| 75. | Jochen S. Hub and Bert L. de Groot. Detection of functional modes in protein dynamics. PLoS Comput. Biol. 5: e1000480 (2009).[pdf] |
| 74. | Dirk Matthes and Bert L. de Groot. Secondary structure propensities in peptide folding simulations: A systematic comparison of molecular mechanics interaction schemes. Biophys. J. 97:599-608 (2009).[pdf] [supplement pdf] |
| 73. | Christian M. Stegmann, Daniel Seeliger, George M. Sheldrick, Bert L. de Groot and Markus Wahl. Thermodynamic signature of trapped water molecules in a protein-ligand interaction. Angewandte Chemie. 48:5207-5210 (2009).[pdf] |
| 72. | Gerhard Fischer, Urszula Kosinska-Eriksson, Camilo Aponte-Santamaria, Madelene Palmgren, Cecilia Geijer, Kristina Hedfalk, Stefan Hohmann, Bert L. de Groot, Richard Neutze, Karin Lindkvist-Petersson. Crystal Structure of a Yeast Aquaporin at 1.15A Reveals a Novel Gating Mechanism. PLoS Biology. 7: e1000130 (2009).[pdf] |
| 71. | Marcus B. Kubitzki, Bert L. de Groot and Daniel Seeliger. Protein dynamics: from structure to function. In: From Protein Structure to Function with Bioinformatics. pp. 217-249 (2009).[pdf] |
| 70. | Jochen S. Hub, Helmut Grubmüller and Bert L. de Groot. Dynamics and Energetics of Permeation Through Aquaporins. What Do We Learn from Molecular Dynamics Simulations? In: Handbook of Experimental Pharmacology. Aquaporins. Vol. 190: 57-76 (2009).[pdf] |
| 69. | Alexander Benedix, Caroline M. Becker, Bert L. de Groot, Amedeo Caflisch, Rainer A. Böckmann. Predicting Free Energy Changes Using Structural Ensembles. Nature Methods. 6: 3-4 (2009).[pdf] |
| 68. | Harshad V. Joshi, Mark J. Jedrzejas and Bert L. de Groot. Domain motions of hyaluronan lyase underlying processive hyaluronan translocation. Proteins. 76:30-46 (2009).[pdf] |
| 67. | Guillem Portella and Bert L. de Groot. Determinants of water permeability through nanoscopic hydrophilic channels. Biophys. J. 96:925-938 (2009).[pdf].[new & notable pdf] |
| 66. | Daniel Seeliger and Bert L. de Groot. tCONCOORD-GUI: Visually Supported Conformational Sampling of Bioactive Molecules. J. Comp. Chem. 30:1160-1166 (2009).[pdf] |
| 65. | Nils-Alexander Lakomek, Oliver F. Lange, Korvin F.A. Walter, Christophe Fares, Dalia Egger, Peter Lunkenheimer, Jens Meiler, Helmut Grubmüller, Stefan Becker, Bert L. de Groot and Christian Griesinger. Residual dipolar couplings as a tool to study molecular recognition of ubiquitin. Biochemical Society Transactions 36: 1433-437 (2008).[pdf] |
| 64. | Rainer A. Böckmann, Bert L. de Groot, Sergej Kakorin, Eberhard Neumann, Helmut Grubmüller. Kinetics, Statistics, and Energetics of Lipid Membrane Electroporation Studied by Molecular Dynamics Simulations. Biophys. J. 95: 1837-1850 (2008).[pdf] |
| 63. | Guillem Portella, Jochen S. Hub, Martin D. Vesper, and Bert L. de Groot. Not only enthalpy: large entropy contribution to ion permeation barriers in single-file channels. Biophys. J. 95: 2275-2282 (2008).[pdf] |
| 62. | Oliver F. Lange, Nils-Alexander Lakomek, Christophe Fares, Gunnar F. Schröder, Korvin F. A. Walter, Stefan Becker, Jens Meiler, Helmut Grubmüller, Christian Griesinger and Bert L. de Groot. Recognition dynamics up to microseconds revealed from RDC derived ubiquitin ensemble in solution. Science. 320:1471-1475 (2008). [pdf] [supplement pdf] [perspective pdf] |
