The interaction of Clostridium perfringens enterotoxin with receptor claudins

PubMed Central

Shrestha, Archana; Uzal, Francisco A.; McClane, Bruce A.

2016-01-01

Clostridium perfringens enterotoxin (CPE) has significant medical importance due to its involvement in several common human gastrointestinal diseases. This 35 kDa single polypeptide toxin consists of two domains: a C-terminal domain involved in receptor binding and an N-terminal domain involved in oligomerization, membrane insertion and pore formation. The action of CPE starts with its binding to receptors, which include certain members of the claudin tight junction protein family; bound CPE then forms a series of complexes, one of which is a pore that causes the calcium influx responsible for host cell death. Recent studies have revealed that CPE binding to claudin receptors involves interactions between the C-terminal CPE domain and both the 1st and 2nd extracellular loops (ECL-1 and ECL-2) of claudin receptors. Of particular importance for this binding is the docking of ECL-2 into a pocket present in the C-terminal domain of the toxin. This increased understanding of CPE interactions with claudin receptors is now fostering the development of receptor decoy therapeutics for CPE-mediated gastrointestinal disease, reagents for cancer therapy/diagnoses and enhancers of drug delivery. PMID:27090847

Claudin-2-mediated cation and water transport share a common pore

PubMed Central

Rosenthal, Rita; Günzel, Dorothee; Krug, Susanne M.; Schulzke, Jörg-Dieter; Fromm, Michael; Yu, Alan S.L.

2016-01-01

Aim Claudin-2 is a tight junction protein typically located in “leaky” epithelia exhibiting large paracellular permeabilities like small intestine and proximal kidney tubule. Former studies revealed that claudin-2 forms paracellular channels for small cations like sodium and potassium and also paracellular channels for water. This study analyzes whether the diffusive transport of sodium and water occurs through a common pore of the claudin-2 channel. Methods Wild-type claudin-2 and different claudin-2 mutants were expressed in MDCK I kidney tubule cells using an inducible system. Ion and water permeability and the effect of blocking reagents on both were investigated on different clones of the mutants. Results Neutralization of a negatively charged cation interaction site in the pore with the mutation, D65N, decreased both, sodium permeability and water permeability. Claudin-2 mutants (I66C and S68C) with substitution of the pore-lining amino acids with cysteine were used to test the effect of steric blocking of the claudin-2 pore by thiol-reactive reagents. Addition of thiol-reactive reagents to these mutants simultaneously decreased conductance and water permeability. Remarkably, all experimental perturbations caused parallel changes in ion conductance and water permeability, disproving different or independent passage pathways. Conclusion Our results indicate that claudin-2-mediated cation and water transport are frictionally coupled and share a common pore. This pore is lined and determined in permeability by amino acid residues of the first extracellular loop of claudin-2. PMID:27359349

Molecular basis of usher pore gating in Escherichia coli pilus biogenesis.

PubMed

Volkan, Ender; Kalas, Vasilios; Pinkner, Jerome S; Dodson, Karen W; Henderson, Nadine S; Pham, Thieng; Waksman, Gabriel; Delcour, Anne H; Thanassi, David G; Hultgren, Scott J

2013-12-17

Extracellular fibers called chaperone-usher pathway pili are critical virulence factors in a wide range of Gram-negative pathogenic bacteria that facilitate binding and invasion into host tissues and mediate biofilm formation. Chaperone-usher pathway ushers, which catalyze pilus assembly, contain five functional domains: a 24-stranded transmembrane β-barrel translocation domain (TD), a β-sandwich plug domain (PLUG), an N-terminal periplasmic domain, and two C-terminal periplasmic domains (CTD1 and 2). Pore gating occurs by a mechanism whereby the PLUG resides stably within the TD pore when the usher is inactive and then upon activation is translocated into the periplasmic space, where it functions in pilus assembly. Using antibiotic sensitivity and electrophysiology experiments, a single salt bridge was shown to function in maintaining the PLUG in the TD channel of the P pilus usher PapC, and a loop between the 12th and 13th beta strands of the TD (β12-13 loop) was found to facilitate pore opening. Mutation of the β12-13 loop resulted in a closed PapC pore, which was unable to efficiently mediate pilus assembly. Deletion of the PapH terminator/anchor resulted in increased OM permeability, suggesting a role for the proper anchoring of pili in retaining OM integrity. Further, we introduced cysteine residues in the PLUG and N-terminal periplasmic domains that resulted in a FimD usher with a greater propensity to exist in an open conformation, resulting in increased OM permeability but no loss in type 1 pilus assembly. These studies provide insights into the molecular basis of usher pore gating and its roles in pilus biogenesis and OM permeability.

Structural basis of dual Ca2+/pH regulation of the endolysosomal TRPML1 channel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Minghui; Zhang, Wei K.; Benvin, Nicole M.

The activities of organellar ion channels are often regulated by Ca2+ and H+, which are present in high concentrations in many organelles. Here we report a structural element critical for dual Ca2+/pH regulation of TRPML1, a Ca2+-release channel crucial for endolysosomal function. TRPML1 mutations cause mucolipidosis type IV (MLIV), a severe lysosomal storage disorder characterized by neurodegeneration, mental retardation and blindness. We obtained crystal structures of the 213-residue luminal domain of human TRPML1 containing three missense MLIV-causing mutations. This domain forms a tetramer with a highly electronegative central pore formed by a novel luminal pore loop. Cysteine cross-linking and cryo-EMmore » analyses confirmed that this architecture occurs in the full-length channel. Structure–function studies demonstrated that Ca2+ and H+ interact with the luminal pore and exert physiologically important regulation. The MLIV-causing mutations disrupt the luminal-domain structure and cause TRPML1 mislocalization. Our study reveals the structural underpinnings of TRPML1's regulation, assembly and pathogenesis.« less

Selectivity filters and cysteine-rich extracellular loops in voltage-gated sodium, calcium, and NALCN channels

PubMed Central

Stephens, Robert F.; Guan, W.; Zhorov, Boris S.; Spafford, J. David

2015-01-01

How nature discriminates sodium from calcium ions in eukaryotic channels has been difficult to resolve because they contain four homologous, but markedly different repeat domains. We glean clues from analyzing the changing pore region in sodium, calcium and NALCN channels, from single-cell eukaryotes to mammals. Alternative splicing in invertebrate homologs provides insights into different structural features underlying calcium and sodium selectivity. NALCN generates alternative ion selectivity with splicing that changes the high field strength (HFS) site at the narrowest level of the hourglass shaped pore where the selectivity filter is located. Alternative splicing creates NALCN isoforms, in which the HFS site has a ring of glutamates contributed by all four repeat domains (EEEE), or three glutamates and a lysine residue in the third (EEKE) or second (EKEE) position. Alternative splicing provides sodium and/or calcium selectivity in T-type channels with extracellular loops between S5 and P-helices (S5P) of different lengths that contain three or five cysteines. All eukaryotic channels have a set of eight core cysteines in extracellular regions, but the T-type channels have an infusion of 4–12 extra cysteines in extracellular regions. The pattern of conservation suggests a possible pairing of long loops in Domains I and III, which are bridged with core cysteines in NALCN, Cav, and Nav channels, and pairing of shorter loops in Domains II and IV in T-type channel through disulfide bonds involving T-type specific cysteines. Extracellular turrets of increasing lengths in potassium channels (Kir2.2, hERG, and K2P1) contribute to a changing landscape above the pore selectivity filter that can limit drug access and serve as an ion pre-filter before ions reach the pore selectivity filter below. Pairing of extended loops likely contributes to the large extracellular appendage as seen in single particle electron cryo-microscopy images of the eel Nav1 channel. PMID:26042044

A refined model of claudin-15 tight junction paracellular architecture by molecular dynamics simulations

PubMed Central

Alberini, Giulio; Benfenati, Fabio

2017-01-01

Tight-junctions between epithelial cells of biological barriers are specialized molecular structures that regulate the flux of solutes across the barrier, parallel to cell walls. The tight-junction backbone is made of strands of transmembrane proteins from the claudin family, but the molecular mechanism of its function is still not completely understood. Recently, the crystal structure of a mammalian claudin-15 was reported, displaying for the first time the detailed features of transmembrane and extracellular domains. Successively, a structural model of claudin-15-based paracellular channels has been proposed, suggesting a putative assembly that illustrates how claudins associate in the same cell (via cis interactions) and across adjacent cells (via trans interactions). Although very promising, the model offers only a static conformation, with residues missing in the most important extracellular regions and potential steric clashes. Here we present detailed atomic models of paracellular single and double pore architectures, obtained from the putative assembly and refined via structural modeling and all-atom molecular dynamics simulations in double membrane bilayer and water environment. Our results show an overall stable configuration of the complex with a fluctuating pore size. Extracellular residue loops in trans interaction are able to form stable contacts and regulate the size of the pore, which displays a stationary radius of 2.5–3.0 Å at the narrowest region. The side-by-side interactions of the cis configuration are preserved via stable hydrogen bonds, already predicted by cysteine crosslinking experiments. Overall, this work introduces an improved version of the claudin-15-based paracellular channel model that strengthens its validity and that can be used in further computational studies to understand the structural features of tight-junctions regulation. PMID:28863193

Closing the loop of the soil water retention curve

USGS Publications Warehouse

Lu, Ning; Alsherif, N; Wayllace, Alexandra; Godt, Jonathan W.

2015-01-01

The authors, to their knowledge for the first time, produced two complete principal soil water retention curves (SWRCs) under both positive and negative matric suction regimes. An innovative testing technique combining the transient water release and imbibition method (TRIM) and constant flow method (CFM) was used to identify the principal paths of SWRC in the positive pore-water pressure regime under unsaturated conditions. A negative matric suction of 9.8 kPa is needed to reach full saturation or close the loop of the SWRC for a silty soil. This work pushes the understanding of the interaction of soil and water into new territory by quantifying the boundaries of the SWRC over the entire suction domain, including both wetting and drying conditions that are relevant to field conditions such as slope wetting under heavy rainfall or rapid groundwater table rise in earthen dams or levees.

Mechanism of action of chromogranin A on catecholamine release: molecular modeling of the catestatin region reveals a β-strand/loop/β-strand structure secured by hydrophobic interactions and predictive of activity

PubMed Central

Tsigelny, Igor; Mahata, Sushil K.; Taupenot, Laurent; Preece, Nicholas E.; Mahata, Manjula; Khan, Imran; Parmer, Robert J.; O’Connor, Daniel T.

2009-01-01

A novel fragment of chromogranin A, known as ‘catestatin’ (bovine chromogranin A344–364), inhibits catecholamine release from chromaffin cells and noradrenergic neurons by acting as a non-competitive nicotinic cholinergic antagonist, and may therefore constitute an endogenous autocrine feedback regulator of sympathoadrenal activity. To characterize how this activity depends on the peptide’s structure, we searched for common 3-dimensional motifs for this primary structure or its homologs. Catestatin’s primary structure bore significant (29–35.5% identity, general alignment score 44–57) sequence homology to fragment sequences within three homologs of known 3-dimensional structures, based on solved X-ray crystals: 8FAB, 1PKM, and 2IG2. Each of these sequences exists in nature as a β-strand/loop/β-strand structure, stabilized by hydrophobic interactions between the β-strands. The catestatin structure was stable during molecular dynamics simulations. The catestatin loop contains three Arg residues, whose electropositive side chains form the terminus of the structure, and give rise to substantial uncompensated charge asymmetry in the molecule. A hydrophobic moment plot revealed that catestatin is the only segment of chromogranin A predicted to contain amphiphilic β-strand. Circular dichroism in the far ultraviolet showed substantial (63%) β-sheet structure, especially in a hydrophobic environment. Alanine-substitution mutants of catestatin established a crucial role for the three central arginine residues in the loop (Arg351, Arg353, and Arg358), though not for two arginine residues in the strand region toward the amino-terminus. [125I]Catestatin bound to Torpedo membranes at a site other than the nicotinic agonist binding site. When the catestatin structure was ‘docked’ with the extracellular domain of the Torpedo nicotinic cholinergic receptor, it interacted principally with the β and δ subunits, in a relatively hydrophobic region of the cation pore extracellular orifice, and the complex of ligand and receptor largely occluded the cation pore, providing a structural basis for the non-competitive nicotinic cholinergic antagonist properties of the peptide. We conclude that a homology model of catestatin correctly predicts actual features of the peptide, both physical and biological. The model suggests particular spatial and charge features of the peptide which may serve as starting points in the development of non-peptide mimetics of this endogenous nicotinic cholinergic antagonist. PMID:9809795

Genotype-phenotype aspects of type 2 long QT syndrome.

PubMed

Shimizu, Wataru; Moss, Arthur J; Wilde, Arthur A M; Towbin, Jeffrey A; Ackerman, Michael J; January, Craig T; Tester, David J; Zareba, Wojciech; Robinson, Jennifer L; Qi, Ming; Vincent, G Michael; Kaufman, Elizabeth S; Hofman, Nynke; Noda, Takashi; Kamakura, Shiro; Miyamoto, Yoshihiro; Shah, Samit; Amin, Vinit; Goldenberg, Ilan; Andrews, Mark L; McNitt, Scott

2009-11-24

The purpose of this study was to investigate the effect of location, coding type, and topology of KCNH2(hERG) mutations on clinical phenotype in type 2 long QT syndrome (LQTS). Previous studies were limited by population size in their ability to examine phenotypic effect of location, type, and topology. Study subjects included 858 type 2 LQTS patients with 162 different KCNH2 mutations in 213 proband-identified families. The Cox proportional-hazards survivorship model was used to evaluate independent contributions of clinical and genetic factors to the first cardiac events. For patients with missense mutations, the transmembrane pore (S5-loop-S6) and N-terminus regions were a significantly greater risk than the C-terminus region (hazard ratio [HR]: 2.87 and 1.86, respectively), but the transmembrane nonpore (S1-S4) region was not (HR: 1.19). Additionally, the transmembrane pore region was significantly riskier than the N-terminus or transmembrane nonpore regions (HR: 1.54 and 2.42, respectively). However, for nonmissense mutations, these other regions were no longer riskier than the C-terminus (HR: 1.13, 0.77, and 0.46, respectively). Likewise, subjects with nonmissense mutations were at significantly higher risk than were subjects with missense mutations in the C-terminus region (HR: 2.00), but that was not the case in other regions. This mutation location-type interaction was significant (p = 0.008). A significantly higher risk was found in subjects with mutations located in alpha-helical domains than in subjects with mutations in beta-sheet domains or other locations (HR: 1.74 and 1.33, respectively). Time-dependent beta-blocker use was associated with a significant 63% reduction in the risk of first cardiac events (p < 0.001). The KCNH2 missense mutations located in the transmembrane S5-loop-S6 region are associated with the greatest risk.

Structural basis for nuclear import complex dissociation by RanGTP.

PubMed

Lee, Soo Jae; Matsuura, Yoshiyuki; Liu, Sai Man; Stewart, Murray

2005-06-02

Nuclear protein import is mediated mainly by the transport factor importin-beta that binds cytoplasmic cargo, most often via the importin-alpha adaptor, and then transports it through nuclear pore complexes. This active transport is driven by disassembly of the import complex by nuclear RanGTP. The switch I and II loops of Ran change conformation with nucleotide state, and regulate its interactions with nuclear trafficking components. Importin-beta consists of 19 HEAT repeats that are based on a pair of antiparallel alpha-helices (referred to as the A- and B-helices). The HEAT repeats stack to yield two C-shaped arches, linked together to form a helicoidal molecule that has considerable conformational flexibility. Here we present the structure of full-length yeast importin-beta (Kap95p or karyopherin-beta) complexed with RanGTP, which provides a basis for understanding the crucial cargo-release step of nuclear import. We identify a key interaction site where the RanGTP switch I loop binds to the carboxy-terminal arch of Kap95p. This interaction produces a change in helicoidal pitch that locks Kap95p in a conformation that cannot bind importin-alpha or cargo. We suggest an allosteric mechanism for nuclear import complex disassembly by RanGTP.

Structure of the Nav1.4-β1 Complex from Electric Eel.

PubMed

Yan, Zhen; Zhou, Qiang; Wang, Lin; Wu, Jianping; Zhao, Yanyu; Huang, Gaoxingyu; Peng, Wei; Shen, Huaizong; Lei, Jianlin; Yan, Nieng

2017-07-27

Voltage-gated sodium (Na v ) channels initiate and propagate action potentials. Here, we present the cryo-EM structure of EeNa v 1.4, the Na v channel from electric eel, in complex with the β1 subunit at 4.0 Å resolution. The immunoglobulin domain of β1 docks onto the extracellular L5 I and L6 IV loops of EeNa v 1.4 via extensive polar interactions, and the single transmembrane helix interacts with the third voltage-sensing domain (VSD III ). The VSDs exhibit "up" conformations, while the intracellular gate of the pore domain is kept open by a digitonin-like molecule. Structural comparison with closed Na v PaS shows that the outward transfer of gating charges is coupled to the iris-like pore domain dilation through intricate force transmissions involving multiple channel segments. The IFM fast inactivation motif on the III-IV linker is plugged into the corner enclosed by the outer S4-S5 and inner S6 segments in repeats III and IV, suggesting a potential allosteric blocking mechanism for fast inactivation. Copyright © 2017 Elsevier Inc. All rights reserved.

Claudins and the Kidney Volume 75: Annual Review of Physiology

PubMed Central

Hou, Jianghui; Rajagopal, Madhumitha; Yu, Alan S. L.

2013-01-01

Claudins are tight junction membrane proteins that regulate paracellular permeability of renal epithelia to small ions, solutes and water. Claudins interact within the cell membrane and between neighboring cells to form tight junction strands and constitute both the paracellular barrier and pore. The first extracellular domain of claudins is thought to be the pore-lining domain and contains the determinants of charge selectivity. Multiple claudins are expressed in different nephron segments and this likely determines the permeability properties of each segment. Recent evidence has identified claudin-2 as constituting the cation-reabsorptive pathway in the proximal tubule, claudin-14, -16 and -19 as forming a complex that regulates calcium transport in the thick ascending limb of the loop of Henle, and claudin-4, -7 and -8 as determinants of collecting duct choride permeability. Mutations in claudin-16 and -19 cause familial hypercalciuric hypomagnesemia. The roles of other claudins in kidney diseases remain to be fully elucidated. PMID:23140368

Quasithermodynamic Contributions to the Fluctuations of a Protein Nanopore

PubMed Central

2015-01-01

Proteins undergo thermally activated conformational fluctuations among two or more substates, but a quantitative inquiry on their kinetics is persistently challenged by numerous factors, including the complexity and dynamics of various interactions, along with the inability to detect functional substates within a resolvable time scale. Here, we analyzed in detail the current fluctuations of a monomeric β-barrel protein nanopore of known high-resolution X-ray crystal structure. We demonstrated that targeted perturbations of the protein nanopore system, in the form of loop-deletion mutagenesis, accompanying alterations of electrostatic interactions between long extracellular loops, produced modest changes of the differential activation free energies calculated at 25 °C, ΔΔG⧧, in the range near the thermal energy but substantial and correlated modifications of the differential activation enthalpies, ΔΔH⧧, and entropies, ΔΔS⧧. This finding indicates that the local conformational reorganizations of the packing and flexibility of the fluctuating loops lining the central constriction of this protein nanopore were supplemented by changes in the single-channel kinetics. These changes were reflected in the enthalpy–entropy reconversions of the interactions between the loop partners with a compensating temperature, TC, of ∼300 K, and an activation free energy constant of ∼41 kJ/mol. We also determined that temperature has a much greater effect on the energetics of the equilibrium gating fluctuations of a protein nanopore than other environmental parameters, such as the ionic strength of the aqueous phase as well as the applied transmembrane potential, likely due to ample changes in the solvation activation enthalpies. There is no fundamental limitation for applying this approach to other complex, multistate membrane protein systems. Therefore, this methodology has major implications in the area of membrane protein design and dynamics, primarily by revealing a better quantitative assessment on the equilibrium transitions among multiple well-defined and functionally distinct substates of protein channels and pores. PMID:25479108

Amino acid screening based on structural modeling identifies critical residues for the function, ion selectivity and structure of Arabidopsis MTP1.

PubMed

Kawachi, Miki; Kobae, Yoshihiro; Kogawa, Sayaka; Mimura, Tetsuro; Krämer, Ute; Maeshima, Masayoshi

2012-07-01

Arabidopsis thaliana MTP1 is a vacuolar membrane Zn(2+)/H(+) antiporter of the cation diffusion facilitator family. Here we present a structure-function analysis of AtMTP1-mediated transport and its remarkable Zn(2+) selectivity by functional complementation tests of more than 50 mutant variants in metal-sensitive yeast strains. This was combined with homology modeling of AtMTP1 based on the crystal structure of the Escherichia coli broad-specificity divalent cation transporter YiiP. The Zn(2+)-binding sites of EcYiiP in the cytoplasmic C-terminus, and the pore formed by transmembrane helices TM2 and TM5, are conserved in AtMTP1. Although absent in EcYiiP, Cys31 and Cys36 in the extended N-terminal cytosolic domain of AtMTP1 are necessary for complementation of a Zn-sensitive yeast strain. On the cytosolic side of the active Zn(2+)-binding site inside the transmembrane pore, Ala substitution of either Asn258 in TM5 or Ser101 in TM2 non-selectively enhanced the metal tolerance conferred by AtMTP1. Modeling predicts that these residues obstruct the movement of cytosolic Zn(2+) into the intra-membrane Zn(2+)-binding site of AtMTP1. A conformational change in the immediately preceding His-rich cytosolic loop may displace Asn258 and permit Zn(2+) entry into the pore. This would allow dynamic coupling of Zn(2+) transport to the His-rich loop, thus acting as selectivity filter or sensor of cytoplasmic Zn(2+) levels. Individual mutations at diverse sites within AtMTP1 conferred Co and Cd tolerance in yeast, and included deletions in N-terminal and His-rich intra-molecular cytosolic domains, and mutations of single residues flanking the transmembrane pore or participating in intra- or inter-molecular domain interactions, all of which are not conserved in the non-selective EcYiiP. © 2012 The Authors Journal compilation © 2012 FEBS.

Influence of the Location of Attractive Polymer-Pore Interactions on Translocation Dynamics.

PubMed

Ghosh, Bappa; Chaudhury, Srabanti

2018-01-11

We probe the influence of polymer-pore interactions on the translocation dynamics using Langevin dynamics simulations. We investigate the effect of the strength and location of the polymer-pore interaction using nanopores that are partially charged either at the entry or the exit or on both sides of the pore. We study the change in the translocation time as a function of the strength of the polymer-pore interaction for a given chain length and under the effect of an externally applied field. Under a moderate driving force and a chain length longer than the length of the pore, the translocation time shows a nonmonotonic increase with an increase in the attractive interaction. Also, an interaction on the cis side of the pore can increase the translocation probability. In the presence of an external field and a strong attractive force, the translocation time for shorter chains is independent of the polymer-pore interaction at the entry side of the pore, whereas an interaction on the trans side dominates the translocation process. Our simulation results are rationalized by a qualitative analysis of the free energy landscape for polymer translocation.

Threading dynamics of a polymer through parallel pores: Potential applications to DNA size separation

NASA Astrophysics Data System (ADS)

Åkerman, Björn

1997-04-01

DNA orientation measurements by linear dichroism (LD) spectroscopy and single molecule imaging by fluorescence microscopy are used to investigate the effect of DNA size (71-740 kilo base pairs) and field strength E (1-5.9 V/cm) on the conformation dynamics during the field-driven threading of DNA molecules through a set of parallel pores in agarose gels, with average pore radii between 380 Å and 1400 Å. Locally relaxed but globally oriented DNA molecules are subjected to a perpendicular field, and the observed LD time profile is compared with a recent theory for the threading [D. Long and J.-L. Viovy, Phys. Rev. E 53, 803 (1996)] which assumes the same initial state. As predicted the DNA is driven by the ends into a U-form, leading to an overshoot in the LD. The overshoot-time scales as E-(1.2-1.4) as predicted, but grows more slowly with DNA size than the predicted linear dependence. For long molecules loops form initially in the threading process but are finally consumed by the ends, and the process of transfer of DNA segments, from the loops to the arms of the U, leads to a shoulder in the LD as predicted. The critical size below which loops do not form (as indicated by the LD shoulder being absent) is between 71 and 105 kbp (0.5% agarose, 5.9 V/cm), and considerably larger than predicted because in the initial state the DNA molecules are housed in gel cavities with effective pore sizes about four times larger than the average pore size. From the data, the separation of DNA by exploiting the threading dynamics in pulsed fields [D. Long et al., CR Acad. Sci. Paris, Ser. IIb 321, 239 (1995)] is shown to be feasible in principle in an agarose-based system.

Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution

PubMed Central

Wu, Jianping; Li, Zhangqiang; Xie, Tian; Peng, Wei; Yin, Changcheng; Li, Xueming; Scheres, Sjors H.W.; Shi, Yigong; Yan, Nieng

2014-01-01

The ryanodine receptors (RyRs) are high-conductance intracellular Ca2+ channels that play a pivotal role in the excitation-contraction coupling of skeletal and cardiac muscles. RyRs are the largest known ion channels, with a homotetrameric organization and approximately 5000 residues in each protomer. Here we report the structure of the rabbit RyR1 in complex with its modulator FKBP12 at an overall resolution of 3.8 Å, determined by single-particle electron cryo-microscopy. Three previously uncharacterized domains, named Central, Handle, and Helical domains, display the armadillo repeat fold. These domains, together with the amino-terminal domain, constitute a network of superhelical scaffold for binding and propagation of conformational changes. The channel domain exhibits the voltage-gated ion channel superfamily fold with distinct features. A negative charge-enriched hairpin loop connecting S5 and the pore helix is positioned above the entrance to the selectivity filter vestibule. The four elongated S6 segments form a right-handed helical bundle that closes the pore at the cytoplasmic border of the membrane. Allosteric regulation of the pore by the cytoplasmic domains is mediated through extensive interactions between the Central domains and the channel domain. These structural features explain high ion conductance by RyRs and the long-range allosteric regulation of channel activities. PMID:25517095

Exploring the Structure of the Voltage-gated Na+ Channel by an Engineered Drug Access Pathway to the Receptor Site for Local Anesthetics*

PubMed Central

Lukacs, Peter; Gawali, Vaibhavkumar S.; Cervenka, Rene; Ke, Song; Koenig, Xaver; Rubi, Lena; Zarrabi, Touran; Hilber, Karlheinz; Stary-Weinzinger, Anna; Todt, Hannes

2014-01-01

Despite the availability of several crystal structures of bacterial voltage-gated Na+ channels, the structure of eukaryotic Na+ channels is still undefined. We used predictions from available homology models and crystal structures to modulate an external access pathway for the membrane-impermeant local anesthetic derivative QX-222 into the internal vestibule of the mammalian rNaV1.4 channel. Potassium channel-based homology models predict amino acid Ile-1575 in domain IV segment 6 to be in close proximity to Lys-1237 of the domain III pore-loop selectivity filter. The mutation K1237E has been shown previously to increase the diameter of the selectivity filter. We found that an access pathway for external QX-222 created by mutations of Ile-1575 was abolished by the additional mutation K1237E, supporting the notion of a close spatial relationship between sites 1237 and 1575. Crystal structures of bacterial voltage-gated Na+ channels predict that the side chain of rNaV1.4 Trp-1531 of the domain IV pore-loop projects into the space between domain IV segment 6 and domain III pore-loop and, therefore, should obstruct the putative external access pathway. Indeed, mutations W1531A and W1531G allowed for exceptionally rapid access of QX-222. In addition, W1531G created a second non-selective ion-conducting pore, bypassing the outer vestibule but probably merging into the internal vestibule, allowing for control by the activation gate. These data suggest a strong structural similarity between bacterial and eukaryotic voltage-gated Na+ channels. PMID:24947510

Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase.

PubMed

Deville, Célia; Carroni, Marta; Franke, Kamila B; Topf, Maya; Bukau, Bernd; Mogk, Axel; Saibil, Helen R

2017-08-01

Refolding aggregated proteins is essential in combating cellular proteotoxic stress. Together with Hsp70, Hsp100 chaperones, including Escherichia coli ClpB, form a powerful disaggregation machine that threads aggregated polypeptides through the central pore of tandem adenosine triphosphatase (ATPase) rings. To visualize protein disaggregation, we determined cryo-electron microscopy structures of inactive and substrate-bound ClpB in the presence of adenosine 5'- O -(3-thiotriphosphate), revealing closed AAA+ rings with a pronounced seam. In the substrate-free state, a marked gradient of resolution, likely corresponding to mobility, spans across the AAA+ rings with a dynamic hotspot at the seam. On the seam side, the coiled-coil regulatory domains are locked in a horizontal, inactive orientation. On the opposite side, the regulatory domains are accessible for Hsp70 binding, substrate targeting, and activation. In the presence of the model substrate casein, the polypeptide threads through the entire pore channel and increased nucleotide occupancy correlates with higher ATPase activity. Substrate-induced domain displacements indicate a pathway of regulated substrate transfer from Hsp70 to the ClpB pore, inside which a spiral of loops contacts the substrate. The seam pore loops undergo marked displacements, along with ordering of the regulatory domains. These asymmetric movements suggest a mechanism for ATPase activation and substrate threading during disaggregation.

Sulphation of CaO-Based Sorbent Modified in CO2 Looping Cycles

NASA Astrophysics Data System (ADS)

Manovic, Vasilije; Anthony, Edward J.; Loncarevic, Davor

CaO-based looping cycles for CO2 capture at high temperatures are based on cyclical carbonation of CaO and regeneration of CaCO3. The main limitation of natural sorbents is the loss of carrying capacity with increasing numbers of reaction cycles, resulting in spent sorbent ballast. Use of spent sorbent from CO2 looping cycles for SO2 capture is a possible solution investigated in this study. Three limestones were investigated: Kelly Rock (Canada), La Blanca (Spain) and Katowice (Poland). Carbonation/calcination cycles were performed in a tube furnace with original limestones and samples thermally pretreated for different times (i.e., sintered). The spent sorbent samples were sulphated in a thermogravimetric analyzer. Changes in the resulting pore structure were then investigated using mercury porosimetry. Final conversions of both spent and pretreated sorbents after longer sulphation times were comparable or higher than those observed for the original sorbents. Maximum sulphation levels strongly depend on sorbent porosity and pore surface area. The shrinkage of sorbent particles during calcination/cycling resulted in a loss of sorbent porosity (≤48%), which corresponds to maximum sulphation levels ˜55% for spent Kelly Rock and Katowice. However, this is ˜10% higher than for the original samples. By contrast, La Blanca limestone had more pronounced particle shrinkage during pretreatment and cycling, leading to lower porosity, <35%, resulting in sulphation conversion of spent samples <30%, significantly lower than for the original sample (45%). These results showed that spent sorbent samples from CO2 looping cycles can be used as sorbents for SO2 retention if significant porosity loss does not occur during CO2 reaction cycles. For spent Kelly Rock and Katowice samples final conversions are determined by the total pore volume available for the bulky CaSO4 product.

Peptides selected for the protein nanocage pores change the rate of iron recovery from the ferritin mineral.

PubMed

Liu, Xiaofeng S; Patterson, Leslie D; Miller, Marvin J; Theil, Elizabeth C

2007-11-02

Pores regulate access between ferric-oxy biomineral inside and reductants/chelators outside the ferritin protein nanocage to control iron demineralization rates. The pore helix/loop/helix motifs that are contributed by three subunits unfold independently of the protein cage, as observed by crystallography, Fe removal rates, and CD spectroscopy. Pore unfolding is induced in wild type ferritin by increased temperature or urea (1-10 mM), a physiological urea range, 0.1 mM guanidine, or mutation of conserved pore amino acids. A peptide selected for ferritin pore binding from a combinatorial, heptapeptide library increased the rate of Fe demineralization 3-fold (p<0.001), similarly to a mutation that unfolded the pores. Conjugating the peptide to Desferal (desferrioxamine B mesylate), a chelator in therapeutic use, increased the rates to 8-fold (p<0.001). A second pore binding peptide had the opposite effect and decreased the rate of Fe demineralization 60% (p<0.001). The peptides could have pharmacological uses and may model regulators of ferritin demineralization rates in vivo or peptide regulators of gated pores in membranes. The results emphasize that small peptides can exploit the structural plasticity of protein pores to modulate function.

Mapping the Interaction Site for a β-Scorpion Toxin in the Pore Module of Domain III of Voltage-gated Na+ Channels*

PubMed Central

Zhang, Joel Z.; Yarov-Yarovoy, Vladimir; Scheuer, Todd; Karbat, Izhar; Cohen, Lior; Gordon, Dalia; Gurevitz, Michael; Catterall, William A.

2012-01-01

Activation of voltage-gated sodium (Nav) channels initiates and propagates action potentials in electrically excitable cells. β-Scorpion toxins, including toxin IV from Centruroides suffusus suffusus (CssIV), enhance activation of NaV channels. CssIV stabilizes the voltage sensor in domain II in its activated state via a voltage-sensor trapping mechanism. Amino acid residues required for the action of CssIV have been identified in the S1-S2 and S3-S4 extracellular loops of domain II. The extracellular loops of domain III are also involved in toxin action, but individual amino acid residues have not been identified. We used site-directed mutagenesis and voltage clamp recording to investigate amino acid residues of domain III that are involved in CssIV action. In the IIISS2-S6 loop, five substitutions at four positions altered voltage-sensor trapping by CssIVE15A. Three substitutions (E1438A, D1445A, and D1445Y) markedly decreased voltage-sensor trapping, whereas the other two substitutions (N1436G and L1439A) increased voltage-sensor trapping. These bidirectional effects suggest that residues in IIISS2-S6 make both positive and negative interactions with CssIV. N1436G enhanced voltage-sensor trapping via increased binding affinity to the resting state, whereas L1439A increased voltage-sensor trapping efficacy. Based on these results, a three-dimensional model of the toxin-channel interaction was developed using the Rosetta modeling method. These data provide additional molecular insight into the voltage-sensor trapping mechanism of toxin action and define a three-point interaction site for β-scorpion toxins on NaV channels. Binding of α- and β-scorpion toxins to two distinct, pseudo-symmetrically organized receptor sites on NaV channels acts synergistically to modify channel gating and paralyze prey. PMID:22761417

Functional analysis of a frame-shift mutant of the dihydropyridine receptor pore subunit (α1S) expressing two complementary protein fragments

PubMed Central

Ahern, Chris A; Vallejo, Paola; Mortenson, Lindsay; Coronado, Roberto

2001-01-01

Background The L-type Ca2+ channel formed by the dihydropyridine receptor (DHPR) of skeletal muscle senses the membrane voltage and opens the ryanodine receptor (RyR1). This channel-to-channel coupling is essential for Ca2+ signaling but poorly understood. We characterized a single-base frame-shift mutant of α1S, the pore subunit of the DHPR, that has the unusual ability to function voltage sensor for excitation-contraction (EC) coupling by virtue of expressing two complementary hemi-Ca2+ channel fragments. Results Functional analysis of cDNA transfected dysgenic myotubes lacking α1S were carried out using voltage-clamp, confocal Ca2+ indicator fluoresence, epitope immunofluorescence and immunoblots of expressed proteins. The frame-shift mutant (fs-α1S) expressed the N-terminal half of α1S (M1 to L670) and the C-terminal half starting at M701 separately. The C-terminal fragment was generated by an unexpected restart of translation of the fs-α1S message at M701 and was eliminated by a M701I mutation. Protein-protein complementation between the two fragments produced recovery of skeletal-type EC coupling but not L-type Ca2+ current. Discussion A premature stop codon in the II-III loop may not necessarily cause a loss of DHPR function due to a restart of translation within the II-III loop, presumably by a mechanism involving leaky ribosomal scanning. In these cases, function is recovered by expression of complementary protein fragments from the same cDNA. DHPR-RyR1 interactions can be achieved via protein-protein complementation between hemi-Ca2+ channel proteins, hence an intact II-III loop is not essential for coupling the DHPR voltage sensor to the opening of RyR1 channel. PMID:11806762

Resolved single-molecule detection of individual species within a mixture of anti-biotin antibodies using an engineered monomeric nanopore.

PubMed

Fahie, Monifa; Chisholm, Christina; Chen, Min

2015-02-24

Oligomeric protein nanopores with rigid structures have been engineered for the purpose of sensing a wide range of analytes including small molecules and biological species such as proteins and DNA. We chose a monomeric β-barrel porin, OmpG, as the platform from which to derive the nanopore sensor. OmpG is decorated with seven flexible loops that move dynamically to create a distinct gating pattern when ionic current passes through the pore. Biotin was chemically tethered to the most flexible one of these loops. The gating characteristic of the loop's movement in and out of the porin was substantially altered by analyte protein binding. The gating characteristics of the pore with bound targets were remarkably sensitive to molecular identity, even providing the ability to distinguish between homologues within an antibody mixture. A total of five gating parameters were analyzed for each analyte to create a unique fingerprint for each biotin-binding protein. Our exploitation of gating noise as a molecular identifier may allow more sophisticated sensor design, while OmpG's monomeric structure greatly simplifies nanopore production.

Negative gating modulation by (R)-N-(benzimidazol-2-yl)-1,2,3,4-tetrahydro-1-naphthylamine (NS8593) depends on residues in the inner pore vestibule: pharmacological evidence of deep-pore gating of K(Ca)2 channels.

PubMed

Jenkins, David Paul; Strøbæk, Dorte; Hougaard, Charlotte; Jensen, Marianne L; Hummel, Rene; Sørensen, Ulrik S; Christophersen, Palle; Wulff, Heike

2011-06-01

Acting as a negative gating modulator, (R)-N-(benzimidazol-2-yl)-1,2,3,4-tetrahydro-1-naphthylamine (NS8593) shifts the apparent Ca(2+)-dependence of the small-conductance Ca(2+)-activated K(+) channels K(Ca)2.1-2.3 to higher Ca(2+) concentrations. Similar to the positive K(Ca) channel-gating modulators 1-ethyl-2-benzimidazolinone (1-EBIO) and cyclohexyl-[2-(3,5-dimethyl-pyrazol-1-yl)-6-methylpyrimidin-4-yl]-amine (CyPPA), the binding site for NS8593 has been assumed to be located in the C-terminal region, in which these channels interact with their Ca(2+) sensor calmodulin. However, by using a progressive chimeric approach, we were able to localize the site-of-action of NS8593 to the K(Ca)2 pore. For example, when we transferred the C terminus from the NS8593-insensitive intermediate-conductance K(Ca)3.1 channel to K(Ca)2.3, the chimeric channel remained as sensitive to NS8593 as wild-type K(Ca)2.3. In contrast, when we transferred the K(Ca)2.3 pore to K(Ca)3.1, the channel became sensitive to NS8593. Using site-directed mutagenesis, we subsequently identified two specific residues in the inner vestibule of K(Ca)2.3 (Ser507 and Ala532) that determined the effect of NS8593. Mutation of these residues to the corresponding residues in K(Ca)3.1 (Thr250 and Val275) made K(Ca)2.3 insensitive to NS8593, whereas introduction of serine and alanine into K(Ca)3.1 was sufficient to render this channel highly sensitive to NS8593. It is noteworthy that the same two residue positions have been found previously to mediate sensitivity of K(Ca)3.1 to clotrimazole and 1-[(2-chlorophenyl)diphenylmethyl]-1H-pyrazole (TRAM-34). The location of Ser507 in the pore-loop near the selectivity filter and Ala532 in an adjacent position in S6 are within the region predicted to contain the K(Ca)2 channel gate. Hence, we propose that NS8593-mediated gating modulation occurs via interaction with gating structures at a position deep within the inner pore vestibule.

Capacitance, charge dynamics, and electrolyte-surface interactions in functionalized carbide-derived carbon electrodes

DOE PAGES

Dyatkin, Boris; Mamontov, Eugene; Cook, Kevin M.; ...

2015-12-24

Our study analyzed the dynamics of ionic liquid electrolyte inside of defunctionalized, hydrogenated, and aminated pores of carbide-derived carbon supercapacitor electrodes. The approach tailors surface functionalities and tunes nanoporous structures to decouple the influence of pore wall composition on capacitance, ionic resistance, and long-term cyclability. Moreover, quasi-elastic neutron scattering probes the self-diffusion properties and electrode-ion interactions of electrolyte molecules confined in functionalized pores. Room-temperature ionic liquid interactions in confined pores are strongest when the hydrogen-containing groups are present on the surface. This property translates into higher capacitance and greater ion transport through pores during electrochemical cycling. Aminated pores, unlike hydrogenatedmore » pores, do not favorably interact with ionic liquid ions and, subsequently, are outperformed by defunctionalized surfaces.« less

Interaction of gases with lunar materials. [analysis of lunar samples from Apollo 17 flight

NASA Technical Reports Server (NTRS)

Holmes, H. F.; Fuller, E. L., Jr.; Gammage, R. B.

1974-01-01

The surface chemistry of Apollo 17 lunar fines samples 74220 (the orange soil) and 74241 (the gray control soil) has been studied by measuring the adsorption of nitrogen, argon, and oxygen (all at 77 K) and also water vapor (at 20 or 22 C). In agreement with results for samples from other missions, both samples had low initial specific surface areas, consisted of nonporous particles, and were attacked by water vapor at high relative pressure to give an increased specific surface area and create a pore system which gave rise to a capillary condensation hysteresis loop in the adsorption isotherms. In contrast to previous samples, both of the Apollo 17 soils were partially hydrophobic in their initial interaction with water vapor (both samples were completely hydrophilic after the reaction with water). The results are consistent with formation at high temperatures without subsequent exposure to significant amounts of water.

Pore structure characterization of Chang-7 tight sandstone using MICP combined with N2GA techniques and its geological control factors

NASA Astrophysics Data System (ADS)

Cao, Zhe; Liu, Guangdi; Zhan, Hongbin; Li, Chaozheng; You, Yuan; Yang, Chengyu; Jiang, Hang

2016-11-01

Understanding the pore networks of unconventional tight reservoirs such as tight sandstones and shales is crucial for extracting oil/gas from such reservoirs. Mercury injection capillary pressure (MICP) and N2 gas adsorption (N2GA) are performed to evaluate pore structure of Chang-7 tight sandstone. Thin section observation, scanning electron microscope, grain size analysis, mineral composition analysis, and porosity measurement are applied to investigate geological control factors of pore structure. Grain size is positively correlated with detrital mineral content and grain size standard deviation while negatively related to clay content. Detrital mineral content and grain size are positively correlated with porosity, pore throat radius and withdrawal efficiency and negatively related to capillary pressure and pore-to-throat size ratio; while interstitial material is negatively correlated with above mentioned factors. Well sorted sediments with high debris usually possess strong compaction resistance to preserve original pores. Although many inter-crystalline pores are produced in clay minerals, this type of pores is not the most important contributor to porosity. Besides this, pore shape determined by N2GA hysteresis loop is consistent with SEM observation on clay inter-crystalline pores while BJH pore volume is positively related with clay content, suggesting N2GA is suitable for describing clay inter-crystalline pores in tight sandstones.

Pore structure characterization of Chang-7 tight sandstone using MICP combined with N2GA techniques and its geological control factors

PubMed Central

Cao, Zhe; Liu, Guangdi; Zhan, Hongbin; Li, Chaozheng; You, Yuan; Yang, Chengyu; Jiang, Hang

2016-01-01

Understanding the pore networks of unconventional tight reservoirs such as tight sandstones and shales is crucial for extracting oil/gas from such reservoirs. Mercury injection capillary pressure (MICP) and N2 gas adsorption (N2GA) are performed to evaluate pore structure of Chang-7 tight sandstone. Thin section observation, scanning electron microscope, grain size analysis, mineral composition analysis, and porosity measurement are applied to investigate geological control factors of pore structure. Grain size is positively correlated with detrital mineral content and grain size standard deviation while negatively related to clay content. Detrital mineral content and grain size are positively correlated with porosity, pore throat radius and withdrawal efficiency and negatively related to capillary pressure and pore-to-throat size ratio; while interstitial material is negatively correlated with above mentioned factors. Well sorted sediments with high debris usually possess strong compaction resistance to preserve original pores. Although many inter-crystalline pores are produced in clay minerals, this type of pores is not the most important contributor to porosity. Besides this, pore shape determined by N2GA hysteresis loop is consistent with SEM observation on clay inter-crystalline pores while BJH pore volume is positively related with clay content, suggesting N2GA is suitable for describing clay inter-crystalline pores in tight sandstones. PMID:27830731

A Specific Two-pore Domain Potassium Channel Blocker Defines the Structure of the TASK-1 Open Pore*

PubMed Central

Streit, Anne K.; Netter, Michael F.; Kempf, Franca; Walecki, Magdalena; Rinné, Susanne; Bollepalli, Murali K.; Preisig-Müller, Regina; Renigunta, Vijay; Daut, Jürgen; Baukrowitz, Thomas; Sansom, Mark S. P.; Stansfeld, Phillip J.; Decher, Niels

2011-01-01

Two-pore domain potassium (K2P) channels play a key role in setting the membrane potential of excitable cells. Despite their role as putative targets for drugs and general anesthetics, little is known about the structure and the drug binding site of K2P channels. We describe A1899 as a potent and highly selective blocker of the K2P channel TASK-1. As A1899 acts as an open-channel blocker and binds to residues forming the wall of the central cavity, the drug was used to further our understanding of the channel pore. Using alanine mutagenesis screens, we have identified residues in both pore loops, the M2 and M4 segments, and the halothane response element to form the drug binding site of TASK-1. Our experimental data were used to validate a K2P open-pore homology model of TASK-1, providing structural insights for future rational design of drugs targeting K2P channels. PMID:21362619

Functional Architecture of the Cytoplasmic Entrance to the Cystic Fibrosis Transmembrane Conductance Regulator Chloride Channel Pore*

PubMed Central

El Hiani, Yassine; Linsdell, Paul

2015-01-01

As an ion channel, the cystic fibrosis transmembrane conductance regulator must form a continuous pathway for the movement of Cl− and other anions between the cytoplasm and the extracellular solution. Both the structure and the function of the membrane-spanning part of this pathway are well defined. In contrast, the structure of the pathway that connects the cytoplasm to the membrane-spanning regions is unknown, and functional roles for different parts of the protein forming this pathway have not been described. We used patch clamp recording and substituted cysteine accessibility mutagenesis to identify positively charged amino acid side chains that attract cytoplasmic Cl− ions to the inner mouth of the pore. Our results indicate that the side chains of Lys-190, Arg-248, Arg-303, Lys-370, Lys-1041, and Arg-1048, located in different intracellular loops of the protein, play important roles in the electrostatic attraction of Cl− ions. Mutation and covalent modification of these residues have charge-dependent effects on the rate of Cl− permeation, demonstrating their functional role in maximization of Cl− flux. Other nearby positively charged side chains were not involved in electrostatic interactions with Cl−. The location of these Cl−-attractive residues suggests that cytoplasmic Cl− ions enter the pore via a lateral portal located between the cytoplasmic extensions to the fourth and sixth transmembrane helices; a secondary, functionally less relevant portal might exist between the extensions to the 10th and 12th transmembrane helices. These results define the cytoplasmic mouth of the pore and show how it attracts Cl− ions from the cytoplasm. PMID:25944907

A hydrophobic gate in an ion channel: the closed state of the nicotinic acetylcholine receptor

NASA Astrophysics Data System (ADS)

Beckstein, Oliver; Sansom, Mark S. P.

2006-06-01

The nicotinic acetylcholine receptor (nAChR) is the prototypic member of the 'Cys-loop' superfamily of ligand-gated ion channels which mediate synaptic neurotransmission, and whose other members include receptors for glycine, γ-aminobutyric acid and serotonin. Cryo-electron microscopy has yielded a three-dimensional structure of the nAChR in its closed state. However, the exact nature and location of the channel gate remains uncertain. Although the transmembrane pore is constricted close to its center, it is not completely occluded. Rather, the pore has a central hydrophobic zone of radius about 3 Å. Model calculations suggest that such a constriction may form a hydrophobic gate, preventing movement of ions through a channel. We present a detailed and quantitative simulation study of the hydrophobic gating model of the nicotinic receptor, in order to fully evaluate this hypothesis. We demonstrate that the hydrophobic constriction of the nAChR pore indeed forms a closed gate. Potential of mean force (PMF) calculations reveal that the constriction presents a barrier of height about 10 kT to the permeation of sodium ions, placing an upper bound on the closed channel conductance of 0.3 pS. Thus, a 3 Å radius hydrophobic pore can form a functional barrier to the permeation of a 1 Å radius Na+ ion. Using a united-atom force field for the protein instead of an all-atom one retains the qualitative features but results in differing conductances, showing that the PMF is sensitive to the detailed molecular interactions.

Structural and functional analysis of an essential nucleoporin heterotrimer on the cytoplasmic face of the nuclear pore complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoshida, Kimihisa; Seo, Hyuk-Soo; Debler, Erik W.

2012-07-25

So far, only a few of the interactions between the {approx}30 nucleoporins comprising the modular structure of the nuclear pore complex have been defined at atomic resolution. Here we report the crystal structure, at 2.6 {angstrom} resolution, of a heterotrimeric complex, composed of fragments of three cytoplasmically oriented nucleoporins of yeast: Nup82, Nup116, and Nup159. Our data show that the Nup82 fragment, representing more than the N-terminal half of the molecule, folds into an extensively decorated, seven-bladed {beta}-propeller that forms the centerpiece of this heterotrimeric complex and anchors both a C-terminal fragment of Nup116 and the C-terminal tail of Nup159.more » Binding between Nup116 and Nup82 is mutually reinforced via two loops, one emanating from the Nup82 {beta}-propeller and the other one from the {beta}-sandwich fold of Nup116, each contacting binding pockets in their counterparts. The Nup82-Nup159 interaction occurs through an amphipathic {alpha}-helix of Nup159, which is cradled in a large hydrophobic groove that is generated from several large surface decorations of the Nup82 {beta}-propeller. Although Nup159 and Nup116 fragments bind to the Nup82 {beta}-propeller in close vicinity, there are no direct contacts between them, consistent with the noncooperative binding that was detected biochemically. Extensive mutagenesis delineated hot-spot residues for these interactions. We also showed that the Nup82 {beta}-propeller binds to other yeast Nup116 family members, Nup145N, Nup100 and to the mammalian homolog, Nup98. Notably, each of the three nucleoporins contains additional nuclear pore complex binding sites, distinct from those that were defined here in the heterotrimeric Nup82 {center_dot} Nup159 {center_dot} Nup116 complex.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manovic, V.; Anthony, E.J.; Loncarevic, D.

CaO-based looping cycles are promising processes for CO{sub 2} Capture from both syngas and flue gas. The technology is based on cyclical carbonation of CaO and regeneration of CaCO{sub 3} in a dual fluidized-bed reactor to produce a pure CO{sub 2} stream suitable for sequestration. Use of spent sorbent from CO{sub 2} looping cycles for SO{sub 2} capture is investigated. Three limestones were investigated: Kelly Rock (Canada), La Blanca (Spain), and Katowice (Poland, Upper Silesia). Carbonation/calcination cycles were performed in a tube furnace with both the original limestones and samples thermally pretreated for different times (i.e., sintered). The spent sorbentmore » samples were sulfated in a thermogravimetric analyzer (TGA). The changes in the resulting sorbent pore structure were then investigated using mercury porosimetry. It has been shown that the sulfation rates of both thermally pretreated and spent sorbent samples are lower in comparison with those of the original samples. However, final conversions of both spent and pretreated sorbents after longer sulfation time were comparable or higher than those observed for the original sorbents under comparable conditions. Maximum sulfation levels strongly depend on sorbent porosity and pore surface area. The results showed that spent sorbent samples from CO{sub 2} looping cycles can be used as sorbents for SO{sub 2} retention in cases where significant porosity loss does not occur during CO{sub 2} reaction cycles. In the case of spent Kelly Rock and Katowice samples, sorbent particles are practically uniformly sulfated, achieving final conversions that are determined by the total pore volume available for the bulky CaSO{sub 4} product.« less

Molecular basis of the interaction between gating modifier spider toxins and the voltage sensor of voltage-gated ion channels

NASA Astrophysics Data System (ADS)

Lau, Carus H. Y.; King, Glenn F.; Mobli, Mehdi

2016-09-01

Voltage-sensor domains (VSDs) are modular transmembrane domains of voltage-gated ion channels that respond to changes in membrane potential by undergoing conformational changes that are coupled to gating of the ion-conducting pore. Most spider-venom peptides function as gating modifiers by binding to the VSDs of voltage-gated channels and trapping them in a closed or open state. To understand the molecular basis underlying this mode of action, we used nuclear magnetic resonance to delineate the atomic details of the interaction between the VSD of the voltage-gated potassium channel KvAP and the spider-venom peptide VSTx1. Our data reveal that the toxin interacts with residues in an aqueous cleft formed between the extracellular S1-S2 and S3-S4 loops of the VSD whilst maintaining lipid interactions in the gaps formed between the S1-S4 and S2-S3 helices. The resulting network of interactions increases the energetic barrier to the conformational changes required for channel gating, and we propose that this is the mechanism by which gating modifier toxins inhibit voltage-gated ion channels.

Local electrostatic interactions determine the diameter of fusion pores

PubMed Central

Guček, Alenka; Jorgačevski, Jernej; Górska, Urszula; Rituper, Boštjan; Kreft, Marko; Zorec, Robert

2015-01-01

In regulated exocytosis vesicular and plasma membranes merge to form a fusion pore in response to stimulation. The nonselective cation HCN channels are involved in the regulation of unitary exocytotic events by at least 2 mechanisms. They can affect SNARE-dependent exocytotic activity indirectly, via the modulation of free intracellular calcium; and/or directly, by altering local cation concentration, which affects fusion pore geometry likely via electrostatic interactions. By monitoring membrane capacitance, we investigated how extracellular cation concentration affects fusion pore diameter in pituitary cells and astrocytes. At low extracellular divalent cation levels predominantly transient fusion events with widely open fusion pores were detected. However, fusion events with predominately narrow fusion pores were present at elevated levels of extracellular trivalent cations. These results show that electrostatic interactions likely help determine the stability of discrete fusion pore states by affecting fusion pore membrane composition. PMID:25835258

An intermolecular electrostatic interaction controls the prepore-to-pore transition in a cholesterol-dependent cytolysin.

PubMed

Wade, Kristin R; Hotze, Eileen M; Kuiper, Michael J; Morton, Craig J; Parker, Michael W; Tweten, Rodney K

2015-02-17

β-Barrel pore-forming toxins (βPFTs) form an obligatory oligomeric prepore intermediate before the formation of the β-barrel pore. The molecular components that control the critical prepore-to-pore transition remain unknown for βPFTs. Using the archetype βPFT perfringolysin O, we show that E183 of each monomer within the prepore complex forms an intermolecular electrostatic interaction with K336 of the adjacent monomer on completion of the prepore complex. The signal generated throughout the prepore complex by this interaction irrevocably commits it to the formation of the membrane-inserted giant β-barrel pore. This interaction supplies the free energy to overcome the energy barrier (determined here to be ∼ 19 kcal/mol) to the prepore-to-pore transition by the coordinated disruption of a critical interface within each monomer. These studies provide the first insight to our knowledge into the molecular mechanism that controls the prepore-to-pore transition for a βPFT.

Polymer translocation under time-dependent driving forces: resonant activation induced by attractive polymer-pore interactions.

PubMed

Ikonen, Timo; Shin, Jaeoh; Sung, Wokyung; Ala-Nissila, Tapio

2012-05-28

We study the driven translocation of polymers under time-dependent driving forces using N-particle Langevin dynamics simulations. We consider the force to be either sinusoidally oscillating in time or dichotomic noise with exponential correlation time, to mimic both plausible experimental setups and naturally occurring biological conditions. In addition, we consider both the case of purely repulsive polymer-pore interactions and the case with additional attractive polymer-pore interactions, typically occurring inside biological pores. We find that the nature of the interaction fundamentally affects the translocation dynamics. For the non-attractive pore, the translocation time crosses over to a fast translocation regime as the frequency of the driving force decreases. In the attractive pore case, because of a free energy well induced inside the pore, the translocation time can be a minimum at the optimal frequency of the force, the so-called resonant activation. In the latter case, we examine the effect of various physical parameters on the resonant activation, and explain our observations using simple theoretical arguments.

An intermolecular electrostatic interaction controls the prepore-to-pore transition in a cholesterol-dependent cytolysin

PubMed Central

Wade, Kristin R.; Hotze, Eileen M.; Kuiper, Michael J.; Morton, Craig J.; Parker, Michael W.; Tweten, Rodney K.

2015-01-01

β-Barrel pore-forming toxins (βPFTs) form an obligatory oligomeric prepore intermediate before the formation of the β-barrel pore. The molecular components that control the critical prepore-to-pore transition remain unknown for βPFTs. Using the archetype βPFT perfringolysin O, we show that E183 of each monomer within the prepore complex forms an intermolecular electrostatic interaction with K336 of the adjacent monomer on completion of the prepore complex. The signal generated throughout the prepore complex by this interaction irrevocably commits it to the formation of the membrane-inserted giant β-barrel pore. This interaction supplies the free energy to overcome the energy barrier (determined here to be ∼19 kcal/mol) to the prepore-to-pore transition by the coordinated disruption of a critical interface within each monomer. These studies provide the first insight to our knowledge into the molecular mechanism that controls the prepore-to-pore transition for a βPFT. PMID:25646411

Induction of autoimmune response to the extracellular loop of the HERG channel pore induces QTc prolongation in guinea‐pigs

PubMed Central

Fabris, Frank; Yue, Yuankun; Qu, Yongxia; Chahine, Mohamed; Sobie, Eric; Lee, Peng; Wieczorek, Rosemary; Jiang, Xian‐Cheng; Capecchi, Pier‐Leopoldo; Laghi‐Pasini, Franco; Lazzerini, Pietro‐Enea

2016-01-01

Key points Channelopathies of autoimmune origin are novel and are associated with corrected QT (QTc) prolongation and complex ventricular arrhythmias.We have recently demonstrated that anti‐SSA/Ro antibodies from patients with autoimmune diseases and with QTc prolongation on the ECG target the human ether‐à‐go‐go‐related gene (HERG) K+ channel by inhibiting the corresponding current, I Kr, at the pore region.Immunization of guinea‐pigs with a peptide (E‐pore peptide) corresponding to the extracellular loop region connecting the S5 and S6 segments of the HERG channel induces high titres of antibodies that inhibit I Kr, lengthen the action potential and cause QTc prolongation on the surface ECG. In addition, anti‐SSA/Ro‐positive sera from patients with connective tissue diseases showed high reactivity to the E‐pore peptide.The translational impact is the development of a peptide‐based approach for the diagnosis and treatment of autoimmune‐associated long QT syndrome. Abstract We recently demonstrated that anti‐SSA/52 kDa Ro antibodies (Abs) from patients with autoimmune diseases and corrected QT (QTc) prolongation directly target and inhibit the human ether‐à‐go‐go‐related gene (HERG) K+ channel at the extracellular pore (E‐pore) region, where homology with SSA/52 kDa Ro antigen was demonstrated. We tested the hypothesis that immunization of guinea‐pigs with a peptide corresponding to the E‐pore region (E‐pore peptide) will generate pathogenic inhibitory Abs and cause QTc prolongation. Guinea‐pigs were immunized with a 31‐amino‐acid peptide corresponding to the E‐pore region of HERG. On days 10–62 after immunization, ECGs were recorded and blood was sampled for the detection of E‐pore peptide Abs. Serum samples from patients with autoimmune diseases were evaluated for reactivity to E‐pore peptide by enzyme‐linked immunosorbent assay (ELISA), and histology was performed on hearts using Masson's Trichrome. Inhibition of the HERG channel was assessed by electrophysiology and by computational modelling of the human ventricular action potential. The ELISA results revealed the presence of high titres of E‐pore peptide Abs and significant QTc prolongation after immunization. High reactivity to E‐pore peptide was found using anti‐SSA/Ro Ab‐positive sera from patients with QTc prolongation. Histological data showed no evidence of fibrosis in immunized hearts. Simulations of simultaneous inhibition of repolarizing currents by anti‐SSA/Ro Ab‐positive sera showed the predominance of the HERG channel in controlling action potential duration and the QT interval. These results are the first to demonstrate that inhibitory Abs to the HERG E‐pore region induce QTc prolongation in immunized guinea‐pigs by targeting the HERG channel independently from fibrosis. The reactivity of anti‐SSA/Ro Ab‐positive sera from patients with connective tissue diseases with the E‐pore peptide opens novel pharmacotherapeutic avenues in the diagnosis and management of autoimmune‐associated QTc prolongation. PMID:27296897

Functional Architecture of the Cytoplasmic Entrance to the Cystic Fibrosis Transmembrane Conductance Regulator Chloride Channel Pore.

PubMed

El Hiani, Yassine; Linsdell, Paul

2015-06-19

As an ion channel, the cystic fibrosis transmembrane conductance regulator must form a continuous pathway for the movement of Cl(-) and other anions between the cytoplasm and the extracellular solution. Both the structure and the function of the membrane-spanning part of this pathway are well defined. In contrast, the structure of the pathway that connects the cytoplasm to the membrane-spanning regions is unknown, and functional roles for different parts of the protein forming this pathway have not been described. We used patch clamp recording and substituted cysteine accessibility mutagenesis to identify positively charged amino acid side chains that attract cytoplasmic Cl(-) ions to the inner mouth of the pore. Our results indicate that the side chains of Lys-190, Arg-248, Arg-303, Lys-370, Lys-1041, and Arg-1048, located in different intracellular loops of the protein, play important roles in the electrostatic attraction of Cl(-) ions. Mutation and covalent modification of these residues have charge-dependent effects on the rate of Cl(-) permeation, demonstrating their functional role in maximization of Cl(-) flux. Other nearby positively charged side chains were not involved in electrostatic interactions with Cl(-). The location of these Cl(-)-attractive residues suggests that cytoplasmic Cl(-) ions enter the pore via a lateral portal located between the cytoplasmic extensions to the fourth and sixth transmembrane helices; a secondary, functionally less relevant portal might exist between the extensions to the 10th and 12th transmembrane helices. These results define the cytoplasmic mouth of the pore and show how it attracts Cl(-) ions from the cytoplasm. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Change in desorption mechanism from pore blocking to cavitation with temperature for nitrogen in ordered silica with cagelike pores.

PubMed

Morishige, Kunimitsu; Tateishi, Masayoshi; Hirose, Fumi; Aramaki, Kenji

2006-10-24

To verify pore blocking controlled desorption in ink-bottle pores, we measured the temperature dependence of the adsorption-desorption isotherms of nitrogen on four kinds of KIT-5 samples with expanded cavities hydrothermally treated for different periods of time at 393 K. In the samples, almost spherical cavities are arranged in a face-centered cubic array and the cavities are connected through small channels. The pore size of the channels increased with an increase in the hydrothermal treatment time. At lower temperatures a steep desorption branch changed to a gradual one as the hydrothermal treatment was prolonged. For the sample hydrothermally treated only for 1 day, the rectangular hysteresis loop shrank gradually with increasing temperature while keeping its shape. The temperature dependence of the evaporation pressure observed was identical with that expected for cavitation-controlled desorption. On the other hand, for the samples hydrothermally treated for long times, the gradual desorption branch became a sharp one with increasing temperature. This strongly suggests that the desorption mechanism is altered from pore blocking to cavitation with temperature. Application of percolation theory to the pore blocking controlled desorption observed here is discussed.

Structural mechanisms of chaperone mediated protein disaggregation

PubMed Central

Sousa, Rui

2014-01-01

The ClpB/Hsp104 and Hsp70 classes of molecular chaperones use ATP hydrolysis to dissociate protein aggregates and complexes, and to move proteins through membranes. ClpB/Hsp104 are members of the AAA+ family of proteins which form ring-shaped hexamers. Loops lining the pore in the ring engage substrate proteins as extended polypeptides. Interdomain rotations and conformational changes in these loops coupled to ATP hydrolysis unfold and pull proteins through the pore. This provides a mechanism that progressively disrupts local secondary and tertiary structure in substrates, allowing these chaperones to dissociate stable aggregates such as β-sheet rich prions or coiled coil SNARE complexes. While the ClpB/Hsp104 mechanism appears to embody a true power-stroke in which an ATP powered conformational change in one protein is directly coupled to movement or structural change in another, the mechanism of force generation by Hsp70s is distinct and less well understood. Both active power-stroke and purely passive mechanisms in which Hsp70 captures spontaneous fluctuations in a substrate have been proposed, while a third proposed mechanism—entropic pulling—may be able to generate forces larger than seen in ATP-driven molecular motors without the conformational coupling required for a power-stroke. The disaggregase activity of these chaperones is required for thermotolerance, but unrestrained protein complex/aggregate dissociation is potentially detrimental. Disaggregating chaperones are strongly auto-repressed, and are regulated by co-chaperones which recruit them to protein substrates and activate the disaggregases via mechanisms involving either sequential transfer of substrate from one chaperone to another and/or simultaneous interaction of substrate with multiple chaperones. By effectively subjecting substrates to multiple levels of selection by multiple chaperones, this may insure that these potent disaggregases are only activated in the appropriate context. PMID:25988153

Role of Mex67-Mtr2 in the Nuclear Export of 40S Pre-Ribosomes

PubMed Central

Occhipinti, Laura; Kemmler, Stefan; Panse, Vikram G.

2012-01-01

Nuclear export of mRNAs and pre-ribosomal subunits (pre40S and pre60S) is fundamental to all eukaryotes. While genetic approaches in budding yeast have identified bona fide export factors for mRNAs and pre60S subunits, little is known regarding nuclear export of pre40S subunits. The yeast heterodimeric transport receptor Mex67-Mtr2 (TAP-p15 in humans) binds mRNAs and pre60S subunits in the nucleus and facilitates their passage through the nuclear pore complex (NPC) into the cytoplasm by interacting with Phe-Gly (FG)-rich nucleoporins that line its transport channel. By exploiting a combination of genetic, cell-biological, and biochemical approaches, we uncovered an unanticipated role of Mex67-Mtr2 in the nuclear export of 40S pre-ribosomes. We show that recruitment of Mex67-Mtr2 to pre40S subunits requires loops emanating from its NTF2-like domains and that the C-terminal FG-rich nucleoporin interacting UBA-like domain within Mex67 contributes to the transport of pre40S subunits to the cytoplasm. Remarkably, the same loops also recruit Mex67-Mtr2 to pre60S subunits and to the Nup84 complex, the respective interactions crucial for nuclear export of pre60S subunits and mRNAs. Thus Mex67-Mtr2 is a unique transport receptor that employs a common interaction surface to participate in the nuclear export of both pre-ribosomal subunits and mRNAs. Mex67-Mtr2 could engage a regulatory crosstalk among the three major export pathways for optimal cellular growth and proliferation. PMID:22956913

The homogeneity of levitation force in single domain YBCO bulk

NASA Astrophysics Data System (ADS)

Zhou, Keran; Xu, Ke-Xi; Wu, Xing-da; Pan, Peng-jun

2007-11-01

The pellet homogeneity of levitation force versus the position in comparison to the seed or to the top surface has been studied in the entire volume of a single domain YBa 2Cu 3O 7-δ bulk sample processed by the top-seeded melt texturing growth (TSMTG). It is found that the levitation forces increase and peak at a depth of 3 mm from the top of the sample at liquid nitrogen temperature. In other words, the second disk has the largest levitation force density. The phenomenon can be interpreted by the interaction between the microcracks or pores produced by crystal growth and the oxygenation. We propose a model in which Y211 particles distribution leading to microcracks and pores reduces the effective induced shielding current loops (ISCL) and increases the perimeters of ISCL. This corresponds to a decrease in the grain size and results in greatly reduced levitation forces of the bottom of the bulk. From the research, we know that the density of the YBCO bulk is also an important parameter for the levitation properties. The result is very attractive and useful for the fundamental studies and fabrication of TSMTG YBa 2Cu 3O 7-δ bulk.

The first transmembrane domain (TM1) of β2-subunit binds to the transmembrane domain S1 of α-subunit in BK potassium channels

PubMed Central

Morera, Francisco J.; Alioua, Abderrahmane; Kundu, Pallob; Salazar, Marcelo; Gonzalez, Carlos; Martinez, Agustin D.; Stefani, Enrico; Toro, Ligia; Latorre, Ramon

2012-01-01

The BK channel is one of the most broadly expressed ion channels in mammals. In many tissues, the BK channel pore-forming α-subunit is associated to an auxiliary β-subunit that modulates the voltage- and Ca2+-dependent activation of the channel. Structural components present in β-subunits that are important for the physical association with the α-subunit are yet unknown. Here, we show through co-immunoprecipitation that the intracellular C-terminus, the second transmembrane domain (TM2) and the extracellular loop of the β2-subunit are dispensable for association with the α-subunit pointing transmembrane domain 1 (TM1) as responsible for the interaction. Indeed, the TOXCAT assay for transmembrane protein–protein interactions demonstrated for the first time that TM1 of the β2-subunit physically binds to the transmembrane S1 domain of the α-subunit. PMID:22710124

Nucleation and hysteresis of vapor-liquid phase transitions in confined spaces: effects of fluid-wall interaction.

PubMed

Men, Yumei; Yan, Qingzhao; Jiang, Guangfeng; Zhang, Xianren; Wang, Wenchuan

2009-05-01

In this work, we propose a method to stabilize a nucleus in the framework of lattice density-functional theory (LDFT) by imposing a suitable constraint. Using this method, the shape of critical nucleus and height of the nucleation barrier can be determined without using a predefined nucleus as input. As an application of this method, we study the nucleation behavior of vapor-liquid transition in nanosquare pores with infinite length and relate the observed hysteresis loop on an adsorption isotherm to the nucleation mechanism. According to the dependence of hysteresis and the nucleation mechanism on the fluid-wall interaction, w , in this work, we have classified w into three regions ( w>0.9 , 0.1< or =w< or =0.9 , and w<0.1 ), which are denoted as strongly, moderately, and weakly attractive fluid-wall interaction, respectively. The dependence of hysteresis on the fluid-wall interaction is interpreted by the different nucleation mechanisms. Our constrained LDFT calculations also show that the different transition paths may induce different nucleation behaviors. The transition path dependence should be considered if morphological transition of nuclei exists during a nucleation process.

Inter-subunit interactions across the upper voltage sensing-pore domain interface contribute to the concerted pore opening transition of Kv channels.

PubMed

Shem-Ad, Tzilhav; Irit, Orr; Yifrach, Ofer

2013-01-01

The tight electro-mechanical coupling between the voltage-sensing and pore domains of Kv channels lies at the heart of their fundamental roles in electrical signaling. Structural data have identified two voltage sensor pore inter-domain interaction surfaces, thus providing a framework to explain the molecular basis for the tight coupling of these domains. While the contribution of the intra-subunit lower domain interface to the electro-mechanical coupling that underlies channel opening is relatively well understood, the contribution of the inter-subunit upper interface to channel gating is not yet clear. Relying on energy perturbation and thermodynamic coupling analyses of tandem-dimeric Shaker Kv channels, we show that mutation of upper interface residues from both sides of the voltage sensor-pore domain interface stabilizes the closed channel state. These mutations, however, do not affect slow inactivation gating. We, moreover, find that upper interface residues form a network of state-dependent interactions that stabilize the open channel state. Finally, we note that the observed residue interaction network does not change during slow inactivation gating. The upper voltage sensing-pore interaction surface thus only undergoes conformational rearrangements during channel activation gating. We suggest that inter-subunit interactions across the upper domain interface mediate allosteric communication between channel subunits that contributes to the concerted nature of the late pore opening transition of Kv channels.

Active Region Formation and Subsurface Structure

NASA Astrophysics Data System (ADS)

Stein, F.; Nordlund, Robert A.

2016-10-01

We present results from emerging magnetic flux simulations showing how several different active regions form and their very different subsurface structures. The simulations assumed an infinite sheet of uniform, untwisted, horizontal field advected into the computational domain by inflows at a depth of 20 Mm. Results from two different horizontal field strengths, 1 and 5 kG, will be presented. Convective up and down flows buckle the horizontal field into Omega and U loops. Upflows and magnetic buoyancy carry the field toward the surface, while fast downflows pin down the field. Small (granular) convective motions, near the surface, shred the emerging field into fine filaments that emerge as the observed "pepper and salt" pattern. The large (supergranular) motions, at depth, keep the overall loop structure intact, so that as the overall omega-loop emerges through the surface the opposite polarity fields counter-stream into large unipolar flux concentrations producing first pores which then coalesce into spots. These tend to be located over the supergranular downflow lanes near the bottom of the domain. The pores and spots exhibit a great variety of subsurface field structures - from monolithic but twisted bundles to intertwined separate spaghetti sturctures. We will show movies of the surface evolution of the field and emergent continuum intensity and of the subsurface evolution of the magnetic field lines.

Isothermal Oxidation of Magnetite to Hematite in Air and Cyclic Reduction/Oxidation Under Carbon Looping Combustion Conditions

NASA Astrophysics Data System (ADS)

Simmonds, Tegan; Hayes, Peter C.

2017-12-01

In the carbon looping combustion process the oxygen carrier is regenerated through oxidation in air; this process has been simulated by the oxidation of dense synthetic magnetite for selected temperatures and times. The oxidation of magnetite in air is shown to occur through the formation of dense hematite layers on the particle surface. This dense hematite forms through lath type shear transformations or solid-state diffusion through the product layer. Cyclic reduction in CO-CO2/oxidation in air of hematite single crystals has been carried out under controlled laboratory conditions at 1173 K (900 °C). It has been shown that the initial reduction step is critical to determining the product microstructure, which consists of gas pore dendrites in the magnetite matrix with blocky hematite formed on the pore surfaces. The progressive growth of the magnetite layer with the application of subsequent cycles appears to continue until no original hematite remains, after which physical disintegration of the particles takes place.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Xin; Chen, Hao; Shaffer, Paul L.

Ivermectin acts as a positive allosteric modulator of several Cys-loop receptors including the glutamate-gated chloride channels (GluCls), γ-aminobutyric acid receptors (GABA ARs), glycine receptors (GlyRs), and neuronal α7-nicotinic receptors (α7 nAChRs). The crystal structure of Caenorhabditis elegans GluCl complexed with ivermectin revealed the details of its ivermectin binding site. Although the electron microscopy structure of zebrafish GlyRα1 complexed with ivermectin demonstrated a similar binding orientation, detailed structural information on the ivermectin binding and pore opening for Cys-loop receptors in vertebrates has been elusive. Here we present the crystal structures of human GlyRα3 in complex with ivermectin at 2.85 and 3.08more » Å resolution. Our structures allow us to explore in detail the molecular recognition of ivermectin by GlyRs, GABA ARs, and α7 nAChRs. Comparisons with previous structures reveal how the ivermectin binding expands the ion channel pore. Our results hold promise in structure-based design of GlyR modulators for the treatment of neuropathic pain.« less

Polymeric heat pipe wick

NASA Technical Reports Server (NTRS)

Seidenberg, Benjamin

1988-01-01

A wick for use in a capillary loop pump heat pipe is described. The wick material is an essentially uniformly porous, permeable, open-cell, polyethylene thermoplastic foam having an ultrahigh average molecular weight of from approximately 1 to 5 million, and an average pore size of about 10 to 12 microns. A representative material having these characteristics is POREX UF, which has an average molecular weight of about 3 million. This material is fully compatible with the FREONs and anhydrous ammonia and allows for the use of these very efficient working fluids in capillary loops.

Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.

PubMed

Golebiowski, Jérôme; Antonczak, Serge; Fernandez-Carmona, Juan; Condom, Roger; Cabrol-Bass, Daniel

2004-12-01

Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the loop of an RNA in complementary interaction with HIV-1 TAR. The simulations reveal that the mismatch GA base, mediated by a water molecule, leads to a complex that presents the best compromise between flexibility and energetic contributions. The mismatch CU base pair, in spite of the presence of an inserted water molecule, is too short to achieve a tight interaction at the closing-loop junction and seems to force TAR to reorganize upon binding. An energetic analysis has allowed us to quantify the strength of the interactions of the closing and the loop-loop pairs throughout the simulations. Although the water-mediated GA closing base pair presents an interaction energy similar to that found on fully geometry-optimized structure, the water-mediated CU closing base pair energy interaction reaches less than half the optimal value.

A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer.

PubMed

Tieleman, D P; Berendsen, H J

1998-06-01

In this paper we study the properties of pores formed by OmpF porin from Escherichia coli, based on a molecular dynamics simulation of the OmpF trimer, 318 palmitoyl-oleoyl-phosphatidylethanolamine lipids, 27 Na+ ions, and 12,992 water molecules. After equilibration and a nanosecond production run, the OmpF trimer exhibits a C-alpha root mean square deviation from the crystal structure of 0.23 nm and a stable secondary structure. No evidence is found for large-scale motions of the L3 loop. We investigate the pore dimensions, conductance, and the properties of water inside the pore. This water forms a complicated pattern, even when averaged over 1 ns of simulation time. Around the pore constriction zone the water dipoles are highly structured in the plane of the membrane, oriented by the strong transversal electric field. In addition, there is a net orientation along the pore axis pointing from the extracellular to the intracellular side of the bilayer. The diffusion coefficients of water inside the pore are greatly reduced compared to bulk. We compare our results to results from model pores (Breed et al., 1996. Biophys. J. 70:1 643-1 661; Sansom et al. 1997. Biophys. J. 73:2404-241 5) and discuss implications for further theoretical work.

Molecular dynamics simulations of electrostatics and hydration distributions around RNA and DNA motifs

NASA Astrophysics Data System (ADS)

Marlowe, Ashley E.; Singh, Abhishek; Semichaevsky, Andrey V.; Yingling, Yaroslava G.

