TY - JOUR A1 - Senf, Deborah A1 - Ruprecht, Colin A1 - Kishani, Saina A1 - Matic, Aleksandar A1 - Toriz, Guillermo A1 - Gatenholm, Paul A1 - Wagberg, Lars A1 - Pfrengle, Fabian T1 - Tailormade polysaccharides with defined branching patterns BT - Enzymatic polymerization of arabinoxylan oligosaccharides JF - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition N2 - The heterogeneous nature of non-cellulosic polysaccharides, such as arabinoxylan, makes it difficult to correlate molecular structure with macroscopic properties. To study the impact of specific structural features of the polysaccharides on crystallinity or affinity to other cell wall components, collections of polysaccharides with defined repeating units are required. Herein, a chemoenzymatic approach to artificial arabinoxylan polysaccharides with systematically altered branching patterns is described. The polysaccharides were obtained by glycosynthase-catalyzed polymerization of glycosyl fluorides derived from arabinoxylan oligosaccharides. X-ray diffraction and adsorption experiments on cellulosic surfaces revealed that the physicochemical properties of the synthetic polysaccharides strongly depend on the specific nature of their substitution patterns. The artificial polysaccharides allow structure-property relationship studies that are not accessible by other means. KW - carbohydrates KW - enzymes KW - glycosynthases KW - structure elucidation KW - synthetic methods Y1 - 2018 U6 - https://doi.org/10.1002/anie.201806871 SN - 1433-7851 SN - 1521-3773 VL - 57 IS - 37 SP - 11987 EP - 11992 PB - Wiley-VCH CY - Weinheim ER - TY - THES A1 - Pavashe, Prashant T1 - Synthesis and transformations of 2-thiocarbohydrates T1 - Synthese und Transformationen von 2-Thiokohlenhydraten BT - a practical approach for functionalization of thiosugars BT - ein Praktischer Zugang zur Funktionalisierung von Thiozuckern N2 - I. Ceric ammonium nitrate (CAN) mediated thiocyanate radical additions to glycals In this dissertation, a facile entry was developed for the synthesis of 2-thiocarbohydrates and their transformations. Initially, CAN mediated thiocyanation of carbohydrates was carried out to obtain the basic building blocks (2-thiocyanates) for the entire studies. Subsequently, 2-thiocyanates were reduced to the corresponding thiols using appropriate reagents and reaction conditions. The screening of substrates, stereochemical outcome and the reaction mechanism are discussed briefly (Scheme I). Scheme I. Synthesis of the 2-thiocyanates II and reductions to 2-thiols III & IV. An interesting mechanism was proposed for the reduction of 2-thiocyanates II to 2-thiols III via formation of a disulfide intermediate. The water soluble free thiols IV were obtained by cleaving the thiocyanate and benzyl groups in a single step. In the subsequent part of studies, the synthetic potential of the 2-thiols was successfully expanded by simple synthetic transformations. II. Transformations of the 2-thiocarbohydrates The 2-thiols were utilized for convenient transformations including sulfa-Michael additions, nucleophilic substitutions, oxidation to disulfides and functionalization at the anomeric position. The diverse functionalizations of the carbohydrates at the C-2 position by means of the sulfur linkage are the highlighting feature of these studies. Thus, it creates an opportunity to expand the utility of 2-thiocarbohydrates for biological studies. Reagents and conditions: a) I2, pyridine, THF, rt, 15 min; b) K2CO3, MeCN, rt, 1 h; c) MeI, K2CO3, DMF, 0 °C, 5 min; d) Ac2O, H2SO4 (1 drop), rt, 10 min; e) CAN, MeCN/H2O, NH4SCN, rt, 1 h; f) NaN3, ZnBr2, iPrOH/H2O, reflux, 15 h; g) NaOH (1 M), TBAI, benzene, rt, 2 h; h) ZnCl2, CHCl3, reflux, 3 h. Scheme II. Functionalization of 2-thiocarbohydrates. These transformations have enhanced the synthetic value of 2-thiocarbohydrates for the preparative scale. Worth