Core shell hybrids based on noble metal nanoparticles and conjugated polymers: synthesis and characterization

Noble metal nanoparticles of different sizes and shapes combined with conjugated functional polymers give rise to advanced core shell hybrids with interesting physical characteristics and potential applications in sensors or cancer therapy. In this paper, a versatile and facile synthesis of core shell systems based on noble metal nanoparticles (AuNPs, AgNPs, PtNPs), coated by copolymers belonging to the class of substituted polyacetylenes has been developed. The polymeric shells containing functionalities such as phenyl, ammonium, or thiol pending groups have been chosen in order to tune hydrophilic and hydrophobic properties and solubility of the target core shell hybrids. The Au, Ag, or Pt nanoparticles coated by poly(dimethylpropargylamonium chloride), or poly(phenylacetylene-co-allylmercaptan). The chemical structure of polymeric shell, size and size distribution and optical properties of hybrids have been assessed. The mean diameter of the metal core has been measured (about 10-30 nm) with polymeric shell of about 2 nm

Computationally Designed Epitope-Mediated Imprinted Polymers versus Conventional Epitope Imprints for the Detection of Human Adenovirus in Water and Human Serum Samples

Detection of pathogenic viruses for point-of-care applications has attracted great attention since the COVID-19 pandemic. Current virus diagnostic tools are laborious and expensive, while requiring medically trained staff. Although user-friendly and cost-effective biosensors are utilized for virus detection, many of them rely on recognition elements that suffer major drawbacks. Herein, computationally designed epitope-imprinted polymers (eIPs) are conjugated with a portable piezoelectric sensing platform to establish a sensitive and robust biosensor for the human pathogenic adenovirus (HAdV). The template epitope is selected from the knob part of the HAdV capsid, ensuring surface accessibility. Computational simulations are performed to evaluate the conformational stability of the selected epitope. Further, molecular dynamics simulations are executed to investigate the interactions between the epitope and the different functional monomers for the smart design of eIPs. The HAdV epitope is imprinted via the solid-phase synthesis method to produce eIPs using in silico-selected ingredients. The synthetic receptors show a remarkable detection sensitivity (LOD: 102 pfu mL–1) and affinity (dissociation constant (Kd): 6.48 × 10–12 M) for HAdV. Moreover, the computational eIPs lead to around twofold improved binding behavior than the eIPs synthesized with a well-established conventional recipe. The proposed computational strategy holds enormous potential for the intelligent design of ultrasensitive imprinted polymer binders

Synthesis and Microstructural Investigations of Organometallic Pd(II) Thiol-Gold Nanoparticles Hybrids

In this work the synthesis and characterization of gold nanoparticles functionalized by a novel thiol-organometallic complex containing Pd(II) centers is presented. Pd(II) thiol,trans, trans-[dithiolate-dibis(tributylphosphine)dipalladium(II)-4,4′-diethynylbiphenyl] was synthesized and linked to Au nanoparticles by the chemical reduction of a metal salt precursor. The new hybrid made of organometallic Pd(II) thiol-gold nanoparticles, shows through a single S bridge a direct link between Pd(II) and Au nanoparticles. The size-control of the Au nanoparticles (diameter range 2–10 nm) was achieved by choosing the suitable AuCl4−/thiol molar ratio. The size, strain, shape, and crystalline structure of these functionalized nanoparticles were determined by a full-pattern X-ray powder diffraction analysis, high-resolution TEM, and X-ray photoelectron spectroscopy. Photoluminescence spectroscopy measurements of the hybrid system show emission peaks at 418 and 440 nm. The hybrid was exposed to gaseous NOxwith the aim to evaluate the suitability for applications in sensor devices; XPS measurements permitted to ascertain and investigate the hybrid –gas interaction

Structural basis for the Pr-Pfr long-range signaling mechanism of a full-length bacterial phytochrome at the atomic level

