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Over the past few decades, Single-Particle Analysis (SPA), in combination with cryo-transmission electron microscopy, has evolved into one of the leading technologies for structural analysis of biological macromolecules. It allows the investigation of biological structures in a close to native state at the molecular level. Within the last five years the achievable resolution of SPA surpassed 2°A and is now approaching atomic resolution, which so far has only been possible with Xray crystallography in a far from native environment. One remaining problem of Cryo-Electron Microscopy (cryo-EM) is the weak image contrast. Since the introduction of cryo-EM in the 1980s phase plates have been investigated as a potential tool to overcome these contrast limitations. Until now, technical problems and instrumental deficiencies have made the use of phase plates difficult; an automated workflow, crucial for the acquisition of 1000s of micrographs needed for SPA, was not possible. In this thesis, a new Zernike-type Phase Plate (PP) was developed and investigated. Freestanding metal films were used as a PP material to overcome the ageing and contamination problems of standard carbon-based PPs. Several experiments, evaluating and testing various metals, ended with iridium as the best-suited material. A thorough investigation of the properties of iridium PP followed in the second part of this thesis. One key outcome is a new operation mode, the rocking PP. By using this rocking-mode, fringing artifacts, another obstacle of Zernike PPs, could be solved. In the last part of this work, acquisition and reconstruction of SPA data of apoferritin was performed using the iridium PP in rocking-mode. A special semi-automated workflow for the acquisition of PP data was developed and tested. The recorded PP data was compared to an additional reference dataset without a PP, acquired following a conventional workflow.
Nanotemplates for the combined structural and functional analysis of membrane-associated proteins
(2019)
Plasma membranes are essential for life because they give cells an identity. Plasma membranes are almost impermeable to fluids and substances. Still, transport between inside and outside needs to be possible. An important transport way is endocytosis. This mechanism relies on membrane-associated proteins that sense and induce curvature to the plasma membrane. However, the physics and structural dynamics behind proteins acting on membranes is not well understood. There is a standard method in vitro to investigate membrane-associated proteins sensing spherical geometries: They are incubated on unilamellar vesicles. This procedure allows to analyze these proteins in their bound state. This approach is inappropriate for GRAF1 (GTPase Regulator Associated with Focal Adhesion Kinase-1), a key player in endocytosis because it senses tubular geometries instead. However, GRAF1 extrudes lipid tubes from vesicles that can be analyzed. Still, this is a limited method because these tubes suffer from inhomogeneity and they do not enable the observation of intermediate and lower concentration binding states. To overcome this issue they can be incubated on pre-tubular structures called nanotemplates. There have been studies using carbon nanotubes and Galactosylceramide lipid tubes as nanotemplates. These approaches require complex chemical modifications or expensive components and they are not necessarily flexible. In this work we present a simple and easy new approach to prepare nanotemplates using Folch lipid mixture. We show on the basis of BPG, a truncate of GRAF1, that our nanotemplates are suitable for Cryo-EM and that it is possible to use IHRSR (Iterative Helical Real Space Reconstruction) to analyze the structure of BPG in its bound state. Moreover, the qualification for Cryo-EM allows to use plunge freezing to interrupt the incubation on our nanotemplates abruptly. This enables the analysis of intermediate binding states to understand the binding process.
The three biodegradable polymers polylactic acid (PLA), polyhydroxybutyrate (PHB) and polybutylene adipate terephthalate (PBAT) were coated with hydrogenated amorphous carbon layers (a-C:H) in the context of this thesis. A direct alignment of the sample surface to the source was chosen, resulting in the deposition of a robust, r-type a-C:H. At the same time, a partly covered silicon wafer was placed together with the polymers in the coating chamber and was coated. Silicon is a hard material and serves as a reference for the applied layers. Due to the hardness of the material, no mixed phase occurs between the substrate and the applied layer (no interlayer formation). In addition, the thickness of the applied layer can be estimated with the help of the silicon sample.
The deposition of the layer was realized by radio frequency plasma enhanced chemical vapor deposition (RF-PECVD). For the coating the samples were pre-treated with an oxygen plasma. Acetylene was used as precursor gas for the plasma coating. Coatings with increasing thickness in 50 nm steps from 0-500 nm were realised.
The surface analysis was performed using several techniques: The morphology and layer stability were analyzed with scanning electron microscopy (SEM) measurements. The wettability was determined by contact angle technique. In addition, the contact angles provide macroscopic information about the bond types of the carbon atoms present on the surface. For microscopic analysis of the chemical composition of the sample and layer surfaces, diffuse reflectance Fourier transform infrared spectroscopy (DRIFT) as well as synchrotron based X-ray photon spectroscopy (XPS) and near edge X-ray absorption fine structure spectroscopy (NEXAFS) were used.
All coated polymers showed several cases of layer failure due to internal stress in the layers. However, these were at different layer thicknesses, so there was a substrate effect. In addition, it is visible in the SEM images that the coatings of PLA and PHB can cause the applied layer to wave, the so-called cord buckling. This does not occur with polymer PBAT, which indicates a possible better bonding of the layer to the polymer. The chemical analyses of the layer surfaces show for each material a layer thickness dependent ratio of sp² to sp³ bonds of carbon, which alternately dominate the layer. In all polymers, the sp³ bond initially dominates, but the sp² to sp³ ratio changes at different intervals. Although the polymers were coated in the same plasma, i.e. the respective layer thicknesses (50 nm, 100 nm, ...) were applied in the same plasma process, the respective systems differed considerably from each other. A substrate effect is therefore demonstrably present. In addition, it was found that a change in the dominant bond from sp³ to sp² is an indication ofan upcoming layer failure of the a-C:H layer deposited on the polymer. In the case of PLA, this occurs immediately with change to sp² as the dominant bond; in the case of PHB and PBAT, this occurs with different delay to increased layer thicknesses (at PHB 100 nm, at PBAT approx. 200 nm.
Overall, this thesis shows that there is a substrate effect in the coating of the biodegradable polymers PLA, PHB and PBAT, since despite the same coating there is a different chemical composition of the surface at the respective layer thicknesses. In addition, a layer failure can be predicted by analyzing the existing bond.