https://researchdata.se/sv/catalogue Search results sv Data published here is the basis for the manuscript for Spectrochimica Acta Part A with the title: The structure of amyloid-beta(1-42) oligomers in membrane-mimetic environments. Here, we demonstrate that Aβ42 oligomers preserve their β-sheet structure in aqueous solution and in a membrane-mimicking environment consisting of either anionic or zwitterionic membranes. Structure and Aβ42 aggregation kinetics were hardly affected by the presence of lipids, showing only slight effects observed during the initial oligomer formation at low temperatures. Our isotope-edited infrared experiments reveal that the backbone carbonyl of V18 residue is located in β-sheets in the presence and in the absence of lipids. Such insensitivity of Aβ42 to the presence of lipid vesicles suggests a distinct aggregation behaviour of Aβ42, compared to Aβ40. The data is in .DPT format, which can be viewed using any text editing program. Tue, 02 Sep 2025 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17045-sthlmuni-29910311 https://researchdata.se/sv/catalogue/dataset/doi-10-17045-sthlmuni-29910311 Stockholms universitet Oleksandra Kurysheva Nina Mann Uliana Afonina Andreas Barth Analysis of the amide I band of proteins is probably the most wide-spread application of bioanalytical infrared spectroscopy. Although highly desirable for a more detailed structural interpretation, a quantitative description of this absorption band is still difficult. This work optimized several electrostatic models with the aim to reproduce the effect of the protein environment on the intrinsic wavenumber of a local amide I oscillator. We considered the main secondary structures – α-helices, parallel and antiparallel β-sheets – with a maximum of 21 amide groups. The models were based on the electric potential and/or the electric field component along the C=O bond at up to four atoms in an amide group. They were bench-marked by comparison to Hessian matrices reconstructed from density functional theory calculations at the BPW91, 6-31G** level. The performance of the electrostatic models depended on the charge set used to calculate the electric field and potential. Gromos and DSSP charge sets, used in common force fields, were not optimal for the better performing models. A good compromise between performance and the stability of model parameters was achieved by a model that considered the electric field at the positions of the oxygen, nitrogen, and hydrogen atoms of the considered amide group. The model describes also some aspects of the local conformation effect and performs similar on its own as in combination with an explicit implementation of the local conformation effect. It is better than a combination of a local hydrogen bonding model with the local conformation effect. Even though the short-range hydrogen bonding model performs worse, it captures important aspects of the local wavenumber sensitivity to the molecular surroundings. We improved also the description of the coupling between local amide I oscillators by developing an electrostatic model for the dependency of the dipole derivative magnitude on the protein environment. Tue, 12 Dec 2023 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17045-sthlmuni-24324886 https://researchdata.se/sv/catalogue/dataset/doi-10-17045-sthlmuni-24324886 Stockholms universitet Andreas Barth Cesare M. Baronio 1. "fig_1a.csv": Small-angle scattering intensity I(Q) as a function of the momentum transfer Q measured for 10 mg/ml lysozyme in 23 mol% glycerol-water at different temperatures upon cooling down after subtracting the scattering intensity measured on the pure solvent. (Note: I(Q) in arbitrary units). 2. "fig_1_inset.csv": Radii of gyration as a function of temperature upon cooling and warming as extracted from fitting the I(q)s for the dilute sample with an elliptical form factor.  3. "fig_1b.csv": Small-angle scattering intensity I(Q) as a function of the momentum transfer Q measured for 200 mg/ml lysozyme in 23 mol% glycerol-water at different temperatures upon cooling down after subtracting the scattering intensity measured on the pure solvent. (Note: I(Q) in arbitrary units). 4. "fig_2a.csv": Wide-angle scattering intensity I(Q) as a function of the momentum transfer Q measured for 200 mg/ml lysozyme in 23 mol% glycerol-water for different temperatures upon cooling. (Note: I(Q) in arbitrary units). 5. "fig_2b.csv": Wide-angle scattering intensity I(Q) as a function of the momentum transfer Q measured for 200 mg/ml lysozyme in 23 mol% glycerol-water for different temperatures upon warming up. (Note: I(Q) in arbitrary units). 6. "fig_2c.csv": 2D scattering pattern in the vicinity of Q ≈ 16-20 nm-¹ measured at T = 197 K during heating. 7. "fig_2d.csv": 2D scattering pattern in the vicinity of Q ≈ 16-20 nm-¹ measured at T = 245 K during heating. 8. "fig_2e.csv": Temperature evolution of the I(Q) around the ice Ih[002] diffraction peak centered at Q ≈ 17 nm−¹ upon cooling. 