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Publications

  1. L. Sun and R.A. Böckmann. Membrane Phase Transition during Heating and Cooling: Molecular Insight into Reversible Melting. Europ. Biophys. J. in press (2017)
  2. L. Lautner, K. Pluhackova, N.K.H.Barth, T. Seydel, W. Lohstroh, R. A. Böckmann, T. Unruh. Dynamic processes in biological membrane mimics revealed by quasielastic neutron scattering. Chemistry and Physics of Lipids  206:28-42 (2017) [link]
  3. A. Sandoval-Perez, K. Pluhackova, R.A. Böckmann. A Critical Comparison of Biomembrane Force Fields: Protein-Lipid Interactions at the Membrane Interface. J. Chem. Theory Comput. 13:2310-2321 (2017) [link][pdf]
  4. J. Han, K. Pluhackova, and R.A. Böckmann. The multifaceted role of SNARE proteins in membrane fusionFront. Physiol. 8:5 (2017) [link] [pdf]
  5. S. Gahbauer and R.A. Böckmann. Membrane-mediated oligomerization of G protein coupled receptors and its implications for GPCR function. Front. Physiol. 7:494 (2016) [link] [pdf]
  6. M. Rabe, C. Aisenbrey , K. Pluhackova , V. de Wert , A. L. Boyle , D. F. Bruggeman , S. A. Kirsch , R.A. Böckmann, A. Kros, J. Raap, B. Bechinger. A Coiled-Coil Peptide Shaping Lipid Bilayers upon Fusion. Biophys. J. 11(10):2162-2175  (2016) [link] [pdf]
  7. K. Pluhackova, S. Gahbauer, F. Kranz, T.A. Wassenaar, and R.A. Böckmann. Dynamic Cholesterol-conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4. PLoS Comp. Biol. 12(11):e1005169 (2016) [link] [pdf]
  8. H. Zhang, K. Pluhackova, Z. Jiang, and R.A. Böckmann. Binding Characteristics of Sphingosine-1-Phosphate to ApoM hints to Assisted Release Mechanism via the ApoM Calyx-Opening. Scientific Reports 6:30655 (2016) [pdf]
  9. M. Dhara, A. Yarzagaray, M. Makke, B. Schindeldecker, Y. Schwarz, A. Shaaban, S. Sharma, R.A. Böckmann, M. Lindau, R. Mohrmann, D. Bruns. v-SNARE transmembrane domains function as catalysts for Ca2+-triggered vesicle fusion. eLife 5:e17571 (2016) [pdf]
  10. A. Sandoval, S. Eichler, S. Madathil, P. J. Reeves, K. Fahmy, and R.A. Böckmann. The molecular switching mechanism at the conserved D(E)RY motif in class-A GPCRs. Biophys. J. 111:79-89 (2016) [pdf]
  11. S. B. Fillenberg, M. D. Friess, S. Körner, R.A. Böckmann, Y.A. Muller. Crystal structures of the global regulator DasR from Streptomyces coelicolor: Implications for the allosteric regulation of GntR/HutC repressors. PLoS One 11(6): e0157691 (2016) [pdf]
  12. J. Han, K. Pluhackova, R.A. Böckmann. Exploring the formation and the structure of synaptobrevin oligomers in a model membrane. Biophys. J.110:2004-2015 (2016) [pdf]
  13. K. Pluhackova, S.A. Kirsch, J. Han, L. Sun, Z. Jiang, T. Unruh, R.A. Böckmann. A Critical Comparison of Biomembrane Force Fields: Structure and Dynamics of Model DMPC, POPC, and POPE Bilayers. J. Phys. Chem. B120:3888-3903 (2016)  [pdf]
  14. J. Han, K. Pluhackova, D. Bruns, R.A. Böckmann. Synaptobrevin transmembrane domain determines the structure and dynamics of the SNARE motif and the linker region. BBA-Biomembranes 1858:855-865 (2016) [pdf]
  15. L. Sun, F. Bertelshofer, G. Greiner, R.A. Böckmann. Characteristics of Sucrose Transport through the Sucrose-Specific Porin ScrY Studied by Molecular Dynamics Simulations. Frontiers in Bioengineering and Biotechnology 4:9 (2016) [pdf]
