Ewelina Lipiec

Infrared nanospectroscopy characterization of oligomeric and fibrillar aggregates during amyloid formation

Amyloids are insoluble protein fibrillar aggregates. The importance of characterizing their aggregation has steadily increased because of their link to human diseases and material science applications. In particular, misfolding and aggregation of the Josephin domain of ataxin-3 is implicated in spinocerebellar ataxia-3. Infrared nanospectroscopy, simultaneously exploiting atomic force microscopy and infrared spectroscopy, can characterize at the nanoscale the conformational rearrangements of proteins during their aggregation. Here we demonstrate that we can individually characterize the oligomeric and fibrillar species formed along the amyloid aggregation. We describe their secondary structure, monitoring at the nanoscale an α-to-β transition, and couple these studies with an independent measurement of the evolution of their intrinsic stiffness. These results suggest that the aggregation of Josephin proceeds from the monomer state to the formation of spheroidal intermediates with a native structure. Only successively, these intermediates evolve into misfolded aggregates and into the final fibrils.

Chemical state of chromium in sewage sludge ash based phosphorus-fertilisers

Sewage sludge ash (SSA) based P-fertilisers were produced by thermochemical treatment of SSA with Cl-donors at approximately 1000°C. During this thermochemical process heavy metals are separated as heavy metal chlorides via the gas phase. Chromium cannot be separated under normal conditions. The risk of the development of toxic Cr(VI) during the thermochemical process was investigated. X-ray Absorption Spectroscopy measurements showed that SSA and thermochemically treated SSA with CaCl2, MgCl2 and NaCl contain Cr(III) compounds only. In contrast, treating SSA with elevated quantities of Na2CO3, to enhance the plant-availability of the phosphate phases of the fertiliser, developed approximately 10-15% Cr(VI). Furthermore, Raman microspectroscopy showed that using Mg-carbonate reduces the risk of a Cr(VI) development during thermochemical treatment. Additionally, leaching tests showed that only a Cr-water solubility>10% is an indicator for Cr(VI) in SSA based P-fertilisers.

Determination of phosphorus fertilizer soil reactions by Raman and synchrotron infrared microspectroscopy

The reaction mechanisms of phosphate-bearing mineral phases from sewage sludge ash-based fertilizers in soil were determined by Raman and synchrotron infrared microspectroscopy. Different reaction mechanisms in wet soil were found for calcium and magnesium (pyro-) phosphates. Calcium orthophosphates were converted over time to hydroxyapatite. Conversely, different magnesium phosphates were transformed to trimagnesium phosphate. Since the magnesium phosphates are unable to form an apatite structure, the plant-available phosphorus remains in the soil, leading to better growth results observed in agricultural pot experiments. The pyrophosphates also reacted very differently. Calcium pyrophosphate is unreactive in soil. In contrast, magnesium pyrophosphate quickly formed plant-available dimagnesium phosphate.

Novel in situ methodology to observe the interactions of chemotherapeutical Pt drugs with DNA under physiological conditions

The binding of the antitumor drug cisplatin with DNA was determined by means of in situ resonant inelastic X-ray scattering (RIXS) spectroscopy. Because of the penetrating properties of hard X-rays, we could determine, under physiological conditions, the identity and number of platinum complexes present. In situ RIXS revealed that under physiological conditions, water molecules replace chloride ligands owing to drug hydration. The subsequent interaction with DNA, led to the bonding of the aqua complexes into the DNA structure with simultaneous loss of the coordinating water and chloride ion. The data analysis reveals that Pt is coordinated by two adjacent guanines giving cis-[Pt(NH3)2{d(GpG)-N7(1),-N7(2)}] upon losing its coordinating water or chloride ligands.

Preparation of Well-Defined DNA Samples for Reproducible Nanospectroscopic Measurements.

Due to its well-defined topology and chemical structure, DNA could become a biological standard sample in the field of nanospectroscopy. Tip-enhanced Raman spectroscopy (TERS) provides new insights into individual DNA molecules immobilized on flat mica crystals. The high sensitivity of TERS is used to assess the chemical changes that appear in DNA upon different surface immobilization protocols.

