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Oligomeric organization of membrane proteins from native membranes at nanoscale spatial and single-molecule resolution

Nature Nanotechnology volume 19, pages 85–94 (2024)Cite this article

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Abstract

The oligomeric organization of membrane proteins in native cell membranes is a critical regulator of their function. High-resolution quantitative measurements of oligomeric assemblies and how they change under different conditions are indispensable to understanding membrane protein biology. We report Native-nanoBleach, a total internal reflection fluorescence microscopy-based single-molecule photobleaching step analysis technique to determine the oligomeric distribution of membrane proteins directly from native membranes at an effective spatial resolution of ~10 nm. We achieved this by capturing target membrane proteins in native nanodiscs with their proximal native membrane environment using amphipathic copolymers. We applied Native-nanoBleach to quantify the oligomerization status of structurally and functionally diverse membrane proteins, including a receptor tyrosine kinase (TrkA) and a small GTPase (KRas) under growth-factor binding and oncogenic mutations, respectively. Our data suggest that Native-nanoBleach provides a sensitive, single-molecule platform to quantify membrane protein oligomeric distributions in native membranes under physiologically and clinically relevant conditions.

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Fig. 1: Native-nanoBleach approach to detect the oligomeric distribution of membrane proteins in their native membrane environments.
Fig. 2: Establishing Native-nanoBleach analysis using membrane proteins with well-established oligomeric states.
Fig. 3: Oligomeric distribution of TrkA in the presence and absence of NGF within native nanodiscs (SMA) isolated from SH-SY5Y cells.
Fig. 4: Oligomeric distribution of KRas and its oncogenic mutants within native nanodiscs (SMA) isolated from Expi293 cells.
Fig. 5: Oligomeric distribution of KRas and its oncogenic mutants within native nanodiscs (SMA) isolated from PDAC cells.

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Data availability

The data supporting the findings of this study are available within the paper and its Supplementary Information. Other relevant data are available from the corresponding author on reasonable request. Source Data are provided with this paper.

Code availability

The calculations for single-molecule photobleaching step analysis, conversion of step distribution to oligomeric distribution, and the theoretical probability of coincidental overlap as a function of surface expression density, as described above and in Supplementary Methods, have been formulated as Matlab codes that are available via Zenodo at the following link (https://doi.org/10.5281/zenodo.8429321)68.

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Acknowledgements

We thank members of the Bhattacharyya, Gupta and Muzumdar laboratories for helpful discussions. We especially thank Anthony Quinnert (Bhattacharyya laboratory) for maintenance of our microscopy set-up, and Dr. Felix Rivera-Molina for help with confocal microscopy. We thank Dr. Marc Llaguno for help with negative stain electron microscopy data collection, and Tathagata Das for help with Matlab codes. The pQE60-KcsA and pET16b-LeuT constructs were a gift from Dr. Crina Nimigean’s and Dr. Eric Gouaux’s laboratories, respectively. Expi293 and SF9 cells were a gift from Dr. Karin Reinisch’s and Dr. Joel Butterwick’s laboratories, respectively. NGF was a gift from Genentech. G.W. acknowledges support from the PPTP training grant (grant no. T32-GM007324), C.B. acknowledges support from the NSF GRFP fellowship (grant no. DGE-2139841) and the P.E.O. Scholar Award. X.G. was a CSC-Yale Scholar. M.D.M. acknowledges support from an National Cancer Institute Mentored Clinical Scientist Research Career Development Award (grant no. K08-CA208016), a NIH New Innovator Award (grant no. DP2-CA248136), a Lustgarten Foundation Therapeutics Focused Research Program award, an American Cancer Society Institutional Research Grant (grant no. IRG 17-172-57) and, in part, the Yale Comprehensive Cancer Center Support Grant (grant no. P30CA016359). K.G. acknowledges support from NIGMS (grant nos. R01GM141192 and RM1GM149406). M.B. acknowledges support from NIGMS (grant nos. R00GM126145 and R35GM147095) for funding.