2009-03-01

Nucleic acid nanoparticles can self-assembly through the formation of complementary loop-loop interactions or stem-stem interactions. Presence and concentration of ions can significantly affect the self-assembly process and the stability of the nanostructure. In this presentation we use explicit molecular dynamics simulations to examine the variations in cationic distributions and hydration environment around DNA and RNA helices and loop-loop interactions. Our simulations show that the potassium and sodium ionic distributions are different around RNA and DNA motifs which could be indicative of ion mediated relative stability of loop-loop complexes. Moreover in RNA loop-loop motifs ions are consistently present and exchanged through a distinct electronegative channel. We will also show how we used the specific RNA loop-loop motif to design a RNA hexagonal nanoparticle.

Pom121 links two essential subcomplexes of the nuclear pore complex core to the membrane

PubMed Central

Mitchell, Jana M.; Mansfeld, Jörg; Capitanio, Juliana; Kutay, Ulrike

2010-01-01

Nuclear pore complexes (NPCs) control the movement of molecules across the nuclear envelope (NE). We investigated the molecular interactions that exist at the interface between the NPC scaffold and the pore membrane. We show that key players mediating these interactions in mammalian cells are the nucleoporins Nup155 and Nup160. Nup155 depletion massively alters NE structure, causing a dramatic decrease in NPC numbers and the improper targeting of membrane proteins to the inner nuclear membrane. The role of Nup155 in assembly is likely closely linked to events at the membrane as we show that Nup155 interacts with pore membrane proteins Pom121 and NDC1. Furthermore, we demonstrate that the N terminus of Pom121 directly binds the β-propeller regions of Nup155 and Nup160. We propose a model in which the interactions of Pom121 with Nup155 and Nup160 are predicted to assist in the formation of the nuclear pore and the anchoring of the NPC to the pore membrane. PMID:20974814

Molecular simulation of fluid adsorption in buckytubes and MCM-41

NASA Astrophysics Data System (ADS)

Maddox, M. W.; Gubbins, K. E.

1994-11-01

We report grand canonical Monte Carlo (GCMC) molecular-simulation studies of argon and nitrogen in models of two novel adsorbents, buckytubes and MCM-41. Buckytubes are monodisperse carbon tubes with internal diameters of 1 5 nm and a regular pore structure. MCM-41 is one member of a new family of highly uniform mesoporous aluminosilicates produced by Mobil. The pore size of MCM-41 can be accurately controlled within the range 1.5-I.0 nm. The adsorption of argon in a buckytube and the adsorption of nitrogen in two different MCM-41 pores are studied at 77 K. Both fluids are modeled as Lennard-Jones spheres. and an averaged fluid-wall potential, dependent only on the distance of the adsorbed molecule from the center of the tube or pore is used. Isotherms and isosteric heats are calculated. Layering transitions and a hysteresis loop are observed for the buckytube and good agreement is found between simulated and experimental isotherms for the MCM-41 systems.

Surface area and pore size characteristics of nanoporous gold subjected to thermal, mechanical, or surface modification studied using gas adsorption isotherms, cyclic voltammetry, thermogravimetric analysis, and scanning electron microscopy

PubMed Central

Tan, Yih Horng; Davis, Jason A.; Fujikawa, Kohki; Ganesh, N. Vijaya; Demchenko, Alexei V.

2012-01-01

Nitrogen adsorption/desorption isotherms are used to investigate the Brunauer, Emmett, and Teller (BET) surface area and Barrett-Joyner-Halenda (BJH) pore size distribution of physically modified, thermally annealed, and octadecanethiol functionalized np-Au monoliths. We present the full adsorption-desorption isotherms for N2 gas on np-Au, and observe type IV isotherms and type H1 hysteresis loops. The evolution of the np-Au under various thermal annealing treatments was examined using scanning electron microscopy (SEM). The images of both the exterior and interior of the thermally annealed np-Au show that the porosity of all free standing np-Au structures decreases as the heat treatment temperature increases. The modification of the np-Au surface with a self-assembled monolayer (SAM) of C18-SH (coverage of 2.94 × 1014 molecules cm−2 based from the decomposition of the C18-SH using thermogravimetric analysis (TGA)), was found to reduce the strength of the interaction of nitrogen gas with the np-Au surface, as reflected by a decrease in the ‘C’ parameter of the BET equation. From cyclic voltammetry studies, we found that the surface area of the np-Au monoliths annealed at elevated temperatures followed the same trend with annealing temperature as found in the BET surface area study and SEM morphology characterization. The study highlights the ability to control free-standing nanoporous gold monoliths with high surface area, and well-defined, tunable pore morphology. PMID:22822294

Te homogeneous precipitation in Ge dislocation loop vicinity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perrin Toinin, J.; Portavoce, A., E-mail: alain.portavoce@im2np.fr; Texier, M.

2016-06-06

High resolution microscopies were used to study the interactions of Te atoms with Ge dislocation loops, after a standard n-type doping process in Ge. Te atoms neither segregate nor precipitate on dislocation loops, but form Te-Ge clusters at the same depth as dislocation loops, in contradiction with usual dopant behavior and thermodynamic expectations. Atomistic kinetic Monte Carlo simulations show that Te atoms are repulsed from dislocation loops due to elastic interactions, promoting homogeneous Te-Ge nucleation between dislocation loops. This phenomenon is enhanced by coulombic interactions between activated Te{sup 2+} or Te{sup 1+} ions.

Guest–host interactions of a rigid organic molecule in porous silica frameworks

PubMed Central

Wu, Di; Hwang, Son-Jong; Zones, Stacey I.; Navrotsky, Alexandra

2014-01-01

Molecular-level interactions at organic–inorganic interfaces play crucial roles in many fields including catalysis, drug delivery, and geological mineral precipitation in the presence of organic matter. To seek insights into organic–inorganic interactions in porous framework materials, we investigated the phase evolution and energetics of confinement of a rigid organic guest, N,N,N-trimethyl-1-adamantammonium iodide (TMAAI), in inorganic porous silica frameworks (SSZ-24, MCM-41, and SBA-15) as a function of pore size (0.8 nm to 20.0 nm). We used hydrofluoric acid solution calorimetry to obtain the enthalpies of interaction between silica framework materials and TMAAI, and the values range from −56 to −177 kJ per mole of TMAAI. The phase evolution as a function of pore size was investigated by X-ray diffraction, IR, thermogravimetric differential scanning calorimetry, and solid-state NMR. The results suggest the existence of three types of inclusion depending on the pore size of the framework: single-molecule confinement in a small pore, multiple-molecule confinement/adsorption of an amorphous and possibly mobile assemblage of molecules near the pore walls, and nanocrystal confinement in the pore interior. These changes in structure probably represent equilibrium and minimize the free energy of the system for each pore size, as indicated by trends in the enthalpy of interaction and differential scanning calorimetry profiles, as well as the reversible changes in structure and mobility seen by variable temperature NMR. PMID:24449886

Ceramic heat pipe wick

NASA Technical Reports Server (NTRS)

Seidenberg, Benjamin (Inventor); Swanson, Theodore (Inventor)

1989-01-01

A wick for use in a capillary loop pump heat pipe is disclosed. The wick material is an essentially uniformly porous, permeable, open-cell, silicon dioxide/aluminum oxide inorganic ceramic foam having a silica fiber ratio, by weight, of about 78 to 22, respectively, a density of 6 lbs/cu ft, and an average pore size of less than 5 microns. A representative material having these characteristics is Lockheed Missile and Space Company, Inc.'s HTP 6-22. This material is fully compatible with the freons and anhydrous ammonia and allows for the use of these very efficient working fluids, and others, in capillary loops.

PolyA Single Strand DNA Translocation Through an Alpha-Hemolysin Pore Stem

NASA Technical Reports Server (NTRS)

OKeeffe, James; Cozmuta, Ioana; Stolc, Viktor

2003-01-01

A new model for the polymer-pore interaction energy is introduced, based on an atomic-scale description of coulombic polymer-pore interaction. The enhanced drift velocity, experimentally observed for short polymers, is successfully accounted for, using this interaction energy model. For R/R(sub 0)>4 (R(sub 0)=7 angstroms) the translocation velocity approaches the free space drift velocity v(sub 0). This motivates the need to appropriately derivatize artificial nanopores, where R>R(sub 0).

Structure insight of GSDMD reveals the basis of GSDMD autoinhibition in cell pyroptosis

PubMed Central

Kuang, Siyun; Zheng, Jun; Yang, Hui; Li, Suhua; Duan, Shuyan; Shen, Yanfang; Ji, Chaoneng; Gan, Jianhua; Xu, Xue-Wei; Li, Jixi

2017-01-01

Recent findings have revealed that the protein gasdermin D (GSDMD) plays key roles in cell pyroptosis. GSDMD binds lipids and forms pore structures to induce pyroptosis upon microbial infection and associated danger signals. However, detailed structural information for GSDMD remains unknown. Here, we report the crystal structure of the C-terminal domain of human GSDMD (GSDMD-C) at 2.64-Å resolution. The first loop on GSDMD-C inserts into the N-terminal domain (GSDMD-N), which helps stabilize the conformation of the full-length GSDMD. Substitution of this region by a short linker sequence increased levels of cell death. Mutants F283A and F283R can increase protein heterogeneity in vitro and are capable of undergoing cell pyroptosis in 293T cells. The small-angle X-ray–scattering envelope of human GSDMD is consistent with the modeled GSDMD structure and mouse GSDMA3 structure, which suggests that GSDMD adopts an autoinhibited conformation in solution. The positive potential surface of GSDMD-N covered by GSDMD-C is exposed after being released from the autoinhibition state and can form high-order oligomers via a charge–charge interaction. Furthermore, by mapping different regions of GSDMD, we determined that one short segment is sufficient to kill bacteria in vitro and can efficiently inhibit cell growth in Escherichia coli and Mycobacterium Smegmatis. These findings reveal that GSDMD-C acts as an auto-inhibition executor and GSDMD-N could form pore structures via a charge–charge interaction upon cleavage by caspases during cell pyroptosis. PMID:28928145

Structure insight of GSDMD reveals the basis of GSDMD autoinhibition in cell pyroptosis.

PubMed

Kuang, Siyun; Zheng, Jun; Yang, Hui; Li, Suhua; Duan, Shuyan; Shen, Yanfang; Ji, Chaoneng; Gan, Jianhua; Xu, Xue-Wei; Li, Jixi

2017-10-03

Recent findings have revealed that the protein gasdermin D (GSDMD) plays key roles in cell pyroptosis. GSDMD binds lipids and forms pore structures to induce pyroptosis upon microbial infection and associated danger signals. However, detailed structural information for GSDMD remains unknown. Here, we report the crystal structure of the C-terminal domain of human GSDMD (GSDMD-C) at 2.64-Å resolution. The first loop on GSDMD-C inserts into the N-terminal domain (GSDMD-N), which helps stabilize the conformation of the full-length GSDMD. Substitution of this region by a short linker sequence increased levels of cell death. Mutants F283A and F283R can increase protein heterogeneity in vitro and are capable of undergoing cell pyroptosis in 293T cells. The small-angle X-ray-scattering envelope of human GSDMD is consistent with the modeled GSDMD structure and mouse GSDMA3 structure, which suggests that GSDMD adopts an autoinhibited conformation in solution. The positive potential surface of GSDMD-N covered by GSDMD-C is exposed after being released from the autoinhibition state and can form high-order oligomers via a charge-charge interaction. Furthermore, by mapping different regions of GSDMD, we determined that one short segment is sufficient to kill bacteria in vitro and can efficiently inhibit cell growth in Escherichia coli and Mycobacterium Smegmatis These findings reveal that GSDMD-C acts as an auto-inhibition executor and GSDMD-N could form pore structures via a charge-charge interaction upon cleavage by caspases during cell pyroptosis.

Clostridium perfringens Enterotoxin Interacts with Claudins via Electrostatic Attraction*

PubMed Central

Kimura, Jun; Abe, Hiroyuki; Kamitani, Shigeki; Toshima, Hirono; Fukui, Aya; Miyake, Masami; Kamata, Yoichi; Sugita-Konishi, Yoshiko; Yamamoto, Shigeki; Horiguchi, Yasuhiko

2010-01-01

Clostridium perfringens enterotoxin (CPE), a causative agent of food poisoning, is a pore-forming toxin disrupting the selective permeability of the plasma membrane of target cells, resulting in cell death. We previously identified claudin as the cell surface receptor for CPE. Claudin, a component of tight junctions, is a tetratransmembrane protein and constitutes a large family of more than 20 members, not all of which serve as the receptor for CPE. The mechanism by which the toxin distinguishes the sensitive claudins is unknown. In this study, we localized the region of claudin responsible for interaction with CPE to the C-terminal part of the second extracellular loop and found that the isoelectric point of this region in sensitive claudins was higher than insensitive claudins. Amino acid substitutions to lower the pI resulted in reduced sensitivity to CPE among sensitive claudins, whereas substitutions to raise the pI endowed CPE-insensitive claudins with sensitivity. The steric structure of the claudin-binding domain of CPE reveals an acidic cleft surrounded by Tyr306, Tyr310, Tyr312, and Leu315, which were reported to be essential for interaction with the sensitive claudins. These results imply that an electrostatic attraction between the basic claudin region and the acidic CPE cleft is involved in their interaction. PMID:19903817

Real-time sensing of epithelial cell-cell and cell-substrate interactions by impedance spectroscopy on porous substrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mondal, D.; RoyChaudhuri, C., E-mail: chirosreepram@yahoo.com; Pal, D.

2015-07-28

Oxidized porous silicon (PS) is a common topographical biocompatible substrate that potentially provides a distinct in vitro environment for better understanding of in vivo behavior. But in the reported studies on oxidized PS, cell-cell and cell-substrate interactions have been detected only by fluorescent labeling. This paper is the first attempt to investigate real-time sensing of these interactions on HaCaT cells by label-free impedance spectroscopy on oxidized PS of two pore diameters (50 and 500 nm). One of the major requirements for successful impedance spectroscopy measurement is to restrict the channeling of electric field lines through the pores. To satisfy this criterion,more » we have designed the pore depths after analyzing the penetration of the medium by using computational fluid dynamics simulation. A distributed electrical model was also developed for estimating the various cellular attributes by considering a pseudorandom distribution of pores. It is observed from the impedance measurements and from the model that the proliferation rate increases for 50 nm pores but decreases for 500 nm pores compared to that for planar substrates. The rate of decrease in cell substrate separation (h) in the initial stage is more than the rate of increase in cell-cell junction resistance (R{sub b}) corresponding to the initial adhesion phase of cells. It is observed that R{sub b} and h are higher for 50 nm pores than those for planar substrates, corresponding to the fact that substrates more conducive toward cell adhesion encourage cell-cell interactions than direct cell-substrate interactions. Thus, the impedance spectroscopy coupled with the proposed theoretical framework for PS substrates can sense and quantify the cellular interactions.« less

Modeling failure in brittle porous ceramics

NASA Astrophysics Data System (ADS)

Keles, Ozgur

Brittle porous materials (BPMs) are used for battery, fuel cell, catalyst, membrane, filter, bone graft, and pharmacy applications due to the multi-functionality of their underlying porosity. However, in spite of its technological benefits the effects of porosity on BPM fracture strength and Weibull statistics are not fully understood--limiting a wider use. In this context, classical fracture mechanics was combined with two-dimensional finite element simulations not only to account for pore-pore stress interactions, but also to numerically quantify the relationship between the local pore volume fraction and fracture statistics. Simulations show that even the microstructures with the same porosity level and size of pores differ substantially in fracture strength. The maximum reliability of BPMs was shown to be limited by the underlying pore--pore interactions. Fracture strength of BMPs decreases at a faster rate under biaxial loading than under uniaxial loading. Three different types of deviation from classic Weibull behavior are identified: P-type corresponding to a positive lower tail deviation, N-type corresponding to a negative lower tail deviation, and S-type corresponding to both positive upper and lower tail deviations. Pore-pore interactions result in either P-type or N-type deviation in the limit of low porosity, whereas S-type behavior occurs when clusters of low and high fracture strengths coexist in a fracture data.

Bistable collective behavior of polymers tethered in a nanopore

NASA Astrophysics Data System (ADS)

Osmanovic, Dino; Bailey, Joe; Harker, Anthony H.; Fassati, Ariberto; Hoogenboom, Bart W.; Ford, Ian J.

2012-06-01

Polymer-coated pores play a crucial role in nucleo-cytoplasmic transport and in a number of biomimetic and nanotechnological applications. Here we present Monte Carlo and Density Functional Theory approaches to identify different collective phases of end-grafted polymers in a nanopore and to study their relative stability as a function of intermolecular interactions. Over a range of system parameters that is relevant for nuclear pore complexes, we observe two distinct phases: one with the bulk of the polymers condensed at the wall of the pore, and the other with the polymers condensed along its central axis. The relative stability of these two phases depends on the interpolymer interactions. The existence the two phases suggests a mechanism in which marginal changes in these interactions, possibly induced by nuclear transport receptors, cause the pore to transform between open and closed configurations, which will influence transport through the pore.

Structure of the TRPV1 ion channel determined by electron cryo-microscopy.

PubMed

Liao, Maofu; Cao, Erhu; Julius, David; Cheng, Yifan

2013-12-05

Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels respond to physical and chemical stimuli has been hampered by a lack of detailed structural information. Here we exploit advances in electron cryo-microscopy to determine the structure of a mammalian TRP channel, TRPV1, at 3.4 Å resolution, breaking the side-chain resolution barrier for membrane proteins without crystallization. Like voltage-gated channels, TRPV1 exhibits four-fold symmetry around a central ion pathway formed by transmembrane segments 5-6 (S5-S6) and the intervening pore loop, which is flanked by S1-S4 voltage-sensor-like domains. TRPV1 has a wide extracellular 'mouth' with a short selectivity filter. The conserved 'TRP domain' interacts with the S4-S5 linker, consistent with its contribution to allosteric modulation. Subunit organization is facilitated by interactions among cytoplasmic domains, including amino-terminal ankyrin repeats. These observations provide a structural blueprint for understanding unique aspects of TRP channel function.

Structure of the TRPV1 ion channel determined by electron cryo-microscopy

PubMed Central

Liao, Maofu; Cao, Erhu; Julius, David; Cheng, Yifan

2014-01-01

Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels respond to physical and chemical stimuli has been hampered by a lack of detailed structural information. Here, we exploit advances in electron cryo-microscopy to determine the structure of a mammalian TRP channel, TRPV1, at 3.4Å resolution, breaking the side-chain resolution barrier for membrane proteins without crystallization. Like voltage-gated channels, TRPV1 exhibits four-fold symmetry around a central ion pathway formed by transmembrane helices S5–S6 and the intervening pore loop, which is flanked by S1–S4 voltage sensor-like domains. TRPV1 has a wide extracellular ‘mouth’ with short selectivity filter. The conserved ‘TRP domain’ interacts with the S4–S5 linker, consistent with its contribution to allosteric modulation. Subunit organization is facilitated by interactions among cytoplasmic domains, including N-terminal ankyrin repeats. These observations provide a structural blueprint for understanding unique aspects of TRP channel function. PMID:24305160

Probe DNA-Cisplatin Interaction with Solid-State Nanopores

NASA Astrophysics Data System (ADS)

Zhou, Zhi; Hu, Ying; Li, Wei; Xu, Zhi; Wang, Pengye; Bai, Xuedong; Shan, Xinyan; Lu, Xinghua; Nanopore Collaboration

2014-03-01

Understanding the mechanism of DNA-cisplatin interaction is essential for clinical application and novel drug design. As an emerging single-molecule technology, solid-state nanopore has been employed in biomolecule detection and probing DNA-molecule interactions. Herein, we reported a real-time monitoring of DNA-cisplatin interaction by employing solid-state SiN nanopores. The DNA-cisplatin interacting process is clearly classified into three stages by measuring the capture rate of DNA-cisplatin adducts. In the first stage, the negative charged DNA molecules were partially discharged due to the bonding of positive charged cisplatin and forming of mono-adducts. In the second stage, forming of DNA-cisplatin di-adducts with the adjacent bases results in DNA bending and softening. The capture rate increases since the softened bi-adducts experience a lower barrier to thread into the nanopores. In the third stage, complex structures, such as micro-loop, are formed and the DNA-cisplatin adducts are aggregated. The capture rate decreases to zero as the aggregated adduct grows to the size of the pore. The characteristic time of this stage was found to be linear with the diameter of the nanopore and this dynamic process can be described with a second-order reaction model. We are grateful to Laboratory of Microfabrication, Dr. Y. Yao, and Prof. R.C. Yu (Institute of Physics, Chinese Academy of Sciences) for technical assistance.

Voltage-dependent conformational changes in connexin channels.

PubMed

Bargiello, Thaddeus A; Tang, Qingxiu; Oh, Seunghoon; Kwon, Taekyung

2012-08-01

Channels formed by connexins display two distinct types of voltage-dependent gating, termed V(j)- or fast-gating and loop- or slow-gating. Recent studies, using metal bridge formation and chemical cross-linking have identified a region within the channel pore that contributes to the formation of the loop-gate permeability barrier. The conformational changes are remarkably large, reducing the channel pore diameter from 15 to 20Å to less than 4Å. Surprisingly, the largest conformational change occurs in the most stable region of the channel pore, the 3(10) or parahelix formed by amino acids in the 42-51 segment. The data provide a set of positional constraints that can be used to model the structure of the loop-gate closed state. Less is known about the conformation of the V(j)-gate closed state. There appear to be two different mechanisms; one in which conformational changes in channel structure are linked to a voltage sensor contained in the N-terminus of Cx26 and Cx32 and a second in which the C-terminus of Cx43 and Cx40 may act either as a gating particle to block the channel pore or alternatively to stabilize the closed state. The later mechanism utilizes the same domains as implicated in effecting pH gating of Cx43 channels. It is unclear if the two V(j)-gating mechanisms are related or if they represent different gating mechanisms that operate separately in different subsets of connexin channels. A model of the V(j)-closed state of Cx26 hemichannel that is based on the X-ray structure of Cx26 and electron crystallographic structures of a Cx26 mutation suggests that the permeability barrier for V(j)-gating is formed exclusively by the N-terminus, but recent information suggests that this conformation may not represent a voltage-closed state. Closed state models are considered from a thermodynamic perspective based on information from the 3.5Å Cx26 crystal structure and molecular dynamics (MD) simulations. The applications of computational and experimental methods to define the path of allosteric molecular transitions that link the open and closed states are discussed. This article is part of a Special Issue entitled: The Communicating junctions, composition, structure and characteristics. Copyright © 2011 Elsevier B.V. All rights reserved.

Polymer translocation in solid-state nanopores: Dependence on hydrodynamic interactions and polymer configuration

NASA Astrophysics Data System (ADS)

Edmonds, Christopher M.; Hesketh, Peter J.; Nair, Sankar

2013-11-01

We present a Brownian dynamics investigation of 3-D Rouse and Zimm polymer translocation through solid-state nanopores. We obtain different scaling exponents α for both polymers using two initial configurations: minimum energy, and 'steady-state'. For forced translocation, Rouse polymers (no hydrodynamic interactions), shows a large dependence of α on initial configuration and voltage. Higher voltages result in crowding at the nanopore exit and reduced α. When the radius of gyration is in equilibrium at the beginning and end of translocation, α = 1 + υ where υ is the Flory exponent. For Zimm polymers (including hydrodynamic interactions), crowding is reduced and α = 2υ. Increased pore diameter does not affect α at moderate voltages that reduce diffusion effects. For unforced translocation using narrow pores, both polymers give α = 1 + 2υ. Due to increased polymer-pore interactions in the narrow pore, hydrodynamic drag effects are reduced, resulting in identical scaling.

Thermodynamics-hydration relationships within loops that affect G-quadruplexes under molecular crowding conditions.

PubMed

Fujimoto, Takeshi; Nakano, Shu-ichi; Sugimoto, Naoki; Miyoshi, Daisuke

2013-01-31

We systematically investigated the effects of loop length on the conformation, thermodynamic stability, and hydration of DNA G-quadruplexes under dilute and molecular crowding conditions in the presence of Na(+). Structural analysis showed that molecular crowding induced conformational switches of oligonucleotides with the longer guanine stretch and the shorter thymine loop. Thermodynamic parameters further demonstrated that the thermodynamic stability of G-quadruplexes increased by increasing the loop length from two to four, whereas it decreased by increasing the loop length from four to six. Interestingly, we found by osmotic pressure analysis that the number of water molecules released from the G-quadruplex decreased with increasing thermodynamic stability. We assumed that base-stacking interactions within the loops not only stabilized the whole G-quadruplex structure but also created hydration sites by accumulating nucleotide functional groups. The molecular crowding effects on the stability of G-quadruplexes composed of abasic sites, which reduce the stacking interactions at the loops, further demonstrated that G-quadruplexes with fewer stacking interactions within the loops released a larger number of water molecules upon folding. These results showed that the stacking interactions within the loops determined the thermodynamic stability and hydration of the whole G-quadruplex.

Influence of system size on the properties of a fluid adsorbed in a nanopore: Physical manifestations and methodological consequences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Puibasset, Joël, E-mail: puibasset@cnrs-orleans.fr; Kierlik, Edouard, E-mail: edouard.kierlik@upmc.fr; Tarjus, Gilles, E-mail: tarjus@lptl.jussieu.fr

Hysteresis and discontinuities in the isotherms of a fluid adsorbed in a nanopore in general hamper the determination of equilibrium thermodynamic properties, even in computer simulations. A way around this has been to consider both a reservoir of small size and a pore of small extent in order to restrict the fluctuations of density and approach a classical van der Waals loop. We assess this suggestion by thoroughly studying through Monte Carlo simulations and density functional theory the influence of system size on the equilibrium configurations of the adsorbed fluid and on the resulting isotherms. We stress the importance ofmore » pore-symmetry-breaking states that even for modest pore sizes lead to discontinuous isotherms and we discuss the physical relevance of these states and the methodological consequences for computing thermodynamic quantities.« less

Hyporheic less-mobile porosity and solute transport in porous media

NASA Astrophysics Data System (ADS)

MahmoodPoorDehkordy, F.; Briggs, M. A.; Day-Lewis, F. D.; Scruggs, C.; Singha, K.; Zarnetske, J. P.; Lane, J. W., Jr.; Bagtzoglou, A. C.

2017-12-01

Solute transport and reactive processes are strongly influenced by hydrodynamic exchange with the hyporheic zone. Contaminant transport and redox zonation in the hyporheic zone and near-stream aquifer can be impacted by the exchange between mobile and less-mobile porosity zones in heterogeneous porous media. Less-mobile porosity zones can be created by fine materials with tight pore throats (e.g. clay, organics) and in larger, well-connected pores down gradient of flow obstructions (e.g. sand behind cobbles). Whereas fluid sampling is primarily responsive to the more-mobile domain, tracking solute tracer dynamics by geoelectrical methods provides direct information about both more- and less-mobile zones. During tracer injection through porous media of varied pore connectivity, a lag between fluid and bulk electrical conductivity is observed, creating a hysteresis loop when plotted in conductivity space. Thus, the combination of simultaneous fluid and bulk electrical conductivity measurements enables a much improved quantification of less-mobile solute dynamics compared to traditional fluid-only sampling approaches. We have demonstrated the less-mobile porosity exchange in laboratory-scale column experiments verified by simulation models. The experimental approach has also been applied to streambed sediments in column and reach-scale field experiments and verified using numerical simulation. Properties of the resultant hysteresis loops can be used to estimate exchange parameters of less-mobile porosity. Our integrated approach combining field experiments, laboratory experiments, and numerical modeling provides new insights into the effect of less-mobile porosity on solute transport in the hyporheic zone.

Control-structure interaction in precision pointing servo loops

NASA Technical Reports Server (NTRS)

Spanos, John T.

1989-01-01

The control-structure interaction problem is addressed via stability analysis of a generic linear servo loop model. With the plant described by the rigid body mode and a single elastic mode, structural flexibility is categorized into one of three types: (1) appendage, (2) in-the-loop minimum phase, and (3) in-the-loop nonminimum phase. Closing the loop with proportional-derivative (PD) control action and introducing sensor roll-off dynamics in the feedback path, stability conditions are obtained. Trade studies are conducted with modal frequency, modal participation, modal damping, loop bandwidth, and sensor bandwidth treated as free parameters. Results indicate that appendage modes are most likely to produce instability if they are near the sensor rolloff, whereas in-the-loop modes are most dangerous near the loop bandwidth. The main goal of this paper is to provide a fundamental understanding of the control-structure interaction problem so that it may benefit the design of complex spacecraft and pointing system servo loops. In this framework, the JPL Pathfinder gimbal pointer is considered as an example.

Damped transverse oscillations of interacting coronal loops

NASA Astrophysics Data System (ADS)

Soler, Roberto; Luna, Manuel

2015-10-01

Damped transverse oscillations of magnetic loops are routinely observed in the solar corona. This phenomenon is interpreted as standing kink magnetohydrodynamic waves, which are damped by resonant absorption owing to plasma inhomogeneity across the magnetic field. The periods and damping times of these oscillations can be used to probe the physical conditions of the coronal medium. Some observations suggest that interaction between neighboring oscillating loops in an active region may be important and can modify the properties of the oscillations. Here we theoretically investigate resonantly damped transverse oscillations of interacting nonuniform coronal loops. We provide a semi-analytic method, based on the T-matrix theory of scattering, to compute the frequencies and damping rates of collective oscillations of an arbitrary configuration of parallel cylindrical loops. The effect of resonant damping is included in the T-matrix scheme in the thin boundary approximation. Analytic and numerical results in the specific case of two interacting loops are given as an application.

Conserved Aromatic Residue Confers Cation Selectivity in Claudin-2 and Claudin-10b*

PubMed Central

Li, Jiahua; Zhuo, Min; Pei, Lei; Yu, Alan S. L.

2013-01-01

In tight junctions, both claudin-2 and claudin-10b form paracellular cation-selective pores by the interaction of the first ECL 1 with permeating ions. We hypothesized that a highly conserved aromatic residue near the pore selectivity filter of claudins contributes to cation selectivity by cation-π interaction with the permeating cation. To test this, we generated MDCK I Tet-off cells stably transfected with claudin-2 Tyr67 mutants. The Y67L mutant showed reduced cation selectivity compared with wild-type claudin-2 due to a decrease in Na+ permeability, without affecting the Cl− permeability. The Y67A mutant enlarged the pore size and further decreased the charge selectivity due to an increase in Cl− permeability. The Y67F mutant restored the Na+ permeability, Cl− permeability, and pore size back to wild-type. The accessibility of Y67C to methanethiosulfonate modification indicated that its side chain faces the lumen of the pore. In claudin-10b, the F66L mutant reduced cation selectivity, and the F66A mutant lost pore conductance. We conclude that the conserved aromatic residue near the cation pore domain of claudins contributes to cation selectivity by a dual role of cation-π interaction and a luminal steric effect. Our findings provide new insight into how ion selectivity is achieved in the paracellular pore. PMID:23760508

Chromatin loops as allosteric modulators of enhancer-promoter interactions.

PubMed

Doyle, Boryana; Fudenberg, Geoffrey; Imakaev, Maxim; Mirny, Leonid A

2014-10-01

The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a complex network of looping interactions. Here we use a polymer model of chromatin fiber to investigate whether, and to what extent, looping interactions between elements in the vicinity of an enhancer-promoter pair can influence their contact frequency. Our equilibrium polymer simulations show that a chromatin loop, formed by elements flanking either an enhancer or a promoter, suppresses enhancer-promoter interactions, working as an insulator. A loop formed by elements located in the region between an enhancer and a promoter, on the contrary, facilitates their interactions. We find that different mechanisms underlie insulation and facilitation; insulation occurs due to steric exclusion by the loop, and is a global effect, while facilitation occurs due to an effective shortening of the enhancer-promoter genomic distance, and is a local effect. Consistently, we find that these effects manifest quite differently for in silico 3C and microscopy. Our results show that looping interactions that do not directly involve an enhancer-promoter pair can nevertheless significantly modulate their interactions. This phenomenon is analogous to allosteric regulation in proteins, where a conformational change triggered by binding of a regulatory molecule to one site affects the state of another site.

DNA–DNA kissing complexes as a new tool for the assembly of DNA nanostructures

PubMed Central

Barth, Anna; Kobbe, Daniela; Focke, Manfred

2016-01-01

Kissing-loop annealing of nucleic acids occurs in nature in several viruses and in prokaryotic replication, among other circumstances. Nucleobases of two nucleic acid strands (loops) interact with each other, although the two strands cannot wrap around each other completely because of the adjacent double-stranded regions (stems). In this study, we exploited DNA kissing-loop interaction for nanotechnological application. We functionalized the vertices of DNA tetrahedrons with DNA stem-loop sequences. The complementary loop sequence design allowed the hybridization of different tetrahedrons via kissing-loop interaction, which might be further exploited for nanotechnology applications like cargo transport and logical elements. Importantly, we were able to manipulate the stability of those kissing-loop complexes based on the choice and concentration of cations, the temperature and the number of complementary loops per tetrahedron either at the same or at different vertices. Moreover, variations in loop sequences allowed the characterization of necessary sequences within the loop as well as additional stability control of the kissing complexes. Therefore, the properties of the presented nanostructures make them an important tool for DNA nanotechnology. PMID:26773051

Effect of pore structure on the removal of clofibric acid by magnetic anion exchange resin.

PubMed

Tan, Liang; Shuang, Chendong; Wang, Yunshu; Wang, Jun; Su, Yihong; Li, Aimin

2018-01-01

The effect of pore structure of resin on clofibric acid (CA) adsorption behavior was investigated by using magnetic anion exchange resins (ND-1, ND-2, ND-3) with increasing pore diameter by 11.68, 15.37, 24.94 nm. Resin with larger pores showed faster adsorption rates and a higher adsorption capacity because the more opened tunnels provided by larger pores benefit the CA diffusion into the resin matrix. The ion exchange by the electrostatic interactions between Cl-type resin and CA resulted in chloride releasing to the solution, and the ratio of released chloride to CA adsorption amount decreased from 0.90 to 0.65 for ND-1, ND-2 and ND-3, indicating that non-electrostatic interactions obtain a larger proportional part of the adsorption into the pores. Co-existing inorganic anions and organic acids reduced the CA adsorption amounts by the competition effect of electrostatic interaction, whereas resins with more opened pore structures weakened the negative influence on CA adsorption because of the existence of non-electrostatic interactions. 85.2% and 65.1% adsorption amounts decrease are calculated for resin ND-1 and ND-3 by the negative influence of 1 mmol L -1 NaCl. This weaken effect of organic acid is generally depends on its hydrophobicity (Log Kow) for carboxylic acid and its ionization degree (pKb) for sulfonic acid. The resins could be reused with the slightly decreases by 1.9%, 3.2% and 5.4% after 7 cycles of regeneration, respectively for ND-1, ND-2 and ND-3, suggesting the ion exchange resin with larger pores are against its reuse by the brine solution regeneration. Copyright © 2017 Elsevier Ltd. All rights reserved.

A localized interaction surface for voltage-sensing domains on the pore domain of a K+ channel.

PubMed

Li-Smerin, Y; Hackos, D H; Swartz, K J

2000-02-01

Voltage-gated K+ channels contain a central pore domain and four surrounding voltage-sensing domains. How and where changes in the structure of the voltage-sensing domains couple to the pore domain so as to gate ion conduction is not understood. The crystal structure of KcsA, a bacterial K+ channel homologous to the pore domain of voltage-gated K+ channels, provides a starting point for addressing this question. Guided by this structure, we used tryptophan-scanning mutagenesis on the transmembrane shell of the pore domain in the Shaker voltage-gated K+ channel to localize potential protein-protein and protein-lipid interfaces. Some mutants cause only minor changes in gating and when mapped onto the KcsA structure cluster away from the interface between pore domain subunits. In contrast, mutants producing large changes in gating tend to cluster near this interface. These results imply that voltage-sensing domains interact with localized regions near the interface between adjacent pore domain subunits.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahmed, K.; Tonks, M.; Zhang, Y.

A detailed phase field model for the effect of pore drag on grain growth kinetics was implemented in MARMOT. The model takes into consideration both the curvature-driven grain boundary motion and pore migration by surface diffusion. As such, the model accounts for the interaction between pore and grain boundary kinetics, which tends to retard the grain growth process. Our 2D and 3D simulations demonstrate that the model capture all possible pore-grain boundary interactions proposed in theoretical models. For high enough surface mobility, the pores move along with the migrating boundary as a quasi-rigid-body, albeit hindering its migration rate compared tomore » the pore-free case. For less mobile pores, the migrating boundary can separate from the pores. For the pore-controlled grain growth kinetics, the model predicts a strong dependence of the growth rate on the number of pores, pore size, and surface diffusivity in agreement with theroretical models. An evolution equation for the grain size that includes these parameters was derived and showed to agree well with numerical solution. It shows a smooth transition from boundary-controlled kinetics to pore-controlled kinetics as the surface diffusivity decreases or the number of pores or their size increases. This equation can be utilized in BISON to give accurate estimate for the grain size evolution. This will be accomplished in the near future. The effect of solute drag and anisotropy of grain boundary on grain growth will be investigated in future studies.« less

Local free energies for the coarse-graining of adsorption phenomena: The interacting pair approximation

NASA Astrophysics Data System (ADS)

Pazzona, Federico G.; Pireddu, Giovanni; Gabrieli, Andrea; Pintus, Alberto M.; Demontis, Pierfranco

2018-05-01

We investigate the coarse-graining of host-guest systems under the perspective of the local distribution of pore occupancies, along with the physical meaning and actual computability of the coarse-interaction terms. We show that the widely accepted approach, in which the contributions to the free energy given by the molecules located in two neighboring pores are estimated through Monte Carlo simulations where the two pores are kept separated from the rest of the system, leads to inaccurate results at high sorbate densities. In the coarse-graining strategy that we propose, which is based on the Bethe-Peierls approximation, density-independent interaction terms are instead computed according to local effective potentials that take into account the correlations between the pore pair and its surroundings by means of mean-field correction terms without the need for simulating the pore pair separately. Use of the interaction parameters obtained this way allows the coarse-grained system to reproduce more closely the equilibrium properties of the original one. Results are shown for lattice-gases where the local free energy can be computed exactly and for a system of Lennard-Jones particles under the effect of a static confining field.

Spatial-pattern-induced evolution of a self-replicating loop network.

PubMed

Suzuki, Keisuke; Ikegami, Takashi

2006-01-01

We study a system of self-replicating loops in which interaction rules between individuals allow competition that leads to the formation of a hypercycle-like network. The main feature of the model is the multiple layers of interaction between loops, which lead to both global spatial patterns and local replication. The network of loops manifests itself as a spiral structure from which new kinds of self-replicating loops emerge at the boundaries between different species. In these regions, larger and more complex self-replicating loops live for longer periods of time, managing to self-replicate in spite of their slower replication. Of particular interest is how micro-scale interactions between replicators lead to macro-scale spatial pattern formation, and how these macro-scale patterns in turn perturb the micro-scale replication dynamics.

Attenuation of Phosphorylation-dependent Activation of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) by Disease-causing Mutations at the Transmission Interface*

PubMed Central

Chin, Stephanie; Yang, Donghe; Miles, Andrew J.; Eckford, Paul D. W.; Molinski, Steven; Wallace, B. A.; Bear, Christine E.

2017-01-01

Cystic fibrosis transmembrane conductance regulator (CFTR) is a multidomain membrane protein that functions as a phosphorylation-regulated anion channel. The interface between its two cytosolic nucleotide binding domains and coupling helices conferred by intracellular loops extending from the channel pore domains has been referred to as a transmission interface and is thought to be critical for the regulated channel activity of CFTR. Phosphorylation of the regulatory domain of CFTR by protein kinase A (PKA) is required for its channel activity. However, it was unclear if phosphorylation modifies the transmission interface. Here, we studied purified full-length CFTR protein using spectroscopic techniques to determine the consequences of PKA-mediated phosphorylation. Synchrotron radiation circular dichroism spectroscopy confirmed that purified full-length wild-type CFTR is folded and structurally responsive to phosphorylation. Intrinsic tryptophan fluorescence studies of CFTR showed that phosphorylation reduced iodide-mediated quenching, consistent with an effect of phosphorylation in burying tryptophans at the transmission interface. Importantly, the rate of phosphorylation-dependent channel activation was compromised by the introduction of disease-causing mutations in either of the two coupling helices predicted to interact with nucleotide binding domain 1 at the interface. Together, these results suggest that phosphorylation modifies the interface between the catalytic and pore domains of CFTR and that this modification facilitates CFTR channel activation. PMID:28003367

Identification of Bacillus thuringiensis Cry3Aa toxin domain II loop 1 as the binding site of Tenebrio molitor cadherin repeat CR12.

PubMed

Zúñiga-Navarrete, Fernando; Gómez, Isabel; Peña, Guadalupe; Amaro, Itzel; Ortíz, Ernesto; Becerril, Baltazar; Ibarra, Jorge E; Bravo, Alejandra; Soberón, Mario

2015-04-01

Bacillus thuringiensis Cry toxins exert their toxic effect by specific recognition of larval midgut proteins leading to oligomerization of the toxin, membrane insertion and pore formation. The exposed domain II loop regions of Cry toxins have been shown to be involved in receptor binding. Insect cadherins have shown to be functionally involved in toxin binding facilitating toxin oligomerization. Here, we isolated a VHH (VHHA5) antibody by phage display that binds Cry3Aa loop 1 and competed with the binding of Cry3Aa to Tenebrio molitor brush border membranes. VHHA5 also competed with the binding of Cry3Aa to a cadherin fragment (CR12) that was previously shown to be involved in binding and toxicity of Cry3Aa, indicating that Cry3Aa binds CR12 through domain II loop 1. Moreover, we show that a loop 1 mutant, previously characterized to have increased toxicity to T. molitor, displayed a correlative enhanced binding affinity to T. molitor CR12 and to VHHA5. These results show that Cry3Aa domain II loop 1 is a binding site of CR12 T. molitor cadherin. Copyright © 2015 Elsevier Ltd. All rights reserved.

Temperature-sensitive gating of TRPV1 channel as probed by atomistic simulations of its trans- and juxtamembrane domains

NASA Astrophysics Data System (ADS)

Chugunov, Anton O.; Volynsky, Pavel E.; Krylov, Nikolay A.; Nolde, Dmitry E.; Efremov, Roman G.

2016-09-01

Heat-activated transient receptor potential channel TRPV1 is one of the most studied eukaryotic proteins involved in temperature sensation. Upon heating, it exhibits rapid reversible pore gating, which depolarizes neurons and generates action potentials. Underlying molecular details of such effects in the pore region of TRPV1 is of a crucial importance to control temperature responses of the organism. Despite the spatial structure of the channel in both open (O) and closed (C) states is known, microscopic nature of channel gating and mechanism of thermal sensitivity are still poorly understood. In this work, we used unrestrained atomistic molecular dynamics simulations of TRPV1 (without N- and C-terminal cytoplasmic domains) embedded into explicit lipid bilayer in its O- and C-states. We found that the pore domain with its neighboring loops undergoes large temperature-dependent conformational transitions in an asymmetric way, when fragments of only one monomer move with large amplitude, freeing the pore upon heating. Such an asymmetrical gating looks rather biologically relevant because it is faster and more reliable than traditionally proposed “iris-like” symmetric scheme of channel opening. Analysis of structural, dynamic, and hydrophobic organization of the pore domain revealed entropy growth upon TRPV1 gating, which is in line with current concepts of thermal sensitivity.

Coupling root architecture and pore network modeling - an attempt towards better understanding root-soil interactions

NASA Astrophysics Data System (ADS)

Leitner, Daniel; Bodner, Gernot; Raoof, Amir

2013-04-01

Understanding root-soil interactions is of high importance for environmental and agricultural management. Root uptake is an essential component in water and solute transport modeling. The amount of groundwater recharge and solute leaching significantly depends on the demand based plant extraction via its root system. Plant uptake however not only responds to the potential demand, but in most situations is limited by supply form the soil. The ability of the plant to access water and solutes in the soil is governed mainly by root distribution. Particularly under conditions of heterogeneous distribution of water and solutes in the soil, it is essential to capture the interaction between soil and roots. Root architecture models allow studying plant uptake from soil by describing growth and branching of root axes in the soil. Currently root architecture models are able to respond dynamically to water and nutrient distribution in the soil by directed growth (tropism), modified branching and enhanced exudation. The porous soil medium as rooting environment in these models is generally described by classical macroscopic water retention and sorption models, average over the pore scale. In our opinion this simplified description of the root growth medium implies several shortcomings for better understanding root-soil interactions: (i) It is well known that roots grow preferentially in preexisting pores, particularly in more rigid/dry soil. Thus the pore network contributes to the architectural form of the root system; (ii) roots themselves can influence the pore network by creating preferential flow paths (biopores) which are an essential element of structural porosity with strong impact on transport processes; (iii) plant uptake depend on both the spatial location of water/solutes in the pore network as well as the spatial distribution of roots. We therefore consider that for advancing our understanding in root-soil interactions, we need not only to extend our root models, but also improve the description of the rooting environment. Until now there have been no attempts to couple root architecture and pore network models. In our work we present a first attempt to join both types of models using the root architecture model of Leitner et al., (2010) and a pore network model presented by Raoof et al. (2010). The two main objectives of coupling both models are: (i) Representing the effect of root induced biopores on flow and transport processes: For this purpose a fixed root architecture created by the root model is superimposed as a secondary root induced pore network to the primary soil network, thus influencing the final pore topology in the network generation. (ii) Representing the influence of pre-existing pores on root branching: Using a given network of (rigid) pores, the root architecture model allocates its root axes into these preexisting pores as preferential growth paths with thereby shape the final root architecture. The main objective of our study is to reveal the potential of using a pore scale description of the plant growth medium for an improved representation of interaction processes at the interface of root and soil. References Raoof, A., Hassanizadeh, S.M. 2010. A New Method for Generating Pore-Network Models. Transp. Porous Med. 81, 391-407. Leitner, D, Klepsch, S., Bodner, G., Schnepf, S. 2010. A dynamic root system growth model based on L-Systems. Tropisms and coupling to nutrient uptake from soil. Plant Soil 332, 177-192.

Structural basis of clade-specific HIV-1 neutralization by humanized anti-V3 monoclonal antibody KD-247.

PubMed

Kirby, Karen A; Ong, Yee Tsuey; Hachiya, Atsuko; Laughlin, Thomas G; Chiang, Leslie A; Pan, Yun; Moran, Jennifer L; Marchand, Bruno; Singh, Kamalendra; Gallazzi, Fabio; Quinn, Thomas P; Yoshimura, Kazuhisa; Murakami, Toshio; Matsushita, Shuzo; Sarafianos, Stefan G

2015-01-01

Humanized monoclonal antibody KD-247 targets the Gly(312)-Pro(313)-Gly(314)-Arg(315) arch of the third hypervariable (V3) loop of the HIV-1 surface glycoprotein. It potently neutralizes many HIV-1 clade B isolates, but not of other clades. To understand the molecular basis of this specificity, we solved a high-resolution (1.55 Å) crystal structure of the KD-247 antigen binding fragment and examined the potential interactions with various V3 loop targets. Unlike most antibodies, KD-247 appears to interact with its target primarily through light chain residues. Several of these interactions involve Arg(315) of the V3 loop. To evaluate the role of light chain residues in the recognition of the V3 loop, we generated 20 variants of KD-247 single-chain variable fragments with mutations in the antigen-binding site. Purified proteins were assessed for V3 loop binding using AlphaScreen technology and for HIV-1 neutralization. Our data revealed that recognition of the clade-specificity defining residue Arg(315) of the V3 loop is based on a network of interactions that involve Tyr(L32), Tyr(L92), and Asn(L27d) that directly interact with Arg(315), thus elucidating the molecular interactions of KD-247 with its V3 loop target. © FASEB.

Reduction of Hematite to Magnetite in CO/CO2 Gas Mixtures Under Carbon Looping Combustion Conditions

NASA Astrophysics Data System (ADS)

Simmonds, Tegan; Hayes, Peter C.

2017-12-01

Iron oxides have been identified as promising materials for use as oxygen carriers in chemical looping combustion technologies as there are abundant resources available in the form of ore and in industrial wastes. The isothermal reduction of hematite (Fe2O3) in the fuel reactor and the subsequent oxidation of magnetite (Fe3O4) in air are the principal reactions of interest for these applications. Experimental investigations have been carried out to characterize the microstructural changes taking place as a result of the reduction reactions for a range of CO/CO2 gas compositions at temperatures between 1073 K and 1373 K (800 °C and 1100 °C). It has been shown that magnetite spinel is formed directly from hematite under these conditions and that porous magnetite or dense platelet or "lath" type morphologies can be formed depending on gas composition and reaction temperature. The conditions for the lath/pore transition are established. Dendritic gas pores are formed during the creation of the porous magnetite. This morphology allows continuous contact between the gas reactant and reaction interface and results in high reduction reaction rates.

Crystal structure of human glycine receptor-α3 bound to antagonist strychnine.

PubMed

Huang, Xin; Chen, Hao; Michelsen, Klaus; Schneider, Stephen; Shaffer, Paul L

2015-10-08

Neurotransmitter-gated ion channels of the Cys-loop receptor family are essential mediators of fast neurotransmission throughout the nervous system and are implicated in many neurological disorders. Available X-ray structures of prokaryotic and eukaryotic Cys-loop receptors provide tremendous insights into the binding of agonists, the subsequent opening of the ion channel, and the mechanism of channel activation. Yet the mechanism of inactivation by antagonists remains unknown. Here we present a 3.0 Å X-ray structure of the human glycine receptor-α3 homopentamer in complex with a high affinity, high-specificity antagonist, strychnine. Our structure allows us to explore in detail the molecular recognition of antagonists. Comparisons with previous structures reveal a mechanism for antagonist-induced inactivation of Cys-loop receptors, involving an expansion of the orthosteric binding site in the extracellular domain that is coupled to closure of the ion pore in the transmembrane domain.

Inverse colloidal crystal membranes for hydrophobic interaction membrane chromatography.

PubMed

Vu, Anh T; Wang, Xinying; Wickramasinghe, S Ranil; Yu, Bing; Yuan, Hua; Cong, Hailin; Luo, Yongli; Tang, Jianguo

2015-08-01

Hydrophobic interaction membrane chromatography has gained interest due to its excellent performance in the purification of humanized monoclonal antibodies. The membrane material used in hydrophobic interaction membrane chromatography has typically been commercially available polyvinylidene fluoride. In this contribution, newly developed inverse colloidal crystal membranes that have uniform pores, high porosity and, therefore, high surface area for protein binding are used as hydrophobic interaction membrane chromatography membranes for humanized monoclonal antibody immunoglobulin G purification. The capacity of the inverse colloidal crystal membranes developed here is up to ten times greater than commercially available polyvinylidene fluoride membranes with a similar pore size. This work highlights the importance of developing uniform pore size high porosity membranes in order to maximize the capacity of hydrophobic interaction membrane chromatography. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations.

PubMed

Di Palma, Francesco; Bottaro, Sandro; Bussi, Giovanni

2015-01-01

Riboswitches are cis-acting regulatory RNA elements prevalently located in the leader sequences of bacterial mRNA. An adenine sensing riboswitch cis-regulates adeninosine deaminase gene (add) in Vibrio vulnificus. The structural mechanism regulating its conformational changes upon ligand binding mostly remains to be elucidated. In this open framework it has been suggested that the ligand stabilizes the interaction of the distal "kissing loop" complex. Using accurate full-atom molecular dynamics with explicit solvent in combination with enhanced sampling techniques and advanced analysis methods it could be possible to provide a more detailed perspective on the formation of these tertiary contacts. In this work, we used umbrella sampling simulations to study the thermodynamics of the kissing loop complex in the presence and in the absence of the cognate ligand. We enforced the breaking/formation of the loop-loop interaction restraining the distance between the two loops. We also assessed the convergence of the results by using two alternative initialization protocols. A structural analysis was performed using a novel approach to analyze base contacts. Contacts between the two loops were progressively lost when larger inter-loop distances were enforced. Inter-loop Watson-Crick contacts survived at larger separation when compared with non-canonical pairing and stacking interactions. Intra-loop stacking contacts remained formed upon loop undocking. Our simulations qualitatively indicated that the ligand could stabilize the kissing loop complex. We also compared with previously published simulation studies. Kissing complex stabilization given by the ligand was compatible with available experimental data. However, the dependence of its value on the initialization protocol of the umbrella sampling simulations posed some questions on the quantitative interpretation of the results and called for better converged enhanced sampling simulations.

The free-energy cost of interaction between DNA loops.

PubMed

Huang, Lifang; Liu, Peijiang; Yuan, Zhanjiang; Zhou, Tianshou; Yu, Jianshe

2017-10-03

From the viewpoint of thermodynamics, the formation of DNA loops and the interaction between them, which are all non-equilibrium processes, result in the change of free energy, affecting gene expression and further cell-to-cell variability as observed experimentally. However, how these processes dissipate free energy remains largely unclear. Here, by analyzing a mechanic model that maps three fundamental topologies of two interacting DNA loops into a 4-state model of gene transcription, we first show that a longer DNA loop needs more mean free energy consumption. Then, independent of the type of interacting two DNA loops (nested, side-by-side or alternating), the promotion between them always consumes less mean free energy whereas the suppression dissipates more mean free energy. More interestingly, we find that in contrast to the mechanism of direct looping between promoter and enhancer, the facilitated-tracking mechanism dissipates less mean free energy but enhances the mean mRNA expression, justifying the facilitated-tracking hypothesis, a long-standing debate in biology. Based on minimal energy principle, we thus speculate that organisms would utilize the mechanisms of loop-loop promotion and facilitated tracking to survive in complex environments. Our studies provide insights into the understanding of gene expression regulation mechanism from the view of energy consumption.

New general pore size distribution model by classical thermodynamics application: Activated carbon

USGS Publications Warehouse

Lordgooei, M.; Rood, M.J.; Rostam-Abadi, M.

2001-01-01

A model is developed using classical thermodynamics to characterize pore size distributions (PSDs) of materials containing micropores and mesopores. The thermal equation of equilibrium adsorption (TEEA) is used to provide thermodynamic properties and relate the relative pore filling pressure of vapors to the characteristic pore energies of the adsorbent/adsorbate system for micropore sizes. Pore characteristic energies are calculated by averaging of interaction energies between adsorbate molecules and adsorbent pore walls as well as considering adsorbate-adsorbate interactions. A modified Kelvin equation is used to characterize mesopore sizes by considering variation of the adsorbate surface tension and by excluding the adsorbed film layer for the pore size. The modified-Kelvin equation provides similar pore filling pressures as predicted by density functional theory. Combination of these models provides a complete PSD of the adsorbent for the micropores and mesopores. The resulting PSD is compared with the PSDs from Jaroniec and Choma and Horvath and Kawazoe models as well as a first-order approximation model using Polanyi theory. The major importance of this model is its basis on classical thermodynamic properties, less simplifying assumptions in its derivation compared to other methods, and ease of use.

Nucleation in mesoscopic systems under transient conditions: Peptide-induced pore formation in vesicles

NASA Astrophysics Data System (ADS)

Zhdanov, Vladimir P.; Höök, Fredrik

2013-04-01

Attachment of lytic peptides to the lipid membrane of virions or bacteria is often accompanied by their aggregation and pore formation, resulting eventually in membrane rupture and pathogen neutralization. The membrane rupture may occur gradually via formation of many pores or abruptly after the formation of the first pore. In academic studies, this process is observed during interaction of peptides with lipid vesicles. We present an analytical model and the corresponding Monte Carlo simulations focused on the pore formation in such situations. Specifically, we calculate the time of the first nucleation-limited pore-formation event and show the distribution of this time in the regime when the fluctuations of the number of peptides attached to a vesicle are appreciable. The results obtained are used to clarify the mechanism of the pore formation and membrane destabilization observed recently during interaction of highly active α-helical peptide with sub-100-nm lipid vesicles that mimic enveloped viruses with nanoscale membrane curvature. The model proposed and the analysis presented are generic and may be applicable to other meso- and nanosystems.

The strainrange conversion principle for treating cumulative fatigue damage in the creep range

NASA Technical Reports Server (NTRS)

Manson, S. S.

1983-01-01

A formula is derived for combining effects of successive hysteresis loops in the creep range of materials when one loop has excess tensile creep, while the other contains excess compressive creep. The resultant effect resembles single loops involving balanced tensile and compressive creep. The attempt to use the Interaction Damage Rule as a tool in combining loops of non-equal size and complex strainrange content has led to important new concepts useful in future studies of creep-fatigue. It turns out that the Interaction Damage Rule is basically an expression of how a set of hysteresis loops involving only single generic strains can combine to produce the same micromechanistic damage as the loop containing the combined strainranges which it analyzes. Making use of the underlying concept of Strainrange Partitioning that only the strainrange content of a hysteresis loop governs fatigue life, not order of introducing strainranges, a rational derivation of the Interaction Damage Rule is provided, showing also how it can effectively be used to synthesize independent loops and determine both damaging and healing effects.

Direct Transmembrane Interaction between Actin and the Pore-Competent, Cholesterol-Dependent Cytolysin Pneumolysin

PubMed Central

Hupp, Sabrina; Förtsch, Christina; Wippel, Carolin; Ma, Jiangtao; Mitchell, Timothy J.; Iliev, Asparouh I.

2013-01-01

The eukaryotic actin cytoskeleton is an evolutionarily well-established pathogen target, as a large number of bacterial factors disturb its dynamics to alter the function of the host cells. These pathogenic factors modulate or mimic actin effector proteins or they modify actin directly, leading to an imbalance of the precisely regulated actin turnover. Here, we show that the pore-forming, cholesterol-dependent cytolysin pneumolysin (PLY), a major neurotoxin of Streptococcus pneumoniae, has the capacity to bind actin directly and to enhance actin polymerisation in vitro. In cells, the toxin co-localised with F-actin shortly after exposure, and this direct interaction was verified by Förster resonance energy transfer. PLY was capable of exerting its effect on actin through the lipid bilayer of giant unilamellar vesicles, but only when its pore competence was preserved. The dissociation constant of G-actin binding to PLY in a biochemical environment was 170–190 nM, which is indicative of a high-affinity interaction, comparable to the affinity of other intracellular actin-binding factors. Our results demonstrate the first example of a direct interaction of a pore-forming toxin with cytoskeletal components, suggesting that the cross talk between pore-forming cytolysins and cells is more complex than previously thought. PMID:23219469

Aromatic–aromatic interactions between residues in KCa3.1 pore helix and S5 transmembrane segment control the channel gating process

PubMed Central

Garneau, Line; Klein, Hélène; Lavoie, Marie-France; Brochiero, Emmanuelle; Parent, Lucie

2014-01-01

The Ca2+-activated potassium channel KCa3.1 is emerging as a therapeutic target for a large variety of health disorders. One distinguishing feature of KCa3.1 is that the channel open probability at saturating Ca2+ concentrations (Pomax) is low, typically 0.1–0.2 for KCa3.1 wild type. This observation argues for the binding of Ca2+ to the calmodulin (CaM)–KCa3.1 complex, promoting the formation of a preopen closed-state configuration leading to channel opening. We have previously shown that the KCa3.1 active gate is most likely located at the level of the selectivity filter. As Ca2+-dependent gating of KCa3.1 originates from the binding of Ca2+ to CaM in the C terminus, the hypothesis of a gate located at the level of the selectivity filter requires that the conformational change initiated in the C terminus be transmitted to the S5 and S6 transmembrane helices, with a resulting effect on the channel pore helix directly connected to the selectivity filter. A study was thus undertaken to determine to what extent the interactions between the channel pore helix with the S5 and S6 transmembrane segments contribute to KCa3.1 gating. Molecular dynamics simulations first revealed that the largest contact area between the pore helix and the S5 plus S6 transmembrane helices involves residue F248 at the C-terminal end of the pore helix. Unitary current recordings next confirmed that modulating aromatic–aromatic interactions between F248 and W216 of the S5 transmembrane helical segment and/or perturbing the interactions between F248 and residues in S6 surrounding the glycine hinge G274 cause important changes in Pomax. This work thus provides the first evidence for a key contribution of the pore helix in setting Pomax by stabilizing the channel closed configuration through aromatic–aromatic interactions involving F248 of the pore helix. We propose that the interface pore helix/S5 constitutes a promising site for designing KCa3.1 potentiators. PMID:24470490

Catalytic conversion in nanoporous materials: Concentration oscillations and spatial correlations due to inhibited transport and intermolecular interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garcia, Andres; Evans, James W.

2016-11-03

We show that steady-state catalytic conversion in nanoporous materials can occur in a quasi-counter-diffusion mode with the reactant (product) concentration strongly decaying (growing) into the pore, but also with oscillations in the total concentration. These oscillations reflect the response of the fluid to the transition from an extended to a confined environment near the pore opening. We focus on the regime of strongly inhibited transport in narrow pores corresponding to single-file diffusion. Here, limited penetration of the reactant into the pores and the associated low reaction yield is impacted by strong spatial correlations induced by both reaction (non-equilibrium correlations) andmore » also by intermolecular interactions (thermodynamic correlations). We develop a generalized hydrodynamic formulation to effectively describe inhibited transport accounting for the effect of these correlations, and incorporate this description of transport into appropriate reaction-diffusion equations. These equations accurately describe both shorter-range concentration oscillations near the pore opening and the longer-range mesoscale variation of concentration profiles in the pore (and thus also describe reaction yield). Success of the analytic theory is validated by comparison with a precise kinetic Monte Carlo simulation of an appropriate molecular-level stochastic reaction-diffusion model. As a result, this work elucidates unconventional chemical kinetics in interacting confined systems.« less

The effect of initial resident fluid saturation on the interaction between resident and infiltrating fluids in porous media

NASA Astrophysics Data System (ADS)

Hsu, S. Y.; Chen, H.; Huang, Q. Z.; Lee, T. Y.; Chiu, Y.; Chang, L. C.; Lamorski, K.; Sławiński, C.; Tsao, C. W.

2017-12-01

The interplay between resident ("old") fluid already in the vadose zone and infiltrating ("new") fluid was examined with micromodel experiments. The geometric patterns of the micromodels are based on a pore doublet and a 2D pore geometry of a sand-packing soil scanned by Micro X-Ray CT. We studied the old and new fluid interaction during imbibition process subject to different evaporation times (different the initial old fluid saturations). The results found that, in the pore-doublet micromodel experiment, the old fluid was mixed and displaced by the new fluid, and an increase in the initial old fluid saturation led to a decrease in the amount of old fluid displaced by the new fluid. On the other hand, the most of the old fluid in the micromodel of 2D sand-packing pore geometry was displaced by and mixed with the new fluid. However, a small amount of the initial old fluid that occupied pore throats remained untouched by the new fluid due to the air blockage. The amount of untouched old fluid increased as the initial old fluid saturation decreased. Our finding reveals the effect of pore geometry and inital old fluid distribution on the interaction between resident and infiltrating fluids.

A novel feedforward compensation canceling input filter-regulator interaction

NASA Technical Reports Server (NTRS)

Kelkar, S. S.; Lee, F. C.

1983-01-01

The interaction between the input and the control loop of switching regulators often results in deterimental effects, such as loop instability, degradation of transient response, and audiosusceptibility, etc. The concept of pole-zero cancelation is employed to mitigate some of these detrimental effects and is implemented using a novel feedforward loop, in addition to existing feedback loops of a buck regulator. Experimental results are presented which show excellent correlation with theory.

Stability in Real Food Webs: Weak Links in Long Loops

NASA Astrophysics Data System (ADS)

Neutel, Anje-Margriet; Heesterbeek, Johan A. P.; de Ruiter, Peter C.

2002-05-01

Increasing evidence that the strengths of interactions among populations in biological communities form patterns that are crucial for system stability requires clarification of the precise form of these patterns, how they come about, and why they influence stability. We show that in real food webs, interaction strengths are organized in trophic loops in such a way that long loops contain relatively many weak links. We show and explain mathematically that this patterning enhances stability, because it reduces maximum ``loop weight'' and thus reduces the amount of intraspecific interaction needed for matrix stability. The patterns are brought about by biomass pyramids, a feature common to most ecosystems. Incorporation of biomass pyramids in 104 food-web descriptions reveals that the low weight of the long loops stabilizes complex food webs. Loop-weight analysis could be a useful tool for exploring the structure and organization of complex communities.

Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein

NASA Astrophysics Data System (ADS)

Bokori-Brown, Monika; Martin, Thomas G.; Naylor, Claire E.; Basak, Ajit K.; Titball, Richard W.; Savva, Christos G.

2016-04-01

Lysenin from the coelomic fluid of the earthworm Eisenia fetida belongs to the aerolysin family of small β-pore-forming toxins (β-PFTs), some members of which are pathogenic to humans and animals. Despite efforts, a high-resolution structure of a channel for this family of proteins has been elusive and therefore the mechanism of activation and membrane insertion remains unclear. Here we determine the pore structure of lysenin by single particle cryo-EM, to 3.1 Å resolution. The nonameric assembly reveals a long β-barrel channel spanning the length of the complex that, unexpectedly, includes the two pre-insertion strands flanking the hypothetical membrane-insertion loop. Examination of other members of the aerolysin family reveals high structural preservation in this region, indicating that the membrane-insertion pathway in this family is conserved. For some toxins, proteolytic activation and pro-peptide removal will facilitate unfolding of the pre-insertion strands, allowing them to form the β-barrel of the channel.

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus

PubMed Central

Smith, Emily M.; Lajoie, Bryan R.; Jain, Gaurav; Dekker, Job

2016-01-01

Three-dimensional genome structure plays an important role in gene regulation. Globally, chromosomes are organized into active and inactive compartments while, at the gene level, looping interactions connect promoters to regulatory elements. Topologically associating domains (TADs), typically several hundred kilobases in size, form an intermediate level of organization. Major questions include how TADs are formed and how they are related to looping interactions between genes and regulatory elements. Here we performed a focused 5C analysis of a 2.8 Mb chromosome 7 region surrounding CFTR in a panel of cell types. We find that the same TAD boundaries are present in all cell types, indicating that TADs represent a universal chromosome architecture. Furthermore, we find that these TAD boundaries are present irrespective of the expression and looping of genes located between them. In contrast, looping interactions between promoters and regulatory elements are cell-type specific and occur mostly within TADs. This is exemplified by the CFTR promoter that in different cell types interacts with distinct sets of distal cell-type-specific regulatory elements that are all located within the same TAD. Finally, we find that long-range associations between loci located in different TADs are also detected, but these display much lower interaction frequencies than looping interactions within TADs. Interestingly, interactions between TADs are also highly cell-type-specific and often involve loci clustered around TAD boundaries. These data point to key roles of invariant TAD boundaries in constraining as well as mediating cell-type-specific long-range interactions and gene regulation. PMID:26748519

Modeling the interaction of ultrasound with pores

NASA Technical Reports Server (NTRS)

Lu, Yichi; Wadley, Haydn N. G.; Parthasarathi, Sanjai

1991-01-01

Factors that affect ultrasonic velocity sensing of density during consolidation of metal powders are examined. A comparison is made between experimental results obtained during the final stage of densification and the predictions of models that assume either a spherical or a spheroidal pore shape. It is found that for measurements made at low frequencies during the final stage of densification, relative density (pore fraction) and pore shape are the two most important factors determining the ultrasonic velocity, the effect of pore size is negligible.

Pore formation and pore closure in poly(D,L-lactide-co-glycolide) films.

PubMed

Fredenberg, Susanne; Wahlgren, Marie; Reslow, Mats; Axelsson, Anders

2011-03-10

Pore formation and pore closure in poly(D,L-lactide-co-glycolide)-based drug delivery systems are two important processes as they control the release of the encapsulated drug. The phenomenon pore closure was investigated by studying the effects of the pH and the temperature of the release medium, and the properties of the polymer. Poly(D,L-lactide-co-glycolide) (PLG) films were subjected to a pore forming pre-treatment, and then pore closure was observed simultaneously with changes in glass transition temperature, wettability (contact angle), water absorption and mass remaining. To further understand the effect of pH, combined pore formation and pore closure were studied at different pH values. Pore closure was increased in a release medium with low pH, with a low-molecular-weight PLG of relatively low degree of hydrophobicity, or at high temperature. Pore closure occurred by two different mechanisms, one based on polymer-polymer interactions and one on polymer-water interactions. The mobility of the PLG chains also played an important role. The surface of the PLG films were more porous at pH 5-6 than at lower or higher pH, as pore formation was relatively fast and pore closure were less pronounced in this pH range. The pH had a significant impact on the porous structure, which should be kept in mind when evaluating experimental results, as the pH may be significantly decreased in vitro, in vivo and in situ. The results also show that the initial porosity is very important when using a high-molecular-weight PLG. Copyright © 2010 Elsevier B.V. All rights reserved.

Two-pore channels: Regulation by NAADP and customized roles in triggering calcium signals

PubMed Central

Patel, Sandip; Marchant, Jonathan; Brailoiu, Eugen

2010-01-01

NAADP is a potent regulator of cytosolic calcium levels. Much evidence suggests that NAADP activates a novel channel located on an acidic (lysosomal-like) calcium store, the mobilisation of which results in further calcium release from the endoplasmic reticulum. Here, we discuss the recent identification of a family of poorly characterized ion channels (the two-pore channels) as endo-lysosomal NAADP receptors. The generation of calcium signals by these channels is likened to those evoked by depolarisation during excitation-contraction coupling in muscle. We discuss the idea that two pore-channels can mediate a trigger release of calcium which is then amplified by calcium-induced calcium release from the endoplasmic reticulum. This is similar to the activation of voltage-sensitive calcium channels and subsequent mobilisation of sarcoplasmic reticulum calcium stores in cardiac tissue. We suggest that two-pore channels may physically interact with ryanodine receptors to account for more direct release of calcium from the endoplasmic reticulum in analogy with the conformational coupling of voltage-sensitive calcium channels and ryanodine receptors in skeletal muscle. Interaction of two-pore channels with other calcium release channels likely occurs between stores “trans-chatter” and possibly within the same store “cis-chatter”. We also speculate that trafficking of two-pore channels through the endolysosomal system facilitates interactions with calcium entry channels. Strategic placing of two-pore channels thus provides a versatile means of generating spatiotemporally complex cellular calcium signals. PMID:20621760

Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix.

PubMed

Pley, H W; Flaherty, K M; McKay, D B

1994-11-03

In large structured RNAs, RNA hairpins in which the strands of the duplex stem are connected by a tetraloop of the consensus sequence 5'-GNRA (where N is any nucleotide, and R is either G or A) are unusually frequent. In group I introns there is a covariation in sequence between nucleotides in the third and fourth positions of the loop with specific distant base pairs in putative RNA duplex stems: GNAA loops correlate with successive 5'-C-C.G-C base pairs in stems, whereas GNGA loops correlate with 5'-C-U.G-A. This has led to the suggestion that GNRA tetraloops may be involved in specific long-range tertiary interactions, with each A in position 3 or 4 of the loop interacting with a C-G base pair in the duplex, and G in position 3 interacting with a U-A base pair. This idea is supported experimentally for the GAAA loop of the P5b extension of the group I intron of Tetrahymena thermophila and the L9 GUGA terminal loop of the td intron of bacteriophage T4 (ref. 4). NMR has revealed the overall structure of the tetraloop for 12-nucleotide hairpins with GCAA and GAAA loops and models have been proposed for the interaction of GNRA tetraloops with base pairs in the minor groove of A-form RNA. Here we describe the crystal structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. The interactions we observe correlate with the specificity of GNRA tetraloops inferred from phylogenetic studies, suggesting that this complex is a legitimate model for intramolecular tertiary interactions mediated by GNRA tetraloops in large structured RNAs.

Controls on the physical properties of gas-hydrate-bearing sediments because of the interaction between gas hydrate and porous media

USGS Publications Warehouse

Lee, Myung W.; Collett, Timothy S.

2005-01-01

Physical properties of gas-hydrate-bearing sediments depend on the pore-scale interaction between gas hydrate and porous media as well as the amount of gas hydrate present. Well log measurements such as proton nuclear magnetic resonance (NMR) relaxation and electromagnetic propagation tool (EPT) techniques depend primarily on the bulk volume of gas hydrate in the pore space irrespective of the pore-scale interaction. However, elastic velocities or permeability depend on how gas hydrate is distributed in the pore space as well as the amount of gas hydrate. Gas-hydrate saturations estimated from NMR and EPT measurements are free of adjustable parameters; thus, the estimations are unbiased estimates of gas hydrate if the measurement is accurate. However, the amount of gas hydrate estimated from elastic velocities or electrical resistivities depends on many adjustable parameters and models related to the interaction of gas hydrate and porous media, so these estimates are model dependent and biased. NMR, EPT, elastic-wave velocity, electrical resistivity, and permeability measurements acquired in the Mallik 5L-38 well in the Mackenzie Delta, Canada, show that all of the well log evaluation techniques considered provide comparable gas-hydrate saturations in clean (low shale content) sandstone intervals with high gas-hydrate saturations. However, in shaly intervals, estimates from log measurement depending on the pore-scale interaction between gas hydrate and host sediments are higher than those estimates from measurements depending on the bulk volume of gas hydrate.

Topological Interaction by Entangled DNA Loops

NASA Astrophysics Data System (ADS)

Feng, Lang; Sha, Ruojie; Seeman, Nadrian. C.; Chaikin, Paul. M.

2012-11-01

We have discovered a new type of interaction between micro- or nanoscale particles that results from the entanglement of strands attached to their surfaces. Self-complementary DNA single strands on a particle can hybridize to form loops. A similar proximal particle can have its loops catenate with those of the first. Unlike conventional thermodynamic interparticle interactions, the catenation interaction is strongly history and protocol dependent, allowing for nonequilibrium particle assembly. The interactions can be controlled by an interesting combination of forces, temperature, light sensitive cross-linking and enzymatic unwinding of the topological links. This novel topological interaction may lead to new materials and phenomena such as particles strung on necklaces, confined motions on designed contours and surfaces, and colloidal Olympic gels.

Molecular Dynamic Simulation of Water Vapor and Determination of Diffusion Characteristics in the Pore

NASA Astrophysics Data System (ADS)

Nikonov, Eduard G.; Pavluš, Miron; Popovičová, Mária

2018-02-01

One of the varieties of pores, often found in natural or artificial building materials, are the so-called blind pores of dead-end or saccate type. Three-dimensional model of such kind of pore has been developed in this work. This model has been used for simulation of water vapor interaction with individual pore by molecular dynamics in combination with the diffusion equation method. Special investigations have been done to find dependencies between thermostats implementations and conservation of thermodynamic and statistical values of water vapor - pore system. The two types of evolution of water - pore system have been investigated: drying and wetting of the pore. Full research of diffusion coefficient, diffusion velocity and other diffusion parameters has been made.

Analysis of electrolyte transport through charged nanopores.

PubMed

Peters, P B; van Roij, R; Bazant, M Z; Biesheuvel, P M

2016-05-01

We revisit the classical problem of flow of electrolyte solutions through charged capillary nanopores or nanotubes as described by the capillary pore model (also called "space charge" theory). This theory assumes very long and thin pores and uses a one-dimensional flux-force formalism which relates fluxes (electrical current, salt flux, and fluid velocity) and driving forces (difference in electric potential, salt concentration, and pressure). We analyze the general case with overlapping electric double layers in the pore and a nonzero axial salt concentration gradient. The 3×3 matrix relating these quantities exhibits Onsager symmetry and we report a significant new simplification for the diagonal element relating axial salt flux to the gradient in chemical potential. We prove that Onsager symmetry is preserved under changes of variables, which we illustrate by transformation to a different flux-force matrix given by Gross and Osterle [J. Chem. Phys. 49, 228 (1968)JCPSA60021-960610.1063/1.1669814]. The capillary pore model is well suited to describe the nonlinear response of charged membranes or nanofluidic devices for electrokinetic energy conversion and water desalination, as long as the transverse ion profiles remain in local quasiequilibrium. As an example, we evaluate electrical power production from a salt concentration difference by reverse electrodialysis, using an efficiency versus power diagram. We show that since the capillary pore model allows for axial gradients in salt concentration, partial loops in current, salt flux, or fluid flow can develop in the pore. Predictions for macroscopic transport properties using a reduced model, where the potential and concentration are assumed to be invariant with radial coordinate ("uniform potential" or "fine capillary pore" model), are close to results of the full model.

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus.

