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1

Molecular cloning, overexpression and characterization of a novel water channel protein from Rhodobacter sphaeroides.  

PubMed

Aquaporins are highly selective water channel proteins integrated into plasma membranes of single cell organisms; plant roots and stromae; eye lenses, renal and red blood cells in vertebrates. To date, only a few microbial aquaporins have been characterized and their physiological importance is not well understood. Here we report on the cloning, expression and characterization of a novel aquaporin, RsAqpZ, from a purple photosynthetic bacterium, Rhodobacter sphaeroides ATCC 17023. The protein was expressed homologously at a high yield (?20 mg/L culture) under anaerobic photoheterotrophic growth conditions. Stopped-flow light scattering experiments demonstrated its high water permeability (0.17±0.05 cm/s) and low energy of activation for water transport (2.93±0.60 kcal/mol) in reconstituted proteoliposomes at a protein to lipid ratio (w/w) of 0.04. We developed a fluorescence correlation spectroscopy based technique and utilized a fluorescent protein fusion of RsAqpZ, to estimate the single channel water permeability of RsAqpZ as 1.24 (±0.41) x 10(-12) cm(3)/s or 4.17 (±1.38)×10(10) H2O molecules/s, which is among the highest single channel permeability reported for aquaporins. Towards application to water purification technologies, we also demonstrated functional incorporation of RsAqpZ in amphiphilic block copolymer membranes. PMID:24497982

Erbakan, Mustafa; Shen, Yue-xiao; Grzelakowski, Mariusz; Butler, Peter J; Kumar, Manish; Curtis, Wayne R

2014-01-01

2

Highly permeable polymeric membranes based on the incorporation of the functional water channel protein Aquaporin Z  

PubMed Central

The permeability and solute transport characteristics of amphiphilic triblock-polymer vesicles containing the bacterial water-channel protein Aquaporin Z (AqpZ) were investigated. The vesicles were made of a block copolymer with symmetric poly-(2-methyloxazoline)-poly-(dimethylsiloxane)-poly-(2-methyloxazoline) (PMOXA15-PDMS110-PMOXA15) repeat units. Light-scattering measurements on pure polymer vesicles subject to an outwardly directed salt gradient in a stopped-flow apparatus indicated that the polymer vesicles were highly impermeable. However, a large enhancement in water productivity (permeability per unit driving force) of up to ?800 times that of pure polymer was observed when AqpZ was incorporated. The activation energy (Ea) of water transport for the protein-polymer vesicles (3.4 kcal/mol) corresponded to that reported for water-channel-mediated water transport in lipid membranes. The solute reflection coefficients of glucose, glycerol, salt, and urea were also calculated, and indicated that these solutes are completely rejected. The productivity of AqpZ-incorporated polymer membranes was at least an order of magnitude larger than values for existing salt-rejecting polymeric membranes. The approach followed here may lead to more productive and sustainable water treatment membranes, whereas the variable levels of permeability obtained with different concentrations of AqpZ may provide a key property for drug delivery applications. PMID:18077364

Kumar, Manish; Grzelakowski, Mariusz; Zilles, Julie; Clark, Mark; Meier, Wolfgang

2007-01-01

3

Molecular and functional characterization of multiple aquaporin water channel proteins from the western tarnished plant bug, Lygus hesperus  

Technology Transfer Automated Retrieval System (TEKTRAN)

Aquaporins (AQPs) are integral membrane channel proteins that facilitate the bidirectional transfer of water or other small solutes across biological membranes involved in numerous essential physiological processes. In arthropods, AQPs belong to several subfamilies, which contribute to osmoregulatio...

4

Immunolocalization of the Mercurial-Insensitive Water Channel and Glycerol Intrinsic Protein in Epithelial Cell Plasma Membranes  

Microsoft Academic Search

Two water channel homologs were cloned recently from rat kidney, mercurial-insensitive water channel (MIWC) and glycerol intrinsic protein (GLIP). Polyclonal antibodies were raised against synthetic C-terminal peptides and purified by affinity chromatography. MIWC and GLIP antibodies recognized proteins in rat kidney with an apparent molecular mass of 30 and 27 kDa, respectively, and did not cross-react. By immunofluorescence, MIWC and

Antonio Frigeri; Michael A. Gropper; C. W. Turck; A. S. Verkman

1995-01-01

5

Mutations in AQP5, Encoding a Water-Channel Protein, Cause Autosomal-Dominant Diffuse Nonepidermolytic Palmoplantar Keratoderma  

PubMed Central

Autosomal-dominant diffuse nonepidermolytic palmoplantar keratoderma is characterized by the adoption of a white, spongy appearance of affected areas upon exposure to water. After exome sequencing, missense mutations were identified in AQP5, encoding water-channel protein aquaporin-5 (AQP5). Protein-structure analysis indicates that these AQP5 variants have the potential to elicit an effect on normal channel regulation. Immunofluorescence data reveal the presence of AQP5 at the plasma membrane in the stratum granulosum of both normal and affected palmar epidermis, indicating that the altered AQP5 proteins are trafficked in the normal manner. We demonstrate here a role for AQP5 in the palmoplantar epidermis and propose that the altered AQP5 proteins retain the ability to form open channels in the cell membrane and conduct water. PMID:23830519

Blaydon, Diana C.; Lind, Lisbet K.; Plagnol, Vincent; Linton, Kenneth J.; Smith, Francis J.D.; Wilson, Neil J.; McLean, W.H. Irwin; Munro, Colin S.; South, Andrew P.; Leigh, Irene M.; O’Toole, Edel A.; Lundström, Anita; Kelsell, David P.

2013-01-01

6

Mutations in AQP5, encoding a water-channel protein, cause autosomal-dominant diffuse nonepidermolytic palmoplantar keratoderma.  

PubMed

Autosomal-dominant diffuse nonepidermolytic palmoplantar keratoderma is characterized by the adoption of a white, spongy appearance of affected areas upon exposure to water. After exome sequencing, missense mutations were identified in AQP5, encoding water-channel protein aquaporin-5 (AQP5). Protein-structure analysis indicates that these AQP5 variants have the potential to elicit an effect on normal channel regulation. Immunofluorescence data reveal the presence of AQP5 at the plasma membrane in the stratum granulosum of both normal and affected palmar epidermis, indicating that the altered AQP5 proteins are trafficked in the normal manner. We demonstrate here a role for AQP5 in the palmoplantar epidermis and propose that the altered AQP5 proteins retain the ability to form open channels in the cell membrane and conduct water. PMID:23830519

Blaydon, Diana C; Lind, Lisbet K; Plagnol, Vincent; Linton, Kenneth J; Smith, Francis J D; Wilson, Neil J; McLean, W H Irwin; Munro, Colin S; South, Andrew P; Leigh, Irene M; O'Toole, Edel A; Lundström, Anita; Kelsell, David P

2013-08-01

7

The Role of Water Channel Proteins in Facilitating Recovery of Leaf Hydraulic Conductance from Water Stress in Populus trichocarpa  

PubMed Central

Gas exchange is constrained by the whole-plant hydraulic conductance (Kplant). Leaves account for an important fraction of Kplant and may therefore represent a major determinant of plant productivity. Leaf hydraulic conductance (Kleaf) decreases with increasing water stress, which is due to xylem embolism in leaf veins and/or the properties of the extra-xylary pathway. Water flow through living tissues is facilitated and regulated by water channel proteins called aquaporins (AQPs). Here we assessed changes in the hydraulic conductance of Populus trichocarpa leaves during a dehydration-rewatering episode. While leaves were highly sensitive to drought, Kleaf recovered only 2 hours after plants were rewatered. Recovery of Kleaf was absent when excised leaves were bench-dried and subsequently xylem-perfused with a solution containing AQP inhibitors. We examined the expression patterns of 12 highly expressed AQP genes during a dehydration-rehydration episode to identify isoforms that may be involved in leaf hydraulic adjustments. Among the AQPs tested, several genes encoding tonoplast intrinsic proteins (TIPs) showed large increases in expression in rehydrated leaves, suggesting that TIPs contribute to reversing drought-induced reductions in Kleaf. TIPs were localized in xylem parenchyma, consistent with a role in facilitating water exchange between xylem vessels and adjacent living cells. Dye uptake experiments suggested that reversible embolism formation in minor leaf veins contributed to the observed changes in Kleaf. PMID:25406088

Laur, Joan; Hacke, Uwe G.

2014-01-01

8

Molecular cloning and characterization of a novel chloride intracellular channel-related protein, parchorin, expressed in water-secreting cells.  

PubMed

We previously reported a 120-kDa phosphoprotein that translocated from cytosol to the apical membrane of gastric parietal cells in association with stimulation of HCl secretion. To determine the molecular identity of the protein, we performed molecular cloning and expression of the protein. Immunoblot analysis showed that this protein was highly enriched in tissues that secrete water, such as parietal cell, choroid plexus, salivary duct, lacrimal gland, kidney, airway epithelia, and chorioretinal epithelia. We named this protein "parchorin" based on its highest enrichment in parietal cells and choroid plexus. We obtained cDNA for parchorin from rabbit choroid plexus coding a protein consisting of 637 amino acids with a predicted molecular mass of 65 kDa. The discrepancy in size on 6% SDS-polyacrylamide gel electrophoresis is considered to be due to its highly acidic nature (pI = 4.18), because COS-7 cells transfected with parchorin cDNA produced a protein with apparent molecular mass of 120 kDa on 6% SDS-polyacrylamide gel electrophoresis. Parchorin is a novel protein that has significant homology to the family of chloride intracellular channels (CLIC), especially the chloride channel from bovine kidney, p64, in the C-terminal 235 amino acids. When expressed as a fusion protein with green fluorescent protein (GFP) in the LLC-PK1 kidney cell line, GFP-parchorin, unlike other CLIC family members, existed mainly in the cytosol. Furthermore, when Cl(-) efflux from the cell was elicited, GFP-parchorin translocated to the plasma membrane. These results suggest that parchorin generally plays a critical role in water-secreting cells, possibly through the regulation of chloride ion transport. PMID:10753923

Nishizawa, T; Nagao, T; Iwatsubo, T; Forte, J G; Urushidani, T

2000-04-14

9

Molecular and functional characterization of multiple aquaporin water channel proteins from the western tarnished plant bug, Lygus hesperus.  

PubMed

Aquaporins (AQPs) are integral membrane channel proteins that facilitate the bidirectional transfer of water or other small solutes across biological membranes involved in numerous essential physiological processes. In arthropods, AQPs belong to several subfamilies, which contribute to osmoregulation, respiration, cryoprotection, anhydrobiosis, and excretion. We cloned and characterized five novel AQPs from the western tarnished plant bug, Lygus hesperus, a polyphagous insect pest of food and fiber crops throughout western North America. The L. hesperus AQPs (LhAQP1-5) belong to different phylogenetic subfamilies, have unique transcription profiles and cellular localizations, and all transport water (but not glycerol) when heterologously expressed in Xenopus laevis oocytes. Our results demonstrate that multiple AQPs with possible compensatory functions are produced in L. hesperus that likely play important roles in maintaining water homeostasis in this important insect pest. PMID:24333473

Fabrick, Jeffrey A; Pei, Jinxin; Hull, J Joe; Yool, Andrea J

2014-02-01

10

Rat kidney papilla contains abundant synaptobrevin protein that participates in the fusion of antidiuretic hormone-regulated water channel-containing endosomes in vitro.  

PubMed Central

Antidiuretic hormone (ADH) regulates renal water excretion by altering the permeability of the collecting duct to water. ADH-responsive epithelial cells are the major cell type lining kidney tubules in the inner medulla and papilla. ADH modulates apical membrane water permeability by the insertion and removal of vesicles containing aquaporin collecting duct water channel protein (now termed AQP-2). To identify and characterize proteins responsible for trafficking of AQP-2-containing vesicles, we utilized antibody and cDNA probes to synaptobrevin b (also termed VAMP-2, for vesicle-associated membrane protein 2), a protein that mediates synaptic vesicle exocytosis in the brain and whose structural homologs are now considered to be components of a complex responsible for intracellular vesicle fusion in all cells. We now report that rat kidney inner medulla and papilla contain abundant synaptobrevin protein. Only light endosomes, one of two types of purified papillary AQP-2-containing endosomes, possess synaptobrevin. Light endosomes fuse in vitro by means of an ATP-dependent process that is significantly inhibited when endosomes are preincubated with either anti-synaptobrevin antibody or tetanus toxin. These data define a functional role for a synaptobrevin protein in the fusion of endosomes in vitro. The presence of abundant synaptobrevin proteins in endosomes containing AQP-2 water channels, as well as insulin-sensitive glucose transporters [Cain, C. C., Trimble, W. S. & Lienhard, G. E. (1992) J. Biol. Chem. 267, 11681-11684], and in cells of Malpighian tubules responsible for urine formation in insects [Chin, A. S., Burgess, R. W., Wong, B. R., Schwartz, T. L. & Scheller, R. H. (1993) Gene 131, 175-181] suggests a specialized role for synaptobrevin in vesicle-mediated membrane transport modulated by peptide hormones. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:7534405

Jo, I; Harris, H W; Amendt-Raduege, A M; Majewski, R R; Hammond, T G

1995-01-01

11

Aquaporin water channels - from atomic structure to clinical medicine  

Microsoft Academic Search

The water permeability of biological membranes has been a longstanding problem in physiology, but the proteins responsible for this remained unknown until discovery of the aquaporin 1 (AQP1) water channel protein. AQP1 is selectively permeated by water driven by osmotic gradients. The atomic structure of human AQP1 has recently been defined. Each subunit of the tetramer contains an individual aqueous

Peter Agre; Landon S. King; Masato Yasui; Wm B. Guggino; Ole Petter Ottersen; Yoshinori Fujiyoshi; Andreas Engel; Søren Nielsen

2002-01-01

12

Computational optimization of synthetic water channels.  

SciTech Connect

Membranes for liquid and gas separations and ion transport are critical to water purification, osmotic energy generation, fuel cells, batteries, supercapacitors, and catalysis. Often these membranes lack pore uniformity and robustness under operating conditions, which can lead to a decrease in performance. The lack of uniformity means that many pores are non-functional. Traditional membranes overcome these limitations by using thick membrane materials that impede transport and selectivity, which results in decreased performance and increased operating costs. For example, limitations in membrane performance demand high applied pressures to deionize water using reverse osmosis. In contrast, cellular membranes combine high flux and selective transport using membrane-bound protein channels operating at small pressure differences. Pore size and chemistry in the cellular channels is defined uniformly and with sub-nanometer precision through protein folding. The thickness of these cellular membranes is limited to that of the cellular membrane bilayer, about 4 nm thick, which enhances transport. Pores in the cellular membranes are robust under operating conditions in the body. Recent efforts to mimic cellular water channels for efficient water deionization produced a significant advance in membrane function. The novel biomimetic design achieved a 10-fold increase in membrane permeability to water flow compared to commercial membranes and still maintained high salt rejection. Despite this success, there is a lack of understanding about why this membrane performs so well. To address this lack of knowledge, we used highperformance computing to interrogate the structural and chemical environments experienced by water and electrolytes in the newly created biomimetic membranes. We also compared the solvation environments between the biomimetic membrane and cellular water channels. These results will help inform future efforts to optimize and tune the performance of synthetic biomimetic membranes for applications in water purification, energy, and catalysis.

Rogers, David Michael; Rempe, Susan L. B.

2012-12-01

13

Heteromultimeric channels formed by rat brain potassium-channel proteins  

Microsoft Academic Search

AN important step towards understanding the molecular basis of the functional diversity of voltage-gated K+ channels in the mammalian brain has been the discovery of a family of genes encoding rat brain K+ channel-forming (RCK) proteins1-6. All species of these RCK proteins form homomultimeric voltage-gated K+ channels with distinct functional characteristics in Xenopus laevis oocytes following injection of the respective

J. Peter Ruppersberg; Klaus H. Schröter; Bert Sakmann; Martin Stocker; Sabine Sewing; Olaf Pongs

1990-01-01

14

Channel Regulation by Extracellular Redox Protein  

PubMed Central

The most widely studied stimuli for ion channel activation are changes in membrane voltage and binding of a chemical ligand in a pocket of the channel protein. While modulation by redox potential has also been appreciated our study shows previously unrecognised channel activation via electron donation from the extracellular redox protein thioredoxin (TRX)1. The ion channel type involved is a member of the Transient Receptor Potential (TRP) family. Activation by TRX led us to consider the relevance of TRP channels to the inflammatory condition of rheumatoid arthritis, where functions of ion channels are relatively unknown and TRX concentrations are high. TRP channel activation was found to be inhibitory for secretion of matrix metalloproteinases, suggesting activation by TRX may have a protective role against disease. Here we expand on our original article and discuss the potential wider implications of the findings in terms of concepts for channel activation and relevance to other ion channel types and systems. PMID:18690048

Beech, David J; Sukumar, Piruthivi

2009-01-01

15

Regulation of Ion Channels by G Proteins  

NSDL National Science Digital Library

This Teaching Resource provides lecture notes and slides for a class covering regulation of ion channels by G proteins and is part of the course "Cell Signaling Systems: A Course for Graduate Students." The lecture begins with an overview of calcium channels and then proceeds to describe the interaction of signaling molecules with calcium channels.

Maria Diverse-Pierluissi (Mount Sinai School of Medicine.;Department of Pharmacology and Biological Chemistry REV)

2005-08-16

16

The plasma membrane of Arabidopsis thaliana contains a mercury- insensitive aquaporin that is a homolog of the tonoplast water channel protein TIP  

Microsoft Academic Search

Plant cells contain proteins that are members of the major intrinsic protein (MIP) family, an ancient family of membrane channel proteins characterized by six membrane-spanning domains and two asparagine-proline-alanine (NPA) amino acid motifs in the two halves of the protein. We recently demonstrated that y- TIP, one of the MIP homologs found in the vacuolar membrane of plant cells, is

Mark J. Daniels; T. Erik Mirkov; Maarten J. Chrispeels

1994-01-01

17

Complex micropatterning of proteins within microfluidic channels.  

PubMed

Microfluidic channels containing protein micropatterned surfaces are useful in many bioanalytical and biological applications. In this study, we developed a new method to integrate microfluidics and protein micropatterning by attaching poly(dimethylsiloxane) (PDMS) microfluidic channels to bio-friendly photoresist films via poly(dopamine) (PDA) adhesive. A bio-friendly photoresist poly(2,2-dimethoxy nitrobenzyl methacrylate-r-methyl methacrylate-r-poly(ethylene glycol) methacrylate) (PDMP) was synthesized and used. By performing microscope projection photolithography (MPP) to the PDMP thin films within PDMS microchannels, complex micropatterns of proteins were successfully generated within microfluidic channels. PMID:25570075

Miju Kim; Junsang Doh

2014-08-01

18

Water-protein interactions  

SciTech Connect

The interaction of macromolecules with solvent water is an important determinant of their properties, but this relationship has not yet been described satisfactorily. The following experiments focus on the process of protein hydration - the addition of water to dry protein to obtain the solution state. A detailed description of the sequence of hydration events is expected to produce a fuller understanding of the protein in dilute solution. This approach is analogous to the use of studies of protein unfolding for understanding the folded state. Heat capacity measurements (1) are of particular interest. These can be carried out over the full range of system composition, from dry protein to the dilute solution, and they serve to correlate information obtained by other techniques that can be applied only to solution or solid state but not both. The dependence of the heat capacity on water activity defines stages in the hydration process and suggests the following simple picture of it: water at the lowest activity, 0-0.07 h (g of water/g of protein), bound principally to ionizable groups; in the mid-range of water activity, 0.07 to 0.25 h, surface clusters form, probably centered on polar surface elements; these clusters are mobile, with heat capacity greater than bulk water, and grow with increased water activity until after the polar sites are saturated at 0.25 h. There is a condensation of water over the most weakly interacting portions of the surface, resulting in completion of a water monolayer containing approx. 300 molecules. From this hydration level, 0.38 h, to the dilute solution there are no changes in thermal properties of the protein.

Rupley, J.A.; Yang, P.H.; Tollin, G.

1980-10-01

19

Membrane-Protein Interactions in Mechanosensitive Channels  

PubMed Central

In this article, we examine the mechanical role of the lipid bilayer in ion channel conformation and function with specific reference to the case of the mechanosensitive channel of large conductance (MscL). In a recent article we argued that mechanotransduction very naturally arises from lipid-protein interactions by invoking a simple analytic model of the MscL channel and the surrounding lipid bilayer. In this article, we focus on improving and expanding this analytic framework for studying lipid-protein interactions with special attention to MscL. Our goal is to generate simple scaling relations which can be used to provide qualitative understanding of the role of membrane mechanics in protein function and to quantitatively interpret experimental results. For the MscL channel, we find that the free energies induced by lipid-protein interaction are of the same order as the measured free energy differences between conductance states. We therefore conclude that the mechanics of the bilayer plays an essential role in determining the conformation and function of the channel. Finally, we compare the predictions of our model to experimental results from the recent investigations of the MscL channel by a variety of investigators and suggest a suite of new experiments. PMID:15542561

Wiggins, Paul; Phillips, Rob

2005-01-01

20

Quaternary Ammonium Compounds as Water Channel Blockers  

E-print Network

, West Mains Road, EH9 3JJ Scotland, United Kingdom Excessive water uptake through Aquaporins (AQP) canQuaternary Ammonium Compounds as Water Channel Blockers SPECIFICITY, POTENCY, AND SITE OF ACTION, potency, and binding site of tetraethyl- ammonium (TEA) to block Aquaporin water permeability. Using

de Groot, Bert

21

Reconstitution of a chloroplast protein import channel.  

PubMed Central

The chloroplastic outer envelope protein OEP75 with a molecular weight of 75 kDa probably forms the central pore of the protein import machinery of the outer chloroplastic membrane. Patch-clamp analysis shows that heterologously expressed, purified and reconstituted OEP75 constitutes a voltage-gated ion channel with a unit conductance of Lambda = 145pS. Activation of the OEP75 channel in vitro is completely dependent on the magnitude and direction of the voltage gradient. Therefore, movements of protein charges of parts of OEP75 in the membrane electric field are required either for pore formation or its opening. In the presence of precursor protein from only one side of the bilayer, strong flickering and partial closing of the channel was observed, indicating a specific interaction of the precursor with OEP75. The comparatively low ionic conductance of OEP75 is compatible with a rather narrow aqueous pore (dporeapproximately equal to 8-9 A). Provided that protein and ion translocation occur through the same pore, this implies that the environment of the polypeptide during the transit is mainly hydrophilic and that protein translocation requires almost complete unfolding of the precursor. PMID:9405364

Hinnah, S C; Hill, K; Wagner, R; Schlicher, T; Soll, J

1997-01-01

22

Chlorella virus MT325 encodes water and potassium channels that interact synergistically  

PubMed Central

Fast and selective transport of water through cell membranes is facilitated by water channels. Water channels belonging to the major intrinsic proteins (MIPs) family have been found in all three domains of life, Archaea, Bacteria, and Eukarya. Here we show that Chlorella virus MT325 has a water channel gene, aqpv1, that forms a functional aquaglyceroporin in oocytes. aqpv1 is transcribed during infection together with MT325 kcv, a gene encoding a previously undescribed type of viral potassium channel. Coexpression of AQPV1 and MT325-Kcv in Xenopus oocytes synergistically increases water transport, suggesting a possible concerted action of the two channels in the infection cycle. The two channels operate by a thermodynamically coupled mechanism that simultaneously alters water conductance and driving force for water movement. Considering the universal role of osmosis, this mechanism is relevant to any cell coexpressing water and potassium channels and could have pathological as well as basic physiological relevance. PMID:16569697

Gazzarrini, Sabrina; Kang, Ming; Epimashko, Svetlana; Van Etten, James L.; Dainty, Jack; Thiel, Gerhard; Moroni, Anna

2006-01-01

23

ThermoTRP channels as modular proteins with allosteric gating  

Microsoft Academic Search

Ion channels activate by sensing stimuli such as membrane voltage, ligand binding or temperature and transduce this information into conformational changes that open the channel pore. Thus, a key question in understanding ion channel function is how do the protein domains involved in sensing stimuli (sensors) and opening the pore (gates) communicate. In this regard, transient receptor potential (TRP) channels

Ramon Latorre; Sebastian Brauchi; Gerardo Orta; Cristián Zaelzer; Guillermo Vargas

2007-01-01

24

Water at interface with proteins  

E-print Network

Water is essential for the activity of proteins. However, the effect of the properties of water on the behavior of proteins is only partially understood. Recently, several experiments have investigated the relation between the dynamics of the hydration water and the dynamics of protein. These works have generated a large amount of data whose interpretation is debated. New experiments measure the dynamics of water at low temperature on the surface of proteins, finding a qualitative change (crossover) that might be related to the slowing down and stop of the protein's activity (protein glass transition), possibly relevant for the safe preservation of organic material at low temperature. To better understand the experimental data several scenarios have been discussed. Here, we review these experiments and discuss their interpretations in relation with the anomalous properties of water. We summarize the results for the thermodynamics and dynamics of supercooled water at an interface. We consider also the effect of water on protein stability, making a step in the direction of understanding, by means of Monte Carlo simulations and theoretical calculations, how the interplay of water cooperativity and hydrogen bonds interfacial strengthening affects the protein cold denaturation.

Giancarlo Franzese; Valentino Bianco; Svilen Iskrov

2010-12-07

25

Alternative splicing switches potassium channel sensitivity to protein phosphorylation.  

PubMed

Alternative exon splicing and reversible protein phosphorylation of large conductance calcium-activated potassium (BK) channels represent fundamental control mechanisms for the regulation of cellular excitability. BK channels are encoded by a single gene that undergoes extensive, hormonally regulated exon splicing. In native tissues BK channels display considerable diversity and plasticity in their regulation by cAMP-dependent protein kinase (PKA). Differential regulation of alternatively spliced BK channels by PKA may provide a molecular basis for the diversity and plasticity of BK channel sensitivities to PKA. Here we demonstrate that PKA activates BK channels lacking splice inserts (ZERO) but inhibits channels expressing a 59-amino acid exon at splice site 2 (STREX-1). Channel activation is dependent upon a conserved C-terminal PKA consensus motif (S869), whereas inhibition is mediated via a STREX-1 exon-specific PKA consensus site. Thus, alternative splicing acts as a molecular switch to determine the sensitivity of potassium channels to protein phosphorylation. PMID:11244090

Tian, L; Duncan, R R; Hammond, M S; Coghill, L S; Wen, H; Rusinova, R; Clark, A G; Levitan, I B; Shipston, M J

2001-03-16

26

Lipid ion channels and the role of proteins.  

PubMed

In the absence of proteins, synthetic lipid membranes can display quantized conduction events for ions that are virtually indistinguishable from those of protein channels. The phenomenological similarities between typical conductances are striking: they are of equal order and show similar lifetime distributions and current histograms. They can include conduction bursts, flickering, and multistep conductance. Lipid channels can be gated by voltage and blocked by drugs. They respond to changes in lateral membrane tension and temperature. Thus, they behave like voltage-gated, temperature-gated, and mechano-sensitive protein channels, or like receptors. The similarity between lipid and protein channels poses an important problem for the interpretation of protein channel data. For example, the Hodgkin-Huxley theory for nerve pulse conduction requires a selective mechanism for the conduction of sodium and potassium ions. To this end, the lipid membrane must act both as a capacitor and as an insulator. Nonselective ion conductance by mechanisms other than the gated protein channels challenges the proposed mechanism for pulse propagation. Nevertheless, textbooks rarely describe the properties of the lipid membrane surrounding the proteins in their discussions of membrane models. These similarities lead to important questions: Do these similarities in lipid and protein channels result from a common mechanism, or are these similarities fortuitous? What distinguishes protein channels from lipid channels, if anything? In this Account, we document experimental and theoretical findings that show the similarity between lipid and protein channels. We discuss important cases where protein channel function strongly correlates with the properties of the lipid. Based on statistical thermodynamics simulations, we discuss how such correlations could come about. We suggest that proteins can act as catalysts for lipid channel formation and that this hypothesis can explain some of the unexplained correlations between protein and lipid membrane function. PMID:23902303

Mosgaard, Lars D; Heimburg, Thomas

2013-12-17

27

1. INTAKE CHANNEL LOOKING NORTHEAST; WATER FROM BEAVER BROOK ENTERS ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1. INTAKE CHANNEL LOOKING NORTHEAST; WATER FROM BEAVER BROOK ENTERS THE INTAKE CHANNEL HERE. - Hondius Water Line, 1.6 miles Northwest of Park headquarters building & 1 mile Northwest of Beaver Meadows entrance station, Estes Park, Larimer County, CO

28

Aquaporin water channels in the nervous system  

PubMed Central

The aquaporins (AQPs) are plasma membrane water-transporting proteins. AQP4 is the principal member of this protein family in the CNS, where it is expressed in astrocytes and is involved in water movement, cell migration and neuroexcitation. AQP1 is expressed in the choroid plexus, where it facilitates cerebrospinal fluid secretion, and in dorsal root ganglion neurons, where it tunes pain perception. The AQPs are potential drug targets for several neurological conditions. Astrocytoma cells strongly express AQP4, which may facilitate their infiltration into the brain, and the neuroinflammatory disease neuromyelitis optica is caused by AQP4-specific autoantibodies that produce complement-mediated astrocytic damage. PMID:23481483

Papadopoulos, Marios C.; Verkman, Alan S.

2013-01-01

29

Gating of the mechanosensitive channel protein MscL: the interplay of membrane and protein.  

PubMed

The mechanosensitive channel of large conductance (MscL) belongs to a family of transmembrane channel proteins in bacteria and functions as a safety valve that relieves the turgor pressure produced by osmotic downshock. MscL gating can be triggered solely by stretching of the membrane. This work reports an effort to understand this mechanotransduction by means of molecular dynamics (MD) simulation on the MscL of mycobacterium tuberculosis embedded in a palmitoyloleoylphosphatidylethanolamine membrane. Equilibrium MD under zero membrane tension produced a more compact protein structure, as measured by its radii of gyration, compared to the crystal structure, in agreement with previous experimental findings. Even under a large applied tension up to 1000 dyn/cm, the MscL lateral dimension largely remained unchanged after up to 20 ns of simulation. A nonequilibrium MD simulation of 3% membrane expansion showed a significant increase in membrane rigidity upon MscL inclusion, which can contribute to efficient mechanotransduction. Direct observation of channel opening was possible only when an explicit lateral bias force was applied to each of the five subunits of MscL in the radially outward direction. Using this force, open structures with a large pore of radius 10 A could be obtained. The channel opening takes place in a stepwise manner and concurrently with the water chain formation across the channel, which occurs without direct involvement of protein hydrophilic residues. The N-terminal S1 helices stabilize the open structure, and the membrane asymmetry (different lipid density on the two leaflets of membrane) promotes channel opening. PMID:18212020

Jeon, Jonggu; Voth, Gregory A

2008-05-01

30

The enigma of the CLIC proteins: Ion channels, redox proteins, enzymes, scaffolding proteins?  

PubMed

Chloride intracellular channel proteins (CLICs) are distinct from most ion channels in that they have both soluble and integral membrane forms. CLICs are highly conserved in chordates, with six vertebrate paralogues. CLIC-like proteins are found in other metazoans. CLICs form channels in artificial bilayers in a process favoured by oxidising conditions and low pH. They are structurally plastic, with CLIC1 adopting two distinct soluble conformations. Phylogenetic and structural data indicate that CLICs are likely to have enzymatic function. The physiological role of CLICs appears to be maintenance of intracellular membranes, which is associated with tubulogenesis but may involve other substructures. PMID:20085760

Littler, Dene R; Harrop, Stephen J; Goodchild, Sophia C; Phang, Juanita M; Mynott, Andrew V; Jiang, Lele; Valenzuela, Stella M; Mazzanti, Michele; Brown, Louise J; Breit, Samuel N; Curmi, Paul M G

2010-05-17

31

Efficient mapping of ligand migration channel networks in dynamic proteins.  

PubMed

For many proteins such as myoglobin, the binding site lies in the interior, and there is no obvious route from the exterior to the binding site in the average structure. Although computer simulations for a limited number of proteins have found some transiently open channels, it is not clear if there exist more channels elsewhere or how the channels are regulated. A systematic approach that can map out the whole ligand migration channel network is lacking. Ligand migration in a dynamic protein resembles closely a well-studied problem in robotics, namely, the navigation of a mobile robot in a dynamic environment. In this work, we present a novel robotic motion planning inspired approach that can map the ligand migration channel network in a dynamic protein. The method combines an efficient spatial mapping of protein inner space with a temporal exploration of protein structural heterogeneity, which is represented by a structure ensemble. The spatial mapping of each conformation in the ensemble produces a partial map of protein inner cavities and their inter-connectivity. These maps are then merged to form a super map that contains all the channels that open dynamically. Results on the pathways in myoglobin for gaseous ligands demonstrate the efficiency of our approach in mapping the ligand migration channel networks. The results, obtained in a significantly less amount of time than trajectory-based approaches, are in agreement with previous simulation results. Additionally, the method clearly illustrates how and what conformational changes open or close a channel. PMID:21638334

Lin, Tu-Liang; Song, Guang

2011-08-01

32

Aquaporin water channels in transepithelial fluid transport  

PubMed Central

Aquaporins (AQPs) are membrane water channels that are involved in a diverse set of functions in mammalian physiology including epithelial fluid transport, brain water balance, cell migration, cell proliferation, neuroexcitation, fat metabolism, epidermal hydration, and others. Phenotype analysis of knockout mice has demonstrated an important role for AQPs in transepithelial fluid transport in kidney tubules, salivary and airway submucosal glands, choroid plexus and ciliary epithelium. The physiological functions of these epithelia, such as absorption of glomerular filtrate by proximal tubule and secretion of saliva by salivary gland, involve rapid transcellular water transport across epithelial cell barriers. Studies in knockout mice have also provided evidence that AQPs are not physiologically important in some epithelia where they are expressed, including lacrimal gland, sweat gland, gallbladder, alveoli and airways. Rates of transepithelial fluid transport per unit membrane surface area in these epithelia are substantially lower than transepithelial fluid transport rates in proximal tubule and salivary gland. Pharmacological inhibition of AQP water permeability in epithelia, with consequent reduced fluid transport, offers potential therapy for human diseases involving water imbalance such as congestive heart failure, hypertension and glaucoma. PMID:20224178

Tradtrantip, Lukmanee; Tajima, Masato; Li, Lihua; Verkman, AS

2013-01-01

33

Iterative Water-filling for Gaussian Vector Multiple Access Channels  

E-print Network

Iterative Water-filling for Gaussian Vector Multiple Access Channels W. Yu, W. Rhee, S. Boyd, and J. Cioffi Zhenlei Shen Lehigh University March 29, 2005 Zhenlei Shen (Lehigh) Iterative Water-filling for Gaussian Vector Multiple Access ChannelsMarch 29, 2005 1 / 13 #12;1 Quick Review 2 Iterative Water

Li, Tiffany Jing

34

Ion channel regulation by protein S-acylation.  

PubMed

Protein S-acylation, the reversible covalent fatty-acid modification of cysteine residues, has emerged as a dynamic posttranslational modification (PTM) that controls the diversity, life cycle, and physiological function of numerous ligand- and voltage-gated ion channels. S-acylation is enzymatically mediated by a diverse family of acyltransferases (zDHHCs) and is reversed by acylthioesterases. However, for most ion channels, the dynamics and subcellular localization at which S-acylation and deacylation cycles occur are not known. S-acylation can control the two fundamental determinants of ion channel function: (1) the number of channels resident in a membrane and (2) the activity of the channel at the membrane. It controls the former by regulating channel trafficking and the latter by controlling channel kinetics and modulation by other PTMs. Ion channel function may be modulated by S-acylation of both pore-forming and regulatory subunits as well as through control of adapter, signaling, and scaffolding proteins in ion channel complexes. Importantly, cross-talk of S-acylation with other PTMs of both cysteine residues by themselves and neighboring sites of phosphorylation is an emerging concept in the control of ion channel physiology. In this review, I discuss the fundamentals of protein S-acylation and the tools available to investigate ion channel S-acylation. The mechanisms and role of S-acylation in controlling diverse stages of the ion channel life cycle and its effect on ion channel function are highlighted. Finally, I discuss future goals and challenges for the field to understand both the mechanistic basis for S-acylation control of ion channels and the functional consequence and implications for understanding the physiological function of ion channel S-acylation in health and disease. PMID:24821965

Shipston, Michael J

2014-06-01

35

Water transport by the bacterial channel alpha-hemolysin  

NASA Technical Reports Server (NTRS)

This study is an investigation of the ability of the bacterial channel alpha-hemolysin to facilitate water permeation across biological membranes. alpha-Hemolysin channels were incorporated into rabbit erythrocyte ghosts at varying concentrations, and water permeation was induced by mixing the ghosts with hypertonic sucrose solutions. The resulting volume decrease of the ghosts was followed by time-resolved optical absorption at pH 5, 6, and 7. The average single-channel permeability coefficient of alpha-hemolysin for water ranged between 1.3x10-12 cm/s and 1.5x10-12 cm/s, depending on pH. The slightly increased single-channel permeability coefficient at lower pH-values was attributed to an increase in the effective pore size. The activation energy of water transport through the channel was low (Ea=5.4 kcal/mol), suggesting that the properties of water inside the alpha-hemolysin channel resemble those of bulk water. This conclusion was supported by calculations based on macroscopic hydrodynamic laws of laminar water flow. Using the known three-dimensional structure of the channel, the calculations accurately predicted the rate of water flow through the channel. The latter finding also indicated that water permeation data can provide a good estimate of the pore size for large channels.

Paula, S.; Akeson, M.; Deamer, D.

1999-01-01

36

BIOCHEMISTRY: TRP Ion Channels--Two Proteins in One  

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. It is well established that some proteins carry out more than one job in the cell, but so far, ion channels do not appear to exhibit this versatility. In their Perspective, Levitan and Cibulsky discuss a cluster of new findings showing that two members of the long TRP ion channel family, LTRPC7 and LTRPC2, are both ion channels and enzymes.

Irwin B. Levitan (University of Pennsylvania School of Medicine;Department of Neuroscience); Susan M. Cibulsky (University of Pennsylvania School of Medicine;Department of Neuroscience)

2001-08-17

37

Small potassium ion channel proteins encoded by chlorella viruses  

PubMed Central

Kcv, a 94-aa protein encoded by Paramecium bursaria chlorella virus 1, is the smallest known protein to form a functional potassium ion channel and basically corresponds to the “pore module” of potassium channels. Both viral replication and channel activity are inhibited by the ion channel blockers barium and amantadine but not by cesium. Genes encoding Kcv-like proteins were isolated from 40 additional chlorella viruses. Differences in 16 of the 94 amino acids were detected, producing six Kcv-like proteins with amino acid substitutions occurring in most of the functional domains of the protein (N terminus, transmembrane 1, pore helix, selectivity filter, and transmembrane 2). The six proteins form functional potassium selective channels in Xenopus oocytes with different properties including altered current kinetics and inhibition by cesium. The amino acid changes together with the different properties observed in the six Kcv-like channels will be used to guide site-directed mutations, either singularly or in combination, to identify key amino acids that confer specific properties to Kcv. PMID:14762169

Kang, Ming; Moroni, Anna; Gazzarrini, Sabrina; DiFrancesco, Dario; Thiel, Gerhard; Severino, Maria; Van Etten, James L.

2004-01-01

38

Viral channel forming proteins — Modeling the target  

Microsoft Academic Search

The cellular and subcellular membranes encounter an important playground for the activity of membrane proteins encoded by viruses. Viral membrane proteins, similar to their host companions, can be integral or attached to the membrane. They are involved in directing the cellular and viral reproduction, the fusion and budding processes. This review focuses especially on those integral viral membrane proteins which

Wolfgang B. Fischer; Hao-Jen Hsu

2011-01-01

39

G protein inhibition of CaV2 calcium channels  

PubMed Central

Voltage-gated Ca2+ channels translate the electrical inputs of excitable cells into biochemical outputs by controlling influx of the ubiquitous second messenger Ca2+. As such the channels play pivotal roles in many cellular functions including the triggering of neurotransmitter and hormone release by CaV2.1 (P/Q-type) and CaV2.2 (N-type) channels. It is well established that G protein coupled receptors (GPCRs) orchestrate precise regulation neurotransmitter and hormone release through inhibition of CaV2 channels. Although the GPCRs recruit a number of different pathways, perhaps the most prominent, and certainly most studied among these is the so-called voltage-dependent inhibition mediated by direct binding of G?? to the ?1 subunit of CaV2 channels. This article will review the basics of Ca2+-channels and G protein signaling, and the functional impact of this now classical inhibitory mechanism on channel function. It will also provide an update on more recent developments in the field, both related to functional effects and crosstalk with other signaling pathways, and advances made toward understanding the molecular interactions that underlie binding of G?? to the channel and the voltage-dependence that is a signature characteristic of this mechanism. PMID:21150298

2010-01-01

40

Physiological evidence that pyramidal neurons lack functional water channels.  

PubMed

The physiological conditions that swell mammalian neurons are clinically important but contentious. Distinguishing the neuronal component of brain swelling requires viewing intact neuronal cell bodies, dendrites, and axons and measuring their changing volume in real time. Cultured or dissociated neuronal somata swell within minutes under acutely overhydrated conditions and shrink when strongly dehydrated. But paradoxically, most central nervous system (CNS) neurons do not express aquaporins, the membrane channels that conduct osmotically driven water. Using 2-photon laser scanning microscopy (2PLSM), we monitored neuronal volume under osmotic stress in real time. Specifically, the volume of pyramidal neurons in cerebral cortex and axon terminals comprising cerebellar mossy fibers was measured deep within live brain slices. The expected swelling or shrinking of the gray matter was confirmed by recording altered light transmittance and by indirectly measuring extracellular resistance over a wide osmotic range of -80 to +80 milliOsmoles (mOsm). Neurons expressing green fluorescent protein were then imaged with 2PLSM between -40 and +80 mOsm over 20 min. Surprisingly, pyramidal somata, dendrites, and spines steadfastly maintained their volume, as did the cerebellar axon terminals. This precluded a need for the neurons to acutely regulate volume, preserved their intrinsic electrophysiological stability, and confirmed that these CNS nerve cells lack functional aquaporins. Thus, whereas water easily permeates the aquaporin-rich endothelia and glia driving osmotic brain swelling, neurons tenatiously maintain their volume. However, these same neurons then swell dramatically upon oxygen/glucose deprivation or [K+]0 elevation, so prolonged depolarization (as during stroke or seizure) apparently swells neurons by opening nonaquaporin channels to water. PMID:16723408

Andrew, R David; Labron, Mark W; Boehnke, Susan E; Carnduff, Lisa; Kirov, Sergei A

2007-04-01

41

The ammonia channel protein AmtB from Escherichia coli is a polytopic membrane protein with a cleavable signal peptide  

E-print Network

The ammonia channel protein AmtB from Escherichia coli is a polytopic membrane protein protein. Abstract The Escherichia coli ammonia channel protein, AmtB, is a homotrimeric polytopic inner et al., 2003; K¨all et al., 2004). The Amt proteins constitute a family of ammonia chan- nel proteins

Merrick, Mike

42

Water Transport in Hydrophilic Channels of Nafion (DMR 0819860)  

E-print Network

Water Transport in Hydrophilic Channels of Nafion (DMR 0819860) Qiao Zhao, Paul Majsztrik and Jay, consists of sulfonic acid groups dispersed in a teflon-like hydrophobic matrix. It was shown that water of the sulfonic acids; (ii) (10%water forms a hydration shell and forms a hydrophilic percolation pathway

Petta, Jason

43

Conductance and block of hair-cell mechanotransducer channels in transmembrane channel–like protein mutants  

PubMed Central

Transmembrane channel–like (TMC) proteins TMC1 and TMC2 are crucial to the function of the mechanotransducer (MT) channel of inner ear hair cells, but their precise function has been controversial. To provide more insight, we characterized single MT channels in cochlear hair cells from wild-type mice and mice with mutations in Tmc1, Tmc2, or both. Channels were recorded in whole-cell mode after tip link destruction with BAPTA or after attenuating the MT current with GsMTx-4, a peptide toxin we found to block the channels with high affinity. In both cases, the MT channels in outer hair cells (OHCs) of wild-type mice displayed a tonotopic gradient in conductance, with channels from the cochlear base having a conductance (110 pS) nearly twice that of those at the apex (62 pS). This gradient was absent, with channels at both cochlear locations having similar small conductances, with two different Tmc1 mutations. The conductance of MT channels in inner hair cells was invariant with cochlear location but, as in OHCs, was reduced in either Tmc1 mutant. The gradient of OHC conductance also disappeared in Tmc1/Tmc2 double mutants, in which a mechanically sensitive current could be activated by anomalous negative displacements of the hair bundle. This “reversed stimulus–polarity” current was seen with two different Tmc1/Tmc2 double mutants, and with Tmc1/Tmc2/Tmc3 triple mutants, and had a pharmacological sensitivity comparable to that of native MT currents for most antagonists, except dihydrostreptomycin, for which the affinity was less, and for curare, which exhibited incomplete block. The existence in the Tmc1/Tmc2 double mutants of MT channels with most properties resembling those of wild-type channels indicates that proteins other than TMCs must be part of the channel pore. We suggest that an external vestibule of the MT channel may partly account for the channel’s large unitary conductance, high Ca2+ permeability, and pharmacological profile, and that this vestibule is disrupted in Tmc mutants. PMID:24981230

Beurg, Maryline; Kim, Kyunghee X.

2014-01-01

44

Zn2+ interaction with Alzheimer amyloid beta protein calcium channels.  

PubMed Central

The Alzheimer disease 40-residue amyloid beta protein (AbetaP[1-40]) forms cation-selective channels across acidic phospholipid bilayer membranes with spontaneous transitions over a wide range of conductances ranging from 40 to 4000 pS. Zn2+ has been reported to bind to AbetaP[1-40] with high affinity, and it has been implicated in the formation of amyloid plaques. We now report the functional consequences of such Zn2+ binding for the AbetaP[1-40] channel. Provided the AbetaP[1-40] channel is expressed in the low conductance (<400 pS) mode, Zn2+ blocks the open channel in a dose- dependent manner. For AbetaP[1-40] channels in the giant conductance mode (>400 pS), Zn2+ doses in the millimolar range were required to exert substantial blockade. The Zn2+ chelator o-phenanthroline reverses the blockade. We also found that Zn2+ modulates AbetaP[1-40] channel gating and conductance only from one side of the channel. These data are consistent with predictions of our recent molecular modeling studies on AbetaP[1-40] channels indicating asymmetric Zn(2+)-AbetaP[1-40] interactions at the entrance to the pore. PMID:8643694

Arispe, N; Pollard, H B; Rojas, E

1996-01-01

45

Regulation of ion channels by CAMP-dependent protein kinase and A-kinase anchoring proteins  

E-print Network

-dependent protein kinase is achieved, in part, through association with A-kinase anchoring proteins (AKAPs). Recent evidence suggests that specific AKAPs direct the kinase to submembrane sites to facilitate phosphorylation and modulation of a variety of ion channels. A new membrane-anchored AKAP targets CAMP-dependent protein kinase

Scott, John D.

46

Determinants of G protein inhibition of presynaptic calcium channels  

Microsoft Academic Search

The modulation of presynaptic calcium (Ca) channels by heterotrimeric G proteins is a key factor for the regulation of neurotransmission.\\u000a Over the past 20 yr, a significant understanding of the molecular events underlying this regulation has been acquired. It\\u000a is now widely accepted that binding of G protein ?? dimers directly to the cytoplasmic region linking domains I and II

Gerald W. Zamponi

2001-01-01

47

Protein Properties in Water-Reduced & Water-Free Media  

E-print Network

Protein Properties in Water-Reduced & Water-Free Media Alpay Taralp, Sabanci University, IstanbulH & temperature extremes Locating/purifying thermophiles, etc. Genetic manipulation Low-tech chemical strategies Native search for robustness: Approach 1: use proteins in water-free media ApproachApproachApproach 2

Taralp, Alpay

48

Engineering Proteins for Custom Inhibition of CaV Channels  

NSDL National Science Digital Library

The influx of Ca2+ ions through voltage-dependent calcium (CaV) channels links electrical signals to physiological responses in all excitable cells. Not surprisingly, blocking CaV channel activity is a powerful method to regulate the function of excitable cells, and this is exploited for both physiological and therapeutic benefit. Nevertheless, the full potential for CaV channel inhibition is not being realized by currently available small-molecule blockers or second-messenger modulators due to limitations in targeting them either to defined groups of cells in an organism or to distinct subcellular regions within a single cell. Here, we review early efforts to engineer protein molecule blockers of CaV channels to fill this crucial niche. This technology would greatly expand the toolbox available to physiologists studying the biology of excitable cells at the cellular and systems level.

Xianghua Xu (College of Physicians and Surgeons, Columbia University Physiology and Cellular Biophysics); Henry Colecraft (Columbia University)

2009-08-01

49

Sansom Group: Simulation of Ion Channels and Membrane Proteins  

NSDL National Science Digital Library

Dr. Mark Sansom of the Department of Biochemistry at Oxford University (UK) heads up this research group on Simulation of Ion Channels and Membrane Proteins. Dedicated to understanding the physiological properties of ion channels -- conductance, ion selectivity, and gating -- this lab uses molecular modeling (and other approaches) to generate "plausible molecular models of ion channels." Targeting those in the know, the homepage provides a wealth of technical information and resource links. The Introduction section outlines the research project, while technical publications, including FTP access to several papers, are offered in the Bibliography and FTP sections. The heart of the site is the Research section, which gives detailed, color-illustrated descriptions of the (currently) six main projects, including Antimicrobial Peptides and Molecular Dynamics Simulations of Ion Permeation in Channels, among others. A hefty selection of academic links rounds out the site.

50

Model studies of dense water overflows in the Faroese Channels  

NASA Astrophysics Data System (ADS)

The overflow of dense water from the Nordic Seas through the Faroese Channel system was investigated through combined laboratory experiments and numerical simulations using the Massachusetts Institute of Technology General Circulation Model. In the experimental study, a scaled, topographic representation of the Faroe-Shetland Channel, Wyville-Thomson Basin and Ridge and Faroe Bank Channel seabed bathymetry was constructed and mounted in a rotating tank. A series of parametric experiments was conducted using dye-tracing and drogue-tracking techniques to investigate deep-water overflow pathways and circulation patterns within the modelled region. In addition, the structure of the outflowing dense bottom water was investigated through density profiling along three cross-channel transects located in the Wyville-Thomson Basin and the converging, up-sloping approach to the Faroe Bank Channel. Results from the dye-tracing studies demonstrate a range of parametric conditions under which dense water overflow across the Wyville-Thomson Ridge is shown to occur, as defined by the Burger number, a non-dimensional length ratio and a dimensionless dense water volume flux parameter specified at the Faroe-Shetland Channel inlet boundary. Drogue-tracking measurements reveal the complex nature of flow paths and circulations generated in the modelled topography, particularly the development of a large anti-cyclonic gyre in the Wyville-Thompson Basin and up-sloping approach to the Faroe Bank Channel, which diverts the dense water outflow from the Faroese shelf towards the Wyville-Thomson Ridge, potentially promoting dense water spillage across the ridge itself. The presence of this circulation is also indicated by associated undulations in density isopycnals across the Wyville-Thomson Basin. Numerical simulations of parametric test cases for the main outflow pathways and density structure in a similarly-scaled Faroese Channels model domain indicate excellent qualitative agreement with the experimental observations and measurements. In addition, the comparisons show that strong temporal variability in the predicted outflow pathways and circulations have a strong influence in regulating the Faroe Bank Channel and Wyville-Thomson Ridge overflows, as well as in determining the overall response in the Faroese Channels to changes in the Faroe-Shetland Channel inlet boundary conditions.

Cuthbertson, Alan; Davies, Peter; Stashchuk, Nataliya; Vlasenko, Vasiliy

2014-01-01

51

G Protein Regulation of Ion Channels and Abscisic Acid  

E-print Network

channels. Stomatal opening in gpa1 plants is insensitive to inhibition by ABA, and the rate of water loss controls stomatal apertures. Sto- matal opening relies on increases in K , Cl­ , malate2­ , and sucrose of the guard cell pair and an increase in pore aper- ture. During stomatal opening, K uptake is mediated

Jones, Alan M.

52

Highly sensitive spectroscopic detection of heme-protein submonolayer films by channel integrated optical waveguide  

Microsoft Academic Search

A highly sensitive technique based on optical absorption using a single-mode, channel integrated optical waveguide is described for broad spectral band detection and analysis of heme-containing protein films at a glass\\/water interface. Fabrication steps and device characteristics of optical waveguides suitable for operation in the wavelength range of 400 - 650 nm are described. Experimental results reported here show a

Ismail E. Araci; Sergio B. Mendes; Nasuhi Yurt; Seppo Honkanen; N. Peyghambarian

2007-01-01

53

Pregabalin activates ROMK1 channels via cAMP-dependent protein kinase and protein kinase C.  