to mention is the Lewis acid catalyzed replacement of the methoxy group by other nucleophiles and the synthesis of the (2→1) thiodisaccharides, which were obtained with complete β-selectivity. Additionally, for the first time, the carbohydrate linked thiotetrazole was synthesized by a (3 + 2) cycloaddition approach at the C-2 position. III. Synthesis of thiodisaccharides by thiol-ene coupling. In the final part of studies, the synthesis of thiodisaccharides by a classical photoinduced thiol-ene coupling was successfully achieved. Reagents and conditions: 2,2-Dimethoxy-2-phenylacetophenone (DPAP), CH2Cl2/EtOH, hv, rt. Scheme III. Thiol-ene coupling between 2-thiols and exo-glycals. During the course of investigations, it was found that the steric hindrance plays an important role in the addition of bulky thiols to endo-glycals. Thus, we successfully screened the suitable substrates for addition of various thiols to sterically less hindered alkenes (Scheme III). The photochemical addition of 2-thiols to three different exo-glycals delivered excellent regio- and diastereoselectivities as well as yields, which underlines the synthetic potential of this convenient methodology. N2 - I. Cerammoniumnitrat (CAN) vermittelte Thiocyanat Radikaladditionen an Glycale In dieser Dissertation wurde ein einfacher synthetischer Zugang zu 2-Thiokohlenhydraten und dessen Transformationsprodukten entwickelt. Zu Beginn wurden CAN vermittelte Funktionalisierungen von Kohlenhydraten mit Thiocyanat durchgeführt, um die notwendigen Ausgangsverbindungen (2-Thiocyanate) für die weiteren Studien zu erhalten. Im Folgenden wurden diese 2-Thiocyanate mit entsprechenden Reagenzien unter geeigneten Reduktionsbedingungen zu den Thiolen reduziert. Das Screening der Substrate, der stereochemische Verlauf und der Reaktionsmechanismus wird kurz diskutiert (Schema I). Schema I. Synthese der 2-Thiocyanate II und Reduktionen zu den 2-Thiolen III & IV. Es wurde ein interessanter Mechanismus für die Reduktion der 2-Thiocyanate II zu den 2-Thiolen III via Bildung von Disulfid-Zwischenstufen vorgeschlagen. Die wasserlöslichen freien Thiole IV wurden durch Spaltung der Thiocyanat- und Benzylgruppen in einem Einzelschritt freigesetzt. Im darauf folgenden Teil der Arbeit wurde das synthetische Potenzial der 2-Tiole erfolgreich durch einfache synthetische Transformationen erweitert. II. Transformationen der 2-Thiokohlenhydrate Die 2-Thiole wurden für die Ausführung praktischer Transformationen eingesetzt, die Sulfa-Michael Additionen, nukleophile Substitutionen, Oxidationen zu Disulfiden und Funktionalisierungen an der anomeren Position beinhalten. Die mannigfaltigen Funktionalisierungen der Kohlenhydrate an den C-2 Positionen mittels der Schwefel Gruppe ist das hervortretende Merkmal dieser Arbeit. Reagenzien und Reaktionsbedingungen: a) I2, Pyridin, THF, rt, 15 min; b) K2CO3, MeCN, rt, 1 h; c) MeI, K2CO3, DMF, 0 °C, 5 min; d) Ac2O, H2SO4 (1 Tropfen), rt, 10 min; e) CAN, MeCN/H2O, NH4SCN, rt, 1 h; f) NaN3; ZnBr2; iPrOH/H2O, Rückfluss 15 h; g) NaOH (1 M), TBAI, Benzol, rt 2 h; h) ZnCl2, CHCl3, Rückfluss, 3 h. Schema II. Funktionalisierungen von 2-Thiokohlenhydraten Daraus eröffnet sich die Möglichkeit, den Nutzwert von 2-Thiokohlenhydraten auf biologische Studien auszuweiten. Diese Transformationen haben den synthetischen Wert von 2-Thiokohlenhydraten für den präparativen Maßstab gesteigert. Hervorzuheben ist hier der Lewis Säure katalysierte Austausch der Methoxygruppe durch weitere Nukleophile und die Synthese von (2→1) Thiodisacchariden, die mit quantitativer β-Selektivität erhalten wurden. Zusätzlich wurde zum ersten Mal ein Zucker gebundenes Thiotetrazol über eine (3+2) Cycloaddition an der C-2 Position synthetisiert. III. Synthese von Thiodisacchariden durch Thiol-En-Kopplungen Im letzten Teil der Arbeit gelang die Synthese von Thiodisacchariden durch eine klassische