PubMed

Smith, Emily M; Lajoie, Bryan R; Jain, Gaurav; Dekker, Job

2016-01-07

Three-dimensional genome structure plays an important role in gene regulation. Globally, chromosomes are organized into active and inactive compartments while, at the gene level, looping interactions connect promoters to regulatory elements. Topologically associating domains (TADs), typically several hundred kilobases in size, form an intermediate level of organization. Major questions include how TADs are formed and how they are related to looping interactions between genes and regulatory elements. Here we performed a focused 5C analysis of a 2.8 Mb chromosome 7 region surrounding CFTR in a panel of cell types. We find that the same TAD boundaries are present in all cell types, indicating that TADs represent a universal chromosome architecture. Furthermore, we find that these TAD boundaries are present irrespective of the expression and looping of genes located between them. In contrast, looping interactions between promoters and regulatory elements are cell-type specific and occur mostly within TADs. This is exemplified by the CFTR promoter that in different cell types interacts with distinct sets of distal cell-type-specific regulatory elements that are all located within the same TAD. Finally, we find that long-range associations between loci located in different TADs are also detected, but these display much lower interaction frequencies than looping interactions within TADs. Interestingly, interactions between TADs are also highly cell-type-specific and often involve loci clustered around TAD boundaries. These data point to key roles of invariant TAD boundaries in constraining as well as mediating cell-type-specific long-range interactions and gene regulation. Copyright © 2016 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Long-pore Electrostatics in Inward-rectifier Potassium Channels

PubMed Central

Robertson, Janice L.; Palmer, Lawrence G.; Roux, Benoît

2008-01-01

Inward-rectifier potassium (Kir) channels differ from the canonical K+ channel structure in that they possess a long extended pore (∼85 Å) for ion conduction that reaches deeply into the cytoplasm. This unique structural feature is presumably involved in regulating functional properties specific to Kir channels, such as conductance, rectification block, and ligand-dependent gating. To elucidate the underpinnings of these functional roles, we examine the electrostatics of an ion along this extended pore. Homology models are constructed based on the open-state model of KirBac1.1 for four mammalian Kir channels: Kir1.1/ROMK, Kir2.1/IRK, Kir3.1/GIRK, and Kir6.2/KATP. By solving the Poisson-Boltzmann equation, the electrostatic free energy of a K+ ion is determined along each pore, revealing that mammalian Kir channels provide a favorable environment for cations and suggesting the existence of high-density regions in the cytoplasmic domain and cavity. The contribution from the reaction field (the self-energy arising from the dielectric polarization induced by the ion's charge in the complex geometry of the pore) is unfavorable inside the long pore. However, this is well compensated by the electrostatic interaction with the static field arising from the protein charges and shielded by the dielectric surrounding. Decomposition of the static field provides a list of residues that display remarkable correspondence with existing mutagenesis data identifying amino acids that affect conduction and rectification. Many of these residues demonstrate interactions with the ion over long distances, up to 40 Å, suggesting that mutations potentially affect ion or blocker energetics over the entire pore. These results provide a foundation for understanding ion interactions in Kir channels and extend to the study of ion permeation, block, and gating in long, cation-specific pores. PMID:19001143

Pore Characterization of Shale Rock and Shale Interaction with Fluids at Reservoir Pressure-Temperature Conditions Using Small-Angle Neutron Scattering

NASA Astrophysics Data System (ADS)

Ding, M.; Hjelm, R.; Watkins, E.; Xu, H.; Pawar, R.

2015-12-01

Oil/gas produced from unconventional reservoirs has become strategically important for the US domestic energy independence. In unconventional realm, hydrocarbons are generated and stored in nanopores media ranging from a few to hundreds of nanometers. Fundamental knowledge of coupled thermo-hydro-mechanical-chemical (THMC) processes that control fluid flow and propagation within nano-pore confinement is critical for maximizing unconventional oil/gas production. The size and confinement of the nanometer pores creates many complex rock-fluid interface interactions. It is imperative to promote innovative experimental studies to decipher physical and chemical processes at the nanopore scale that govern hydrocarbon generation and mass transport of hydrocarbon mixtures in tight shale and other low permeability formations at reservoir pressure-temperature conditions. We have carried out laboratory investigations exploring quantitative relationship between pore characteristics of the Wolfcamp shale from Western Texas and the shale interaction with fluids at reservoir P-T conditions using small-angle neutron scattering (SANS). We have performed SANS measurements of the shale rock in single fluid (e.g., H2O and D2O) and multifluid (CH4/(30% H2O+70% D2O)) systems at various pressures up to 20000 psi and temperature up to 150 oF. Figure 1 shows our SANS data at different pressures with H2O as the pressure medium. Our data analysis using IRENA software suggests that the principal changes of pore volume in the shale occurred on smaller than 50 nm pores and pressure at 5000 psi (Figure 2). Our results also suggest that with increasing P, more water flows into pores; with decreasing P, water is retained in the pores.

Molecular dynamics study of the interaction between nanoscale interstitial dislocation loops and grain boundaries in BCC iron

NASA Astrophysics Data System (ADS)

Gao, N.; Perez, D.; Lu, G. H.; Wang, Z. G.

2018-01-01

Atomic simulations are used to investigate the interaction between nanoscale interstitial dislocation loops and grain boundaries (GBs), the subsequent evolution of the GBs' structures, and the resulting impact on mechanical properties, in BCC iron. The interaction between loops and GBs - Σ 3 { 111 } and Σ 3 { 112 } - is affected by the angle (θ) between the Burgers vector and the normal to the GB plane, as well as by the distribution of free volume (FV) and stress. Loops can be totally absorbed by Σ 3 { 111 } boundaries, while the interaction with Σ 3 { 112 } boundaries is found to change the Burgers vector and habit plane after absorption, but to otherwise leave the loop intact, resulting in selective absorption. When θ =90o , no absorption occurs in Σ 3 { 112 } . The stress accumulation induced by the absorption affects the local mechanical properties of GBs. In nanocrystalline iron sample, a similar phenomenon is also observed, resulting in rearrangement of GBs and grain growth.

Dynamics of the active site loops in catalyzing aminoacylation reaction in seryl and histidyl tRNA synthetases.

PubMed

Dutta, Saheb; Kundu, Soumya; Saha, Amrita; Nandi, Nilashis

2018-03-01

Aminoacylation reaction is the first step of protein biosynthesis. The catalytic reorganization at the active site of aminoacyl tRNA synthetases (aaRSs) is driven by the loop motions. There remain lacunae of understanding concerning the catalytic loop dynamics in aaRSs. We analyzed the functional loop dynamics in seryl tRNA synthetase from Methanopyrus kandleri ( mk SerRS) and histidyl tRNA synthetases from Thermus thermophilus ( tt HisRS), respectively, using molecular dynamics. Results confirm that the motif 2 loop and other active site loops are flexible spots within the catalytic domain. Catalytic residues of the loops form a network of interaction with the substrates to form a reactive state. The loops undergo transitions between closed state and open state and the relaxation of the constituent residues occurs in femtosecond to nanosecond time scale. Order parameters are higher for constituent catalytic residues which form a specific network of interaction with the substrates to form a reactive state compared to the Gly residues within the loop. The development of interaction is supported from mutation studies where the catalytic domain with mutated loop exhibits unfavorable binding energy with the substrates. During the open-close motion of the loops, the catalytic residues make relaxation by ultrafast librational motion as well as fast diffusive motion and subsequently relax rather slowly via slower diffusive motion. The Gly residues act as a hinge to facilitate the loop closing and opening by their faster relaxation behavior. The role of bound water is analyzed by comparing implicit solvent-based and explicit solvent-based simulations. Loops fail to form catalytically competent geometry in absence of water. The present result, for the first time reveals the nature of the active site loop dynamics in aaRS and their influence on catalysis.

The functional interaction between abaecin and pore-forming peptides indicates a general mechanism of antibacterial potentiation.

PubMed

Rahnamaeian, Mohammad; Cytryńska, Małgorzata; Zdybicka-Barabas, Agnieszka; Vilcinskas, Andreas

2016-04-01

Long-chain proline-rich antimicrobial peptides such as bumblebee abaecin show minimal activity against Gram-negative bacteria despite binding efficiently to specific intracellular targets. We recently reported that bumblebee abaecin interacts with Escherichia coli DnaK but shows negligible antibacterial activity unless it is combined with sublethal doses of the pore-forming peptide hymenoptaecin. These two bumblebee peptides are co-expressed in vivo in response to a bacterial challenge. Here we investigated whether abaecin interacts similarly with pore-forming peptides from other organisms by replacing hymenoptaecin with sublethal concentrations of cecropin A (0.3 μM) or stomoxyn (0.05 μM). We found that abaecin increased the membrane permeabilization effects of both peptides, confirming that it can reduce the minimal inhibitory concentrations of pore-forming peptides from other species. We also used atomic force microscopy to show that 20 μM abaecin combined with sublethal concentrations of cecropin A or stomoxyn causes profound structural changes to the bacterial cell surface. Our data indicate that the potentiating functional interaction between abaecin and pore-forming peptides is not restricted to specific co-expressed peptides from the same species but is likely to be a general mechanism. Combination therapies based on diverse insect-derived peptides could therefore be used to tackle bacteria that are recalcitrant to current antibiotics. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Cohesiveness tunes assembly and morphology of FG nucleoporin domain meshworks – Implications for nuclear pore permeability

PubMed Central

Eisele, Nico B.; Labokha, Aksana A.; Frey, Steffen; Görlich, Dirk; Richter, Ralf P.

2013-01-01

Nuclear pore complexes control the exchange of macromolecules between the cytoplasm and the nucleus. A selective permeability barrier that arises from a supramolecular assembly of intrinsically unfolded nucleoporin domains rich in phenylalanine-glycine dipeptides (FG domains) fills the nuclear pore. There is increasing evidence that selective transport requires cohesive FG domain interactions. To understand the functional roles of cohesive interactions, we studied monolayers of end-grafted FG domains as a bottom-up nanoscale model system of the permeability barrier. Based on detailed physicochemical analysis of the model films and comparison of the data with polymer theory, we propose that cohesiveness is tuned to promote rapid assembly of the permeability barrier and to generate a stable and compact pore-filling meshwork with a small mesh size. Our results highlight the functional importance of weak interactions, typically a few kBT per chain, and contribute important information to understand the mechanism of size-selective transport. PMID:24138862

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Qingqing; Li, Huilin; Wang, Tong

Perfringolysin O (PFO) is a transmembrane (TM) β-barrel protein that inserts into mammalian cell membranes. Once inserted into membranes, PFO assembles into pore-forming oligomers containing 30–50 PFO monomers. These form a pore of up to 300 Å, far exceeding the size of most other proteinaceous pores. In this study, we found that altering PFO TM segment length can alter the size of PFO pores. A PFO mutant with lengthened TM segments oligomerized to a similar extent as wild-type PFO, and exhibited pore-forming activity and a pore size very similar to wild-type PFO as measured by electron microscopy and a leakagemore » assay. In contrast, PFO with shortened TM segments exhibited a large reduction in pore-forming activity and pore size. This suggests that the interaction between TM segments can greatly affect the size of pores formed by TM β-barrel proteins. PFO may be a promising candidate for engineering pore size for various applications.« less

Experimental investigation on variation of physical properties of coal samples subjected to microwave irradiation

NASA Astrophysics Data System (ADS)

Hu, Guozhong; Yang, Nan; Xu, Guang; Xu, Jialin

2018-03-01

The gas drainage rate of low-permeability coal seam is generally less than satisfactory. This leads to the gas disaster of coal mine, and largely restricts the extraction of coalbed methane (CBM), and increases the emission of greenhouse gases in the mining area. Consequently, enhancing the gas drainage rate is an urgent challenge. To solve this problem, a new approach of using microwave irradiation (MWR) as a non-contact physical field excitation method to enhance gas drainage has been attempted. In order to evaluate the feasibility of this method, the methane adsorption, diffusion and penetrability of coal subjected to MWR were experimentally investigated. The variation of methane adsorbed amount, methane diffusion speed and absorption loop for the coal sample before and after MWR were obtained. The findings show that the MWR can change the adsorption property and reduce the methane adsorption capacity of coal. Moreover, the methane diffusion characteristic curves for both the irradiated coal samples and theoriginal coal samples present the same trend. The irradiated coal samples have better methane diffusion ability than the original ones. As the adsorbed methane decreases, the methane diffusion speed increases or remain the same for the sample subjected to MWR. Furthermore, compared to the original coal samples, the area of the absorption loop for irradiated samples increases, especially for the micro-pore and medium-pore stage. This leads to the increase of open pores in the coal, thus improving the gas penetrability of coal. This study provides supports for positive MWR effects on changing the methane adsorption and improving the methane diffusion and the gas penetrability properties of coal samples.

Structural dynamics of the MecA-ClpC complex: a type II AAA+ protein unfolding machine.

PubMed

Liu, Jing; Mei, Ziqing; Li, Ningning; Qi, Yutao; Xu, Yanji; Shi, Yigong; Wang, Feng; Lei, Jianlin; Gao, Ning

2013-06-14

The MecA-ClpC complex is a bacterial type II AAA(+) molecular machine responsible for regulated unfolding of substrates, such as transcription factors ComK and ComS, and targeting them to ClpP for degradation. The six subunits of the MecA-ClpC complex form a closed barrel-like structure, featured with three stacked rings and a hollow passage, where substrates are threaded and translocated through successive pores. Although the general concepts of how polypeptides are unfolded and translocated by internal pore loops of AAA(+) proteins have long been conceived, the detailed mechanistic model remains elusive. With cryoelectron microscopy, we captured four different structures of the MecA-ClpC complexes. These complexes differ in the nucleotide binding states of the two AAA(+) rings and therefore might presumably reflect distinctive, representative snapshots from a dynamic unfolding cycle of this hexameric complex. Structural analysis reveals that nucleotide binding and hydrolysis modulate the hexameric complex in a number of ways, including the opening of the N-terminal ring, the axial and radial positions of pore loops, the compactness of the C-terminal ring, as well as the relative rotation between the two nucleotide-binding domain rings. More importantly, our structural and biochemical data indicate there is an active allosteric communication between the two AAA(+) rings and suggest that concerted actions of the two AAA(+) rings are required for the efficiency of the substrate unfolding and translocation. These findings provide important mechanistic insights into the dynamic cycle of the MecA-ClpC unfoldase and especially lay a foundation toward the complete understanding of the structural dynamics of the general type II AAA(+) hexamers.

Fluxoids configurations in finite superconducting networks

NASA Astrophysics Data System (ADS)

Sharon, Omri J.; Haham, Noam; Shaulov, Avner A.; Yeshurun, Yosef

2017-12-01

Analysis of superconducting ladders consisting of rectangular loops, yields an Ising like expression for the total energy of the ladders as a function of the loops vorticities and the applied magnetic field. This expression shows that fluxoids can be treated as repulsively interacting objects driven towards the ladder center by the applied field. Distinctive repulsive interactions between fluxoids are obtained depending on the ratio l between the loops length and the common width of adjacent loops. A 'short range' and a 'long range' interactions obtained for l ≳ 1 and l ≪ 1, respectively, give rise to remarkably different fluxoid configurations. The different configurations of fluxoids in different types of ladders are illustrated by simulations.

Chemotherapy drugs form ion pores in membranes due to physical interactions with lipids.

PubMed

Ashrafuzzaman, Mohammad; Tseng, Chih-Yuan; Duszyk, Marek; Tuszynski, Jack A

2012-12-01

We demonstrate the effects on membrane of the tubulin-binding chemotherapy drugs: thiocolchicoside and taxol. Electrophysiology recordings across lipid membranes in aqueous phases containing drugs were used to investigate the drug effects on membrane conductance. Molecular dynamics simulation of the chemotherapy drug-lipid complexes was used to elucidate the mechanism at an atomistic level. Both drugs are observed to induce stable ion-flowing pores across membranes. Discrete pore current-time plots exhibit triangular conductance events in contrast to rectangular ones found for ion channels. Molecular dynamics simulations indicate that drugs and lipids experience electrostatic and van der Waals interactions for short periods of time when found within each other's proximity. The energies from these two interactions are found to be similar to the energies derived theoretically using the screened Coulomb and the van der Waals interactions between peptides and lipids due to mainly their charge properties while forming peptide-induced ion channels in lipid bilayers. Experimental and in silico studies together suggest that the chemotherapy drugs induce ion pores inside lipid membranes due to drug-lipid physical interactions. The findings reveal cytotoxic effects of drugs on the cell membrane, which may aid in novel drug development for treatment of cancer and other diseases. © 2012 John Wiley & Sons A/S.

Multiscale modeling of shock wave localization in porous energetic material

NASA Astrophysics Data System (ADS)

Wood, M. A.; Kittell, D. E.; Yarrington, C. D.; Thompson, A. P.

2018-01-01

Shock wave interactions with defects, such as pores, are known to play a key role in the chemical initiation of energetic materials. The shock response of hexanitrostilbene is studied through a combination of large-scale reactive molecular dynamics and mesoscale hydrodynamic simulations. In order to extend our simulation capability at the mesoscale to include weak shock conditions (<6 GPa), atomistic simulations of pore collapse are used to define a strain-rate-dependent strength model. Comparing these simulation methods allows us to impose physically reasonable constraints on the mesoscale model parameters. In doing so, we have been able to study shock waves interacting with pores as a function of this viscoplastic material response. We find that the pore collapse behavior of weak shocks is characteristically different than that of strong shocks.

Immobilized glucose oxidase--catalase and their deactivation in a differential-bed loop reactor.

PubMed

Prenosil, J E

1979-01-01

Glucose oxidase containing catalase was immobilized with a copolymer of phenylenediamine and glutaraldehyde on pumice and titania carrier to study the enzymatic oxidation of glucose in a differential-bed loop reactor. The reaction rate was found to be first order with respect to the concentration of limiting oxygen substrate, suggesting a strong external mass-transfer resistance for all the flow rates used. The partial pressure of oxygen was varied from 21.3 up to 202.6 kPa. The use of a differential-bed loop reactor for the determination of the active enzyme concentration in the catalyst with negligible internal pore diffusion resistance is shown. Catalyst deactivation was studied, especially with respect to the presence of catalase. It is believed that the hydrogen peroxide formed in the oxidation reaction deactivates catalase first; if an excess of catalase is present, the deactivation of glucose oxidase remains small. The mathematical model subsequently developed adequately describes the experimental results.

Heat removal from bipolar transistor by loop heat pipe with nickel and copper porous structures.

PubMed

Nemec, Patrik; Smitka, Martin; Malcho, Milan

2014-01-01

Loop heat pipes (LHPs) are used in many branches of industry, mainly for cooling of electrical elements and systems. The loop heat pipe is a vapour-liquid phase-change device that transfers heat from evaporator to condenser. One of the most important parts of the LHP is the porous wick structure. The wick structure provides capillary force to circulate the working fluid. To achieve good thermal performance of LHP, capillary wicks with high permeability and porosity and fine pore radius are expected. The aim of this work was to develop porous structures from copper and nickel powder with different grain sizes. For experiment copper powder with grain size of 50 and 100 μm and nickel powder with grain size of 10 and 25 μm were used. Analysis of these porous structures and LHP design are described in the paper. And the measurements' influences of porous structures in LHP on heat removal from the insulated gate bipolar transistor (IGBT) have been made.

Heat Removal from Bipolar Transistor by Loop Heat Pipe with Nickel and Copper Porous Structures

PubMed Central

Smitka, Martin; Malcho, Milan

2014-01-01

Loop heat pipes (LHPs) are used in many branches of industry, mainly for cooling of electrical elements and systems. The loop heat pipe is a vapour-liquid phase-change device that transfers heat from evaporator to condenser. One of the most important parts of the LHP is the porous wick structure. The wick structure provides capillary force to circulate the working fluid. To achieve good thermal performance of LHP, capillary wicks with high permeability and porosity and fine pore radius are expected. The aim of this work was to develop porous structures from copper and nickel powder with different grain sizes. For experiment copper powder with grain size of 50 and 100 μm and nickel powder with grain size of 10 and 25 μm were used. Analysis of these porous structures and LHP design are described in the paper. And the measurements' influences of porous structures in LHP on heat removal from the insulated gate bipolar transistor (IGBT) have been made. PMID:24959622

Val-407 and Ile-408 in the β5′-Loop of Pancreatic Lipase Mediate Lipase-Colipase Interactions in the Presence of Bile Salt Micelles*

PubMed Central

Freie, Angela Bourbon; Ferrato, Francine; Carrière, Frédéric; Lowe, Mark E.

2013-01-01

In a previous study, we demonstrated that the β5′-loop in the C-terminal domain of human pancreatic triglyceride lipase (hPTL) makes a major contribution in the function of hPTL (Chahinian et al. (2002) Biochemistry 41, 13725–13735). In the present study, we characterized the contribution of three residues in the β5′-loop, Val-407, Ile-408, and Leu-412, to the function of hPTL. By substituting charged residues, aspartate or lysine, in these positions, we altered the hydrophilic to lipophilic ratio of the β5′-loop. Each of the mutants was expressed, purified, and characterized for activity and binding with both monolayers and emulsions and for binding to colipase. Experiments with monolayers and with emulsions suggested that the interaction of hPTL with a phospholipid monolayer differs from the interaction of the hPTL-colipase complex with a dicaprin monolayer or a triglyceride emulsion (i.e. neutral lipids). Val-407, Ile-408, and Leu-412 make major contributions to interactions with monolayers, whereas only Val-407 and Ile-408 appear essential for activity on triglyceride emulsions in the presence of bile salt micelles. In solutions of taurodeoxycholate at micellar concentrations, a major effect of the β5′-loop mutations is to change the interaction between hPTL and colipase. These observations support a major contribution of residues in the β5′-loop in the function of hPTL and suggest that a third partner, bile salt micelles or the lipid interface or both, influence the binding of colipase and hPTL through interactions with the β5′-loop. PMID:16431912

A new karst-dwelling bent-toed gecko (Squamata: Gekkonidae: Cyrtodactylus) from Xiangkhoang Province, northeastern Laos.

PubMed

Nazarov, Roman A; Pauwels, Olivier S G; Konstantinov, Evgeniy L; Chulisov, Anatoliy S; Orlov, Nikolai L; Poyarkov, Nikolay A

2018-05-18

We describe a new karst-dwelling Cyrtodactylus from Ban Thathom, Xiangkhoang Province, northeastern Laos. The new species can be distinguished from other congeners by having four dark dorsal bands between limb insertions, a discontinuous nuchal loop, 10 precloacal pores in males or 10-12 precloacal pits (females) separated by a diastema from a series of enlarged femoral scales bearing 18 or 19 pores (male) or 8-10 pits (females) along each femur, 14-18 dorsal tubercle rows at midbody, no precloacal groove, 30-36 midbody scale rows across belly between ventrolateral skin folds, transversely enlarged subcaudal plates, and a maximal known snout-vent length of 75.5 mm. Our description brings to 22 the number of Cyrtodactylus species recorded from Laos.

Reversal modes in FeCoNi nanowire arrays: Correlation between magnetostatic interactions and nanowires length

NASA Astrophysics Data System (ADS)

Samanifar, S.; Almasi Kashi, M.; Ramazani, A.; Alikhani, M.

2015-03-01

FeCoNi nanowire arrays (175 nm in diameter and lengths ranging from 5 to 40 μm) were fabricated into nanopores of hard-anodized aluminum oxide templates using pulsed ac electrodeposition technique. Increasing the length had no considerable effect on the composition and crystalline characteristics of Fe47Co38Ni15 nanowires (NWs). By eliminating the dendrites formed at the bottom of the pores, we report a careful investigation on the effect of magnetostatic interactions on magnetic properties and the effect of nanowire length on reversal modes. Hysteresis loop measurements indicated that increasing the length decreases coercivity and squareness values. On the other hand, first-order reversal curve measurements show a linear correlation between the magnetostatic interactions and length of NWs. Comparing reversal modes of the NWs both experimentally and theoretically using angular dependence of coercivity, we find that when L≤22 μm, a vortex domain wall mode is only occurred. When L>22 μm, a non-monotonic behavior indicates a transition from the vortex to transverse domain wall propagation. As a result, a critical length was found above which the transition between the reversal modes is occurred due the enhanced interactions. The transition angle also shifts toward a lower angle as the length increases. Moreover, with increasing length from 22 to 31 μm, the single domain structure of NWs changes to a pseudo single domain state. A multidomain-like behavior is also found for the longest NWs length.

Charged string loops in Reissner-Nordström black hole background

NASA Astrophysics Data System (ADS)

Oteev, Tursinbay; Kološ, Martin; Stuchlík, Zdeněk

2018-03-01

We study the motion of current carrying charged string loops in the Reissner-Nordström black hole background combining the gravitational and electromagnetic field. Introducing new electromagnetic interaction between central charge and charged string loop makes the string loop equations of motion to be non-integrable even in the flat spacetime limit, but it can be governed by an effective potential even in the black hole background. We classify different types of the string loop trajectories using effective potential approach, and we compare the innermost stable string loop positions with loci of the charged particle innermost stable orbits. We examine string loop small oscillations around minima of the string loop effective potential, and we plot radial profiles of the string loop oscillation frequencies for both the radial and vertical modes. We construct charged string loop quasi-periodic oscillations model and we compare it with observed data from microquasars GRO 1655-40, XTE 1550-564, and GRS 1915+105. We also study the acceleration of current carrying string loops along the vertical axis and the string loop ejection from RN black hole neighbourhood, taking also into account the electromagnetic interaction.

Effect of orientation of prismatic dislocation loops on interaction with free surfaces in BCC iron

NASA Astrophysics Data System (ADS)

Fikar, Jan; Gröger, Roman; Schäublin, Robin

2017-12-01

The prismatic loops appear in metals as a result of high-energy irradiation. Understanding their formation and interaction is important for quantification of irradiation-induced deterioration of mechanical properties. Characterization of dislocation loops in thin foils is commonly made using transmission electron microscopy (TEM), but the results are inevitably influenced by the proximity of free surfaces. The prismatic loops are attracted to free surfaces by image forces. Depending on the type, shape, size, orientation and depth of the loop in the foil, they can escape to the free surface creating denuded loop-free zones and thus invalidating TEM observations. In our previous studies we described a simple general method to determine the critical depth and the critical stress to move prismatic dislocation loops. The critical depths can be further used to correct measurements of the loop density by TEM. Here, we use this procedure to compare 〈100〉 loops and 1/2 〈111〉 loops in body-centered cubic (BCC) iron. The influences of the interatomic potential and the loop orientation are studied in detail. The difference between interstitial and vacancy type loop is also investigated.

Interaction of Zwitterionic Penicillins with the OmpF Channel Facilitates Their Translocation

PubMed Central

Danelon, Christophe; Nestorovich, Ekaterina M.; Winterhalter, Mathias; Ceccarelli, Matteo; Bezrukov, Sergey M.

2006-01-01

To study translocation of β-lactam antibiotics of different size and charge across the outer bacterial membrane, we combine an analysis of ion currents through single trimeric outer membrane protein F (OmpF) porins in planar lipid bilayers with molecular dynamics simulations. Because the size of penicillin molecules is close to the size of the narrowest part of the OmpF pore, penicillins occlude the pore during their translocation. Favorably interacting penicillins cause time-resolvable transient blockages of the small-ion current through the channel and thereby provide information about their dynamics within the pore. Analyzing these random fluctuations, we find that ampicillin and amoxicillin have a relatively high affinity for OmpF. In contrast, no or only a weak interaction is detected for carbenicillin, azlocillin, and piperacillin. Molecular dynamics simulations suggest a possible pathway of these drugs through the OmpF channel and rationalize our experimental findings. For zwitterionic ampicillin and amoxicillin, we identify a region of binding sites near the narrowest part of the channel pore. Interactions with these sites partially compensate for the entropic cost of drug confinement by the channel. Whereas azlocillin and piperacillin are clearly too big to pass through the channel constriction, dianionic carbenicillin does not find an efficient binding region in the constriction zone. Carbenicillin's favorable interactions are limited to the extracellular vestibule. These observations confirm our earlier suggestion that a set of high-affinity sites at the narrowest part of the OmpF channel improves a drug's ability to cross the membrane via the pore. PMID:16339889

Decreasing transmembrane segment length greatly decreases perfringolysin O pore size

DOE PAGES

Lin, Qingqing; Li, Huilin; Wang, Tong; ...

2015-04-08

Perfringolysin O (PFO) is a transmembrane (TM) β-barrel protein that inserts into mammalian cell membranes. Once inserted into membranes, PFO assembles into pore-forming oligomers containing 30–50 PFO monomers. These form a pore of up to 300 Å, far exceeding the size of most other proteinaceous pores. In this study, we found that altering PFO TM segment length can alter the size of PFO pores. A PFO mutant with lengthened TM segments oligomerized to a similar extent as wild-type PFO, and exhibited pore-forming activity and a pore size very similar to wild-type PFO as measured by electron microscopy and a leakagemore » assay. In contrast, PFO with shortened TM segments exhibited a large reduction in pore-forming activity and pore size. This suggests that the interaction between TM segments can greatly affect the size of pores formed by TM β-barrel proteins. PFO may be a promising candidate for engineering pore size for various applications.« less

High heat flux loop heat pipes

NASA Astrophysics Data System (ADS)

North, Mark T.; Sarraf, David B.; Rosenfeld, John H.; Maidanik, Yuri F.; Vershinin, Sergey

1997-01-01

Loop Heat Pipes (LHPs) can transport very large thermal power loads, over long distances, through flexible, small diameter tubes and against high gravitational heads. While recent LHPs have transported as much as 1500 W, the peak heat flux through a LHP's evaporator has been limited to about 0.07 MW/m2. This limitation is due to the arrangement of vapor passages next to the heat load which is one of the conditions necessary to ensure self priming of the device. This paper describes work aimed at raising this limit by threefold to tenfold. Two approaches were pursued. One optimized the vapor passage geometry for the high heat flux conditions. The geometry improved the heat flow into the wick and working fluid. This approach also employed a finer pored wick to support higher vapor flow losses. The second approach used a bidisperse wick material within the circumferential vapor passages. The bidisperse material increased the thermal conductivity and the evaporative surface area in the region of highest heat flux, while providing a flow path for the vapor. Proof-of-concept devices were fabricated and tested for each approach. Both devices operated as designed and both demonstrated operation at a heat flux of 0.70 MW/m2. This performance exceeded the known state of the art by a factor of more than six for both conventional heat pipes and for loop heat pipes using ammonia. In addition, the bidisperse-wick device demonstrated boiling heat transfer coefficients up to 100,000 W/m2.K, and the fine pored device demonstrated an orientation independence with its performance essentially unaffected by whether its evaporator was positioned above, below or level with the condenser.

Effects of human chromosome 12 on interactions between Tat and TAR of human immunodeficiency virus type 1.

PubMed Central

Alonso, A; Cujec, T P; Peterlin, B M

1994-01-01

Rates of transcriptions of the human immunodeficiency virus are greatly increased by the viral trans activator Tat. In vitro, Tat binds to the 5' bulge of the trans-activation response (TAR) RNA stem-loop, which is present in all viral transcripts. In human cells, the central loop in TAR and its cellular RNA-binding proteins are also critical for the function of Tat. Previously, we demonstrated that in rodent cells (CHO cells), but not in those which contain the human chromosome 12 (CHO12 cells), Tat-TAR interactions are compromised. In this study, we examined the roles of the bulge and loop in TAR in Tat trans activation in these cells. Whereas low levels of trans activation depended solely on interactions between Tat and the bulge in CHO cells, high levels of trans activation depended also on interactions between Tat and the loop in CHO12 cells. Since the TAR loop binding proteins in these two cell lines were identical and different from their human counterpart, the human chromosome 12 does not encode TAR loop binding proteins. In vivo binding competition studies with TAR decoys confirmed that the binding of Tat to TAR is more efficient in CHO12 cells. Thus, the protein(s) encoded on human chromosome 12 helps to tether Tat to TAR via its loop, which results in high levels of trans activation. Images PMID:8083988

A conformational landscape for alginate secretion across the outer membrane of Pseudomonas aeruginosa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tan, Jingquan; Rouse, Sarah L.; Li, Dianfan

2014-08-01

Crystal structures of the β-barrel porin AlgE reveal a mechanism whereby alginate is exported from P. aeruginosa for biofilm formation. The exopolysaccharide alginate is an important component of biofilms produced by Pseudomonas aeruginosa, a major pathogen that contributes to the demise of cystic fibrosis patients. Alginate exits the cell via the outer membrane porin AlgE. X-ray structures of several AlgE crystal forms are reported here. Whilst all share a common β-barrel constitution, they differ in the degree to which loops L2 and T8 are ordered. L2 and T8 have been identified as an extracellular gate (E-gate) and a periplasmic gatemore » (P-gate), respectively, that reside on either side of an alginate-selectivity pore located midway through AlgE. Passage of alginate across the membrane is proposed to be regulated by the sequential opening and closing of the two gates. In one crystal form, the selectivity pore contains a bound citrate. Because citrate mimics the uronate monomers of alginate, its location is taken to highlight a route through AlgE taken by alginate as it crosses the pore. Docking and molecular-dynamics simulations support and extend the proposed transport mechanism. Specifically, the P-gate and E-gate are flexible and move between open and closed states. Citrate can leave the selectivity pore bidirectionally. Alginate docks stably in a linear conformation through the open pore. To translate across the pore, a force is required that presumably is provided by the alginate-synthesis machinery. Accessing the open pore is facilitated by complex formation between AlgE and the periplasmic protein AlgK. Alginate can thread through a continuous pore in the complex, suggesting that AlgK pre-orients newly synthesized exopolysaccharide for delivery to AlgE.« less

Possible pore size effects on the state of tris(8-quinolinato)aluminum(III) (Alq3) adsorbed in mesoporous silicas and their temperature dependence.

PubMed

Tagaya, Motohiro; Ogawa, Makoto

2008-12-07

The states of tris(8-quinolinato)aluminum(III) (Alq3) adsorbed in mesoporous silicas with different pore sizes (2.5, 3.1 and 5.0 nm) were investigated. Alq3 was successfully occluded into the mesoporous silicas from solution and the adsorbed amount of Alq3 per BET surface area was effectively controlled by changing the added amount Alq3 to the solution. The state of Alq3 in the mesopore varied depending on the pore size as well as the adsorbed amount of Alq3 as revealed by variation of the photoluminescence spectra. The luminescence of the adsorbed Alq3 was found to be temperature-dependent, indicating the mobility of the adsorbed Alq3 to temperature variations. The temperature-dependence also depended on the pore size. The guest-guest interactions between Alq3 molecules as well as the host-guest interactions between Alq3 and the mesopore were controlled by the pore size.

Atomistic study of the hardening of ferritic iron by Ni-Cr decorated dislocation loops

NASA Astrophysics Data System (ADS)

Bonny, G.; Bakaev, A.; Terentyev, D.; Zhurkin, E.; Posselt, M.

2018-01-01

The exact nature of the radiation defects causing hardening in reactor structural steels consists of several components that are not yet clearly determined. While generally, the hardening is attributed to dislocation loops, voids and secondary phases (radiation-induced precipitates), recent advanced experimental and computational studies point to the importance of solute-rich clusters (SRCs). Depending on the exact composition of the steel, SRCs may contain Mn, Ni and Cu (e.g. in reactor pressure vessel steels) or Ni, Cr, Si, Mn (e.g. in high-chromium steels for generation IV and fusion applications). One of the hypotheses currently implied to explain their formation is the process of radiation-induced diffusion and segregation of these elements to small dislocation loops (heterogeneous nucleation), so that the distinction between SRCs and loops becomes somewhat blurred. In this work, we perform an atomistic study to investigate the enrichment of loops by Ni and Cr solutes and their interaction with an edge dislocation. The dislocation loops decorated with Ni and Cr solutes are obtained by Monte Carlo simulations, while the effect of solute segregation on the loop's strength and interaction mechanism is then addressed by large scale molecular dynamics simulations. The synergy of the Cr-Ni interaction and their competition to occupy positions in the dislocation loop core are specifically clarified.

Annealing effect on thermodynamic and physical properties of mesoporous silicon: A simulation and nitrogen sorption study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Pushpendra, E-mail: pkumar-iitd@yahoo.com; Huber, Patrick, E-mail: patrick.huber@tuhh.de

Discovery of porous silicon formation in silicon substrate in 1956 while electro-polishing crystalline Si in hydrofluoric acid (HF), has triggered large scale investigations of porous silicon formation and their changes in physical and chemical properties with thermal and chemical treatment. A nitrogen sorption study is used to investigate the effect of thermal annealing on electrochemically etched mesoporous silicon (PS). The PS was thermally annealed from 200°C to 800°C for 1 hr in the presence of air. It was shown that the pore diameter and porosity of PS vary with annealing temperature. The experimentally obtained adsorption / desorption isotherms show hysteresis typicalmore » for capillary condensation in porous materials. A simulation study based on Saam and Cole model was performed and compared with experimentally observed sorption isotherms to study the physics behind of hysteresis formation. We discuss the shape of the hysteresis loops in the framework of the morphology of the layers. The different behavior of adsorption and desorption of nitrogen in PS with pore diameter was discussed in terms of concave menisci formation inside the pore space, which was shown to related with the induced pressure in varying the pore diameter from 7.2 nm to 3.4 nm.« less

Thermodynamic characterization of the multivalent interactions underlying rapid and selective translocation through the nuclear pore complex

PubMed Central

Hayama, Ryo; Sparks, Samuel; Hecht, Lee M.; Dutta, Kaushik; Karp, Jerome M.; Cabana, Christina M.; Rout, Michael P.; Cowburn, David

2018-01-01

Intrinsically disordered proteins (IDPs) play important roles in many biological systems. Given the vast conformational space that IDPs can explore, the thermodynamics of the interactions with their partners is closely linked to their biological functions. Intrinsically disordered regions of Phe–Gly nucleoporins (FG Nups) that contain multiple phenylalanine–glycine repeats are of particular interest, as their interactions with transport factors (TFs) underlie the paradoxically rapid yet also highly selective transport of macromolecules mediated by the nuclear pore complex. Here, we used NMR and isothermal titration calorimetry to thermodynamically characterize these multivalent interactions. These analyses revealed that a combination of low per-FG motif affinity and the enthalpy–entropy balance prevents high-avidity interaction between FG Nups and TFs, whereas the large number of FG motifs promotes frequent FG–TF contacts, resulting in enhanced selectivity. Our thermodynamic model underlines the importance of functional disorder of FG Nups. It helps explain the rapid and selective translocation of TFs through the nuclear pore complex and further expands our understanding of the mechanisms of “fuzzy” interactions involving IDPs. PMID:29374059

Multiscale modeling of shock wave localization in porous energetic material

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wood, M. A.; Kittell, D. E.; Yarrington, C. D.

Shock wave interactions with defects, such as pores, are known to play a key role in the chemical initiation of energetic materials. The shock response of hexanitrostilbene is studied through a combination of large-scale reactive molecular dynamics and mesoscale hydrodynamic simulations. In order to extend our simulation capability at the mesoscale to include weak shock conditions (< 6 GPa), atomistic simulations of pore collapse are used here to define a strain-rate-dependent strength model. Comparing these simulation methods allows us to impose physically reasonable constraints on the mesoscale model parameters. In doing so, we have been able to study shock wavesmore » interacting with pores as a function of this viscoplastic material response. Finally, we find that the pore collapse behavior of weak shocks is characteristically different than that of strong shocks.« less

Multiscale modeling of shock wave localization in porous energetic material

DOE PAGES

Wood, M. A.; Kittell, D. E.; Yarrington, C. D.; ...

2018-01-30

Shock wave interactions with defects, such as pores, are known to play a key role in the chemical initiation of energetic materials. The shock response of hexanitrostilbene is studied through a combination of large-scale reactive molecular dynamics and mesoscale hydrodynamic simulations. In order to extend our simulation capability at the mesoscale to include weak shock conditions (< 6 GPa), atomistic simulations of pore collapse are used here to define a strain-rate-dependent strength model. Comparing these simulation methods allows us to impose physically reasonable constraints on the mesoscale model parameters. In doing so, we have been able to study shock wavesmore » interacting with pores as a function of this viscoplastic material response. Finally, we find that the pore collapse behavior of weak shocks is characteristically different than that of strong shocks.« less

Nanoengineered field induced charge separation membranes manufacture thereof

DOEpatents

O'Brien, Kevin C.; Haslam, Jeffery J.; Bourcier, William L.; Floyd, III, William Clary

2016-08-02

A device according to one embodiment includes a porous membrane having a surface charge and pore configuration characterized by a double layer overlap effect being present in pores of the membrane, where the porous membrane includes functional groups that preferentially interact with either cations or anions. A device according to another embodiment includes a porous membrane having a surface charge in pores thereof sufficient to impart anion or cation selectivity in the pores. Additional devices, systems and methods are also presented.

The Influence of Pores in Track Etched Membranes and Prepared on their Base Polymer/Metal Composites on their Fracture Strength

NASA Astrophysics Data System (ADS)

Gumirova, V. N.; Bedin, S. A.; Abdurashidova, G. S.; Razumovskaya, I. V.

The strength of track etched membranes and prepared on their base polymer/metal composites is analysed in point of view of the pores form evolution during the extension and the interaction of elastic mechanical fields on closely positioned pores. The stress-strain curves for track membranes and composites PET/Cu are demonstrated for pore density 1.2×107сm-2 and diameters from 0.06 μm to 2.9 μm

Replacing the Axial Ligand Tyrosine 75 or Its Hydrogen Bond Partner Histidine 83 Minimally Affects Hemin Acquisition by the Hemophore HasAp from Pseudomonas aeruginosa

PubMed Central

2015-01-01

Hemophores from Pseudomonas aeruginosa (HasAp), Serratia marcescens (HasAsm), and Yersinia pestis (HasAyp) bind hemin between two loops. One of the loops harbors conserved axial ligand Tyr75 (Y75 loop) in all three structures, whereas the second loop (H32 loop) contains axial ligand His32 in HasAp and HasAsm, but a noncoordinating Gln32 in HasAyp. Binding of hemin to the Y75 loop of HasAp or HasAsm causes a large rearrangement of the H32 loop that allows His32 coordination. The Q32 loop in apo-HasAyp is already in the closed conformation, such that binding of hemin to the conserved Y75 loop occurs with minimal structural rearrangement and without coordinative interaction with the Q32 loop. In this study, structural and spectroscopic investigations of the hemophore HasAp were conducted to probe (i) the role of the conserved Tyr75 loop in hemin binding and (ii) the proposed requirement of the His83–Tyr75 hydrogen bond to allow the coordination of hemin by Tyr75. High-resolution crystal structures of H83A holo-HasAp obtained at pH 6.5 (0.89 Å) and pH 5.4 (1.25 Å) show that Tyr75 remains coordinated to the heme iron, and that a water molecule can substitute for Nδ of His83 to interact with the Oη atom of Tyr75, likely stabilizing the Tyr75–Fe interaction. Nuclear magnetic resonance spectroscopy revealed that in apo-Y75A and apo-H83A HasAp, the Y75 loop is disordered, and that disorder propagates to nearby elements of secondary structure, suggesting that His83 Nδ–Tyr75 Oη interaction is important to the organization of the Y75 loop in apo-HasA. Kinetic analysis of hemin loading conducted via stopped-flow UV–vis and rapid-freeze-quench resonance Raman shows that both mutants load hemin with biphasic kinetic parameters that are not significantly dissimilar from those previously observed for wild-type HasAp. When the structural and kinetic data are taken together, a tentative model emerges, which suggests that HasA hemophores utilize hydrophobic, π–π stacking, and van der Waals interactions to load hemin efficiently, while axial ligation likely functions to slow hemin release, thus allowing the hemophore to meet the challenge of capturing hemin under inhospitable conditions and delivering it selectively to its cognate receptor. PMID:24625274

The Effect of the Pore Entrance on Particle Motion in Slit Pores: Implications for Ultrathin Membranes

PubMed Central

Delavari, Armin; Baltus, Ruth

2017-01-01

Membrane rejection models generally neglect the effect of the pore entrance on intrapore particle transport. However, entrance effects are expected to be particularly important with ultrathin membranes, where membrane thickness is typically comparable to pore size. In this work, a 2D model was developed to simulate particle motion for spherical particles moving at small Re and infinite Pe from the reservoir outside the pore into a slit pore. Using a finite element method, particles were tracked as they accelerated across the pore entrance until they reached a steady velocity in the pore. The axial position in the pore where particle motion becomes steady is defined as the particle entrance length (PEL). PELs were found to be comparable to the fluid entrance length, larger than the pore size and larger than the thickness typical of many ultrathin membranes. Results also show that, in the absence of particle diffusion, hydrodynamic particle–membrane interactions at the pore mouth result in particle “funneling” in the pore, yielding cross-pore particle concentration profiles focused at the pore centerline. The implications of these phenomena on rejection from ultrathin membranes are examined. PMID:28796197

Efficient Ligation of the Schistosoma Hammerhead Ribozyme †

PubMed Central

Canny, Marella D.; Jucker, Fiona M.; Pardi, Arthur

2011-01-01

The hammerhead ribozyme from Schistosoma mansoni is the best characterized of the natural hammerhead ribozymes. Biophysical, biochemical, and structural studies have shown that the formation of the loop-loop tertiary interaction between stems I and II alters the global folding, cleavage kinetics, and conformation of the catalytic core of this hammerhead, leading to a ribozyme that is readily cleaved under physiological conditions. This study investigates the ligation kinetics and the internal equilibrium between cleavage and ligation for the Schistosoma hammerhead. Single turnover kinetic studies on a construct where the ribozyme cleaves and ligates substrate(s) in trans showed up to 23% ligation when starting from fully cleaved products. This was achieved by a ~2,000-fold increase in the rate of ligation compared to a minimal hammerhead without the loop-loop tertiary interaction, yielding an internal equilibrium that ranges from 2–3 at physiological Mg2+ ion concentrations (0.1 –1 mM). Thus, the natural Schistosoma hammerhead ribozyme is almost as efficient at ligation as it is at cleavage. The results here are consistent with a model where formation of the loop-loop tertiary interaction leads to a higher population of catalytically active molecules, and where formation of this tertiary interaction has a much larger effect on the ligation than the cleavage activity of the Schistosoma hammerhead ribozyme. PMID:17319693

Activation loop targeting strategy for design of receptor-interacting protein kinase 2 (RIPK2) inhibitors.

PubMed

Suebsuwong, Chalada; Pinkas, Daniel M; Ray, Soumya S; Bufton, Joshua C; Dai, Bing; Bullock, Alex N; Degterev, Alexei; Cuny, Gregory D

2018-02-15

Development of selective kinase inhibitors remains a challenge due to considerable amino acid sequence similarity among family members particularly in the ATP binding site. Targeting the activation loop might offer improved inhibitor selectivity since this region of kinases is less conserved. However, the strategy presents difficulties due to activation loop flexibility. Herein, we report the design of receptor-interacting protein kinase 2 (RIPK2) inhibitors based on pan-kinase inhibitor regorafenib that aim to engage basic activation loop residues Lys169 or Arg171. We report development of CSR35 that displayed >10-fold selective inhibition of RIPK2 versus VEGFR2, the target of regorafenib. A co-crystal structure of CSR35 with RIPK2 revealed a resolved activation loop with an ionic interaction between the carboxylic acid installed in the inhibitor and the side-chain of Lys169. Our data provides principle feasibility of developing activation loop targeting type II inhibitors as a complementary strategy for achieving improved selectivity. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Dislocation dynamics simulations of interactions between gliding dislocations and radiation induced prismatic loops in zirconium

NASA Astrophysics Data System (ADS)

Drouet, Julie; Dupuy, Laurent; Onimus, Fabien; Mompiou, Frédéric; Perusin, Simon; Ambard, Antoine

2014-06-01

The mechanical behavior of Pressurized Water Reactor fuel cladding tubes made of zirconium alloys is strongly affected by neutron irradiation due to the high density of radiation induced dislocation loops. In order to investigate the interaction mechanisms between gliding dislocations and loops in zirconium, a new nodal dislocation dynamics code, adapted to Hexagonal Close Packed metals, has been used. Various configurations have been systematically computed considering different glide planes, basal or prismatic, and different characters, edge or screw, for gliding dislocations with -type Burgers vectors. Simulations show various interaction mechanisms such as (i) absorption of a loop on an edge dislocation leading to the formation of a double super-jog, (ii) creation of a helical turn, on a screw dislocation, that acts as a strong pinning point or (iii) sweeping of a loop by a gliding dislocation. It is shown that the clearing of loops is more favorable when the dislocation glides in the basal plane than in the prismatic plane explaining the easy dislocation channeling in the basal plane observed after neutron irradiation by transmission electron microscopy.

Pore-scale simulation of CO2-water-rock interactions

NASA Astrophysics Data System (ADS)

Deng, H.; Molins, S.; Steefel, C. I.; DePaolo, D. J.

2017-12-01

In Geologic Carbon Storage (GCS) systems, the migration of scCO2 versus CO2-acidifed brine ultimately determines the extent of mineral trapping and caprock integrity, i.e. the long-term storage efficiency and security. While continuum scale multiphase reactive transport models are valuable for large scale investigations, they typically (over-)simplify pore-scale dynamics and cannot capture local heterogeneities that may be important. Therefore, pore-scale models are needed in order to provide mechanistic understanding of how fine scale structural variations and heterogeneous processes influence the transport and geochemistry in the context of multiphase flow, and to inform parameterization of continuum scale modeling. In this study, we investigate the interplay of different processes at pore scale (e.g. diffusion, reactions, and multiphase flow) through the coupling of a well-developed multiphase flow simulator with a sophisticated reactive transport code. The objectives are to understand where brine displaced by scCO2 will reside in a rough pore/fracture, and how the CO2-water-rock interactions may affect the redistribution of different phases. In addition, the coupled code will provide a platform for model testing in pore-scale multiphase reactive transport problems.

Thermal characterization of static and dynamical properties of the confined molecular systems interacting through dispersion force.

PubMed

Ramos, Sergio Luis L M; Ogino, Michihiko; Oguni, Masaharu

2015-01-28

We investigated the thermal properties of liquid methylcyclohexane and racemic sec-butylcyclohexane, as representatives of a molecular system with only dispersion-force intermolecular interactions, confined in the pores (thickness/diameter d = 12, 6, 1.1 nm) of silica gels by adiabatic calorimetry. The results imply a heterogeneous picture for molecular aggregate under confinement consisting of an interfacial region and an inner pore one. In the vicinity of a glass-transition temperature T(g,bulk) of bulk liquid, two distinguishable relaxation phenomena were observed for the confined systems and their origins were attributed to the devitrification, namely glass transition, processes of (1) a layer of interfacial molecules adjacent to the pore walls and (2) the molecules located in the middle of the pore. A third glass-transition phenomenon was observed at lower temperatures and ascribed to a secondary relaxation process. The glass transition of the interfacial-layer molecules was found to proceed at temperatures rather above T(g,bulk), whereas that of the molecules located in the inner pore region occurred at temperatures below T(g,bulk). We discuss the reason why the molecules located in different places in the pores reveal the respectively different dynamical properties.

Disrupting a key hydrophobic pair in the oligomerization interface of the actinoporins impairs their pore‐forming activity

PubMed Central

Mesa‐Galloso, Haydeé; Delgado‐Magnero, Karelia H.; Cabezas, Sheila; López‐Castilla, Aracelys; Hernández‐González, Jorge E.; Pedrera, Lohans; Alvarez, Carlos; Peter Tieleman, D.; García‐Sáez, Ana J.; Lanio, Maria E.; Valiente, Pedro A.

2017-01-01

Abstract Crystallographic data of the dimeric and octameric forms of fragaceatoxin C (FraC) suggested the key role of a small hydrophobic protein–protein interaction surface for actinoporins oligomerization and pore formation in membranes. However, site‐directed mutagenesis studies supporting this hypothesis for others actinoporins are still lacking. Here, we demonstrate that disrupting the key hydrophobic interaction between V60 and F163 (FraC numbering scheme) in the oligomerization interface of FraC, equinatoxin II (EqtII), and sticholysin II (StII) impairs the pore formation activity of these proteins. Our results allow for the extension of the importance of FraC protein–protein interactions in the stabilization of the oligomeric intermediates of StII and EqtII pointing out that all of these proteins follow a similar pathway of membrane disruption. These findings support the hybrid pore proposal as the universal model of actinoporins pore formation. Moreover, we reinforce the relevance of dimer formation, which appears to be a functional intermediate in the assembly pathway of some different pore‐forming proteins. PMID:28000294

Structure-function relationships of curaremimetic neurotoxin loop 2 and of a structurally similar segment of rabies virus glycoprotein in their interaction with the nicotinic acetylcholine receptor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lentz, T.L.

1991-11-12

Peptides corresponding to portions of curaremimetic neurotoxin loop 2 and to a structurally similar segment of rabies virus glycoprotein were synthetically modified in order to gain information on structure-function relationships of neurotoxin loop 2 interactions with the acetylcholine receptor. Binding of synthetic peptides to the acetylcholine receptor of Torpedo electric organ membranes was assessed by measuring their ability to inhibit the binding of {sup 125}I-{alpha}-bungarotoxin to the receptor. The peptides showing the highest affinity for the receptor were a peptide corresponding to the sequence of loop 2 (residues 25-44) of Ophiophagus hannah (king cobra) toxin b and the structurally similarmore » segment of CVS rabies virus glycoprotein. These affinities were comparable to those of d-tubocurarine and suberyldicholine. These results demonstrate the importance of loop 2 in the neurotoxin interaction with the receptor. N- and C-terminal deletions of the loop 2 peptides and substitution of residues invariant or highly conserved among neurotoxins were performed in order to determine the role of individual residues in binding. Residues 25-40 are the most crucial in the interaction with the acetylcholine receptor. Since this region of the glycoprotein contains residues corresponding to all of the functionally invariant neurotoxin residues, it may interact with the acetylcholine receptor through a mechanism similar to that of the neurotoxins.« less

RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription

PubMed Central

Huang, Xuhui; Wang, Dong; Weiss, Dahlia R.; Bushnell, David A.; Kornberg, Roger D.; Levitt, Michael

2010-01-01

A structurally conserved element, the trigger loop, has been suggested to play a key role in substrate selection and catalysis of RNA polymerase II (pol II) transcription elongation. Recently resolved X-ray structures showed that the trigger loop forms direct interactions with the β-phosphate and base of the matched nucleotide triphosphate (NTP) through residues His1085 and Leu1081, respectively. In order to understand the role of these two critical residues in stabilizing active site conformation in the dynamic complex, we performed all-atom molecular dynamics simulations of the wild-type pol II elongation complex and its mutants in explicit solvent. In the wild-type complex, we found that the trigger loop is stabilized in the “closed” conformation, and His1085 forms a stable interaction with the NTP. Simulations of point mutations of His1085 are shown to affect this interaction; simulations of alternative protonation states, which are inaccessible through experiment, indicate that only the protonated form is able to stabilize the His1085-NTP interaction. Another trigger loop residue, Leu1081, stabilizes the incoming nucleotide position through interaction with the nucleotide base. Our simulations of this Leu mutant suggest a three-component mechanism for correctly positioning the incoming NTP in which (i) hydrophobic contact through Leu1081, (ii) base stacking, and (iii) base pairing work together to minimize the motion of the incoming NTP base. These results complement experimental observations and provide insight into the role of the trigger loop on transcription fidelity. PMID:20798057

Geometrical criteria for characterizing open and closed states of WPD-loop in PTP1B

NASA Astrophysics Data System (ADS)

Shinde, Ranajit Nivrutti; Elizabeth Sobhia, M.

2012-06-01

Distinctive movement of WPD-loop occurs during the catalysis of phosphotyrosine by protein tyrosine phosphatase 1B (PTP1B). This loop is in the "open" state in apo-form whereas it is catalytically competent in the "closed" state. During the closure of this loop, unique hydrogen bond interactions are formed between different residues of the PTP1B. Present study examines such interactions from the available 118 crystal structures of PTP1B. It gives insights into the five novel hydrogen bonds essentially formed in the "closed" loop structures. Additionally, the study provides distance ranges between the atoms involved in the hydrogen bonds. This information can be used as a geometrical criterion in the characterization of conformational state of the WPD-loop especially in the molecular dynamics simulations.

Pore formation during dehydration of polycrystalline gypsum observed and quantified in a time-series synchrotron radiation based X-ray micro-tomography experiment

NASA Astrophysics Data System (ADS)

Fusseis, F.; Schrank, C.; Liu, J.; Karrech, A.; Llana-Fúnez, S.; Xiao, X.; Regenauer-Lieb, K.

2011-10-01

We conducted an in-situ X-ray micro-computed tomography heating experiment at the Advanced Photon Source (USA) to dehydrate an unconfined 2.3 mm diameter cylinder of Volterra Gypsum. We used a purpose-built X-ray transparent furnace to heat the sample to 388 K for a total of 310 min to acquire a three-dimensional time-series tomography dataset comprising nine time steps. The voxel size of 2.2 μm3 proved sufficient to pinpoint reaction initiation and the organization of drainage architecture in space and time. We observed that dehydration commences across a narrow front, which propagates from the margins to the centre of the sample in more than four hours. The advance of this front can be fitted with a square-root function, implying that the initiation of the reaction in the sample can be described as a diffusion process. Novel parallelized computer codes allow quantifying the geometry of the porosity and the drainage architecture from the very large tomographic datasets (6.4 × 109 voxel each) in unprecedented detail. We determined position, volume, shape and orientation of each resolvable pore and tracked these properties over the duration of the experiment. We found that the pore-size distribution follows a power law. Pores tend to be anisotropic but rarely crack-shaped and have a preferred orientation, likely controlled by a pre-existing fabric in the sample. With on-going dehydration, pores coalesce into a single interconnected pore cluster that is connected to the surface of the sample cylinder and provides an effective drainage pathway. Our observations can be summarized in a model in which gypsum is stabilized by thermal expansion stresses and locally increased pore fluid pressures until the dehydration front approaches to within about 100 μm. Then, the internal stresses are released and dehydration happens efficiently, resulting in new pore space. Pressure release, the production of pores and the advance of the front are coupled in a feedback loop. We discuss our findings in the context of previous studies.

Pore formation during dehydration of a polycrystalline gypsum sample observed and quantified in a time-series synchrotron X-ray micro-tomography experiment

NASA Astrophysics Data System (ADS)

Fusseis, F.; Schrank, C.; Liu, J.; Karrech, A.; Llana-Fúnez, S.; Xiao, X.; Regenauer-Lieb, K.

2012-03-01

We conducted an in-situ X-ray micro-computed tomography heating experiment at the Advanced Photon Source (USA) to dehydrate an unconfined 2.3 mm diameter cylinder of Volterra Gypsum. We used a purpose-built X-ray transparent furnace to heat the sample to 388 K for a total of 310 min to acquire a three-dimensional time-series tomography dataset comprising nine time steps. The voxel size of 2.2 μm3 proved sufficient to pinpoint reaction initiation and the organization of drainage architecture in space and time. We observed that dehydration commences across a narrow front, which propagates from the margins to the centre of the sample in more than four hours. The advance of this front can be fitted with a square-root function, implying that the initiation of the reaction in the sample can be described as a diffusion process. Novel parallelized computer codes allow quantifying the geometry of the porosity and the drainage architecture from the very large tomographic datasets (20483 voxels) in unprecedented detail. We determined position, volume, shape and orientation of each resolvable pore and tracked these properties over the duration of the experiment. We found that the pore-size distribution follows a power law. Pores tend to be anisotropic but rarely crack-shaped and have a preferred orientation, likely controlled by a pre-existing fabric in the sample. With on-going dehydration, pores coalesce into a single interconnected pore cluster that is connected to the surface of the sample cylinder and provides an effective drainage pathway. Our observations can be summarized in a model in which gypsum is stabilized by thermal expansion stresses and locally increased pore fluid pressures until the dehydration front approaches to within about 100 μm. Then, the internal stresses are released and dehydration happens efficiently, resulting in new pore space. Pressure release, the production of pores and the advance of the front are coupled in a feedback loop.

FAST TRACK COMMUNICATION: A Temperley-Lieb quantum chain with two- and three-site interactions

NASA Astrophysics Data System (ADS)

Ikhlef, Y.; Jacobsen, J. L.; Saleur, H.

2009-07-01

We study the phase diagram of a quantum chain of spin-1/2 particles whose world lines form a dense loop gas with loop weight n. In addition to the usual two-site interaction corresponding to the XXZ spin chain, we introduce a three-site interaction. The resulting model contains a Majumdar-Ghosh-like gapped phase and a new integrable point, which we solve exactly. We also locate a critical line realizing dilute O(n) criticality, without introducing explicit dilution in the loops. Our results have implications for anisotropic spin chains, as well as anyonic quantum chains.

Successive Two-sided Loop Jets Caused by Magnetic Reconnection between Two Adjacent Filamentary Threads

NASA Astrophysics Data System (ADS)

Tian, Zhanjun; Liu, Yu; Shen, Yuandeng; Elmhamdi, Abouazza; Su, Jiangtao; Liu, Ying D.; Kordi, Ayman. S.

2017-08-01

We present observational analysis of two successive two-sided loop jets observed by the ground-based New Vacuum Solar Telescope and the space-borne Solar Dynamics Observatory. The two successive two-sided loop jets manifested similar evolution processes and both were associated with the interaction of two small-scale adjacent filamentary threads, magnetic emerging, and cancellation processes at the jet’s source region. High temporal and high spatial resolution observations reveal that the two adjacent ends of the two filamentary threads are rooted in opposite magnetic polarities within the source region. The two threads approached each other, and then an obvious brightening patch is observed at the interaction position. Subsequently, a pair of hot plasma ejections are observed heading in opposite directions along the paths of the two filamentary threads at a typical speed for two-sided loop jets of the order 150 km s-1. Close to the end of the second jet, we report the formation of a bright hot loop structure at the source region, which suggests the formation of new loops during the interaction. Based on the observational results, we propose that the observed two-sided loop jets are caused by magnetic reconnection between the two adjacent filamentary threads, largely different from the previous scenario that a two-sided loop jet is generated by magnetic reconnection between an emerging bipole and the overlying horizontal magnetic fields.

Direct observation of gold nanoparticle assemblies with the porin MspA on mica.

PubMed

Basel, Matthew T; Dani, Raj Kumar; Kang, Myungshim; Pavlenok, Mikhail; Chikan, Viktor; Smith, Paul E; Niederweis, Michael; Bossmann, Stefan H

2009-02-24

The octameric porin MspA from Mycobacterium smegmatis is sufficiently stable to form a nonmembrane-supported stand-alone porin on mica surfaces. About 98% of all MspA octamers were found to stand upright on mica, with their periplasmic loop regions bound to the hydrophilic mica surface. Both, small (d = 3.7 nm) and large (d = 17 nm) gold nanoparticles bind to MspA, however, in different positions: small gold nanoparticles bind within the MspA pore, whereas the large gold nanoparticles bind to the upper region of MspA. These experiments demonstrate that gold nanoparticles can be positioned at different, well-defined distances from the underlying surface using the MspA pore as a template. These findings represent a significant step toward the use of electrically insulating stable proteins in combination with metal nanoparticles in nanodevices.

Active membrane having uniform physico-chemically functionalized ion channels

DOEpatents

Gerald, II, Rex E; Ruscic, Katarina J; Sears, Devin N; Smith, Luis J; Klingler, Robert J; Rathke, Jerome W

2012-09-24

The present invention relates to a physicochemically-active porous membrane for electrochemical cells that purports dual functions: an electronic insulator (separator) and a unidirectional ion-transporter (electrolyte). The electrochemical cell membrane is activated for the transport of ions by contiguous ion coordination sites on the interior two-dimensional surfaces of the trans-membrane unidirectional pores. One dimension of the pore surface has a macroscopic length (1 nm-1000 .mu.m) and is directed parallel to the direction of an electric field, which is produced between the cathode and the anode electrodes of an electrochemical cell. The membrane material is designed to have physicochemical interaction with ions. Control of the extent of the interactions between the ions and the interior pore walls of the membrane and other materials, chemicals, or structures contained within the pores provides adjustability of the ionic conductivity of the membrane.

The SH2 domain of Abl kinases regulates kinase autophosphorylation by controlling activation loop accessibility.

PubMed

Lamontanara, Allan Joaquim; Georgeon, Sandrine; Tria, Giancarlo; Svergun, Dmitri I; Hantschel, Oliver

2014-11-17

The activity of protein kinases is regulated by multiple molecular mechanisms, and their disruption is a common driver of oncogenesis. A central and almost universal control element of protein kinase activity is the activation loop that utilizes both conformation and phosphorylation status to determine substrate access. In this study, we use recombinant Abl tyrosine kinases and conformation-specific kinase inhibitors to quantitatively analyse structural changes that occur after Abl activation. Allosteric SH2-kinase domain interactions were previously shown to be essential for the leukemogenesis caused by the Bcr-Abl oncoprotein. We find that these allosteric interactions switch the Abl activation loop from a closed to a fully open conformation. This enables the trans-autophosphorylation of the activation loop and requires prior phosphorylation of the SH2-kinase linker. Disruption of the SH2-kinase interaction abolishes activation loop phosphorylation. Our analysis provides a molecular mechanism for the SH2 domain-dependent activation of Abl that may also regulate other tyrosine kinases.

The SH2 domain of Abl kinases regulates kinase autophosphorylation by controlling activation loop accessibility

NASA Astrophysics Data System (ADS)

Lamontanara, Allan Joaquim; Georgeon, Sandrine; Tria, Giancarlo; Svergun, Dmitri I.; Hantschel, Oliver

2014-11-01

The activity of protein kinases is regulated by multiple molecular mechanisms, and their disruption is a common driver of oncogenesis. A central and almost universal control element of protein kinase activity is the activation loop that utilizes both conformation and phosphorylation status to determine substrate access. In this study, we use recombinant Abl tyrosine kinases and conformation-specific kinase inhibitors to quantitatively analyse structural changes that occur after Abl activation. Allosteric SH2-kinase domain interactions were previously shown to be essential for the leukemogenesis caused by the Bcr-Abl oncoprotein. We find that these allosteric interactions switch the Abl activation loop from a closed to a fully open conformation. This enables the trans-autophosphorylation of the activation loop and requires prior phosphorylation of the SH2-kinase linker. Disruption of the SH2-kinase interaction abolishes activation loop phosphorylation. Our analysis provides a molecular mechanism for the SH2 domain-dependent activation of Abl that may also regulate other tyrosine kinases.

Energy profile of maltooligosaccharide permeation through maltoporin as derived from the structure and from a statistical analysis of saccharide-protein interactions.

PubMed Central

Meyer, J. E.; Schulz, G. E.

1997-01-01

The crystal structure of the maltodextrin-specific porin from Salmonella typhimurium ligated with a maltotrioside at the pore eyelet is known at 2.4 A resolution. The three glucose units assume a conformation close to the natural amylose helix. The pore eyelet fits exactly the cross-section of a maltooligosaccharide chain and thus functions as a constraining orifice. The oligomer permeates the membrane by screwing along the amylose helix through this orifice. Because each glucose glides along the given helix, its interactions can be sampled at any point along the pathway. The interactions are mostly hydrogen bonds, but also contacts to aromatic rings at one side of the pore. We have derived the energy profile of a gliding maltooligosaccharide by following formation and breakage of hydrogen bonds and by assessing the saccharide-aromatics interactions from a statistical analysis of saccharide binding sites in proteins. The resulting profile indicates smooth permeation despite extensive hydrogen bonding at the orifice. PMID:9144780

A macroscopic model of proton transport through the membrane-ionomer interface of a polymer electrolyte membrane fuel cell.

PubMed

Kumar, Milan; Edwards, Brian J; Paddison, Stephen J

2013-02-14

The membrane-ionomer interface is the critical interlink of the electrodes and catalyst to the polymer electrolyte membrane (PEM); together forming the membrane electrode assembly in current state-of-the-art PEM fuel cells. In this paper, proton conduction through the interface is investigated to understand its effect on the performance of a PEM fuel cell. The water containing domains at this interface were modeled as cylindrical pores/channels with the anionic groups (i.e., -SO(3)(-)) assumed to be fixed on the pore wall. The interactions of each species with all other species and an applied external field were examined. Molecular-based interaction potential energies were computed in a small test element of the pore and were scaled up in terms of macroscopic variables. Evolution equations of the density and momentum of the species (water molecules and hydronium ions) were derived within a framework of nonequilibrium thermodynamics. The resulting evolution equations for the species were solved analytically using an order-of-magnitude analysis to obtain an expression for the proton conductivity. Results show that the conductivity increases with increasing water content and pore radius, and strongly depends on the separation distance between the sulfonate groups and their distribution on the pore wall. It was also determined that the conductivity of two similar pores of different radii in series is limited by the pore with the smaller radius.

Analysis of Adsorbate-Adsorbate and Adsorbate-Adsorbent Interactions to Decode Isosteric Heats of Gas Adsorption.

PubMed

Madani, S Hadi; Sedghi, Saeid; Biggs, Mark J; Pendleton, Phillip

2015-12-21

A qualitative interpretation is proposed to interpret isosteric heats of adsorption by considering contributions from three general classes of interaction energy: fluid-fluid heat, fluid-solid heat, and fluid-high-energy site (HES) heat. Multiple temperature adsorption isotherms are defined for nitrogen, T=(75, 77, 79) K, argon at T=(85, 87, 89) K, and for water and methanol at T=(278, 288, 298) K on a well-characterized polymer-based, activated carbon. Nitrogen and argon are subjected to isosteric heat analyses; their zero filling isosteric heats of adsorption are consistent with slit-pore, adsorption energy enhancement modelling. Water adsorbs entirely via specific interactions, offering decreasing isosteric heat at low pore filling followed by a constant heat slightly in excess of water condensation enthalpy, demonstrating the effects of micropores. Methanol offers both specific adsorption via the alcohol group and non-specific interactions via its methyl group; the isosteric heat increases at low pore filling, indicating the predominance of non-specific interactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Site-Directed Spin Labeling Reveals Pentameric Ligand-Gated Ion Channel Gating Motions

PubMed Central

Dellisanti, Cosma D.; Ghosh, Borna; Hanson, Susan M.; Raspanti, James M.; Grant, Valerie A.; Diarra, Gaoussou M.; Schuh, Abby M.; Satyshur, Kenneth; Klug, Candice S.; Czajkowski, Cynthia

2013-01-01

Pentameric ligand-gated ion channels (pLGICs) are neurotransmitter-activated receptors that mediate fast synaptic transmission. In pLGICs, binding of agonist to the extracellular domain triggers a structural rearrangement that leads to the opening of an ion-conducting pore in the transmembrane domain and, in the continued presence of neurotransmitter, the channels desensitize (close). The flexible loops in each subunit that connect the extracellular binding domain (loops 2, 7, and 9) to the transmembrane channel domain (M2–M3 loop) are essential for coupling ligand binding to channel gating. Comparing the crystal structures of two bacterial pLGIC homologues, ELIC and the proton-activated GLIC, suggests channel gating is associated with rearrangements in these loops, but whether these motions accurately predict the motions in functional lipid-embedded pLGICs is unknown. Here, using site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy and functional GLIC channels reconstituted into liposomes, we examined if, and how far, the loops at the ECD/TMD gating interface move during proton-dependent gating transitions from the resting to desensitized state. Loop 9 moves ∼9 Å inward toward the channel lumen in response to proton-induced desensitization. Loop 9 motions were not observed when GLIC was in detergent micelles, suggesting detergent solubilization traps the protein in a nonactivatable state and lipids are required for functional gating transitions. Proton-induced desensitization immobilizes loop 2 with little change in position. Proton-induced motion of the M2–M3 loop was not observed, suggesting its conformation is nearly identical in closed and desensitized states. Our experimentally derived distance measurements of spin-labeled GLIC suggest ELIC is not a good model for the functional resting state of GLIC, and that the crystal structure of GLIC does not correspond to a desensitized state. These findings advance our understanding of the molecular mechanisms underlying pLGIC gating. PMID:24260024

Controlling reactivity of nanoporous catalyst materials by tuning reaction product-pore interior interactions: Statistical mechanical modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jing; Ackerman, David M.; Lin, Victor S.-Y.

2013-04-02

Statistical mechanical modeling is performed of a catalytic conversion reaction within a functionalized nanoporous material to assess the effect of varying the reaction product-pore interior interaction from attractive to repulsive. A strong enhancement in reactivity is observed not just due to the shift in reaction equilibrium towards completion but also due to enhanced transport within the pore resulting from reduced loading. The latter effect is strongest for highly restricted transport (single-file diffusion), and applies even for irreversible reactions. The analysis is performed utilizing a generalized hydrodynamic formulation of the reaction-diffusion equations which can reliably capture the complex interplay between reactionmore » and restricted transport.« less

Water-mediated interactions between hydrophobic and ionic species in cylindrical nanopores

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vaitheeswaran, S.; Reddy, G.; Thirumalai, D.

2009-03-07

We use Metropolis Monte Carlo and umbrella sampling to calculate the free energies of interaction of two methane molecules and their charged derivatives in cylindrical water-filled pores. Confinement strongly alters the interactions between the nonpolar solutes and completely eliminates the solvent separated minimum (SSM) that is seen in bulk water. The free energy profiles show that the methane molecules are either in contact or at separations corresponding to the diameter and the length of the cylindrical pore. Analytic calculations that estimate the entropy of the solutes, which are solvated at the pore surface, qualitatively explain the shape of the freemore » energy profiles. Adding charges of opposite sign and magnitude 0.4e or e (where e is the electronic charge) to the methane molecules decreases their tendency for surface solvation and restores the SSM. We show that confinement induced ion-pair formation occurs whenever l{sub B}/D{approx}O(1), where l{sub B} is the Bjerrum length and D is the pore diameter. The extent of stabilization of the SSM increases with ion charge density as long as l{sub B}/D<1. In pores with D{<=}1.2 nm, in which the water is strongly layered, increasing the charge magnitude from 0.4e to e reduces the stability of the SSM. As a result, ion-pair formation that occurs with negligible probability in the bulk is promoted. In larger diameter pores that can accommodate a complete hydration layer around the solutes, the stability of the SSM is enhanced.« less

Low pH-Induced Pore Formation by the T Domain of Botulinum Toxin Type A is Dependent upon NaCl Concentration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lai, B.; Swaminathan, S.; Agarwal, R.

2010-07-19

Botulinum neurotoxins (BoNTs) undergo low pH-triggered membrane insertion, resulting in the translocation of their light (catalytic) chains into the cytoplasm. The T (translocation) domain of the BoNT heavy chain is believed to carry out translocation. Here, the behavior of isolated T domain from BoNT type A has been characterized, both in solution and when associated with model membranes. When BoNT T domain prepared in the detergent dodecylmaltoside was diluted into aqueous solution, it exhibited a low pH-dependent conformational change below pH 6. At low pH the T domain associated with, and formed pores within, model membrane vesicles composed of 30more » mol% dioleoylphosphatidylglycerol/70 mol% dioleoylphosphatidylcholine. Although T domain interacted with vesicles at low (50 mM) and high (400 mM) NaCl concentrations, the interaction required much less lipid at low salt. However, even at high lipid concentrations pore formation was much more pronounced at low NaCl concentrations than at high NaCl concentration. Increasing salt concentration after insertion in the presence of 50 mM NaCl did not decrease pore formation. A similar effect of NaCl concentration upon pore formation was observed in vesicles composed solely of dioleoylphosphatidylcholine, showing that the effect of NaCl did not solely involve modulation of electrostatic interactions between protein and anionic lipids. These results indicate that some feature of membrane-bound T domain tertiary structure critical for pore formation is highly dependent upon salt concentration.« less

Mechanism of auxiliary β-subunit-mediated membrane targeting of L-type (CaV1.2) channels

PubMed Central

Fang, Kun; Colecraft, Henry M

2011-01-01

Abstract Ca2+ influx via CaV1/CaV2 channels drives processes ranging from neurotransmission to muscle contraction. Association of a pore-forming α1 and cytosolic β is necessary for trafficking CaV1/CaV2 channels to the cell surface through poorly understood mechanisms. A prevalent idea suggests β binds the α1 intracellular I–II loop, masking an endoplasmic reticulum (ER) retention signal as the dominant mechanism for CaV1/CaV2 channel membrane trafficking. There are hints that other α1 subunit cytoplasmic domains may play a significant role, but the nature of their potential contribution is unclear. We assessed the roles of all intracellular domains of CaV1.2-α1C by generating chimeras featuring substitutions of all possible permutations of intracellular loops/termini of α1C into the β-independent CaV3.1-α1G channel. Surprisingly, functional analyses demonstrated α1C I–II loop strongly increases channel surface density while other cytoplasmic domains had a competing opposing effect. Alanine-scanning mutagenesis identified an acidic-residue putative ER export motif responsible for the I–II loop-mediated increase in channel surface density. β-dependent increase in current arose as an emergent property requiring four α1C intracellular domains, with the I–II loop and C-terminus being essential. The results suggest β binding to the α1C I–II loop causes a C-terminus-dependent rearrangement of intracellular domains, shifting a balance of power between export signals on the I–II loop and retention signals elsewhere. PMID:21746784

Topological Interaction by Entanglement of DNA

NASA Astrophysics Data System (ADS)

Feng, Lang; Sha, Ruojie; Seeman, Nadrian; Chaikin, Paul

2012-02-01

We find and study a new type of interaction between colloids, Topological Interaction by Entanglement of DNA (TIED), due to concatenation of loops formed by palindromic DNA. Consider a particle coated with palindromic DNA of sequence ``P1.'' Below the DNA hybridization temperature (Tm), loops of the self-complementary DNA form on the particle surface. Direct hybridization with similar particle covered with a different sequence P2 do not occur. However when particles are held together at T > Tm, then cooled to T < Tm, some of the loops entangle and link, similar to a Olympic Gel. We quantitatively observe and measure this topological interaction between colloids in a ˜5^o C temperature window, ˜6^o C lower than direct binding of complementary DNA with similar strength and introduce the concept of entanglement binding free energy. To prove our interaction to be topological, we unknot the purely entangled binding sites between colloids by adding Topoisomerase I which unconcatenates our loops. This research suggests novel history dependent ways of binding particles and serves as a new design tool in colloidal self-assembly.

Loop vertex expansion for higher-order interactions

NASA Astrophysics Data System (ADS)

Rivasseau, Vincent

2018-05-01

This note provides an extension of the constructive loop vertex expansion to stable interactions of arbitrarily high order, opening the way to many applications. We treat in detail the example of the (\\bar{φ } φ )^p field theory in zero dimension. We find that the important feature to extend the loop vertex expansion is not to use an intermediate field representation, but rather to force integration of exactly one particular field per vertex of the initial action.

Non-FG mediated transport of the large pre-ribosomal subunit through the nuclear pore complex by the mRNA export factor Gle2

PubMed Central

Occhipinti, Laura; Chang, Yiming; Altvater, Martin; Menet, Anna M.; Kemmler, Stefan; Panse, Vikram G.

