{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T02:28:49Z","timestamp":1781058529400,"version":"3.54.1"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,22]],"date-time":"2022-12-22T00:00:00Z","timestamp":1671667200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100005562","name":"North Carolina Biotechnology Center","doi-asserted-by":"publisher","award":["2014-IDG-1017"],"award-info":[{"award-number":["2014-IDG-1017"]}],"id":[{"id":"10.13039\/100005562","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006510","name":"Duke University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006510","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R01-GM145035"],"award-info":[{"award-number":["1R01-GM145035"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Metal cations have been exploited for their precipitation properties in a wide variety of studies, ranging from differentiating proteins from serum and blood to identifying the protein targets of drugs. Despite widespread recognition of this phenomenon, the mechanisms of metal-induced protein aggregation have not been fully elucidated. Recent studies have suggested that copper's (Cu) ability to induce protein aggregation may be a main contributor to Cu-induced cell death. Here, we provide the first proteome-wide analysis of the relative sensitivities of proteins across the Escherichia coli proteome to Cu-induced aggregation. We utilize a metal-induced protein precipitation (MiPP) methodology that relies on quantitative bottom\u2013up proteomics to define the metal concentration\u2013dependent precipitation properties of proteins on a proteomic scale. Our results establish that Cu far surpasses other metals in promoting protein aggregation and that the protein aggregation is reversible upon metal chelation. The bulk of the Cu bound in the protein aggregates is Cu1+, regardless of the Cu2+ source. Analysis of our MiPP data allows us to investigate underlying biophysical characteristics that determine a protein's sensitivity to Cu-induced aggregation, which is independent of the relative concentration of protein in the lysate. Overall, this analysis provides new insights into the mechanism behind Cu cytotoxicity, as well as metal cation\u2013induced protein aggregation.<\/jats:p>","DOI":"10.1093\/mtomcs\/mfac098","type":"journal-article","created":{"date-parts":[[2022,12,23]],"date-time":"2022-12-23T00:20:50Z","timestamp":1671754850000},"source":"Crossref","is-referenced-by-count":22,"title":["Analysis of copper-induced protein precipitation across the <i>E. coli<\/i> proteome"],"prefix":"10.1093","volume":"15","author":[{"given":"Amy T R","family":"Robison","sequence":"first","affiliation":[{"name":"Department of Chemistry, Duke University , Durham, NC 27708, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Grace R","family":"Sturrock","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Duke University , Durham, NC 27708, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacqueline M","family":"Zaengle-Barone","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Duke University , Durham, NC 27708, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nancy","family":"Wiebelhaus","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Duke University , Durham, NC 27708, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Azim","family":"Dharani","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Duke University , Durham, NC 27708, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabella G","family":"Williams","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Duke University , Durham, NC 27708, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael C","family":"Fitzgerald","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Duke University , Durham, NC 27708, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9015-0998","authenticated-orcid":false,"given":"Katherine J","family":"Franz","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Duke University , Durham, NC 27708, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,12,22]]},"reference":[{"issue":"4-5","key":"2024012010365488000_bib1","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1113\/jphysiol.1907.sp001234","article-title":"The precipitation of the proteins of horse serum","volume":"36","author":"Mellanby","year":"1907","journal-title":"J. Physiol."