{"entity": "journal", "iuid": "169c783ccdb14570a7df23eb61a0d758", "timestamp": "2026-06-09T23:49:43.923Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Protein%20Sci..json"}, "display": {"href": "https://publications.scilifelab.se/journal/Protein%20Sci."}}, "title": "Protein Sci.", "issn": "1469-896X", "issn-l": "0961-8368", "publications_count": 12, "publications": [{"entity": "publication", "iuid": "33c0bbe9b62046fe9c45cf73bd92f4cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33c0bbe9b62046fe9c45cf73bd92f4cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33c0bbe9b62046fe9c45cf73bd92f4cc"}}, "title": "Dynamic interaction of the Yersinia pseudotuberculosis type three secretion system proteins LcrV and LcrG.", "authors": [{"family": "Mangu", "given": "Jagadish Chandra Kumar", "initials": "JCK", "orcid": "0000-0003-1850-1412", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a3713eb7af24389a3f32c1e5d8dd7c9.json"}}, {"family": "Rogne", "given": "Per", "initials": "P", "orcid": "0000-0002-3687-9200", "researcher": {"href": "https://publications.scilifelab.se/researcher/31042ecc88a94cd6b97cef0508da93fd.json"}}, {"family": "Mattsson", "given": "Jonna", "initials": "J", "orcid": "0000-0002-5294-7808", "researcher": {"href": "https://publications.scilifelab.se/researcher/894626ea67fd459eb08e4a9c4768fb09.json"}}, {"family": "Hultgren", "given": "Lucas", "initials": "L"}, {"family": "Gahlot", "given": "Kumar D", "initials": "KD"}, {"family": "Lamy", "given": "Ana\u00efs", "initials": "A", "orcid": "0000-0001-9757-100X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3886e3714e8142778455c4b96e1a2983.json"}}, {"family": "Berntsson", "given": "Ronnie P-A", "initials": "RP"}, {"family": "Johansson", "given": "Lennart B-\u00c5", "initials": "LB"}, {"family": "Francis", "given": "Matthew S", "initials": "MS"}, {"family": "Wolf-Watz", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2026-01-00", "journal": {"title": "Protein Sci.", "issn": "1469-896X", "volume": "35", "issue": "1", "pages": "e70400", "issn-l": "0961-8368"}, "abstract": "Yersinia pathogenicity is dependent on polarized translocation of effector proteins via the type III secretion system (T3SS). The tip complex situated on the needle structure of the T3SS is required for contact with the eukaryotic host membrane and is to an extent composed of pentameric LcrV. LcrV is a multifunctional protein that also acts as a regulator of the T3SS by virtue of forming a high-affinity complex in the cytoplasm with its chaperone, LcrG. By employing a structure-based approach centered on mass spectrometry, FRET and NMR spectroscopy, we demonstrated that the LcrV-LcrG complex is best described as a multivalent complex, and that the N-terminal domain of LcrV contributes by negatively affecting the LcrG binding affinity. The N-terminal domain of LcrV is dynamic and undergoes a conformational change to accommodate LcrG binding. 19F NMR spectroscopy analysis suggests that the conformational change is an intrinsic property of the protein, which agrees with a conformational selection model. An analysis of effector secretion into a culture supernatant demonstrated that the low synthesis and low secretion phenotypes of a LcrV mutant where the N-terminal domain has been removed are linked to the structure, interactions and stability of the LcrV N-terminal domain. In summary, our results add insights into the dynamics of LcrV and its complex with LcrG.", "doi": "10.1002/pro.70400", "pmid": "41427733", "labels": {"Swedish NMR Centre": "Service", "Structural Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12720783"}], "notes": [], "created": "2026-02-20T13:00:10.096Z", "modified": "2026-04-24T09:00:04.729Z"}, {"entity": "publication", "iuid": "db8859e1f60843cfb22193244670316d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db8859e1f60843cfb22193244670316d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db8859e1f60843cfb22193244670316d"}}, "title": "Deep sequencing combined with high-throughput screening enables efficient development of a pH-dependent high-affinity binding domain targeting HER3.", "authors": [{"family": "M\u00f6ller", "given": "Marit", "initials": "M"}, {"family": "J\u00f6nsson", "given": "Malin", "initials": "M"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "L\u00f6fblom", "given": "John", "initials": "J"}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d733dbd7b84a6b88f7f5fcff7165f6.