TY - JOUR A1 - Dai, Xiaolin A1 - Mate, Diana M. A1 - Glebe, Ulrich A1 - Garakani, Tayebeh Mirzaei A1 - Körner, Andrea A1 - Schwaneberg, Ulrich A1 - Böker, Alexander T1 - Sortase-mediated ligation of purely artificial building blocks JF - Polymers N2 - Sortase A (SrtA) from Staphylococcus aureus has been often used for ligating a protein with other natural or synthetic compounds in recent years. Here we show that SrtA-mediated ligation (SML) is universally applicable for the linkage of two purely artificial building blocks. Silica nanoparticles (NPs), poly(ethylene glycol) and poly(N-isopropyl acrylamide) are chosen as synthetic building blocks. As a proof of concept, NP-polymer, NP-NP, and polymer-polymer structures are formed by SrtA catalysis. Therefore, the building blocks are equipped with the recognition sequence needed for SrtA reaction-the conserved peptide LPETG-and a pentaglycine motif. The successful formation of the reaction products is shown by means of transmission electron microscopy (TEM), matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-ToF MS), and dynamic light scattering (DLS). The sortase catalyzed linkage of artificial building blocks sets the stage for the development of a new approach to link synthetic structures in cases where their synthesis by established chemical methods is complicated. KW - sortase-mediated ligation KW - enzymes KW - block copolymers KW - nanoparticles Y1 - 2018 U6 - https://doi.org/10.3390/polym10020151 SN - 2073-4360 VL - 10 IS - 2 PB - MDPI CY - Basel ER - TY - JOUR A1 - Holland-Moritz, Henry A1 - Graupner, Julia A1 - Möller, Wolfhard A1 - Pacholski, Claudia A1 - Ronning, Carsten T1 - Dynamics of nanoparticle morphology under low energy ion irradiation JF - Nanotechnology N2 - If nanostructures are irradiated with energetic ions, the mechanism of sputtering becomes important when the ion range matches about the size of the nanoparticle. Gold nanoparticles with diameters of similar to 50 nm on top of silicon substrates with a native oxide layer were irradiated by gallium ions with energies ranging from 1 to 30 keV in a focused ion beam system. High resolution in situ scanning electron microscopy imaging permits detailed insights in the dynamics of the morphology change and sputter yield. Compared to bulk-like structures or thin films, a pronounced shaping and enhanced sputtering in the nanostructures occurs, which enables a specific shaping of these structures using ion beams. This effect depends on the ratio of nanoparticle size and ion energy. In the investigated energy regime, the sputter yield increases at increasing ion energy and shows a distinct dependence on the nanoparticle size. The experimental findings are directly compared to Monte Carlo simulations obtained from iradina and TRI3DYN, where the latter takes into account dynamic morphological and compositional changes of the target. KW - ion beam KW - nanoparticles KW - sputtering KW - Monte Carlo KW - in situ Y1 - 2018 U6 - https://doi.org/10.1088/1361-6528/aac36c SN - 0957-4484 SN - 1361-6528 VL - 29 IS - 31 PB - IOP Publ. Ltd. CY - Bristol ER - TY - THES A1 - Dai, Xiaolin T1 - Synthesis of artificial building blocks for sortase-mediated ligation and their enzymatic linkage T1 - Synthese von artifiziellen Bausteinen für Sortase-vermittelte Ligationen und deren enzymatische Verknüpfung N2 - Das Enzym Sortase A katalysiert die Bildung einer Peptidbindung zwischen der Erkennungssequenz LPXTG und einem Oligoglycin. Während vielfältige Ligationen zwischen Proteinen und verschiedenen Biomolekülen, Proteinen und kleinen synthetischen Molekülen, sowie Proteinen und Oberflächen durchgeführt wurden, besteht das Ziel dieser Arbeit darin, die Sortase-katalysierte Verlinkung von synthetischen Bausteinen zu untersuchen. Dies könnte den Weg bereiten für die Anwendung von Sortase A für chemische Aufgabenstellungen und eventuell sogar in den Materialwissenschaften. Für diese grundsätzliche Untersuchung wurden die verwendeten Bausteine zunächst so einfach wie möglich gehalten und leicht zugängliche SiO2 Nanopartikel und kommerziell erhältliche Polymerblöcke ausgewählt. Die Bausteine wurden als erstes mit den Peptidsequenzen für Sortase-vermittelte Ligationen funktionalisiert. SiO2 Nanopartikel wurden mit Durchmessern von 60 und 200 nm hergestellt und mit C=C Doppelbindungen oberflächenmodifiziert. Dann wurden Peptide mit einem terminalen Cystein kovalent durch eine Thiol-en Reaktion angebunden. An die 60 nm NP wurden Peptide mit einem Pentaglycin und an die 200 nm Partikel Peptide mit LPETG Sequenz gebunden. Auf die gleiche Art und Weise wurden Peptide mit terminalem Cystein an die Polymere Polyethylenglykol (PEG) und Poly(N Isopropylacrylamid) (PNIPAM), die beide über C=C Endgruppen verfügen, gebunden und G5-PEG und PNIPAM-LPETG Konjugate erhalten. Mit den vier Bausteinen wurden nun durch Sortase-vermittelte Ligation NP–Polymer Hybride, NP–NP und Polymer–Polymer Strukturen hergestellt und die Produkte u. a. durch Transmissionselektronen-mikroskopie, MALDI-ToF Massenspektrometrie