Publications
2019
| Sonja A. Kirsch and Rainer A. Böckmann. Coupling of membrane nanodomain formation and enhanced electroporation near phase transition. Biophys. J. 116(11): 2131-2148 [pdf] [cover image] |
2018
| M. Friess, K. Pluhackova, R.A. Böckmann. Structural Model of the mIgM B-cell Receptor Transmembrane Domain from Self-Association Molecular Dynamics Simulations. Front. Immunol. 9:2947 [link] |
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Sonja Kirsch*, Andreas Kugemann*, Armando Carpaneto, Rainer A. Böckmann#, Petra Dietrich#: Phosphatidylinositol-3,5-bisphosphate lipid binding-induced activation of the human two-pore channel 2. Cell. Mol. Life Sci. 75(20): 3803-3815 [link]
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Schmidt, K., Gardill, B. R., Kern, A., Kirchweger, P., Börsch, M. & Muller, Y. A. (2018) Design of an allosterically modulated doxycycline and doxorubicin drug-binding protein. Proc. Natl. Acad. Sci. USA 115(22):5744-5749 [link]
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Christoph Mark, Claus Metzner, Lena Lautscham, Pamela L. Strissel, Reiner Strick, and Ben Fabry
Bayesian model selection for complex dynamic systems. Nature Communications 9:1803 [link]
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| Heger, L., Balk, S., Lühr, J.L., Heidkamp, G.F., Lehmann, C.H.K., Hatscher, L., Purbojo, A., Hartmann, A., Garcia-Martin, F., Nishimura, S.-I., Cesjnevar, R., Nimmerjahn, F. and Dudziak: D.CLEC10A is a specific marker for human CD1c+ DCs and enhances their Toll-like receptor 7/8 induced cytokine secretion. Front. Immunol. doi: 10.3389/fimmu.2018.00744 [link] |
| Ilyaskin, A.V., Kirsch, S.A., Böckmann, R.A., Sticht, H., Korbmacher, C., Haerteis, S., Diakov, A: The degenerin region of the human bile acid-sensitive ion channel (BASIC) is involved in channel inhibition by calcium and activation by bile acids. Pflügers Arch – Eur. J. Physiol. 470(7):1087-1102; doi: 10.1007/s00424-018-2142-z [link] |
| Gahbauer, S., Pluhackova, K. & Böckmann, R.A. Closely related, yet unique: Distinct homo- and heterodimerization patterns of G protein coupled chemokine receptors and their fine-tuning by cholesterol. PLoS Comp. Biol. 14(3): e1006062 ; doi: 10.1371/journal.pcbi.1006062 [link] |
| L. Sun and R.A. Böckmann. Membrane Phase Transition during Heating and Cooling: Molecular Insight into Reversible Melting. Europ. Biophys. J. 47(2), 151-164 [link] |
2017
| Condor, M. and Steinwachs, J. and Mark, C. and Garcia Aznar, J. M. and Fabry, B. Traction Force Microscopy in 3-Dimensional Extracellular Matrix Networks. Curr Protoc Cell Biol. 2017 Jun 19;75:10.22.1-10.22.20. |
| Thum, S. and Kokornaczyk, A. and Seki, T. and De Maria, M. and Ortiz Zacarias, N. V. and de Vries, H. and Weiss, C. and Koch, M. and Schepmann, D. and Kitamura, M. and Tschammer, N. and Heitman, L. H. and Junker, A. and Wünsch, B. Synthesis and biological evaluation of chemokine receptor ligands with 2-benzazepine scaffold. Eur J Med Chem. 2017 Jul 28;135:401-413. |
| Cvitkovic, A. and Smith, A.-S. and Pande, J.. Asymptotic expansions of the hypergeometric function with two large parameters — application to the partition function of a lattice gas in a field of traps. , , |
| Susanne F. Fenz, Timo Bihr, Daniel Schmidt, Rudolf Merkel, Udo Seifert, Kheya Sengupta, and Ana-Sunčana Smith: Membrane fluctuations mediate lateral interaction between cadherin bonds. Nature Physics doi:10.1038/nphys4138 [link] |
| L. Lautner, K. Pluhackova, Nicolai 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 [link] |
