Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating.
Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating.
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DOI：
10.1371/journal.pcbi.1003488
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发表时间：
2014-03
影响因子：
4.3
通讯作者：
Schulten K
中科院分区：
文献类型：
--
作者：
Gamini R;Han W;Stone JE;Schulten K
核孔复合体 (NPC) 形成穿过真核细胞核膜的物质转移的门户。富含苯丙氨酸-甘氨酸重复基序 (FG-nups) 的无序蛋白质形成中央运输通道。了解 nups 在 NPC 内部的排列方式可以解释 NPC 如何充当用于传输大分子的选择性过滤器和用于扩散小分子的筛状过滤器（< 或 ）。我们利用分子动力学对一种 nup 的各种组装形成的结构进行建模，即 Nsp1 的 609 个氨基酸长的 FG 结构域 (Nsp1-FG)。模拟从 Nsp1-FG 的不同初始构象和几何排列开始。在所有情况下，Nsp1-FG 共同形成刷状结构，其刷毛由 2-27 个结点束组成，然而，这些束通过单个结点交联，留下一束并加入附近的一束。交联程度随初始nup构象和排列的不同而变化。结构分析表明，nups 的 FG 重复序列不仅涉及束结构的形成，而且大量存在于 FG 重复序列表位易于接近的交联区域中。在转运因子 (TF) 辅助下的大分子显然是通过 TF 表面上填充的 FG 结合袋与 FG-nups 结合而选择性地转运通过 NPC。因此，我们的研究结果表明，TF 与交联区域中的多个 FG 协同结合，并分解束，为自身及其货物通过创造宽阔的孔隙。此外，通过模拟，发现 Nsp1-FG 束之间的交联为分子的被动扩散设定了 < 的分子尺寸限制。我们的模拟表明，NPC 中央通道在靠近外围的地方，纽带束缚占主导地位，具有刷状适度交联的束，但在束缚失去作用的中心区域，具有筛状结构的束和频繁的交联。高等生命形式的细胞将其基因组与细胞核中的其余部分分开，该核被核膜包围着基因组。数百个孔，每个孔都是由许多蛋白质组成的复合体，通过高度选择性的运输确保进出细胞核的交通：小生物分子可以不受阻碍地通过，而大生物分子需要与称为运输因子的蛋白质结合才能通过。人们对核孔复合体的功能知之甚少，观察的一个主要障碍是它们的巨大尺寸和孔内部的无序性质。我们通过计算研究了核孔蛋白（nups）形成的结构类型。在计算中，我们将许多核（每个核有 600 个氨基酸长的蛋白质）放入被认为代表核孔的排列中，并模拟随后的分子行为。我们发现，nup 形成 2-27 个蛋白质的束，当单个 nup 离开束并加入相邻的束时，这些束就会交联。这一发现提出了核孔中核团的适应性分子网状排列，并解释了选择性运输是如何实现的，即足够小的分子的通过不受交联的阻碍，但大分子需要运输因子的帮助来熔化交联。
Nuclear pore complexes (NPCs) form gateways for material transfer across the nuclear envelope of eukaryotic cells. Disordered proteins, rich in phenylalanine-glycine repeat motifs (FG-nups), form the central transport channel. Understanding how nups are arranged in the interior of the NPC may explain how NPC functions as a selectivity filter for transport of large molecules and a sieve-like filter for diffusion of small molecules (< or ). We employed molecular dynamics to model the structures formed by various assemblies of one kind of nup, namely the 609-aa-long FG domain of Nsp1 (Nsp1-FG). The simulations started from different initial conformations and geometrical arrangements of Nsp1-FGs. In all cases Nsp1-FGs collectively formed brush-like structures with bristles made of bundles of 2–27 nups, however, the bundles being cross-linked through single nups leaving one bundle and joining a nearby one. The degree of cross-linking varies with different initial nup conformations and arrangements. Structural analysis reveals that FG-repeats of the nups not only involve formation of bundle structures, but are abundantly present in cross-linking regions where the epitopes of FG-repeats are highly accessible. Large molecules that are assisted by transport factors (TFs) are selectively transported through NPC apparently by binding to FG-nups through populated FG-binding pockets on the TF surface. Therefore, our finding suggests that TFs bind concertedly to multiple FGs in cross-linking regions and break-up the bundles to create wide pores for themselves and their cargoes to pass. In addition, the cross-linking between Nsp1-FG bundles, arising from simulations, is found to set a molecular size limit of < for passive diffusion of molecules. Our simulations suggest that the NPC central channel, near the periphery where tethering of nups is dominant, features brush-like moderately cross-linked bundles, but in the central region, where tethering loses its effect, features a sieve-like structure of bundles and frequent cross-links. Cells of higher life forms separate their genomes from the rest of the cell in a nucleus that surrounds the genome by a nuclear envelope. Hundreds of pores, each a complex made of many proteins, assure traffic into and out of the nucleus through highly selective transport: small biomolecules can pass unhindered, whereas large biomolecules need to associate with proteins called transport factors, to pass. Little is known about how the nuclear pore complexes function, a key impediment to observation being their huge size and the disordered nature of the pore interior. We investigated computationally what kind of structure the nuclear pore proteins (nups) form. In the computation we place many nups, each a 600 amino acid-long protein, into arrangements considered representative for the nuclear pore, and simulate the subsequent molecular behavior. We find that the nups form bundles of 2–27 proteins, the bundles being cross-linked when a single nup leaves a bundle and joins an adjacent one. The finding suggests an adaptive molecular mesh arrangement of nups in the nuclear pore and explains how selective transport is accomplished, namely that passage of sufficiently small molecules is unhindered by the cross-linking, but that large molecules need the assistance of transport factors to melt the cross-linking.
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DOI：
10.1073/pnas.0910163107
发表时间：
2010-04-06
影响因子：
11.1
作者：
Ader, Christian;Frey, Steffen;Baldus, Marc
通讯作者：
Baldus, Marc
影响因子：
56.9
作者：
Frey, Steffen;Richter, Ralf P.;Goerlich, Dirk
通讯作者：
Goerlich, Dirk
影响因子：
4.4
作者：
FELLER, SE;ZHANG, YH;BROOKS, BR
通讯作者：
BROOKS, BR
DOI：
10.1073/pnas.0603521103
发表时间：
2006-06-20
影响因子：
11.1
作者：
Lim, Roderick Y. H.;Huang, Ning-Ping;Aebi, Ueli
通讯作者：
Aebi, Ueli
影响因子：
5.6
作者：
Isgro, Timothy A.;Schulten, Klaus
通讯作者：
Schulten, Klaus