PubMed

Pregabalin (PGB) displays analgesic and anticonvulsant activities. Regulation of the resting membrane potential (RMP) by renal outer medullary potassium (ROMK1) channels may provide a mechanism for these activities. We examined the effects of PGB on ROMK1 channel activity. To investigate the regulatory effect of PGB on the activity of ROMK1 channel, we used inside-out excised membrane patches to measure the K+ current in Xenopus oocytes expressed either the wild-type (WT) or mutant ROMK1 channels. PGB concentration-dependently enhanced the activity of ROMK1 channels. PGB increases the WT channels, pHi gating residue mutant channels (K80M) and the mutant channels at phosphatidylinositol bisphosphate (PIP2)-binding sites (R188Q, R217A, and K218A). Our study suggests that PGB in the regulating of ROMK1 channel function are neither by pHi- nor PIP2-dependent mechanism. We found PGB failed to prompt the activity of consensus phosphorylation sites for protein kinase C (PKC) mutated channels (S183A, T191A, T193A, S201A and T234A). Furthermore, PGB did not stimulate the activity of channels in the presence of cAMP-dependent protein kinase (PKA) inhibitors, the mutants of the C-terminal PKA-phosphorylation sites (S219A and S313A), and the mutants constructed (S219D and S313D) which mimic the addition of negative charged associated with phosphorylation bound to a serine. These results demonstrated that PKA- and PKC-mediated phosphorylation represents a novel mechanism for PGB-activated ROMK1 channels. The enhancement of ROMK1 currents proves to an important molecular mechanism underlying the analgesic/anticonvulsant property of PGB for the restoration of RMP. PMID:25008072

Lee, Chien-Hsing; Liou, Horng-Huei

2014-10-01

54

Hydration water, charge transport and protein dynamics.  

PubMed

The hydration water of proteins is essential to biological activity but its properties are not yet fully understood. A recent study of dielectric relaxation of hydrated proteins [A. Levstik et al., Phys. Rev E.60 7604 (1999)] has found a behavior typical of a proton glass, with a glass transition of about 268 K. In order to analyze these results, we investigate the statistical mechanics and dynamics of a model of `two-dimensional water' which describes the hydrogen bonding scheme of bounded water molecules. We discuss the connection between the dynamics of bound water and charge transport on the protein surface as observed in the dielectric measurements. PMID:23345745

Peyrard, M

2001-06-01

55

Challenging accepted ion channel biology: p64 and the CLIC family of putative intracellular anion channel proteins (Review).  

PubMed

Parchorin, p64 and the related chloride intracellular channel (CLIC) proteins are widely expressed in multicellular organisms and have emerged as candidates for novel, auto-inserting, self-assembling intracellular anion channels involved in a wide variety of fundamental cellular events including regulated secretion, cell division and apoptosis. Although the mammalian phosphoproteins p64 and parchorin (49 and 65K, respectively) have only been indirectly implicated in anion channel activity, two CLIC proteins (CLIC1 and CLIC4, 27 and 29K, respectively) appear to be essential molecular components of anion channels, and CLIC1 can form anion channels in planar lipid bilayers in the absence of other cellular proteins. However, these putative ion channel proteins are controversial because they exist in both soluble and membrane forms, with at least one transmembrane domain. Even more surprisingly, soluble CLICs share the same glutaredoxin fold as soluble omega class glutathione-S-transferases. Working out how these ubiquitous, soluble proteins unfold, insert into membranes and then refold to form integral membrane proteins, and how cells control this potentially dangerous process and make use of the associated ion channels, are challenging prospects. Critical to this future work is the need for better characterization of membrane topology, careful functional analysis of reconstituted and native channels, including their conductances and selectivities, and detailed structure/function studies including targeted mutagenesis to investigate the structure of the putative pore, the role of protein phosphorylation and the role of conserved cysteine residues. PMID:12745921

Ashley, R H

2003-01-01

56

Properties of underwater acoustic communication channels in shallow water.  

PubMed

Underwater acoustic channels are band-limited and reverberant, posing many obstacles to reliable, phase-coherent acoustic communications. While many high frequency communication experiments have been conducted in shallow water, few have carried out systematic studies on the channel properties at a time scale relevant for communications. To aid communication system design, this paper analyzes at-sea data collected in shallow water under various conditions to illustrate how the ocean environments (sea surface waves and random ocean medium) can affect the signal properties. Channel properties studied include amplitude and phase variations, and temporal coherence of individual paths as well as the temporal and spatial coherence of multipaths at different time scales. Reasons for the coherence loss are hypothesized. PMID:22280578

Yang, T C

2012-01-01

57

Regulation of recombinant cardiac cystic fibrosis transmembrane conductance regulator chloride channels by protein kinase C.  

PubMed Central

We investigated the regulation of cardiac cystic fibrosis transmembrane conductance regulator (CFTR) Cl- channels by protein kinase C (PKC) in Xenopus oocytes injected with cRNA encoding the cardiac (exon 5-) CFTR Cl- channel isoform. Membrane currents were recorded using a two-electrode voltage clamp technique. Activators of PKC or a cAMP cocktail elicited robust time-independent Cl- currents in cardiac CFTR-injected oocytes, but not in control water-injected oocytes. The effects of costimulation of both pathways were additive; however, maximum protein kinase A (PKA) activation occluded further activation by PKC. In oocytes expressing either the cardiac (exon 5-) or epithelial (exon 5+) CFTR isoform, Cl- currents activated by PKA were sustained, whereas PKC-activated currents were transient, with initial activation followed by slow current decay in the continued presence of phorbol esters, the latter effect likely due to down-regulation of endogenous PKC activity. The specific PKA inhibitor, adenosine 3',5'-cyclic monophosphothioate (Rp-cAMPS), and various protein phosphatase inhibitors were used to determine whether the stimulatory effects of PKC are dependent upon the PKA phosphorylation state of cardiac CFTR channels. Intraoocyte injection of 1,2-bis(2-aminophenoxy)ethane-N,N, N,N-tetraacetic acid (BAPTA) or pretreatment of oocytes with BAPTA-acetoxymethyl-ester (BAPTA-AM) nearly completely prevented dephosphorylation of CFTR currents activated by cAMP, an effect consistent with inhibition of protein phosphatase 2C (PP2C) by chelation of intracellular Mg2+. PKC-induced stimulation of CFTR channels was prevented by inhibition of basal endogenous PKA activity, and phorbol esters failed to stimulate CFTR channels trapped into either the partially PKA phosphorylated (P1) or the fully PKA phosphorylated (P1P2) channel states. Site-directed mutagenesis of serines (S686 and S790) within two consensus PKC phosphorylation sites on the cardiac CFTR regulatory domain attentuated, but did not eliminate, the stimulatory effects of phorbol esters on mutant CFTR channels. The effects of PKC on cardiac CFTR Cl- channels are consistent with a simple model in which PKC phosphorylation of the R domain facilitates PKA-induced transitions from dephosphorylated (D) to partially (P1) phosphorylated and fully (P1P2) phosphorylated channel states. PMID:10096895

Yamazaki, J; Britton, F; Collier, M L; Horowitz, B; Hume, J R

1999-01-01

58

Interference avoidance versus iterative water filling in multiaccess vector channels  

Microsoft Academic Search

We present an analysis of the relationship between the application of greedy interference avoidance and that of iterative water filling for vector multiaccess channels. The two methods converge to fixed points with similar properties corresponding to maximum sum capacity. However, the former is used for optimizing CDMA codewords, whereas the latter is used for optimizing transmit covariance matrices. We present

Dimitrie C. Popescu; Otilia Popescu; Christopher Rose

2004-01-01

59

Patterning multiplex protein microarrays in a single microfluidic channel.  

PubMed

The development of versatile biofunctional surfaces is a fundamental prerequisite in designing Lab on a Chip (LOC) devices for applications in biosensing interfaces and microbioreactors. The current paper presents a rapid combinatorial approach to create multiplex protein patterns in a single microfluidic channel. This approach consists of coupling microcontact printing with microfluidic patterning, where microcontact printing is employed for silanization using (3-Aminopropyl) triethoxysilane (APTES), followed by microfluidic patterning of multiple antibodies. As a result, the biomolecules of choice could be covalently attached to the microchannel surface, thus creating a durable and highly resistant functional interface. Moreover, the experimental procedure was designed to create a microfluidic platform that maintains functionality at high flow rates. The functionalized surfaces were characterized using X-ray photoelectron spectroscopy (XPS) and monitored with fluorescence microscopy at each step of functionalization. To illustrate the possibility of patterning multiple biomolecules along the cross section of a single microfluidic channel, microarrays of five different primary antibodies were patterned onto a single channel and their functionality was evaluated accordingly through a multiplex immunoassay using secondary antibodies specific to each patterned primary antibody. The resulting patterns remained stable at shear stresses of up to 50 dyn/cm(2). The overall findings suggest that the developed multiplex functional interface on a single channel can successfully lead to highly resistant multiplex functional surfaces for high throughput biological assays. PMID:22124457

Didar, Tohid Fatanat; Foudeh, Amir M; Tabrizian, Maryam

2012-01-17

60

Filter gate closure inhibits ion but not water transport through potassium channels  

PubMed Central

The selectivity filter of K+ channels is conserved throughout all kingdoms of life. Carbonyl groups of highly conserved amino acids point toward the lumen to act as surrogates for the water molecules of K+ hydration. Ion conductivity is abrogated if some of these carbonyl groups flip out of the lumen, which happens (i) in the process of C-type inactivation or (ii) during filter collapse in the absence of K+. Here, we show that K+ channels remain permeable to water, even after entering such an electrically silent conformation. We reconstituted fluorescently labeled and constitutively open mutants of the bacterial K+ channel KcsA into lipid vesicles that were either C-type inactivating or noninactivating. Fluorescence correlation spectroscopy allowed us to count both the number of proteoliposomes and the number of protein-containing micelles after solubilization, providing the number of reconstituted channels per proteoliposome. Quantification of the per-channel increment in proteoliposome water permeability with the aid of stopped-flow experiments yielded a unitary water permeability pf of (6.9 ± 0.6) × 10?13 cm3?s?1 for both mutants. “Collapse” of the selectivity filter upon K+ removal did not alter pf and was fully reversible, as demonstrated by current measurements through planar bilayers in a K+-containing medium to which K+-free proteoliposomes were fused. Water flow through KcsA is halved by 200 mM K+ in the aqueous solution, which indicates an effective K+ dissociation constant in that range for a singly occupied channel. This questions the widely accepted hypothesis that multiple K+ ions in the selectivity filter act to mutually destabilize binding. PMID:23754382

Hoomann, Torben; Jahnke, Nadin; Horner, Andreas; Keller, Sandro; Pohl, Peter

2013-01-01

61

Filter gate closure inhibits ion but not water transport through potassium channels.  

PubMed

The selectivity filter of K(+) channels is conserved throughout all kingdoms of life. Carbonyl groups of highly conserved amino acids point toward the lumen to act as surrogates for the water molecules of K(+) hydration. Ion conductivity is abrogated if some of these carbonyl groups flip out of the lumen, which happens (i) in the process of C-type inactivation or (ii) during filter collapse in the absence of K(+). Here, we show that K(+) channels remain permeable to water, even after entering such an electrically silent conformation. We reconstituted fluorescently labeled and constitutively open mutants of the bacterial K(+) channel KcsA into lipid vesicles that were either C-type inactivating or noninactivating. Fluorescence correlation spectroscopy allowed us to count both the number of proteoliposomes and the number of protein-containing micelles after solubilization, providing the number of reconstituted channels per proteoliposome. Quantification of the per-channel increment in proteoliposome water permeability with the aid of stopped-flow experiments yielded a unitary water permeability pf of (6.9 ± 0.6) × 10(-13) cm(3)?s(-1) for both mutants. "Collapse" of the selectivity filter upon K(+) removal did not alter pf and was fully reversible, as demonstrated by current measurements through planar bilayers in a K(+)-containing medium to which K(+)-free proteoliposomes were fused. Water flow through KcsA is halved by 200 mM K(+) in the aqueous solution, which indicates an effective K(+) dissociation constant in that range for a singly occupied channel. This questions the widely accepted hypothesis that multiple K(+) ions in the selectivity filter act to mutually destabilize binding. PMID:23754382

Hoomann, Torben; Jahnke, Nadin; Horner, Andreas; Keller, Sandro; Pohl, Peter

2013-06-25

62

Voltage Gated Ion Channel Function: Gating, Conduction, and the Role of Water and Protons  

SciTech Connect

Ion channels, which are found in every biological cell, regulate the concentration of electrolytes, and are responsible for multiple biological functions, including in particular the propagation of nerve impulses. The channels with the latter function are gated (opened) by a voltage signal, which allows Na+ into the cell and K+ out. These channels have several positively charged amino acids on a transmembrane domain of their voltage sensor, and it is generally considered, based primarily on two lines of experimental evidence, that these charges move with respect to the membrane to open the channel. At least three forms of motion, with greatly differing extents and mechanisms of motion, have been proposed. There is a “gating current”, a capacitative current preceding the channel opening, that corresponds to several charges (for one class of channel typically 12–13) crossing the membrane field, which may not require protein physically crossing a large fraction of the membrane. The coupling to the opening of the channel would in these models depend on the motion. The conduction itself is usually assumed to require the “gate” of the channel to be pulled apart to allow ions to enter as a section of the protein partially crosses the membrane, and a selectivity filter at the opposite end of the channel determines the ion which is allowed to pass through. We will here primarily consider K+ channels, although Na+ channels are similar. We propose that the mechanism of gating differs from that which is generally accepted, in that the positively charged residues need not move (there may be some motion, but not as gating current). Instead, protons may constitute the gating current, causing the gate to open; opening consists of only increasing the diameter at the gate from approximately 6 Å to approximately 12 Å. We propose in addition that the gate oscillates rather than simply opens, and the ion experiences a barrier to its motion across the channel that is tuned by the water present within the channel. Our own quantum calculations as well as numerous experiments of others are interpreted in terms of this hypothesis. It is also shown that the evidence that supports the motion of the sensor as the gating current can also be consistent with the hypothesis we present.

Kariev, Alisher M.; Green, Michael E.

2012-02-26

63

Nanosecond Relaxation Dynamics of Hydrated Proteins: Water versus protein contributions  

SciTech Connect

We have studied picosecond to nanosecond dynamics of hydrated protein powders using dielectric spectroscopy and molecular dynamics (MD) simulations. Our analysis of hydrogen-atom single particle dynamics from MD simulations focused on main ( main tens of picoseconds) and slow ( slow nanosecond) relaxation processes that were observed in dielectric spectra of similar hydrated protein samples. Traditionally, the interpretation of these processes observed in dielectric spectra has been ascribed to the relaxation behavior of hydration water tightly bounded to a protein and not to protein atoms. Detailed analysis of the MD simulations and comparison to dielectric data indicate that the observed relaxation process in the nanosecond time range of hydrated protein spectra is mainly due to protein atoms. The relaxation processes involve the entire structure of protein including atoms in the protein backbone, side chains, and turns. Both surface and buried protein atoms contribute to the slow processes; however, surface atoms demonstrate slightly faster relaxation dynamics. Analysis of the water molecule residence and dipolar relaxation correlation behavior indicates that the hydration water relaxes at much shorter time scales.

Khodadadi, S [University of Akron; Curtis, J. E. [National Institute of Standards and Technology (NIST), Gaithersburg, MD; Sokolov, Alexei P [ORNL

2011-01-01

64

Protein and cell patterning in closed polymer channels by photoimmobilizing proteins on photografted poly(ethylene glycol) diacrylate.  

PubMed

Definable surface chemistry is essential for many applications of microfluidic polymer systems. However, small cross-section channels with a high surface to volume ratio enhance passive adsorption of molecules that depletes active molecules in solution and contaminates the channel surface. Here, we present a one-step photochemical process to coat the inner surfaces of closed microfluidic channels with a nanometer thick layer of poly(ethylene glycol) (PEG), well known to strongly reduce non-specific adsorption, using only commercially available reagents in an aqueous environment. The coating consists of PEG diacrylate (PEGDA) covalently grafted to polymer surfaces via UV light activation of the water soluble photoinitiator benzoyl benzylamine, a benzophenone derivative. The PEGDA coating was shown to efficiently limit the adsorption of antibodies and other proteins to <5% of the adsorbed amount on uncoated polymer surfaces. The coating could also efficiently suppress the adhesion of mammalian cells as demonstrated using the HT-29 cancer cell line. In a subsequent equivalent process step, protein in aqueous solution could be anchored onto the PEGDA coating in spatially defined patterns with a resolution of <15??m using an inverted microscope as a projection lithography system. Surface patterns of the cell binding protein fibronectin were photochemically defined inside a closed microfluidic device that was initially homogeneously coated by PEGDA. The resulting fibronectin patterns were shown to greatly improve cell adhesion compared to unexposed areas. This method opens for easy surface modification of closed microfluidic systems through combining a low protein binding PEG-based coating with spatially defined protein patterns of interest. PMID:25587375

Larsen, Esben Kjær Unmack; Mikkelsen, Morten Bo Lindholm; Larsen, Niels B

2014-11-01

65

No Mystery! Water Carved the Outflow Channels on Mars  

NASA Astrophysics Data System (ADS)

The enormous outflow channels of Chryse Planitia provide the best evidence that large amounts of water were once released onto the martian surface. The role of water has recently been challenged by the White Mars hypothesis, which claims that the channels were cut by CO2 gas-supported debris flows that also resurfaced the northern plains. Hoffman [Icarus, 2000] refers to a volumetric "misfit" between outburst channels and the chaos source zones. He explains that chaos collapse "...involves regolith alone which generates its own fluids from liquid CO2 and CO2-bearing ices within its own volume." Hoffman [LPSC 32, #1257] argues that release of liquid CO2 produced Aromatum Chaos, and a hypothetical energetic "jet" of gas and debris carved Ravi Vallis. He notes that water would have had to be locally recharged in many episodes to provide enough discharge to form the chaos and channel. However, these assertions appear incorrect because the fluid source was a distant surface impoundment, not local recharge. Carr [Water on Mars, 1996] describes a 400-km-long zone of subsidence that extends northward from Ganges Chasma to the source of Shalbatana Vallis. MOLA data reveal that this subsidence also extends eastward to Aromatum Chaos, the source of Ravi Vallis. The field relations show that a liquid-filled impoundment in Ganges Chasma drained northward via subterranean flowpaths to maintain surface flows in Shalbatana and Ravi Valles. The fact that the flows began at a surface impoundment virtually eliminates liquid CO2 as the flowing agent. Liquid CO2 would not be stable at the surface unless the atmospheric pressure exceeded 5 atm. A recent study by Stewart and Nimmo [JGR, in press] suggests that CO2 in liquid, solid, or clathrate form could not be preserved within the crust over geologic time. Liquid water is much closer to its stability field even on present-day Mars. Large outflow channels, such as Kasei and Tiu-Simud Valles, likely formed through the release of floodwaters dammed by ice and debris, analogous to the scabland flooding of eastern Washington. The water sources were probably ice-covered impoundments in ancestral Valles Marineris canyons. Subice volcanism was a possible source of heat to create liquid water. The former existence of transient water bodies near the surface can help to calibrate models of a volcanic-hydrologic climax during the Hesperian.

Coleman, N.

2002-12-01

66

Dispersion of buoyant emissions from low level sources in urban areas: water channel modelling  

E-print Network

sources in urban areas: water channel modelling’, Int. J.level sources in urban areas: water channel modelling Sammodelling the dispersion from low level buoyant sources: Dispersion of buoyant emissions from low level sources in urban

Pournazeri, Sam; Schulte, Nico; Tan, Si; Princevac, Marko; Venkatram, Akula

2013-01-01

67

Functionality and Protein-Water Interactions  

E-print Network

The structures of proteins exhibit secondary elements composed of helices and loops. Comparison of several water-only hydrophobicity scales with the functionalities of two repeat proteins shows that these secondary elements possess water-induced medium-range order that is sometimes similar, but can also be complementary, to structural order. Study of these hitherto "phantom" order parameters promises far-reaching incremental improvements in the theory of protein dynamics. A by-product of the theory is an independent evaluation of the reliability of different hydrophobicity scales.

J. C. Phillips

2008-03-02

68

Dynamics of Protein Hydration Water  

E-print Network

We present the frequency- and temperature-dependent dielectric properties of lysozyme solutions in a broad concentration regime, measured at subzero temperatures and compare the results with measurements above the freezing point of water and on hydrated lysozyme powder. Our experiments allow examining the dynamics of unfreezable hydration water in a broad temperature range including the so-called No Man's Land (160 - 235 K). The obtained results prove the bimodality of the hydration shell dynamics and are discussed in the context of the highly-debated fragile-to-strong transition of water.

M. Wolf; S. Emmert; R. Gulich; P. Lunkenheimer; A. Loidl

2014-12-08

69

Microfabricated Patch Clamp Electrodes for Improved Ion Channel Protein Measurements  

NASA Astrophysics Data System (ADS)

Ion channels are trans-membrane proteins that underlie many cell functions including hormone and neurotransmitter release, muscle contraction and cell signaling cascades. Ion channel proteins are commonly characterized via the patch clamp method in which an extruded glass tube containing ionic solution, manipulated by an expert technician, is brought into contact with a living cell to record ionic current through the cell membrane. Microfabricated planar patch electrodes, micromolded in the silicone elastomer poly-dimethylsiloxane (PDMS) from microlithographically patterned structures, have been developed that improve on this method. Microfabrication techniques allow arrays of patch electrodes to be fabricated, increasing the throughput of the measurement technique. Planar patch electrodes readily allow the automation of cell sealing, further increasing throughput. Microfabricated electrode arrays may be readily integrated with microfluidic structures to allow fast, in situ solution exchange. Miniaturization of the electrode geometry should increase both the signal to noise and the bandwidth of the measurement. Microfabricated patch electrode arrays have been fabricated and measurements have been taken.

Klemic, James; Klemic, Kathryn; Reed, Mark; Sigworth, Frederick

2002-03-01

70

The role of transmembrane channel–like proteins in the operation of hair cell mechanotransducer channels  

PubMed Central

Sound stimuli elicit movement of the stereocilia that make up the hair bundle of cochlear hair cells, putting tension on the tip links connecting the stereocilia and thereby opening mechanotransducer (MT) channels. Tmc1 and Tmc2, two members of the transmembrane channel–like family, are necessary for mechanotransduction. To assess their precise role, we recorded MT currents elicited by hair bundle deflections in mice with null mutations of Tmc1, Tmc2, or both. During the first postnatal week, we observed a normal MT current in hair cells lacking Tmc1 or Tmc2; however, in the absence of both isoforms, we recorded a large MT current that was phase-shifted 180°, being evoked by displacements of the hair bundle away from its tallest edge rather than toward it as in wild-type hair cells. The anomalous MT current in hair cells lacking Tmc1 and Tmc2 was blocked by FM1-43, dihydrostreptomycin, and extracellular Ca2+ at concentrations similar to those that blocked wild type. MT channels in the double knockouts carried Ca2+ with a lower permeability than wild-type or single mutants. The MT current in double knockouts persisted during exposure to submicromolar Ca2+, even though this treatment destroyed the tip links. We conclude that the Tmc isoforms do not themselves constitute the MT channel but are essential for targeting and interaction with the tip link. Changes in the MT conductance and Ca2+ permeability observed in the absence of Tmc1 mutants may stem from loss of interaction with protein partners in the transduction complex. PMID:24127526

Kim, Kyunghee X.; Beurg, Maryline; Hackney, Carole M.; Furness, David N.; Mahendrasingam, Shanthini

2013-01-01

71

A ligand channel through the G protein coupled receptor opsin.  

PubMed

The G protein coupled receptor rhodopsin contains a pocket within its seven-transmembrane helix (TM) structure, which bears the inactivating 11-cis-retinal bound by a protonated Schiff-base to Lys296 in TM7. Light-induced 11-cis-/all-trans-isomerization leads to the Schiff-base deprotonated active Meta II intermediate. With Meta II decay, the Schiff-base bond is hydrolyzed, all-trans-retinal is released from the pocket, and the apoprotein opsin reloaded with new 11-cis-retinal. The crystal structure of opsin in its active Ops* conformation provides the basis for computational modeling of retinal release and uptake. The ligand-free 7TM bundle of opsin opens into the hydrophobic membrane layer through openings A (between TM1 and 7), and B (between TM5 and 6), respectively. Using skeleton search and molecular docking, we find a continuous channel through the protein that connects these two openings and comprises in its central part the retinal binding pocket. The channel traverses the receptor over a distance of ca. 70 A and is between 11.6 and 3.2 A wide. Both openings are lined with aromatic residues, while the central part is highly polar. Four constrictions within the channel are so narrow that they must stretch to allow passage of the retinal beta-ionone-ring. Constrictions are at openings A and B, respectively, and at Trp265 and Lys296 within the retinal pocket. The lysine enforces a 90 degrees elbow-like kink in the channel which limits retinal passage. With a favorable Lys side chain conformation, 11-cis-retinal can take the turn, whereas passage of the all-trans isomer would require more global conformational changes. We discuss possible scenarios for the uptake of 11-cis- and release of all-trans-retinal. If the uptake gate of 11-cis-retinal is assigned to opening B, all-trans is likely to leave through the same gate. The unidirectional passage proposed previously requires uptake of 11-cis-retinal through A and release of photolyzed all-trans-retinal through B. PMID:19194506

Hildebrand, Peter W; Scheerer, Patrick; Park, Jung Hee; Choe, Hui-Woog; Piechnick, Ronny; Ernst, Oliver P; Hofmann, Klaus Peter; Heck, Martin

2009-01-01

72

Actin directly interacts with different membrane channel proteins and influences channel activities: AQP2 as a model.  

PubMed

The interplay between actin and 10 membrane channel proteins that have been shown to directly bind to actin are reviewed. The 10 membrane channel proteins covered in this review are aquaporin 2 (AQP2), cystic fibrosis transmembrane conductance regulator (CFTR), ClC2, short form of ClC3 (sClC3), chloride intracellular channel 1 (CLIC1), chloride intracellular channel 5 (CLIC5), epithelial sodium channel (ENaC), large-conductance calcium-activated potassium channel (Maxi-K), transient receptor potential vanilloid 4 (TRPV4), and voltage-dependent anion channel (VDAC), with particular attention to AQP2. In regard to AQP2, most reciprocal interactions between actin and AQP2 occur during intracellular trafficking, which are largely mediated through indirect binding. Actin and the actin cytoskeleton work as cables, barriers, stabilizers, and force generators for motility. However, as with ENaC, the effects of actin cytoskeleton on channel gating should be investigated further. This article is part of a Special Issue entitled: Reciprocal influences between cell cytoskeleton and membrane channels, receptors and transporters. Guest Editor: Jean Claude Hervé. PMID:23770358

Sasaki, Sei; Yui, Naofumi; Noda, Yumi

2014-02-01

73

Kinetics of gravity-driven water channels under steady rainfall  

NASA Astrophysics Data System (ADS)

We investigate the formation of fingered flow in dry granular media under simulated rainfall using a quasi-two-dimensional experimental setup composed of a random close packing of monodisperse glass beads. Using controlled experiments, we analyze the finger instabilities that develop from the wetting front as a function of fundamental granular (particle size) and fluid properties (rainfall, viscosity). These finger instabilities act as precursors for water channels, which serve as outlets for water drainage. We look into the characteristics of the homogeneous wetting front and channel size as well as estimate relevant time scales involved in the instability formation and the velocity of the channel fingertip. We compare our experimental results with that of the well-known prediction developed by Parlange and Hill [D. E. Hill and J. Y. Parlange, Soil Sci. Soc. Am. Proc. 36, 697 (1972), 10.2136/sssaj1972.03615995003600050010x]. This model is based on linear stability analysis of the growth of perturbations arising at the interface between two immiscible fluids. Results show that, in terms of morphology, experiments agree with the proposed model. However, in terms of kinetics we nevertheless account for another term that describes the homogenization of the wetting front. This result shows that the manner we introduce the fluid to a porous medium can also influence the formation of finger instabilities. The results also help us to calculate the ideal flow rate needed for homogeneous distribution of water in the soil and minimization of runoff, given the grain size, fluid density, and fluid viscosity. This could have applications in optimizing use of irrigation water.

Cejas, Cesare M.; Wei, Yuli; Barrois, Remi; Frétigny, Christian; Durian, Douglas J.; Dreyfus, Rémi

2014-10-01

74

Kinetics of gravity-driven water channels under steady rainfall.  

PubMed

We investigate the formation of fingered flow in dry granular media under simulated rainfall using a quasi-two-dimensional experimental setup composed of a random close packing of monodisperse glass beads. Using controlled experiments, we analyze the finger instabilities that develop from the wetting front as a function of fundamental granular (particle size) and fluid properties (rainfall, viscosity). These finger instabilities act as precursors for water channels, which serve as outlets for water drainage. We look into the characteristics of the homogeneous wetting front and channel size as well as estimate relevant time scales involved in the instability formation and the velocity of the channel fingertip. We compare our experimental results with that of the well-known prediction developed by Parlange and Hill [D. E. Hill and J. Y. Parlange, Soil Sci. Soc. Am. Proc. 36, 697 (1972)]. This model is based on linear stability analysis of the growth of perturbations arising at the interface between two immiscible fluids. Results show that, in terms of morphology, experiments agree with the proposed model. However, in terms of kinetics we nevertheless account for another term that describes the homogenization of the wetting front. This result shows that the manner we introduce the fluid to a porous medium can also influence the formation of finger instabilities. The results also help us to calculate the ideal flow rate needed for homogeneous distribution of water in the soil and minimization of runoff, given the grain size, fluid density, and fluid viscosity. This could have applications in optimizing use of irrigation water. PMID:25375487

Cejas, Cesare M; Wei, Yuli; Barrois, Remi; Frétigny, Christian; Durian, Douglas J; Dreyfus, Rémi

2014-10-01

75

Proton transfer via a transient linear water-molecule chain in a membrane protein  

PubMed Central

High-resolution protein ground-state structures of proton pumps and channels have revealed internal protein-bound water molecules. Their possible active involvement in protein function has recently come into focus. An illustration of the formation of a protonated protein-bound water cluster that is actively involved in proton transfer was described for the membrane protein bacteriorhodopsin (bR) [Garczarek F, Gerwert K (2006) Nature 439:109–112]. Here we show through a combination of time-resolved FTIR spectroscopy and molecular dynamics simulations that three protein-bound water molecules are rearranged by a protein conformational change that resulted in a transient Grotthuss-type proton-transfer chain extending through a hydrophobic protein region of bR. This transient linear water chain facilitates proton transfer at an intermediate conformation only, thereby directing proton transfer within the protein. The rearrangement of protein-bound water molecules that we describe, from inactive positions in the ground state to an active chain in an intermediate state, appears to be energetically favored relative to transient incorporation of water molecules from the bulk. Our discovery provides insight into proton-transfer mechanisms through hydrophobic core regions of ubiquitous membrane spanning proteins such as G-protein coupled receptors or cytochrome C oxidases. PMID:21709261

Freier, Erik; Wolf, Steffen; Gerwert, Klaus

2011-01-01

76

Alcohol modulation of G-protein-gated inwardly rectifying potassium channels: from binding to therapeutics  

PubMed Central

Alcohol (ethanol)-induced behaviors may arise from direct interaction of alcohol with discrete protein cavities within brain proteins. Recent structural and biochemical studies have provided new insights into the mechanism of alcohol-dependent activation of G protein-gated inwardly rectifying potassium (GIRK) channels, which regulate neuronal responses in the brain reward circuit. GIRK channels contain an alcohol binding pocket formed at the interface of two adjacent channel subunits. Here, we discuss the physiochemical properties of the alcohol pocket and the roles of G protein ?? subunits and membrane phospholipid PIP2 in regulating the alcohol response of GIRK channels. Some of the features of alcohol modulation of GIRK channels may be common to other alcohol-sensitive brain proteins. We discuss the possibility of alcohol-selective therapeutics that block alcohol access to the pocket. Understanding alcohol recognition and modulation of brain proteins is essential for development of therapeutics for alcohol abuse and addiction. PMID:24611054

Bodhinathan, Karthik; Slesinger, Paul A.

2014-01-01

77

Effects of water temperature and dissolved oxygen on daily feed consumption, feed utilization and growth of channel catfish ( Ictalurus punctatus)  

Microsoft Academic Search

Feed intake (FI), feed efficiency (FE), protein efficiency ratio (PER) and weight gain (WG) of juvenile channel catfish initially weighing 15.0±0.23 g (10–12 cm initial total length) were evaluated under three regimes of time-varying water temperature (mean daily water temperature for Stoneville, MS, USA; mean +3; and, mean ?3°C) and three of dissolved oxygen (DO; 100, 70 and 30% air

J. Alejandro Buentello; Delbert M Gatlin; William H Neill

2000-01-01

78

Protein expression of G-protein inwardly rectifying potassium channels (GIRK) in breast cancer cells  

Microsoft Academic Search

BACKGROUND: Previous data from our laboratory has indicated that a functional link exists between the G-protein-coupled inwardly rectifying potassium (GIRK) channel and the beta-adrenergic receptor pathway in breast cancer cell lines, and these pathways were involved in growth regulation of these cells. Alcohol is an established risk factor for breast cancer and has been found to open GIRK. In order

Madhu S Dhar; Howard K Plummer III

2006-01-01

79

Phycodnavirus Potassium Ion Channel Proteins Question the Virus Molecular Piracy Hypothesis  

Microsoft Academic Search

Phycodnaviruses are large dsDNA, algal-infecting viruses that encode many genes with homologs in prokaryotes and eukaryotes. Among the viral gene products are the smallest proteins known to form functional K+ channels. To determine if these viral K+ channels are the product of molecular piracy from their hosts, we compared the sequences of the K+ channel pore modules from seven phycodnaviruses

Kay Hamacher; Timo Greiner; Hiroyuki Ogata; James L. Van Etten; Manuela Gebhardt; Luis P. Villarreal; Cristian Cosentino; Anna Moroni; Gerhard Thiel

2012-01-01

80

Protein Kinase Modulation of Dendritic K Channels in Hippocampus Involves a Mitogen-Activated Protein Kinase Pathway  

Microsoft Academic Search

We investigated mitogen-activated protein kinase (MAPK) mod- ulation of dendritic, A-type K channels in CA1 pyramidal neurons in the hippocampus. Activation of cAMP-dependent protein kinase A (PKA) and protein kinase C (PKC) leads to an increase in the amplitude of backpropagating action potentials in distal dendrites through downregulation of transient K channels in CA1 pyramidal neurons in the hippocampus. We

Li-Lian Yuan; J. Paige Adams; Michael Swank; J. David Sweatt; Daniel Johnston

2002-01-01

81

Selectivity and conductance among the glycerol and water conducting aquaporin family of channels  

E-print Network

Minireview Selectivity and conductance among the glycerol and water conducting aquaporin family water plus glycerol conducting channel (GlpF), and now of aquaporin Z (AqpZ) from the same species in the glycerol plus water channel paradigm, GlpF. Water molecules form a single hydrogen bonded ¢le throughout

82

Formation of Ravi Vallis outflow channel, Mars: Morphological development, water discharge, and duration estimates  

Microsoft Academic Search

We infer that the morphology of the Ravi Vallis channel system is consistent with it having been eroded by water in a single flood event, and we have used the topography of the channel system to estimate the depth of water in the channel at various stages during its development. Values lie in the range 50–150 m. Measured bed slopes,

Harald J. Leask; Lionel Wilson; Karl L. Mitchell

2006-01-01

83

Comparison of Channel and Blue Catfish Fed Diets Containing Various Levels of Protein  

Technology Transfer Automated Retrieval System (TEKTRAN)

A comparative study was conducted on growth and protein requirements of channel catfish, Ictalurus punctatus, and blue catfish, Ictalurus furcatus. Four diets containing 24, 28, 32, or 36% protein were fed to both channel (initial weight 6.9 g/fish) and blue (6.6 g/fish) catfish for two growing seas...

84

Suppression of aquaporin, a mediator of water channel control in the carcinogenic liver fluke, Opisthorchis viverrini  

PubMed Central

Background Opisthorchiasis and Opisthorchis viverrini-associated bile duct cancer represent major public health threats in Thailand and Laos. The tegument of this food borne fluke plays pivotal roles in parasite metabolism, homeostasis and osmoregulation. Excretory/secretory products also pass from the fluke to the biliary environment, products that likely underlie pathogenesis of liver fluke infection. Aquaporins (AQPs), belong to the major intrinsic protein superfamily of integral plasma membrane channel proteins that selectively transport water across cell membranes. AQPs play key roles as water and ion transport channels through the tegument of helminth parasites. Methods Here, two forms of AQP mRNAs from the adult developmental stage of O. viverrini, termed O. viverrini aquaporin-1 and -2 (Ov-aqp-1 and -2) were investigated. Roles of Ov-aqp-1 and -2 in the movement of water across the tegument of this carcinogenic liver fluke were investigated using RNA interference. Results Ov-AQP-1 and Ov-AQP-2 contain unique characteristic asparagine-proline-alanine (NPA) motifs of AQP transmembrane proteins. Phylogenetic analysis indicated that Ov-AQPs belong to an expanding group of aquaglyceroporin-like water channel proteins characterized from helminth and protozoan parasites, which is pivotal to the specialized requirements of water and solute control during parasitism. Elevated transcription of Ov-aqp-1 was evident in the egg, cercaria, metacercaria and adult stages of O. viverrini, whereas Ov-aqp-2 transcripts were detected at higher level in egg, metacercaria, cercaria and adult stage, respectively. RNA interference using electroporated dsRNA suppressed transcript levels of Ov-aqp-1 and Ov-aqp-2 in adult worms by 58-99% over periods of up to 16 days in vitro. Suppression of Ov-aqp-1 and Ov-aqp-2 in vitro disabled water transport in adult flukes. Conclusion The apparently pivotal roles of Ov-AQP in solute homeostasis at the fluke surface suggest that deeper investigation will be informative for the pathophysiology of O. viverrini, and may uncover intervention targets, particularly in view of the singularly notable predilection of this pathogen for residence within ducts of the biliary tree. PMID:24885060

2014-01-01

85

Identification of characteristic protein folding channels in a coarse-grained hydrophobic-polar peptide model  

E-print Network

Identification of characteristic protein folding channels in a coarse-grained hydrophobic of protein folding is one of the major challenges of modern interdisciplinary science. Proteins are linear simulations of protein folding are difficult, mainly for two reasons. Firstly, the folding process is so slow

Bachmann, Michael

86

Morphology of rain water channelization in systematically varied model sandy soils  

E-print Network

We visualize the formation of fingered flow in dry model sandy soils under different raining conditions using a quasi-2d experimental set-up, and systematically determine the impact of soil grain diameter and surface wetting property on water channelization phenomenon. The model sandy soils we use are random closely-packed glass beads with varied diameters and surface treatments. For hydrophilic sandy soils, our experiments show that rain water infiltrates into a shallow top layer of soil and creates a horizontal water wetting front that grows downward homogeneously until instabilities occur to form fingered flows. For hydrophobic sandy soils, in contrast, we observe that rain water ponds on the top of soil surface until the hydraulic pressure is strong enough to overcome the capillary repellency of soil and create narrow water channels that penetrate the soil packing. Varying the raindrop impinging speed has little influence on water channel formation. However, varying the rain rate causes significant changes in water infiltration depth, water channel width, and water channel separation. At a fixed raining condition, we combine the effects of grain diameter and surface hydrophobicity into a single parameter and determine its influence on water infiltration depth, water channel width, and water channel separation. We also demonstrate the efficiency of several soil water improvement methods that relate to rain water channelization phenomenon, including pre-wetting sandy soils at different level before rainfall, modifying soil surface flatness, and applying superabsorbent hydrogel particles as soil modifiers.

Y. Wei; C. M. Cejas; R. Barrois; R. Dreyfus; D. J. Durian

2014-03-13

87

Morphology of Rain Water Channeling in Systematically Varied Model Sandy Soils  

NASA Astrophysics Data System (ADS)

We visualize the formation of fingered flow in dry model sandy soils under different rain conditions using a quasi-2D experimental setup and systematically determine the impact of the soil grain diameter and surface wetting properties on the water channeling phenomenon. The model sandy soils we use are random closely packed glass beads with varied diameters and surface treatments. For hydrophilic sandy soils, our experiments show that rain water infiltrates a shallow top layer of soil and creates a horizontal water wetting front that grows downward homogeneously until instabilities occur to form fingered flows. For hydrophobic sandy soils, in contrast, we observe that rain water ponds on the top of the soil surface until the hydraulic pressure is strong enough to overcome the capillary repellency of soil and create narrow water channels that penetrate the soil packing. Varying the raindrop impinging speed has little influence on water channel formation. However, varying the rain rate causes significant changes in the water infiltration depth, water channel width, and water channel separation. At a fixed rain condition, we combine the effects of the grain diameter and surface hydrophobicity into a single parameter and determine its influence on the water infiltration depth, water channel width, and water channel separation. We also demonstrate the efficiency of several soil water improvement methods that relate to the rain water channeling phenomenon, including prewetting sandy soils at different levels before rainfall, modifying soil surface flatness, and applying superabsorbent hydrogel particles as soil modifiers.

Wei, Yuli; Cejas, Cesare M.; Barrois, Rémi; Dreyfus, Rémi; Durian, Douglas J.

2014-10-01

88

Biological gas channels for NH3 and CO2: evidence that Rh (Rhesus) proteins are CO2 channels.  

PubMed

Physiological evidence from our laboratory indicates that Amt/Mep proteins are gas channels for NH3, the first biological gas channels to be described. This view has now been confirmed by structural evidence and is displacing the previous belief that Amt/Mep proteins were active transporters for the NH4+ ion. Still disputed is the physiological substrate for Rh proteins, the only known homologues of Amt/Mep proteins. Many think they are mammalian ammonium (NH4+ or NH3) transporters. Following Monod's famous dictum, "Anything found to be true of E. coli must also be true of elephants" [Perspect. Biol. Med. 47(1) (2004) 47], we explored the substrate for Rh proteins in the unicellular green alga Chlamydomonas reinhardtii. C. reinhardtii is one of the simplest organisms to have Rh proteins and it also has Amt proteins. Physiological studies in this microbe indicate that the substrate for Rh proteins is CO2 and confirm that the substrate for Amt proteins is NH3. Both are readily hydrated gases. Knowing that transport of CO2 is the ancestral function of Rh proteins supports the inference from hematological research that a newly evolving role of the human Rh30 proteins, RhCcEe and RhD, is to help maintain the flexible, flattened shape of the red cell. PMID:16563833

Kustu, S; Inwood, W

2006-01-01

89

Structural basis for allosteric coupling at the membrane-protein interface in Gloeobacter violaceus ligand-gated ion channel (GLIC).  

PubMed

Ligand binding at the extracellular domain of pentameric ligand-gated ion channels initiates a relay of conformational changes that culminates at the gate within the transmembrane domain. The interface between the two domains is a key structural entity that governs gating. Molecular events in signal transduction at the interface are poorly defined because of its intrinsically dynamic nature combined with functional modulation by membrane lipid and water vestibules. Here we used electron paramagnetic resonance spectroscopy to delineate protein motions underlying Gloeobacter violaceus ligand-gated ion channel gating in a membrane environment and report the interface conformation in the closed and the desensitized states. Extensive intrasubunit interactions were observed in the closed state that are weakened upon desensitization and replaced by newer intersubunit contacts. Gating involves major rearrangements of the interfacial loops, accompanied by reorganization of the protein-lipid-water interface. These structural changes may serve as targets for modulation of gating by lipids, alcohols, and amphipathic drug molecules. PMID:24338475

Velisetty, Phanindra; Chalamalasetti, Sreevatsa V; Chakrapani, Sudha

2014-01-31

90

Short Paper: OFDM in Deep Water Acoustic Channels with Extremely Long Delay Spread  

E-print Network

Short Paper: OFDM in Deep Water Acoustic Channels with Extremely Long Delay Spread Zhaohui Wang ABSTRACT Deep water horizontal channels usually have very long de- lay spreads relative to shallow water and the other from surface reflections. Viewing the signals arrived along the two clusters as from two virtual

Zhou, Shengli

91

On the Coupling Between Channel Level and Surface Ground Water Flows  

E-print Network

On the Coupling Between Channel Level and Surface Ground Water Flows S. N. Antontsev (1), , J.I. D@mail.ru Abbreviated Title: CHANNEL LEVEL AND GROUND WATER FLOWS Abstract. This paper is devoted to a mathematical in simultaneous flows of surface, soil and ground waters. Such models are widely used for forecasting (numerical

Díaz, Jesús Ildefonso

92

Vasopressin Increases Water Permeability of Kidney Collecting Duct by Inducing Translocation of Aquaporin-CD Water Channels to Plasma Membrane  

Microsoft Academic Search

Water excretion by the kidney is regulated by the peptide hormone vasopressin. Vasopressin increases the water permeability of the renal collecting duct cells, allowing more water to be reabsorbed from collecting duct urine to blood. Despite long-standing interest in this process, the mechanism of the water permeability increase has remained undetermined. Recently, a molecular water channel (AQP-CD) has been cloned

Soren Nielsen; Chung-Lin Chou; David Marples; Erik I. Christensen; Bellamkonda K. Kishore; Mark A. Knepper

1995-01-01

93

Dramatic nano-fluidic properties of carbon nanotube membranes as a platform for protein channel mimetics  

NASA Astrophysics Data System (ADS)

Carbon nanotubes have three key attributes that make them of great interest for novel membrane applications: 1) atomically flat graphite surface allows for ideal fluid slip boundary conditions and extremely fast flow rates 2) the cutting process to open CNTs inherently places functional chemistry at CNT core entrance for chemical selectivity and 3) CNT are electrically conductive allowing for electrochemical reactions and application of electric fields gradients at CNT tips. Pressure driven flux of a variety of solvents (H2O, hexane, decane ethanol, methanol) are 4-5 orders of magnitude higher than conventional Newtonian flow [Nature 2005, 438, 44] due to atomically flat graphite planes inducing nearly ideal slip conditions. However this is eliminated with selective chemical functionalization [ACS Nano 2011 5(5) 3867-3877] needed to give chemical selectivity. These unique properties allow us to explore the hypothesis of producing ``Gatekeeper'' membranes that mimic natural protein channels to actively pump through rapid nm-scale channels. With anionic tip functionality strong electroosmotic flow is induced by unimpeded cation flow with similar 10,000 fold enhancements [Nature Nano 2012 7(2) 133-39]. With enhanced power efficiency, carbon nanotube membranes were employed as the active element of a switchable transdermal drug delivery device that can facilitate more effective treatments of drug abuse and addiction. Recently methods to deposit Pt monolayers on CNT surface have been developed making for highly efficient catalytic platforms. Discussed are other applications of CNT protein channel mimetics, for large area robust engineering platforms, including water purification, flow battery energy storage, and biochemical/biomass separations.

Hinds, Bruce

2013-03-01

94

Multiple Scales in the Simulation of Ion Channels and Proteins  

PubMed Central

Computation of living processes creates great promise for the everyday life of mankind and great challenges for physical scientists. Simulations molecular dynamics have great appeal to biologists as a natural extension of structural biology. Once a biologist sees a structure, she/he wants to see it move. Molecular biology has shown that a small number of atoms, sometimes even one messenger ion, like Ca2+, can control biological function on the scale of cells, organs, tissues, and organisms. Enormously concentrated ions—at number densities of ~20 M—in protein channels and enzymes are responsible for many of the characteristics of living systems, just as highly concentrated ions near electrodes are responsible for many of the characteristics of electrochemical systems. Here we confront the reality of the scale differences of ions. We show that the scale differences needed to simulate all the atoms of biological cells are 107 in linear dimension, 1021 in three dimensions, 109 in resolution, 1011 in time, and 1013 in particle number (to deal with concentrations of Ca2+). These scales must be dealt with simultaneously if the simulation is to deal with most biological functions. Biological function extends across all of them, all at once in most cases. We suggest a computational approach using explicit multiscale analysis instead of implicit simulation of all scales. The approach is based on an energy variational principle EnVarA introduced by Chun Liu to deal with complex fluids. Variational methods deal automatically with multiple interacting components and scales. When an additional component is added to the system, the resulting Euler Lagrange field equations change form automatically—by algebra alone—without additional unknown parameters. Multifaceted interactions are solutions of the resulting equations. We suggest that ionic solutions should be viewed as complex fluids with simple components. Highly concentrated solutions—dominated by interactions of components—are easily computed by EnVarA. Successful computation of ions concentrated in special places may be a significant step to understanding the defining characteristics of biological and electrochemical systems. Indeed, computing ions near proteins and nucleic acids may prove as important to molecular biology and chemical technology as computing holes and electrons has been to our semiconductor and digital technology. PMID:21135913

Eisenberg, Bob

2010-01-01

95

Remodeling of channel-forming ORAI proteins determines an oncogenic switch in prostate cancer.  

PubMed

ORAI family channels have emerged as important players in malignant transformation, yet the way in which they reprogram cancer cells remains elusive. Here we show that the relative expression levels of ORAI proteins in prostate cancer are different from that in noncancerous tissue. By mimicking ORAI protein remodeling observed in primary tumors, we demonstrate in in vitro models that enhanced ORAI3 expression favors heteromerization with ORAI1 to form a novel channel. These channels support store-independent Ca(2+) entry, thereby promoting cell proliferation and a smaller number of functional homomeric ORAI1-based store-operated channels, which are important in supporting susceptibility to apoptosis. Thus, our findings highlight disrupted dynamic equilibrium of channel-forming proteins as an oncogenic mechanism. PMID:24954132

Dubois, Charlotte; Vanden Abeele, Fabien; Lehen'kyi, V'yacheslav; Gkika, Dimitra; Guarmit, Basma; Lepage, Gilbert; Slomianny, Christian; Borowiec, Anne Sophie; Bidaux, Gabriel; Benahmed, Mohamed; Shuba, Yaroslav; Prevarskaya, Natalia

2014-07-14

96

Control of Neuronal Voltage-Gated Calcium Ion Channels From RNA to Protein  

PubMed Central

Voltage-gated calcium (CaV) ion channels convert neuronal activity into rapid intracellular calcium signals to trigger a myriad of cellular responses. Their involvement in major neurological and psychiatric diseases, and importance as therapeutic targets, has propelled interest in subcellular-specific mechanisms that align CaV channel activity to specific tasks. Here we highlight recent studies that delineate mechanisms controlling the expression of CaV channels at the level of RNA and protein. We discuss the roles of RNA editing and alternative pre-mRNA splicing in generating CaV channel isoforms with activities specific to the demands of individual cells; the roles of ubiquitination and accessory proteins in regulating CaV channel expression; and the specific binding partners which contribute to both pre- and post- synaptic CaV channel function. PMID:23907011

Lipscombe, Diane; Allen, Summer E; Toro, Cecilia P.

2013-01-01

97

Specificity of Gbetagamma signaling depends on Galpha subunit coupling with G-protein-sensitive K(+) channels.  

PubMed

Many neurotransmitters activate G-protein-gated inwardly rectifying K(+) (Kir3) channels by stimulating G-protein-coupled receptors. However, in native systems, only receptors coupled to pertussis-toxin (PTX)-sensitive G proteins (Gi/Go) have been shown to be able to activate Kir3 channels through the betagamma subunits of G proteins (Gbetagamma), whereas activation of receptors coupled to PTX-insensitive G proteins such as Gq or Gs do not activate Kir3 channels. The question remains as to how signaling specificity is achieved and what are its key determinants. In this study, we have used the Xenopus oocyte expression system to investigate specific activation of Kir3 channels by heterotrimeric G proteins. We have demonstrated the activation of Kir3.4 channels by agonist stimulation of non-PTX-sensitive G proteins under conditions of Galpha subunit overexpression. We present evidence to suggest a key role for the coupling efficiency of Galpha subunits in determining the specificity of Gbetagamma signaling to the channel. PMID:19590257

Geng, Xian; Du, Xiao-na; Rusinova, Radda; Liu, Bo-yi; Li, Fang; Zhang, Xuan; Chen, Xing-juan; Logothetis, Diomedes E; Zhang, Hai-lin

2009-01-01

98

Bioluminescence Methodology for the Detection of Protein–Protein Interactions Within the Voltage-Gated Sodium Channel Macromolecular Complex  

PubMed Central

Abstract Protein–protein interactions are critical molecular determinants of ion channel function and emerging targets for pharmacological interventions. Yet, current methodologies for the rapid detection of ion channel macromolecular complexes are still lacking. In this study we have adapted a split-luciferase complementation assay (LCA) for detecting the assembly of the voltage-gated Na+ (Nav) channel C-tail and the intracellular fibroblast growth factor 14 (FGF14), a functionally relevant component of the Nav channelosome that controls gating and targeting of Nav channels through direct interaction with the channel C-tail. In the LCA, two complementary N-terminus and C-terminus fragments of the firefly luciferase were fused, respectively, to a chimera of the CD4 transmembrane segment and the C-tail of Nav1.6 channel (CD4-Nav1.6-NLuc) or FGF14 (CLuc-FGF14). Co-expression of CLuc-FGF14 and CD4-Nav1.6-NLuc in live cells led to a robust assembly of the FGF14:Nav1.6 C-tail complex, which was attenuated by introducing single-point mutations at the predicted FGF14:Nav channel interface. To evaluate the dynamic regulation of the FGF14:Nav1.6 C-tail complex by signaling pathways, we investigated the effect of kinase inhibitors on the complex formation. Through a platform of counter screenings, we show that the p38/MAPK inhibitor, PD169316, and the I?B kinase inhibitor, BAY 11-7082, reduce the FGF14:Nav1.6 C-tail complementation, highlighting a potential role of the p38MAPK and the I?B/NF?B pathways in controlling neuronal excitability through protein–protein interactions. We envision the methodology presented here as a new valuable tool to allow functional evaluations of protein–channel complexes toward probe development and drug discovery targeting ion channels implicated in human disorders. PMID:22364545

Shavkunov, Alexander; Panova, Neli; Prasai, Anesh; Veselenak, Ron; Bourne, Nigel; Stoilova-McPhie, Svetla

2012-01-01

99

Bioluminescence methodology for the detection of protein-protein interactions within the voltage-gated sodium channel macromolecular complex.  