Thiol-En-Kopplung. Reagenzien und Reaktionsbedingungen: 2,2-Dimethoxy-2-phenylacetophenone (DPAP), CH2Cl2/EtOH, hv, rt. Schema III. Thiol-En-Kopplungen zwischen 2-Thiolen und exo-Glycalen. Im Verlauf der Untersuchungen wurde aufgezeigt, dass die räumlische Hinderung bei der Addition von sterisch anspruchsvollen 2-Thiolen an endo-Glycale eine wichtige Rolle spielt. Dazu erprobten wir geeignete Substrate zur Addition von 2-Thiolen an sterisch wenig anspruchsvolle Alkene (Schema III). Die photochemische Addition der 2-Thiole an drei verschiedene exo-Glycale lieferte exzellente Regio- und Diastereoselektivitäten und Ausbeuten, was das synthetische Potenzial dieser bequem durchführbaren Methodik unterstreicht. KW - carbohydrates KW - 2-Thiodisaccharides KW - radical reactions KW - Ceric Ammonium Nitrate (CAN) KW - photochemistry KW - Kohlenhydrate KW - 2-Thiodisaccharide KW - Radikalreaktionen KW - Cer Ammonium Nitrat (CAN) KW - Photochemie Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-397739 ER - TY - JOUR A1 - Bauch, Marcel A1 - Fudickar, Werner A1 - Linker, Torsten T1 - Stereoselective [4+2] Cycloaddition of Singlet Oxygen to Naphthalenes Controlled by Carbohydrates JF - Molecules : a journal of synthetic chemistry and natural product chemistry N2 - Stereoselective reactions of singlet oxygen are of current interest. Since enantioselective photooxygenations have not been realized efficiently, auxiliary control is an attractive alternative. However, the obtained peroxides are often too labile for isolation or further transformations into enantiomerically pure products. Herein, we describe the oxidation of naphthalenes by singlet oxygen, where the face selectivity is controlled by carbohydrates for the first time. The synthesis of the precursors is easily achieved starting from naphthoquinone and a protected glucose derivative in only two steps. Photooxygenations proceed smoothly at low temperature, and we detected the corresponding endoperoxides as sole products by NMR. They are labile and can thermally react back to the parent naphthalenes and singlet oxygen. However, we could isolate and characterize two enantiomerically pure peroxides, which are sufficiently stable at room temperature. An interesting influence of substituents on the stereoselectivities of the photooxygenations has been found, ranging from 51:49 to up to 91:9 dr (diastereomeric ratio). We explain this by a hindered rotation of the carbohydrate substituents, substantiated by a combination of NOESY measurements and theoretical calculations. Finally, we could transfer the chiral information from a pure endoperoxide to an epoxide, which was isolated after cleavage of the sugar chiral auxiliary in enantiomerically pure form. KW - singlet oxygen KW - photooxygenation KW - naphthalenes KW - carbohydrates KW - stereoselectivity KW - auxiliary control KW - [4+2] cycloaddition Y1 - 2021 U6 - https://doi.org/10.3390/molecules26040804 SN - 1420-3049 VL - 16 IS - 4 PB - MDPI CY - Basel ER - TY - GEN A1 - Bauch, Marcel A1 - Fudickar, Werner A1 - Linker, Torsten T1 - Stereoselective [4+2] Cycloaddition of Singlet Oxygen to Naphthalenes Controlled by Carbohydrates T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Stereoselective reactions of singlet oxygen are of current interest. Since enantioselective photooxygenations have not been realized efficiently, auxiliary control is an attractive alternative. However, the obtained peroxides are often too labile for isolation or further transformations into enantiomerically pure products. Herein, we describe the oxidation of naphthalenes by singlet oxygen, where the face selectivity is controlled by carbohydrates for the first time. The synthesis of the precursors is easily achieved starting from naphthoquinone and a protected glucose derivative in only two steps. Photooxygenations proceed smoothly at low temperature, and we detected