@misc{LeproNagelKlumppetal.2019,
  author    = {Lepro, Valentino and Nagel, Oliver and Klumpp, Stefan and Lipowsky, Reinhard and Beta, Carsten},
  title     = {Cooperative Transport by Amoeboid Cells},
  series = {Biophysical journal},
  volume    = {116},
  journal   = {Biophysical journal},
  number    = {3},
  publisher = {Cell Press},
  address   = {Cambridge},
  issn      = {0006-3495},
  doi       = {10.1016/j.bpj.2018.11.682},
  pages     = {122A -- 122A},
  year      = {2019},
  language  = {en}
}
@article{SchimkaSanterMujkicNinnemannetal.2016,
  author    = {Schimka, Selina and Santer, Svetlana and Mujkic-Ninnemann, Nina M. and Bleger, David and Hartmann, Laura and Wehle, Marko and Lipowsky, Reinhard and Santer, Mark},
  title     = {Photosensitive Peptidomimetic for Light-Controlled, Reversible DNA Compaction},
  series = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences},
  volume    = {17},
  journal   = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1525-7797},
  doi       = {10.1021/acs.biomac.6b00052},
  pages     = {1959 -- 1968},
  year      = {2016},
  abstract  = {Light-induced DNA compaction as part of nonviral gene delivery was investigated intensively in the past years, although the bridging between the artificial light switchable compacting.agents and biodompatible light insensitive compacting agents was not achieved until now. In this paper, we report on light-induced compaction and decompaction of DNA molecules in the presence of a new typeof agent, a multivalent cationic peptidomimetic molecule containing a photosensitive Azo-group as a branch (Azo-PM). Az-o-PM is synthesized using a solid-phase procedure during Which anrazoberizene unit is attached as a side chain to an Oligo(arnidoamine) backbone. We shoW, that within a-certain Tange,of concentrations and under illumination with light of appropriate-wavelengths, these cationic Molecules induce reversible DNA compaction/decompaction by photo-isomerization of the incorporated azobenzene unit between a hydrophobic trans- and 4 hydrophilic cis-conformation, as characterized by dynamic light scattering and AFM measurements. In contrast to other molecular Species used for invasive DNA compaction, such as-widely used azobenzene containing cationic surfactant (Azo-TAR, C-4-Azo-OCX-TMAB), the presented peptidomimetic agent appears to lead to different compleication/compaction mechanisms., An investigation of Ato-PM in close proximity to a DNA segment by means of a molecular dynamics simulation sustains a picture in which Azo-PM acts as a multivalent counterion, with its rather large cationic oligo(amidoamine) backbone dominating the interaction with the double helix, fine-tuned or assisted by the presence" andisomerization state of the Azo-moiety. However, due to its peptidomimetic backbone, Azo-PM should be far less toxic than photosensitive surfactants and might represent a starting point for a conscious design of photoswitchable, biocompatible vectors for gene delivery.},
  language  = {en}
}
@article{KangBarbirzLipowskyetal.2014,
  author    = {Kang, Yu and Barbirz, Stefanie and Lipowsky, Reinhard and Santer, Mark},
  title     = {Conformational Diversity of O-Antigen Polysaccharides of the Gram-Negative Bacterium Shigella flexneri Serotype Y},
  series = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry},
  volume    = {118},
  journal   = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry},
  number    = {9},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1520-6106},
  doi       = {10.1021/jp4111713},
  pages     = {2523 -- 2534},
  year      = {2014},
  language  = {en}
}
@article{VallerianiZhangNagaretal.2011,
  author    = {Valleriani, Angelo and Zhang, Gong and Nagar, Apoorva and Ignatova, Zoya and Lipowsky, Reinhard},
  title     = {Length-dependent translation of messenger RNA by ribosomes},
  series = {Physical review : E, Statistical, nonlinear and soft matter physics},
  volume    = {83},
  journal   = {Physical review : E, Statistical, nonlinear and soft matter physics},
  number    = {4},
  publisher = {American Physical Society},
  address   = {College Park},
  issn      = {1539-3755},
  doi       = {10.1103/PhysRevE.83.042903},
  pages     = {4},
  year      = {2011},
  abstract  = {A simple measure for the efficiency of protein synthesis by ribosomes is provided by the steady state amount of protein per messenger RNA (mRNA), the so-called translational ratio, which is proportional to the translation rate. Taking the degradation of mRNA into account, we show theoretically that both the translation rate and the translational ratio decrease with increasing mRNA length, in agreement with available experimental data for the prokaryote Escherichia coli. We also show that, compared to prokaryotes, mRNA degradation in eukaryotes leads to a less rapid decrease of the translational ratio. This finding is consistent with the fact that, compared to prokaryotes, eukaryotes tend to have longer proteins.},
  language  = {en}
}
@article{KarLipowskyKnecht2011,
  author    = {Kar, Parimal and Lipowsky, Reinhard and Knecht, Volker},
  title     = {Importance of polar solvation for cross-reactivity of antibody and its variants with steroids},
  series = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry},
  volume    = {115},
  journal   = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry},
  number    = {23},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1520-6106},
  doi       = {10.1021/jp201538t},
  pages     = {7661 -- 7669},
  year      = {2011},
  abstract  = {Understanding the factors determining the binding of ligands to receptors in detail is essential for rational drug design. Here, the free energies of binding of the steroids progesterone (PRG) and 5 beta-androstane-3,17-dione (SAD) to the Diels-Alderase antibody 1E9, as well as the Leu(H47)Trp/Arg(H100)Trp 1E9 double mutant (1E9dm) and the corresponding single mutants, have been estimated and decomposed using the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method. Also the difference in binding free energies between the PRG-1E9dm complex and the complex of PRG with the antiprogesterone antibody DB3 have been evaluated and decomposed. The steroids bind less strongly to 1E9 than to DB3, but the mutations tend to improve the steroid affinity, in quantitative agreement with experimental data. Although the complexes formed by PRG or SAD with 1E9dm and by PRG with DB3 have similar affinity, the binding mechanisms are different. Reduced Waals for SAD-1E9dm versus PRG-1E9dm or for PRG-1E9dm versus PRG-DB3 are energetically compensated by an increased solvation of polar groups, partly contrasting previous conclusions based on structural inspection. Our study illustrates that deducing binding mechanisms from structural models alone can be misleading. Therefore, taking into account solvation effects as in MM-PBSA calculations is essential to elucidate molecular recognition.},
  language  = {en}
}