PubMed

Protein-protein interactions are critical molecular determinants of ion channel function and emerging targets for pharmacological interventions. Yet, current methodologies for the rapid detection of ion channel macromolecular complexes are still lacking. In this study we have adapted a split-luciferase complementation assay (LCA) for detecting the assembly of the voltage-gated Na+ (Nav) channel C-tail and the intracellular fibroblast growth factor 14 (FGF14), a functionally relevant component of the Nav channelosome that controls gating and targeting of Nav channels through direct interaction with the channel C-tail. In the LCA, two complementary N-terminus and C-terminus fragments of the firefly luciferase were fused, respectively, to a chimera of the CD4 transmembrane segment and the C-tail of Nav1.6 channel (CD4-Nav1.6-NLuc) or FGF14 (CLuc-FGF14). Co-expression of CLuc-FGF14 and CD4-Nav1.6-NLuc in live cells led to a robust assembly of the FGF14:Nav1.6 C-tail complex, which was attenuated by introducing single-point mutations at the predicted FGF14:Nav channel interface. To evaluate the dynamic regulation of the FGF14:Nav1.6 C-tail complex by signaling pathways, we investigated the effect of kinase inhibitors on the complex formation. Through a platform of counter screenings, we show that the p38/MAPK inhibitor, PD169316, and the I?B kinase inhibitor, BAY 11-7082, reduce the FGF14:Nav1.6 C-tail complementation, highlighting a potential role of the p38MAPK and the I?B/NF?B pathways in controlling neuronal excitability through protein-protein interactions. We envision the methodology presented here as a new valuable tool to allow functional evaluations of protein-channel complexes toward probe development and drug discovery targeting ion channels implicated in human disorders. PMID:22364545

Shavkunov, Alexander; Panova, Neli; Prasai, Anesh; Veselenak, Ron; Bourne, Nigel; Stoilova-McPhie, Svetla; Laezza, Fernanda

2012-04-01

100

A protein kinase-phosphatase pair interacts with an ion channel to regulate ABA signaling in plant guard cells  

PubMed Central

The plant hormone abscisic acid (ABA) serves as a physiological monitor to assess the water status of plants and, under drought conditions, induces stomatal pore closure by activating specific ion channels, such as a slow-anion channel (SLAC1) that, in turn, mediate ion efflux from the guard cells. Earlier genetic analyses uncovered a protein kinase (OST1) and several 2C-type phosphatases, as respective positive and negative regulators of ABA-induced stomatal closure. Here we show that the OST1 kinase interacts with the SLAC1 anion channel, leading to its activation via phosphorylation. PP2CA, one of the PP2C phosphatase family members acts in an opposing manner and inhibits the activity of SLAC1 by two mechanisms: (1) direct interaction with SLAC1 itself, and (2) physical interaction with OSTI leading to inhibition of the kinase independently of phosphatase activity. The results suggest that ABA signaling is mediated by a physical interaction chain consisting of several components, including a PP2C member, SnRK2-type kinase (OST1), and an ion channel, SLAC1, to regulate stomatal movements. The findings are in keeping with a paradigm in which a protein kinase-phosphatase pair interacts physically with a target protein to couple a signal with a specific response. PMID:19955427

Lee, Sung Chul; Lan, Wenzhi; Buchanan, Bob B.; Luan, Sheng

2009-01-01

101

Phycodnavirus Potassium Ion Channel Proteins Question the Virus Molecular Piracy Hypothesis  

PubMed Central

Phycodnaviruses are large dsDNA, algal-infecting viruses that encode many genes with homologs in prokaryotes and eukaryotes. Among the viral gene products are the smallest proteins known to form functional K+ channels. To determine if these viral K+ channels are the product of molecular piracy from their hosts, we compared the sequences of the K+ channel pore modules from seven phycodnaviruses to the K+ channels from Chlorella variabilis and Ectocarpus siliculosus, whose genomes have recently been sequenced. C. variabilis is the host for two of the viruses PBCV-1 and NY-2A and E. siliculosus is the host for the virus EsV-1. Systematic phylogenetic analyses consistently indicate that the viral K+ channels are not related to any lineage of the host channel homologs and that they are more closely related to each other than to their host homologs. A consensus sequence of the viral channels resembles a protein of unknown function from a proteobacterium. However, the bacterial protein lacks the consensus motif of all K+ channels and it does not form a functional channel in yeast, suggesting that the viral channels did not come from a proteobacterium. Collectively, our results indicate that the viruses did not acquire their K+ channel-encoding genes from their current algal hosts by gene transfer; thus alternative explanations are required. One possibility is that the viral genes arose from ancient organisms, which served as their hosts before the viruses developed their current host specificity. Alternatively the viral proteins could be the origin of K+ channels in algae and perhaps even all cellular organisms. PMID:22685610

Hamacher, Kay; Greiner, Timo; Ogata, Hiroyuki; Van Etten, James L.; Gebhardt, Manuela; Villarreal, Luis P.; Cosentino, Cristian; Moroni, Anna; Thiel, Gerhard

2012-01-01

102

Regulation of excitatory and inhibitory neurotransmitter-gated ion channels by protein phosphorylation  

Microsoft Academic Search

Phosphorylation of ligand-gated ion channels is recognised as a potentially important mechanism for short- and long-term modulation of ion-channel function. Following the discovery of numerous sites of phosphorylation on ligand-gated ion channel proteins, recent studies have demonstrated that neurotransmitter-induced activation of serine\\/threonine, tyrosine and other kinases can result in the modulation of glutamate, type A ?-aminobutyric acid (GABAA) and glycine

Trevor G Smart

1997-01-01

103

Protein-directed synthesis of Mn-doped ZnS quantum dots: a dual-channel biosensor for two proteins.  

PubMed

Proteins typically have nanoscale dimensions and multiple binding sites with inorganic ions, which facilitates the templated synthesis of nanoparticles to yield nanoparticle-protein hybrids with tailored functionality, water solubility, and tunable frameworks with well-defined structure. In this work, we report a protein-templated synthesis of Mn-doped ZnS quantum dots (QDs) by exploring bovine serum albumin (BSA) as the template. The obtained Mn-doped ZnS QDs give phosphorescence emission centered at 590?nm, with a decay time of about 1.9?ms. A dual-channel sensing system for two different proteins was developed through integration of the optical responses (phosphorescence emission and resonant light scattering (RLS)) of Mn-doped ZnS QDs and recognition of them by surface BSA phosphorescent sensing of trypsin and RLS sensing of lysozyme. Trypsin can digest BSA and remove BSA from the surface of Mn-doped ZnS QDs, thus quenching the phosphorescence of QDs, whereas lysozyme can assemble with BSA to lead to aggregation of QDs and enhanced RLS intensity. The detection limits for trypsin and lysozyme were 40 and 3?nM, respectively. The selectivity of the respective channel for trypsin and lysozyme was evaluated with a series of other proteins. Unlike other protein sensors based on nanobioconjugates, the proposed dual-channel sensor employs only one type of QDs but can detect two different proteins. Further, we found the RLS of QDs can also be useful for studying the BSA-lysozyme binding stoichiometry, which has not been reported in the literature. These successful biosensor applications clearly demonstrate that BSA not only serves as a template for growth of Mn-doped ZnS QDs, but also impacts the QDs for selective recognition of analyte proteins. PMID:23576296

Wu, Peng; Zhao, Ting; Tian, Yunfei; Wu, Lan; Hou, Xiandeng

2013-06-01

104

ADAM22, A KV1 CHANNEL INTERACTING PROTEIN, RECRUITS MAGUKS TO JUXTAPARANODES OF MYELINATED AXONS  

PubMed Central

Clustered Kv1 K+ channels regulate neuronal excitability at juxtaparanodes of myelinated axons, axon initial segments (AIS), and cerebellar basket cell terminals (BCTs). These channels are part of a larger protein complex that includes cell adhesion molecules and scaffolding proteins. To identify proteins that regulate assembly, clustering, and/or maintenance of axonal Kv1 channel protein complexes, we immunoprecipitated Kv1.2 ? subunits, then used mass-spectrometry to identify interacting proteins. We found that ADAM22 (A Disintegrin And Metalloproteinase 22) is a component of the Kv1 channel complex, and that ADAM22 co-immunoprecipitates Kv1.2 and the MAGUKs PSD-93 and PSD-95. When co-expressed with MAGUKs in heterologous cells, ADAM22 and Kv1 channels are recruited into membrane surface clusters. However, co-expression of Kv1.2 with ADAM22 and MAGUKs does not alter channel properties. Among all the known Kv1 channel interacting proteins, only ADAM22 is found at every site where Kv1 channels are clustered. Analysis of Caspr-null mice showed that like other previously described juxtaparanodal proteins, disruption of the paranodal junction resulted in redistribution of ADAM22 into paranodal zones. Analysis of Caspr2-, PSD-93-, PSD-95-, and double PSD-93/PSD-95-null mice showed ADAM22 clustering at BCTs requires PSD-95, but ADAM22 clustering at juxtaparanodes requires neither PSD-93 nor PSD-95. In direct contrast, analysis of ADAM22-null mice demonstrated juxtaparanodal clustering of PSD-93 and PSD-95 requires ADAM22, whereas Kv1.2 and Caspr2 clustering is normal in ADAM22-null mice. Thus, ADAM22 is an axonal component of the Kv1 K+ channel complex that recruits MAGUKs to juxtaparanodes. PMID:20089912

Ogawa, Yasuhiro; Oses-Prieto, Juan; Kim, Moon Young; Horresh, Ido; Peles, Elior; Burlingame, Alma L.; Trimmer, James S.; Meijer, Dies; Rasband, Matthew N.

2009-01-01

105

Ferritin Protein Nanocages Use Ion Channels, Catalytic Sites, and Nucleation Channels To Manage Iron/Oxygen Chemistry  

PubMed Central

The ferritin superfamily is composed of ancient, nanocage proteins with an internal cavity, 60% of total volume, that reversibly synthesize solid minerals of hydrated ferric oxide; the minerals are iron concentrates for cell nutrition as well as antioxidants due to ferrous and oxygen consumption during mineralization. The cages have multiple iron entry/exit channels, oxidoreductase enzyme sites, and, in eukaryotes, Fe(III)O nucleation channels with clustered exits that extend protein activity to include facilitated mineral growth. Ferritin protein cage differences include size, amino acid sequence, and location of the active sites, oxidant substrate and crystallinity of the iron mineral. Genetic regulation depends on iron and oxygen signals, which in animals includes direct ferrous signaling to RNA to release and to ubiquitin-ligases to degrade the protein repressors. Ferritin biosynthesis forms, with DNA, mRNA and the protein product, a feedback loop where the genetic signals are also protein substrates. The ferritin protein nanocages, which are required for normal iron homeostasis and are finding current use in delivery of nanodrugs, novel nanomaterials, and nanocatalysts, are likely contributors to survival and success during the transition from anaerobic to aerobic life. PMID:21296609

Theil, Elizabeth C.

2011-01-01

106

Probing membrane protein structure using water polarization transfer solid-state NMR  

NASA Astrophysics Data System (ADS)

Water plays an essential role in the structure and function of proteins, lipid membranes and other biological macromolecules. Solid-state NMR heteronuclear-detected 1H polarization transfer from water to biomolecules is a versatile approach for studying water-protein, water-membrane, and water-carbohydrate interactions in biology. We review radiofrequency pulse sequences for measuring water polarization transfer to biomolecules, the mechanisms of polarization transfer, and the application of this method to various biological systems. Three polarization transfer mechanisms, chemical exchange, spin diffusion and NOE, manifest themselves at different temperatures, magic-angle-spinning frequencies, and pulse irradiations. Chemical exchange is ubiquitous in all systems examined so far, and spin diffusion plays the key role in polarization transfer within the macromolecule. Tightly bound water molecules with long residence times are rare in proteins at ambient temperature. The water polarization-transfer technique has been used to study the hydration of microcrystalline proteins, lipid membranes, and plant cell wall polysaccharides, and to derive atomic-resolution details of the kinetics and mechanism of ion conduction in channels and pumps. Using this approach, we have measured the water polarization transfer to the transmembrane domain of the influenza M2 protein to obtain information on the structure of this tetrameric proton channel. At short mixing times, the polarization transfer rates are site-specific and depend on the pH, labile protons, sidechain conformation, as well as the radial position of the residues in this four-helix bundle. Despite the multiple dependences, the initial transfer rates reflect the periodic nature of the residue positions from the water-filled pore, thus this technique provides a way of gleaning secondary structure information, helix tilt angle, and the oligomeric structure of membrane proteins.

Williams, Jonathan K.; Hong, Mei

2014-10-01

107

GIRK4 Confers Appropriate Processing and Cell Surface Localization to G-protein-gated Potassium Channels*  

E-print Network

stimulation of G-protein-coupled receptors (6). ACh released from the vagus nerve binds and activates mus of their voltage-gated K channel relatives (see Refs. 1­3 for review). Like the Shaker family of K channels, IRKs- carinic M2 receptors located on cardiac pacemaker cells. M2 receptors selectively couple to the pertussis

Clapham, David E.

108

The jellyfish green fluorescent protein: A new tool for studying ion channel expression and function  

Microsoft Academic Search

Two methods are described for using the jellyfish green fluorescent protein (GFP) as a reporter gene for ion channel expression. GFP fluorescence can be used to identify the transfected cells, and to estimate the relative levels of ion channel expression, in cotransfection experiments. A GFP-NMDAR1 chimera can be constructed that produces a functional, fluorescent receptor subunit. These methods should facilitate

John Marshall; Raymond Molloy; Guy W. J Moss; James R Howe; Thomas E Hughes

1995-01-01

109

Inhibition of a background potassium channel by Gq protein alpha-subunits.  

PubMed

Two-pore-domain K(+) channels provide neuronal background currents that establish resting membrane potential and input resistance; their modulation provides a prevalent mechanism for regulating cellular excitability. The so-called TASK channel subunits (TASK-1 and TASK-3) are widely expressed, and they are robustly inhibited by receptors that signal through Galphaq family proteins. Here, we manipulated G protein expression and membrane phosphatidylinositol 4,5-bisphosphate (PIP(2)) levels in intact and cell-free systems to provide electrophysiological and biochemical evidence that inhibition of TASK channels by Galphaq-linked receptors proceeds unabated in the absence of phospholipase C (PLC) activity, and instead involves association of activated Galphaq subunits with the channels. Receptor-mediated inhibition of TASK channels was faster and less sensitive to a PLCbeta1-ct minigene construct than inhibition of PIP(2)-sensitive Kir3.4(S143T) homomeric channels that is known to be dependent on PLC. TASK channels were strongly inhibited by constitutively active Galphaq, even by a mutated version that is deficient in PLC activation. Receptor-mediated TASK channel inhibition required exogenous Galphaq expression in fibroblasts derived from Galphaq/11 knockout mice, but proceeded unabated in a cell line in which PIP(2) levels were reduced by regulated overexpression of a lipid phosphatase. Direct application of activated Galphaq, but not other G protein subunits, inhibited TASK channels in excised patches, and constitutively active Galphaq subunits were selectively coimmunoprecipitated with TASK channels. These data indicate that receptor-mediated TASK channel inhibition is independent of PIP(2) depletion, and they suggest a mechanism whereby channel modulation by Galphaq occurs through direct interaction with the ion channel or a closely associated intermediary. PMID:16492788

Chen, Xiangdong; Talley, Edmund M; Patel, Nitin; Gomis, Ana; McIntire, William E; Dong, Biwei; Viana, Félix; Garrison, James C; Bayliss, Douglas A

2006-02-28

110

Ancient association between cation leak channels and Mid1 proteins is conserved in fungi and animals  

PubMed Central

Neuronal resting potential can tune the excitability of neural networks, affecting downstream behavior. Sodium leak channels (NALCN) play a key role in rhythmic behaviors by helping set, or subtly changing neuronal resting potential. The full complexity of these newly described channels is just beginning to be appreciated, however. NALCN channels can associate with numerous subunits in different tissues and can be activated by several different peptides and second messengers. We recently showed that NALCN channels are closely related to fungal calcium channels, which they functionally resemble. Here, we use this relationship to predict a family of NALCN-associated proteins in animals on the basis of homology with the yeast protein Mid1, the subunit of the yeast calcium channel. These proteins all share a cysteine-rich region that is necessary for Mid1 function in yeast. We validate this predicted association by showing that the Mid1 homolog in Drosophila, encoded by the CG33988 gene, is coordinately expressed with NALCN, and that knockdown of either protein creates identical phenotypes in several behaviors associated with NALCN function. The relationship between Mid1 and leak channels has therefore persisted over a billion years of evolution, despite drastic changes to both proteins and the organisms in which they exist. PMID:24639627

Ghezzi, Alfredo; Liebeskind, Benjamin J.; Thompson, Ammon; Atkinson, Nigel S.; Zakon, Harold H.

2014-01-01

111

Immunosuppressants Implicate Protein Phosphatase Regulation of K^+ Channels in Guard Cells  

Microsoft Academic Search

The elevation of Ca2+ levels in the cytoplasm inactivates inward-rectifying K^+ channels that play a central role in regulating the apertures of stomatal pores in higher plants. However, the mechanism for the Ca2+-mediated inhibition of K^+-channel function is unknown. Using patch-clamp techniques, we show that cyclophilin-cyclosporin A and FK506-binding protein-FK506 complexes, which are highly specific inhibitors of protein phosphatase 2B

Sheng Luan; Weiwei Li; Frank Rusnak; Sarah M. Assmann; Stuart L. Schreiber

1993-01-01

112

Adrenergic Regulation of HCN4 Channel Requires Protein Association with ?2-Adrenergic Receptor*  

PubMed Central

?1- and ?2-adrenergic receptors utilize different signaling mechanisms to control cardiac function. Recent studies demonstrated that ?2-adrenergic receptors (?2ARs) colocalize with some ion channels that are critical for proper cardiac function. Here, we demonstrate that ?2ARs form protein complexes with the pacemaker HCN4 channel, as well as with other subtypes of HCN channels. The adrenergic receptor-binding site was identified at a proximal region of the N-terminal tail of the HCN4 channel. A synthetic peptide derived from the ?2AR-binding domain of the HCN4 channel disrupted interaction between HCN4 and ?2AR. In addition, treatment with this peptide prevented adrenergic augmentation of pacemaker currents and spontaneous contraction rates but did not affect adrenergic regulation of voltage-gated calcium currents. These results suggest that the ion channel-receptor complex is a critical mechanism in ion channel regulation. PMID:22613709

Greene, Derek; Kang, Seungwoo; Kosenko, Anastasia; Hoshi, Naoto

2012-01-01

113

EFFECT OF ELEVATED WATER TEMPERATURE ON INSECT EMERGENCE IN OUTDOOR EXPERIMENTAL CHANNELS  

EPA Science Inventory

Emergence of adult aquatic insects was evaluated weekly with plexiglass traps positioned in two outdoor experimental channels from April through August 1977. One channel was seasonal Mississippi River water temperature and the other maintained at 10C above. Maximum water temperat...

114

On the circulation of bottom water in the region of the Vema Channel  

Microsoft Academic Search

The circulation and transport of Antarctic Bottom Water (?4<45.87) in the region of the Vema Channel are studied along three WOCE hydrographic lines, the geostrophic velocities referenced to previously published direct current measurements. The primary supply of water to the deep Vema Channel is from the Argentine Basin's deep western boundary current, with no indication of an inflow from the

Elaine L. McDonagh; Michel Arhan; Karen J. Heywood

2002-01-01

115

Optimum Dietary Protein to Energy Ratio for Channel Catfish Fingerlings, Ictalurus punctatus 1-4  

Microsoft Academic Search

Twenty-one semipurified diets were formulated to deter mine the optimum protein :energy ratio (P\\/E) for channel catfish finger- lings. Seven crude protein levels and three energy levels at each protein level were utilized. The protein, lipid, and digestible carbohydrate sources were hexane-extracted whole egg powder, salmon-corn oil mixture, and white dextrin, respectively. After an initial 2 week conditioning period, the

DONALD L. GARLING; J. R. ANDROBERT; P. WILSON

116

Interactions between proteins implicated in exocytosis and voltage-gated calcium channels.  

PubMed Central

Neurotransmitter release from synaptic vesicles is triggered by voltage-gated calcium influx through P/Q-type or N-type calcium channels. Purification of N-type channels from rat brain synaptosomes initially suggested molecular interactions between calcium channels and two key proteins implicated in exocytosis: synaptotagmin I and syntaxin 1. Co-immunoprecipitation experiments were consistent with the hypothesis that both N- and P/Q-type calcium channels, but not L-type channels, are associated with the 7S complex containing syntaxin 1, SNAP-25, VAMP and synaptotagmin I or II. Immunofluorescence confocal microscopy at the frog neuromuscular junction confirmed that calcium channels, syntaxin 1 and SNAP-25 are co-localized at active zones of the presynaptic plasma membrane where transmitter release occurs. Experiments with recombinant proteins were performed to map synaptic protein interaction sites on the alpha 1A subunit, which forms the pore of the P/Q-type calcium channel. In vitro-translated 35S-synaptotagmin I bound to a site located on the cytoplasmic loop linking homologous domains II and III of the alpha 1A subunit. This direct link would target synaptotagmin, a putative calcium sensor for exocytosis, to a microdomain of calcium influx close to the channel mouth. Cysteine string proteins (CSPs) contain a J-domain characteristic of molecular chaperones that cooperate with Hsp70. They are located on synaptic vesicles and thought to be involved in modulating the activity of presynaptic calcium channels. CSPs were found to bind to the same domain of the calcium channel as synaptotagmin, and also to associate with VAMP. CSPs may act as molecular chaperones in association with Hsp70 to direct assembly or dissociation of multiprotein complexes at the calcium channel. PMID:10212477

Seagar, M; Lévêque, C; Charvin, N; Marquèze, B; Martin-Moutot, N; Boudier, J A; Boudier, J L; Shoji-Kasai, Y; Sato, K; Takahashi, M

1999-01-01

117

The ABC protein turned chloride channel whose failure causes cystic fibrosis  

NASA Astrophysics Data System (ADS)

CFTR chloride channels are encoded by the gene mutated in patients with cystic fibrosis. These channels belong to the superfamily of ABC transporter ATPases. ATP-driven conformational changes, which in other ABC proteins fuel uphill substrate transport across cellular membranes, in CFTR open and close a gate to allow transmembrane flow of anions down their electrochemical gradient. New structural and biochemical information from prokaryotic ABC proteins and functional information from CFTR channels has led to a unifying mechanism explaining those ATP-driven conformational changes.

Gadsby, David C.; Vergani, Paola; Csanády, László

2006-03-01

118

Elementary events underlying voltage-dependent G-protein inhibition of N-type calcium channels.  

PubMed Central

Voltage-dependent G-protein inhibition of N-type calcium channels reduces presynaptic calcium entry, sharply attenuating neurotransmitter release. Studies in neurons demonstrate that G-proteins have multiple modulatory effects on N-type channels. The observed changes may reflect genuine complexity in G-protein action and/or the intricate interactions of multiple channels and receptors in neurons. Expression of recombinant M2-muscarinic receptors and N-type channels in HEK 293 cells allowed voltage-dependent inhibition to be studied in isolation. In this system, receptor-activated G-proteins had only one effect: a 10-fold increase in the time required for channels to first open following membrane depolarization. There were no changes in gating after the channel first opened, and unitary currents were not detectably altered by modulation. Despite its simplicity, this single change successfully accounts for the complex alterations in whole-cell current observed during G-protein inhibition in neurons. PMID:8913590

Patil, P G; de Leon, M; Reed, R R; Dubel, S; Snutch, T P; Yue, D T

1996-01-01

119

Structure, function and translational relevance of aquaporin dual water and ion channels  

PubMed Central

Aquaporins have been assumed to be selective for water alone, and aquaglyceroporins are accepted as carrying water and small uncharged solutes including glycerol. This review presents an expanded view of aquaporins as channels with more complex mechanisms of regulation and diverse repertoires of substrate permeabilities than were originally appreciated in the early establishment of the field. The role of aquaporins as dual water and gated ion channels is likely to have physiological and potentially translational relevance, and can be evaluated with newly developed molecular and pharmacological tools. Ion channel activity has been shown for Aquaporins -0, -1, and -6, Drosphila Big Brain, and plant Nodulin-26. Although the concept of ion channel function in aquaporins remains controversial, research advances are beginning to define not only the ion channel function but also the detailed molecular mechanisms that govern and mediate the multifunctional capabilities. With regard to physiological relevance, the adaptive benefit of expression of ion channel activity in aquaporins, implied by amino acid sequence conservation of the ion channel gating domains, suggests they provide more than water or glycerol and solute transport. Dual ion and water channels are of interest for understanding the modulation of transmembrane fluid gradients, volume regulation, and possible signal transduction in tissues expressing classes of aquaporins that have the dual function capability. Other aquaporin classes might be found in future work to have ion channel activities, pending identification of the possible signaling pathways that could govern activation. PMID:22342689

Yool, Andrea J; Campbell, Ewan M

2012-01-01

120

Raman spectroscopy of protein-water interactions in aqueous solutions  

Microsoft Academic Search

Some conclusions about the effect of protein presence on water structure, as found by Raman spectroscopy, are presented here. An overall intensity decrease and strong spectral shape changes which are encountered in the OH stretching region when increasing protein concentration are explained in terms of a water model taking into account three water species with different Raman efficiency. The hydration

Fabrizio Cavatorta; Marco P. Fontana; Arnaldo Vecli

1976-01-01

121

Membrane Protein Biosensor with Multi-Channel CMOS Impedance Extractor and Digitizer  

E-print Network

Membrane Protein Biosensor with Multi-Channel CMOS Impedance Extractor and Digitizer Chao Yang the development of biosensor arrays that harness the unique sensitivity and selectivity of membrane proteins frequency spectrum. This paper described the design and characterization of a biosensor array microsystem

Mason, Andrew

122

Regulation of CRAC channels by protein interactions and post-translational modification  

PubMed Central

Store-operated Ca2+ entry (SOCE) is a widespread mechanism to elevate the intracellular Ca2+ concentrations and stimulate downstream signaling pathways affecting proliferation, secretion, differentiation and death in different cell types. In immune cells, immune receptor stimulation induces intracellular Ca2+ store depletion that subsequently activates Ca2+-release-activated-Ca2+ (CRAC) channels, a prototype of store-operated Ca2+ (SOC) channels. CRAC channel opening leads to activation of diverse downstream signaling pathways affecting proliferation, differentiation, cytokine production and cell death. Recent identification of STIM1 as the endoplasmic reticulum Ca2+ sensor and Orai1 as the pore subunit of CRAC channels has provided the much-needed molecular tools to dissect the mechanism of activation and regulation of CRAC channels. In this review, we discuss the recent advances in understanding the associating partners and posttranslational modifications of Orai1 and STIM1 proteins that regulate diverse aspects of CRAC channel function. PMID:23454861

Srikanth, Sonal; Ribalet, Bernard; Gwack, Yousang

2013-01-01

123

Investigation of water droplet dynamics in PEM fuel cell gas channels  

NASA Astrophysics Data System (ADS)

Water management in Proton Exchange Membrane Fuel Cell (PEMFC) has remained one of the most important issues that need to be addressed before its commercialization in automotive applications. Accumulation of water on the gas diffusion layer (GDL) surface in a PEMFC introduces a barrier for transport of reactant gases through the GDL to the catalyst layer. Despite the fact that the channel geometry is one of the key design parameters of a fluidic system, very limited research is available to study the effect of microchannel geometry on the two-phase flow structure. In this study, the droplet-wall dynamics and two-phase pressure drop across the water droplet present in a typical PEMFC channel, were examined in auto-competitive gas channel designs (0.4 x 0.7 mm channel cross section). The liquid water flow pattern inside the gas channel was analyzed for different air velocities. Experimental data was analyzed using the Concus-Finn condition to determine the wettability characteristics in the corner region. It was confirmed that the channel angle along with the air velocity and the channel material influences the water distribution and holdup within the channel. Dynamic contact angle emerged as an important parameter in controlling the droplet-wall interaction. Experiments were also performed to understand how the inlet location of the liquid droplet on the GDL surface affects the droplet dynamic behavior in the system. It was found that droplets emerging near the channel wall or under the land lead to corner filling of the channel. Improvements in the channel design has been proposed based on the artificial channel roughness created to act as capillary grooves to transport the liquid water away from the land area. For droplets emerging near the center of the channel, beside the filling and no-filling behavior reported in the literature, a new droplet jumping behavior was observed. As droplets grew and touched the sidewalls, they jumped off to the sidewall leaving the whole GDL exposed for gases to diffuse to the catalyst layer. A theoretical model was developed and a criterion was proposed to predict the droplet jumping behavior in the gas channel. A theoretical force balance model was proposed to predict the pressure force and air velocity required to remove the droplet from the channel to avoid complete channel blockage. The overall goal of this work was to identify the gas channel configuration that provides efficient water removal with a lower pressure drop in the system efficiency while meeting the US Department of Energy's specifications for a PEMFC for automotive application.

Gopalan, Preethi

124

Structure of the water channel AqpZ from Escherichia coli revealed by electron crystallography1  

Microsoft Academic Search

Molecular water channels (aquaporins) allow living cells to adapt to osmotic variations by rapid and specific diffusion of water molecules. Aquaporins are present in animals, plants, algae, fungi and bacteria. Here we present an electron microscopic analysis of the most ancient water channel described so far: the aquaporin Z (AqpZ) of Escherichia coli. A recombinant AqpZ with a poly(histidine) tag

P. Ringler; M. J. Borgnia; H. Stahlberg; P. C. Maloney; P. Agre; A. Engel

1999-01-01

125

SecA Alone Can Promote Protein Translocation and Ion Channel Activity  

PubMed Central

SecA is an essential component of the Sec-dependent protein translocation pathway across cytoplasmic membranes in bacteria. Escherichia coli SecA binds to cytoplasmic membranes at SecYEG high affinity sites and at phospholipid low affinity sites. It has been widely viewed that SecYEG functions as the essential protein-conducting channel through which precursors cross the membranes in bacterial Sec-dependent pathways, and that SecA functions as a motor to hydrolyze ATP in translocating precursors through SecYEG channels. We have now found that SecA alone can promote precursor translocation into phospholiposomes. Moreover, SecA-liposomes elicit ionic currents in Xenopus oocytes. Patch-clamp recordings further show that SecA alone promotes signal peptide- or precursor-dependent single channel activity. These activities were observed with the functional SecA at about 1–2 ?m. The results show that SecA alone is sufficient to promote protein translocation into liposomes and to elicit ionic channel activity at the phospholipids low affinity binding sites, thus indicating that SecA is able to form the protein-conducting channels. Even so, such SecA-liposomes are less efficient than those with a full complement of Sec proteins, and lose the signal-peptide proofreading function, resembling the effects of PrlA mutations. Addition of purified SecYEG restores the signal peptide specificity and increases protein translocation and ion channel activities. These data show that SecA can promote protein translocation and ion channel activities both when it is bound to lipids at low affinity sites and when it is bound to SecYEG with high affinity. The latter of the two interactions confers high efficiency and specificity. PMID:22033925

Hsieh, Ying-hsin; Zhang, Hao; Lin, Bor-ruei; Cui, Ningren; Na, Bing; Yang, Hsiuchin; Jiang, Chun; Sui, Sen-fang; Tai, Phang C.

2011-01-01

126

Natural channel protein inserts and functions in a completely artificial, solid-supported bilayer membrane  

PubMed Central

Reconstitution of membrane proteins in artificial membrane systems creates a platform for exploring their potential for pharmacological or biotechnological applications. Previously, we demonstrated amphiphilic block copolymers as promising building blocks for artificial membranes with long-term stability and tailorable structural parameters. However, the insertion of membrane proteins has not previously been realized in a large-area, stable, and solid-supported artificial membrane. Here, we show the first, preliminary model of a channel membrane protein that is functionally incorporated in a completely artificial polymer, tethered, solid-supported bilayer membrane (TSSBM). Unprecedented ionic transport characteristics that differ from previous results on protein insertion into planar, free-standing membranes, are identified. Our findings mark a change in understanding protein insertion and ion flow within natural channel proteins when inserted in an artificial TSSBM, thus holding great potential for numerous applications such as drug screening, trace analyzing, and biosensing. PMID:23846807

Zhang, Xiaoyan; Fu, Wangyang; Palivan, Cornelia G.; Meier, Wolfgang

2013-01-01

127

INTRODUCTION Aquaporins (AQPs) are membrane proteins that facilitate water  

E-print Network

3630 INTRODUCTION Aquaporins (AQPs) are membrane proteins that facilitate water transport, and have-length transmembrane helices and the two NPA-containing loops, B and E. This conformation in the plasma membrane Aquaporins (AQPs) are membrane proteins that for

Piulachs, M. Dolors

128

The synaptic vesicle protein synaptophysin: purification and characterization of its channel activity.  

PubMed

The synaptic vesicle protein synaptophysin was solubilized from rat brain synaptosomes with a relatively low concentration of Triton X-100 (0.2%) and was highly purified (above 95%) using a rapid single chromatography step on hydroxyapatite/celite resin. Purified synaptophysin was reconstituted into a planar lipid bilayer and the channel activity of synaptophysin was characterized. In asymmetric KCl solutions (cis 300 mM/trans 100 mM), synaptophysin formed a fast-fluctuating channel with a conductance of 414 +/- 13 pS at +60 mV. The open probability of synaptophysin channels was decreased upon depolarization, and channels were found to be cation-selective. Synaptophysin channels showed higher selectivity for K(+) over Cl(-) (P(K(+))/P(Cl(-)) > 8) and preferred K(+) over Li(+), Na(+), Rb(+), Cs(+), or choline(+). The synaptophysin channel is impermeable to Ca(2+), which has no effect on its channel activity. This study is the second demonstration of purified synaptophysin channel activity, but the first biophysical characterization of its channel properties. The availability of large amounts of purified synaptophysin and of its characteristic channel properties might help to establish the role of synaptophysin in synaptic transmission. PMID:12496091

Gincel, Dan; Shoshan-Barmatz, Varda

2002-12-01

129

Control performance and biomembrane disturbance of carbon nanotube artificial water channels by nitrogen-doping.  

PubMed

To establish ways to control the performance of artificial water channels is a big challenge. With molecular dynamics studies, we found that water flow inside the water channels of carbon nanotubes (CNTs) can be controlled by reducing or intensifying interaction energy between water molecules and the wall of the CNTs channel. A way of example toward this significant goal was demonstrated by the doping of nitrogen into the wall of CNTs. Different ratios of nitrogen doping result in different controllable water performance which is dominated mainly through a gradient of van der Waals forces created by the heteroatom doping in the wall of CNTs. Further results revealed that the nitrogen-doped CNT channels show less influence on the integrality of biomembrane than the pristine one, while the nitrogen-doped double-walled carbon nanotube exhibits fewer disturbances to the cellular membrane integrality than the nitrogen-doped single-walled carbon nanotube when interacting with biomembranes. PMID:20919730

Yang, Yuling; Li, Xiaoyi; Jiang, Jinliang; Du, Huailiang; Zhao, Lina; Zhao, Yuliang

2010-10-26

130

A MultiChannel Continuous Water Toxicity Monitoring System: Its Evaluation and Application to Water Discharged from a Power Plant  

Microsoft Academic Search

A multi-channel continuous water toxicity monitoring system was, after confirming the systems' performance, implemented to samples of water discharged from power plants to detect and classify their toxicity using several recombinant bioluminescent bacteria. Each channel of the system is composed of a series of two mini-bioreactors to enable a continuous operation, i.e., without system interruption due to highly toxic samples.

Byoung Chan Kim; Man Bock Gu

2005-01-01

131

SDS capillary gel electrophoresis of proteins in microfabricated channels  

PubMed Central

Analysis of variations in the concentrations or structures of biomolecules (e.g., mRNAs, proteins, peptides, natural products) that occur either naturally or in response to environmental or genetic perturbations can provide important insight into complex biological processes. Many biological samples are mixtures that require a separation step before quantitation of variations in the individual components. Two-dimensional denaturing gel electrophoresis has been used very effectively to separate complex mixtures of proteins, but it is time consuming and requires considerable amounts of sample. Microchannel-based separations have proven very effective in rapidly separating small amounts of nucleic acids; more recently, isoelectric focusing of proteins also has been adapted to the microchannel format. Here, we describe microchannel-based SDS capillary gel electrophoresis of proteins and demonstrate the speed and high resolution it provides. This development is an important step toward the miniaturization and integration of multidimensional and array separation methods for complex protein mixtures. PMID:10318890

Yao, Shao; Anex, Deon S.; Caldwell, W. Brett; Arnold, Don W.; Smith, Katherine B.; Schultz, Peter G.

1999-01-01

132

Structure of the SecY channel during initiation of protein translocation  

PubMed Central

Many secretory proteins are targeted by signal sequences to a protein-conducting channel, formed by prokaryotic SecY- or eukaryotic Sec61-complexes, and are translocated across the membrane during their synthesis1,2. Crystal structures of the inactive channel show that the SecY subunit of the heterotrimeric complex consists of two halves that form an hourglass-shaped pore with a constriction in the middle of the membrane and a lateral gate that faces the lipid phase3-5. The closed channel has an empty cytoplasmic funnel and an extracellular funnel that is filled with a small helical domain, called the plug. During initiation of translocation, a ribosome–nascent chain complex binds to the SecY/Sec61 complex, resulting in insertion of the nascent chain. However, the mechanism of channel opening during translocation is unclear. Here, we have addressed this question by determining structures of inactive and active ribosome–channel complexes with cryo-electron microscopy. Non-translating ribosome–SecY channel complexes derived from Methanococcus jannaschii or Escherichia coli show the channel in its closed state, and indicate that ribosome binding per se causes only minor changes. The structure of an active E. coli ribosome–channel complex demonstrates that the nascent chain opens the channel, causing mostly rigid body movements of the N- and C-terminal halves of SecY. In this early translocation intermediate, the polypeptide inserts as a loop into the SecY channel with the hydrophobic signal sequence intercalated into the open lateral gate. The nascent chain also forms a loop on the cytoplasmic surface of SecY rather than directly entering the channel. PMID:24153188

Park, Eunyong; Ménétret, Jean-François; Gumbart, James C.; Ludtke, Steven J.; Li, Weikai; Whynot, Andrew

2013-01-01

133

Flow characteristics of water in straight and serpentine micro-channels with miter bends  

Microsoft Academic Search

Flow characteristics of pressure-driven de-ionized water were investigated experimentally in straight and serpentine micro-channels with miter bends. The micro-channels had rectangular cross-sections with hydraulic diameters of 0.209mm, 0.395mm and 0.549mm. To evaluate bend loss coefficient in the serpentine micro-channel and micro-scale size effect on it, the additional pressure drop due to the miter bend must be obtained. This additional pressure

Renqiang Xiong; Jacob N. Chung

2007-01-01

134

Cloning and expression of apical membrane water channel of rat kidney collecting tubule  

Microsoft Academic Search

CONCENTRATING urine is mandatory for most mammals to prevent water loss from the body. Concentrated urine is produced in response to vasopressin by the transepithelial recovery of water from the lumen of the kidney collecting tubule through highly water-permeable membranes1,2. In this nephron segment, vaso-pressin regulates water permeability by endo- and exocytosis of water channels from or to the apical

Kiyohide Fushimi; Shinichi Uchida; Yukichi Harat; Yukio Hirata; Fumiaki Marumo; Sei Sasaki

1993-01-01

135

Vasoconstrictors inhibit ATP-sensitive K+ channels in arterial smooth muscle through protein kinase C  

Microsoft Academic Search

A B S T RA C T The effects of vasoconstrictor-receptor (neuropeptide Y, a-adrenergic, serotonergic, histaminergic) stimulation on currents through ATP-sensitive potassium (KATe) channels in arterial smooth muscle cells were ex- amined. Whole-cell KAT e currents, activated by the synthetic KAT e channel opener pinacidil or by the endogenous vasodilator, calcitonin gene-related peptide, which acts through protein kinase A, were

ADRIAN D. BONEV; MARK T. NELSON

1996-01-01

136

Changes in Channel Trafficking and Protein Stability Caused by LQT2 Mutations in the PAS Domain of the HERG Channel  

PubMed Central

Inherited human long-QT2 syndrome (LQTS) results from mutations in the gene encoding the HERG channel. Several LQT2-associated mutations have been mapped to the amino terminal cytoplasmic Per-Arnt-Sim (PAS) domain of the HERG1a channel subunit. Here we have characterized the trafficking properties of some LQT2-associated PAS domain mutants and analyzed rescue of the trafficking mutants by low temperature (27°C) or by the pore blocker drug E4031. We show that the LQT2-associated mutations in the PAS domain of the HERG channel display molecular properties that are distinct from the properties of LQT2-associated mutations in the trans-membrane region. Unlike the latter, many of the tested PAS domain LQT2-associated mutations do not result in trafficking deficiency of the channel. Moreover, the majority of the PAS domain mutations that cause trafficking deficiencies are not rescued by a pore blocking drug. We have also explored the in vitro folding stability properties of isolated mutant PAS domain proteins using a thermal unfolding fluorescence assay and a chemical unfolding assay. PMID:22396785

Harley, Carol A.; Jesus, Catarina S. H.; Carvalho, Ricardo; Brito, Rui M. M.; Morais-Cabral, João H.

2012-01-01

137

Multicriteria decision analysis in water resources management: the malnichara channel improvement  

Microsoft Academic Search

Multicriteria decision analysis tool is used in many water resources and environmental management projects. The Malnichara is one of the natural channels in Sylhet city (Bangladesh) responsible for storm runoff conveyance to the downstream Surma river. The channel is found to be encroached at many locations of the city and found to be very vulnerable. The authority has taken decision

R. K. Chowdhury; R. Rahman

2008-01-01

138

Ricean Shadowed Statistical Characterization of Shallow Water Acoustic Channels for Wireless Communications  

E-print Network

In this letter, the statistical behaviour of the shallow water acoustic channel for wireless communications is shown to be well characterized by the Ricean shadowed distribution, which has never been proposed for communication purposes on this type of channel. This characterization is clearly motivated from statistical and physical perspectives and has both theoretical and practical advantages compared to previously proposed models.

Ruiz-Vega, F; Otero, P; Paris, J F

2011-01-01

139

Efficient water-filling algorithms for a Gaussian multiaccess channel with ISI  

Microsoft Academic Search

Although the optimum transmit power spectral density (PSD) of each user in a Gaussian multiaccess channel is theoretically available, efficient algorithms are needed to obtain the optimal PSD numerically. This paper presents two water-filling algorithms for the scenario where all users have the same priorities. First we propose for a two-user channel an exact algorithm with a computational complexity of

Chaohuang Zeng; Louise M. C. Hoo; John M. Cioffi

2000-01-01

140

Suspended marine particulate proteins in coastal and oligotrophic waters  

NASA Astrophysics Data System (ADS)

Metaproteomic analyses were performed on suspended sediments collected in one coastal environment (Washington margin, Pacific Ocean, n = 5) and two oligotrophic environments (Atlantic Ocean near BATS, n = 5, and Pacific Ocean near HOTS, n = 5). Using a database of 2.3 million marine proteins developed using the NCBI database, 443 unique peptides were detected from which 363 unique proteins were identified. Samples from the euphotic zone contained on average 2-3x more identifiable proteins than deeper waters (150-1500 m) and these proteins were predominately from photosynthetic organisms. Diatom peptides dominate the spectra of the Washington margin while peptides from cyanobacteria, such as Synechococcus sp. dominated the spectra of both oligotrophic sites. Despite differences in the exact proteins identified at each location, there is good agreement for protein function and cellular location. Proteins in surface waters code for a variety of cellular functions including photosynthesis (24% of detected proteins), energy production (10%), membrane production (9%) and genetic coding and reading (9%), and are split 60-40 between membrane proteins and intracellular cytoplasmic proteins. Sargasso Sea surface waters contain a suite of peptides consistent with proteins involved in circadian rhythms that promote both C and N fixation at night. At depth in the Sargasso Sea, both muscle-derived myosin protein and the muscle-hydrolyzing proteases deseasin MCP-01 and metalloprotease Mcp02 from ?-proteobacteria were observed. Deeper waters contain peptides predominately sourced from ?-proteobacteria (37% of detected proteins) and ?-proteobacteria (26%), although peptides from membrane and photosynthetic proteins attributable to phytoplankton were still observed (13%). Relative to surface values, detection frequencies for bacterial membrane proteins and extracellular enzymes rose from 9 to 16 and 2 to 4% respectively below the thermocline and the overall balance between membrane proteins and intracellular proteins grows to an approximate 75-25 split. Unlike the phytoplankton membrane proteins, which are detrital in nature, the bacterial protein suite at depth is consistent with living biomass.

Bridoux, Maxime C.; Neibauer, Jaqui; Ingalls, Anitra E.; Nunn, Brook L.; Keil, Richard G.

2015-03-01

141

Channel Bow in Boiling Water Reactors - Hot Cell Examination Results and Correlation to Measured Bow  

SciTech Connect

An increase in frequency of fuel channel-control blade interference has been observed in Boiling Water Reactors (BWR) in recent years. Many of the channels leading to interference were found to bow towards the control blade in a manner that was inconsistent with the expected bow due to other effects. The pattern of bow appeared to indicate a new channel bow mechanism that differed from the predominant bow mechanism caused by differential growth due to fast-fluence gradients. In order to investigate this new type of channel bow, coupons from several channels with varying degrees of bow were returned to the GE Vallecitos Nuclear Center (VNC) for Post-Irradiation Examination (PIE). This paper describes the characteristics of channel corrosion and hydrogen pickup observed, and relates the observations to the channel exposure level, control history, and measured channel bow. The channels selected for PIE had exposures in the range of 36-48 GWd/MTU and covered a wide range of measured bow. The coupons were obtained at 4 elevations from opposing channel sides adjacent and away from the control blade. The PIE performed on these coupons included visual examination, metallography, and hydrogen concentration measurements. A new mechanism of control-blade shadow corrosion-induced channel bow was found to correlate with differences in the extent of corrosion and corresponding differences in the hydrogen concentration between opposite sides of the channels. The increased corrosion on the control blade sides was found to be dependent on the level of control early in the life of the channel. The contributions of other potential factors leading to increased channel bow and channel-control blade interference are also discussed in this paper. (authors)

Mahmood, S.T. [Global Nuclear Fuel, GE Vallecitos Nuclear Center, 6705 Vallecitos Road, Sunol, CA 94586 (United States); Lin, Y.P.; Dubecky, M.A. [Global Nuclear Fuel, 3901 Castle Hayne Road, m/c H25, Wilmington, NC 28401 (United States); Edsinger, K. [Electric Power Research Institute, 3420 Hillview Avenue, Palo Alto, CA 94304 (United States); Mader, E.V. [Electric Power Research Institute, 1000 River Walk Dr. no. 340, Idaho Falls, ID 83402 (United States)

2007-07-01

142

Influence of the scaffolding protein Zonula Occludens (ZOs) on membrane channels.  

PubMed

Zonula Occludens (ZO) proteins are ubiquitous scaffolding proteins providing the structural basis for the assembly of multiprotein complexes at the cytoplasmic surface of the plasma membrane and linking transmembrane proteins to the filamentous cytoskeleton. They belong to the large family of membrane-associated guanylate kinase (MAGUK)-like proteins comprising a number of subfamilies based on domain content and sequence similarity. ZO proteins were originally described to localize specifically to tight junctions, or Zonulae Occludentes, but this notion was rapidly reconsidered since ZO proteins were found to associate with adherens junctions as well as with gap junctions, particularly with connexin-made intercellular channels, and also with a few other membrane channels. Accumulating evidence reveals that in addition to having passive scaffolding functions in organizing gap junction complexes, including connexins and cytoskeletals, ZO proteins (particularly ZO-1) also actively take part in the dynamic function as well as in the remodeling of junctional complexes in a number of cellular systems. This article is part of a Special Issue entitled: Reciprocal influences between cell cytoskeleton and membrane channels, receptors and transporters. Guest Editor: Jean Claude Hervé. PMID:23867773

Hervé, Jean-Claude; Derangeon, Mickaël; Sarrouilhe, Denis; Bourmeyster, Nicolas

2014-02-01

143

Members of the chloride intracellular ion channel protein family demonstrate glutaredoxin-like enzymatic activity.  

PubMed

The Chloride Intracellular Ion Channel (CLIC) family consists of six evolutionarily conserved proteins in humans. Members of this family are unusual, existing as both monomeric soluble proteins and as integral membrane proteins where they function as chloride selective ion channels, however no function has previously been assigned to their soluble form. Structural studies have shown that in the soluble form, CLIC proteins adopt a glutathione S-transferase (GST) fold, however, they have an active site with a conserved glutaredoxin monothiol motif, similar to the omega class GSTs. We demonstrate that CLIC proteins have glutaredoxin-like glutathione-dependent oxidoreductase enzymatic activity. CLICs 1, 2 and 4 demonstrate typical glutaredoxin-like activity using 2-hydroxyethyl disulfide as a substrate. Mutagenesis experiments identify cysteine 24 as the catalytic cysteine residue in CLIC1, which is consistent with its structure. CLIC1 was shown to reduce sodium selenite and dehydroascorbate in a glutathione-dependent manner. Previous electrophysiological studies have shown that the drugs IAA-94 and A9C specifically block CLIC channel activity. These same compounds inhibit CLIC1 oxidoreductase activity. This work for the first time assigns a functional activity to the soluble form of the CLIC proteins. Our results demonstrate that the soluble form of the CLIC proteins has an enzymatic activity that is distinct from the channel activity of their integral membrane form. This CLIC enzymatic activity may be important for protecting the intracellular environment against oxidation. It is also likely that this enzymatic activity regulates the CLIC ion channel function. PMID:25581026

Al Khamici, Heba; Brown, Louise J; Hossain, Khondker R; Hudson, Amanda L; Sinclair-Burton, Alxcia A; Ng, Jane Phui Mun; Daniel, Elizabeth L; Hare, Joanna E; Cornell, Bruce A; Curmi, Paul M G; Davey, Mary W; Valenzuela, Stella M

2015-01-01

144

Members of the Chloride Intracellular Ion Channel Protein Family Demonstrate Glutaredoxin-Like Enzymatic Activity  

PubMed Central

The Chloride Intracellular Ion Channel (CLIC) family consists of six evolutionarily conserved proteins in humans. Members of this family are unusual, existing as both monomeric soluble proteins and as integral membrane proteins where they function as chloride selective ion channels, however no function has previously been assigned to their soluble form. Structural studies have shown that in the soluble form, CLIC proteins adopt a glutathione S-transferase (GST) fold, however, they have an active site with a conserved glutaredoxin monothiol motif, similar to the omega class GSTs. We demonstrate that CLIC proteins have glutaredoxin-like glutathione-dependent oxidoreductase enzymatic activity. CLICs 1, 2 and 4 demonstrate typical glutaredoxin-like activity using 2-hydroxyethyl disulfide as a substrate. Mutagenesis experiments identify cysteine 24 as the catalytic cysteine residue in CLIC1, which is consistent with its structure. CLIC1 was shown to reduce sodium selenite and dehydroascorbate in a glutathione-dependent manner. Previous electrophysiological studies have shown that the drugs IAA-94 and A9C specifically block CLIC channel activity. These same compounds inhibit CLIC1 oxidoreductase activity. This work for the first time assigns a functional activity to the soluble form of the CLIC proteins. Our results demonstrate that the soluble form of the CLIC proteins has an enzymatic activity that is distinct from the channel activity of their integral membrane form. This CLIC enzymatic activity may be important for protecting the intracellular environment against oxidation. It is also likely that this enzymatic activity regulates the CLIC ion channel function. PMID:25581026

Al Khamici, Heba; Brown, Louise J.; Hossain, Khondker R.; Hudson, Amanda L.; Sinclair-Burton, Alxcia A.; Ng, Jane Phui Mun; Daniel, Elizabeth L.; Hare, Joanna E.; Cornell, Bruce A.; Curmi, Paul M. G.; Davey, Mary W.; Valenzuela, Stella M.

