Segrest, J. P., Jones, M. K., De Loof, H. & Dashti, N. Structure of apolipoprotein B-100 in low density lipoproteins. J. Lipid Res. 42, 1346â1367 (2001).
Suryawanshi, Y. N. & Warbhe, R. A. Familial hypercholesterolemia: a literature review of the pathophysiology and current and novel treatments. Cureus 15, e49121 (2023).
Borén, J. et al. Low-density lipoproteins cause atherosclerotic cardiovascular disease: pathophysiological, genetic, and therapeutic insights: a consensus statement from the European Atherosclerosis Society Consensus Panel. Eur. Heart J. 41, 2313â2330 (2020).
Yu, Y. et al. Polyhedral 3D structure of human plasma very low density lipoproteins by individual particle cryo-electron tomography1. J. Lipid Res. 57, 1879â1888 (2016).
Ehrlich, M. et al. Endocytosis by random initiation and stabilization of clathrin-coated pits. Cell 118, 591â605 (2004).
Rudenko, G. et al. Structure of the LDL receptor extracellular domain at endosomal pH. Science 298, 2353â2358 (2002).
Jeon, H. & Blacklow, S. C. Structure and physiologic function of the low-density lipoprotein receptor. Annu. Rev. Biochem. 74, 535â562 (2005).
Mhaimeed, O. et al. The importance of LDL-C lowering in atherosclerotic cardiovascular disease prevention: lower for longer is better. Am. J. Prev. Cardiol. 18, 100649 (2024).
Chora, J. R., Medeiros, A. M., Alves, A. C. & Bourbon, M. Analysis of publicly available LDLR, APOB, and PCSK9 variants associated with familial hypercholesterolemia: application of ACMG guidelines and implications for familial hypercholesterolemia diagnosis. Genet. Med. 20, 591â598 (2018).
Blacklow, S. C. Versatility in ligand recognition by LDL receptor family proteins: advances and frontiers. Curr. Opin. Struct. Biol. 17, 419â426 (2007).
Wu, X. & Rapoport, T. A. Cryo-EM structure determination of small proteins by nanobody-binding scaffolds (Legobodies). Proc. Natl Acad. Sci. USA 118, e2115001118 (2021).
Nykjaer, A. & Willnow, T. E. The low-density lipoprotein receptor gene family: a cellular Swiss army knife. Trends Cell Biol. 12, 273â280 (2002).
Ren, G. et al. Model of human low-density lipoprotein and bound receptor based on cryoEM. Proc. Natl Acad. Sci. USA 107, 1059â1064 (2010).
Kumar, V. et al. Three-dimensional cryoEM reconstruction of native LDL particles to 16Ã resolution at physiological body temperature. PLoS One 6, e18841 (2011).
Cisse, A. et al. Targeting structural flexibility in low density lipoprotein by integrating cryo-electron microscopy and high-speed atomic force microscopy. Int. J. Biol. Macromol. 252, 126345 (2023).
Li, H. et al. Construction of a biotinylated cameloid-like antibody for lable-free detection of apolipoprotein B-100. Biosens. Bioelectron. 64, 111â118 (2015).
Jeiran, K. et al. A new structural model of apolipoprotein B100 based on computational modeling and cross linking. Int. J. Mol. Sci. 23, 11480 (2022).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583â589 (2021).
Thompson, J. R. & Banaszak, L. J. Lipidâprotein interactions in lipovitellin. Biochemistry 41, 9398â9409 (2002).
Biterova, E. I. et al. The crystal structure of human microsomal triglyceride transfer protein. Proc. Natl Acad. Sci. USA 116, 17251â17260 (2019).
Huang, R. et al. Apolipoprotein A-I structural organization in high-density lipoproteins isolated from human plasma. Nat. Struct. Mol. Biol. 18, 416â422 (2011).