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Protein Sci.", "issn": "1469-896X", "volume": "34", "issue": "8", "pages": "e70247", "issn-l": "0961-8368"}, "abstract": "In vitro methods for developing binding domains have been well-established for many years, owing to the cost-efficient synthesis of DNA and high-throughput selection and screening technologies. However, generating high-affinity binding domains often requires the development of focused maturation libraries for a second selection, which typically demands a detailed understanding of the binding surfaces from the initial selection, a process that can be time-consuming. In this study, we accelerated this process by using deep sequencing data from the first selection to guide the design of the maturation library. Additionally, we employed a high-throughput screening system using flow cytometry based on Escherichia coli display to identify conditional binding domains from the selection output. This approach enabled the development of a high-affinity binder targeting the cancer biomarker HER3, with a binding affinity of 3.3 nM at extracellular pH 7.4, 100 times higher than the first-generation binding domain. Notably, the binding domain features a pH-dependent release mechanism, enabling rapid release in slightly acidic environments (pH \u22486), which resemble endosomal conditions. When conjugated to the cytotoxin mertansine (DM1), the binding domain demonstrated specific cytotoxic activity against HER3-expressing cell lines, with an IC50 of 2-5 nM. The presented approach enables the efficient development of conditional binding domains which hold promise for therapeutic applications.", "doi": "10.1002/pro.70247", "pmid": "40716110", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-21T18:09:51.575Z", "modified": "2025-11-21T18:09:51.723Z"}, {"entity": "publication", "iuid": "3cba993176914d9489704b83ceb80532", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3cba993176914d9489704b83ceb80532.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3cba993176914d9489704b83ceb80532"}}, "title": "Defining short linear motif binding determinants by phage display-based deep mutational scanning.", "authors": [{"family": "Benz", "given": "Caroline", "initials": "C"}, {"family": "Maassen", "given": "Lars", "initials": "L"}, {"family": "Simonetti", "given": "Leandro", "initials": "L"}, {"family": "Mihalic", "given": "Filip", "initials": "F", "orcid": "0000-0002-6840-2319", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f57a961e98e4e15b1b96ec8efc95d4f.json"}}, {"family": "Lindqvist", "given": "Richard", "initials": "R"}, {"family": "Tsitsa", "given": "Ifigenia", "initials": "I", "orcid": "0000-0001-8154-5528", "researcher": {"href": "https://publications.scilifelab.se/researcher/9afb0faf7a4c435cbba2b4aa63b99b51.json"}}, {"family": "Konstantinou", "given": "Aimiliani", "initials": "A"}, {"family": "Jemth", "given": "Per", "initials": "P", "orcid": "0000-0003-1516-7228", "researcher": {"href": "https://publications.scilifelab.se/researcher/91bb46ceba74462498354a328886b982.json"}}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK"}, {"family": "Davey", "given": "Norman E", "initials": "NE"}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-7081-3846", "researcher": {"href": "https://publications.scilifelab.se/researcher/f51534acce8c4214a55a3e7387850d53.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Protein Sci.", "issn": "1469-896X", "volume": "34", "issue": "6", "pages": "e70174", "issn-l": "0961-8368"}, "abstract": "Deep mutational scanning (DMS) has emerged as a powerful approach for evaluating the effects of mutations on binding or function. Here, we developed a DMS by phage display protocol to define the specificity determinants of short linear motifs (SLiMs) binding to peptide-binding domains. We first designed a benchmarking DMS library to evaluate the performance of the approach on well-known ligands for 11 different peptide-binding domains, including the talin-1 PTB domain, the G3BP1 NTF2 domain, and the MDM2 SWIB domain. Comparison with a set of reference motifs from the eukaryotic linear motif (ELM) database confirmed that the DMS by phage display analysis correctly identifies known motif binding determinants and provides novel insights into specificity determinants, including defining a non-canonical talin-1 PTB binding motif with a putative extended conformation. A second DMS library was designed, aiming to provide information on the binding determinants for 19 SLiM-based interactions between human and SARS-CoV-2 proteins. The analysis confirmed the affinity determining residues of viral peptides binding to host proteins and refined the consensus motifs in human peptides binding to five domains from SARS-CoV-2 proteins, including the non-structural protein (NSP) 9. The DMS analysis further pinpointed mutations that increased the affinity of ligands for NSP3 and NSP9. An affinity-improved cell-permeable NSP9-binding peptide