Publications — PEPTIDISC LAB

Some Research Publications and Applications using the Peptidisc membrane mimetic:

Horne J, Kaplan E, Jin BHS, Petsolari E, Gradon JM, Ntsogo Y, Harris A, Yu D, Luisi BF (2025) A lipoprotein partner for the Escherichia coli outer membrane protein TolC. bioRxiv 2025.03.19.644130;
Rimle L, Phillips BP, Codo Costa Barra IM, Arnold N, Hennebert C, Meier T, von Ballmoos C. (2025) A splendid molecular factory: De- and reconstruction of the mammalian respiratory chain. Proc Natl Acad Sci U S A. 122(12):e2416162122.
Tania S, Petsolar E, et al. (2025). Disassembly of the Escherichia coli AcrABZ-TolC efflux pump by ligand-mediated disruption of TolC-AcrA interfacial contacts bioRxiv 2025.02.18.638599; doi: https://doi.org/10.1101/2025.02.18.638599
Jain BK, Duan HD, Valentine L, Ariana Samiha, Huilin Li, Todd R Graham (2025). P4-ATPase control over phosphoinositide membrane asymmetry and neomycin resistance. bioRxiv 2025.03.03.641220; doi: https://doi.org/10.1101/2025.03.03.641220
Miki K, Miyata T, Makino F, Imada K, Namba K, Minamino T. (2025) Structural basis of flagellar rod assembly on the FliPQR protein-export channel bioRxiv 2025.02.07.637169; doi: https://doi.org/10.1101/2025.02.07.637169.
Fang S, Yang Y, Zhang X, Yang Z, Zhang M, Zhao Y, Zhang C, Yu F, Wang YF, Zhang P. (2025)* Structural mechanism underlying PHO1:H1-mediated phosphate transport in Arabidopsis. Nat Plants. 10.1038/s41477-024-01895-6.
Morizumi T, Kim K, Li H, Nag P, Dogon T, Sineshchekov OA, Wang Y, Brown LS, Hwang S, Sun H, Bondar AN, Schapiro I, Govorunova EG, Spudich JL, Ernst OP. (2025)*Structural insights into light-gating of potassium-selective channelrhodopsin. Nat Commun. 16(1):1283. d

