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Conformation switch of NPC1 epitomizes a luminal alternating access for nonpolar substrates

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作者

    Xuelan Wu， 
    Xuelan Wu
    • Department of Chemistry, Princeton University, Princeton, NJ 08544
    Sepehr Dehghani-Ghahnaviyeh， 
    Sepehr Dehghani-Ghahnaviyeh
    • Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
    Ali Rasouli， 
    Ali Rasouli
    • Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
    John A. Malona， 
    John A. Malona
    • Jnana Therapeutics Inc., Boston, MA 02210
    Mitchell Antalek， 
    Mitchell Antalek
    • Jnana Therapeutics Inc., Boston, MA 02210
    Lyn H. Jones， 
    Lyn H. Jones
    • Jnana Therapeutics Inc., Boston, MA 02210
    Xiao Fan， 
    Xiao Fan
    • Institute of Bio-Architecture and Bio-Interaction (IBABI), Shenzhen Medical Academy of Research and Translation, Guangdong, China 518107
    • Department of Molecular Biology, Princeton University, Princeton, NJ 08544
    Adele Peng， 
    Adele Peng
    • Department of Molecular Biology, Princeton University, Princeton, NJ 08544
    Emad Tajkhorshid， 
    Emad Tajkhorshid
    • Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
    Hongwu Qian， 
    Hongwu Qian
    • 中国科学技术大学生命科学与医学部
    • University of Science and Technology of China image/svg+xml
    Nieng Yan
    Nieng Yan
    • Department of Molecular Biology, Princeton University, Princeton, NJ 08544
    • Institute of Bio-Architecture and Bio-Interaction (IBABI), Shenzhen Medical Academy of Research and Translation, Guangdong, China 518107
    • Institute of Chemical Biology, Shenzhen Bay Laboratory, Guangming District, Shenzhen 518132, Guangdong, China
分类
生物化学与生物物理学
关键词
Cryo-EM; Niemann-Pick disease type c; alternating access

摘要

Niemann-Pick disease type C (NPC) arises from failure of the NPC1 and/or NPC2 proteins to mobilize lysosomal cholesterol, yet the mechanism by which the complex drives sterol translocation lacks a thorough understanding (1, 2). Here, we capture an NPC1-NPC2 complex conformation at lysosomal pH using a bis-sterol ligand (JM046), fortifying NPC2 engagement with NPC1 and enabling structural characterization of an alternative transport state. In this complex, the sterol moiety is absent from the NPC1 central tunnel, and the neck site adopts an expanded architecture that resembles a previously observed NPC1 conformation at neutral pH, indicating that the tunnel geometry is not influenced by the pH alone. Instead, we provide evidence that cholesterol occupancy in the neck site is a key determinant of tunnel contraction. Supporting this notion, NPC1 purified from cholesterol-auxotrophic insect cells exhibits a similar expanded neck conformation. Integrating these structures and molecular dynamics (MD) simulations exploring the directional cholesterol handoff from NPC2 to the NPC1 tunnel, we propose a substrate-induced gating cycle where luminal and membrane-facing openings of NPC1 switch states in a coordinated manner to transfer cholesterol across the hydrophilic glycocalyx. This mechanism is reminiscent of the alternating access mechanism for hydrophobic substrate transfer. This framework synthesizes NPC1 conformational states into a mechanistic basis to classify pathogenic NPC variants by relevant transport steps, which will illuminate mechanism-guided therapeutic strategies.

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Wu, X., Dehghani-Ghahnaviyeh, S., Rasouli, A., A. Malona, J., Antalek, M., H. Jones, L., Fan, X., Peng, A., Tajkhorshid, E., Qian, H., & Yan, N. (2026). Conformation switch of NPC1 epitomizes a luminal alternating access for nonpolar substrates. 浪淘沙预印本平台. https://doi.org/10.65215/LTSpreprints.2026.09.18.000345

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