{"entity": "journal", "iuid": "e45fad587b7d463d8e1c9fa6aa9a705c", "timestamp": "2026-07-17T04:45:01.449Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/J.%20Mol.%20Recognit..json"}, "display": {"href": "https://publications.scilifelab.se/journal/J.%20Mol.%20Recognit."}}, "title": "J. Mol. Recognit.", "issn": "1099-1352", "issn-l": "0952-3499", "publications_count": 2, "publications": [{"entity": "publication", "iuid": "ebaf9ab9161e4097ab0a1fbce2e73615", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ebaf9ab9161e4097ab0a1fbce2e73615.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ebaf9ab9161e4097ab0a1fbce2e73615"}}, "title": "Molecularly imprinted polymers synthesized via template immobilization on fumed silica nanoparticles for the enrichment of phosphopeptides.", "authors": [{"family": "Duarte", "given": "Mariana", "initials": "M"}, {"family": "Subedi", "given": "Prabal", "initials": "P"}, {"family": "Yilmaz", "given": "Ecevit", "initials": "E"}, {"family": "Marcus", "given": "Katrin", "initials": "K"}, {"family": "Laurell", "given": "Thomas", "initials": "T"}, {"family": "Ekstr\u00f6m", "given": "Simon", "initials": "S"}], "type": "journal article", "published": "2018-03-00", "journal": {"title": "J. Mol. Recognit.", "issn": "1099-1352", "volume": "31", "issue": "3", "issn-l": "0952-3499"}, "abstract": "Phosphorylation is a protein post-translational modification (PTM) that plays an important role in cell signaling, cell differentiation, and metabolism. The hyper phosphorylated forms of certain proteins have been appointed as biomarkers for neurodegenerative diseases, and phosphorylation-related mutations are important for detecting cancer pathways. Due to the low abundance of phosphorylated proteins in biological fluids, sample enrichment is beneficial prior to detection. Thus, a need to find new strategies for enriching phosphopeptides has emerged. Molecularly imprinted polymers (MIPs) are synthetic polymeric materials manufactured to exhibit affinity for a target molecule. In this study, MIPs have been synthesized using a new approach based on the use of fumed silica as sacrificial support acting as solid porogen with the template (phosphotyrosine) immobilized on its surface. Phosphotyrosine MIPs were tested against a mixture of peptides and phosphopeptides by performing micro-solid phase extraction using MIPs (\u03bcMISPE) packed in a pipette tip. First, the capability of the materials to preferentially enrich phosphopeptides was evaluated. In a next step, the enrichment of phosphopeptides from a whole-cell lysate of human embryonic kidney (HEK) 293T cells was performed. The eluates were analyzed using MALDI-MS in the first case and with nano-HPLC-ESI-MS/MS in the second case. The results showed that the MIPs provided affinity for phosphopeptides, binding preferentially to multi-site phosphorylated peptides. The MIPs could enrich phosphopeptides in over 10-fold compared with the number of phosphopeptides found in a cell lysate without enrichment.", "doi": "10.1002/jmr.2677", "pmid": "29024117", "labels": {"Structural Proteomics": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-27T10:07:51.196Z", "modified": "2021-05-24T15:39:50.424Z"}, {"entity": "publication", "iuid": "dbe52e1f133d4beb8fd0c3a4cc18ef06", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dbe52e1f133d4beb8fd0c3a4cc18ef06.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dbe52e1f133d4beb8fd0c3a4cc18ef06"}}, "title": "Structure and assembly-disassembly properties of wild-type transthyretin amyloid protofibrils observed with atomic force microscopy.", "authors": [{"family": "Pires", "given": "Ricardo H", "initials": "RH"}, {"family": "Saraiva", "given": "Maria J", "initials": "MJ"}, {"family": "Damas", "given": "Ana M", "initials": "AM"}, {"family": "Kellermayer", "given": "Mikl\u00f3s S Z", "initials": "MS"}], "type": "journal article", "published": "2011-04-20", "journal": {"volume": "24", "issn": "1099-1352", "issue": "3", "pages": "467-476", "title": "J. Mol. Recognit.", "issn-l": "0952-3499"}, "abstract": "Transthyretin (TTR) is an important human transport protein present in the serum and the cerebrospinal fluid. Aggregation of TTR in the form of amyloid fibrils is associated with neurodegeneration, but the mechanisms of cytotoxicity are likely to stem from the presence of intermediate assembly states. Characterization of these intermediate species is therefore essential to understand the etiology and pathogenesis of TTR-related amyloidoses. In the present work we used atomic force microscopy to investigate the morphological features of wild-type (WT) TTR amyloid protofibrils that appear in the early stages of aggregation. TTR protofibrils obtained by mild acidification appeared as flexible filaments with variable length and were able to bind amyloid markers (thioflavin T and Congo red). Surface topology and contour-length distribution displayed a periodic pattern of \u223c 15 nm, suggesting that the protofibrils assemble via an end-binding oligomer fusion mechanism. The average height and periodic substructure found in protofibrils is compatible with the double-helical model of the TTR amyloid protofilament. Over time protofibrils aggregated into bundles and did not form mature amyloid-like fibrils. Unlike amyloid fibrils that are typically stable under physiological conditions, the bundles dissociated into component protofibrils with axially compacted and radially dilated structure when exposed to phosphate-buffered saline solution. Thus, WT TTR can form metastable filamentous aggregates that may represent an important transient state along the pathway towards the formation of cytotoxic TTR species.", "doi": "10.1002/jmr.1112", "pmid": "21504025", "labels": {"Mass Spectrometry-based Proteomics, Uppsala": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:57:55.227Z", "modified": "2017-05-30T13:13:09.485Z"}], "created": "2017-05-09T09:12:02.469Z", "modified": "2020-11-27T13:14:01.451Z"}