@article{GeorgievGrafmuellerBlegeretal.2018,
  author    = {Georgiev, Vasil N. and Grafm{\"u}ller, Andrea and Bl{\´e}ger, David and Hecht, Stefan and Kunstmann, Sonja and Barbirz, Stefanie and Lipowsky, Reinhard and Dimova, Rumiana},
  title     = {Area increase and budding in giant vesicles triggered by light},
  series = {Advanced science},
  volume    = {5},
  journal   = {Advanced science},
  number    = {8},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2198-3844},
  doi       = {10.1002/advs.201800432},
  pages     = {9},
  year      = {2018},
  abstract  = {Biomembranes are constantly remodeled and in cells, these processes are controlled and modulated by an assortment of membrane proteins. Here, it is shown that such remodeling can also be induced by photoresponsive molecules. The morphological control of giant vesicles in the presence of a water-soluble ortho-tetrafluoroazobenzene photoswitch (F-azo) is demonstrated and it is shown that the shape transformations are based on an increase in membrane area and generation of spontaneous curvature. The vesicles exhibit budding and the buds can be retracted by using light of a different wavelength. In the presence of F-azo, the membrane area can increase by more than 5\% as assessed from vesicle electrodeformation. To elucidate the underlying molecular mechanism and the partitioning of F-azo in the membrane, molecular dynamics simulations are employed. Comparison with theoretically calculated shapes reveals that the budded shapes are governed by curvature elasticity, that the spontaneous curvature can be decomposed into a local and a nonlocal contribution, and that the local spontaneous curvature is about 1/(2.5 mu m). The results show that exo- and endocytotic events can be controlled by light and that these photoinduced processes provide an attractive method to change membrane area and morphology.},
  language  = {en}
}
@article{MetjeLeverMayeretal.2020,
  author    = {Metje, Jan and Lever, Fabiano and Mayer, Dennis and Squibb, Richard James and Robinson, Matthew Scott and Niebuhr, Mario and Feifel, Raimund and D{\"u}sterer, Stefan and G{\"u}hr, Markus},
  title     = {URSA-PQ},
  series = {Applied Sciences},
  volume    = {10},
  journal   = {Applied Sciences},
  number    = {21},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2076-3417},
  doi       = {10.3390/app10217882},
  pages     = {13},
  year      = {2020},
  abstract  = {We present a highly flexible and portable instrument to perform pump-probe spectroscopy with an optical and an X-ray pulse in the gas phase. The so-called URSA-PQ (German for 'Ultraschnelle R{\"o}ntgenspektroskopie zur Abfrage der Photoenergiekonversion an Quantensystemen', Engl. 'ultrafast X-ray spectroscopy for probing photoenergy conversion in quantum systems') instrument is equipped with a magnetic bottle electron spectrometer (MBES) and tools to characterize the spatial and temporal overlap of optical and X-ray laser pulses. Its adherence to the CAMP instrument dimensions allows for a wide range of sample sources as well as other spectrometers to be included in the setup. We present the main design and technical features of the instrument. The MBES performance was evaluated using Kr M4,5NN Auger lines using backfilled Kr gas, with an energy resolution ΔE/E ≅ 1/40 in the integrating operative mode. The time resolution of the setup at FLASH 2 FL 24 has been characterized with the help of an experiment on 2-thiouracil that is inserted via the instruments' capillary oven. We find a time resolution of 190 fs using the molecular 2p photoline shift and attribute this to different origins in the UV-pump—the X-ray probe setup.},
  language  = {en}
}
@article{RakersSchumacherMeinletal.2016,
  author    = {Rakers, Christin and Schumacher, Fabian and Meinl, Walter and Glatt, Hansruedi and Kleuser, Burkhard and Wolber, Gerhard},
  title     = {In Silico Prediction of Human Sulfotransferase 1E1 Activity Guided by Pharmacophores from Molecular Dynamics Simulations},
  series = {The journal of biological chemistry},
  volume    = {291},
  journal   = {The journal of biological chemistry},
  publisher = {American Society for Biochemistry and Molecular Biology},
  address   = {Bethesda},
  issn      = {0021-9258},
  doi       = {10.1074/jbc.M115.685610},
  pages     = {58 -- 71},
  year      = {2016},
