@article{BanerjeeLipowskySanter2020,
  author    = {Banerjee, Pallavi and Lipowsky, Reinhard and Santer, Mark},
  title     = {Coarse-grained molecular model for the Glycosylphosphatidylinositol anchor with and without protein},
  series = {Journal of Chemical Theory and Computation},
  volume    = {16},
  journal   = {Journal of Chemical Theory and Computation},
  number    = {6},
  publisher = {ACS Publications},
  address   = {Washington DC},
  issn      = {1549-9626},
  doi       = {10.1021/acs.jctc.0c00056},
  pages     = {15},
  year      = {2020},
  abstract  = {Glycosylphosphatidylinositol (GPI) anchors are a unique class of complex glycolipids that anchor a great variety of proteins to the extracellular leaflet of plasma membranes of eukaryotic cells. These anchors can exist either with or without an attached protein called GPI-anchored protein (GPI-AP) both in vitro and in vivo. Although GPIs are known to participate in a broad range of cellular functions, it is to a large extent unknown how these are related to GPI structure and composition. Their conformational flexibility and microheterogeneity make it difficult to study them experimentally. Simplified atomistic models are amenable to all-atom computer simulations in small lipid bilayer patches but not suitable for studying their partitioning and trafficking in complex and heterogeneous membranes. Here, we present a coarse-grained model of the GPI anchor constructed with a modified version of the MARTINI force field that is suited for modeling carbohydrates, proteins, and lipids in an aqueous environment using MARTINI's polarizable water. The nonbonded interactions for sugars were reparametrized by calculating their partitioning free energies between polar and apolar phases. In addition, sugar-sugar interactions were optimized by adjusting the second virial coefficients of osmotic pressures for solutions of glucose, sucrose, and trehalose to match with experimental data. With respect to the conformational dynamics of GPI-anchored green fluorescent protein, the accessible time scales are now at least an order of magnitude larger than for the all-atom system. This is particularly important for fine-tuning the mutual interactions of lipids, carbohydrates, and amino acids when comparing to experimental results. We discuss the prospective use of the coarse-grained GPI model for studying protein-sorting and trafficking in membrane models.},
  language  = {en}
}
@misc{BanerjeeLipowskySanter2020,
  author    = {Banerjee, Pallavi and Lipowsky, Reinhard and Santer, Mark},
  title     = {Coarse-grained molecular model for the Glycosylphosphatidylinositol anchor with and without protein},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {6},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-52374},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-523742},
  pages     = {17},
  year      = {2020},
  abstract  = {Glycosylphosphatidylinositol (GPI) anchors are a unique class of complex glycolipids that anchor a great variety of proteins to the extracellular leaflet of plasma membranes of eukaryotic cells. These anchors can exist either with or without an attached protein called GPI-anchored protein (GPI-AP) both in vitro and in vivo. Although GPIs are known to participate in a broad range of cellular functions, it is to a large extent unknown how these are related to GPI structure and composition. Their conformational flexibility and microheterogeneity make it difficult to study them experimentally. Simplified atomistic models are amenable to all-atom computer simulations in small lipid bilayer patches but not suitable for studying their partitioning and trafficking in complex and heterogeneous membranes. Here, we present a coarse-grained model of the GPI anchor constructed with a modified version of the MARTINI force field that is suited for modeling carbohydrates, proteins, and lipids in an aqueous environment using MARTINI's polarizable water. The nonbonded interactions for sugars were reparametrized by calculating their partitioning free energies between polar and apolar phases. In addition, sugar-sugar interactions were optimized by adjusting the second virial coefficients of osmotic pressures for solutions of glucose, sucrose, and trehalose to match with experimental data. With respect to the conformational dynamics of GPI-anchored green fluorescent protein, the accessible time scales are now at least an order of magnitude larger than for the all-atom system. This is particularly important for fine-tuning the mutual interactions of lipids, carbohydrates, and amino acids when comparing to experimental results. We discuss the prospective use of the coarse-grained GPI model for studying protein-sorting and trafficking in membrane models.},
  language  = {en}
}
@inproceedings{KangBarbirzLipowskyetal.2013,
  author    = {Kang, Y. and Barbirz, Stefanie and Lipowsky, Reinhard and Santer, Mark},
  title     = {Conformational Insights into Recognition Mechanism of O-Antigen Polysaccharides by Tailspike Protein},
  series = {European biophysics journal : with biophysics letters ; an international journal of biophysics},
  volume    = {42},
  booktitle = {European biophysics journal : with biophysics letters ; an international journal of biophysics},
  number    = {1},
  publisher = {Springer},
  address   = {New York},
  issn      = {0175-7571},
  pages     = {S112 -- S112},
  year      = {2013},
  language  = {en}
}
@article{VallerianiIgnatovaNagaretal.2010,
  author    = {Valleriani, Angelo and Ignatova, Zoya and Nagar, Apoorva and Lipowsky, Reinhard},
  title     = {Turnover of messenger RNA : polysome statistics beyond the steady state},
  issn      = {0295-5075},
  doi       = {10.1209/0295-5075/89/58003},
  year      = {2010},
  abstract  = {The interplay between turnover or degradation and ribosome loading of messenger RNA (mRNA) is studied theoretically using a stochastic model that is motivated by recent experimental results. Random mRNA degradation affects the statistics of polysomes, i.e., the statistics of the number of ribosomes per mRNA as extracted from cells. Since ribosome loading of newly created mRNA chains requires some time to reach steady state, a fraction of the extracted mRNA/ ribosome complexes does not represent steady state conditions. As a consequence, the mean ribosome density obtained from the extracted complexes is found to be inversely proportional to the mRNA length. On the other hand, the ribosome density profile shows an exponential decrease along the mRNA for prokaryotes and becomes uniform in eukaryotic cells. Copyright (C) EPLA, 2010},
  language  = {en}
}