2015-01-01

145

Cooperative endocytosis of the endosomal SNARE protein syntaxin-8 and the potassium channel TASK-1  

PubMed Central

The endosomal SNARE protein syntaxin-8 interacts with the acid-sensitive potassium channel TASK-1. The functional relevance of this interaction was studied by heterologous expression of these proteins (and mutants thereof) in Xenopus oocytes and in mammalian cell lines. Coexpression of syntaxin-8 caused a fourfold reduction in TASK-1 current, a corresponding reduction in the expression of TASK-1 at the cell surface, and a marked increase in the rate of endocytosis of the channel. TASK-1 and syntaxin-8 colocalized in the early endosomal compartment, as indicated by the endosomal markers 2xFYVE and rab5. The stimulatory effect of the SNARE protein on the endocytosis of the channel was abolished when both an endocytosis signal in TASK-1 and an endocytosis signal in syntaxin-8 were mutated. A syntaxin-8 mutant that cannot assemble with other SNARE proteins had virtually the same effect as wild-type syntaxin-8. Total internal reflection fluorescence microscopy showed formation and endocytosis of vesicles containing fluorescence-tagged clathrin, TASK-1, and/or syntaxin-8. Our results suggest that the unassembled form of syntaxin-8 and the potassium channel TASK-1 are internalized via clathrin-mediated endocytosis in a cooperative manner. This implies that syntaxin-8 regulates the endocytosis of TASK-1. Our study supports the idea that endosomal SNARE proteins can have functions unrelated to membrane fusion. PMID:24743596

Renigunta, Vijay; Fischer, Thomas; Zuzarte, Marylou; Kling, Stefan; Zou, Xinle; Siebert, Kai; Limberg, Maren M.; Rinné, Susanne; Decher, Niels; Schlichthörl, Günter; Daut, Jürgen

2014-01-01

146

CONCENTRATING TOXOPLASMA GONDII AND CYCLOSPORA CAYETANENSIS FROM SURFACE WATER AND DRINKING WATER BY CONTINUOUS SEPARATION CHANNEL CENTRIFUGATION  

Technology Transfer Automated Retrieval System (TEKTRAN)

Aims: To evaluate the effectiveness of continuous separation channel centrifugation for concentrating Toxoplasma gondii and Cyclospora cayetanensis from drinking water and environmental waters.Methods and Results: Ready-to-seed vials with known quantities of Toxoplasma gondii and Cyclospora cayetane...

147

Performance analysis of a LDPC coded OFDM communication system in shallow water acoustic channels  

NASA Astrophysics Data System (ADS)

Time-varying significant multipath interference is the major obstacle to reliable data communication in shallow water acoustic channels. In this paper, the performance of a low density parity check (LDPC) coded orthogonal frequency division multiplexing (OFDM) communication system is investigated for these channels. The initial message for LDPC, decoded by using the belief propagation (BP) algorithm, is deduced for OFDM underwater acoustic channels; based on this deduction, the noise thresholds of regular LDPC codes with different code rates are obtained by using the density evolution algorithm. Furthermore, a communication system model, developed with LDPC code, OFDM and channel interleaver for shallow water acoustic channels, is introduced. The effect of modulation and coding schemes on the LDPC codes performance is investigated by simulation. The results show that the system can achieve remarkable performance in shallow water acoustic channels, and the performance improves with increasing code length and decreasing code rate. The bit error rate (BER) of the system, under conditions with QPSK modulation, 1280-code length and 1/2-code rate, is less than 10-5 when the signal to noise ratio (SNR) is greater than 6.8dB. These values are obtained for a five-path shallow water acoustic channel of Xiamen harbor.

Liu, Shengxing; Xu, Xiaomei

2012-11-01

148

Comparisons of the hydraulics of water flows in Martian outflow channels with flows of similar scale on earth  

Microsoft Academic Search

The hydraulics of channelized water flows on Mars and the resulting sediment transport rates are calculated, and similar computations are performed for such terrestrial analogs as the Mississippi River and the catastrophic Lake Missoula floods that formed the Channeled Scabland in eastern Washington State. The morphologies of deep-sea channels formed by catastrophic turbidity currents are compared with the Martian channels,

P. D. Komar

1979-01-01

149

Mercury-sensitive water channels as possible sensors of water potentials in pollen.  

PubMed

The growing pollen tube is central to plant reproduction and is a long-standing model for cellular tip growth in biology. Rapid osmotically driven growth is maintained under variable conditions, which requires osmosensing and regulation. This study explores the mechanism of water entry and the potential role of osmosensory regulation in maintaining pollen growth. The osmotic permeability of the plasmalemma of Lilium pollen tubes was measured from plasmolysis rates to be 1.32±0.31×10(-3) cm s(-1). Mercuric ions reduce this permeability by 65%. Simulations using an osmotic model of pollen tube growth predict that an osmosensor at the cell membrane controls pectin deposition at the cell tip; inhibiting the sensor is predicted to cause tip bursting due to cell wall thinning. It was found that adding mercury to growing pollen tubes caused such a bursting of the tips. The model indicates that lowering the osmotic permeability per se does not lead to bursting but rather to thickening of the tip. The time course of induced bursting showed no time lag and was independent of mercury concentration, compatible with a surface site of action. The submaximal bursting response to intermediate mercuric ion concentration was independent of the concentration of calcium ions, showing that bursting is not due to a competitive inhibition of calcium binding or entry. Bursting with the same time course was also shown by cells growing on potassium-free media, indicating that potassium channels (implicated in mechanosensing) are not involved in the bursting response. The possible involvement of mercury-sensitive water channels as osmosensors and current knowledge of these in pollen cells are discussed. PMID:24098048

Shachar-Hill, Bruria; Hill, Adrian E; Powell, Janet; Skepper, Jeremy N; Shachar-Hill, Yair

2013-11-01

150

Mercury-sensitive water channels as possible sensors of water potentials in pollen  

PubMed Central

The growing pollen tube is central to plant reproduction and is a long-standing model for cellular tip growth in biology. Rapid osmotically driven growth is maintained under variable conditions, which requires osmosensing and regulation. This study explores the mechanism of water entry and the potential role of osmosensory regulation in maintaining pollen growth. The osmotic permeability of the plasmalemma of Lilium pollen tubes was measured from plasmolysis rates to be 1.32±0.31×10–3 cm s–1. Mercuric ions reduce this permeability by 65%. Simulations using an osmotic model of pollen tube growth predict that an osmosensor at the cell membrane controls pectin deposition at the cell tip; inhibiting the sensor is predicted to cause tip bursting due to cell wall thinning. It was found that adding mercury to growing pollen tubes caused such a bursting of the tips. The model indicates that lowering the osmotic permeability per se does not lead to bursting but rather to thickening of the tip. The time course of induced bursting showed no time lag and was independent of mercury concentration, compatible with a surface site of action. The submaximal bursting response to intermediate mercuric ion concentration was independent of the concentration of calcium ions, showing that bursting is not due to a competitive inhibition of calcium binding or entry. Bursting with the same time course was also shown by cells growing on potassium-free media, indicating that potassium channels (implicated in mechanosensing) are not involved in the bursting response. The possible involvement of mercury-sensitive water channels as osmosensors and current knowledge of these in pollen cells are discussed. PMID:24098048

Hill, Adrian E.

2013-01-01

151

Formation of Ravi Vallis outflow channel, Mars: Morphological development, water discharge, and duration estimates  

NASA Astrophysics Data System (ADS)

We infer that the morphology of the Ravi Vallis channel system is consistent with it having been eroded by water in a single flood event, and we have used the topography of the channel system to estimate the depth of water in the channel at various stages during its development. Values lie in the range 50-150 m. Measured bed slopes, estimated water depths, and corresponding channel widths are used to obtain mean water flow speeds and volume flow rates. Water flow speeds are found to lie in the range ~10-25 m s-1, and the discharge estimates vary from a maximum volume flux of ~30 × 106 m3 s-1 just after the start of the flood to less than 10 × 106 m3 s-1 in the late stages. Using assumptions about the sediment-carrying capability of the water, estimates are obtained for the minimum duration of the water release event, the minimum total volume of water involved, and the crustal erosion rate. The duration is inferred to have been between 2 and 10 weeks, and the minimum total water volume was between 11,000 and 65,000 km3. The corresponding bed erosion rate was possibly as much as ~100 but more likely ~20-50 m/d. It is estimated that during the early stages of the flood event, flow conditions were supercritical, with maximum Froude numbers between 1.4 and 2 depending on the bed roughness.

Leask, Harald J.; Wilson, Lionel; Mitchell, Karl L.

2006-06-01

152

Time-Resolved Images of the Decay of the Gas Channel Induced by Pulsed Positive Streamer Discharge in Water  

Microsoft Academic Search

In an underwater streamer discharge, plasma chan- nels are created and propagate in water. After the discharge, the ionized gas channels gradually cool down and decay. In this paper, a time-resolved study on the decay process of the gas channels induced by pulsed positive streamer discharge in water is performed by using a high-speed camera system. The gas channels created

Xiao Qiong Wen; Gui Shi Liu; Zhen Feng Ding

2011-01-01

153

The small envelope protein of porcine reproductive and respiratory syndrome virus possesses ion channel protein-like properties  

SciTech Connect

The small envelope (E) protein of porcine reproductive and respiratory syndrome virus (PRRSV) is a hydrophobic 73 amino acid protein encoded in the internal open reading frame (ORF) of the bicistronic mRNA2. As a first step towards understanding the biological role of E protein during PRRSV replication, E gene expression was blocked in a full-length infectious clone by mutating the ATG translational initiation to GTG, such that the full-length mutant genomic clone was unable to synthesize the E protein. DNA transfection of PRRSV-susceptible cells with the E gene knocked-out genomic clone showed the absence of virus infectivity. P129-{delta}E-transfected cells however produced virion particles in the culture supernatant, and these particles contained viral genomic RNA, demonstrating that the E protein is essential for PRRSV infection but dispensable for virion assembly. Electron microscopy suggests that the P129-{delta}E virions assembled in the absence of E had a similar appearance to the wild-type particles. Strand-specific RT-PCR demonstrated that the E protein-negative, non-infectious P129-{delta}E virus particles were able to enter cells but further steps of replication were interrupted. The entry of PRRSV has been suggested to be via receptor-mediated endocytosis, and lysomotropic basic compounds and known ion-channel blocking agents both inhibited PRRSV replication effectively during the uncoating process. The expression of E protein in Escherichia coli-mediated cell growth arrests and increased the membrane permeability. Cross-linking experiments in cells infected with PRRSV or transfected with E gene showed that the E protein was able to form homo-oligomers. Taken together, our data suggest that the PRRSV E protein is likely an ion-channel protein embedded in the viral envelope and facilitates uncoating of virus and release of the genome in the cytoplasm.

Lee, Changhee [Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2W1 (Canada); Yoo, Dongwan [Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2W1 (Canada)]. E-mail: dyoo@uoguelph.ca

2006-11-10

154

A virus-encoded potassium ion channel is a structural protein in the chlorovirus Paramecium bursaria chlorella virus 1 virion.  

PubMed

Most chloroviruses encode small K(+) channels, which are functional in electrophysiological assays. The experimental finding that initial steps in viral infection exhibit the same sensitivity to channel inhibitors as the viral K(+) channels has led to the hypothesis that the channels are structural proteins located in the internal membrane of the virus particles. This hypothesis was questioned recently because proteomic studies failed to detect the channel protein in virions of the prototype chlorovirus Paramecium bursaria chlorella virus 1 (PBCV-1). Here, we used a mAb raised against the functional K(+) channel from chlorovirus MA-1D to search for the viral K(+) channel in the virus particle. The results showed that the antibody was specific and bound to the tetrameric channel on the extracellular side. The antibody reacted in a virus-specific manner with protein extracts from chloroviruses that encoded channels similar to that from MA-1D. There was no cross-reactivity with chloroviruses that encoded more diverse channels or with a chlorovirus that lacked a K(+) channel gene. Together with electron microscopic imaging, which revealed labelling of individual virus particles with the channel antibody, these results establish that the viral particles contain an active K(+) channel, presumably located in the lipid membrane that surrounds the DNA in the mature virions. PMID:23918407

Romani, Giulia; Piotrowski, Adrianna; Hillmer, Stefan; Gurnon, James; Van Etten, James L; Moroni, Anna; Thiel, Gerhard; Hertel, Brigitte

2013-11-01

155

A virus-encoded potassium ion channel is a structural protein in the chlorovirus Paramecium bursaria chlorella virus 1 virion  

PubMed Central

Most chloroviruses encode small K+ channels, which are functional in electrophysiological assays. The experimental finding that initial steps in viral infection exhibit the same sensitivity to channel inhibitors as the viral K+ channels has led to the hypothesis that the channels are structural proteins located in the internal membrane of the virus particles. This hypothesis was questioned recently because proteomic studies failed to detect the channel protein in virions of the prototype chlorovirus Paramecium bursaria chlorella virus 1 (PBCV-1). Here, we used a mAb raised against the functional K+ channel from chlorovirus MA-1D to search for the viral K+ channel in the virus particle. The results showed that the antibody was specific and bound to the tetrameric channel on the extracellular side. The antibody reacted in a virus-specific manner with protein extracts from chloroviruses that encoded channels similar to that from MA-1D. There was no cross-reactivity with chloroviruses that encoded more diverse channels or with a chlorovirus that lacked a K+ channel gene. Together with electron microscopic imaging, which revealed labelling of individual virus particles with the channel antibody, these results establish that the viral particles contain an active K+ channel, presumably located in the lipid membrane that surrounds the DNA in the mature virions. PMID:23918407

Romani, Giulia; Piotrowski, Adrianna; Hillmer, Stefan; Gurnon, James; Van Etten, James L.; Moroni, Anna; Thiel, Gerhard

2013-01-01

156

Intra-membrane molecular interactions of K%2B channel proteins : application to problems in biodefense and bioenergy.  

SciTech Connect

Ion channel proteins regulate complex patterns of cellular electrical activity and ionic signaling. Certain K+ channels play an important role in immunological biodefense mechanisms of adaptive and innate immunity. Most ion channel proteins are oligomeric complexes with the conductive pore located at the central subunit interface. The long-term activity of many K+ channel proteins is dependent on the concentration of extracellular K+; however, the mechanism is unclear. Thus, this project focused on mechanisms underlying structural stability of tetrameric K+ channels. Using KcsA of Streptomyces lividans as a model K+ channel of known structure, the molecular basis of tetramer stability was investigated by: 1. Bioinformatic analysis of the tetramer interface. 2. Effect of two local anesthetics (lidocaine, tetracaine) on tetramer stability. 3. Molecular simulation of drug docking to the ion conduction pore. The results provide new insights regarding the structural stability of K+ channels and its possible role in cell physiology.

Moczydlowski, Edward G.

2013-07-01

157

EVALUATION OF PROTEIN REDUCTION AND LYSINE SUPPLEMENTATION OF PRODUCTION DIETS FOR CHANNEL CATFISH ICTALURUS PUNCTATUS  

Technology Transfer Automated Retrieval System (TEKTRAN)

A 2-year continuous production trial was conducted in earthen ponds to evaluate lysine supplementation of practical diets as a means to reduce the need for total dietary protein and limit nitrogenous waste production of channel catfish. Experimental diets consisted of three practical diets containi...

158

Interaction of the synaptic protein PICK1 (protein interacting with C kinase 1) with the non-voltage gated sodium channels BNC1 (brain Na+ channel 1) and ASIC (acid-sensing ion channel).  

PubMed Central

Neuronal members of the degenerin/epithelial Na(+) channel (DEG/ENaC) family of cation channels include the mammalian brain Na(+) channel 1 (BNC1), acid-sensing ion channel (ASIC) and dorsal-root acid-sensing ion channel (DRASIC). Their response to acidic pH, their sequence similarity to nematode proteins involved in mechanotransduction and their modulation by neuropeptides suggest that they may function as receptors for a number of different stimuli. Using the yeast two-hybrid assay, we found that the PDZ domain-containing protein PICK1 (protein interacting with C kinase) interacts specifically with the C-termini of BNC1 and ASIC, but not DRASIC or the related alphaENaC or betaENaC. In both the yeast two-hybrid system and mammalian cells, deletion of the BNC1 and ASIC C-termini abolished the interaction with PICK1. Likewise, mutating the PDZ domain in PICK1 abolished its interaction with BNC1 and ASIC. In addition, in a heterologous expression system PICK1 altered the distribution of BNC1 channels; this effect was dependent on the PDZ domain of PICK1 and the C-terminus of BNC1. We found crude synaptosomal fractions of brain to be enriched in ASIC, suggesting a possible synaptic localization. Moreover, in transfected hippocampal neurons ASIC co-localized with PICK1 in a punctate pattern at synapses. These data suggest that PICK1 binds ASIC and BNC1 via its PDZ domain. This interaction may be important for the localization and/or function of these channels in both the central and peripheral nervous systems. PMID:11802773

Hruska-Hageman, Alesia M; Wemmie, John A; Price, Margaret P; Welsh, Michael J

2002-01-01

159

The hepatitis C virus p7 protein forms an ion channel that is inhibited by long-alkyl-chain  

E-print Network

flaviviruses such as dengue virus and Jap- anese encephalitis virus (8), which do not contain p7The hepatitis C virus p7 protein forms an ion channel that is inhibited by long Blumberg, March 17, 2003 We show that hepatitis C virus (HCV) p7 protein forms ion channels in black lipid

Fischer, Wolfgang

160

Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel  

PubMed Central

Traditional macroscale protein crystallization is accomplished non-trivially by exploring a range of protein concentrations and buffers in solution until a suitable combination is attained. This methodology is time consuming and resource intensive, hindering protein structure determination. Even more difficulties arise when crystallizing large membrane protein complexes such as photosystem I (PSI) due to their large unit cells dominated by solvent and complex characteristics that call for even stricter buffer requirements. Structure determination techniques tailored for these ‘difficult to crystallize’ proteins such as femtosecond nanocrystallography are being developed, yet still need specific crystal characteristics. Here, we demonstrate a simple and robust method to screen protein crystallization conditions at low ionic strength in a microfluidic device. This is realized in one microfluidic experiment using low sample amounts, unlike traditional methods where each solution condition is set up separately. Second harmonic generation microscopy via Second Order Nonlinear Imaging of Chiral Crystals (SONICC) was applied for the detection of nanometer and micrometer sized PSI crystals within microchannels. To develop a crystallization phase diagram, crystals imaged with SONICC at specific channel locations were correlated to protein and salt concentrations determined by numerical simulations of the time-dependent diffusion process along the channel. Our method demonstrated that a portion of the PSI crystallization phase diagram could be reconstructed in excellent agreement with crystallization conditions determined by traditional methods. We postulate that this approach could be utilized to efficiently study and optimize crystallization conditions for a wide range of proteins that are poorly understood to date. PMID:24191698

Abdallah, Bahige G.; Kupitz, Christopher; Fromme, Petra; Ros, Alexandra

2014-01-01

161

33 CFR 207.640 - Sacramento Deep Water Ship Channel Barge Lock and Approach Canals; use, administration, and...  

Code of Federal Regulations, 2013 CFR

33 Navigation and Navigable Waters 3 2013-07-01 2013-07-01 false Sacramento Deep Water Ship Channel Barge Lock and Approach Canals...Section 207.640 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF...

2013-07-01

162

33 CFR 207.640 - Sacramento Deep Water Ship Channel Barge Lock and Approach Canals; use, administration, and...  

Code of Federal Regulations, 2011 CFR

33 Navigation and Navigable Waters 3 2011-07-01 2011-07-01 false Sacramento Deep Water Ship Channel Barge Lock and Approach Canals...Section 207.640 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF...

2011-07-01

163

33 CFR 207.640 - Sacramento Deep Water Ship Channel Barge Lock and Approach Canals; use, administration, and...  

Code of Federal Regulations, 2014 CFR

33 Navigation and Navigable Waters 3 2014-07-01 2014-07-01 false Sacramento Deep Water Ship Channel Barge Lock and Approach Canals...Section 207.640 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF...

2014-07-01

164

Water and sediment transport of channel-flat systems in a mesotidal mudflat: Willapa Bay, Washington  

NASA Astrophysics Data System (ADS)

The muddy tidal flats of southern Willapa Bay, Washington are tidally dominated and receive little direct freshwater input. We use data from instruments deployed in channels of different size and on their adjacent flats to investigate the hydrodynamics and sediment dynamics of each morphological setting under a range of seasonal and meteorological conditions, including rain and wind events. Interaction between the morphology of the channel/flat complex and tidal water-level variations produces well-defined velocity pulses during both flooding and ebbing tides. These pulses represent about 27% of the total along-channel water transport and 35% of the suspended-sediment transport of the system. Maintenance of continuity produces the velocity pulse, and pulse magnitude is determined by tidal range. Wind alters the flow regime in channels and on the flat, enhancing over-flat ebb flow in this study location while decreasing ebb-pulse intensity. Wind speed was positively correlated with minimum suspended-sediment concentration. Precipitation falling directly on flats was found to erode flat sediment, which subsequently formed a temporary deposit in the adjacent channel. Residual along-channel water transport in channels and on nearby flats was flood dominant under all seasonal conditions sampled, and sediment flux was flood dominant during winter and spring deployments.

Nowacki, Daniel J.; Ogston, Andrea S.

2013-06-01

165

Partitioning of Water Discharge by Distributary Channels in the Prograding, Wax Lake Delta, Coastal Louisiana, USA  

Microsoft Academic Search

How water and sediment is routed through distributary networks on river deltas is incompletely known and a topic of much active research. We have undertaken a study to determine the controls on partitioning of water and sediment discharge in distributary channels of the Wax Lake Delta and to connect these transport processes to the land building associated with the growth

J. Buttles; D. Mohrig; J. Nittrouer; B. McElroy; E. Baitis; M. Allison; C. Paola; G. Parker; W. Kim

2007-01-01

166

Mapping functional domains of chloride intracellular channel (CLIC) proteins in vivo.  

PubMed

Chloride intracellular channel (CLIC) proteins are small proteins distantly related to the omega family of glutathione S-transferases (GSTs). CLIC proteins are expressed in a wide variety of tissues in multicellular organisms and are targeted to specific cellular membranes. Members of this family are capable in vitro of changing conformation from a globular, soluble state to a membrane-inserted state in which they provide chloride conductance. The structural basis for in vivo CLIC protein function, however, is not well understood. We have mapped the functional domains of CLIC family members using an in vivo assay for membrane localization and function of CLIC proteins in the nematode Caenorhabditis elegans. A<70 amino acid N-terminal domain is a key determinant of membrane localization and function of invertebrate CLIC proteins. This domain, which we term the ''PTM'' domain, named after an amphipathic putative transmembrane helix contained within it, directs distinct C. elegans CLIC homologs to distinct subcellular membranes. We find that within the PTM region, the cysteine residues required for GST-type activity are unnecessary for invertebrate CLIC function, but that specific residues within the proposed transmembrane helix are necessary for correct targeting and protein function. We find that among all tested invertebrate CLIC proteins, function appears to be completely conserved despite striking differences in the charged residues contained within the amphipathic helix. This indicates that these residues do not contribute to anion selectivity as previously suggested. We find that outside the PTM region, the remaining three-quarters of CLIC protein sequence is functionally equivalent not only among vertebrate and invertebrate CLIC proteins, but also among the more distantly related GST-omega and GST-sigma proteins. The PTM region thus provides both targeting information and CLIC functional specificity, possibly adapting GST-type proteins to function as ion channels. PMID:16737711

Berry, Katherine L; Hobert, Oliver

2006-06-23

167

Laboratory Modeling of Self-Formed Leveed Channels From Sediment-Laden Flows Entering Still Water  

NASA Astrophysics Data System (ADS)

Self-formed leveed channels constructed by deposition of suspended sediment from sediment-laden flows entering still water are common features in nature. Such channels drive delta progradation, develop at tidal inlets and occur where mainstem river flows empty into oxbows and blocked valley lakes. Presently there is no theory for the formation of such channels. This lack of theory is partly due to a lack of field or laboratory studies that provide insight about the mechanism controlling these self-formed, propagating channels. The creation of such features in the laboratory, have proved illusive to date. Our ongoing experiments aimed at modeling the formation of floodplain tie channels provide insight into the necessary conditions for levee formation and channel growth. Under conditions of steady water discharge, constant sediment feed rate, unimodal sediment distribution and invariant basin stage we are able to create subaqueous lateral bars (submerged levees) along the margins of a sediment laden jet. Our results highlight the sensitivity of channel formation to issues of scaling and experimental design. In the laboratory, levee formation has only been possible with the use of plastic particles (specific gravity ~1.5); complete bed alluviation and dune formation results from the use of particles with specific gravities of ~ 2.65 across a range grain diameters and shapes. We hypothesize this effect is related to high entrainment thresholds relative to suspension thresholds of small (< 100 mm) natural particles under conditions of reduced turbulence in laboratory scaled flows. Additionally, both the width to depth ratio and the form of the outlet channel introducing the sediment laden flow into the experimental basin exert a strong control on sedimentation pattern and levee growth. Continuing experiments are focused on generating emergent channel levees and a basin ward propagation of the channel by adjusting the form of the feed channel, varying basin stage, and the use of unsteady discharge.

Rowland, J. C.; Dietrich, W. E.

2004-12-01

168

Protein conformational modifications and kinetics of water-protein interactions in milk protein concentrate powder upon aging: effect on solubility.  

PubMed

Protein conformational modifications and water-protein interactions are two major factors believed to induce instability of protein and eventually affect the solubility of milk protein concentrate (MPC) powder. To test these hypotheses, MPC was stored at different water activities (a(w) 0.0-0.85) and temperatures (25 and 45 degrees C) for up to 12 weeks. Samples were examined periodically to determine solubility, change in protein conformation by Fourier transform infrared (FTIR) spectroscopy and principal component analysis (PCA), and water status (interaction of water with the protein molecule/surface) by measuring the transverse relaxation time (T(2)) with proton nuclear magnetic resonance ((1)H NMR). The solubility of MPC decreased significantly with aging, and this process was enhanced by increasing water activity (a(w)) and storage temperature. Minor changes in protein secondary structure were observed with FTIR, which indicated some degree of unfolding of protein molecules. PCA of the FTIR data was able to discriminate samples according to moisture content and storage period. Partial least-squares (PLS) analysis showed some correlation between FTIR spectral feature and solubility. The NMR T(2) results indicated the presence of three distinct populations of water molecules, and the proton signal intensity and T(2) values of proton fractions varied with storage conditions (humidity, temperature) and aging. Results suggest that protein/protein interactions may be initiated by unfolding of protein molecules that eventually affects solubility. PMID:20536137

Haque, Enamul; Bhandari, Bhesh R; Gidley, Michael J; Deeth, Hilton C; Møller, Sandie M; Whittaker, Andrew K

2010-07-14

169

Water slug to drop and film transitions in gas-flow channels.  

PubMed

Water emerging from micrometer-sized pores into millimeter-sized gas-flow channels forms drops. The drops grow until the force from the flowing gas is sufficient to detach the drops as either (1) slugs that completely occlude the cross section of the channel and move at the superficial gas velocity, (2) drops that partially occlude the channel and move at a velocity that is less than the gas velocity, or (3) films that flow continuously, occluding part of the channel. At steady state, small residual water droplets, ?100 ?m in diameter, left in corners and on surface defects from previous drops, are key in determining the shape of water drops at detachment. Slugs are formed at low-gas-phase Reynolds numbers (ReG) in both hydrophilic and hydrophobic channels. Drops are shed in Teflon-coated hydrophobic channels for ReG > 30. Films are formed in acrylic hydrophilic channels for ReG > 30. Slugs form when growing drops encounter residual water droplets that nucleate the drop to slug transition. Drops are shed when the force exerted by the flowing gas on growing drops exceeds the force needed to advance the gas/liquid/solid contact line before they grow to the critical size for the drop to slug transition. Drops grow by "stick-slip" of the solid-liquid-gas contact lines and with pinned contact lines until the force on the drops results in either the downstream contact angle becoming greater than the dynamic advancing contact angle or the upstream contact angle becoming less than the dynamic receding contact angle. The upstream contact line never detaches for hydrophilic channels, which is why films form. The shape of water drops and the detachment energies are shown to be well approximated by the force balance between the force needed to advance the drop's contact lines and the force that the flowing gas exerts on a stationary drop. PMID:24206393

Cheah, May Jean; Kevrekidis, Ioannis G; Benziger, Jay B

2013-12-01

170

The threshold of vapor channel formation in water induced by pulsed CO2 laser  

NASA Astrophysics Data System (ADS)

Water plays an important role in laser ablation. There are two main interpretations of laser-water interaction: hydrokinetic effect and vapor phenomenon. The two explanations are reasonable in some way, but they can't explain the mechanism of laser-water interaction completely. In this study, the dynamic process of vapor channel formation induced by pulsed CO2 laser in static water layer was monitored by high-speed camera. The wavelength of pulsed CO2 laser is 10.64 um, and pulse repetition rate is 60 Hz. The laser power ranged from 1 to 7 W with a step of 0.5 W. The frame rate of high-speed camera used in the experiment was 80025 fps. Based on high-speed camera pictures, the dynamic process of vapor channel formation was examined, and the threshold of vapor channel formation, pulsation period, the volume, the maximum depth and corresponding width of vapor channel were determined. The results showed that the threshold of vapor channel formation was about 2.5 W. Moreover, pulsation period, the maximum depth and corresponding width of vapor channel increased with the increasing of the laser power.

Guo, Wenqing; Zhang, Xianzeng; Zhan, Zhenlin; Xie, Shusen

2012-12-01

171

Water dynamics clue to key residues in protein folding  

SciTech Connect

A computational method independent of experimental protein structure information is proposed to recognize key residues in protein folding, from the study of hydration water dynamics. Based on all-atom molecular dynamics simulation, two key residues are recognized with distinct water dynamical behavior in a folding process of the Trp-cage protein. The identified key residues are shown to play an essential role in both 3D structure and hydrophobic-induced collapse. With observations on hydration water dynamics around key residues, a dynamical pathway of folding can be interpreted.

Gao, Meng [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Zhu, Huaiqiu, E-mail: hqzhu@pku.edu.cn [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Yao, Xin-Qiu [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China) [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Department of Biophysics, Kyoto University, Sakyo Kyoto 606-8502 (Japan); She, Zhen-Su, E-mail: she@pku.edu.cn [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)

2010-01-29

172

NMR-based structural biology of proteins in supercooled water.  

PubMed

NMR-based structural biology of proteins can be pursued efficiently in supercooled water at temperatures well below the freezing point of water. This enables one to study protein structure, dynamics, hydration and cold denaturation in an unperturbed aqueous solution at very low temperatures. Furthermore, such studies enable one to accurately measure thermodynamic parameters associated with protein cold denaturation. Presently available approaches to acquire NMR data for supercooled aqueous protein solutions are surveyed, new insights obtained from such studies are summarized, and future perspectives are discussed. PMID:21533787

Szyperski, Thomas; Mills, Jeffrey L

2011-03-01

173

Computational analysis of the soluble form of the intracellular chloride ion channel protein CLIC1.  

PubMed

The chloride intracellular channel (CLIC) family of proteins has the remarkable property of maintaining both a soluble form and an integral membrane form acting as an ion channel. The soluble form is structurally related to the glutathione-S-transferase family, and CLIC can covalently bind glutathione via an active site cysteine. We report approximately 0.6??s of molecular dynamics simulations, encompassing the three possible ligand-bound states of CLIC1, using the structure of GSH-bound human CLIC1. Noncovalently bound GSH was rapidly released from the protein, whereas the covalently ligand-bound protein remained close to the starting structure over 0.25??s of simulation. In the unliganded state, conformational changes in the vicinity of the glutathione-binding site resulted in reduced reactivity of the active site thiol. Elastic network analysis indicated that the changes in the unliganded state are intrinsic to the protein architecture and likely represent functional transitions. Overall, our results are consistent with a model of CLIC function in which covalent binding of glutathione does not occur spontaneously but requires interaction with another protein to stabilise the GSH binding site and/or transfer of the ligand. The results do not indicate how CLIC1 undergoes a radical conformational change to form a transmembrane chloride channel but further elucidate the mechanism by which CLICs are redox controlled. PMID:24089665

Jones, Peter M; Curmi, Paul M G; Valenzuela, Stella M; George, Anthony M

2013-01-01

174

Computational Analysis of the Soluble Form of the Intracellular Chloride Ion Channel Protein CLIC1  

PubMed Central

The chloride intracellular channel (CLIC) family of proteins has the remarkable property of maintaining both a soluble form and an integral membrane form acting as an ion channel. The soluble form is structurally related to the glutathione-S-transferase family, and CLIC can covalently bind glutathione via an active site cysteine. We report approximately 0.6??s of molecular dynamics simulations, encompassing the three possible ligand-bound states of CLIC1, using the structure of GSH-bound human CLIC1. Noncovalently bound GSH was rapidly released from the protein, whereas the covalently ligand-bound protein remained close to the starting structure over 0.25??s of simulation. In the unliganded state, conformational changes in the vicinity of the glutathione-binding site resulted in reduced reactivity of the active site thiol. Elastic network analysis indicated that the changes in the unliganded state are intrinsic to the protein architecture and likely represent functional transitions. Overall, our results are consistent with a model of CLIC function in which covalent binding of glutathione does not occur spontaneously but requires interaction with another protein to stabilise the GSH binding site and/or transfer of the ligand. The results do not indicate how CLIC1 undergoes a radical conformational change to form a transmembrane chloride channel but further elucidate the mechanism by which CLICs are redox controlled. PMID:24089665

Jones, Peter M.; Curmi, Paul M. G.; Valenzuela, Stella M.; George, Anthony M.

2013-01-01

175

Vibrational energy flow through the green fluorescent protein-water interface: communication maps and thermal boundary conductance.  

PubMed

We calculate communication maps for green fluorescent protein (GFP) to elucidate energy transfer pathways between the chromophore and other parts of the protein in the ground and excited state. The approach locates energy transport channels from the chromophore to remote regions of the protein via residues and water molecules that hydrogen bond to the chromophore. We calculate the thermal boundary conductance between GFP and water over a wide range of temperature and find that the interface between the protein and the cluster of water molecules in the ?-barrel poses negligible resistance to thermal flow, consistent with facile vibrational energy transfer from the chromophore to the ?-barrel waters observed in the communication maps. PMID:24471982

Xu, Yao; Leitner, David M

2014-07-17

176

Isolation and identification of a sodium channel-inhibiting protein from eggs of black widow spiders.  

PubMed

The eggs of black widow spider (L. tredecimguttatus) have been demonstrated to be rich in biologically active components that exhibit great research value and application foreground. In the present study, a protein toxin, named Latroeggtoxin-II, was isolated from the eggs using the combination of gel filtration, ion exchange chromatography and reversed-phase high performance liquid chromatography. Electrospray mass spectrometric analysis indicated that the molecular weight of the protein was 28.69 kDa, and Edman degradation revealed that its N-terminal sequence was ESIQT STYVP NTPNQ KFDYE VGKDY-. After being abdominally injected into mice and P. americana, the protein could make the animals especially P. americana display a series of poisoning symptoms. Electrophysiological experiments demonstrated that the protein could selectively inhibit tetrodotoxin-resistant Na(+) channel currents in rat dorsal root ganglion neurons, without significant effect on the tetrodotoxin-sensitive Na(+) channel currents. Using multiple proteomic strategies, the purified protein was shown to have only a few similarities to the existing proteins in the databases, suggesting that it was a novel protein isolated from the eggs of black widow spiders. PMID:24412150

Li, Jianjun; Yan, Yizhong; Yu, Hai; Peng, Xiaozhen; Zhang, Yiya; Hu, Weijun; Duan, Zhigui; Wang, Xianchun; Liang, Songping

2014-04-01

177

Preparation of semi-solid aluminum alloy slurry poured through a water-cooled serpentine channel  

NASA Astrophysics Data System (ADS)

A water-cooled serpentine channel pouring process was invented to produce semi-solid A356 aluminum alloy slurry for rheocasting, and the effects of pouring temperature and circulating cooling water flux on the microstructure of the slurry were investigated. The results show that at the pouring temperature of 640-680°C and the circulating cooling water flux of 0.9 m3/h, the semi-solid A356 aluminum alloy slurry with spherical primary ?(Al) grains can be obtained, whose shape factors are between 0.78 and 0.86 and the grain diameter can reach 48-68 ?m. When the pouring temperatures are at 660-680°C, only a very thin solidified shell remains inside the serpentine channel and can be removed easily. When the serpentine channel is cooled with circulating water, the microstructure of the semi-solid slurry can be improved, and the serpentine channel is quickly cooled to room temperature after the completion of one pouring. In terms of the productivity of the special equipment, the water-cooled serpentine channel is economical and efficient.

Chen, Zheng-Zhou; Mao, Wei-Min; Wu, Zong-Chuang

2012-01-01

178

Gating of the TrkH Ion Channel by its Associated RCK Protein, Trka  

PubMed Central

TrkH belongs to a superfamily of K+ transport proteins required for growth of bacteria in low external K+ concentrations. The crystal structure of TrkH from Vibrio parahaemolyticus showed that TrkH resembles a K+ channel, and may have a gating mechanism substantially different from K+ channels. TrkH assembles with TrkA, a cytosolic protein comprising two Regulate-the-Conductance-of-K+, or RCK domains, which are found in certain K+ channels and control their gating. However, fundamental questions on whether TrkH is an ion channel and how it is regulated by TrkA remain unresolved. Here we show single-channel activity of TrkH that is upregulated by ATP via TrkA. We report two structures of the tetrameric TrkA ring, one in complex with TrkH and one in isolation, in which the ring assumes two dramatically different conformations. These results suggest a mechanism for how ATP increases TrkH activity by inducing conformational changes in TrkA. PMID:23598339

Cao, Yu; Pan, Yaping; Huang, Hua; Jin, Xiangshu; Levin, Elena J.; Kloss, Brian; Zhou, Ming

2013-01-01

179

Regulation of CaV2 calcium channels by G protein coupled receptors  

PubMed Central

Voltage gated calcium channels (Ca2+ channels) are key mediators of depolarization induced calcium influx into excitable cells, and thereby play pivotal roles in a wide array of physiological responses. This review focuses on the inhibition of CaV2 (N- and P/Q-type) Ca2+-channels by G protein coupled receptors (GPCRs), which exerts important autocrine/paracrine control over synaptic transmission and neuroendocrine secretion. Voltage-dependent inhibition is the most widespread mechanism, and involves direct binding of the G protein ?? dimer (G??) to the ?1 subunit of CaV2 channels. GPCRs can also recruit several other distinct mechanisms including phosphorylation, lipid signaling pathways, and channel trafficking that result in voltage-independent inhibition. Current knowledge of G??-mediated inhibition is reviewed, including the molecular interactions involved, determinants of voltage-dependence, and crosstalk with other cell signaling pathways. A summary of recent developments in understanding the voltage-independent mechanisms prominent in sympathetic and sensory neurons is also included. PMID:23063655

Zamponi, Gerald W.; Currie, Kevin P.M.

2012-01-01

180

KCl Mediates K+ Channel-Activated Mitogen-Activated Protein Kinases Signaling in Wound Healing  

PubMed Central

Background Wound healing is an interaction of a complex signaling cascade of cellular events, including inflammation, proliferation, and maturation. K+ channels modulate the mitogen-activated protein kinase (MAPK) signaling pathway. Here, we investigated whether K+ channel-activated MAPK signaling directs collagen synthesis and angiogenesis in wound healing. Methods The human skin fibroblast HS27 cell line was used to examine cell viability and collagen synthesis after potassium chloride (KCl) treatment by Cell Counting Kit-8 (CCK-8) and western blotting. To investigate whether K+ ion channels function upstream of MAPK signaling, thus affecting collagen synthesis and angiogenesis, we examined alteration of MAPK expression after treatment with KCl (channel inhibitor), NS1619 (channel activator), or kinase inhibitors. To research the effect of KCl on angiogenesis, angiogenesis-related proteins such as thrombospondin 1 (TSP1), anti-angiogenic factor, basic fibroblast growth factor (bFGF) and vascular endothelial growth factor (VEGF), pro-angiogenic factor were assayed by western blot. Results The viability of HS27 cells was not affected by 25 mM KCl. Collagen synthesis increased dependent on time and concentration of KCl exposure. The phosphorylations of MAPK proteins such as extracellular-signal-regulated kinase (ERK) and p38 increased about 2.5-3 fold in the KCl treatment cells and were inhibited by treatment of NS1619. TSP1 expression increased by 100%, bFGF expression decreased by 40%, and there is no significant differences in the VEGF level by KCl treatment, TSP1 was inhibited by NS1619 or kinase inhibitors. Conclusions Our results suggest that KCl may function as a therapeutic agent for wound healing in the skin through MAPK signaling mediated by the K+ ion channel. PMID:25606484

Shim, Jung Hee; Lim, Jong Woo; Kim, Byeong Kyu; Park, Soo Jin; Kim, Suk Wha

2015-01-01

181

Heat Transfer Enhancement using Synthetic Jet Actuators in Forced Convection Water Filled Micro-Channels  

Microsoft Academic Search

The effect of a synthetic jet on heat transfer rates in forced convection of water in micro-channels has been studied numerically. Unsteady computations of laminar flow have been performed for a two- dimensional micro-channel, 200 µm high and 4.2 mm long, open at either end with the top surface hot and all other solid wall adiabatic. The orifice width was

V. Timchenko; J. A. Reizes; E. Leonardi; F. Stella

2005-01-01

182

A flow through water system for channel catfish fingerling culture  

E-print Network

. This relationship was reported by Fry (1957). Increasing high values of incoming oxygen (Figure 10) enabled the fish to continue to gain weight, though at a lesser rate as the total biomass increased. The greater demand for oxygen (Figure 12) of the higher... Two studies were conducted, one in 1975 and the second in 1976, with 16, 208-liter drums which were modified to culture channel catfish fry to fingerling size. In 1975, five trials were initiated, three to examine stocking rates of fry and two...

Steinbach, Donny W

1977-01-01

183

Dynamics of channel incision in a granular bed driven by subsurface water flow  

E-print Network

We propose a dynamical model for the erosive growth of a channel in a granular medium driven by subsurface water flow. The model is inferred from experimental data acquired with a laser-aided imaging technique. The evolution equation for transverse sections of a channel has the form of a non-locally driven Burgers equation. With fixed coefficients this equation admits an asymptotic similarity solution. Ratios of the granular transport coefficients can therefore be extracted from the shape of channels that have evolved in steady driving conditions.

A. E. Lobkovsky; B. Smith; A. Kudrolli; D. H. Rothman

2005-05-13

184

PROFILE: Hungry Water: Effects of Dams and Gravel Mining on River Channels  

PubMed

/ Rivers transport sediment from eroding uplands to depositional areas near sea level. If the continuity of sediment transport is interrupted by dams or removal of sediment from the channel by gravel mining, the flow may become sediment-starved (hungry water) and prone to erode the channel bed and banks, producing channel incision (downcutting), coarsening of bed material, and loss of spawning gravels for salmon and trout (as smaller gravels are transported without replacement from upstream). Gravel is artificially added to the River Rhine to prevent further incision and to many other rivers in attempts to restore spawning habitat. It is possible to pass incoming sediment through some small reservoirs, thereby maintaining the continuity of sediment transport through the system. Damming and mining have reduced sediment delivery from rivers to many coastal areas, leading to accelerated beach erosion. Sand and gravel are mined for construction aggregate from river channel and floodplains. In-channel mining commonly causes incision, which may propagate up- and downstream of the mine, undermining bridges, inducing channel instability, and lowering alluvial water tables. Floodplain gravel pits have the potential to become wildlife habitat upon reclamation, but may be captured by the active channel and thereby become instream pits. Management of sand and gravel in rivers must be done on a regional basis, restoring the continuity of sediment transport where possible and encouraging alternatives to river-derived aggregate sources.KEY WORDS: Dams; Aquatic habitat; Sediment transport; Erosion; Sedimentation; Gravel mining PMID:9175542

Kondolf

1997-07-01

185

Hungry water: Effects of dams and gravel mining on river channels  

SciTech Connect

Rivers transport sediment from eroding uplands to depositional areas near sea level. If the continuity of sediment transport is interrupted by dams or removal of sediment from the channel by gravel mining, the flow may become sediment-starved (hungry water) and prone to erode the channel bed and banks, producing channel incision (downcutting), coarsening of bed material, and loss of spawning gravels for salmon and trout (as smaller gravels are transported without replacement from upstream), Gravel is artificially added to the River Rhine to prevent further incision and to many other rivers in attempts to restore spawning habitat. It is possible to pass incoming sediment through some small reservoirs, thereby maintaining the continuity of sediment transport through the system. Damming and mining have reduced sediment delivery from rivers to many coastal areas, leading to accelerated beach erosion. Sand and gravel are mined for construction aggregate from river channel and floodplains. In-channel mining commonly causes incision, which may propagate up- and downstream of the mine, undermining bridges, inducing channel instability, and lowering alluvial water tables. Floodplain gravel pits have the potential to become wildlife habitat upon reclamation, but may be captured by the active channel and thereby become instream pits. Management of sand and gravel in rivers must be done on a regional basis, restoring the continuity of sediment transport where possible and encouraging alternatives to river-derived aggregate sources. 80 refs., 17 figs.

Kondolf, G.M. [Univ. of California, Berkeley, CA (United States)] [Univ. of California, Berkeley, CA (United States)

1997-07-01

186

A macromolecular trafficking complex composed of ??-adrenergic receptors, A-Kinase Anchoring Proteins and L-type calcium channels.  

PubMed

Abstract Sympathetic modulation of cardiac L-type calcium channels is an important mechanism for regulating heart rate and cardiac contractility. At the molecular level, activation of ?-adrenergic receptors (?AR) increases calcium influx into cardiac myocytes by activating protein kinase A (PKA), leading to subsequent phosphorylation of L-type calcium channels. In the case of the ?2AR, this process is facilitated by the presence of A-Kinase Anchoring Proteins (AKAPs) that serve as scaffolding proteins for the L-type calcium channel and the ?2AR complex. Our work has shown that, in addition to facilitating PKA phosphorylation of the channel, AKAPs also promote an increase in the Cav1.2 channel surface expression. Here we review the molecular mechanisms of ?2AR/AKAP/L-type channel interactions and trafficking. PMID:23557075

Flynn, Robyn; Altier, Christophe

2013-06-01

187

Numerical simulation of shallow-water dam break flows in open channels using smoothed particle hydrodynamics  

NASA Astrophysics Data System (ADS)

SummaryA meshless numerical model is proposed to investigate shallow-water dam break flows in 1D open channels. The numerical model is to solve the shallow water equations (SWE) based on smoothed particle hydrodynamics (SPH). The concept of slice water particles (SWP) is adopted in the SPH-SWE formulation. The numerical sensitivity analysis is first performed to study the appropriate SWP number and variable smoothing length through dam break flows in an idealized 1D channel with dry/wet beds. Extensive validation by comparison with laboratory and field data is next conducted for four benchmark problems, including dam break flows through a rough flat channel, a rough bumpy channel with various downstream boundary conditions, a nonprismatic channel, and a realistic scale model of the Toce river in Italy. The simulated results indicate that accurate performance is reached in the presence of shock discontinuities, shock front motion, hydraulic jumps, dry/wet bed flow, supercritical/subcritical/transcritical flow, reverse flow, contraction flow, overtopping flow, partial reflections and multiple wave interaction without special numerical treatment. All of the simulations are carried out by PC within 10 min. Thus, the proposed numerical model has proved its efficiency and reliability for dam break flow computations in open channels.

Chang, Tsang-Jung; Kao, Hong-Ming; Chang, Kao-Hua; Hsu, Ming-Hsi

2011-09-01

188

A minimal isoform of the TMEM16A protein associated with chloride channel activity  

PubMed Central

TMEM16A protein, also known as anoctamin-1, has been recently identified as an essential component of Ca2+-activated Cl? channels. We previously reported the existence of different TMEM16A isoforms generated by alternative splicing. In the present study, we have determined the functional properties of a minimal TMEM16A protein. This isoform, called TMEM16A(0), has a significantly shortened amino-terminus and lacks three alternative segments localized in the intracellular regions of the protein (total length: 840 amino acids). TMEM16A(0) expression is associated with Ca2+-activated Cl? channel activity as measured by three different functional assays based on the halide-sensitive yellow fluorescent protein, short-circuit current recordings, and patch-clamp technique. However, compared to a longer isoform, TMEM16(abc) (total length: 982 amino acids), TMEM16A(0) completely lacks voltage-dependent activation. Furthermore, TMEM16A(0) and TMEM16A(abc) have similar but not identical responses to extracellular anion replacement, thus suggesting a difference in ion selectivity and conductance. Our results indicate that TMEM16A(0) has the basic domains required for anion transport and Ca2+-sensitivity. However, the absence of alternative segments, which are present in more complex isoforms of TMEM16A, modifies the channel gating and ion transport ability. PMID:21645494

Ferrera, Loretta; Scudieri, Paolo; Sondo, Elvira; Caputo, Antonella; Caci, Emanuela; Zegarra-Moran, Olga; Ravazzolo, Roberto; Galietta, Luis J.V.

2011-01-01

189

Increasing mutagenicity of São Gonçalo Channel waters based on the Allium cepa test.  

PubMed

The São Gonçalo Channel is of great importance to the conservation of local biodiversity; it also is a water supply source of the city of Pelotas, Brazil, and the surrounding region. We examined the mutagenic activity of its waters. The following items were seasonally investigated in Allium cepa root radicular meristem cells: mitotic index, mitotic anomalies, interphase anomalies, and total anomalies. Water samples were collected from four different stations, Lock Dam, Santa Bárbara Channel, Pelotas Creek, and Barra do Laranjal. A drinking water negative control was used. For each sampling station, 8000 cells were counted, 2000 of which by repetition. The data were computed on a database (SPSS), and then analyzed by the chi-square test and the Mann-Whitney U-test. In 2005, the channel water provoked a significantly greater number of anomalies than the control water. The number of anomalies increased in 2007. This suggests that there was an increase in toxic substances in the channel over the years. PMID:19291879

Paiva, T S; Garcias, G L; Martino-Roth, M G

2009-01-01

190

Energetics of the protein-DNA-water interaction  

Microsoft Academic Search

BACKGROUND: To understand the energetics of the interaction between protein and DNA we analyzed 39 crystallographically characterized complexes with the HINT (Hydropathic INTeractions) computational model. HINT is an empirical free energy force field based on solvent partitioning of small molecules between water and 1-octanol. Our previous studies on protein-ligand complexes demonstrated that free energy predictions were significantly improved by taking

Francesca Spyrakis; Pietro Cozzini; Chiara Bertoli; Anna Marabotti; Glen E Kellogg; Andrea Mozzarelli

2007-01-01

191

A single WW domain is the predominant mediator of the interaction between the human ubiquitin-protein ligase Nedd4 and the human epithelial sodium channel.  

PubMed Central

The activity of the epithelial Na(+) channel (ENaC) is required for the maintenance of salt and water balance in the body. Channel activity is regulated by the ubiquitin-protein ligase Nedd4 ['neuronal precursor cell-expressed developmentally down-regulated (gene 4)'] that interacts with the channel via its WW domains. Mutations in channel subunits that disrupt this interaction cause Liddle's syndrome, a severe inherited form of hypertension. In previous studies we showed that WW domains 2, 3 and 4 of human Nedd4 bound to the human ENaC (hENaC) subunits, whereas WW domain 1 did not. Here we extend this observation to determine the binding affinities of the human Nedd4 WW domains for hENaC C-terminal peptides. We show that WW domains 2, 3 and 4 bind with differing affinities to Na(+) channel subunit peptides. WW domain 3 has the highest affinity and we predict that WW domain 3 contributes most of the binding because a construct containing the three WW domains bound no better than WW domain 3 alone. Further, a single amino acid change (Arg(165)-->Thr) in WW domain 1 enables binding to the alpha subunit of the channel to occur, with an affinity comparable with that of WW domain 4. Differential binding propensities between the various WW domains and Na(+) channel subunit peptides are explained on the basis of quantitative structural modelling of the complexes and their isolated components. PMID:11802777

Lott, J Shaun; Coddington-Lawson, Sarah J; Teesdale-Spittle, Paul H; McDonald, Fiona J

2002-01-01

192

Lipid bilayer regulation of membrane protein function: gramicidin channels as molecular force probes  

PubMed Central

Membrane protein function is regulated by the host lipid bilayer composition. This regulation may depend on specific chemical interactions between proteins and individual molecules in the bilayer, as well as on non-specific interactions between proteins and the bilayer behaving as a physical entity with collective physical properties (e.g. thickness, intrinsic monolayer curvature or elastic moduli). Studies in physico-chemical model systems have demonstrated that changes in bilayer physical properties can regulate membrane protein function by altering the energetic cost of the bilayer deformation associated with a protein conformational change. This type of regulation is well characterized, and its mechanistic elucidation is an interdisciplinary field bordering on physics, chemistry and biology. Changes in lipid composition that alter bilayer physical properties (including cholesterol, polyunsaturated fatty acids, other lipid metabolites and amphiphiles) regulate a wide range of membrane proteins in a seemingly non-specific manner. The commonality of the changes in protein function suggests an underlying physical mechanism, and recent studies show that at least some of the changes are caused by altered bilayer physical properties. This advance is because of the introduction of new tools for studying lipid bilayer regulation of protein function. The present review provides an introduction to the regulation of membrane protein function by the bilayer physical properties. We further describe the use of gramicidin channels as molecular force probes for studying this mechanism, with a unique ability to discriminate between consequences of changes in monolayer curvature and bilayer elastic moduli. PMID:19940001

Lundbæk, Jens A.; Collingwood, Shemille A.; Ingólfsson, Helgi I.; Kapoor, Ruchi; Andersen, Olaf S.

