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Annual Review of Biochemistry Jun 2019The nuclear pore complex (NPC) serves as the sole bidirectional gateway of macromolecules in and out of the nucleus. Owing to its size and complexity (∼1,000 protein... (Review)
Review
The nuclear pore complex (NPC) serves as the sole bidirectional gateway of macromolecules in and out of the nucleus. Owing to its size and complexity (∼1,000 protein subunits, ∼110 MDa in humans), the NPC has remained one of the foremost challenges for structure determination. Structural studies have now provided atomic-resolution crystal structures of most nucleoporins. The acquisition of these structures, combined with biochemical reconstitution experiments, cross-linking mass spectrometry, and cryo-electron tomography, has facilitated the determination of the near-atomic overall architecture of the symmetric core of the human, fungal, and algal NPCs. Here, we discuss the insights gained from these new advances and outstanding issues regarding NPC structure and function. The powerful combination of bottom-up and top-down approaches toward determining the structure of the NPC offers a paradigm for uncovering the architectures of other complex biological machines to near-atomic resolution.
Topics: Active Transport, Cell Nucleus; Animals; Cell Nucleus; Cryoelectron Microscopy; Crystallography, X-Ray; Eukaryota; Humans; Models, Molecular; Nuclear Pore; Nuclear Pore Complex Proteins; Protein Conformation; Protein Subunits; RNA, Messenger
PubMed: 30883195
DOI: 10.1146/annurev-biochem-062917-011901 -
Toxins Sep 2019Perforation of cellular membranes by pore-forming proteins can affect cell physiology, tissue integrity, or immune response. Since many pore-forming proteins are toxins... (Review)
Review
Perforation of cellular membranes by pore-forming proteins can affect cell physiology, tissue integrity, or immune response. Since many pore-forming proteins are toxins or highly potent virulence factors, they represent an attractive target for the development of molecules that neutralize their actions with high efficacy. There has been an assortment of inhibitors developed to specifically obstruct the activity of pore-forming proteins, in addition to vaccination and antibiotics that serve as a plausible treatment for the majority of diseases caused by bacterial infections. Here we review a wide range of potential inhibitors that can specifically and effectively block the activity of pore-forming proteins, from small molecules to more specific macromolecular systems, such as synthetic nanoparticles, antibodies, antibody mimetics, polyvalent inhibitors, and dominant negative mutants. We discuss their mechanism of inhibition, as well as advantages and disadvantages.
Topics: Animals; Cell Membrane; Humans; Pore Forming Cytotoxic Proteins
PubMed: 31546810
DOI: 10.3390/toxins11090545 -
Nature Reviews. Molecular Cell Biology Feb 2017Nuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes to form channels across the nuclear envelope. They are large macromolecular assemblies with a... (Review)
Review
Nuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes to form channels across the nuclear envelope. They are large macromolecular assemblies with a complex composition and diverse functions. Apart from facilitating nucleocytoplasmic transport, NPCs are involved in chromatin organization, the regulation of gene expression and DNA repair. Understanding the molecular mechanisms underlying these functions has been hampered by a lack of structural knowledge about the NPC. The recent convergence of crystallographic and biochemical in vitro analysis of nucleoporins (NUPs), the components of the NPC, with cryo-electron microscopic imaging of the entire NPC in situ has provided first pseudo-atomic view of its central core and revealed that an unexpected network of short linear motifs is an important spatial organization principle. These breakthroughs have transformed the way we understand NPC structure, and they provide an important base for functional investigations, including the elucidation of the molecular mechanisms underlying clinically manifested mutations of the nucleocytoplasmic transport system.
Topics: Active Transport, Cell Nucleus; Humans; Mutation; Nuclear Pore; Nuclear Pore Complex Proteins
PubMed: 27999437
DOI: 10.1038/nrm.2016.147 -
Seminars in Cell & Developmental Biology Dec 2017The ancient phylum of Cnidaria contains many aquatic species with peculiar lifestyle. In order to survive, these organisms have evolved attack and defense mechanisms... (Review)
Review
The ancient phylum of Cnidaria contains many aquatic species with peculiar lifestyle. In order to survive, these organisms have evolved attack and defense mechanisms that are enabled by specialized cells and highly developed venoms. Pore-forming toxins are an important part of their venomous arsenal. Along some other types, the most representative are examples of four protein families that are commonly found in other kingdoms of life: actinoporins, Cry-like proteins, aerolysin-like toxins and MACPF/CDC toxins. Some of the homologues of pore-forming toxins may serve other functions, such as in food digestion, development and response against pathogenic organisms. Due to their interesting physico-chemical properties, the cnidarian pore-forming toxins may also serve as tools in medical research and nanobiotechnological applications.
