=========== HEADER =========== Readme.txt for [dataset title]________________________________ Item Handle: [to be added after record is created] Documentation written on 2026-04-23 By Corey Barber, Heather Coates, Updated , by ________________________ =========== SUGGESTED DATA CITATION =========== Please cite this data in the references for any publication which uses it. Kimble-Hill, A. C., Biak, R. C., Zathang, S., Ray, B. D., Petrache, H. I. (2026). Nanopeptide based on Amot80 AEKEYEGSE, KKQVYVDKV, LEGCYEKVA, SSASYQPVP, VSEAYENLV [Data set]. IU Indianapolis University Library. =========== PRIMARY STUDY INFORMATION =========== ACKNOWLEDGEMENTS Project title: Nanopeptide based on Amot80 SSASYQPVP Funding agency: Award Number: Award Period: Investigator Name: Ann C. Kimble-Hill Investigator Institution: Indiana University Indianapolis Investigator Address: 635 Barnhill Dr, Indianapolis, IN 46202 Investigator Email: ankimble@iu.edu Investigator Role (related to this dataset): PI Investigator ID (ORCID): https://orcid.org/0000-0001-9575-5454 Investigator Name: Roger C. Biak Investigator Institution: Indiana University Indianapolis Investigator Address: 402 N. Blackford St. Indianapolis, IN 46202 Investigator Email: rogerbiak@yahoo.com Investigator Role (related to this dataset): data analysis, data visualization Investigator ID (ORCID): N/A Investigator Name: Suitintial Zathang Investigator Institution: Indiana University Indianapolis Investigator Address: 402 N. Blackford St. Indianapolis, IN 46202 Investigator Email: suitintial2@gmail.com Investigator Role (related to this dataset): data collection, data processing/cleaning, data analysis, data visualization Investigator ID (ORCID): N/A Investigator Name: Bruce D. Ray Investigator Institution: Indiana University Indianapolis Investigator Address: 402 N. Blackford St. Indianapolis, IN 46202 Investigator Email: bray@iu.edu Investigator Role (related to this dataset): supervision, data collection, data processing/cleaning, data analysis, data visualization, & lab manager Investigator ID (ORCID): https://orcid.org/0000-0002-7663-2333 Investigator Name: Horia I. Petrache Investigator Institution: Indiana University Indianapolis Investigator Address: 402 N. Blackford St. Indianapolis, IN 46202 Investigator Email: hpetrach@iu.edu Investigator Role (related to this dataset): Co-PI Investigator ID (ORCID): https://orcid.org/0000-0003-4363-9456 DATE(S) of DATA COLLECTION 20150705 to 20150709 INSTRUMENT INFORMATION Instrument information: Varian Inova 500 NMR spectrometer Instrument affiliation Indiana University Indianapolis Physics Department Instrument location Indianapolis, Indiana FILE INFORMATION *.pdb files can be opened and worked with any of the following applications: PyMOL: Highly recommended for visualization, featuring an open-source version. VMD (Visual Molecular Dynamics): Used for rendering, capable of downloading PDB files directly. Swiss-PDBViewer: A specialized application for analyzing protein structures. UCSF ChimeraX: An advanced, free, and widely used tool for molecular modeling, visualization, and analysis. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. Mol* (Molstar): The default 3D viewer for the RCSB PDB website, offering fast and interactive visualization directly in the browser. iCn3D: A National Institutes of Health tool that runs in browsers, allowing for specialized viewing of 3D, 2D, and 1D data. Jmol: A free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. *.nef files can be opened and worked with any of the following applications: CCPN Analysis 3.2.2, open source NMR spectroscopy software that runs on Windows, Mac OS X, and Linux/Unix systems. NMRFAM-SPARKY, open source software from National Magnetic Resonance Facility, University of Wisconsin, Madison that runs on Windows, Mac OS X, and Linux/Unix systems. When referring to membrane docking results, cite the Orientations of Proteins in Membranes (OPM) database and refer to: Lomize MA, Pogozheva ID, Joo H., Mosberg HI, Lomize AL (2012) OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res. 40 (Database issue), D370-D376. For an explanation of our method please refer to: Lomize AL, Todd SC, Pogozheva ID. (2022) Spatial arrangement of proteins in planar and curved membranes by PPM 3.0. Protein Sci. 31: 930-946. When referring to results from Alphafold, cite the following paper: Fleming, J., Magana, P., Nair, S., Tsenkov, M., Bertoni, D., Pidruchna, I., Afonso, M.Q.L., Midlik, A., Paramval, U., Žídek, A. and Laydon, A., 2025. AlphaFold protein structure database and 3D-Beacons: new data and capabilities. Journal of Molecular Biology, 437(15), p.168967. dot: 10.1016/j.jmb.2025.168967. Files Included in the SSASYQPVP.zip folder SSASYQPVP-water.nef SSASYQPVP_water.pdb Alphafold structure excised from AF-Q4VCS5-F1-model (Protein Angiomotin, Gene AMOT, Source organism Homo sapiens, UniProt Q4VCS5): SSASYQPVP alphafold model.pdb In SSASYQPVP_azara spectrum (*.spc) and parameter files (*.par) as follows: SSASYQPVP-cosy-07-05-2015.par SSASYQPVP-cosy-07-05-2015.spc SSASYQPVP-dqcosy-07-06-2015.par SSASYQPVP-dqcosy-07-06-2015.spc SSASYQPVP-roesy-07-09-2015.par SSASYQPVP-roesy-07-09-2015.spc SSASYQPVP-roesyb-07-09-2015.par SSASYQPVP-roesyb-07-09-2015.spc SSASYQPVP-tocsy-07-05-2015.par SSASYQPVP-tocsy-07-05-2015.spc PDB files from OPM PPM 3.0 modeling as follows where lipid membrane included 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), lysosome, Endoplasmic reticulum membrane (ER), Golgi apparatus (Golgi), Mitochondrial outer membrane (OuterMito), Eukaryotic plasma membranes (PM): OPM PPM membrane compositions.pdf SSASYQPVP_DMPC docked PPM report.PDF SSASYQPVP_DMPC docked.pdb SSASYQPVP_DOPC docked PPM report.pdf SSASYQPVP_DOPC docked.pdb SSASYQPVP_Endosome docked PPM report.pdf SSASYQPVP_Endosome docked.pdb SSASYQPVP_ER docked PPM report.pdf SSASYQPVP_ER docked.pdb SSASYQPVP_Golgi docked PPM report.pdf SSASYQPVP_Golgi docked.pdb SSASYQPVP_Lysosome docked PPM report.pdf SSASYQPVP_Lysosome docked.pdb SSASYQPVP_OuterMito docking PPM report.pdf SSASYQPVP_OuterMito docking.pdb SSASYQPVP_PM docking PPM report.pdf SSASYQPVP_PM docking.pdb ACCESS & SHARING Links to thesis, dissertation, reports, or publications that cite or use the data (include DOI): Links/relationships to other data files/sets: =========== CREDITS =========== Template provided by Indiana University UITS Research Storage, Indiana University Bloomington Libraries, IUPUI University Library