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The molecular mechanism of lipid uptake by membrane-anchored bridge-like lipid transfer proteins
Open accessPreprint — published as 10.1073/pnas.2520399123 · Paper page
Abstract
Lipid transport by bridge-like lipid transfer proteins (BLTPs) is emerging as a key process in lipid and cellular metabolism in both physiological and pathological conditions. However, the precise mechanism of lipid transport by BLTPs has remained elusive. Here, we use extensive all-atom molecular dynamics simulations to characterize the precise mechanism of lipid transfer into the BLTP hydrophobic cavity from donor membranes. For multiple BLTPs, we observe the ability to extract and solubilize lipids without lipid selectivity, and we identify membrane destabilization as a critical parameter to achieve effective lipid desorption. We rationally design a mutant BLTP with altered ability to destabilize lipid bilayers, and we show that this abolishes lipid desorption in silico and protein function in vivo . Taken together, our data provide an atomic-level description of the mechanism of lipid transport by BLTPs, ultimately suggesting alternative strategies to interfere with their activity.
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Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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Research works printed but not linked: 80
- 10.1038/nrm2330 · DOI · Paper page
- 10.1038/nrm.2017.138 · DOI
- 10.1194/jlr.R800049-JLR200 · DOI
- Egea, P. F . Mechanisms of Non-Vesicular Exchange of Lipids at Membrane Contact Sites: Of Shuttles, Tunnels and Funnels. Front Cell Dev Biol 9, (2021). · DOI
- 10.1016/j.tibs.2017.05.001 · DOI
- 10.1038/s41580-018-0071-5 · DOI · Paper page
- 10.1016/j.ceb.2011.04.006 · DOI
- 10.1016/J.TCB.2022.03.011 · DOI
- Reinisch, K. M. & Prinz, W. A . Mechanisms of nonvesicular lipid transport. J Cell Biol 220, (2021). · DOI
- 10.1186/s12860-019-0226-z · DOI
- Melia, T. J. & Reinisch, K. M . A possible role for VPS13-family proteins in bulk lipid transfer, membrane expansion and organelle biogenesis. J Cell Sci 135, (2022). · DOI
- 10.1038/s41598-022-13717-w · DOI
- 2020, A novel VPS13B mutation in Cohen syndrome: a case report and review of literature, BMC Med Genet, 21, 140, 10.1186/s12881-020-01075-1 · DOI
- 10.1002/mds.27516 · DOI
- 10.1016/j.ajhg.2016.01.014 · DOI
- 10.1002/ana.25220 · DOI · Paper page
- 10.1038/88821 · DOI
- 10.1091/mbc.E19-08-0439-T · DOI
- Cai, S. et al. In situ architecture of the lipid transport protein VPS13C at ER–lysosome membrane contacts. Proc Natl Acad Sci U S A 119, (2022). · DOI · Paper page
- Hanna, M. G. , Suen, P. H. , Wu, Y. , Reinisch, K. M. & De Camilli, P . SHIP164 is a chorein motif lipid transfer protein that controls endosome–Golgi membrane traffic. J Cell Biol 221, (2022). · DOI · Paper page
- Chowdhury, S. et al. Insights into autophagosome biogenesis from structural and biochemical analyses of the ATG2A-WIPI4 complex. Proc Natl Acad Sci U S A 115, (2018). · DOI
- 10.1038/s41594-019-0203-4 · DOI
- 10.1083/jcb.201807019 · DOI
- 10.1038/s41586-025-08918-y · DOI
- 2022, Sequence Analysis and Structural Predictions of Lipid Transfer Bridges in the Repeating Beta Groove (RBG) Superfamily Reveal Past and Present Domain Variations Affecting Form, Function and Interactions of VPS13, ATG2, SHIP164, Hobbit and Tweek, Contact, 5, 251525642211343, 10.1177/25152564221134328 · DOI
- 2022, The bridge-like lipid transfer protein (BLTP) gene group: introducing new nomenclature based on structural homology indicating shared function, Hum Genomics, 16, 66, 10.1186/s40246-022-00439-3 · DOI
- 10.1038/s41467-022-34450-y · DOI
- Neuman, S. D. et al. The Hob proteins are novel and conserved lipid-binding proteins at ER–PM contact sites. J Cell Sci 135, (2022). · DOI
- 2025, The bridge-like lipid transport protein VPS13C/PARK23 mediates ER–lysosome contacts following lysosome damage, Nat Cell Biol, 27, 776, 10.1038/s41556-025-01653-6 · DOI
- 2024, Specificity of lipid transfer proteins: An in vitro story, Biochimie, 227, 85, 10.1016/j.biochi.2024.09.007 · DOI
- Maeda, S. , Otomo, C. & Otomo, T . The autophagic membrane tether ATG2A transfers lipids between membranes. Elife 8, (2019). · DOI
- 10.1083/jcb.201811139 · DOI
- 10.1038/s41586-022-05164-4 · DOI
- Li, P. , Lees, J. A. , Lusk, C. P. & Reinisch, K. M . Cryo-EM reconstruction of a VPS13 fragment reveals a long groove to channel lipids between membranes. J Cell Biol 219, (2020). · DOI
