{"id":21507,"date":"2023-09-07T10:52:06","date_gmt":"2023-09-07T14:52:06","guid":{"rendered":"http:\/\/www.bumc.bu.edu\/ppb\/?page_id=21507"},"modified":"2026-03-11T11:30:57","modified_gmt":"2026-03-11T15:30:57","slug":"the-akey-lab","status":"publish","type":"page","link":"https:\/\/www.bumc.bu.edu\/ppb\/the-akey-lab\/","title":{"rendered":""},"content":{"rendered":"

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Towards a comprehensive model of the yeast NPC<\/h4>\n
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Density maps for yeast NPCs imaged after a 1-step purification (left, with M.P. Rout Rockefeller) and in situ within growing cells after plunge freezing and FIB milling (right, with D. Singh, E. Villa UCSD; S.J. Ludtke Baylor College of Medicine). [Cell, 2022]<\/figcaption><\/figure>\n


The nucleus is compartmentalized by double membranes of the Nuclear Envelope (NE) and macromolecules must cross this barrier during growth and differentiation. The Nuclear Pore Complex (NPC) forms a conduit for the bidirectional transport of proteins and RNA-protein complexes between the cytoplasm and nuclear interior. The large size, modular construction and dynamic nature of the 8-fold symmetric, yeast NPC (~600\u00c5 by 1100\u00c5; 52-60 MDa ~550 nucleoporins\/Nups) requires a multi-scale approach to obtain a complete model of this translocation machine, which spans large pores in the nuclear envelope. This work will inform us on the roles of different Nups in hierarchical assembly of the spoke-ring scaffold, pore membrane stabilization, spoke dynamics, structure and function of the central transporter and NPC evolution. We extended our analysis of the isolated NPC in an active collaboration with the Villa laboratory (UCSD) and are thus able to compare structures of contracted and radially expanded conformations in the isolated and in situ yeast pore complex.<\/p>\n

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Composite multiscale model of a yeast NPC with color coded surface renderings of 16 density maps for regions of the Form II NPC with FG-Nup connectors modeled as cylinders. [Molecular Cell, 2023] <\/span><\/figcaption><\/figure>\n

Click on the figure for animation<\/strong><\/span><\/p>\n

We extended our work on the isolated NPC with cryogenic-EM and single particle methods to provide a composite, multiscale structure of the 8-fold symmetric core scaffold. To date, we have analyzed yeast NPCs from growing cells engaged in transport, which contain a plug-like feature in the central channel comprised of cylindrically-arrayed FG repeats, transport factors and cargo. However, the dynamic core scaffold contracts to a ground state configuration during purification, due to the loss of lateral membrane tension during solubilization of the NE. There are many take home messages from our ongoing work: we now have a better understanding of how these large machines may assemble, how they flex and adapt to changes in transport by expansion of their central passageway, and how Nups have evolved to form 3 different co-axial rings, while some Nups share similar interaction motifs with transport factors that help guide cargo through the central channel. Moreover, multiple NPC isoforms are present in the same cell, which reflects the lego-like ability of this assembly to use interchangeable parts to modify the outer rings. This mutability may play a role in adapting these machines for specialized functions at the nuclear periphery.<\/p>\n

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top – Radial expansion and contraction of the yeast NPC. (left) Radially-contracted NPC in white with FG connectors. (right) Radially-expanded conformation of the in situ NPC. bottom – The plug-like central transporter (grey) may become “unplugged” during radial expansion. [Molecular Cell, 2023]<\/figcaption><\/figure>\n

FG-repeats in the central transport channel of the NPC have two functions: they may act as a plug-like barrier that entraps transport factors and cargo complexes in radially contracted NPCs due to their higher packing density, while reorganization of the FG matrix during radial expansion \u201cunplugs\u201d the central channel to facilitate a higher rate of transport. However, the link between the conformation of the core scaffold and the distribution of FG-repeats in the central channel may be modulated by transport factor-cargo complexes and lateral tension in the NE.<\/p>\n