Yilun Chen, Franck Duong van Hoa (2025). Peptidisc-assisted hydrophobic clustering towards the production of multimeric and multispecific nanobody proteins. Biochemistry. 10.1021/acs.biochem.4c00793.
Jandu, RJ, Al-Seragi M, Aoki H, Babu M, Duong van Hoa F (2025) Membrane mimetic thermal proteome profiling (MM-TPP) towards mapping membrane protein-ligand dynamics. eLife 14:RP104549.
Kindig K, Gibbs E, Seiferth D, Biggin PC, Chakrapani S. (2024) Mechanisms underlying modulation of human GlyRα3 by Zn2+ and pH. Sci Adv. 10(51):eadr5920. doi: 10.1126/sciadv.adr5920.
Thach T, Dhanabalan K, Nandekar PP, Stauffer S, Heisler I, Alvarado S, Snyder J, Subramanian R. (2024).*Mechanistic insights into the selective targeting of P2X3 receptor by camlipixant antagonist. J Biol Chem. 108109. doi: 10.1016/j.jbc.2024.108109.
Mitrovic SA, Demalgiriya-Gamage C, Winter LM, Kiechle T, Ebenhoch R, Neubauer H, Stierstorfer B, Frego L, Wolfrum C, Reindl S, Nar H (2024)*. GPR180 is a new member of the Golgi-dynamics domain seven-transmembrane helix protein family. Commun Biol. 7(1):1588. doi: 10.1038/s42003-024-07260-9.
Antony, F., Brough, Z., Orangi, M., Al-Seragi, M., Aoki, H., Babu, M., Duong van Hoa, F. (2024) Sensitive profiling of mouse liver membrane proteome dysregulation following a high-fat and alcohol diet treatment. PROTEOMICS Sep 23:e202300599. PMID: 39313981
Zheng YY, Chung WH, Leung YC, Wong KY. (2024) Heterogenous Expression and Purification of Lipid II Flippase from Staphylococcus aureus. Protein Pept Lett. 31(5):e040724231578.
Huang Q, Chan KY, Wu J, Botticello-Romero NR, Zheng Q, Lou S, Keyes C, Svanbergsson A, Johnston J, Mills A, Lin CY, Brauer PP, Clouse G, Pacouret S, Harvey JW, Beddow T, Hurley JK, Tobey IG, Powell M, Chen AT, Barry AJ, Eid FE, Chan YA, Deverman BE. (2024). An AAV capsid reprogrammed to bind human Transferrin Receptor mediates brain-wide gene delivery. Science. doi: 10.1126/science.adm8386.
Gao Y, Zhang Y, Hakke S, Mohren R, Sijbers LJPM, Peters PJ, Ravelli RBG. (2024) Cryo-EM structure of cytochrome bo3 quinol oxidase assembled in peptidiscs reveals an "open" conformation for potential ubiquinone-8 release. Biochim Biophys Acta Bioenerg. 2024 Apr 11:149045. doi: 10.1016/j.bbabio.2024.149045.
Jandu, R.S., Yu, H., Zhao, Z., Le, H.T., Kim, S., Huan, T., Duong van Hoa, F. (2024) Capture of Endogenous Lipids in Peptidiscs and Effect on Protein Stability and Activity, iScience (2024), doi: https://doi.org/10.1016/j.isci.2024.109382.
Zhao, Z., Young, J.W., Duong van hoa, F. (2024). Affinity Purification of Membrane β-Barrel Proteins via Biotin-Tagged Peptidiscs. In: Ieva, R. (eds) Transmembrane β-Barrel Proteins. Methods in Molecular Biology (2024). vol 2778. doi.org/10.1007/978-1-0716-3734-0_10
Shin J, Park J, Jeong J, Lam JH, Qiu X, Wu D, Kim K, Lee JY, Robinson CV, Hyun J, Katritch V, Kim KP, Cho Y. (2024) Constitutive activation mechanism of a class C GPCR. Nat Struct Mol Biol. 2024 Feb 8. doi: 10.1038/s41594-024-01224-7. Online ahead of print.
Young JW, Pfitzner E, van Wee R, Kirschbaum C, Kukura P, Robinson CV. (2024) Characterization of membrane protein interactions by peptidisc-mediated mass photometry. iScience. 2024 Jan 4;27(2):108785. doi: 10.1016/j.isci.2024.108785.
Antony F, Brough Z, Zhao Z, Duong van hoa F. (2023). Capture of the Mouse Organ Membrane Proteome Specificity in Peptidisc Libraries. J Proteome Res. 2023 Dec. doi:10.1021/acs.
Yu L, Xu X, Chua WZ, Feng H, Ser Z, Shao K, Shi J, Wang Y, Li Z, Sobota RM, Sham LT, Luo M. (2023) Structural basis of peptide secretion for Quorum sensing by ComA. Nat Commun. 2023 Nov 7;14(1):7178. doi: 10.1038/s41467-023-42852-9.
Li J, Xu X, Shi J, Hermoso JA, Sham LT, Luo M. (2023) Regulation of the cell division hydrolase RipC by the FtsEX system in Mycobacterium tuberculosis. Nat Commun. 2023 Dec 4;14(1):7999. doi: 10.1038/s41467-023-43770-6.
Morizumi T, Kim K, Li H, Govorunova EG, Sineshchekov OA, Wang Y, Zheng L, Bertalan É, Bondar A-N, Askari A, et al. (2023).*Structures of channelrhodopsin paralogs in peptidiscs explain their contrasting K+ and Na+ selectivities. Nat Commun. 14(1):4365.