2013-01-01

Multiple export receptors passage bound pre-ribosomes through nuclear pore complexes (NPCs) by transiently interacting with the Phe-Gly (FG) meshwork of their transport channels. Here, we reveal how the non-FG interacting yeast mRNA export factor Gly-Leu-FG lethal 2 (Gle2) functions in the export of the large pre-ribosomal subunit (pre-60S). Structure-guided studies uncovered conserved platforms used by Gle2 to export pre-60S: an uncharacterized basic patch required to bind pre-60S, and a second surface that makes non-FG contacts with the nucleoporin Nup116. A basic patch mutant of Gle2 is able to function in mRNA export, but not pre-60S export. Thus, Gle2 provides a distinct interaction platform to transport pre-60S to the cytoplasm. Notably, Gle2’s interaction platforms become crucial for pre-60S export when FG-interacting receptors are either not recruited to pre-60S or are impaired. We propose that large complex cargos rely on non-FG as well as FG-interactions for their efficient translocation through the nuclear pore complex channel. PMID:23907389

DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics

PubMed Central

Laurens, Niels; Rusling, David A.; Pernstich, Christian; Brouwer, Ineke; Halford, Stephen E.; Wuite, Gijs J. L.

2012-01-01

Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariably aligning the sites in parallel. On account of the fixed alignment, the topology of the DNA loop is set by the orientation of the sites along the DNA. We show that both the separation of the FokI sites and their orientation, altering, respectively, the twisting and the bending of the DNA needed to juxtapose the sites, have profound effects on the dynamics of the looping interaction. Surprisingly, the presence of a nick within the loop does not affect the observed rigidity of the DNA. In contrast, the introduction of a 4-nt gap fully relaxes all of the torque present in the system but does not necessarily enhance loop stability. FokI therefore employs torque to stabilise its DNA-looping interaction by acting as a ‘torsional’ catch bond. PMID:22373924

An interacting loop model of solar flare bursts

NASA Technical Reports Server (NTRS)

Emslie, A. G.

1981-01-01

As a result of the strong heating produced at chromospheric levels during a solar flare burst, the local gas pressure can transiently attain very large values in certain regions. The effectiveness of the surrounding magnetic field at confining this high pressure plasma is therefore reduced and the flaring loop becomes free to expand laterally. In so doing it may drive magnetic field lines into neighboring, nonflaring, loops in the same active region, causing magnetic reconnection to take place and triggering another flare burst. The features of this interacting loop model are found to be in good agreement with the energetics and time structure of flare associated solar hard X-ray bursts.

Motor-sensory confluence in tactile perception.

PubMed

Saig, Avraham; Gordon, Goren; Assa, Eldad; Arieli, Amos; Ahissar, Ehud

2012-10-03

Perception involves motor control of sensory organs. However, the dynamics underlying emergence of perception from motor-sensory interactions are not yet known. Two extreme possibilities are as follows: (1) motor and sensory signals interact within an open-loop scheme in which motor signals determine sensory sampling but are not affected by sensory processing and (2) motor and sensory signals are affected by each other within a closed-loop scheme. We studied the scheme of motor-sensory interactions in humans using a novel object localization task that enabled monitoring the relevant overt motor and sensory variables. We found that motor variables were dynamically controlled within each perceptual trial, such that they gradually converged to steady values. Training on this task resulted in improvement in perceptual acuity, which was achieved solely by changes in motor variables, without any change in the acuity of sensory readout. The within-trial dynamics is captured by a hierarchical closed-loop model in which lower loops actively maintain constant sensory coding, and higher loops maintain constant sensory update flow. These findings demonstrate interchangeability of motor and sensory variables in perception, motor convergence during perception, and a consistent hierarchical closed-loop perceptual model.

Tailoring the hydrophobicity of graphene for its use as nanopores for DNA translocation

NASA Astrophysics Data System (ADS)

Schneider, Grégory F.; Xu, Qiang; Hage, Susanne; Luik, Stephanie; Spoor, Johannes N. H.; Malladi, Sairam; Zandbergen, Henny; Dekker, Cees

2013-10-01

Graphene nanopores are potential successors to biological and silicon-based nanopores. For sensing applications, it is however crucial to understand and block the strong nonspecific hydrophobic interactions between DNA and graphene. Here we demonstrate a novel scheme to prevent DNA-graphene interactions, based on a tailored self-assembled monolayer. For bare graphene, we encounter a paradox: whereas contaminated graphene nanopores facilitated DNA translocation well, clean crystalline graphene pores very quickly exhibit clogging of the pore. We attribute this to strong interactions between DNA nucleotides and graphene, yielding sticking and irreversible pore closure. We develop a general strategy to noncovalently tailor the hydrophobic surface of graphene by designing a dedicated self-assembled monolayer of pyrene ethylene glycol, which renders the surface hydrophilic. We demonstrate that this prevents DNA to adsorb on graphene and show that single-stranded DNA can now be detected in graphene nanopores with excellent nanopore durability and reproducibility.

Interactions of a Charged Nanoparticle with a Lipid Membrane: Implications for Gene Delivery

PubMed Central

Ting, Christina L.; Wang, Zhen-Gang

2011-01-01

We employ self-consistent field theory to study the thermodynamics of membrane-particle interactions in the context of gene delivery systems, with the aim to guide the design of dendrimers that can overcome the endosomal escape barrier by inserting into membranes and creating pores. We consider the interaction between a model polyamidoamine dendrimer and a membrane under controlled tension as a function of the separation between the dendrimer and the membrane. In all the cases we have studied, the lowest free energy state corresponds to the membrane partially wrapping the dendrimer. However, with moderate tension, we find that a G5 (or larger) generation dendrimer, through thermal fluctuation, can induce the formation of metastable pores. These metastable pores are subsequently shown to significantly lower the critical tension necessary for membrane rupture, thus possibly enhancing the release of the trapped genetic material from the endosome. PMID:21354402

Unique battery with an active membrane separator having uniform physico-chemically functionalized ion channels and a method making the same

DOEpatents

Gerald, II, Rex E.; Ruscic, Katarina J [Chicago, IL; Sears, Devin N [Spruce Grove, CA; Smith, Luis J [Natick, MA; Klingler, Robert J [Glenview, IL; Rathke, Jerome W [Homer Glen, IL

2012-02-21

The invention relates to a unique battery having an active, porous membrane and method of making the same. More specifically the invention relates to a sealed battery system having a porous, metal oxide membrane with uniform, physicochemically functionalized ion channels capable of adjustable ionic interaction. The physicochemically-active porous membrane purports dual functions: an electronic insulator (separator) and a unidirectional ion-transporter (electrolyte). The electrochemical cell membrane is activated for the transport of ions by contiguous ion coordination sites on the interior two-dimensional surfaces of the trans-membrane unidirectional pores. The membrane material is designed to have physicochemical interaction with ions. Control of the extent of the interactions between the ions and the interior pore walls of the membrane and other materials, chemicals, or structures contained within the pores provides adjustability of the ionic conductivity of the membrane.

A Culture-Behavior-Brain Loop Model of Human Development.

PubMed

Han, Shihui; Ma, Yina

2015-11-01

Increasing evidence suggests that cultural influences on brain activity are associated with multiple cognitive and affective processes. These findings prompt an integrative framework to account for dynamic interactions between culture, behavior, and the brain. We put forward a culture-behavior-brain (CBB) loop model of human development that proposes that culture shapes the brain by contextualizing behavior, and the brain fits and modifies culture via behavioral influences. Genes provide a fundamental basis for, and interact with, the CBB loop at both individual and population levels. The CBB loop model advances our understanding of the dynamic relationships between culture, behavior, and the brain, which are crucial for human phylogeny and ontogeny. Future brain changes due to cultural influences are discussed based on the CBB loop model. Copyright © 2015 Elsevier Ltd. All rights reserved.

Interplay between short-range correlated disorder and Coulomb interaction in nodal-line semimetals

NASA Astrophysics Data System (ADS)

Wang, Yuxuan; Nandkishore, Rahul M.

2017-09-01

In nodal-line semimetals, Coulomb interactions and short-range correlated disorder are both marginal perturbations to the clean noninteracting Hamiltonian. We analyze their interplay using a weak-coupling renormalization group approach. In the clean case, the Coulomb interaction has been found to be marginally irrelevant, leading to Fermi liquid behavior. We extend the analysis to incorporate the effects of disorder. The nodal line structure gives rise to kinematical constraints similar to that for a two-dimensional Fermi surface, which plays a crucial role in the one-loop renormalization of the disorder couplings. For a twofold degenerate nodal loop (Weyl loop), we show that disorder flows to strong coupling along a unique fixed trajectory in the space of symmetry inequivalent disorder couplings. Along this fixed trajectory, all symmetry inequivalent disorder strengths become equal. For a fourfold degenerate nodal loop (Dirac loop), disorder also flows to strong coupling, however, the strengths of symmetry inequivalent disorder couplings remain different. We show that feedback from disorder reverses the sign of the beta function for the Coulomb interaction, causing the Coulomb interaction to flow to strong coupling as well. However, the Coulomb interaction flows to strong coupling asymptotically more slowly than disorder. Extrapolating our results to strong coupling, we conjecture that at low energies nodal line semimetals should be described by a noninteracting nonlinear sigma model. We discuss the relation of our results with possible many-body localization at zero temperatures in such materials.

Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations

PubMed Central

McDowell, S. Elizabeth; Jun, Jesse M.; Walter, Nils G.

2010-01-01

Enzymes generally are thought to derive their functional activity from conformational motions. The limited chemical variation in RNA suggests that such structural dynamics may play a particularly important role in RNA function. Minimal hammerhead ribozymes are known to cleave efficiently only in ∼10-fold higher than physiologic concentrations of Mg2+ ions. Extended versions containing native loop–loop interactions, however, show greatly enhanced catalytic activity at physiologically relevant Mg2+ concentrations, for reasons that are still ill-understood. Here, we use Mg2+ titrations, activity assays, ensemble, and single molecule fluorescence resonance energy transfer (FRET) approaches, combined with molecular dynamics (MD) simulations, to ask what influence the spatially distant tertiary loop–loop interactions of an extended hammerhead ribozyme have on its structural dynamics. By comparing hammerhead variants with wild-type, partially disrupted, and fully disrupted loop–loop interaction sequences we find that the tertiary interactions lead to a dynamic motional sampling that increasingly populates catalytically active conformations. At the global level the wild-type tertiary interactions lead to more frequent, if transient, encounters of the loop-carrying stems, whereas at the local level they lead to an enrichment in favorable in-line attack angles at the cleavage site. These results invoke a linkage between RNA structural dynamics and function and suggest that loop–loop interactions in extended hammerhead ribozymes—and Mg2+ ions that bind to minimal ribozymes—may generally allow more frequent access to a catalytically relevant conformation(s), rather than simply locking the ribozyme into a single active state. PMID:20921269

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu Wei; Leal, Walter S.

Pheromone-binding proteins (PBPs) are involved in the uptake of pheromones from pores on the antennae, transport through an aqueous environment surrounding the olfactory receptor neurons, and fast delivery to pheromone receptors. We tested the hypothesis that a C-terminal segment and a flexible loop are involved in the release of pheromones to membrane-bound receptors. We expressed in Escherichia coli 11 mutants of the PBP from the silkworm moth, BmorPBP, taking into consideration structural differences between the forms with high and low binding affinity. The N-terminus was truncated and His-69, His-70 and His-95 at the base of a flexible loop, and amore » cluster of acidic residues at the C-terminus were mutated. Binding assays and circular dichroism analyses support a mechanism involving protonation of acidic residues Asp-132 and Glu-141 at the C-terminus and histidines, His-70 and His-95, in the base of a loop covering the binding pocket. The former leads to the formation of a new {alpha}-helix, which competes with pheromone for the binding pocket, whereas positive charge repulsion of the histidines opens the opposite side of the binding pocket.« less

Simulation of gas adsorption on a surface and in slit pores with grand canonical and canonical kinetic Monte Carlo methods.

PubMed

Ustinov, E A; Do, D D

2012-08-21

We present for the first time in the literature a new scheme of kinetic Monte Carlo method applied on a grand canonical ensemble, which we call hereafter GC-kMC. It was shown recently that the kinetic Monte Carlo (kMC) scheme is a very effective tool for the analysis of equilibrium systems. It had been applied in a canonical ensemble to describe vapor-liquid equilibrium of argon over a wide range of temperatures, gas adsorption on a graphite open surface and in graphitic slit pores. However, in spite of the conformity of canonical and grand canonical ensembles, the latter is more relevant in the correct description of open systems; for example, the hysteresis loop observed in adsorption of gases in pores under sub-critical conditions can only be described with a grand canonical ensemble. Therefore, the present paper is aimed at an extension of the kMC to open systems. The developed GC-kMC was proved to be consistent with the results obtained with the canonical kMC (C-kMC) for argon adsorption on a graphite surface at 77 K and in graphitic slit pores at 87.3 K. We showed that in slit micropores the hexagonal packing in the layers adjacent to the pore walls is observed at high loadings even at temperatures above the triple point of the bulk phase. The potential and applicability of the GC-kMC are further shown with the correct description of the heat of adsorption and the pressure tensor of the adsorbed phase.

Successive Two-sided Loop Jets Caused by Magnetic Reconnection between Two Adjacent Filamentary Threads

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Zhanjun; Liu, Yu; Shen, Yuandeng

We present observational analysis of two successive two-sided loop jets observed by the ground-based New Vacuum Solar Telescope and the space-borne Solar Dynamics Observatory . The two successive two-sided loop jets manifested similar evolution processes and both were associated with the interaction of two small-scale adjacent filamentary threads, magnetic emerging, and cancellation processes at the jet’s source region. High temporal and high spatial resolution observations reveal that the two adjacent ends of the two filamentary threads are rooted in opposite magnetic polarities within the source region. The two threads approached each other, and then an obvious brightening patch is observedmore » at the interaction position. Subsequently, a pair of hot plasma ejections are observed heading in opposite directions along the paths of the two filamentary threads at a typical speed for two-sided loop jets of the order 150 km s{sup −1}. Close to the end of the second jet, we report the formation of a bright hot loop structure at the source region, which suggests the formation of new loops during the interaction. Based on the observational results, we propose that the observed two-sided loop jets are caused by magnetic reconnection between the two adjacent filamentary threads, largely different from the previous scenario that a two-sided loop jet is generated by magnetic reconnection between an emerging bipole and the overlying horizontal magnetic fields.« less

Non-perturbative Quantification of Ionic Charge Transfer through Nm-Scale Protein Pores Using Graphene Microelectrodes

NASA Astrophysics Data System (ADS)

Ping, Jinglei; Johnson, A. T. Charlie; A. T. Charlie Johnson Team

Conventional electrical methods for detecting charge transfer through protein pores perturb the electrostatic condition of the solution and chemical reactivity of the pore, and are not suitable to be used for complex biofluids. We developed a non-perturbative methodology ( fW input power) for quantifying trans-pore electrical current and detecting the pore status (i.e., open vs. closes) via graphene microelectrodes. Ferritin was used as a model protein featuring a large interior compartment, well-separated from the exterior solution with discrete pores as charge commuting channels. The charge flowing through the ferritin pores transfers into the graphene microelectrode and is recorded by an electrometer. In this example, our methodology enables the quantification of an inorganic nanoparticle-protein nanopore interaction in complex biofluids. The authors acknowledge the support from the Defense Advanced Research Projects Agency (DARPA) and the U.S. Army Research Office under Grant Number W911NF1010093.

Impact of pore size variability and network coupling on electrokinetic transport in porous media

NASA Astrophysics Data System (ADS)

Alizadeh, Shima; Bazant, Martin Z.; Mani, Ali

2016-11-01

We have developed and validated an efficient and robust computational model to study the coupled fluid and ion transport through electrokinetic porous media, which are exposed to external gradients of pressure, electric potential, and concentration. In our approach a porous media is modeled as a network of many pores through which the transport is described by the coupled Poisson-Nernst-Planck-Stokes equations. When the pore sizes are random, the interactions between various modes of transport may provoke complexities such as concentration polarization shocks and internal flow circulations. These phenomena impact mixing and transport in various systems including deionization and filtration systems, supercapacitors, and lab-on-a-chip devices. In this work, we present simulations of massive networks of pores and we demonstrate the impact of pore size variation, and pore-pore coupling on the overall electrokinetic transport in porous media.

A Theoretical Analysis of the Interaction Between Pores and Inclusions During the Continuous Casting of Steel

NASA Astrophysics Data System (ADS)

Nick, Arash Safavi; Vynnycky, Michael; Fredriksson, Hasse

2016-06-01

A mathematical model is derived to predict the trajectories of pores and inclusions that are nucleated in the interdendritic region during the continuous casting of steel. Using basic fluid mechanics and heat transfer, scaling analysis, and asymptotic methods, the model accounts for the possible lateral drift of the pores as a result of the dependence of the surface tension on temperature and sulfur concentration. Moreover, the soluto-thermocapillary drift of such pores prior to final solidification, coupled to the fact that any inclusions present can only have a vertical trajectory, can help interpret recent experimental observations of pore-inclusion clusters in solidified steel castings.

Structural and Mechanistic Insights into the Latrophilin3-FLRT3 Complex that Mediates Glutamatergic Synapse Development.

PubMed

Ranaivoson, Fanomezana M; Liu, Qun; Martini, Francesca; Bergami, Francesco; von Daake, Sventja; Li, Sheng; Lee, David; Demeler, Borries; Hendrickson, Wayne A; Comoletti, Davide

2015-09-01

Latrophilins (LPHNs) are adhesion-like G-protein-coupled receptors implicated in attention-deficit/hyperactivity disorder. Recently, LPHN3 was found to regulate excitatory synapse number through trans interactions with fibronectin leucine-rich repeat transmembrane 3 (FLRT3). By isothermal titration calorimetry, we determined that only the olfactomedin (OLF) domain of LPHN3 is necessary for FLRT3 association. By multi-crystal native single-wavelength anomalous diffraction phasing, we determined the crystal structure of the OLF domain. This structure is a five-bladed β propeller with a Ca(2+) ion bound in the central pore, which is capped by a mobile loop that allows the ion to exchange with the solvent. The crystal structure of the OLF/FLRT3 complex shows that LPHN3-OLF in the closed state binds with high affinity to the concave face of FLRT3-LRR with a combination of hydrophobic and charged residues. Our study provides structural and functional insights into the molecular mechanism underlying the contribution of LPHN3/FLRT3 to the development of glutamatergic synapses. Copyright © 2015 Elsevier Ltd. All rights reserved.

Cryo-EM structures of the human endolysosomal TRPML3 channel in three distinct states.

PubMed

Zhou, Xiaoyuan; Li, Minghui; Su, Deyuan; Jia, Qi; Li, Huan; Li, Xueming; Yang, Jian

2017-12-01

TRPML3 channels are mainly localized to endolysosomes and play a critical role in the endocytic pathway. Their dysfunction causes deafness and pigmentation defects in mice. TRPML3 activity is inhibited by low endolysosomal pH. Here we present cryo-electron microscopy (cryo-EM) structures of human TRPML3 in the closed, agonist-activated, and low-pH-inhibited states, with resolutions of 4.06, 3.62, and 4.65 Å, respectively. The agonist ML-SA1 lodges between S5 and S6 and opens an S6 gate. A polycystin-mucolipin domain (PMD) forms a luminal cap. S1 extends into this cap, forming a 'gating rod' that connects directly to a luminal pore loop, which undergoes dramatic conformational changes in response to low pH. S2 extends intracellularly and interacts with several intracellular regions to form a 'gating knob'. These unique structural features, combined with the results of electrophysiological studies, indicate a new mechanism by which luminal pH and other physiological modulators such as PIP 2 regulate TRPML3 by changing S1 and S2 conformations.

Structural Elements Regulating AAA+ Protein Quality Control Machines.

PubMed

Chang, Chiung-Wen; Lee, Sukyeong; Tsai, Francis T F

2017-01-01

Members of the ATPases Associated with various cellular Activities (AAA+) superfamily participate in essential and diverse cellular pathways in all kingdoms of life by harnessing the energy of ATP binding and hydrolysis to drive their biological functions. Although most AAA+ proteins share a ring-shaped architecture, AAA+ proteins have evolved distinct structural elements that are fine-tuned to their specific functions. A central question in the field is how ATP binding and hydrolysis are coupled to substrate translocation through the central channel of ring-forming AAA+ proteins. In this mini-review, we will discuss structural elements present in AAA+ proteins involved in protein quality control, drawing similarities to their known role in substrate interaction by AAA+ proteins involved in DNA translocation. Elements to be discussed include the pore loop-1, the Inter-Subunit Signaling (ISS) motif, and the Pre-Sensor I insert (PS-I) motif. Lastly, we will summarize our current understanding on the inter-relationship of those structural elements and propose a model how ATP binding and hydrolysis might be coupled to polypeptide translocation in protein quality control machines.

Voltage Sensor Inactivation in Potassium Channels

PubMed Central

Bähring, Robert; Barghaan, Jan; Westermeier, Regina; Wollberg, Jessica

2012-01-01

In voltage-gated potassium (Kv) channels membrane depolarization causes movement of a voltage sensor domain. This conformational change of the protein is transmitted to the pore domain and eventually leads to pore opening. However, the voltage sensor domain may interact with two distinct gates in the pore domain: the activation gate (A-gate), involving the cytoplasmic S6 bundle crossing, and the pore gate (P-gate), located externally in the selectivity filter. How the voltage sensor moves and how tightly it interacts with these two gates on its way to adopt a relaxed conformation when the membrane is depolarized may critically determine the mode of Kv channel inactivation. In certain Kv channels, voltage sensor movement leads to a tight interaction with the P-gate, which may cause conformational changes that render the selectivity filter non-conductive (“P/C-type inactivation”). Other Kv channels may preferably undergo inactivation from pre-open closed-states during voltage sensor movement, because the voltage sensor temporarily uncouples from the A-gate. For this behavior, known as “preferential” closed-state inactivation, we introduce the term “A/C-type inactivation”. Mechanistically, P/C- and A/C-type inactivation represent two forms of “voltage sensor inactivation.” PMID:22654758

Tuning the band structure of graphene nanoribbons through defect-interaction-driven edge patterning

NASA Astrophysics Data System (ADS)

Du, Lin; Nguyen, Tam N.; Gilman, Ari; Muniz, André R.; Maroudas, Dimitrios

2017-12-01

We report a systematic analysis of pore-edge interactions in graphene nanoribbons (GNRs) and their outcomes based on first-principles calculations and classical molecular-dynamics simulations. We find a strong attractive interaction between nanopores and GNR edges that drives the pores to migrate toward and coalesce with the GNR edges, which can be exploited to form GNR edge patterns that impact the GNR electronic band structure and tune the GNR band gap. Our analysis introduces a viable physical processing strategy for modifying GNR properties by combining defect engineering and thermal annealing.

Analysis of the mechanism of nucleosome survival during transcription

PubMed Central

Chang, Han-Wen; Kulaeva, Olga I.; Shaytan, Alexey K.; Kibanov, Mikhail; Kuznedelov, Konstantin; Severinov, Konstantin V.; Kirpichnikov, Mikhail P.; Clark, David J.; Studitsky, Vasily M.

2014-01-01

Maintenance of nucleosomal structure in the cell nuclei is essential for cell viability, regulation of gene expression and normal aging. Our previous data identified a key intermediate (a small intranucleosomal DNA loop, Ø-loop) that is likely required for nucleosome survival during transcription by RNA polymerase II (Pol II) through chromatin, and suggested that strong nucleosomal pausing guarantees efficient nucleosome survival. To evaluate these predictions, we analysed transcription through a nucleosome by different, structurally related RNA polymerases and mutant yeast Pol II having different histone-interacting surfaces that presumably stabilize the Ø-loop. The height of the nucleosomal barrier to transcription and efficiency of nucleosome survival correlate with the net negative charges of the histone-interacting surfaces. Molecular modeling and analysis of Pol II-nucleosome intermediates by DNase I footprinting suggest that efficient Ø-loop formation and nucleosome survival are mediated by electrostatic interactions between the largest subunit of Pol II and core histones. PMID:24234452

Direct Observation of Gold Nanoparticle Assemblies with the Porin MspA on Mica

PubMed Central

Basel, Matthew T.; Dani, Raj Kumar; Kang, Myungshim; Pavlenok, Mikhail; Chikan, Viktor; Smith, Paul E.; Niederweis, Michael

2009-01-01

The octameric porin MspA from Mycobacterium smegmatis is sufficiently stable to form a non-membrane-supported stand-alone porin on Mica surfaces. About 98% of all MspA octamers were found to stand upright on Mica, with their periplasmic loop regions bound to the hydrophilic Mica surface. Both, small (d = 3.7 nm) and large (d = 17 nm) gold nanoparticles bind to MspA, however in different positions: small gold nanoparticles bind within the MspA pore, whereas the large gold nanoparticles bind to the upper region of MspA. These experiments demonstrate that gold nanoparticles can be positioned at different, well-defined distances from the underlying surface using the MspA pore as a template. These findings represent a significant step towards the use of electrically insulating stable proteins in combination with metal nanoparticles in nanodevices. PMID:19236086

Characterization of Pore Defects and Fatigue Cracks in Die Cast AM60 Using 3D X-ray Computed Tomography

NASA Astrophysics Data System (ADS)

Yang, Zhuofei; Kang, Jidong; Wilkinson, David S.

2015-08-01

AM60 high pressure die castings have been used in automobile applications to reduce the weight of vehicles. However, the pore defects that are inherent in die casting may negatively affect mechanical properties, especially the fatigue properties. Here we have studied damage ( e.g., pore defects, fatigue cracks) during strained-controlled fatigue using 3-dimensional X-ray computed tomography (XCT). The fatigue test was interrupted every 2000 cycles and the specimen was removed to be scanned using a desktop micro-CT system. XCT reveals pore defects, cracks, and fracture surfaces. The results show that pores can be accurately measured and modeled in 3D. Defect bands are found to be made of pores under 50 µm (based on volume-equivalent sphere diameter). Larger pores are randomly distributed in the region between the defect bands. Observation of fatigue cracks by XCT is performed in three ways such that the 3D model gives the best illustration of crack-porosity interaction while the other two methods, with the cracks being viewed on transverse or longitudinal cross sections, have better detectability on crack initiation and crack tip observation. XCT is also of value in failure analysis on fracture surfaces. By assessing XCT data during fatigue testing and observing fracture surfaces on a 3D model, a better understanding on the crack initiation, crack-porosity interaction, and the morphology of fracture surface is achieved.

Molecular understanding of osmosis in semipermeable membranes.

PubMed

Raghunathan, A V; Aluru, N R

2006-07-14

We investigate single-file osmosis of water through a semipermeable membrane with an uncharged, a positively and a negatively charged nanopore. Molecular dynamics simulations indicate that the osmotic flux through a negatively charged pore (J_) is higher compared to the osmotic flux in a positively charged pore (J+) followed by the osmotic flux in the uncharged pore (J(0)), i.e., J_ > J+ > J(0). The molecular mechanisms governing osmosis, steady state osmosis, and the observed osmotic flux dependence on the nanopore charge are explained by computing all the molecular interactions involved and identifying the molecular interactions that play an important role during and after osmosis. This study helps in a fundamental understanding of osmosis and in the design of advanced nanoporous membranes for various applications of osmosis.

Different designs of kinase-phosphatase interactions and phosphatase sequestration shapes the robustness and signal flow in the MAPK cascade

PubMed Central

2012-01-01

Background The three layer mitogen activated protein kinase (MAPK) signaling cascade exhibits different designs of interactions between its kinases and phosphatases. While the sequential interactions between the three kinases of the cascade are tightly preserved, the phosphatases of the cascade, such as MKP3 and PP2A, exhibit relatively diverse interactions with their substrate kinases. Additionally, the kinases of the MAPK cascade can also sequester their phosphatases. Thus, each topologically distinct interaction design of kinases and phosphatases could exhibit unique signal processing characteristics, and the presence of phosphatase sequestration may lead to further fine tuning of the propagated signal. Results We have built four architecturally distinct types of models of the MAPK cascade, each model with identical kinase-kinase interactions but unique kinases-phosphatases interactions. Our simulations unravelled that MAPK cascade’s robustness to external perturbations is a function of nature of interaction between its kinases and phosphatases. The cascade’s output robustness was enhanced when phosphatases were sequestrated by their target kinases. We uncovered a novel implicit/hidden negative feedback loop from the phosphatase MKP3 to its upstream kinase Raf-1, in a cascade resembling the B cell MAPK cascade. Notably, strength of the feedback loop was reciprocal to the strength of phosphatases’ sequestration and stronger sequestration abolished the feedback loop completely. An experimental method to verify the presence of the feedback loop is also proposed. We further showed, when the models were activated by transient signal, memory (total time taken by the cascade output to reach its unstimulated level after removal of signal) of a cascade was determined by the specific designs of interaction among its kinases and phosphatases. Conclusions Differences in interaction designs among the kinases and phosphatases can differentially shape the robustness and signal response behaviour of the MAPK cascade and phosphatase sequestration dramatically enhances the robustness to perturbations in each of the cascade. An implicit negative feedback loop was uncovered from our analysis and we found that strength of the negative feedback loop is reciprocally related to the strength of phosphatase sequestration. Duration of output phosphorylation in response to a transient signal was also found to be determined by the individual cascade’s kinase-phosphatase interaction design. PMID:22748295

Nup93, a Vertebrate Homologue of Yeast Nic96p, Forms a Complex with a Novel 205-kDa Protein and Is Required for Correct Nuclear Pore Assembly

PubMed Central

Grandi, Paola; Dang, Tam; Pané, Nelly; Shevchenko, Andrej; Mann, Matthias; Forbes, Douglass; Hurt, Ed

1997-01-01

Yeast and vertebrate nuclear pores display significant morphological similarity by electron microscopy, but sequence similarity between the respective proteins has been more difficult to observe. Herein we have identified a vertebrate nucleoporin, Nup93, in both human and Xenopus that has proved to be an evolutionarily related homologue of the yeast nucleoporin Nic96p. Polyclonal antiserum to human Nup93 detects corresponding proteins in human, rat, and Xenopus cells. Immunofluorescence and immunoelectron microscopy localize vertebrate Nup93 at the nuclear basket and at or near the nuclear entry to the gated channel of the pore. Immunoprecipitation from both mammalian and Xenopus cell extracts indicates that a small fraction of Nup93 physically interacts with the nucleoporin p62, just as yeast Nic96p interacts with the yeast p62 homologue. However, a large fraction of vertebrate Nup93 is extracted from pores and is also present in Xenopus egg extracts in complex with a newly discovered 205-kDa protein. Mass spectrometric sequencing of the human 205-kDa protein reveals that this protein is encoded by an open reading frame, KIAAO225, present in the human database. The putative human nucleoporin of 205 kDa has related sequence homologues in Caenorhabditis elegans and Saccharomyces cerevisiae. To analyze the role of the Nup93 complex in the pore, nuclei were assembled that lack the Nup93 complex after immunodepletion of a Xenopus nuclear reconstitution extract. The Nup93-complex–depleted nuclei are clearly defective for correct nuclear pore assembly. From these experiments, we conclude that the vertebrate and yeast pore have significant homology in their functionally important cores and that, with the identification of Nup93 and the 205-kDa protein, we have extended the knowledge of the nearest-neighbor interactions of this core in both yeast and vertebrates. PMID:9348540

New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies.

PubMed

Farid, Ramy; Day, Tyler; Friesner, Richard A; Pearlstein, Robert A

2006-05-01

We created a homology model of the homo-tetrameric pore domain of HERG using the crystal structure of the bacterial potassium channel, KvAP, as a template. We docked a set of known blockers with well-characterized effects on channel function into the lumen of the pore between the selectivity filter and extracellular entrance using a novel docking and refinement procedure incorporating Glide and Prime. Key aromatic groups of the blockers are predicted to form multiple simultaneous ring stacking and hydrophobic interactions among the eight aromatic residues lining the pore. Furthermore, each blocker can achieve these interactions via multiple docking configurations. To further interpret the docking results, we mapped hydrophobic and hydrophilic potentials within the lumen of each refined docked complex. Hydrophilic iso-potential contours define a 'propeller-shaped' volume at the selectivity filter entrance. Hydrophobic contours define a hollow 'crown-shaped' volume located above the 'propeller', whose hydrophobic 'rim' extends along the pore axis between Tyr652 and Phe656. Blockers adopt conformations/binding orientations that closely mimic the shapes and properties of these contours. Blocker basic groups are localized in the hydrophilic 'propeller', forming electrostatic interactions with Ser624 rather than a generally accepted pi-cation interaction with Tyr652. Terfenadine, cisapride, sertindole, ibutilide, and clofilium adopt similar docked poses, in which their N-substituents bridge radially across the hollow interior of the 'crown' (analogous to the hub and spokes of a wheel), and project aromatic/hydrophobic portions into the hydrophobic 'rim'. MK-499 docks with its longitudinal axis parallel to the axis of the pore and 'crown', and its hydrophobic groups buried within the hydrophobic 'rim'.

Dynamic properties of individual water molecules in a hydrophobic pore lined with acyl chains: a molecular dynamics study.

PubMed

Qi, Z; Sokabe, M

1998-03-30

Recently, a certain class of synthetic molecules has been shown to form ion channels, the pore of which is lined with hydrophobic acyl chains [M. Sokabe, in: F. Oosawa, H. Hayashi, T. Yoshioka (Eds.), Transmembrane Signaling and Sensation, JSSP/VNU Science Press BV, Tokyo, 1984, p. 119; F. Hayashi, M. Sokabe, M. Takagi, K. Hayashi, U. Kishimoto, Biochim. Biophys. Acta, 510 (1978) 305; M.J. Pregel, L. Jullien, J. Canceill, L. Lacombe, J.M. Lehn, J. Chem. Soc. Perkin Trans., 2 (1995) 417; Y. Tanaka, Y. Kobuke, M. Sokabe, Angew. Chem. Int. Ed. Engl., 34 (1995) 693; M. Sokabe, Z. Qi, K. Donowaki, H. Ishida, K. Okubo, Biophys. J., 70 (1996) A201; H. Ishida, K. Donowaki, Y. Inoue, Z. Qi, M. Sokabe, Chem. Lett. (1997) p. 953]. As an initial step towards understanding the physical mechanisms of ion permeation across such a hydrophobic pore, systematic molecular dynamics simulations were performed to investigate dynamic and energetic properties of water molecules inside the pore using a dimer of alanine-N'-acylated cyclic peptide as a channel model. Dynamic energy profiles for water molecules indicated that the energy barrier at the middle region of the pore is approximately 2-3 kcal/mol higher than that in the cap water region which was defined as a vicinity region of the channel entrance. Energetics analyses demonstrated that the mutual interactions among intrapore water molecules are the major factor to give favorable interaction (negative energy contribution) for themselves. The pore, despite being lined with acyl chains, has a favorable van der Waals interaction with intrapore water molecules. These results may help to explain why water-filled channels can be formed by the hydrophobic helices in natural channels.

Mechanism and molecular basis for the sodium channel subtype specificity of µ-conopeptide CnIIIC

PubMed Central

Markgraf, René; Leipold, Enrico; Schirmeyer, Jana; Paolini-Bertrand, Marianne; Hartley, Oliver; Heinemann, Stefan H

2012-01-01

BACKGROUND AND PURPOSE Voltage-gated sodium channels (NaV channels) are key players in the generation and propagation of action potentials, and selective blockade of these channels is a promising strategy for clinically useful suppression of electrical activity. The conotoxin µ-CnIIIC from the cone snail Conus consors exhibits myorelaxing activity in rodents through specific blockade of skeletal muscle (NaV1.4) NaV channels. EXPERIMENTAL APPROACH We investigated the activity of µ-CnIIIC on human NaV channels and characterized its inhibitory mechanism, as well as the molecular basis, for its channel specificity. KEY RESULTS Similar to rat paralogs, human NaV1.4 and NaV1.2 were potently blocked by µ-CnIIIC, the sensitivity of NaV1.7 was intermediate, and NaV1.5 and NaV1.8 were insensitive. Half-channel chimeras revealed that determinants for the insensitivity of NaV1.8 must reside in both the first and second halves of the channel, while those for NaV1.5 are restricted to domains I and II. Furthermore, domain I pore loop affected the total block and therefore harbours the major determinants for the subtype specificity. Domain II pore loop only affected the kinetics of toxin binding and dissociation. Blockade by µ-CnIIIC of NaV1.4 was virtually irreversible but left a residual current of about 5%, reflecting a ‘leaky’ block; therefore, Na+ ions still passed through µ-CnIIIC-occupied NaV1.4 to some extent. TTX was excluded from this binding site but was trapped inside the pore by µ-CnIIIC. CONCLUSION AND IMPLICATIONS Of clinical significance, µ-CnIIIC is a potent and persistent blocker of human skeletal muscle NaV1.4 that does not affect activity of cardiac NaV1.5. PMID:22537004

Crystallization and textural porosity of synthetic clay minerals.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carrado, K. A.; Csencsits, R.; Thiyagarajan, P.

2002-12-01

The crystallization of synthetic layered magnesium silicate hectorite clays from both silica sol and organosilane sources is compared. For the silica sol-derived clays, a templating method is employed wherein organic or polymeric molecules are included during clay crystallization that are then removed from the composites via calcination. The mechanism of silane-derived hectorite formation is followed by XRD, TGA, 29Si MAS NMR, and small angle X-ray scattering (SAXS), and results are compared to those obtained for the sol-derived hectorite. The mechanism appears to be similar but the rate is approximately doubled when the silane is used rather than silica sol. Analyticalmore » transmission electron microscopy (TEM) is exploited to glean structural morphology information towards resolving the nature of the resulting pore network structures. Results are compared with nitrogen adsorption-desorption isotherm behavior; dominant hysteresis loops are present in the type IV isotherms. Pore size distributions based on both the adsorption and desorption isotherms are compared. Small angle neutron scattering (SANS) experiments reveal that the average particle size increases as synthetic laponite < sol-derived hectorite < silane-derived hectorite < natural hectorite. Contrast matching SANS studies in aqueous and organic solvents are carried out to extract information about pore accessibility.« less

Efficiently computing exact geodesic loops within finite steps.

PubMed

Xin, Shi-Qing; He, Ying; Fu, Chi-Wing

2012-06-01

Closed geodesics, or geodesic loops, are crucial to the study of differential topology and differential geometry. Although the existence and properties of closed geodesics on smooth surfaces have been widely studied in mathematics community, relatively little progress has been made on how to compute them on polygonal surfaces. Most existing algorithms simply consider the mesh as a graph and so the resultant loops are restricted only on mesh edges, which are far from the actual geodesics. This paper is the first to prove the existence and uniqueness of geodesic loop restricted on a closed face sequence; it contributes also with an efficient algorithm to iteratively evolve an initial closed path on a given mesh into an exact geodesic loop within finite steps. Our proposed algorithm takes only an O(k) space complexity and an O(mk) time complexity (experimentally), where m is the number of vertices in the region bounded by the initial loop and the resultant geodesic loop, and k is the average number of edges in the edge sequences that the evolving loop passes through. In contrast to the existing geodesic curvature flow methods which compute an approximate geodesic loop within a predefined threshold, our method is exact and can apply directly to triangular meshes without needing to solve any differential equation with a numerical solver; it can run at interactive speed, e.g., in the order of milliseconds, for a mesh with around 50K vertices, and hence, significantly outperforms existing algorithms. Actually, our algorithm could run at interactive speed even for larger meshes. Besides the complexity of the input mesh, the geometric shape could also affect the number of evolving steps, i.e., the performance. We motivate our algorithm with an interactive shape segmentation example shown later in the paper.

A dihydropyridine receptor alpha1s loop region critical for skeletal muscle contraction is intrinsically unstructured and binds to a SPRY domain of the type 1 ryanodine receptor.

PubMed

Cui, Yanfang; Tae, Han-Shen; Norris, Nicole C; Karunasekara, Yamuna; Pouliquin, Pierre; Board, Philip G; Dulhunty, Angela F; Casarotto, Marco G

2009-03-01

The II-III loop of the dihydropyridine receptor (DHPR) alpha(1s) subunit is a modulator of the ryanodine receptor (RyR1) Ca(2+) release channel in vitro and is essential for skeletal muscle contraction in vivo. Despite its importance, the structure of this loop has not been reported. We have investigated its structure using a suite of NMR techniques which revealed that the DHPR II-III loop is an intrinsically unstructured protein (IUP) and as such belongs to a burgeoning structural class of functionally important proteins. The loop does not possess a stable tertiary fold: it is highly flexible, with a strong N-terminal helix followed by nascent helical/turn elements and unstructured segments. Its residual structure is loosely globular with the N and C termini in close proximity. The unstructured nature of the II-III loop may allow it to easily modify its interaction with RyR1 following a surface action potential and thus initiate rapid Ca(2+) release and contraction. The in vitro binding partner for the II-III was investigated. The II-III loop interacts with the second of three structurally distinct SPRY domains in RyR1, whose function is unknown. This interaction occurs through two preformed N-terminal alpha-helical regions and a C-terminal hydrophobic element. The A peptide corresponding to the helical N-terminal region is a common probe of RyR function and binds to the same SPRY domain as the full II-III loop. Thus the second SPRY domain is an in vitro binding site for the II-III loop. The possible in vivo role of this region is discussed.

Mini-filament Eruption as the Initiation of a Jet along Coronal Loops

NASA Astrophysics Data System (ADS)

Hong, Junchao; Jiang, Yunchun; Yang, Jiayan; Yang, Bo; Xu, Zhe; Xiang, Yongyuan

2016-10-01

Minifilament eruptions (MFEs) and coronal jets are different types of solar small-scale explosive events. We report an MFE observed at the New Vacuum Solar Telescope (NVST). As seen in the NVST Hα images, during the rising phase, the minifilament erupts outward orthogonally to its length, accompanied with a flare-like brightening at the bottom. Afterward, dark materials are found to possibly extend along the axis of the expanded filament body. The MFE is analogous to large filament eruptions. However, a simultaneous observation of the Solar Dynamics Observatory shows that a jet is initiated and flows out along nearby coronal loops during the rising phase of the MFE. Meanwhile, small hot loops, which connect the original eruptive site of the minifilament to the footpoints of the coronal loops, are formed successively. A differential emission measure analysis demonstrates that, on the top of the new small loops, a hot cusp structure exists. We conjecture that the magnetic fields of the MFE interact with magnetic fields of the coronal loops. This interaction is interpreted as magnetic reconnection that produces the jet and the small hot loops.

Free-energy calculations reveal the subtle differences in the interactions of DNA bases with α-hemolysin.

PubMed

Manara, Richard M A; Guy, Andrew T; Wallace, E Jayne; Khalid, Syma

2015-02-10

Next generation DNA sequencing methods that utilize protein nanopores have the potential to revolutionize this area of biotechnology. While the technique is underpinned by simple physics, the wild-type protein pores do not have all of the desired properties for efficient and accurate DNA sequencing. Much of the research efforts have focused on protein nanopores, such as α-hemolysin from Staphylococcus aureus. However, the speed of DNA translocation has historically been an issue, hampered in part by incomplete knowledge of the energetics of translocation. Here we have utilized atomistic molecular dynamics simulations of nucleotide fragments in order to calculate the potential of mean force (PMF) through α-hemolysin. Our results reveal specific regions within the pore that play a key role in the interaction with DNA. In particular, charged residues such as D127 and K131 provide stabilizing interactions with the anionic DNA and therefore are likely to reduce the speed of translocation. These regions provide rational targets for pore optimization. Furthermore, we show that the energetic contributions to the protein-DNA interactions are a complex combination of electrostatics and short-range interactions, often mediated by water molecules.

Functional Loop Dynamics of the Streptavidin-Biotin Complex

PubMed Central

Song, Jianing; Li, Yongle; Ji, Changge; Zhang, John Z. H.

2015-01-01

Accelerated molecular dynamics (aMD) simulation is employed to study the functional dynamics of the flexible loop3-4 in the strong-binding streptavidin-biotin complex system. Conventional molecular (cMD) simulation is also performed for comparison. The present study reveals the following important properties of the loop dynamics: (1) The transition of loop3-4 from open to closed state is observed in 200 ns aMD simulation. (2) In the absence of biotin binding, the open-state streptavidin is more stable, which is consistent with experimental evidences. The free energy (ΔG) difference is about 5 kcal/mol between two states. But with biotin binding, the closed state is more stable due to electrostatic and hydrophobic interactions between the loop3-4 and biotin. (3) The closure of loop3-4 is concerted to the stable binding of biotin to streptavidin. When the loop3-4 is in its open-state, biotin moves out of the binding pocket, indicating that the interactions between the loop3-4 and biotin are essential in trapping biotin in the binding pocket. (4) In the tetrameric streptavidin system, the conformational change of the loop3-4 in each monomer is independent of each other. That is, there is no cooperative binding for biotin bound to the four subunits of the tetramer. PMID:25601277

Architecture of the TIM23 inner mitochondrial translocon and interactions with the matrix import motor.

PubMed

Ting, See-Yeun; Schilke, Brenda A; Hayashi, Masaya; Craig, Elizabeth A

2014-10-10

Translocation of proteins from the cytosol across the mitochondrial inner membrane is driven by action of the matrix-localized multi-subunit import motor, which is associated with the TIM23 translocon. The architecture of the import apparatus is not well understood. Here, we report results of site-specific in vivo photocross-linking along with genetic and coimmunoprecipitation analyses dissecting interactions between import motor subunits and the translocon. The translocon is composed of the two integral membrane proteins Tim23 and Tim17, each containing four membrane-spanning segments. We found that Tim23 having a photoactivatable cross-linker in the matrix exposed loop between transmembrane domains 1 and 2 (loop 1) cross-linked to Tim44. Alterations in this loop destabilized interaction of Tim44 with the translocon. Analogously, Tim17 having a photoactivatable cross-linker in the matrix exposed loop between transmembrane segments 1 and 2 (loop 1) cross-linked to Pam17. Alterations in this loop caused destabilization of the interaction of Pam17 with the translocon. Substitution of individual photoactivatable residues in Tim44 and Pam17 in regions we previously identified as important for translocon association resulted in cross-linking to Tim23 and Tim17, respectively. Our results are consistent with a model in which motor association is achieved via interaction of Tim23 with Tim44, which serves as a scaffold for association of other motor components, and of Tim17 with Pam17. As both Tim44 and Pam17 have been implicated as regulatory subunits of the motor, this positioning is conducive for responding to conformational changes in the translocon upon a translocating polypeptide entering the channel. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Assessing the Impact of Riparian Soil-Water Dynamics on Streambank Erosion

USDA-ARS?s Scientific Manuscript database

Occurrence of streambank failure is closely related to changes in pore-water pressure. Pore-water pressure in a streambank is affected, among others, by infiltrating rainfall, streambank-material texture, riparian vegetation, and interactions between surface water and groundwater. Also, the reduct...

Irradiation behavior of the interaction product of U-Mo fuel particle dispersion in an Al matrix

NASA Astrophysics Data System (ADS)

Kim, Yeon Soo; Hofman, G. L.

2012-06-01

Irradiation performance of U-Mo fuel particles dispersed in Al matrix is stable in terms of fuel swelling and is suitable for the conversion of research and test reactors from highly enriched uranium (HEU) to low enriched uranium (LEU). However, tests of the fuel at high temperatures and high burnups revealed obstacles caused by the interaction layers forming between the fuel particle and matrix. In some cases, fission gas filled pores grow and interconnect in the interdiffusion layer resulting in fuel plate failure. Postirradiation observations are made to examine the behavior of the interdiffusion layers. The interdiffusion layers show a fluid-like behavior characteristic of amorphous materials. In the amorphous interdiffusion layers, fission gas diffusivity is high and the material viscosity is low so that the fission gas pores readily form and grow. Based on the observations, a pore formation mechanism is proposed and potential remedies to suppress the pore growth are also introduced.

A Method to Predict the Structure and Stability of RNA/RNA Complexes.

PubMed

Xu, Xiaojun; Chen, Shi-Jie

2016-01-01

RNA/RNA interactions are essential for genomic RNA dimerization and regulation of gene expression. Intermolecular loop-loop base pairing is a widespread and functionally important tertiary structure motif in RNA machinery. However, computational prediction of intermolecular loop-loop base pairing is challenged by the entropy and free energy calculation due to the conformational constraint and the intermolecular interactions. In this chapter, we describe a recently developed statistical mechanics-based method for the prediction of RNA/RNA complex structures and stabilities. The method is based on the virtual bond RNA folding model (Vfold). The main emphasis in the method is placed on the evaluation of the entropy and free energy for the loops, especially tertiary kissing loops. The method also uses recursive partition function calculations and two-step screening algorithm for large, complicated structures of RNA/RNA complexes. As case studies, we use the HIV-1 Mal dimer and the siRNA/HIV-1 mutant (T4) to illustrate the method.

Structure-Directed and Tailored Diversity Synthetic Antibody Libraries Yield Novel Anti-EGFR Antagonists.

PubMed

Miersch, Shane; Maruthachalam, Bharathikumar Vellalore; Geyer, C Ronald; Sidhu, Sachdev S

2017-05-19

We tested whether grafting an interaction domain into the hypervariable loop of a combinatorial antibody library could promote targeting to a specific epitope. Formation of the epidermal growth factor receptor (EGFR) signaling heterodimer involves extensive contacts mediated by a "dimerization loop." We grafted the dimerization loop into the third hypervariable loop of a synthetic antigen-binding fragment (Fab) library and diversified other loops using a tailored diversity strategy. This structure-directed Fab library and a naı̈ve synthetic Fab library were used to select Fabs against EGFR. Both libraries yielded high affinity Fabs that bound to overlapping epitopes on cell-surface EGFR, inhibited receptor activation, and targeted epitopes distinct from those of cetuximab and panitumumab. Epitope mapping experiments revealed complex sites of interaction, comprised of domains I and II but not exclusively localized to the receptor dimerization loop. These results validate the grafting approach for designing Fab libraries and also underscore the versatility of naı̈ve synthetic libraries.

Kinetics of interior loop formation in semiflexible chains.

PubMed

Hyeon, Changbong; Thirumalai, D

2006-03-14

Loop formation between monomers in the interior of semiflexible chains describes elementary events in biomolecular folding and DNA bending. We calculate analytically the interior distance distribution function for semiflexible chains using a mean field approach. Using the potential of mean force derived from the distance distribution function we present a simple expression for the kinetics of interior looping by adopting Kramers theory. For the parameters, that are appropriate for DNA, the theoretical predictions in comparison with the case are in excellent agreement with explicit Brownian dynamics simulations of wormlike chain (WLC) model. The interior looping times (tauIC) can be greatly altered in the cases when the stiffness of the loop differs from that of the dangling ends. If the dangling end is stiffer than the loop then tauIC increases for the case of the WLC with uniform persistence length. In contrast, attachment of flexible dangling ends enhances rate of interior loop formation. The theory also shows that if the monomers are charged and interact via screened Coulomb potential then both the cyclization (tauc) and interior looping (tauIC) times greatly increase at low ionic concentration. Because both tauc and tauIC are determined essentially by the effective persistence length [lp(R)] we computed lp(R) by varying the range of the repulsive interaction between the monomers. For short range interactions lp(R) nearly coincides with the bare persistence length which is determined largely by the backbone chain connectivity. This finding rationalizes the efficacy of describing a number of experimental observations (response of biopolymers to force and cyclization kinetics) in biomolecules using WLC model with an effective persistence length.

Pore size regulates cell and tissue interactions with PLGA-CaP scaffolds used for bone engineering.

PubMed

Sicchieri, Luciana Gonçalves; Crippa, Grasiele Edilaine; de Oliveira, Paulo Tambasco; Beloti, Marcio Mateus; Rosa, Adalberto Luiz

2012-02-01

A common subject in bone tissue engineering is the need for porous scaffolds to support cell and tissue interactions aiming at repairing bone tissue. As poly(lactide-co-glycolide)-calcium phosphate (PLGA-CaP) scaffolds can be manufactured with different pore sizes, the aim of this study was to evaluate the effect of pore diameter on osteoblastic cell responses and bone tissue formation. Scaffolds were prepared with 85% porosity, with pore diameters in the ranges 470-590, 590-850 and 850-1200 µm. Rat bone marrow stem cells differentiated into osteoblasts were cultured on the scaffolds for up to 10 days to evaluate cell growth, alkaline phosphatase (ALP) activity and the gene expression of the osteoblast markers RUNX2, OSX, COL, MSX2, ALP, OC and BSP by real-time PCR. Scaffolds were implanted in critical size rat calvarial defects for 2, 4, and 8 weeks for histomorphometric analysis. Cell growth and ALP activity were not affected by the pore size; however, there was an increase in the gene expression of osteoblastic markers with the increase in the pore sizes. At 2 weeks all scaffolds displayed a similar amount of bone and blood vessels formation. At 4 and 8 weeks much more bone formation and an increased number of blood vessels were observed in scaffolds with pores of 470-590 µm. These results show that PLGA-CaP is a promising biomaterial for bone engineering. However, ideally, combinations of larger (-1000 µm) and smaller (-500 µm) pores in a single scaffold would optimize cellular and tissue responses during bone healing. Copyright © 2011 John Wiley & Sons, Ltd.

Root induced changes of effective 1D hydraulic properties in a soil column.

PubMed

Scholl, P; Leitner, D; Kammerer, G; Loiskandl, W; Kaul, H-P; Bodner, G

Roots are essential drivers of soil structure and pore formation. This study aimed at quantifying root induced changes of the pore size distribution (PSD). The focus was on the extent of clogging vs. formation of pores during active root growth. Parameters of Kosugi's lognormal PSD model were determined by inverse estimation in a column experiment with two cover crops (mustard, rye) and an unplanted control. Pore dynamics were described using a convection-dispersion like pore evolution model. Rooted treatments showed a wider range of pore radii with increasing volumes of large macropores >500 μm and micropores <2.5 μm, while fine macropores, mesopores and larger micropores decreased. The non-rooted control showed narrowing of the PSD and reduced porosity over all radius classes. The pore evolution model accurately described root induced changes, while structure degradation in the non-rooted control was not captured properly. Our study demonstrated significant short term root effects with heterogenization of the pore system as dominant process of root induced structure formation. Pore clogging is suggested as a partial cause for reduced pore volume. The important change in micro- and large macropores however indicates that multiple mechanic and biochemical processes are involved in root-pore interactions.

Isolated pores dissected from human two-pore channel 2 are functional

PubMed Central

Penny, Christopher J.; Rahman, Taufiq; Sula, Altin; Miles, Andrew J.; Wallace, B. A.; Patel, Sandip

2016-01-01

Multi-domain voltage-gated ion channels appear to have evolved through sequential rounds of intragenic duplication from a primordial one-domain precursor. Whereas modularity within one-domain symmetrical channels is established, little is known about the roles of individual regions within more complex asymmetrical channels where the domains have undergone substantial divergence. Here we isolated and characterised both of the divergent pore regions from human TPC2, a two-domain channel that holds a key intermediate position in the evolution of voltage-gated ion channels. In HeLa cells, each pore localised to the ER and caused Ca2+ depletion, whereas an ER-targeted pore mutated at a residue that inactivates full-length TPC2 did not. Additionally, one of the pores expressed at high levels in E. coli. When purified, it formed a stable, folded tetramer. Liposomes reconstituted with the pore supported Ca2+ and Na+ uptake that was inhibited by known blockers of full-length channels. Computational modelling of the pore corroborated cationic permeability and drug interaction. Therefore, despite divergence, both pores are constitutively active in the absence of their partners and retain several properties of the wild-type pore. Such symmetrical ‘pore-only’ proteins derived from divergent channel domains may therefore provide tractable tools for probing the functional architecture of complex ion channels. PMID:27941820

Modeling for stress-strain curve of a porous NiTi under compressive loading

NASA Astrophysics Data System (ADS)

Zhao, Ying; Taya, Minoru

2005-05-01

Two models for predicting the stress-strain curve of porous NiTi under compressive loading are presented in this paper. Porous NiTi shape memory alloy is investigated as a composite composed of solid NiTi as matrix and pores as inclusions. Eshelby"s equivalent inclusion method and Mori-Tanaka"s mean-field theory are employed in both models. In the first model, the geometry of the pores is assumed as sphere. The composite is with close-cells. While in the second model, two geometries of the pores, sphere and ellipsoid, are investigated. The pores are interconnected to each other forming an open-cell microstructure. The two adjacent pores connected along equator ring are investigated as a unit. Two pores interact with each other as they are connected. The average eigenstrain of each unit is obtained by taking the average of each pore"s eigenstrain. The stress-strain curves of porous shape memory alloy with spherical pores and ellipsoidal pores are compared, it is found that the shape of the pores has a nonignorable influence on the mechanical property of the porous NiTi. Comparison of the stress-strain curves of the two models shows that introducing of the average eigenstrains in the second model makes the predictions more agreeable to the experimental results.

Isolated pores dissected from human two-pore channel 2 are functional.

PubMed

Penny, Christopher J; Rahman, Taufiq; Sula, Altin; Miles, Andrew J; Wallace, B A; Patel, Sandip

2016-12-12

Multi-domain voltage-gated ion channels appear to have evolved through sequential rounds of intragenic duplication from a primordial one-domain precursor. Whereas modularity within one-domain symmetrical channels is established, little is known about the roles of individual regions within more complex asymmetrical channels where the domains have undergone substantial divergence. Here we isolated and characterised both of the divergent pore regions from human TPC2, a two-domain channel that holds a key intermediate position in the evolution of voltage-gated ion channels. In HeLa cells, each pore localised to the ER and caused Ca 2+ depletion, whereas an ER-targeted pore mutated at a residue that inactivates full-length TPC2 did not. Additionally, one of the pores expressed at high levels in E. coli. When purified, it formed a stable, folded tetramer. Liposomes reconstituted with the pore supported Ca 2+ and Na + uptake that was inhibited by known blockers of full-length channels. Computational modelling of the pore corroborated cationic permeability and drug interaction. Therefore, despite divergence, both pores are constitutively active in the absence of their partners and retain several properties of the wild-type pore. Such symmetrical 'pore-only' proteins derived from divergent channel domains may therefore provide tractable tools for probing the functional architecture of complex ion channels.

Modeling and control of non-square MIMO system using relay feedback.

PubMed

Kalpana, D; Thyagarajan, T; Gokulraj, N

2015-11-01

This paper proposes a systematic approach for the modeling and control of non-square MIMO systems in time domain using relay feedback. Conventionally, modeling, selection of the control configuration and controller design of non-square MIMO systems are performed using input/output information of direct loop, while the output of undesired responses that bears valuable information on interaction among the loops are not considered. However, in this paper, the undesired response obtained from relay feedback test is also taken into consideration to extract the information about the interaction between the loops. The studies are performed on an Air Path Scheme of Turbocharged Diesel Engine (APSTDE) model, which is a typical non-square MIMO system, with input and output variables being 3 and 2 respectively. From the relay test response, the generalized analytical expressions are derived and these analytical expressions are used to estimate unknown system parameters and also to evaluate interaction measures. The interaction is analyzed by using Block Relative Gain (BRG) method. The model thus identified is later used to design appropriate controller to carry out closed loop studies. Closed loop simulation studies were performed for both servo and regulatory operations. Integral of Squared Error (ISE) performance criterion is employed to quantitatively evaluate performance of the proposed scheme. The usefulness of the proposed method is demonstrated on a lab-scale Two-Tank Cylindrical Interacting System (TTCIS), which is configured as a non-square system. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

A New Poisson-Nernst-Planck Model with Ion-Water Interactions for Charge Transport in Ion Channels.

PubMed

Chen, Duan

2016-08-01

In this work, we propose a new Poisson-Nernst-Planck (PNP) model with ion-water interactions for biological charge transport in ion channels. Due to narrow geometries of these membrane proteins, ion-water interaction is critical for both dielectric property of water molecules in channel pore and transport dynamics of mobile ions. We model the ion-water interaction energy based on realistic experimental observations in an efficient mean-field approach. Variation of a total energy functional of the biological system yields a new PNP-type continuum model. Numerical simulations show that the proposed model with ion-water interaction energy has the new features that quantitatively describe dielectric properties of water molecules in narrow pores and are possible to model the selectivity of some ion channels.

Structural comparison of four different antibodies interacting with human papillomavirus 16 and mechanisms of neutralization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guan, Jian; Bywaters, Stephanie M.; Brendle, Sarah A.

2015-09-15

Cryo-electron microscopy (cryo-EM) was used to solve the structures of human papillomavirus type 16 (HPV16) complexed with fragments of antibody (Fab) from three different neutralizing monoclonals (mAbs): H16.1A, H16.14J, and H263.A2. The structure-function analysis revealed predominantly monovalent binding of each Fab with capsid interactions that involved multiple loops from symmetry related copies of the major capsid protein. The residues identified in each Fab-virus interface map to a conformational groove on the surface of the capsomer. In addition to the known involvement of the FG and HI loops, the DE loop was also found to constitute the core of each epitope.more » Surprisingly, the epitope mapping also identified minor contributions by EF and BC loops. Complementary immunological assays included mAb and Fab neutralization. The specific binding characteristics of mAbs correlated with different neutralizing behaviors in pre- and post-attachment neutralization assays. - Highlights: • We present HPV16-Fab complexes from neutralizing mAbs: H16.1A, H16.14J, and H263.A2. • The structure-function analysis revealed predominantly monovalent binding of each mAb. • Capsid–Fab interactions involved multiple loops from symmetry related L1 proteins. • Besides the known FG and HI loops, epitope mapping also identified DE, EF, and BC loops. • Neutralizing assays complement the structures to show multiple neutralization mechanisms.« less

A short autocomplementary sequence plays an essential role in avian sarcoma-leukosis virus RNA dimerization.

PubMed

Fossé, P; Motté, N; Roumier, A; Gabus, C; Muriaux, D; Darlix, J L; Paoletti, J

1996-12-24

Retroviral genomes consist of two identical RNA molecules joined noncovalently near their 5'-ends. Recently, two models have been proposed for RNA dimer formation on the basis of results obtained in vitro with human immunodeficiency virus type 1 RNA and Moloney murine leukemia virus RNA. It was first proposed that viral RNA dimerizes by forming an interstrand quadruple helix with purine tetrads. The second model postulates that RNA dimerization is initiated by a loop-loop interaction between the two RNA molecules. In order to better characterize the dimerization process of retroviral genomic RNA, we analyzed the in vitro dimerization of avian sarcoma-leukosis virus (ASLV) RNA using different transcripts. We determined the requirements for heterodimer formation, the thermal dissociation of RNA dimers, and the influence of antisense DNA oligonucleotides on dimer formation. Our results strongly suggest that purine tetrads are not involved in dimer formation. Data show that an autocomplementary sequence located upstream from the splice donor site and within a major packaging signal plays a crucial role in ASLV RNA dimer formation in vitro. This sequence is able to form a stem-loop structure, and phylogenetic analysis reveals that it is conserved in 28 different avian sarcoma and leukosis viruses. These results suggest that dimerization of ASLV RNA is initiated by a loop-loop interaction between two RNA molecules and provide an additional argument for the ubiquity of the dimerization process via loop-loop interaction.

Investigating the development of less-mobile porosity in realistic hyporheic zone sediments with COMSOL Multiphysics

NASA Astrophysics Data System (ADS)

MahmoodPoorDehkordy, F.; Briggs, M. A.; Day-Lewis, F. D.; Bagtzoglou, A. C.

2017-12-01

Although hyporheic zones are often modeled at the reach scale as homogeneous "boxes" of exchange, heterogeneity caused by variations of pore sizes and connectivity is not uncommon. This heterogeneity leads to the creation of more- and less-mobile zones of hydraulic exchange that influence reactive solute transport processes. Whereas fluid sampling is generally sensitive to more-mobile zones, geoelectrical measurement is sensitive to ionic tracer dynamics in both less- and more-mobile zones. Heterogeneity in pore connectivity leads to a lag between fluid and bulk electrical conductivity (EC) resulting in a hysteresis loop, observed during tracer breakthrough tests, that contains information about the less-mobile porosity attributes of the medium. Here, we present a macro-scale model of solute transport and electrical conduction developed using COMSOL Multiphysics. The model is used to simulate geoelectrical monitoring of ionic transport for bed sediments based on (1) a stochastic sand-and-cobble mixture and (2) a dune feature with strong permeability layering. In both of these disparate sediment types, hysteresis between fluid and bulk EC is observed, and depends in part on fluid flux rate through the model domain. Using the hysteresis loop, the ratio of less-mobile to mobile porosity and mass-transfer coefficient are estimated graphically. The results indicate the presence and significance of less-mobile porosity in the hyporheic zones and demonstrate the capability of the proposed model to detect heterogeneity in flow processes and estimate less-mobile zone parameters.

Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements

PubMed Central

PENEDO, J. CARLOS; WILSON, TIMOTHY J.; JAYASENA, SUMEDHA D.; KHVOROVA, ANASTASIA; LILLEY, DAVID M.J.

2004-01-01

It has been shown that the activity of the hammerhead ribozyme at μM magnesium ion concentrations is markedly increased by the inclusion of loops in helices I and II. We have studied the effect of such loops on the magnesium ion-induced folding of the ribozyme, using fluorescence resonance energy transfer. We find that with the loops in place, folding into the active conformation occurs in a single step, in the μM range of magnesium ion concentration. Disruption of the loop–loop interaction leads to a reversion to two-step folding, with the second stage requiring mM concentrations of magnesium ion. Sodium ions also promote the folding of the natural form of the ribozyme at high concentrations, but the folding occurs as a two-stage process. The loops clearly act as important auxiliary elements in the function of the ribozyme, permitting folding to occur efficiently under physiological conditions. PMID:15100442

Probing the closed-loop model of mRNA translation in living cells

PubMed Central

Archer, Stuart K; Shirokikh, Nikolay E; Hallwirth, Claus V; Beilharz, Traude H; Preiss, Thomas

2015-01-01

The mRNA closed-loop, formed through interactions between the cap structure, poly(A) tail, eIF4E, eIF4G and PAB, features centrally in models of eukaryotic translation initiation, although direct support for its existence in vivo is not well established. Here, we investigated the closed-loop using a combination of mRNP isolation from rapidly cross-linked cells and high-throughput qPCR. Using the interaction between these factors and the opposing ends of mRNAs as a proxy for the closed-loop, we provide evidence that it is prevalent for eIF4E/4G-bound but unexpectedly sparse for PAB1-bound mRNAs, suggesting it primarily occurs during a distinct phase of polysome assembly. We observed mRNA-specific variation in the extent of closed-loop formation, consistent with a role for polysome topology in the control of gene expression. PMID:25826658

Characterization of a Novel Association between Two Trypanosome-Specific Proteins and 5S rRNA

PubMed Central

Ciganda, Martin; Williams, Noreen

2012-01-01

P34 and P37 are two previously identified RNA binding proteins in the flagellate protozoan Trypanosoma brucei. RNA interference studies have determined that the proteins are essential and are involved in ribosome biogenesis. Here, we show that these proteins interact in vitro with the 5S rRNA with nearly identical binding characteristics in the absence of other cellular factors. The T. brucei 5S rRNA has a complex secondary structure and presents four accessible loops (A to D) for interactions with RNA-binding proteins. In other eukaryotes, loop C is bound by the L5 ribosomal protein and loop A mainly by TFIIIA. The binding of P34 and P37 to T. brucei 5S rRNA involves the LoopA region of the RNA, but these proteins also protect the L5 binding site located on LoopC. PMID:22253864

Coverage Dependent Assembly of Anthraquinone on Au(111)

NASA Astrophysics Data System (ADS)

Conrad, Brad; Deloach, Andrew; Einstein, Theodore; Dougherty, Daniel

A study of adsorbate-adsorbate and surface state mediated interactions of anthraquinone (AnQ) on Au(111) is presented. We utilize scanning tunneling microscopy (STM) to characterize the coverage dependence of AnQ structure formation. Ordered structures are observed up to a single monolayer (ML) and are found to be strongly dependent on molecular surface density. While the complete ML forms a well-ordered close-packed layer, for a narrow range of sub-ML coverages irregular close-packed islands are observed to coexist with a disordered pore network linking neighboring islands. This network displays a characteristic pore size and at lower coverages, the soliton walls of the herringbone reconstruction are shown to promote formation of distinct pore nanostructures. We will discuss these nanostructure formations in the context of surface mediated and more direct adsorbate interactions.

A reentrant loop domain in the glutamate carrier EAAT1 participates in substrate binding and translocation.

PubMed

Seal, R P; Amara, S G

1998-12-01

To investigate the structural determinants underlying transport by the glutamate transporter EAAT1, we mutated each of 24 highly conserved residues (P392 to Q415) to cysteine. A majority of these substituted cysteines react with the sulfhydryl-modifying reagent MTSEA, suggesting that they reside in an aqueous environment. The impermeant reagents MTSES and MTSET react with residues at each end of the domain (A395C and A414C), supporting a model that places these residues near the extracellular surface. Substrates and inhibitors block the reaction between MTS derivatives and A395C, and the cosubstrate, sodium, slows reaction of MTSEA with Y405C and E406C. From these results, we propose that this domain forms a reentrant membrane loop at the cell surface and may comprise part of the translocation pore for substrates and cotransported ions.

Man-in-the-control-loop simulation of manipulators

NASA Technical Reports Server (NTRS)

Chang, J. L.; Lin, Tsung-Chieh; Yae, K. Harold

1989-01-01

A method to achieve man-in-the-control-loop simulation is presented. Emerging real-time dynamics simulation suggests a potential for creating an interactive design workstation with a human operator in the control loop. The recursive formulation for multibody dynamics simulation is studied to determine requirements for man-in-the-control-loop simulation. High speed computer graphics techniques provides realistic visual cues for the simulator. Backhoe and robot arm simulations are implemented to demonstrate the capability of man-in-the-control-loop simulation.

Shifts in pore connectivity from precipitation versus groundwater rewetting increases soil carbon loss after drought

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, A. Peyton; Bond-Lamberty, Ben; Benscoter, Brian W.

Droughts and other extreme precipitation events are predicted to increase in intensity, duration and extent, with uncertain implications for terrestrial carbon (C) sequestration. Soil wetting from above (precipitation) results in a characteristically different pattern of pore-filling than wetting from below (groundwater), with larger, well-connected pores filling before finer pore spaces, unlike groundwater rise in which capillary forces saturate the finest pores first. Here we demonstrate that pore-scale wetting patterns interact with antecedent soil moisture conditions to alter pore-, core- and field-scale C dynamics. Drought legacy and wetting direction are perhaps more important determinants of short-term C mineralization than current soilmore » moisture content in these soils. Our results highlight that microbial access to C is not solely limited by physical protection, but also by drought or wetting-induced shifts in hydrologic connectivity. We argue that models should treat soil moisture within a three-dimensional framework emphasizing hydrologic conduits for C and resource diffusion.« less

Mechanics of water pore formation in lipid membrane under electric field

NASA Astrophysics Data System (ADS)

Bu, Bing; Li, Dechang; Diao, Jiajie; Ji, Baohua

2017-04-01

Transmembrane water pores are crucial for substance transport through cell membranes via membrane fusion, such as in neural communication. However, the molecular mechanism of water pore formation is not clear. In this study, we apply all-atom molecular dynamics and bias-exchange metadynamics simulations to study the process of water pore formation under an electric field. We show that water molecules can enter a membrane under an electric field and form a water pore of a few nanometers in diameter. These water molecules disturb the interactions between lipid head groups and the ordered arrangement of lipids. Following the movement of water molecules, the lipid head groups are rotated and driven into the hydrophobic region of the membrane. The reorientated lipid head groups inside the membrane form a hydrophilic surface of the water pore. This study reveals the atomic details of how an electric field influences the movement of water molecules and lipid head groups, resulting in water pore formation.

Controllable self-assembly of mesoporous hydroxyapatite.

PubMed

Chen, Jingdi; Wang, Zihao; Wen, Zhenliang; Yang, Shen; Wang, Jianhua; Zhang, Qiqing

2015-03-01

In this paper, mesoporous hydroxyapatite (HAp) of controllable pore size was tailored with the template of a biodegradable mono-alkyl phosphate (MAP) via a simple route by hydrothermal treatment. A serial study of the various experimental parameters on pore size of HAp was investigated. The additive amount of MAP and hydrothermal temperature were important factors for the pore structure and pore size. Powder X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and nitrogen adsorption-desorption (BET, BJH) were used to characterize the structure and composition of the HAp samples. Both XRD and BJH results indicated that regular mesoporous HAp nanoparticles (with a mean pore size of 3.5nm) were successfully produced. As shown in transmission electron microscopy (TEM), orderly uniform pore structure appeared in the HAp particles. Because of the special structure of the MAP and the interaction between ionized MAP and other ions in solution, the product presents uniform mesoporous structure with well-defined pore size. Copyright © 2015 Elsevier B.V. All rights reserved.

Determination of pore size distributions of porous chromatographic adsorbents by inverse size-exclusion chromatography.

PubMed

Yao, Yan; Lenhoff, Abraham M

2004-05-28

The macroscopic properties of porous chromatographic adsorbents are directly influenced by the pore structure, with the pore size distribution (PSD) playing a major role beyond simply the mean pore size. Inverse size-exclusion chromatography (ISEC), a widely used chromatographic method for determining the PSD of porous media, provides more relevant information on liquid chromatographic materials in situ than traditional methods, such as gas sorption and mercury intrusion. The fundamentals and applications of ISEC in the characterization of the pore structure are reviewed. The description of the probe solutes and the pore space, as well as theoretical models for deriving the PSD from solute partitioning behavior, are discussed. Precautions to ensure integrity of the experiments are also outlined, including accounting for probe polydispersity and minimization of solute-adsorbent interactions. The results that emerge are necessarily model-dependent, but ISEC nonetheless represents a powerful and non-destructive source of quantitative pore structure information that can help to elucidate chromatographic performance observations covering both retention and rate aspects.

Functional interactions at the interface between voltage-sensing and pore domains in the Shaker K(v) channel.

PubMed

Soler-Llavina, Gilberto J; Chang, Tsg-Hui; Swartz, Kenton J

2006-11-22

Voltage-activated potassium (K(v)) channels contain a central pore domain that is partially surrounded by four voltage-sensing domains. Recent X-ray structures suggest that the two domains lack extensive protein-protein contacts within presumed transmembrane regions, but whether this is the case for functional channels embedded in lipid membranes remains to be tested. We investigated domain interactions in the Shaker K(v) channel by systematically mutating the pore domain and assessing tolerance by examining channel maturation, S4 gating charge movement, and channel opening. When mapped onto the X-ray structure of the K(v)1.2 channel the large number of permissive mutations support the notion of relatively independent domains, consistent with crystallographic studies. Inspection of the maps also identifies portions of the interface where residues are sensitive to mutation, an external cluster where mutations hinder voltage sensor activation, and an internal cluster where domain interactions between S4 and S5 helices from adjacent subunits appear crucial for the concerted opening transition.

Crystal structure of listeriolysin O reveals molecular details of oligomerization and pore formation

NASA Astrophysics Data System (ADS)

Köster, Stefan; van Pee, Katharina; Hudel, Martina; Leustik, Martin; Rhinow, Daniel; Kühlbrandt, Werner; Chakraborty, Trinad; Yildiz, Özkan

2014-04-01

Listeriolysin O (LLO) is an essential virulence factor of Listeria monocytogenes that causes listeriosis. Listeria monocytogenes owes its ability to live within cells to the pH- and temperature-dependent pore-forming activity of LLO, which is unique among cholesterol-dependent cytolysins. LLO enables the bacteria to cross the phagosomal membrane and is also involved in activation of cellular processes, including the modulation of gene expression or intracellular Ca2+ oscillations. Neither the pore-forming mechanism nor the mechanisms triggering the signalling processes in the host cell are known in detail. Here, we report the crystal structure of LLO, in which we identified regions important for oligomerization and pore formation. Mutants were characterized by determining their haemolytic and Ca2+ uptake activity. We analysed the pore formation of LLO and its variants on erythrocyte ghosts by electron microscopy and show that pore formation requires precise interface interactions during toxin oligomerization on the membrane.

Stress fields around two pores in an elastic body: exact quadrature domain solutions.

PubMed

Crowdy, Darren

2015-08-08

Analytical solutions are given for the stress fields, in both compression and far-field shear, in a two-dimensional elastic body containing two interacting non-circular pores. The two complex potentials governing the solutions are found by using a conformal mapping from a pre-image annulus with those potentials expressed in terms of the Schottky-Klein prime function for the annulus. Solutions for a three-parameter family of elastic bodies with two equal symmetric pores are presented and the compressibility of a special family of pore pairs is studied in detail. The methodology extends to two unequal pores. The importance for boundary value problems of plane elasticity of a special class of planar domains known as quadrature domains is also elucidated. This observation provides the route to generalization of the mathematical approach here to finding analytical solutions for the stress fields in bodies containing any finite number of pores.

Integrative structure and functional anatomy of a nuclear pore complex

NASA Astrophysics Data System (ADS)

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D.; Hogan, Joanna A.; Upla, Paula; Chemmama, Ilan E.; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S.; Wang, Junjie; Williams, Rosemary; Unruh, Jay R.; Greenberg, Charles H.; Jacobs, Erica Y.; Yu, Zhiheng; de La Cruz, M. Jason; Mironska, Roxana; Stokes, David L.; Aitchison, John D.; Jarrold, Martin F.; Gerton, Jennifer L.; Ludtke, Steven J.; Akey, Christopher W.; Chait, Brian T.; Sali, Andrej; Rout, Michael P.

2018-03-01

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

Integrative structure and functional anatomy of a nuclear pore complex.

PubMed

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D; Hogan, Joanna A; Upla, Paula; Chemmama, Ilan E; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S; Wang, Junjie; Williams, Rosemary; Unruh, Jay R; Greenberg, Charles H; Jacobs, Erica Y; Yu, Zhiheng; de la Cruz, M Jason; Mironska, Roxana; Stokes, David L; Aitchison, John D; Jarrold, Martin F; Gerton, Jennifer L; Ludtke, Steven J; Akey, Christopher W; Chait, Brian T; Sali, Andrej; Rout, Michael P

2018-03-22

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

The C-terminal coiled-coil of the bacterial voltage-gated sodium channel NaChBac is not essential for tetramer formation, but stabilizes subunit-to-subunit interactions.