the corresponding endoperoxides as sole products by NMR. They are labile and can thermally react back to the parent naphthalenes and singlet oxygen. However, we could isolate and characterize two enantiomerically pure peroxides, which are sufficiently stable at room temperature. An interesting influence of substituents on the stereoselectivities of the photooxygenations has been found, ranging from 51:49 to up to 91:9 dr (diastereomeric ratio). We explain this by a hindered rotation of the carbohydrate substituents, substantiated by a combination of NOESY measurements and theoretical calculations. Finally, we could transfer the chiral information from a pure endoperoxide to an epoxide, which was isolated after cleavage of the sugar chiral auxiliary in enantiomerically pure form. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1116 KW - singlet oxygen KW - photooxygenation KW - naphthalenes KW - carbohydrates KW - stereoselectivity KW - auxiliary control KW - [4+2] cycloaddition Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-493361 SN - 1866-8372 IS - 1116 ER - TY - JOUR A1 - Umbreen, Sumaira A1 - Linker, Torsten T1 - Simple Synthesis of Conformationally Fixed Glycosamine Analogues by Beckmann Rearrangement at the Carbohydrate Ring JF - Chemistry - a European journal N2 - Conformationally fixed carbohydrate analogues are promising small-molecule inhibitors for hydrolases like O-GlcNAcase (OGA); however, their synthesis usually requires many steps. Herein we describe cycloadditions of dichloroketene to various glycals and subsequent Beckmann rearrangements, which offer an easy and stereoselective entry to glycosamine derivatives in good yields. The reactions are applicable for hexoses, pentoses, and disaccharides, and transformations to the corresponding imidates proceed smoothly. First biological tests reveal that such imidates indeed inhibit human OGA. KW - carbohydrates KW - cycloaddition KW - enzyme inhibitors KW - rearrangement KW - selective syntheses Y1 - 2015 U6 - https://doi.org/10.1002/chem.201406546 SN - 0947-6539 SN - 1521-3765 VL - 21 IS - 20 SP - 7340 EP - 7344 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Schmidt, Bernd A1 - Hauke, Sylvia T1 - Olefin cross metathesis based de novo synthesis of a partially protected L-amicetose and a fully protected L-cinerulose derivative JF - Beilstein journal of organic chemistry N2 - Cross metathesis of a lactate derived allylic alcohol and acrolein is the entry point to a de novo synthesis of 4-benzoate protected L-amicetose and a cinerulose derivative protected at C5 and C1. KW - carbohydrates KW - de novo synthesis KW - lactate KW - metathesis KW - ruthenium Y1 - 2014 U6 - https://doi.org/10.3762/bjoc.10.102 SN - 1860-5397 VL - 10 SP - 1023 EP - 1031 PB - Beilstein-Institut zur Förderung der Chemischen Wissenschaften CY - Frankfurt, Main ER - TY - JOUR A1 - Salama, Ahmed A1 - Neumann, Mike A1 - Günter, Christina A1 - Taubert, Andreas T1 - Ionic liquid-assisted formation of cellulose/calcium phosphate hybrid materials JF - Beilstein journal of nanotechnology N2 - Cellulose/calcium phosphate hybrid materials were synthesized via an ionic liquid-assisted route. Scanning electron microscopy, transmission electron microscopy, energy-dispersive X-ray spectroscopy, X-ray diffraction, infrared spectroscopy, and thermogravimetric analysis/differential thermal analysis show that, depending on the reaction conditions, cellulose/hydroxyapatite, cellulose/ chlorapatite, or cellulose/monetite composites form. Preliminary studies with MC3T3-E1 pre-osteoblasts show that the cells proliferate on the hybrid materials suggesting that the ionic liquid-based process yields materials that are potentially useful as scaffolds for regenerative therapies. KW - biomineralization KW - calcium phosphate KW - carbohydrates KW - cellulose KW - hybrid materials KW - ionic liquid Y1 - 2014 U6 - https://doi.org/10.3762/bjnano.5.167 SN - 2190-4286 VL - 5 SP - 1553 EP - 1568 PB - Beilstein-Institut zur Förderung der Chemischen Wissenschaften CY - Frankfurt, Main ER - TY - GEN A1 - Kunstmann, Ruth Sonja A1 - Engström, Olof A1 - Wehle, Marko A1 - Widmalm, Göran A1 - Santer, Mark A1 - Barbirz, Stefanie T1 - Increasing the affinity of an O-Antigen polysaccharide binding site in Shigella flexneri bacteriophage Sf6 tailspike protein T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Broad and unspecific use of antibiotics accelerates spread of resistances. Sensitive and robust pathogen detection is thus important for a more targeted application. Bacteriophages contain a large repertoire of pathogen-binding proteins. These tailspike proteins (TSP) often bind surface glycans and represent a promising design platform for specific pathogen sensors. We analysed bacteriophage Sf6 TSP that recognizes the O-polysaccharide of dysentery-causing Shigella flexneri to develop variants with increased sensitivity for sensor applications. Ligand polyrhamnose backbone conformations were obtained from 2D H-1,H-1-trNOESY NMR utilizing methine-methine and methine-methyl correlations. They agreed well with conformations obtained from molecular dynamics (MD), validating the method for further predictions. In a set of mutants, MD predicted ligand flexibilities that were in good correlation with binding strength as confirmed on immobilized S. flexneri O-polysaccharide (PS) with surface plasmon resonance. In silico approaches combined with rapid screening on PS surfaces hence provide valuable strategies for TSP-based pathogen sensor design. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1417 KW - carbohydrates KW - molecular dynamics simulations KW - NMR spectroscopy KW - protein-carbohydrate interactions KW - surface plasmon resonance Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-519418 SN - 1866-8372 IS - 32 ER - TY - JOUR A1 - Kunstmann, Ruth Sonja A1 - Engström, Olof A1 - Wehle, Marko A1 - Widmalm, Göran A1 - Santer, Mark A1 - Barbirz, Stefanie T1 - Increasing the affinity of an O-Antigen polysaccharide binding site in Shigella flexneri bacteriophage Sf6 tailspike protein JF - Chemistry – A European Journal N2 - Broad and unspecific use of antibiotics accelerates spread of resistances. Sensitive and robust pathogen detection is thus important for a more targeted application. Bacteriophages contain a large repertoire of pathogen-binding proteins. These tailspike proteins (TSP) often bind surface glycans and represent a promising design platform for specific pathogen sensors. We analysed bacteriophage Sf6 TSP that recognizes the O-polysaccharide of dysentery-causing Shigella flexneri to develop variants with increased sensitivity for sensor applications. Ligand polyrhamnose backbone conformations were obtained from 2D H-1,H-1-trNOESY NMR utilizing methine-methine and methine-methyl correlations. They agreed well with conformations obtained from molecular dynamics (MD), validating the method for further predictions. In a set of mutants, MD predicted ligand flexibilities that were in good correlation with binding strength as confirmed on immobilized S. flexneri O-polysaccharide (PS) with surface plasmon resonance. In silico approaches combined with rapid screening on PS surfaces hence provide valuable strategies for TSP-based pathogen sensor design. KW - carbohydrates KW - molecular dynamics simulations KW - NMR spectroscopy KW - protein-carbohydrate interactions KW - surface plasmon resonance Y1 - 2020 U6 - https://doi.org/10.1002/chem.202000495 SN - 0947-6539 SN - 1521-3765 VL - 26 IS - 32 SP - 7263 EP - 7273 PB - Wiley-VCH CY - Weinheim ER - TY - THES A1 - Banerjee, Pallavi T1 - Glycosylphosphatidylinositols (GPIs) and GPI-anchored proteins tethered to lipid bilayers BT - modelling a complex interplay of carbohydrates, proteins and lipids BT - Modellierung eines komplexen Zusammenspiels von Kohlenhydraten, Proteinen und Lipiden N2 - Glycosylphosphatidylinositols (GPIs) are highly complex glycolipids that serve as membrane anchors to a large variety of eukaryotic proteins. These are covalently attached to a group of peripheral proteins called GPI-anchored proteins (GPI-APs) through a post-translational modification in the endoplasmic reticulum. The GPI anchor is a unique structure composed of a glycan, with phospholipid tail at one end and a phosphoethanolamine linker at the other where the protein attaches. The glycan part of the GPI comprises a conserved pseudopentasaccharide core that could branch out to carry additional glycosyl or phosphoethanolamine units. GPI-APs are involved in a diverse range of cellular processes, few of which are signal transduction, protein trafficking, pathogenesis by protozoan parasites like the malaria- causing parasite Plasmodium falciparum. GPIs can also exist freely on the membrane surface without an attached protein such as those found in parasites like Toxoplasma gondii, the causative agent of Toxoplasmosis. These molecules are both structurally and functionally diverse, however, their structure-function relationship is still poorly understood. This is mainly because no clear picture exists regarding how the protein and the glycan arrange with respect to the lipid layer. Direct experimental evidence is rather scarce, due to which inconclusive pictures have emerged, especially regarding the orientation of GPIs and GPI-APs on membrane surfaces and the role of GPIs in membrane organization. It appears that computational modelling through molecular dynamics simulations would be a useful method to make progress. In this thesis, we attempt to explore characteristics of GPI anchors and GPI-APs embedded in lipid bilayers by constructing molecular models at two different resolutions – all-atom and coarse-grained. First, we show how to construct a modular molecular model of GPIs and GPI-anchored proteins that can be readily extended to a broad variety of systems, addressing the micro-heterogeneity of GPIs. We do so by creating a hybrid link to which GPIs of diverse branching and lipid tails of varying saturation with their optimized force fields, GLYCAM06 and Lipid14 respectively, can be attached. Using microsecond simulations, we demonstrate that GPI prefers to “flop-down” on the membrane, thereby, strongly interacting with the lipid heads, over standing upright like a “lollipop”. Secondly, we extend the model of the GPI core to carry out a systematic study of the structural aspects of GPIs carrying different side chains (parasitic and human GPI variants) inserted in lipid bilayers. Our results demonstrate the importance of the side branch residues as these are the most accessible, and thereby, recognizable epitopes. This finding qualitatively agrees with experimental observations that highlight the role of the side branches in immunogenicity of GPIs and the specificity thereof. The overall flop-down orientation of the GPIs with respect to the bilayer surface presents the side chain residues to face the solvent. Upon attaching the green fluorescent protein (GFP) to the GPI, it is seen to lie in close proximity to the bilayer, interacting both with the lipid heads and glycan part of the GPI. However the orientation of GFP is sensitive to the type of GPI it is attached to. Finally, we construct a coarse-grained model of the GPI and GPI-anchored GFP using a modified version of the MARTINI force-field, using which the timescale is enhanced by at least an order of magnitude compared to the atomistic system. This study provides a theoretical perspective on the conformational behavior of the GPI core and some of its branched variations in presence of lipid bilayers, as well as draws comparisons with experimental observations. Our modular atomistic