2010-01-01

193

Severe Acute Respiratory Syndrome Coronavirus Envelope Protein Ion Channel Activity Promotes Virus Fitness and Pathogenesis  

PubMed Central

Deletion of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) envelope (E) gene attenuates the virus. E gene encodes a small multifunctional protein that possesses ion channel (IC) activity, an important function in virus-host interaction. To test the contribution of E protein IC activity in virus pathogenesis, two recombinant mouse-adapted SARS-CoVs, each containing one single amino acid mutation that suppressed ion conductivity, were engineered. After serial infections, mutant viruses, in general, incorporated compensatory mutations within E gene that rendered active ion channels. Furthermore, IC activity conferred better fitness in competition assays, suggesting that ion conductivity represents an advantage for the virus. Interestingly, mice infected with viruses displaying E protein IC activity, either with the wild-type E protein sequence or with the revertants that restored ion transport, rapidly lost weight and died. In contrast, mice infected with mutants lacking IC activity, which did not incorporate mutations within E gene during the experiment, recovered from disease and most survived. Knocking down E protein IC activity did not significantly affect virus growth in infected mice but decreased edema accumulation, the major determinant of acute respiratory distress syndrome (ARDS) leading to death. Reduced edema correlated with lung epithelia integrity and proper localization of Na+/K+ ATPase, which participates in edema resolution. Levels of inflammasome-activated IL-1? were reduced in the lung airways of the animals infected with viruses lacking E protein IC activity, indicating that E protein IC function is required for inflammasome activation. Reduction of IL-1? was accompanied by diminished amounts of TNF and IL-6 in the absence of E protein ion conductivity. All these key cytokines promote the progression of lung damage and ARDS pathology. In conclusion, E protein IC activity represents a new determinant for SARS-CoV virulence. PMID:24788150

Nieto-Torres, Jose L.; DeDiego, Marta L.; Verdiá-Báguena, Carmina; Jimenez-Guardeño, Jose M.; Regla-Nava, Jose A.; Fernandez-Delgado, Raul; Castaño-Rodriguez, Carlos; Alcaraz, Antonio; Torres, Jaume; Aguilella, Vicente M.; Enjuanes, Luis

2014-01-01

194

Protein arginine methyl transferases-3 and -5 increase cell surface expression of cardiac sodium channel.  

PubMed

The ?-subunit of the cardiac voltage-gated sodium channel (NaV1.5) plays a central role in cardiomyocyte excitability. We have recently reported that NaV1.5 is post-translationally modified by arginine methylation. Here, we aimed to identify the enzymes that methylate NaV1.5, and to describe the role of arginine methylation on NaV1.5 function. Our results show that protein arginine methyl transferase (PRMT)-3 and -5 methylate NaV1.5 in vitro, interact with NaV1.5 in human embryonic kidney (HEK) cells, and increase NaV1.5 current density by enhancing NaV1.5 cell surface expression. Our observations are the first evidence of regulation of a voltage-gated ion channel, including calcium, potassium, sodium and TRP channels, by arginine methylation. PMID:23912080

Beltran-Alvarez, Pedro; Espejo, Alexsandra; Schmauder, Ralf; Beltran, Carlos; Mrowka, Ralf; Linke, Thomas; Batlle, Montserrat; Pérez-Villa, Félix; Pérez, Guillermo J; Scornik, Fabiana S; Benndorf, Klaus; Pagans, Sara; Zimmer, Thomas; Brugada, Ramon

2013-10-01

195

A large iris-like expansion of a mechanosensitive channel protein induced by membrane tension  

NASA Technical Reports Server (NTRS)

MscL, a bacterial mechanosensitive channel of large conductance, is the first structurally characterized mechanosensor protein. Molecular models of its gating mechanisms are tested here. Disulfide crosslinking shows that M1 transmembrane alpha-helices in MscL of resting Escherichia coli are arranged similarly to those in the crystal structure of MscL from Mycobacterium tuberculosis. An expanded conformation was trapped in osmotically shocked cells by the specific bridging between Cys 20 and Cys 36 of adjacent M1 helices. These bridges stabilized the open channel. Disulfide bonds engineered between the M1 and M2 helices of adjacent subunits (Cys 32-Cys 81) do not prevent channel gating. These findings support gating models in which interactions between M1 and M2 of adjacent subunits remain unaltered while their tilts simultaneously increase. The MscL barrel, therefore, undergoes a large concerted iris-like expansion and flattening when perturbed by membrane tension.

Betanzos, Monica; Chiang, Chien-Sung; Guy, H. Robert; Sukharev, Sergei

2002-01-01

196

Hydration water dynamics and instigation of protein structuralrelaxation  

SciTech Connect

Until a critical hydration level is reached, proteins do not function. This critical level of hydration is analogous to a similar lack of protein function observed for temperatures below a dynamical temperature range of 180-220K that also is connected to the dynamics of protein surface water. Restoration of some enzymatic activity is observed in partially hydrated protein powders, sometimes corresponding to less than a single hydration layer on the protein surface, which indicates that the dynamical and structural properties of the surface water is intimately connected to protein stability and function. Many elegant studies using both experiment and simulation have contributed important information about protein hydration structure and timescales. The molecular mechanism of the solvent motion that is required to instigate the protein structural relaxation above a critical hydration level or transition temperature has yet to be determined. In this work we use experimental quasi-elastic neutron scattering (QENS) and molecular dynamics simulation to investigate hydration water dynamics near a greatly simplified protein system. We consider the hydration water dynamics near the completely deuterated N-acetyl-leucine-methylamide (NALMA) solute, a hydrophobic amino acid side chain attached to a polar blocked polypeptide backbone, as a function of concentration between 0.5M-2.0M under ambient conditions. We note that roughly 50-60% of a folded protein's surface is equally distributed between hydrophobic and hydrophilic domains, domains whose lengths are on the order of a few water diameters, that justify our study of hydration dynamics of this simple model protein system. The QENS experiment was performed at the NIST Center for Neutron Research, using the disk chopper time of flight spectrometer (DCS). In order to separate the translational and rotational components in the spectra, two sets of experiments were carried out using different incident neutron wavelengths of 7.5{angstrom} and 5.5{angstrom} to give two different time resolutions. All the spectra have been measure at room temperature. The spectra were corrected for the sample holder contribution and normalized using the vanadium standard. The resulting data were analyzed with DAVE programs (http://www.ncnr.nist.gov/dave/). The AMBER force field and SPCE water model were used for modeling the NALMA solute and water, respectively. For the analysis of the water dynamics in the NALMA aqueous solutions, we performed simulations of a dispersed solute configuration consistent with our previous structural analysis, where we had primarily focused on the structural organization of these peptide solutions and their connection to protein folding. Further details of the QENS experiment and molecular dynamics simulations are reported elsewhere.

Russo, Daniela; Hura, Greg; Head-Gordon, Teresa

2003-09-01

197

Vertical arrival structure of shipping noise in deep water channels  

Microsoft Academic Search

In passive sonar systems, knowledge of low-frequency shipping noise is significant for target detection performance. However, an accurate model for the shipping noise structure is difficult to obtain, because of the varying distributions of ships and complicated underwater environment. This work characterizes low-frequency distant shipping noise observed in deep water environments as a function of receiver depth and vertical arrival

Zizheng Li; Lisa M. Zurk; Barry Ma

2010-01-01

198

An outer membrane channel protein of Mycobacterium tuberculosis with exotoxin activity.  

PubMed

The ability to control the timing and mode of host cell death plays a pivotal role in microbial infections. Many bacteria use toxins to kill host cells and evade immune responses. Such toxins are unknown in Mycobacterium tuberculosis. Virulent M. tuberculosis strains induce necrotic cell death in macrophages by an obscure molecular mechanism. Here we show that the M. tuberculosis protein Rv3903c (channel protein with necrosis-inducing toxin, CpnT) consists of an N-terminal channel domain that is used for uptake of nutrients across the outer membrane and a secreted toxic C-terminal domain. Infection experiments revealed that CpnT is required for survival and cytotoxicity of M. tuberculosis in macrophages. Furthermore, we demonstrate that the C-terminal domain of CpnT causes necrotic cell death in eukaryotic cells. Thus, CpnT has a dual function in uptake of nutrients and induction of host cell death by M. tuberculosis. PMID:24753609

Danilchanka, Olga; Sun, Jim; Pavlenok, Mikhail; Maueröder, Christian; Speer, Alexander; Siroy, Axel; Marrero, Joeli; Trujillo, Carolina; Mayhew, David L; Doornbos, Kathryn S; Muñoz, Luis E; Herrmann, Martin; Ehrt, Sabine; Berens, Christian; Niederweis, Michael

2014-05-01

199

Coupled Radon and Water Temperature Measurements to Characterize the Effects of Altered Stream Channel Planform  

NASA Astrophysics Data System (ADS)

In summer 2011, a 2.6 km reach of Meacham Creek, Oregon, USA, was altered from a straight, steep wall-based channel to more a sinuous, low-gradient channel. Key objectives of this restoration project were to increase the rate and magnitude of hyporheic exchange. The overarching goal was to initiate increased buffering and lagging of water temperature in the subsurface to mitigate warm surface water temperature in Meacham Creek, an important spawning and rearing stream for depressed populations of Chinook salmon and summer steelhead. To evaluate progress toward project goals and objectives, stream temperature and groundwater temperature in 22 wells have been measured hourly at the restoration site since March 2011. In addition, the radioactive isotope 222Rn was measured in each well and in the surface water on two occasions. The relative residence time of down welling stream water measured in the wells can be determined by ranked amplitude depression and lagged phase of annual temperature signals in the wells relative to that of the open channel flow. Residence times predicted by annual temperature signal dynamics are corroborated by 222Rn concentrations in each well. The data collected to date provide a foundation for developing a groundwater thermal model to predict the effects of channel reconfiguration on ground-surface water exchange and associated temperature effects at the reach scale.

Amerson, B. E.; Poole, G. C.; O'Daniel, S. J.

2013-12-01

200

Inhibition of Ca2+ Channels and Adrenal Catecholamine Release by G Protein Coupled Receptors  

PubMed Central

Catecholamines and other transmitters released from adrenal chromaffin cells play central roles in the “fight-or-flight” response and exert profound effects on cardiovascular, endocrine, immune, and nervous system function. As such, precise regulation of chromaffin cell exocytosis is key to maintaining normal physiological function and appropriate responsiveness to acute stress. Chromaffin cells express a number of different G protein coupled receptors (GPCRs) that sense the local environment and orchestrate this precise control of transmitter release. The primary trigger for catecholamine release is Ca2+ entry through voltage-gated Ca2+ channels, so it makes sense that these channels are subject to complex regulation by GPCRs. In particular G protein ?? heterodimers (G??) bind to and inhibit Ca2+ channels. Here I review the mechanisms by which GPCRs inhibit Ca2+ channels in chromaffin cells and how this might be altered by cellular context. This is related to the potent autocrine inhibition of Ca2+ entry and transmitter release seen in chromaffin cells. Recent data that implicate an additional inhibitory target of G?? on the exocytotic machinery and how this might fine tune neuroendocrine secretion are also discussed. PMID:21061161

2011-01-01

201

The Dynamic Transition of Protein Hydration Water  

E-print Network

Thin layers of water on biomolecular and other nanostructured surfaces can be supercooled to temperatures not accessible with bulk water. Chen et al. [PNAS 103, 9012 (2006)] suggested that anomalies near 220 K observed by quasi-elastic neutron scattering can be explained by a hidden critical point of bulk water. Based on more sensitive measurements of water on perdeuterated phycocyanin, using the new neutron backscattering spectrometer SPHERES, and an improved data analysis, we present results that show no sign of such a fragile-to-strong transition. The inflection of the elastic intensity at 220 K has a dynamic origin that is compatible with a calorimetric glass transition at 170 K. The temperature dependence of the relaxation times is highly sensitive to data evaluation; it can be brought into perfect agreement with the results of other techniques, without any anomaly.

W. Doster; S. Busch; A. M. Gaspar; M. -S. Appavou; J. Wuttke; H. Scheer

2010-02-12

202

TMEM16A Protein: A New Identity for Ca2+-Dependent Cl? Channels  

NSDL National Science Digital Library

Ca+-dependent Cl? channels (CaCCs) play a variety of physiological roles in different organs and tissues, including transepithelial Cl? secretion, smooth muscle contraction, regulation of neuronal excitability, and transduction of sensory stimuli. The recent identification of TMEM16A protein as an important component of CaCCs should allow a better understanding of their physiological role, structure-function relationship, and regulatory mechanisms.

Loretta Ferrera (Istituto Giannina Gaslini)

2010-12-01

203

AL0671, A new potassium channel opener, inhibits nonenzymatic glycation of protein and LDL oxidation  

Microsoft Academic Search

1.1. The effects of AL0671, a novel potassium channel opener, on protein glycation and low-density lipoprotein (LDL) oxidation were tested.2.2. AL0671 dose-dependently inhibited both fluorescence development of bovine serum albumin and cross-linking of lysozyme. These inhibitory effects for glycation were no Impotent than aminoguanidine.3.3. AL0671 dose-dependently inhibited both increase in negative charge and apo B-100 fragmentation during incubation of LDL

Takeshi Yamauchi; Sumio Matzno; Teruaki Imada; Masahiro Eda; Yoshihisa Inoue; Norifumi Nakamura

1996-01-01

204

Evidence from oocyte expression that the erythrocyte water channel is distinct from band 3 and the glucose transporter.  

PubMed Central

It has been proposed that the mercurial-sensitive water transporter in mammalian erythrocytes is the anion exchanger band 3 (AE1) and/or the glucose transporter, band 4.5 (GLUT1). Using a functional assay for water channel expression in Xenopus oocytes (Zhang, R., K. A. Logee, and A. S. Verkman. 1990. J. Biol. Chem. 265:15375-15378), we compared osmotic water permeability (Pf) of oocytes injected with water, reticulocyte mRNA, AE1 mRNA, and GLUT1 mRNA. Injection of oocytes with 5-50 ng of in vitro-transcribed AE1 mRNA had no effect on Pf, but increased trans-stimulated 36Cl uptake greater than fourfold in a dinitro-disulfonic stilbene (DNDS)-inhibitable manner. Injection with 1-50 ng of in vitro-transcribed GLUT1 mRNA increased 3H-methylglucose uptake greater than 15-fold in a cytochalasin B-sensitive manner and increased Pf from (3.7 +/- 0.4) x 10(-4) cm/s (SE, n = 16, 10 degrees C) in water-injected oocytes up to (13 +/- 1) x 10(-4) cm/s (n = 18). Both the increments in sugar and water transport were inhibited by cytochalasin B (25 microM) and phloretin (0.2 mM); neither was inhibited by 0.3 mM HgCl2. In oocytes injected with 50 ng of rabbit reticulocyte mRNA, the Pf of (18 +/- 2) x 10(-4) cm/s (n = 18) was reduced to (4.0 +/- 0.6) x 10(-4) cm/s (n = 10) by HgCl2, but was not inhibited by DNDS (0.4 mM), cytochalasin B or phloretin. Coinjection of reticulocyte mRNA with antisense oligodeoxyribonucleotides against AE1 or GLUT1 did not affect Pf, but inhibited completely the incremental uptake of 36Cl or 3H-methylglucose, respectively. Expression of size-fractionated mRNA from reticulocyte gave a 2-2.5-kb size for water channel mRNA, less than the 4-4.5-kb size for the Cl transporter. These results provide evidence that facilitated water transport in erythrocytes is mediated not by bands 3 or 4.5, but by distinct water transport protein(s). Images PMID:1939644

Zhang, R; Alper, S L; Thorens, B; Verkman, A S

1991-01-01

205

Molecular cloning and characterization of a mitogen-activated protein kinase-associated intracellular chloride channel.  

PubMed

ERK7, a member of the mitogen-activated protein kinase family, has a carboxyl-terminal tail that is required for ERK7 activation, cellular localization, and its ability to inhibit DNA synthesis. To identify proteins that interact with ERK7, we utilized a yeast two-hybrid screen with the COOH-terminal tail of ERK7 as bait and isolated the cDNA for a novel protein termed CLIC3. The interaction between CLIC3 and ERK7 in mammalian cells was confirmed by co-immunoprecipitation. CLIC3 has significant homology to human intracellular chloride channels 1 (NCC27/CLIC1) and 2 and bovine kidney chloride channel p64. Like NCC27/CLIC1, CLIC3 is predominantly localized in the nucleus and stimulates chloride conductance when expressed in cells. Taken together, these results suggest that CLIC3 is a new member of the human CLIC family. The observed interaction between CLIC3 and ERK7 is the first demonstration of a stable complex between a protein that activates chloride ion transport and a member of the mitogen-activated protein kinase family of signal transducers. The specific association of CLIC3 with the COOH-terminal tail of ERK7 suggests that CLIC3 may play a role in the regulation of cell growth. PMID:9880541

Qian, Z; Okuhara, D; Abe, M K; Rosner, M R

1999-01-15

206

Polypyrrole-supported membrane proteins for bio-inspired ion channels.  

PubMed

Biomedical platforms constructed by immobilizing membrane proteins in matrixes made of synthetic organic polymers is a challenge because the structure and function of these proteins are affected by environmental conditions. In this work, an operative composite that regulates the diffusion of alkali ions has been prepared by functionalizing a supporting matrix made of poly(N-methylpyrrole) (PNMPy) with a ?-barrel membrane protein (Omp2a) that forms channels and pores. The protein has been unequivocally identified in the composite, and its structure has been shown to remain unaltered. The PNMPy-Omp2a platform fulfills properties typically associated with functional bio-interfaces with biomedical applications (e.g., biocompatibility, biodegrabadility, and hydrophilicity). The functionality of the immobilized protein has been examined by studying the passive ion transport response in the presence of electrolytic solutions with Na(+) and K(+) concentrations close to those found in blood. Although the behavior of PNMPy and PNMPy-Omp2a is very similar for solutions with very low concentration, the resistance of the latter decreases drastically when the concentration of ions increases to ?100 mM. This reduction reflects an enhanced ion exchange between the biocomposite and the electrolytic medium, which is not observed in PNMPy, evidencing that PNMPy-Omp2a is particularly well suited to prepare bioinspired channels and smart biosensors. PMID:25585165

Pérez-Madrigal, Maria M; Del Valle, Luis J; Armelin, Elaine; Michaux, Catherine; Roussel, Guillaume; Perpète, Eric A; Alemán, Carlos

2015-01-28

207

Functional reconstitution of a rice aquaporin water channel, PIP1;1, by a micro-batchwise methodology.  

PubMed

Assessing the selectivity, regulation and physiological relevance of aquaporin membrane channels (AQPs) requires structural and functional studies of wild type and modified proteins. In particular, when characterizing their transport properties, reconstitution in isolation from native cellular or membrane processes is of pivotal importance. Here, we describe rapid and efficient incorporation of OsPIP1;1, a rice AQP, in liposomes at analytical scale. PIP1;1 was produced as a histidine-tagged form, 10His-OsPIP1;1, in an Escherichia coli-based expression system. The recombinant protein was purified by affinity chromatography and incorporated into liposomes by a micro-batchwise technology using egg-yolk phospholipids and the non-polar Amberlite resin. PIP1;1 proteoliposomes and control empty liposomes had good size homogeneity as seen by quasi-elastic light scattering and electron microscopy analyses. By stopped-flow light scattering, indicating correct protein folding of the incorporated protein, the osmotic water permeability exhibited by the PIP1;1 proteoliposomes was markedly higher than empty liposomes. Functional reconstitution of OsPIP1;1 was further confirmed by the low Arrhenius activation energy (3.37 kcal/mol) and sensitivity to HgCl2, a known AQP blocker, of the PIP1;1-mediated osmotic water conductance. These results provide a valuable contribution in fully elucidating the regulation and water-conducting property of PIP1;1, an AQP that needs to hetero-multimerize with AQPs of the PIP2 subgroup to reach the native plasma membrane and play its role. The micro-batchwise methodology is suitable for the functional reconstitution of whichever AQPs and other membrane transport proteins. PMID:25394803

Scalera, Vito; Gena, Patrizia; Mastrodonato, Maria; Kitagawa, Yoshichika; Carulli, Salvatore; Svelto, Maria; Calamita, Giuseppe

2014-10-30

208

2D IR spectroscopy reveals the role of water in the binding of channel-blocking drugs to the influenza M2 channel  

NASA Astrophysics Data System (ADS)

Water is an integral part of the homotetrameric M2 proton channel of the influenza A virus, which not only assists proton conduction but could also play an important role in stabilizing channel-blocking drugs. Herein, we employ two dimensional infrared (2D IR) spectroscopy and site-specific IR probes, i.e., the amide I bands arising from isotopically labeled Ala30 and Gly34 residues, to probe how binding of either rimantadine or 7,7-spiran amine affects the water dynamics inside the M2 channel. Our results show, at neutral pH where the channel is non-conducting, that drug binding leads to a significant increase in the mobility of the channel water. A similar trend is also observed at pH 5.0 although the difference becomes smaller. Taken together, these results indicate that the channel water facilitates drug binding by increasing its entropy. Furthermore, the 2D IR spectral signatures obtained for both probes under different conditions collectively support a binding mechanism whereby amantadine-like drugs dock in the channel with their ammonium moiety pointing toward the histidine residues and interacting with a nearby water cluster, as predicted by molecular dynamics simulations. We believe these findings have important implications for designing new anti-influenza drugs.

Ghosh, Ayanjeet; Wang, Jun; Moroz, Yurii S.; Korendovych, Ivan V.; Zanni, Martin; DeGrado, William F.; Gai, Feng; Hochstrasser, Robin M.

2014-06-01

209

G protein-mediated inhibition of Cav3.2 T-type channels revisited.  

PubMed

T-type calcium channels are important modulators of both membrane potential and intracellular Ca(2+) concentration, allowing them to play key roles in such diverse processes as aldosterone production from adrenal glomerulosa cells to boosting pain signals in nociceptors. In both these examples, the Ca(v)3.2 isoform mediates Ca(2+) influx. This isoform is also of particular interest because mutations in its gene (CACNA1H) that enhance channel activity have been associated with idiopathic generalized epilepsies, whereas mutations that disrupt its activity have been associated with autism spectrum disorders. Block of T-channel activity has been proposed to contribute to the therapeutic usefulness of a wide variety of drugs, such as antihypertensives, antipsychotics, and antidepressants. Recent evidence strongly supports the hypothesis that block of Ca(v)3.2 channels might be useful in the treatment of neuropathic pain. Therefore, it is of particular interest that Ca(v)3.2 channels are exquisitely regulated by G protein-coupled receptors and various downstream effectors. This Perspective summarizes recent findings (p. 202) on this regulation and the novel pathways specifically activated by either neurokinin I, corticotropin-releasing factor receptor 1, or dopamine D(1) receptors. PMID:19903827

Perez-Reyes, Edward

2010-02-01

210

Polyester modification of the mammalian TRPM8 channel protein: Implications for structure and function  

PubMed Central

SUMMARY The TRPM8 ion channel is expressed in sensory neurons and is responsible for sensing environmental cues such as cold temperatures and chemical compounds, including menthol and icilin. The channel functional activity is regulated by various physical and chemical factors, and is likely to be pre-conditioned by its molecular composition. Our studies indicate that TRPM8 channel forms a structural-functional complex with the polyester, poly-(R)-3hydroxybutyrate (PHB). We identified by mass spectrometry a number of PHB-modified peptides in the N-terminus of the TRPM8 protein and in its extracellular S3–S4 linker. Removal of PHB by enzymatic hydrolysis, and site-directed mutagenesis of both the serine residues that serve as covalent anchors for PHB and adjacent hydrophobic residues that interact with the methyl groups of the polymer, resulted in significant inhibition of TRPM8 channel activity. We conclude that the TRPM8 channel undergoes post-translational modification by PHB and that this modification is required for its normal function. PMID:23850286

Bikard, Yann; Chen, Wei; Liu, Tong; Li, Hong; Jendrossek, Dieter; Cohen, Alejandro; Pavlov, Evgeny; Rohacs, Tibor; Zakharian, Eleonora

2013-01-01

211

Capacitation and Ca(2+) influx in spermatozoa: role of CNG channels and protein kinase G.  

PubMed

Cyclic guanosine monophosphate (cGMP) has been recently shown to modulate in vitro capacitation of mammalian spermatozoa, but the mechanisms through which it influences sperm functions have not been clarified. There are at least two targets of cGMP, cyclic nucleotide-gated (CNG) channels and cGMP-dependent protein kinase (PKG), involved in several physiological events in mammalian spermatozoa. It has been suggested that CNG channels allow the influx of Ca(2+) to cytoplasm during capacitation, whereas PKG could trigger a phosphorylation pathway which might also, indirectly, mediate calcium entry. Using the patch-clamp technique in whole-cell configuration, we showed how l-cis-Diltiazem (a CNG-channel inhibitor) and KT5823 (a PKG inhibitor) decreased significantly the amplitude of macroscopic ion currents in a dose-response manner, and decreased in vitro capacitation. The inhibition of CNG channels completely abolishes the Ca(2+) influx induced by cyclic nucleotides in mouse spermatozoa. This work suggests that the downstream cGMP pathway is required in mammalian sperm capacitation and the mechanisms involved include CNG channels and PKG, highlighting these molecules as important therapeutic targets for infertility treatments or to develop new male contraceptives. PMID:24293181

Cisneros-Mejorado, A; Hernández-Soberanis, L; Islas-Carbajal, M C; Sánchez, D

2014-01-01

212

Intracellular chloride channel protein CLIC1 regulates macrophage function through modulation of phagosomal acidification  

PubMed Central

Summary Intracellular chloride channel protein 1 (CLIC1) is a 241 amino acid protein of the glutathione S transferase fold family with redox- and pH-dependent membrane association and chloride ion channel activity. Whilst CLIC proteins are evolutionarily conserved in Metazoa, indicating an important role, little is known about their biology. CLIC1 was first cloned on the basis of increased expression in activated macrophages. We therefore examined its subcellular localisation in murine peritoneal macrophages by immunofluorescence confocal microscopy. In resting cells, CLIC1 is observed in punctate cytoplasmic structures that do not colocalise with markers for endosomes or secretory vesicles. However, when these macrophages phagocytose serum-opsonised zymosan, CLIC1 translocates onto the phagosomal membrane. Macrophages from CLIC1?/? mice display a defect in phagosome acidification as determined by imaging live cells phagocytosing zymosan tagged with the pH-sensitive fluorophore Oregon Green. This altered phagosomal acidification was not accompanied by a detectable impairment in phagosomal-lysosomal fusion. However, consistent with a defect in acidification, CLIC1?/? macrophages also displayed impaired phagosomal proteolytic capacity and reduced reactive oxygen species production. Further, CLIC1?/? mice were protected from development of serum transfer induced K/BxN arthritis. These data all point to an important role for CLIC1 in regulating macrophage function through its ion channel activity and suggest it is a suitable target for the development of anti-inflammatory drugs. PMID:22956539

Jiang, Lele; Salao, Kanin; Li, Hui; Rybicka, Joanna M.; Yates, Robin M.; Luo, Xu Wei; Shi, Xin Xin; Kuffner, Tamara; Tsai, Vicky Wang-Wei; Husaini, Yasmin; Wu, Liyun; Brown, David A.; Grewal, Thomas; Brown, Louise J.; Curmi, Paul M. G.; Breit, Samuel N.

2012-01-01

213

Slip effects on mixed convective peristaltic transport of copper-water nanofluid in an inclined channel.  

PubMed

Peristaltic transport of copper-water nanofluid in an inclined channel is reported in the presence of mixed convection. Both velocity and thermal slip conditions are considered. Mathematical modelling has been carried out using the long wavelength and low Reynolds number approximations. Resulting coupled system of equations is solved numerically. Quantities of interest are analyzed through graphs. Numerical values of heat transfer rate at the wall for different parameters are obtained and examined. Results showed that addition of copper nanoparticles reduces the pressure gradient, axial velocity at the center of channel, trapping and temperature. Velocity slip parameter has a decreasing effect on the velocity near the center of channel. Temperature of nanofluid increases with increase in the Grashoff number and channel inclination angle. It is further concluded that the heat transfer rate at the wall increases considerably in the presence of copper nanoparticles. PMID:25170908

Abbasi, Fahad Munir; Hayat, Tasawar; Ahmad, Bashir; Chen, Guo-Qian

2014-01-01

214

Slip Effects on Mixed Convective Peristaltic Transport of Copper-Water Nanofluid in an Inclined Channel  

PubMed Central

Peristaltic transport of copper-water nanofluid in an inclined channel is reported in the presence of mixed convection. Both velocity and thermal slip conditions are considered. Mathematical modelling has been carried out using the long wavelength and low Reynolds number approximations. Resulting coupled system of equations is solved numerically. Quantities of interest are analyzed through graphs. Numerical values of heat transfer rate at the wall for different parameters are obtained and examined. Results showed that addition of copper nanoparticles reduces the pressure gradient, axial velocity at the center of channel, trapping and temperature. Velocity slip parameter has a decreasing effect on the velocity near the center of channel. Temperature of nanofluid increases with increase in the Grashoff number and channel inclination angle. It is further concluded that the heat transfer rate at the wall increases considerably in the presence of copper nanoparticles. PMID:25170908

Abbasi, Fahad Munir; Hayat, Tasawar; Ahmad, Bashir; Chen, Guo-Qian

2014-01-01

215

On the Coupling Between Channel Level and Surface Ground-Water Flows  

NASA Astrophysics Data System (ADS)

This paper is devoted to a mathematical analysis of some general models of mass transport and other coupled physical processes developed in simultaneous flows of surface, soil and ground waters. Such models are widely used for forecasting (numerical simulation) of a hydrological cycle for concrete territories. The mathematical models that proved a more realistic approach are obtained by combining several mathematical models for local processes. The water-exchange models take into account the following factors: Water flows in confined and unconfined aquifers, vertical moisture migration allowing earth surface evaporation, open-channel flow simulated by one-dimensional hydraulic equations, transport of contamination, etc. These models may have different levels of sophistication. We illustrate the type of mathematical singularities which may appear by considering a simple model on the coupling of a surface flow of surface and ground waters with the flow of a line channel or river.

Antontsev, S. N.; Díaz, J. I.

2008-08-01

216

MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein?Protein Interface  

PubMed Central

The calculation of protein interaction energetics is of fundamental interest, yet accurate quantities are difficult to obtain due to the complex and dynamic nature of protein interfaces. This is further complicated by the presence of water molecules, which can exhibit transient interactions of variable duration and strength with the protein surface. The T-cell receptor (TCR) and its staphylococcal enterotoxin 3 (SEC3) binding partner are well-characterized examples of a protein?protein interaction system exhibiting interfacial plasticity, cooperativity, and additivity among mutants. Specifically engineered mutants induce intercalating interfacial water molecules, which subsequently enhance protein?protein binding affinity. In this work, we perform a set of molecular mechanics (MM) Poisson?Boltzmann (PB) surface area (SA) calculations on the wild type and two mutant TCR-SEC3 systems and show that the method is able to discriminate between weak and strong binders only when key explicit water molecules are included in the analysis. The results presented here point to the promise of MM-PBSA toward rationalizing molecular recognition at protein?protein interfaces, while establishing a general approach to handle explicit interfacial water molecules in such calculations. PMID:19461869

2009-01-01

217

Pore waters regulate ion permeation in a calcium release-activated calcium channel  

PubMed Central

The recent crystal structure of Orai, the pore unit of a calcium release-activated calcium (CRAC) channel, is used as the starting point for molecular dynamics and free-energy calculations designed to probe this channel’s conduction properties. In free molecular dynamics simulations, cations localize preferentially at the extracellular channel entrance near the ring of Glu residues identified in the crystal structure, whereas anions localize in the basic intracellular half of the pore. To begin to understand ion permeation, the potential of mean force (PMF) was calculated for displacing a single Na+ ion along the pore of the CRAC channel. The computed PMF indicates that the central hydrophobic region provides the major hindrance for ion diffusion along the permeation pathway, thereby illustrating the nonconducting nature of the crystal structure conformation. Strikingly, further PMF calculations demonstrate that the mutation V174A decreases the free energy barrier for conduction, rendering the channel effectively open. This seemingly dramatic effect of mutating a nonpolar residue for a smaller nonpolar residue in the pore hydrophobic region suggests an important role for the latter in conduction. Indeed, our computations show that even without significant channel-gating motions, a subtle change in the number of pore waters is sufficient to reshape the local electrostatic field and modulate the energetics of conduction, a result that rationalizes recent experimental findings. The present work suggests the activation mechanism for the wild-type CRAC channel is likely regulated by the number of pore waters and hence pore hydration governs the conductance. PMID:24101457

Dong, Hao; Fiorin, Giacomo; Carnevale, Vincenzo; Treptow, Werner; Klein, Michael L.

2013-01-01

218

Enantioselective Protein-Sterol Interactions Mediate Regulation of Both Prokaryotic and Eukaryotic Inward Rectifier K+ Channels by Cholesterol  

PubMed Central

Cholesterol is the major sterol component of all mammalian cell plasma membranes and plays a critical role in cell function and growth. Previous studies have shown that cholesterol inhibits inward rectifier K+ (Kir) channels, but have not distinguished whether this is due directly to protein-sterol interactions or indirectly to changes in the physical properties of the lipid bilayer. Using purified bacterial and eukaryotic Kir channels reconstituted into liposomes of controlled lipid composition, we demonstrate by 86Rb+ influx assays that bacterial Kir channels (KirBac1.1 and KirBac3.1) and human Kir2.1 are all inhibited by cholesterol, most likely by locking the channels into prolonged closed states, whereas the enantiomer, ent-cholesterol, does not inhibit these channels. These data indicate that cholesterol regulates Kir channels through direct protein-sterol interactions likely taking advantage of an evolutionarily conserved binding pocket. PMID:21559361

D'Avanzo, Nazzareno; Hyrc, Krzysztof; Enkvetchakul, Decha; Covey, Douglas F.; Nichols, Colin G.

2011-01-01

219

Ultrafast viscous water flow through nanostrand-channelled graphene oxide membranes.  

PubMed

Pressure-driven ultrafiltration membranes are important in separation applications. Advanced filtration membranes with high permeance and enhanced rejection must be developed to meet rising worldwide demand. Here we report nanostrand-channelled graphene oxide ultrafiltration membranes with a network of nanochannels with a narrow size distribution (3-5 nm) and superior separation performance. This permeance offers a 10-fold enhancement without sacrificing the rejection rate compared with that of graphene oxide membranes, and is more than 100 times higher than that of commercial ultrafiltration membranes with similar rejection. The flow enhancement is attributed to the porous structure and significantly reduced channel length. An abnormal pressure-dependent separation behaviour is also reported, where the elastic deformation of nanochannels offers tunable permeation and rejection. The water flow through these hydrophilic graphene oxide nanochannels is identified as viscous. This nanostrand-channelling approach is also extendable to other laminate membranes, providing potential for accelerating separation and water-purification processes. PMID:24352165

Huang, Hubiao; Song, Zhigong; Wei, Ning; Shi, Li; Mao, Yiyin; Ying, Yulong; Sun, Luwei; Xu, Zhiping; Peng, Xinsheng

2013-01-01

220

A central scheme for shallow water flows along channels with irregular geometry  

Microsoft Academic Search

We present a new semi-discrete central scheme for one-dimensional shallow water flows along channels with non-uniform rectangular cross sections and bottom topography. The scheme preserves the positivity of the water height, and it is preserves steady-states of rest (i.e., it is well- balanced). Along with a detailed description of the scheme, numerous numerical examples are presented for unsteady and steady

Jorge Balbás; Smadar Karni

2009-01-01

221

Integration of thermal and osmotic regulation of water homeostasis: the role of TRPV channels  

PubMed Central

Maintenance of body water homeostasis is critical for preventing hyperthermia, because evaporative cooling is the most efficient means of dissipating excess body heat. Water homeostasis is achieved by regulation of water intake and water loss by the kidneys. The former is achieved by sensations of thirst that motivate water acquisition, whereas the latter is regulated by the antidiuretic action of vasopressin. Vasopressin secretion and thirst are stimulated by increases in the osmolality of the extracellular fluid as well as decreases in blood pressure and/or blood volume, signals that are precipitated by water depletion associated with the excess evaporative water loss required to prevent hyperthermia. In addition, they are stimulated by increases in body temperature. The sites and molecular mechanisms involved in integrating thermal and osmotic regulation of thirst and vasopressin secretion are reviewed here with a focus on the role of the thermal and mechanosensitive transient receptor potential-vanilloid (TRPV) family of ion channels. PMID:23883678

Johnson, Alan Kim

2013-01-01

222

Mars outflow channels: A reappraisal of the estimation of water flow velocities from water depths, regional slopes, and channel floor  

E-print Network

2004; revised 25 June 2004; accepted 14 July 2004; published 10 September 2004. [1] Methods used so far to corresponding overestimates of subsurface aquifer permeabilities, rates of filling of depressions with water. Geophys. Res., 109, E09003, doi:10.1029/2004JE002281. 1. Introduction [2] The discharge rates and volumes

Head III, James William

223

Short Paper:R&D of a Dual mode acoustic modem testbed for shallow water channels  

E-print Network

Short Paper:R&D of a Dual mode acoustic modem testbed for shallow water channels Feng TONG1, which urged the R&D of high performance underwater acoustic (UWA) modems. However, as underwater modem testbed system, which enables the switch between DSSS and OFDM scheme to accommodate different

Kastner, Ryan

224

Assessment of a nuclear fuel assembly performance with different inner water channels  

Microsoft Academic Search

Advanced fuel designs have been developed with the cycle efficiency. With this idea, in boiling water reactor fuel assemblies has been improved. The current work analyzes two 9 x 9 fuel assemblies with different inner channel designs. The first design corresponds to an actual assembly, whereas the second is proposed with the aim of making comparisons between their performances. The

G. Alonso-Vargas; J. L. Montes; M. R. Perusquia

1995-01-01

225

Water-filled channels constructed by supramolecular complex of partial-cone thiacalix[4]arene tetrasulfonate  

NASA Astrophysics Data System (ADS)

A novel crystal containing water-filled channel structures was prepared under hydrothermal conditions utilizing thiacalix[4]arene tetrasulfonate, Ni(ClO 4) 2, and 2,2'-bipyridine, in which thiacalix[4]arene tetrasulfonate molecules assumed the so-called partial-cone conformation.

Liu, Yu; Guo, Dong-Sheng; Zhang, Heng-Yi

2005-01-01

226

A MODELING STUDY OF WATER QUALITY IN MAIN CHANNEL AND ESTUARINE WETLAND  

Microsoft Academic Search

A simple computation framework is applied to include estuarine wetland and their interaction with main channels in estuarine modeling. The concept and the model implementation of the scheme are explained using a vertical two-dimensional model of estuarine hydrodynamics and water quality. The model was applied to the Tanshui River estuary and Kuan-Du wetland. The model is calibrated and verified by

Wen-Cheng Liu; Ming-Hsi Hsu; Albert Y. Kuo

2001-01-01

227

Evolutionary and comparative analysis of aquaporin water channel genes in fish  

Microsoft Academic Search

The role of aquaporin water channels in some teleost fish has been described for some (orthologues of mammalian) aquaporins, especially aquaporins 1 (AQP) 0, 1 and 3, however to date the role of aquaporins in other more ancient fish lineages such as the Elasmobranches and Agnathans remains almost completely uninvestigated. The goal of this project is to identify homologous aquaporin

Christopher P. Cutler; Lara Meischke; Gordon Cramb

228

Interannual variability of water mass properties in the Tunisia-Sicily Channel  

NASA Astrophysics Data System (ADS)

We analysed in situ CTD data collected on 36 joint Tunisian-Italian oceanographic cruises in the Tunisia-Sicily Channel (Cap Bon-Mazara del Vallo section) from 1995 to 2009 in order to identify the water masses in the region and to estimate the interannual variability of their hydrological characteristics. Besides the well-known AW (Atlantic Water) and LIW (Levantine Intermediate Water), other water masses have been identified though their presence is neither as steady nor as stable as the aforementioned ones. The WIW (Western Intermediate Water) flows beneath the AW towards the eastern basin while the IW (Ionian Water), with a highly intermittent character, flows within the subsurface layer towards the western basin. The flow of subsurface water (WIW and IW) is affected by intense mixing which modifies the water masses, tending to make them disappear. Moreover, the same hydrological time series produced interesting results concerning the increase in both temperature and salinity in the Tunisia-Sicily Channel. This trend especially concerns the deeper layers (LIW and tEMDW, i.e. transitional Eastern Mediterranean Deep Water) and we hypothesise that this is a direct response to climatic change occurring in the eastern basin.

Ben Ismail, Sana; Schroeder, Katrin; Sammari, Chérif; Gasparini, Gian Pietro; Borghini, Mireno; Aleya, Lotfi

2014-07-01

229

On the turbulent flow around water turbines placed in an open channel: an experimental study  

NASA Astrophysics Data System (ADS)

A growing interest in water turbines (using tidal, river, marine currents) has been observed during the last few years. Fundamental understanding of the turbulent flow around the water turbines is crucial to predict the potential effects of these structures on the local morphology, water flow and power available in the current, among others. In this study, a series of model water turbines (single and an aligned array) of 50 cm rotor diameter were placed in the main channel of the Saint Anthony Falls Laboratory at the University of Minnesota. The main channel is approx 2.5 m wide, 1.8 m height and 85 m long. Flow around the water turbines were analyzed under subcritical conditions. Turbine hub heights coincided with the channel mid height. A series of acoustic Doppler anemometers (ADV) were used to obtain 3 velocity components of the flow at a rate of 200 Hz. Selected streamwise and spanwise vertical planes were measured to describe the kinematics around the water turbines. Potential interactions with the lateral walls were also addressed. High order statistics (mean velocity, turbulence intensities and Reynolds stresses) as well as two point correlations and spectra were computed to infer fundamental differences and similitude with their counterparts, the wind turbines.

Sotiropoulos, F.; Chamorro, L. P.; Arndt, R.

2010-12-01

230

Energetics of the protein-DNA-water interaction  

PubMed Central

Background To understand the energetics of the interaction between protein and DNA we analyzed 39 crystallographically characterized complexes with the HINT (Hydropathic INTeractions) computational model. HINT is an empirical free energy force field based on solvent partitioning of small molecules between water and 1-octanol. Our previous studies on protein-ligand complexes demonstrated that free energy predictions were significantly improved by taking into account the energetic contribution of water molecules that form at least one hydrogen bond with each interacting species. Results An initial correlation between the calculated HINT scores and the experimentally determined binding free energies in the protein-DNA system exhibited a relatively poor r2 of 0.21 and standard error of ± 1.71 kcal mol-1. However, the inclusion of 261 waters that bridge protein and DNA improved the HINT score-free energy correlation to an r2 of 0.56 and standard error of ± 1.28 kcal mol-1. Analysis of the water role and energy contributions indicate that 46% of the bridging waters act as linkers between amino acids and nucleotide bases at the protein-DNA interface, while the remaining 54% are largely involved in screening unfavorable electrostatic contacts. Conclusion This study quantifies the key energetic role of bridging waters in protein-DNA associations. In addition, the relevant role of hydrophobic interactions and entropy in driving protein-DNA association is indicated by analyses of interaction character showing that, together, the favorable polar and unfavorable polar/hydrophobic-polar interactions (i.e., desolvation) mostly cancel. PMID:17214883

Spyrakis, Francesca; Cozzini, Pietro; Bertoli, Chiara; Marabotti, Anna; Kellogg, Glen E; Mozzarelli, Andrea

2007-01-01

231

Triggering a Wet Climate on Mars: The Role of Outflow Channels in Martian Water Cycles  

NASA Astrophysics Data System (ADS)

The triggering of a robust water cycle on Mars has been hypothesized to be caused by gigantic flooding events evidenced by outflow channels. Here we use the Ames Mars General Circulation Model (MGCM) to study how these presumably abrupt eruptions of water (Carr,1996) affected the climate of Mars. We model where the water ultimately went as part of a transient hydrologic cycle. Chryse Planitia, east of Tharsis, has evidence for multiple water outflow channels. One of the largest channels is Ares Valles, which was carved by floods with estimated water volumes of order 10^5 km^2 (Andrews-Hanna, 2007 & Carr, 1996). Outflow discharge rate estimates range from 10^6 to 10^7 m^3/seconds or greater (Andrews-Hanna & Phillips, 2007, Harrison & Grimm, 2008). Studies suggest that outflow channels formed with smaller, successive floods instead of a single large flood (Wilson, et al.,2004). Warner et al. (2009) suggest up to six outflow events for the formation of Ares Valles, while estimates for another large outflow, Kasei Valles, might have been flooded by over two thousand floods with a total water volume of 5.5 x 10^5 km^3 (Harrison & Grimm, 2008). By adding water to the surface of Mars at the given outflow rate, as an expanding one-layer lake, we are able to study quantitatively how these outflow events influenced Mars climate, particularly the hydrologic cycle. In particular: Could sudden introductions of large amounts of water on the Martian surface lead to a new equilibrated water cycle? Can we tie certain fluvial surface features to transient or sustained water cycles? What are the roles of water vapor and water ice clouds to sudden changes in the water cycle on Mars? How are radiative feedbacks involved with this? What is the ultimate fate of the outflow water? This work uses the NASA Ames MGCM version 2.1 and other schemes that are part of the NASA Ames MGCM suite of tools. Various versions of the MGCM developed at Ames have been used extensively to examine dust and volatile distributions on Mars (e.g., Kahre et al., 2006, 2008). The MGCM 2.1 currently has a well-developed water ice cloud formation scheme (Montmessin et al., 2002, 2004a), which includes calculation of cloud particle concentrations, nucleation, growth, and gravitational sedimentation. For examining the effect of a large water outflow on the climate of Mars, we include water tracers, with an advanced cloud particle scheme Preliminary results suggest that water may have been transported globally for years post-outflow. Post-outflow water cloud formation increases dramatically, with water ice clouds and water vapor potentially transporting water globally. The global mass of water vapor and of water ice clouds increases substantially, with the post-outflow patterns settling into annual cycles, with increasing water entering the atmosphere from the surface over time. Future work will examine the radiative effects of the water vapor and water ice clouds, and the longer-term persistence of a new hydrological or climate regime Detailed comparisons of post-outflow precipitation locations with fluvial features on Mars will be done.

Santiago, D.; Asphaug, E. I.; Colaprete, A.

2011-12-01

232

The nature of ion and water barrier crossings in a simulated ion channel.  

PubMed Central

Using a combination of techniques, including molecular dynamics, time-correlation analysis, stochastic dynamics, and fitting of continuum diffusion theory to electrophysiological data, a characterization is made of thermally driven sodium, water, and D2O motion within the gramicidin A channel. Since the channel contents are constrained to move in a single-file fashion, the motion that corresponds to experimentally measurable rates of permeation of the membrane is the motion of the center of mass of the channel contents. We therefore emphasize channel contents center-of-mass motion in our analysis of molecular dynamics computations. The usual free energy calculation techniques would be of questionable validity when applied to such motion. As an alternative to those techniques, we postulate a periodic sinusoidal free energy profile (related to the periodic structure of the helical channel) and deduce the fluid dynamic diffusion coefficient and the height and spacing of the free energy barriers from the form of the mean-square-deviation function, using stochastic computations. The fluid dynamic friction in each case appears similar to that for aqueous solution. However, the diffusive motions are modulated by a spatially periodic free energy profile with a periodicity characteristic of an L-D pair of amino acids in the gramicidin helix, approximately 1.7 A in the model we use. The barrier height depends on which substance is moving in the channel, but in each case is several times thermal energy. For barriers of this width and height, the motion is intermediate between the low-friction (transition-state) and high-friction (Brownian) limits. Thus, neither of these formalisms that have been used commonly to describe membrane permeation gives an accurate picture of the underlying physical process (although the Brownian description seems closer to correct). The non-Markovian Langevin equation must be solved to describe properly the statistics of the process. The "channel state of matter" characteristic of the channel contents appears to have some properties typical of the solid and some typical of the liquid state. The magnitude of the local friction and nature of the ion solvation are similar to the liquid state, but the periodicities of structure, free energy, and dynamics are somewhat solid-like. The alignment of water dipoles in the channel bears some resemblance to the orientational ordering of a nematic liquid crystal, but unlike a nematic liquid crystal, the waters have a degree of translational order as well. Thus, the "channel state" is not adequately described by analogy to either the solid or liquid states or to liquid crystals but must be dealt with as its own characteristic type of condensed matter. PMID:7679301

Chiu, S. W.; Novotny, J. A.; Jakobsson, E.

1993-01-01

233

AMP-activated protein kinase in BK-channel regulation and protection against hearing loss following acoustic overstimulation.  

PubMed

The energy-sensing AMP-activated serine/threonine protein kinase (AMPK) confers cell survival in part by stimulation of cellular energy production and limitation of cellular energy utilization. AMPK-sensitive functions further include activities of epithelial Na+ channel ENaC and voltage-gated K+ channel KCNE1/KCNQ1. AMPK is activated by an increased cytosolic Ca2+ concentration. The present study explored whether AMPK regulates the Ca2+-sensitive large conductance and voltage-gated potassium (BK) channel. cRNA encoding BK channel was injected into Xenopus oocytes with and without additional injection of wild-type AMPK (AMPK?1+AMPK?1+AMPK?1), constitutively active AMPK?R70Q, or inactive AMPK?K45R. BK-channel activity was determined utilizing the 2-electrode voltage-clamp. Moreover, BK-channel protein abundance in the cell membrane was determined by confocal immunomicroscopy. As BK channels are expressed in outer hair cells (OHC) of the inner ear and lack of BK channels increases noise vulnerability, OHC BK-channel expression was examined by immunohistochemistry and hearing function analyzed by auditory brain stem response measurements in AMPK?1-deficient mice (ampk-/-) and in wild-type mice (ampk+/+). As a result, coexpression of AMPK or AMPK?R70Q but not of AMPK?K45R significantly enhanced BK-channel-mediated currents and BK-channel protein abundance in the oocyte cell membrane. BK-channel expression in the inner ear was lower in ampk-/- mice than in ampk+/+ mice. The hearing thresholds prior to and immediately after an acoustic overexposure were similar in ampk-/- and ampk+/+ mice. However, the recovery from the acoustic trauma was significantly impaired in ampk-/- mice compared to ampk+/+ mice. In summary, AMPK is a potent regulator of BK channels. It may thus participate in the signaling cascades that protect the inner ear from damage following acoustic overstimulation. PMID:22767231

Föller, Michael; Jaumann, Mirko; Dettling, Juliane; Saxena, Ambrish; Pakladok, Tatsiana; Munoz, Carlos; Ruth, Peter; Sopjani, Mentor; Seebohm, Guiscard; Rüttiger, Lukas; Knipper, Marlies; Lang, Florian

2012-10-01

234

Ancient Origins of RGK Protein Function: Modulation of Voltage-Gated Calcium Channels Preceded the Protostome and Deuterostome Split  

PubMed Central

RGK proteins, Gem, Rad, Rem1, and Rem2, are members of the Ras superfamily of small GTP-binding proteins that interact with Ca2+ channel ? subunits to modify voltage-gated Ca2+ channel function. In addition, RGK proteins affect several cellular processes such as cytoskeletal rearrangement, neuronal dendritic complexity, and synapse formation. To probe the phylogenetic origins of RGK protein–Ca2+ channel interactions, we identified potential RGK-like protein homologs in genomes for genetically diverse organisms from both the deuterostome and protostome animal superphyla. RGK-like protein homologs cloned from Danio rerio (zebrafish) and Drosophila melanogaster (fruit flies) expressed in mammalian sympathetic neurons decreased Ca2+ current density as reported for expression of mammalian RGK proteins. Sequence alignments from evolutionarily diverse organisms spanning the protostome/deuterostome divide revealed conservation of residues within the RGK G-domain involved in RGK protein – Cav? subunit interaction. In addition, the C-terminal eleven residues were highly conserved and constituted a signature sequence unique to RGK proteins but of unknown function. Taken together, these data suggest that RGK proteins, and the ability to modify Ca2+ channel function, arose from an ancestor predating the protostomes split from deuterostomes approximately 550 million years ago. PMID:24992013

Puhl, Henry L.; Lu, Van B.; Won, Yu-Jin; Sasson, Yehezkel; Hirsch, Joel A.; Ono, Fumihito; Ikeda, Stephen R.

2014-01-01

235

Online multi-channel microfluidic chip-mass spectrometry and its application for quantifying noncovalent protein-protein interactions.  

