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From Protein Structure to Function: Ring Cycle for Dilating and Constricting the Nuclear Pore Print
Wednesday, 28 August 2013 00:00

Nuclear pore complexes (NPCs) act as the central gatekeepers for selective transport between the cytoplasm and the nucleus. They allow the exchange of selected proteins and ribonucleoproteins, while preventing the transport of material not meant to cross the nuclear envelope. The NPC transport channel is the largest and most complex transport conduit in the eukaryotic kingdom and it is likely composed of only 3 out of 30 nuclear pore complex proteins (nups). Researchers from the Howard Hughes Medical Institute at the Rockefeller University have determined crystal structures of interacting domains of these centrally located channel nups, Nup54, Nup58, and Nup62, using data collected at ALS  Beamline 8.2.1. These structures allowed them to elucidate the molecular mechanism that underlies large-scale diameter changes of NPCs and propose a 'ring cycle' for dilating and constricting NPCs from 10–50 nm. The ring cycle would provide a method to adjust transport activities to cellular demands with a rapid response time.

Nuclear Transport: Evolution in Understanding

In evolution from prokaryotes to eukaryotes, the myriad of reactions yielding cotranscriptional and posttranscriptional assembly of ribonucleoproteins was largely confined to the nuclear compartment. This required the concomitant evolution of transport conduits of a sufficiently large diameter to allow passage of assembled ribonucleoproteins to the cytoplasm. Among these, ribosomal subunits presented a special challenge, as they are relatively rigid bodies. Hence, a correspondingly large nuclear pore had to evolve to accommodate the passage of ribosomal subunits, but also to protect against concomitant bidirectional leakage of the myriad of proteins, which are generally much smaller than ribonucleoproteins, to help maintain distinct nucleoplasmic and cytoplasmic proteomes. One way for meeting the challenge to transport diverse substrates of a large size range would be to endow the nuclear pore with the ability to have its central transport channel undergo dilation and constriction.

However, in several current models, key aspects of NPC function are not controlled by dilation and constriction of a central transport channel, but are collectively delegated instead to natively unstructured, FG repeat containing regions, which have a dual role as the NPC's permeability barrier and transport facilitator. This widely held view of nups as merely forming a static transport conduit that strategically places those nups containing FG repeats to exert their dual function, has recently been challenged by ALS studies that have led researchers to propose their "ring cycle hypothesis," a molecular architecture for the central transport channel of the nuclear pore complex. Its hallmark is a flexible mid-plane ring that is reversibly dilated and constricted from 10–50 nm. The ring cycle would provide a method to adjust transport activities to cellular demands with a rapid response time.

Left: Structure-derived model of the dilated transport channel consisting of helical regions of the channel nups Nup54 (blue), Nup58 (red) and Nup62 (gray).  Right: Constricted state of the transport channel, consisting of the same helical regions of Nup54, Nup58, and Nup62. Cycling between dilated and constricted states allows diameter adjustments from 10–50 nm.

This work represents a paradigm shift in the field of nuclear transport, in the sense that for the first time, it provides evidence for the presence of a moving structural feature in the NPC that can control nucleo-cytoplasmic traffic. This novel structural feature is a flexible midplane ring that has the ability to cycle between dilated and constricted states. The midplane ring is composed of portions of two nuclear pore proteins that interact with one another, Nup54 and Nup58. In the dilated state, a large midplane ring is formed by the interacting domains of 64 copies of Nup54 and 32 copies of Nup58. The dilated midplane ring has a flexible diameter range of 40–50 nm, sufficiently large to accommodate transit of the largest cargo that has so far been reported to pass through the NPC. A local, intramodular derailment of the ring could even open a "lateral gate" for transport of integral membrane proteins from the outer to the inner membrane of the nuclear envelope.

Nuclear pore complexes embedded in the nuclear envelope, viewed from the cytoplasmic side. Nuclear pore complexes are shown with dilated (40- to 50-nm diameter) and constricted (10- to 20-nm) transport channels.

For constricting the pore to a diameter range of 10–20 nm, the 96 constituents of the midplane ring undergo structural rearrangements and resolve into three stacked rings. The central ring consists of 32 protomers of Nup58. It is sandwiched between two rings, each consisting of 32 protomers of Nup54, which are tentatively placed above and below (or tucked into) the central ring. Transitions between constricted and dilated states are enabled by central patches of polar hydrogen-bonded residues, which structurally condition the midplane rings for instability. The extraordinary "molecular ballet" of the ring cycle allows cycling between the dilated and constricted states, leading to substantial diameter adjustments of the transport channel.

The ring cycle hypothesis also suggests a mechanism for regulation of these large-scale diameter changes. In the full-length channel nups, the α-helical regions are flanked by natively unfolded Phe-Gly (FG)-repeats. While the exact mechanism of action of FG-repeats is debated, it is very clear that they have a dual role in nuclear transport, by forming the permeability barrier and at the same time enabling selective transport by providing docking sites for transport factor•cargo complexes. Beyond these two accepted functions, the ring cycle hypothesis suggests that FG-repeats act as sensors for transport demands and adjust the moving gate of the NPC. When the FG-repeats are engaged by a large number of transport factor•cargo complexes in transit, the midplane ring transitions to its dilated state. In the absence of traffic, the FG-repeats could interact with each other to reinforce the constricted state of the transport channel.

In summary, the ring cycle hypothesis describes a molecular mechanism for large-scale diameter changes of the transport channel of the NPC, which could explain the ability of NPCs to achieve selective transport for various classes of substrates with a large size range, from single proteins to large ribosomal subunits.

Researchers Sozanne Solmaz, Gunter Blobel, and Ivo Melčák.


 

Research conducted by: S.R. Solmaz, G. Blobel, and I. Melčák (Howard Hughes Medical Institute at The Rockefeller University).

Research funding: Howard Hughes Medical Institute. Operation of the ALS is supported by the U.S. Department of Energy, Office of Basic Energy Sciences.

Publication about this research: S. R. Solmaz, G. Blobel, and I. Melčák, “Ring Cycle for Dilating and Constricting the Nuclear Pore,” PNAS 110, 5858 (2013).

ALS Science Highlight #277

 

ALSNews Vol. 345