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Developmental Cell Sep 2016Nuclear pore proteins at the base of cilia were thought to regulate transport into cilia. In this issue of Developmental Cell, Del Viso et al. (2016) challenge this...
Nuclear pore proteins at the base of cilia were thought to regulate transport into cilia. In this issue of Developmental Cell, Del Viso et al. (2016) challenge this view, showing instead that pore proteins localize to ciliary basal bodies and that their perturbation leads to congenital heart disease.
Topics: Cilia; Heart Defects, Congenital; Humans; Nuclear Pore; Nuclear Pore Complex Proteins; Protein Transport
PubMed: 27623377
DOI: 10.1016/j.devcel.2016.08.019 -
Biochimica Et Biophysica Acta Apr 2012The cholesterol-dependent cytolysins (CDCs) are a large family of pore-forming toxins that are produced, secreted and contribute to the pathogenesis of many species of... (Review)
Review
The cholesterol-dependent cytolysins (CDCs) are a large family of pore-forming toxins that are produced, secreted and contribute to the pathogenesis of many species of Gram-positive bacteria. The assembly of the CDC pore-forming complex has been under intense study for the past 20 years. These studies have revealed a molecular mechanism of pore formation that exhibits many novel features. The CDCs form large β-barrel pore complexes that are assembled from 35 to 40 soluble CDC monomers. Pore formation is dependent on the presence of membrane cholesterol, which functions as the receptor for most CDCs. Cholesterol binding initiates significant secondary and tertiary structural changes in the monomers, which lead to the assembly of a large membrane embedded β-barrel pore complex. This review will focus on the molecular mechanism of assembly of the CDC membrane pore complex and how these studies have led to insights into the mechanism of pore formation for other pore-forming proteins. This article is part of a Special Issue entitled: Protein Folding in Membranes.
Topics: Cell Membrane; Cholesterol; Complement Membrane Attack Complex; Humans; Perforin; Protein Structure, Secondary
PubMed: 21835159
DOI: 10.1016/j.bbamem.2011.07.036 -
Annual Review of Microbiology 2015The mechanism by which the cholesterol-dependent cytolysins (CDCs) assemble their giant β-barrel pore in cholesterol-rich membranes has been the subject of intense... (Review)
Review
The mechanism by which the cholesterol-dependent cytolysins (CDCs) assemble their giant β-barrel pore in cholesterol-rich membranes has been the subject of intense study in the past two decades. A combination of structural, biophysical, and biochemical analyses has revealed deep insights into the series of complex and highly choreographed secondary and tertiary structural transitions that the CDCs undergo to assemble their β-barrel pore in eukaryotic membranes. Our knowledge of the molecular details of these dramatic structural changes in CDCs has transformed our understanding of how giant pore complexes are assembled and has been critical to our understanding of the mechanisms of other important classes of pore-forming toxins and proteins across the kingdoms of life. Finally, there are tantalizing hints that the CDC pore-forming mechanism is more sophisticated than previously imagined and that some CDCs are employed in pore-independent processes.
Topics: Bacterial Toxins; Cell Membrane; Cholesterol; Cytotoxins; Gram-Positive Bacteria; Humans; Models, Molecular; Pore Forming Cytotoxic Proteins; Protein Structure, Secondary
PubMed: 26488276
DOI: 10.1146/annurev-micro-091014-104233 -
Biophysical Journal Nov 2014The productive fusion pore in membrane fusion is generally thought to be toroidally shaped. Theoretical studies and recent experiments suggest that its formation, in...
The productive fusion pore in membrane fusion is generally thought to be toroidally shaped. Theoretical studies and recent experiments suggest that its formation, in some scenarios, may be preceded by an initial pore formed near the rim of the extended hemifusion diaphragm (HD), a rim-pore. This rim-pore is characterized by a nontoroidal shape that changes with size. To determine this shape as well as the free energy along the pathway of rim-pore expansion, we derived a simple analytical free energy model. We argue that dilation of HD material via expansion of a rim-pore is favored over a regular, circular pore. Further, the expanding rim-pore faces a free energy barrier that linearly increases with HD size. In contrast, the tension required to expand the rim-pore decreases with HD size. Pore flickering, followed by sudden opening, occurs when the tension in the HD competes with the line energy of the rim-pore, and the rim-pore reaches its equilibrium size before reaching the critical pore size. The experimental observation of flickering and closing fusion pores (kiss-and-run) is very well explained by the observed behavior of rim-pores. Finally, the free energy landscape of rim-pore expansion/HD dilation may very well explain why some cellular fusion reactions, in their attempt to minimize energetic costs, progress via alternative formation and dilation of microscopic hemifusion intermediates.
