (2011)

Boggio-Pasqua, M.; Groenhof, G.: Controlling the photoreactivity of the photoactive yellow protein chromophore by substituting at the p-coumaric acid group. The Journal of Physical Chemistry B 115 (21), pp. 7021 - 7028 (2011)

Donnini, S.; Tegeler, F.; Groenhof, G.; Grubmüller, H.: Constant pH molecular dynamics in explicit solvent with lambda-dynamics. Journal of Chemical Theory and Computation 7 (6), pp. 1962 - 1978 (2011)

van den Bogaart, G.; Thutupalli, S.; Risselada, H. J.; Meyenberg, K.; Holt, M.; Riedel, D.; Diederichsen, U.; Herminghaus, S.; Grubmüller, H.; Jahn, R.: Synaptotagmin-1 may be a distance regulator acting upstream of SNARE nucleation. Nature Structural and Molecular Biology 18 (7), pp. 805 - 812 (2011)

Höfling, M.; Lima, N.; Haenni, D.; Seidel, C. A. M.; Schuler, B.; Grubmüller, H.: Structural heterogeneity and quantitative FRET efficiency distributions of polyprolines through a hybrid atomistic simulation and Monte Carlo approach. PLoS One 6 (5), e19791 (2011)

Czub, J.; Grubmüller, H.: Torsional elasticity and energetics of F-1-ATPase. Proceedings of the National Academy of Sciences of the United States of America 108 (18), pp. 7408 - 7413 (2011)

Matthes, D.; Gapsys, V.; Daebel, V.; de Groot, B. L.: Mapping the conformational dynamics and pathways of spontaneous steric zipper peptide oligomerization. Plos One 6 (5), e19129 (2011)

Kutzner, C.; Czub, J.; Grubmüller, H.: Keep it flexible: Driving macromolecular rotary motions in atomistic simulations with GROMACS. Journal of Chemical Theory and Computation 7 (5), pp. 1381 - 1393 (2011)

Risselada, H. J.; Kutzner, C.; Grubmüller, H.: Caught in the act: Visualization of SNARE-mediated fusion events in molecular detail. Chembiochem 12 (7), pp. 1049 - 1055 (2011)

Risselada, H. J.; Marrink, S. J.; Mueller, M.: Curvature-dependent elastic properties of liquid-ordered domains result in inverted domain sorting on uniaxially compressed vesicles. Pysical Review Letters 106 (14), 148102 (2011)

de Groot, B. L.; Hub, J. S.: A decade of debate: Significance of CO2 permeation through membrane channels still controversial. Chemphyschem 12 (5), pp. 1021 - 1022 (2011)

Kappel, C.; Grubmüller, H.: Velocity-dependent mechanical unfolding of bacteriorhodopsin is governed by a dynamic interaction network. Biophysical Journal 100 (4), pp. 1109 - 1119 (2011)

Godec, A.; Ukmar, T.; Gaberscek, M.; Merzel, F.: Inversion of pore size dependence of solute transport kinetics from increasingly attractive ordered porous matrix. Europhysics Letters 92 (6), 60011 (2011)

Ukmar, T.; Gaberscek, M.; Merzel, F.; Godec, A.: Modus operandi of controlled release from mesoporous matrices: A theoretical perspective. Physical Chemistry Chemical Physics 13 (3), pp. 15311 - 15317 (2011)

Ukmar, T.; Godec, A.; Planinsek, O.; Kaucic, V.; Mali, G.; Gaberscek, M.: The phase (trans)formation and physical state of a model drug in mesoscopic confinement. Physical Chemistry Chemical Physics 13 (35), pp. 16046 - 16054 (2011)

van den Bogaart, G.; Meyenberg, K.; Risselada, H. J.; Amin, H.; Willig, K.; Hubrich, B. E.; Dier, M.; Hell, S. W.; Grubmüller, H.; Diederichsen, U. et al.; Jahn, R.: Membrane protein sequestering by ionic protein–lipid interactions. Nature 479 (7374), doi:10.1038/nature10545, pp. 552 - 555 (2011)