},{"issue":"3","key":"2024012010365488000_bib2","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1016\/S0021-9258(18)76632-5","article-title":"The use of copper and iron salts for the deproteinization of blood","volume":"90","author":"Somogyi","year":"1931","journal-title":"J. Biol. Chem."},{"issue":"4","key":"2024012010365488000_bib3","doi-asserted-by":"crossref","first-page":"2286","DOI":"10.1021\/cr200271j","article-title":"Hofmeister phenomena: an update on ion specificity in biology","volume":"112","author":"Lo Nostro","year":"2012","journal-title":"Chem. Rev."},{"issue":"4","key":"2024012010365488000_bib4","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/nchem.1899","article-title":"Beyond Hofmeister","volume":"6","author":"Jungwirth","year":"2014","journal-title":"Nat. Chem."},{"issue":"11","key":"2024012010365488000_bib5","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1038\/s41557-019-0355-1","article-title":"Hofmeister's curse","volume":"11","author":"Gibb","year":"2019","journal-title":"Nat. Chem."},{"issue":"9","key":"2024012010365488000_bib6","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1007\/BF00241693","article-title":"Copper affinity precipitation as an initial step in protein purification","volume":"8","author":"Agarwal","year":"1994","journal-title":"Biotechnol. Tech."},{"issue":"2","key":"2024012010365488000_bib7","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1006\/jcis.1996.0049","article-title":"A model for metal affinity protein precipitation","volume":"177","author":"Iyer","year":"1996","journal-title":"J. Colloid Interface Sci."},{"issue":"2","key":"2024012010365488000_bib8","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/S1570-0232(02)00914-5","article-title":"Optimization of protein precipitation based upon effectiveness of protein removal and ionization effect in liquid chromatography-tandem mass spectrometry","volume":"785","author":"Polson","year":"2003","journal-title":"J. Chromatogr. B. Analyt. Technol. Biomed. Life. Sci."},{"issue":"19","key":"2024012010365488000_bib9","doi-asserted-by":"crossref","first-page":"7066","DOI":"10.1021\/acs.analchem.2c00391","article-title":"Ion-based proteome-integrated solubility alteration assays for systemwide profiling of protein\u2014molecule interactions","volume":"94","author":"Beusch","year":"2022","journal-title":"Anal. Chem."},{"issue":"19","key":"2024012010365488000_bib10","doi-asserted-by":"crossref","first-page":"2253","DOI":"10.1016\/j.ccr.2012.04.004","article-title":"Metal ions as modulators of protein conformation and misfolding in neurodegeneration","volume":"256","author":"Leal","year":"2012","journal-title":"Coord. Chem. Rev."},{"issue":"8","key":"2024012010365488000_bib11","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1038\/sj.bjp.0706416","article-title":"The crucial role of metal ions in neurodegeneration: the basis for a promising therapeutic strategy","volume":"146","author":"Gaeta","year":"2005","journal-title":"Br. J. Pharmacol."},{"issue":"1","key":"2024012010365488000_bib12","doi-asserted-by":"crossref","first-page":"252","DOI":"10.3390\/biom4010252","article-title":"Heavy metals and metalloids as a cause for protein misfolding and aggregation","volume":"4","author":"Tam\u00e1s","year":"2014","journal-title":"Biomolecules"},{"issue":"12","key":"2024012010365488000_bib13","doi-asserted-by":"crossref","first-page":"1743","DOI":"10.1039\/C8MT00182K","article-title":"Copper-induced cell death and the protective role of glutathione: the implication of impaired protein folding rather than oxidative stress","volume":"10","author":"Saporito-Magri\u00f1\u00e1","year":"2018","journal-title":"Metallomics"},{"issue":"2","key":"2024012010365488000_bib14","doi-asserted-by":"crossref","first-page":"e03251","DOI":"10.1128\/mbio.03251-21","article-title":"Copper induces protein