Dataset for article Novel glycogen-based materials for scavenging cationic antimicrobial peptides

---------------------------------------------------------------------------------------------------------------------------Dataset for article Novel glycogen-based materials for scavenging cationic antimicrobial peptides--------------------------------------------------------------------------------------------------------------------------- ReadMe version: 1.0 (2026-06-24; completed with tracked edits on 2026-06-25) Dataset version: 1.0 (2026-06-24) Dataset DOI: 10.5281/zenodo.20845029 Related article: Mariia Rabyk, Natalia Podhorska, Nadiia Velychkivska, Ewa Pavlova, Marcela Filipova, Martin Hruby, Novel glycogen-based materials for scavenging cationic antimicrobial peptides, Colloids and Surfaces B: Biointerfaces 257 (2026) 115084, https://doi.org/10.1016/j.colsurfb.2025.115084 --------------------------------------------------------------------CONTACT-------------------------------------------------------------------- Martin Hruby [e-mail]; [e-mail] ORCID: 0000-0002-5075-261X Institute of Macromolecular Chemistry, Czech Academy of Sciences (IMC CAS) Heyrovsky sq. 2, 162 06 Prague 6, Czech Republic ______Creators______ Mariia Rabyk (ORCiD: 0000-0002-9169-6271; IMC CAS), Writing - original draft; Visualization; Software; Methodology; Investigation; Data curation Natalia Podhorska (IMC CAS), Visualization; Methodology; Investigation; Data curation Nadiia Velychkivska (ORCiD: 0000-0002-4950-1071; IMC CAS), Visualization; Software; Investigation; Data curation Ewa Pavlova (ORCiD: 0000-0002-6693-9040; IMC CAS), Visualization; Software; Investigation Marcela Filipova (ORCiD: 0000-0003-3503-7973; IMC CAS), Validation; Methodology; Formal analysis; Data curation Martin Hruby (ORCiD: 0000-0002-5075-261X; IMC CAS), Writing - review & editing; Validation; Supervision; Methodology; Funding acquisition; Formal analysis; Conceptualization ______Contributors______ No additional contributors. --------------------------------------------------------------------DATA AVAILABILITY AND ACCESS INSTRUCTIONS--------------------------------------------------------------------The dataset is intended for open repository deposition together with this ReadMe. Until the repository DOI is assigned, cite the related article DOI above and the dataset title. The license and terms of reuse are shown in the following chapter below. --------------------------------------------------------------------LICENSE--------------------------------------------------------------------______ReadMe file license______ ReadMe by Martin Hruby and co-authors is licensed under CC BY 4.0 License information: https://creativecommons.org/licenses/by/4.0/ ______Dataset license______ Dataset for article Novel glycogen-based materials for scavenging cationic antimicrobial peptides by Mariia Rabyk, Natalia Podhorska, Nadiia Velychkivska, Ewa Pavlova, Marcela Filipova, and Martin Hruby is licensed under CC BY 4.0 License information: https://creativecommons.org/licenses/by/4.0/ --------------------------------------------------------------------DESCRIPTION AND METHODOLOGY-------------------------------------------------------------------- ______About the dataset______Cationic antimicrobial peptides (CAMPs) are associated with inflammatory diseases such as psoriasis. The related study developed sulfated glycogen (GGS) as a natural, biodegradable, polysaccharide-based polyanion for scavenging cationic peptides and proteins. Glycogen was functionalized with sulfate groups at different degrees of substitution by varying the amount of sulfur trioxide-pyridine complex and reaction time. The selected samples were native glycogen (GG) and sulfated glycogens GGS1, GGS3, GGS10, and GGS20, where the number indicates approximately the number of glucose units per one SO3Na group.The dataset contains raw and instrument-exported data supporting physicochemical characterization of the prepared materials: 1H NMR spectra, ATR-FTIR spectra, dynamic/electrophoretic light-scattering data including complexation with lysozyme and melittin, and transmission electron microscopy images with particle-size spreadsheets. These data support the article conclusions that highly sulfated glycogens, especially GGS1 and GGS3, form complexes with cationic model peptides/proteins and suppress melittin-caused hemolysis in vitro. ______Ethics______No sensitive or personal data are included in the supplied dataset. Because the article reports in vitro hemolysis testing with human red blood cells but the supplied ZIP contains no raw personal or donor-level data, the