| 61. | Nils-Alexander Lakomek, Korvin F. A. Walter, Christophe Fares, Oliver F. Lange, Bert L. de Groot, Helmut Grubmüller, Rafael Brüschweiler, Axel Munk, Stefan Becker, Jens Meiler and Christian Griesinger. Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics J. Biomol. NMR. 41: 139-155 (2008).[pdf] |
| 60. | Marcus B. Kubitzki and Bert L. de Groot. The Atomistic Mechanism of Conformational Transition in Adenylate Kinase: a TEE-REX Molecular Dynamics Study. Structure. 8:1175-1182 (2008).[pdf] |
| 59. | Ulrich Zachariae, Robert Schneider, Phanindra Velisetty, Adam Lange, Daniel Seeliger, Sören J. Wacker, Yasmin Karimi-Nejad, Gert Vriend, Stefan Becker, Olaf Pongs, Marc Baldus and Bert L. de Groot. The molecular mechanism of toxin-induced conformational changes in a potassium channel: relation to C-type inactivation. Structure. 16:747-754 (2008).[pdf] |
| 58. | Claudia Hartmann, Mohamed Chami, Ulrich Zachariae, Bert L. de Groot, Andreas Engel and Markus G. Grütter. Vacuolar protein sorting: Two different functional states of the AAA-ATPase Vps4p. J. Mol. Biol. 377:352-363 (2008).[pdf] |
| 57. | Jochen S. Hub and Bert L. de Groot. Mechanism of selectivity in aquaporins and aquaglyceroporins Proc. Nat. Acad. Sci. 105:1198-1203 (2008).[pdf] |
| 56. | Matthias E. Müller, Jochen S. Hub, Helmut Grubmüller and Bert L. de Groot. Is TEA an inhibitor for human Aquaporin-1? Pflügers Archiv. 456:663-669 (2008).[pdf] |
| 55. | Daniel Seeliger, Jürgen Haas, and Bert L. de Groot. Geometry-based Sampling of Conformational Transitions in Proteins. Structure 15: 1482-1492 (2007).[pdf] |
| 54. | Jochen S. Hub, Tim Salditt, Maikel C Rheinstädter, and Bert L. de Groot. Short range order and collective dynamics of DMPC bilayers. A comparison between molecular dynamics simulations, x-ray, and neutron scattering experiments. Biophys. J. 93: 3156-3168 (2007).[pdf] |
| 53. | Louic S. Vermeer, Bert L. de Groot, Valerie Reat, Alain Milon, Jerzy Czaplicki. Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments. Eur. Biophys. J. 36: 919-931 (2007). [pdf] |
| 52. | Carsten Kutzner, David Van Der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. De Groot, Helmut Grubmüller. Speeding up parallel GROMACS on high-latency networks. J. Comp. Chem. 28:2075-2084 (2007). [pdf] |
| 51. | Marcus B. Kubitzki and Bert L. de Groot. Molecular Dynamics Simulations using Temperature Enhanced Essential dynamics Replica EXchange (TEE-REX). Biophys. J. 92:4262-4270 (2007). [pdf] |
| 50. | Guillem Portella, Peter Pohl and Bert L. de Groot. Invariance of Single-File Water Permeability in Gramicidin-like Peptidic Pores as function of Pore Length. Biophys. J. 92:3930-3937 (2007). [pdf] |
| 49. | Daniel Seeliger and Bert L. de Groot. Atomic contacts in protein structures. A detailed analysis of atomic radii, packing and overlaps. Proteins. 68: 595-601 (2007). [pdf] |
| 48. | S. Takamori, M. Holt, K. Stenius, E.A. Lemke, M. Grĝnborg, D. Riedel, H. Urlaub, S. Schenck, B. Brügger, Ph. Ringler, S.A. Müller, B. Rammner, F. Gräter, J. S. Hub, B.L. De Groot, G. Mieskes, Y. Moriyama, J. Klingauf, H. Grubmüller, J. Heuser, F. Wieland, and R. Jahn. Molecular Anatomy of a Trafficking Organelle. Cell 127:831-846 (2006). [pdf] |
| 47. | Steven Hayward and Bert L. de Groot. Normal Modes and Essential Dynamics. in: Methods in molecular biology, vol 443, Molecular modelling of proteins 89-106 (2008). [pdf] |