9. "fig_2f.csv": Temperature evolution of the I(Q) around the ice Ih[002] diffraction peak centered at Q ≈ 17 nm−¹ upon warming up. 10. "fig_3a.csv": Temperature dependence of the Q-value of the SAXS I(Q) peak position for a 200 mg/ml lysozyme in glycerol-water solution during a deep temperature cycle down to 195 K. 11. "fig_3b.csv": Temperature dependence of the Q-value of the SAXS I(Q) peak position for a 200 mg/ml lysozyme in glycerol-water solution during a medium temperature cycle down to 225 K. 12. "fig_3c.csv": Temperature dependence of the Q-value of the SAXS I(Q) peak position for a 200 mg/ml lysozyme in glycerol-water solution during a shallow temperature cycle down to 245 K. 13. "fig_3d.csv": Temperature dependence of the Q-value of the WAXS I(Q) peak position for a 200 mg/ml lysozyme in glycerol-water solution during a deep temperature cycle down to 195 K. 14. "fig_3e.csv": Temperature dependence of the Q-value of the WAXS I(Q) peak position for a 200 mg/ml lysozyme in glycerol-water solution during a medium temperature cycle down to 225 K. 15. "fig_3f.csv": Temperature dependence of the Q-value of the WAXS I(Q) peak position for a 200 mg/ml lysozyme in glycerol-water solution during a shallow temperature cycle down to 245 K 16. "fig_4a.csv": The protein-protein structure factor S(Q) at different temperatures (T = 195-300 K) upon cooling obtained from the fits using the two-Yukawa model. 17. "fig_4b.csv": Temperature dependence of the attraction strength parameter K₁ (in units of kbT) extracted from fitting the SAXS curves upon cooling down and warming up.  18. "fig_4c.csv": The two-Yukawa potential at different temperatures (T = 195-300 K) upon cooling down.  19. "fig_4d.csv": The pair distribution function g(r) at different temperatures (T = 195-300 K) derived from the modeled structure factors. Additionally, a Jupyter notebook "open-data.ipynb" which shows how to load and plot the data from the csv files in Python. Mon, 21 Aug 2023 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17045-sthlmuni-23295626 https://researchdata.se/sv/catalogue/dataset/doi-10-17045-sthlmuni-23295626 Stockholms universitet Mariia Filianina Foivos Perakis Maddalena Bin Sharon Berkowicz The data published here are the basis for the article by Paul et al. in Commun. Chem. with the title 13C- and 15N-labeling of amyloid-β and inhibitory polypeptides to study their interaction via nanoscale infrared spectroscopy and for the Research Square preprint by Paul et al. with DOI: 10.21203/rs.3.rs-2141341/v1 (https://doi.org/10.21203/rs.3.rs-2141341/v1) and title 13C-isotope-editing of nanoscale infrared images reveals the action of an inhibi­tory peptide against amyloid-β aggregation.   These publications show that 13C, 15N-labeling can be used to discriminate between two peptides in nanoscale images of their infrared absorption, even when they have similar secondary structure. We studied different aggregation states of the amyloid-β peptide (Aβ) and its interaction with an inhibitory cell-penetrating peptide (NCAM1-PrP) using scattering-type scanning near-field optical microscopy (s-SNOM). Labeled and unlabeled peptides could be distinguished by comparing images of the optical phase taken at wavenumbers characteristic for either the labeled or the unlabeled peptide. Some of the provided files require particular software to view them: Gwyddion (http://gwyddion.net/) is needed for image files, neaPLOT (attocube) for nano-FTIR spectra, and OPUS (Bruker) for FTIR spectra. Processed neaPLOT files were stored as csv files. OPUS files were converted to txt files but can also be read by Spectragryph (https://www.effemm2.de/spectragryph/about.html), which is free for private and academic use. Mon, 03 Jul 2023 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17045-sthlmuni-23609580 https://researchdata.se/sv/catalogue/dataset/doi-10-17045-sthlmuni-23609580 Stockholms universitet Suman Paul Adéla Jeništová Faraz Vosough Elina Berntsson Cecilia Mörman Jüri Jarvet Astrid Gräslund Sebastian K. T. S. Wärmländer Andreas Barth Datasets: - "Figure1a.csv": scattering intensity of hydrated proteins in Wide-Angle X-ray Scattering for different fluences  (in units of photons/second/area). - "Figure1a_inset.csv": scattering intensity of hydrated proteins in Small-Angle X-ray Scattering for different fluences (in units of photons/second/area). - "Figure1b.csv": Intensity autocorrelation functions g2 at momentum transfer Q = 0.08 1/nm for different fluences (in units of photons/second/area).  - "Figure1b_inset.csv":  decay rate (in second) as a function of the momentum transfer Q (in 1/nm) for different fluences (in units of photons/second/area). - "Figure1c.csv": decay rate (in second) for variable fluence (in photons/second/um^2) at the momentum transfer Q = 0.08 1/nm. - "Figure1d.csv": renormalised intensity autocorrelation functions g2 at momentum transfer Q = 0.08 1/nm for variable fluence (in photons/second/um^2), where the time axis is normalised to the corresponding fluence F by calculating t/(1 + a · F·τ0), where τ0 is the equilibrium time constant extracted by extrapolation to F=0 (from data in "Figure1c.csv)" - "Figure2a.csv": The Wide-Angle X-ray Scattering scattering intensity at different temperatures T=180-290 K - "Figure2b.csv": The Small-Angle X-ray Scattering scattering intensity at different temperatures T=180-290 K - "Figure2c.csv": Intensity autocorrelation functions g2 for different temperatures (T=180-290 K) at momentum transfer Q = 0.1 1/nm. - "Figure2d-2e.csv": time constants (in second) and the Kohlrausch-Williams-Watts (KWW) exponent extracted from the fits of data in "Figure2c.csv" as a function of temperature (in K) - "Figure3b.csv": The normalised variance Chi_T at different temperatures (T=180-290 K) extracted from the two-time correlation functions. - "Figure3c.csv": The maximum of the normalised variance Chi_0 as a function of temperature (in K). Additionally, a Jupyter notebook "open-data.ipynb" which shows how to load and plot the data from the csv files in Python. Tue, 23 May 2023 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17045-sthlmuni-22756400 https://researchdata.se/sv/catalogue/dataset/doi-10-17045-sthlmuni-22756400 Stockholms universitet Maddalena Bin