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Author notes

  1. These authors contributed equally: Gerard Walker, Caroline Brown.

Authors and Affiliations

  1. Department of Pharmacology, Yale University, New Haven, CT, USA

    Gerard Walker, Shailesh Kumar & Moitrayee Bhattacharyya

  2. Department of Cell Biology, Yale University, New Haven, CT, USA

    Gerard Walker, Caroline Brown & Kallol Gupta

  3. Nanobiology Institute, Yale University, West Haven, CT, USA

    Gerard Walker, Caroline Brown & Kallol Gupta

  4. Department of Pathology, Yale University, New Haven, CT, USA

    Xiangyu Ge

  5. Yale Cancer Biology Institute, Yale University, West Haven, CT, USA

    Xiangyu Ge & Mandar D. Muzumdar

  6. Department of Genetics, Yale University, New Haven, CT, USA

    Mandar D. Muzumdar

  7. Department of Internal Medicine, Yale University, New Haven, CT, USA

    Mandar D. Muzumdar

  8. Yale Cancer Center, New Haven, USA

    Mandar D. Muzumdar

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Contributions

M.B. conceived the study and designed the experiments with all of the authors. G.W., C.B., X.G. and S.K. performed the experiments and analyzed the data in consultation with M.D.M., K.G. and M.B. X.G. and M.D.M. contributed the engineered PDAC cells. K.G. contributed key bacterial membrane protein constructs. M.B. and G.W. wrote the paper in consultation with all of the co-authors. All of the authors discussed the results and implications, and commented on the manuscript at all stages.

Corresponding author

Correspondence to Moitrayee Bhattacharyya.

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Nature Nanotechnology thanks Henriette Autzen, Yamuna Krishnan, and Kabir Biswas for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–10, Tables 1–3, Methods, and Source Data (1–4) for blots and scans reported in the supplementary figures.

Reporting Summary

Source data

Source Data Fig. 1

The first file: ‘source-data-Fig-1c-nanodisc-size-distribution.pzfx’ presents the nanodisc size distribution from negative stain electron microscopy data (for Fig. 1c), including statistical analysis. The second file: ‘example-single-molecule-image-G12D_rep2-Fig1e.png’ shows a representative single-molecule TIRF image (for Fig. 1e).

Source Data Fig. 2

The first file: ‘oligomeric-distribution-amtb-semisweet-kcsa-omp25.pzfx’ contains source data for Fig. 2a, including statistical analysis. The second: ‘oligomeric-distribution-model-systems-LeuT.pzfx’ contains source data for Fig. 2c,d, including statistical analysis. Finally, ‘theoretical-calculation-overlap-surface-density’ contains data that is plotted in Fig. 2e and generated through a MATLAB code that is made available (see ‘Code availability’ section).

Source Data Fig. 3

The first file: ‘fsec-trkA-shsy5y.pzfx’ is source data for Fig. 3b. The second file: ‘oligomeric-distribution-TrkA’ contains data for Fig. 3c, including statistical analysis.

Source Data Fig. 4

The first file: ‘oligomeric-distribution-KRas-WT+mutants-Expi293-and-BI-2853-treatment.pzfx’ contains source data for Fig. 4a,c, including statistical analysis. The second file: ‘norm-BI-2852-FSEC-overlay.pzfx’ shows data for the FSEC shown in Fig. 4b. Finally, ‘KRAS_recip_pulldown_quant.pzfx’ represents the source data for western blot quantification in Fig. 4d, including statistical analysis.

Source Data Fig. 5

The first file: ‘final-PDAC-lines-western-blots-quantification.pzfx’ contains data for western blot quantifications shown in Fig. 5b. We also provided another file for Fig. 5b, ‘final-PDAC-lines-western-statistics.pzfx’, which contains the statistical analysis shown in this figure. The third and fourth files: ‘NP10-low-analysis’ and ‘NP10-high-analysis.pzfx’ contain source data for the oligomeric distributions shown in Fig. 5c,d, including statistical analysis.

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Walker, G., Brown, C., Ge, X. et al. Oligomeric organization of membrane proteins from native membranes at nanoscale spatial and single-molecule resolution. Nat. Nanotechnol. 19, 85–94 (2024). https://doi.org/10.1038/s41565-023-01547-4

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