was found to exert stronger antiviral effects than the wild-type peptide. Our study demonstrates that DMS by phage display can efficiently be multiplexed and applied to refine binding determinants and shows how the results can guide peptide-engineering efforts.", "doi": "10.1002/pro.70174", "pmid": "40411416", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12102759"}], "notes": [], "created": "2025-09-08T11:37:16.206Z", "modified": "2025-11-21T18:30:05.510Z"}, {"entity": "publication", "iuid": "4d18e85087514f59b370cda0f3182fae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4d18e85087514f59b370cda0f3182fae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4d18e85087514f59b370cda0f3182fae"}}, "title": "Dynamic networks connect the USP14 active site region with the proteasome interaction surface", "authors": [{"family": "Salomonsson", "given": "Johannes", "initials": "J", "orcid": "0000-0003-4810-3669", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcc65f9dd43440adb6da73997653fb20.json"}}, {"family": "Sj\u00f6strand", "given": "Linda", "initials": "L"}, {"family": "Eskilson", "given": "Arvid", "initials": "A"}, {"family": "Derbyshire", "given": "Dean", "initials": "D"}, {"family": "D'Arcy", "given": "P\u00e1draig", "initials": "P"}, {"family": "Sunnerhagen", "given": "Maria", "initials": "M"}, {"family": "Ahlner", "given": "Alexandra", "initials": "A", "orcid": "0000-0001-7004-8251", "researcher": {"href": "https://publications.scilifelab.se/researcher/08cd17a1108045b5be32cd492a082453.json"}}], "type": "journal-article", "published": "2025-04-00", "journal": {"title": "Protein Sci.", "issn": "0961-8368", "volume": "34", "issue": "4", "issn-l": null}, "abstract": null, "doi": "10.1002/pro.70077", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:05:11.667Z", "modified": "2025-11-27T08:05:11.806Z"}, {"entity": "publication", "iuid": "7b520e6896954b47943166f96bc43806", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b520e6896954b47943166f96bc43806.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b520e6896954b47943166f96bc43806"}}, "title": "Molecular basis for different substrate-binding sites and chaperone functions of the BRICHOS domain.", "authors": [{"family": "Chen", "given": "Gefei", "initials": "G", "orcid": "0000-0002-5543-5963", "researcher": {"href": "https://publications.scilifelab.se/researcher/18ba91366ee94a1282e7b2b0bd8044d2.json"}}, {"family": "Wang", "given": "Yu", "initials": "Y"}, {"family": "Zheng", "given": "Zihan", "initials": "Z"}, {"family": "Jiang", "given": "Wangshu", "initials": "W"}, {"family": "Leppert", "given": "Axel", "initials": "A", "orcid": "0000-0001-6223-3350", "researcher": {"href": "https://publications.scilifelab.se/researcher/e89c2b7f8a294cfdae4848e96be7520b.json"}}, {"family": "Zhong", "given": "Xueying", "initials": "X"}, {"family": "Belorusova", "given": "Anna", "initials": "A"}, {"family": "Siegal", "given": "Gregg", "initials": "G"}, {"family": "Jegersch\u00f6ld", "given": "Caroline", "initials": "C"}, {"family": "Koeck", "given": "Philip J B", "initials": "PJB"}, {"family": "Abelein", "given": "Axel", "initials": "A", "orcid": "0000-0002-8079-3017", "researcher": {"href": "https://publications.scilifelab.se/researcher/22767062bdf549e1ae365d603e081817.json"}}, {"family": "Hebert", "given": "Hans", "initials": "H"}, {"family": "Knight", "given": "Stefan D", "initials": "SD"}, {"family": "Johansson", "given": "Jan", "initials": "J", "orcid": "0000-0002-8719-4703", "researcher": {"href": "https://publications.scilifelab.se/researcher/54c887805e9f4212857eb26efad3dcd9.json"}}], "type": "journal article", "published": "2024-07-00", "journal": {"title": "Protein Sci.", "issn": "1469-896X", "volume": "33", "issue": "7", "pages": "e5063", "issn-l": "0961-8368"}, "abstract": "Proteins can misfold into fibrillar or amorphous aggregates and molecular chaperones act as crucial guardians against these undesirable processes. The BRICHOS chaperone domain, found in several otherwise unrelated proproteins that contain amyloidogenic regions, effectively inhibits amyloid formation and toxicity but can in some cases also prevent non-fibrillar, amorphous protein aggregation. Here, we elucidate the molecular basis behind the multifaceted chaperone activities of the BRICHOS domain from the Bri2 proprotein. High-confidence AlphaFold2 and RoseTTAFold predictions suggest that the intramolecular amyloidogenic region (Bri23) is part of the hydrophobic core of the proprotein, where it occupies the proposed amyloid binding site, explaining the markedly reduced ability of the proprotein to prevent an exogenous amyloidogenic peptide from aggregating. However, the BRICHOS-Bri23 complex maintains its