{"entity": "journal", "iuid": "9508df98bdf54e7b8d544cd4e9a59888", "timestamp": "2026-10-13T19:38:12.985Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/Protein%20Eng.%20Des.%20Sel..json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/Protein%20Eng.%20Des.%20Sel."}}, "title": "Protein Eng. Des. Sel.", "issn": "1741-0134", "issn-l": "1741-0126", "publications_count": 3, "publications": [{"entity": "publication", "iuid": "c69f5ca7fbea408085ab9c6a08a4129e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c69f5ca7fbea408085ab9c6a08a4129e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c69f5ca7fbea408085ab9c6a08a4129e"}}, "title": "Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids.", "authors": [{"family": "Haloi", "given": "Nandan", "initials": "N"}, {"family": "Huang", "given": "Shan", "initials": "S"}, {"family": "Nichols", "given": "Aaron L", "initials": "AL"}, {"family": "Fine", "given": "Eve J", "initials": "EJ"}, {"family": "Friesenhahn", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0002-8129-0171", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d577502b32c43d7873ae44895b0791a.json"}}, {"family": "Marotta", "given": "Christopher B", "initials": "CB"}, {"family": "Dougherty", "given": "Dennis A", "initials": "DA"}, {"family": "Lindahl", "given": "Erik", "initials": "E"}, {"family": "Howard", "given": "Rebecca J", "initials": "RJ"}, {"family": "Mayo", "given": "Stephen L", "initials": "SL", "orcid": "0000-0002-9785-5018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f800b169c3f427ebfaca3731358643a.json"}}, {"family": "Lester", "given": "Henry A", "initials": "HA", "orcid": "0000-0002-5470-5255", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebe59757b5b9402486ee19bfe8f1b991.json"}}], "type": "journal article", "published": "2024-01-29", "journal": {"title": "Protein Eng. Des. Sel.", "issn": "1741-0134", "volume": "37", "issn-l": "1741-0126"}, "abstract": "We developed fluorescent protein sensors for nicotine with improved sensitivity. For iNicSnFR12 at pH 7.4, the proportionality constant for \u2206F/F0vs [nicotine] (\u03b4-slope, 2.7 \u03bcM-1) is 6.1-fold higher than the previously reported iNicSnFR3a. The activated state of iNicSnFR12 has a fluorescence quantum yield of at least 0.6. We measured similar dose-response relations for the nicotine-induced absorbance increase and fluorescence increase, suggesting that the absorbance increase leads to the fluorescence increase via the previously described nicotine-induced conformational change, the 'candle snuffer' mechanism. Molecular dynamics (MD) simulations identified a binding pose for nicotine, previously indeterminate from experimental data. MD simulations also showed that Helix 4 of the periplasmic binding protein (PBP) domain appears tilted in iNicSnFR12 relative to iNicSnFR3a, likely altering allosteric network(s) that link the ligand binding site to the fluorophore. In thermal melt experiments, nicotine stabilized the PBP of the tested iNicSnFR variants. iNicSnFR12 resolved nicotine in diluted mouse and human serum at 100 nM, the peak [nicotine] that occurs during smoking or vaping, and possibly at the decreasing levels during intervals between sessions. NicSnFR12 was also partially activated by unidentified endogenous ligand(s) in biofluids. Improved iNicSnFR12 variants could become the molecular sensors in continuous nicotine monitors for animal and human biofluids.", "doi": "10.1093/protein/gzae003", "pmid": "38302088", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10896302"}, {"db": "pii", "key": "7596259"}], "notes": [], "created": "2026-08-20T09:51:41.821Z", "modified": "2026-09-23T12:59:47.280Z"}, {"entity": "publication", "iuid": "4ac5904ce17e42aab5162c02b0c4369e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4ac5904ce17e42aab5162c02b0c4369e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4ac5904ce17e42aab5162c02b0c4369e"}}, "title": "Generation and analyses of human synthetic antibody libraries and their application for protein