{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T18:28:08Z","timestamp":1790620088151,"version":"4.1.0"},"reference-count":70,"publisher":"MDPI AG","issue":"19","license":[{"start":{"date-parts":[[2022,9,29]],"date-time":"2022-09-29T00:00:00Z","timestamp":1664409600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000050","name":"National Heart, Lung and Blood institute","doi-asserted-by":"publisher","award":["HL006095-13"],"award-info":[{"award-number":["HL006095-13"]}],"id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>ApoB-100 is a member of a large lipid transfer protein superfamily and is one of the main apolipoproteins found on low-density lipoprotein (LDL) and very low-density lipoprotein (VLDL) particles. Despite its clinical significance for the development of cardiovascular disease, there is limited information on apoB-100 structure. We have developed a novel method based on the \u201cdivide and conquer\u201d algorithm, using PSIPRED software, by dividing apoB-100 into five subunits and 11 domains. Models of each domain were prepared using I-TASSER, DEMO, RoseTTAFold, Phyre2, and MODELLER. Subsequently, we used disuccinimidyl sulfoxide (DSSO), a new mass spectrometry cleavable cross-linker, and the known position of disulfide bonds to experimentally validate each model. We obtained 65 unique DSSO cross-links, of which 87.5% were within a 26 \u00c5 threshold in the final model. We also evaluated the positions of cysteine residues involved in the eight known disulfide bonds in apoB-100, and each pair was measured within the expected 5.6 \u00c5 constraint. Finally, multiple domains were combined by applying constraints based on detected long-range DSSO cross-links to generate five subunits, which were subsequently merged to achieve an uninterrupted architecture for apoB-100 around a lipoprotein particle. Moreover, the dynamics of apoB-100 during particle size transitions was examined by comparing VLDL and LDL computational models and using experimental cross-linking data. In addition, the proposed model of receptor ligand binding of apoB-100 provides new insights into some of its functions.<\/jats:p>","DOI":"10.3390\/ijms231911480","type":"journal-article","created":{"date-parts":[[2022,9,29]],"date-time":"2022-09-29T21:03:10Z","timestamp":1664485390000},"page":"11480","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["A New Structural Model of Apolipoprotein B100 Based on Computational Modeling and Cross Linking"],"prefix":"10.3390","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0901-034X","authenticated-orcid":false,"given":"Kianoush","family":"Jeiran","sequence":"first","affiliation":[{"name":"Lipoprotein Metabolism Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA"},{"name":"School of Systems Biology, George Mason University, Manassas, VA 20110, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott M.","family":"Gordon","sequence":"additional","affiliation":[{"name":"Department of Physiology and Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY 40536, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Denis O.","family":"Sviridov","sequence":"additional","affiliation":[{"name":"Lipoprotein Metabolism Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angel M.","family":"Aponte","sequence":"additional","affiliation":[{"name":"Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amanda","family":"Haymond","sequence":"additional","affiliation":[{"name":"Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5270-3678","authenticated-orcid":false,"given":"Grzegorz","family":"Piszczek","sequence":"additional","affiliation":[{"name":"Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2833-5681","authenticated-orcid":false,"given":"Diego","family":"Lucero","sequence":"additional","affiliation":[{"name":"Lipoprotein Metabolism Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1248-6613","authenticated-orcid":false,"given":"Edward B.","family":"Neufeld","sequence":"additional","affiliation":[{"name":"Lipoprotein Metabolism Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6858-1516","authenticated-orcid":false,"given":"Iosif I.","family":"Vaisman","sequence":"additional","affiliation":[{"name":"School of Systems Biology, George Mason University, Manassas, VA 20110, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lance","family":"Liotta","sequence":"additional","affiliation":[{"name":"Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ancha","family":"Baranova","sequence":"additional","affiliation":[{"name":"School of Systems Biology, George Mason University, Manassas, VA 20110, USA"},{"name":"Research Center for Medical Genetics, 115522 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alan T.","family":"Remaley","sequence":"additional","affiliation":[{"name":"Lipoprotein Metabolism Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,9,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1111\/j.1365-2796.2005.01556.x","article-title":"Apolipoprotein B: A clinically important apolipoprotein which assembles atherogenic lipoproteins and promotes the development of atherosclerosis","volume":"258","author":"Olofsson","year":"2005","journal-title":"J. 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