| Janina R. Lange, Claus Metzner, Sebastian Richter, Werner Schneider, Monika Spermann, Thorsten Kolb, Graeme Whyte, Ben Fabry (2017). Unbiased High-Precision Cell Mechanical Measurements with Microconstrictions. Biophysical Journal, Volume 112, Issue 7, 11 April 2017, Pages 1472–1480. [link] |
| Grebnev, G., Ntefidou, M., & Kost, B. (2017). Secretion and Endocytosis in Pollen Tubes: Models of Tip Growth in the Spot Light. Frontiers in Plant Science, 8, 154 [link] |
| Reimann, R., Kost, B., & Dettmer, J. (2017). TETRASPANINs in Plants. Frontiers in Plant Science, 8, 545. [link] |
| 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] |
| H. Stein, S. Spindler, N. Bonakdar, C. Wang, and V. Sandoghdar. Production of isolated giant unilamellar vesicles under high salt concentrations. Front. Physiol. 8, doi: 10.3389/fphys.2017.00063 [link] |
| Han, Kristyna Pluhackova, and Rainer A. Böckmann. The multifaceted role of SNARE proteins in membrane fusion. Front. Physiol. 8:5 [link] |
| Lehmann, C. H. K. and Baranska, A. and Heidkamp, G. and Heger, L. and Neubert, K. and Lühr, J. J. and Hoffmann, A. and Reimer, K. and Beck, S. and Seeling, M. and et al.. DC subset specific induction of {CD4 and CD8 T} cell responses upon antigen uptake via activating or inhibitory {Fc$\gamma$} receptors in vivo. J Exp Med. 2017 May 1; 214(5): 1509–1528. [link] |
2016
| Bartsch, T. F. and Kochanczyk, M. D. and Lissek, E. N. and Lange, J. R. and Florin, E.-L. Nanoscopic imaging of thick, heterogeneous soft-matter structures in aqueous solution. Nat Commun. 2016; 7: 12729. |
| Heidkamp, G. F. and Sander, J. and Lehmann, C. H. K. and Heger, L. and Eissing, N. and Baranska, A. and Lühr, J. J. and Hoffmann, A. and Reimer K. C. and Lux, A. and Söder, S. and et al. Human lymphoid organ dendritic cell identity is predominantly dictated by ontogeny, not tissue microenvironment. Science Immunology 16 Dec 2016: Vol. 1, Issue 6, eaai7677. [link] |
| Heidkamp, G. F. and Lehmann, C. H. K. and Heger, L. and Baranska, A. and Hoffmann, A. and Lühr, J.J. and Dudziak, D. Functional Specialization of Dendritic Cell Subsets. Encyclopedia of Cell Biology Stahl, pp.588-604. [link] |
| Lehmann, C. and Heger, L. and Heidkamp, G. and Baranska, A. and Lühr, J. J. and Hoffmann, A. and and Dudziak, D. Direct Delivery of Antigens to Dendritic Cells via Antibodies Specific for Endocytic Receptors as a Promising Strategy for Future Therapie. Vaccines (Basel). 2016 Jun; 4(2): 8. [link] |
| Julian Steinwachs, Claus Metzner, Kai Skodzek, Nadine Lang, Ingo Thievessen, Christoph Mark, Stefan Münster, Katerina E Aifantis, Ben Fabry (2016). Three-dimensional force microscopy of cells in biopolymer networks. Nature Methods 13, 171–176 (2016). [link] |
| S. Kaliman, C. Jayachandran, F. Rehfeldt, and A.-S. Smith. Limits of applicability of the Voronoi tessellation determined by centres of cell nuclei to epithelium morphology. Front. Physiol. 7:551 [link] |
| Stefan Gahbauer and Rainer A. Böckmann. Membrane-mediated oligomerization of G protein coupled receptors and its implications for GPCR function. Front. Physiol. 7:494 [link] |
| 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. 11:2162-2175 [link] |
| 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:e1005169 [link] |
| Janina R. Lange, Wolfgang H. Goldmann, Jose Luis Alonso. Influence of avb3 integrin on the mechanical properties and the morphology of M21 and K562 cells. BBRC 478:1280-1285 [link] |
| Susann Spindler, Jens Ehrig, Katharina König, Tristan Nowak, Marek Piliarik, Hannah E Stein, Richard W Taylor, Elisabeth Garanger, Sébastien Lecommandoux, Isabel D Alves, and Vahid Sandoghdar. Visualization of lipids and proteins at high spatial and temporal resolution via interferometric scattering (iSCAT) microscopy. J. Phys. D: Appl. Phys. 49:274002 [link] |