PubMed

Mio, Kazuhiro; Mio, Muneyo; Arisaka, Fumio; Sato, Masahiko; Sato, Chikara

2010-09-01

The NaChBac is a prokaryotic homologue of the voltage-gated sodium channel found in the genome of the alkalophilic bacterium Bacillus halodurans C-125. Like a repeating cassette of mammalian sodium channel, the NaChBac possesses hydrophobic domains corresponding to six putative transmembrane segments and a pore loop, and exerts channel function by forming a tetramer although detailed mechanisms of subunit assembly remain unclear. We generated truncated mutants from NaChBac, and investigated their ability to form tetramers in relation to their channel functions. A mutant that deletes almost all of the C-terminal coiled-coil structure lost its voltage-dependent ion permeability, although it was properly translocated to the cell surface. The mutant protein was purified as a tetramer using a reduced concentration of detergent, but the association between the subunits was shown to be much weaker than the wild type. The chemical cross-linking, blue native PAGE, sedimentation velocity experiments, size exclusion chromatography, immunoprecipitation, and electron microscopy all supported its tetrameric assembly. We further purified the C-terminal cytoplasmic domain alone and confirmed its self-oligomerization. These data suggest that the C-terminal coiled-coil structure stabilizes subunit-to-subunit interactions of NaChBac, but is not critical for their tetramer formation. 2010 Elsevier Ltd. All rights reserved.

Visualizing Active-Site Dynamics in Single Crystals of HePTP: Opening of the WPD Loop Involves Coordinated Movement of the E Loop

DOE Office of Scientific and Technical Information (OSTI.GOV)

D Critton; L Tautz; R Page

2011-12-31

Phosphotyrosine hydrolysis by protein tyrosine phosphatases (PTPs) involves substrate binding by the PTP loop and closure over the active site by the WPD loop. The E loop, located immediately adjacent to the PTP and WPD loops, is conserved among human PTPs in both sequence and structure, yet the role of this loop in substrate binding and catalysis is comparatively unexplored. Hematopoietic PTP (HePTP) is a member of the kinase interaction motif (KIM) PTP family. Compared to other PTPs, KIM-PTPs have E loops that are unique in both sequence and structure. In order to understand the role of the E loopmore » in the transition between the closed state and the open state of HePTP, we identified a novel crystal form of HePTP that allowed the closed-state-to-open-state transition to be observed within a single crystal form. These structures, which include the first structure of the HePTP open state, show that the WPD loop adopts an 'atypically open' conformation and, importantly, that ligands can be exchanged at the active site, which is critical for HePTP inhibitor development. These structures also show that tetrahedral oxyanions bind at a novel secondary site and function to coordinate the PTP, WPD, and E loops. Finally, using both structural and kinetic data, we reveal a novel role for E-loop residue Lys182 in enhancing HePTP catalytic activity through its interaction with Asp236 of the WPD loop, providing the first evidence for the coordinated dynamics of the WPD and E loops in the catalytic cycle, which, as we show, is relevant to multiple PTP families.« less

Methane and CO2 Adsorption and Transport in Carbon-based Systems from Experiments and Molecular Simulation

NASA Astrophysics Data System (ADS)

Wilcox, Jennifer; Firouzi, Mahnaz; Rupp, Erik; Haghapanah, Reza; Wang, Beibei

2013-04-01

Carbon capture and sequestration is one strategy that could potentially mitigate gigatons of CO2 emissions per year; however, technical obstacles have thus far hindered wide-scale deployment of this strategy. To design efficient and reliable strategies for either carbon capture or sequestration at the full-scale, one needs to understand the chemical and physical properties of CO2 and its interaction with its local surroundings at the molecular-scale. To investigate the chemical and physical properties of CO2 and its local surroundings at the molecular-scale, surface characterization studies are carried out alongside theoretical model efforts. Experimental investigation of CO2 interactions with organic-based porous materials ranging in complexity from functionalized graphene and activated carbon to various-rank coal and gas shale samples to create a set of realistic models that take into account both surface and pore heterogeneity. Integration of theory and experiments takes place to allow for the relevant physics at the molecular-level to be revealed. Determining adsorption and transport phenomena of CO2 (and mixtures, including H2O, and CH4) within the model pore systems can be used to understand the complex pore matrices of carbon-based sorbents, coal, and the organic components of gas shale that are crucial to determining their carbon capture or sequestration potential. Non-equilibrium molecular dynamics (NEMD) simulations of pure carbon dioxide, methane, helium and their mixtures have been carried out in carbon slit pores to investigate gas slippage and Klinkenberg effects in the organic matrices of coal and gas shale rocks. NEMD techniques are ideally suited for the experimental situation in which an external driving force, such as a chemical potential or pressure gradient, are applied on the system. Simulations have been conducted to determine the effect of pore size and exposure to an external potential on the velocity profile and slip-stick boundary conditions. The simulations indicate that molecule-wall collisions influence the velocity profile, which deviates significantly from the Navier-Stokes hydrodynamic prediction for micro and mesopores. Also, the shape of the velocity profile is found to be independent of the applied pressure gradient in micropores. The results indicate that the velocity profile is uniform for pore sizes less than 2 nm (micropores). As pore sizes increase to 10 nm, parabolic profiles are observed due to the reduced interaction of gas molecules with the pore walls. Interestingly, in small pores unlike in large pores, the gas velocity at the walls is non-zero and predicted gas transport is somewhat enhanced as the gas flow transitions from a parabolic velocity profile to plug-flow. In addition, a 3-D pore network, representative of porous carbon-based materials, has been generated atomistically using the Voronoi tessellation method. Simulations have been carried out to determine the effect of the pore structure and modeled viscosity on permeability and Klinkenberg parameters. The use of the bulk-phase viscosity for estimating the permeability of CO2 in units of Darcy in a 3-D micropore network is not an appropriate assumption as it significantly underestimates the CO2 permeability given that CO2 is an adsorbing gas with strong pore wall interactions. On the other hand, since the transport properties of CH4 are less influenced by the pore walls compared with CO2, the use of the bulk-phase CH4 viscosity estimates are a reasonable assumption. The application of this work is to advance our understanding of gas transport and to provide insight into mechanisms of gas-surface interactions in the complex natural systems such as gas shale so that we can make accurate capacity estimates in addition to assisting in enhancing natural gas recovery from these systems. These results will potentially have important implications on CO2 adsorption and transport in carbon-based materials and geologic formations and may provide an understanding of the limitations of the use of bulk-phase fluid viscosities to model transport properties for nanoconfined fluids.

Antimicrobial Peptide Simulations and the Influence of Force Field on the Free Energy for Pore Formation in Lipid Bilayers.

PubMed

Bennett, W F Drew; Hong, Chun Kit; Wang, Yi; Tieleman, D Peter

2016-09-13

Due to antimicrobial resistance, the development of new drugs to combat bacterial and fungal infections is an important area of research. Nature uses short, charged, and amphipathic peptides for antimicrobial defense, many of which disrupt the lipid membrane in addition to other possible targets inside the cell. Computer simulations have revealed atomistic details for the interactions of antimicrobial peptides and cell-penetrating peptides with lipid bilayers. Strong interactions between the polar interface and the charged peptides can induce bilayer deformations - including membrane rupture and peptide stabilization of a hydrophilic pore. Here, we performed microsecond-long simulations of the antimicrobial peptide CM15 in a POPC bilayer expecting to observe pore formation (based on previous molecular dynamics simulations). We show that caution is needed when interpreting results of equilibrium peptide-membrane simulations, given the length of time single trajectories can dwell in local energy minima for 100's of ns to microseconds. While we did record significant membrane perturbations from the CM15 peptide, pores were not observed. We explain this discrepancy by computing the free energy for pore formation with different force fields. Our results show a large difference in the free energy barrier (ca. 40 kJ/mol) against pore formation predicted by the different force fields that would result in orders of magnitude differences in the simulation time required to observe spontaneous pore formation. This explains why previous simulations using the Berger lipid parameters reported pores induced by charged peptides, while with CHARMM based models pores were not observed in our long time-scale simulations. We reconcile some of the differences in the distance dependent free energies by shifting the free energy profiles to account for thickness differences between force fields. The shifted curves show that all the models describe small defects in lipid bilayers in a consistent manner, suggesting a common physical basis.

Interaction between the Pore and a Fast Gate of the Cardiac Sodium Channel

PubMed Central

Townsend, Claire; Horn, Richard

1999-01-01

Permeant ions affect a fast gating process observed in human cardiac sodium channels (Townsend, C., H.A. Hartmann, and R. Horn. 1997. J. Gen. Physiol. 110:11–21). Removal of extracellular permeant ions causes a reduction of open probability at positive membrane potentials. These results suggest an intimate relationship between the ion-conducting pore and the gates of the channel. We tested this hypothesis by three sets of manipulations designed to affect the binding of cations within the pore: application of intracellular pore blockers, mutagenesis of residues known to contribute to permeation, and chemical modification of a native cysteine residue (C373) near the extracellular mouth of the pore. The coupling between extracellular permeant ions and this fast gating process is abolished both by pore blockers and by a mutation that severely affects selectivity. A more superficial pore mutation or chemical modification of C373 reduces single channel conductance while preserving both selectivity of the pore and the modulatory effects of extracellular cations. Our results demonstrate a modulatory gating role for a region deep within the pore and suggest that the structure of the permeation pathway is largely preserved when a channel is closed. PMID:9925827

Electrochemical pore filling strategy for controlled growth of magnetic and metallic nanowire arrays with large area uniformity

NASA Astrophysics Data System (ADS)

Arefpour, M.; Almasi Kashi, M.; Ramazani, A.; Montazer, A. H.

2016-07-01

While a variety of template-based strategies have been developed in the fabrication of nanowires (NWs), a uniform pore filling across the template still poses a major challenge. Here, we present a large area controlled pore filling strategy in the reproducible fabrication of various magnetic and metallic NW arrays, embedded inside anodic aluminum oxide templates. Using a diffusive pulsed electrodeposition (DPED) technique, this versatile strategy relies on the optimized filling of branched nanopores at the bottom of templates with Cu. Serving the Cu filled nanopores as appropriate nucleation sites, the DPED is followed by a uniform and homogeneous deposition of magnetic (Ni and Fe) and metallic (Cu and Zn) NWs at a current density of 50 mA cm-2 for an optimal thickness of alumina barrier layer (˜18 nm). Our strategy provides large area uniformity (exceeding 400 μm2) in the fabrication of 16 μm long free-standing NW arrays. Using hysteresis loop measurements and scanning electron microscopy images, the electrodeposition efficiency (EE) and pore filling percentage (F p) are evaluated, leading to maximum EE and F p values of 91% and 95% for Ni and Zn, respectively. Moreover, the resulting NW arrays are found to be highly crystalline. Accordingly, the DPED technique is capable of cheaply and efficiently controlling NW growth over a large area, providing a tool for various nanoscale applications including biomedical devices, electronics, photonics, magnetic storage medium and nanomagnet computing.

Electrochemical pore filling strategy for controlled growth of magnetic and metallic nanowire arrays with large area uniformity.

PubMed

Arefpour, M; Kashi, M Almasi; Ramazani, A; Montazer, A H

2016-06-01

While a variety of template-based strategies have been developed in the fabrication of nanowires (NWs), a uniform pore filling across the template still poses a major challenge. Here, we present a large area controlled pore filling strategy in the reproducible fabrication of various magnetic and metallic NW arrays, embedded inside anodic aluminum oxide templates. Using a diffusive pulsed electrodeposition (DPED) technique, this versatile strategy relies on the optimized filling of branched nanopores at the bottom of templates with Cu. Serving the Cu filled nanopores as appropriate nucleation sites, the DPED is followed by a uniform and homogeneous deposition of magnetic (Ni and Fe) and metallic (Cu and Zn) NWs at a current density of 50 mA cm -2 for an optimal thickness of alumina barrier layer (∼18 nm). Our strategy provides large area uniformity (exceeding 400 μm 2 ) in the fabrication of 16 μm long free-standing NW arrays. Using hysteresis loop measurements and scanning electron microscopy images, the electrodeposition efficiency (EE) and pore filling percentage (F p ) are evaluated, leading to maximum EE and F p values of 91% and 95% for Ni and Zn, respectively. Moreover, the resulting NW arrays are found to be highly crystalline. Accordingly, the DPED technique is capable of cheaply and efficiently controlling NW growth over a large area, providing a tool for various nanoscale applications including biomedical devices, electronics, photonics, magnetic storage medium and nanomagnet computing.

Mesoporous Akaganeite of Adjustable Pore Size Synthesized using Mixed Templates

NASA Astrophysics Data System (ADS)

Zhang, Y.; Ge, D. L.; Ren, H. P.; Fan, Y. J.; Wu, L. M.; Sun, Z. X.

2017-12-01

Mesoporous akaganeite with large and adjustable pore size was synthesized through a co-template method, which was achieved by the combined interaction between PEG2000 and alkyl amines with different lengths of the straight carbon chain. The characterized results indicate that the synthesized samples show comparatively narrow BJH pore size distributions and centered at 14.3 nm when PEG and HEPA was used, and it could be enlarged to 16.8 and 19.4 nm respectively through changing the alkyl amines to DDA and HDA. Meanwhile, all the synthesized akaganeite possess relativity high specific surface area ranging from 183 to 281 m2/g and high total pore volume of 0.98 to 1.5 cm3/g. A possible mechanism leading to the pore size changing was also proposed.

Blowout Surge due to Interaction between a Solar Filament and Coronal Loops

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Haidong; Jiang, Yunchun; Yang, Jiayan

2017-06-20

We present an observation of the interaction between a filament and the outer spine-like loops that produces a blowout surge within one footpoint of large-scale coronal loops on 2015 February 6. Based the observation of the AIA 304 and 94 Å, the activated filament is initially embedded below a dome of a fan-spine configuration. Due to the ascending motion, the erupting filament reconnects with the outer spine-like field. We note that the material in the filament blows out along the outer spine-like field to form the surge with a wider spire, and a two-ribbon flare appears at the site ofmore » the filament eruption. In this process, small bright blobs appear at the interaction region and stream up along the outer spine-like field and down along the eastern fan-like field. As a result, a leg of the filament becomes radial and the material in it erupts, while another leg forms the new closed loops. Our results confirm that the successive reconnection occurring between the erupting filament and the coronal loops may lead to a strong thermal/magnetic pressure imbalance, resulting in a blowout surge.« less

Simultaneous Activation of Multiple Memory Systems during Learning: Insights from Electrophysiology and Modeling

DTIC Science & Technology

2010-06-01

autonomic and pain functions, and facilitating/inhibiting voluntary movements. The external segment of the globus pallidus (globus pallidus externa, GPe...or less responsive to pain stimuli. 1.2.4. Other cortico-basal ganglia loops Alexander, Strick and colleagues have additionally defined a number of... orofacial loop and loops through inferotemporal and posterior parietal cortical areas have also been defined. 1.2.5. Interactions between loops Once

Diagonal dominance for the multivariable Nyquist array using function minimization

NASA Technical Reports Server (NTRS)

Leininger, G. G.

1977-01-01

A new technique for the design of multivariable control systems using the multivariable Nyquist array method was developed. A conjugate direction function minimization algorithm is utilized to achieve a diagonal dominant condition over the extended frequency range of the control system. The minimization is performed on the ratio of the moduli of the off-diagonal terms to the moduli of the diagonal terms of either the inverse or direct open loop transfer function matrix. Several new feedback design concepts were also developed, including: (1) dominance control parameters for each control loop; (2) compensator normalization to evaluate open loop conditions for alternative design configurations; and (3) an interaction index to determine the degree and type of system interaction when all feedback loops are closed simultaneously. This new design capability was implemented on an IBM 360/75 in a batch mode but can be easily adapted to an interactive computer facility. The method was applied to the Pratt and Whitney F100 turbofan engine.

Interaction of irradiation-induced prismatic dislocation loops with free surfaces in tungsten

NASA Astrophysics Data System (ADS)

Fikar, Jan; Gröger, Roman; Schäublin, Robin

2017-02-01

The prismatic dislocation loops appear in metals as a result of high-energy irradiation. Understanding their formation and interaction is important for quantification of irradiation-induced deterioration of mechanical properties. Characterization of dislocation loops in thin foils is commonly made using transmission electron microscopy (TEM), but the results are inevitably influenced by the proximity of free surfaces. The prismatic loops are attracted to free surfaces by image forces. Depending on the type, size and depth of the loop in the foil, they can escape to the free surface, thus invalidating TEM observations and conclusions. In this article small prismatic hexagonal and circular dislocation loops in tungsten with the Burgers vectors 1/2 〈 1 1 1 〉 and 〈 1 0 0 〉 are studied by molecular statics simulations using three embedded atom method (EAM) potentials. The calculated image forces are compared to known elastic solutions. A particular attention is paid to the critical stress to move edge dislocations. The escape of the loop to the free surface is quantified by a combination of atomistic simulations and elastic calculations. For example, for the 1/2 〈 1 1 1 〉 loop with diameter 7.4 nm in a 55 nm thick foil we calculated that about one half of the loops will escape to the free surface. This implies that TEM observations detect only approx. 50% of the loops that were originally present in the foil.

Identification of a high affinity nucleocapsid protein binding element within the Moloney murine leukemia virus Psi-RNA packaging signal: implications for genome recognition.

PubMed

D'Souza, V; Melamed, J; Habib, D; Pullen, K; Wallace, K; Summers, M F

2001-11-23

Murine leukemia virus (MLV) is currently the most widely used gene delivery system in gene therapy trials. The simple retrovirus packages two copies of its RNA genome by a mechanism that involves interactions between the nucleocapsid (NC) domain of a virally-encoded Gag polyprotein and a segment of the RNA genome located just upstream of the Gag initiation codon, known as the Psi-site. Previous studies indicated that the MLV Psi-site contains three stem loops (SLB-SLD), and that stem loops SLC and SLD play prominent roles in packaging. We have developed a method for the preparation and purification of large quantities of recombinant Moloney MLV NC protein, and have studied its interactions with a series of oligoribonucleotides that contain one or more of the Psi-RNA stem loops. At RNA concentrations above approximately 0.3 mM, isolated stem loop SLB forms a duplex and stem loops SL-C and SL-D form kissing complexes, as expected from previous studies. However, neither the monomeric nor the dimeric forms of these isolated stem loops binds NC with significant affinity. Longer constructs containing two stem loops (SL-BC and SL-CD) also exhibit low affinities for NC. However, NC binds with high affinity and stoichiometrically to both the monomeric and dimeric forms of an RNA construct that contains all three stem loops (SL-BCD; K(d)=132(+/-55) nM). Titration of SL-BCD with NC also shifts monomer-dimer equilibrium toward the dimer. Mutagenesis experiments demonstrate that the conserved GACG tetraloops of stem loops C and D do not influence the monomer-dimer equilibrium of SL-BCD, that the tetraloop of stem loop B does not participate directly in NC binding, and that the tetraloops of stem loops C and D probably also do not bind to NC. These surprising results differ considerably from those observed for HIV-1, where NC binds to individual stem loops with high affinity via interactions with exposed residues of the tetraloops. The present results indicate that MLV NC binds to a pocket or surface that only exists in the presence of all three stem loops. Copyright 2001 Academic Press.

Meiotic Clade AAA ATPases: Protein Polymer Disassembly Machines.

PubMed

Monroe, Nicole; Hill, Christopher P

2016-05-08

Meiotic clade AAA ATPases (ATPases associated with diverse cellular activities), which were initially grouped on the basis of phylogenetic classification of their AAA ATPase cassette, include four relatively well characterized family members, Vps4, spastin, katanin and fidgetin. These enzymes all function to disassemble specific polymeric protein structures, with Vps4 disassembling the ESCRT-III polymers that are central to the many membrane-remodeling activities of the ESCRT (endosomal sorting complexes required for transport) pathway and spastin, katanin p60 and fidgetin affecting multiple aspects of cellular dynamics by severing microtubules. They share a common domain architecture that features an N-terminal MIT (microtubule interacting and trafficking) domain followed by a single AAA ATPase cassette. Meiotic clade AAA ATPases function as hexamers that can cycle between the active assembly and inactive monomers/dimers in a regulated process, and they appear to disassemble their polymeric substrates by translocating subunits through the central pore of their hexameric ring. Recent studies with Vps4 have shown that nucleotide-induced asymmetry is a requirement for substrate binding to the pore loops and that recruitment to the protein lattice via MIT domains also relieves autoinhibition and primes the AAA ATPase cassettes for substrate binding. The most striking, unifying feature of meiotic clade AAA ATPases may be their MIT domain, which is a module that is found in a wide variety of proteins that localize to ESCRT-III polymers. Spastin also displays an adjacent microtubule binding sequence, and the presence of both ESCRT-III and microtubule binding elements may underlie the recent findings that the ESCRT-III disassembly function of Vps4 and the microtubule-severing function of spastin, as well as potentially katanin and fidgetin, are highly coordinated. Copyright © 2015 Elsevier Ltd. All rights reserved.

RNA polymerase gate loop guides the nontemplate DNA strand in transcription complexes.

PubMed

NandyMazumdar, Monali; Nedialkov, Yuri; Svetlov, Dmitri; Sevostyanova, Anastasia; Belogurov, Georgiy A; Artsimovitch, Irina

2016-12-27

Upon RNA polymerase (RNAP) binding to a promoter, the σ factor initiates DNA strand separation and captures the melted nontemplate DNA, whereas the core enzyme establishes interactions with the duplex DNA in front of the active site that stabilize initiation complexes and persist throughout elongation. Among many core RNAP elements that participate in these interactions, the β' clamp domain plays the most prominent role. In this work, we investigate the role of the β gate loop, a conserved and essential structural element that lies across the DNA channel from the clamp, in transcription regulation. The gate loop was proposed to control DNA loading during initiation and to interact with NusG-like proteins to lock RNAP in a closed, processive state during elongation. We show that the removal of the gate loop has large effects on promoter complexes, trapping an unstable intermediate in which the RNAP contacts with the nontemplate strand discriminator region and the downstream duplex DNA are not yet fully established. We find that although RNAP lacking the gate loop displays moderate defects in pausing, transcript cleavage, and termination, it is fully responsive to the transcription elongation factor NusG. Together with the structural data, our results support a model in which the gate loop, acting in concert with initiation or elongation factors, guides the nontemplate DNA in transcription complexes, thereby modulating their regulatory properties.

Insulators form gene loops by interacting with promoters in Drosophila.

PubMed

Erokhin, Maksim; Davydova, Anna; Kyrchanova, Olga; Parshikov, Alexander; Georgiev, Pavel; Chetverina, Darya

2011-09-01

Chromatin insulators are regulatory elements involved in the modulation of enhancer-promoter communication. The 1A2 and Wari insulators are located immediately downstream of the Drosophila yellow and white genes, respectively. Using an assay based on the yeast GAL4 activator, we have found that both insulators are able to interact with their target promoters in transgenic lines, forming gene loops. The existence of an insulator-promoter loop is confirmed by the fact that insulator proteins could be detected on the promoter only in the presence of an insulator in the transgene. The upstream promoter regions, which are required for long-distance stimulation by enhancers, are not essential for promoter-insulator interactions. Both insulators support basal activity of the yellow and white promoters in eyes. Thus, the ability of insulators to interact with promoters might play an important role in the regulation of basal gene transcription.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rikvold, Per Arne; Brown, Gregory; Miyashita, Seiji

Phase diagrams and hysteresis loops were obtained by Monte Carlo simulations and a mean- field method for a simplified model of a spin-crossovermaterialwith a two-step transition between the high-spin and low-spin states. This model is a mapping onto a square-lattice S = 1/2 Ising model with antiferromagnetic nearest-neighbor and ferromagnetic Husimi-Temperley ( equivalent-neighbor) long-range interactions. Phase diagrams obtained by the two methods for weak and strong long-range interactions are found to be similar. However, for intermediate-strength long-range interactions, the Monte Carlo simulations show that tricritical points decompose into pairs of critical end points and mean-field critical points surrounded by horn-shapedmore » regions of metastability. Hysteresis loops along paths traversing the horn regions are strongly reminiscent of thermal two-step transition loops with hysteresis, recently observed experimentally in several spin-crossover materials. As a result, we believe analogous phenomena should be observable in experiments and simulations for many systems that exhibit competition between local antiferromagnetic-like interactions and long-range ferromagnetic-like interactions caused by elastic distortions.« less

Interactions of Twisted Ω-loops in a Model Solar Convection Zone

NASA Astrophysics Data System (ADS)

Jouve, L.; Brun, A. S.; Aulanier, G.

2018-04-01

This study aims at investigating the ability of strong interactions between magnetic field concentrations during their rise through the convection zone to produce complex active regions at the solar surface. To do so, we perform numerical simulations of buoyant magnetic structures evolving and interacting in a model solar convection zone. We first produce a 3D model of rotating convection and then introduce idealized magnetic structures close to the bottom of the computational domain. These structures possess a certain degree of field line twist and they are made buoyant on a particular extension in longitude. The resulting twisted Ω-loops will thus evolve inside a spherical convective shell possessing large-scale mean flows. We present results on the interaction between two such loops with various initial parameters (mainly buoyancy and twist) and on the complexity of the emerging magnetic field. In agreement with analytical predictions, we find that if the loops are introduced with opposite handedness and same axial field direction or the same handedness but opposite axial field, they bounce against each other. The emerging region is then constituted of two separated bipolar structures. On the contrary, if the loops are introduced with the same direction of axial and peripheral magnetic fields and are sufficiently close, they merge while rising. This more interesting case produces complex magnetic structures with a high degree of non-neutralized currents, especially when the convective motions act significantly on the magnetic field. This indicates that those interactions could be good candidates to produce eruptive events like flares or CMEs.

Microgrids | Grid Modernization | NREL

Science.gov Websites

algorithms for microgrid integration Controller hardware-in-the-loop testing, where the physical controller interacts with a model of the microgrid and associated power devices Power hardware-in-the-loop testing of operation was validated in a power hardware-in-the-loop experiment using a programmable DC power supply to

Expression, purification and biochemical characterization of the cytoplasmic loop of PomA, a stator component of the Na+ driven flagellar motor

PubMed Central

Abe-Yoshizumi, Rei; Kobayashi, Shiori; Gohara, Mizuki; Hayashi, Kokoro; Kojima, Chojiro; Kojima, Seiji; Sudo, Yuki; Asami, Yasuo; Homma, Michio

2013-01-01

Flagellar motors embedded in bacterial membranes are molecular machines powered by specific ion flows. Each motor is composed of a stator and a rotor and the interactions of those components are believed to generate the torque. Na+ influx through the PomA/PomB stator complex of Vibrio alginolyticus is coupled to torque generation and is speculated to trigger structural changes in the cytoplasmic domain of PomA that interacts with a rotor protein in the C-ring, FliG, to drive the rotation. In this study, we tried to overproduce the cytoplasmic loop of PomA (PomA-Loop), but it was insoluble. Thus, we made a fusion protein with a small soluble tag (GB1) which allowed us to express and characterize the recombinant protein. The structure of the PomA-Loop seems to be very elongated or has a loose tertiary structure. When the PomA-Loop protein was produced in E. coli, a slight dominant effect was observed on motility. We conclude that the cytoplasmic loop alone retains a certain function. PMID:27493537

The magnetosphere as system

NASA Astrophysics Data System (ADS)

Siscoe, G. L.

2012-12-01

What is a system? A group of elements interacting with each other so as to create feedback loops. A system gets complex as the number of feedback loops increases and as the feedback loops exhibit time delays. Positive and negative feedback loops with time delays can give a system intrinsic time dependence and emergent properties. A system generally has input and output flows of something (matter, energy, money), which, if time variable, add an extrinsic component to its behavior. The magnetosphere is a group of elements interacting through feedback loops, some with time delays, driven by energy and mass inflow from a variable solar wind and outflow into the atmosphere and solar wind. The magnetosphere is a complex system. With no solar wind, there is no behavior. With solar wind, there is behavior from intrinsic and extrinsic causes. As a contribution to taking a macroscopic view of magnetospheric dynamics, to treating the magnetosphere as a globally integrated, complex entity, I will discus the magnetosphere as a system, its feedback loops, time delays, emergent behavior, and intrinsic and extrinsic behavior modes.

An emerging case for membrane pore formation as a common mechanism for the unconventional secretion of FGF2 and IL-1β.

PubMed

Brough, David; Pelegrin, Pablo; Nickel, Walter

2017-10-01

Extracellular proteins with important signalling roles in processes, such as inflammation and angiogenesis, are known to employ unconventional routes of protein secretion. Although mechanisms of unconventional protein secretion are beginning to emerge, the precise molecular details have remained elusive for the majority of cargo proteins secreted by unconventional means. Recent findings suggest that for two examples of unconventionally secreted proteins, interleukin 1β (IL-1β) and fibroblast growth factor 2 (FGF2), the common molecular principle of pore formation may be shared. Under specific experimental conditions, secretion of IL-1β and FGF2 is triggered by phosphatidylinositol 4,5-bisphosphate [PI(4,5)P 2 ]-dependent formation of pores across the plasma membrane. However, the underlying mechanisms are different, with FGF2 known to directly interact with PI(4,5)P 2 , whereas in the case of IL-1β secretion, it is proposed that the N-terminal fragment of gasdermin D interacts with PI(4,5)P 2 to form the pore. Thus, although implemented in different ways, these findings suggest that pore formation may be shared by the unconventional secretion mechanisms for FGF2 and IL-1β in at least some cases. In this Opinion article, we discuss the unconventional mechanisms of FGF2 and IL-1β release with a particular emphasis on recent discoveries suggesting the importance of pore formation on the plasma membrane. © 2017. Published by The Company of Biologists Ltd.

Interactions of GSK-3β with mitochondrial permeability transition pore modulators during preconditioning: age-associated differences.

PubMed

Zhu, Jiang; Rebecchi, Mario J; Glass, Peter S A; Brink, Peter R; Liu, Lixin

2013-04-01

Anesthetic preconditioning (APC) and ischemic preconditioning (IPC) are lost with normal aging. Here, we investigated age-related difference between phosphoglycogen synthase kinase-3beta (pGSK-3β) and pGSK-3β with modulators of mitochondrial permeability transition pore, including adenine nucleotide translocase (ANT), cyclophilin-D, or voltage-dependent anion channel. APC or IPC significantly increased pGSK-3β in the young groups in both the cytosol and the mitochondria and also significantly increased pGSK-3β in co-immunoprecipitates with ANT. Importantly, the level of cyclophilin-D in co-immunoprecipitates with ANT was significantly decreased in the young APC and IPC groups, but not in old rats. We also found that APC or IPC significantly prolonged mitochondrial permeability transition pore opening time in the young cardiomyocytes under oxidative stress, but not in the elderly. Attenuation of APC or IPC protection in the aging heart is associated with failure to reduce ANT-cyclophilin-D interactions and to decreased pGSK-3β responsiveness of ANT, critical modulators of mitochondrial permeability transition pore.

Nuclear pore proteins are involved in the biogenesis of functional tRNA.

PubMed

Simos, G; Tekotte, H; Grosjean, H; Segref, A; Sharma, K; Tollervey, D; Hurt, E C

1996-05-01

Los1p and Pus1p, which are involved in tRNA biogenesis, were found in a genetic screen for components interacting with the nuclear pore protein Nsp1p. LOS1, PUS1 and NSP1 interact functionally, since the combination of mutations in the three genes causes synthetic lethality. Pus1p is an intranuclear protein which exhibits a nucleotide-specific and intron-dependent tRNA pseudouridine synthase activity. Los1p was shown previously to be required for efficient pre-tRNA splicing; we report here that Los1p localizes to the nuclear pores and is linked functionally to several components of the tRNA biogenesis machinery including Pus1p and Tfc4p. When the formation of functional tRNA was analyzed by an in vivo assay, the los1(-) pus1(-) double mutant, as well as several thermosensitive nucleoporin mutants including nsp1, nup116, nup133 and nup85, exhibited loss of suppressor tRNA activity even at permissive temperatures. These data suggest that nuclear pore proteins are required for the biogenesis of functional tRNA.

Pore-Water Carbonate and Phosphate As Predictors of Arsenate Toxicity in Soil.

PubMed

Lamb, Dane T; Kader, Mohammed; Wang, Liang; Choppala, Girish; Rahman, Mohammad Mahmudur; Megharaj, Mallavarapu; Naidu, Ravi

2016-12-06

Phytotoxicity of inorganic contaminants is influenced by the presence of competing ions at the site of uptake. In this study, interaction of soil pore-water constituents with arsenate toxicity was investigated in cucumber (Cucumis sativa L) using 10 contrasting soils. Arsenate phytotoxicity was shown to be related to soluble carbonate and phosphate. The data indicated that dissolved phosphate and carbonate had an antagonistic impact on arsenate toxicity to cucumber. To predict arsenate phytotoxicity in soils with a diverse range of soil solution properties, both carbonate and phosphate were required. The relationship between arsenic and pore-water toxicity parameters was established initially using multiple regression. In addition, based on the relationship with carbonate and phosphate we successively applied a terrestrial biotic ligand-like model (BLM) including carbonate and phosphate. Estimated effective concentrations from the BLM-like parametrization were strongly correlated to measured arsenate values in pore-water (R 2 = 0.76, P < 0.001). The data indicates that an ion interaction model similar to the BLM for arsenate is possible, potentially improving current risk assessments at arsenic and co-contaminated soils.

Atomistic Structure of Mineral Nano-aggregates from Simulated Compaction and Dewatering.

PubMed

Ho, Tuan Anh; Greathouse, Jeffery A; Wang, Yifeng; Criscenti, Louise J

2017-11-10

The porosity of clay aggregates is an important property governing chemical reactions and fluid flow in low-permeability geologic formations and clay-based engineered barrier systems. Pore spaces in clays include interlayer and interparticle pores. Under compaction and dewatering, the size and geometry of such pore spaces may vary significantly (sub-nanometer to microns) depending on ambient physical and chemical conditions. Here we report a molecular dynamics simulation method to construct a complex and realistic clay-like nanoparticle aggregate with interparticle pores and grain boundaries. The model structure is then used to investigate the effect of dewatering and water content on micro-porosity of the aggregates. The results suggest that slow dewatering would create more compact aggregates compared to fast dewatering. Furthermore, the amount of water present in the aggregates strongly affects the particle-particle interactions and hence the aggregate structure. Detailed analyses of particle-particle and water-particle interactions provide a molecular-scale view of porosity and texture development of the aggregates. The simulation method developed here may also aid in modeling the synthesis of nanostructured materials through self-assembly of nanoparticles.

Atomistic Structure of Mineral Nano-aggregates from Simulated Compaction and Dewatering

DOE PAGES

Ho, Tuan Anh; Greathouse, Jeffery A.; Wang, Yifeng; ...

2017-11-10

The porosity of clay aggregates is an important property governing chemical reactions and fluid flow in low-permeability geologic formations and clay-based engineered barrier systems. Pore spaces in clays include interlayer and interparticle pores. Under compaction and dewatering, the size and geometry of such pore spaces may vary significantly (sub-nanometer to microns) depending on ambient physical and chemical conditions. Here we report a molecular dynamics simulation method to construct a complex and realistic clay-like nanoparticle aggregate with interparticle pores and grain boundaries. The model structure is then used to investigate the effect of dewatering and water content on micro-porosity of themore » aggregates. The results suggest that slow dewatering would create more compact aggregates compared to fast dewatering. Furthermore, the amount of water present in the aggregates strongly affects the particle-particle interactions and hence the aggregate structure. Detailed analyses of particle-particle and water-particle interactions provide a molecular-scale view of porosity and texture development of the aggregates. The simulation method developed here may also aid in modeling the synthesis of nanostructured materials through self-assembly of nanoparticles.« less

Equilibrium, metastability, and hysteresis in a model spin-crossover material with nearest-neighbor antiferromagnetic-like and long-range ferromagnetic-like interactions

NASA Astrophysics Data System (ADS)

Rikvold, Per Arne; Brown, Gregory; Miyashita, Seiji; Omand, Conor; Nishino, Masamichi

2016-02-01

Phase diagrams and hysteresis loops were obtained by Monte Carlo simulations and a mean-field method for a simplified model of a spin-crossover material with a two-step transition between the high-spin and low-spin states. This model is a mapping onto a square-lattice S =1 /2 Ising model with antiferromagnetic nearest-neighbor and ferromagnetic Husimi-Temperley (equivalent-neighbor) long-range interactions. Phase diagrams obtained by the two methods for weak and strong long-range interactions are found to be similar. However, for intermediate-strength long-range interactions, the Monte Carlo simulations show that tricritical points decompose into pairs of critical end points and mean-field critical points surrounded by horn-shaped regions of metastability. Hysteresis loops along paths traversing the horn regions are strongly reminiscent of thermal two-step transition loops with hysteresis, recently observed experimentally in several spin-crossover materials. We believe analogous phenomena should be observable in experiments and simulations for many systems that exhibit competition between local antiferromagnetic-like interactions and long-range ferromagnetic-like interactions caused by elastic distortions.

Radiation Enhanced Absorption of Frank Loops by Nanovoids in Cu

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Youxing; Zhang, Xinghang; Wang, Jian

Neutron and heavy ion irradiation generally induces voids in metallic materials, and continuous radiations typically result in void swelling and mechanical failure of the irradiated materials. Recent experiments showed that nanovoids in nanotwinned copper could act as sinks for radiation-induced Frank loops, significantly mitigating radiation damage [Y. Chen et al., Nat. Commun. 6:7036 (2015)]. In this paper, we report on structural evolution of Frank loops under cascades and address the role of nanovoids in absorbing Frank loops in detail by using molecular dynamics simulations. Results show that a stand-alone Frank loop is stable under cascades. When Frank loops are adjacentmore » to nanovoids, the diffusion of a group of atoms from the loop into nanovoids is accomplished via the formation and propagation of dislocation loops. The loop-nanovoid interactions result in the shrinkage of the nanovoids and the Frank loops.« less

Radiation Enhanced Absorption of Frank Loops by Nanovoids in Cu

DOE PAGES

Chen, Youxing; Zhang, Xinghang; Wang, Jian

2016-11-01

Neutron and heavy ion irradiation generally induces voids in metallic materials, and continuous radiations typically result in void swelling and mechanical failure of the irradiated materials. Recent experiments showed that nanovoids in nanotwinned copper could act as sinks for radiation-induced Frank loops, significantly mitigating radiation damage [Y. Chen et al., Nat. Commun. 6:7036 (2015)]. In this paper, we report on structural evolution of Frank loops under cascades and address the role of nanovoids in absorbing Frank loops in detail by using molecular dynamics simulations. Results show that a stand-alone Frank loop is stable under cascades. When Frank loops are adjacentmore » to nanovoids, the diffusion of a group of atoms from the loop into nanovoids is accomplished via the formation and propagation of dislocation loops. The loop-nanovoid interactions result in the shrinkage of the nanovoids and the Frank loops.« less

Microfluidic Experiments Studying Pore Scale Interactions of Microbes and Geochemistry

NASA Astrophysics Data System (ADS)

Chen, M.; Kocar, B. D.

2016-12-01

Understanding how physical phenomena, chemical reactions, and microbial behavior interact at the pore-scale is crucial to understanding larger scale trends in groundwater chemistry. Recent studies illustrate the utility of microfluidic devices for illuminating pore-scale physical-biogeochemical processes and their control(s) on the cycling of iron, uranium, and other important elements 1-3. These experimental systems are ideal for examining geochemical reactions mediated by microbes, which include processes governed by complex biological phenomenon (e.g. biofilm formation, etc.)4. We present results of microfluidic experiments using a model metal reducing bacteria and varying pore geometries, exploring the limitations of the microorganisms' ability to access tight pore spaces, and examining coupled biogeochemical-physical controls on the cycling of redox sensitive metals. Experimental results will provide an enhanced understanding of coupled physical-biogeochemical processes transpiring at the pore-scale, and will constrain and compliment continuum models used to predict and describe the subsurface cycling of redox-sensitive elements5. 1. Vrionis, H. A. et al. Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. Appl. Environ. Microbiol. 71, 6308-6318 (2005). 2. Pearce, C. I. et al. Pore-scale characterization of biogeochemical controls on iron and uranium speciation under flow conditions. Environ. Sci. Technol. 46, 7992-8000 (2012). 3. Zhang, C., Liu, C. & Shi, Z. Micromodel investigation of transport effect on the kinetics of reductive dissolution of hematite. Environ. Sci. Technol. 47, 4131-4139 (2013). 4. Ginn, T. R. et al. Processes in microbial transport in the natural subsurface. Adv. Water Resour. 25, 1017-1042 (2002). 5. Scheibe, T. D. et al. Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation. Microb. Biotechnol. 2, 274-286 (2009).

The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA

PubMed Central

Law, Michael J.; Rice, Andrew J.; Lin, Patti; Laird-Offringa, Ite A.

2006-01-01

The N-terminal RNA Recognition Motif (RRM1) of the spliceosomal protein U1A interacting with its target U1 hairpin II (U1hpII) has been used as a paradigm for RRM-containing proteins interacting with their RNA targets. U1A binds to U1hpII via direct interactions with a 7-nucleotide (nt) consensus binding sequence at the 5′ end of a 10-nt loop, and via hydrogen bonds with the closing C–G base pair at the top of the RNA stem. Using surface plasmon resonance (Biacore), we have examined the role of structural features of U1hpII in binding to U1A RRM1. Mutational analysis of the closing base pair suggests it plays a minor role in binding and mainly prevents “breathing” of the loop. Lengthening the stem and nontarget part of the loop suggests that the increased negative charge of the RNA might slightly aid association. However, this is offset by an increase in dissociation, which may be caused by attraction of the RRM to nontarget parts of the RNA. Studies of a single stranded target and RNAs with untethered loops indicate that structure is not very relevant for association but is important for complex stability. In particular, breaking the link between the stem and the 5′ side of the loop greatly increases complex dissociation, presumably by hindering simultaneous contacts between the RRM and stem and loop nucleotides. While binding of U1A to a single stranded target is much weaker than to U1hpII, it occurs with nanomolar affinity, supporting recent evidence that binding of unstructured RNA by U1A has physiological significance. PMID:16738410

The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA.

PubMed

Law, Michael J; Rice, Andrew J; Lin, Patti; Laird-Offringa, Ite A

2006-07-01

The N-terminal RNA Recognition Motif (RRM1) of the spliceosomal protein U1A interacting with its target U1 hairpin II (U1hpII) has been used as a paradigm for RRM-containing proteins interacting with their RNA targets. U1A binds to U1hpII via direct interactions with a 7-nucleotide (nt) consensus binding sequence at the 5' end of a 10-nt loop, and via hydrogen bonds with the closing C-G base pair at the top of the RNA stem. Using surface plasmon resonance (Biacore), we have examined the role of structural features of U1hpII in binding to U1A RRM1. Mutational analysis of the closing base pair suggests it plays a minor role in binding and mainly prevents "breathing" of the loop. Lengthening the stem and nontarget part of the loop suggests that the increased negative charge of the RNA might slightly aid association. However, this is offset by an increase in dissociation, which may be caused by attraction of the RRM to nontarget parts of the RNA. Studies of a single stranded target and RNAs with untethered loops indicate that structure is not very relevant for association but is important for complex stability. In particular, breaking the link between the stem and the 5' side of the loop greatly increases complex dissociation, presumably by hindering simultaneous contacts between the RRM and stem and loop nucleotides. While binding of U1A to a single stranded target is much weaker than to U1hpII, it occurs with nanomolar affinity, supporting recent evidence that binding of unstructured RNA by U1A has physiological significance.

Looping and clustering model for the organization of protein-DNA complexes on the bacterial genome

NASA Astrophysics Data System (ADS)

Walter, Jean-Charles; Walliser, Nils-Ole; David, Gabriel; Dorignac, Jérôme; Geniet, Frédéric; Palmeri, John; Parmeggiani, Andrea; Wingreen, Ned S.; Broedersz, Chase P.

2018-03-01

The bacterial genome is organized by a variety of associated proteins inside a structure called the nucleoid. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the looping and clustering model, which employs a statistical physics approach to describe protein-DNA complexes. The looping and clustering model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins that is organized around a single high-affinity binding site. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and loop closure entropy of this protein-DNA cluster on the one hand, and the positional entropy for placing loops within the cluster on the other. Indeed, we show that the protein interaction strength determines the ‘tightness’ of the loopy protein-DNA complex. Thus, our model provides a theoretical framework for quantitatively computing the binding profiles of ParB-like proteins around a cognate (parS) binding site.

Effect of urea and alkylureas on the stability and structural fluctuation of the M80-containing Ω-loop of horse cytochrome c.

PubMed

Kumar, Sandeep; Sharma, Deepak; Kumar, Rajesh

2014-03-01

The effect of denaturants on the structural fluctuation of M80-containing Ω-loop of ferrocytochrome c was determined by measuring the rate coefficient of CO-association with ferrocytochrome c under varying concentrations of urea and alkylureas (methylurea (MU), N,N'-dimethylurea (DMU), ethylurea (EU), tetramethylurea (TMU)) at pH7.0, 25°C. As denaturant concentration is increased within the subdenaturing limit, the CO-association reaction is decelerated indicating that subdenaturing concentrations of denaturant reduce the structural fluctuation of the Ω-loop. Structural fluctuation of the Ω-loop is reduced more for urea and least for TMU. Intermolecular docking between horse cytochrome c and denaturant molecule (urea, MU, DMU, EU and TMU) reveals that polyfunctional interactions between the denaturant and different groups of Ω-loop and other part of protein decrease with an increase of alkyl group on urea molecule, which suggests that the decrease in the extent of restricted dynamics of Ω-loop with a corresponding increase of alkyl groups on urea molecule is due to the decrease of denaturant-mediated cross-linking interactions. These denaturant-mediated interactions are expected to reduce the conformational entropy of protein. Analysis of rate-temperature data shows a progressive decrease in conformational entropy of protein in the native to subdenaturing region. Thermodynamic analysis of denaturant (urea, MU, DMU, EU, TMU) effects on the thermal unfolding of ferrocytochrome c reveals that (i) thermodynamic stability of protein decreases with increasing concentration of denaturant or hydrophobicity of urea derivatives, (ii) water activity plays an important role in stabilization of ferrocytochrome c, and (iii) destabilization of ferrocytochrome c by denaturant occurs through the disturbance of hydrophobic interactions and hydrogen-bonding. Copyright © 2014 Elsevier B.V. All rights reserved.

Determinants of Chromosome Architecture: Insulator Pairing in cis and in trans

PubMed Central

Fujioka, Miki; Mistry, Hemlata; Schedl, Paul; Jaynes, James B.

2016-01-01

The chromosomes of multicellular animals are organized into a series of topologically independent looped domains. This domain organization is critical for the proper utilization and propagation of the genetic information encoded by the chromosome. A special set of architectural elements, called boundaries or insulators, are responsible both for subdividing the chromatin into discrete domains and for determining the topological organization of these domains. Central to the architectural functions of insulators are homologous and heterologous insulator:insulator pairing interactions. The former (pairing between copies of the same insulator) dictates the process of homolog alignment and pairing in trans, while the latter (pairing between different insulators) defines the topology of looped domains in cis. To elucidate the principles governing these architectural functions, we use two insulators, Homie and Nhomie, that flank the Drosophila even skipped locus. We show that homologous insulator interactions in trans, between Homie on one homolog and Homie on the other, or between Nhomie on one homolog and Nhomie on the other, mediate transvection. Critically, these homologous insulator:insulator interactions are orientation-dependent. Consistent with a role in the alignment and pairing of homologs, self-pairing in trans is head-to-head. Head-to-head self-interactions in cis have been reported for other fly insulators, suggesting that this is a general principle of self-pairing. Homie and Nhomie not only pair with themselves, but with each other. Heterologous Homie-Nhomie interactions occur in cis, and we show that they serve to delimit a looped chromosomal domain that contains the even skipped transcription unit and its associated enhancers. The topology of this loop is defined by the heterologous pairing properties of Homie and Nhomie. Instead of being head-to-head, which would generate a circular loop, Homie-Nhomie pairing is head-to-tail. Head-to-tail pairing in cis generates a stem-loop, a configuration much like that observed in classical lampbrush chromosomes. These pairing principles provide a mechanistic underpinning for the observed topologies within and between chromosomes. PMID:26910731

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Hongcai J

In the past decades, there has been an escalation of interest in the study of MOFs due to their fascinating structures and intriguing application potentials. Their exceptionally high surface areas, uniform yet tunable pore sizes, and well-defined adsorbate-MOF interaction sites make them suitable for hydrogen storage. Various strategies to increase the hydrogen capacity of MOFs, such as constructing pore sizes comparable to hydrogen molecules, increasing surface area and pore volume, utilizing catenation, and introducing coordinatively unsaturated metal centers (UMCs) have been widely explored to increase the hydrogen uptake of the MOFs. MOFs with hydrogen uptake approaching the DOE gravimetric storagemore » goal under reasonable pressure but cryo- temperature (typically 77 K) were achieved. However, the weak interaction between hydrogen molecules and MOFs has been the major hurdle limiting the hydrogen uptake of MOFs at ambient temperature. Along the road, we have realized both high surface area and strong interaction between framework and hydrogen are equally essential for porous materials to be practically applicable in Hydrogen storage. Increasing the isosteric heats of adsorption for hydrogen through the introduction of active centers into the framework could have great potential on rendering the framework with strong interaction toward hydrogen. Approaches on increasing the surface areas and improving hydrogen affinity by optimizing size and structure of the pores and the alignment of active centers around the pores in frameworks have been pursued, for example: (a) the introduction of coordinatively UMC (represents a metal center missing multiple ligands) with potential capability of multiple dihydrogen-binding (Kubas type, non-dissociative) per UMC, (b) the design and synthesis of proton-rich MOFs in which a + H3 binds dihydrogen just like a metal ion does, and (c) the preparation of MOFs and PPNs with well aligned internal electric fields. We believe the accomplishments of this DOE supported research will greatly benefit the future pursuit of hydrogen storage materials. The ultimate goal to increase the gravimetric and volumetric hydrogen storage capacity to meet DOE targets for Light-Duty Vehicles is achievable.« less

Ebullition, Plant-Mediated Transport, and Subsurface Horizontal Water Flow Dominate Methane Transport in an Arctic Sphagnum Bog

NASA Astrophysics Data System (ADS)

Wehr, R. A.; McCalley, C. K.; Logan, T. A.; Chanton, J.; Crill, P. M.; Rich, V. I.; Saleska, S. R.

2017-12-01

Emission of the greenhouse gas methane from wetlands is of prime concern in the prediction of climate change - especially emission associated with thawing permafrost, which may drive a positive feedback loop of emission and warming. In addition to the biochemistry of methane production and consumption, wetland methane emission depends critically on the transport mechanisms by which methane moves through and out of the ecosystem. We therefore developed a model of methane biochemistry and transport for a sphagnum bog representing an intermediate permafrost thaw stage in Stordalen Mire, Sweden. In order to simultaneously reproduce measured profiles of both the concentrations and isotopic compositions of both methane and carbon dioxide in the peat pore water (Fig. 1) - as well as the surface methane emission - it was necessary for the model to include ebullition, plant-mediated transport via aerenchyma, and subsurface horizontal water flow. Diffusion of gas through the pore water was relatively unimportant. As a result, 90% of the produced methane escaped the wetland rather than being consumed by methanotrophic organisms in the near-surface pore water. Our model provides a comprehensive picture of methane emission from this bog site by quantifying the vertical profiles of: acetoclastic methanogenesis, hydrogenotrophic methanogenesis, methane oxidation, aerobic respiration, ebullition, plant-mediated transport, subsurface horizontal water flow, and diffusion.

Outward Rectification of Voltage-Gated K+ Channels Evolved at Least Twice in Life History

PubMed Central

Riedelsberger, Janin; Dreyer, Ingo; Gonzalez, Wendy

2015-01-01

Voltage-gated potassium (K+) channels are present in all living systems. Despite high structural similarities in the transmembrane domains (TMD), this K+ channel type segregates into at least two main functional categories—hyperpolarization-activated, inward-rectifying (Kin) and depolarization-activated, outward-rectifying (Kout) channels. Voltage-gated K+ channels sense the membrane voltage via a voltage-sensing domain that is connected to the conduction pathway of the channel. It has been shown that the voltage-sensing mechanism is the same in Kin and Kout channels, but its performance results in opposite pore conformations. It is not known how the different coupling of voltage-sensor and pore is implemented. Here, we studied sequence and structural data of voltage-gated K+ channels from animals and plants with emphasis on the property of opposite rectification. We identified structural hotspots that alone allow already the distinction between Kin and Kout channels. Among them is a loop between TMD S5 and the pore that is very short in animal Kout, longer in plant and animal Kin and the longest in plant Kout channels. In combination with further structural and phylogenetic analyses this finding suggests that outward-rectification evolved twice and independently in the animal and plant kingdom. PMID:26356684

Outward Rectification of Voltage-Gated K+ Channels Evolved at Least Twice in Life History.

PubMed

Riedelsberger, Janin; Dreyer, Ingo; Gonzalez, Wendy

2015-01-01

Voltage-gated potassium (K+) channels are present in all living systems. Despite high structural similarities in the transmembrane domains (TMD), this K+ channel type segregates into at least two main functional categories-hyperpolarization-activated, inward-rectifying (Kin) and depolarization-activated, outward-rectifying (Kout) channels. Voltage-gated K+ channels sense the membrane voltage via a voltage-sensing domain that is connected to the conduction pathway of the channel. It has been shown that the voltage-sensing mechanism is the same in Kin and Kout channels, but its performance results in opposite pore conformations. It is not known how the different coupling of voltage-sensor and pore is implemented. Here, we studied sequence and structural data of voltage-gated K+ channels from animals and plants with emphasis on the property of opposite rectification. We identified structural hotspots that alone allow already the distinction between Kin and Kout channels. Among them is a loop between TMD S5 and the pore that is very short in animal Kout, longer in plant and animal Kin and the longest in plant Kout channels. In combination with further structural and phylogenetic analyses this finding suggests that outward-rectification evolved twice and independently in the animal and plant kingdom.

Cryo-EM structure of the gasdermin A3 membrane pore.

PubMed

Ruan, Jianbin; Xia, Shiyu; Liu, Xing; Lieberman, Judy; Wu, Hao

2018-05-01

Gasdermins mediate inflammatory cell death after cleavage by caspases or other, unknown enzymes. The cleaved N-terminal fragments bind to acidic membrane lipids to form pores, but the mechanism of pore formation remains unresolved. Here we present the cryo-electron microscopy structures of the 27-fold and 28-fold single-ring pores formed by the N-terminal fragment of mouse GSDMA3 (GSDMA3-NT) at 3.8 and 4.2 Å resolutions, and of a double-ring pore at 4.6 Å resolution. In the 27-fold pore, a 108-stranded anti-parallel β-barrel is formed by two β-hairpins from each subunit capped by a globular domain. We identify a positively charged helix that interacts with the acidic lipid cardiolipin. GSDMA3-NT undergoes radical conformational changes upon membrane insertion to form long, membrane-spanning β-strands. We also observe an unexpected additional symmetric ring of GSDMA3-NT subunits that does not insert into the membrane in the double-ring pore, which may represent a pre-pore state of GSDMA3-NT. These structures provide a basis that explains the activities of several mutant gasdermins, including defective mutants that are associated with cancer.

The mitochondrial intermembrane loop region of rat carnitine palmitoyltransferase 1A is a major determinant of its malonyl-CoA sensitivity.

PubMed

Borthwick, Karen; Jackson, Vicky N; Price, Nigel T; Zammit, Victor A

2006-11-03

Carnitine palmitoyltransferase (CPT) 1A adopts a polytopic conformation within the mitochondrial outer membrane, having both the N- and C-terminal segments on the cytosolic aspect of the membrane and a loop region connecting the two transmembrane (TM) segments protruding into the inter membrane space. In this study we demonstrate that the loop exerts major effects on the sensitivity of the enzyme to its inhibitor, malonyl-CoA. Insertion of a 16-residue spacer between the C-terminal part of the loop sequence (i.e. between residues 100 and 101) and TM2 (which is predicted to start at residue 102) increased the sensitivity to malonyl-CoA inhibition of the resultant mutant protein by more than 10-fold. By contrast, the same insertion made between TM1 and the loop had no effects on the kinetic properties of the enzyme, indicating that effects on the catalytic C-terminal segment were specifically induced by loop-TM2 interactions. Enhanced sensitivity was also observed in all mutants in which the native TM2-loop pairing was disrupted either by making chimeras in which the loops and TM2 segments of CPT 1A and CPT 1B were exchanged or by deleting successive 9-residue segments from the loop sequence. The data suggest that the sequence spanning the loop-TM2 boundary determines the disposition of this TM in the membrane so as to alter the conformation of the C-terminal segment and thus affect its interaction with malonyl-CoA.

Structural determinants of Kvbeta1.3-induced channel inactivation: a hairpin modulated by PIP2.

PubMed

Decher, Niels; Gonzalez, Teresa; Streit, Anne Kathrin; Sachse, Frank B; Renigunta, Vijay; Soom, Malle; Heinemann, Stefan H; Daut, Jürgen; Sanguinetti, Michael C

2008-12-03

Inactivation of voltage-gated Kv1 channels can be altered by Kvbeta subunits, which block the ion-conducting pore to induce a rapid ('N-type') inactivation. Here, we investigate the mechanisms and structural basis of Kvbeta1.3 interaction with the pore domain of Kv1.5 channels. Inactivation induced by Kvbeta1.3 was antagonized by intracellular PIP(2). Mutations of R5 or T6 in Kvbeta1.3 enhanced Kv1.5 inactivation and markedly reduced the effects of PIP(2). R5C or T6C Kvbeta1.3 also exhibited diminished binding of PIP(2) compared with wild-type channels in an in vitro lipid-binding assay. Further, scanning mutagenesis of the N terminus of Kvbeta1.3 revealed that mutations of L2 and A3 eliminated N-type inactivation. Double-mutant cycle analysis indicates that R5 interacts with A501 and T480 of Kv1.5, residues located deep within the pore of the channel. These interactions indicate that Kvbeta1.3, in contrast to Kvbeta1.1, assumes a hairpin structure to inactivate Kv1 channels. Taken together, our findings indicate that inactivation of Kv1.5 is mediated by an equilibrium binding of the N terminus of Kvbeta1.3 between phosphoinositides (PIPs) and the inner pore region of the channel.

Characterization of a native hammerhead ribozyme derived from schistosomes

PubMed Central

OSBORNE, EDITH M.; SCHAAK, JANELL E.; DEROSE, VICTORIA J.

2005-01-01

A recent re-examination of the role of the helices surrounding the conserved core of the hammerhead ribozyme has identified putative loop–loop interactions between stems I and II in native hammerhead sequences. These extended hammerhead sequences are more active at low concentrations of divalent cations than are minimal hammerheads. The loop–loop interactions are proposed to stabilize a more active conformation of the conserved core. Here, a kinetic and thermodynamic characterization of an extended hammerhead sequence derived from Schistosoma mansoni is performed. Biphasic kinetics are observed, suggesting the presence of at least two conformers, one cleaving with a fast rate and the other with a slow rate. Replacing loop II with a poly(U) sequence designed to eliminate the interaction between the two loops results in greatly diminished activity, suggesting that the loop–loop interactions do aid in forming a more active conformation. Previous studies with minimal hammerheads have shown deleterious effects of Rp-phosphorothioate substitutions at the cleavage site and 5′ to A9, both of which could be rescued with Cd2+. Here, phosphorothioate modifications at the cleavage site and 5′ to A9 were made in the schistosome-derived sequence. In Mg2+, both phosphorothioate substitutions decreased the overall fraction cleaved without significantly affecting the observed rate of cleavage. The addition of Cd2+ rescued cleavage in both cases, suggesting that these are still putative metal binding sites in this native sequence. PMID:15659358

Evidence for two-loop interaction from IRIS and SDO observations of penumbral brightenings

NASA Astrophysics Data System (ADS)

Alissandrakis, C. E.; Koukras, A.; Patsourakos, S.; Nindos, A.

2017-07-01

Aims: We investigate small scale energy release events which can provide clues on the heating mechanism of the solar corona. Methods: We analyzed spectral and imaging data from the Interface Region Imaging Spectrograph (IRIS), images from the Atmospheric Imaging Assembly (AIA) aboard the Solar Dynamics Observatoty (SDO), and magnetograms from the Helioseismic and Magnetic Imager (HMI) aboard SDO. Results: We report observations of small flaring loops in the penumbra of a large sunspot on July 19, 2013. Our main event consisted of a loop spanning 15'', from the umbral-penumbral boundary to an opposite polarity region outside the penumbra. It lasted approximately 10 min with a two minute impulsive peak and was observed in all AIA/SDO channels, while the IRIS slit was located near its penumbral footpoint. Mass motions with an apparent velocity of 100 km s-1 were detected beyond the brightening, starting in the rise phase of the impulsive peak; these were apparently associated with a higher-lying loop. We interpret these motions in terms of two-loop interaction. IRIS spectra in both the C II and Si iv lines showed very extended wings, up to about 400 km s-1, first in the blue (upflows) and subsequently in the red wing. In addition to the strong lines, emission was detected in the weak lines of Cl I, O I and C I, as well as in the Mg II triplet lines. Absorption features in the profiles of the C II doublet, the Si iv doublet and the Mg II h and k lines indicate the existence of material with a lower source function between the brightening and the observer. We attribute this absorption to the higher loop and this adds further credibility to the two-loop interaction hypothesis. Tilts were detected in the absorption spectra, as well as in the spectra of Cl I, O I, and C I lines, possibly indicating rotational motions from the untwisting of magnetic flux tubes. Conclusions: We conclude that the absorption features in the C II, Si iv and Mg II profiles originate in a higher-lying, descending loop; as this approached the already activated lower-lying loop, their interaction gave rise to the impulsive peak, the very broad line profiles and the mass motions. Movies associated to Figs. A.1-A.3 are available at http://www.aanda.org

Evaluation of the influence of sulfur-based functional groups on the embedding of silver nanoparticles into the pores of MCM-41

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oliveira, Roselaine da S.; Camilo, Fernanda F.; Bizeto, Marcos A., E-mail: mabizeto@unifesp.br

The incorporation of noble metals in the pores of mesoporous silicas might produce materials with interesting catalytic and sensing capabilities, but the proper control of pore filling and the avoidance of nanoparticles migration to outside the pores are processes not yet completely understood. In this work, we evaluated the role of –SH and –SO{sub 3}H groups post-grafted into MCM-41 on the production of silver nanoparticles by using 1-butanol as reducing agent. Thiol groups were the most efficient on promoting the formation of nanoparticles within the pores. Conversely, sulfonic groups establish electrostatic interactions with silver cations that preclude the formation ofmore » nanoparticle in yields comparable to thiol groups. MCM-41 without functional groups did not have good affinity to silver and the nanoparticles are produced outside the pores. This study showed the importance on selecting an adequate surface functional group in order to obtain silver nanoparticles filling the pores of MCM-41. - Graphical abstract: Silver nanoparticles formation inside the pores of sulfur-groups functionalized mesoporous silica. - Highlights: • Silver nanoparticles formation inside the pores of mesoporous silica. • n-butanol as reducing agent of impregnated silver cations. • Tuning the silica surface properties by grafting sulfur-based functional groups. • Influence on the loading and distribution of the nanoparticles through the pores.« less

Lennard-Jones fluids in two-dimensional nano-pores. Multi-phase coexistence and fluid structure

NASA Astrophysics Data System (ADS)

Yatsyshin, Petr; Savva, Nikos; Kalliadasis, Serafim

2014-03-01

We present a number of fundamental findings on the wetting behaviour of nano-pores. A popular model for fluid confinement is a one-dimensional (1D) slit pore formed by two parallel planar walls and it exhibits capillary condensation (CC): a first-order phase transition from vapour to capillary-liquid (Kelvin shift). Capping such a pore at one end by a third orthogonal wall forms a prototypical two-dimensional (2D) pore. We show that 2D pores possess a wetting temperature such that below this temperature CC remains of first order, above it becomes a continuous phase transition manifested by a slab of capillary-liquid filling the pore from the capping wall. Continuous CC exhibits hysteresis and can be preceded by a first-order capillary prewetting transition. Additionally, liquid drops can form in the corners of the 2D pore (remnant of 2D wedge prewetting). The three fluid phases, vapour, capillary-liquid slab and corner drops, can coexist at the pore triple point. Our model is based on the statistical mechanics of fluids in the density functional formulation. The fluid-fluid and fluid-substrate interactions are dispersive. We analyze in detail the microscopic fluid structure, isotherms and full phase diagrams. Our findings also suggest novel ways to control wetting of nano-pores. We are grateful to the European Research Council via Advanced Grant No. 247031 for support.

Cool transition region loops observed by the Interface Region Imaging Spectrograph

NASA Astrophysics Data System (ADS)

Huang, Z.; Xia, L.; Li, B.; Madjarska, M. S.

2015-12-01

An important class of loops in the solar atmosphere, cool transition region loops, have received little attention mainly due to instrumental limitations. We analyze a cluster of these loops in the on-disk active region NOAA 11934 recorded in a Si IV 1402.8 Å spectral raster and 1400Å slit-jaw (SJ) images taken by the Interface Region Imaging Spectrograph. We divide these loops into three groups and study their dynamics, evolution and interaction.The first group comprises geometrically relatively stable loops, which are finely scaled with 382~626 km cross-sections. Siphon flows in these loops are suggested by the Doppler velocities gradually changing from -10 km/s (blue-shifts) in one end to 20 km/s (red-shifts) in the other. Nonthermal velocities from 15 to 25 km/s were determined. The obtained physical properties suggest that these loops are impulsively heated by magnetic reconnection occurring at the blue-shifted footpoints where magnetic cancellation with a rate of 1015 Mx/s is found. The released magnetic energy is redistributed by the siphon flows. The second group corresponds to two active footpoints rooted in mixed-magnetic-polarity regions. Magnetic reconnection in both footpoints is suggested by explosive-event line profiles with enhanced wings up to 200 km/s and magnetic cancellation with a rate of ~1015 Mx/s. In the third group, an interaction between two cool loop systems is observed. Mixed-magnetic polarities are seen in their conjunction area where explosive-event line profiles and magnetic cancellation with a rate of 3×1015 Mx/s are found. This is a clear indication that magnetic reconnection occurs between these two loop systems. Our observations suggest that the cool transition region loops are heated impulsively most likely by sequences of magnetic reconnection events.

Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process

NASA Astrophysics Data System (ADS)

Iacovache, Ioan; de Carlo, Sacha; Cirauqui, Nuria; Dal Peraro, Matteo; van der Goot, F. Gisou; Zuber, Benoît

2016-07-01

Owing to their pathogenical role and unique ability to exist both as soluble proteins and transmembrane complexes, pore-forming toxins (PFTs) have been a focus of microbiologists and structural biologists for decades. PFTs are generally secreted as water-soluble monomers and subsequently bind the membrane of target cells. Then, they assemble into circular oligomers, which undergo conformational changes that allow membrane insertion leading to pore formation and potentially cell death. Aerolysin, produced by the human pathogen Aeromonas hydrophila, is the founding member of a major PFT family found throughout all kingdoms of life. We report cryo-electron microscopy structures of three conformational intermediates and of the final aerolysin pore, jointly providing insight into the conformational changes that allow pore formation. Moreover, the structures reveal a protein fold consisting of two concentric β-barrels, tightly kept together by hydrophobic interactions. This fold suggests a basis for the prion-like ultrastability of aerolysin pore and its stoichiometry.

Anomalous or regular capacitance? The influence of pore size dispersity on double-layer formation

NASA Astrophysics Data System (ADS)

Jäckel, N.; Rodner, M.; Schreiber, A.; Jeongwook, J.; Zeiger, M.; Aslan, M.; Weingarth, D.; Presser, V.

2016-09-01

The energy storage mechanism of electric double-layer capacitors is governed by ion electrosorption at the electrode surface. This process requires high surface area electrodes, typically highly porous carbons. In common organic electrolytes, bare ion sizes are below one nanometer but they are larger when we consider their solvation shell. In contrast, ionic liquid electrolytes are free of solvent molecules, but cation-anion coordination requires special consideration. By matching pore size and ion size, two seemingly conflicting views have emerged: either an increase in specific capacitance with smaller pore size or a constant capacitance contribution of all micro- and mesopores. In our work, we revisit this issue by using a comprehensive set of electrochemical data and a pore size incremental analysis to identify the influence of certain ranges in the pore size distribution to the ion electrosorption capacity. We see a difference in solvation of ions in organic electrolytes depending on the applied voltage and a cation-anion interaction of ionic liquids in nanometer sized pores.

Experimental validation of the predicted binding site of Escherichia coli K1 outer membrane protein A to human brain microvascular endothelial cells: identification of critical mutations that prevent E. coli meningitis.

PubMed

Pascal, Tod A; Abrol, Ravinder; Mittal, Rahul; Wang, Ying; Prasadarao, Nemani V; Goddard, William A

2010-11-26

Escherichia coli K1, the most common cause of meningitis in neonates, has been shown to interact with GlcNAc1-4GlcNAc epitopes of Ecgp96 on human brain microvascular endothelial cells (HBMECs) via OmpA (outer membrane protein A). However, the precise domains of extracellular loops of OmpA interacting with the chitobiose epitopes have not been elucidated. We report the loop-barrel model of these OmpA interactions with the carbohydrate moieties of Ecgp96 predicted from molecular modeling. To test this model experimentally, we generated E. coli K1 strains expressing OmpA with mutations of residues predicted to be critical for interaction with the HBMEC and tested E. coli invasion efficiency. For these same mutations, we predicted the interaction free energies (including explicit calculation of the entropy) from molecular dynamics (MD), finding excellent correlation (R(2) = 90%) with experimental invasion efficiency. Particularly important is that mutating specific residues in loops 1, 2, and 4 to alanines resulted in significant inhibition of E. coli K1 invasion in HBMECs, which is consistent with the complete lack of binding found in the MD simulations for these two cases. These studies suggest that inhibition of the interactions of these residues of Loop 1, 2, and 4 with Ecgp96 could provide a therapeutic strategy to prevent neonatal meningitis due to E. coli K1.

Evidence for an RNA pseudoknot loop-helix interaction essential for efficient -1 ribosomal frameshifting.

PubMed

Liphardt, J; Napthine, S; Kontos, H; Brierley, I

1999-05-07

RNA pseudoknots are structural elements that participate in a variety of biological processes. At -1 ribosomal frameshifting sites, several types of pseudoknot have been identified which differ in their organisation and functionality. The pseudoknot found in infectious bronchitis virus (IBV) is typical of those that possess a long stem 1 of 11-12 bp and a long loop 2 (30-164 nt). A second group of pseudoknots are distinguishable that contain stems of only 5 to 7 bp and shorter loops. The NMR structure of one such pseudoknot, that of mouse mammary tumor virus (MMTV), has revealed that it is kinked at the stem 1-stem 2 junction, and that this kinked conformation is essential for efficient frameshifting. We recently investigated the effect on frameshifting of modulating stem 1 length and stability in IBV-based pseudoknots, and found that a stem 1 with at least 11 bp was needed for efficient frameshifting. Here, we describe the sequence manipulations that are necessary to bypass the requirement for an 11 bp stem 1 and to convert a short non-functional IBV-derived pseudoknot into a highly efficient, kinked frameshifter pseudoknot. Simple insertion of an adenine residue at the stem 1-stem 2 junction (an essential feature of a kinked pseudoknot) was not sufficient to create a functional pseudoknot. An additional change was needed: efficient frameshifting was recovered only when the last nucleotide of loop 2 was changed from a G to an A. The requirement for an A at the end of loop 2 is consistent with a loop-helix contact similar to those described in other RNA tertiary structures. A mutational analysis of both partners of the proposed interaction, the loop 2 terminal adenine residue and two G.C pairs near the top of stem 1, revealed that the interaction was essential for efficient frameshifting. The specific requirement for a 3'-terminal A residue was lost when loop 2 was increased from 8 to 14 nt, suggesting that the loop-helix contact may be required only in those pseudoknots with a short loop 2. Copyright 1999 Academic Press.

Optimizing the inner loop of the gravitational force interaction on modern processors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Warren, Michael S

2010-12-08

We have achieved superior performance on multiple generations of the fastest supercomputers in the world with our hashed oct-tree N-body code (HOT), spanning almost two decades and garnering multiple Gordon Bell Prizes for significant achievement in parallel processing. Execution time for our N-body code is largely influenced by the force calculation in the inner loop. Improvements to the inner loop using SSE3 instructions has enabled the calculation of over 200 million gravitational interactions per second per processor on a 2.6 GHz Opteron, for a computational rate of over 7 Gflops in single precision (700/0 of peak). We obtain optimal performancemore » some processors (including the Cell) by decomposing the reciprocal square root function required for a gravitational interaction into a table lookup, Chebychev polynomial interpolation, and Newton-Raphson iteration, using the algorithm of Karp. By unrolling the loop by a factor of six, and using SPU intrinsics to compute on vectors, we obtain performance of over 16 Gflops on a single Cell SPE. Aggregated over the 8 SPEs on a Cell processor, the overall performance is roughly 130 Gflops. In comparison, the ordinary C version of our inner loop only obtains 1.6 Gflops per SPE with the spuxlc compiler.« less

Structure of the voltage-gated K⁺ channel Eag1 reveals an alternative voltage sensing mechanism.

PubMed

Whicher, Jonathan R; MacKinnon, Roderick

2016-08-12

Voltage-gated potassium (K(v)) channels are gated by the movement of the transmembrane voltage sensor, which is coupled, through the helical S4-S5 linker, to the potassium pore. We determined the single-particle cryo-electron microscopy structure of mammalian K(v)10.1, or Eag1, bound to the channel inhibitor calmodulin, at 3.78 angstrom resolution. Unlike previous K(v) structures, the S4-S5 linker of Eag1 is a five-residue loop and the transmembrane segments are not domain swapped, which suggest an alternative mechanism of voltage-dependent gating. Additionally, the structure and position of the S4-S5 linker allow calmodulin to bind to the intracellular domains and to close the potassium pore, independent of voltage-sensor position. The structure reveals an alternative gating mechanism for K(v) channels and provides a template to further understand the gating properties of Eag1 and related channels. Copyright © 2016, American Association for the Advancement of Science.

Atomistic Simulations of Pore Formation and Closure in Lipid Bilayers

PubMed Central

Bennett, W. F. Drew; Sapay, Nicolas; Tieleman, D. Peter

2014-01-01

Cellular membranes separate distinct aqueous compartments, but can be breached by transient hydrophilic pores. A large energetic cost prevents pore formation, which is largely dependent on the composition and structure of the lipid bilayer. The softness of bilayers and the disordered structure of pores make their characterization difficult. We use molecular-dynamics simulations with atomistic detail to study the thermodynamics, kinetics, and mechanism of pore formation and closure in DLPC, DMPC, and DPPC bilayers, with pore formation free energies of 17, 45, and 78 kJ/mol, respectively. By using atomistic computer simulations, we are able to determine not only the free energy for pore formation, but also the enthalpy and entropy, which yields what is believed to be significant new insights in the molecular driving forces behind membrane defects. The free energy cost for pore formation is due to a large unfavorable entropic contribution and a favorable change in enthalpy. Changes in hydrogen bonding patterns occur, with increased lipid-water interactions, and fewer water-water hydrogen bonds, but the total number of overall hydrogen bonds is constant. Equilibrium pore formation is directly observed in the thin DLPC lipid bilayer. Multiple long timescale simulations of pore closure are used to predict pore lifetimes. Our results are important for biological applications, including the activity of antimicrobial peptides and a better understanding of membrane protein folding, and improve our understanding of the fundamental physicochemical nature of membranes. PMID:24411253

Behavior of P85 and P188 Poloxamer Molecules: Computer Simulations Using United Atom Force Field.

DOE PAGES

Goliaei, Ardeshir; Lau, Edmond Y.; Adhikari, Upendra; ...

2016-05-27

To study the interaction between poloxamer molecules and lipid bilayers using molecular dynamics simulation technique with the united atom resolution, we augmented the GROMOS force field to include poloxamers. We validated the force field by calculating the radii of gyration of two poloxamers, P85 and P188, solvated in water and by considering the poloxamer density distributions at the air/water interface. The emphasis of our simulations was on the study of the interaction between poloxamers and lipid bilayer. At the water/lipid bilayer interface, we observed that both poloxamers studied, P85 and P188, behaved like surfactants: the hydrophilic blocks of poloxamers becamemore » adsorbed at the polar interface, while their hydrophobic block penetrated the interface into the aliphatic tail region of the lipid bilayer. We also observed that when P85 and P188 poloxamers interacted with damaged membranes that contained pores, the hydrophobic blocks of copolymers penetrated into the membrane in the vicinity of the pore and compressed the membrane. Lastly, due to this compression, water molecules were evacuated from the pore.« less

pH controlled gating of toxic protein pores by dendrimers

NASA Astrophysics Data System (ADS)

Mandal, Taraknath; Kanchi, Subbarao; Ayappa, K. G.; Maiti, Prabal K.