Phytochromes constitute a widespread photoreceptor family that typically interconverts between two photostates called Pr (red light-absorbing) and Pfr (far-red light-absorbing). The lack of full-length structures solved at the (near-)atomic level in both pure Pr and Pfr states leaves gaps in the structural mechanisms involved in the signal transmission pathways during the photoconversion. Here, we present the crystallographic structures of three versions from the plant pathogen Xanthomonas campestris virulence regulator XccBphP bacteriophytochrome, including two full-length proteins, in the Pr and Pfr states. The structures show a reorganization of the interaction networks within and around the chromophore-binding pocket, an α-helix/β-sheet tongue transition, and specific domain reorientations, along with interchanging kinks and breaks at the helical spine as a result of the photoswitching, which subsequently affect the quaternary assembly. These structural findings, combined with multidisciplinary studies, allow us to describe the signaling mechanism of a full-length bacterial phytochrome at the atomic level.Fil: Otero, Lisandro Horacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Plataforma Argentina de Biología Estructural y Metabolómica; ArgentinaFil: Foscaldi, Sabrina Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Antelo, Giuliano Tomás. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Rosano, German Leandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Sirigu, Serena. Soleil Synchrotron; FranciaFil: Klinke, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Plataforma Argentina de Biología Estructural y Metabolómica; ArgentinaFil: Defelipe, Lucas Alfredo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. European Molecular Biology Laboratory Hamburg; AlemaniaFil: Sánchez Lamas, Maximiliano. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Battocchio, Giovanni. Technishe Universitat Berlin; AlemaniaFil: Conforte, Valeria Paola. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Ciencia y Tecnología "Dr. César Milstein". Fundación Pablo Cassará. Instituto de Ciencia y Tecnología "Dr. César Milstein"; ArgentinaFil: Vojnov, Adrián Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Ciencia y Tecnología "Dr. César Milstein". Fundación Pablo Cassará. Instituto de Ciencia y Tecnología "Dr. César Milstein"; ArgentinaFil: Chavas, Leonard M.G.. Soleil Synchrotron; Francia. Nagoya University; JapónFil: Goldbaum, Fernando Alberto. Plataforma Argentina de Biología Estructural y Metabolómica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Mroginski, Maria Andrea. Technishe Universitat Berlin; AlemaniaFil: Rinaldi, Jimena Julieta. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Bonomi, Hernán Ruy. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentin

Mono- and bi-functional arenethiols as surfactants for gold nanoparticles: synthesis and characterization

Stable gold nanoparticles stabilized by different mono and bi-functional arenethiols, namely, benzylthiol and 1,4-benzenedimethanethiol, have been prepared by using a modified Brust's two-phase synthesis. The size, shape, and crystalline structure of the gold nanoparticles have been determined by high-resolution electron microscopy and full-pattern X-ray powder diffraction analyses. Nanocrystals diameters have been tuned in the range 2 ÷ 9 nm by a proper variation of Au/S molar ratio. The chemical composition of gold nanoparticles and their interaction with thiols have been investigated by X-ray photoelectron spectroscopy. In particular, the formation of networks has been observed with interconnected gold nanoparticles containing 1,4-benzenedimethanethiol as ligand

Structural basis for the Pr-Pfr long-range signaling mechanism of a full-length bacterial phytochrome at the atomic level

Phytochromes constitute a widespread photoreceptor family that typically interconverts between two photostates called Pr (red light–absorbing) and Pfr (far-red light–absorbing). The lack of full-length structures solved at the (near-)atomic level in both pure Pr and Pfr states leaves gaps in the structural mechanisms involved in the signal transmission pathways during the photoconversion. Here, we present the crystallographic structures of three versions from the plant pathogen Xanthomonas campestris virulence regulator XccBphP bacteriophytochrome, including two full-length proteins, in the Pr and Pfr states. The structures show a reorganization of the interaction networks within and around the chromophore-binding pocket, an α-helix/β-sheet tongue transition, and specific domain reorientations, along with interchanging kinks and breaks at the helical spine as a result of the photoswitching, which subsequently affect the quaternary assembly. These structural findings, combined with multidisciplinary studies, allow us to describe the signaling mechanism of a full-length bacterial phytochrome at the atomic level.DFG, 221545957, SFB 1078: Proteinfunktion durch ProtonierungsdynamikEC/H2020/664726/EU/EMBL Interdisciplinary, International and Intersectorial Postdocs/EI3PO