model of GPI can be further employed to study GPIs of variable branching, and thereby, aid in designing future experiments especially in the area of vaccines and drug therapies. Our coarse-grained model can be used to study dynamic aspects of GPIs and GPI-APs w.r.t plasma membrane organization. Furthermore, the backmapping technique of converting coarse-grained trajectory back to the atomistic model would enable in-depth structural analysis with ample conformational sampling. N2 - Glykosylphosphatidyl-Inositole (GPIs) sind komplex Glykolipide, die insbesondere auf der Oberfläche eukaryotischer Zellen als Verankerung einer Reihe unterschiedlicher Proteine dienen. GPIs werden den Proteinen als post-translationale Modifikationen im endoplasmotischen Reticulum hinzugefügt. Die Verankerung in der Membran wird durch einen Phospholipidrest hergestellt, das Protein ist dann über ein sich daran anschließendes Pseudo-Pentasaccharid und einen Phospoethanolaminrest kovalent an den GPI Anker gebunden. Das Pseudo-Pentasaccharid ist dabei proteinunabhängig eine invariante Struktur, kann aber an bestimmten Stellen durch weitere Carbohydratseitenketten und/oder Phosphoethanolaminreste wesentlich erweitert werden. GPI-verankerte Proteine (engl. GPI-anchored proteins, GPI-APs) sind an einer Reihe zellulärer Prozesse beteiligt; einige davon betreffen intra- und interzelluläre Signalübermittlung oder Proteintransport auf der Zelloberfläche; die Pathogenese vieler Parasiten, wie etwa Plasmodium falciparum (Malaria) wird entscheidend durch GPI-APs bestimmt; es können aber auch die bei vielen parasitischen Einzellern freien, ohne Protein auftretenden GPIs pathogene Wirkung entfalten wie etwa bei der Toxoplasmose (Toxoplasma gondii). Der allgemeine Zusammenhang von Struktur eines GPI-AP und seiner Funktion ist allerdings bis heute zum größten Teil unbekannt. Dies liegt zum einen daran, dass sich kein klares Bild zeichnen lässt, wie ein GPI-AP relativ zur Zellmembran exponiert wird. Die relevanten Zeit- und Längenskalen sind experimentell unzugänglich, und entsprechende in vivo oder in vitro Untersuchungen liefern lediglich indirekte Hinweise. Der Fall GPI-verankerter Proteine ist daher ein Beispiel, in dem computergestützte Modellierung einen wesentlichen Beitrag zur Aufklärung leisten kann. In der vorliegenden Arbeit wird zunächst ein atomistisches, molekulardynamisches Modell für GPIs und GPI-APs konstruiert und vorgestellt, mit dem sich GPI-APs auf der Längenskala einiger 10 Nanometer und einer Zeitskala von etwa 10 Mikrosekunden effizient untersuchen lassen. Modularität des Modells ist hierbei ein entscheidender Aspekt: mit den entwickelten Modellen lassen sich eine breite Palette von GPI Variationen darstellen. GPIs weisen, wie auch andere Proteinglykolysierungen eine sogenannte Mikroheterogenität auf; die Modifikation durch den Zucker kann sich zwischen den Kopien ein und desselben Proteins unterscheiden. Die technische Umsetzung erfolgt im Rahmen der sogenannten AMBER- Familie atomistischer Kraftfelder, die nach einem bestimmten Schema für biomolekulare Simulationen entwickelt wurden. Dabei werden existierende Modelle für Zucker (GLYCAM06) und Lipide (Lipid14) durch die Optimierung und Herleitung fehlender Parameter so angepasst, dass sich ein vollständiges GPI-AP in einer Lipid-Doppelschicht darstellen lässt. Dabei zeigt sich, dass das Protein vermittelt über den flexiblen Anker über einen beachtlichen Bewegungsspielraum verfügt. Im Falle des hier betrachteten Green Fluorescent Protein (GFP) kann man daher das Bild einer festen Orientierung des Proteins in Bezug auf die Lipidoberfläche verwerfen; wie in der Mehrzahl der Simulationen beobachtet, kann das GFP sogar vollständig auf der Lipidschicht zu liegen kommen. Weiterhin konnte nachgewiesen werden, dass eine Reihe möglicher Seitenketten des GPI Ankers, die zu Parasiten wie Toxoplasma gondii gehören