SR-FTIR Coupled with Principal Component Analysis Shows Evidence for the Cellular Bystander Effect

Synchrotron radiation-Fourier transform infrared (SR-FTIR) microscopy coupled with multivariate data analysis was used as an independent modality to monitor the cellular bystander effect. Single, living prostate cancer PC-3 cells were irradiated with various numbers of protons, ranging from 50–2,000, with an energy of either 1 or 2 MeV using a proton microprobe. SR-FTIR spectra of cells, fixed after exposure to protons and nonirradiated neighboring cells (bystander cells), were recorded. Spectral differences were observed in both the directly targeted and bystander cells and included changes in the DNA backbone and nucleic bases, along with changes in the protein secondary structure. Principal component analysis (PCA) was used to investigate the variance in the entire data set. The percentage of bystander cells relative to the applied number of protons with two different energies was calculated. Of all the applied quantities, the dose of 400 protons at 2 MeV was found to be the most effective for causing significant macromolecular perturbation in bystander PC-3 cells.

Vibrational Changes Induced by Electron Transfer in Surface Bound Azurin Metalloprotein Studied by Tip-Enhanced Raman Spectroscopy and Scanning Tunneling Microscopy

The copper protein azurin, due to the peculiar coupling of its optical and vibronic properties with electron transfer (ET) and its biorecognition capabilities, is a very promising candidate for bioelectronic, bio-optoelectronic and biosensor applications. However, a complete understanding of the fundamental processes relating azurin ET and its optical and vibronic characteristics with the charge transport mechanisms occurring in proteins bound to a conductive surface, the typical scenario for a biosensor or bioelectronic component, is still lacking. We studied azurin proteins bound to a gold electrode surface by scanning tunneling microscopy combined with tip-enhanced Raman spectroscopy (STM-TERS). Robust TER spectra were obtained, and the proteins vibronic response under optical excitation in resonance with its ligand-to-metal charge transfer band was found to be affected by the tunneling parameters, indicating a direct involvement of the active site vibrations in the electron transport process.

Basis set dependence using DFT/B3LYP calculations to model the Raman spectrum of thymine.

Raman spectroscopy (including surface enhanced Raman spectroscopy (SERS) and tip enhanced Raman spectroscopy (TERS)) is a highly promising experimental method for investigations of biomolecule damage induced by ionizing radiation. However, proper interpretation of changes in experimental spectra for complex systems is often difficult or impossible, thus Raman spectra calculations based on density functional theory (DFT) provide an invaluable tool as an additional layer of understanding of underlying processes. There are many works that address the problem of basis set dependence for energy and bond length consideration, nevertheless there is still lack of consistent research on basis set influence on Raman spectra intensities for biomolecules. This study fills this gap by investigating of the influence of basis set choice for the interpretation of Raman spectra of the thymine molecule calculated using the DFT/B3LYP framework and comparing these results with experimental spectra. Among 19 selected Poples basis sets, the best agreement was achieved using 6-31[Formula: see text](d,p), 6-31[Formula: see text](d,p) and 6-11[Formula: see text]G(d,p) sets. Adding diffuse functions or polarized functions for small basis set or use of a medium or large basis set without diffuse or polarized functions is not sufficient to reproduce Raman intensities correctly. The introduction of the diffuse functions ([Formula: see text]) on hydrogen atoms is not necessary for gas phase calculations. This work serves as a benchmark for further research on the interaction of ionizing radiation with DNA molecules by means of ab initio calculations and Raman spectroscopy. Moreover, this work provides a set of new scaling factors for Raman spectra calculation in the framework of DFT/B3LYP method.

Nanoscale Investigation into the Cellular Response of Glioblastoma Cells Exposed to Protons

Exposure to ionizing radiation can induce cellular defense mechanisms including cell activation and rapid proliferation prior to metastasis and in extreme cases can result in cell death. Herewith we apply infrared nano- and microspectroscopy combined with multidimensional data analysis to characterize the effect of ionizing radiation on single glioblastoma nuclei isolated from cells treated with 10 Gy of X-rays or 1 and 10 Gy of protons. We observed chromatin fragmentation related to the formation of apoptotic bodies following X-ray exposure. Following proton irradiation we detected evidence of a DNA conformational change (B-DNA to A-DNA transition) related to DNA repair and accompanied by an increase in protein content related to the synthesis of peptide enzymes involved in DNA repair. We also show that proton exposure can increase cholesterol and sterol ester synthesis, which are important lipids involved in the metastatic process changing the fluidity of the cellular membrane in preparation for rapid proliferation.