PubMed

To establish an automatic and online microfluidic chip-mass spectrometry (chip-MS) system, a device was designed and fabricated for microsampling by a hybrid capillary. The movement of the capillary was programmed by a computer to aspirate samples from different microfluidic channels in the form of microdroplets (typically tens of nanoliters in volume), which were separated by air plugs. The droplets were then directly analyzed by MS via paper spray ionization without any pretreatment. The feasibility and performance were demonstrated by a concentration gradient experiment. Furthermore, after eliminating the effect of nonuniform response factors by an internal standard method, determination of the association constant within a noncovalent protein-protein complex was successfully accomplished with the MS-based titration indicating the versatility and the potential of this novel platform for widespread applications. PMID:25597452

Liu, Wu; Chen, Qiushui; Lin, Xuexia; Lin, Jin-Ming

2015-03-01

236

Evidence for G-Protein Regulation of Inward K+ Channel Current in Guard Cells of Fava Bean  

Microsoft Academic Search

Recent reports have shown that GTP-binding proteins (G-proteins) are present in plants but have given limited indication as to their site of action. G-proteins in animal cells transduce extracellular signals into intracellular or membrane-mediated events, including the regulation of ion channels. Using whole-cell patch clamp, we provide evidence that a G-protein in guard cells of fava bean regulates the magnitude

Katrina Fairley-Grenot; Sarah M. Assmann

1991-01-01

237

Liquid water transport in parallel serpentine channels with manifolds on cathode side of a PEM fuel cell stack  

NASA Astrophysics Data System (ADS)

Water management in a proton exchange membrane (PEM) fuel cell stack has been a challenging issue on the road to commercialization. This paper presents a numerical investigation of air-water flow in parallel serpentine channels on cathode side of a PEM fuel cell stack by use of the commercial Computational Fluid Dynamics (CFD) software package FLUENT. Different air-water flow behaviours inside the serpentine flow channels with inlet and outlet manifolds were discussed. The results showed that there were significant variations of water distribution and pressure drop in different cells at different times. The "collecting-and-separating effect" due to the serpentine shape of the gas flow channels, the pressure drop change due to the water distribution inside the inlet and outlet manifolds were observed. Several gas flow problems of this type of parallel serpentine channels were identified and useful suggestions were given through investigating the flow patterns inside the channels and manifolds.

Jiao, Kui; Zhou, Biao; Quan, Peng

238

Adaptive resolution simulation of an atomistic protein in MARTINI water  

SciTech Connect

We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15?ns long molecular dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.

Zavadlav, Julija [Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana (Slovenia)] [Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana (Slovenia); Melo, Manuel Nuno; Marrink, Siewert J., E-mail: s.j.marrink@rug.nl [Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen (Netherlands); Praprotnik, Matej, E-mail: praprot@cmm.ki.si [Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana (Slovenia) [Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana (Slovenia); Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000 Ljubljana (Slovenia)

2014-02-07

239

The Structure and Transport of Water and Hydrated Ions Within Hydrophobic, Nanoscale Channels  

SciTech Connect

The purpose of this project includes an experimental and modeling investigation into water and hydrated ion structure and transport at nanomaterials interfaces. This is a topic relevant to understanding the function of many biological systems such as aquaporins that efficiently shuttle water and ion channels that permit selective transport of specific ions across cell membranes. Carbon nanotubes (CNT) are model nanoscale, hydrophobic channels that can be functionalized, making them artificial analogs for these biological channels. This project investigates the microscopic properties of water such as water density distributions and dynamics within CNTs using Nuclear Magnetic Resonance (NMR) and the structure of hydrated ions at CNT interfaces via X-ray Absorption Spectroscopy (XAS). Another component of this work is molecular simulation, which can predict experimental measurables such as the proton relaxation times, chemical shifts, and can compute the electronic structure of CNTs. Some of the fundamental questions this work is addressing are: (1) what is the length scale below which nanoscale effects such as molecular ordering become important, (2) is there a relationship between molecular ordering and transport?, and (3) how do ions interact with CNT interfaces? These are questions of interest to the scientific community, but they also impact the future generation of sensors, filters, and other devices that operate on the nanometer length scale. To enable some of the proposed applications of CNTs as ion filtration media and electrolytic supercapacitors, a detailed knowledge of water and ion structure at CNT interfaces is critical.

Holt, J K; Herberg, J L; Wu, Y; Schwegler, E; Mehta, A

2009-06-15

240

Generation, Comparison, and Merging of Pathways between Protein Conformations: Gating in K-Channels  

PubMed Central

We present a general framework for the generation, alignment, comparison, and hybridization of motion pathways between two known protein conformations. The framework, which is rooted in probabilistic motion-planning techniques in robotics, allows for the efficient generation of collision-free motion pathways, while considering a wide range of degrees of freedom involved in the motion. Within the framework, we provide the means to hybridize pathways, thus producing, the motion pathway of the lowest energy barrier out of the many pathways proposed by our algorithm. This method for comparing and hybridizing pathways is modular, and may be used within the context of molecular dynamics and Monte Carlo simulations. The framework was implemented within the Rosetta software suite, where the protein is represented in atomic detail. The K-channels switch between open and closed conformations, and we used the overall framework to investigate this transition. Our analysis suggests that channel-opening may follow a three-phase pathway. First, the channel unlocks itself from the closed state; second, it opens; and third, it locks itself in the open conformation. A movie that depicts the proposed pathway is available in the Supplementary Material (Movie S1) and at http://www.cs.tau.ac.il/?angela/SuppKcsA.html. PMID:18621834

Enosh, Angela; Raveh, Barak; Furman-Schueler, Ora; Halperin, Dan; Ben-Tal, Nir

2008-01-01

241

Physiological roles and diseases of tmem16/anoctamin proteins: are they all chloride channels?  

PubMed Central

The Tmem16 gene family was first identified by bioinformatic analysis in 2004. In 2008, it was shown independently by 3 laboratories that the first two members (Tmem16A and Tmem16B) of this 10-gene family are Ca2+-activated Cl? channels. Because these proteins are thought to have 8 transmembrane domains and be anion-selective channels, the alternative name, Anoctamin (anion and octa=8), has been proposed. However, it remains unclear whether all members of this family are, in fact, anion channels or have the same 8-transmembrane domain topology. Since 2008, there have been nearly 100 papers published on this gene family. The excitement about Tmem16 proteins has been enhanced by the finding that Ano1 has been linked to cancer, mutations in Ano5 are linked to several forms of muscular dystrophy (LGMDL2 and MMD-3), mutations in Ano10 are linked to autosomal recessive spinocerebellar ataxia, and mutations in Ano6 are linked to Scott syndrome, a rare bleeding disorder. Here we review some of the recent developments in understanding the physiology and structure-function of the Tmem16 gene family. PMID:21642943

Duran, Charity; Hartzell, H Criss

2011-01-01

242

Transmembrane extension and oligomerization of the CLIC1 chloride intracellular channel protein upon membrane interaction.  

PubMed

Chloride intracellular channel proteins (CLICs) differ from most ion channels as they can exist in both soluble and integral membrane forms. The CLICs are expressed as soluble proteins but can reversibly autoinsert into the membrane to form active ion channels. For CLIC1, the interaction with the lipid bilayer is enhanced under oxidative conditions. At present, little evidence is available characterizing the structure of the putative oligomeric CLIC integral membrane form. Previously, fluorescence resonance energy transfer (FRET) was used to monitor and model the conformational transition within CLIC1 as it interacts with the membrane bilayer. These results revealed a large-scale unfolding between the C- and N-domains of CLIC1 as it interacts with the membrane. In the present study, FRET was used to probe lipid-induced structural changes arising in the vicinity of the putative transmembrane region of CLIC1 (residues 24-46) under oxidative conditions. Intramolecular FRET distances are consistent with the model in which the N-terminal domain inserts into the bilayer as an extended ?-helix. Further, intermolecular FRET was performed between fluorescently labeled CLIC1 monomers within membranes. The intermolecular FRET shows that CLIC1 forms oligomers upon oxidation in the presence of the membranes. Fitting the data to symmetric oligomer models of the CLIC1 transmembrane form indicates that the structure is large and most consistent with a model comprising approximately six to eight subunits. PMID:22082111

Goodchild, Sophia C; Angstmann, Christopher N; Breit, Samuel N; Curmi, Paul M G; Brown, Louise J

2011-12-20

243

Pentameric Assembly of Potassium Channel Tetramerization Domain-Containing Protein 5 (KCTD5)  

PubMed Central

We report the X-ray crystal structure of human potassium channel tetramerization domain-containing protein 5 (KCTD5), the first member of the family to be so characterized. Four findings were unexpected. First, the structure reveals assemblies of five subunits while tetramers were anticipated; pentameric stoichiometry is observed also in solution by scanning transmission electron microscopy mass analysis and analytical ultracentrifugation. Second, the same Bric-a-brac, Tramtrack, Broad Complex (BTB) domain surface mediates assembly of five KCTD5 and four voltage-gated potassium (Kv) channel subunits; four amino acid differences appear crucial. Third, KCTD5 complexes have well-defined N- and C-terminal modules separated by a flexible linker that swivels ~30°; the C-module shows a new fold and is required to bind Golgi re-assembling stacking protein 55 with ~1 ?M affinity as judged by surface plasmon resonance and ultracentrifugation. Fourth, despite the homology reflected in its name, KCTD5 does not impact operation of Kv4.2, Kv3.4, Kv2.1 or Kv1.2 channels. PMID:19361449

Dementieva, Irina S.; Tereshko, Valentina; McCrossan, Zoe A.; Solomaha, Elena; Araki, Daniel; Xu, Chen; Grigorieff, Nikolaus; Goldstein, Steve A. N.

2009-01-01

244

Antioxidative activity of protein hydrolysates prepared from alkaline-aided channel catfish protein isolates.  

PubMed

Antioxidative activity of hydrolyzed protein prepared from alkali-solubilized catfish protein isolates was studied. The isolates were hydrolyzed to 5, 15, and 30% degree of hydrolysis using the protease enzyme, Protamex. Hydrolyzed protein was separated into hydrolysates and soluble supernatants, and both of these fractions were studied for their metal chelating ability, 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging ability, ferric reducing antioxidant power (FRAP), oxygen radical absorbance capacity (ORAC), and their ability to inhibit the formation of thiobarbituric acid reactive substances (TBARS) in washed tilapia muscle containing tilapia hemolysate. Both hydrolysates and supernatants were characterized using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Results showed that DPPH radical scavenging ability and reducing power of catfish protein hydrolysates decreased, whereas the ORAC value, metal chelating ability, and ability to inhibit TBARS increased, with an increase in the degree of hydrolysis. Hydrolysate samples showed higher DPPH radical scavenging ability and Fe(3+) reducing ability, and supernatant samples had higher metal chelating ability. In general, low molecular weight (MW) peptides had high ORAC values and high metal chelating ability, and high MW peptides had a higher reducing power (FRAP) and were more effective in scavenging DPPH radicals. In a washed muscle model system, the ability of catfish protein hydrolysates and their corresponding supernatants to inhibit the formation of TBARS increased with an increase in the degree of hydrolysis. PMID:18662014

Theodore, Ann E; Raghavan, Sivakumar; Kristinsson, Hordur G

2008-08-27

245

Collective motion of symmetric camphor papers in an annular water channel  

NASA Astrophysics Data System (ADS)

We investigate the collective motion of symmetric self-propelled objects that are driven by a difference in the surface tension. The objects move around an annular water channel spontaneously and interact through the camphor layer that develops on the water surface. We found that two collective motion modes, discrete and continuous density waves, are generated depending on the number of self-propelled objects. The two modes are characterized by examining the local and global dynamics, and the collective motion mechanism is discussed in relation to the distribution of camphor concentration in the annular water channel. We conclude that the difference between these two modes originates from that of the driving mechanism that pushes a camphor paper away from a cluster, through which mechanism density waves are generated and maintained.

Ikura, Yumihiko S.; Heisler, Eric; Awazu, Akinori; Nishimori, Hiraku; Nakata, Satoshi

2013-07-01

246

Structure-function of proteins interacting with the ?1 pore-forming subunit of high-voltage-activated calcium channels  

PubMed Central

Openings of high-voltage-activated (HVA) calcium channels lead to a transient increase in calcium concentration that in turn activate a plethora of cellular functions, including muscle contraction, secretion and gene transcription. To coordinate all these responses calcium channels form supramolecular assemblies containing effectors and regulatory proteins that couple calcium influx to the downstream signal cascades and to feedback elements. According to the original biochemical characterization of skeletal muscle Dihydropyridine receptors, HVA calcium channels are multi-subunit protein complexes consisting of a pore-forming subunit (?1) associated with four additional polypeptide chains ?, ?2, ?, and ?, often referred to as accessory subunits. Twenty-five years after the first purification of a high-voltage calcium channel, the concept of a flexible stoichiometry to expand the repertoire of mechanisms that regulate calcium channel influx has emerged. Several other proteins have been identified that associate directly with the ?1-subunit, including calmodulin and multiple members of the small and large GTPase family. Some of these proteins only interact with a subset of ?1-subunits and during specific stages of biogenesis. More strikingly, most of the ?1-subunit interacting proteins, such as the ?-subunit and small GTPases, regulate both gating and trafficking through a variety of mechanisms. Modulation of channel activity covers almost all biophysical properties of the channel. Likewise, regulation of the number of channels in the plasma membrane is performed by altering the release of the ?1-subunit from the endoplasmic reticulum, by reducing its degradation or enhancing its recycling back to the cell surface. In this review, we discuss the structural basis, interplay and functional role of selected proteins that interact with the central pore-forming subunit of HVA calcium channels. PMID:24917826

Neely, Alan; Hidalgo, Patricia

2014-01-01

247

Groundwater-surface water interaction in the riparian zone of an incised channel, Walnut Creek, Iowa  

USGS Publications Warehouse

Riparian zones of many incised channels in agricultural regions are cropped to the channel edge leaving them unvegetated for large portions of the year. In this study we evaluated surface and groundwater interaction in the riparian zone of an incised stream during a spring high flow period using detailed stream stage and hydraulic head data from six wells, and water quality sampling to determine whether the riparian zone can be a source of nitrate pollution to streams. Study results indicated that bank storage of stream water from Walnut Creek during a large storm water runoff event was limited to a narrow 1.6 m zone immediately adjacent to the channel. Nitrate concentrations in riparian groundwater were highest near the incised stream where the unsaturated zone was thickest. Nitrate and dissolved oxygen concentrations and nitrate-chloride ratios increased during a spring recharge period then decreased in the latter portion of the study. We used MODFLOW and MT3DMS to evaluate dilution and denitrification processes that would contribute to decreasing nitrate concentrations in riparian groundwater over time. MT3DMS model simulations were improved with a denitrification rate of 0.02 1/d assigned to the floodplain sediments implying that denitrification plays an important role in reducing nitrate concentrations in groundwater. We conclude that riparian zones of incised channels can potentially be a source of nitrate to streams during spring recharge periods when the near-stream riparian zone is largely unvegetated. ?? 2005 Elsevier B.V. All rights reserved.

Schilling, K.E.; Li, Z.; Zhang, Y.-K.

2006-01-01

248

Protein-spanning water networks and implications for prediction of protein-protein interactions mediated through hydrophobic effects.  

PubMed

Hydrophobic effects, often conflated with hydrophobic forces, are implicated as major determinants in biological association and self-assembly processes. Protein-protein interactions involved in signaling pathways in living systems are a prime example where hydrophobic effects have profound implications. In the context of protein-protein interactions, a priori knowledge of relevant binding interfaces (i.e., clusters of residues involved directly with binding interactions) is difficult. In the case of hydrophobically mediated interactions, use of hydropathy-based methods relying on single residue hydrophobicity properties are routinely and widely used to predict propensities for such residues to be present in hydrophobic interfaces. However, recent studies suggest that consideration of hydrophobicity for single residues on a protein surface require accounting of the local environment dictated by neighboring residues and local water. In this study, we use a method derived from percolation theory to evaluate spanning water networks in the first hydration shells of a series of small proteins. We use residue-based water density and single-linkage clustering methods to predict hydrophobic regions of proteins; these regions are putatively involved in binding interactions. We find that this simple method is able to predict with sufficient accuracy and coverage the binding interface residues of a series of proteins. The approach is competitive with automated servers. The results of this study highlight the importance of accounting of local environment in determining the hydrophobic nature of individual residues on protein surfaces. PMID:25204743

Cui, Di; Ou, Shuching; Patel, Sandeep

2014-12-01

249

Why do proteins aggregate? “Intrinsically insoluble proteins” and “dark mediators” revealed by studies on “insoluble proteins” solubilized in pure water  

PubMed Central

In 2008, I reviewed and proposed a model for our discovery in 2005 that unrefoldable and insoluble proteins could in fact be solubilized in unsalted water. Since then, this discovery has offered us and other groups a powerful tool to characterize insoluble proteins, and we have further addressed several fundamental and disease-relevant issues associated with this discovery. Here I review these results, which are conceptualized into several novel scenarios. 1) Unlike 'misfolded proteins', which still retain the capacity to fold into well-defined structures but are misled to 'off-pathway' aggregation, unrefoldable and insoluble proteins completely lack this ability and will unavoidably aggregate in vivo with ~150 mM ions, thus designated as 'intrinsically insoluble proteins (IIPs)' here. IIPs may largely account for the 'wastefully synthesized' DRiPs identified in human cells. 2) The fact that IIPs including membrane proteins are all soluble in unsalted water, but get aggregated upon being exposed to ions, logically suggests that ions existing in the background play a central role in mediating protein aggregation, thus acting as 'dark mediators'. Our study with 14 salts confirms that IIPs lack the capacity to fold into any well-defined structures. We uncover that salts modulate protein dynamics and anions bind proteins with high selectivity and affinity, which is surprisingly masked by pre-existing ions. Accordingly, I modified my previous model. 3) Insoluble proteins interact with lipids to different degrees. Remarkably, an ALS-causing P56S mutation transforms the ?-sandwich MSP domain into a helical integral membrane protein. Consequently, the number of membrane-interacting proteins might be much larger than currently recognized. To attack biological membranes may represent a common mechanism by which aggregated proteins initiate human diseases. 4) Our discovery also implies a solution to the 'chicken-and-egg paradox' for the origin of primitive membranes embedded with integral membrane proteins, if proteins originally emerged in unsalted prebiotic media. PMID:24555050

Song, Jianxing

2013-01-01

250

Water slug formation and motion in gas flow channels: the effects of geometry, surface wettability, and gravity.  

PubMed

Water emerging from ?100 ?m pores into millimeter-size gas flow channels forms drops that grow and become slugs which span the flow channel. Flowing gas causes the slugs to detach and move down the channel. The effect of channel geometry, surface wettability, and gravity on the formation and motion of water slugs has been analyzed using high-speed video images of the drops and differential pressure-time traces. Drops grow and appear, assuming a sequence of shapes that minimize the total interfacial energy of the gas-liquid and liquid-solid interfaces. The drops are initially spherical caps centered on the pore (the liquid contacts one wall). Above a certain size, the drops move to the corner, forming "corner drops" (the liquid contacts two walls). Corner drops grow across the channel, evolving into partial liquid bridges (drops confined by three walls), and finally the drops span the channel cross-section forming slugs (contacting all four walls). Smaller slugs are formed in channels with hydrophobic walls than in channels with hydrophilic walls. Smaller slugs are formed in channels with curved walls than in square or rectangular channels. Slugs move when the differential gas pressure overcomes the force to move the advancing and receding gas-liquid-solid contact lines of the slugs. Residual water left behind in corners by moving slugs reduces the barriers for drops to form slugs, causing the steady-state slug volumes to be smaller than those seen at start-up in dry channels. PMID:23876035

Cheah, May J; Kevrekidis, Ioannis G; Benziger, Jay B

2013-08-01

251

Rh proteins vs Amt proteins: an organismal and phylogenetic perspective on CO2 and NH3 gas channels.  

PubMed

Rh (Rhesus) proteins are homologues of ammonium transport (Amt) proteins. Physiological and structural evidence shows that Amt proteins are gas channels for NH(3), but the substrate of Rh proteins, be it CO2 as shown in green alga, or NH3/NH4+ as shown in mammalian cells, remains disputed. We assembled a large dataset generated of Rh and Amt to explore how Rh originated from and evolved independently of Amt relatives. Analysis of this rich data implies that Rh was split from Amt first to emerge in archaeal species. The Rh ancestor underwent divergence and duplication along speciation, leading to neofunctionalization and subfunctionalization of the Rh family. The characteristic organismal distribution of Rh vs. Amt reflects their early separation and subsequent independent evolution: they coexist in microbes and invertebrates but do not in fungi, vascular plants or vertebrates. Rh gene-duplication was prominent in vertebrates: while epithelial RhBG/RhCG displayed strong purifying selection, erythroid Rh30 and RhAG experienced different episodes of positive selection in each of which adaptive evolution occurred at certain time points and in a few codon sites. Mammalian Rh30 and RhAG were subject to particularly strong positive selection in some codon sites in the lineage from rodents to human. The grounds of this adaptive evolution may be driven by the necessity to increase the surface/volume ratio of biconcave erythrocytes for facilitative gas diffusion. Altogether, these results are consistent with Rh proteins not being the orthologue of Amt proteins but having gained the function for CO2/HCO3- transport, with important roles in systemic pH regulation. PMID:16564193

Peng, J; Huang, C H

2006-01-01

252

Protein and solvent dynamics of the water-soluble chlorophyll-binding protein (WSCP)  

NASA Astrophysics Data System (ADS)

This study presents quasielastic neutron scattering data of the water-soluble chlorophyll-binding protein (WSCP) and the corresponding buffer solution at room temperature. The contributions of protein and buffer solution to the overall scattering are carefully separated. Otherwise, the fast water dynamics dominating the buffer contribution is likely to mask the slow protein dynamics. In the case of WSCP, the protein scattering can be described by two contributions: i) internal protein dynamics represented by a diffusion in a sphere with an average radius of 2.7 Å and ii) global (Brownian) diffusion of the WSCP macromolecule with an upper limit for the translational diffusion coefficient of 9.4 ? 10-7 cm2/s.

Rusevich, Leonid; Embs, Jan; Bektas, Inga; Paulsen, Harald; Renger, Gernot; Pieper, Jörg

2015-01-01

253

Metamorphic response of the CLIC1 chloride intracellular ion channel protein upon membrane interaction.  

PubMed

A striking feature of the CLIC (chloride intracellular channel) protein family is the ability of its members to convert between a soluble state and an integral membrane channel form. Direct evidence of the structural transition required for the CLIC protein to autonomously insert into the membrane is lacking, largely because of the challenge of probing the conformation of the membrane-bound protein. However, insights into the CLIC transmembrane form can be gained by biophysical methods such as fluorescence resonance energy transfer (FRET) spectroscopy. This approach was used to measure distances from tryptophan 35, located within the CLIC1 putative N-domain transmembrane region, to three native cysteine residues within the C-terminal domain. These distances were computed both in aqueous solution and upon the addition of membrane vesicles. The FRET distances were used as constraints for modeling of a structure for the CLIC1 integral membrane form. The data are suggestive of a large conformational unfolding occurring between the N- and C-domains of CLIC1 upon interaction with the membrane. Consistent with previous findings, the N-terminal domain of CLIC1 is likely to insert into the lipid bilayer, while the C-domain remains in solution on the extravesicular side of the membrane. PMID:20507120

Goodchild, Sophia C; Howell, Michael W; Littler, Dene R; Mandyam, Ramya A; Sale, Kenneth L; Mazzanti, Michele; Breit, Samuel N; Curmi, Paul M G; Brown, Louise J

2010-06-29

254

Exploration of cone cyclic nucleotide-gated channel-interacting proteins using affinity purification and mass spectrometry.  

PubMed

Photopic (cone) vision essential for color sensation, central vision, and visual acuity is mediated by the activation of photoreceptor cyclic nucleotide-gated (CNG) channels. Naturally occurring mutations in the cone channel subunits CNGA3 and CNGB3 are associated with achromatopsia and cone dystrophies. This work investigated the functional modulation of cone CNG channel by exploring the channel-interacting proteins. Retinal protein extracts prepared from cone-dominant Nrl (- / -) mice were used in CNGA3 antibody affinity purification, followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) separation and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry analysis. The peptide mass fingerprinting of the tryptic digests and database search identified a number of proteins including spectrin alpha-2, ATPase (Na(+)/K(+) transporting) alpha-3, alpha and beta subunits of ATP synthase (H(+) transporting, mitochondrial F1 complex), and alpha-2 subunit of the guanine nucleotide-binding protein. In addition, the affinity-binding assays demonstrated an interaction between cone CNG channel and calmodulin but not cone Na(+)/Ca(2+)-K(+) exchanger in the mouse retina. Results of this study provide insight into our understanding of cone CNG channel-interacting proteins and the functional modulations. PMID:24664681

Ding, Xi-Qin; Matveev, Alexander; Singh, Anil; Komori, Naoka; Matsumoto, Hiroyuki

2014-01-01

255

Modeling water droplet condensation and evaporation in DNS of turbulent channel flow  

NASA Astrophysics Data System (ADS)

In this paper a point particle model for two-way coupling in water droplet-laden incompressible turbulent flow of air is proposed. The model is based on conservation laws and semi-empirical correlations. It has been implemented and tested in a DNS code based for turbulent channel flow with an Eulerian-Lagrangian approach. The two-way coupling is investigated in terms of the effects of mass and heat transfer on the droplets distributions along the channel wall-normal direction and by comparison of the droplet temperature statistics with respect to the case without evaporation and condensation. A remarkable conclusion is that the presence of evaporating and condensing droplets results in an increase in the non-dimensional heat transfer coefficient of the channel flow represented by the Nusselt number.

Russo, E.; Kuerten, J. G. M.; van der Geld, C. W. M.; Geurts, B. J.

2011-12-01

256

Stability analysis of a square rod bundle sub-channel in supercritical water reactor  

NASA Astrophysics Data System (ADS)

Extensive investigations on the flow and heat transfer behavior in SCWR fuel assembly have been undertaken worldwide. However, stability analysis of supercritical water in the sub-channels of tight lattices is still lacking. In this paper, the flow stability of a fuel bundle channel with square pitches has been analyzed using commercial CFD code-ANSYS Fluent. Typical dynamic instability of Density Wave Oscillation (DWO) has occurred in heated channel containing fluids at supercritical pressure. A further discussion about the impacts of various operational parameters (e.g. power input, system pressure, mass velocity, inlet temperature, etc) shows that the system becomes more stable as system pressure and/or mass flow rate increases. An increase in inlet temperature also has a stabilizing effect on the system.

Hai-jun, Wang; Ting, You; Lei, Zhang; Hong-fang, Gu; Yu-shan, Luo; Ji-lian, Bian

2013-07-01

257

Grazing Land Management Strongly Controls Water Quality, Sediment and Channel Dynamics in Tallgrass Prairie Headwater Networks  

NASA Astrophysics Data System (ADS)

In the prairie remnants of North America, watershed sediment regimes are heavily influenced by livestock grazing practices. Despite dramatic declines in stream water quality and ecosystem function concomitant with increasing gazing pressures, there have been no studies to quantitatively assess the relationship between various grazing treatments and sediment production in natural grassland ecosystems. In this study, we evaluate suspended sediment transport and channel morphology in the Flint Hills physiographic province using a paired whole-watershed approach, including 2 replicates of high density cattle grazing, 2 replicates of low density cattle grazing, 3 replicates of bison grazing and 3 replicates of no grazing. As expected, results demonstrate that cattle grazing operations increase e-coli, sediment concentrations and increase channel width. However, no significant differences in e-coli, suspended sediment dynamics or channel geomorphology were found between bison grazed and ungrazed watersheds.

Grudzinski, B. G.; Daniels, M. D.

2013-12-01

258

Carbon nanotube sensors integrated inside a microfluidic channel for water quality monitoring  

NASA Astrophysics Data System (ADS)

Single-walled carbon nanotubes (SWNTs) with their unique electrical properties and large surface area are remarkable materials for detecting low concentration of toxic and hazardous chemicals (both from the gaseous and liquid phases). Ionic adsorbates in water will attach on to SWNTs and drastically alter their electrical properties. Several SWNTs based pH and chemical sensors have been demonstrated. However, most of them require external components to test and analyze the response of SWNTs to ions inside the liquid samples. Here, we report a water quality monitoring sensor composed of SWNTs integrated inside microfluidic channels and on-chip testing components with a wireless transmission board. To detect multiple analytes in water requires the functionalization of SWNTs with different chemistries. In addition, microfluidic channels are used to guide liquid samples to individual nanotube sensors in an efficient manner. Furthermore, the microfluidic system enables sample mixing and separation before testing. To realize the nanosensors, first microelectrodes were fabricated on an oxidized silicon substrate. Next, PDMS micro channels were fabricated and bonded on the substrate. These channels can be incorporated with a microfluidic system which can be designed to manipulate different analytes for specific molecule detection. Low temperature, solution based Dielectrophoretic (DEP) assembly was conducted inside this microfluidic system which successfully bridged SWNTs between the microelectrodes. The SWNTs sensors were next characterized with different pH buffer solutions. The resistance of SWNTs had a linearly increase as the pH values ranged from 5 to 8. The nanosensor incorporated within the microfluidic system is a versatile platform and can be utilized to detect numerous water pollutants, including toxic organics and microorganisms down to low concentrations. On-chip processing and wireless transmission enables the realization of a full autonomous system for real time monitoring of water quality.

Liu, Yu; Li, Xinghui; Dokmeci, Mehmet R.; Wang, Ming L.

2011-04-01

259

Hydrophobic free energy eigenfunctions of pore, channel, and transporter proteins contain beta-burst patterns.  

PubMed Central

Hydropathy plots are often used in place of missing physical data to model transmembrane proteins that are difficult to crystallize. The sequential maxima of their graphs approximate the number and locations of transmembrane segments, but potentially useful additional information about sequential hydrophobic variation is lost in this smoothing procedure. To explore a broader range of hydrophobic variations without loss of the transmembrane segment-relevant sequential maxima, we utilize a sequence of linear decompositions and transformations of the n-length hydrophobic free energy sequences, Hi, i = 1...n, of proteins. Constructions of hydrophobic free energy eigenfunctions, psil, from M-lagged, M x M autocovariance matrices, CM, were followed by their all-poles, maximum entropy power spectral, Somega(psil), and Mexican Hat wavelet, Wa,b(psil), transformations. These procedures yielded graphs indicative of inverse frequencies, omega-1, and sequence locations of hydrophobic modes suggestive of secondary and supersecondary protein structures. The graphs of these computations discriminated between Greek Key, Jelly Role, and Up and Down categories of antiparallel beta-barrel proteins. With these methods, examples of porins, connexins, hexose transporters, nuclear membrane proteins, and potassium but not sodium channels appear to belong to the Up and Down antiparallel beta-barrel variety. PMID:9788928

Selz, K A; Mandell, A J; Shlesinger, M F

1998-01-01

260

Simulations of the Effects of Water Vapor, Cloud Liquid Water, and Ice on AMSU Moisture Channel Brightness Temperatures.  

NASA Astrophysics Data System (ADS)

Radiative transfer simulations are performed to determine how water vapor and nonprecipitating cloud liquid water and ice particles within typical midlatitude atmospheres affect brightness temperatures TB's of moisture sounding channels used in the Advanced Microwave Sounding Unit (AMSU) and AMSU-like instruments. The purpose is to promote a general understanding of passive top-of-atmosphere TB's for window frequencies at 23.8, 89.0, and 157.0 GHz, and water vapor frequencies at 176.31, 180.3 1, and 182.31 GHz by documenting specific examples. This is accomplished through detailed analyses of TB's for idealized atmospheres, mostly representing temperate conditions over land. Cloud effects are considered in terms of five basic properties: droplet size distribution, phase, liquid or ice water content, altitude, and thickness. Effects on TB of changing surface emissivity also are addressed. The brightness temperature contribution functions are presented as an aid to physically interpreting AMSU TB's.Both liquid and ice clouds impact the TB's in a variety of ways. The TB's at 23.8 and 89 GHZ are more strongly affected by altostratus liquid clouds than by cirrus clouds for equivalent water paths. In contrast, channels near 157 and 183 GHz are more strongly affected by ice clouds. Higher clouds have a water impact on 157- and 183-GHz TB's than do lower clouds. Clouds depress TB's of the higher-frequency channels by suppressing, but not necessarily obscuring, radiance contributions from below. Thus, TB's are less closely associated with cloud-top temperatures than are IR radiometric temperatures. Water vapor alone accounts for up to 89% of the total attenuation by a midtropospheric liquid cloud for channels near 183 GHz. The Rayleigh approximation is found to be adequate for typical droplet size distributions; however, Mie scattering effects from liquid droplets become important for droplet size distribution functions with modal radii greater than 20 µm near 157 and 183 GHz, and greater than 30 40 µm at 89 GHz. This is due mainly to the relatively small concentrations of droplets much larger than the mode radius. Orographic clouds and tropical cumuli have been observed to contain droplet size distributions with mode radii in the 30 40-µm range. Thus, as new instruments bridge the gap between microwave and infrared to frequencies even higher than 183 GHz, radiative transfer modelers are cautioned to explicitly address scattering characteristics of such clouds.

Muller, Bradley M.; Fuelberg, Henry E.; Xiang, Xuwu

1994-10-01

261

Protein tyrosine kinase PYK2 involved in Ca2+-induced regulation of ion channel and MAP kinase functions  

Microsoft Academic Search

The protein tyrosine kinase PYK2, which is highly expressed in the central nervous system, is rapidly phosphorylated on tyrosine residues in response to various stimuli that elevate the intracellular calcium concentration, as well as by protein kinase C activation. Activation of PYK2 leads to modulation of ion channel function and activation of the MAP kinase signalling pathway. PYK2 activation may

S. Lev; H. Moreno; R. Martinez; P. Canoll; E. Peles; J. M. Musacchio; G. D. Plowman; B. Rudy; J. Schlessinger

1995-01-01

262

Dynamics of protein and mixed protein/surfactant adsorption layers at the water/fluid interface.  

PubMed

The adsorption behaviour of proteins and systems mixed with surfactants of different nature is described. In the absence of surfactants the proteins mainly adsorb in a diffusion controlled manner. Due to lack of quantitative models the experimental results are discussed partly qualitatively. There are different types of interaction between proteins and surfactant molecules. These interactions lead to protein/surfactant complexes the surface activity and conformation of which are different from those of the pure protein. Complexes formed with ionic surfactants via electrostatic interaction have usually a higher surface activity, which becomes evident from the more than additive surface pressure increase. The presence of only small amounts of ionic surfactants can significantly modify the structure of adsorbed proteins. With increasing amounts of ionic surfactants, however, an opposite effect is reached as due to hydrophobic interaction and the complexes become less surface active and can be displaced from the interface due to competitive adsorption. In the presence of non-ionic surfactants the adsorption layer is mainly formed by competitive adsorption between the compounds and the only interaction is of hydrophobic nature. Such complexes are typically less surface active than the pure protein. From a certain surfactant concentration of the interface is covered almost exclusively by the non-ionic surfactant. Mixed layers of proteins and lipids formed by penetration at the water/air or by competitive adsorption at the water/chloroform interface are formed such that at a certain pressure the components start to separate. Using Brewster angle microscopy in penetration experiments of proteins into lipid monolayers this interfacial separation can be visualised. A brief comparison of the protein adsorption at the water/air and water/n-tetradecane shows that the adsorbed amount at the water/oil interface is much stronger and the change in interfacial tension much larger than at the water/air interface. Also some experimental data on the dilational elasticity of proteins at both interfaces measured by a transient relaxation technique are discussed on the basis of the derived thermodynamic model. As a fast developing field of application the use of surface tensiometry and rheometry of mixed protein/surfactant mixed layers is demonstrated as a new tool in the diagnostics of various diseases and for monitoring the progress of therapies. PMID:10798350

Miller, R; Fainerman, V B; Makievski, A V; Krägel, J; Grigoriev, D O; Kazakov, V N; Sinyachenko, O V

2000-05-24

263

Role of pertussis toxin-sensitive G-protein, K+ channels, and voltage-gated Ca2+ channels in the antinociceptive effect of inosine.  

PubMed

Inosine is the first metabolite of adenosine. It exerts an antinociceptive effect by activating the adenosine A(1) and A(2A) receptors. We have previously demonstrated that inosine exhibits antinociceptive properties in acute and chronic mice models of nociception. The aim of this study was to investigate the involvement of pertussis toxin-sensitive G-protein-coupled receptors, as well as K(+) and Ca(2+) channels, in the antinociception promoted by inosine in the formalin test. Mice were pretreated with pertussis toxin (2.5 ?g/site, i.t., an inactivator of G(i/0) protein); after 7 days, they received inosine (10 mg/kg, i.p.) or morphine (2.5 mg/kg, s.c., used as positive control) immediately before the formalin test. Another group of animals received tetraethylammonium (TEA) or 4-aminopyridine (4-AP) (1 ?g/site, i.t., a non-specific voltage-gated K(+) channel blockers), apamin (50 ng/site, i.t., a small conductance Ca(2+)-activated K(+) channel blocker), charybdotoxin (250 pg/site, i.t., a large-conductance Ca(2+)-activated K(+) channel blocker), glibenclamide (100 ?g/site, i.t., an ATP-sensitive K(+) channel blocker) or CaCl(2) (200 nmol/site, i.t.). Afterwards, the mice received inosine (10 mg/kg, i.p.), diclofenac (10 mg/kg, i.p., a positive control), or morphine (2.5 mg/kg, s.c., a positive control) immediately before the formalin test. The antinociceptive effect of inosine was reversed by the pre-administration of pertussis toxin (2.5 ?g/site, i.t.), TEA, 4-aminopyridine, charybdotoxin, glibenclamide, and CaCl(2), but not apamin. Further, all K(+) channel blockers and CaCl(2) reversed the antinociception induced by diclofenac and morphine, respectively. Taken together, these data suggest that the antinociceptive effect of inosine is mediated, in part, by pertussis toxin-sensitive G-protein coupled receptors and the subsequent activation of voltage gated K(+) channel, large conductance Ca(2+)-activated and ATP-sensitive K(+) channels or inactivation of voltage-gated Ca(2+) channels. Finally, small conductance Ca(2+)-activated K(+) channels are not involved in the antinociceptive effect of inosine. PMID:22806273

Macedo-Junior, Sérgio José; Nascimento, Francisney Pinto; Luiz-Cerutti, Murilo; Santos, Adair Roberto Soares

2013-03-01

264

Free enthalpies of replacing water molecules in protein binding pockets.  

PubMed

Water molecules in the binding pocket of a protein and their role in ligand binding have increasingly raised interest in recent years. Displacement of such water molecules by ligand atoms can be either favourable or unfavourable for ligand binding depending on the change in free enthalpy. In this study, we investigate the displacement of water molecules by an apolar probe in the binding pocket of two proteins, cyclin-dependent kinase 2 and tRNA-guanine transglycosylase, using the method of enveloping distribution sampling (EDS) to obtain free enthalpy differences. In both cases, a ligand core is placed inside the respective pocket and the remaining water molecules are converted to apolar probes, both individually and in pairs. The free enthalpy difference between a water molecule and a CH(3) group at the same location in the pocket in comparison to their presence in bulk solution calculated from EDS molecular dynamics simulations corresponds to the binding free enthalpy of CH(3) at this location. From the free enthalpy difference and the enthalpy difference, the entropic contribution of the displacement can be obtained too. The overlay of the resulting occupancy volumes of the water molecules with crystal structures of analogous ligands shows qualitative correlation between experimentally measured inhibition constants and the calculated free enthalpy differences. Thus, such an EDS analysis of the water molecules in the binding pocket may give valuable insight for potency optimization in drug design. PMID:23247390

Riniker, Sereina; Barandun, Luzi J; Diederich, François; Krämer, Oliver; Steffen, Andreas; van Gunsteren, Wilfred F

2012-12-01

265

Reaction enthalpies along the two channels of geminate electron recombination in liquid-to-supercritical water  

NASA Astrophysics Data System (ADS)

Ionizing radiation or UV light produces electrons and H2O+ ions in water. These species transform into hydrated electron, e-aq, hydrated H3O+ ion, and ·OH radical in each other's neighborhood much faster than any forthcoming chemical transformation. Part of the electrons escapes their geminate partners. There exists two possible paths for the remaining fraction to react: H3O++e-aq=H3O· [channel (A)] and ·OH+e-aq=OH- [channel (B)]. We devised two thermodynamic cycles for the computation of the reaction enthalpies of both channels. Channel (A) was found to be endothermic with an enthalpy of 3.61 eV at room temperature. The enthalpy is seen to be almost constant up to 500 K, to increase at 600 K and to drop abruptly around 650 K, i.e. in the region where the dielectric constant is below 20. Channel (B) was found to be exothermic with an enthalpy of -2.33 eV at room temperature. It is becoming gradually less exothermic with increasing temperature the variation becoming fast around 650 K. The tendency of these thermochemical results parallel with recent kinetic calculations by Torres-Alacan et al. (J. Torres-Alacan, S. Kratz, P. Vöhringer, 2011. Phys. Chem. Chem. Phys. 13, 20806-20819)

Schiller, Robert; Horváth, Ákos

2013-11-01

266

Modulation of proton transfer in the water wire of dioxolane-linked gramicidin channels by lipid membranes.  

PubMed

Proton conductance (g(H)) in single SS stereoisomers of dioxolane-linked gramicidin A (gA) channels were measured in different phospholipid bilayers at different HCl concentrations. In particular, measurements were obtained in bilayers made of 1,2-diphytanoyl 3-phosphocholine (DiPhPC) or its ethylated derivative 1,2-diphytanoyl 3-ethyl-phosphocholine (et-DiPhPC,). The difference between these phospholipids is that in et-DiPhPC one of the phosphate oxygens is covalently linked to an ethyl group and cannot be protonated. In relatively dilute acid solutions, g(H) in DiPhPC is significantly higher than in et-DiPhPC. At high acid concentrations, g(H) is the same in both diphytanoyl bilayers. Such differences in g(H) can be accounted for by surface charge effects at the membrane/solution interfaces. In the linear portion of the log g(H)-log [H] relationship, g(H) values in diphytanoyl bilayers were significantly larger (approximately 10-fold) than in neutral glyceryl monooleate (GMO) membranes. The slopes of the linear log-log relationships between g(H) and [H] in diphytanoyl and GMO bilayers are essentially the same (approximately 0.76). This slope is significantly lower than the slope of the log-log plot of proton conductivity versus proton concentration in aqueous solutions (approximately 1.00). Because the chemical composition of the membrane-channel/solution interface is strikingly different in GMO and diphytanoyl bilayers, the reduced slope in g(H)-[HCl] relationships may be a characteristic of proton transfer in the water wire inside the SS channel. Values of g(H) in diphytanoyl bilayers were also significantly larger than in membranes made of the more common biological phospholipids 1-palmitoyl 2-oleoyl phosphocholine (POPC) or 1-palmitoyl 2-oleoyl phosphoethanolamine (POPE). These differences, however, cannot be accounted for by different surface charge effects or by different internal dipole potentials. On the other hand, maximum g(H) measured in the SS channel does not depend on the composition of the bilayer and is determined essentially by the reduced mobility of protons in concentrated acid solutions. Finally, no experimental evidence was found in support of a lateral proton movement at the phospholipid/solution interface contributing to g(H) in single SS channels. Protein-lipid interactions are likely to modulate g(H) in the SS channel. PMID:11509357

de Godoy, C M; Cukierman, S

2001-09-01

267

Origin of dark-channel X-ray fluorescence from transition-metal ions in water.  

PubMed

The nonradiative dark channels in the L-edge fluorescence spectra from transition-metal aqueous solution identify the ultrafast charge-transfer processes playing an important role in many biological and chemical systems. Yet, the exact origin of such spectral dips with respect to the X-ray transmission spectrum has remained unclear. In the present study we explore the nature of the underlying decay mechanism of 2p core-excited Co(2+) in water by probing the nonradiative Auger-type electron emission channel using photoelectron spectroscopy from a liquid microjet. Our measurements demonstrate unequivocally that metal-to-water charge transfer quenches fluorescence and will inevitably lead to a dip in the total-fluorescence-yield X-ray absorption spectrum. This is directly revealed from the resonant enhancement of valence signal intensity arising from the interference of two identical final states created by a direct and Auger-electron emission, respectively. PMID:22175947

Seidel, Robert; Ghadimi, Samira; Lange, Kathrin M; Bonhommeau, Sébastien; Soldatov, Mikhail A; Golnak, Ronny; Kothe, Alexander; Könnecke, René; Soldatov, Alexander; Thürmer, Stephan; Winter, Bernd; Aziz, Emad F

2012-01-25

268

Dual-Color Fluorescence-Burst Analysis to Probe Protein Efflux through the Mechanosensitive Channel MscL  

PubMed Central

The mechanosensitive channel protein of large conductance, MscL, from Escherichia coli has been implicated in protein efflux, but the passage of proteins through the channel has never been demonstrated. We used dual-color fluorescence-burst analysis to evaluate the efflux of fluorescent labeled compounds through MscL. The method correlates the fluctuations in intensity of fluorescent labeled membranes and encapsulated (macro)molecules (labeled with second fluorophore) for each liposome diffusing through the observation volume. The analysis provides quantitative information on the concentration of macromolecules inside the liposomes and the fraction of functional channel proteins. For MscL, reconstituted in large unilamellar vesicles, we show that insulin, bovine pancreas trypsin inhibitor, and other compounds smaller than 6.5 kDa can pass through MscL, whereas larger macromolecules cannot. PMID:17142294

van den Bogaart, Geert; Krasnikov, Victor; Poolman, Bert

2007-01-01

269

Soy protein polymers: Enhancing the water stability property  

NASA Astrophysics Data System (ADS)

Soy protein based plastics have been processed in the past by researchers for various short-term applications; however a common issue is the high water sensitivity of these plastics. This work concentrates on resolving this water sensitivity issue of soy protein polymers by employing chemical and mechanical interaction at the molecular level during extrusion. The primary chemical interactions employed were anhydride chemistries such as maleic anhydride (MA), phthalic anhydride (PTA), and butylated hydroxyanisole (BHA). These were respectively used in conjunction with glycerol as a plasticizer to produce relatively water stable soy protein based plastics. Formulations with varying additive levels of the chemistries were extruded and injection molded to form the samples for characterization. The additive levels of anhydrides were varied between 3-10% tw/tw (total mass). Results indicated that phthalic anhydride formulations resulted in highest water stability. Plastic formulations with concentration up to 10% phthalic anhydride were observed to have water absorption as low as 21.5% after 24 hrs of exposure to water with respect to 250% for the control formulation. Fourier transform infrared spectroscopy (FTIR) was utilized to characterize and confirm the fundamental mechanisms of water stability achieved by phthalic and maleic anhydride chemistries. In addition, the anhydride formulations were modified by inclusion of cotton fibers and pretreated cotton powder in order to improve mechanical properties. The incorporation of cotton fibers improved the dry strength by 18%, but did not significantly improve the wet state strength of the plastics. It was also observed that the butylated-hydroxy anisole (BHA) formulation exhibited high extension values in the dry state and had inferior water absorption properties in comparison with anhydride formulations.

Srinivasan, Gowrishankar

270

Simulations of the effects of water vapor, cloud liquid water, and ice on AMSU moisture channel brightness temperatures  

NASA Technical Reports Server (NTRS)

Radiative transfer simulations are performed to determine how water vapor and nonprecipitating cloud liquid water and ice particles within typical midlatitude atmospheres affect brightness temperatures T(sub B)'s of moisture sounding channels used in the Advanced Microwave Sounding Unit (AMSU) and AMSU-like instruments. The purpose is to promote a general understanding of passive top-of-atmosphere T(sub B)'s for window frequencies at 23.8, 89.0, and 157.0 GHz, and water vapor frequencies at 176.31, 180.31, and 182.31 GHz by documenting specific examples. This is accomplished through detailed analyses of T(sub B)'s for idealized atmospheres, mostly representing temperate conditions over land. Cloud effects are considered in terms of five basic properties: droplet size distribution, phase, liquid or ice water content, altitude, and thickness. Effects on T(sub B) of changing surface emissivity also are addressed. The brightness temperature contribution functions are presented as an aid to physically interpreting AMSU T(sub B)'s. Both liquid and ice clouds impact the T(sub B)'s in a variety of ways. The T(sub B)'s at 23.8 and 89 GHz are more strongly affected by altostratus liquid clouds than by cirrus clouds for equivalent water paths. In contrast, channels near 157 and 183 GHz are more strongly affected by ice clouds. Higher clouds have a greater impact on 157- and 183-GHz T(sub B)'s than do lower clouds. Clouds depress T(sub B)'s of the higher-frequency channels by suppressing, but not necessarily obscuring, radiance contributions from below. Thus, T(sub B)'s are less closely associated with cloud-top temperatures than are IR radiometric temperatures. Water vapor alone accounts for up to 89% of the total attenuation by a midtropospheric liquid cloud for channels near 183 GHz. The Rayleigh approximation is found to be adequate for typical droplet size distributions; however, Mie scattering effects from liquid droplets become important for droplet size distribution functions with modal radii greater than 20 micrometers near 157 and 183 GHz, and greater than 30-40 micrometers at 89 GHz. This is due mainly to the relatively small concentrations of droplets much larger than the mode radius. Orographic clouds and tropical cumuli have been observed to contain droplet size distributions with mode radii in the 30-40 micrometers range. Thus, as new instruments bridge the gap between microwave and infrared to frequencies even higher than 183 GHz, radiative transfer modelers are cautioned to explicitly address scattering characteristics of such clouds.

Muller, Bradley M.; Fuelberg, Henry E.; Xiang, Xuwu

1994-01-01

271

Gas-discharge probe microscopy of water-carrying channels in wood  

NASA Astrophysics Data System (ADS)

We have used a gas-discharge imaging technique to study the water transport channels (tracheids) in wood samples. Results obtained for the samples of bitch and aspen show features of this variant of the probe microscopy and show its additional possibilities as compared to optical microscopy. It is concluded that gas-discharge probe microscopy can be used for additional diagnostics of the structure of plant and animal tissues.

Ivanov-Omskii, V. I.; Ivanova, E. I.

2012-04-01

272

Neonatal ureteral obstruction alters expression of renal sodium transporters and aquaporin water channels  

Microsoft Academic Search

Neonatal ureteral obstruction alters expression of renal sodium transporters and aquaporin water channels.BackgroundCongenital urinary tract obstruction is a common cause of renal insufficiency in the neonate and during infancy. Recently, we demonstrated that ureteral obstruction in adult rats is associated with reduction in the abundance of renal aquaporins (AQPs) and renal sodium transporters, which paralleled an impaired urinary concentrating capacity.MethodsIn

YIMIN SHI; CHUNLING LI; KLAUS THOMSEN; TROELS MUNCH JøRGENSEN; Mark A. Knepper; SøREN NIELSEN; JENS CHRISTIAN DJURHUUS; JøRGEN FRøKIæR

2004-01-01

273

Wind-forced circulation model and water exchanges through the channel in the Bay of Toulon  

NASA Astrophysics Data System (ADS)

A hydrodynamic model of the Bay of Toulon has been developed for use as a post-accident radionuclide dispersion simulation tool. Located in a Mediterranean urban area, the Bay of Toulon is separated into two basins by a 1.4-km long seawall. The Little Bay is semi-enclosed and connected to the Large Bay by a fairway channel. This channel is the site of significant water mass exchange as a result of both wind-driven currents and bathymetry. It is therefore a focal point for marine contamination. As part of the model calibration and validation process, the first step consisted of studying the water mass exchange between the two basins. An Acoustic Doppler Current Profiler was moored in the channel for 1 year. The present study analyses in situ data to determine the current intensity and direction, and also to better understand the vertical current profile, which is highly correlated with meteorological forcing. Comparisons of model-generated and measured data are presented, and various atmospheric forcing datasets are used to enhance computed results. It appears that accurate meteorological forcing data is needed to enhance the accuracy of the hydrodynamic model. This channel is an important location for water mass renewal in the Bay of Toulon, and model results are used to quantify these exchanges. The mean calculated annual water exchange time is approximately 3.4 days. However, this duration is strongly wind dependent and shortens during windy winter months. It ranges from 1.5 days during strong wind periods to 7.5 days during calm weather. Residence time values calculated through tracer dispersion modelling after release at the back of the Little Bay are found to be comparable to the mean exchange time values, especially for windy conditions.

Dufresne, Christiane; Duffa, Céline; Rey, Vincent

2014-01-01

274

Coupling of Retinal, Protein, and Water Dynamics in Squid Rhodopsin  

PubMed Central

The light-induced isomerization of the retinal from 11-cis to all-trans triggers changes in the conformation of visual rhodopsins that lead to the formation of the activated state, which is ready to interact with the G protein. To begin to understand how changes in the structure and dynamics of the retinal are transmitted to the protein, we performed molecular dynamics simulations of squid rhodopsin with 11-cis and all-trans retinal, and with two different force fields for describing the retinal molecule. The results indicate that structural rearrangements in the binding pocket, albeit small, propagate toward the cytoplasmic side of the protein, and affect the dynamics of internal water molecules. The sensitivity of the active-site interactions on the retinal force-field parameters highlights the coupling between the retinal molecule and its immediate protein environment. PMID:20923654

Jardón-Valadez, Eduardo; Bondar, Ana-Nicoleta; Tobias, Douglas J.

2010-01-01

275

Moving Fe2+ from ferritin ion channels to catalytic OH centers depends on conserved protein cage carboxylates.  

