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An Architectural Guide to the Nuclear Pore Complex

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Credit: The Rockefeller University, New York

Sixty years ago, folk singer Pete Seeger recorded a song about helping those in need. The song starts like this: “Oh, had I a golden thread/And a needle so fine/I’d weave a magic strand/Of rainbow design.” In this brief animation, it seems like a golden thread and a needle are fast at work. But this rainbow design helps to answer a longstanding need for cell biologists: a comprehensive model of the thousands of pores embedded in the double-membrane barrier, or nuclear envelope, that divides the nucleus and its DNA from the rest of the cell.

These channels, called nuclear pore complexes (NPCs), are essential for life, tightly controlling which large macromolecules get in or out of the nucleus. Such activities include allowing vital proteins to enter the nucleus, blocking out harmful viruses, and shuttling messenger RNAs from the nucleus to the cytoplasm, where they are translated into proteins.

This computer simulation starts with an overhead view of the fully formed NPC structure. From this angle, the pore membrane (gray) appears to be at the base and is embroidered in four rings that are the channel’s main architectural support beams. There’s the cytoplasmic outer ring (yellow), the inner rings (purple, blue), the membrane ring (brown), and the nucleoplasmic outer ring (yellow). Each color represents different protein complexes, not rings per se, and the hole in the middle is the central channel through which molecules are transported. Filling the hole is a selective gating mechanism made of disordered protein (anchored to green) that helps to get the right molecules in and out.

Pretty cool stuff. The simulation comes from a groundbreaking paper published recently in the journal Nature [1]. The work was led by a number of NIH-supported researchers, including Mike Rout and Brian Chait at The Rockefeller University, New York; Andrej Sali at University of California, San Francisco; Chris Akey at Boston University Medical School; and Steve Ludkte at Baylor College of Medicine, Houston.

Rout and Chait have spent more than 20 years trying to solve the structure of NPCs. Not only are NPCs large and constantly engaged in shuttling molecules in and out, they also represent moving machines. About a third of the complex moves around while processing molecules, making its flexible architecture more akin to a suspension bridge than a bricks-and-mortar building. In the animation, you can see this built-in flexibility in the connectors (green) that run between the rings.

This is where the collaboration became key. The researchers availed themselves of all variety of biochemical and imaging technologies to identify the constituent proteins, their locations relative to one another, and the dimensions of their protein complexes.

The model system in which this work was conducted was brewer’s yeast, or Saccharomyces cerevisiae. While brewer’s yeast is best known for its uses in baking bread or brewing beer, the simple, single-cell organism is also used in sophisticated biological studies because it possesses the same eukaryotic cell structure as humans. This detailed 3D map of NPCs in brewer’s yeast, computed from data, now provides a comprehensive guide to study these critical portals in far greater detail in human cells, as well as to help determine how changes to NPCs can lead to human disease, including neurodegenerative disorders, autoimmune conditions, and cancers.

Reference:

[1] Integrative structure and functional anatomy of a nuclear pore complex. 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, Akey CW, Chait BT, Sali A, Rout MP. Nature. 2018 Mar 22;555(7697):475-482

Links:

Michael Rout (The Rockefeller University, New York)

Brian Chait (The Rockefeller University)

National Center for Dynamic Interactome Research

NIH Support: National Institute of General Medical Sciences; National Institute of Diabetes and Digestive and Kidney Diseases