Computergestützte Studien zu den dynamischen Eigenschaften von Phytochromen

Phytochromes are superfamily of bistable photoreceptor molecules found in several organisms, such as plants, bacteria, algae and fungi. They serve as light sensors, mainly detecting red and far red light, governing a range of functions, such as seed germination, greening, stem extension, and flowering in plants. Due to their important role in several organism they have been studied for decades, tough their full mechanism of action remains elusive. In this work we investigated the dynamical properties of phytochromes by means of computational methods. Furthermore we extended the studies to the vibrational properties of the light sensitive chromophore, an open tetrapyrrol bilin, contained inside the phytochromes. In the first chapter of this work we start with a general description of phytochromes and their structure, including peculiar features such as a knot like structure connecting two domains. We give a brief exposition of differences and varieties of phytochromes found in plants, bacteria and other organism based on their light sensitivity and photocycle behaviour. We discuss the known conformational changes that happen during the photocycle, both in the chromophore and in the protein scaffold. In the second chapter we briefly summarise the theory behind the computational methods used, from molecular dynamic (MD) to quantum mechanic (QM). We outlined the foundations of MD, a computational method widely employed for the studify of large biomolecules such as complex proteins. We give a short exposition on how to include the effect of the environment, with whom the protein interacts during the simulations. Of the many algorithm developed since the introduction of MD method, we list the ones employed in our simulations. We continue then with a section on two methods we employed developed to improve conformational sampling, an issue that affects all MD simulations and has been tackled by many researcher over the years. In the last part we give a description of the employed QM/MM method adopted to evaluate vibrational properties of the chromophore, whose results can then be compared with experimental results. In the third chapter we include a summary of the computational details of our calculations. Beginning with how models are prepared, a starting step sometimes overlooked, but that has deep repercussion on all the simulations that follow. We also give a brief exposition of the used softwares and their capabilities, we then conclude with a section on analysis tools. A proper analysis of the results is as or even more important than the simulations itself, so the choice of the adequate analysis method that better correlates trajectories with actual physical properties, is of greatest importance for the final interpretation of the vast amount of gathered data. The fourth chapter should be the most interesting for the reader, since it contains the highlights of the results obtained during this PhD period. Results are grouped by system and their observed dynamical behaviour, starting with arguably the most studied phytochrome, Deinocccus radiodurans(DrBph), followed by Agp2 from Agrobacterium tumefaciens, Xantomonas campestris (XccBph) phytochromes and lastly GAF-3, a cyanobacteriochrome derived from Synechocystis sp. PCC6803. Thanks to the the use of enhanced sampling methods, we were able to study the dynamics of these phyotchromes in a wider variety of conformations and relating them to some specific structural features. Example is the effect of simulating the monomer versus the naturally occurring dimer in solution, or the deletion of a linker knot from the protein scaffold, in DrBph. These enhanced methods made possible to sample secondary structural transitions in Agp2, a phenomenon that would otherwise require order of magnitudes longer conventional MD. In addition was possible to assess the stability of different dimer construct on the longer time scale and determine if one conformation is more or less stable than another one in XccBph, a question that has always driven curiosity, since most of naturally occurring phytochromes appears as parallel dimer, but few physiological functional ones adopt an antiparallel configuration. Other computational methods were adopted, including constant pH calculations, giving accurate pKa values predictions for key residues in the chromophore vicinity and their most likely protonation states in Agp2. This is turn influences the correspondent MD sampling, giving a better and more physiologically accurate representation of the dynamic proton interchange between residues happening in the protein. Finally the results of QM/MM calculations on GAF-3, an interesting red-green photo-switch, aimed to reproduce and help interpret experimental spectra and to link spectra to conformations.Phytochromen sind eine Superfamilie von bistabilen Photorezeptormolekülen, die in verschiedenen Organismen wie Pflanzen, Bakterien, Algen und Pilzen vorkommen. Sie dienen als Lichtsensoren, die hauptsächlich rotes und fernes rotes Licht erkennen und eine Reihe von Funktionen steuern, wie z. B. die Keimung von Samen, das Ergrünen, die