Cruz SJ, Burendei B, Lee WH, Ward A (2023) Structure of mechanically activated ion channel OSCA2.3 reveals mobile elements in the transmembrane domain. Structure. 2023 Dec 6:S0969-2126(23)00411-2. doi: 10.1016/j.str.2023.11.009.
Itskanov S, Wang L, Junne T, Sherriff R, Xiao L, Blanchard N, Shi WQ, Forsyth C, Hoepfner D, Spiess M, Park E. (2023) A common mechanism of Sec61 translocon inhibition by small molecules. Nat Chem Biol. 2023 May 11. doi: 10.1038/s41589-023-01337-y.
Zhao Z, Khurana A, Antony F, Young JW, Hewton KG, Brough Z, Zhong T, Parker ST, Duong van Hoa F. (2023) A Peptidisc-based Survey of the Plasma Membrane Proteome of a Mammalian Cell. Mol Cell Proteomics. 2023 Jun 7:100588. doi: 10.1016/j.mcpro.2023.100588.
Xu X, Li J, Chua WZ, Pages MA, Shi J, Hermoso JA, Bernhardt T, Sham LT, Luo (2023) Mechanistic insights into the regulation of cell wall hydrolysis by FtsEX and EnvC at the bacterial division site. Proc Natl Acad Sci USA. 2023 May 23;120(21):e2301897120.
Kim S, Lee SS, Park JG, Kim JW, Ju S, Choi SH, Kim S, Kim NJ, Hong S, Kang JY, Jin MS. (2022) Structural Insights into Porphyrin Recognition by the Human ATP-Binding Cassette Transporter ABCB6. Mol Cells. 2022 Aug 31;45(8):575-587.
Young JW, Wason IS, Zhao Z, Kim S, Aoki H, Phanse S, Rattray DG, Foster LJ, Babu M, Duong van Hoa F. (2022) Development of a Method Combining Peptidiscs and Proteomics to Identify, Stabilize, and Purify a Detergent-Sensitive Membrane Protein Assembly. J Proteome Res. 2022 Jul 1;21(7):1748-1758.
Ung KL, Winkler M, Schulz L, Kolb M, Janacek DP, Dedic E, Stokes DL, Hammes UZ, Pedersen BP. (2022)* Structures and mechanism of the plant PIN-FORMED auxin transporter. Nature. Sep;609(7927):605-610.
Demmer JK, Phillips BP, Uhrig OL, Filloux A, Allsopp LP, Bublitz M, Meier T. (2022) Structure of ATP synthase from ESKAPE pathogen Acinetobacter baumannii. Sci Adv. 2022 Feb 18;8(7):5966.
Xu P, Huang S, Zhang H, Mao C, Zhou XE, Cheng X, Simon IA, Shen DD, Yen HY, Robinson CV, Harpsøe K, Svensson B, Guo J, Jiang H, Gloriam DE, Melcher K, Jiang Y, Zhang Y, Xu HE. (2021) Structural insights into the lipid and ligand regulation of serotonin receptors. Nature. 2021 Apr;592(7854):469-473.
Harris A, Wagner M, Du D, Raschka S, Nentwig LM, Gohlke H, Smits SHJ, Luisi BF, Schmitt L. (2021) Structure and efflux mechanism of the yeast pleiotropic drug resistance transporter Pdr5. Nat Commun. 2021 Sep 6;12(1):5254.
Wu JX, Liu R, Song K, Chen L. (2021). Structures of human dual oxidase 1 complex in low-calcium and high-calcium states. Nat Commun. 2021 Jan 8;12(1):155.
Zeytuni N, Dickey SW, Hu J, Chou HT, Worrall LJ, Alexander JAN, Carlson ML, Nosella M, Duong F, Yu Z, Otto M, Strynadka NCJ. (2020). Structural insight into the Staphylococcus aureus ATP-driven exporter of virulent peptide toxins. Sci Adv. 2020 Sep 30;6(40):8219.
Young JW, Wason IS, Zhao Z, Rattray DG, Foster LJ, Duong Van Hoa F. (2020) His-Tagged Peptidiscs Enable Affinity Purification of the Membrane Proteome for Downstream Mass Spectrometry Analysis. J Proteome Res. 2020 Jul 2;19(7):2553-2562.
Kuo YC, Chen H, Shang G, Uchikawa E, Tian H, Bai XC, Zhang X. (2020). Cryo-EM structure of the PlexinC1/A39R complex reveals inter-domain interactions critical for ligand-induced activation. Nat Commun. 2020 Apr 23;11(1):1953.
Angiulli G, Dhupar HS, Suzuki H, Wason IS, Duong Van Hoa F, Walz T. (2020) New approach for membrane protein reconstitution into peptidiscs and basis for their adaptability to different proteins. Elife. 2020 Mar 3;9:e53530.
Rantalainen K, Berndsen ZT, Antanasijevic A, Schiffner T, Zhang X, Lee WH, Torres JL, Zhang L, Irimia A, Copps J, Zhou KH, Kwon YD, Law WH, Schramm CA, Verardi R, Krebs SJ, Kwong PD, Doria-Rose NA, Wilson IA, Zwick MB, Yates JR 3rd, Schief WR, Ward AB. (2020) HIV-1 Envelope and MPER Antibody Structures in Lipid Assemblies. Cell Rep. 2020 Apr 28;31(4):107583.
Saville JW, Troman L, Duong Van Hoa F. (2019) PeptiQuick, a One-Step Incorporation of Membrane Proteins into Biotinylated Peptidiscs for Streamlined Protein Binding Assays. J Vis Exp. 2019 Nov 2;(153).
Carlson ML, Stacey RG, Young JW, Wason IS, Zhao Z, Rattray DG, Scott N, Kerr CH, Babu M, Foster LJ, Duong Van Hoa F. (2019) Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries. Elife. 2019 Jul 31;8:e46615.