dataset is non-sensitive. ______Sample preparation______Native glycogen (GG) from Crassostrea gigas (Pacific oyster; molecular weight about 12 MDa; Sigma-Aldrich G8751) was used as the polysaccharide scaffold. Sulfation was performed with sulfur trioxide-pyridine complex in DMF/pyridine. In the general procedure, 500 mg GG (3.09 mmol glucose units) was added to 10 mL DMF and 1.4 mL pyridine, heated to 65 °C and stirred for 2 h. SO3-pyridine complex was added portionwise, and the suspension was stirred at 65 °C for a further 2-12 h depending on the targeted substitution degree. After cooling, 4 M NaOH was added, the precipitate was centrifuged, washed with ethanol, dissolved in water, dialyzed against water using 3.5 kDa MWCO membrane for 145 h at room temperature, centrifuged again, and lyophilized.Sample-code mapping from the supplied file GG_sulf_samples names.docx: GG = native glycogen; GGS20 (20 glucose units per SO3Na) = MR24/09; GGS10 (10 glucose units per SO3Na) = MR24/11; GGS3 (3 glucose units per SO3Na) = MR23/43_rep plus MR24/12; GGS1 (1 glucose unit per SO3Na) = MR23/43 plus MR24/08. Some folder and file names use the working labels MR23-43, MR23-43_rep, MR24-08, MR24-09, MR24-11, and MR24-12. ______Methods of data collection______*1H NMR spectra Instrument: Bruker AVANCE NEO 400 MHz spectrometer operating at 400.13 MHz. Acquisition: 90° 1H pulse width 16.5 microseconds, relaxation delay 10 s, acquisition time 3.28 s, 64 scans; samples dissolved in D2O; HDO reference at delta = 4.80 ppm; temperature controlled within +/-0.2 K using a BVT 3000 temperature unit. Software: TopSpin 4.1.x. TopSpin 4.1.0 for processing; TopSpin 4.1.4 for opening the raw NMR data. *ATR-FTIR spectra Instrument: Perkin-Elmer Spectrum 100T FTIR spectrometer with Specac MKII Golden Gate single-reflection ATR accessory. Export/software: Generic ASCII export from Spectrum 10 ES software. Spectra are saved as .asc files. Data units: wavenumber in cm^-1 and transmittance in percent (%T), as indicated in the ASCII headers. *Dynamic and electrophoretic light scattering (DLS/ELS) Instrument: Malvern Zetasizer Nano ZS ZEN3600 with Zetasizer Software Version 7.13. Conditions: measurements at 25 +/-0.1 °C; Dhyd measured at scattering angle theta = 173° and processed with the REPES algorithm; zeta-potential evaluated using the Smoluchowski model. Measurements included aqueous solutions of GG/GGS at 0.5, 1.0, and 2.0 mg/mL with or without NaCl to a final concentration of 0.01 M; pH-dependent measurements in acetate buffer pH 5.0 and phosphate-buffered saline pH 7.4; lysozyme titration experiments with GGS at 0.5 mg/mL and lysozyme at 6.0 mg/mL; and melittin complexation experiments in PBS pH 7.4 for the more highly sulfated samples. *Transmission electron microscopy (TEM) Instrument: Tecnai G2 Spirit Twin 12 (FEI, Brno, Czech Republic). Grid preparation: polymer solutions were dropped onto 300-mesh copper TEM grids coated with thin carbon film; excess solution was removed after 1 min; samples were negatively stained with 2 wt% uranyl acetate for 45 s, air-dried, and imaged. Imaging: acceleration voltage 120 kV, bright-field mode. Particle diameters were evaluated from at least 300 particles from TEM micrographs using Atlas software (Tescan Digital Microscopy Imaging, Brno, Czech Republic). ______Methods of data processing______The dataset contains raw instrument files and instrument/export files as supplied.For NMR, the archive includes Bruker acquisition files (for example acqu/acqus, fid) and processed-data folders (pdata/1 with 1r/1i and processing metadata) generated by TopSpin. For FTIR, .asc files are generic ASCII exports from Spectrum 10 ES and are considered instrument-exported raw spectra. For DLS/ELS, .dts and .del files are native Zetasizer files containing measurement records and analyses. For TEM, .tif image files are raw/primary microscope images, and .xls/.xlsx files contain particle-size measurements and summarized sizes.Published values such as Dhyd, zeta-potential, TEM number-average diameter, and complexation thresholds were calculated from these instrumental data according to the methods described in the article and ESI. --------------------------------------------------------------------DATASET STRUCTURE--------------------------------------------------------------------000_ReadMe.txt001_Documentation.zip├── GG_sulf_samples names.csv - mapping between article sample names, degree of sulfation, and working sample names├── Software.txt - software needed to open/inspect the raw data002_Data.zip ├── 1H NMR/│ ├── MR23-43.pdf; MR23-43_rep.pdf - exported/rendered NMR spectra