ability to form large polydisperse oligomers that prevent amorphous protein aggregation. A cryo-EM-derived model of the Bri2 BRICHOS oligomer is compatible with surface-exposed hydrophobic motifs that get exposed and come together during oligomerization, explaining its effects against amorphous aggregation. These findings provide a molecular basis for the BRICHOS chaperone domain function, where distinct surfaces are employed against different forms of protein aggregation.", "doi": "10.1002/pro.5063", "pmid": "38864729", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11168071"}], "notes": [], "created": "2024-10-08T09:34:32.077Z", "modified": "2024-11-15T13:43:08.812Z"}, {"entity": "publication", "iuid": "0da0ae4f148b4c269b2e050772b012bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0da0ae4f148b4c269b2e050772b012bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0da0ae4f148b4c269b2e050772b012bc"}}, "title": "Establishing Trypanosoma cruzi farnesyl pyrophosphate synthase as a viable target for biosensor driven fragment-based lead discovery.", "authors": [{"family": "Opassi", "given": "Giulia", "initials": "G"}, {"family": "Nordstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Lundin", "given": "Arne", "initials": "A"}, {"family": "Napolitano", "given": "Valeria", "initials": "V"}, {"family": "Magari", "given": "Francesca", "initials": "F"}, {"family": "Dzus", "given": "Tom", "initials": "T"}, {"family": "Klebe", "given": "Gerhard", "initials": "G", "orcid": "0000-0003-0177-537X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6afa0eddded142f2a16043d896012024.json"}}, {"family": "Danielson", "given": "U Helena", "initials": "UH", "orcid": "0000-0003-2728-0340", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2bf7dffedf44237807c23718c72efa6.json"}}], "type": "journal article", "published": "2020-04-00", "journal": {"title": "Protein Sci.", "issn": "1469-896X", "volume": "29", "issue": "4", "pages": "991-1003", "issn-l": "0961-8368"}, "abstract": "Procedures for producing and exploring Trypanosoma cruzi farnesyl pyrophosphate synthase (tcFPPS) for surface plasmon resonance (SPR) biosensor-driven fragment-based discovery have been established. The method requires functional sensor surfaces with high sensitivity for extended times and appropriate controls. Initial problems with protein stability and lack of useful reference compounds motivated optimization of experimental procedures and conditions. The improved methods enabled the production of pure, folded and dimeric protein, and identified procedures for storage and handling. A new coupled enzymatic assay, using luciferase for detection of pyrophosphate, was developed and used to confirm that the purified enzyme was active after purification and storage. It also confirmed that sensor surfaces prepared with structurally intact protein was active. An SPR-biosensor assay for fragment library screening and hit confirmation was developed. A thermal shift assay was used in parallel. A library of 90 fragments was efficiently screened by both assays at a single concentration in the presence and absence of the catalytic cofactor Mg2+ . Hits were selected on the basis of response levels or \u0394T m > 1\u00b0C and selectivity for tcFPPS in the presence of Mg2+ . Characterization of hits by SPR showed that all had low affinities and the relationships between steady-state responses and concentrations were not sufficiently hyperbolic for determination of KD -values. Instead, ranking could be performed from the slope of the linear relationship at low concentrations. This pilot screen confirms that the procedures developed herein enables SPR-biosensor driven fragment-based discovery of leads targeting tcFPPS, despite the lack of a reference compound. SIGNIFICANCE STATEMENT: To enable the discovery of drugs, it is essential to have access to relevant forms of the target protein and valid biochemical methods for studying the protein and effects of compounds that may be evolved into drugs. We have established methods for the discovery of drugs for treatment of American Trypanosomiasis (Chagas disease), using farnesyl pyrophosphate synthase from Trypanosoma cruzi as a target.", "doi": "10.1002/pro.3834", "pmid": "31994261", "labels": {"Drug Discovery and Development": null}, "xrefs": [{"db": "pmc", "key": "PMC7096706"}], "notes": [], "created": "2020-12-04T23:38:48.809Z", "modified": "2025-10-17T13:05:08.047Z"}, {"entity": "publication", "iuid": "35ee67ba38754d2e8cf529e8a42afa25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/35ee67ba38754d2e8cf529e8a42afa25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/35ee67ba38754d2e8cf529e8a42afa25"}}, "title": "IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions-Insights