Some Research Publications and Applications using the Peptidisc membrane mimetic:

Horne J, Kaplan E, Jin BHS, Petsolari E, Gradon JM, Ntsogo Y, Harris A, Yu D, Luisi BF (2025) A lipoprotein partner for the Escherichia coli outer membrane protein TolC. bioRxiv 2025.03.19.644130;

Rimle L, Phillips BP, Codo Costa Barra IM, Arnold N, Hennebert C, Meier T, von Ballmoos C. (2025) A splendid molecular factory: De- and reconstruction of the mammalian respiratory chain. Proc Natl Acad Sci U S A. 122(12):e2416162122.

Tania S, Petsolar E, et al. (2025). Disassembly of the Escherichia coli AcrABZ-TolC efflux pump by ligand-mediated disruption of TolC-AcrA interfacial contacts bioRxiv 2025.02.18.638599; doi: https://doi.org/10.1101/2025.02.18.638599

Jain BK, Duan HD, Valentine L, Ariana Samiha, Huilin Li, Todd R Graham (2025). P4-ATPase control over phosphoinositide membrane asymmetry and neomycin resistance. bioRxiv 2025.03.03.641220; doi: https://doi.org/10.1101/2025.03.03.641220

Miki K, Miyata T, Makino F, Imada K, Namba K, Minamino T. (2025) Structural basis of flagellar rod assembly on the FliPQR protein-export channel bioRxiv 2025.02.07.637169; doi: https://doi.org/10.1101/2025.02.07.637169.

Fang S, Yang Y, Zhang X, Yang Z, Zhang M, Zhao Y, Zhang C, Yu F, Wang YF, Zhang P. (2025)* Structural mechanism underlying PHO1:H1-mediated phosphate transport in Arabidopsis. Nat Plants. 10.1038/s41477-024-01895-6.

Morizumi T, Kim K, Li H, Nag P, Dogon T, Sineshchekov OA, Wang Y, Brown LS, Hwang S, Sun H, Bondar AN, Schapiro I, Govorunova EG, Spudich JL, Ernst OP. (2025)*Structural insights into light-gating of potassium-selective channelrhodopsin. Nat Commun. 16(1):1283. d

Yilun Chen, Franck Duong van Hoa (2025). Peptidisc-assisted hydrophobic clustering towards the production of multimeric and multispecific nanobody proteins. Biochemistry. 10.1021/acs.biochem.4c00793.

Jandu, RJ, Al-Seragi M, Aoki H, Babu M, Duong van Hoa F (2025) Membrane mimetic thermal proteome profiling (MM-TPP) towards mapping membrane protein-ligand dynamics. eLife 14:RP104549.

Kindig K, Gibbs E, Seiferth D, Biggin PC, Chakrapani S. (2024) Mechanisms underlying modulation of human GlyRα3 by Zn2+ and pH. Sci Adv. 10(51):eadr5920. doi: 10.1126/sciadv.adr5920.

Thach T, Dhanabalan K, Nandekar PP, Stauffer S, Heisler I, Alvarado S, Snyder J, Subramanian R. (2024).*Mechanistic insights into the selective targeting of P2X3 receptor by camlipixant antagonist. J Biol Chem. 108109. doi: 10.1016/j.jbc.2024.108109.