Ausdehnung des Stängels und die Blüte bei Pflanzen. Aufgrund ihrer wichtigen Rolle in verschiedenen Organismen werden sie seit Jahrzehnten erforscht, obwohl ihr vollständiger Wirkmechanismus noch immer schwer zu verstehen ist. In dieser Arbeit haben wir die dynamischen Eigenschaften von Phytochromen mit Hilfe von Berechnungsmethoden untersucht. Darüber hinaus haben wir die Untersuchungen auf die Schwingungseigenschaften des lichtempfindlichen Chromophors, eines offenen Tetrapyrrol-Bilins, das im Inneren der Phytochrome enthalten ist, ausgeweitet. Im ersten Kapitel dieser Arbeit beginnen wir mit einer allgemeinen Beschreibung der Phytochrome und ihrer Struktur, einschließlich besonderer Merkmale wie einer knotenartigen Struktur, die zwei Domänen verbindet. Wir geben eine kurze Darstellung der Unterschiede und Varietäten von Phytochromen, die in Pflanzen, Bakterien und anderen Organismen gefunden werden, basierend auf ihrer Lichtempfindlichkeit und ihrem Verhalten im Photozyklus. Des Weiteren diskutieren wir die bekannten Konformationsänderungen, die während des Photozyklus stattfinden, sowohl im Chromophor als auch im Proteingerüst. Im zweiten Kapitel fassen wir kurz die Theorie hinter den verwendeten Berechnungsmethoden zusammen, von der Molekulardynamik (MD) bis zur Quantenmechanik (QM). Unter anderem skizzieren wir die Grundlagen der MD, einer Berechnungsmethode, die häufig für die Untersuchung großer Biomoleküle wie komplexer Proteine eingesetzt wird und geben eine kurze Darstellung, wie man den Effekt der Umgebung, mit der das Protein während der Simulationen interagiert, einbezieht. Darüber hinaus listen wir von den vielen Algorithmen, die seit der Einführung der MD-Methode entwickelt wurden, die in unseren Simulationen verwendeten auf. Im weiteren Verlauf dieses Kapitels fahren wir mit einem Abschnitt über zwei von uns verwendete Methoden fort, die entwickelt wurden, um das Konformations-Sampling zu verbessern, ein Problem, das alle MD-Simulationen betrifft und im Laufe der Jahre von vielen Forschern angegangen wurde. Im letzten Teil beschreiben wir die eingesetzte QM/MM-Methode, die zur Auswertung der Schwingungseigenschaften des Chromophors verwendet wurde, deren Ergebnisse dann mit experimentellen Ergebnissen verglichen werden können. Im dritten Kapitel fassen wir die rechnerischen Details unserer Berechnungen zusammen. Wir beginnen damit, wie die Modelle vorbereitet werden. Dieser Anfangsschritt wird manchmal übersehen wird, hat aber tiefgreifende Auswirkungen auf alle folgenden Simulationen. Hierbei geben wir auch eine kurze Darstellung der verwendeten Software und ihrer Möglichkeiten und schließen dann mit einem Abschnitt über Analysewerkzeuge. Die Wahl der geeigneten Analysemethode, die die Trajektorien besser mit den tatsächlichen physikalischen Eigenschaften korreliert, ist daher von größter Bedeutung für die endgültige Interpretation der riesigen Menge an gesammelten Daten. Das vierte Kapitel dürfte für den Leser das interessanteste sein, da es die Höhepunkte der während dieser Promotionszeit erzielten Ergebnisse enthält. Die Ergebnisse sind nach Systemen und ihrem beobachteten dynamischen Verhalten gruppiert, beginnend mit dem wohl am besten untersuchten Phytochrom, Deinocccus radiodurans(DrBph), gefolgt von Agp2 aus Agrobacterium tumefaciens, Xantomonas campestris (XccBph) Phytochrome und schließlich GAF-3, ein Cyanobakteriochrom, das aus Synechocystis sp. PCC6803 stammt. Dank der Verwendung erweiterter Sampling-Methoden konnten wir die Dynamik dieser Phyotchrome in einer größeren Vielfalt von Konformationen un- tersuchen und sie mit einigen spezifischen strukturellen Merkmalen in Verbindung bringen. Ein Beispiel dafür ist der Effekt der Simulation des Monomers gegenüber dem natürlich vorkommenden Dimer in Lösung oder der Deletion eines Linkerknotens aus dem Proteingerüst, in DrBph. Diese verbesserten Methoden ermöglichten es, sekundärstrukturelle Übergänge in Agp2 zu untersuchen, ein Phänomen, für das sonst eine um Größenordnungen längere konventionelle MD erforderlich wäre. Außerdem war es möglich, die Stabilität verschiedener Dimerkonstrukte auf der längeren Zeitskala zu bewerten und zu bestimmen, ob eine Konformation mehr oder weniger stabil ist als eine andere in XccBph. Dies ist eine Frage, die schon immer das wissenschaftliche Interesse geweckt hat, da die meisten natürlich vorkommenden Phytochrome als parallele Dimere auftreten, aber nur wenige physiologisch funktionale eine antiparallele Konfiguration annehmen. Es wurden weitere Berechnungsmethoden angewandt, darunter Berechnungen mit konstantem pH-Wert, die genaue Vorhersagen der pKa-Werte für Schlüsselreste in der Nähe des Chromophors und ihrer wahrscheinlichsten Protonierungszustände in Agp2 liefern. Dies wiederum beeinflusst das entsprechende MD-Sampling, was eine bessere und physiologisch genauere Darstellung des dynamischen Protonenaustauschs zwischen den Resten im Protein ergibt. Schließlich wurden die Ergebnisse von QM/MM-Rechnungen an GAF-3, einem interessanten Rot-Grün-Photoschalter, vorgestellt, die darauf abzielen, experimentelle Spektren zu reproduzieren und zu interpretieren sowie Spektren mit Konformationen zu verknüpfen