Beenken A, Cerutti G, Brasch J, Guo Y, Sheng Z, Erdjument-Bromage H, Aziz Z, Robbins-Juarez SY, Chavez EY, Ahlsen G, Katsamba PS, Neubert TA, Fitzpatrick AW, Barasch J, Shapiro L. Structures of LRP2 reveal a molecular machine for endocytosis. Cell. 2023 Feb 16;186(4):821-836.e13. Epub 2023 Feb 6 PubMed.

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  1. We’ve known for a long time that members of this receptor family play a critical role in biology. What has been missing is a detailed understanding of how they accomplish their function at the molecular level. Solving the structure of LRP2 represents a significant achievement and offers critical insight into important biological questions.

    In addition to providing mechanistic insight into how ligand uncoupling occurs in the low-pH environment of endosomal compartments, this study reveals two unexpected findings. First, while studies performed on isolated ligand binding clusters from LRP2 have similar ligand binding properties, the data reveal structural-based control of each ligand-binding region, indicating a level of regulation that was not anticipated.

    Second, the pH-induced conformational change results in a dramatic separation of the intracellular domains in the dimer, from the 25 Å at extracellular pH to 140 Å at endosomal pH. This could impact assembly of adaptor molecules involved in trafficking and signaling events. Finally, it is likely that information learned from the structure of LRP2 will be applicable to LRP1 as well, as many of the critical structural elements are also found in LRP1.

    View all comments by Dudley Strickland

  2. In this landmark paper, Andrew Beenken et al. used cryoEM to solve the structure of LRP2, which is part of the LDL-receptor-related family of proteins, at both extracellular and endosomal pH. This family of proteins is able to bind ApoE isoforms, which greatly affect the risk for late-onset AD. Competition between ApoE and other ligands such as tau and Aβ for binding to these receptors is implicated in Aβ plaque deposition and tau seeding and spreading.

    The proper recycling of receptors like LRP1, LRP2, and LDLR is important for clearing Aβ and tau from the ISF. In fact, overexpression of LDLR has been shown to be protective in a mouse model of tau pathology. Similarly, polymorphisms in the promoter region of LRP2, which lowers LRP2 expression, are associated with higher AD risk, possibly due to the decreased clearance of proteins like Aβ and tau. However, despite the importance of these receptors to AD pathology, the molecular mechanisms underlying their function and ligand binding had not been well described until now.

    The structure resolved in this paper greatly alters the model predicted by Alphafold, whereby the unique hairpin folding and dimerization states “overturn” the textbook depiction of lipoprotein receptor family as “tube men” at the cell surface. This study provides a mechanistic description of how the pH changes LRP2 experiences while trafficking from the plasma membrane to the endosome regulate ligand binding and release. The structural model shows how LRP2 mutations associated with Donnai-Barrow Syndrome disrupt pH-sensitive sites that would interfere with the conformational change that LRP2 undergoes when at endosomal pH, preventing intramolecular ligands to bind EGF-like domains in order to release LRP2’s cargo.

    This study now gives us a framework to try to better understand how mutations in other LDL receptor family proteins could be playing a role in AD pathology. Interestingly, SORL1, which is a risk factor for late-onset AD, is an endosomal-sorting protein containing an EGF-like domain and 11 LDLR class A repeats. SORL1 has been shown to be involved in APP processing, and it is intriguing to think that mutations that disrupt cargo release throughout trafficking, in a manner similar to LRP2, could have implications for APP processing and trafficking.

    A critical question that remains is how extramolecular ligands bind receptors like LRP2. This would be important for understanding how ApoE competes with Aβ or tau for binding to LDL-receptor-related receptors. Future studies characterizing this family of proteins and their ligands will expand our understanding of the molecular mechanisms underlying disease risk variants and how LDL-receptor-related proteins are contributing to AD pathogenesis.

    Beyond the AD-related ligands, the structural dependence on pH of those lipoprotein receptors may imply new roles for themselves as well as ApoE and other lipoproteins and molecules involved in lysosomal storage disorders. This paper also provides new thoughts for basic science in this area. One important question is how different lipoprotein receptors modulate their interactions with ligands by changing numbers and arrangement of those conserved domains. This further raises the question how exactly the pH change drives such a huge tertiary structure movement from ligand-binding conformation into the closed conformation at pH 5.2. In line with this paper, the conserved domains of L repeats and β-propellers with Ca2+-coordinating interactions might be the answer. The interactions between L repeats and β-propellers in this structure indicate a universal pH-dependent domain-level sliding that governs the ligand-catch-and-release mechanism in lipoproteins. Different numbers of conserved domains among different lipoprotein receptors seem to have a more profound impact on a variety of superdomain movements that eventually determine the capture-and-release efficiency of subtype lipoproteins. Some of the essential Ca2+ ions would contribute to the electron transfers across different residues. Molecular dynamics paired with CryoEM 3D classification at intermediate pH between 5.2 and 7.4 could be important in  future studies to fully understand the process.

    As the authors discussed, one limitation of this study is the lack of determinations of the intracellular domain. However, it is observable that the last two EGF-like domains experience considerable spatial movements at different pH conditions, which leads to a reasonable prediction that the cytoplasmic domain undergoes substantial confirmational changes because of the former movements. Although the authors encountered technical challenges to visualize the disordered cytoplasmic domain, it would be interesting to complex LRP2 protein with known endosomal sorting proteins such as WASH/CCC family to investigate the pH-dependent sorting system.

    View all comments by Michael Strickland

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  1. Catch and Release: Cryo-EM Reveals How LRP2 Receptor Recycles Cargo