sowie Dynamische Lichtstreuung charakterisiert. Die Verlinkung dieser synthetischen Bausteine konnte eindeutig gezeigt werden. Das Verwenden von kommerziell erhältlichen Polymeren hat jedoch zu einem Gemisch der Polymer-Peptid Konjugate mit unmodifiziertem Polymer geführt, welches nicht gereinigt werden konnte. Deswegen wurden anschließend Synthesestrategien für reine Peptid-Polymer und Polymer-Peptid Konjugate als Bausteine für Sortase-vermittelte Ligationen entwickelt. Diese basieren auf der RAFT Polymerisation mit CTAs, die entweder an N- oder C-Terminus eines Peptids gebunden sind. GG-PNIPAM wurde durch das Anbinden eines geeigneten RAFT CTAs an Fmoc-GG in einer Veresterungsreaktion, Polymerisation von NIPAM und Abspalten der Fmoc Schutzgruppe synthetisiert. Weiterhin wurden mehrere Peptide durch Festphasen-Peptidsynthese erhalten. Die Anbindung eines RAFT CTAs (oder eines Polymerisationsinitiators) an den N-Terminus eines Peptids kann automatisiert als letzter Schritt in einem Peptid-Synthetisierer erfolgen. Die Synthese eines solchen Konjugats konnte in dem Zeithorizont dieser Arbeit noch nicht erreicht werden. Jedoch existieren mehrere vielversprechende Strategien, um diesen Ansatz mit verschiedenen Kopplungsreagenzien zur Anbindung des CTAs fortzusetzen. Solche Polymer Bausteine können in Zukunft für die Synthese von Protein-Polymer Konjugaten durch Sortase-Katalyse verwendet werden. Außerdem kann der Ansatz auch für die Synthese von Block-Copolymeren aus Polymerblöcken mit Peptidmotiven an beiden Enden ausgebaut werden. Auch wenn bei der grundsätzlichen Untersuchung im Rahmen dieser Arbeit Hybridstrukturen hergestellt wurden, die auch durch traditionelle chemische Synthesen erhalten werden könnten, wird ein Bausatz solcher Bausteine in Zukunft die Synthese neuer Materialien ermöglichen und kann auch den Weg für die Anwendung von Enzymen in den Materialwissenschaften ebnen. In Ergänzung zu Nanopartikeln und Block-Copolymeren können dann auch Hybridmaterialien unter Einbezug von Protein-basierten Bausteinen hergestellt werden. Daher könnten Sortase Enzyme zu einem Werkzeug werden, welches etablierte chemische Verlinkungstechniken ergänzt und mit den hoch spezifischen Peptidmotiven über funktionale Einheiten verfügt, die orthogonal zu allen chemischen Gruppen sind. N2 - The enzyme Sortase A catalyzes the formation of a peptide bond between the recognition sequence LPXTG and an oligoglycine. While manifold ligations between proteins and various biomolecules, proteins and small synthetic molecules as well as proteins and surfaces have been reported, the aim of this thesis was to investigate the sortase-catalyzed linkage between artificial building blocks. Hence, this could pave the way for the use of sortase A for tasks from a chemical point of view and maybe even materials science. For the proof of concept, the studied systems were kept as simple as possible at first by choosing easily accessible silica NPs and commercially available polymers. These building blocks were functionalized with peptide motifs for sortase-mediated ligation. Silica nanoparticles were synthesized with diameters of 60 and 200 nm and surface modified with C=C functionalities. Then, peptides bearing a terminal cysteine were covalently linked by means of a thiol-ene reaction. 60 nm SiO2 NPs were functionalized with pentaglycines, while peptides with LPETG motif were linked to 200 nm silica particles. Polyethyleneglycol (PEG) and poly(N isopropylacrylamide) (PNIPAM) were likewise functionalized with peptides by thiol-ene reaction between cysteine residues and C=C units in the polymer end groups. Hence, G5-PEG and PNIPAM-LPETG conjugates were obtained. With this set of building blocks, NP–polymer hybrids, NP–NP, and polymer–polymer structures were generated by sortase-mediated ligation and the product formation shown by transmission electron microscopy, MALDI-ToF mass spectrometry and dynamic light scatting, among others. Thus, the linkage of these artificial building blocks by the enzyme sortase A could be demonstrated. However, when using commercially available polymers, the purification of the polymer–peptide conjugates was impossible and resulted in a mixture containing unmodified polymer. Therefore, strategies were developed for the own synthesis of pure peptide-polymer and polymer-peptide conjugates as building blocks for sortase-mediated ligation. The designed routes are based on preparing polymer blocks via RAFT polymerization from CTAs that are attached to N- or C-terminus, respectively, of a peptide. GG-PNIPAM was synthesized through attachment of a suitable RAFT CTA to Fmoc-GG in an esterification reaction, followed by polymerization of NIPAM and cleavage of the Fmoc protection group. Furthermore, several peptides were synthesized by solid-phase peptide synthesis. The linkage of a RAFT CTA (or polymerization initiator) to the N-terminus of a peptide can be conducted in an automated fashion as last step in a peptide synthesizer. The synthesis of such a conjugate couldn’t be realized in the time