aggregation, a toxic process compensated by molecular chaperones","volume":"13","author":"Zuily","year":"2022","journal-title":"mBio"},{"issue":"6586","key":"2024012010365488000_bib15","doi-asserted-by":"crossref","first-page":"1254","DOI":"10.1126\/science.abf0529","article-title":"Copper induces cell death by targeting lipoylated TCA cycle proteins","volume":"375","author":"Tsvetkov","year":"2022","journal-title":"Science"},{"issue":"1","key":"2024012010365488000_bib16","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1021\/acschembio.0c00900","article-title":"Protein folding stability changes across the proteome reveal targets of Cu toxicity in E. coli","volume":"16","author":"Wiebelhaus","year":"2021","journal-title":"ACS Chem. Biol."},{"issue":"5","key":"2024012010365488000_bib17","doi-asserted-by":"crossref","first-page":"1616","DOI":"10.1128\/JB.01357-06","article-title":"Intracellular copper does not catalyze the formation of oxidative DNA damage in escherichia coli","volume":"189","author":"Macomber","year":"2007","journal-title":"J. Bacteriol."},{"issue":"20","key":"2024012010365488000_bib18","doi-asserted-by":"crossref","first-page":"8344","DOI":"10.1073\/pnas.0812808106","article-title":"The iron-sulfur clusters of dehydratases are primary intracellular targets of copper toxicity","volume":"106","author":"Macomber","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"issue":"1","key":"2024012010365488000_bib19","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/S0300-483X(03)00159-8","article-title":"Copper toxicity, oxidative stress, and antioxidant nutrients","volume":"189","author":"Gaetke","year":"2003","journal-title":"Toxicology"},{"key":"2024012010365488000_bib20","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/B978-0-12-811077-5.00006-2","article-title":"Chapter 6 cellular copper toxicity: a critical appraisal of fenton-chemistry-based oxidative stress in Wilson disease","volume-title":"Wilson Disease","author":"Zischka","year":"2019"},{"issue":"2","key":"2024012010365488000_bib21","doi-asserted-by":"crossref","first-page":"eESP00142020","DOI":"10.1128\/ecosalplus.ESP-0014-2020","article-title":"Copper homeostatic mechanisms and their role in the virulence of escherichia coli and salmonella enterica","volume":"9","author":"Hyre","year":"2021","journal-title":"EcoSal Plus"},{"issue":"3","key":"2024012010365488000_bib22","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/s41589-018-0211-4","article-title":"Bacterial sensors define intracellular free energies for correct enzyme metalation","volume":"15","author":"Osman","year":"2019","journal-title":"Nat. Chem. Biol."},{"issue":"9","key":"2024012010365488000_bib23","doi-asserted-by":"crossref","first-page":"e7052","DOI":"10.1371\/journal.pone.0007052","article-title":"Copper-triggered aggregation of ubiquitin","volume":"4","author":"Arnesano","year":"2009","journal-title":"PLoS One"},{"issue":"7-8","key":"2024012010365488000_bib24","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1007\/s00018-003-3447-3","article-title":"Investigation of the effects of copper ions on protein aggregation using a model system","volume":"61","author":"Capanni","year":"2004","journal-title":"Cell. Mol. Life Sci."},{"key":"2024012010365488000_bib25","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1016\/j.jinorgbio.2014.04.003","article-title":"Metal ions modulate thermal aggregation of beta-lactoglobulin: a joint chemical and physical characterization","volume":"137","author":"Navarra","year":"2014","journal-title":"J. Inorg. Biochem."},{"issue":"8","key":"2024012010365488000_bib26","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1007\/s00249-008-0346-4","article-title":"Thermally induced denaturation and aggregation of blg-a: effect of the Cu2+ and Zn2+ metal ions","volume":"37","author":"Stirpe","year":"2008","journal-title":"Eur. Biophys. J."},{"issue":"6","key":"2024012010365488000_bib27","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1038\/nrmicro3028","article-title":"Antimicrobial activity of metals: mechanisms, molecular targets and applications","volume":"11","author":"Lemire","year":"2013","journal-title":"Nat. Rev. Microbiol."