PubMed

Ferritin biominerals are protein-caged metabolic iron concentrates used for iron-protein cofactors and oxidant protection (Fe(2+) and O2 sequestration). Fe(2+) passage through ion channels in the protein cages, like membrane ion channels, required for ferritin biomineral synthesis, is followed by Fe(2+) substrate movement to ferritin enzyme (Fox) sites. Fe(2+) and O2 substrates are coupled via a diferric peroxo (DFP) intermediate, ?max 650 nm, which decays to [Fe(3+)-O-Fe(3+)] precursors of caged ferritin biominerals. Structural studies show multiple conformations for conserved, carboxylate residues E136 and E57, which are between ferritin ion channel exits and enzymatic sites, suggesting functional connections. Here we show that E136 and E57 are required for ferritin enzyme activity and thus are functional links between ferritin ion channels and enzymatic sites. DFP formation (Kcat and kcat/Km), DFP decay, and protein-caged hydrated ferric oxide accumulation decreased in ferritin E57A and E136A; saturation required higher Fe(2+) concentrations. Divalent cations (both ion channel and intracage binding) selectively inhibit ferritin enzyme activity (block Fe(2+) access), Mn(2+) < Co(2+) < Cu(2+) < Zn(2+), reflecting metal ion-protein binding stabilities. Fe(2+)-Cys126 binding in ferritin ion channels, observed as Cu(2+)-S-Cys126 charge-transfer bands in ferritin E130D UV-vis spectra and resistance to Cu(2+) inhibition in ferritin C126S, was unpredicted. Identifying E57 and E136 links in Fe(2+) movement from ferritin ion channels to ferritin enzyme sites completes a bucket brigade that moves external Fe(2+) into ferritin enzymatic sites. The results clarify Fe(2+) transport within ferritin and model molecular links between membrane ion channels and cytoplasmic destinations. PMID:24843174

Behera, Rabindra K; Theil, Elizabeth C

2014-06-01

276

Moving Fe2+ from ferritin ion channels to catalytic OH centers depends on conserved protein cage carboxylates  

PubMed Central

Ferritin biominerals are protein-caged metabolic iron concentrates used for iron–protein cofactors and oxidant protection (Fe2+ and O2 sequestration). Fe2+ passage through ion channels in the protein cages, like membrane ion channels, required for ferritin biomineral synthesis, is followed by Fe2+ substrate movement to ferritin enzyme (Fox) sites. Fe2+ and O2 substrates are coupled via a diferric peroxo (DFP) intermediate, ?max 650 nm, which decays to [Fe3+–O–Fe3+] precursors of caged ferritin biominerals. Structural studies show multiple conformations for conserved, carboxylate residues E136 and E57, which are between ferritin ion channel exits and enzymatic sites, suggesting functional connections. Here we show that E136 and E57 are required for ferritin enzyme activity and thus are functional links between ferritin ion channels and enzymatic sites. DFP formation (Kcat and kcat/Km), DFP decay, and protein-caged hydrated ferric oxide accumulation decreased in ferritin E57A and E136A; saturation required higher Fe2+ concentrations. Divalent cations (both ion channel and intracage binding) selectively inhibit ferritin enzyme activity (block Fe2+ access), Mn2+ << Co2+ < Cu2+ < Zn2+, reflecting metal ion–protein binding stabilities. Fe2+–Cys126 binding in ferritin ion channels, observed as Cu2+–S–Cys126 charge-transfer bands in ferritin E130D UV-vis spectra and resistance to Cu2+ inhibition in ferritin C126S, was unpredicted. Identifying E57 and E136 links in Fe2+ movement from ferritin ion channels to ferritin enzyme sites completes a bucket brigade that moves external Fe2+ into ferritin enzymatic sites. The results clarify Fe2+ transport within ferritin and model molecular links between membrane ion channels and cytoplasmic destinations. PMID:24843174

Behera, Rabindra K.; Theil, Elizabeth C.

2014-01-01

277

A discrete water exit pathway in the membrane protein cytochrome c oxidase.  

PubMed

By using the non-redox-active Mg2+/Mn2+ site of cytochrome c oxidase as a probe, water access from the outside of the enzyme and water escape from the buried active site were studied. Water movement was time-resolved by monitoring the magnetic interaction of the oxygen isotope 17O with the Mn2+ by using a rapid freeze-quench-electron spin echo envelope modulation technique. Rapid (msec) access of water from the bulk phase to the Mn2+ was demonstrated by mixing cytochrome c oxidase with H217O. To determine whether a channel involving the Mn2+ was used for water exit from the active site, samples incubated in 17O2 were allowed to turn over approximately five times before freezing. The 17O, now in the form of H217O, was detected at the Mn2+. The significant broadening of the Mn2+ signal after the limited number of turnovers strongly suggests that the water exits the protein by means of one discrete pathway, not by random diffusion. PMID:14660787

Schmidt, Bryan; McCracken, John; Ferguson-Miller, Shelagh

2003-12-23

278

Comparisons of the hydraulics of water flows in Martian outflow channels with flows of similar scale on earth  

NASA Technical Reports Server (NTRS)

The hydraulics of channelized water flows on Mars and the resulting sediment transport rates are calculated, and similar computations are performed for such terrestrial analogs as the Mississippi River and the catastrophic Lake Missoula floods that formed the Channeled Scabland in eastern Washington State. The morphologies of deep-sea channels formed by catastrophic turbidity currents are compared with the Martian channels, many similarities are pointed out, and the hydraulics of the various flows are compared. The results indicate that the velocities, discharges, bottom shear stresses, and sediment-transport capacity of water flows along the Martian channels would be comparable to those of the oceanic turbidity currents and the Lake Missoula floods. It is suggested that the submarine canyons from which turbidity currents originate are the terrestrial counterparts to the chaotic-terrain areas or craters that serve as sources for many of the Martian channels.

Komar, P. D.

1979-01-01

279

Downregulation of the renal outer medullary K(+) channel ROMK by the AMP-activated protein kinase.  

PubMed

The 5'-adenosine monophosphate-activated serine/threonine protein kinase (AMPK) is stimulated by energy depletion, increase in cytosolic Ca(2+) activity, oxidative stress, and nitric oxide. AMPK participates in the regulation of the epithelial Na(+) channel ENaC and the voltage-gated K(+) channel KCNE1/KCNQ1. It is partially effective by decreasing PIP(2) formation through the PI3K pathway. The present study explored whether AMPK regulates the renal outer medullary K(+) channel ROMK. To this end, cRNA encoding ROMK was injected into Xenopus oocytes with and without additional injection of constitutively active AMPK(?R70Q) (AMPK(?1)-HA+AMPK(?1)-Flag+AMPK?1(R70Q)), or of inactive AMPK(?K45R) (AMPK(?1K45R)+AMPK(?1)-Flag+AMPK(?1)-HA), and the current determined utilizing two-electrode voltage-clamp and single channel patch clamp. ROMK protein abundance was measured utilizing chemiluminescence in Xenopus oocytes and western blot in whole kidney tissue. Moreover, renal Na(+) and K(+) excretion were determined in AMPK(?1)-deficient mice (ampk ( -/- )) and wild-type mice (ampk ( +/+ )) prior to and following an acute K(+) load (111 mM KCl, 30 mM NaHCO(3), 4.7 mM NaCl, and 2.25 g/dl BSA) at a rate of 500 ?l/h. As a result, coexpression of AMPK(?R70Q) but not of AMPK(?K45R) significantly decreased the current in ROMK1-expressing Xenopus oocytes. Injection of phosphatidylinositol PI((4,5))P(2) significantly increased the current in ROMK1-expressing Xenopus oocytes, an effect reversed in the presence of AMPK(?R70Q). Under control conditions, no significant differences between ampk ( -/- ) and ampk ( +/+ ) mice were observed in glomerular filtration rate (GFR), urinary flow rate, serum aldosterone, plasma Na(+), and K(+) concentrations as well as absolute and fractional Na(+) and K(+) excretion. Following an acute K(+) load, GFR, urinary flow rate, serum aldosterone, plasma Na(+), and K(+) concentration were again similar in both genotypes, but renal absolute and fractional Na(+) and K(+) excretion were higher in ampk ( -/- ) than in ampk ( +/+ ) mice. According to micropuncture following a K(+) load, delivery of Na(+) to the early distal tubule but not delivery of K(+) to late proximal and early distal tubules was increased in ampk (-/-) mice. The upregulation of renal ROMK1 protein expression by acute K(+) load was more pronounced in ampk (-/-) than in ampk ( +/+ ) mice. In conclusion, AMPK downregulates ROMK, an effect compromising the ability of the kidney to excrete K(+) following an acute K(+) load. PMID:23179379

Siraskar, Balasaheb; Huang, Dan Yang; Pakladok, Tatsiana; Siraskar, Gulab; Sopjani, Mentor; Alesutan, Ioana; Kucherenko, Yulia; Almilaji, Ahmad; Devanathan, Vasudharani; Shumilina, Ekaterina; Föller, Michael; Munoz, Carlos; Lang, Florian

2013-02-01

280

Reversible Adsorption of Proteins at the Oil\\/Water Interface. I. Preferential Adsorption of Proteins at Charged Oil\\/Water Interfaces  

Microsoft Academic Search

The behaviour of positively and negatively charged oil-in-water emulsions, stabilized with hexadecyl trimethyl ammonium bromide and sodium hexadecyl sulphate respectively in the presence of protein solutions has been studied. Under certain conditions proteins will adsorb to a charged oil\\/water interface. When finely dispersed oil-in-water emulsion was used to provide this oil\\/water interface, adsorption of protein resulted in flocculation of the

J. J. Elkes; A. C. Frazer; J. H. Schulman; H. C. Stewart

1943-01-01

281

Reversible Adsorption of Proteins at the Oil\\/Water Interface. I. Preferential Adsorption of Proteins at Charged Oil\\/Water Interfaces  

Microsoft Academic Search

The behaviour of positively and negatively charged oil-in-water emulsions, stabilized with hexadecyl trimethyl ammonium bromide and sodium hexadecyl sulphate respectively in the presence of protein solutions has been studied. Under certain conditions proteins will adsorb to a charged oil\\/water interface. When finely dispersed oil-in-water emulsion was used to provide this oil\\/water interface, adsorption of protein resulted in flocculation of the

J. J. Elkes; A. C. Frazer; J. H. Schulman; H. C. Stewart

1946-01-01

282

CLIC4, an intracellular chloride channel protein, is a novel molecular target for cancer therapy.  

PubMed

Chloride intracellular channel (CLIC)4 is a p53- and tumor necrosis factor alpha (TNFalpha)-regulated chloride channel protein that is localized to the mitochondria and cytoplasm of mouse and human keratinocytes. CLIC4 protein increases in differentiating keratinocytes and in keratinocytes exposed to DNA-damaging agents and metabolic inhibitors. Increasing CLIC4 levels by transduction of recombinant CLIC4 causes apoptosis. CLIC4 translocates to the nucleus under a variety of conditions of cell stress, and nuclear CLIC4 is associated with cell cycle arrest and accelerated apoptosis. Reduction of CLIC4 and several other CLIC family members by expressing a doxycycline-regulated CLIC4 antisense also causes apoptosis in squamous cancer cell lines. Expressing antisense CLIC4 in tumors derived from transplanting these cells into nude mice inhibits tumor growth, increases tumor apoptosis, and reduces tumor cell proliferation. Co-administration of TNFalpha intraperitoneally enhances the tumor-inhibitory influence of CLIC4 antisense expression. Together, these results suggest that CLIC4 is important for keratinocyte viability and may be a novel target for anti-cancer therapy. PMID:16358817

Suh, Kwang S; Mutoh, Michihiro; Gerdes, Michael; Yuspa, Stuart H

2005-11-01

283

Protein Kinase A Mediates Activity-Dependent Kv4.2 Channel Trafficking  

PubMed Central

The A-type potassium channel subunit Kv4.2 influences hippocampal function through regulation of dendritic excitability, and changes in Kv4.2 surface expression alter synaptic plasticity. Recent data from our laboratory demonstrate that EGFP (enhanced green fluorescent protein)-tagged Kv4.2 channels located in dendritic spines are internalized in an activity-dependent manner after synaptic stimulation and during chemically induced long-term potentiation. However, the molecular trigger for Kv4.2 internalization remains unknown. Here we examined the role of protein kinase A (PKA) in Kv4.2 activity-dependent trafficking. In hippocampal neurons, PKA activation with forskolin or 8-Br-cAMP induced Kv4.2 internalization from dendritic spines, whereas PKA inhibition with H89 prevented AMPA-induced internalization. Furthermore, introduction of a point mutation at the C-terminal PKA phosphorylation site of Kv4.2 (S552A) prevented the AMPA-induced internalization of Kv4.2. Together, these data demonstrate that Kv4.2 activity-dependent internalization requires PKA phosphorylation of Kv4.2 at serine 522. PMID:18650329

Hammond, Rebecca S.; Lin, Lin; Sidorov, Michael S.; Wikenheiser, Andrew M.; Hoffman, Dax A.

2009-01-01

284

Control of muscle ryanodine receptor calcium release channels by proteins in the sarcoplasmic reticulum lumen.  

PubMed

1. Many biological processes that are governed by intracellular calcium signals rely on intracellular stores, which provide a reliable, controlled release of calcium into the cytoplasm. Calcium release through the ryanodine receptor (RyR), the main ion channel in the sarcoplasmic reticulum (the calcium store in muscle) is the key determinant of muscle force. 2. Calsequestrin, the main calcium buffer in the sarcoplasmic reticulum, provides a pool of calcium for release through the RyR and acts as a luminal calcium sensor for the channel via its interactions with triadin and junctin. Until recently, how calsequestrin communicated the store Ca(2+) load to the RyR remained unknown. 3. Calsequestrin 1 (skeletal calsequestrin) has been shown to both inhibit and activate the skeletal RyR1, dependent on whether it's bound to the RyR1 directly or indirectly via anchoring proteins. 4. The phosphorylation status of calsequestrin 1 is deemed important: it influences the Ca(2+) binding capacity of calsequestrin, the way in which calsequestrin 1 regulates the RyR1 and how calsequestrin 1 interacts with the key anchoring protein junctin. 5. In skeletal muscle, junctin plays a more critical role than triadin in the mechanism that controls Ca(2+) release from the sarcoplasmic reticulum. 6. The close relationship between altered expression and dysfunction of calsequestrin in several skeletal and cardiac disorders highlights the critical role that calsequestrin plays in maintaining Ca(2+) homeostasis and regulation of muscle contraction. PMID:19278523

Beard, Nicole A; Wei, Lan; Dulhunty, Angela F

2009-03-01

285

Subunit-specific inhibition of acid sensing ion channels by stomatin-like protein 1  

PubMed Central

There are five mammalian stomatin-domain genes, all of which encode peripheral membrane proteins that can modulate ion channel function. Here we examined the ability of stomatin-like protein 1 (STOML1) to modulate the proton-sensitive members of the acid-sensing ion channel (ASIC) family. STOML1 profoundly inhibits ASIC1a, but has no effect on the splice variant ASIC1b. The inactivation time constant of ASIC3 is also accelerated by STOML1. We examined STOML1 null mutant mice with a ?-galactosidase-neomycin cassette gene-trap reporter driven from the STOML1 gene locus, which indicated that STOML1 is expressed in at least 50% of dorsal root ganglion (DRG) neurones. Patch clamp recordings from mouse DRG neurones identified a trend for larger proton-gated currents in neurones lacking STOML1, which was due to a contribution of effects upon both transient and sustained currents, at different pH, a finding consistent with an endogenous inhibitory function for STOML1. PMID:24247984

Kozlenkov, Alexey; Lapatsina, Liudmila; Lewin, Gary R; Smith, Ewan St John

2014-01-01

286

Sec61?, a subunit of the Sec61 protein translocation channel at the Endoplasmic Reticulum, is involved in the transport of Gurken to the plasma membrane  

Microsoft Academic Search

BACKGROUND: Protein translocation across the membrane of the Endoplasmic Reticulum (ER) is the first step in the biogenesis of secretory and membrane proteins. Proteins enter the ER by the Sec61 translocon, a proteinaceous channel composed of three subunits, ?, ? and ?. While it is known that Sec61? forms the actual channel, the function of the other two subunits remains

Anshuman Kelkar; Bernhard Dobberstein

2009-01-01

287

Ions at Aqueous Interfaces: From Water Surface to Hydrated Proteins  

NASA Astrophysics Data System (ADS)

The surfaces of aqueous solutions are traditionally viewed as devoid of inorganic ions. Molecular simulations and surface-selective spectroscopic techniques show, however, that large polarizable anions and hydronium cations can be found (and even enhanced) at the surface and are involved in chemistry at the air/water interface. Here, we review recent studies of ions at the air/water interface and compare from this perspective water with other polar solvents. For water, we focus in particular on the surface behavior of its ionic product (i.e., hydronium and hydroxide ions). We also investigate the feasibility of dielectric models for the description of the protein/water interface, in analogy to the air/water interface. Little correlation is found between these two interfaces in terms of ion segregation. Therefore, we suggest a local model of pairing of ions from the solution with charged and polar groups at the protein surface. We also describe corresponding results of experimental studies on aqueous model systems.

Jungwirth, Pavel; Winter, Bernd

2008-05-01

288

Water stress inhibits hydraulic conductance and leaf growth in rice seedlings but not the transport of water via mercury-sensitive water channels in the root  

PubMed

The mechanisms by which moderate water stress (adding polyethylene glycol 6000 to the root medium) induces a sustained inhibition of growth in emerging first leaves of intact rice (Oryza sativa) seedlings was investigated under growth-chamber conditions. Early (24 h) inhibition of leaf growth was not related to changes in root size or in osmotic potential gradients and cell wall-yielding characteristics in the leaf-expansion zone of stressed seedlings. However, reductions in root-to-leaf hydraulic conductance (L) were measured in two rice cultivars after 4 or 24 h at various levels of water stress, and these reductions correlated well with the inhibition of leaf growth. We assayed L by a psychrometric method and, in intact seedlings, by a novel osmotic-jump method. The addition of 0.5 mM HgCl2 to the root medium to inhibit water transport through Hg-sensitive water channels in the roots did not inhibit leaf growth in unstressed seedlings. However, both leaf growth and L were additionally reduced (by 49% and 43%, respectively) within minutes of adding HgCl2 to roots of water-stressed seedlings. Water stress therefore appeared to increase the transport of water via Hg-sensitive water channels. Other mechanisms were apparently involved in inhibiting overall L and leaf growth. PMID:10318692

Lu; Neumann

1999-05-01

289

Water Stress Inhibits Hydraulic Conductance and Leaf Growth in Rice Seedlings but Not the Transport of Water via Mercury-Sensitive Water Channels in the Root1  

PubMed Central

The mechanisms by which moderate water stress (adding polyethylene glycol 6000 to the root medium) induces a sustained inhibition of growth in emerging first leaves of intact rice (Oryza sativa) seedlings was investigated under growth-chamber conditions. Early (24 h) inhibition of leaf growth was not related to changes in root size or in osmotic potential gradients and cell wall-yielding characteristics in the leaf-expansion zone of stressed seedlings. However, reductions in root-to-leaf hydraulic conductance (L) were measured in two rice cultivars after 4 or 24 h at various levels of water stress, and these reductions correlated well with the inhibition of leaf growth. We assayed L by a psychrometric method and, in intact seedlings, by a novel osmotic-jump method. The addition of 0.5 mm HgCl2 to the root medium to inhibit water transport through Hg-sensitive water channels in the roots did not inhibit leaf growth in unstressed seedlings. However, both leaf growth and L were additionally reduced (by 49% and 43%, respectively) within minutes of adding HgCl2 to roots of water-stressed seedlings. Water stress therefore appeared to increase the transport of water via Hg-sensitive water channels. Other mechanisms were apparently involved in inhibiting overall L and leaf growth. PMID:10318692

Lu, Zhongjin; Neumann, Peter M.

1999-01-01

290

Cytocompatible and water stable ultrafine protein fibers for tissue engineering  

NASA Astrophysics Data System (ADS)

This dissertation proposal focuses on the development of cytocompatible and water stable protein ultrafine fibers for tissue engineering. The protein-based ultrafine fibers have the potential to be used for biomedicine, due to their biocompatibility, biodegradability, similarity to natural extracellular matrix (ECM) in physical structure and chemical composition, and superior adsorption properties due to their high surface to volume ratio. However, the current technologies to produce the protein-based ultrafine fibers for biomedical applications still have several problems. For instance, the current electrospinning and phase separation technologies generate scaffolds composed of densely compacted ultrafine fibers, and cells can spread just on the surface of the fiber bulk, and hardly penetrate into the inner sections of scaffolds. Thus, these scaffolds can merely emulate the ECM as a two dimensional basement membrane, but are difficult to mimic the three dimensional ECM stroma. Moreover, the protein-based ultrafine fibers do not possess sufficient water stability and strength for biomedical applications, and need modifications such as crosslinking. However, current crosslinking methods are either high in toxicity or low in crosslinking efficiency. To solve the problems mentioned above, zein, collagen, and gelatin were selected as the raw materials to represent plant proteins, animal proteins, and denatured proteins in this dissertation. A benign solvent system was developed specifically for the fabrication of collagen ultrafine fibers. In addition, the gelatin scaffolds with a loose fibrous structure, high cell-accessibility and cell viability were produced by a novel ultralow concentration phase separation method aiming to simulate the structure of three dimensional (3D) ECM stroma. Non-toxic crosslinking methods using citric acid as the crosslinker were also developed for electrospun or phase separated scaffolds from these three proteins, and proved to be efficient to enhance the strength and water stability of scaffolds. The crosslinked protein scaffolds showed higher cytocompatibility than the polylactic acid scaffolds and the fibers crosslinked by glutaraldehyde. The potential of using these protein-based ultrafine fibers crosslinked by citric acid for tissue engineering has been proved in this dissertation.

Jiang, Qiuran

291

AMP-activated protein kinase regulates hERG potassium channel.  

PubMed

Besides their role in cardiac repolarization, human ether-a-go-go-related gene potassium (hERG) channels are expressed in several tumor cells including rhabdomyosarcoma cells. The channels foster cell proliferation. Ubiquitously expressed AMP-dependent protein kinase (AMPK) is a serine-/threonine kinase, stimulating energy-generating and inhibiting energy-consuming processes thereby helping cells survive periods of energy depletion. AMPK has previously been shown to regulate Na?/K? ATPase, Na?/Ca²? exchangers, Ca²? channels and K? channels. The present study tested whether AMPK regulates hERG channel activity. Wild type AMPK (?1?1?1), constitutively active (?R70Q)AMPK (?1?1?1(R70Q)), or catalytically inactive (?K45R)AMPK (?1(K45R)?1?1) were expressed in Xenopus oocytes with hERG. Tail currents were determined as a measure of hERG channel activity by two-electrode-voltage clamp. hERG membrane abundance was quantified by chemiluminescence and visualized by immunocytochemistry and confocal microscopy. Moreover, hERG currents were measured in RD rhabdomyosarcoma cells after pharmacological modification of AMPK activity using the patch clamp technique. Coexpression of wild-type AMPK and of constitutively active (?R70Q)AMPK significantly downregulated the tail currents in hERG-expressing Xenopus oocytes. Pharmacological activation of AMPK with AICAR or with phenformin inhibited hERG currents in Xenopus oocytes, an effect abrogated by AMPK inhibitor compound C. (?R70Q)AMPK enhanced the Nedd4-2-dependent downregulation of hERG currents. Coexpression of constitutively active (?R70Q)AMPK decreased membrane expression of hERG in Xenopus oocytes. Compound C significantly enhanced whereas AICAR tended to inhibit hERG currents in RD rhabdomyosarcoma cells. AMPK is a powerful regulator of hERG-mediated currents in both, Xenopus oocytes and RD rhabdomyosarcoma cells. AMPK-dependent regulation of hERG may be particularly relevant in cardiac hypertrophy and tumor growth. PMID:23716168

Almilaji, Ahmad; Munoz, Carlos; Elvira, Bernat; Fajol, Abul; Pakladok, Tatsiana; Honisch, Sabina; Shumilina, Ekaterina; Lang, Florian; Föller, Michael

2013-11-01

292

Formation of ion-conducting channels by the membrane attack complex proteins of complement.  

PubMed Central

The effects of sequential additions of purified human complement proteins C5b-6, C7, C8, and C9 to assemble the C5b-9 membrane attack complex (MAC) of complement on electrical properties of planar lipid bilayers have been analyzed. The high resistance state of such membranes was impaired after assembly of large numbers of C5b-8 complexes as indicated by the appearance of rapidly fluctuating membrane currents. The C5b-8 induced conductance was voltage dependent and rectifying at higher voltages. Addition of C9 to membranes with very few C5b-8 complexes caused appearance of few discrete single channels of low conductance (5-25 pS) but after some time very large (greater than 0.5 nS) jumps in conductance could be monitored. This high macroscopic conductance state was dominated by 125-pS channels having a lifetime of approximately 1 s. The high conductance state was not stable and declined again after a period of 1-3 h. Incorporation of MAC extracted from complement-lysed erythrocytes into liposomes and subsequent transformation of such complexes into planar bilayers via an intermediate monolayer state resulted in channels with characteristics similar to the ones produced by sequential assembly of C5b-9. Comparison of the high-conductance C5b-9 channel characteristics (lifetime, ion preference, ionic-strength dependence) with those produced by poly(C9) (the circular or tubular aggregation product of C9) as published by Young, J.D.-E., Z.A. Cohn, and E.R. Podack. (1986. Science [Wash. DC]. 233:184-190.) indicates that the two are significantly different. PMID:1720679

Shiver, J W; Dankert, J R; Esser, A F

1991-01-01

293

S-nitrosylation regulates nuclear translocation of chloride intracellular channel protein CLIC4.  

PubMed

Nuclear translocation of chloride intracellular channel protein CLIC4 is essential for its role in Ca(2+)-induced differentiation, stress-induced apoptosis, and modulating TGF-beta signaling in mouse epidermal keratinocytes. However, post-translational modifications on CLIC4 that govern nuclear translocation and thus these activities remain to be elucidated. The structure of CLIC4 is dependent on the redox environment, in vitro, and translocation may depend on reactive oxygen and nitrogen species in the cell. Here we show that NO directly induces nuclear translocation of CLIC4 that is independent of the NO-cGMP pathway. Indeed, CLIC4 is directly modified by NO through S-nitrosylation of a cysteine residue, as measured by the biotin switch assay. NO enhances association of CLIC4 with the nuclear import proteins importin alpha and Ran. This is likely a result of the conformational change induced by S-nitrosylated CLIC4 that leads to unfolding of the protein, as exhibited by CD spectra analysis and trypsinolysis of the modified protein. Cysteine mutants of CLIC4 exhibit altered nitrosylation, nuclear residence, and stability, compared with the wild type protein likely as a consequence of altered tertiary structure. Moreover, tumor necrosis factor alpha-induced nuclear translocation of CLIC4 is dependent on nitric-oxide synthase activity. Inhibition of nitric-oxide synthase activity inhibits tumor necrosis factor alpha-induced nitrosylation and association with importin alpha and Ran and ablates CLIC4 nuclear translocation. These results suggest that S-nitrosylation governs CLIC4 structure, its association with protein partners, and thus its intracellular distribution. PMID:20504765

Malik, Mariam; Shukla, Anjali; Amin, Palak; Niedelman, Wendy; Lee, Jessica; Jividen, Kasey; Phang, Juanita M; Ding, Jinhui; Suh, Kwang S; Curmi, Paul M G; Yuspa, Stuart H

2010-07-30

294

Liquid water transport in parallel serpentine channels with manifolds on cathode side of a PEM fuel cell stack  

Microsoft Academic Search

Water management in a proton exchange membrane (PEM) fuel cell stack has been a challenging issue on the road to commercialization. This paper presents a numerical investigation of air–water flow in parallel serpentine channels on cathode side of a PEM fuel cell stack by use of the commercial Computational Fluid Dynamics (CFD) software package FLUENT. Different air–water flow behaviours inside

Kui Jiao; Biao Zhou; Peng Quan

2006-01-01

295

Real-time visualization of oxygen partial pressures in straight channels of running polymer electrolyte fuel cell with water plugging  

NASA Astrophysics Data System (ADS)

Visualization inside polymer electrolyte fuel cells (PEFCs) for elucidating the reaction distributions is expected to improve the performance, durability, and stability. An oxygen-sensitive film of a luminescent porphyrin was used to visualize the oxygen partial pressures in five straight gas-flow channels of a running PEFC with liquid-water blockages formed at the end of the channels. The blockage greatly lowered and unstabilized the cell voltage. The oxygen partial pressure decreased nearly to 0 kPa in the blocked channel. With a water blockage in a channel, the oxygen partial pressures in the adjacent channels were lowered due to an extra demand of oxygen consumption. When the number of the blocked channels increased, the oxygen partial pressure in the unblocked channels became much lowered. When the water blockages disappeared, the oxygen partial pressures quickly returned to the values before plugging. The influence of the cross flows of air through the gas diffusion layers in straight channels was much smaller than that in serpentine flow channels.

Nagase, Katsuya; Suga, Takeo; Nagumo, Yuzo; Uchida, Makoto; Inukai, Junji; Nishide, Hiroyuki; Watanabe, Masahiro

2015-01-01

296

Ion-water and ion-polypeptide correlations in a gramicidin-like channel. A molecular dynamics study.  

PubMed Central

This work describes a molecular dynamics study of ion-water and ion-polypeptide correlation in a model gramicidin-like channel (the polyglycine analogue) based upon interaction between polarizable, multipolar groups. The model suggests that the vicinity of the dimer junction and of the ethanolamine tail are regions of unusual flexibility. Cs+ binds weakly in the mouth of the channel: there it coordinates five water molecules and the #11CO group with which it interacts strongly and is ideally aligned. In the channel interior it is generally pentacoordinate; at the dimer junction, because of increased channel flexibility, it again becomes essentially hexacoordinate. The ion is also strongly coupled to the #13 CO but not to either #9 or #15, consistent with 13C NMR data. Water in the channel interior is strikingly different from bulk water; it has a much lower mean dipole moment. This correlates with our observation (which differs from that of previous studies) that water-water angular correlations do not persist within the channel, a result independent of ion occupancy or ionic polarity. In agreement with streaming potential measurements, there are seven single file water molecules associated with Cs+ permeation; one of these is always in direct contact with bulk water. At the mouth of an ion-free channel, there is a pattern of dipole moment alteration among the polar groups. Due to differential interaction with water, exo-carbonyls have unusually large dipole moments whereas those of the endo-carbonyls are low. The computed potential of mean force for CS+ translocation is qualitatively reasonable. However, it only exhibits a weakly articulated binding site and it does not quantitatively account for channel energetics. Correction for membrane polarization reduces, but does not eliminate, these problems. PMID:1705448

Jordan, P C

1990-01-01

297

Denaturation of proteins in methanol/water mixtures.  

PubMed

The solvophobic theory developed earlier by Sinanoglu introducing the use of molecular surface areas and microthermodynamic surface and interfacial tensions at molecular dimensions is applied to the interpretation of calorimetric data on denaturation of lysozyme in a wide range of methanol/water mixtures. The experimental values of standard unitary free energies of denaturation correlate well with our predictions. The molecular surface area change of the protein upon denaturation is evaluated using the solvophobic theory. The maximum in the stability of the native form of the protein is predicted to occur at 8% (v/v) methanol. This is found to be in agreement with the experimental results. PMID:17007768

Fernández, A; Sinanoglu, O

1985-03-01

298

Numerical investigation of interfacial transport resistance due to water droplets in proton exchange membrane fuel cell air channels  

E-print Network

Nusselt number a b s t r a c t Oxygen transport resistance at the air flow channel and gas diffusion layerNumerical investigation of interfacial transport resistance due to water droplets in proton exchange membrane fuel cell air channels Mustafa Koz a , Satish G. Kandlikar a,b,* a Microsystems

Kandlikar, Satish

299

76 FR 47529 - Port Access Route Study: In the Waters of Montauk Channel and Block Island Sound  

Federal Register 2010, 2011, 2012, 2013, 2014

...USCG-2005-21650] Port Access Route Study: In the Waters of Montauk Channel and...Notice of availability of Preliminary Study Recommendations with request for comments...announces the availability of Preliminary Study Recommendations of a Port Access...

2011-08-05

300

Evidence for the Existence of a Sulfonylurea-Receptor-Like Protein in Plants: Modulation of Stomatal Movements and Guard Cell Potassium Channels by Sulfonylureas and Potassium Channel Openers  

Microsoft Academic Search

Limitation of water loss and control of gas exchange is accomplished in plant leaves via stomatal guard cells. Stomata open in response to light when an increase in guard cell turgor is triggered by ions and water influx across the plasma membrane. Recent evidence demonstrating the existence of ATP-binding cassette proteins in plants led us to analyze the effect of

Nathalie Leonhardt; Elena Marin; Alain Vavasseur; Cyrille Forestier

1997-01-01

301

Sensitivity of polarization fluctuations to the nature of protein-water interactions: Study of biological water in four different protein-water systems  

NASA Astrophysics Data System (ADS)

Since the time of Kirkwood, observed deviations in magnitude of the dielectric constant of aqueous protein solution from that of neat water (˜80) and slower decay of polarization have been subjects of enormous interest, controversy, and debate. Most of the common proteins have large permanent dipole moments (often more than 100 D) that can influence structure and dynamics of even distant water molecules, thereby affecting collective polarization fluctuation of the solution, which in turn can significantly alter solution's dielectric constant. Therefore, distance dependence of polarization fluctuation can provide important insight into the nature of biological water. We explore these aspects by studying aqueous solutions of four different proteins of different characteristics and varying sizes, chicken villin headpiece subdomain (HP-36), immunoglobulin binding domain protein G (GB1), hen-egg white lysozyme (LYS), and Myoglobin (MYO). We simulate fairly large systems consisting of single protein molecule and 20000-30000 water molecules (varied according to the protein size), providing a concentration in the range of ˜2-3 mM. We find that the calculated dielectric constant of the system shows a noticeable increment in all the cases compared to that of neat water. Total dipole moment auto time correlation function of water ??MW(0)?MW(t)? is found to be sensitive to the nature of the protein. Surprisingly, dipole moment of the protein and total dipole moment of the water molecules are found to be only weakly coupled. Shellwise decomposition of water molecules around protein reveals higher density of first layer compared to the succeeding ones. We also calculate heuristic effective dielectric constant of successive layers and find that the layer adjacent to protein has much lower value (˜50). However, progressive layers exhibit successive increment of dielectric constant, finally reaching a value close to that of bulk 4-5 layers away. We also calculate shellwise orientational correlation function and tetrahedral order parameter to understand the local dynamics and structural re-arrangement of water. Theoretical analysis providing simple method for calculation of shellwise local dielectric constant and implication of these findings are elaborately discussed in the present work.

Ghosh, Rikhia; Banerjee, Saikat; Hazra, Milan; Roy, Susmita; Bagchi, Biman

2014-12-01

302

Sensitivity of polarization fluctuations to the nature of protein-water interactions: Study of biological water in four different protein-water systems.  

PubMed

Since the time of Kirkwood, observed deviations in magnitude of the dielectric constant of aqueous protein solution from that of neat water (?80) and slower decay of polarization have been subjects of enormous interest, controversy, and debate. Most of the common proteins have large permanent dipole moments (often more than 100 D) that can influence structure and dynamics of even distant water molecules, thereby affecting collective polarization fluctuation of the solution, which in turn can significantly alter solution's dielectric constant. Therefore, distance dependence of polarization fluctuation can provide important insight into the nature of biological water. We explore these aspects by studying aqueous solutions of four different proteins of different characteristics and varying sizes, chicken villin headpiece subdomain (HP-36), immunoglobulin binding domain protein G (GB1), hen-egg white lysozyme (LYS), and Myoglobin (MYO). We simulate fairly large systems consisting of single protein molecule and 20000-30000 water molecules (varied according to the protein size), providing a concentration in the range of ?2-3 mM. We find that the calculated dielectric constant of the system shows a noticeable increment in all the cases compared to that of neat water. Total dipole moment auto time correlation function of water ??MW(0)?MW(t)? is found to be sensitive to the nature of the protein. Surprisingly, dipole moment of the protein and total dipole moment of the water molecules are found to be only weakly coupled. Shellwise decomposition of water molecules around protein reveals higher density of first layer compared to the succeeding ones. We also calculate heuristic effective dielectric constant of successive layers and find that the layer adjacent to protein has much lower value (?50). However, progressive layers exhibit successive increment of dielectric constant, finally reaching a value close to that of bulk 4-5 layers away. We also calculate shellwise orientational correlation function and tetrahedral order parameter to understand the local dynamics and structural re-arrangement of water. Theoretical analysis providing simple method for calculation of shellwise local dielectric constant and implication of these findings are elaborately discussed in the present work. PMID:25494802

Ghosh, Rikhia; Banerjee, Saikat; Hazra, Milan; Roy, Susmita; Bagchi, Biman

2014-12-14

303

Thromboxane A2 receptor and MaxiK-channel intimate interaction supports channel trans-inhibition independent of G-protein activation  

PubMed Central

Large conductance voltage- and calcium-activated potassium channels (MaxiK, BKCa) are well known for sustaining cerebral and coronary arterial tone and for their linkage to vasodilator ?-adrenergic receptors. However, how MaxiK channels are linked to counterbalancing vasoconstrictor receptors is unknown. Here, we show that vasopressive thromboxane A2 receptors (TP) can intimately couple with and inhibit MaxiK channels. Activation of the receptor with its agonist trans-inhibits MaxiK independently of G-protein activation. This unconventional mechanism is supported by independent lines of evidence: (i) inhibition of MaxiK current by thromboxane A2 mimetic, U46619, occurs even when G-protein activity is suppressed; (ii) MaxiK and TP physically associate and display a high degree of proximity; and (iii) Förster resonance energy transfer occurs between fluorescently labeled MaxiK and TP, supporting a direct interaction. The molecular mechanism of MaxiK–TP intimate interaction involves the receptor's first intracellular loop and C terminus, and it entails the voltage-sensing conduction cassette of MaxiK channel. Further, physiological evidence of MaxiK–TP physical interaction is given in human coronaries and rat aorta, and by confirming TP role (with antagonist SQ29,548) in the U46619-induced MaxiK inhibition in human coronaries. We propose that vasoconstrictor TP receptor and MaxiK-channel direct interaction facilitates G-protein–independent TP to MaxiK trans-inhibition, which would promote vasoconstriction. PMID:20959415

Tanaka, Yoshio; Alioua, Abderrahmane; Wu, Yong; Lu, Rong; Kundu, Pallob; Sanchez-Pastor, Enrique; Marijic, Jure; Stefani, Enrico; Toro, Ligia

2010-01-01

304

A trace component of ginseng that inhibits Ca2+ channels through a pertussis toxin-sensitive G protein.  

PubMed Central

A crude extract from ginseng root inhibits high-threshold, voltage-dependent Ca2+ channels through an unknown receptor linked to a pertussis toxin-sensitive G protein. We now have found the particular compound that seems responsible for the effect: it is a saponin, called ginsenoside Rf (Rf), that is present in only trace amounts within ginseng. At saturating concentrations, Rf rapidly and reversibly inhibits N-type, and other high-threshold, Ca2+ channels in rat sensory neurons to the same degree as a maximal dose of opioids. The effect is dose-dependent (half-maximal inhibition: 40 microM) and it is virtually eliminated by pretreatment of the neurons with pertussis toxin, an inhibitor of G(o) and Gi GTP-binding proteins. Other ginseng saponins--ginsenosides Rb1, Rc, Re, and Rg1--caused relatively little inhibition of Ca2+ channels, and lipophilic components of ginseng root had no effect. Antagonists of a variety of neurotransmitter receptors that inhibit Ca2+ channels fail to alter the effect of Rf, raising the possibility that Rf acts through another G protein-linked receptor. Rf also inhibits Ca2+ channels in the hybrid F-11 cell line, which might, therefore, be useful for molecular characterization of the putative receptor for Rf. Because it is not a peptide and it shares important cellular and molecular targets with opioids, Rf might be useful in itself or as a template for designing additional modulators of neuronal Ca2+ channels. PMID:7568008

Nah, S Y; Park, H J; McCleskey, E W

1995-01-01

305

GFP-mut2 Proteins in Trehalose-Water Matrixes: Spatially Heterogeneous Protein-Water-Sugar Structures  

PubMed Central

We report investigations on the properties of nanoenvironments around single-GFP-mut2 proteins in trehalose-water matrixes. Single-GFPmut2 molecules embedded in thin trehalose-water films were characterized in terms of their fluorescence brightness, bleaching dynamics, excited state lifetime, and fluorescence polarization. For each property, sets of ?100–150 single molecules have been investigated as a function of trehalose content and hydration. Three distinct and interconverting families of proteins have been found which differ widely in terms of bleaching dynamics, brightness, and fluorescence polarization, whose relative populations sizably depend on sample hydration. The reported results evidence the simultaneous presence of different protein-trehalose-water nanostructures whose rigidity increases by lowering the sample hydration. Such spatial inhomogeneity is in line with the well-known heterogeneous dynamics in supercooled fluids and in nonsolid carbohydrate glasses and gives a pictorial representation of the sharp, sudden reorganization of the above structures after uptake ? release of water molecules. PMID:17416616

D'Alfonso, Laura; Collini, Maddalena; Cannone, Fabio; Chirico, Giuseppe; Campanini, Barbara; Cottone, Grazia; Cordone, Lorenzo

2007-01-01

306

Ground-water and surface-water-level data at Rindge Tract on the Stockton Deep Water Ship Channel, San Joaquin County, California, 1983-84  

USGS Publications Warehouse

The Sacramento-San Joaquin Delta is formed at the confluence of the two major rivers that drain the Central Valley of California. The Sacramento and San Joaquin Rivers and many interconnecting sloughs meandered back and forth across the tidelands, frequently overflowing their banks. Approximately 1 ,100 miles of levees were constructed to form about 60 tracts or islands that protect these lands from periodic flooding. The levees were constructed of sand, silt, and peat dredged from the channel bottom and are subject to erosion and failure. Owing to compaction, oxidation of the peat, and other related conditions, the islands are subsiding at rates of up to 0.25 ft/yr. The altitude of the land surface of the islands is often below sea level and below the surface water level in the channel. This condition causes stresses that may contribute to high groundwater levels and levee failure. The U.S. Army Corps of Engineers requested that the U.S. Geological Survey install and maintain continuous recorders to monitor water levels in each of four wells. Monitoring which began in July 1983 also provided data to show the relation between surface water levels in the channel and groundwater levels in the wells. Dredging began in the area of the Rindge Tract site during the latter part of July 1983. Water levels in all four wells dropped 1.5 to 2 ft between September 1983 and September 1984 and continued to drop thorough December 1984. (Lantz-PTT)

Pierce, Michael J.; Johnson, Karen L.

1986-01-01

307

Characterization of vegetative storage protein (VSP) and low molecular proteins induced by water deficit in stolon of white clover.  

PubMed

In stolon of white clover (Trifolium repens L.), the 17.3 kDa protein has been newly identified as a vegetative storage protein (VSP) which has preponderant roles in N accumulation and mobilization to sustain growth when capacity of N uptake is strongly reduced. To characterize the water deficit effect on this protein, the kinetic pattern of soluble protein, SDS-PAGE, Western blotting, and proteomic analysis was studied in the stolon of white clover during 28 days of water-deficit. Water deficit led to decrease protein concentration. SDS-PAGE revealed that two major proteins of 17.3 and 16 kDa were accumulated to high level in response to water stress. These proteins cross-reacted positively with antibodies raised against the 17.3 kDa VSP, a protein which shared biochemical features with stress proteins implied in dehydration tolerance. Using two-dimensional electrophoresis (2-DE) gel and matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF-MS) analysis, it was demonstrated that 19.5 and 17.3 kDa protein spots were up-regulated by water stress, and both spots were identical to nucleoside diphosphate kinase (NDPK) and lipid transfer proteins (LTPs), respectively. These results suggest that low molecular proteins induced by water-deficit in the stolon of white clover act as an alternative N reserves or play significant roles in plant protection against water-deficit stress. PMID:24299955

Lee, Bok-Rye; Lee, Dong-Gi; Avice, Jean-Christophe; Kim, Tae-Hwan

2014-01-01

308

Recovery from Slow Inactivation in K+ Channels is Controlled by Water Molecules  

PubMed Central

The bacterial K+ channel KcsA can be used to help elucidate questions about channel inactivation and recovery at the atomic level. Although KcsA contains only a pore domain, without voltage-sensing machinery, it has the structural elements necessary for ion conduction, activation and inactivation1–7. Available X-ray structures of KcsA provide an atomic view of the four most important functional states in which the intracellular gate is either closed or open, and the selectivity filter is either conductive or inactivated8–10. Application of a specific stimulus opens the intracellular gate of a K+ channel (activation), yielding a transient period of ion conduction until the selectivity filter spontaneously undergoes a conformational change toward a non-conductive state (inactivation). Removal of the stimulus closes the gate and allows the selectivity filter to interconvert back to its conductive conformation (recovery). In this manuscript, a series of long molecular dynamics (MD) simulations reveal how the selectivity filter is sterically locked in the inactive conformation by buried water molecules bound behind the selectivity filter. Potential of mean force calculations show how the recovery process is affected by the buried waters and the rebinding of an external K+ ion. A kinetic model deduced from the simulations shows how releasing the buried waters can stretch the timescale of recovery to seconds. This leads to the prediction that reducing the occupancy of the buried waters by imposing a high osmotic stress should accelerate the rate of recovery, which was verified experimentally by measuring the recovery rate in the presence of 2M sucrose. PMID:23892782

Ostmeyer, Jared; Chakrapani, Sudha; Pan, Albert C.; Perozo, Eduardo; Roux, Benoît

2013-01-01

309

Crystal Structure of the Mammalian GIRK2 KplusChannel and Gating Regulation by G Proteins PIP2 and Sodium  

SciTech Connect

G protein-gated K{sup +} channels (Kir3.1--Kir3.4) control electrical excitability in many different cells. Among their functions relevant to human physiology and disease, they regulate the heart rate and govern a wide range of neuronal activities. Here, we present the first crystal structures of a G protein-gated K{sup +} channel. By comparing the wild-type structure to that of a constitutively active mutant, we identify a global conformational change through which G proteins could open a G loop gate in the cytoplasmic domain. The structures of both channels in the absence and presence of PIP{sub 2} suggest that G proteins open only the G loop gate in the absence of PIP{sub 2}, but in the presence of PIP{sub 2} the G loop gate and a second inner helix gate become coupled, so that both gates open. We also identify a strategically located Na{sup +} ion-binding site, which would allow intracellular Na{sup +} to modulate GIRK channel activity. These data provide a structural basis for understanding multiligand regulation of GIRK channel gating.

M Whorton; R MacKinnon

2011-12-31

310

Enhanced water and cryoprotectant permeability of porcine oocytes after artificial expression of human and zebrafish aquaporin-3 channels.  

PubMed

One of the major obstacles for the vitrification of mature porcine oocytes with ethylene glycol is their low permeability to this cryoprotectant, which results in osmotic stress-induced cell damage and low survival. Pig blastocysts, on the other hand, show enhanced water and cryoprotectant permeability, which has been related to the transcriptional activation of aquaporin-3 (AQP3) channels at this stage of development. In this study, we asked if expression of cRNAs encoding two aquaglyceroporins, human AQP3 (hAQP3) or the zebrafish Aqp3b-T85A mutant, in porcine oocytes can increase their permeability. Microinjection of germinal-vesicle-stage oocytes with enhanced green fluorescent protein (EGFP) or AQP3 cRNAs resulted in the expression of the corresponding proteins in ?26% of the metaphase-II stage oocytes at 40-44?hr of in vitro culture; co-injection of EGFP cRNA appeared to be a suitable marker for oocyte selection since all EGFP-positive oocytes also expressed the corresponding aquaporin. Using this method, we found that mature oocytes co-expressing EGFP and hAQP3 or EGFP and Aqp3b-T85A showed approximately a twofold increase of the hydraulic conductivity (Lp ) with respect non-injected or EGFP alone-injected oocytes in a 0.43?M sucrose or 1.3?M ethylene glycol solution, whereas the ethylene glycol permeability (PEG ) of EGFP?+?hAQP3 and EGFP?+?Aqp3b-T85A oocytes was 6.7- and 12-fold higher, respectively, than control oocytes. These data demonstrate that the artificial expression of aquaglyceroporins in porcine metaphase-II oocytes improves their permeability, and that the zebrafish Aqp3b-T85A mutant is more efficient than the human channel at increasing the oocyte permeability to ethylene glycol. PMID:24488947

Morató, Roser; Chauvigné, François; Novo, Sergi; Bonet, Sergi; Cerdà, Joan

2014-05-01

311

Early Fluid and Protein Shifts in Men During Water Immersion  

NASA Technical Reports Server (NTRS)

High precision blood and plasma densitometry was used to measure transvascular fluid shifts during water immersion to the neck. Six men (28-49 years) undertook 30 min of standing immersion in water at 35.0 +/- 0.2 C; immersion was preceded by 30 min control standing in air at 28 +/- 1 C. Blood was sampled from an antecubital catheter for determination of Blood Density (BD), Plasma Density (PD), Haematocrit (Ht), total Plasma Protein Concentration (PPC), and Plasma Albumin Concentration (PAC). Compared to control, significant decreases (p less than 0.01) in all these measures were observed after 20 min immersion. At 30 min, plasma volume had increased by 11.0 +/- 2.8%; the average density of the fluid shifted from extravascular fluid into the vascular compartment was 1006.3 g/l; albumin moved with the fluid and its albumin concentration was about one-third of the plasma protein concentration during early immersion. These calculations are based on the assumption that the F-cell ratio remained unchanged. No changes in erythrocyte water content during immersion were found. Thus, immersion-induced haemodilution is probably accompanied by protein (mainly albumin) augmentation which accompanies the intra-vascular fluid shift.

Hinghofer-Szalkay, H.; Harrison, M. H.; Greenleaf, J. E.

1987-01-01

312

Inhibition of protein synthesis in loblolly pine hypocotyls by mannitol-induced water stress.  

PubMed

The relationship between mannitol-induced water stress and protein synthesis was investigated in hypocotyl slices of loblolly pine (Pinus taeda L.). Mannitol-induced water stress inhibited the incorporation of L-[(35)S]methionine into protein. As the water potential decreased, incorporation of label into protein decreased in both the soluble- and membrane-protein fractions. There were no significant differences in response to water stress among seed sources from four different geographical regions. PMID:14972832

Hulbert, C; Funkhouser, E A; Soltes, E J; Newton, R J

1988-03-01

313

Channel Stability and Water Quality of the Alagnak River, Southwestern Alaska  

USGS Publications Warehouse

The Alagnak River, a National Wild River located in southwestern Alaska, drains an area of 3,600 square kilometers and is used for recreational and subsistence activities, primarily angling, camping, rafting, and hunting by visitors and seasonal residents, and for commercial guiding by several lodges. Increases in visitor use in the 1990s included an increase in the use of high-horsepower motorboats on the river, primarily for angling, and raised concerns regarding human impacts on water quality. Downstream from its confluence with the Nonvianuk River at river kilometer (RK) 93, the Alagnak River is formed in glacial drift and outwash with a single, low bedrock outcrop. Analysis of aerial photography from 1951, 1982, and 2001 shows that the river's multiple channels from RK 57 to 93 have been relatively stable. In contrast, long reaches of multiple channels from RK 35 to 57 changed substantially between 1951 and 1982, creating a new complex of channels. Downstream from RK 35, channel changes in the past 50 years consist largely of minor meander migration. Analysis of water samples collected during this study at RK 21, 46, and 93 and in the Alagnak and Nonvianuk Rivers at the outlets of the lakes that form their source shows that the Alagnak River is a nutrient-poor, calcium-bicarbonate water with low suspended-sediment concentrations. Water chemistry changes little over time or in a downstream direction. Weak patterns over time include high late May/early June concentrations of some nutrients, carbon, and iron. Weak patterns over distance include downstream increases in iron, manganese, and phosphorous. No pervasive human impacts on Alagnak River water chemistry were detected. Local effects that could be diluted within a kilometer downstream of the source were not detectable by this study. Data collected at three continuously recording wake gaging stations at RK 21, 46, and 93 showed that 1999-2000 motorboat use was heaviest in the lower reaches of the river, moderate in the middle reaches, and very light in the upper reaches. Maximum boat use was 137, 40, and 4 wakes per day at RK 21, 46, and 93, respectively. The mean height of the maximum wave generated in each wake was about 0.15 m (meters) at all three gaging stations. Bank erosion monitoring at 14 sites between RK 21 and 93 quantified erosion rates ranging from 0 to 1.1 m/yr (meters per year). Erodibility (based on grain-size analysis) increases in a downstream direction, as do measured erosion rates. Alagnak River banks are noncohesive and erode by grain-by-grain removal of sediment in an alternating pattern of water-driven erosion and gravitydriven erosion. Periodic surveys at bank erosion monitoring sites detected the development of a shallow underwater shelf formed by the action of wind waves and boat wakes at several sites. This shelf contains sediment eroded from the bank and redeposited adjacent to the bank; the shelf reformed as water levels changed but maintained the same wave-generated form throughout much of the season. Measurements of bank erosion processes, particularly the development of a wave-generated shelf, and visual observations suggest that boat wakes increase bank erosion rates, especially at high, exposed banks. Analysis of aerial photography and other assessments of bank erosion processes indicate that this increase in erosion rates has not altered the mechanisms of channel change, which in the past 50 years have included complex, compound channel changes and meander migration.

Curran, Janet H.