Summary: A detailed understanding of the architecture and mechanics of the NPC is providing an in-depth view of how the nucleus and cell body communicate, which underscores an important range of biology and disease processes.<\/p>\n

This project is a team effort and major collaborators include Michael Rout, PhD<\/a> and Brian Chait, PhD<\/a> (Rockefeller University), Javier Fernandez-Martinez, PhD<\/a> (Basque Foundation of Science); Ignacia Echeverria, PhD<\/a> and Andrej Sali, PhD<\/a> (University of California, San Francisco) Steve Ludtke, PhD<\/a> (Baylor College of Medicine) and Elizabeth Villa, PhD<\/a>, (University of California, San Diego).<\/p>\n

Molecular Cell Editors choice: 20 papers from 2023> yeast NPC<\/a><\/h4>\n

Previews and paper links –<\/h4>\n

[Nature] Integrative structure and functional anatomy of a nuclear pore complex.<\/em><\/a><\/p>\n

An Architectural Guide to the Nuclear Pore Complex \u2013 NIH Director\u2019s Blog (2018)<\/a><\/em><\/p>\n

New Model of Yeast Nuclear Pore Complex Revealed (2022)<\/a><\/p>\n

[Open Access from Cell] Comprehensive structure and functional adaptations of the yeast nuclear pore complex.<\/a><\/p>\n

Preview: Megan R. McCarthy and C. Patrick Lusk (2022), One ring doesn\u2019t rule them all: Distinct nuclear pore complexes in a single cell.<\/a><\/p>\n

[Molecular Cell] Implications of a multiscale structure of the yeast nuclear pore complex.<\/em><\/a><\/p>\n

Preview – Fellowship of two rings: Unprecedented insights into the structure of the yeast nuclear pore complex. <\/em><\/a><\/p>\n

Selected NPC Publications:<\/h4>\n

Akey CW<\/strong>, Echeverria I, Ouch C, Nudelman I, Shi Y, Wang J, Chait BT, Sali A, Fernandez-Martinez J, Rout MP. (2023). Implications of a multiscale structure of the yeast nuclear pore complex. Molecular Cell 83:3283-3302.<\/p>\n

Akey CW<\/strong>, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, Unruh J, Jaspersen SL, Chait BT, Sali A, Fernandez-Martinez J, Ludtke SJ, Villa E, Rout MP. (2022). Comprehensive structure and functional adaptations of the yeast nuclear pore complex. Cell 185:361-378. doi: 10.1016\/j.cell.2021.12.015. PMID: 34982960.<\/p>\n

Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, Unruh JR, Greenberg CH, Jacobs EY, Yu Z, de la Cruz MJ, Mironska R, Stokes DL, Aitchison JD, Jarrold MF, Gerton JL, Ludtke SJ\u2020, Akey CW<\/strong>\u2020, Chait BT\u2020, Sali A\u2020, and Rout MP\u2020, \u2020Co-last authors. (2018). Integrative structure and functional anatomy of a nuclear pore complex. Nature. 555:475-482. doi: 10.1038\/nature26003. Epub 2018 Mar 14. PMID: 29539637.<\/p>\n

Yang, Q., Rout, MP and Akey CW<\/strong> (1998). Three-dimensional architecture of the isolated yeast nuclear pore complex: Functional and evolutionary implications. Molecular Cell 1, 223-234. PMID: 9659919.<\/p>\n

Akey CW<\/strong> and Radermacher M (1993). Architecture of the Xenopus nuclear pore complex revealed by three-dimensional cryo-electron microscopy. The Journal of Cell Biology 122, 1-19. 10.1083\/jcb.122.1.1.<\/p>\n

<\/h5>\n
NPC PubMed publications list<\/a><\/h5>\n
NPC EMDB entries<\/strong><\/a><\/h5>\n

Early Projects<\/span><\/h4>\n