2016-06-01

Designing effective nanoscale blockers for membrane inserted pores formed by pore forming toxins, which are expressed by several virulent bacterial strains, on a target cell membrane is a challenging and active area of research. Here we demonstrate that PAMAM dendrimers can act as effective pH controlled gating devices once the pore has been formed. We have used fully atomistic molecular dynamics (MD) simulations to characterize the cytolysin A (ClyA) protein pores modified with fifth generation (G5) PAMAM dendrimers. Our results show that the PAMAM dendrimer, in either its protonated (P) or non-protonated (NP) states can spontaneously enter the protein lumen. Protonated dendrimers interact strongly with the negatively charged protein pore lumen. As a consequence, P dendrimers assume a more expanded configuration efficiently blocking the pore when compared with the more compact configuration adopted by the neutral NP dendrimers creating a greater void space for the passage of water and ions. To quantify the effective blockage of the protein pore, we have calculated the pore conductance as well as the residence times by applying a weak force on the ions/water. Ionic currents are reduced by 91% for the P dendrimers and 31% for the NP dendrimers. The preferential binding of Cl- counter ions to the P dendrimer creates a zone of high Cl- concentration in the vicinity of the internalized dendrimer and a high concentration of K+ ions in the transmembrane region of the pore lumen. In addition to steric effects, this induced charge segregation for the P dendrimer effectively blocks ionic transport through the pore. Our investigation shows that the bio-compatible PAMAM dendrimers can potentially be used to develop therapeutic protocols based on the pH sensitive gating of pores formed by pore forming toxins to mitigate bacterial infections.Designing effective nanoscale blockers for membrane inserted pores formed by pore forming toxins, which are expressed by several virulent bacterial strains, on a target cell membrane is a challenging and active area of research. Here we demonstrate that PAMAM dendrimers can act as effective pH controlled gating devices once the pore has been formed. We have used fully atomistic molecular dynamics (MD) simulations to characterize the cytolysin A (ClyA) protein pores modified with fifth generation (G5) PAMAM dendrimers. Our results show that the PAMAM dendrimer, in either its protonated (P) or non-protonated (NP) states can spontaneously enter the protein lumen. Protonated dendrimers interact strongly with the negatively charged protein pore lumen. As a consequence, P dendrimers assume a more expanded configuration efficiently blocking the pore when compared with the more compact configuration adopted by the neutral NP dendrimers creating a greater void space for the passage of water and ions. To quantify the effective blockage of the protein pore, we have calculated the pore conductance as well as the residence times by applying a weak force on the ions/water. Ionic currents are reduced by 91% for the P dendrimers and 31% for the NP dendrimers. The preferential binding of Cl- counter ions to the P dendrimer creates a zone of high Cl- concentration in the vicinity of the internalized dendrimer and a high concentration of K+ ions in the transmembrane region of the pore lumen. In addition to steric effects, this induced charge segregation for the P dendrimer effectively blocks ionic transport through the pore. Our investigation shows that the bio-compatible PAMAM dendrimers can potentially be used to develop therapeutic protocols based on the pH sensitive gating of pores formed by pore forming toxins to mitigate bacterial infections. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr02963a

Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice.

PubMed

Dong, Qianli; Li, Ning; Li, Xiaochong; Yuan, Zan; Xie, Dejian; Wang, Xiaofei; Li, Jianing; Yu, Yanan; Wang, Jinbin; Ding, Baoxu; Zhang, Zhibin; Li, Changping; Bian, Yao; Zhang, Ai; Wu, Ying; Liu, Bao; Gong, Lei

2018-06-01

The non-random spatial packing of chromosomes in the nucleus plays a critical role in orchestrating gene expression and genome function. Here, we present a Hi-C analysis of the chromatin interaction patterns in rice (Oryza sativa L.) at hierarchical architectural levels. We confirm that rice chromosomes occupy their own territories with certain preferential inter-chromosomal associations. Moderate compartment delimitation and extensive TADs (Topologically Associated Domains) were determined to be associated with heterogeneous genomic compositions and epigenetic marks in the rice genome. We found subtle features including chromatin loops, gene loops, and off-/near-diagonal intensive interaction regions. Gene chromatin loops associated with H3K27me3 could be positively involved in gene expression. In addition to insulated enhancing effects for neighbor gene expression, the identified rice gene loops could bi-directionally (+/-) affect the expression of looped genes themselves. Finally, web-interleaved off-diagonal IHIs/KEEs (Interactive Heterochromatic Islands or KNOT ENGAGED ELEMENTs) could trap transposable elements (TEs) via the enrichment of silencing epigenetic marks. In parallel, the near-diagonal FIREs (Frequently Interacting Regions) could positively affect the expression of involved genes. Our results suggest that the chromatin packing pattern in rice is generally similar to that in Arabidopsis thaliana but with clear differences at specific structural levels. We conclude that genomic composition, epigenetic modification, and transcriptional activity could act in combination to shape global and local chromatin packing in rice. Our results confirm recent observations in rice and A. thaliana but also provide additional insights into the patterns and features of chromatin organization in higher plants. © 2018 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

Causal transfer function analysis to describe closed loop interactions between cardiovascular and cardiorespiratory variability signals.

PubMed

Faes, L; Porta, A; Cucino, R; Cerutti, S; Antolini, R; Nollo, G

2004-06-01

Although the concept of transfer function is intrinsically related to an input-output relationship, the traditional and widely used estimation method merges both feedback and feedforward interactions between the two analyzed signals. This limitation may endanger the reliability of transfer function analysis in biological systems characterized by closed loop interactions. In this study, a method for estimating the transfer function between closed loop interacting signals was proposed and validated in the field of cardiovascular and cardiorespiratory variability. The two analyzed signals x and y were described by a bivariate autoregressive model, and the causal transfer function from x to y was estimated after imposing causality by setting to zero the model coefficients representative of the reverse effects from y to x. The method was tested in simulations reproducing linear open and closed loop interactions, showing a better adherence of the causal transfer function to the theoretical curves with respect to the traditional approach in presence of non-negligible reverse effects. It was then applied in ten healthy young subjects to characterize the transfer functions from respiration to heart period (RR interval) and to systolic arterial pressure (SAP), and from SAP to RR interval. In the first two cases, the causal and non-causal transfer function estimates were comparable, indicating that respiration, acting as exogenous signal, sets an open loop relationship upon SAP and RR interval. On the contrary, causal and traditional transfer functions from SAP to RR were significantly different, suggesting the presence of a considerable influence on the opposite causal direction. Thus, the proposed causal approach seems to be appropriate for the estimation of parameters, like the gain and the phase lag from SAP to RR interval, which have a large clinical and physiological relevance.

Probing the dynamics of restriction endonuclease NgoMIV-DNA interaction by single-molecule FRET.

PubMed

Tutkus, Marijonas; Sasnauskas, Giedrius; Rutkauskas, Danielis

2017-12-01

Many type II restriction endonucleases require two copies of their recognition sequence for optimal activity. Concomitant binding of two DNA sites by such an enzyme produces a DNA loop. Here we exploit single-molecule Förster resonance energy transfer (smFRET) of surface-immobilized DNA fragments to study the dynamics of DNA looping induced by tetrameric endonuclease NgoMIV. We have employed a DNA fragment with two NgoMIV recognition sites and a FRET dye pair such that upon protein-induced DNA looping the dyes are brought to close proximity resulting in a FRET signal. The dynamics of DNA-NgoMIV interactions proved to be heterogeneous, with individual smFRET trajectories exhibiting broadly different average looped state durations. Distinct types of the dynamics were attributed to different types of DNA-protein complexes, mediated either by one NgoMIV tetramer simultaneously bound to two specific sites ("slow" trajectories) or by semi-specific interactions of two DNA-bound NgoMIV tetramers ("fast" trajectories), as well as to conformational heterogeneity of individual NgoMIV molecules. © 2017 Wiley Periodicals, Inc.

The effects of intraparticle and interparticle interactions on the magnetic hysteresis loop of frozen suspensions of bionized nanoferrite particles

NASA Astrophysics Data System (ADS)

Boekelheide, Zoe; Gruettner, Cordula; Dennis, Cindi

Bionized nano-ferrite (iron oxide/dextran) nanoparticles have been shown to have a large heating response in an alternating magnetic field, making them very promising for applications in magnetic nanoparticle hyperthermia cancer treatment. Magnetic hysteresis loop measurements of these particles provide insight into the magnetic reversal behavior of these particles, and thus their heating response. Measurements have been performed on frozen suspensions of nanoparticles dispersed in H2O, which have been frozen in a range of applied fields in order to tune the interparticle dipolar interactions through formation of linear chains. These experimental results are compared with micromagnetic models of both monolithic (single-domain) and internally structured (multi-grain) particles. It is found that the internal structure of the nanoparticles, which are made up of parallelepiped-shaped grains, is important for describing the magnetic reversal behavior of the particles and the resulting shape of the hysteresis loops. In addition to this, interparticle interactions between particles in a linear chain modify the reversal behavior and thus the shape of the hysteresis loop.

A bioprosthetic ovary created using 3D printed microporous scaffolds restores ovarian function in sterilized mice.

PubMed

Laronda, Monica M; Rutz, Alexandra L; Xiao, Shuo; Whelan, Kelly A; Duncan, Francesca E; Roth, Eric W; Woodruff, Teresa K; Shah, Ramille N

2017-05-16

Emerging additive manufacturing techniques enable investigation of the effects of pore geometry on cell behavior and function. Here, we 3D print microporous hydrogel scaffolds to test how varying pore geometry, accomplished by manipulating the advancing angle between printed layers, affects the survival of ovarian follicles. 30° and 60° scaffolds provide corners that surround follicles on multiple sides while 90° scaffolds have an open porosity that limits follicle-scaffold interaction. As the amount of scaffold interaction increases, follicle spreading is limited and survival increases. Follicle-seeded scaffolds become highly vascularized and ovarian function is fully restored when implanted in surgically sterilized mice. Moreover, pups are born through natural mating and thrive through maternal lactation. These findings present an in vivo functional ovarian implant designed with 3D printing, and indicate that scaffold pore architecture is a critical variable in additively manufactured scaffold design for functional tissue engineering.

Channel Size Conversion of Phi29 DNA-Packaging Nanomotor for Discrimination of Single- and Double-Stranded Nucleic Acids

PubMed Central

Geng, Jia; Wang, Shaoying; Fang, Huaming; Guo, Peixuan

2013-01-01

Nanopores have been utilized to detect the conformation and dynamics of polymers, including DNA and RNA. Biological pores are extremely reproducible at the atomic level with uniform channel sizes. The channel of the bacterial virus phi29 DNA packaging motor is a natural conduit for the transportation of double-stranded DNA (dsDNA), and has the largest diameter among the well-studied biological channels. The larger channel facilitates translocation of dsDNA, and offers more space for further channel modification and conjugation. Interestingly, the relatively large wild type channel, which translocates dsDNA, cannot detect single-stranded nucleic acids (ssDNA or ssRNA) under the current experimental conditions. Herein, we reengineered this motor channel by removing the internal loop segment of the channel. The modification resulted in two classes of channels. One class was the same size as the wild type channel, while the other class had a cross-sectional area about 60% of the wild type. This smaller channel was able to detect the real-time translocation of single stranded nucleic acids at single-molecule level. While the wild type connector exhibited a one-way traffic property with respect to dsDNA translocation, the loop deleted connector was able to translocate ssDNA and ssRNA with equal competencies from both termini. This finding of size alterations in reengineered motor channels expands the potential application of the phi29 DNA packaging motor in nanomedicine, nanobiotechnology, and high-throughput single pore DNA sequencing. PMID:23488809

Partial deletion of beta9 loop in pancreatic lipase-related protein 2 reduces enzyme activity with a larger effect on long acyl chain substrates.

PubMed

Dridi, Kaouthar; Amara, Sawsan; Bezzine, Sofiane; Rodriguez, Jorge A; Carrière, Frédéric; Gaussier, Hélène

2013-07-01

Structural studies on pancreatic lipase have revealed a complex architecture of surface loops surrounding the enzyme active site and potentially involved in interactions with lipids. Two of them, the lid and beta loop, expose a large hydrophobic surface and are considered as acyl chain binding sites based on their interaction with an alkyl phosphonate inhibitor. While the role of the lid in substrate recognition and selectivity has been extensively studied, the implication of beta9 loop in acyl chain stabilization remained hypothetical. The characterization of an enzyme with a natural deletion of the lid, guinea pig pancreatic lipase-related protein 2 (GPLRP2), suggests however an essential contribution of the beta9 loop in the stabilization of the acyl enzyme intermediate formed during the lipolysis reaction. A GPLRP2 mutant with a seven-residue deletion of beta9 loop (GPLRP2-deltabeta9) was produced and its enzyme activity was measured using various substrates (triglycerides, monoglycerides, galactolipids, phospholipids, vinyl esters) with short, medium and long acyl chains. Whatever the substrate tested, GPLRP2-deltabeta9 activity is drastically reduced compared to that of wild-type GPLRP2 and this effect is more pronounced as the length of substrate acyl chain increases. Changes in relative substrate selectivity and stereoselectivity remained however weak. The deletion within beta9 loop has also a negative effect on the rate of enzyme inhibition by alkyl phosphonates. All these findings indicate that the reduced enzyme turnover observed with GPLRP2-deltabeta9 results from a weaker stabilization of the acyl enzyme intermediate due to a loss of hydrophobic interactions.

Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot

NASA Technical Reports Server (NTRS)

Su, L.; Chen, L.; Egli, M.; Berger, J. M.; Rich, A.

1999-01-01

Many viruses regulate translation of polycistronic mRNA using a -1 ribosomal frameshift induced by an RNA pseudoknot. A pseudoknot has two stems that form a quasi-continuous helix and two connecting loops. A 1.6 A crystal structure of the beet western yellow virus (BWYV) pseudoknot reveals rotation and a bend at the junction of the two stems. A loop base is inserted in the major groove of one stem with quadruple-base interactions. The second loop forms a new minor-groove triplex motif with the other stem, involving 2'-OH and triple-base interactions, as well as sodium ion coordination. Overall, the number of hydrogen bonds stabilizing the tertiary interactions exceeds the number involved in Watson-Crick base pairs. This structure will aid mechanistic analyses of ribosomal frameshifting.

Multiprotein DNA Looping

NASA Astrophysics Data System (ADS)

Vilar, Jose M. G.; Saiz, Leonor

2006-06-01

DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switchlike transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.

Crystal structure of Streptococcus pneumoniae pneumolysin provides key insights into early steps of pore formation

PubMed Central

Lawrence, Sara L.; Feil, Susanne C.; Morton, Craig J.; Farrand, Allison J.; Mulhern, Terrence D.; Gorman, Michael A.; Wade, Kristin R.; Tweten, Rodney K.; Parker, Michael W.

2015-01-01

Pore-forming proteins are weapons often used by bacterial pathogens to breach the membrane barrier of target cells. Despite their critical role in infection important structural aspects of the mechanism of how these proteins assemble into pores remain unknown. Streptococcus pneumoniae is the world’s leading cause of pneumonia, meningitis, bacteremia and otitis media. Pneumolysin (PLY) is a major virulence factor of S. pneumoniae and a target for both small molecule drug development and vaccines. PLY is a member of the cholesterol-dependent cytolysins (CDCs), a family of pore-forming toxins that form gigantic pores in cell membranes. Here we present the structure of PLY determined by X-ray crystallography and, in solution, by small-angle X-ray scattering. The crystal structure reveals PLY assembles as a linear oligomer that provides key structural insights into the poorly understood early monomer-monomer interactions of CDCs at the membrane surface. PMID:26403197

Superficially Porous Particles with 1000 Å Pores for Large Biomolecule High Performance Liquid Chromatography and Polymer Size Exclusion Chromatography

PubMed Central

Wagner, Brian M.; Schuster, Stephanie A.; Boyes, Barry E.; Shields, Taylor J.; Miles, William L.; Haynes, Mark J.; Moran, Robert E.; Kirkland, Joseph J.; Schure, Mark R.

2017-01-01

To facilitate mass transport and column efficiency, solutes must have free access to particle pores to facilitate interactions with the stationary phase. To ensure this feature, particles should be used for HPLC separations which have pores sufficiently large to accommodate the solute without restricted diffusion. This paper describes the design and properties of superficially porous (also called Fused-Core®, core shell or porous shell) particles with very large (1000 Å) pores specifically developed for separating very large biomolecules and polymers. Separations of DNA fragments, monoclonal antibodies, large proteins and large polystyrene standards are used to illustrate the utility of these particles for efficient, high-resolution applications. PMID:28213987

Superficially porous particles with 1000Å pores for large biomolecule high performance liquid chromatography and polymer size exclusion chromatography.

PubMed

Wagner, Brian M; Schuster, Stephanie A; Boyes, Barry E; Shields, Taylor J; Miles, William L; Haynes, Mark J; Moran, Robert E; Kirkland, Joseph J; Schure, Mark R

2017-03-17

To facilitate mass transport and column efficiency, solutes must have free access to particle pores to facilitate interactions with the stationary phase. To ensure this feature, particles should be used for HPLC separations which have pores sufficiently large to accommodate the solute without restricted diffusion. This paper describes the design and properties of superficially porous (also called Fused-Core ® , core shell or porous shell) particles with very large (1000Å) pores specifically developed for separating very large biomolecules and polymers. Separations of DNA fragments, monoclonal antibodies, large proteins and large polystyrene standards are used to illustrate the utility of these particles for efficient, high-resolution applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Response to Extreme Temperatures of Mesoporous Silica MCM-41: Porous Structure Transformation Simulation and Modification of Gas Adsorption Properties.

PubMed

Zhang, Shenli; Perez-Page, Maria; Guan, Kelly; Yu, Erick; Tringe, Joseph; Castro, Ricardo H R; Faller, Roland; Stroeve, Pieter

2016-11-08

Molecular dynamics (MD) and Monte Carlo (MC) simulations were applied together for the first time to reveal the porous structure transformation mechanisms of mesoporous silica MCM-41 subjected to temperatures up to 2885 K. Silica was experimentally characterized to inform the models and enable prediction of changes in gas adsorption/separation properties. MD simulations suggest that the pore closure process is activated by a collective diffusion of matrix atoms into the porous region, accompanied by bond reformation at the surface. Degradation is kinetically limited, such that complete pore closure is postponed at high heating rates. We experimentally observe decreased gas adsorption with increasing temperature in mesoporous silica heated at fixed rates, due to pore closure and structural degradation consistent with simulation predictions. Applying the Kissinger equation, we find a strong correlation between the simulated pore collapse temperatures and the experimental values which implies an activation energy of 416 ± 17 kJ/mol for pore closure. MC simulations give the adsorption and selectivity for thermally treated MCM-41, for N 2 , Ar, Kr, and Xe at room temperature within the 1-10 000 kPa pressure range. Relative to pristine MCM-41, we observe that increased surface roughness due to decreasing pore size amplifies the difference of the absolute adsorption amount differently for different adsorbate molecules. In particular, we find that adsorption of strongly interacting molecules can be enhanced in the low-pressure region while adsorption of weakly interacting molecules is inhibited. This then results in higher selectivity in binary mixture adsorption in mesoporous silica.

Optimal design strategy of switching converters employing current injected control

NASA Astrophysics Data System (ADS)

Lee, F. C.; Fang, Z. D.; Lee, T. H.

1985-01-01

This paper analyzes a buck/boost regulator employing current-injected control (CIC). It reveals the complex interactions between the dc loop and the current-injected loop and underlines the fundamental principle that governs the loop gain determination. Three commonly used compensation techniques are compared. The integral and lead/lag compensation are shown to be most desirable for performance optimization and stability.

Effect of confinement in nano-porous materials on the solubility of a supercritical gas

NASA Astrophysics Data System (ADS)

Hu, Yaofeng; Huang, Liangliang; Zhao, Shuangliang; Liu, Honglai; Gubbins, Keith E.

2016-11-01

By combining Gibbs Ensemble Monte Carlo simulations and density functional theory, we investigate the influence of confinement in a slit-shaped carbon pore on the solubility of a supercritical solute gas in a liquid solvent. In the cases studied here, competing adsorption of the solvent and solute determines whether the solubility is enhanced or suppressed for larger pores. We find that the solubility in the confined system is strongly dependent on pore width, and that molecular packing effects are important for small pore widths. In addition, the solubility decreases on increase in the temperature, as for the bulk mixture, but the rate of decrease is greater in the pore due to a decrease in the partial molar enthalpy of the solute in the pore; this effect becomes greater as pore width is decreased. The solubility is increased on increasing the bulk pressure of the gas in equilibrium with the pore, and obeys Henry's law at lower pressures. However, the Henry constant differs significantly from that for the bulk mixture, and the range of pressure over which Henry's law applies is reduced relative to that for the bulk mixture. The latter observation indicates that solute-solute interactions become more important in the pore than for the bulk at a given bulk pressure. Finally, we note that different authors use different definitions of the solubility in pores, leading to some confusion over the reported phenomenon of 'oversolubility'. We recommend that solubility be defined as the overall mole fraction of solute in the pores, since it takes into account the increase in density of the solvent in the pores, and avoids ambiguity in the definition of the pore volume.

MINI-FILAMENT ERUPTION AS THE INITIATION OF A JET ALONG CORONAL LOOPS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hong, Junchao; Jiang, Yunchun; Yang, Jiayan

Minifilament eruptions (MFEs) and coronal jets are different types of solar small-scale explosive events. We report an MFE observed at the New Vacuum Solar Telescope (NVST). As seen in the NVST H α images, during the rising phase, the minifilament erupts outward orthogonally to its length, accompanied with a flare-like brightening at the bottom. Afterward, dark materials are found to possibly extend along the axis of the expanded filament body. The MFE is analogous to large filament eruptions. However, a simultaneous observation of the Solar Dynamics Observatory shows that a jet is initiated and flows out along nearby coronal loopsmore » during the rising phase of the MFE. Meanwhile, small hot loops, which connect the original eruptive site of the minifilament to the footpoints of the coronal loops, are formed successively. A differential emission measure analysis demonstrates that, on the top of the new small loops, a hot cusp structure exists. We conjecture that the magnetic fields of the MFE interact with magnetic fields of the coronal loops. This interaction is interpreted as magnetic reconnection that produces the jet and the small hot loops.« less

TRF2 Recruits RTEL1 to Telomeres in S Phase to Promote T-Loop Unwinding

PubMed Central

Sarek, Grzegorz; Vannier, Jean-Baptiste; Panier, Stephanie; Petrini, John H.J.; Boulton, Simon J.

2015-01-01

Summary The helicase RTEL1 promotes t-loop unwinding and suppresses telomere fragility to maintain the integrity of vertebrate telomeres. An interaction between RTEL1 and PCNA is important to prevent telomere fragility, but how RTEL1 engages with the telomere to promote t-loop unwinding is unclear. Here, we establish that the shelterin protein TRF2 recruits RTEL1 to telomeres in S phase, which is required to prevent catastrophic t-loop processing by structure-specific nucleases. We show that the TRF2-RTEL1 interaction is mediated by a metal-coordinating C4C4 motif in RTEL1, which is compromised by the Hoyeraal-Hreidarsson syndrome (HHS) mutation, RTEL1R1264H. Conversely, we define a TRF2I124D substitution mutation within the TRFH domain of TRF2, which eliminates RTEL1 binding and phenocopies the RTEL1R1264H mutation, giving rise to aberrant t-loop excision, telomere length heterogeneity, and loss of the telomere as a circle. These results implicate TRF2 in the recruitment of RTEL1 to facilitate t-loop disassembly at telomeres in S phase. PMID:25620558

TRF2 recruits RTEL1 to telomeres in S phase to promote t-loop unwinding.

PubMed

Sarek, Grzegorz; Vannier, Jean-Baptiste; Panier, Stephanie; Petrini, John H J; Boulton, Simon J

2015-02-19

The helicase RTEL1 promotes t-loop unwinding and suppresses telomere fragility to maintain the integrity of vertebrate telomeres. An interaction between RTEL1 and PCNA is important to prevent telomere fragility, but how RTEL1 engages with the telomere to promote t-loop unwinding is unclear. Here, we establish that the shelterin protein TRF2 recruits RTEL1 to telomeres in S phase, which is required to prevent catastrophic t-loop processing by structure-specific nucleases. We show that the TRF2-RTEL1 interaction is mediated by a metal-coordinating C4C4 motif in RTEL1, which is compromised by the Hoyeraal-Hreidarsson syndrome (HHS) mutation, RTEL1(R1264H). Conversely, we define a TRF2(I124D) substitution mutation within the TRFH domain of TRF2, which eliminates RTEL1 binding and phenocopies the RTEL1(R1264H) mutation, giving rise to aberrant t-loop excision, telomere length heterogeneity, and loss of the telomere as a circle. These results implicate TRF2 in the recruitment of RTEL1 to facilitate t-loop disassembly at telomeres in S phase. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Spontaneous crystalline-to-amorphous phase transformation of organic or medicinal compounds in the presence of porous media, part 2: amorphization capacity and mechanisms of interaction.

PubMed

Qian, Ken K; Suib, Steven L; Bogner, Robin H

2011-11-01

Amorphization of crystalline compounds using mesoporous media is a promising technique to improve the solubility and dissolution rate of poorly soluble compounds. The objective of this paper is to determine the capacity of amorphization and understand the mechanisms of phase transformation. Commercial grades of mesoporous silicon dioxide (SiO(2)) samples (5- to 30-nm mean pore diameters) with either constant surface area or constant pore volume were used. The amorphization capacity of naphthalene was not proportional to either the surface area or the pore volume measured using adsorption chambers. Instead, the amorphization capacity correlated with surface curvature, that is, the smaller the pore diameter and the higher the surface curvature, the greater the amorphization capacity. The change in surface chemistry due to a highly curved surface may be responsible for the enhanced amorphization capacity as well. The amorphization of crystalline compounds was facilitated through capillary condensation, with the decrease in pore volume as the direct experimental evidence. The amorphization capacity was also enhanced by the dipole-dipole or dipole-induced dipole interaction, promoted by the hydroxyl groups on the surface of SiO(2). The enthalpy of vapor-solid condensation of crystalline compounds was a useful indicator to predict the rank order of amorphization capacity. Copyright © 2011 Wiley-Liss, Inc.

On the influence of the intermolecular potential on the wetting properties of water on silica surfaces

NASA Astrophysics Data System (ADS)

Pafong, E.; Geske, J.; Drossel, B.

2016-09-01

We study the wetting properties of water on silica surfaces using molecular dynamics (MD) simulations. To describe the intermolecular interaction between water and silica atoms, two types of interaction potential models are used: the standard BródkA and Zerda (BZ) model and the Gulmen and Thompson (GT) model. We perform an in-depth analysis of the influence of the choice of the potential on the arrangement of the water molecules in partially filled pores and on top of silica slabs. We find that at moderate pore filling ratios, the GT silica surface is completely wetted by water molecules, which agrees well with experimental findings, while the commonly used BZ surface is less hydrophilic and is only partially wetted. We interpret our simulation results using an analytical calculation of the phase diagram of water in partially filled pores. Moreover, an evaluation of the contact angle of the water droplet on top of the silica slab reveals that the interaction becomes more hydrophilic with increasing slab thickness and saturates around 2.5-3 nm, in agreement with the experimentally found value. Our analysis also shows that the hydroaffinity of the surface is mainly determined by the electrostatic interaction, but the van der Waals interaction nevertheless is strong enough that it can turn a hydrophobic surface into a hydrophilic surface.

Quantum corrections to the generalized Proca theory via a matter field

NASA Astrophysics Data System (ADS)

Amado, André; Haghani, Zahra; Mohammadi, Azadeh; Shahidi, Shahab

2017-09-01

We study the quantum corrections to the generalized Proca theory via matter loops. We consider two types of interactions, linear and nonlinear in the vector field. Calculating the one-loop correction to the vector field propagator, three- and four-point functions, we show that the non-linear interactions are harmless, although they renormalize the theory. The linear matter-vector field interactions introduce ghost degrees of freedom to the generalized Proca theory. Treating the theory as an effective theory, we calculate the energy scale up to which the theory remains healthy.

Ferroelectric-like hysteresis loop originated from non-ferroelectric effects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Bora; Seol, Daehee; Lee, Shinbuhm

Piezoresponse force microscopy (PFM) has provided advanced nanoscale understanding and analysis of ferroelectric and piezoelectric properties. In PFM-based studies, electromechanical strain induced by the converse piezoelectric effect is probed and analyzed as a PFM response. However, electromechanical strain can also arise from several non-piezoelectric origins that may lead to a misinterpretation of the observed response. Among them, electrostatic interaction can significantly affect the PFM response. Nonetheless, previous studies explored solely the influence of electrostatic interaction on the PFM response under the situation accompanied with polarization switching. Here, we show the influence of the electrostatic interaction in the absence of polarizationmore » switching by using unipolar voltage sweep. The obtained results reveal that the electromechanical neutralization between piezoresponse of polarization and electrostatic interaction plays a crucial role in the observed ferroelectric-like hysteresis loop despite the absence of polarization switching. Furthermore, our work can provide a basic guideline for the correct interpretation of the hysteresis loop in PFM-based studies.« less

Ferroelectric-like hysteresis loop originated from non-ferroelectric effects

DOE PAGES

Kim, Bora; Seol, Daehee; Lee, Shinbuhm; ...

2016-09-06

Piezoresponse force microscopy (PFM) has provided advanced nanoscale understanding and analysis of ferroelectric and piezoelectric properties. In PFM-based studies, electromechanical strain induced by the converse piezoelectric effect is probed and analyzed as a PFM response. However, electromechanical strain can also arise from several non-piezoelectric origins that may lead to a misinterpretation of the observed response. Among them, electrostatic interaction can significantly affect the PFM response. Nonetheless, previous studies explored solely the influence of electrostatic interaction on the PFM response under the situation accompanied with polarization switching. Here, we show the influence of the electrostatic interaction in the absence of polarizationmore » switching by using unipolar voltage sweep. The obtained results reveal that the electromechanical neutralization between piezoresponse of polarization and electrostatic interaction plays a crucial role in the observed ferroelectric-like hysteresis loop despite the absence of polarization switching. Furthermore, our work can provide a basic guideline for the correct interpretation of the hysteresis loop in PFM-based studies.« less

Structural rearrangements at the translocation pore of the human glutamate transporter, EAAT1.

PubMed

Leighton, Barbara H; Seal, Rebecca P; Watts, Spencer D; Skyba, Mary O; Amara, Susan G

2006-10-06

Structure-function studies of mammalian and bacterial excitatory amino acid transporters (EAATs), as well as the crystal structure of a related archaeal glutamate transporter, support a model in which TM7, TM8, and the re-entrant loops HP1 and HP2 participate in forming a substrate translocation pathway within each subunit of a trimer. However, the transport mechanism, including precise binding sites for substrates and co-transported ions and changes in the tertiary structure underlying transport, is still not known. In this study, we used chemical cross-linking of introduced cysteine pairs in a cysteine-less version of EAAT1 to examine the dynamics of key domains associated with the translocation pore. Here we show that cysteine substitution at Ala-395, Ala-367, and Ala-440 results in functional single and double cysteine transporters and that in the absence of glutamate or dl-threo-beta-benzyloxyaspartate (dl-TBOA), A395C in the highly conserved TM7 can be cross-linked to A367C in HP1 and to A440C in HP2. The formation of these disulfide bonds is reversible and occurs intra-molecularly. Interestingly, cross-linking A395C to A367C appears to abolish transport, whereas cross-linking A395C to A440C lowers the affinities for glutamate and dl-TBOA but does not change the maximal transport rate. Additionally, glutamate and dl-TBOA binding prevent cross-linking in both double cysteine transporters, whereas sodium binding facilitates cross-linking in the A395C/A367C transporter. These data provide evidence that within each subunit of EAAT1, Ala-395 in TM7 resides close to a residue at the tip of each re-entrant loop (HP1 and HP2) and that these residues are repositioned relative to one another at different steps in the transport cycle. Such behavior likely reflects rearrangements in the tertiary structure of the translocation pore during transport and thus provides constraints for modeling the structural dynamics associated with transport.

Equilibrium, metastability, and hysteresis in a model spin-crossover material with nearest-neighbor antiferromagnetic-like and long-range ferromagnetic-like interactions

DOE PAGES

Rikvold, Per Arne; Brown, Gregory; Miyashita, Seiji; ...

2016-02-16

Phase diagrams and hysteresis loops were obtained by Monte Carlo simulations and a mean- field method for a simplified model of a spin-crossovermaterialwith a two-step transition between the high-spin and low-spin states. This model is a mapping onto a square-lattice S = 1/2 Ising model with antiferromagnetic nearest-neighbor and ferromagnetic Husimi-Temperley ( equivalent-neighbor) long-range interactions. Phase diagrams obtained by the two methods for weak and strong long-range interactions are found to be similar. However, for intermediate-strength long-range interactions, the Monte Carlo simulations show that tricritical points decompose into pairs of critical end points and mean-field critical points surrounded by horn-shapedmore » regions of metastability. Hysteresis loops along paths traversing the horn regions are strongly reminiscent of thermal two-step transition loops with hysteresis, recently observed experimentally in several spin-crossover materials. As a result, we believe analogous phenomena should be observable in experiments and simulations for many systems that exhibit competition between local antiferromagnetic-like interactions and long-range ferromagnetic-like interactions caused by elastic distortions.« less

Superdiffusive gas recovery from nanopores

NASA Astrophysics Data System (ADS)

Wu, Haiyi; He, Yadong; Qiao, Rui

2016-11-01

Understanding the recovery of gas from reservoirs featuring pervasive nanopores is essential for effective shale gas extraction. Classical theories cannot accurately predict such gas recovery and many experimental observations are not well understood. Here we report molecular simulations of the recovery of gas from single nanopores, explicitly taking into account molecular gas-wall interactions. We show that, in very narrow pores, the strong gas-wall interactions are essential in determining the gas recovery behavior both quantitatively and qualitatively. These interactions cause the total diffusion coefficients of the gas molecules in nanopores to be smaller than those predicted by kinetic theories, hence slowing down the rate of gas recovery. These interactions also lead to significant adsorption of gas molecules on the pore walls. Because of the desorption of these gas molecules during gas recovery, the gas recovery from the nanopore does not exhibit the usual diffusive scaling law (i.e., the accumulative recovery scales as R ˜t1 /2 ) but follows a superdiffusive scaling law R ˜tn (n >0.5 ), which is similar to that observed in some field experiments. For the system studied here, the superdiffusive gas recovery scaling law can be captured well by continuum models in which the gas adsorption and desorption from pore walls are taken into account using the Langmuir model.

Interaction of Porosity with a Planar Solid/Liquid Interface

NASA Technical Reports Server (NTRS)

Catalina, Adrian V.; Stefanescu, Doru M.; Sen, Subhayu; Kaukler, William F.

2004-01-01

In this article, an investigation of the interaction between gas porosity and a planar solid/liquid (SL) interface is reported. A two-dimensional numerical model able to accurately track sharp SL interfaces during solidification of pure metals and alloys is proposed. The finite-difference method and a rectangular undeformed grid are used for computation. The SL interface is described through the points of intersection with the grid lines. Its motion is determined by the thermal and solute gradients at each particular point. Changes of the interface temperature because of capillarity or solute redistribution as well as any perturbation of the thermal and solute field produced by the presence of non-metallic inclusions can be computed. To validate the model, the dynamics of the interaction between a gas pore and a solidification front in metal alloys was observed using a state of the art X-ray transmission microscope (XTM). The experiments included observation of the distortion of the SL interface near a pore, real-time measurements of the growth rate, and the change in shape of the porosity during interaction with the SL interface in pure Al and Al-0.25 wt pct Au alloy. In addition, porosity-induced solute segregation patterns surrounding a pore were also quantified.

Understanding controlled drug release from mesoporous silicates: theory and experiment.

PubMed

Ukmar, T; Maver, U; Planinšek, O; Kaučič, V; Gaberšček, M; Godec, A

2011-11-07

Based on the results of carefully designed experiments upgraded with appropriate theoretical modeling, we present clear evidence that the release curves from mesoporous materials are significantly affected by drug-matrix interactions. In experimental curves, these interactions are manifested as a non-convergence at long times and an inverse dependence of release kinetics on pore size. Neither of these phenomena is expected in non-interacting systems. Although both phenomena have, rather sporadically, been observed in previous research, they have not been explained in terms of a general and consistent theoretical model. The concept is demonstrated on a model drug indomethacin embedded into SBA-15 and MCM-41 porous silicates. The experimental release curves agree exceptionally well with theoretical predictions in the case of significant drug-wall attractions. The latter are described using a 2D Fokker-Planck equation. One could say that the interactions affect the relative cross-section of pores where the local flux has a non-vanishing axial component and in turn control the effective transfer of drug into bulk solution. Finally, we identify the critical parameters determining the pore size dependence of release kinetics and construct a dynamic phase diagram of the various resulting transport regimes. Copyright © 2011 Elsevier B.V. All rights reserved.

Undamped transverse oscillations of coronal loops as a self-oscillatory process

NASA Astrophysics Data System (ADS)

Nakariakov, V. M.; Anfinogentov, S. A.; Nisticò, G.; Lee, D.-H.

2016-06-01

Context. Standing transverse oscillations of coronal loops are observed to operate in two regimes: rapidly decaying, large amplitude oscillations and undamped small amplitude oscillations. In the latter regime the damping should be compensated by energy supply, which allows the loop to perform almost monochromatic oscillations with almost constant amplitude and phase. Different loops oscillate with different periods. The oscillation amplitude does not show dependence on the loop length or the oscillation period. Aims: We aim to develop a low-dimensional model explaining the undamped kink oscillations as a self-oscillatory process caused by the effect of negative friction. The source of energy is an external quasi-steady flow, for example, supergranulation motions near the loop footpoints or external flows in the corona. Methods: We demonstrate that the interaction of a quasi-steady flow with a loop can be described by a Rayleigh oscillator equation that is a non-linear ordinary differential equation, with the damping and resonant terms determined empirically. Results: Small-amplitude self-oscillatory solutions to the Rayleigh oscillator equation are harmonic signals of constant amplitude, which is consistent with the observed properties of undamped kink oscillations. The period of self-oscillations is determined by the frequency of the kink mode. The damping by dissipation and mode conversion is compensated by the continuous energy deposition at the frequency of the natural oscillation. Conclusions: We propose that undamped kink oscillations of coronal loops may be caused by the interaction of the loops with quasi-steady flows, and hence are self-oscillations, which is analogous to producing a tune by moving a bow across a violin string.

Structural mechanism of Smad4 recognition by the nuclear oncoprotein Ski: insights on Ski-mediated repression of TGF-beta signaling.

PubMed

Wu, Jia Wei; Krawitz, Ariel R; Chai, Jijie; Li, Wenyu; Zhang, Fangjiu; Luo, Kunxin; Shi, Yigong

2002-11-01

The Ski family of nuclear oncoproteins represses TGF-beta signaling through interactions with the Smad proteins. The crystal structure of the Smad4 binding domain of human c-Ski in complex with the MH2 domain of Smad4 reveals specific recognition of the Smad4 L3 loop region by a highly conserved interaction loop (I loop) from Ski. The Ski binding surface on Smad4 significantly overlaps with that required for binding of the R-Smads. Indeed, Ski disrupts the formation of a functional complex between the Co- and R-Smads, explaining how it could lead to repression of TGF-beta, activin, and BMP responses. Intriguingly, the structure of the Ski fragment, stabilized by a bound zinc atom, resembles the SAND domain, in which the corresponding I loop is responsible for DNA binding.

Effects of polymer graft properties on protein adsorption and transport in ion exchange chromatography: a multiscale modeling study.

PubMed

Basconi, Joseph E; Carta, Giorgio; Shirts, Michael R

2015-04-14

Multiscale simulation is used to study the adsorption of lysozyme onto ion exchangers obtained by grafting charged polymers into a porous matrix, in systems with various polymer properties and strengths of electrostatic interaction. Molecular dynamics simulations show that protein partitioning into the polymer-filled pore space increases with the overall charge content of the polymers, while the diffusivity in the pore space decreases. However, the combination of greatly increased partitioning and modestly decreased diffusion results in macroscopic transport rates that increase as a function of charge content, as the large concentration driving force due to enhanced pore space partitioning outweighs the reduction in the pore space diffusivity. Matrices having greater charge associated with the grafted polymers also exhibit more diffuse intraparticle concentration profiles during transient adsorption. In systems with a high charge content per polymer and a low protein loading, the polymers preferentially partition toward the surface due to favorable interactions with the surface-bound protein. These results demonstrate the potential of multiscale modeling to illuminate qualitative trends between molecular properties and the adsorption equilibria and kinetic properties observable on macroscopic scales.

Nuclear pore proteins are involved in the biogenesis of functional tRNA.

PubMed Central

Simos, G; Tekotte, H; Grosjean, H; Segref, A; Sharma, K; Tollervey, D; Hurt, E C

1996-01-01

Los1p and Pus1p, which are involved in tRNA biogenesis, were found in a genetic screen for components interacting with the nuclear pore protein Nsp1p. LOS1, PUS1 and NSP1 interact functionally, since the combination of mutations in the three genes causes synthetic lethality. Pus1p is an intranuclear protein which exhibits a nucleotide-specific and intron-dependent tRNA pseudouridine synthase activity. Los1p was shown previously to be required for efficient pre-tRNA splicing; we report here that Los1p localizes to the nuclear pores and is linked functionally to several components of the tRNA biogenesis machinery including Pus1p and Tfc4p. When the formation of functional tRNA was analyzed by an in vivo assay, the los1(-) pus1(-) double mutant, as well as several thermosensitive nucleoporin mutants including nsp1, nup116, nup133 and nup85, exhibited loss of suppressor tRNA activity even at permissive temperatures. These data suggest that nuclear pore proteins are required for the biogenesis of functional tRNA. Images PMID:8641292

Interactions of the H5 pore region and hydroxylamine with N-type inactivation in the Shaker K+ channel.

PubMed Central

Yool, A J; Schwarz, T L

1995-01-01

Mutations at sites in the H5 region of the Shaker B K+ channel were used to analyze the influence of the pore on N-type inactivation. Single-channel and two-electrode voltage clamp analyses showed that mutations at residues T441 and T442, which are thought to lie at the internal mouth of the pore, produced opposite effects on inactivation: the inactivated state is stabilized by T441S and destabilized by T442S. In addition, an ammonium derivative, hydroxylamine (OH-(NH3)+), appears to bind in the pore region of T441S and further decreases the rate of recovery from N-type inactivation. This effect relies on the presence of the amino-terminal. The effect of hydroxylamine on the T441S mutation of this K+ channel shows several properties analogous to those of local anesthetics on the Na+ channel. These results can be interpreted to suggest that part of the H5 region contributes to the receptor for the inactivation particle and that a hydroxylamine ion trapped near that site can stabilize their interaction. Images FIGURE 8 PMID:7696498

Nonlinear transport of soft droplets in pore networks

NASA Astrophysics Data System (ADS)

Vernerey, Franck; Benet Cerda, Eduard; Koo, Kanghyeon

A large number of biological and technological processes depend on the transport of soft colloidal particles through porous media; this includes the transport and separation of cells, viruses or drugs through tissues, membranes and microfluidic devices. In these systems, the interactions between soft particles, background fluid and the surrounding pore space yield complex, nonlinear behaviors such as non-Darcy flows, localization and jamming. We devise a computational strategy to investigate the transport of non-wetting and deformable water droplets in a microfluidic device made of a random distribution of cylindrical obstacles. We first derive scaling laws for the entry of the droplet in a single pore and discuss the role of surface tension, contact angle and size in this process. This information is then used to study the transport of multiple droplets in an obstacle network. We find that when the droplet size is close to the pore size, fluid flow and droplet trafficking strongly interact, leading to local redistributions in pressure fields, intermittent clogging and jamming. Importantly, it is found that the overall droplet and fluid transport display three different scaling regimes depending on the forcing pressure, and that these regimes can be related to droplet properties.

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).

PubMed

Pravda, Lukáš; Sehnal, David; Toušek, Dominik; Navrátilová, Veronika; Bazgier, Václav; Berka, Karel; Svobodová Vareková, Radka; Koca, Jaroslav; Otyepka, Michal

2018-04-30

MOLEonline is an interactive, web-based application for the detection and characterization of channels (pores and tunnels) within biomacromolecular structures. The updated version of MOLEonline overcomes limitations of the previous version by incorporating the recently developed LiteMol Viewer visualization engine and providing a simple, fully interactive user experience. The application enables two modes of calculation: one is dedicated to the analysis of channels while the other was specifically designed for transmembrane pores. As the application can use both PDB and mmCIF formats, it can be leveraged to analyze a wide spectrum of biomacromolecular structures, e.g. stemming from NMR, X-ray and cryo-EM techniques. The tool is interconnected with other bioinformatics tools (e.g., PDBe, CSA, ChannelsDB, OPM, UniProt) to help both setup and the analysis of acquired results. MOLEonline provides unprecedented analytics for the detection and structural characterization of channels, as well as information about their numerous physicochemical features. Here we present the application of MOLEonline for structural analyses of α-hemolysin and transient receptor potential mucolipin 1 (TRMP1) pores. The MOLEonline application is freely available via the Internet at https://mole.upol.cz.

Characterization of nanoporous shales with gas sorption

NASA Astrophysics Data System (ADS)

Joewondo, N.; Prasad, M.

2017-12-01

The understanding of the fluid flow in porous media requires the knowledge of the pore system involved. Fluid flow in fine grained shales falls under different regime than transport regime in conventional reservoir due to the different average pore sizes in the two materials; the average pore diameter of conventional sandstones is on the micrometer scale, while of shales can be as small as several nanometers. Mercury intrusion porosimetry is normally used to characterize the pores of conventional reservoir, however with increasingly small pores, the injection pressure required to imbibe the pores becomes infinitely large due to surface tension. Characterization of pores can be expressed by a pore size distribution (PSD) plot, which reflects distribution of pore volume or surface area with respect to pore size. For the case of nanoporous materials, the surface area, which serves as the interface between the rock matrix and fluid, becomes increasingly large and important. Physisorption of gas has been extensively studied as a method of nanoporous solid characterization (particularly for the application of catalysis, metal organic frameworks, etc). The PSD is obtained by matching the experimental result to the calculated theoretical result (using Density Functional Theory (DFT), a quantum mechanics based modelling method for molecular scale interactions). We present the challenges and experimental result of Nitrogen and CO2 gas sorption on shales with various mineralogy and the interpreted PSD obtained by DFT method. Our result shows significant surface area contributed by the nanopores of shales, hence the importance of surface area measurements for the characterization of shales.

Modeling of Processing-Induced Pore Morphology in an Additively-Manufactured Ti-6Al-4V Alloy

PubMed Central

Kabir, Mohammad Rizviul; Richter, Henning

2017-01-01

A selective laser melting (SLM)-based, additively-manufactured Ti-6Al-4V alloy is prone to the accumulation of undesirable defects during layer-by-layer material build-up. Defects in the form of complex-shaped pores are one of the critical issues that need to be considered during the processing of this alloy. Depending on the process parameters, pores with concave or convex boundaries may occur. To exploit the full potential of additively-manufactured Ti-6Al-4V, the interdependency between the process parameters, pore morphology, and resultant mechanical properties, needs to be understood. By incorporating morphological details into numerical models for micromechanical analyses, an in-depth understanding of how these pores interact with the Ti-6Al-4V microstructure can be gained. However, available models for pore analysis lack a realistic description of both the Ti-6Al-4V grain microstructure, and the pore geometry. To overcome this, we propose a comprehensive approach for modeling and discretizing pores with complex geometry, situated in a polycrystalline microstructure. In this approach, the polycrystalline microstructure is modeled by means of Voronoi tessellations, and the complex pore geometry is approximated by strategically combining overlapping spheres of varied sizes. The proposed approach provides an elegant way to model the microstructure of SLM-processed Ti-6Al-4V containing pores or crack-like voids, and makes it possible to investigate the relationship between process parameters, pore morphology, and resultant mechanical properties in a finite-element-based simulation framework. PMID:28772504

Modeling of Processing-Induced Pore Morphology in an Additively-Manufactured Ti-6Al-4V Alloy.

PubMed

Kabir, Mohammad Rizviul; Richter, Henning

2017-02-08

A selective laser melting (SLM)-based, additively-manufactured Ti-6Al-4V alloy is prone to the accumulation of undesirable defects during layer-by-layer material build-up. Defects in the form of complex-shaped pores are one of the critical issues that need to be considered during the processing of this alloy. Depending on the process parameters, pores with concave or convex boundaries may occur. To exploit the full potential of additively-manufactured Ti-6Al-4V, the interdependency between the process parameters, pore morphology, and resultant mechanical properties, needs to be understood. By incorporating morphological details into numerical models for micromechanical analyses, an in-depth understanding of how these pores interact with the Ti-6Al-4V microstructure can be gained. However, available models for pore analysis lack a realistic description of both the Ti-6Al-4V grain microstructure, and the pore geometry. To overcome this, we propose a comprehensive approach for modeling and discretizing pores with complex geometry, situated in a polycrystalline microstructure. In this approach, the polycrystalline microstructure is modeled by means of Voronoi tessellations, and the complex pore geometry is approximated by strategically combining overlapping spheres of varied sizes. The proposed approach provides an elegant way to model the microstructure of SLM-processed Ti-6Al-4V containing pores or crack-like voids, and makes it possible to investigate the relationship between process parameters, pore morphology, and resultant mechanical properties in a finite-element-based simulation framework.

The pore-forming bacterial effector, VopQ, halts autophagic turnover.

PubMed

Sreelatha, Anju; Orth, Kim; Starai, Vincent J

2013-12-01

Vibrio parahemolyticus Type III effector VopQ is both necessary and sufficient to induce autophagy within one hour of infection. We demonstrated that VopQ interacts with the Vo domain of the conserved vacuolar H(+)-ATPase. Membrane-associated VopQ subsequently forms pores in the membranes of acidic compartments, resulting in immediate release of protons without concomitant release of lumenal protein contents. These studies show how a bacterial pathogen can compromise host ion potentials using a gated pore-forming effector to equilibrate levels of small molecules found in endolysosomal compartments and disrupt cellular processes such as autophagy.

Modeling the hydro-mechanical responses of strip and circular punch loadings on water-saturated collapsible geomaterials

DOE PAGES

Sun, WaiChing; Chen, Qiushi; Ostien, Jakob T.

2013-11-22

A stabilized enhanced strain finite element procedure for poromechanics is fully integrated with an elasto-plastic cap model to simulate the hydro-mechanical interactions of fluid-infiltrating porous rocks with associative and non-associative plastic flow. We present a quantitative analysis on how macroscopic plastic volumetric response caused by pore collapse and grain rearrangement affects the seepage of pore fluid, and vice versa. Results of finite element simulations imply that the dissipation of excess pore pressure may significantly affect the stress path and thus alter the volumetric plastic responses.

Limit cycles in piecewise-affine gene network models with multiple interaction loops

NASA Astrophysics Data System (ADS)

Farcot, Etienne; Gouzé, Jean-Luc

2010-01-01

In this article, we consider piecewise affine differential equations modelling gene networks. We work with arbitrary decay rates, and under a local hypothesis expressed as an alignment condition of successive focal points. The interaction graph of the system may be rather complex (multiple intricate loops of any sign, multiple thresholds, etc.). Our main result is an alternative theorem showing that if a sequence of region is periodically visited by trajectories, then under our hypotheses, there exists either a unique stable periodic solution, or the origin attracts all trajectories in this sequence of regions. This result extends greatly our previous work on a single negative feedback loop. We give several examples and simulations illustrating different cases.

Free energy and phase transition of the matrix model on a plane wave

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hadizadeh, Shirin; Ramadanovic, Bojan; Semenoff, Gordon W.

2005-03-15

It has recently been observed that the weakly coupled plane-wave matrix model has a density of states which grows exponentially at high energy. This implies that the model has a phase transition. The transition appears to be of first order. However, its exact nature is sensitive to interactions. In this paper, we analyze the effect of interactions by computing the relevant parts of the effective potential for the Polyakov loop operator in the finite temperature plane-wave matrix model to three-loop order. We show that the phase transition is indeed of first order. We also compute the correction to the Hagedornmore » temperature to order two loops.« less

A new approximation for pore pressure accumulation in marine sediment due to water waves

NASA Astrophysics Data System (ADS)

Jeng, D.-S.; Seymour, B. R.; Li, J.

2007-01-01

The residual mechanism of wave-induced pore water pressure accumulation in marine sediments is re-examined. An analytical approximation is derived using a linear relation for pore pressure generation in cyclic loading, and mistakes in previous solutions (Int. J. Numer. Anal. Methods Geomech. 2001; 25:885-907; J. Offshore Mech. Arctic Eng. (ASME) 1989; 111(1):1-11) are corrected. A numerical scheme is then employed to solve the case with a non-linear relation for pore pressure generation. Both analytical and numerical solutions are verified with experimental data (Laboratory and field investigation of wave-sediment interaction. Joseph H. Defrees Hydraulics Laboratory, School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 1983), and provide a better prediction of pore pressure accumulation than the previous solution (J. Offshore Mech. Arctic Eng. (ASME) 1989; 111(1):1-11). The parametric study concludes that the pore pressure accumulation and use of full non-linear relation of pore pressure become more important under the following conditions: (1) large wave amplitude, (2) longer wave period, (3) shallow water, (4) shallow soil and (5) softer soils with a low consolidation coefficient. Copyright

Glycine receptor mechanism illuminated by electron cryo-microscopy

PubMed Central

Du, Juan; Lü, Wei; Wu, Shenping; Cheng, Yifan; Gouaux, Eric

2015-01-01

Summary The strychnine-sensitive glycine receptor (GlyR) mediates inhibitory synaptic transmission in the spinal cord and brainstem and is linked to neurological disorders including autism and hyperekplexia. Understanding of molecular mechanisms and pharmacology of GlyRs has been hindered by a dearth of high-resolution structures. Here we report electron cryo-microscopy structures of the α1 GlyR with strychnine, glycine, or glycine/ivermectin. Strychnine arrests the receptor in an antagonist-bound, closed ion channel state, glycine stabilizes the receptor in an agonist-bound open channel state, and the glycine/ivermectin complex adopts a potentially desensitized or partially open state. Relative to the glycine-bound state, strychnine expands the agonist-binding pocket via outward movement of the C loop, promotes rearrangement of the extracellular and transmembrane domain ‘wrist’ interface, and leads to rotation of the transmembrane domain toward the pore axis, occluding the ion conduction pathway. These structures illuminate GlyR mechanism and define a rubric to interpret structures of Cys-loop receptors. PMID:26344198

Glycine receptor mechanism elucidated by electron cryo-microscopy.

PubMed

Du, Juan; Lü, Wei; Wu, Shenping; Cheng, Yifan; Gouaux, Eric

2015-10-08

The strychnine-sensitive glycine receptor (GlyR) mediates inhibitory synaptic transmission in the spinal cord and brainstem and is linked to neurological disorders, including autism and hyperekplexia. Understanding of molecular mechanisms and pharmacology of glycine receptors has been hindered by a lack of high-resolution structures. Here we report electron cryo-microscopy structures of the zebrafish α1 GlyR with strychnine, glycine, or glycine and ivermectin (glycine/ivermectin). Strychnine arrests the receptor in an antagonist-bound closed ion channel state, glycine stabilizes the receptor in an agonist-bound open channel state, and the glycine/ivermectin complex adopts a potentially desensitized or partially open state. Relative to the glycine-bound state, strychnine expands the agonist-binding pocket via outward movement of the C loop, promotes rearrangement of the extracellular and transmembrane domain 'wrist' interface, and leads to rotation of the transmembrane domain towards the pore axis, occluding the ion conduction pathway. These structures illuminate the GlyR mechanism and define a rubric to interpret structures of Cys-loop receptors.

Ddx19 links mRNA nuclear export with progression of transcription and replication and suppresses genomic instability upon DNA damage in proliferating cells.

PubMed

Hodroj, Dana; Serhal, Kamar; Maiorano, Domenico

2017-09-03

The DEAD-box Helicase 19 (Ddx19) gene codes for an RNA helicase involved in both mRNA (mRNA) export from the nucleus into the cytoplasm and in mRNA translation. In unperturbed cells, Ddx19 localizes in the cytoplasm and at the cytoplasmic face of the nuclear pore. Here we review recent findings related to an additional Ddx19 function in the nucleus in resolving RNA:DNA hybrids (R-loops) generated during collision between transcription and replication, and upon DNA damage. Activation of a DNA damage response pathway dependent upon the ATR kinase, a major regulator of replication fork progression, stimulates translocation of the Ddx19 protein from the cytoplasm into the nucleus. Only nuclear Ddx19 is competent to resolve R-loops, and down regulation of Ddx19 expression induces DNA double strand breaks only in proliferating cells. Overall these observations put forward Ddx19 as an important novel mediator of the crosstalk between transcription and replication.

A novel fast mass transfer anaerobic inner loop fluidized bed biofilm reactor for PTA wastewater treatment.

PubMed

Chen, Yingwen; Zhao, Jinlong; Li, Kai; Xie, Shitao

In this paper, a fast mass transfer anaerobic inner loop fluidized bed biofilm reactor (ILFBBR) was developed to improve purified terephthalic acid (PTA) wastewater treatment. The emphasis of this study was on the start-up mode of the anaerobic ILFBBR, the hydraulic loadings and the operation stability. The biological morphology of the anaerobic biofilm in the reactors was also analyzed. The anaerobic column could operate successfully for 46 days due to the pre-aerating process. The anaerobic column had the capacity to resist shock loadings and maintained a high stable chemical oxygen demand (COD) and terephthalic acid removal rates at a hydraulic retention time of 5-10 h, even under conditions of organic volumetric loadings as high as 28.8 kg COD·m(-3).d(-1). The scanning electron microscope analysis of the anaerobic carrier demonstrated that clusters of prokaryotes grew inside of pores and that the filaments generated by pre-aeration contributed to the anaerobic biofilm formation and stability.

Interdomain Hydrophobic Interactions Modulate the Thermostability of Microbial Esterases from the Hormone-Sensitive Lipase Family*

PubMed Central

Li, Ping-Yi; Chen, Xiu-Lan; Ji, Peng; Li, Chun-Yang; Wang, Peng; Zhang, Yi; Xie, Bin-Bin; Qin, Qi-Long; Su, Hai-Nan; Zhou, Bai-Cheng; Zhang, Yu-Zhong; Zhang, Xi-Ying

2015-01-01

Microbial hormone-sensitive lipases (HSLs) contain a CAP domain and a catalytic domain. However, it remains unclear how the CAP domain interacts with the catalytic domain to maintain the stability of microbial HSLs. Here, we isolated an HSL esterase, E40, from a marine sedimental metagenomic library. E40 exhibited the maximal activity at 45 °C and was quite thermolabile, with a half-life of only 2 min at 40 °C, which may be an adaptation of E40 to the permanently cold sediment environment. The structure of E40 was solved to study its thermolability. Structural analysis showed that E40 lacks the interdomain hydrophobic interactions between loop 1 of the CAP domain and α7 of the catalytic domain compared with its thermostable homologs. Mutational analysis showed that the introduction of hydrophobic residues Trp202 and Phe203 in α7 significantly improved E40 stability and that a further introduction of hydrophobic residues in loop 1 made E40 more thermostable because of the formation of interdomain hydrophobic interactions. Altogether, the results indicate that the absence of interdomain hydrophobic interactions between loop 1 and α7 leads to the thermolability of E40. In addition, a comparative analysis of the structures of E40 and other thermolabile and thermostable HSLs suggests that the interdomain hydrophobic interactions between loop 1 and α7 are a key element for the thermostability of microbial HSLs. Therefore, this study not only illustrates the structural element leading to the thermolability of E40 but also reveals a structural determinant for HSL thermostability. PMID:25771540

The pH sensor of the plant K+-uptake channel KAT1 is built from a sensory cloud rather than from single key amino acids.

PubMed

González, Wendy; Riedelsberger, Janin; Morales-Navarro, Samuel E; Caballero, Julio; Alzate-Morales, Jans H; González-Nilo, Fernando D; Dreyer, Ingo

2012-02-15

The uptake of potassium ions (K+) accompanied by an acidification of the apoplasm is a prerequisite for stomatal opening. The acidification (approximately 2-2.5 pH units) is perceived by voltage-gated inward potassium channels (K(in)) that then can open their pores with lower energy cost. The sensory units for extracellular pH in stomatal K(in) channels are proposed to be histidines exposed to the apoplasm. However, in the Arabidopsis thaliana stomatal K(in) channel KAT1, mutations in the unique histidine exposed to the solvent (His267) do not affect the pH dependency. We demonstrate in the present study that His267 of the KAT1 channel cannot sense pH changes since the neighbouring residue Phe266 shifts its pKa to undetectable values through a cation-π interaction. Instead, we show that Glu240 placed in the extracellular loop between transmembrane segments S5 and S6 is involved in the extracellular acid activation mechanism. Based on structural models we propose that this region may serve as a molecular link between the pH- and the voltage-sensor. Like Glu240, several other titratable residues could contribute to the pH-sensor of KAT1, interact with each other and even connect such residues far away from the voltage-sensor with the gating machinery of the channel.

Interactions between voltage sensor and pore domains in a hERG K+ channel model from molecular simulations and the effects of a voltage sensor mutation.

PubMed

Colenso, Charlotte K; Sessions, Richard B; Zhang, Yi H; Hancox, Jules C; Dempsey, Christopher E

2013-06-24

The hERG K(+) channel is important for establishing normal electrical activity in the human heart. The channel's unique gating response to membrane potential changes indicates specific interactions between voltage sensor and pore domains that are poorly understood. In the absence of a crystal structure we constructed a homology model of the full hERG membrane domain and performed 0.5 μs molecular dynamics (MD) simulations in a hydrated membrane. The simulations identify potential interactions involving residues at the extracellular surface of S1 in the voltage sensor and at the N-terminal end of the pore helix in the hERG model. In addition, a diffuse interface involving hydrophobic residues on S4 (voltage sensor) and pore domain S5 of an adjacent subunit was stable during 0.5 μs of simulation. To assess the ability of the model to give insight into the effects of channel mutation we simulated a hERG mutant that contains a Leu to Pro substitution in the voltage sensor S4 helical segment (hERG L532P). Consistent with the retention of gated K(+) conductance, the L532P mutation was accommodated in the S4 helix with little disruption of helical structure. The mutation reduced the extent of interaction across the S4-S5 interface, suggesting a structural basis for the greatly enhanced deactivation rate in hERG L532P. The study indicates that pairwise comparison of wild-type and mutated channel models is a useful approach to interpreting functional data where uncertainty in model structures exist.

Interaction of ordinary Portland cement and Opalinus Clay: Dual porosity modelling compared to experimental data

NASA Astrophysics Data System (ADS)

Jenni, A.; Gimmi, T.; Alt-Epping, P.; Mäder, U.; Cloet, V.

2017-06-01

Interactions between concrete and clays are driven by the strong chemical gradients in pore water and involve mineral reactions in both materials. In the context of a radioactive waste repository, these reactions may influence safety-relevant clay properties such as swelling pressure, permeability or radionuclide retention. Interfaces between ordinary Portland cement and Opalinus Clay show weaker, but more extensive chemical disturbance compared to a contact between low-pH cement and Opalinus Clay. As a consequence of chemical reactions porosity changes occur at cement-clay interfaces. These changes are stronger and may lead to complete pore clogging in the case of low-pH cements. The prediction of pore clogging by reactive transport simulations is very sensitive to the magnitude of diffusive solute fluxes, cement clinker chemistry, and phase reaction kinetics. For instance, the consideration of anion-depleted porosity in clays substantially influences overall diffusion and pore clogging at interfaces. A new concept of dual porosity modelling approximating Donnan equilibrium is developed and applied to an ordinary Portland cement - Opalinus Clay interface. The model predictions are compared with data from the cement-clay interaction (CI) field experiment in the Mt Terri underground rock laboratory (Switzerland), which represent 5 y of interaction. The main observations such as the decalcification of the cement at the interface, the Mg enrichment in the clay detached from the interface, and the S enrichment in the cement detached from the interface, are qualitatively predicted by the new model approach. The model results reveal multiple coupled processes that create the observed features. The quantitative agreement of modelled and measured data can be improved if uncertainties of key input parameters (tortuosities, reaction kinetics, especially of clay minerals) can be reduced.

Inactivation gating of Kv7.1 channels does not involve concerted cooperative subunit interactions.

PubMed

Meisel, Eshcar; Tobelaim, William; Dvir, Meidan; Haitin, Yoni; Peretz, Asher; Attali, Bernard

2018-01-01

Inactivation is an intrinsic property of numerous voltage-gated K + (Kv) channels and can occur by N-type or/and C-type mechanisms. N-type inactivation is a fast, voltage independent process, coupled to activation, with each inactivation particle of a tetrameric channel acting independently. In N-type inactivation, a single inactivation particle is necessary and sufficient to occlude the pore. C-type inactivation is a slower process, involving the outermost region of the pore and is mediated by a concerted, highly cooperative interaction between all four subunits. Inactivation of Kv7.1 channels does not exhibit the hallmarks of N- and C-type inactivation. Inactivation of WT Kv7.1 channels can be revealed by hooked tail currents that reflects the recovery from a fast and voltage-independent inactivation process. However, several Kv7.1 mutants such as the pore mutant L273F generate an additional voltage-dependent slow inactivation. The subunit interactions during this slow inactivation gating remain unexplored. The goal of the present study was to study the nature of subunit interactions along Kv7.1 inactivation gating, using concatenated tetrameric Kv7.1 channel and introducing sequentially into each of the four subunits the slow inactivating pore mutation L273F. Incorporating an incremental number of inactivating mutant subunits did not affect the inactivation kinetics but slowed down the recovery kinetics from inactivation. Results indicate that Kv7.1 inactivation gating is not compatible with a concerted cooperative process. Instead, adding an inactivating subunit L273F into the Kv7.1 tetramer incrementally stabilizes the inactivated state, which suggests that like for activation gating, Kv7.1 slow inactivation gating is not a concerted process.

Formation of prismatic loops from C15 Laves phase interstitial clusters in body-centered cubic iron

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yongfeng; Bai, Xian-Ming; Tonks, Michael R.

2015-03-01

This Letter reports the transition of C15 phase self-interstitial clusters to loops in body-centered-cubic Iron. Molecular dynamics simulations are performed to evaluate the relative stabilities of difference interstitial cluster configurations including C15 phase structure and <100> and <111>/2 loops. Within a certain size range, C15 cluster are found more stable than loops, and the relative stabilities are reversed beyond that range. In accordance to the crossover in relative stabilities, C15 clusters may grow by absorbing individual interstitials at small sizes and transitions into loops eventually. The transition takes place by nucleation and reaction of <111>/2 loop segments. These observations explainmore » the absence of C15 phase interstitial clusters predicted by density-functional-theory calculations in previous experimental observations. More importantly, the current results provide a new formation mechanism of <100> loops which requires no interaction of loops.« less

Propagation of a plasma streamer in catalyst pores

NASA Astrophysics Data System (ADS)

Zhang, Quan-Zhi; Bogaerts, Annemie

2018-03-01

Although plasma catalysis is gaining increasing interest for various environmental applications, the underlying mechanisms are still far from understood. For instance, it is not yet clear whether and how plasma streamers can propagate in catalyst pores, and what is the minimum pore size to make this happen. As this is crucial information to ensure good plasma-catalyst interaction, we study here the mechanism of plasma streamer propagation in a catalyst pore, by means of a two-dimensional particle-in-cell/Monte Carlo collision model, for various pore diameters in the nm-range to μm-range. The so-called Debye length is an important criterion for plasma penetration into catalyst pores, i.e. a plasma streamer can penetrate into pores when their diameter is larger than the Debye length. The Debye length is typically in the order of a few 100 nm up to 1 μm at the conditions under study, depending on electron density and temperature in the plasma streamer. For pores in the range of ∼50 nm, plasma can thus only penetrate to some extent and at very short times, i.e. at the beginning of a micro-discharge, before the actual plasma streamer reaches the catalyst surface and a sheath is formed in front of the surface. We can make plasma streamers penetrate into smaller pores (down to ca. 500 nm at the conditions under study) by increasing the applied voltage, which yields a higher plasma density, and thus reduces the Debye length. Our simulations also reveal that the plasma streamers induce surface charging of the catalyst pore sidewalls, causing discharge enhancement inside the pore, depending on pore diameter and depth.

Alteration of the mode of antibacterial action of a defensin by the amino-terminal loop substitution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Bin; Zhu, Shunyi, E-mail: Zhusy@ioz.ac.cn

Highlights: Black-Right-Pointing-Pointer Al-M is an engineered fungal defensin with the n-loop of an insect defensin. Black-Right-Pointing-Pointer Al-M adopts a native defensin-like structure with high antibacterial potency. Black-Right-Pointing-Pointer Al-M kills bacteria through a membrane disruptive mechanism. Black-Right-Pointing-Pointer This work sheds light on the functional evolution of CS{alpha}{beta}-type defensins. -- Abstract: Ancient invertebrate-type and classical insect-type defensins (AITDs and CITDs) are two groups of evolutionarily related antimicrobial peptides (AMPs) that adopt a conserved cysteine-stabilized {alpha}-helical and {beta}-sheet (CS{alpha}{beta}) fold with a different amino-terminal loop (n-loop) size and diverse modes of antibacterial action. Although they both are identified as inhibitors of cell wallmore » biosynthesis, only CITDs evolved membrane disruptive ability by peptide oligomerization to form pores. To understand how this occurred, we modified micasin, a fungus-derived AITDs with a non-membrane disruptive mechanism, by substituting its n-loop with that of an insect-derived CITDs. After air oxidization, the synthetic hybrid defensin (termed Al-M) was structurally identified by circular dichroism (CD) and functionally evaluated by antibacterial and membrane permeability assays and electronic microscopic observation. Results showed that Al-M folded into a native-like defensin structure, as determined by its CD spectrum that is similar to that of micasin. Al-M was highly efficacious against the Gram-positive bacterium Bacillus megaterium with a lethal concentration of 1.76 {mu}M. As expected, in contrast to micasin, Al-M killed the bacteria through a membrane disruptive mechanism of action. The alteration in modes of action supports a key role of the n-loop extension in assembling functional surface of CITDs for membrane disruption. Our work provides mechanical evidence for evolutionary relationship between AITDs and CITDs.« less

CASPASE-9 CARD:CORE DOMAIN INTERACTIONS REQUIRE A PROPERLY-FORMED ACTIVE SITE

PubMed Central

Huber, Kristen L.; Serrano, Banyuhay P.; Hardy, Jeanne A.

2018-01-01

Caspase-9 is a critical factor in the initiation of apoptosis, and as a result is tightly regulated by a number of mechanisms. Caspase-9 contains a Caspase Activation and Recruitment Domain (CARD), which enables caspase-9 to form a tight interaction with the apoptosome, a heptameric activating platform. The caspase-9 CARD has been thought to be principally involved in recruitment to the apoptosome, but its roles outside this interaction have yet to be uncovered. In this work we show that the CARD is involved in physical interactions with the catalytic core of caspase-9 in the absence of the apoptosome; this interaction requires a properly formed caspase-9 active site. The active sites of caspases are composed of four extremely mobile loops. When the active-site loops are not properly ordered, the CARD and core domains of caspase-9 do not interact and behave independently, like loosely tethered beads. When the active-site loop bundle is properly ordered, the CARD domain interacts with the catalytic core, forming a single folding unit. Together these findings provide mechanistic insight into a new level of caspase-9 regulation, prompting speculation that the CARD may also play a role in the recruitment or recognition of substrate. PMID:29500231

PHO-ERK1/2 interaction with mitochondria regulates the permeability transition pore in cardioprotective signaling.

PubMed

Hernández-Reséndiz, Sauri; Zazueta, Cecilia

2014-07-11

The molecular mechanism(s) by which extracellular signal-regulated kinase 1/2 (ERK1/2) and other kinases communicate with downstream targets have not been fully determined. Multiprotein signaling complexes undergoing spatiotemporal redistribution may enhance their interaction with effector proteins promoting cardioprotective response. Particularly, it has been proposed that some active kinases in association with caveolae may converge into mitochondria. Therefore, in this study we investigate if PHO-ERK1/2 interaction with mitochondria may provide a mechanistic link in the regulation of these organelles in cardioprotective signaling. Using a model of dilated cardiomyopathy followed by ischemia-reperfusion injury, we determined ERK1/2 signaling at the level of mitochondria and evaluated its effect on the permeability transition pore. The most important finding of the present study is that, under cardioprotective conditions, a subpopulation of activated ERK1/2 was directed to the mitochondrial membranes through vesicular trafficking, concurring with increased phosphorylation of mitochondrial proteins and inhibition of the mitochondrial permeability transition pore opening. In addition, our results suggest that vesicles enriched with caveolin-3 could form structures that may drive ERK1/2, GSK3β and Akt to mitochondria. Signaling complexes including PHO-ERK, PHO-Akt, PHO-eNOS and caveolin-3 contribute to cardioprotection by directly targeting the mitochondrial proteome and regulating the opening of the permeability transition pore in this model. Copyright © 2013 Elsevier Inc. All rights reserved.

Modeling the relaxation dynamics of fluids in nanoporous materials

NASA Astrophysics Data System (ADS)

Edison, John R.

Mesoporous materials are being widely used in the chemical industry in various environmentally friendly separation processes and as catalysts. Our research can be broadly described as an effort to understand the behavior of fluids confined in such materials. More specifically we try to understand the influence of state variables like temperature and pore variables like size, shape, connectivity and structural heterogeneity on both the dynamic and equilibrium behavior of confined fluids. The dynamic processes associated with the approach to equilibrium are largely unexplored. It is important to look into the dynamic behavior for two reasons. First, confined fluids experience enhanced metastabilities and large equilibration times in certain classes of mesoporous materials, and the approach to the metastable/stable equilibrium is of tremendous interest. Secondly, understanding the transport resistances in a microscopic scale will help better engineer heterogeneous catalysts and separation processes. Here we present some of our preliminary studies on dynamics of fluids in ideal pore geometries. The tool that we have used extensively to investigate the relaxation dynamics of fluids in pores is the dynamic mean field theory (DMFT) as developed by Monson [P. A. Monson, J. Chem. Phys., 128, 084701 (2008)]. The theory is based on a lattice gas model of the system and can be viewed as a highly computationally efficient approximation to the dynamics averaged over an ensemble of Kawasaki dynamics Monte Carlo trajectories of the system. It provides a theory of the dynamics of the system consistent with the thermodynamics in mean field theory. The nucleation mechanisms associated with confined fluid phase transitions are emergent features in the calculations. We begin by describing the details of the theory and then present several applications of DMFT. First we present applications to three model pore networks (a) a network of slit pores with a single pore width; (b) a network of slit pores with two pore widths arranged in intersecting channels with a single pore width in each channel; (c) a network of slit pores with two pore widths forming an array of ink-bottles. The results illustrate the effects of pore connectivity upon the dynamics of vapor liquid phase transformations as well as on the mass transfer resistances to equilibration. We then present an application to a case where the solid-fluid interactions lead to partial wetting on a planar surface. The pore filling process in such systems features an asymmetric density distribution where a liquid droplet appears on one of the walls. We also present studies on systems where there is partial drying or drying associated with weakly attractive or repulsive interactions between the fluid and the pore walls. We describe the symmetries exhibited by the lattice model between pore filling for wetting states and pore emptying for drying states, for both the thermodynamics and dynamics. We then present an extension of DMFT to mixtures and present some examples that illustrate the utility of the approach. Finally we present an assessment the accuracy of the DMFT through comparisons with a higher order approximation based on the path probability method as well as Kawasaki dynamics.

A novel actin binding site of myosin required for effective muscle contraction.

PubMed

Várkuti, Boglárka H; Yang, Zhenhui; Kintses, Bálint; Erdélyi, Péter; Bárdos-Nagy, Irén; Kovács, Attila L; Hári, Péter; Kellermayer, Miklós; Vellai, Tibor; Málnási-Csizmadia, András

2012-02-12

F-actin serves as a track for myosin's motor functions and activates its ATPase activity by several orders of magnitude, enabling actomyosin to produce effective force against load. Although actin activation is a ubiquitous property of all myosin isoforms, the molecular mechanism and physiological role of this activation are unclear. Here we describe a conserved actin-binding region of myosin named the 'activation loop', which interacts with the N-terminal segment of actin. We demonstrate by biochemical, biophysical and in vivo approaches using transgenic Caenorhabditis elegans strains that the interaction between the activation loop and actin accelerates the movement of the relay, stimulating myosin's ATPase activity. This interaction results in efficient force generation, but it is not essential for the unloaded motility. We conclude that the binding of actin to myosin's activation loop specifically increases the ratio of mechanically productive to futile myosin heads, leading to efficient muscle contraction.

Preparation and magnetic properties of cylindrical NiFe films and antidot arrays.

PubMed

Sanz, R; Navas, D; Vazquez, M; Hernández-Vélez, M; Ross, C A

2010-10-01

Continuous NiFe (Permalloy) cylindrical films and arrays of cylindrical NiFe antidots 7 nm thick have been prepared by sputtering onto cylindrical aluminum wires and onto wires anodized to form a porous anodic alumina layer. The antidots are arranged in a close-packed pattern determined by the hexagonal pore arrangement in the porous alumina, with period 103 nm and diameter 42 nm. Hysteresis loops were measured at different angles with respect to the cylinder axis and indicate an easy plane normal to the radius of the wire. The antidots enhance the coercivity compared to the continuous cylindrical film.

Complexities of high temperature metal fatigue: Some steps toward understanding

NASA Technical Reports Server (NTRS)

Manson, S. S.; Halford, G. R.

1983-01-01

After pointing out many of the complexities that attend high temperature metal fatigue beyond those already studied in the sub-creep range, a description of the micromechanisms of deformation and fracture is presented for several classes of materials that were studied over the past dozen years. Strainrange Partitioning (SRP) is used as a framework for interpreting the results. Several generic types of behavior were observed with regard both to deformation and fracture and each is discussed in the context of the micromechanisms involved. Treatment of cumulative fatigue damage and the possibility of ""healing'' of damage in successive loading loops, has led to a new interpretation of the Interaction Damage Rule of SRP. Using the concept of ""equivalent micromechanistic damage'' -- that the same damage on a microscopic scale is induced if the same hysteresis loops are generated, element for element -- it turns out the Interaction Damage Rule essentially compounds a number of variants of hysteresis loops, all of which have the same damage according to SRP concepts, into a set of loops each containing only one of the generic SRP strainranges. Thus the damage associcated with complex loops comprising several types of strainrange is analyzed by considering a combination of loops each containing only one type of strainrange. This concept is expanded to show how several independent loops can combine to ""heal'' creep damage in a complex loading history.