| 46. | Frauke Gräter, Bert L. de Groot, Hualiang Jiang and Helmut Grubmüller Ligand-Release Pathways in the Pheromone-Binding Protein of Bombyx mori Structure 14:1567-1576 (2006). [pdf] |
| 45. | Jochen S. Hub and Bert L. de Groot. Does CO2 Permeate through Aquaporin-1? Biophys. J. 91:842-848 (2006). [pdf] |
| 44. | Frank J. M. Detmers, Bert L. de Groot, E. Matthias Müller, Andrew Hinton, Irene B. M. Konings, Mozes Sze, Sabine L. Flitsch, Helmut Grubmüller, and Peter M. T. Deen. Quaternary Ammonium Compounds as Water Channel Blockers. J. Biol. Chem. 281:14207-14214 (2006). [pdf] |
| 43. | Daniel Seeliger and Bert L. de Groot. Prediction of protein flexibility from geometrical constraints. Biotech International. 18:20-22 (2006). [pdf] |
| 42. | Daniel J. Rigden, James E. Littlejohn, Harshad V. Joshi, Bert L. de Groot and Mark J. Jedrzejas. Alternate Structural Conformations of Streptococcus pneumoniae Hyaluronan Lyase: Insights into Enzyme Flexibility and Underlying Molecular Mechanism of Action. J. Mol. Biol. 358:1165-1178 (2006). [pdf] |
| 41. | Sapar M. Saparov, Jochen R. Pfeifer, Loay Al-Momani, Guillem Portella, Bert L. de Groot, Ulrich Koert and Peter Pohl. Mobility of a One-Dimensional Confined File of Water Molecules as a Function of File Length. Phys. Rev. Lett. 96:148101 (2006). [pdf] |
| 40. | J. B. Sĝrensen, K. Wiederhold, E. M. Müller, I. Milosevic, G. Nagy, B. L de Groot, H. Grubmüller, and D. Fasshauer. Sequential N- to C-terminal SNARE complex assembly drives priming and fusion of secretory vesicles. EMBO J. 25:955-966 (2006). [pdf] |
| 39. | Bert L. de Groot, Rainer A. Böckmann, and Helmut Grubmüller. Proteindynamik-Simulationen. Molekulare Nanomaschinen unter der Lupe. Physik in unserer Zeit 37: 73-79 (2006). [pdf] [cover] |
| 38. | Gabor Nagy, Ira Milosevic, Dirk Fasshauer, E. Matthias Müller, Bert L. de Groot, Thorsten Lang, Michael C. Wilson and Jakob B. Sorensen Alternative Splicing of SNAP-25 Regulates Secretion through Nonconservative Substitutions in the SNARE Domain Molecular Biology of the Cell 16: 5675-5685 (2005). [pdf] |
| 37. | Heise H, Luca S, de Groot BL, Grubmüller H, Baldus M.; Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations. Biophys J. 89: 2113-2120 (2005). [pdf] |
| 36. | W. Kukulski, A.D. Schenk, U. Johanson, T. Braun, B.L. de Groot, D. Fotiadis, P. Kjellbom and A. Engel; The 5 A Structure of Heterologously Expressed Plant Aquaporin SoPIP2;1. J. Mol. Biol. 350:611-616 (2005). [pdf] |
| 35. | Andreas D. Schenk, Paul J.L. Werten, Simon Scheuring, Bert L. de Groot, Shirley A. Müller, Henning Stahlberg, Ansgar Philippsen and Andreas Engel;The 4.5 A Structure of Human AQP2 J. Mol. Biol. 350:278-289 (2005). [pdf] |
| 34. | Oliver F. Lange, H. Grubmüller, and Bert L. de Groot; Molecular Dynamics Simulations of Protein G Challenge NMR-Derived Correlated Backbone Motions. Angew. Chem. Int. Ed. 44:3394-3399 (2005). [pdf] |
| 33. | Bert L. de Groot and Helmut Grubmüller; The dynamics and energetics of water permeation and proton exclusion in aquaporins Curr. Opin. Struct. Biol. 15: 176-183 (2005). [pdf] |
| 32. | B. L. de Groot and H. Grubmüller; Aquaporine: Die perfekten Wasserfilter der Zelle. BIOspektrum 4:384-386 (2004). [pdf] |