  abstract  = {Acting during phase II metabolism, sulfotransferases (SULTs) serve detoxification by transforming a broad spectrum of compounds from pharmaceutical, nutritional, or environmental sources into more easily excretable metabolites. However, SULT activity has also been shown to promote formation of reactive metabolites that may have genotoxic effects. SULT subtype 1E1 (SULT1E1) was identified as a key player in estrogen homeostasis, which is involved in many physiological processes and the pathogenesis of breast and endometrial cancer. The development of an in silico prediction model for SULT1E1 ligands would therefore support the development of metabolically inert drugs and help to assess health risks related to hormonal imbalances. Here, we report on a novel approach to develop a model that enables prediction of substrates and inhibitors of SULT1E1. Molecular dynamics simulations were performed to investigate enzyme flexibility and sample protein conformations. Pharmacophores were developed that served as a cornerstone of the model, and machine learning techniques were applied for prediction refinement. The prediction model was used to screen the DrugBank (a database of experimental and approved drugs): 28\% of the predicted hits were reported in literature as ligands of SULT1E1. From the remaining hits, a selection of nine molecules was subjected to biochemical assay validation and experimental results were in accordance with the in silico prediction of SULT1E1 inhibitors and substrates, thus affirming our prediction hypotheses.},
  language  = {en}
}
@article{GoetzeGrecoMitricetal.2012,
  author    = {Goetze, Jan P. and Greco, Claudio and Mitric, Roland and Bonacic-Koutecky, Vlasta and Saalfrank, Peter},
  title     = {BLUF Hydrogen network dynamics and UV/Vis spectra: A combined molecular dynamics and quantum chemical study},
  series = {JOURNAL OF COMPUTATIONAL CHEMISTRY},
  volume    = {33},
  journal   = {JOURNAL OF COMPUTATIONAL CHEMISTRY},
  number    = {28},
  publisher = {WILEY-BLACKWELL},
  address   = {HOBOKEN},
  issn      = {0192-8651},
  doi       = {10.1002/jcc.23056},
  pages     = {2233 -- 2242},
  year      = {2012},
  abstract  = {Blue light sensing using flavin (BLUF) protein photoreceptor domains change their hydrogen bond network after photoexcitation. To explore this phenomenon, BLUF domains from R. sphaeroides were simulated using Amber99 molecular dynamics (MD). Five starting configurations were considered, to study different BLUF proteins (AppA/BlrB), Trp conformations (Win/Wout), structure determination (X-ray/NMR), and finally, His protonation states. We found dependencies of the hydrogen bonds on almost all parameters. Our data show an especially strong correlation of the Trp position and hydrogen bonds involving Gln63. The latter is in some contradiction to earlier results (Obanayama et al., Photochem. Photobiol. 2008, 84 10031010). Possible origins and implications are discussed. Our calculations support conjectures that Gln63 is more flexible with Trp104 in Win position. Using snapshots from MD and time-dependent density functional theory, UV/vis spectra for the chromophore were determined, which account for molecular motion of the protein under ambient conditions. In accord with experiment, it is found that the UV/vis spectra of BLUF bound flavin are red-shifted and thermally broadened for all calculated p ? p* transitions, relative to gas phase flavin at T = 0 K. However, differences in the spectra between the various BLUF configurations cannot be resolved with the present approach. (c) 2012 Wiley Periodicals, Inc.},
  language  = {en}
}
@article{ZuoGandhiArndtetal.2012,
  author    = {Zuo, Zhili and Gandhi, Neha S. and Arndt, Katja Maren and Mancera, Ricardo L.},
  title     = {Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein},
  series = {Biopolymers},
  volume    = {97},
  journal   = {Biopolymers},
  number    = {11},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0006-3525},
  doi       = {10.1002/bip.22099},
  pages     = {899 -- 909},
  year      = {2012},
  abstract  = {The c-Fosc-Jun complex forms the activator protein 1 transcription factor, a therapeutic target in the treatment of cancer. Various synthetic peptides have been designed to try to selectively disrupt the interaction between c-Fos and c-Jun at its leucine zipper domain. To evaluate the binding affinity between these synthetic peptides and c-Fos, polarizable and nonpolarizable molecular dynamics (MD) simulations were conducted, and the resulting conformations were analyzed using the molecular mechanics generalized Born surface area (MM/GBSA) method to compute free energies of binding. In contrast to empirical and semiempirical approaches, the estimation of free energies of binding using a combination of MD simulations and the MM/GBSA approach takes into account dynamical properties such as conformational changes, as well as solvation effects and hydrophobic and hydrophilic interactions. The predicted binding affinities of the series of c-Jun-based peptides targeting the c-Fos peptide show good correlation with experimental melting temperatures. This provides the basis for the rational design of peptides based on internal, van der Waals, and electrostatic interactions.},
  language  = {en}
}