Esser, V., Limbird, L. E., Brown, M. S., Goldstein, J. L. & Russell, D. W. Mutational analysis of the ligand binding domain of the low density lipoprotein receptor. J. Biol. Chem. 263, 13282â13290 (1988).
Russell, D. W., Brown, M. S. & Goldstein, J. L. Different combinations of cysteine-rich repeats mediate binding of low density lipoprotein receptor to two different proteins. J. Biol. Chem. 264, 21682â21688 (1989).
Boren, J. et al. Identification of the low density lipoprotein receptor-binding site in apolipoprotein B100 and the modulation of its binding activity by the carboxyl terminus in familial defective apo-B100. J. Clin. Invest. 101, 1084â1093 (1998).
Motazacker, M. M. et al. Advances in genetics show the need for extending screening strategies for autosomal dominant hypercholesterolaemia. Eur. Heart J. 33, 1360â1366 (2012).
RodrÃguez-Jiménez, C. et al. Identification and functional analysis of APOB variants in a cohort of hypercholesterolemic patients. Int. J. Mol. Sci. 24, 7635 (2023).
Fernández-Higuero, J. A. et al. Structural analysis of APOB variants, p.(Arg3527Gln), p.(Arg1164Thr) and p.(Gln4494del), causing familial hypercholesterolaemia provides novel insights into variant pathogenicity. Sci. Rep. 5, 18184 (2015).
Gaffney, D. et al. Independent mutations at codon 3500 of the apolipoprotein B gene are associated with hyperlipidemia. Arterioscler. Thromb. Vasc. Biol. 15, 1025â1029 (1995).
Pullinger, C. R. et al. Familial ligand-defective apolipoprotein B. Identification of a new mutation that decreases LDL receptor binding affinity. J. Clin. Invest. 95, 1225â1234 (1995).
Huang, S., Henry, L., Ho, Y. K., Pownall, H. J. & Rudenko, G. Mechanism of LDL binding and release probed by structure-based mutagenesis of the LDL receptor. J. Lipid Res. 51, 297â308 (2010).
Gomez, A. et al. Functional analysis of six uncharacterised mutations in LDLR gene. Atherosclerosis 291, 44â51 (2019).
Benito-Vicente, A. et al. The importance of an integrated analysis of clinical, molecular, and functional data for the genetic diagnosis of familial hypercholesterolemia. Genet. Med. 17, 980â988 (2015).
Duskova, L. et al. Low density lipoprotein receptor variants in the beta-propeller subdomain and their functional impact. Front. Genet. 11, 691 (2020).
Wang, M. et al. Novel LDLR variants affecting low density lipoprotein metabolism identified in familial hypercholesterolemia. Mol. Biol. Rep. 51, 153 (2024).
Shen, H. et al. Familial defective apolipoprotein B-100 and increased low-density lipoprotein cholesterol and coronary artery calcification in the Old Order Amish. Arch. Intern. Med. 170, 1850â1855 (2010).
Soria, L. F. et al. Association between a specific apolipoprotein B mutation and familial defective apolipoprotein B-100. Proc. Natl Acad. Sci. USA 86, 587â591 (1989).
Montasser, M. E. et al. Genetic and functional evidence links a missense variant in B4GALT1 to lower LDL and fibrinogen. Science 374, 1221â1227 (2021).
Zhao, Y. et al. In-depth mass spectrometry analysis reveals the plasma proteomic and N-glycoproteomic impact of an Amish-enriched cardioprotective variant in B4GALT1. Mol. Cell. Proteomics 22, 100595 (2023).
Zou, P. & Ting, A. Y. Imaging LDL receptor oligomerization during endocytosis using a co-internalization assay. ACS Chem. Biol. 6, 308â313 (2011).
van Driel, I. R., Davis, C. G., Goldstein, J. L. & Brown, M. S. Self-association of the low density lipoprotein receptor mediated by the cytoplasmic domain. J. Biol. Chem. 262, 16127â16134 (1987).