  16. Nina Larisch, Sonja A. Kirsch, Alexandra Schambony, Tanja Studtrucker, Rainer A. Böckmann, and Petra Dietrich. The function of the two-pore channel TPC1 depends on dimerization of its carboxy-terminal helix. Cell. Mol. Life Sci. 73:2565-2581 (2016) [pdf]
  17. Sonja A. Kirsch and Rainer A. Böckmann. Membrane Pore Formation in Atomistic and Coarse-Grained Simulations (Review). BBA-Biomembranes 1858:2266-2277 (2016) [pdf] [link]
  18. Zhenyan Jiang, Hansi Zhang, Rainer A. Böckmann. Allostery in BAX Protein Activation. J. Biomol. Struct. Dyn. 34:2469-2480 (2016)  [pdf]
  19. Pluhackova, K., H. Morhenn, L. Lautner, W. Lohstroh, K. Nemkovskiy, T. Unruh, R.A. Böckmann. Extension of the LOPLS-AA Force Field for Alcohols, Esters and Monoolein Bilayers and Its Validation by Neutron Scattering Experiments. J. Phys. Chem. B 119:15287-15299 (2015)  [pdf] [link]
  20. F. Bertelshofer, L. Sun, G. Greiner, R.A. Böckmann. GroPBS: Fast Solver for Implicit Electrostatics of Biomolecules. Frontiers in Bioengineering and Biotechnology 3:186 (2015)  [pdf] [link]
  21. R. Kociurzynski, M. Pannuzzo, R.A. Böckmann. Phase Transition of Glycolipid Membranes Studied by Coarse-Grained Simulations. Langmuir 31:9379-9387 (2015)  [pdf]  [link]
  22. J. Han, K. Pluhackova, T.A. Wassenaar, R.A. Böckmann. Synaptobrevin Transmembrane Domain Dimerization Studied by Multiscale Molecular Dynamics Simulations. Biophys. J. 109:760-771 (2015) [pdf]
  23. K. Pluhackova and R.A. Böckmann. Biomembranes in atomistic and coarse grained simulations (Review). J. Phys. Cond. Mat. 27:323103 (2015)  [pdf][link]
  24. T.A. Wassenaar, H. Ingolfsson, A. Moussatova, R.A. Böckmann, D.P Tieleman, S.J. Marrink. Computational lipidomics with insane: a versatile tool for generating custom membranes for molecular simulations. J. Chem. Theory Comput. 11:2144-2155 (2015) [link]
  25. T.A. Wassenaar, K. Pluhackova, A. Moussatova, D. Sengupta, S.J. Marrink, D.P. Tieleman, R.A. Böckmann. High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach. J. Chem. Theory Comput. 11:2278-2291 (2015) [link]
  26. K. Pluhackova, T.A. Wassenaar, S. Kirsch, R.A. Böckmann. Spontaneous Adsorption of Coiled-Coil Model Peptides K and E to a Mixed Lipid Bilayer. J. Phys. Chem. B 119:4396-4408 (2015) [link]
  27. M. Pannuzzo, A. Raudino, R.A. Böckmann. Peptide-Induced Membrane Curvature in Edge-Stabilized Open Bilayers: A Theoretical and Molecular Dynamics Study. J. Chem. Phys. 141:024901(2014) [link]
  28. T.A. Wassenaar, K. Pluhackova, R.A. Böckmann, S.J. Marrink, D.P. Tieleman. Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models. J. Chem. Theory Comput. 10:676-690 (2014) [pdf]
  29. M. Pannuzzo, R.A. Böckmann. Energetic View on Membrane Pore Formation.Biophys. J. 106:1-2 (2014) [pdf]
  30. R. Sorrentino, R.A. Böckmann, M.T. Fiorillo. HLA-B27 and antigen presentation: At the crossroads between immune defense and autoimmunity. In Molecular Immunology 57:22-27 (2014) [pdf]
  31. K. Pluhackova, T. Wassenaar, R.A. Böckmann. Molecular Dynamics Simulations of Membrane Proteins. In Membrane Biogenesis (Methods in Molecular Biology) p. 85-101 (2013) [pdf]
  32. S.W.I. Siu, K. Pluhackova, R.A. Böckmann. Optimization of the OPLS-AA Force Field for Long Hydrocarbons. J. Chem. Theory Comput. 8:1459-1470 (2012) [pdf]
  33. M. Borisovska, Y.N. Schwarz, M. Dhara, A. Yarzagaray, S. Hugo, D. Narzi, S.W.I. Siu, J. Kesavan, R. Mohrmann, R.A. Böckmann, D. Bruns. Membrane-proximal tryptophanes of synaptobrevinII stabilize priming of secretory vesicles. J. Neurosci. 32:15983-15997 (2012) [pdf]