| Hansi Zhang, Kristyna Pluhackova, Zhenyan Jiang, and Rainer A. Böckmann. Binding Characteristics of Sphingosine-1-Phosphate to ApoM hints to Assisted Release Mechanism via the ApoM Calyx-Opening. Sci. Rep. 6:30655 [link] |
| Angelica Sandoval, Stefanie Eichler, Sineej Madathil, Philip J. Reeves, Karim Fahmy, and Rainer A. Böckmann. The molecular switching mechanism at the conserved D(E)RY motif in class-A GPCRs. Biophys. J. 111:79-89 [link] |
| Fillenberg, S. B. and Friess, M. D. and Körner, S. and Böckmann, R. A. and Muller, Y. A. Crystal Structures of the Global Regulator {DasR} from Streptomyces coelicolor: Implications for the Allosteric Regulation of GntR/HutC Repressors. PLoS ONE 11(6): e0157691. [link] |
| Dhara, M. and Yarzagaray, A. and Makke, M. and Schindeldecker, B. and Schwarz, Y. and Shaaban, A. and Sharma, S. and Böckmann, R. A. and Lindau, M. and Mohrmann, R. and Bruns, D. v-SNARE transmembrane domains function as catalysts for vesicle fusion. eLife 2016;5:e17571 [link] |
| Jing Han, Kristyna Pluhackova, and Rainer A. Böckmann. Exploring the formation and the structure of synaptobrevin oligomers in a model membrane. Biophys. J. 110:2004-2015 [link] |
| Kristyna Pluhackova, Sonja A. Kirsch, Jing Han, Liping Sun, Zhenyan Jiang, Tobias Unruh, and Rainer A. Böckmann. A Critical Comparison of Biomembrane Force Fields: Structure and Dynamics of Model DMPC, POPC, and POPE Bilayers. J. Phys. Chem. B 120:3888-3903 [link] |
| Cornelia Monzel, Daniel Schmidt, Udo Seifert, Ana-Suncana Smith, Rudolf Merkel, and Kheya Sengupta. Nanometric thermal fluctuations of weakly confined biomembranes measured with microsecond time-resolution. Soft Matter 12:4755-4768 [link] |
| Jing Han, Kristyna Pluhackova, Dieter Bruns, and Rainer A. Böckmann. Synaptobrevin transmembrane domain determines the structure and dynamics of the SNARE motif and the linker region. BBA-Biomembranes 1858:855-865 [link] |
| Liping Sun, Franziska Bertelshofer, Günther Greiner, and Rainer A. Böckmann. Characteristics of Sucrose Transport through the Sucrose-Specific Porin ScrY Studied by Molecular Dynamics Simulations. Frontiers in Bioengineering and Biotechnology 4:9 [link] |
| Nina Larisch, Sonja A. Kirsch, Alexandra Schambony, Tanja Studtrucker, Rainer A. Böckmann, and Petra Dietrich. Antiparallel dimerization of the carboxy-terminal helix is essential for the function of the vacuolar two-pore channel TPC1. Cell. Mol. Life Sci. 73:2565-2581 [link] |
| Calmet, P. and De Maria, M. and Harte, E. and Lamb, D. and Serrano-Vega, M. and Jazayeri, A. and Tschammer, N. and Alves, I. D. Real monitoring of membrane GPCR reconstitution by plasmon waveguide resonance: on the role of lipids. Scientific Reports 6, Article number: 36181 (2016) [link] |
| Sonja A. Kirsch and Rainer A. Böckmann. Membrane Pore Formation in Atomistic and Coarse-Grained Simulations. BBA-Biomembranes1858:2266-2277 [link] |
| Jiang, Z. and Zhang, H. and Böckmann, R. A. Allostery in BAX Protein Activation. J Biomol Struct Dyn. 2016 Nov;34(11):2469-80. [link] |
2015
| C. Monzel, D. Schmidt, C. Kleusch, D. Kirchenbühler, U. Seifert, A.-S. Smith, K. Sengupta, R. Merkel. Measuring fast stochastic displacements of bio-membranes with dynamic optical displacement spectroscopy. Nature Commun.6:8162 [link] |
| Kristyna Pluhackova, Humphrey Morhenn, Lisa Lautner, Wiebke Lohstroh, Kirill Nemkovskiy, Tobias Unruh, Rainer 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. B119:15287–15299 [link] |
