TY  - GEN
A1  - Banerjee, Pallavi
A1  - Lipowsky, Reinhard
A1  - Santer, Mark
T1  - Coarse-grained molecular model for the Glycosylphosphatidylinositol anchor with and without protein
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1216 
KW  - Martini force-field
KW  - osmotic-pressure
KW  - potential-functions
KW  - aqueous-solution
KW  - dynamics
KW  - coefficient
KW  - simulation
KW  - trypanosoma
KW  - transition
KW  - parameters
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523742
SN  - 1866-8372
IS  - 6
ER  - 
TY  - GEN
A1  - Thete, Aniket
A1  - Rojas, Oscar
A1  - Neumeyer, David
A1  - Koetz, Joachim
A1  - Dujardin, Erik
T1  - Ionic liquid-assisted morphosynthesis of gold nanorods using polyethyleneimine-capped seeds
N2  - Seed-mediated gold nanorods with tunable lengths are prepared using new polyethyleneimine-capped gold nanoparticles synthesized in ionic liquid. The effect of polyethyleneimine and ionic liquid during nanorod growth is investigated and shows a marked effect on their final aspect ratio.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 245 
KW  - aqueous-solution
KW  - aspect-ratio
KW  - cationic surfactants
KW  - chemical-synthesis
KW  - delivery
KW  - metal nanoparticles
KW  - mixtures
KW  - shape
KW  - silver nanowires
KW  - surface-plasmon resonance
Y1  - 2013
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-95196
SP  - 14294
EP  - 14298
ER  - 
TY  - GEN
A1  - Junginger, Mathias
A1  - Kübel, Christian
A1  - Schacher, Felix H.
A1  - Müller, Axel H. E.
A1  - Taubert, Andreas
T1  - Crystal structure and chemical composition of biomimetic calcium phosphate nanofibers
N2  - Calcium phosphate nanofibers with a diameter of only a few nanometers and a cotton-ball-like aggregate morphology have been reported several times in the literature. Although fiber formation seems reproducible in a variety of conditions, the crystal structure and chemical composition of the fibers have been elusive. Using scanning transmission electron microscopy, low dose electron (nano)diffraction, energy-dispersive X-ray spectroscopy, and energy-filtered transmission electron microscopy, we have assigned crystal structures and chemical compositions to the fibers. Moreover, we demonstrate that the mineralization process yields true polymer/calcium phosphate hybrid materials where the block copolymer template is closely associated with the calcium phosphate.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 244 
KW  - air-water-interface
KW  - polycationic monolayer
KW  - mineralization beneath
KW  - block-copolymers
KW  - aqueous-solution
KW  - morphology
KW  - orthophosphates
KW  - biomaterials
KW  - nucleation
KW  - clusters
Y1  - 2013
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-95176
SP  - 11301
EP  - 11308
ER  -