  34. E. Nurzia, D. Narzi, A. Cauli, A. Mathieu, V. Tedeschi, S. Caristi, R. Sorrentino, R.A. Böckmann, M.T. Fiorillo. Interaction pattern of Arg62 in the A-pocket of differentially disease-associated HLA-B27 subtypes suggests distinct TCR binding modes. PLoS ONE 7:e32865 (2012) [pdf]
  35. D. Narzi, C. M. Becker, M.T. Fiorillo, B. Uchanska-Ziegler, A. Ziegler, R.A. Böckmann. Dynamical characterization of two differentially disease-associated MHC Class I proteins in complex with viral and self-peptides. J. Mol. Biol. 415:429-442 (2012) [pdf]
  36. R.A. Böckmann. Effects of Alkanols on Lipid Bilayers. In Encyclopedia of Biophysics in press (2011) [pdf]
  37. S.A. Jusoh, C. Welsch, S.W.I. Siu, R.A. Böckmann, V. Helms. Contribution of charged and polar residues for the formation of the E1-E2 heterodimer from Hepatitis C Virus. J. Mol. Model. 16:1625-1637 (2010) [pdf]
  38. Beate Griepernau and Rainer A. Böckmann. Influence of Anesthetics on a Membrane Ion Channel Studied by Molecular Dynamics Simulations.submitted
  39. R. Vacha, P. Jurkiewicz, M. Petrov, M. Berkowitz, R.A. Böckmann, J. Barucha-Kraszewska, M. Hof, P. Jungwirth. Mechanism of Interaction of Monovalent Ions with Phosphatidylcholine Lipid Membranes. J. Phys. Chem. B 114:9504-9509 (2010) [pdf]
  40. R. Vacha, S.W.I. Siu, M. Petrov, R.A. Böckmann, J. Barucha-Kraszewska, P. Jurkiewicz, M. Hof, M. L. Berkowitz, P. Jungwirth. Effects of Alkali Cations and Halide Anions on the DOPC Lipid Membrane. J. Phys. Chem. A113:7235-7243 (2009) [pdf]
  41. Shirley W.I. Siu and Rainer A. Böckmann. Low Free Energy Barrier for Ion Permeation Through Double-Helical Gramicidin. J. Phys. Chem. B113:3195-3202 (2009) [pdf]
  42. 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][Supplementary]
  43. Rui Wang, Shirley W.I. Siu, Rainer A. Böckmann. Fine-Grained Protein Mutation Extraction from Biological Literature. ICECT 2009 (Macau)
  44. Andreas Ziegler, Claudia A. Müller, Rainer A. Böckmann, Barbara Uchanska-Ziegler. Low Affinity Peptides and T Cell Selection. Trends in Immunology30:53-60 (2009) [pdf]
  45. Beate Griepernau and Rainer A. Böckmann. The Influence of 1-Alkanols and External Pressure on the Lateral Pressure Profiles of Lipid Bilayers. Biophys. J. 95:5766-5778 (2008) [pdf]
  46. Daniele Narzi, Shirley W.I. Siu, Christian U. Stirnimann, John P.A. Grimshaw, Rudi Glockshuber, Guido Capitani, Rainer A. Böckmann. Evidence for proton shuffling in a thioredoxin-like protein during catalysis. J. Mol. Biol.382:978-986 (2008) [pdf] [Supplementary] [Cover]
  47. 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]
  48. Daniele Narzi, Kathrin Winkler, Jürgen Saidowski, Rolf Misselwitz, Andreas Ziegler, Rainer A. Böckmann, Ulrike Alexiev. Molecular determinants of MHC class I complex stability: shaping antigenic features through long-range electrostatic interactions. J. Biol. Chem. 283:23093-23103 (2008) [pdf][Supplementary]
  49. B. Griepernau, C. Hanke, L. Santen, and R.A. Böckmann. Coarse-grained protein adsorption on solid surfaces. In From Computational Biophysics to Systems Biology (CBSB08) (NUC Series 40, Jülich) 223-225 (2008)[pdf]
  50. S.W.I. Siu and R.A. Böckmann. Free energy study of ion permeation through gramicidin. In From Computational Biophysics to Systems Biology(CBSB08) (NUC Series 40, Jülich) 377-379 (2008) [pdf]