| Franziska Bertelshofer, Liping Sun, Günther Greiner, Rainer A. Böckmann. GroPBS: Fast Solver for Implicit Electrostatics of Biomolecules. Frontiers in Bioengineering and Biotechnology 3:186 [link] |
| Lena A. Lautscham, Christoph Kämmerer, Janina R. Lange, Thorsten Kolb, Christoph Mark, Achim Schilling, Pamela L. Strissel, Reiner Strick, Caroline Gluth, Amy C. Rowat, Claus Metzner, Ben Fabry. Migration in Confined 3D Environments Is Determined by a Combination of Adhesiveness, Nuclear Volume, Contractility, and Cell Stiffness. Biophys. J. 109: 900-913 [link] |
| Timo Bihr, Udo Seifert and Ana-Sunčana Smith. Multiscale approaches to protein-mediated interactions between membranes -relating microscopic and macroscopic dynamics in radially growing adhesions. New J. Phys. 17: 083016 [link] |
| Daniel Schmidt, Timo Bihr, Susanne Fenz, Rudolf Merkel, Udo Seifert, Kheya Sengupta, Ana-Sunčana Smith. Crowding of receptors induces ring-like adhesions in model membranes. BBA: Mol. Cell Res. 1853: 2984 [link] |
| Raisa Kociurzynski, Martina Pannuzzo, and Rainer A. Böckmann. Phase Transition of Glycolipid Membranes Studied by Coarse-Grained Simulations. Langmuir DOI: 10.1021/acs.langmuir.5b01617 [bibtex] [link] |
| Jing Han, Kristyna Pluhackova, Tsjerk Wassenaar, and Rainer A. Böckmann. Synaptobrevin Transmembrane Domain Dimerization Studied by Multiscale Molecular Dynamics Simulations. Biophys. J. 109:760-771 [bibtex] [link] |
| Claus Metzner, Christoph Mark, Julian Steinwachs, Lena Lautscham, Franz Stadler and Ben Fabry. Superstatistical Analysis and Modelling of Heterogeneous Random Walks. Nat. Comm. accepted [link] |
| Kristyna Pluhackova and Rainer A. Böckmann. Biomembranes in atomistic and coarse grained simulations (Review). J. Phys. Cond. Mat. 27:323103 [bibtex] [link] |
| Wassenaar, T. A. and Ingolfsson, H. I. and Böckmann, R. A. and Tieleman, D. P. and Marrink, S. J. Computational Lipidomics with INSANE: A versatile Tool for Generating Custom Membranes for Molecular Simulations. J. Chem. Theory Comput., 2015, 11 (5), pp 2144–2155 [link] |
| Tsjerk Wassenaar, Kristyna Pluhackova, Anastassiia Moussatova, Durba Sengupta, Siewert J. Marrink, D. Peter Tieleman, and Rainer A. Böckmann. High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach. J. Chem. Theory Comput. 11:2278-2291 [bibtex] [link] |
| Kristyna Pluhackova, Tsjerk Wassenaar, Sonja Kirsch, and Rainer A. Böckmann. Spontaneous Adsorption of Coiled-Coil Model Peptides K and E to a Mixed Lipid Bilayer. J. Phys. Chem. B 119:4396-4408 [bibtex] [link] |
2014
| Timo Bihr, Susanne Fenz, Erich Sackmann, Rudolf Merkel, Udo Seifert, Kheya Sengupta, and Ana-Suncana Smith. Association Rates of Membrane-Coupled Cell Adhesion Molecules. Biophys. J. 107:L33-L36 [link] |
| Martina Pannuzzo, Antonio Raudino, Rainer A. Böckmann. Peptide-Induced Membrane Curvature in Edge-Stabilized Open Bilayers: A Theoretical and Molecular Dynamics Study. J. Chem. Phys. 141:024901 [cover] [bibtex] [link] |
| Wassenaar, T. A. and Pluhackova, K. and Böckmann, R. A. and Marrink, S. J. and Tieleman, D. P. Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models. J. Chem. Theory Comput., 2014, 10 (2), pp 676–690 [link] |
| Pannuzzo, M. and Böckmann, R. A. Energetic View on Membrane Pore Formation. Biophys J. 2014 Jan 7; 106(1): 1–2. [link] |
| C.-L. Hsieh, S. Spindler, J. Ehrig, V. Sandoghdar. Tracking single particles on supported lipid membranes: multi-mobility diffusion and nanoscopic confinement. J. Phys. Chem. B. 118, 1545 [link] |
| J. T. Kim, S. Spindler, V. Sandoghdar. Scanning-aperture trapping and manipulation of single charged nanoparticles. Nature Communications. 5, 3380 [link] |