Mitrovic SA, Demalgiriya-Gamage C, Winter LM, Kiechle T, Ebenhoch R, Neubauer H, Stierstorfer B, Frego L, Wolfrum C, Reindl S, Nar H (2024)*. GPR180 is a new member of the Golgi-dynamics domain seven-transmembrane helix protein family. Commun Biol. 7(1):1588. doi: 10.1038/s42003-024-07260-9.

Antony, F., Brough, Z., Orangi, M., Al-Seragi, M., Aoki, H., Babu, M., Duong van Hoa, F. (2024) Sensitive profiling of mouse liver membrane proteome dysregulation following a high-fat and alcohol diet treatment. PROTEOMICS Sep 23:e202300599. PMID: 39313981

Zheng YY, Chung WH, Leung YC, Wong KY. (2024) Heterogenous Expression and Purification of Lipid II Flippase from Staphylococcus aureus. Protein Pept Lett. 31(5):e040724231578.

Jandu, R.S., Yu, H., Zhao, Z., Le, H.T., Kim, S., Huan, T., Duong van Hoa, F. (2024) Capture of Endogenous Lipids in Peptidiscs and Effect on Protein Stability and Activity, iScience (2024), doi: https://doi.org/10.1016/j.isci.2024.109382.

Zhao, Z., Young, J.W., Duong van hoa, F. (2024). Affinity Purification of Membrane β-Barrel Proteins via Biotin-Tagged Peptidiscs. In: Ieva, R. (eds) Transmembrane β-Barrel Proteins. Methods in Molecular Biology (2024). vol 2778. doi.org/10.1007/978-1-0716-3734-0_10

Shin J, Park J, Jeong J, Lam JH, Qiu X, Wu D, Kim K, Lee JY, Robinson CV, Hyun J, Katritch V, Kim KP, Cho Y. (2024) Constitutive activation mechanism of a class C GPCR. Nat Struct Mol Biol. 2024 Feb 8. doi: 10.1038/s41594-024-01224-7. Online ahead of print.

Young JW, Pfitzner E, van Wee R, Kirschbaum C, Kukura P, Robinson CV. (2024) Characterization of membrane protein interactions by peptidisc-mediated mass photometry. iScience. 2024 Jan 4;27(2):108785. doi: 10.1016/j.isci.2024.108785.

Antony F, Brough Z, Zhao Z, Duong van hoa F. (2023). Capture of the Mouse Organ Membrane Proteome Specificity in Peptidisc Libraries. J Proteome Res. 2023 Dec. doi:10.1021/acs.

Yu L, Xu X, Chua WZ, Feng H, Ser Z, Shao K, Shi J, Wang Y, Li Z, Sobota RM, Sham LT, Luo M. (2023) Structural basis of peptide secretion for Quorum sensing by ComA. Nat Commun. 2023 Nov 7;14(1):7178. doi: 10.1038/s41467-023-42852-9.

Li J, Xu X, Shi J, Hermoso JA, Sham LT, Luo M. (2023) Regulation of the cell division hydrolase RipC by the FtsEX system in Mycobacterium tuberculosis. Nat Commun. 2023 Dec 4;14(1):7999. doi: 10.1038/s41467-023-43770-6.

Morizumi T, Kim K, Li H, Govorunova EG, Sineshchekov OA, Wang Y, Zheng L, Bertalan É, Bondar A-N, Askari A, et al. (2023).*Structures of channelrhodopsin paralogs in peptidiscs explain their contrasting K+ and Na+ selectivities. Nat Commun. 14(1):4365.

Cruz SJ, Burendei B, Lee WH, Ward A (2023) Structure of mechanically activated ion channel OSCA2.3 reveals mobile elements in the transmembrane domain. Structure. 2023 Dec 6:S0969-2126(23)00411-2. doi: 10.1016/j.str.2023.11.009.

Itskanov S, Wang L, Junne T, Sherriff R, Xiao L, Blanchard N, Shi WQ, Forsyth C, Hoepfner D, Spiess M, Park E. (2023) A common mechanism of Sec61 translocon inhibition by small molecules. Nat Chem Biol. 2023 May 11. doi: 10.1038/s41589-023-01337-y.

