Model-based analysis of interferon-β induced signaling pathway
http://bioinformatics.oxfordjournals.org –
Interferon-β induced JAK-STAT signaling pathways contribute to mucosal immune recognition and an anti-viral state. Though the main molecular mechanisms constituting these pathways are known, neither the detailed structure of the regulatory network, nor its dynamics has yet been investigated. Read more »
Dimples, pores, star-rings, and thin rings on growing nuclear envelopes: evidence for structural intermediates in nuclear pore complex assembly
Year of publication:
1997
Journal name:
Journal of Cell Science
Nucleocytoplasmic transport: a thermodynamic mechanism
http://www.pubmedcentral.nih.gov –
The nuclear pore supports molecular communication between cytoplasm and
nucleus in eukaryotic cells. Selective transport of proteins is mediated by soluble
receptors, whose regulation by the small GTPase Ran leads to cargo
accumulation in, or depletion from, the nucleus, i.e., nuclear import or nuclear
export. We consider the operation of this transport system by a combined
analytical and experimental approach. Provocative predictions of a simple model
were tested using cell-free nuclei reconstituted in Xenopus egg extract, a system Read more »
Year of publication:
2009
Journal name:
HFSP
Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models
http://www.ploscompbiol.org –
The nuclear pore complex (NPC) is the gate to the nucleus. Recent determination of the configuration of proteins in the yeast NPC at ~5 nm resolution permits us to study the NPC global dynamics using coarse-grained structural models. We investigate these large-scale motions by using an extended elastic network model (ENM) formalism applied to several coarse-grained representations of the NPC. Two types of collective motions (global modes) are predicted by the ENMs to be intrinsically favored by the NPC architecture: global bending and extension/contraction from circular to elliptical shapes. Read more »
Year of publication:
2009
Journal name:
PLoS Comput Biol
Nanomechanical Basis of Selective
http://www.sciencemag.org –
The nuclear pore complex regulates cargo transport between the cytoplasm and the nucleus. We set out to correlate the governing biochemical interactions to the nanoscopic responses of the phenylalanineglycine (FG)–rich nucleoporin domains, which are involved in attenuating or promoting cargo translocation. We found that binding interactions with the transport receptor karyopherin-b1 caused the FG domains of the human nucleoporin Nup153 to collapse into compact molecular conformations. Read more »
Year of publication:
2007
Journal name:
Science
Structure, Dynamics and Function of Nuclear Pore Complexes
http://www.sciencedirect.com –
Nuclear pore complexes are large aqueous channels that penetrate the nuclear envelope, thereby connecting the nuclear interior with the cytoplasm. Until recently, these macromolecular complexes were viewed as static structures, the only function of which was to control the molecular trafficking between the two compartments. It has now become evident that this simplistic scenario is inaccurate and that nuclear pore complexes are highly dynamic multiprotein assemblies involved in diverse cellular processes ranging from the organization of the cytoskeleton to gene expression. Read more »
Year of publication:
2008
Journal name:
Trends in Cell Biology
Crossing the Nuclear Envelope: Hierarchical Regulation of Nucleocytoplasmic Transport
http://www.sciencemag.org –
Transport of macromolecules between the nucleus and cytoplasm is a critical cellular process for eukaryotes, and the machinery that mediates nucleocytoplasmic exchange is subject to multiple levels of control. Regulation is achieved by modulating the expression or function of single cargoes, transport receptors, or the transport channel. Each of these mechanisms has increasingly broad impacts on transport patterns and capacity, and this hierarchy of control directly affects gene expression, signal transduction, development, and disease. Read more »
Year of publication:
2007
Journal name:
Science
Nuclear pore complex assembly through the cell cycle: Regulation and membrane organization
http://www.sciencedirect.com –
In eukaryotes, all macromolecules traffic between the nucleus and the cytoplasm through nuclear pore complexes (NPCs), which are among the largest supramolecular assemblies in cells. Although their composition in yeast and metazoa is well characterized, understanding how NPCs are assembled and form the pore through the double membrane of the nuclear envelope and how both processes are controlled still remains a challenge. Read more »
Year of publication:
2008
Journal name:
Federation of European Biochemical Societies
Cryo-electron Tomography Provides Novel Insights into Nuclear Pore Architecture: Implications for Nucleocytoplasmic Transport
http://www.sciencedirect.com –
To go beyond the current structural consensus model of the nuclear pore complex (NPC), we performed cryo-electron tomography of fully native NPCs from Xenopus oocyte nuclear envelopes (NEs). The cytoplasmic face of the NPC revealed distinct anchoring sites for the cytoplasmic filaments, whereas the nuclear face was topped with a massive distal ring positioned above the central pore with indications of the anchoring sites for the nuclear basket filaments and putative intranuclear filaments. Read more »
Year of publication:
2003
Journal name:
Journal of Molecular Biology
The molecular architecture of the nuclear pore complex
http://www.nature.com –
Nuclear pore complexes (NPCs) are proteinaceous assemblies of approximately 50MDa that selectively transport cargoes across the nuclear envelope. To determine the molecular architecture of the yeast NPC, we collected a diverse set of biophysical and proteomic data, and developed a method for using these data to localize the NPC’s 456 constituent proteins (see the accompanying paper). Our structure reveals that half of the NPC is made up of a core scaffold, which is structurally analogous to vesicle-coating complexes. Read more »
Year of publication:
2007
Journal name:
Nature
Acting Out of Character: Regulatory Roles of Nuclear Pore Complex Proteins
http://www.sciencedirect.com –
Nuclear pore complexes (NPCs) mediate all selective bidirectional transport between the nucleus and the cytoplasm. Additional functions for NPCs and their constituent proteins (nucleoporins) are emerging, some independent of classical transport. Specifically, enzymatic activities at the NPC regulate nucleocytoplasmic transport and use the NPC as a regulatory scaffold. Also, nucleoporins may regulate gene expression by contacting chromatin. Read more »
Year of publication:
2009
Journal name:
Developmental Cell
On the Octagonal Structure of the Nuclear Pore Complex: Insights from Coarse-Grained Models
http://www.sciencedirect.com –
The basic structure of the nuclear pore complex (NPC), conserved across almost all organisms from yeast to humans, persists in featuring an octagonal symmetry involving the nucleoporins that constitute the NPC ring. In this article, we seek to understand and evaluate the potential biomechanical reasons for this eightfold symmetry. Our analytical investigation shows that the eightfold symmetry maximizes the bending stiffness of each of the eight NPC spokes while our computational analyses identify the most likely deformation modes, frequencies, and associated kinetic energies of the NPC. Read more »
Year of publication:
2008
Journal name:
Biophysical Journal
The Yeast Nuclear Pore Complex: Composition, Architecture, and Transport Mechanism
http://jcb.rupress.org –
An understanding of how the nuclear pore complex (NPC) mediates nucleocytoplasmic exchange requires a comprehensive inventory of the molecular components of the NPC and a knowledge of how each component contributes to the overall structure of this large molecular translocation machine. Therefore, we have taken a comprehensive approach to classify all components of the yeast NPC (nucleoporins). This involved identifying all the proteins present in a highly enriched NPC fraction, determining which of these proteins were nucleoporins, and localizing each nucleoporin within the NPC. Read more »
Year of publication:
2000
Journal name:
The Journal of Cell Biology
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