Topics: Lipid Bilayers; Membrane Fusion; Molecular Conformation; Molecular Dynamics Simulation; Porosity; Thermodynamics
PubMed: 25418297
DOI: 10.1016/j.bpj.2014.08.022 -
Materials (Basel, Switzerland) Jul 2022Concrete structures have to withstand the combined effects of external load and environmental factors. Therefore, it is meaningful to study the durability of concrete...
Concrete structures have to withstand the combined effects of external load and environmental factors. Therefore, it is meaningful to study the durability of concrete under compression and carbonation. The air permeability coefficient () and pore structure of concrete under uniaxial compression and carbonation were measured by the Autoclam method and mercury intrusion porosimetry (MIP). The Autoclam test results showed that the concrete changed in a concave parabolic manner with the compressive stress level, and the inflection point of the stress level was 45%. The MIP results showed that the characteristic pore structural parameters (porosity, average pore diameter, median pore diameter by area, and median pore diameter by volume) first decreased and then increased with the stress level change. The change in concrete microstructure was a result of the combined effect of pore filling, decalcification, and densification, as well as the split effect. The key pore structural parameters affecting were confirmed using gray relational analysis (GRA). The top three parameters with the highest correlation with the carbonated concrete were porosity (gray relational grade = 0.789), median pore diameter by volume ( = 0.763), and proportion of transition pore volume ( = 0.827). Furthermore, the regression analysis showed a good linear relation between and the important pore structural parameters.
PubMed: 35888239
DOI: 10.3390/ma15144775 -
ACS Omega May 2023The characterization of the pore structure of tight sandstones is of great importance for the exploration and development of tight oil reservoirs. However, little...
Pore Structure and Fractal Characteristics of Tight Sandstones Based on Nuclear Magnetic Resonance: A Case Study in the Triassic Yanchang Formation of the Ordos Basin, China.
The characterization of the pore structure of tight sandstones is of great importance for the exploration and development of tight oil reservoirs. However, little attention has been given to the geometrical features of pores with various scales, which implies that the effect of pores on the fluid flow and storage capacity is still ambiguous and presents a significant challenge to the risk assessment of tight oil reservoirs. This study investigates the pore structure characteristics of tight sandstones by applying thin section petrography, scanning electron microscopy, nuclear magnetic resonance, fractal theory, and geometric analysis. The results indicate that the tight sandstones have a binary pore system, consisting of small pores and combine pores. A shuttlecock model expresses the shape of the small pore. The radius of the small pore is comparable to the throat radius, and the connectivity of the small pore is poor. A spiny spherical model describes the shape of the combine pore. The connectivity of the combine pore is good, and the pore radius is larger than the throat radius. The most significant contribution to the storage space of the tight sandstones is attributed to the small pores, while permeability is primarily controlled by the combine pores. The heterogeneity of the combine pore has a strong positive correlation with flow capacity, which is associated with the multiple throats of the combine pores that developed during diagenesis. Therefore, the sandstones that are dominated by combine pores and are located near the source rocks represent the most favorable area for the exploitation and development of tight sandstone reservoirs.
PubMed: 37179599
DOI: 10.1021/acsomega.3c00937 -
The Journal of Physiology Sep 2010Two-pore-domain potassium (K2P) channels are responsible for background leak currents which regulate the membrane potential and excitability of many cell types. Their... (Review)
Review
Two-pore-domain potassium (K2P) channels are responsible for background leak currents which regulate the membrane potential and excitability of many cell types. Their activity is modulated by a variety of chemical and physical stimuli which act to increase or decrease the open probability of individual K2P channels. Crystallographic data and homology modelling suggest that all K(+) channels possess a highly conserved structure for ion selectivity and gating mechanisms. Like other K(+) channels, K2P channels are thought to have two primary conserved gating mechanisms: an inactivation (or C-type) gate at the selectivity filter close to the extracellular side of the channel and an activation gate at the intracellular entrance to the channel involving key, identified, hinge glycine residues. Zinc and hydrogen ions regulate Drosophila KCNK0 and mammalian TASK channels, respectively, by interacting with the inactivation gate of these channels. In contrast, the voltage dependence of TASK3 channels is mediated through its activation gate. For KCNK0 it has been shown that the gates display positive cooperativity. It is of much interest to determine whether other K2P regulatory compounds interact with either the activation gate or the inactivation gate to alter channel activity or, indeed, whether additional regulatory gating pathways exist.
Topics: Amino Acid Motifs; Animals; Humans; Ion Channel Gating; Potassium Channels, Tandem Pore Domain; Protein Structure, Tertiary
PubMed: 20566661
DOI: 10.1113/jphysiol.2010.192344 -
PloS One 2021The distribution of multiscale pores and fractures in coal and rock is an important basis for reflecting the capacity of fluid flow in coal seam seepage passages....