Proline Restricts Loop I Conformation of the High Affinity WW Domain from Human Nedd4-1 to a Ligand Binding-Competent Type I β-Turn.

PubMed

Schulte, Marianne; Panwalkar, Vineet; Freischem, Stefan; Willbold, Dieter; Dingley, Andrew J

2018-04-19

Sequence alignment of the four WW domains from human Nedd4-1 (neuronal precursor cell expressed developmentally down-regulated gene 4-1) reveals that the highest sequence diversity exists in loop I. Three residues in this type I β-turn interact with the PPxY motif of the human epithelial Na + channel (hENaC) subunits, indicating that peptide affinity is defined by the loop I sequence. The third WW domain (WW3*) has the highest ligand affinity and unlike the other three hNedd4-1 WW domains or other WW domains studied contains the highly statistically preferred proline at the ( i + 1) position found in β-turns. In this report, molecular dynamics simulations and experimental data were combined to characterize loop I stability and dynamics. Exchange of the proline to the equivalent residue in WW4 (Thr) results in the presence of a predominantly open seven residue Ω loop rather than the type I β-turn conformation for the wild-type apo-WW3*. In the presence of the ligand, the structure of the mutated loop I is locked into a type I β-turn. Thus, proline in loop I ensures a stable peptide binding-competent β-turn conformation, indicating that amino acid sequence modulates local flexibility to tune binding preferences and stability of dynamic interaction motifs.

Role of the DELSEED Loop in Torque Transmission of F1-ATPase

PubMed Central

Tanigawara, Mizue; Tabata, Kazuhito V.; Ito, Yuko; Ito, Jotaro; Watanabe, Rikiya; Ueno, Hiroshi; Ikeguchi, Mitsunori; Noji, Hiroyuki

2012-01-01

F1-ATPase is an ATP-driven rotary motor that generates torque at the interface between the catalytic β-subunits and the rotor γ-subunit. The β-subunit inwardly rotates the C-terminal domain upon nucleotide binding/dissociation; hence, the region of the C-terminal domain that is in direct contact with γ—termed the DELSEED loop—is thought to play a critical role in torque transmission. We substituted all the DELSEED loop residues with alanine to diminish specific DELSEED loop-γ interactions and with glycine to disrupt the loop structure. All the mutants rotated unidirectionally with kinetic parameters comparable to those of the wild-type F1, suggesting that the specific interactions between DELSEED loop and γ is not involved in cooperative interplays between the catalytic β-subunits. Glycine substitution mutants generated half the torque of the wild-type F1, whereas the alanine mutant generated comparable torque. Fluctuation analyses of the glycine/alanine mutants revealed that the γ-subunit was less tightly held in the α3β3-stator ring of the glycine mutant than in the wild-type F1 and the alanine mutant. Molecular dynamics simulation showed that the DELSEED loop was disordered by the glycine substitution, whereas it formed an α-helix in the alanine mutant. Our results emphasize the importance of loop rigidity for efficient torque transmissions. PMID:23009846

Investigation of Congenital Myasthenia Reveals Functional Asymmetry of Invariant Acetylcholine Receptor (AChR) Cys-loop Aspartates.

PubMed

Shen, Xin-Ming; Brengman, Joan; Neubauer, David; Sine, Steven M; Engel, Andrew G

2016-02-12

We identify two heteroallelic mutations in the acetylcholine receptor δ-subunit from a patient with severe myasthenic symptoms since birth: a novel δD140N mutation in the signature Cys-loop and a mutation in intron 7 of the δ-subunit gene that disrupts splicing of exon 8. The mutated Asp residue, which determines the disease phenotype, is conserved in all eukaryotic members of the Cys-loop receptor superfamily. Studies of the mutant acetylcholine receptor expressed in HEK 293 cells reveal that δD140N attenuates cell surface expression and apparent channel gating, predicting a reduced magnitude and an accelerated decay of the synaptic response, thus reducing the safety margin for neuromuscular transmission. Substituting Asn for Asp at equivalent positions in the α-, β-, and ϵ-subunits also suppresses apparent channel gating, but the suppression is much greater in the α-subunit. Mutant cycle analysis applied to single and pairwise mutations reveals that αAsp-138 is energetically coupled to αArg-209 in the neighboring pre-M1 domain. Our findings suggest that the conserved αAsp-138 and αArg-209 contribute to a principal pathway that functionally links the ligand binding and pore domains. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Structure and Function of Thermostable Direct Hemolysin (TDH) from Vibrio Parahaemolyticus

NASA Astrophysics Data System (ADS)

Hashimoto, Hiroshi; Yamane, Tsutomu; Ikeguchi, Mitsunori; Nakahira, Kumiko; Yanagihara, Itaru

Thermostable direct hemolysin (TDH) is a major virulence factor of Vibrio parahaemolyticus that causes pandemic food-borne enterocolitis mediated by seafood. TDH exists as a tetramer in solution, and it possesses extreme hemolytic activity. Here, we present the crystal structure of the TDH tetramer at 1.5 Å resolution. The TDH tetramer forms a central pore with dimensions of 23 Å in diameter and ∼50 Å in depth. π-cation interactions between protomers comprising the tetramer were indispensable for hemolytic activity of TDH. The N-terminal region was intrinsically disordered outside the pore. Molecular dynamics (MD) simulations suggested that water molecules permeate freely through the central and side channel pores. These findings imply a novel membrane attachment mechanism by a soluble tetrameric pore-forming toxin.

Kv7.1 ion channels require a lipid to couple voltage sensing to pore opening.

PubMed

Zaydman, Mark A; Silva, Jonathan R; Delaloye, Kelli; Li, Yang; Liang, Hongwu; Larsson, H Peter; Shi, Jingyi; Cui, Jianmin

2013-08-06

Voltage-gated ion channels generate dynamic ionic currents that are vital to the physiological functions of many tissues. These proteins contain separate voltage-sensing domains, which detect changes in transmembrane voltage, and pore domains, which conduct ions. Coupling of voltage sensing and pore opening is critical to the channel function and has been modeled as a protein-protein interaction between the two domains. Here, we show that coupling in Kv7.1 channels requires the lipid phosphatidylinositol 4,5-bisphosphate (PIP2). We found that voltage-sensing domain activation failed to open the pore in the absence of PIP2. This result is due to loss of coupling because PIP2 was also required for pore opening to affect voltage-sensing domain activation. We identified a critical site for PIP2-dependent coupling at the interface between the voltage-sensing domain and the pore domain. This site is actually a conserved lipid-binding site among different K(+) channels, suggesting that lipids play an important role in coupling in many ion channels.

An alternative for presenting interactive dynamic data sets in electronic presentations: a scrollable flash movie loop.

PubMed

Yam, Chun-Shan

2007-11-01

The purpose of this article is to describe an alternative for creating scrollable movie loops for electronic presentations including PowerPoint. The alternative provided in this article enables academic radiologists to present scrollable movie loops in PowerPoint. The scrolling capability is created using Flash ActionScript. A Flash template with the required ActionScript code is provided. Users can simply download the template and follow the step-by-step demonstration to create scrollable movie loops. No previous ActionScript programming knowledge is necessary.

The elusive role of the SPRY2 domain in RyR1

PubMed Central

Willemse, Hermia; Mirza, Shamaruh; Gallant, Esther M; Board, Philip G

2011-01-01

The second of three SPRY domains (SPRY2, S1085-V1208) located in the skeletal muscle ryanodine receptor (RyR1) is contained within regions of RyR1 that influence EC coupling and bind to imperatoxin A, a toxin probe of RyR1 channel gating. We examined the binding of the F loop (P1107-A1121) in SPRY2 to the ASI/basic region in RyR1 (T3471-G3500, containing both alternatively spliced (ASI) residues and neighboring basic amino acids). We then investigated the possible influence of this interaction on excitation contraction (EC) coupling. A peptide with the F loop sequence and an antibody to the SPRY2 domain each enhanced RyR1 activity at low concentrations and inhibited at higher concentrations. A peptide containing the ASI/basic sequence bound to SPRY2 and binding decreased ∼10-fold following mutation or structural disruption of the basic residues. Binding was abolished by mutation of three critical acidic F loop residues. Together these results suggest that the ASI/basic and SPRY2 domains interact in an F loop regulatory module. Although a region that includes the SPRY2 domain influences EC coupling, as does the ASI/basic region, Ca2+ release during ligand- and depolarization-induced RyR1 activation were not altered by mutation of the three critical F loop residues following expression of mutant RyR1 in RyR1-null myotubes. Therefore the electrostatic regulatory interaction between the SPRY2 F loop residues (that bind to imperatoxin A) and the ASI/basic residues of RyR1 does not influence bi-directional DHPR-RyR1 signaling during skeletal EC coupling, possibly because the interaction is interrupted by the influence of factors present in intact muscle cells. PMID:21239886

Concerted Motions Networking Pores and Distant Ferroxidase Centers Enable Bacterioferritin Function and Iron Traffic£ξ

PubMed Central

Yao, Huili; Rui, Huan; Kumar, Ritesh; Eshelman, Kate; Lovell, Scott; Battaile, Kevin P.; Im, Wonpil; Rivera, Mario

2015-01-01

X-ray crystallography, molecular dynamics (MD) simulations and biochemistry were utilized to investigate the effect of introducing hydrophobic interactions in the 4-fold (N148L and Q151L) and B-pores (D34F) of Pseudomonas aeruginosa bacterioferritin B (BfrB) on BfrB function. The structures show only local structural perturbations and confirm the anticipated hydrophobic interactions. Surprisingly, structures obtained after soaking crystals in Fe2+-containing crystallization solution revealed that although iron loads into the ferroxidase centers of the mutants, the side chains of ferroxidase ligands E51 and H130 do not reorganize to bind the iron ions, as is seen in the wt BfrB structures. Similar experiments with a double mutant (C89S/K96C) prepared to introduce changes outside the pores show competent ferroxidase centers that function akin to those in wt BfrB. MD simulations comparing wt BfrB with the D34F and N148L mutants show that the mutants exhibit significantly reduced flexibility, and reveal a network of concerted motions linking ferroxidase centers and 4-fold and B-pores, which are important for imparting ferroxidase centers in BfrB with the required flexibility to function efficiently. In agreement, the efficiency of Fe2+ oxidation and uptake of the 4-fold and B-pore mutants in solution is significantly compromised relative to wt or C89S/K96C BfrB. Finally, our structures show a large number of previously unknown iron binding sites in the interior cavity and B-pores of BfrB, which reveal in unprecedented detail conduits followed by iron and phosphate ions across the BfrB shell, as well as paths in the interior cavity that may facilitate nucleation of the iron phosphate mineral. PMID:25640193

EUV Waves Driven by the Sudden Expansion of Transequatorial Loops Caused by Coronal Jets

NASA Astrophysics Data System (ADS)

Shen, Yuandeng; Tang, Zehao; Miao, Yuhu; Su, Jiangtao; Liu, Yu

2018-06-01

We present two events to study the driving mechanism of extreme-ultraviolet (EUV) waves that are not associated with coronal mass ejections (CMEs), by using high-resolution observations taken by the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory. Observational results indicate that the observed EUV waves were accompanied by flares and coronal jets, but not the CMEs that were regarded as drivers of most EUV waves in previous studies. In the first case, it is observed that a coronal jet is ejected along a transequatorial loop system at a plane-of-the-sky (POS) speed of 335 ± 22 km s{}-1; in the meantime, an arc-shaped EUV wave appeared on the eastern side of the loop system. In addition, the EUV wave further interacted with another interconnecting loop system and launched a fast propagating (QFP) magnetosonic wave along the loop system, which had a period of 200 s and a speed of 388 ± 65 km s{}-1, respectively. In the second case, we observed a coronal jet that ejected at a POS speed of 282 ± 44 km s{}-1 along a transequatorial loop system as well as the generation of bright EUV waves on the eastern side of the loop system. Based on the observational results, we propose that the observed EUV waves on the eastern side of the transequatorial loop systems are fast-mode magnetosonic waves and that they are driven by the sudden lateral expansion of the transequatorial loop systems due to the direct impingement of the associated coronal jets, while the QFP wave in the fist case formed due to the dispersive evolution of the disturbance caused by the interaction between the EUV wave and the interconnecting coronal loops. It is noted that EUV waves driven by sudden loop expansions have shorter lifetimes than those driven by CMEs.

Interactive Textiles Front End Analysis. Phase 1

DTIC Science & Technology

1998-11-01

demonstrated. Active ultrasound and radar were investigated as means to detect the track of projectiles and acoustic signatures were obtained using...technique was used to incorporate pore-forming proteins into various lipid and protein matrices. At a constant pressure the pore-forming protein when added...report. Polymer Gel Sensors and Devices controlled by Infrared Light and Ultrasound Principle Investigator: Z. Hu North Texas State University

Comparison of Effective Medium Schemes For Seismic Velocities in Cracked Anisotropic Rock

NASA Astrophysics Data System (ADS)

Morshed, S.; Chesnokov, E.

2017-12-01

Understanding of elastic properties of reservoir rock is necessary for meaningful interpretation and analysis of seismic measurements. The elastic properties of a rock are controlled by the microstructural properties such as mineralogical composition, pore and crack distribution, texture and pore connectivity. However, seismic scale is much larger than microstructure scale. Understanding of macroscopic properties at relevant seismic scale (e.g. borehole sonic data) comes from effective medium theory (EMT). However, most of the effective medium theories fail at high crack density as the interactions of strain fields of the cracks can't be ignored. We compare major EMT schemes from low to high crack density. While at low crack density all method gives similar results, at high crack density they differ significantly. Then, we focus on generalized singular approximation (GSA) and effective field (EF) method as they allow cracks beyond the limit of dilute concentrations. Additionally, we use grain contact (GC) method to examine the stiffness constants of the rock matrix. We prepare simple models of a multiphase media containing low to high concentrations of isolated pores. Randomly oriented spherical pores and horizontally oriented ellipsoidal (aspect ratio =0.1) pores have been considered. For isolated spherical pores, all the three methods show exactly same or similar results. However, inclusion interactions are different in different directions in case of horizontal ellipsoidal pores and individual stiffness constants differ greatly from one method to another at different crack density. Stiffness constants remain consistent in GSA method whereas some components become unusual in EF method at a higher crack density (>0.15). Finally, we applied GSA method to interpret ultrasonic velocities of core samples. Mineralogical composition from X-ray diffraction (XRD) data and lab measured porosity data have been utilized. Both compressional and shear wave velocities from GSA method show good fit with the lab measured velocities.

Challenging AQP4 druggability for NMO-IgG antibody binding using molecular dynamics and molecular interaction fields.

PubMed

Mangiatordi, Giuseppe Felice; Alberga, Domenico; Siragusa, Lydia; Goracci, Laura; Lattanzi, Gianluca; Nicolotti, Orazio

2015-07-01

Neuromyelitis optica (NMO) is a multiple sclerosis-like immunopathology disease affecting optic nerves and the spinal cord. Its pathological hallmark is the deposition of a typical immunoglobulin, called NMO-IgG, against the water channel Aquaporin-4 (AQP4). Preventing NMO-IgG binding would represent a valuable molecular strategy for a focused NMO therapy. The recent observation that aspartate in position 69 (D69) is determinant for the formation of NMO-IgG epitopes prompted us to carry out intensive Molecular Dynamics (MD) studies on a number of single-point AQP4 mutants. Here, we report a domino effect originating from the point mutation at position 69: we find that the side chain of T62 is reoriented far from its expected position leaning on the lumen of the pore. More importantly, the strength of the H-bond interaction between L53 and T56, at the basis of the loop A, is substantially weakened. These events represent important pieces of a clear-cut mechanistic rationale behind the failure of the NMO-IgG binding, while the water channel function as well as the propensity to aggregate into OAPs remains unaltered. The molecular interaction fields (MIF)-based analysis of cavities complemented MD findings indicating a putative binding site comprising the same residues determining epitope reorganization. In this respect, docking studies unveiled an intriguing perspective to address the future design of small drug-like compounds against NMO. In agreement with recent experimental observations, the present study is the first computational attempt to elucidate NMO-IgG binding at the molecular level, as well as a first effort toward a less elusive AQP4 druggability. Copyright © 2015 Elsevier B.V. All rights reserved.

Claudin Loss-of-Function Disrupts Tight Junctions and Impairs Amelogenesis

PubMed Central

Bardet, Claire; Ribes, Sandy; Wu, Yong; Diallo, Mamadou Tidiane; Salmon, Benjamin; Breiderhoff, Tilman; Houillier, Pascal; Müller, Dominik; Chaussain, Catherine

2017-01-01

Claudins are a family of proteins that forms paracellular barriers and pores determining tight junctions (TJ) permeability. Claudin-16 and -19 are pore forming TJ proteins allowing calcium and magnesium reabsorption in the thick ascending limb of Henle's loop (TAL). Loss-of-function mutations in the encoding genes, initially identified to cause Familial Hypomagnesemia with Hypercalciuria and Nephrocalcinosis (FHHNC), were recently shown to be also involved in Amelogenesis Imperfecta (AI). In addition, both claudins were expressed in the murine tooth germ and Claudin-16 knockout (KO) mice displayed abnormal enamel formation. Claudin-3, an ubiquitous claudin expressed in epithelia including kidney, acts as a barrier-forming tight junction protein. We determined that, similarly to claudin-16 and claudin-19, claudin-3 was expressed in the tooth germ, more precisely in the TJ located at the apical end of secretory ameloblasts. The observation of Claudin-3 KO teeth revealed enamel defects associated to impaired TJ structure at the secretory ends of ameloblasts and accumulation of matrix proteins in the forming enamel. Thus, claudin-3 protein loss-of-function disturbs amelogenesis similarly to claudin-16 loss-of-function, highlighting the importance of claudin proteins for the TJ structure. These findings unravel that loss-of-function of either pore or barrier-forming TJ proteins leads to enamel defects. Hence, the major structural function of claudin proteins appears essential for amelogenesis. PMID:28596736

Thermal-hydraulic performance of metal foam heat exchangers under dry operating conditions

DOE PAGES

Nawaz, Kashif; Bock, Jessica; Jacobi, Anthony M.

2017-03-14

High porosity metal foams with novel thermal, mechanical, electrical, and acoustic properties are being more widely adopted for application. Due to their large surface-area-to-volume ratio and complex structure which induces better fluid mixing, boundary layer restarting and wake destruction, they hold promise for heat transfer applications. In this study, the thermal-hydraulic performance of open-cell aluminum metal foam heat exchanger has been evaluated. The impact of flow conditions and metal foam geometry on the heat transfer coefficient and gradient have been investigated. Metal foam heat exchanger with same geometry (face area, flow depth and fin dimensions) consisting of four different typemore » of metal foams have been built for the study. Experiments are conducted in a closed-loop wind tunnel at different flow rate under dry operating condition. Metal foams with a smaller pore size (40 PPI) have a larger heat transfer coefficient compared to foams with a larger pore size (5 PPI). However, foams with larger pores result in relatively smaller pressure gradients. Current thermal-hydraulic modeling practices have been reviewed and potential issues have been identified. Permeability and inertia coefficients are determined and compared to data reported in open literature. Finally, on the basis of the new experimental results, correlations are developed relating the foam characteristics and flow conditions through the friction factor f and the Colburn j factor.« less

Claudin Loss-of-Function Disrupts Tight Junctions and Impairs Amelogenesis.

PubMed

Bardet, Claire; Ribes, Sandy; Wu, Yong; Diallo, Mamadou Tidiane; Salmon, Benjamin; Breiderhoff, Tilman; Houillier, Pascal; Müller, Dominik; Chaussain, Catherine

2017-01-01

Claudins are a family of proteins that forms paracellular barriers and pores determining tight junctions (TJ) permeability. Claudin-16 and -19 are pore forming TJ proteins allowing calcium and magnesium reabsorption in the thick ascending limb of Henle's loop (TAL). Loss-of-function mutations in the encoding genes, initially identified to cause Familial Hypomagnesemia with Hypercalciuria and Nephrocalcinosis (FHHNC), were recently shown to be also involved in Amelogenesis Imperfecta (AI). In addition, both claudins were expressed in the murine tooth germ and Claudin-16 knockout (KO) mice displayed abnormal enamel formation. Claudin-3, an ubiquitous claudin expressed in epithelia including kidney, acts as a barrier-forming tight junction protein. We determined that, similarly to claudin-16 and claudin-19, claudin-3 was expressed in the tooth germ, more precisely in the TJ located at the apical end of secretory ameloblasts. The observation of Claudin-3 KO teeth revealed enamel defects associated to impaired TJ structure at the secretory ends of ameloblasts and accumulation of matrix proteins in the forming enamel. Thus, claudin-3 protein loss-of-function disturbs amelogenesis similarly to claudin-16 loss-of-function, highlighting the importance of claudin proteins for the TJ structure. These findings unravel that loss-of-function of either pore or barrier-forming TJ proteins leads to enamel defects. Hence, the major structural function of claudin proteins appears essential for amelogenesis.

Thermal-hydraulic performance of metal foam heat exchangers under dry operating conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nawaz, Kashif; Bock, Jessica; Jacobi, Anthony M.

High porosity metal foams with novel thermal, mechanical, electrical, and acoustic properties are being more widely adopted for application. Due to their large surface-area-to-volume ratio and complex structure which induces better fluid mixing, boundary layer restarting and wake destruction, they hold promise for heat transfer applications. In this study, the thermal-hydraulic performance of open-cell aluminum metal foam heat exchanger has been evaluated. The impact of flow conditions and metal foam geometry on the heat transfer coefficient and gradient have been investigated. Metal foam heat exchanger with same geometry (face area, flow depth and fin dimensions) consisting of four different typemore » of metal foams have been built for the study. Experiments are conducted in a closed-loop wind tunnel at different flow rate under dry operating condition. Metal foams with a smaller pore size (40 PPI) have a larger heat transfer coefficient compared to foams with a larger pore size (5 PPI). However, foams with larger pores result in relatively smaller pressure gradients. Current thermal-hydraulic modeling practices have been reviewed and potential issues have been identified. Permeability and inertia coefficients are determined and compared to data reported in open literature. Finally, on the basis of the new experimental results, correlations are developed relating the foam characteristics and flow conditions through the friction factor f and the Colburn j factor.« less

Molecular and functional characterization of Anopheles gambiae inward rectifier potassium (Kir1) channels: a novel role in egg production.

PubMed

Raphemot, Rene; Estévez-Lao, Tania Y; Rouhier, Matthew F; Piermarini, Peter M; Denton, Jerod S; Hillyer, Julián F

2014-08-01

Inward rectifier potassium (Kir) channels play essential roles in regulating diverse physiological processes. Although Kir channels are encoded in mosquito genomes, their functions remain largely unknown. In this study, we identified the members of the Anopheles gambiae Kir gene family and began to investigate their function. Notably, we sequenced the A. gambiae Kir1 (AgKir1) gene and showed that it encodes all the canonical features of a Kir channel: an ion pore that is composed of a pore helix and a selectivity filter, two transmembrane domains that flank the ion pore, and the so-called G-loop. Heterologous expression of AgKir1 in Xenopus oocytes revealed that this gene encodes a functional, barium-sensitive Kir channel. Quantitative RT-PCR experiments then showed that relative AgKir1 mRNA levels are highest in the pupal stage, and that AgKir1 mRNA is enriched in the adult ovaries. Gene silencing of AgKir1 by RNA interference did not affect the survival of female mosquitoes following a blood meal, but decreased their egg output. These data provide evidence for a new role of Kir channels in mosquito fecundity, and further validates them as promising molecular targets for the development of a new class of mosquitocides to be used in vector control. Copyright © 2014 Elsevier Ltd. All rights reserved.

An Integrated Loop Model of Corrective Feedback and Oral English Learning: A Case of International Students in the United States

ERIC Educational Resources Information Center

Lee, Eun Jeong

2017-01-01

The author in this study introduces an integrated corrective feedback (CF) loop to schematize the interplay between CF and independent practice in L2 oral English learning among advanced-level adult ESL students. The CF loop integrates insights from the Interaction, Output, and Noticing Hypotheses to show how CF can help or harm L2 learners'…

Autopilot, Mind Wandering, and the Out of the Loop Performance Problem.

PubMed

Gouraud, Jonas; Delorme, Arnaud; Berberian, Bruno

2017-01-01

To satisfy the increasing demand for safer critical systems, engineers have integrated higher levels of automation, such as glass cockpits in aircraft, power plants, and driverless cars. These guiding principles relegate the operator to a monitoring role, increasing risks for humans to lack system understanding. The out of the loop performance problem arises when operators suffer from complacency and vigilance decrement; consequently, when automation does not behave as expected, understanding the system or taking back manual control may be difficult. Close to the out of the loop problem, mind wandering points to the propensity of the human mind to think about matters unrelated to the task at hand. This article reviews the literature related to both mind wandering and the out of the loop performance problem as it relates to task automation. We highlight studies showing how these phenomena interact with each other while impacting human performance within highly automated systems. We analyze how this proximity is supported by effects observed in automated environment, such as decoupling, sensory attention, and cognitive comprehension decrease. We also show that this link could be useful for detecting out of the loop situations through mind wandering markers. Finally, we examine the limitations of the current knowledge because many questions remain open to characterize interactions between out of the loop, mind wandering, and automation.

Protein nanopore-based, single-molecule exploration of copper binding to an antimicrobial-derived, histidine-containing chimera peptide.

PubMed

Mereuta, Loredana; Schiopu, Irina; Asandei, Alina; Park, Yoonkyung; Hahm, Kyung-Soo; Luchian, Tudor

2012-12-11

Metal ions binding exert a crucial influence upon the aggregation properties and stability of peptides, and the propensity of folding in various substates. Herein, we demonstrate the use of the α-HL protein as a powerful nanoscopic tool to probe Cu(2+)-triggered physicochemical changes of a 20 aminoacids long, antimicrobial-derived chimera peptide with a His residue as metal-binding site, and simultaneously dissect the kinetics of the free- and Cu(2+)-bound peptide interaction to the α-HL pore. Combining single-molecule electrophysiology on reconstituted lipid membranes and fluorescence spectroscopy, we show that the association rate constant between the α-HL pore and a Cu(2+)-free peptide is higher than that of a Cu(2+)-complexed peptide. We posit that mainly due to conformational changes induced by the bound Cu(2+) on the peptide, the resulting complex encounters a higher energy barrier toward its association with the protein pore, stemming most likely from an extra entropy cost needed to fit the Cu(2+)-complexed peptide within the α-HL lumen region. The lower dissociation rate constant of the Cu(2+)-complexed peptide from α-HL pore, as compared to that of Cu(2+)-free peptide, supports the existence of a deeper free energy well for the protein interaction with a Cu(2+)-complexed peptide, which may be indicative of specific Cu(2+)-mediated contributions to the binding of the Cu(2+)-complexed peptide within the pore lumen.

Cyclic deformation-induced solute transport in tissue scaffolds with computer designed, interconnected, pore networks: experiments and simulations.

PubMed

Den Buijs, Jorn Op; Dragomir-Daescu, Dan; Ritman, Erik L

2009-08-01

Nutrient supply and waste removal in porous tissue engineering scaffolds decrease from the periphery to the center, leading to limited depth of ingrowth of new tissue into the scaffold. However, as many tissues experience cyclic physiological strains, this may provide a mechanism to enhance solute transport in vivo before vascularization of the scaffold. The hypothesis of this study was that pore cross-sectional geometry and interconnectivity are of major importance for the effectiveness of cyclic deformation-induced solute transport. Transparent elastic polyurethane scaffolds, with computer-programmed design of pore networks in the form of interconnected channels, were fabricated using a 3D printing and injection molding technique. The scaffold pores were loaded with a colored tracer for optical contrast, cyclically compressed with deformations of 10 and 15% of the original undeformed height at 1.0 Hz. Digital imaging was used to quantify the spatial distribution of the tracer concentration within the pores. Numerical simulations of a fluid-structure interaction model of deformation-induced solute transport were compared to the experimental data. The results of experiments and modeling agreed well and showed that pore interconnectivity heavily influences deformation-induced solute transport. Pore cross-sectional geometry appears to be of less relative importance in interconnected pore networks. Validated computer models of solute transport can be used to design optimal scaffold pore geometries that will enhance the convective transport of nutrients inside the scaffold and the removal of waste, thus improving the cell survivability deep inside the scaffold.

A streamline splitting pore-network approach for computationally inexpensive and accurate simulation of transport in porous media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mehmani, Yashar; Oostrom, Martinus; Balhoff, Matthew

2014-03-20

Several approaches have been developed in the literature for solving flow and transport at the pore-scale. Some authors use a direct modeling approach where the fundamental flow and transport equations are solved on the actual pore-space geometry. Such direct modeling, while very accurate, comes at a great computational cost. Network models are computationally more efficient because the pore-space morphology is approximated. Typically, a mixed cell method (MCM) is employed for solving the flow and transport system which assumes pore-level perfect mixing. This assumption is invalid at moderate to high Peclet regimes. In this work, a novel Eulerian perspective on modelingmore » flow and transport at the pore-scale is developed. The new streamline splitting method (SSM) allows for circumventing the pore-level perfect mixing assumption, while maintaining the computational efficiency of pore-network models. SSM was verified with direct simulations and excellent matches were obtained against micromodel experiments across a wide range of pore-structure and fluid-flow parameters. The increase in the computational cost from MCM to SSM is shown to be minimal, while the accuracy of SSM is much higher than that of MCM and comparable to direct modeling approaches. Therefore, SSM can be regarded as an appropriate balance between incorporating detailed physics and controlling computational cost. The truly predictive capability of the model allows for the study of pore-level interactions of fluid flow and transport in different porous materials. In this paper, we apply SSM and MCM to study the effects of pore-level mixing on transverse dispersion in 3D disordered granular media.« less

Pomeron calculus in zero transverse dimensions: Summation of pomeron loops and generating functional for multiparticle production processes

NASA Astrophysics Data System (ADS)

Levin, E.; Prygarin, A.

2008-02-01

In this paper we address two problems in pomeron calculus in zero transverse dimensions: the summation of the pomeron loops and the calculation of the processes of multiparticle generation. We introduce a new generating functional for these processes and obtain the evolution equation for it. We argue that in the kinematic range given by 1 ≪ln(1/α_{text{S}}2) ≪α_{text{S}} Y ≪1/α_{text{S}}, we can reduce the pomeron calculus to the exchange of non-interacting pomerons with the renormalized amplitude of their interaction with the target. Therefore, the summation of the pomeron loops can be performed using the Mueller Patel Salam Iancu approximation.

Effect of Cavity Size of Mesoporous Silica on Short DNA Duplex Stability.

PubMed

Masuda, Tsubasa; Shibuya, Yuuta; Arai, Shota; Kobayashi, Sayaka; Suzuki, Sotaro; Kijima, Jun; Itoh, Tetsuji; Sato, Yusuke; Nishizawa, Seiichi; Yamaguchi, Akira

2018-05-15

We studied the stabilities of short (4- and 3-bp) DNA duplexes within silica mesopores modified with a positively charged trimethyl aminopropyl (TMAP) monolayer (BJH pore diameter 1.6-7.4 nm). The DNA fragments with fluorescent dye were introduced into the pores, and their fluorescence resonance energy transfer (FRET) response was measured to estimate the structuring energies of the short DNA duplexes under cryogenic conditions (temperature 233-323 K). The results confirmed the enthalpic stability gain of the duplex within size-matched pores (1.6 and 2.3 nm). The hybridization equilibrium constants found for the size-matched pores were 2 orders of magnitude larger than those for large pores (≥3.5 nm), and this size-matching effect for the enhanced duplex stability was explained by a tight electrostatic interaction between the duplex and the surface TMAP groups. These results indicate the requirement of the precise regulation of mesopore size to ensure the stabilization of hydrogen-bonded supramolecular assemblies.

Identification of contact sites between ankyrin and band 3 in the human erythrocyte membrane.

PubMed

Grey, Jesse L; Kodippili, Gayani C; Simon, Katya; Low, Philip S

2012-08-28

The red cell membrane is stabilized by a spectrin/actin-based cortical cytoskeleton connected to the phospholipid bilayer via multiple protein bridges. By virtue of its interaction with ankyrin and adducin, the anion transporter, band 3 (AE1), contributes prominently to these bridges. In a previous study, we demonstrated that an exposed loop comprising residues 175-185 of the cytoplasmic domain of band 3 (cdB3) constitutes a critical docking site for ankyrin on band 3. In this paper, we demonstrate that an adjacent loop, comprising residues 63-73 of cdB3, is also essential for ankyrin binding. Data that support this hypothesis include the following. (1) Deletion or mutation of residues within the latter loop abrogates ankyrin binding without affecting cdB3 structure or its other functions. (2) Association of cdB3 with ankyrin is inhibited by competition with the loop peptide. (3) Resealing of the loop peptide into erythrocyte ghosts alters membrane morphology and stability. To characterize cdB3-ankyrin interaction further, we identified their interfacial contact sites using molecular docking software and the crystal structures of D(3)D(4)-ankyrin and cdB3. The best fit for the interaction reveals multiple salt bridges and hydrophobic contacts between the two proteins. The most important ion pair interactions are (i) cdB3 K69-ankyrin E645, (ii) cdB3 E72-ankyrin K611, and (iii) cdB3 D183-ankyrin N601 and Q634. Mutation of these four residues on ankyrin yielded an ankyrin with a native CD spectrum but little or no affinity for cdB3. These data define the docking interface between cdB3 and ankyrin in greater detail.

Identification of contact sites between ankyrin and band 3 in the human erythrocyte membrane

PubMed Central

Grey, Jesse L.; Kodippili, Gayani C.; Simon, Katya; Low, Philip S.

2012-01-01

The red cell membrane is stabilized by a spectrin/actin-based cortical cytoskeleton connected to the phospholipid-bilayer via multiple protein bridges. By virtue of its interaction with ankyrin and adducin, the anion transporter, band 3 (AE1), contributes prominently to these bridges. In a previous study, we demonstrated that an exposed loop comprising residues 175–185 of the cytoplasmic domain of band 3 (cdB3) constitutes a critical docking site for ankyrin on band 3. In this paper, we demonstrate that an adjacent loop, comprising residues 63–73 of cdB3, is also essential for ankyrin binding. Data in support of this hypothesis include: 1) deletion or mutation of residues within the latter loop abrogates ankyrin binding without affecting cdB3 structure or its other functions, 2) association of cdB3 with ankyrin is inhibited by competition with the loop peptide, and 3) resealing of the loop peptide into erythrocyte ghosts alters membrane morphology and stability. To characterize cdB3-ankyrin interaction further, we identified their interfacial contact sites using molecular docking software and the crystal structures of D3D4-ankyrin and cdB3. The best fit for the interaction reveals multiple salt bridges and hydrophobic contacts between the two proteins. The most important ion pair interactions are: i) cdB3 K69 to ankyrin E645, ii) cdB3 E72 to ankyrin K611, and iii) cdB3 D183 to ankyrin N601 and Q634. Mutation of the above four residues on ankyrin yielded an ankyrin with native CD spectrum, but little or no affinity for cdB3. These data define the docking interface between cdB3 and ankyrin in greater detail. PMID:22861190

Osmotic mechanism of the loop extrusion process

NASA Astrophysics Data System (ADS)

Yamamoto, Tetsuya; Schiessel, Helmut

2017-09-01

The loop extrusion theory assumes that protein factors, such as cohesin rings, act as molecular motors that extrude chromatin loops. However, recent single molecule experiments have shown that cohesin does not show motor activity. To predict the physical mechanism involved in loop extrusion, we here theoretically analyze the dynamics of cohesin rings on a loop, where a cohesin loader is in the middle and unloaders at the ends. Cohesin monomers bind to the loader rather frequently and cohesin dimers bind to this site only occasionally. Our theory predicts that a cohesin dimer extrudes loops by the osmotic pressure of cohesin monomers on the chromatin fiber between the two connected rings. With this mechanism, the frequency of the interactions between chromatin segments depends on the loading and unloading rates of dimers at the corresponding sites.

Prediction of relative and absolute permeabilities for gas and water from soil water retention curves using a pore-scale network model

NASA Astrophysics Data System (ADS)

Fischer, Ulrich; Celia, Michael A.

1999-04-01

Functional relationships for unsaturated flow in soils, including those between capillary pressure, saturation, and relative permeabilities, are often described using analytical models based on the bundle-of-tubes concept. These models are often limited by, for example, inherent difficulties in prediction of absolute permeabilities, and in incorporation of a discontinuous nonwetting phase. To overcome these difficulties, an alternative approach may be formulated using pore-scale network models. In this approach, the pore space of the network model is adjusted to match retention data, and absolute and relative permeabilities are then calculated. A new approach that allows more general assignments of pore sizes within the network model provides for greater flexibility to match measured data. This additional flexibility is especially important for simultaneous modeling of main imbibition and drainage branches. Through comparisons between the network model results, analytical model results, and measured data for a variety of both undisturbed and repacked soils, the network model is seen to match capillary pressure-saturation data nearly as well as the analytical model, to predict water phase relative permeabilities equally well, and to predict gas phase relative permeabilities significantly better than the analytical model. The network model also provides very good estimates for intrinsic permeability and thus for absolute permeabilities. Both the network model and the analytical model lost accuracy in predicting relative water permeabilities for soils characterized by a van Genuchten exponent n≲3. Overall, the computational results indicate that reliable predictions of both relative and absolute permeabilities are obtained with the network model when the model matches the capillary pressure-saturation data well. The results also indicate that measured imbibition data are crucial to good predictions of the complete hysteresis loop.

A new mechanism of voltage-dependent gating exposed by KV10.1 channels interrupted between voltage sensor and pore.

PubMed

Tomczak, Adam P; Fernández-Trillo, Jorge; Bharill, Shashank; Papp, Ferenc; Panyi, Gyorgy; Stühmer, Walter; Isacoff, Ehud Y; Pardo, Luis A

2017-05-01

Voltage-gated ion channels couple transmembrane potential changes to ion flow. Conformational changes in the voltage-sensing domain (VSD) of the channel are thought to be transmitted to the pore domain (PD) through an α-helical linker between them (S4-S5 linker). However, our recent work on channels disrupted in the S4-S5 linker has challenged this interpretation for the KCNH family. Furthermore, a recent single-particle cryo-electron microscopy structure of K V 10.1 revealed that the S4-S5 linker is a short loop in this KCNH family member, confirming the need for an alternative gating model. Here we use "split" channels made by expression of VSD and PD as separate fragments to investigate the mechanism of gating in K V 10.1. We find that disruption of the covalent connection within the S4 helix compromises the ability of channels to close at negative voltage, whereas disconnecting the S4-S5 linker from S5 slows down activation and deactivation kinetics. Surprisingly, voltage-clamp fluorometry and MTS accessibility assays show that the motion of the S4 voltage sensor is virtually unaffected when VSD and PD are not covalently bound. Finally, experiments using constitutively open PD mutants suggest that the presence of the VSD is structurally important for the conducting conformation of the pore. Collectively, our observations offer partial support to the gating model that assumes that an inward motion of the C-terminal S4 helix, rather than the S4-S5 linker, closes the channel gate, while also suggesting that control of the pore by the voltage sensor involves more than one mechanism. © 2017 Tomczak et al.

A new mechanism of voltage-dependent gating exposed by KV10.1 channels interrupted between voltage sensor and pore

PubMed Central

Fernández-Trillo, Jorge; Bharill, Shashank; Panyi, Gyorgy; Stühmer, Walter; Isacoff, Ehud Y.

2017-01-01

Voltage-gated ion channels couple transmembrane potential changes to ion flow. Conformational changes in the voltage-sensing domain (VSD) of the channel are thought to be transmitted to the pore domain (PD) through an α-helical linker between them (S4–S5 linker). However, our recent work on channels disrupted in the S4–S5 linker has challenged this interpretation for the KCNH family. Furthermore, a recent single-particle cryo-electron microscopy structure of KV10.1 revealed that the S4–S5 linker is a short loop in this KCNH family member, confirming the need for an alternative gating model. Here we use “split” channels made by expression of VSD and PD as separate fragments to investigate the mechanism of gating in KV10.1. We find that disruption of the covalent connection within the S4 helix compromises the ability of channels to close at negative voltage, whereas disconnecting the S4–S5 linker from S5 slows down activation and deactivation kinetics. Surprisingly, voltage-clamp fluorometry and MTS accessibility assays show that the motion of the S4 voltage sensor is virtually unaffected when VSD and PD are not covalently bound. Finally, experiments using constitutively open PD mutants suggest that the presence of the VSD is structurally important for the conducting conformation of the pore. Collectively, our observations offer partial support to the gating model that assumes that an inward motion of the C-terminal S4 helix, rather than the S4–S5 linker, closes the channel gate, while also suggesting that control of the pore by the voltage sensor involves more than one mechanism. PMID:28360219

Optimizing Voltage Control for Large-Scale Solar - Text version | Energy

Science.gov Websites

system software in the loop during simulations, both for long term studies, as well as in some hardware in the loop studies, where we had actual devices interacting with this. So this is a fairly unique

Characterization of the Interaction of Sclerostin with the Low Density Lipoprotein Receptor-related Protein (LRP) Family of Wnt Co-receptors*

PubMed Central

Holdsworth, Gill; Slocombe, Patrick; Doyle, Carl; Sweeney, Bernadette; Veverka, Vaclav; Le Riche, Kelly; Franklin, Richard J.; Compson, Joanne; Brookings, Daniel; Turner, James; Kennedy, Jeffery; Garlish, Rachael; Shi, Jiye; Newnham, Laura; McMillan, David; Muzylak, Mariusz; Carr, Mark D.; Henry, Alistair J.; Ceska, Thomas; Robinson, Martyn K.

2012-01-01

LRP5 and LRP6 are proteins predicted to contain four six-bladed β-propeller domains and both bind the bone-specific Wnt signaling antagonist sclerostin. Here, we report the crystal structure of the amino-terminal region of LRP6 and using NMR show that the ability of sclerostin to bind to this molecule is mediated by the central core of sclerostin and does not involve the amino- and carboxyl-terminal flexible arm regions. We show that this structured core region interacts with LRP5 and LRP6 via an NXI motif (found in the sequence PNAIG) within a flexible loop region (loop 2) within the central core region. This sequence is related closely to a previously identified motif in laminin that mediates its interaction with the β-propeller domain of nidogen. However, the NXI motif is not involved in the interaction of sclerostin with LRP4 (another β-propeller containing protein in the LRP family). A peptide derived from the loop 2 region of sclerostin blocked the interaction of sclerostin with LRP5/6 and also inhibited Wnt1 but not Wnt3A or Wnt9B signaling. This suggests that these Wnts interact with LRP6 in different ways. PMID:22696217

Imaging carbon nanotube interactions, diffusion, and stability in nanopores.

PubMed

Eichmann, Shannon L; Smith, Billy; Meric, Gulsum; Fairbrother, D Howard; Bevan, Michael A

2011-07-26

We report optical microscopy measurements of three-dimensional trajectories of individual multiwalled carbon nanotubes (MWCNTs) in nanoscale silica slit pores. Trajectories are analyzed to nonintrusively measure MWCNT interactions, diffusion, and stability as a function of pH and ionic strength. Evanescent wave scattering is used to track MWCNT positions normal to pore walls with nanometer-scale resolution, and video microscopy is used to track lateral positions with spatial resolution comparable to the diffraction limit. Analysis of MWCNT excursions normal to pore walls yields particle-wall potentials that agree with theoretical electrostatic and van der Waals potentials assuming a rotationally averaged potential of mean force. MWCNT lateral mean square displacements are used to quantify translational diffusivities, which are comparable to predictions based on the best available theories. Finally, measured MWCNT pH and ionic strength dependent stabilities are in excellent agreement with predictions. Our findings demonstrate novel measurement and modeling tools to understand the behavior of confined MWCNTs relevant to a broad range of applications.

A pain-inducing centipede toxin targets the heat activation machinery of nociceptor TRPV1

NASA Astrophysics Data System (ADS)

Yang, Shilong; Yang, Fan; Wei, Ningning; Hong, Jing; Li, Bowen; Luo, Lei; Rong, Mingqiang; Yarov-Yarovoy, Vladimir; Zheng, Jie; Wang, Kewei; Lai, Ren

2015-09-01

The capsaicin receptor TRPV1 ion channel is a polymodal nociceptor that responds to heat with exquisite sensitivity through an unknown mechanism. Here we report the identification of a novel toxin, RhTx, from the venom of the Chinese red-headed centipede that potently activates TRPV1 to produce excruciating pain. RhTx is a 27-amino-acid small peptide that forms a compact polarized molecule with very rapid binding kinetics and high affinity for TRPV1. We show that RhTx targets the channel's heat activation machinery to cause powerful heat activation at body temperature. The RhTx-TRPV1 interaction is mediated by the toxin's highly charged C terminus, which associates tightly to the charge-rich outer pore region of the channel where it can directly interact with the pore helix and turret. These findings demonstrate that RhTx binding to the outer pore can induce TRPV1 heat activation, therefore providing crucial new structural information on the heat activation machinery.

Penetration Barrier of Water through Graphynes' Pores: First-Principles Predictions and Force Field Optimization.

PubMed

Bartolomei, Massimiliano; Carmona-Novillo, Estela; Hernández, Marta I; Campos-Martínez, José; Pirani, Fernando; Giorgi, Giacomo; Yamashita, Koichi

2014-02-20

Graphynes are novel two-dimensional carbon-based materials that have been proposed as molecular filters, especially for water purification technologies. We carry out first-principles electronic structure calculations at the MP2C level of theory to assess the interaction between water and graphyne, graphdiyne, and graphtriyne pores. The computed penetration barriers suggest that water transport is unfeasible through graphyne while being unimpeded for graphtriyne. For graphdiyne, with a pore size almost matching that of water, a low barrier is found that in turn disappears if an active hydrogen bond with an additional water molecule on the opposite side of the opening is considered. Thus, in contrast with previous determinations, our results do not exclude graphdiyne as a promising membrane for water filtration. In fact, present calculations lead to water permeation probabilities that are 2 orders of magnitude larger than estimations based on common force fields. A new pair potential for the water-carbon noncovalent component of the interaction is proposed for molecular dynamics simulations involving graphdiyne and water.

A deeper analysis of the epitope/paratope of PLY-5, a mouse monoclonal antibody which recognises the conserved undecapeptide tryptophan-rich loop (ECTGLAWEWWR) of bacterial cholesterol-dependent cytolysins.

PubMed

González-Menéndez, Pedro; García-Ocaña, Marcos; de los Toyos, Juan R

2013-01-04

A previous study showed that the minimal epitope recognised by the PLY-5 mAb in the conserved undecapeptide Trp-rich loop of bacterial CDCs should consist of WEWWRT (Jacobs et al., 1999) [5]. Now, through immunoscreening of amino acid substitution analogues, it is concluded that the second Trp and the Arg residues are essential in the PLY-5 epitope. The E residue is an auxiliary epitope contributor. Antibody modelling and docking simulations provided support for these findings. For recognition by the antibody, the Trp-rich loop flipped out, mimicking the mechanism of membrane insertion. The displaced second Trp was seen to establish aromatic stacking interactions with aromatic residues of the antibody paratope and the notably extruded guanidium tip of the arginine residue mediated electrostatic interactions with well-exposed carboxylic groups of glutamic residues on the surface of the paratope. Thus, the epitope/paratope interaction is mainly mediated by aromatic and by ionic interactions. Copyright © 2012 Elsevier Inc. All rights reserved.

Contribution of seawater recirculation to submarine groundwater discharge and related nutrient fluxes in two tropical bays

NASA Astrophysics Data System (ADS)

Vautier, Camille; Dulaiova, Henrietta

2017-04-01

Hawaiian coastal waters suffer from excess terrestrial nutrient loading, most of which comes from submarine groundwater discharge (SGD). This study quantifies and distinguishes the role of the fresh terrestrial and tidally pumped salt water components of SGD into the nearshore zone of two reefs on the island of Oahu: Maunalua Bay and Kāneohe Bay. The two components of SGD are characterized using isotopic techniques, and the study mainly focuses on the less understood recirculation component. A two-step approach is implemented: first, a conceptual model of groundwater circulation is established; second, nutrient fluxes associated with seawater recirculation are quantified. Groundwater circulation through the beach berm is quantified and characterized using 222Rn and 224Ra activity measurements. Nutrient fluxes are obtained by coupling nutrient concentration measurements and discharge estimates. The isotopic signatures inform us about the influence of the tidal cycle on groundwater circulation. 222Rn, 224Ra, and δ18O isotopes are used to derive apparent ages of the infiltrated seawater and allow us to quantify recirculation rates. The method is also complemented with the use of silicate concentration as tracers of the recirculation process. The trends in apparent ages observed in pore water in Maunalua match previously published conceptual groundwater circulation models and show a sequentially aging pore water circulation loop. However, the ages obtained in Kāneohe suggest a different tidal pumping dynamic that lacks a circulation loop, perhaps resulting from the absence of freshwater discharge. Derived nutrient fluxes show that the autochthonous production of inorganic nitrogen and phosphorus that occurs during seawater recirculation has a significant impact on nutrient cycles in the nearshore areas of the bays. This result suggests that seawater recirculation should be taken into account in biogeochemical studies of coastal areas.

Slow DNA Transport through Nanopores in Hafnium Oxide Membranes

PubMed Central

Bell, David C.; Cohen-Karni, Tzahi; Rosenstein, Jacob K.; Wanunu, Meni

2016-01-01

We present a study of double- and single-stranded DNA transport through nanopores fabricated in ultrathin (2–7 nm thick) free-standing hafnium oxide (HfO2) membranes. The high chemical stability of ultrathin HfO2 enables long-lived experiments with <2 nm diameter pores that last several hours, in which we observe >50 000 DNA translocations with no detectable pore expansion. Mean DNA velocities are slower than velocities through comparable silicon nitride pores, providing evidence that HfO2 nanopores have favorable physicochemical interactions with nucleic acids that can be leveraged to slow down DNA in a nanopore. PMID:24083444

Experimental Investigation on Pore Structure Characterization of Concrete Exposed to Water and Chlorides

PubMed Central

Liu, Jun; Tang, Kaifeng; Qiu, Qiwen; Pan, Dong; Lei, Zongru; Xing, Feng

2014-01-01

In this paper, the pore structure characterization of concrete exposed to deionised water and 5% NaCl solution was evaluated using mercury intrusion porosity (MIP), scanning electron microscopy (SEM) and X-ray diffraction (XRD). The effects of calcium leaching, fly ash incorporation, and chloride ions on the evolution of pore structure characteristics were investigated. The results demonstrate that: (i) in ordinary concrete without any fly ash, the leaching effect of the cement products is more evident than the cement hydration effect. From the experimental data, Ca(OH)2 is leached considerably with the increase in immersion time. The pore structure of concrete can also be affected by the formation of an oriented structure of water in concrete materials; (ii) incorporation of fly ash makes a difference for the performance of concrete submersed in solutions as the total porosity and the pore connectivity can be lower. Especially when the dosage of fly ash is up to 30%, the pores with the diameter of larger than 100 nm show significant decrease. It demonstrates that the pore properties are improved by fly ash, which enhances the resistance against the calcium leaching; (iii) chlorides have a significant impact on microstructure of concrete materials because of the chemical interactions between the chlorides and cement hydrates. PMID:28788204

Smooth DNA transport through a narrowed pore geometry.

PubMed

Carson, Spencer; Wilson, James; Aksimentiev, Aleksei; Wanunu, Meni

2014-11-18

Voltage-driven transport of double-stranded DNA through nanoscale pores holds much potential for applications in quantitative molecular biology and biotechnology, yet the microscopic details of translocation have proven to be challenging to decipher. Earlier experiments showed strong dependence of transport kinetics on pore size: fast regular transport in large pores (> 5 nm diameter), and slower yet heterogeneous transport time distributions in sub-5 nm pores, which imply a large positional uncertainty of the DNA in the pore as a function of the translocation time. In this work, we show that this anomalous transport is a result of DNA self-interaction, a phenomenon that is strictly pore-diameter dependent. We identify a regime in which DNA transport is regular, producing narrow and well-behaved dwell-time distributions that fit a simple drift-diffusion theory. Furthermore, a systematic study of the dependence of dwell time on DNA length reveals a single power-law scaling of 1.37 in the range of 35-20,000 bp. We highlight the resolution of our nanopore device by discriminating via single pulses 100 and 500 bp fragments in a mixture with >98% accuracy. When coupled to an appropriate sequence labeling method, our observation of smooth DNA translocation can pave the way for high-resolution DNA mapping and sizing applications in genomics.

Surface water and groundwater interactions in coastal wetlands

NASA Astrophysics Data System (ADS)

Li, Ling; Xin, Pei; Shen, Chengji

2014-05-01

Salt marshes are an important wetland system in the upper intertidal zone, interfacing the land and coastal water. Dominated by salt-tolerant plants, these wetlands provide essential eco-environmental services for maintaining coastal biodiversity. They also act as sediment traps and help stabilize the coastline. While they play an active role in moderating greenhouse gas emissions, these wetlands have become increasingly vulnerable to the impact of global climate change. Salt marshes are a complex hydrological system characterized by strong, dynamic interactions between surface water and groundwater, which underpin the wetland's eco-functionality. Bordered with coastal water, the marsh system undergoes cycles of inundation and exposure driven by the tide. This leads to dynamic, complex pore-water flow and solute transport in the marsh soil. Pore-water circulations occur at different spatial and temporal scales with strong link to the marsh topography. These circulations control solute transport between the marsh soil and the tidal creek, and ultimately affect the overall nutrient exchange between the marsh and coastal water. The pore-water flows also dictate the soil aeration conditions, which in turn affect marsh plant growth. This talk presents results and findings from recent numerical and experimental studies, focusing on the pore-water flow behaviour in the marsh soil under the influence of tides and density-gradients.

Experimental Quantification of Pore-Scale Flow Phenomena in 2D Heterogeneous Porous Micromodels: Multiphase Flow Towards Coupled Solid-Liquid Interactions

NASA Astrophysics Data System (ADS)

Li, Y.; Kazemifar, F.; Blois, G.; Christensen, K. T.

2017-12-01

Geological sequestration of CO2 within saline aquifers is a viable technology for reducing CO2 emissions. Central to this goal is accurately predicting both the fidelity of candidate sites pre-injection of CO2 and its post-injection migration. Moreover, local fluid pressure buildup may cause activation of small pre-existing unidentified faults, leading to micro-seismic events, which could prove disastrous for societal acceptance of CCS, and possibly compromise seal integrity. Recent evidence shows that large-scale events are coupled with pore-scale phenomena, which necessitates the representation of pore-scale stress, strain, and multiphase flow processes in large-scale modeling. To this end, the pore-scale flow of water and liquid/supercritical CO2 is investigated under reservoir-relevant conditions, over a range of wettability conditions in 2D heterogeneous micromodels that reflect the complexity of a real sandstone. High-speed fluorescent microscopy, complemented by a fast differential pressure transmitter, allows for simultaneous measurement of the flow field within and the instantaneous pressure drop across the micromodels. A flexible micromodel is also designed and fabricated, to be used in conjunction with the micro-PIV technique, enabling the quantification of coupled solid-liquid interactions.

Whisker growth of l-menthol in coexistence with various excipients.

PubMed

Yuasa, H; Ooi, M; Takashima, Y; Kanaya, Y

2000-08-10

The purpose of the present study was to clarify the mechanism for l-menthol whisker growth. l-Menthol was mixed with an excipient, and the interaction was examined by IR measurement, thermal analysis and powder X-ray diffraction. Then we examined the involvement of the capillary condensation using the pore size distribution measurement. By mixing l-menthol with an excipient with whisker growth, the hydroxyl group stretching band of l-menthol was shifted to the higher wavenumber in the IR spectrum, the melting point and heat of fusion of l-menthol became lower in the thermal analysis, and the diffraction intensity of l-menthol became lower in the powder X-ray diffraction. The excipients with whisker growth showed the tendency to have the meso-pore involved in the capillary condensation in the pore size distribution measurement. From the above results, the whisker growth mechanism is considered as follows. When l-menthol was mixed with an excipient with whisker growth, the crystallinity of l-menthol was lowered and the vapor pressure was increased by the interaction mainly consisting of the hydrogen bond. The generated l-menthol vapor entered meso-pore, the saturated vapor pressure was lowered by the capillary condensation, and the nucleation occurred. The vapor was further supplied, generating the growth of whisker.

Structural Dynamics Investigation of Human Family 1 & 2 Cystatin-Cathepsin L1 Interaction: A Comparison of Binding Modes.

PubMed

Nandy, Suman Kumar; Seal, Alpana

2016-01-01

Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory affinity towards C1 family of cysteine proteases and molecular details of these interactions are still elusive. In this study, inhibitory interactions of human family 1 & 2 cystatins with cathepsin L1 are predicted and their stability and viability are verified through protein docking & comparative molecular dynamics. An overall stabilization effect is observed in all cystatins on complex formation. Complexes are mostly dominated by van der Waals interaction but the relative participation of the conserved regions varied extensively. While van der Waals contacts prevail in L1 and L2 loop, N-terminal segment chiefly acts as electrostatic interaction site. In fact the comparative dynamics study points towards the instrumental role of L1 loop in directing the total interaction profile of the complex either towards electrostatic or van der Waals contacts. The key amino acid residues surfaced via interaction energy, hydrogen bonding and solvent accessible surface area analysis for each cystatin-cathepsin L1 complex influence the mode of binding and thus control the diverse inhibitory affinity of cystatins towards cysteine proteases.

PIP2-dependent coupling is prominent in Kv7.1 due to weakened interactions between S4-S5 and S6

NASA Astrophysics Data System (ADS)

Kasimova, Marina A.; Zaydman, Mark A.; Cui, Jianmin; Tarek, Mounir

2015-01-01

Among critical aspects of voltage-gated potassium (Kv) channels' functioning is the effective communication between their two composing domains, the voltage sensor (VSD) and the pore. This communication, called coupling, might be transmitted directly through interactions between these domains and, as recently proposed, indirectly through interactions with phosphatidylinositol-4,5-bisphosphate (PIP2), a minor lipid of the inner plasma membrane leaflet. Here, we show how the two components of coupling, mediated by protein-protein or protein-lipid interactions, both contribute in the Kv7.1 functioning. On the one hand, using molecular dynamics simulations, we identified a Kv7.1 PIP2 binding site that involves residues playing a key role in PIP2-dependent coupling. On the other hand, combined theoretical and experimental approaches have shown that the direct interaction between the segments of the VSD (S4-S5) and the pore (S6) is weakened by electrostatic repulsion. Finally, we conclude that due to weakened protein-protein interactions, the PIP2-dependent coupling is especially prominent in Kv7.1.

Strong competition between ΘI I-loop-current order and d -wave charge order along the diagonal direction in a two-dimensional hot spot model

NASA Astrophysics Data System (ADS)

de Carvalho, Vanuildo S.; Kloss, Thomas; Montiel, Xavier; Freire, Hermann; Pépin, Catherine

2015-08-01

We study the fate of the so-called ΘI I-loop-current order that breaks both time-reversal and parity symmetries in a two-dimensional hot spot model with antiferromagnetically mediated interactions, using Fermi surfaces relevant to the phenomenology of the cuprate superconductors. We start from a three-band Emery model describing the hopping of holes in the CuO2 plane that includes two hopping parameters tp p and tp d, local onsite Coulomb interactions Ud and Up, and nearest-neighbor Vp d couplings between the fermions in the copper [Cu (3 dx2-y2) ] and oxygen [O (2 px) and O (2 py)] orbitals. By focusing on the lowest-energy band, we proceed to decouple the local interaction Ud of the Cu orbital in the spin channel using a Hubbard-Stratonovich transformation to arrive at the interacting part of the so-called spin-fermion model. We also decouple the nearest-neighbor interaction Vp d to introduce the order parameter of the ΘI I-loop-current order. In this way, we are able to construct a consistent mean-field theory that describes the strong competition between the composite order parameter made of a quadrupole-density wave and d -wave pairing fluctuations proposed in Efetov et al. [Nat. Phys. 9, 442 (2013), 10.1038/nphys2641] with the ΘI I-loop-current order parameter that is argued to be relevant for explaining important aspects of the physics of the pseudogap phase displayed in the underdoped cuprates.

Regenerable Sorbent for CO2 Removal

NASA Technical Reports Server (NTRS)

Alptekin, Gokhan; Jayaraman, Ambal

2013-01-01

A durable, high-capacity regenerable sorbent can remove CO2 from the breathing loop under a Martian atmosphere. The system design allows near-ambient temperature operation, needs only a small temperature swing, and sorbent regeneration takes place at or above 8 torr, eliminating the potential for Martian atmosphere to leak into the regeneration bed and into the breathing loop. The physical adsorbent can be used in a metabolic, heat-driven TSA system to remove CO2 from the breathing loop of the astronaut and reject it to the Martian atmosphere. Two (or more) alternating sorbent beds continuously scrub and reject CO2 from the spacesuit ventilation loop. The sorbent beds are cycled, alternately absorbing CO2 from the vent loop and rejecting the adsorbed material into the environment at a high CO2 partial pressure (above 8 torr). The system does not need to run the adsorber at cryogenic temperatures, and uses a much smaller temperature swing. The sorbent removes CO2 via a weak chemical interaction. The interaction is strong enough to enable CO2 adsorption even at 3 to 7.6 torr. However, because the interaction between the surface adsorption sites and the CO2 is relatively weak, the heat input needed to regenerate the sorbent is much lower than that for chemical absorbents. The sorbent developed in this project could potentially find use in a large commercial market in the removal of CO2 emissions from coal-fired power plants, if regulations are put in place to curb carbon emissions from power plants.

Cooperative and noncooperative magnetization reversal in alnicos

DOE PAGES

Skomski, Ralph; Ke, Liqin; Kramer, Matthew J.; ...

2017-02-08

Here, we investigate how magnetostatic interactions affect the coercivity of alnico-type magnets. Starting from exact micromagnetic relations, we also analyze two limits, namely cooperative reversal processes operative on short lengths scales and noncooperative reversal processes on long length scales. Furthermore, in alnicos, intrawire interactions are predominantly cooperative, whereas interwire effects are typically noncooperative. However, the transition between the regimes depends on feature size and hysteresis-loop shape, and interwire cooperative effects are largest for nearly rectangular loops. Our analysis revises the common shape-anisotropy interpretation of alnicos.

Mass gap in the weak coupling limit of (2 +1 )-dimensional SU(2) lattice gauge theory

NASA Astrophysics Data System (ADS)

Anishetty, Ramesh; Sreeraj, T. P.

2018-04-01

We develop the dual description of (2 +1 )-dimensional SU(2) lattice gauge theory as interacting "Abelian-like" electric loops by using Schwinger bosons. "Point splitting" of the lattice enables us to construct explicit Hilbert space for the gauge invariant theory which in turn makes dynamics more transparent. Using path integral representation in phase space, the interacting closed loop dynamics is analyzed in the weak coupling limit to get the mass gap.

A unified approach to fluid-flow, geomechanical, and seismic modelling

NASA Astrophysics Data System (ADS)

Yarushina, Viktoriya; Minakov, Alexander

2016-04-01

The perturbations of pore pressure can generate seismicity. This is supported by observations from human activities that involve fluid injection into rocks at high pressure (hydraulic fracturing, CO2 storage, geothermal energy production) and natural examples such as volcanic earthquakes. Although the seismic signals that emerge during geotechnical operations are small both in amplitude and duration when compared to natural counterparts. A possible explanation for the earthquake source mechanism is based on a number of in situ stress measurements suggesting that the crustal rocks are close to its plastic yield limit. Hence, a rapid increase of the pore pressure decreases the effective normal stress, and, thus, can trigger seismic shear deformation. At the same time, little attention has been paid to the fact that the perturbation of fluid pressure itself represents an acoustic source. Moreover, non-double-couple source mechanisms are frequently reported from the analysis of microseismicity. A consistent formulation of the source mechanism describing microseismic events should include both a shear and isotropic component. Thus, improved understanding of the interaction between fluid flow and seismic deformation is needed. With this study we aim to increase the competence in integrating real-time microseismic monitoring with geomechanical modelling such that there is a feedback loop between monitored deformation and stress field modelling. We propose fully integrated seismic, geomechanical and reservoir modelling. Our mathematical formulation is based on fundamental set of force balance, mass balance, and constitutive poro-elastoplastic equations for two-phase media consisting of deformable solid rock frame and viscous fluid. We consider a simplified 1D modelling setup for consistent acoustic source and wave propagation in poro-elastoplastic media. In this formulation the seismic wave is generated due to local changes of the stress field and pore pressure induced by e.g. fault generation or strain localization. This approach gives unified framework to characterize microseismicity of both class-I (pressure induced) and class-II (stress triggered) type of events. We consider two modelling setups. In the first setup the event is located within the reservoir and associated with pressure/stress drop due to fracture initiation. In the second setup we assume that seismic wave from a distant source hits a reservoir. The unified formulation of poro-elastoplastic deformation allows us to link the macroscopic stresses to local seismic instability.

Loop-loop interactions govern multiple steps in indole-3-glycerol phosphate synthase catalysis

PubMed Central

Zaccardi, Margot J; O'Rourke, Kathleen F; Yezdimer, Eric M; Loggia, Laura J; Woldt, Svenja; Boehr, David D

2014-01-01

Substrate binding, product release, and likely chemical catalysis in the tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase (IGPS) are dependent on the structural dynamics of the β1α1 active-site loop. Statistical coupling analysis and molecular dynamic simulations had previously indicated that covarying residues in the β1α1 and β2α2 loops, corresponding to Arg54 and Asn90, respectively, in the Sulfolobus sulfataricus enzyme (ssIGPS), are likely important for coordinating functional motions of these loops. To test this hypothesis, we characterized site mutants at these positions for changes in catalytic function, protein stability and structural dynamics for the thermophilic ssIGPS enzyme. Although there were only modest changes in the overall steady-state kinetic parameters, solvent viscosity and solvent deuterium kinetic isotope effects indicated that these amino acid substitutions change the identity of the rate-determining step across multiple temperatures. Surprisingly, the N90A substitution had a dramatic effect on the general acid/base catalysis of the dehydration step, as indicated by the loss of the descending limb in the pH rate profile, which we had previously assigned to Lys53 on the β1α1 loop. These changes in enzyme function are accompanied with a quenching of ps-ns and µs-ms timescale motions in the β1α1 loop as measured by nuclear magnetic resonance studies. Altogether, our studies provide structural, dynamic and functional rationales for the coevolution of residues on the β1α1 and β2α2 loops, and highlight the multiple roles that the β1α1 loop plays in IGPS catalysis. Thus, substitution of covarying residues in the active-site β1α1 and β2α2 loops of indole-3-glycerol phosphate synthase results in functional, structural, and dynamic changes, highlighting the multiple roles that the β1α1 loop plays in enzyme catalysis and the importance of regulating the structural dynamics of this loop through noncovalent interactions with nearby structural elements. PMID:24403092

Structural Determinants of Oligomerization of the Aquaporin-4 Channel.

PubMed

Kitchen, Philip; Conner, Matthew T; Bill, Roslyn M; Conner, Alex C

2016-03-25

The aquaporin (AQP) family of integral membrane protein channels mediate cellular water and solute flow. Although qualitative and quantitative differences in channel permeability, selectivity, subcellular localization, and trafficking responses have been observed for different members of the AQP family, the signature homotetrameric quaternary structure is conserved. Using a variety of biophysical techniques, we show that mutations to an intracellular loop (loop D) of human AQP4 reduce oligomerization. Non-tetrameric AQP4 mutants are unable to relocalize to the plasma membrane in response to changes in extracellular tonicity, despite equivalent constitutive surface expression levels and water permeability to wild-type AQP4. A network of AQP4 loop D hydrogen bonding interactions, identified using molecular dynamics simulations and based on a comparative mutagenic analysis of AQPs 1, 3, and 4, suggest that loop D interactions may provide a general structural framework for tetrameric assembly within the AQP family. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Deciphering the structural framework of glycine receptor anchoring by gephyrin

PubMed Central

Kim, Eun Young; Schrader, Nils; Smolinsky, Birthe; Bedet, Cécile; Vannier, Christian; Schwarz, Günter; Schindelin, Hermann

2006-01-01

Glycine is the major inhibitory neurotransmitter in the spinal cord and brain stem. Gephyrin is required to achieve a high concentration of glycine receptors (GlyRs) in the postsynaptic membrane, which is crucial for efficient glycinergic signal transduction. The interaction between gephyrin and the GlyR involves the E-domain of gephyrin and a cytoplasmic loop located between transmembrane segments three and four of the GlyR β subunit. Here, we present crystal structures of the gephyrin E-domain with and without the GlyR β-loop at 2.4 and 2.7 Å resolutions, respectively. The GlyR β-loop is bound in a symmetric ‘key and lock' fashion to each E-domain monomer in a pocket adjacent to the dimer interface. Structure-guided mutagenesis followed by in vitro binding and in vivo colocalization assays demonstrate that a hydrophobic interaction formed by Phe 330 of gephyrin and Phe 398 and Ile 400 of the GlyR β-loop is crucial for binding. PMID:16511563

Probing a 2-aminobenzimidazole library for binding to RNA internal loops via two-dimensional combinatorial screening.

PubMed

Velagapudi, Sai Pradeep; Pushechnikov, Alexei; Labuda, Lucas P; French, Jonathan M; Disney, Matthew D

2012-11-16

There are many potential RNA drug targets in bacterial, viral, and human transcriptomes. However, there are few small molecules that modulate RNA function. This is due, in part, to a lack of fundamental understanding about RNA-ligand interactions including the types of small molecules that bind to RNA structural elements and the RNA structural elements that bind to small molecules. In an effort to better understand RNA-ligand interactions, we diversified the 2-aminobenzimidazole core (2AB) and probed the resulting library for binding to a library of RNA internal loops. We chose the 2AB core for these studies because it is a privileged scaffold for binding RNA based on previous reports. These studies identified that N-methyl pyrrolidine, imidazole, and propylamine diversity elements at the R1 position increase binding to internal loops; variability at the R2 position is well tolerated. The preferred RNA loop space was also determined for five ligands using a statistical approach and identified trends that lead to selective recognition.

Cyber-Physical Test Platform for Microgrids: Combining Hardware, Hardware-in-the-Loop, and Network-Simulator-in-the-Loop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, Austin; Chakraborty, Sudipta; Wang, Dexin

This paper presents a cyber-physical testbed, developed to investigate the complex interactions between emerging microgrid technologies such as grid-interactive power sources, control systems, and a wide variety of communication platforms and bandwidths. The cyber-physical testbed consists of three major components for testing and validation: real time models of a distribution feeder model with microgrid assets that are integrated into the National Renewable Energy Laboratory's (NREL) power hardware-in-the-loop (PHIL) platform; real-time capable network-simulator-in-the-loop (NSIL) models; and physical hardware including inverters and a simple system controller. Several load profiles and microgrid configurations were tested to examine the effect on system performance withmore » increasing channel delays and router processing delays in the network simulator. Testing demonstrated that the controller's ability to maintain a target grid import power band was severely diminished with increasing network delays and laid the foundation for future testing of more complex cyber-physical systems.« less

Solution structure of an ATP-binding RNA aptamer reveals a novel fold.

PubMed Central

Dieckmann, T; Suzuki, E; Nakamura, G K; Feigon, J

1996-01-01

In vitro selection has been used to isolate several RNA aptamers that bind specifically to biological cofactors. A well-characterized example in the ATP-binding RNA aptamer family, which contains a conserved 11-base loop opposite a bulged G and flanked by regions of double-stranded RNA. The nucleotides in the consensus sequence provide a binding pocket for ATP (or AMP), which binds with a Kd in the micromolar range. Here we present the three-dimensional solution structure of a 36-nucleotide ATP-binding RNA aptamer complexed with AMP, determined from NMR-derived distance and dihedral angle restraints. The conserved loop and bulged G form a novel compact, folded structure around the AMP. The backbone tracing of the loop nucleotides can be described by a Greek zeta (zeta). Consecutive loop nucleotides G, A, A form a U-turn at the bottom of the zeta, and interact with the AMP to form a structure similar to a GNRA tetraloop, with AMP standing in for the final A. Two asymmetric G. G base pairs close the stems flanking the internal loop. Mutated aptamers support the existence of the tertiary interactions within the consensus nucleotides and with the AMP found in the calculated structures. PMID:8756406

Affective loop experiences: designing for interactional embodiment.

PubMed

Höök, Kristina

2009-12-12

Involving our corporeal bodies in interaction can create strong affective experiences. Systems that both can be influenced by and influence users corporeally exhibit a use quality we name an affective loop experience. In an affective loop experience, (i) emotions are seen as processes, constructed in the interaction, starting from everyday bodily, cognitive or social experiences; (ii) the system responds in ways that pull the user into the interaction, touching upon end users' physical experiences; and (iii) throughout the interaction the user is an active, meaning-making individual choosing how to express themselves-the interpretation responsibility does not lie with the system. We have built several systems that attempt to create affective loop experiences with more or less successful results. For example, eMoto lets users send text messages between mobile phones, but in addition to text, the messages also have colourful and animated shapes in the background chosen through emotion-gestures with a sensor-enabled stylus pen. Affective Diary is a digital diary with which users can scribble their notes, but it also allows for bodily memorabilia to be recorded from body sensors mapping to users' movement and arousal and placed along a timeline. Users can see patterns in their bodily reactions and relate them to various events going on in their lives. The experiences of building and deploying these systems gave us insights into design requirements for addressing affective loop experiences, such as how to design for turn-taking between user and system, how to create for 'open' surfaces in the design that can carry users' own meaning-making processes, how to combine modalities to create for a 'unity' of expression, and the importance of mirroring user experience in familiar ways that touch upon their everyday social and corporeal experiences. But a more important lesson gained from deploying the systems is how emotion processes are co-constructed and experienced inseparable from all other aspects of everyday life. Emotion processes are part of our social ways of being in the world; they dye our dreams, hopes and bodily experiences of the world. If we aim to design for affective interaction experiences, we need to place them into this larger picture.

Affective loop experiences: designing for interactional embodiment

PubMed Central

Höök, Kristina

2009-01-01

Involving our corporeal bodies in interaction can create strong affective experiences. Systems that both can be influenced by and influence users corporeally exhibit a use quality we name an affective loop experience. In an affective loop experience, (i) emotions are seen as processes, constructed in the interaction, starting from everyday bodily, cognitive or social experiences; (ii) the system responds in ways that pull the user into the interaction, touching upon end users' physical experiences; and (iii) throughout the interaction the user is an active, meaning-making individual choosing how to express themselves—the interpretation responsibility does not lie with the system. We have built several systems that attempt to create affective loop experiences with more or less successful results. For example, eMoto lets users send text messages between mobile phones, but in addition to text, the messages also have colourful and animated shapes in the background chosen through emotion-gestures with a sensor-enabled stylus pen. Affective Diary is a digital diary with which users can scribble their notes, but it also allows for bodily memorabilia to be recorded from body sensors mapping to users' movement and arousal and placed along a timeline. Users can see patterns in their bodily reactions and relate them to various events going on in their lives. The experiences of building and deploying these systems gave us insights into design requirements for addressing affective loop experiences, such as how to design for turn-taking between user and system, how to create for ‘open’ surfaces in the design that can carry users' own meaning-making processes, how to combine modalities to create for a ‘unity’ of expression, and the importance of mirroring user experience in familiar ways that touch upon their everyday social and corporeal experiences. But a more important lesson gained from deploying the systems is how emotion processes are co-constructed and experienced inseparable from all other aspects of everyday life. Emotion processes are part of our social ways of being in the world; they dye our dreams, hopes and bodily experiences of the world. If we aim to design for affective interaction experiences, we need to place them into this larger picture. PMID:19884153

Surprising features of particle dynamics in channel-facilitated transport

NASA Astrophysics Data System (ADS)

Berezhkovskii, Alexander M.; Bezrukov, Sergey M.

2007-06-01

We analyze the consequences of interactions between the pore and the translocating molecule within the framework of a continuous diffusion model using the Smoluchowski equation with the radiation boundary conditions. We describe the solute-pore interaction in terms of the potential of mean force. Several of our analytical findings are quite counterintuitive. Three of the examples to be discussed here are: (i) "Sticking" to the channel slows down translocation (a particle spends more time in the channel) but increases the flux; (ii) If the potential well modeling the particle-channel interaction occupies only a part of the channel length, the average translocation time is non-monotonic in the width of the potential well, first increasing and then decreasing; (iii) At a finite potential bias applied to the channel, the mean "up-hill" and "downhill" particle translocation times (and their distributions) are identical.