for selected sulfated samples│ ├── Rabyk_GG.tiff - image/export of native glycogen NMR spectrum│ ├── scan/MR23-43.jpg; scan/MR23-43_rep.jpg - scanned or image exports of NMR spectra│ ├── Rabyk_400_24.zip - archived Bruker NMR experiment folder│ └── Rabyk_400_24/1 ... Rabyk_400_24/9/ - Bruker experiment directories with raw fid/acqus files and pdata/1 processed spectra├── DLS/│ ├── MR23_43-43_rep/ - DLS files for MR23-43 and MR23-43_rep, including 2 mg/mL measurements│ ├── MR24-05-08/ - DLS files for MR24-05 to MR24-08 in water│ ├── MR24_09-12/ - DLS files for MR24-09 to MR24-12 in water│ ├── MR23-43_rep_TEMs .dts - Zetasizer data file associated with TEM-related sample set│ └── complaxation/ - original folder name retained; DLS complexation/titration data for GG_II, MR23-43, MR23-43_rep, MR24-08, MR24-09, MR24-11, and Melittin subfolders├── FTIR/│ └── GG_from oyster.asc; MR23-43.asc; MR23-43_REP.asc; MR24-05.asc; MR24-06.asc; MR24-07.asc; MR24-08.asc; MR24-09.asc; MR24-10.asc; MR24-11.asc; MR24-12.asc└── TEM/ ├── *.tif - TEM micrographs for native and sulfated glycogen samples ├── GG-II_1 - Repeated.xls; HR24-09right pcture repeated.xls - particle-size spreadsheets/measurements └── TABLE OF SIZES.xlsx - summarized TEM particle-size table --------------------------------------------------------------------FILENAME STRUCTURE--------------------------------------------------------------------The following interpretation should be used: Article/sample names: GG = native glycogen; GGS1, GGS3, GGS10, and GGS20 = sulfated glycogens with approximately 1, 3, 10, or 20 glucose units per SO3Na group, respectively. Working sample codes: MR23-43 and MR24-08 correspond to GGS1; MR23-43_rep and MR24-12 correspond to GGS3; MR24-11 corresponds to GGS10; MR24-09 corresponds to GGS20; GG_II, native, and GG_from oyster refer to native GG. This mapping is based on GG_sulf_samples names.docx. 1H NMR folders: Rabyk_400_24/<number>/ follows the Bruker experiment-directory structure. Important files include fid (raw free induction decay), acqu/acqus (acquisition parameters), pulseprogram, and pdata/1 (processed spectrum and processing parameters). FTIR files: <sample_code>.asc, for example GG_from oyster.asc, MR23-43.asc, MR23-43_REP.asc, MR24-09.asc. These are Perkin-Elmer/Spectrum ASCII spectral exports. DLS files: <sample_code>_<condition>.dts or .del, where condition labels include H2O/H20, Lys_AcB, Lys_PBS, Lys_H2O, or PBS for melittin experiments. The folder name complaxation is an original misspelling of complexation and is intentionally retained to preserve the data package. TEM files: <sample_code>_<image_number>.tif or descriptive microscope filenames, plus Excel spreadsheets with particle-size measurements or summaries. --------------------------------------------------------------------FILE TYPES & FORMATS, SW TO OPEN AND DIMENSIONS & UNITS--------------------------------------------------------------------*1H NMR spectra original format: Bruker NMR directory structure containing fid, acqu/acqus, pulseprogram, and pdata/1 files SW: Bruker TopSpin 4.1.4 (per Software.txt; the ESI reports TopSpin 4.1.0 for processing) auxiliary formats: .pdf, .jpg, .tiff image/spectrum exports horizontal axis: chemical shift, delta (ppm) vertical axis: signal intensity (a.u.) *ATR-FTIR spectra original/exported format: .asc generic ASCII export from Spectrum 10 ES software SW: Spectrum 10 ES, compatible text editor, spreadsheet software, or custom script horizontal axis/first column: wavenumber (cm^-1) vertical axis/second column: transmittance (%T) *DLS/ELS data original format: .dts and .del Zetasizer data files SW: Zetasizer Software Version 7.13 principal dimensions/units: hydrodynamic diameter Dhyd (nm), intensity-weighted size distribution (% intensity or arbitrary intensity as exported), zeta-potential (mV), scattering/count-rate metadata as stored by the instrument software *TEM data original image format: .tif microscopy images; auxiliary .jpg/.tiff exports where present SW: TEM imaging software, ImageJ/Fiji, Atlas/Tescan Digital Microscopy Imaging, or other TIFF-compatible image software measurement spreadsheets: .xls and .xlsx files readable in Microsoft Excel, LibreOffice Calc, or compatible software dimensions/units: image scale bars and measured particle diameters in nm; summarized metrics include number-average diameter Dn and related particle-size statistics where provided *Documentation and auxiliary files .docx files: Microsoft Word/LibreOffice Writer; include sample-code mapping and this ReadMe .txt files: plain text; Software.txt lists software versions needed to open the data