- Srinivasan, S. , Álvarez, D. , John Peter, A. T. & Vanni, S . Unbiased MD simulations identify lipid binding sites in lipid transfer proteins. J. Cell Biol. 223, (2024). · DOI
- 10.1101/2025.03.27.645728 · DOI
- 10.1146/annurev-cellbio-120420-014634 · DOI
- 10.1371/journal.pcbi.1010992 · DOI
- 2024, Model Mechanism for Lipid Uptake by the Human STARD2/PC-TP Phosphatidylcholine Transfer Protein, J Phys Chem Lett, 15, 8287, 10.1021/acs.jpclett.4c01743 · DOI
- 2021, Impact of PIP2 Lipids, Force Field Parameters, and Mutational Analysis on the Binding of the Osh4’s α 6 –α 7 Domain, J Phys Chem B, 125, 5296, 10.1021/acs.jpcb.0c10393 · DOI
- 2024, Proposed dual membrane contact with full-length Osh4, Biochimica et Biophysica Acta (BBA) - Biomembranes, 1866, 184365, 10.1016/j.bbamem.2024.184365 · DOI
- 10.1101/2025.05.24.655882 · DOI
- 2022, Csf1: A Putative Lipid Transport Protein Required for Homeoviscous Adaptation of the Lipidome, Contact, 5, 251525642211019, 10.1177/25152564221101974 · DOI
- Toulmay, A. et al. Vps13-like proteins provide phosphatidylethanolamine for GPI anchor synthesis in the ER. J Cell Biol 221, (2022). · DOI
- 10.1101/2025.04.30.651444 · DOI
- 10.1186/s12881-020-01074-2 · DOI
- 10.1021/acs.biochem.5b00718 · DOI
- 2020, Breakage of Hydrophobic Contacts Limits the Rate of Passive Lipid Exchange between Membranes, J Phys Chem B, 124, 5884, 10.1021/acs.jpcb.0c04139 · DOI
- 10.1021/ja0624321 · DOI · Paper page
- 10.1039/b902376c · DOI
- 2021, Membrane hydrophobicity determines the activation free energy of passive lipid transport, Biophys J, 120, 3718, 10.1016/j.bpj.2021.07.016 · DOI
- 10.1093/nar/gkn322 · DOI
- 10.1093/bioinformatics/17.8.700 · DOI
- 10.15252/embj.2021109998 · DOI
- 2024, Model Mechanism for Lipid Uptake by the Human STARD2/PC-TP Phosphatidylcholine Transfer Protein, J Phys Chem Lett, 15, 8287, 10.1021/acs.jpclett.4c01743 · DOI
- 2024, Lipid uptake/release by start domains from microsecond-long molecular dynamics simulations, Biophys J, 123, 452a, 10.1016/j.bpj.2023.11.2755 · DOI
- 10.1073/pnas.1806727115 · DOI
- 10.1083/jcb.201606078 · DOI
- 2023, In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms, Proteins: Structure, Function, and Bioinformatics, 91, 439, 10.1002/prot.26446 · DOI
- Ghanbarpour, A. , Valverde, D. P. , Melia, T. J. & Reinisch, K. M . A model for a partnership of lipid transfer proteins and scramblases in membrane expansion and organelle biogenesis. Proc Natl Acad Sci U S A 118, (2021). · DOI
- 10.1038/s41594-020-00518-w · DOI · Paper page
- Guillén-Samander, A. et al. A partnership between the lipid scramblase XK and the lipid transfer protein VPS13A at the plasma membrane. Proc Natl Acad Sci U S A 119, (2022). · DOI
- Eswar, N. et al. Comparative Protein Structure Modeling Using Modeller. Curr Protoc Bioinformatics 15, (2006). · DOI
- 10.1093/nar/gkr703 · DOI
- 10.1016/j.bpj.2009.04.013 · DOI
- 2015, GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers, SoftwareX, 1–2, 19
- 10.1038/nmeth.4067 · DOI
- 10.1063/1.448118 · DOI
- 10.1063/1.449071 · DOI
- 10.1063/1.328693 · DOI
- 10.1063/1.464397 · DOI
- 10.1016/0263-7855(96)00018-5 · DOI · Paper page
- 10.1002/jcc.21787 · DOI
- 10.1038/s41586-020-2649-2 · DOI · Paper page
- 10.25080/Majora-92bf1922-00a · DOI
- 10.1002/yea.1142 · DOI
- 10.1002/(SICI)1097-0061(199807)14:10<953::AID-YEA293>3.0.CO;2-U · DOI
- 10.1371/journal.pone.0003647 · DOI
- 10.1021/sb500366v · DOI
- 10.1002/yea.3065 · DOI
Metadata
- Authors
- Álvarez, D., Blair, P. C., Rocha-Roa, C., Davey, M., Conibear, E., & Vanni, S.
- Affiliations
- University of Fribourg (CH)
- University of British Columbia (CA)
- Corresponding author
- Vanni, Stefano
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- openRxiv
- Published
- 2025-08-02
- Volume
- 123
- Issue
- 4
- Pages
- e2520399123-e2520399123
- ISSN
- 0027-8424 (ISSN-L)
- OpenAlex
- W7125434868
- Cited by
- 6
- References
- 1
- Citations by year
- 2026: 5 · 2025: 1
- FWCI
- 10.33
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- Funders
- Swiss National Science Foundation (CRSII5_189996)
- European Research Council (803952)
- Canada Foundation for Innovation (39914)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Lipid metabolism and biosynthesis
- Keywords
- lipid transfer, membrane perturbation, lipid solubilization, lipid metabolism, protein-lipid interactions, rational protein design
- MeSH terms
- Biological Transport, Carrier Proteins, Cell Membrane, Lipid Bilayers, Lipid Metabolism, Molecular Dynamics Simulation, Hydrophobic and Hydrophilic Interactions
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