from transcription factors.", "authors": [{"family": "Millard", "given": "Peter S", "initials": "PS", "orcid": "0000-0003-1975-952X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2727f453eb524fea9fcdc0c8c3d1fe2b.json"}}, {"family": "Bugge", "given": "Katrine", "initials": "K", "orcid": "0000-0002-6286-6243", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb2ffb2565b43a9b2d4a891575eb611.json"}}, {"family": "Marabini", "given": "Riccardo", "initials": "R", "orcid": "0000-0003-3929-0490", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff6849b36a26415ea6b135100d349fc8.json"}}, {"family": "Boomsma", "given": "Wouter", "initials": "W", "orcid": "0000-0002-8257-3827", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c4fffa2a63147d49079213a8c68e7ed.json"}}, {"family": "Burow", "given": "Meike", "initials": "M", "orcid": "0000-0002-2350-985X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ac8209b3add4a779776052508bc1896.json"}}, {"family": "Kragelund", "given": "Birthe B", "initials": "BB", "orcid": "0000-0002-7454-1761", "researcher": {"href": "https://publications.scilifelab.se/researcher/03962568e1a945968c337cfe46e6c545.json"}}], "type": "journal article", "published": "2020-01-00", "journal": {"title": "Protein Sci.", "issn": "1469-896X", "volume": "29", "issue": "1", "pages": "169-183", "issn-l": "0961-8368"}, "abstract": "Protein domains constitute regions of distinct structural properties and molecular functions that are retained when removed from the rest of the protein. However, due to the lack of tertiary structure, the identification of domains has been largely neglected for long (>50 residues) intrinsically disordered regions. Here we present a sequence-based approach to assess and visualize domain organization in long intrinsically disordered regions based on compositional sequence biases. An online tool to find putative intrinsically disordered domains (IDDomainSpotter) in any protein sequence or sequence alignment using any particular sequence trait is available at http://www.bio.ku.dk/sbinlab/IDDomainSpotter. Using this tool, we have identified a putative domain enriched in hydrophilic and disorder-promoting residues (Pro, Ser, and Thr) and depleted in positive charges (Arg and Lys) bordering the folded DNA-binding domains of several transcription factors (p53, GCR, NAC46, MYB28, and MYB29). This domain, from two different MYB transcription factors, was characterized biophysically to determine its properties. Our analyses show the domain to be extended, dynamic and highly disordered. It connects the DNA-binding domain to other disordered domains and is present and conserved in several transcription factors from different families and domains of life. This example illustrates the potential of IDDomainSpotter to predict, from sequence alone, putative domains of functional interest in otherwise uncharacterized disordered proteins.", "doi": "10.1002/pro.3754", "pmid": "31642121", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6933863"}], "notes": [], "created": "2020-01-07T11:04:11.544Z", "modified": "2025-10-17T13:03:57.280Z"}, {"entity": "publication", "iuid": "bfe8e72ed23542b98cb7ceccc359bfc3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bfe8e72ed23542b98cb7ceccc359bfc3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bfe8e72ed23542b98cb7ceccc359bfc3"}}, "title": "High-efficient bacterial production of human ApoA-I amyloidogenic variants.", "authors": [{"family": "Del Giudice", "given": "Rita", "initials": "R"}, {"family": "Lagerstedt", "given": "Jens O", "initials": "JO"}], "type": "journal article", "published": "2018-12-00", "journal": {"title": "Protein Sci.", "issn": "1469-896X", "volume": "27", "issue": "12", "pages": "2101-2109", "issn-l": "0961-8368"}, "abstract": "Apolipoprotein A-I (ApoA-I)-related amyloidosis is a rare disease caused by missense mutations in the APOA1 gene. These mutations lead to protein aggregation and abnormal accumulation of ApoA-I amyloid fibrils in heart, liver, kidneys, skin, nerves, ovaries, or testes. Consequently, the carriers are at risk of single- or multi-organ failure and of need of organ transplantation. Understanding the basic molecular structure and function of ApoA-I amyloidogenic variants, as well as their biological effects, is, therefore, of great interest. However, the intrinsic low stability of this type of proteins makes their overexpression and purification difficult. To overcome this barrier, we here describe an optimized production and purification procedure for human ApoA-I amyloidogenic proteins that efficiently provides between 46 mg and 91 mg (depending on the protein variant) of pure