| 31. | Bert L. de Groot, Tomaso Frigato, Volkhard Helms and Helmut Grubmüller; The mechanism of proton exclusion in the aquaporin-1 water channel. J. Mol. Biol. 333: 279-293 (2003). [pdf] |
| 30. | Bert L. de Groot, Andreas Engel, and Helmut Grubmüller; The structure of the Aquaporin-1 water channel: a comparison between cryo-electron microscopy and x-ray crystallography. J. Mol. Biol. 325: 485-493 (2003). [pdf] |
| 29. | P. J. L. Werten, H. -W. Remigy, B. L. de Groot, D. Fotiadis,A. Philippsen, H. Stahlberg, H. Grubmüller and A. Engel; Progress in the analysis of membrane protein structure and function.; FEBS Lett. 529:65-72 (2002). [pdf] |
| 28. | Luciane V. Mello, Bert L. de Groot, Songlin Li, and Mark J. Jedrzejas; Structure and flexibility of streptococcus agalactiae hyaluronate lyase complex with its substrate: Insights into the mechanism of processive degradation of hyaluronan; J. Biol. Chem. 277: 36678-36688 (2002). [pdf] |
| 27. | Mark J. Jedrzejas, Luciane V. Mello, Bert L. de Groot, and Songlin Li; Mechanism of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase: Structures of complexes with the substrate; J. Biol. Chem. 277:28287-28297 (2002). [pdf] |
| 26. | Yoshinori Fujiyoshi, Kaoru Mitsuoka, Bert L. de Groot, Ansgar Philippsen, Helmut Grubmüller, Peter Agre, and Andreas Engel; Structure and function of water channels.; Curr. Opin. Struct. Biol. 12:509-515 (2002). [pdf] |
| 25. | Bert L. de Groot, D. Peter Tieleman, Peter Pohl and Helmut Grubmüller; Water permeation through gramicidin A: desformylation and the double helix; a molecular dynamics study; Biophys. J. 82: 2934-2942 (2002). [pdf] |
| 24. | Bert L. de Groot and Helmut Grubmüller; Water Permeation Across Biological Membranes: Mechanism and Dynamics of Aquaporin-1 and GlpF; Science 294:2353-2357 (2001) [pdf] |
| 23. | Bert L. de Groot, Andreas Engel and Helmut Grubmüller; A refined structure of human aquaporin-1; FEBS Lett. 504:206-211 (2001) [pdf] |
| 22. | Bert L. de Groot, Xavier Daura, Alan E. Mark and Helmut Grubmüller; Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds; J. Mol. Biol. 390 (1): 299-313 (2001) [pdf] |
| 21. | Stahlberg H, Braun T, de Groot B, Philippsen A, Borgnia MJ, Agre P, Kuhlbrandt W, Engel A; The 6.9-angstrom structure of GlpF: A basis for homology modeling of the glycerol channel from Escherichia coli; J. Struct. Biol. 132 (2): 133-141 (2000) [pdf] |
| 20. | Rainer Ossig, Hans Dieter Schmitt, Bert de Groot, Dietmar Riedel, Sirkka Keränen, Hans Ronne, Helmut Grubmüller, and Reinhard Jahn; Exocytosis requires asymmetry in the central layer of the snare complex.; EMBO J. 19:6000-6010 (2000) [pdf] |
| 19. | Bert L. de Groot, J. Bernard Heymann, Andreas Engel, Kaoru Mitsuoka, Yoshinori Fujiyoshi and Helmut Grubmüller; The Fold of Human Aquaporin 1; J. Mol. Biol. 300(4): 987-994 (2000) [pdf] |
| 18. | Heymann J.B, Pfeiffer M, Hildebrandt V, Kaback HR, Fotiadis D, de Groot B, Engel A, Oesterhelt D and Müller D.J.; Conformations of the rhodopsin third cytoplasmic loop grafted onto bacteriorhodopsin; Struct. Fold. Des. 8(6): 643-653 (2000) [pdf] |
| 17. | A.Amadei, B.L. de Groot, M.-A. Ceruso, A. Di Nola and H.J.C. Berendsen; A kinetic model for the internal motions of proteins: Diffusion between multiple harmonic wells , PROTEINS: Struct. Funct. Gen. 35: 283-292 (1999). [pdf] |
| 16. | Bert de Groot; |