Zhao Z, Khurana A, Antony F, Young JW, Hewton KG, Brough Z, Zhong T, Parker ST, Duong van Hoa F. (2023) A Peptidisc-based Survey of the Plasma Membrane Proteome of a Mammalian Cell. Mol Cell Proteomics. 2023 Jun 7:100588. doi: 10.1016/j.mcpro.2023.100588.

Xu X, Li J, Chua WZ, Pages MA, Shi J, Hermoso JA, Bernhardt T, Sham LT, Luo (2023) Mechanistic insights into the regulation of cell wall hydrolysis by FtsEX and EnvC at the bacterial division site. Proc Natl Acad Sci USA. 2023 May 23;120(21):e2301897120.

Kim S, Lee SS, Park JG, Kim JW, Ju S, Choi SH, Kim S, Kim NJ, Hong S, Kang JY, Jin MS. (2022) Structural Insights into Porphyrin Recognition by the Human ATP-Binding Cassette Transporter ABCB6. Mol Cells. 2022 Aug 31;45(8):575-587.

Young JW, Wason IS, Zhao Z, Kim S, Aoki H, Phanse S, Rattray DG, Foster LJ, Babu M, Duong van Hoa F. (2022) Development of a Method Combining Peptidiscs and Proteomics to Identify, Stabilize, and Purify a Detergent-Sensitive Membrane Protein Assembly. J Proteome Res. 2022 Jul 1;21(7):1748-1758.

Ung KL, Winkler M, Schulz L, Kolb M, Janacek DP, Dedic E, Stokes DL, Hammes UZ, Pedersen BP. (2022)* Structures and mechanism of the plant PIN-FORMED auxin transporter. Nature. Sep;609(7927):605-610.

Demmer JK, Phillips BP, Uhrig OL, Filloux A, Allsopp LP, Bublitz M, Meier T. (2022) Structure of ATP synthase from ESKAPE pathogen Acinetobacter baumannii. Sci Adv. 2022 Feb 18;8(7):5966.

Harris A, Wagner M, Du D, Raschka S, Nentwig LM, Gohlke H, Smits SHJ, Luisi BF, Schmitt L. (2021) Structure and efflux mechanism of the yeast pleiotropic drug resistance transporter Pdr5. Nat Commun. 2021 Sep 6;12(1):5254.

Wu JX, Liu R, Song K, Chen L. (2021). Structures of human dual oxidase 1 complex in low-calcium and high-calcium states. Nat Commun. 2021 Jan 8;12(1):155.

Zeytuni N, Dickey SW, Hu J, Chou HT, Worrall LJ, Alexander JAN, Carlson ML, Nosella M, Duong F, Yu Z, Otto M, Strynadka NCJ. (2020). Structural insight into the Staphylococcus aureus ATP-driven exporter of virulent peptide toxins. Sci Adv. 2020 Sep 30;6(40):8219.

Young JW, Wason IS, Zhao Z, Rattray DG, Foster LJ, Duong Van Hoa F. (2020) His-Tagged Peptidiscs Enable Affinity Purification of the Membrane Proteome for Downstream Mass Spectrometry Analysis. J Proteome Res. 2020 Jul 2;19(7):2553-2562.

Kuo YC, Chen H, Shang G, Uchikawa E, Tian H, Bai XC, Zhang X. (2020). Cryo-EM structure of the PlexinC1/A39R complex reveals inter-domain interactions critical for ligand-induced activation. Nat Commun. 2020 Apr 23;11(1):1953.

Angiulli G, Dhupar HS, Suzuki H, Wason IS, Duong Van Hoa F, Walz T. (2020) New approach for membrane protein reconstitution into peptidiscs and basis for their adaptability to different proteins. Elife. 2020 Mar 3;9:e53530.

Saville JW, Troman L, Duong Van Hoa F. (2019) PeptiQuick, a One-Step Incorporation of Membrane Proteins into Biotinylated Peptidiscs for Streamlined Protein Binding Assays. J Vis Exp. 2019 Nov 2;(153).

Carlson ML, Stacey RG, Young JW, Wason IS, Zhao Z, Rattray DG, Scott N, Kerr CH, Babu M, Foster LJ, Duong Van Hoa F. (2019) Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries. Elife. 2019 Jul 31;8:e46615.

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