  51. R.A. Böckmann, S.W.I. Siu, S. Leis, B.L. de Groot, S. Kakorin, E. Neumann, and H. Grubmüller. Electroporation studied by molecular dynamics simulations. In From Computational Biophysics to Systems Biology(CBSB08) (NUC Series 40, Jülich) 69-72 (2008) [pdf]
  52. C.M. Becker, A. Benedix, B.L. de Groot, A. Caflisch, and R.A. Böckmann.Fast and accurate structure-based calculation of folding free energies and binding affinities. In From Computational Biophysics to Systems Biology (CBSB08) (NUC Series 40, Jülich) 161-164 (2008) [pdf]
  53. Shirley W. I. Siu, Robert Vacha, Pavel Jungwirth, Rainer A. Böckmann.Biomolecular simulations of membranes: Physical properties from different force fields. J. Chem. Phys.128:125103 (2008) [pdf] selected for April issue of Virtual Journal of Biological Physics Research
  54. Prisca Liberali, Elina Kakkonen, Gabriele Turacchio, Carmen Valente, Alexander Spaar, Giuseppe Perinetti, Rainer A. Böckmann, Daniela Corda, Antonio Colanzi, Varpu Marjomaki, and Alberto Luini. The closure of Pak1-dependent macropinosomes requires the phosphorylation of CtBP1/BARS.EMBO Journal 27:970-981 (2008) [pdf] [Supplementary]
  55. Heinz Fabian, Hans Huser, Daniele Narzi, Rolf Misselwitz, Bernhard Loll, Andreas Ziegler, Rainer A. Böckmann, Barbara Uchanska-Ziegler, and Dieter Naumann. HLA-B27 subtypes differentially associated with disease exhibit conformational differences in solution. J. Mol. Biol.376:798-810 (2008).[pdf]
  56. Beate Griepernau, Simon Leis, Matthias F. Schneider, Martin Sikor, Daniel Steppich, and Rainer A. Böckmann. 1-Alkanols and Membranes: A Story of Attraction. BBA – Biomembranes 1768:2899-2913 (2007) [pdf]
  57. Shirley W.I. Siu and Rainer A. Böckmann. Electric Field Effects on Membranes: Gramicidin A as a Test Ground. Journal of Structural Biology 157:545-556 (2007) [pdf]
  58. 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]
  59. Christian U. Stirnimann, Anna Rozhkova, Ulla Grauschopf, Rainer A. Böckmann, Rudi Glockshuber, Guido Capitani, Markus G. Grütter. High resolution structures of Escherichia coli cDsbD in different redox states: a combined crystallographic, biochemical and computational study. J. Mol. Biol. 358:829-845 (2006) [pdf]
  60. R. A. Böckmann and A. Caflisch. Spontaneous Formation of Detergent Micelles around the Outer Membrane Protein OmpX. Biophys. J.88:3191-3204 (2005) [pdf]
  61. T. Pöhlmann, R. A. Böckmann, H. Grubmüller, B. Uchanska-Ziegler, A. Ziegler and U. Alexiev. Differential Peptide Dynamics is Linked to MHC Polymorphism. J. Biol. Chem. 279(27):28197-28201 (2004) [pdf]
  62. R. A. Böckmann and H. Grubmüller. Multistep Binding of Divalent Cations to Phospholipid Bilayers: A Molecular Dynamics Study. Angew. Chemie Int. Ed. 43(8):1021-1024 (2004) [pdf] [Cover]Angew. Chemie 116(8):1039-1042 (2004) [pdf]
  63. R. A. Böckmann and H. Grubmüller. Conformational Dynamics of the F1-ATPase Beta-Subunit: A Molecular Dynamics Study. Biophys. J. 85(3):1482-149 (2003) [pdf] [Cover]
  64. R. A. Böckmann, A. Hac, T. Heimburg and H. Grubmüller. Effect of Sodium Chloride on a Lipid Bilayer Biophys. J. 85(3):1647-1655 (2003) [pdf]
  65. R. A. Böckmann and H. Grubmüller. Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase.Nature Struct. Biol. 9:198-202 (2002) [pdf]
  66. R. Böckmann, C. Hanhart, O. Krehl, S. Krewald, and J. Speth. Pi NN Vertex Function in a Meson-Theoretical Model. Phys. Rev. C 60:055212 (1999)[pdf]