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 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