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Deconstructing transport-distribution reconstruction in the nuclear-pore complex

Nature Structural & Molecular Biology volume 25, pages 1061–1062 (2018)Cite this article

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To the Editor — Nuclear-pore complexes (NPCs) span the nuclear envelope and mediate bidirectional transport between the nucleus and cytoplasm. Macromolecules (>40 kDa) require transport receptors to transit the NPC efficiently, whereas smaller molecules diffuse through the NPC passively1. The mechanism through which the semipermeable barrier at the center of the NPC regulates selective transport is unknown. Aiming to elucidate this mechanism, Yang and colleagues have investigated spatial cargo distribution within the NPC2 by using single-point edge-excitation subdiffraction (SPEED) microscopy2,3,4,5,6.

SPEED microscopy features innovations in optical microscopy as well as data processing. The potential of SPEED to obtain pseudotomographic data prompted us to systematically analyze the technical aspects of the data-processing method. Through a series of simulations, we examined the data requirements (including precision, dataset size, and symmetry constraints) and the limits to which reconstructed transport densities can be interpreted with confidence.

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Fig. 1: The performance of SPEED depends on the dataset size and overall precision.

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Acknowledgements

This work was funded by grants 1R01GM123541. D.G. acknowledges support from the National Institutes of Health Common Fund 4D Nucleome Program (grant 1U01EB021238) and NIGMS grant R01GM123541. C.S.S. was supported by a Junior Research Fellowship through Merton College, Oxford, UK. We thank S. Musser for critical feedback on the entire project and M. Hammer for critical reading of theory development. L.-C.T. acknowledges support by the NIH through grant K99 GM126810.

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Author notes

  1. These authors contributed equally: Li-Chun Tu, Maximiliaan Huisman, Yu-Chieh Chung.

Authors and Affiliations

  1. RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA

    Li-Chun Tu, Maximiliaan Huisman, Carlas Sierd Smith & David Grunwald

  2. Kavli Institute for the Physics and Mathematics of the Universe, University of Tokyo, Kashiwa, Japan

    Yu-Chieh Chung

  3. Center for Neural Circuits and Behaviour, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK

    Carlas Sierd Smith

Authors
  1. Li-Chun Tu
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  2. Maximiliaan Huisman
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  3. Yu-Chieh Chung
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  4. Carlas Sierd Smith
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  5. David Grunwald
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Contributions

All authors contributed to the study design and data interpretation; L.-C.T., M.H., C.S.S. and Y.-C.C. collected and analyzed data, M.H. led and implemented simulations with support from C.S.S. and Y.-C.C.; Y.-C.C. derived theory with support from L.-C.T. and C.S.S. D.G. initiated the project and provided supervision. All authors wrote, revised, and approved the manuscript.

Corresponding author

Correspondence to David Grunwald.

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The authors declare no competing interests.

Supplementay Infomation

Supplementary Note 1

Theoretical description and analysis of 3D SPEED

Reporting Summary

Supplementary Note 2

Supplemental simulation results

Supplementary Note 3

Simulation methods

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Tu, LC., Huisman, M., Chung, YC. et al. Deconstructing transport-distribution reconstruction in the nuclear-pore complex. Nat Struct Mol Biol 25, 1061–1062 (2018). https://doi.org/10.1038/s41594-018-0161-2

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