protein per liter of Escherichia coli culture. Structural integrity of the amyloidogenic and native ApoA-I proteins were verified by circular dichroism spectroscopy and intrinsic fluorescence analysis, and preserved functionality was demonstrated by use of a lipid clearance assay as well as by reconstitution of high-density lipoprotein (HDL) particles. In conclusion, the use of the described high-yield protein production system to obtain amyloidogenic ApoA-I proteins, and their native counterpart, will enable molecular and cellular experimental studies aimed to explain the molecular basis for this rare disease.", "doi": "10.1002/pro.3522", "pmid": "30291643", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6237697"}], "notes": [], "created": "2020-01-27T10:11:30.317Z", "modified": "2021-05-24T15:39:50.387Z"}, {"entity": "publication", "iuid": "943fcace4f18487990477589f516bde1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/943fcace4f18487990477589f516bde1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/943fcace4f18487990477589f516bde1"}}, "title": "The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction.", "authors": [{"family": "Salvatore", "given": "M", "initials": "M"}, {"family": "Shu", "given": "N", "initials": "N"}, {"family": "Elofsson", "given": "A", "initials": "A"}], "type": "journal article", "published": "2018-01-00", "journal": {"volume": "27", "issn": "1469-896X", "issue": "1", "pages": "195-201", "title": "Protein Sci.", "issn-l": "0961-8368"}, "abstract": "SubCons is a recently developed method that predicts the subcellular localization of a protein. It combines predictions from four predictors using a Random Forest classifier. Here, we present the user-friendly web-interface implementation of SubCons. Starting from a protein sequence, the server rapidly predicts the subcellular localizations of an individual protein. In addition, the server accepts the submission of sets of proteins either by uploading the files or programmatically by using command line WSDL API scripts. This makes SubCons ideal for proteome wide analyses allowing the user to scan a whole proteome in few days. From the web page, it is also possible to download precalculated predictions for several eukaryotic organisms. To evaluate the performance of SubCons we present a benchmark of LocTree3 and SubCons using two recent mass-spectrometry based datasets of mouse and drosophila proteins. The server is available at http://subcons.bioinfo.se/.", "doi": "10.1002/pro.3297", "pmid": "28901589", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5734273"}], "notes": [], "created": "2017-11-10T13:09:49.314Z", "modified": "2024-01-16T13:48:47.161Z"}, {"entity": "publication", "iuid": "04ded7be42f34b5ba55d710ff6d8662a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04ded7be42f34b5ba55d710ff6d8662a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04ded7be42f34b5ba55d710ff6d8662a"}}, "title": "The human protein atlas: A spatial map of the human proteome.", "authors": [{"family": "Thul", "given": "Peter J", "initials": "PJ"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}], "type": "journal article", "published": "2017-09-23", "journal": {"title": "Protein Sci.", "issn": "1469-896X", "volume": null, "issue": null, "issn-l": "0961-8368"}, "abstract": "The correct spatial distribution of proteins is vital for their function and often mis-localization or ectopic expression leads to diseases. For more than a decade, the Human Protein Atlas (HPA) has constituted a valuable tool for researchers studying protein localization and expression in human tissues and cells. The centerpiece of the HPA is its unique antibody collection for mapping the entire human proteome by immunohistochemistry and immunocytochemistry. By these approaches, more than 10 million images showing protein expression patterns at a single-cell level were generated and are publicly available at www.proteinatlas.org. The antibody-based approach is combined with transcriptomics data for an overview of global expression profiles. The present article comprehensively describes the HPA database functions and how users can utilize it for their own research as well as discusses the future path of spatial proteomics.", "doi": "10.1002/pro.3307", "pmid": "28940711", "labels": {"Tissue Profiling": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-05T13:06:43.719Z", "modified": "2017-11-05T13:06:43.736Z"}, {"entity": "publication", "iuid": "c42b4df6aa6a4db9a6b82b4a3a73fd10", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c42b4df6aa6a4db9a6b82b4a3a73fd10.