},{"key":"2024012010365488000_bib28","doi-asserted-by":"crossref","first-page":"213474","DOI":"10.1016\/j.ccr.2020.213474","article-title":"Biomedical applications of copper ionophores","volume":"422","author":"Oliveri","year":"2020","journal-title":"Coord. Chem. Rev."},{"issue":"20","key":"2024012010365488000_bib29","doi-asserted-by":"crossref","first-page":"13528","DOI":"10.1021\/acs.inorgchem.9b01029","article-title":"Emerging opportunities to manipulate metal trafficking for therapeutic benefit","volume":"58","author":"Hunsaker","year":"2019","journal-title":"Inorg. Chem."},{"issue":"6","key":"2024012010365488000_bib30","doi-asserted-by":"crossref","first-page":"1019","DOI":"10.1021\/acsinfecdis.8b00037","article-title":"Copper influences the antibacterial outcomes of a \u03b2-lactamase-activated prochelator against drug-resistant bacteria","volume":"4","author":"Zaengle-Barone","year":"2018","journal-title":"ACS. Infect. Dis."},{"issue":"8","key":"2024012010365488000_bib31","doi-asserted-by":"crossref","first-page":"3809","DOI":"10.1021\/pr400032m","article-title":"iFASP: combining isobaric mass tagging with filter-aided sample preparation","volume":"12","author":"McDowell","year":"2013","journal-title":"J. Proteome Res."},{"issue":"5","key":"2024012010365488000_bib32","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1515\/labmed-2019-0098","article-title":"A colorimetric method to measure oxidized, reduced and total glutathione levels in erythrocytes","volume":"43","author":"Alisik","year":"2019","journal-title":"J. Lab. Med."},{"issue":"15","key":"2024012010365488000_bib33","doi-asserted-by":"crossref","first-page":"9249","DOI":"10.1021\/acs.analchem.8b01772","article-title":"Chemical denaturation and protein precipitation approach for discovery and quantitation of protein\u2014drug interactions","volume":"90","author":"Meng","year":"2018","journal-title":"Anal. Chem."},{"issue":"8","key":"2024012010365488000_bib34","doi-asserted-by":"crossref","first-page":"3809","DOI":"10.1021\/pr400032m","article-title":"iFASP: combining isobaric mass tagging with filter-aided sample preparation","volume":"12","author":"McDowell","year":"2013","journal-title":"J. Proteome Res."},{"issue":"1","key":"2024012010365488000_bib35","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1038\/nprot.2012.146","article-title":"Thermodynamic analysis of protein-ligand binding interactions in complex biological mixtures using the stability of proteins from rates of oxidation","volume":"8","author":"Strickland","year":"2013","journal-title":"Nat. Protoc."},{"issue":"13","key":"2024012010365488000_bib36","doi-asserted-by":"crossref","first-page":"11047","DOI":"10.1074\/jbc.M110.213074","article-title":"Unification of the Copper(I) binding affinities of the metallo-chaperones Atx1, Atox1, and related proteins: detection probes and affinity standards","volume":"286","author":"Xiao","year":"2011","journal-title":"J. Biol. Chem."},{"issue":"8","key":"2024012010365488000_bib37","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1038\/nchembio.186","article-title":"Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli","volume":"5","author":"Bennett","year":"2009","journal-title":"Nat. Chem. Biol."},{"issue":"15","key":"2024012010365488000_bib38","doi-asserted-by":"crossref","first-page":"1130","DOI":"10.1089\/ars.2017.7123","article-title":"The incomplete glutathione puzzle: just guessing at numbers and figures?","volume":"27","author":"Deponte","year":"2017","journal-title":"Antioxid. Redox Signaling"},{"issue":"52","key":"2024012010365488000_bib39","doi-asserted-by":"crossref","first-page":"21558","DOI":"10.1074\/jbc.M117.817452","article-title":"Glutathione limits Aquacopper(I) to sub-femtomolar concentrations through cooperative assembly of a tetranuclear cluster","volume":"292","author":"Morgan","year":"2017","journal-title":"J. Biol. Chem."