Topics: Animals; Cell Membrane; Cnidaria; Cnidarian Venoms; Models, Molecular; Phylogeny; Pore Forming Cytotoxic Proteins; Protein Conformation; Toxins, Biological
PubMed: 28751252
DOI: 10.1016/j.semcdb.2017.07.026 -
Frontiers in Molecular Biosciences 2021Pore forming proteins are a broad class of pathogenic proteins secreted by organisms as virulence factors due to their ability to form pores on the target cell membrane.... (Review)
Review
Pore forming proteins are a broad class of pathogenic proteins secreted by organisms as virulence factors due to their ability to form pores on the target cell membrane. Bacterial pore forming toxins (PFTs) belong to a subclass of pore forming proteins widely implicated in bacterial infections. Although the action of PFTs on target cells have been widely investigated, the underlying membrane response of lipids during membrane binding and pore formation has received less attention. With the advent of superresolution microscopy as well as the ability to carry out molecular dynamics (MD) simulations of the large protein membrane assemblies, novel microscopic insights on the pore forming mechanism have emerged over the last decade. In this review, we focus primarily on results collated in our laboratory which probe dynamic lipid reorganization induced in the plasma membrane during various stages of pore formation by two archetypal bacterial PFTs, cytolysin A (ClyA), an -toxin and listeriolysin O (LLO), a -toxin. The extent of lipid perturbation is dependent on both the secondary structure of the membrane inserted motifs of pore complex as well as the topological variations of the pore complex. Using confocal and superresolution stimulated emission depletion (STED) fluorescence correlation spectroscopy (FCS) and MD simulations, lipid diffusion, cholesterol reorganization and deviations from Brownian diffusion are correlated with the oligomeric state of the membrane bound protein as well as the underlying membrane composition. Deviations from free diffusion are typically observed at length scales below ∼130 nm to reveal the presence of local dynamical heterogeneities that emerge at the nanoscale-driven in part by preferential protein binding to cholesterol and domains present in the lipid membrane. Interrogating the lipid dynamics at the nanoscale allows us further differentiate between binding and pore formation of - and -PFTs to specific domains in the membrane. The molecular insights gained from the intricate coupling that occurs between proteins and membrane lipids and receptors during pore formation are expected to improve our understanding of the virulent action of PFTs.
PubMed: 34568431
DOI: 10.3389/fmolb.2021.737561 -
Microbiology (Reading, England) Mar 2022Pore-forming toxins (PFTs) are widely distributed in both Gram-negative and Gram-positive bacteria. PFTs can act as virulence factors that bacteria utilise in...
Pore-forming toxins (PFTs) are widely distributed in both Gram-negative and Gram-positive bacteria. PFTs can act as virulence factors that bacteria utilise in dissemination and host colonisation or, alternatively, they can be employed to compete with rival microbes in polymicrobial niches. PFTs transition from a soluble form to become membrane-embedded by undergoing large conformational changes. Once inserted, they perforate the membrane, causing uncontrolled efflux of ions and/or nutrients and dissipating the protonmotive force (PMF). In some instances, target cells intoxicated by PFTs display additional effects as part of the cellular response to pore formation. Significant progress has been made in the mechanistic description of pore formation for the different PFTs families, but in several cases a complete understanding of pore structure remains lacking. PFTs have evolved recognition mechanisms to bind specific receptors that define their host tropism, although this can be remarkably diverse even within the same family. Here we summarise the salient features of PFTs and highlight where additional research is necessary to fully understand the mechanism of pore formation by members of this diverse group of protein toxins.