Multiple Loops of the Dihydropyridine Receptor Pore Subunit Are Required for Full-Scale Excitation-Contraction Coupling in Skeletal Muscle

PubMed Central

Carbonneau, Leah; Bhattacharya, Dipankar; Sheridan, David C.; Coronado, Roberto

2005-01-01

Understanding which cytosolic domains of the dihydropyridine receptor participate in excitation-contraction (EC) coupling is critical to validate current structural models. Here we quantified the contribution to skeletal-type EC coupling of the α1S (CaV1.1) II-III loop when alone or in combination with the rest of the cytosolic domains of α1S. Chimeras consisting of α1C (CaV1.2) with α1S substitutions at each of the interrepeat loops (I-II, II-III, and III-IV loops) and N- and C-terminal domains were evaluated in dysgenic (α1S-null) myotubes for phenotypic expression of skeletal-type EC coupling. Myotubes were voltage-clamped, and Ca2+ transients were measured by confocal line-scan imaging of fluo-4 fluorescence. In agreement with previous results, the α1C/α1S II-III loop chimera, but none of the other single-loop chimeras, recovered a sigmoidal fluorescence-voltage curve indicative of skeletal-type EC coupling. To quantify Ca2+ transients in the absence of inward Ca2+ current, but without changing the external solution, a mutation, E736K, was introduced into the P-loop of repeat II of α1C. The Ca2+ transients expressed by the α1C(E736K)/α1S II-III loop chimera were ∼70% smaller than those expressed by the Ca2+-conducting α1C/α1S II-III variant. The low skeletal-type EC coupling expressed by the α1C/α1S II-III loop chimera was confirmed in the Ca2+-conducting α1C/α1S II-III loop variant using Cd2+ (10−4 M) as the Ca2+ current blocker. In contrast to the behavior of the II-III loop chimera, Ca2+ transients expressed by an α1C/α1S chimera carrying all tested skeletal α1S domains (all α1S interrepeat loops, N- and C-terminus) were similar in shape and amplitude to wild-type α1S, and did not change in the presence of the E736K mutation or in the presence of 10−4 M Cd2+. Controls indicated that similar dihydropyridine receptor charge movements were expressed by the non-Ca2+ permeant α1S(E1014K) variant, the α1C(E736K)/α1S II-III loop chimera, and the α1C(E736K)/α1S chimera carrying all tested α1S domains. The data indicate that the functional recovery produced by the α1S II-III loop is incomplete and that multiple cytosolic domains of α1S are necessary for a quantitative recovery of the EC-coupling phenotype of skeletal myotubes. Thus, despite the importance of the II-III loop there may be other critical determinants in α1S that influence the efficiency of EC coupling. PMID:15849247

Collider study on the loop-induced dark matter mediation

NASA Astrophysics Data System (ADS)

Tsai, Yuhsin

2016-06-01

Collider experiments are one of the most promising ways to constrain Dark Matter (DM) interactions. For DM couplings involving light mediators, especially for the loop-mediated interactions, a meaningful interpretation of the results requires to go beyond effective field theory. In this note we discuss the study of the magnetic dipole interacting DM, focusing on a model with anarchic dark flavor structure. By including the momentum-dependent form factors that mediate the coupling - given by the Dark Penguin - in collider processes, we study bounds from monophoton, diphoton, and non-pointing photon searches at the LHC. We also compare our results to constraints from the direct detection experiments.

Can pore-clogging by ash explain post-fire runoff?

USGS Publications Warehouse

Stoof, Cathelijne R.; Gevaert, Anouk I.; Baver, Christine; Hassanpour, Bahareh; Morales, Veronica L.; Zhang, Wei; Martin, Deborah; Giri, Shree K.; Steenhuis, Tammo S.

2016-01-01

Ash plays an important role in controlling runoff and erosion processes after wildfire and has frequently been hypothesised to clog soil pores and reduce infiltration. Yet evidence for clogging is incomplete, as research has focussed on identifying the presence of ash in soil; the actual flow processes remain unknown. We conducted laboratory infiltration experiments coupled with microscope observations in pure sands, saturated hydraulic conductivity analysis, and interaction energy calculations, to test whether ash can clog pores (i.e. block pores such that infiltration is hampered and ponding occurs). Although results confirmed previous observations of ash washing into pores, clogging was not observed in the pure sands tested, nor were conditions found for which this does occur. Clogging by means of strong attachment of ash to sand was deemed unlikely given the negative surface charge of the two materials. Ponding due to washing in of ash was also considered improbable given the high saturated conductivity of pure ash and ash–sand mixtures. This first mechanistic step towards analysing ash transport and attachment processes in field soils therefore suggests that pore clogging by ash is unlikely to occur in sands. Discussion is provided on other mechanisms by which ash can affect post-fire hydrology.

Modeling the Pore Formation Mechanism in UMo/AL Dispersion Fuel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Yeon Soo; Jamison, L.; Hofman, G.

In UMo/Al dispersion fuel meat, pores formed in the ILs or at IL-Al interfaces tend to increase in size with irradiation, potentially limiting performance of this fuel. There has been no universally accepted mechanism for the formation and growth of this type of pore. However, there is a consensus that the stress state determined by meat swelling and fission- induced creep is one of the determinants, and fission gas availability at the pore site is another. Five dispersion RERTR miniplates that have well defined irradiation conditions and PIE data were selected for examination. Meat swelling and pore volume were measuredmore » in each plate. ABAQUS finite element analysis (FEA) package was utilized to obtain the time-dependent evolution of mechanical states in the plates while matching the measured meat swelling and creep. Interpretation of these results give insights on how to model a failure function – a predictor for large pore formation – using variables such as meat swelling, interaction layer growth, stress, and creep. This model can be used for optimizing fuel design parameters to reach the desired goal: meeting high power and performance reactor demand.« less

Tailoring pore properties of MCM-48 silica for selective adsorption of CO2.

PubMed

Kim, Sangil; Ida, Junichi; Guliants, Vadim V; Lin, Jerry Y S

2005-04-07

Four different types of amine-attached MCM-48 silicas were prepared and investigated for CO(2) separation from N(2). Monomeric and polymeric hindered and unhindered amines were attached to the pore surface of the MCM-48 silica and characterized with respect to their CO(2) sorption properties. The pore structures and amino group content in these modified silicas were investigated by XRD, FT-IR, TGA, N(2) adsorption/desorption at 77 K and CHN/Si analysis, which confirmed that in all cases the amino groups were attached to the pore surface of MCM-48 at 1.5-5.2 mmol/g. The N(2) adsorption/desorption analysis showed a considerable decrease of the pore volume and surface area for the MCM-48 silica containing a polymeric amine (e.g., polyethyleneimine). The CO(2) adsorption rates and capacities of the amine-attached MCM-48 samples were studied employing a sorption microbalance. The results obtained indicated that in addition to the concentration of surface-attached amino groups, specific interactions between CO(2) and the surface amino groups, and the resultant pore structure after amine group attachment have a significant impact on CO(2) adsorption properties of these promising adsorbent materials.

An α-subunit loop structure is required for GM2 activator protein binding by β-hexosaminidase A

PubMed Central

Zarghooni, Maryam; Bukovac, Scott; Tropak, Michael; Callahan, John; Mahuran, Don

2010-01-01

The α- and/or β-subunits of human β-hexosaminidase A (αβ) and B (ββ) are ~60% identical. In vivo only β-hexosaminidase A can utilize GM2 ganglioside as a substrate, but requires the GM2 activator protein to bind GM2 ganglioside and then interact with the enzyme, placing the terminal GalNAc residue in the active site of the α-subunit. A model for this interaction suggests that two loop structures, present only in the α-subunit, may be critical to this binding. Three amino acids in one of these loops are not encoded in the HEXB gene, while four from the other are removed posttranslationally from the pro-β-subunit. Natural substrate assays with forms of hexosaminidase A containing mutant α-subunits demonstrate that only the site that is removed from the β-subunit during its maturation is critical for the interaction. Our data suggest an unexpected biological role for such proteolytic processing events. PMID:15485660

Methane gas hydrate effect on sediment acoustic and strength properties

USGS Publications Warehouse

Winters, W.J.; Waite, W.F.; Mason, D.H.; Gilbert, L.Y.; Pecher, I.A.

2007-01-01

To improve our understanding of the interaction of methane gas hydrate with host sediment, we studied: (1) the effects of gas hydrate and ice on acoustic velocity in different sediment types, (2) effect of different hydrate formation mechanisms on measured acoustic properties (3) dependence of shear strength on pore space contents, and (4) pore pressure effects during undrained shear.A wide range in acoustic p-wave velocities (Vp) were measured in coarse-grained sediment for different pore space occupants. Vp ranged from less than 1 km/s for gas-charged sediment to 1.77–1.94 km/s for water-saturated sediment, 2.91–4.00 km/s for sediment with varying degrees of hydrate saturation, and 3.88–4.33 km/s for frozen sediment. Vp measured in fine-grained sediment containing gas hydrate was substantially lower (1.97 km/s). Acoustic models based on measured Vp indicate that hydrate which formed in high gas flux environments can cement coarse-grained sediment, whereas hydrate formed from methane dissolved in the pore fluid may not.The presence of gas hydrate and other solid pore-filling material, such as ice, increased the sediment shear strength. The magnitude of that increase is related to the amount of hydrate in the pore space and cementation characteristics between the hydrate and sediment grains. We have found, that for consolidation stresses associated with the upper several hundred meters of sub-bottom depth, pore pressures decreased during shear in coarse-grained sediment containing gas hydrate, whereas pore pressure in fine-grained sediment typically increased during shear. The presence of free gas in pore spaces damped pore pressure response during shear and reduced the strengthening effect of gas hydrate in sands.

Pore-Lining Composition and Capillary Breakthrough Pressure of Mudstone Caprocks: Sealing Efficiency of Geologic CO2 Storage Sites

NASA Astrophysics Data System (ADS)

Heath, J. E.; Dewers, T. A.; McPherson, B. J.; Kotula, P. G.

2010-12-01

Subsurface containment of CO2 is predicated on effective caprock sealing. Many previous studies have relied on macroscopic measurements of capillary breakthrough pressure and other petrophysical properties without direct examination of solid phases that line pore networks and directly contact fluids. However, pore-lining phases strongly contribute to sealing behavior through interfacial interactions among CO2, brine, and the mineral or non-mineral phases. Our high resolution (i.e., sub-micron) examination of the composition of pore-lining phases of several continental and marine mudstones indicates that sealing efficiency (i.e., breakthrough pressure) is governed by pore shapes and pore-lining phases that are not identifiable except through direct characterization of pores. Bulk X-ray diffraction data does not indicate which phases line the pores and may be especially lacking for mudstones with organic material. Organics can line pores and may represent once-mobile phases that modify the wettability of an originally clay-lined pore network. For shallow formations (i.e., < ~800 m depth), interfacial tension and contact angles result in breakthrough pressures that may be as high as those needed to fracture the rock—thus, in the absence of fractures, capillary sealing efficiency is indicated. Deeper seals have poorer capillary sealing if mica-like wetting dominates the wettability. We thank the U.S. Department of Energy’s National Energy Technology Laboratory and the Office of Basic Energy Sciences, and the Southeast and Southwest Carbon Sequestration Partnerships for supporting this work. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Company, for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-AC04-94AL85000.

Closed-loop for type 1 diabetes - an introduction and appraisal for the generalist.

PubMed

Bally, Lia; Thabit, Hood; Hovorka, Roman

2017-01-23

Rapid progress over the past decade has been made with the development of the 'Artificial Pancreas', also known as the closed-loop system, which emulates the feedback glucose-responsive functionality of the pancreatic beta cell. The recent FDA approval of the first hybrid closed-loop system makes the Artificial Pancreas a realistic therapeutic option for people with type 1 diabetes. In anticipation of its advent into clinical care, we provide a primer and appraisal of this novel therapeutic approach in type 1 diabetes for healthcare professionals and non-specialists in the field. Randomised clinical studies in outpatient and home settings have shown improved glycaemic outcomes, reduced risk of hypoglycaemia and positive user attitudes. User input and interaction with existing closed-loop systems, however, are still required. Therefore, management of user expectations, as well as training and support by healthcare providers are key to ensure optimal uptake, satisfaction and acceptance of the technology. An overview of closed-loop technology and its clinical implications are discussed, complemented by our extensive hands-on experience with closed-loop system use during free daily living. The introduction of the artificial pancreas into clinical practice represents a milestone towards the goal of improving the care of people with type 1 diabetes. There remains a need to understand the impact of user interaction with the technology, and its implication on current diabetes management and care.

Extended Impact of Pin1 Catalytic Loop Phosphorylation Revealed by S71E Phosphomimetic.

PubMed

Mahoney, Brendan J; Zhang, Meiling; Zintsmaster, John S; Peng, Jeffrey W

2018-03-02

Pin1 is a two-domain human protein that catalyzes the cis-trans isomerization of phospho-Ser/Thr-Pro (pS/T-P) motifs in numerous cell-cycle regulatory proteins. These pS/T-P motifs bind to Pin1's peptidyl-prolyl isomerase (PPIase) domain in a catalytic pocket, between an extended catalytic loop and the PPIase domain core. Previous studies showed that post-translational phosphorylation of S71 in the catalytic loop decreases substrate binding affinity and isomerase activity. To define the origins for these effects, we investigated a phosphomimetic Pin1 mutant, S71E-Pin1, using solution NMR. We find that S71E perturbs not only its host loop but also the nearby PPIase core. The perturbations identify a local network of hydrogen bonds and salt bridges that is more extended than previously thought, and includes interactions between the catalytic loop and the α2/α3 turn in the PPIase core. Explicit-solvent molecular dynamics simulations and phylogenetic analysis suggest that these interactions act as conserved "latches" between the loop and PPIase core that enhance binding of phosphorylated substrates, as they are absent in PPIases lacking pS/T-P specificity. Our results suggest that S71 is a hub residue within an electrostatic network primed for phosphorylation, and may illustrate a common mechanism of phosphorylation-mediated allostery. Copyright © 2018 Elsevier Ltd. All rights reserved.

Autopilot, Mind Wandering, and the Out of the Loop Performance Problem

PubMed Central

Gouraud, Jonas; Delorme, Arnaud; Berberian, Bruno

2017-01-01

To satisfy the increasing demand for safer critical systems, engineers have integrated higher levels of automation, such as glass cockpits in aircraft, power plants, and driverless cars. These guiding principles relegate the operator to a monitoring role, increasing risks for humans to lack system understanding. The out of the loop performance problem arises when operators suffer from complacency and vigilance decrement; consequently, when automation does not behave as expected, understanding the system or taking back manual control may be difficult. Close to the out of the loop problem, mind wandering points to the propensity of the human mind to think about matters unrelated to the task at hand. This article reviews the literature related to both mind wandering and the out of the loop performance problem as it relates to task automation. We highlight studies showing how these phenomena interact with each other while impacting human performance within highly automated systems. We analyze how this proximity is supported by effects observed in automated environment, such as decoupling, sensory attention, and cognitive comprehension decrease. We also show that this link could be useful for detecting out of the loop situations through mind wandering markers. Finally, we examine the limitations of the current knowledge because many questions remain open to characterize interactions between out of the loop, mind wandering, and automation. PMID:29051723

Loop Braiding Statistics and Interacting Fermionic Symmetry-Protected Topological Phases in Three Dimensions

NASA Astrophysics Data System (ADS)

Cheng, Meng; Tantivasadakarn, Nathanan; Wang, Chenjie

2018-01-01

We study Abelian braiding statistics of loop excitations in three-dimensional gauge theories with fermionic particles and the closely related problem of classifying 3D fermionic symmetry-protected topological (FSPT) phases with unitary symmetries. It is known that the two problems are related by turning FSPT phases into gauge theories through gauging the global symmetry of the former. We show that there exist certain types of Abelian loop braiding statistics that are allowed only in the presence of fermionic particles, which correspond to 3D "intrinsic" FSPT phases, i.e., those that do not stem from bosonic SPT phases. While such intrinsic FSPT phases are ubiquitous in 2D systems and in 3D systems with antiunitary symmetries, their existence in 3D systems with unitary symmetries was not confirmed previously due to the fact that strong interaction is necessary to realize them. We show that the simplest unitary symmetry to support 3D intrinsic FSPT phases is Z2×Z4. To establish the results, we first derive a complete set of physical constraints on Abelian loop braiding statistics. Solving the constraints, we obtain all possible Abelian loop braiding statistics in 3D gauge theories, including those that correspond to intrinsic FSPT phases. Then, we construct exactly soluble state-sum models to realize the loop braiding statistics. These state-sum models generalize the well-known Crane-Yetter and Dijkgraaf-Witten models.

SDO/AIA AND HINODE/EIS OBSERVATIONS OF INTERACTION BETWEEN AN EUV WAVE AND ACTIVE REGION LOOPS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Liheng; Zhang, Jun; Li, Ting

2013-09-20

We present detailed analysis of an extreme-ultraviolet (EUV) wave and its interaction with active region (AR) loops observed by the Solar Dynamics Observatory/Atmospheric Imaging Assembly and the Hinode EUV Imaging Spectrometer (EIS). This wave was initiated from AR 11261 on 2011 August 4 and propagated at velocities of 430-910 km s{sup –1}. It was observed to traverse another AR and cross over a filament channel on its path. The EUV wave perturbed neighboring AR loops and excited a disturbance that propagated toward the footpoints of these loops. EIS observations of AR loops revealed that at the time of the wavemore » transit, the original redshift increased by about 3 km s{sup –1}, while the original blueshift decreased slightly. After the wave transit, these changes were reversed. When the EUV wave arrived at the boundary of a polar coronal hole, two reflected waves were successively produced and part of them propagated above the solar limb. The first reflected wave above the solar limb encountered a large-scale loop system on its path, and a secondary wave rapidly emerged 144 Mm ahead of it at a higher speed. These findings can be explained in the framework of a fast-mode magnetosonic wave interpretation for EUV waves, in which observed EUV waves are generated by expanding coronal mass ejections.« less

Enzymatic function of loop movement in enolase: preparation and some properties of H159N, H159A, H159F, and N207A enolases.

PubMed

Brewer, John M; Glover, Claiborne V C; Holland, Michael J; Lebioda, Lukasz

2003-05-01

The hypothesis that His159 in yeast enolase moves on a polypeptide loop to protonate the phosphoryl of 2-phosphoglycerate to initiate its conversion to phosphoenolpyruvate was tested by preparing H159N, H159A, and H159F enolases. These have 0.07%-0.25% of the native activity under standard assay conditions and the pH dependence of maximum velocities of H159A and H159N mutants is markedly altered. Activation by Mg2+ is biphasic, with the smaller Mg2+ activation constant closer to that of the "catalytic" Mg2+ binding site of native enolase and the larger in the mM range in which native enolase is inhibited. A third Mg2+ may bind to the phosphoryl, functionally replacing proton donation by His159. N207A enolase lacks an intersubunit interaction that stabilizes the closed loop(s) conformation when 2-phosphoglycerate binds. It has 21% of the native activity, also exhibits biphasic Mg2+ activation, and its reaction with the aldehyde analogue of the substrate is more strongly inhibited than is its normal enzymatic reaction. Polypeptide loop(s) closure may keep a proton from His159 interacting with the substrate phosphoryl oxygen long enough to stabilize a carbanion intermediate.

Cyclic Deformation-Induced Solute Transport in Tissue Scaffolds with Computer Designed, Interconnected, Pore Networks: Experiments and Simulations

PubMed Central

Op Den Buijs, Jorn; Dragomir-Daescu, Dan; Ritman, Erik L.

2014-01-01

Nutrient supply and waste removal in porous tissue engineering scaffolds decrease from the periphery to the center, leading to limited depth of ingrowth of new tissue into the scaffold. However, as many tissues experience cyclic physiological strains, this may provide a mechanism to enhance solute transport in vivo before vascularization of the scaffold. The hypothesis of this study was that pore cross-sectional geometry and interconnectivity are of major importance for the effectiveness of cyclic deformation-induced solute transport. Transparent elastic polyurethane scaffolds, with computer-programmed design of pore networks in the form of interconnected channels, were fabricated using a 3D printing and injection molding technique. The scaffold pores were loaded with a colored tracer for optical contrast, cyclically compressed with deformations of 10 and 15% of the original undeformed height at 1.0 Hz. Digital imaging was used to quantify the spatial distribution of the tracer concentration within the pores. Numerical simulations of a fluid–structure interaction model of deformation-induced solute transport were compared to the experimental data. The results of experiments and modeling agreed well and showed that pore interconnectivity heavily influences deformation-induced solute transport. Pore cross-sectional geometry appears to be of less relative importance in interconnected pore networks. Validated computer models of solute transport can be used to design optimal scaffold pore geometries that will enhance the convective transport of nutrients inside the scaffold and the removal of waste, thus improving the cell survivability deep inside the scaffold. PMID:19466547

Double row loop-coil configuration for high-speed electrodynamic maglev suspension, guidance, propulsion and guideway directional switching

DOEpatents

He, Jianliang; Rote, Donald M.

1996-01-01

A stabilization and propulsion system comprising a series of loop-coils arranged in parallel rows wherein two rows combine to form one of two magnetic rails. Levitation and lateral stability are provided when the induced field in the magnetic rails interacts with the superconducting magnets mounted on the magnetic levitation vehicle. The loop-coils forming the magnetic rails have specified dimensions and a specified number of turns and by constructing differently these specifications, for one rail with respect to the other, the angle of tilt of the vehicle can be controlled during directional switching. Propulsion is provided by the interaction of a traveling magnetic wave associated with the coils forming the rails and the super conducting magnets on the vehicle.

Double row loop-coil configuration for high-speed electrodynamic maglev suspension, guidance, propulsion and guideway directional switching

DOEpatents

He, J.; Rote, D.M.

1996-05-21

A stabilization and propulsion system are disclosed comprising a series of loop-coils arranged in parallel rows wherein two rows combine to form one of two magnetic rails. Levitation and lateral stability are provided when the induced field in the magnetic rails interacts with the superconducting magnets mounted on the magnetic levitation vehicle. The loop-coils forming the magnetic rails have specified dimensions and a specified number of turns and by constructing differently these specifications, for one rail with respect to the other, the angle of tilt of the vehicle can be controlled during directional switching. Propulsion is provided by the interaction of a traveling magnetic wave associated with the coils forming the rails and the superconducting magnets on the vehicle. 12 figs.

Interactions driving the collapse of islet amyloid polypeptide: Implications for amyloid aggregation

NASA Astrophysics Data System (ADS)

Cope, Stephanie M.

Human islet amyloid polypeptide (hIAPP), also known as amylin, is a 37-residue intrinsically disordered hormone involved in glucose regulation and gastric emptying. The aggregation of hIAPP into amyloid fibrils is believed to play a causal role in type 2 diabetes. To date, not much is known about the monomeric state of hIAPP or how it undergoes an irreversible transformation from disordered peptide to insoluble aggregate. IAPP contains a highly conserved disulfide bond that restricts hIAPP(1-8) into a short ring-like structure: N_loop. Removal or chemical reduction of N_loop not only prevents cell response upon binding to the CGRP receptor, but also alters the mass per length distribution of hIAPP fibers and the kinetics of fibril formation. The mechanism by which N_loop affects hIAPP aggregation is not yet understood, but is important for rationalizing kinetics and developing potential inhibitors. By measuring end-to-end contact formation rates, Vaiana et al. showed that N_loop induces collapsed states in IAPP monomers, implying attractive interactions between N_loop and other regions of the disordered polypeptide chain . We show that in addition to being involved in intra-protein interactions, the N_loop is involved in inter-protein interactions, which lead to the formation of extremely long and stable beta-turn fibers. These non-amyloid fibers are present in the 10 muM concentration range, under the same solution conditions in which hIAPP forms amyloid fibers. We discuss the effect of peptide cyclization on both intra- and inter-protein interactions, and its possible implications for aggregation. Our findings indicate a potential role of N_loop-N_loop interactions in hIAPP aggregation, which has not previously been explored. Though our findings suggest that N_loop plays an important role in the pathway of amyloid formation, other naturally occurring IAPP variants that contain this structural feature are incapable of forming amyloids. For example, hIAPP readily forms amyloid fibrils in vitro, whereas the rat variant (rIAPP), differing by six amino acids, does not. In addition to being highly soluble, rIAPP is an effective inhibitor of hIAPP fibril formation . Both of these properties have been attributed to rIAPP's three proline residues: A25P, S28P and S29P. Single proline mutants of hIAPP have also been shown to kinetically inhibit hIAPP fibril formation. Because of their intrinsic dihedral angle preferences, prolines are expected to affect conformational ensembles of intrinsically disordered proteins. The specific effect of proline substitutions on IAPP structure and dynamics has not yet been explored, as the detection of such properties is experimentally challenging due to the low molecular weight, fast reconfiguration times, and very low solubility of IAPP peptides. High-resolution techniques able to measure tertiary contact formations are needed to address this issue. We employ a nanosecond laser spectroscopy technique to measure end-to-end contact formation rates in IAPP mutants. We explore the proline substitutions in IAPP and quantify their effects in terms of intrinsic chain stiffness. We find that the three proline mutations found in rIAPP increase chain stiffness. Interestingly, we also find that residue R18 plays an important role in rIAPP's unique chain stiffness and, together with the proline residues, is a determinant for its non-amyloidogenic properties. We discuss the implications of our findings on the role of prolines in IDPs.

Universality hypothesis breakdown at one-loop order

NASA Astrophysics Data System (ADS)

Carvalho, P. R. S.

2018-05-01

We probe the universality hypothesis by analytically computing the at least two-loop corrections to the critical exponents for q -deformed O (N ) self-interacting λ ϕ4 scalar field theories through six distinct and independent field-theoretic renormalization group methods and ɛ -expansion techniques. We show that the effect of q deformation on the one-loop corrections to the q -deformed critical exponents is null, so the universality hypothesis is broken down at this loop order. Such an effect emerges only at the two-loop and higher levels, and the validity of the universality hypothesis is restored. The q -deformed critical exponents obtained through the six methods are the same and, furthermore, reduce to their nondeformed values in the appropriated limit.

Selection of a platinum-binding sequence in a loop of a four-helix bundle protein.

PubMed

Yagi, Sota; Akanuma, Satoshi; Kaji, Asumi; Niiro, Hiroya; Akiyama, Hayato; Uchida, Tatsuya; Yamagishi, Akihiko

2018-02-01

Protein-metal hybrids are functional materials with various industrial applications. For example, a redox enzyme immobilized on a platinum electrode is a key component of some biofuel cells and biosensors. To create these hybrid materials, protein molecules are bound to metal surfaces. Here, we report the selection of a novel platinum-binding sequence in a loop of a four-helix bundle protein, the Lac repressor four-helix protein (LARFH), an artificial protein in which four identical α-helices are connected via three identical loops. We created a genetic library in which the Ser-Gly-Gln-Gly-Gly-Ser sequence within the first inter-helical loop of LARFH was semi-randomly mutated. The library was then subjected to selection for platinum-binding affinity by using the T7 phage display method. The majority of the selected variants contained the Tyr-Lys-Arg-Gly-Tyr-Lys (YKRGYK) sequence in their randomized segment. We characterized the platinum-binding properties of mutant LARFH by using quartz crystal microbalance analysis. Mutant LARFH seemed to interact with platinum through its loop containing the YKRGYK sequence, as judged by the estimated exclusive area occupied by a single molecule. Furthermore, a 10-residue peptide containing the YKRGYK sequence bound to platinum with reasonably high affinity and basic side chains in the peptide were crucial in mediating this interaction. In conclusion, we have identified an amino acid sequence, YKRGYK, in the loop of a helix-loop-helix motif that shows high platinum-binding affinity. This sequence could be grafted into loops of other polypeptides as an approach to immobilize proteins on platinum electrodes for use as biosensors among other applications. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling.

PubMed

Arnautova, Yelena A; Abagyan, Ruben A; Totrov, Maxim

2011-02-01

We report the development of internal coordinate mechanics force field (ICMFF), new force field parameterized using a combination of experimental data for crystals of small molecules and quantum mechanics calculations. The main features of ICMFF include: (a) parameterization for the dielectric constant relevant to the condensed state (ε = 2) instead of vacuum, (b) an improved description of hydrogen-bond interactions using duplicate sets of van der Waals parameters for heavy atom-hydrogen interactions, and (c) improved backbone covalent geometry and energetics achieved using novel backbone torsional potentials and inclusion of the bond angles at the C(α) atoms into the internal variable set. The performance of ICMFF was evaluated through loop modeling simulations for 4-13 residue loops. ICMFF was combined with a solvent-accessible surface area solvation model optimized using a large set of loop decoys. Conformational sampling was carried out using the biased probability Monte Carlo method. Average/median backbone root-mean-square deviations of the lowest energy conformations from the native structures were 0.25/0.21 Å for four residues loops, 0.84/0.46 Å for eight residue loops, and 1.16/0.73 Å for 12 residue loops. To our knowledge, these results are significantly better than or comparable with those reported to date for any loop modeling method that does not take crystal packing into account. Moreover, the accuracy of our method is on par with the best previously reported results obtained considering the crystal environment. We attribute this success to the high accuracy of the new ICM force field achieved by meticulous parameterization, to the optimized solvent model, and the efficiency of the search method. © 2010 Wiley-Liss, Inc.

Helix-length compensation studies reveal the adaptability of the VS ribozyme architecture.

PubMed

Lacroix-Labonté, Julie; Girard, Nicolas; Lemieux, Sébastien; Legault, Pascale

2012-03-01

Compensatory mutations in RNA are generally regarded as those that maintain base pairing, and their identification forms the basis of phylogenetic predictions of RNA secondary structure. However, other types of compensatory mutations can provide higher-order structural and evolutionary information. Here, we present a helix-length compensation study for investigating structure-function relationships in RNA. The approach is demonstrated for stem-loop I and stem-loop V of the Neurospora VS ribozyme, which form a kissing-loop interaction important for substrate recognition. To rapidly characterize the substrate specificity (k(cat)/K(M)) of several substrate/ribozyme pairs, a procedure was established for simultaneous kinetic characterization of multiple substrates. Several active substrate/ribozyme pairs were identified, indicating the presence of limited substrate promiscuity for stem Ib variants and helix-length compensation between stems Ib and V. 3D models of the I/V interaction were generated that are compatible with the kinetic data. These models further illustrate the adaptability of the VS ribozyme architecture for substrate cleavage and provide global structural information on the I/V kissing-loop interaction. By exploring higher-order compensatory mutations in RNA our approach brings a deeper understanding of the adaptability of RNA structure, while opening new avenues for RNA research.

Structure and function of ameloblastin as an extracellular matrix protein: adhesion, calcium binding, and CD63 interaction in human and mouse.

PubMed

Zhang, Xu; Diekwisch, Thomas G H; Luan, Xianghong

2011-12-01

The functional significance of extracellular matrix proteins in the life of vertebrates is underscored by a high level of sequence variability in tandem with a substantial degree of conservation in terms of cell-cell and cell-matrix adhesion interactions. Many extracellular matrix proteins feature multiple adhesion domains for successful attachment to substrates, such as integrin, CD63, and heparin. Here we have used homology and ab initio modeling algorithms to compare mouse ameloblastin (mAMBN) and human ameloblastin (hABMN) isoforms and to analyze their potential for cell adhesion and interaction with other matrix molecules as well as calcium binding. Sequence comparison between mAMBN and hAMBN revealed a 26-amino-acid deletion in mAMBN, corresponding to a helix-loop-helix frameshift. The human AMBN domain (174Q-201G), homologous to the mAMBN 157E-178I helix-loop-helix region, formed a helix-loop motif with an extended loop, suggesting a higher degree of flexibility of hAMBN compared with mAMBN, as confirmed by molecular dynamics simulation. Heparin-binding domains, CD63-interaction domains, and calcium-binding sites in both hAMBN and mAMBN support the concept of AMBN as an extracellular matrix protein. The high level of conservation between AMBN functional domains related to adhesion and differentiation was remarkable when compared with only 61% amino acid sequence homology. © 2011 Eur J Oral Sci.

External Barium Affects the Gating of KCNQ1 Potassium Channels and Produces a Pore Block via Two Discrete Sites

PubMed Central

Gibor, Gilad; Yakubovich, Daniel; Peretz, Asher; Attali, Bernard

2004-01-01

The pore properties and the reciprocal interactions between permeant ions and the gating of KCNQ channels are poorly understood. Here we used external barium to investigate the permeation characteristics of homomeric KCNQ1 channels. We assessed the Ba2+ binding kinetics and the concentration and voltage dependence of Ba2+ steady-state block. Our results indicate that extracellular Ba2+ exerts a series of complex effects, including a voltage-dependent pore blockade as well as unique gating alterations. External barium interacts with the permeation pathway of KCNQ1 at two discrete and nonsequential sites. (a) A slow deep Ba2+ site that occludes the channel pore and could be simulated by a model of voltage-dependent block. (b) A fast superficial Ba2+ site that barely contributes to channel block and mostly affects channel gating by shifting rightward the voltage dependence of activation, slowing activation, speeding up deactivation kinetics, and inhibiting channel inactivation. A model of voltage-dependent block cannot predict the complex impact of Ba2+ on channel gating in low external K+ solutions. Ba2+ binding to this superficial site likely modifies the gating transitions states of KCNQ1. Both sites appear to reside in the permeation pathway as high external K+ attenuates Ba2+ inhibition of channel conductance and abolishes its impact on channel gating. Our data suggest that despite the high degree of homology of the pore region among the various K+ channels, KCNQ1 channels display significant structural and functional uniqueness. PMID:15226366

Constant fields and constant gradients in open ionic channels.

PubMed Central

Chen, D P; Barcilon, V; Eisenberg, R S

1992-01-01

Ions enter cells through pores in proteins that are holes in dielectrics. The energy of interaction between ion and charge induced on the dielectric is many kT, and so the dielectric properties of channel and pore are important. We describe ionic movement by (three-dimensional) Nemst-Planck equations (including flux and net charge). Potential is described by Poisson's equation in the pore and Laplace's equation in the channel wall, allowing induced but not permanent charge. Asymptotic expansions are constructed exploiting the long narrow shape of the pore and the relatively high dielectric constant of the pore's contents. The resulting one-dimensional equations can be integrated numerically; they can be analyzed when channels are short or long (compared with the Debye length). Traditional constant field equations are derived if the induced charge is small, e.g., if the channel is short or if the total concentration gradient is zero. A constant gradient of concentration is derived if the channel is long. Plots directly comparable to experiments are given of current vs voltage, reversal potential vs. concentration, and slope conductance vs. concentration. This dielectric theory can easily be tested: its parameters can be determined by traditional constant field measurements. The dielectric theory then predicts current-voltage relations quite different from constant field, usually more linear, when gradients of total concentration are imposed. Numerical analysis shows that the interaction of ion and channel can be described by a mean potential if, but only if, the induced charge is negligible, that is to say, the electric field is spatially constant. Images FIGURE 1 PMID:1376159

Binding of Substrates to the Central Pore of the Vps4 ATPase Is Autoinhibited by the Microtubule Interacting and Trafficking (MIT) Domain and Activated by MIT Interacting Motifs (MIMs).

PubMed

Han, Han; Monroe, Nicole; Votteler, Jörg; Shakya, Binita; Sundquist, Wesley I; Hill, Christopher P

2015-05-22

The endosomal sorting complexes required for transport (ESCRT) pathway drives reverse topology membrane fission events within multiple cellular pathways, including cytokinesis, multivesicular body biogenesis, repair of the plasma membrane, nuclear membrane vesicle formation, and HIV budding. The AAA ATPase Vps4 is recruited to membrane necks shortly before fission, where it catalyzes disassembly of the ESCRT-III lattice. The N-terminal Vps4 microtubule-interacting and trafficking (MIT) domains initially bind the C-terminal MIT-interacting motifs (MIMs) of ESCRT-III subunits, but it is unclear how the enzyme then remodels these substrates in response to ATP hydrolysis. Here, we report quantitative binding studies that demonstrate that residues from helix 5 of the Vps2p subunit of ESCRT-III bind to the central pore of an asymmetric Vps4p hexamer in a manner that is dependent upon the presence of flexible nucleotide analogs that can mimic multiple states in the ATP hydrolysis cycle. We also find that substrate engagement is autoinhibited by the Vps4p MIT domain and that this inhibition is relieved by binding of either Type 1 or Type 2 MIM elements, which bind the Vps4p MIT domain through different interfaces. These observations support the model that Vps4 substrates are initially recruited by an MIM-MIT interaction that activates the Vps4 central pore to engage substrates and generate force, thereby triggering ESCRT-III disassembly. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Binding of Substrates to the Central Pore of the Vps4 ATPase Is Autoinhibited by the Microtubule Interacting and Trafficking (MIT) Domain and Activated by MIT Interacting Motifs (MIMs)*

PubMed Central

Han, Han; Monroe, Nicole; Votteler, Jörg; Shakya, Binita; Sundquist, Wesley I.; Hill, Christopher P.

2015-01-01

The endosomal sorting complexes required for transport (ESCRT) pathway drives reverse topology membrane fission events within multiple cellular pathways, including cytokinesis, multivesicular body biogenesis, repair of the plasma membrane, nuclear membrane vesicle formation, and HIV budding. The AAA ATPase Vps4 is recruited to membrane necks shortly before fission, where it catalyzes disassembly of the ESCRT-III lattice. The N-terminal Vps4 microtubule-interacting and trafficking (MIT) domains initially bind the C-terminal MIT-interacting motifs (MIMs) of ESCRT-III subunits, but it is unclear how the enzyme then remodels these substrates in response to ATP hydrolysis. Here, we report quantitative binding studies that demonstrate that residues from helix 5 of the Vps2p subunit of ESCRT-III bind to the central pore of an asymmetric Vps4p hexamer in a manner that is dependent upon the presence of flexible nucleotide analogs that can mimic multiple states in the ATP hydrolysis cycle. We also find that substrate engagement is autoinhibited by the Vps4p MIT domain and that this inhibition is relieved by binding of either Type 1 or Type 2 MIM elements, which bind the Vps4p MIT domain through different interfaces. These observations support the model that Vps4 substrates are initially recruited by an MIM-MIT interaction that activates the Vps4 central pore to engage substrates and generate force, thereby triggering ESCRT-III disassembly. PMID:25833946

Fabrication of channeled scaffolds with ordered array of micro-pores through microsphere leaching and indirect Rapid Prototyping technique.

PubMed

Tan, J Y; Chua, C K; Leong, K F

2013-02-01

Advanced scaffold fabrication techniques such as Rapid Prototyping (RP) are generally recognized to be advantageous over conventional fabrication methods in terms architectural control and reproducibility. Yet, most RP techniques tend to suffer from resolution limitations which result in scaffolds with uncontrollable, random-size pores and low porosity, albeit having interconnected channels which is characteristically present in most RP scaffolds. With the increasing number of studies demonstrating the profound influences of scaffold pore architecture on cell behavior and overall tissue growth, a scaffold fabrication method with sufficient architectural control becomes imperative. The present study demonstrates the use of RP fabrication techniques to create scaffolds having interconnected channels as well as controllable micro-size pores. Adopted from the concepts of porogen leaching and indirect RP techniques, the proposed fabrication method uses monodisperse microspheres to create an ordered, hexagonal closed packed (HCP) array of micro-pores that surrounds the existing channels of the RP scaffold. The pore structure of the scaffold is shaped using a single sacrificial construct which comprises the microspheres and a dissolvable RP mold that were sintered together. As such, the size of pores as well as the channel configuration of the scaffold can be tailored based on the design of the RP mold and the size of microspheres used. The fabrication method developed in this work can be a promising alternative way of preparing scaffolds with customized pore structures that may be required for specific studies concerning cell-scaffold interactions.

An analysis of transient flow in upland watersheds: interactions between structure and process

Treesearch

David Lawrence Brown

1995-01-01

The physical structure and hydrological processes of upland watersheds interact in response to forcing functions such as rainfall, leading to storm runoff generation and pore pressure evolution. Transient fluid flow through distinct flow paths such as the soil matrix, macropores, saprolite, and bedrock may be viewed as a consequence of such interactions. Field...

Structure and Functional Characterization of Vibrio parahaemolyticus Thermostable Direct Hemolysin*

PubMed Central

Yanagihara, Itaru; Nakahira, Kumiko; Yamane, Tsutomu; Kaieda, Shuji; Mayanagi, Kouta; Hamada, Daizo; Fukui, Takashi; Ohnishi, Kiyouhisa; Kajiyama, Shin'ichiro; Shimizu, Toshiyuki; Sato, Mamoru; Ikegami, Takahisa; Ikeguchi, Mitsunori; Honda, Takeshi; Hashimoto, Hiroshi

2010-01-01

Thermostable direct hemolysin (TDH) is a major virulence factor of Vibrio parahaemolyticus that causes pandemic foodborne enterocolitis mediated by seafood. TDH exists as a tetramer in solution, and it possesses extreme hemolytic activity. Here, we present the crystal structure of the TDH tetramer at 1.5 Å resolution. The TDH tetramer forms a central pore with dimensions of 23 Å in diameter and ∼50 Å in depth. π-Cation interactions between protomers comprising the tetramer were indispensable for hemolytic activity of TDH. The N-terminal region was intrinsically disordered outside of the pore. Molecular dynamic simulations suggested that water molecules permeate freely through the central and side channel pores. Electron micrographs showed that tetrameric TDH attached to liposomes, and some of the tetramer associated with liposome via one protomer. These findings imply a novel membrane attachment mechanism by a soluble tetrameric pore-forming toxin. PMID:20335168

Effective Thermal Conductivity of an Aluminum Foam + Water Two Phase System

NASA Technical Reports Server (NTRS)

Moskito, John

1996-01-01

This study examined the effect of volume fraction and pore size on the effective thermal conductivity of an aluminum foam and water system. Nine specimens of aluminum foam representing a matrix of three volume fractions (4-8% by vol.) and three pore sizes (2-4 mm) were tested with water to determine relationships to the effective thermal conductivity. It was determined that increases in volume fraction of the aluminum phase were correlated to increases in the effective thermal conductivity. It was not statistically possible to prove that changes in pore size of the aluminum foam correlated to changes in the effective thermal conductivity. However, interaction effects between the volume fraction and pore size of the foam were statistically significant. Ten theoretical models were selected from the published literature to compare against the experimental data. Models by Asaad, Hadley, and de Vries provided effective thermal conductivity predictions within a 95% confidence interval.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sava Gallis, Dorina F.; Ermanoski, Ivan; Greathouse, Jeffrey A.

Here, we present a combined experimental and Grand Canonical Monte Carlo (GCMC) modeling study on the adsorption of iodine in three classes of nanoporous materials: activated charcoals, zeolites, and metal–organic frameworks (MOFs). Iodine adsorption profiles were measured for the first time in situ, with a uniquely designed sorption apparatus. It was determined that pore size and pore environment are responsible for a dynamic adsorption profile, correlated with distinct pressure ranges. At pressures below 0.3 atm, iodine adsorption is governed by a combination of small pores and extra-framework components (e.g., Ag+ ions in the zeolite mordenite). At regimes above 0.3 atm,more » the amount of iodine gas stored relates with an increase in pore size and specific surface area. GCMC results validate the trends noted experimentally and in addition provide a measure of the strength of the adsorbate–adsorbent interactions in these materials.« less

Conformational Heterogeneity of Bax Helix 9 Dimer for Apoptotic Pore Formation

NASA Astrophysics Data System (ADS)

Liao, Chenyi; Zhang, Zhi; Kale, Justin; Andrews, David W.; Lin, Jialing; Li, Jianing

2016-07-01

Helix α9 of Bax protein can dimerize in the mitochondrial outer membrane (MOM) and lead to apoptotic pores. However, it remains unclear how different conformations of the dimer contribute to the pore formation on the molecular level. Thus we have investigated various conformational states of the α9 dimer in a MOM model — using computer simulations supplemented with site-specific mutagenesis and crosslinking of the α9 helices. Our data not only confirmed the critical membrane environment for the α9 stability and dimerization, but also revealed the distinct lipid-binding preference of the dimer in different conformational states. In our proposed pathway, a crucial iso-parallel dimer that mediates the conformational transition was discovered computationally and validated experimentally. The corroborating evidence from simulations and experiments suggests that, helix α9 assists Bax activation via the dimer heterogeneity and interactions with specific MOM lipids, which eventually facilitate proteolipidic pore formation in apoptosis regulation.

The Immune Adaptor SLP-76 Binds to SUMO-RANGAP1 at Nuclear Pore Complex Filaments to Regulate Nuclear Import of Transcription Factors in T Cells

PubMed Central

Liu, Hebin; Schneider, Helga; Recino, Asha; Richardson, Christine; Goldberg, Martin W.; Rudd, Christopher E.

2015-01-01

Summary While immune cell adaptors regulate proximal T cell signaling, direct regulation of the nuclear pore complex (NPC) has not been reported. NPC has cytoplasmic filaments composed of RanGAP1 and RanBP2 with the potential to interact with cytoplasmic mediators. Here, we show that the immune cell adaptor SLP-76 binds directly to SUMO-RanGAP1 of cytoplasmic fibrils of the NPC, and that this interaction is needed for optimal NFATc1 and NF-κB p65 nuclear entry in T cells. Transmission electron microscopy showed anti-SLP-76 cytoplasmic labeling of the majority of NPCs in anti-CD3 activated T cells. Further, SUMO-RanGAP1 bound to the N-terminal lysine 56 of SLP-76 where the interaction was needed for optimal RanGAP1-NPC localization and GAP exchange activity. While the SLP-76-RanGAP1 (K56E) mutant had no effect on proximal signaling, it impaired NF-ATc1 and p65/RelA nuclear entry and in vivo responses to OVA peptide. Overall, we have identified SLP-76 as a direct regulator of nuclear pore function in T cells. PMID:26321253

The Immune Adaptor SLP-76 Binds to SUMO-RANGAP1 at Nuclear Pore Complex Filaments to Regulate Nuclear Import of Transcription Factors in T Cells.

PubMed

Liu, Hebin; Schneider, Helga; Recino, Asha; Richardson, Christine; Goldberg, Martin W; Rudd, Christopher E

2015-09-03

While immune cell adaptors regulate proximal T cell signaling, direct regulation of the nuclear pore complex (NPC) has not been reported. NPC has cytoplasmic filaments composed of RanGAP1 and RanBP2 with the potential to interact with cytoplasmic mediators. Here, we show that the immune cell adaptor SLP-76 binds directly to SUMO-RanGAP1 of cytoplasmic fibrils of the NPC, and that this interaction is needed for optimal NFATc1 and NF-κB p65 nuclear entry in T cells. Transmission electron microscopy showed anti-SLP-76 cytoplasmic labeling of the majority of NPCs in anti-CD3 activated T cells. Further, SUMO-RanGAP1 bound to the N-terminal lysine 56 of SLP-76 where the interaction was needed for optimal RanGAP1-NPC localization and GAP exchange activity. While the SLP-76-RanGAP1 (K56E) mutant had no effect on proximal signaling, it impaired NF-ATc1 and p65/RelA nuclear entry and in vivo responses to OVA peptide. Overall, we have identified SLP-76 as a direct regulator of nuclear pore function in T cells. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

A Phenylalanine Clamp Catalyzes Protein Translocation Through the Anthrax Toxin Pore

PubMed Central

Krantz, Bryan A.; Melnyk, Roman A.; Zhang, Sen; Juris, Stephen J.; Lacy, D. Borden; Wu, Zhengyan; Finkelstein, Alan; Collier, R. John

2006-01-01

The protective antigen component of anthrax toxin forms a homoheptameric pore in the endosomal membrane, creating a narrow passageway for the enzymatic components of the toxin to enter the cytosol. We found that, during conversion of the heptameric precursor to the pore, the seven phenylalanine-427 residues converged within the lumen, generating a radially symmetric heptad of solvent-exposed aromatic rings. This “φ-clamp” structure was required for protein translocation and comprised the major conductance-blocking site for hydrophobic drugs and model cations. We conclude that the φ clamp serves a chaperone-like function, interacting with hydrophobic sequences presented by the protein substrate as it unfolds during translocation. PMID:16051798

Lattice Boltzmann-Based Approaches for Pore-Scale Reactive Transport

DOE PAGES

Yoon, Hongkyu; Kang, Qinjun; Valocchi, Albert J.

2015-07-29

Here an important geoscience and environmental applications such as geologic carbon storage, environmental remediation, and unconventional oil and gas recovery are best understood in the context of reactive flow and multicomponent transport in the subsurface environment. The coupling of chemical and microbiological reactions with hydrological and mechanical processes can lead to complex behaviors across an enormous range of spatial and temporal scales. These coupled responses are also strongly influenced by the heterogeneity and anisotropy of the geologic formations. Reactive transport processes can change the pore morphology at the pore scale, thereby leading to nonlinear interactions with advective and diffusive transport,more » which can strongly influence larger-scale properties such as permeability and dispersion.« less

Structural Basis for the ATP-dependent Configuration of Adenylation Active Site in Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase*

PubMed Central

Chen, Yaozong; Sun, Yueru; Song, Haigang; Guo, Zhihong

2015-01-01

o-Succinylbenzoyl-CoA synthetase, or MenE, is an essential adenylate-forming enzyme targeted for development of novel antibiotics in the menaquinone biosynthesis. Using its crystal structures in a ligand-free form or in complex with nucleotides, a conserved pattern is identified in the interaction between ATP and adenylating enzymes, including acyl/aryl-CoA synthetases, adenylation domains of nonribosomal peptide synthetases, and luciferases. It involves tight gripping interactions of the phosphate-binding loop (P-loop) with the ATP triphosphate moiety and an open-closed conformational change to form a compact adenylation active site. In MenE catalysis, this ATP-enzyme interaction creates a new binding site for the carboxylate substrate, allowing revelation of the determinants of substrate specificities and in-line alignment of the two substrates for backside nucleophilic substitution reaction by molecular modeling. In addition, the ATP-enzyme interaction is suggested to play a crucial catalytic role by mutation of the P-loop residues hydrogen-bonded to ATP. Moreover, the ATP-enzyme interaction has also clarified the positioning and catalytic role of a conserved lysine residue in stabilization of the transition state. These findings provide new insights into the adenylation half-reaction in the domain alteration catalytic mechanism of the adenylate-forming enzymes. PMID:26276389

Noise in NC-AFM measurements with significant tip–sample interaction

PubMed Central

Lübbe, Jannis; Temmen, Matthias

2016-01-01

The frequency shift noise in non-contact atomic force microscopy (NC-AFM) imaging and spectroscopy consists of thermal noise and detection system noise with an additional contribution from amplitude noise if there are significant tip–sample interactions. The total noise power spectral density D Δ f(f m) is, however, not just the sum of these noise contributions. Instead its magnitude and spectral characteristics are determined by the strongly non-linear tip–sample interaction, by the coupling between the amplitude and tip–sample distance control loops of the NC-AFM system as well as by the characteristics of the phase locked loop (PLL) detector used for frequency demodulation. Here, we measure D Δ f(f m) for various NC-AFM parameter settings representing realistic measurement conditions and compare experimental data to simulations based on a model of the NC-AFM system that includes the tip–sample interaction. The good agreement between predicted and measured noise spectra confirms that the model covers the relevant noise contributions and interactions. Results yield a general understanding of noise generation and propagation in the NC-AFM and provide a quantitative prediction of noise for given experimental parameters. We derive strategies for noise-optimised imaging and spectroscopy and outline a full optimisation procedure for the instrumentation and control loops. PMID:28144538

A small stem-loop structure of the Ebola virus trailer is essential for replication and interacts with heat-shock protein A8

PubMed Central

Sztuba-Solinska, Joanna; Diaz, Larissa; Kumar, Mia R.; Kolb, Gaëlle; Wiley, Michael R.; Jozwick, Lucas; Kuhn, Jens H.; Palacios, Gustavo; Radoshitzky, Sheli R.; J. Le Grice, Stuart F.; Johnson, Reed F.

2016-01-01

Ebola virus (EBOV) is a single-stranded negative-sense RNA virus belonging to the Filoviridae family. The leader and trailer non-coding regions of the EBOV genome likely regulate its transcription, replication, and progeny genome packaging. We investigated the cis-acting RNA signals involved in RNA–RNA and RNA–protein interactions that regulate replication of eGFP-encoding EBOV minigenomic RNA and identified heat shock cognate protein family A (HSC70) member 8 (HSPA8) as an EBOV trailer-interacting host protein. Mutational analysis of the trailer HSPA8 binding motif revealed that this interaction is essential for EBOV minigenome replication. Selective 2′-hydroxyl acylation analyzed by primer extension analysis of the secondary structure of the EBOV minigenomic RNA indicates formation of a small stem-loop composed of the HSPA8 motif, a 3′ stem-loop (nucleotides 1868–1890) that is similar to a previously identified structure in the replicative intermediate (RI) RNA and a panhandle domain involving a trailer-to-leader interaction. Results of minigenome assays and an EBOV reverse genetic system rescue support a role for both the panhandle domain and HSPA8 motif 1 in virus replication. PMID:27651462

Differential manipulation of arrestin-3 binding to basal and agonist-activated G protein-coupled receptors.

PubMed

Prokop, Susanne; Perry, Nicole A; Vishnivetskiy, Sergey A; Toth, Andras D; Inoue, Asuka; Milligan, Graeme; Iverson, Tina M; Hunyady, Laszlo; Gurevich, Vsevolod V

2017-08-01

Non-visual arrestins interact with hundreds of different G protein-coupled receptors (GPCRs). Here we show that by introducing mutations into elements that directly bind receptors, the specificity of arrestin-3 can be altered. Several mutations in the two parts of the central "crest" of the arrestin molecule, middle-loop and C-loop, enhanced or reduced arrestin-3 interactions with several GPCRs in receptor subtype and functional state-specific manner. For example, the Lys139Ile substitution in the middle-loop dramatically enhanced the binding to inactive M 2 muscarinic receptor, so that agonist activation of the M 2 did not further increase arrestin-3 binding. Thus, the Lys139Ile mutation made arrestin-3 essentially an activation-independent binding partner of M 2 , whereas its interactions with other receptors, including the β 2 -adrenergic receptor and the D 1 and D 2 dopamine receptors, retained normal activation dependence. In contrast, the Ala248Val mutation enhanced agonist-induced arrestin-3 binding to the β 2 -adrenergic and D 2 dopamine receptors, while reducing its interaction with the D 1 dopamine receptor. These mutations represent the first example of altering arrestin specificity via enhancement of the arrestin-receptor interactions rather than selective reduction of the binding to certain subtypes. Copyright © 2017. Published by Elsevier Inc.

Noise in NC-AFM measurements with significant tip-sample interaction.

PubMed

Lübbe, Jannis; Temmen, Matthias; Rahe, Philipp; Reichling, Michael

2016-01-01

The frequency shift noise in non-contact atomic force microscopy (NC-AFM) imaging and spectroscopy consists of thermal noise and detection system noise with an additional contribution from amplitude noise if there are significant tip-sample interactions. The total noise power spectral density D Δ f ( f m ) is, however, not just the sum of these noise contributions. Instead its magnitude and spectral characteristics are determined by the strongly non-linear tip-sample interaction, by the coupling between the amplitude and tip-sample distance control loops of the NC-AFM system as well as by the characteristics of the phase locked loop (PLL) detector used for frequency demodulation. Here, we measure D Δ f ( f m ) for various NC-AFM parameter settings representing realistic measurement conditions and compare experimental data to simulations based on a model of the NC-AFM system that includes the tip-sample interaction. The good agreement between predicted and measured noise spectra confirms that the model covers the relevant noise contributions and interactions. Results yield a general understanding of noise generation and propagation in the NC-AFM and provide a quantitative prediction of noise for given experimental parameters. We derive strategies for noise-optimised imaging and spectroscopy and outline a full optimisation procedure for the instrumentation and control loops.

The molecular mechanism of nuclear transport revealed by atomic-scale measurements

PubMed Central

Hough, Loren E; Dutta, Kaushik; Sparks, Samuel; Temel, Deniz B; Kamal, Alia; Tetenbaum-Novatt, Jaclyn; Rout, Michael P; Cowburn, David

2015-01-01

Nuclear pore complexes (NPCs) form a selective filter that allows the rapid passage of transport factors (TFs) and their cargoes across the nuclear envelope, while blocking the passage of other macromolecules. Intrinsically disordered proteins (IDPs) containing phenylalanyl-glycyl (FG)-rich repeats line the pore and interact with TFs. However, the reason that transport can be both fast and specific remains undetermined, through lack of atomic-scale information on the behavior of FGs and their interaction with TFs. We used nuclear magnetic resonance spectroscopy to address these issues. We show that FG repeats are highly dynamic IDPs, stabilized by the cellular environment. Fast transport of TFs is supported because the rapid motion of FG motifs allows them to exchange on and off TFs extremely quickly through transient interactions. Because TFs uniquely carry multiple pockets for FG repeats, only they can form the many frequent interactions needed for specific passage between FG repeats to cross the NPC. DOI: http://dx.doi.org/10.7554/eLife.10027.001 PMID:26371551

Structure of an Arrestin2-clathrin Complex Reveals a Novel Clathrin Binding Domain that Modulates Receptor Trafficking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang, D.; Kern, R; Puthenveedu, M

2009-01-01

Non-visual arrestins play a pivotal role as adaptor proteins in regulating the signaling and trafficking of multiple classes of receptors. Although arrestin interaction with clathrin, AP-2, and phosphoinositides contributes to receptor trafficking, little is known about the configuration and dynamics of these interactions. Here, we identify a novel interface between arrestin2 and clathrin through x-ray diffraction analysis. The intrinsically disordered clathrin binding box of arrestin2 interacts with a groove between blades 1 and 2 in the clathrin {beta}-propeller domain, whereas an 8-amino acid splice loop found solely in the long isoform of arrestin2 (arrestin2L) interacts with a binding pocket formedmore » by blades 4 and 5 in clathrin. The apposition of the two binding sites in arrestin2L suggests that they are exclusive and may function in higher order macromolecular structures. Biochemical analysis demonstrates direct binding of clathrin to the splice loop in arrestin2L, whereas functional analysis reveals that both binding domains contribute to the receptor-dependent redistribution of arrestin2L to clathrin-coated pits. Mutagenesis studies reveal that the clathrin binding motif in the splice loop is (L/I){sub 2}GXL. Taken together, these data provide a framework for understanding the dynamic interactions between arrestin2 and clathrin and reveal an essential role for this interaction in arrestin-mediated endocytosis.« less

Interacting cytoplasmic loops of subunits a and c of Escherichia coli F1F0 ATP synthase gate H+ transport to the cytoplasm.

PubMed

Steed, P Ryan; Kraft, Kaitlin A; Fillingame, Robert H

2014-11-25

H(+)-transporting F1F0 ATP synthase catalyzes the synthesis of ATP via coupled rotary motors within F0 and F1. H(+) transport at the subunit a-c interface in transmembranous F0 drives rotation of a cylindrical c10 oligomer within the membrane, which is coupled to rotation of subunit γ within the α3β3 sector of F1 to mechanically drive ATP synthesis. F1F0 functions in a reversible manner, with ATP hydrolysis driving H(+) transport. ATP-driven H(+) transport in a select group of cysteine mutants in subunits a and c is inhibited after chelation of Ag(+) and/or Cd(+2) with the substituted sulfhydryl groups. The H(+) transport pathway mapped via these Ag(+)(Cd(+2))-sensitive Cys extends from the transmembrane helices (TMHs) of subunits a and c into cytoplasmic loops connecting the TMHs, suggesting these loop regions could be involved in gating H(+) release to the cytoplasm. Here, using select loop-region Cys from the single cytoplasmic loop of subunit c and multiple cytoplasmic loops of subunit a, we show that Cd(+2) directly inhibits passive H(+) transport mediated by F0 reconstituted in liposomes. Further, in extensions of previous studies, we show that the regions mediating passive H(+) transport can be cross-linked to each other. We conclude that the loop-regions in subunits a and c that are implicated in H(+) transport likely interact in a single structural domain, which then functions in gating H(+) release to the cytoplasm.

THERMAL STRUCTURE OF CORONAL LOOPS AS SEEN WITH NORIKURA CORONAGRAPH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prasad, S. Krishna; Singh, Jagdev; Ichimoto, K., E-mail: krishna@iiap.res.in

2013-03-10

The thermal structure of a coronal loop, both along and across the loop, is vital in determining the exact plasma heating mechanism. High-resolution spectroscopic observations of the off-limb corona were made using the 25 cm Norikura coronagraph, located at Norikura, Japan. Observations on a number of days were made simultaneously in four forbidden iron emission lines, namely, the [Fe XI] 7892 A line, the [Fe XIII] 10747 A and 10798 A lines, and the [Fe XIV] 5303 A line and on some days made only in the [Fe XI] 7892 A and [Fe X] 6374 A lines. Using temperature sensitivemore » emission line ratios [Fe XIV] 5303 A/[Fe XIII] 10747 A and [Fe XI] 7892 A/[Fe X] 6374 A, we compute the electron temperatures along 18 different loop structures observed on different days. We find a significant negative temperature gradient in all of the structures observed in Fe XIV and Fe XIII and a positive temperature gradient in the structures observed in Fe XI and Fe X. Combining these results with the previous investigations by Singh and his collaborators, we infer that the loop tops, in general, appear hotter when observed in colder lines and colder when observed in relatively hotter lines as compared to their coronal foot points. We suggest that this contrasting trend observed in the temperature variation along the loop structures can be explained by a gradual interaction of different temperature plasma. The exact mechanism responsible for this interaction must be investigated further and has the potential to constrain loop heating models.« less

Dislocation loops in ultra-high purity Fe(Cr) alloys after 7.2 MeV proton irradiation

NASA Astrophysics Data System (ADS)

Chen, J.; Duval, F.; Jung, P.; Schäublin, R.; Gao, N.; Barthe, M. F.

2018-05-01

Ultra-high purity Fe(Cr) alloys (from 0 wt% Cr to 14 wt% Cr) were 3D homogeneously irradiated by 0-7.2 MeV protons to 0.3 dpa at nominal temperatures from 270 °C to 500 °C. Microstructural changes were observed by transmission electron microscopy (TEM). The results showed that evolution of dislocation loops depends on the Cr content. Below 300 °C, large ½ a0 <111> loops are dominating. Above 300 °C, a0 <100> loops with a habit plane {100} appear. Loop sizes of both types are more or less the same. At temperatures from 310 °C to 400 °C, a0 <100> loops form clusters with the same {100} habit plane as the one of the loops forming them. This indicates that <100> loops of the same variant start gliding under mutual elastic interaction. At 500 °C, dislocation loops form disc shaped clusters about 1000 nm in diameter and sitting on {111} and/or {100} planes in the pure Fe samples. Based on these observations a quantitative analysis of the dislocation loops configurations and their temperature dependence is made, leading to an understanding of the basic mechanisms of formation of these loops.

Pore structure and function of synthetic nanopores with fixed charges: tip shape and rectification properties

NASA Astrophysics Data System (ADS)

Ramírez, Patricio; Apel, Pavel Yu; Cervera, Javier; Mafé, Salvador

2008-08-01

We present a complete theoretical study of the relationship between the structure (tip shape and dimensions) and function (selectivity and rectification) of asymmetric nanopores on the basis of previous experimental studies. The theoretical model uses a continuum approach based on the Nernst-Planck equations. According to our results, the nanopore transport properties, such as current-voltage (I-V) characteristics, conductance, rectification ratio, and selectivity, are dictated mainly by the shape of the pore tip (we have distinguished bullet-like, conical, trumpet-like, and hybrid shapes) and the concentration of pore surface charges. As a consequence, the nanopore performance in practical applications will depend not only on the base and tip openings but also on the pore shape. In particular, we show that the pore opening dimensions estimated from the pore conductance can be very different, depending on the pore shape assumed. The results obtained can also be of practical relevance for the design of nanopores, nanopipettes, and nanoelectrodes, where the electrical interactions between the charges attached to the nanostructure and the mobile charges confined in the reduced volume of the inside solution dictate the device performance in practical applications. Because single tracks are the elementary building blocks for nanoporous membranes, the understanding and control of their individual properties should also be crucial in protein separation, water desalination, and bio-molecule detection using arrays of identical nanopores.

Pore structure and function of synthetic nanopores with fixed charges: tip shape and rectification properties.

PubMed

Ramírez, Patricio; Apel, Pavel Yu; Cervera, Javier; Mafé, Salvador

2008-08-06

We present a complete theoretical study of the relationship between the structure (tip shape and dimensions) and function (selectivity and rectification) of asymmetric nanopores on the basis of previous experimental studies. The theoretical model uses a continuum approach based on the Nernst-Planck equations. According to our results, the nanopore transport properties, such as current-voltage (I-V) characteristics, conductance, rectification ratio, and selectivity, are dictated mainly by the shape of the pore tip (we have distinguished bullet-like, conical, trumpet-like, and hybrid shapes) and the concentration of pore surface charges. As a consequence, the nanopore performance in practical applications will depend not only on the base and tip openings but also on the pore shape. In particular, we show that the pore opening dimensions estimated from the pore conductance can be very different, depending on the pore shape assumed. The results obtained can also be of practical relevance for the design of nanopores, nanopipettes, and nanoelectrodes, where the electrical interactions between the charges attached to the nanostructure and the mobile charges confined in the reduced volume of the inside solution dictate the device performance in practical applications. Because single tracks are the elementary building blocks for nanoporous membranes, the understanding and control of their individual properties should also be crucial in protein separation, water desalination, and bio-molecule detection using arrays of identical nanopores.

Membrane pore formation in atomistic and coarse-grained simulations.

PubMed

Kirsch, Sonja A; Böckmann, Rainer A

2016-10-01

Biological cells and their organelles are protected by ultra thin membranes. These membranes accomplish a broad variety of important tasks like separating the cell content from the outer environment, they are the site for cell-cell interactions and many enzymatic reactions, and control the in- and efflux of metabolites. For certain physiological functions e.g. in the fusion of membranes and also in a number of biotechnological applications like gene transfection the membrane integrity needs to be compromised to allow for instance for the exchange of polar molecules across the membrane barrier. Mechanisms enabling the transport of molecules across the membrane involve membrane proteins that form specific pores or act as transporters, but also so-called lipid pores induced by external fields, stress, or peptides. Recent progress in the simulation field enabled to closely mimic pore formation as supposed to occur in vivo or in vitro. Here, we review different simulation-based approaches in the study of membrane pores with a focus on lipid pore properties such as their size and energetics, poration mechanisms based on the application of external fields, charge imbalances, or surface tension, and on pores that are induced by small molecules, peptides, and lipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. Copyright © 2015 Elsevier B.V. All rights reserved.

Smooth DNA Transport through a Narrowed Pore Geometry

PubMed Central

Carson, Spencer; Wilson, James; Aksimentiev, Aleksei; Wanunu, Meni

2014-01-01

Voltage-driven transport of double-stranded DNA through nanoscale pores holds much potential for applications in quantitative molecular biology and biotechnology, yet the microscopic details of translocation have proven to be challenging to decipher. Earlier experiments showed strong dependence of transport kinetics on pore size: fast regular transport in large pores (> 5 nm diameter), and slower yet heterogeneous transport time distributions in sub-5 nm pores, which imply a large positional uncertainty of the DNA in the pore as a function of the translocation time. In this work, we show that this anomalous transport is a result of DNA self-interaction, a phenomenon that is strictly pore-diameter dependent. We identify a regime in which DNA transport is regular, producing narrow and well-behaved dwell-time distributions that fit a simple drift-diffusion theory. Furthermore, a systematic study of the dependence of dwell time on DNA length reveals a single power-law scaling of 1.37 in the range of 35–20,000 bp. We highlight the resolution of our nanopore device by discriminating via single pulses 100 and 500 bp fragments in a mixture with >98% accuracy. When coupled to an appropriate sequence labeling method, our observation of smooth DNA translocation can pave the way for high-resolution DNA mapping and sizing applications in genomics. PMID:25418307

Fabrication of mesoporous silica for ultra-low-k interlayer dielectrics

NASA Astrophysics Data System (ADS)

Fujii, Nobutoshi; Kohmura, Kazuo; Nakayama, Takahiro; Tanaka, Hirofumi; Hata, Nobuhiro; Seino, Yutaka; Kikkawa, Takamaro

2005-11-01

We have developed sol-gel self-assembly techniques to control the pore structure and diameter of ultra-low-k interlayer dielectric (ILD) films. Porous silica films have been fabricated using cationic and nonionic surfactants as templates, resulting in 2D-hexagonal and disordered pore structures, respectively. The disordered mesoporous silica film has a worm-hole like network of pore channels having a uniform diameter. Precursors of the mesoporous silica films were synthesized by use of tetraethyl-orthosilicate (TEOS), inorganic acid, water, ethanol and various surfactants. The surfactants used were cationic alkyltrimethyl-ammonium (ATMA) chloride surfactants for 2D-hexagonal pores and nonionic tri-block copolymer for disordered structures. Dimethyldiethoxysilane (DMDEOS) was added for forming the disordered mesoporous silica. The disordered cylindrical pore structure with a uniform pore size was fabricated by controlling the static electrical interaction between the surfactant and the silica oligomer with methyl group of DMDEOS. Tetramethylcycrotetrasiloxane (TMCTS) vapor treatment was developed, which improved the mechanical strength of mesoporous silica films. The TMCTS polymer covered the pore wall surface and cross-linked to passivate the mechanical defects in the silica wall. Significant enhancement of mechanical strength was demonstrated by TMCTS vapor treatment. The porous silica film modified with a catalyst and a plasma treatment achieved higher mechanical strength and lower dielectric constant than conventional porous silica films because the TMCTS vapor treatment was more effective for mechanical reinforcement and hydrophobicity.

Pore growth in U-Mo/Al dispersion fuel

NASA Astrophysics Data System (ADS)

Kim, Yeon Soo; Jeong, G. Y.; Sohn, D.-S.; Jamison, L. M.

2016-09-01

U-Mo/Al dispersion fuel is currently under development in the DOE's Material Management and Minimization program to convert HEU-fueled research reactors to LEU-fueled reactors. In some demanding conditions in high-power and high-performance reactors, large pores form in the interaction layers between the U-Mo fuel particles and the Al matrix, which pose a potential to cause fuel failure. In this study, comprehension of the formation and growth of these pores was explored. As a product, a model to predict pore growth and porosity increase was developed. The model includes three major topics: fission gas release from the U-Mo and the IL to the pores, stress evolution in the fuel meat, and the effect of amorphous IL growth. Well-characterized in-pile data from reduced-size plates were used to fit the model parameters. A data set from full-sized plates, independent and distinctively different from those used to fit the model parameters, was used to examine the accuracy of the model. The model showed fair agreement with the measured data. The model suggested that the growth of the IL has a critical effect on pore growth, as both its material properties and energetics are favorable to pore formation. Therefore, one area of the current effort, focused on suppressing IL growth, appears to be on the right track to improve the performance of this fuel.

Electrostatic networks control plug stabilization in the PapC usher.

PubMed

Pham, Thieng; Henderson, Nadine S; Werneburg, Glenn T; Thanassi, David G; Delcour, Anne H

2015-01-01

The PapC usher, a β-barrel pore in the outer membrane of uropathogenic Escherichia coli, is used for assembly of the P pilus, a key virulence factor in bacterial colonization of human kidney cells. Each PapC protein is composed of a 24-stranded β-barrel channel, flanked by N- and C-terminal globular domains protruding into the periplasm, and occluded by a plug domain (PD). The PD is displaced from the channel towards the periplasm during pilus biogenesis, but the molecular mechanism for PD displacement remains unclear. Two structural features within the β-barrel, an α-helix and β5-6 hairpin loop, may play roles in controlling plug stabilization. Here we have tested clusters of residues at the interface of the plug, barrel, α-helix and hairpin, which participate in electrostatic networks. To assess the roles of these residues in plug stabilization, we used patch-clamp electrophysiology to compare the activity of wild-type and mutant PapC channels containing alanine substitutions at these sites. Mutations interrupting each of two salt bridge networks were relatively ineffective in disrupting plug stabilization. However, mutation of two pairs of arginines located at the inner and the outer surfaces of the PD resulted in an enhanced propensity for plug displacement. One arginine pair involved in a repulsive interaction between the linkers that tether the plug to the β-barrel was particularly sensitive to mutation. These results suggest that plug displacement, which is necessary for pilus assembly and translocation, may require a weakening of key electrostatic interactions between the plug linkers, and the plug and the α-helix.

Drosophila TIM binds importin α1, and acts as an adapter to transport PER to the nucleus.

PubMed

Jang, A Reum; Moravcevic, Katarina; Saez, Lino; Young, Michael W; Sehgal, Amita

2015-02-01

Regulated nuclear entry of clock proteins is a conserved feature of eukaryotic circadian clocks and serves to separate the phase of mRNA activation from mRNA repression in the molecular feedback loop. In Drosophila, nuclear entry of the clock proteins, PERIOD (PER) and TIMELESS (TIM), is tightly controlled, and impairments of this process produce profound behavioral phenotypes. We report here that nuclear entry of PER-TIM in clock cells, and consequently behavioral rhythms, require a specific member of a classic nuclear import pathway, Importin α1 (IMPα1). In addition to IMPα1, rhythmic behavior and nuclear expression of PER-TIM require a specific nuclear pore protein, Nup153, and Ran-GTPase. IMPα1 can also drive rapid and efficient nuclear expression of TIM and PER in cultured cells, although the effect on PER is mediated by TIM. Mapping of interaction domains between IMPα1 and TIM/PER suggests that TIM is the primary cargo for the importin machinery. This is supported by attenuated interaction of IMPα1 with TIM carrying a mutation previously shown to prevent nuclear entry of TIM and PER. TIM is detected at the nuclear envelope, and computational modeling suggests that it contains HEAT-ARM repeats typically found in karyopherins, consistent with its role as a co-transporter for PER. These findings suggest that although PER is the major timekeeper of the clock, TIM is the primary target of nuclear import mechanisms. Thus, the circadian clock uses specific components of the importin pathway with a novel twist in that TIM serves a karyopherin-like role for PER.

Backbone dynamics of the antifungal Psd1 pea defensin and its correlation with membrane interaction by NMR spectroscopy.

PubMed

de Medeiros, Luciano Neves; Angeli, Renata; Sarzedas, Carolina G; Barreto-Bergter, Eliana; Valente, Ana Paula; Kurtenbach, Eleonora; Almeida, Fabio C L

2010-02-01

Plant defensins are cysteine-rich cationic peptides, components of the innate immune system. The antifungal sensitivity of certain exemplars was correlated to the level of complex glycosphingolipids in the membrane of fungi strains. Psd1 is a 46 amino acid residue defensin isolated from pea seeds which exhibit antifungal activity. Its structure is characterized by the so-called cysteine-stabilized alpha/beta motif linked by three loops as determined by two-dimensional NMR. In the present work we explored the measurement of heteronuclear Nuclear Overhauser Effects, R1 and R2 (15)N relaxation ratios, and chemical shift to probe the backbone dynamics of Psd1 and its interaction with membrane mimetic systems with phosphatidylcholine (PC) or dodecylphosphocholine (DPC) with glucosylceramide (CMH) isolated from Fusarium solani. The calculated R2 values predicted a slow motion around the highly conserved among Gly12 residue and also in the region of the Turn3 His36-Trp38. The results showed that Psd1 interacts with vesicles of PC or PC:CMH in slightly different forms. The interaction was monitored by chemical shift perturbation and relaxation properties. Using this approach we could map the loops as the binding site of Psd1 with the membrane. The major binding epitope showed conformation exchange properties in the mus-ms timescale supporting the conformation selection as the binding mechanism. Moreover, the peptide corresponding to part of Loop1 (pepLoop1: Gly12 to Ser19) is also able to interact with DPC micelles acquiring a stable structure and in the presence of DPC:CMH the peptide changes to an extended conformation, exhibiting NOE mainly with the carbohydrate and ceramide parts of CMH. Copyright 2009 Elsevier B.V. All rights reserved.

Exploring the Mechanism of Zanamivir Resistance in a Neuraminidase Mutant: A Molecular Dynamics Study

PubMed Central

Han, Nanyu; Liu, Xuewei; Mu, Yuguang

2012-01-01

It is critical to understand the molecular basis of the drug resistance of influenza viruses to efficiently treat this infectious disease. Recently, H1N1 strains of influenza A carrying a mutation of Q136K in neuraminidase were found. The new strain showed a strong Zanamivir neutralization effect. In this study, normal molecular dynamics simulations and metadynamics simulations were employed to explore the mechanism of Zanamivir resistance. The wild-type neuraminidase contained a 310 helix before the 150 loop, and there was interaction between the 150 and 430 loops. However, the helix and the interaction between the two loops were disturbed in the mutant protein due to interaction between K136 and nearby residues. Hydrogen-bond network analysis showed weakened interaction between the Zanamivir drug and E276/D151 on account of the electrostatic interaction between K136 and D151. Metadynamics simulations showed that the free energy landscape was different in the mutant than in the wild-type neuraminidase. Conformation with the global minimum of free energy for the mutant protein was different from the wild-type conformation. While the drug fit completely into the active site of the wild-type neuraminidase, it did not match the active site of the mutant variant. This study indicates that the altered hydrogen-bond network and the deformation of the 150 loop are the key factors in development of Zanamivir resistance. Furthermore, the Q136K mutation has a variable effect on conformation of different N1 variants, with conformation of the 1918 N1 variant being more profoundly affected than that of the other N1 variants studied in this paper. This observation warrants further experimental investigation. PMID:22970161

Exploring the mechanism of zanamivir resistance in a neuraminidase mutant: a molecular dynamics study.

PubMed

Han, Nanyu; Liu, Xuewei; Mu, Yuguang

2012-01-01

It is critical to understand the molecular basis of the drug resistance of influenza viruses to efficiently treat this infectious disease. Recently, H1N1 strains of influenza A carrying a mutation of Q136K in neuraminidase were found. The new strain showed a strong Zanamivir neutralization effect. In this study, normal molecular dynamics simulations and metadynamics simulations were employed to explore the mechanism of Zanamivir resistance. The wild-type neuraminidase contained a 3(10) helix before the 150 loop, and there was interaction between the 150 and 430 loops. However, the helix and the interaction between the two loops were disturbed in the mutant protein due to interaction between K136 and nearby residues. Hydrogen-bond network analysis showed weakened interaction between the Zanamivir drug and E276/D151 on account of the electrostatic interaction between K136 and D151. Metadynamics simulations showed that the free energy landscape was different in the mutant than in the wild-type neuraminidase. Conformation with the global minimum of free energy for the mutant protein was different from the wild-type conformation. While the drug fit completely into the active site of the wild-type neuraminidase, it did not match the active site of the mutant variant. This study indicates that the altered hydrogen-bond network and the deformation of the 150 loop are the key factors in development of Zanamivir resistance. Furthermore, the Q136K mutation has a variable effect on conformation of different N1 variants, with conformation of the 1918 N1 variant being more profoundly affected than that of the other N1 variants studied in this paper. This observation warrants further experimental investigation.