},{"issue":"9","key":"2024012010365488000_bib40","doi-asserted-by":"crossref","first-page":"5079","DOI":"10.1021\/acs.analchem.7b00595","article-title":"Predicting ESI\/MS signal change for anions in different solvents","volume":"89","author":"Kruve","year":"2017","journal-title":"Anal. Chem."},{"issue":"20","key":"2024012010365488000_bib41","doi-asserted-by":"crossref","first-page":"9078","DOI":"10.1073\/pnas.1000148107","article-title":"Quantitative proteomics approach for identifying protein-drug interactions in complex mixtures using protein stability measurements","volume":"107","author":"West","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"issue":"6205","key":"2024012010365488000_bib42","doi-asserted-by":"crossref","first-page":"1255784","DOI":"10.1126\/science.1255784","article-title":"Tracking cancer drugs in living cells by thermal profiling of the proteome","volume":"346","author":"Savitski","year":"2014","journal-title":"Science"},{"issue":"5","key":"2024012010365488000_bib43","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/s41592-020-0801-4","article-title":"Meltome atlas\u2014thermal proteome stability across the tree of life","volume":"17","author":"Jarzab","year":"2020","journal-title":"Nat. Methods"},{"issue":"D1","key":"2024012010365488000_bib44","doi-asserted-by":"crossref","first-page":"D419","DOI":"10.1093\/nar\/gky1038","article-title":"PANTHER version 14: more genomes, a new PANTHER GO-Slim and improvements in enrichment analysis tools","volume":"47","author":"Mi","year":"2019","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"2024012010365488000_bib45","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1021\/mp4004749","article-title":"Lysine and arginine content of proteins: computational analysis suggests a new tool for solubility design","volume":"11","author":"Warwicker","year":"2014","journal-title":"Mol. Pharmaceutics"},{"issue":"38","key":"2024012010365488000_bib46","doi-asserted-by":"crossref","first-page":"12816","DOI":"10.1021\/jp906350s","article-title":"Urea-mediated protein denaturation: a consensus view","volume":"113","author":"Das","year":"2009","journal-title":"J. Phys. Chem. B"},{"issue":"7","key":"2024012010365488000_bib47","doi-asserted-by":"crossref","first-page":"1406","DOI":"10.1110\/ps.0304803","article-title":"Analysis of accessible surface of residues in proteins","volume":"12","author":"Lins","year":"2003","journal-title":"Protein Sci."},{"issue":"1","key":"2024012010365488000_bib48","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1093\/femsre\/fuz026","article-title":"Protein aggregation in bacteria","volume":"44","author":"Schramm","year":"2020","journal-title":"FEMS Microbiol. Rev."},{"issue":"3","key":"2024012010365488000_bib49","first-page":"e00434","article-title":"Copper cytotoxicity: cellular casualties of noncognate coordination chemistry","volume":"13","author":"O'Hern","year":"2022","journal-title":"mBio"},{"issue":"D1","key":"2024012010365488000_bib50","doi-asserted-by":"crossref","first-page":"D543","DOI":"10.1093\/nar\/gkab1038","article-title":"The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences","volume":"50","author":"Perez-Riverol","year":"2022","journal-title":"Nucleic Acids Res."}],"container-title":["Metallomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/metallomics\/advance-article-pdf\/doi\/10.1093\/mtomcs\/mfac098\/48355863\/mfac098.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/metallomics\/article-pdf\/15\/1\/mfac098\/56255027\/mfac098.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/metallomics\/article-pdf\/15\/1\/mfac098\/56255027\/mfac098.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,20]],"date-time":"2024-01-20T10:37:33Z","timestamp":1705747053000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/metallomics\/article\/doi\/10.1093\/mtomcs\/mfac098\/6957399"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,12,22]]},"references-count":50,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,1,10]]}},"URL":"https:\/\/doi.org\/10.1093\/mtomcs\/mfac098","relation":{},"ISSN":["1756-591X"],"issn-type":[{"value":"1756-591X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023]]},"published":{"date-parts":[[2022,12,22]]},"article-number":"mfac098"}}