Topics: Bacteria; Bacterial Toxins; Cell Membrane; Humans; Pore Forming Cytotoxic Proteins; Virulence Factors
PubMed: 35333704
DOI: 10.1099/mic.0.001154 -
Cell Stress Aug 2020Exocytosis is a universal process of eukaryotic cells, consisting of fusion between the vesicle and the plasma membranes, leading to the formation of a fusion pore, a... (Review)
Review
Exocytosis is a universal process of eukaryotic cells, consisting of fusion between the vesicle and the plasma membranes, leading to the formation of a fusion pore, a channel through which vesicle cargo exits into the extracellular space. In 1986, Rand and Parsegian proposed several stages to explain the nature of membrane fusion. Following stimulation, it starts with focused stress destabilization of membranes in contact, followed by the coalescence of two membrane surfaces. In the next fraction of a millisecond, restabilization of fused membranes is considered to occur to maintain the cell's integrity. This view predicted that once a fusion pore is formed, it must widen abruptly, irreversibly and fully, whereby the vesicle membrane completely integrates with and collapses into the plasma membrane (full fusion exocytosis). However, recent experimental evidence has revealed that once the fusion pore opens, it may also reversibly close (transient or kiss-and-run exocytosis). Here, we present a historical perspective on understanding the mechanisms that initiate the membrane merger and fusion pore formation. Next, post-fusion mechanisms that regulate fusion pore stability are considered, reflecting the state in which the forces of widening and constriction of fusion pores are balanced. Although the mechanisms generating these forces are unclear, they may involve lipids and proteins, including SNAREs, which play a role not only in the pre-fusion but also post-fusion stages of exocytosis. How molecules stabilize the fusion pore in the open state is key for a better understanding of fusion pore physiology in health and disease.
PubMed: 32908961
DOI: 10.15698/cst2020.09.230 -
Gels (Basel, Switzerland) Jul 2022This review discusses the most commonly employed methods for determining pore size and pore size distribution in bioaerogels. Aerogels are materials with high porosity... (Review)
Review
This review discusses the most commonly employed methods for determining pore size and pore size distribution in bioaerogels. Aerogels are materials with high porosity and large surface areas. Most of their pores are in the range of mesopores, between 2 and 50 nm. They often have smaller or larger pores, which presents a significant challenge in determining the exact mean pore size and pore size distribution in such materials. The precision and actual value of the pore size are of considerable importance since pore size and pore size distribution are among the main properties of aerogels and are often directly connected with the final application of those materials. However, many recently published papers discuss or present pore size as one of the essential achievements despite the misinterpretation or the wrong assignments of pore size determination. This review will help future research and publications evaluate the pore size of aerogels more precisely and discuss it correctly. The study covers methods such as gas adsorption, from which BJH and DFT models are often used, SEM, mercury porosimetry, and thermoporometry. The methods are described, and the results obtained are discussed. The following paper shows that there is still no precise method for determining pore size distribution or mean pore size in aerogels until now. Knowing that, it is expected that this field will evolve in the future.
PubMed: 35877523
DOI: 10.3390/gels8070438 -
Cold Spring Harbor Perspectives in... Jan 2022The nuclear pore complex (NPC) is a highly conserved channel in the nuclear envelope that mediates mRNA export to the cytosol and bidirectional protein transport. Many... (Review)
Review
The nuclear pore complex (NPC) is a highly conserved channel in the nuclear envelope that mediates mRNA export to the cytosol and bidirectional protein transport. Many chromosomal loci physically interact with nuclear pore proteins (Nups), and interactions with Nups can promote transcriptional repression, transcriptional activation, and transcriptional poising. Interaction with the NPC also affects the spatial arrangement of genes, interchromosomal clustering, and folding of topologically associated domains. Thus, the NPC is a spatial organizer of the genome and regulator of genome function.
Topics: Active Transport, Cell Nucleus; Genome; Nuclear Pore; Nuclear Pore Complex Proteins; Protein Transport
PubMed: 34127448
DOI: 10.1101/cshperspect.a039438 -
The Protein Journal Aug 2019During my postdoc interview in June of 1998, I asked Günter why he was moving more towards the nucleus in his latest studies. He said, "Well Joe, that's where... (Review)
Review
During my postdoc interview in June of 1998, I asked Günter why he was moving more towards the nucleus in his latest studies. He said, "Well Joe, that's where everything starts." By the end of the interview, I accepted the postdoc. He had a way of making everything sound so cool. Günter's progression was natural, since the endoplasmic reticulum and the nucleus are the only organelles that share the same membrane. The nuclear envelope extends into a double membrane system with nuclear pore complexes embedded in the pore membrane openings. Even while writing this review, I remember Günter stressing; it is the nuclear pore complex. Just saying nuclear pore doesn't encompass the full magnitude of its significance. The nuclear pore complex is one of the largest collection of proteins that fit together for an overall function: transport. This review will cover the Blobel lab contributions in the quest for the blueprint of the nuclear pore complex from isolation of the nuclear envelope and nuclear lamin to the ring structures.
Topics: Animals; Biographies as Topic; Cytoskeleton; Famous Persons; Humans; Lamins; Membrane Glycoproteins; Nuclear Lamina; Nuclear Pore; Nuclear Pore Complex Proteins; Rats; Yeasts
PubMed: 31410705
DOI: 10.1007/s10930-019-09858-z