und bei entsprechenden Immunreaktionen relevant sind, tatsächlich so exponiert werden, dass ihre Rolle als Rezeptoren unterstrichen wird. Das Pseudopentasaccharid selbst ist dabei teilweise in die Kopfgruppenregion der Lipidschicht eingebettet. Des Weiteren wurde hier das atomistische Modell auf eine vergröberte Darstellung im Rahmen des MARTINI Kraftfelds projiziert, um die zugänglichen Zeit- und Längenskalen noch einmal um einen Faktor 10 zu erweitern. Somit werden auch Studien GPI-APs möglich, bei denen sich ihre Dynamik in heterogenen Lipidschichten untersuchen lässt, etwa um Fragen zu beantworten, wie diese Proteine mit verschiedenen Membrandomänen assoziieren. Insgesamt werden mit dieser Arbeit eine Reihe von Ansätzen aufgezeigt, wie sich GPI verankerte Proteine möglicherweise effektiver in speziell angepassten Experimenten und in größerem Detail untersuchen lassen, als dies bisher möglich war. T2 - Glykosylphosphatidylinositole (GPIs) und GPI-verankerte Proteine, die an Lipid-Doppelschichten gebunden sind KW - GPI KW - carbohydrates KW - membrane KW - protein KW - molecular dynamics KW - coarse-graining KW - martini KW - GPI KW - Kohlenhydrate KW - grobkörnig KW - martini KW - Membran KW - Molekular-dynamik KW - Protein Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-489561 ER - TY - GEN A1 - Linker, Torsten T1 - Addition of Heteroatom Radicals to endo-Glycals T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Radical reactions have found many applications in carbohydrate chemistry, especially in the construction of carbon–carbon bonds. The formation of carbon–heteroatom bonds has been less intensively studied. This mini-review will summarize the efforts to add heteroatom radicals to unsaturated carbohydrates like endo-glycals. Starting from early examples, developed more than 50 years ago, the importance of such reactions for carbohydrate chemistry and recent applications will be discussed. After a short introduction, the mini-review is divided in sub-chapters according to the heteroatoms halogen, nitrogen, phosphorus, and sulfur. The mechanisms of radical generation by chemical or photochemical processes and the subsequent reactions of the radicals at the 1-position will be discussed. This mini-review cannot cover all aspects of heteroatom-centered radicals in carbohydrate chemistry, but should provide an overview of the various strategies and future perspectives T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 873 KW - radicals KW - carbohydrates KW - heteroatoms KW - synthesis Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-459970 SN - 1866-8372 IS - 873 ER - TY - JOUR A1 - Linker, Torsten T1 - Addition of Heteroatom Radicals to endo-Glycals JF - Chemistry N2 - Radical reactions have found many applications in carbohydrate chemistry, especially in the construction of carbon–carbon bonds. The formation of carbon–heteroatom bonds has been less intensively studied. This mini-review will summarize the efforts to add heteroatom radicals to unsaturated carbohydrates like endo-glycals. Starting from early examples, developed more than 50 years ago, the importance of such reactions for carbohydrate chemistry and recent applications will be discussed. After a short introduction, the mini-review is divided in sub-chapters according to the heteroatoms halogen, nitrogen, phosphorus, and sulfur. The mechanisms of radical generation by chemical or photochemical processes and the subsequent reactions of the radicals at the 1-position will be discussed. This mini-review cannot cover all aspects of heteroatom-centered radicals in carbohydrate chemistry, but should provide an overview of the various strategies and future perspectives KW - radicals KW - carbohydrates KW - heteroatoms KW - synthesis Y1 - 2020 U6 - https://doi.org/10.3390/chemistry2010008 SN - 2624-8549 VL - 2 IS - 1 SP - 80 EP - 92 PB - MDPI CY - Basel ER -