frame of this thesis, but many promising strategies exist to continue this strategy using different coupling reagents. Such polymer building blocks can be used to synthesize protein-polymer conjugates catalyzed by sortase A and the approach can be carried on to the synthesis of block copolymers by using polymer blocks with peptide motifs on both ends. Although the proof of concept demonstrated in this thesis only shows examples that can be also synthesized by exclusively chemical techniques, a toolbox of such building blocks will enable the future formation of new materials and pave the way for the application of enzymes in materials science. In addition to nanoparticle systems and block copolymers, this also includes combination with protein-based building blocks to form hybrid materials. Hence, sortase could become an enzymatic tool that complements established chemical linking technologies and provides specific peptide motifs that are orthogonal to all existing chemical functional groups. KW - sortase-mediated ligation KW - enzyme KW - block copolymers KW - nanoparticles KW - Ligation KW - Enzym KW - Block-Copolymere KW - Nanopartikel Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-420060 ER - TY - GEN A1 - Sarhan, Radwan Mohamed A1 - Koopman, Wouter-Willem Adriaan A1 - Schuetz, Roman A1 - Schmid, Thomas A1 - Liebig, Ferenc A1 - Koetz, Joachim A1 - Bargheer, Matias T1 - The importance of plasmonic heating for the plasmondriven photodimerization of 4-nitrothiophenol T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Metal nanoparticles form potent nanoreactors, driven by the optical generation of energetic electrons and nanoscale heat. The relative influence of these two factors on nanoscale chemistry is strongly debated. This article discusses the temperature dependence of the dimerization of 4-nitrothiophenol (4-NTP) into 4,4′-dimercaptoazobenzene (DMAB) adsorbed on gold nanoflowers by Surface-Enhanced Raman Scattering (SERS). Raman thermometry shows a significant optical heating of the particles. The ratio of the Stokes and the anti-Stokes Raman signal moreover demonstrates that the molecular temperature during the reaction rises beyond the average crystal lattice temperature of the plasmonic particles. The product bands have an even higher temperature than reactant bands, which suggests that the reaction proceeds preferentially at thermal hot spots. In addition, kinetic measurements of the reaction during external heating of the reaction environment yield a considerable rise of the reaction rate with temperature. Despite this significant heating effects, a comparison of SERS spectra recorded after heating the sample by an external heater to spectra recorded after prolonged illumination shows that the reaction is strictly photo-driven. While in both cases the temperature increase is comparable, the dimerization occurs only in the presence of light. Intensity dependent measurements at fixed temperatures confirm this finding. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 698 KW - enhanced raman-scattering KW - charge-transfer KW - metal KW - nanoparticles KW - catalysis KW - AU KW - 4-nitrobenzenethiol KW - aminothiophenol KW - photocatalysis KW - wavelength Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-427197 SN - 1866-8372 IS - 698 ER - TY - JOUR A1 - Dey, Pradip A1 - Bergmann, Tobias A1 - Cuellar-Camacho, Jose Luis A1 - Ehrmann, Svenja A1 - Chowdhury, Mohammad Suman A1 - Zhang, Minze A1 - Dahmani, Ismail A1 - Haag, Rainer A1 - Azad, Walid T1 - Multivalent flexible nanogels exhibit broad-spectrum antiviral activity by blocking virus entry JF - ACS nano N2 - The entry process of viruses into host cells is complex and involves stable but transient multivalent interactions with different cell surface receptors. The initial contact of several viruses begins with attachment to heparan sulfate (HS) proteoglycans on the cell surface, which results in a cascade of events that end up with virus entry. The development of antiviral agents based on multivalent interactions to shield virus particles and block initial interactions with cellular receptors has attracted attention in antiviral research. Here, we designed nanogels with different degrees of flexibility based on dendritic polyglycerol sulfate to mimic cellular HS. The designed nanogels are nontoxic and broad-spectrum, can multivalently interact with viral glycoproteins, shield virus surfaces, and efficiently block infection. We also visualized virus-nanogel interactions as well as the uptake of nanogels by the cells through clathrin-mediated endocytosis using confocal microscopy. As many human viruses attach to the cells through HS moieties, we introduce our flexible nanogels as robust inhibitors for these viruses. KW - multivalent KW - herpes simplex virus KW - heparan sulfate KW - nanoparticles KW - click chemistry KW - polyglycerol Y1 - 2018 U6 - https://doi.org/10.1021/acsnano.8b01616 SN - 1936-0851 SN - 1936-086X VL - 12 IS - 7 SP - 6429 EP - 6442 PB - American Chemical Society CY - Washington ER -