Heymann, J. B. et al. Clathrin-coated vesicles from brain have small payloads: a cryo-electron tomographic study. J. Struct. Biol. 184, 43â51 (2013).
Berndsen Z. T. & Cassidy, C. K. The structure of ApoB100 from human low-density lipoprotein. Preprint at bioRxiv https://doi.org/10.1101/2024.02.28.582555 (2024).
Lu, M. & Gursky, O. Aggregation and fusion of low-density lipoproteins in vivo and in vitro. Biomol. Concepts 4, 501â518 (2013).
Ãörni, K. & Kovanen, P. T. Aggregation susceptibility of low-density lipoproteinsâa novel modifiable biomarker of cardiovascular risk. J. Clin. Med. 10, 1769 (2021).
Maruyama, I. N. Activation of transmembrane cell-surface receptors via a common mechanism? The ârotation modelâ. Bioessays 37, 959â967 (2015).
Feixas, F., Lindert, S., Sinko, W. & McCammon, J. A. Exploring the role of receptor flexibility in structure-based drug discovery. Biophys. Chem. 186, 31â45 (2014).
Heuser, J. E. & Anderson, R. G. Hypertonic media inhibit receptor-mediated endocytosis by blocking clathrin-coated pit formation. J. Cell Biol. 108, 389â400 (1989).
Beglova, N., Jeon, H., Fisher, C. & Blacklow, S. C. Cooperation between fixed and low pH-inducible interfaces controls lipoprotein release by the LDL receptor. Mol. Cell 16, 281â292 (2004).
Havel, R. J., Eder, H. A. & Bragdon, J. H. The distribution and chemical composition of ultracentrifugally separated lipoproteins in human serum. J. Clin. Invest. 34, 1345â1353 (1955).
Schumaker, V. N. & Puppione, D. L. Sequential flotation ultracentrifugation. Methods Enzymol. 128, 155â170 (1986).
Gaubatz, J. W. et al. Dynamics of dense electronegative low density lipoproteins and their preferential association with lipoprotein phospholipase A2. J. Lipid Res. 48, 348â357 (2007).
Banerjee, S. et al. Proteolysis of the low density lipoprotein receptor by bone morphogenetic protein-1 regulates cellular cholesterol uptake. Sci. Rep. 9, 11416 (2019).
Yost, S. A., Whidby, J., Khan, A. G., Wang, Y. & Marcotrigiano, J. Overcoming challenges of hepatitis C virus envelope glycoprotein production in mammalian cells. Methods Mol. Biol. 1911, 305â316 (2019).
Wu, D. & Piszczek, G. Standard protocol for mass photometry experiments. Eur. Biophys. J. 50, 403â409 (2021).
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290â296 (2017).
Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153â1160 (2019).
Cardone, G., Heymann, J. B. & Steven, A. C. One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions. J. Struct. Biol. 184, 226â236 (2013).
Sanchez-Garcia, R. et al. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun. Biol. 4, 874 (2021).
Jakobi, A. J., Wilmanns, M. & Sachse, C. Model-based local density sharpening of cryo-EM maps. eLife 6, e27131 (2017).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486â501 (2010).
Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861â877 (2019).
Williams, C. J. et al. MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci. 27, 293â315 (2018).
Wessel, D. & Flugge, U. I. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal. Biochem. 138, 141â143 (1984).
Rappsilber, J., Mann, M. & Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc. 2, 1896â1906 (2007).
Mendes, M. L. et al. An integrated workflow for crosslinking mass spectrometry. Mol. Syst. Biol. 15, e8994 (2019).
Lenz, S. et al. Reliable identification of protein-protein interactions by crosslinking mass spectrometry. Nat. Commun. 12, 3564 (2021).
Kong, A. T., Leprevost, F. V., Avtonomov, D. M., Mellacheruvu, D. & Nesvizhskii, A. I. MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics. Nat. Methods 14, 513â520 (2017).
da Veiga Leprevost, F. et al. Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat. Methods 17, 869â870 (2020).