The distribution of multiscale pores and fractures in coal and rock is an important basis for reflecting the capacity of fluid flow in coal seam seepage passages. Accurate extraction and qualitative and quantitative analysis of pore-fracture structures are helpful in revealing the flow characteristics of fluid in seepage channels. The relationship between pore and fracture connectivity can provide a scientific reference for optimizing coal seam water injection parameters. Therefore, to analyse the change in permeability caused by the variability in the coal pore-fracture network structure, a CT scanning technique was used to scan coal samples from the Leijia District, Fuxin. A total of 720 sets of original images were collected, a median filter was used to filter out the noise in the obtained images, and to form the basis of a model, the reconstruction and analysis of the three-dimensional pore-fracture morphology of coal samples were carried out. A pore-fracture network model of the coal body was extracted at different scales. Using the maximum sphere algorithm combined with the coordination number, the effect of different quantitative relationships between pore size and pore throat channel permeability was studied. Avizo software was used to simulate the flow path of fluid in the seepage channels. The change trend of the fluid velocity between different seepage channels was discussed. The results of the pore-fracture network models at different scales show that the pore-fracture structure is nonuniform and vertically connected, and the pores are connected at connecting points. The pore size distribution ranges from 104 μm to 9425 μm. The pore throat channel length distribution ranges from 4206 μm to 48073 μm. The size of the coordination number determines the connectivity and thus the porosity of the coal seam. The more connected pore channels there are, the larger the pore diameters and the stronger the percolation ability. During flow in the seepage channels of the coal, the velocity range is divided into a low-speed region, medium-speed region and high-speed region. The fluid seepage in the coal seam is driven by the following factors: pore connectivity > pore and pore throat dimensions > pore and pore throat structure distribution. Ultimately, the pore radius and pore connectivity directly affect the permeability of the coal seam.
Topics: Algorithms; Coal; Computer Simulation; Hydraulic Fracking; Porosity; Tomography, X-Ray Computed; Water Movements
PubMed: 34166372
DOI: 10.1371/journal.pone.0252277 -
ACS Omega Jan 2022Tight sandstone reservoirs have ultralow physical properties and strong heterogeneity, and there is a need to describe the corresponding pore structure characteristics...
Tight sandstone reservoirs have ultralow physical properties and strong heterogeneity, and there is a need to describe the corresponding pore structure characteristics systematically to promote research on unconventional reservoirs. The pore structure, controlled by the diagenesis and volcanic activity of the tight reservoirs in the third member of the Shahejie Formation (Es) of the Gaoshangpu structural belt in the Nanpu Sag, is studied by high-pressure mercury injection, nuclear magnetic resonance, and constant-rate-controlled mercury porosimetry. The results show that the Es reservoir can be divided into three types: the pore radii of Type I reservoirs range from 120 to 180 μm, and the throat radii are larger than 1 μm, resulting in good pore connectivity; pore radii of Type II reservoirs are approximately 100 μm, and the throat radii range from 0.1 to 1 μm, resulting in moderate pore connectivity; and pore radii of Type III reservoirs are much smaller than 100 μm, and the throat radii are smaller than 0.1 μm, resulting in worst pore connectivity. The pore size of Type I reservoirs is most sensitive to compaction, and the pore connectivity is mainly controlled by carbonate cementation; the pore throat size and pore connectivity of Type II reservoirs are seriously affected by clay cementation, and pores are mainly formed by dissolution. However, the pore structure of Type III reservoirs is the worst among those investigated in this study but can be further improved by dissolution to a certain extent. Volcanic activity controls cementation and affects dissolution, thus changing the pore structure. A pore structure evolution model is established, which can provide a reference for future oil gas exploration.
PubMed: 35071869
DOI: 10.1021/acsomega.1c04573 -
Nucleus (Austin, Tex.) 2012The defining feature of eukaryotic cells is the double lipid bilayer of the nuclear envelope (NE) that serves as a physical barrier separating the genome from the... (Review)
Review
The defining feature of eukaryotic cells is the double lipid bilayer of the nuclear envelope (NE) that serves as a physical barrier separating the genome from the cytosol. Nuclear pore complexes (NPCs) are embedded in the NE to facilitate transport of proteins and other macromolecules into and out of the nucleus. In fungi and early embryos where the NE does not completely breakdown during mitosis, microtubule-organizing centers such as the spindle pole body (SPB) must also be inserted into the NE to facilitate organization of the mitotic spindle. Several recent papers have shed light on the mechanism by which SPB complexes are inserted into the NE. An unexpected link between the SPB and NPCs suggests that assembly of these NE complexes is tightly coordinated. We review the findings of these reports in light of our current knowledge of SPB, NPC and NE structure, assembly and function.
Topics: Membrane Proteins; Mitosis; Nuclear Envelope; Nuclear Pore; Nuclear Pore Complex Proteins; Nuclear Proteins; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Spindle Apparatus
PubMed: 22572959
DOI: 10.4161/nucl.20148