| 15. | B.L. de Groot, G. Vriend and H.J.C. Berendsen; Conformational changes in the chaperonin GroEL: New insights into the allosteric mechanism , J. Mol. Biol. 286: 1241-1249 (1999). [pdf] |
| 14. | Johannes P.M. Langedijk, Bert L. de Groot, Herman J.C. Berendsen and Jan T. van Oirschot; Structural homology of the central conserved region of the attachment protein G of the respiratory syncytial virus with the fourth subdomain of 55 kD tumor necrosis factor receptor, Virology 243: 293-302 (1998). [pdf] |
| 13. | B.L. de Groot, S. Hayward, D.M.F. van Aalten, A. Amadei and H.J.C. Berendsen; Domain Motions in Bacteriophage T4 Lysozyme; a Comparison between Molecular Dynamics and Crystallographic Data PROTEINS: Struct. Funct. Gen. 31: 116-127 (1998). [pdf] |
| 12. | B.L. de Groot, D.M.F. van Aalten, R.M. Scheek, A. Amadei, G. Vriend and H.J.C. Berendsen; Prediction of protein conformational freedom from distance constraints, PROTEINS: Struct. Funct. Gen. 29: 240-251 (1997) [pdf] |
| 11. | D.M.F. van Aalten, D.A. Conn, B.L. de Groot, J.B.C. Findlay, H.J.C. Berendsen and A. Amadei; Protein dynamics derived from clusters of crystal structures, Biophys. J. 73(6): 2891-2896 (1997) |
| 10. | D.M.F. van Aalten, B.L. de Groot, H.J.C. Berendsen, J.B.C. Findlay and A. Amadei; A Comparison of Techniques for Calculating Protein Essential Dynamics, J. Comp. Chem. 18:169-181 (1997) [pdf] |
| 9. | D.M.F. van Aalten, B.L. de Groot, H.J.C. Berendsen and J.B.C. Findlay; Conformational analysis of retinoids and restriction of their dynamics by retinoid-binding proteins, The biochemical journal 319(2): 543-550 (1996) [pdf] |
| 8. | D. van der Spoel, B.L. de Groot, S. Hayward, H.J.C. Berendsen and H.J. Vogel; Bending of the Calmodulin Central Helix: A Theoretical Study , Prot. Sci. 5: 2044-2053 (1996) |
| 7. | B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; An extended sampling of the configurational space of HPr from E. coli , PROTEINS: Struct. Funct. Gen. 26: 314-322 (1996) |
| 6. | B.L. de Groot, D.M.F. van Aalten, A. Amadei and H.J.C. Berendsen; The consistency of large concerted motions in proteins in Molecular Dynamics simulations , Biophys. J. 71: 1707-1713 (1996) [pdf] |
| 5. | N.A.J. van Nuland, J.A. Wiersma, D. van der Spoel, B.L. de Groot, R.M. Scheek and G.T. Robillard; Phosphorylation-induced torsion-angle strain in the active center of HPr, detected by NMR and restrained molecular dynamics refinement, Prot. Sci. 5: 442-446 (1996) |
| 4. | B.L. de Groot, A. Amadei, D.M.F. van Aalten and H.J.C. Berendsen; Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin, J. Biomol. Struct. Dyn. 13 : 741-751 (1996) |
| 3. | A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F. van Aalten and H.J.C. Berendsen; An efficient method for sampling the essential subspace of proteins., J. Biomol. Struct. Dyn. 13:615-626 (1996) |
| 2. | R.M. Scheek, N.A.J. van Nuland, B.L. de Groot and A. Amadei; Structure from NMR and molecular dynamics: distance restraining inhibits motion in the essential subspace, J. Biomol. NMR. 6:106-11 (1995) |
| 1. | A. Amadei, A.B.M. Linssen, B.L. de Groot and H.J.C. Berendsen; Essential degrees of freedom of proteins, in "Modelling of Biomolecular Structures and Mechanisms" A. Pullmann et. al. (ed.) pp 85-93 (1995) |
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