microarrays.", "authors": [{"family": "S\u00e4ll", "given": "Anna", "initials": "A"}, {"family": "Walle", "given": "Maria", "initials": "M"}, {"family": "Wingren", "given": "Christer", "initials": "C"}, {"family": "M\u00fcller", "given": "Susanne", "initials": "S"}, {"family": "Nyman", "given": "Tomas", "initials": "T"}, {"family": "Vala", "given": "Andrea", "initials": "A"}, {"family": "Ohlin", "given": "Mats", "initials": "M"}, {"family": "Borrebaeck", "given": "Carl A K", "initials": "CAK"}, {"family": "Persson", "given": "Helena", "initials": "H"}], "type": "journal article", "published": "2016-10-00", "journal": {"title": "Protein Eng. Des. Sel.", "issn": "1741-0134", "volume": "29", "issue": "10", "pages": "427-437", "issn-l": "1741-0126"}, "abstract": "Antibody-based proteomics offers distinct advantages in the analysis of complex samples for discovery and validation of biomarkers associated with disease. However, its large-scale implementation requires tools and technologies that allow development of suitable antibody or antibody fragments in a high-throughput manner. To address this we designed and constructed two human synthetic antibody fragment (scFv) libraries denoted HelL-11 and HelL-13. By the use of phage display technology, in total 466 unique scFv antibodies specific for 114 different antigens were generated. The specificities of these antibodies were analyzed in a variety of immunochemical assays and a subset was further evaluated for functionality in protein microarray applications. This high-throughput approach demonstrates the ability to rapidly generate a wealth of reagents not only for proteome research, but potentially also for diagnostics and therapeutics. In addition, this work provides a great example on how a synthetic approach can be used to optimize library designs. By having precise control of the diversity introduced into the antigen-binding sites, synthetic libraries offer increased understanding of how different diversity contributes to antibody binding reactivity and stability, thereby providing the key to future library optimization.", "doi": "10.1093/protein/gzw042", "pmid": "27590051", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "gzw042"}], "notes": [], "created": "2018-12-05T11:44:53.105Z", "modified": "2018-12-05T11:44:53.132Z"}, {"entity": "publication", "iuid": "b99f7a8faefe416598a172834b3d869c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b99f7a8faefe416598a172834b3d869c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b99f7a8faefe416598a172834b3d869c"}}, "title": "Isolation of novel single-chain Cro proteins targeted for binding to the bcl-2 transcription initiation site by repertoire selection and subunit combinatorics.", "authors": [{"family": "Jonas", "given": "Kristina", "initials": "K"}, {"family": "Van Der Vries", "given": "Erhard", "initials": "E"}, {"family": "Nilsson", "given": "Mikael T I", "initials": "MT"}, {"family": "Widersten", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2005-11-00", "journal": {"title": "Protein Eng. Des. Sel.", "issn": "1741-0126", "volume": "18", "issue": "11", "pages": "537-546", "issn-l": null}, "abstract": "New designed DNA-binding proteins may be recruited to act as transcriptional regulators and could provide new therapeutic agents in the treatment of genetic disorders such as cancer. We have isolated tailored DNA-binding proteins selected for affinity to a region spanning the transcription initiation site of the human bcl-2 gene. The proteins were derived from a single-chain derivative of the lambda Cro protein (scCro), randomly mutated in its recognition helices to construct libraries of protein variants of distinct DNA-binding properties. By phage display-afforded affinity selections combined with recombination of shuffled subunits, protein variants were isolated, which displayed high affinity for the target bcl-2 sequence, as determined by electrophoretic mobility shift and biosensor assays. The proteins analyzed were moderately sequence-specific but provide a starting point for further maturation of desired function.", "doi": "10.1093/protein/gzi058", "pmid": "16186141", "labels": {"Kristina Jonas": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "gzi058"}], "notes": [], "created": "2020-11-30T14:49:04.554Z", "modified": "2022-11-07T11:33:47.354Z"}], "created": "2018-12-05T11:44:53.117Z", "modified": "2020-11-27T13:12:56.622Z"}