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Wang Y, Dahmane S, Ti R, Mai X, Zhu L, Carlson LA, Stjepanovic G. Structural basis for lipid transfer by the ATG2A-ATG9A complex. Nat Struct Mol Biol 2025; 32:35-47. [PMID: 39174844 DOI: 10.1038/s41594-024-01376-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/23/2024] [Indexed: 08/24/2024]
Abstract
Autophagy is characterized by the formation of double-membrane vesicles called autophagosomes. Autophagy-related proteins (ATGs) 2A and 9A have an essential role in autophagy by mediating lipid transfer and re-equilibration between membranes for autophagosome formation. Here we report the cryo-electron microscopy structures of human ATG2A in complex with WD-repeat protein interacting with phosphoinositides 4 (WIPI4) at 3.2 Å and the ATG2A-WIPI4-ATG9A complex at 7 Å global resolution. On the basis of molecular dynamics simulations, we propose a mechanism of lipid extraction from the donor membranes. Our analysis revealed 3:1 stoichiometry of the ATG9A-ATG2A complex, directly aligning the ATG9A lateral pore with ATG2A lipid transfer cavity, and an interaction of the ATG9A trimer with both the N-terminal and the C-terminal tip of rod-shaped ATG2A. Cryo-electron tomography of ATG2A liposome-binding states showed that ATG2A tethers lipid vesicles at different orientations. In summary, this study provides a molecular basis for the growth of the phagophore membrane and lends structural insights into spatially coupled lipid transport and re-equilibration during autophagosome formation.
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Affiliation(s)
- Yang Wang
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China
| | - Selma Dahmane
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Rujuan Ti
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China
| | - Xinyi Mai
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China
| | - Lizhe Zhu
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China.
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China.
| | - Lars-Anders Carlson
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden.
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.
| | - Goran Stjepanovic
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China.
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Halder R, Chu ZT, Ti R, Zhu L, Warshel A. On the Control of Directionality of Myosin. J Am Chem Soc 2024. [PMID: 39367841 DOI: 10.1021/jacs.4c09528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2024]
Abstract
The origin of the unique directionality of myosin has been a problem of fundamental and practical importance. This work establishes in a conclusive way that the directionality is controlled by tuning the barrier for the rate-determining step, namely, the ADP release step. This conclusion is based on exploring the molecular origin behind the reverse directionality of myosins V and VI and the determination of the origin of the change in the barriers of the ADP release for the forward and backward motions. Our investigation is performed by combining different simulation methods such as steer molecular dynamics (SMD), umbrella sampling, renormalization method, and automated path searching method. It is found that in the case of myosin V, the ADP release from the postrigor (trailing head) state overcomes a lower barrier than the prepowerstroke (leading head) state, which is also evident from experimental observation. In the case of myosin VI, we noticed a different trend when compared to myosin V. Since the directionality of myosins V and VI follows a reverse trend, we conclude that such differences in the directionality are controlled by the free energy barrier for the ADP release. Overall, the proof that the directionality of myosin is determined by the activation barrier of the rate-determining step in the cycle, rather than by some unspecified dynamical effects, has general importance.
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Affiliation(s)
- Ritaban Halder
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Zhen Tao Chu
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Rujuan Ti
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Lizhe Zhu
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
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Ti R, Pang B, Yu L, Gan B, Ma W, Warshel A, Ren R, Zhu L. Fine-tuning activation specificity of G-protein-coupled receptors via automated path searching. Proc Natl Acad Sci U S A 2024; 121:e2317893121. [PMID: 38346183 PMCID: PMC10895267 DOI: 10.1073/pnas.2317893121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 01/12/2024] [Indexed: 02/15/2024] Open
Abstract
Physics-based simulation methods can grant atomistic insights into the molecular origin of the function of biomolecules. However, the potential of such approaches has been hindered by their low efficiency, including in the design of selective agonists where simulations of myriad protein-ligand combinations are necessary. Here, we describe an automated input-free path searching protocol that offers (within 14 d using Graphics Processing Unit servers) a minimum free energy path (MFEP) defined in high-dimension configurational space for activating sphingosine-1-phosphate receptors (S1PRs) by arbitrary ligands. The free energy distributions along the MFEP for four distinct ligands and three S1PRs reached a remarkable agreement with Bioluminescence Resonance Energy Transfer (BRET) measurements of G-protein dissociation. In particular, the revealed transition state structures pointed out toward two S1PR3 residues F263/I284, that dictate the preference of existing agonists CBP307 and BAF312 on S1PR1/5. Swapping these residues between S1PR1 and S1PR3 reversed their response to the two agonists in BRET assays. These results inspired us to design improved agonists with both strong polar head and bulky hydrophobic tail for higher selectivity on S1PR1. Through merely three in silico iterations, our tool predicted a unique compound scaffold. BRET assays confirmed that both chiral forms activate S1PR1 at nanomolar concentration, 1 to 2 orders of magnitude less than those for S1PR3/5. Collectively, these results signify the promise of our approach in fine agonist design for G-protein-coupled receptors.
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Affiliation(s)
- Rujuan Ti
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Bin Pang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200437, China
| | - Leiye Yu
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200437, China
| | - Bing Gan
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Wenzhuo Ma
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089
| | - Ruobing Ren
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200437, China
- Shanghai Qi Zhi Institute, Shanghai 200030, China
| | - Lizhe Zhu
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
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