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c42b4df6aa6a4db9a6b82b4a3a73fd10"}}, "title": "Epitope-specificity of recombinant antibodies reveals promiscuous peptide-binding properties.", "authors": [{"family": "Olsson", "given": "Niclas", "initials": "N"}, {"family": "Wallin", "given": "Stefan", "initials": "S"}, {"family": "James", "given": "Peter", "initials": "P"}, {"family": "Borrebaeck", "given": "Carl A K", "initials": "CA"}, {"family": "Wingren", "given": "Christer", "initials": "C"}], "type": "journal article", "published": "2012-12-00", "journal": {"volume": "21", "issn": "1469-896X", "issue": "12", "pages": "1897-1910", "title": "Protein Sci.", "issn-l": "0961-8368"}, "abstract": "Protein-peptide interactions are a common occurrence and essential for numerous cellular processes, and frequently explored in broad applications within biology, medicine, and proteomics. Therefore, understanding the molecular mechanism(s) of protein-peptide recognition, specificity, and binding interactions will be essential. In this study, we report the first detailed analysis of antibody-peptide interaction characteristics, by combining large-scale experimental peptide binding data with the structural analysis of eight human recombinant antibodies and numerous peptides, targeting tryptic mammalian and eukaryote proteomes. The results consistently revealed that promiscuous peptide-binding interactions, that is, both specific and degenerate binding, were exhibited by all antibodies, and the discovery was corroborated by orthogonal data, indicating that this might be a general phenomenon for low-affinity antibody-peptide interactions. The molecular mechanism for the degenerate peptide-binding specificity appeared to be executed through the use of 2-3 semi-conserved anchor residues in the C-terminal part of the peptides, in analogue to the mechanism utilized by the major histocompatibility complex-peptide complexes. In the long-term, this knowledge will be instrumental for advancing our fundamental understanding of protein-peptide interactions, as well as for designing, generating, and applying peptide specific antibodies, or peptide-binding proteins in general, in various biotechnical and medical applications.", "doi": "10.1002/pro.2173", "pmid": "23034898", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pmc", "key": "PMC3575919"}], "notes": [], "created": "2017-05-04T14:56:20.027Z", "modified": "2020-01-21T13:53:20.850Z"}, {"entity": "publication", "iuid": "f1401f1407364e189b734a9b3e1582c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1401f1407364e189b734a9b3e1582c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1401f1407364e189b734a9b3e1582c0"}}, "title": "Generation of monospecific antibodies based on affinity capture of polyclonal antibodies.", "authors": [{"family": "Hjelm", "given": "Barbara", "initials": "B"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Igel", "given": "Ulrika", "initials": "U"}, {"family": "Johannesson", "given": "Henrik", "initials": "H"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Sj\u00f6berg", "given": "Anna", "initials": "A"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Johansson", "given": "Christine", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2011-11-00", "journal": {"volume": "20", "issn": "1469-896X", "issue": "11", "pages": "1824-1835", "title": "Protein Sci.", "issn-l": "0961-8368"}, "abstract": "A method is described to generate and validate antibodies based on mapping the linear epitopes of a polyclonal antibody followed by sequential epitope-specific capture using synthetic peptides. Polyclonal antibodies directed towards four proteins RBM3, SATB2, ANLN, and CNDP1, potentially involved in human cancers, were selected and antibodies to several non-overlapping epitopes were generated and subsequently validated by Western blot, immunohistochemistry, and immunofluorescence. For all four proteins, a dramatic difference in functionality could be observed for these monospecific antibodies directed to the different epitopes. In each case, at least one antibody was obtained with full functionality across all applications, while other epitope-specific fractions showed no or little functionality. These results present a path forward to use the mapped binding sites of polyclonal antibodies to generate epitope-specific antibodies, providing an attractive approach for large-scale efforts to characterize the human proteome by antibodies.", "doi": "10.1002/pro.716", "pmid": "21898641", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Spatial Proteomics": null, "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC3267947"}], "notes": [], "created": "2017-05-04T14:55:09.271Z", "modified": "2021-07-08T13:44:33.721Z"}], "created": "2017-05-09T09:12:35.853Z", "modified": "2020-11-27T13:14:03.278Z"}