2003-01-01

314

Water and sediment budgets for the stormwater-drainage channel at the Navy Ships Parts Control Center near Mechanicsburg, Pennsylvania, water year 1993  

USGS Publications Warehouse

The Navy Ships Parts Control Center near Mechanicsburg, Pa., occupies an area of 824 acres, of which 358 are covered by impervious surfaces. Most of the impervious area is drained by stormwater systems that discharge to an open channel that extends about 7,900 feet from its headwaters to its confluence with Trindle Spring Run. The channel drains an area of 992 acres, of which 435 are covered by impervious surfaces. The entire area of the Center including the stormwater-drainage channel is situated in karst terrain. Parts of the drainage channel contain large sinkholes and most of the storm runoff that enters the channel drains to the sinkholes. From 1992 to 1994, the U.S. Geological Survey, in cooperation with the Department of the Navy, conducted a detailed study of water and sediment flows in the stormwater-drainage channel. The purpose of this study was to quantify the discharge of stormwater and suspended sediment to the ground-water system, by way of sinkholes, and to Trindle Spring Run. From October 1, 1992, to September 30, 1993, the data-collection period for the study, discharge and suspended-sediment concentrations were measured at three sites along the drainage channel. During the period, water inflow to the channel totaled 679 acre-feet and outflow to Trindle Spring Run totaled 131 acre-feet. Water loss to sinkholes in the drainage channel totaled 548 acre-feet or 81 percent of inflow. Total sediment inflow to the drainage channel was 97 tons, outflow to Trindle Spring Run was 22 tons, sediment loss to sinkholes was 63 tons, and the residual 12 tons of sediment was deposited in the channel. The effect of filling the sinkholes on flooding was estimated through use of a step-backwater model. The model was used to simulate undampened water-surface elevations that would result from the maximum instantaneous discharge recorded during October 1992-September 1993. The model is constrained by uncertainty in the values of the channel-roughness parameter. Analysis of the model results indicates that during high flows, inflow to sinkholes results in a moderate reduction in discharge and water-surface elevations in the drainage channel. This analysis shows that filling the sinkholes will result in increased frequency and magnitude of flooding in downstream parts of the drainage channel and increased discharge of storm runoff and suspended sediment to Trindle Spring Run.

Reed, L.A.; Durlin, R.R.; Bender, J.K.

1994-01-01

315

Developmental changes in the cochlear hair cell mechanotransducer channel and their regulation by transmembrane channel–like proteins  

PubMed Central

Vibration of the stereociliary bundles activates calcium-permeable mechanotransducer (MT) channels to initiate sound detection in cochlear hair cells. Different regions of the cochlea respond preferentially to different acoustic frequencies, with variation in the unitary conductance of the MT channels contributing to this tonotopic organization. Although the molecular identity of the MT channel remains uncertain, two members of the transmembrane channel–like family, Tmc1 and Tmc2, are crucial to hair cell mechanotransduction. We measured MT channel current amplitude and Ca2+ permeability along the cochlea’s longitudinal (tonotopic) axis during postnatal development of wild-type mice and mice lacking Tmc1 (Tmc1?/?) or Tmc2 (Tmc2?/?). In wild-type mice older than postnatal day (P) 4, MT current amplitude increased ?1.5-fold from cochlear apex to base in outer hair cells (OHCs) but showed little change in inner hair cells (IHCs), a pattern apparent in mutant mice during the first postnatal week. After P7, the OHC MT current in Tmc1?/? (dn) mice declined to zero, consistent with their deafness phenotype. In wild-type mice before P6, the relative Ca2+ permeability, PCa, of the OHC MT channel decreased from cochlear apex to base. This gradient in PCa was not apparent in IHCs and disappeared after P7 in OHCs. In Tmc1?/? mice, PCa in basal OHCs was larger than that in wild-type mice (to equal that of apical OHCs), whereas in Tmc2?/?, PCa in apical and basal OHCs and IHCs was decreased compared with that in wild-type mice. We postulate that differences in Ca2+ permeability reflect different subunit compositions of the MT channel determined by expression of Tmc1 and Tmc2, with the latter conferring higher PCa in IHCs and immature apical OHCs. Changes in PCa with maturation are consistent with a developmental decrease in abundance of Tmc2 in OHCs but not in IHCs. PMID:23277480

Kim, Kyunghee X.

2013-01-01

316

Bordetella pertussis major outer membrane porin protein forms small, anion-selective channels in lipid bilayer membranes.  

PubMed Central

The major outer membrane protein of molecular weight 40,000 (the 40K protein) of a virulent isolate of Bordetella pertussis was purified to apparent homogeneity. The purified protein formed an oligomer band (of apparent molecular weight 90,000) on sodium dodecyl sulfate-polyacrylamide gels after solubilization at low temperatures. The porin function of this protein was characterized by the black lipid bilayer method. The 40K protein formed channels smaller than all other constitutive major outer membrane porins studied to date. The average single-channel conductance in 1 M KCl was 0.56 nS. This was less than a third of the conductance previously observed for Escherichia coli porins. Zero-current potential measurements made of the porin to determine its ion selectivity revealed the porin to be more than 100-fold selective for anions over cations. The single-channel conductance was measured as a function of salt concentration. The data could be fitted to a Lineweaver-Burk plot suggesting an anion binding site with a Kd of 1.17 M Cl- and a maximum possible conductance through the channel of 1.28 nS. Images PMID:2420780

Armstrong, S K; Parr, T R; Parker, C D; Hancock, R E

1986-01-01

317

Evidence for the formation of a heptameric ion channel complex by the hepatitis C virus p7 protein in vitro.  

PubMed

The p7 protein of hepatitis C virus functions as an ion channel both in vitro and in cell-based assays and is inhibited by amantadine, long alkyl chain imino-sugar derivatives, and amiloride compounds. Future drug design will be greatly aided by information on the stoichiometry and high resolution structure of p7 ion channel complexes. Here, we have refined a bacterial expression system for p7 based on a glutathione S-transferase fusion methodology that circumvents the inherent problems of hydrophobic protein purification and the limitations of chemical synthesis. Rotational averaging and harmonic analysis of transmission electron micrographs of glutathione S-transferase-FLAG-p7 fusion proteins in liposomes revealed a heptameric stoichiometry. The oligomerization of p7 protein was then confirmed by SDS-PAGE and mass spectrometry analysis of pure, concentrated FLAG-p7. The same protein was also confirmed to function as an ion channel in suspended lipid bilayers and was inhibited by amantadine. These data validate this system as a means of generating high resolution structural information on the p7 ion channel complex. PMID:17032656

Clarke, Dean; Griffin, Stephen; Beales, Lucy; Gelais, Corine St; Burgess, Stan; Harris, Mark; Rowlands, David

2006-12-01

318

Influenza matrix protein 2 alters CFTR expression and function through its ion channel activity  

PubMed Central

The human cystic fibrosis transmembrane conductance regulator (CFTR) is a cyclic AMP-activated chloride (Cl?) channel in the lung epithelium that helps regulate the thickness and composition of the lung epithelial lining fluid. We investigated whether influenza M2 protein, a pH-activated proton (H+) channel that traffics to the plasma membrane of infected cells, altered CFTR expression and function. M2 decreased CFTR activity in 1) Xenopus oocytes injected with human CFTR, 2) epithelial cells (HEK-293) stably transfected with CFTR, and 3) human bronchial epithelial cells (16HBE14o?) expressing native CFTR. This inhibition was partially reversed by an inhibitor of the ubiquitin-activating enzyme E1. Next we investigated whether the M2 inhibition of CFTR activity was due to an increase of secretory organelle pH by M2. Incubation of Xenopus oocytes expressing CFTR with ammonium chloride or concanamycin A, two agents that alkalinize the secretory pathway, inhibited CFTR activity in a dose-dependent manner. Treatment of M2- and CFTR-expressing oocytes with the M2 ion channel inhibitor amantadine prevented the loss in CFTR expression and activity; in addition, M2 mutants, lacking the ability to transport H+, did not alter CFTR activity in Xenopus oocytes and HEK cells. Expression of an M2 mutant retained in the endoplasmic reticulum also failed to alter CFTR activity. In summary, our data show that M2 decreases CFTR activity by increasing secretory organelle pH, which targets CFTR for destruction by the ubiquitin system. Alteration of CFTR activity has important consequences for fluid regulation and may potentially modify the immune response to viral infection. PMID:23457187

Londino, James D.; Lazrak, Ahmed; Jurkuvenaite, Asta; Collawn, James F.; Noah, James W.

2013-01-01

319

Protein kinase C modulation of thermo-sensitive transient receptor potential channels: Implications for pain signaling  

PubMed Central

A variety of molecules are reported to be involved in chronic pain. This review outlines the specifics of protein kinase C (PKC), its isoforms and their role in modulating thermo-sensitive transient receptor potential (TRP) channels TRPV1-4, TRPM8, and TRPA1. Anatomically, PKC and thermo-sensitive TRPs are co-expressed in cell bodies of nociceptive dorsal root ganglion (DRG) neurons, which are used as physiological correlates of peripheral and central projections involved in pain transmission. In the past decade, modulation of painful heat-sensitive TRPV1 by PKC has received the most attention. Recently, PKC modulation of other newly discovered thermo-sensitive pain-mediating TRPs has come into focus. Such modulation may occur under conditions of chronic pain resulting from nerve damage or inflammation. Since thermo-TRPs are primary detectors of acute pain stimuli, their modulation by PKC can severely alter their function, resulting in chronic pain. Comprehensive knowledge of pain signaling involving interaction of specific isoforms of PKC with specific thermo-sensitive TRP channels is incomplete. Such information is necessary to dissect out modality specific mechanisms to better manage the complex polymodal nature of chronic pain. This review is an attempt to update the readers on current knowledge of PKC modulation of thermo-sensitive TRPs and highlight implications of such modulation for pain signaling PMID:22470230

Mandadi, Sravan; Armati, Patricia J.; Roufogalis, Basil D.

2011-01-01

320

Identification of G protein-coupled, inward rectifier potassium channel gene products from the rat anterior pituitary gland.  

PubMed

Dopamine (DA) is a physiological regulator of PRL secretion, exerting tonic inhibitory control. DA activates an inward rectifier K(+) (IRK) channel in rat lactotropes, causing membrane hyperpolarization and inhibition of Ca(2+)-dependent action potentials. Both the activation of this effector K(+) channel and the inhibition of PRL release are mediated by D(2)-type receptor activation and pertussis toxin- sensitive G proteins. To study the molecular basis of this physiologically relevant channel, a homology-based PCR approach was employed to identify members of the IRK channel family expressed in the anterior pituitary gland. Nondegenerate primers corresponding to regions specific for IRK channels known to be G protein activated (GIRKs; gene subfamily Kir 3.0) were synthesized and used in the PCR with reverse transcribed female rat anterior pituitary messenger RNA as the template. PCR products of predicted sizes for Kir 3.1, 3.2, and 3.4 were consistently observed by ethidium bromide staining after 16 amplification cycles. The identities of the products were confirmed by subcloning and sequencing. Expression of each of these gene products in anterior pituitary was confirmed by Northern blot analysis. Functional analysis of the GIRK proteins was performed in the heterologous expression system, Xenopus laevis oocytes. Macroscopic K(+) currents were examined in oocytes injected with different combinations of Kir 3.0 complementary RNA (cRNA) and G protein subunit (beta(1)gamma(2)) cRNA. The current-voltage relationships demonstrated strong inward rectification for each individual and pairwise combination of GIRK channel subunits. Oocytes coinjected with any pair of GIRK subunit cRNA exhibited significantly larger inward K(+) currents than oocytes injected with only one GIRK channel subtype. Ligand-dependent activation of only one of the GIRK combinations (GIRK1 and GIRK4) was observed when channel subunits were coexpressed with the D(2) receptor in Xenopus oocytes. Dose-response data fit to a Michaelis-Menten equation gave an apparent K(d) similar to that for DA binding in anterior pituitary tissue. GIRK1 and GIRK4 proteins were coimmunoprecipitated from anterior pituitary lysates, confirming the presence of native GIRK1/GIRK4 oligomers in this tissue. These data indicate that GIRK1 and GIRK4 are excellent candidate subunits for the D(2)-activated, G protein-gated channel in pituitary lactotropes, where they play a critical role in excitation-secretion coupling. PMID:11416001

Gregerson, K A; Flagg, T P; O'Neill, T J; Anderson, M; Lauring, O; Horel, J S; Welling, P A

2001-07-01

321

[Functionally-relevant conformational dynamics of water-soluble proteins].  

PubMed

A study is reported of the functional-relevant dynamics of three typical water-soluble proteins: Calmodulin, Src-tyrosine kinase as well as repressor of Trp operon. Application of the state-of-art methods of structural bioinformatics allowed to identify dynamics seen in the X-ray structures of the investigated proteins associated with their specific biological functions. In addition, Normal Mode analysis technique revealed the most probable directions of the functionally-relevant motions for all that proteins were also predicted. Importantly, overall type of the motions observed on the lowest-frequency modes was very similar to the motions seen from the analysis of the X-ray data of the examined macromolecules. Thereby it was shown that the large-scale as well as local conformational motions of the proteins might be predetermined already at the level of their tertiary structures. In particular, the determining factor might be the specific fold of the alpha-helixes. Thus functionally-relevant in vivo dynamics of the investigated proteins might be evolutionally formed by means of natural selection at the level of the spatial topology. PMID:23705506

Novikov, G V; Sivozhelezov, V S; Sha?tan, K V

2013-01-01

322

Estimating seepage flux from ephemeral stream channels using surface water and groundwater level data  

NASA Astrophysics Data System (ADS)

flux from ephemeral streams can be an important component of the water balance in arid and semiarid regions. An emerging technique for quantifying this flux involves the measurement and simulation of a flood wave as it moves along an initially dry channel. This study investigates the usefulness of including surface water and groundwater data to improve model calibration when using this technique. We trialed this approach using a controlled flow event along a 1387 m reach of artificial stream channel. Observations were then simulated using a numerical model that combines the diffusion-wave approximation of the Saint-Vénant equations for streamflow routing, with Philip's infiltration equation and the groundwater flow equation. Model estimates of seepage flux for the upstream segments of the study reach, where streambed hydraulic conductivities were approximately 101 m d-1, were on the order of 10-4 m3 d-1 m-2. In the downstream segments, streambed hydraulic conductivities were generally much lower but highly variable (˜10-3 to 10-7 m d-1). A Latin Hypercube Monte Carlo sensitivity analysis showed that the flood front timing, surface water stage, groundwater heads, and the predicted streamflow seepage were most influenced by specific yield. Furthermore, inclusion of groundwater data resulted in a higher estimate of total seepage estimates than if the flood front timing were used alone.

Noorduijn, Saskia L.; Shanafield, Margaret; Trigg, Mark A.; Harrington, Glenn A.; Cook, Peter G.; Peeters, L.

2014-02-01

323

Regulation of the Membrane Insertion and Conductance Activity of the Metamorphic Chloride Intracellular Channel Protein CLIC1 by Cholesterol  

PubMed Central

The Chloride Intracellular ion channel protein CLIC1 has the ability to spontaneously insert into lipid membranes from a soluble, globular state. The precise mechanism of how this occurs and what regulates this insertion is still largely unknown, although factors such as pH and redox environment are known contributors. In the current study, we demonstrate that the presence and concentration of cholesterol in the membrane regulates the spontaneous insertion of CLIC1 into the membrane as well as its ion channel activity. The study employed pressure versus area change measurements of Langmuir lipid monolayer films; and impedance spectroscopy measurements using tethered bilayer membranes to monitor membrane conductance during and following the addition of CLIC1 protein. The observed cholesterol dependent behaviour of CLIC1 is highly reminiscent of the cholesterol-dependent-cytolysin family of bacterial pore-forming proteins, suggesting common regulatory mechanisms for spontaneous protein insertion into the membrane bilayer. PMID:23457643

Valenzuela, Stella M.; Alkhamici, Heba; Brown, Louise J.; Almond, Oscar C.; Goodchild, Sophia C.; Carne, Sonia; Curmi, Paul M. G.; Holt, Stephen A.; Cornell, Bruce A.

2013-01-01

324

Plumes and Blooms: Modeling the Case II Waters of the Santa Barbara Channel. Chapter 15  

NASA Technical Reports Server (NTRS)

The goal of the Plumes and Blooms (PnB) project is to develop, validate and apply to imagery state-of-the-art ocean color algorithms for quantifying sediment plumes and phytoplankton blooms for the Case II environment of the Santa Barbara Channel. We conduct monthly to twice-monthly transect observations across the Santa Barbara Channel to develop an algorithm development and product validation data set. The PnB field program started in the summer of 1996. At each of the 7 PnB stations, a complete verification bio-geo-optical data set is collected. Included are redundant measures of apparent optical properties (remote sensing reflectance and diffuse attenuation spectra), as well as in situ profiles of spectral absorption, beam attenuation and backscattering coefficients. Water samples are analyzed for component in vivo absorption spectra, fluorometric chlorophyll, phytoplankton pigment (by the SDSU CHORS laboratory), and inorganic nutrient concentrations. A primary goal is to use the PnB field data set to objectively tune semi-analytical models of ocean color for this site and apply them using available satellite imagery (SeaWiFS and MODIS). In support of this goal, we have also been addressing SeaWiFS ocean color and AVHRR SST imagery. We also are using the PnB data set to address time/space variability of water masses in the Santa Barbara Channel and its relationship to the 1997/1998 El Nino. However, the comparison between PnB field observations and satellite estimates of primary products has been disappointing. We find that field estimates of water-leaving radiance, L(sub wN)(lambda), correspond poorly to satellite estimates for both SeaWiFS and MODIS local area coverage imagery. We believe this is due to poor atmospheric correction due to complex mixtures of aerosol types found in these near-coastal regions. Last, we remain active in outreach activities.

Siegel, D. A.; Maritorena, S.; Nelson, N. B.

2003-01-01

325

Regulation of Cardiac ATP-sensitive Potassium Channel Surface Expression by Calcium/Calmodulin-dependent Protein Kinase II*  

PubMed Central

Cardiac ATP-sensitive potassium (KATP) channels are key sensors and effectors of the metabolic status of cardiomyocytes. Alteration in their expression impacts their effectiveness in maintaining cellular energy homeostasis and resistance to injury. We sought to determine how activation of calcium/calmodulin-dependent protein kinase II (CaMKII), a central regulator of calcium signaling, translates into reduced membrane expression and current capacity of cardiac KATP channels. We used real-time monitoring of KATP channel current density, immunohistochemistry, and biotinylation studies in isolated hearts and cardiomyocytes from wild-type and transgenic mice as well as HEK cells expressing wild-type and mutant KATP channel subunits to track the dynamics of KATP channel surface expression. Results showed that activation of CaMKII triggered dynamin-dependent internalization of KATP channels. This process required phosphorylation of threonine at 180 and 224 and an intact 330YSKF333 endocytosis motif of the KATP channel Kir6.2 pore-forming subunit. A molecular model of the ?2 subunit of the endocytosis adaptor protein, AP2, complexed with Kir6.2 predicted that ?2 docks by interaction with 330YSKF333 and Thr-180 on one and Thr-224 on the adjacent Kir6.2 subunit. Phosphorylation of Thr-180 and Thr-224 would favor interactions with the corresponding arginine- and lysine-rich loops on ?2. We concluded that calcium-dependent activation of CaMKII results in phosphorylation of Kir6.2, which promotes endocytosis of cardiac KATP channel subunits. This mechanism couples the surface expression of cardiac KATP channels with calcium signaling and reveals new targets to improve cardiac energy efficiency and stress resistance. PMID:23223335

Sierra, Ana; Zhu, Zhiyong; Sapay, Nicolas; Sharotri, Vikas; Kline, Crystal F.; Luczak, Elizabeth D.; Subbotina, Ekaterina; Sivaprasadarao, Asipu; Snyder, Peter M.; Mohler, Peter J.; Anderson, Mark E.; Vivaudou, Michel; Zingman, Leonid V.; Hodgson-Zingman, Denice M.

2013-01-01

326

Using Proteins In Unusual Environments: Water-Reduced & Water-Free Examples  

E-print Network

: Bioreactors Textile treatment Medicinal and organic syntheses Protein drugs & drug delivery Biosensors-Ac-L-Phe-OEt + amyl alcohol N-Ac-L-Phe-OAmyl + EtOH in octane NOTE ­ Reactions in water are much faster! The new view

Taralp, Alpay

327

Water-surface elevation controls on sediment-transport dynamics in channel-flat environments of intertidal flats  

NASA Astrophysics Data System (ADS)

Tidal flats are thought to have a balanced sediment budget between export through channels and import via more diffuse processes over flat boundaries. However, little has been done to understand the mechanisms of sediment transport between channels and flats that span multiple morphological and temporal scales. The muddy flats of southeastern Willapa Bay, Washington, are tidally dominated and receive relatively little direct freshwater influence. We use data from instrumented tripods in representative channel and flat pairs of different orders to a) better understand sediment dynamics in each morphological setting, b) investigate whether sediment fluxes are balanced between channels and flats, and c) determine the importance of channel order on these sediment dynamics. Data from intensive field efforts as well as longer-term deployments help to inform how the hydrodynamic regimes of each environment serve to export or retain sediment and to further characterize the total sediment budget of intertidal flats. Results from two month-long deployments in winter 2009-2010 show channels of all orders in southeastern Willapa Bay were flood dominated. This was driven by longer durations of and sustained higher velocities during flooding tides, and suggests that larger circulation patterns were active within the tidal flat complex. The deployment periods were characterized by a range of meteorological conditions, including rain and several wind events. The wind events were correlated with increased flood dominance of water and sediment transport. Near-bed observations of velocity and suspended-sediment concentration (SSC) give insight to processes active when water levels are shallow over the flat. These processes are important in determining the net flux of water and sediment of the system. High-resolution water-column velocity and backscatter profiles reveal complex sediment-flux dynamics between channel and flat environments. Pulses of velocity and SSC were observed in the channel during flooding and ebbing tides when water levels were near the flat elevation, a phenomenon often observed in tidal flats and salt marshes. Instrumentation deployed near the bed on the flat measured elevated SSC when flat water depth dropped below 10 cm. This “skimming” of sediment on the flat contributed to the SSC pulse in the channel during ebbing tides. Water convergence from the flat led to increased channel bottom stresses and resuspension of freshly deposited sediment temporarily stored within the channel. These fine-scale observations allow us to address the mechanisms that govern the total sediment balance of channels and flats within tidal flat systems.

Nowacki, D. J.; Ogston, A. S.

2010-12-01

328

Spacial Distribution of Salinity and the Mechanism of Saltwater Intrusion in the Modaomen Water Channel of Pear River Estuary  

NASA Astrophysics Data System (ADS)

Modaomen channel is an important fresh water resource in Pearl River Delta. It has been impacted by saltwater intrusion frequently in the last decade. This has drawn more and more attention from scientists and engineers. The hydrodynamic mechanism of saltwater intrusion is still impercipient. In the present paper, hydrographs of velocity and salinity in the channel are analyzed based on field observations of velocity and salinity of upper, middle, and lower water layers at several stations along the Modaomen channel. It is found that the transport of salinity in Modaomen channel is obviously different from other estuaries. As the tidal range increases from neap to spring tide, the salinity in each water layer decreases unexpectedly. This peculiar phenomenon is attributed to the extraordinary flow process in the channel. When salinity value in each layer and vertical salinity gradient are lower during spring tide, no matter on rising or ebbing tide, the flow velocity monotonously decreases from water surface to the bottom, which is suggested by common sense. However, when salinity values and vertical salinity gradient are higher during neap tide, the flow velocity unexpectedly increases from water surface to the bottom during flood period, and flood duration of the bottom current is surprisingly as long as 15-18 hours. In addition, an inflexional velocity profile may remain amazingly for about 9 hours. This could be driven by the baroclinic pressure under the condition of tides, topography and upstream runoff discharge of this channel.

Liu, J. B.; Bao, Y.

2011-09-01

329

Automatic Measurement of Water Levels by Using Image Identification Method in Open Channel  

NASA Astrophysics Data System (ADS)

Water level data is indispensable to hydrology research, and it is important information for hydraulic engineering and overall utilization of water resources. The information of water level can be transmitted to management office by the network so that the management office may well understand whether the river level is exceeding the warning line. The existing water level measurement method can only present water levels in a form of data without any of images, the methods which make data just be a data and lack the sense of reality. Those images such as the rising or overflow of river level that the existing measurement method cannot obtain simultaneously. Therefore, this research employs a newly, improved method for water level measurement. Through the Video Surveillance System to record the images on site, an image of water surface will be snapped, and then the snapped image will be pre-processed and be compared with its altitude reference value to obtain a water level altitude value. With the ever-growing technology, the application scope of image identification is widely in increase. This research attempts to use image identification technology to analyze water level automatically. The image observation method used in this research is one of non-contact water level gage but it is quite different from other ones; the image observation method is cheap and the facilities can be set up beside an embankment of river or near the houses, thus the impact coming from external factors will be significantly reduced, and a real scene picture will be transmitted through wireless transmission. According to the dynamic water flow test held in an indoor experimental channel, the results of the research indicated that all of error levels of water level identification were less than 2% which meant the image identification could achieve identification result at different water levels. This new measurement method can offer instant river level figures and on-site video so that a disaster prevention measures can be made accordingly. Keywords: Image identification; Water Level; Video surveillance system.

Chung Yang, Han; Xue Yang, Jia

2014-05-01

330

Role of water in Protein Aggregation and Amyloid Polymorphism  

PubMed Central

Conspectus The link between oligomers and amyloid fibrils and a variety of neurodegenerative diseases raises the need to decipher the principles governing protein aggregation. Mechanisms of in vivo amyloid formation involve a number of coconspirators and complex interactions with membranes. Nevertheless, it is believed that understanding the biophysical basis of in vitro amyloid formation in well-defined systems is important in discovering ligands that preferentially bind to regions that harbor amyloidogenic tendencies. Determination of structures of fibrils of a variety of peptides has set the stage for probing the dynamics of oligomer formation and amyloid growth using computer simulations. Most experimental and simulation studies have been interpreted largely from the perspective of proteins without much consideration of the role of solvent in enabling or inhibiting oligomer formation and assembly to protofilaments and amyloid fibrils. Here, we provide a perspective on how interactions with water affect folding landscapes of A? monomers, oligomer formation in A?16–22 fragment, protofilament formation in a peptide from yeast prion Sup35. Explicit molecular dynamics simulations of these systems illustrate how water controls the self-assembly of higher order structures and provide a structural basis for understanding the kinetics of oligomer and fibril growth. Simulations show that monomers of A?-peptides sample a number of compact conformations. Population of aggregation-prone structures (N*) with salt-bridge, which bear a striking similarity to the peptide structure in the fibril, requires overcoming a high desolvation barrier. In general, sequences for which N* structures are not significantly populated are unlikely to aggregate. Generically oligomers and fibrils form in two steps. In the first stage water is expelled from the region between peptides rich in hydrophobic residues (for example A?16–22) resulting in the disordered oligomers. In the second stage, the peptides align along a preferred axis to form ordered structures with anti-parallel ?-strand arrangement. The rate limiting step in the ordered assembly is the rearrangement of the peptides within a confining volume. The mechanism of protofilament formation in a polar peptide fragment from the yeast prion in which the two sheets are packed against each other creating a dry interface illustrates that water dramatically slows down self-assembly. As the sheets approach each other two perfectly ordered one-dimensional water wires, which are stabilized by hydrogen bonds to the amide groups of the polar side chains, results in the formation of long-lived metastable structures. Release of the trapped water from the pore creates a helically-twisted protofilament with a dry interface. Similarly, the driving force for addition of a solvated monomer to a preformed fibril is the release of water whose entropy gain and favorable inter peptide hydrogen bond formation compensates for loss in entropy of the peptides. We suggest that the two-step mechanism, a model also used in protein crystallization, must hold good for higher order amyloid structure formation. In the first step a liquid droplet rich in proteins containing N* structures form. Conformational rearrangement of the peptides leading to an ordered state occurs within the droplet by incorporation of monomers or collision with other droplets and ultimately results in ?-amyloid formation. Because there is an ensemble of distinct N* structures with varying water content there must be a number of distinct water-laden polymorphic structures. Evidence for this proposal is presented. Water plays multifarious roles, which in the case of predominantly hydrophobic sequences, accelerates fibril formation. In contrast, water-stabilized metastable intermediates dramatically slow down fibril growth rates in hydrophilic sequences. PMID:21761818

Thirumalai, D.; Reddy, Govardhan; Straub, John E.

2011-01-01

331

Guard cell anion channel SLAC1 is regulated by CDPK protein kinases with distinct Ca2+ affinities  

PubMed Central

In response to drought stress, the phytohormone abscisic acid (ABA) induces stomatal closure. Thereby the stress hormone activates guard cell anion channels in a calcium-dependent, as well as –independent, manner. Open stomata 1 protein kinase (OST1) and ABI1 protein phosphatase (ABA insensitive 1) represent key components of calcium-independent ABA signaling. Recently, the guard cell anion channel SLAC1 was identified. When expressed heterologously SLAC1 remained electrically silent. Upon coexpression with Ca2+-independent OST1, however, SLAC1 anion channels appear activated in an ABI1-dependent manner. Mutants lacking distinct calcium-dependent protein kinases (CPKs) appeared impaired in ABA stimulation of guard cell ion channels, too. To study SLAC1 activation via the calcium-dependent ABA pathway, we studied the SLAC1 response to CPKs in the Xenopus laevis oocyte system. Split YFP-based protein–protein interaction assays, using SLAC1 as the bait, identified guard cell expressed CPK21 and 23 as major interacting partners. Upon coexpression of SLAC1 with CPK21 and 23, anion currents document SLAC1 stimulation by these guard cell protein kinases. Ca2+-sensitive activation of SLAC1, however, could be assigned to the CPK21 pathway only because CPK23 turned out to be rather Ca2+-insensitive. In line with activation by OST1, CPK activation of the guard cell anion channel was suppressed by ABI1. Thus the CPK and OST1 branch of ABA signal transduction in guard cells seem to converge on the level of SLAC1 under the control of the ABI1/ABA-receptor complex. PMID:20385816

Geiger, D.; Scherzer, S.; Mumm, P.; Marten, I.; Ache, P.; Matschi, S.; Liese, A.; Wellmann, C.; Al-Rasheid, K. A. S.; Grill, E.; Romeis, T.; Hedrich, R.

2010-01-01

332

TRP channel-associated factors are a novel protein family that regulates TRPM8 trafficking and activity.  

PubMed

TRPM8 is a cold sensor that is highly expressed in the prostate as well as in other non-temperature-sensing organs, and is regulated by downstream receptor-activated signaling pathways. However, little is known about the intracellular proteins necessary for channel function. Here, we identify two previously unknown proteins, which we have named "TRP channel-associated factors" (TCAFs), as new TRPM8 partner proteins, and we demonstrate that they are necessary for channel function. TCAF1 and TCAF2 both bind to the TRPM8 channel and promote its trafficking to the cell surface. However, they exert opposing effects on TRPM8 gating properties. Functional interaction of TCAF1/TRPM8 also leads to a reduction in both the speed and directionality of migration of prostate cancer cells, which is consistent with an observed loss of expression of TCAF1 in metastatic human specimens, whereas TCAF2 promotes migration. The identification of TCAFs introduces a novel mechanism for modulation of TRPM8 channel activity. PMID:25559186

Gkika, Dimitra; Lemonnier, Loic; Shapovalov, George; Gordienko, Dmitri; Poux, Céline; Bernardini, Michela; Bokhobza, Alexandre; Bidaux, Gabriel; Degerny, Cindy; Verreman, Kathye; Guarmit, Basma; Benahmed, Mohamed; de Launoit, Yvan; Bindels, Rene J M; Fiorio Pla, Alessandra; Prevarskaya, Natalia

2015-01-01

333

A multi-channel gel electrophoresis and continuous fraction collection apparatus for high throughput protein separation and characterization  

SciTech Connect

To facilitate a direct interface between protein separation by PAGE and protein identification by mass spectrometry, we developed a multichannel system that continuously collects fractions as protein bands migrate off the bottom of gel electrophoresis columns. The device was constructed using several short linear gel columns, each of a different percent acrylamide, to achieve a separation power similar to that of a long gradient gel. A Counter Free-Flow elution technique then allows continuous and simultaneous fraction collection from multiple channels at low cost. We demonstrate that rapid, high-resolution separation of a complex protein mixture can be achieved on this system using SDS-PAGE. In a 2.5 h electrophoresis run, for example, each sample was separated and eluted into 48-96 fractions over a mass range of 10-150 kDa; sample recovery rates were 50percent or higher; each channel was loaded with up to 0.3 mg of protein in 0.4 mL; and a purified band was eluted in two to three fractions (200 L/fraction). Similar results were obtained when running native gel electrophoresis, but protein aggregation limited the loading capacity to about 50 g per channel and reduced resolution.

Choi, Megan; Nordmeyer, Robert A.; Cornell, Earl; Dong, Ming; Biggin, Mark D.; Jin, Jian

2009-10-02

334

Modulation of cardiac Na+ channels expressed in a mammalian cell line and in ventricular myocytes by protein kinase C.  

PubMed Central

Cardiac rH1 Na+ channel alpha subunits were expressed in cells of the Chinese hamster lung 1610 cell line by transfection, and a stable cell line expressing cardiac Na+ channels (SNa-rH1) was isolated. Mean Na+ currents of 2.2 +/- 1.0 nA were recorded, which corresponds to a cell surface density of approximately 1-2 channels active at the peak of the Na+ current per micron2. The expressed cardiac Na+ current was tetrodotoxin resistant (Kd = 1.8 microM) and had voltage-dependent properties similar to those of the Na+ current in neonatal ventricular myocytes. Activation of protein kinase C by 1-oleoyl-2-acetyl-sn-glycerol (OAG) (10 microM) decreased this current approximately 33% at a holding potential of -114 mV and 56% at -94 mV. This reduction in peak current was caused in part by an 8- to 14-mV shift of steady-state inactivation in the hyperpolarized direction. Na+ channel activation was unchanged. Effects of OAG in SNa-rH1 cells and in neonatal rat cardiac myocytes were similar, except that the time course of inactivation was slowed either transiently or persistently when protein kinase C was activated in myocytes bathed in low-Ca2+ (1 microM) or Ca(2+)-free solution but was unaffected in SNa-rH1 cells. The effects of OAG on cardiac Na+ current were blocked in cells that had been previously microinjected with a peptide inhibitor of protein kinase C but not with a peptide inhibitor of cAMP-dependent protein kinase, indicating that protein kinase C is responsible for the effect of OAG. Single-channel recordings from SNa-rH1 cells showed that the probability of channel opening was reduced by OAG, but the conductance was unaffected. OAG did not induce the late Na+ channel openings observed with PKC modulation of neuronal and skeletal muscle Na+ channels. Thus, the substantial reduction in Na+ current at normal diastolic depolarizations with 10 microM OAG is due to failure of channel opening in response to depolarization. Such Na+ current reductions may have profound effects on cardiac cell excitability. PMID:8159741

Qu, Y; Rogers, J; Tanada, T; Scheuer, T; Catterall, W A

1994-01-01

335

Self-association and precursor protein binding of Saccharomyces cerevisiae Tom40p, the core component of the protein translocation channel of the mitochondrial outer membrane.  

PubMed Central

The precursor protein translocase of the mitochondrial outer membrane (Tom) is a multi-subunit complex containing receptors and a general import channel, of which the core component is Tom40p. Nuclear-encoded mitochondrial precursor proteins are first recognized by surface receptors and then pass through the import channel. The Tom complex has been purified; however, the protein-protein interactions that drive its assembly and maintain its stability have been difficult to study. Here we show that Saccharomyces cerevisiae Tom40p expressed in bacteria and purified to homogeneity associates efficiently with itself. The self-association is very strong and can withstand up to 4 M urea or 1 M salt. The tight self-association does not require the N-terminal segment of Tom40p. Furthermore, purified Tom40p preferentially recognizes the targeting sequence of mitochondrial precursor proteins. Although the binding of the targeting sequence to Tom40p is inhibited by urea concentrations in excess of 1 M, it is moderately resistant to 1 M salt. Simultaneous self-assembly and precursor protein binding suggest that Tom40p contains at least two different domains mediating these processes. The experimental approach described here should be useful for analysing protein-protein interactions involving individual or groups of components of the mitochondrial import machinery. PMID:11336653

Gordon, D M; Wang, J; Amutha, B; Pain, D

2001-01-01

336

Copper accumulation in channel catfish (Ictalurus punctatus) exposed to water borne copper sulfate  

SciTech Connect

Liver and axial muscle of channel catfish (Ictalurus punctatus) was analyzed for residual copper after exposure to water borne copper sulfate. Copper sulfate was continuously introduced into well water in three fiber glass tanks to achieve 1.7 mg/L, 2.7 mg/L and 3.6 mg/L copper sulfate concentrations in exposure waters. Milli-Q quality water was metered into a fourth tank at the same rate for unexposed fish. Actual levels of copper in exposure waters were determined by daily sampling and analysis by graphite furnace atomic absorption spectrophotometry (GFAA). Tissue samples were taken from six fish from each of the exposed and unexposed tanks at two-week intervals, Samples were collected until tissue analysis indicated an equilibrium had been established between the uptake and elimination in both the muscle and liver tissue. Elimination was followed until a clear rate of deputation could be established. Samples were digested in nitric acid in a micro wave digestor and analyzed by GFAA. Results of tissue analysis will be presented to demonstrate bioaccumulation and the effect of copper concentration, length of copper exposure, and gender on copper uptake, establishment of tissue:environmental copper equilibrium, and rate of copper elimination following exposure.

Hobbs, M. [Oak Ridge Inst. for Science and Education, TN (United States); Griffin, B. [National Biological Service, Stuttgart, AR (United States); Schlenk, D. [Univ. of Mississippi, Oxford, MS (United States); Kadlubar, F.; Brand, C.D. [National Center for Toxicological Research, Jefferson, AR (United States)

1995-12-31

337

Phylogeny of immune recognition: processing and presentation of structurally defined proteins in channel catfish immune responses.  

PubMed

This work was undertaken to investigate whether or not antigen processing and presentation are important in channel catfish in vitro secondary immune responses elicited with structurally defined proteins, namely, pigeon heart cytochrome C (pCytC), hen egg lysozyme, and horse myoglobin. The use of in vitro antigen-pulsed and fixed B cells or monocytes as antigen presenting cells (APC) resulted in autologous peripheral blood leukocytes (PBL) responding with vigorous proliferation and antibody production in vitro. In addition, several long-term catfish monocyte lines have been found to function as efficient APC with autologous but not allogeneic responders. Subsequent separation of the responding PBL into sIg- (T-cell-enriched) and B (sIg+) cells subsets showed that both underwent proliferative responses to antigen-pulsed and fixed APC. Moreover, allogeneic cells used as APC were found to induce only strong mixed leukocyte reactions without specific in vitro antibody production. Initial attempts at identifying the immunogenic region(s) of the protein antigens for catfish indicated there are two such regions for pCytC, namely, peptides 66-80 and 81-104. PMID:1668258

Vallejo, A N; Miller, N W; Clem, L W

1991-01-01

338

Students' Understanding of External Representations of the Potassium Ion Channel Protein Part II: Structure-Function Relationships and Fragmented Knowledge  

ERIC Educational Resources Information Center

Research that has focused on external representations in biochemistry has uncovered student difficulties in comprehending and interpreting external representations. This study focuses on students' understanding of three external representations (ribbon diagram, wireframe, and hydrophobic/hydrophilic) of the potassium ion channel protein. Analysis…

Harle, Marissa; Towns, Marcy H.

2012-01-01

339

Light inactivation of water transport and protein–protein interactions of aquaporin–Killer Red chimeras  

PubMed Central

Aquaporins (AQPs) have a broad range of cellular and organ functions; however, nontoxic inhibitors of AQP water transport are not available. Here, we applied chromophore-assisted light inactivation (CALI) to inhibit the water permeability of AQP1, and of two AQP4 isoforms (M1 and M23), one of which (M23) forms aggregates at the cell plasma membrane. Chimeras containing Killer Red (KR) and AQPs were generated with linkers of different lengths. Osmotic water permeability of cells expressing KR/AQP chimeras was measured from osmotic swelling–induced dilution of cytoplasmic chloride, which was detected using a genetically encoded chloride-sensing fluorescent protein. KR-AQP1 red fluorescence was bleached rapidly (?10% per second) by wide-field epifluorescence microscopy. After KR bleaching, KR-AQP1 water permeability was reduced by up to 80% for the chimera with the shortest linker. Remarkably, CALI-induced reduction in AQP4-KR water permeability was approximately twice as efficient for the aggregate-forming M23 isoform; this suggests intermolecular CALI, which was confirmed by native gel electrophoresis on cells coexpressing M23-AQP4-KR and myc-tagged M23-AQP4. CALI also disrupted the interaction of AQP4 with a neuromyelitis optica autoantibody directed against an extracellular epitope on AQP4. CALI thus permits rapid, spatially targeted and irreversible reduction in AQP water permeability and interactions in live cells. Our data also support the utility of CALI to study protein–protein interactions as well as other membrane transporters and receptors. PMID:22200949

Baumgart, Florian; Rossi, Andrea

2012-01-01

340

Effects of water management practices on discharge of nutrients and organic matter from channel catfish ( Ictalurus punctatus) ponds  

Microsoft Academic Search

A water quality data set generated by sampling commercial ponds for 2 years was used in a hydrological model of pond overflow volume to describe the effects of water management practices on discharge of nutrients and organic matter from channel catfish Ictalurus punctatus ponds in northwest Mississippi, USA. Average concentrations of total nitrogen, total phosphorus, chemical oxygen demand, and biochemical

Craig S Tucker; Susan K Kingsbury; Jonathan W Pole; Charles L Wax

1996-01-01

341

Interlayer Water Regulates the Bio-nano Interface of a ?-sheet Protein stacking on Graphene  

NASA Astrophysics Data System (ADS)

Using molecular dynamics simulations, we investigated an integrated bio-nano interface consisting of a ?-sheet protein stacked onto graphene. We found that the stacking assembly of the model protein on graphene could be controlled by water molecules. The interlayer water filled within interstices of the bio-nano interface could suppress the molecular vibration of surface groups on protein, and could impair the CH...? interaction driving the attraction of the protein and graphene. The intermolecular coupling of interlayer water would be relaxed by the relative motion of protein upon graphene due to the interaction between water and protein surface. This effect reduced the hindrance of the interlayer water against the assembly of protein on graphene, resulting an appropriate adsorption status of protein on graphene with a deep free energy trap. Thereby, the confinement and the relative sliding between protein and graphene, the coupling of protein and water, and the interaction between graphene and water all have involved in the modulation of behaviors of water molecules within the bio-nano interface, governing the hindrance of interlayer water against the protein assembly on hydrophobic graphene. These results provide a deep insight into the fundamental mechanism of protein adsorption onto graphene surface in water.

Lv, Wenping; Xu, Guiju; Zhang, Hongyan; Li, Xin; Liu, Shengju; Niu, Huan; Xu, Dongsheng; Wu, Ren'an

2015-01-01

342

The RGK family of GTP-binding Proteins: Regulators of Voltage-dependent Calcium Channels and Cytoskeleton Remodeling  

PubMed Central

RGK proteins constitute a novel subfamily of small Ras-related proteins that function as potent inhibitors of voltage-dependent (VDCC) Ca2+ channels and regulators of actin cytoskeletal dynamics. Within the larger Ras superfamily, RGK proteins have distinct regulatory and structural characteristics, including nonconservative amino acid substitutions within regions known to participate in nucleotide binding and hydrolysis and a C-terminal extension that contains conserved regulatory sites which control both subcellular localization and function. RGK GTPases interact with the VDCC ?-subunit (CaV?) and inhibit Rho/Rho kinase signaling to regulate VDCC activity and the cytoskeleton respectively. Binding of both calmodulin and 14-3-3 to RGK proteins, and regulation by phosphorylation controls cellular trafficking and the downstream signaling of RGK proteins, suggesting that a complex interplay between interacting protein factors and trafficking contribute to their regulation. PMID:18042346

Correll, Robert N.; Pang, Chunyan; Niedowicz, Dana M.; Finlin, Brian S.; Andres, Douglas A.

2008-01-01

343

Drosophila Photoreceptor Cells Exploited for the Production of Eukaryotic Membrane Proteins: Receptors, Transporters and Channels  

PubMed Central

Background Membrane proteins (MPs) play key roles in signal transduction. However, understanding their function at a molecular level is mostly hampered by the lack of protein in suitable amount and quality. Despite impressive developments in the expression of prokaryotic MPs, eukaryotic MP production has lagged behind and there is a need for new expression strategies. In a pilot study, we produced a Drosophila glutamate receptor specifically in the eyes of transgenic flies, exploiting the naturally abundant membrane stacks in the photoreceptor cells (PRCs). Now we address the question whether the PRCs also process different classes of medically relevant target MPs which were so far notoriously difficult to handle with conventional expression strategies. Principal Findings We describe the homologous and heterologous expression of 10 different targets from the three major MP classes - G protein-coupled receptors (GPCRs), transporters and channels in Drosophila eyes. PRCs offered an extraordinary capacity to produce, fold and accommodate massive amounts of MPs. The expression of some MPs reached similar levels as the endogenous rhodopsin, indicating that the PRC membranes were almost unsaturable. Expression of endogenous rhodopsin was not affected by the target MPs and both could coexist in the membrane stacks. Heterologous expression levels reached about 270 to 500 pmol/mg total MP, resulting in 0.2–0.4 mg purified target MP from 1 g of fly heads. The metabotropic glutamate receptor and human serotonin transporter - both involved in synaptic transmission - showed native pharmacological characteristics and could be purified to homogeneity as a prerequisite for further studies. Significance We demonstrate expression in Drosophila PRCs as an efficient and inexpensive tool for the large scale production of functional eukaryotic MPs. The fly eye system offers a number of advantages over conventional expression systems and paves the way for in-depth analyses of eukaryotic MPs that have so far not been accessible to biochemical and biophysical studies. PMID:21494623

Panneels, Valérie; Kock, Ines; Krijnse-Locker, Jacomine; Rezgaoui, Meriem; Sinning, Irmgard

2011-01-01

344

Membrane insertion of gap junction connexins: polytopic channel forming membrane proteins  

PubMed Central

Connexins, the proteins that form gap junction channels, are polytopic plasma membrane (PM) proteins that traverse the plasma membrane bilayer four times. The insertion of five different connexins into the membrane of the ER was studied by synthesizing connexins in translation- competent cell lysates supplemented with pancreatic ER-derived microsomes, and by expressing connexins in vivo in several eucaryotic cell types. In addition, the subcellular distribution of the connexins was determined. In vitro-synthesis in the presence of microsomes resulted in the signal recognition particle-dependent membrane insertion of the connexins. The membrane insertion of all connexins was accompanied by an efficient proteolytic processing that was dependent on the microsome concentration. Endogenous unprocessed connexins were detectable in the microsomes used, indicating that the pancreatic microsomes serve as a competent recipient in vivo for unprocessed full length connexins. Although oriented with their amino terminus in the cytoplasm, the analysis of the cleavage reaction indicated that an unprecedented processing by signal peptidase resulted in the removal of an amino-terminal portion of the connexins. Variable amounts of similar connexin cleavage products were also identified in the ER membranes of connexin overexpressing cells. The amount generated correlated with the level of protein expression. These results demonstrate that the connexins contain a cryptic signal peptidase cleavage site that can be processed by this enzyme in vitro and in vivo in association with their membrane insertion. Consequently, a specific factor or condition must be required to prevent this aberrant processing of connexins under normal conditions in the cell. PMID:7929580

1994-01-01

345

Sensitivity to Abscisic Acid of Guard-Cell K^+ Channels is Suppressed by abi1-1, a Mutant Arabidopsis Gene Encoding a Putative Protein Phosphatase  

Microsoft Academic Search

Abscisic acid (ABA) modulates the activities of three major classes of ion channels-inward- and outward-rectifying K^+ channels (IK,in and IK,out, respectively) and anion channels-at the guard-cell plasma membrane to achieve a net efflux of osmotica and stomatal closure. Disruption of ABA sensitivity in wilty abi1-1 mutants of Arabidopsis and evidence that this gene encodes a protein phosphatase suggest that protein

Fiona Armstrong; Jeffrey Leung; Alexander Grabov; Jane Brearley; Jerome Giraudat; Michael R. Blatt

1995-01-01

346

Memory reconsolidation and its maintenance depend on L-voltage-dependent calcium channels and CaMKII functions regulating protein turnover in the hippocampus  

PubMed Central

Immediate postretrieval bilateral blockade of long-acting voltage–dependent calcium channels (L-VDCCs), but not of glutamatergic NMDA receptors, in the dorsal CA1 region of the hippocampus hinders retention of long-term spatial memory in the Morris water maze. Immediate postretrieval bilateral inhibition of calcium/calmodulin-dependent protein kinase (CaMK) II in dorsal CA1 does not affect retention of this task 24 h later but does hinder it 5 d later. These two distinct amnesic effects are abolished if protein degradation by proteasomes is inhibited concomitantly. These results indicate that spatial memory reconsolidation depends on the functionality of L-VDCC in dorsal CA1, that maintenance of subsequent reconsolidated memory trace depends on CaMKII, and these results also suggest that the role played by both L-VDCC and CaMKII is to promote the retrieval-dependent, synaptically localized enhancement of protein synthesis necessary to counteract a retrieval-dependent, synaptic-localized enhancement of protein degradation, which has been described as underlying the characteristic labilization of the memory trace triggered by retrieval. Thus, conceivably, L-VDCC and CaMKII would enhance activity-dependent localized protein renewal, which may account for the improvement of the long-term efficiency of the synapses responsible for the maintenance of reactivated long-term spatial memory. PMID:23576750

Da Silva, Weber Cláudio; Cardoso, Gabriela; Bonini, Juliana Sartori; Benetti, Fernando; Izquierdo, Ivan

2013-01-01

347

Tentative Study on Performance of Darriues-Type Hydroturbine Operated in Small Open Water Channel  

NASA Astrophysics Data System (ADS)

The development of small hydropower is one of the realistic and preferable utilizations of renewable energy, but the extra-low head hydropower less than 2 m is almost undeveloped yet for some reasons. The authors have developed several types of Darrieus-type hydro-turbine system, and among them, the Darrieus-turbine with a wear and a nozzle installed upstream of turbine is so far in success to obtain more output power, i.e. more shaft torque, by gathering all water into the turbine. However, there can several cases exist, in which installing the wear covering all the flow channel width is unrealistic. Then, in the present study, the hydraulic performances of Darrieus-type hydro-turbine with the inlet nozzle is investigated, putting alone in a small open channel without upstream wear. In the experiment, the five-bladed Darrieus-type runner with the pitch-circle diameter of 300 mm and the blade span of 300 mm is vertically installed in the open channel with the width of 1,200 mm. The effectiveness of the shape of the inlet nozzle is also examined using two types of two-dimensional symmetric nozzle, the straight line nozzle (SL nozzle) with the converging angle of 45 degrees and the half diameter curved nozzle (HD nozzle) whose radius is a half diameter of runner pitch circle. Inlet and outlet nozzle widths are in common for the both nozzles, which are 540 mm and 240 mm respectively. All the experiments are carried out under the conditions with constant flow rate and downstream water level, and performances are evaluated by measured output torque and the measured head difference between the water levels upstream and downstream of the turbine. As a result, it is found that the output power is remarkably increased by installing the inlet nozzle, and the turbine with SL nozzle produces larger power than that with HD nozzle. However, the peak efficiency is deteriorated in both cases. The speed ratio defined by the rotor speed divided by the downstream water velocity at the peak efficiency is larger in both cases with the inlet nozzle, partly due to the increase of inflow velocity into the turbine. In order to understand the cause of the differences of power, i.e. torque characteristics of the turbine with SL and HD nozzles, twodimensional CFD simulation is carried out. It is found that the instantaneous torque variation is important for the overall turbine performances, indicating the possibility of further performance improvement through the optimization of nozzle geometry.

Matsushita, D.; Moriyama, R.; Nakashima, K.; Watanabe, S.; Okuma, K.; Furukawa, A.

2014-12-01

348

Changes of expression of stretch-activated potassium channel TREK-1 mRNA and protein in hypertrophic myocardium.  

PubMed

The expression of stretch-activated potassium channel TREK-1 mRNA and protein of hypertrophic myocardium was measured. Using a model of hypertrophy induced by coarctation of abdominal aorta in male Wistar rats, the expression of TREK-1 mRNA and protein was detected by using semi-quantitative RT PCR and Western blot respectively. At 4th and 8th week after constriction of the abdominal aorta, rats developed significant left ventricular hypertrophy. As compared to sham-operated group, stretch-activated potassium channel TREK-1 mRNA was strongly expressed and protein was up-regulated in operation groups (P < 0.05). It was concluded that the expression of TREK-1 was up-regulated in hypertrophic myocardium induced by chronic pressure overload in Wistar rats. PMID:16711001

Cheng, Longxian; Su, Fengcheng; Ripen, Nsenga; Fan, Hong; Huang, Kai; Wang, Min; Peng, Hongyu; Mei, Chunli; Zhao, Fang; Liao, Yuhua

2006-01-01

349

Electron transfer activation of a second water channel for proton transport in [FeFe]-hydrogenase  

NASA Astrophysics Data System (ADS)

Hydrogenase enzymes are important because they can reversibly catalyze the production of molecular hydrogen. Proton transport mechanisms have been previously studied in residue pathways that lead to the active site of the enzyme via residues Cys299 and Ser319. The importance of this pathway and these residues has been previously exhibited through site-specific mutations, which were shown to interrupt the enzyme activity. It has been shown recently that a separate water channel (WC2) is coupled with electron transport to the active site of the [FeFe]-hydrogenase. The water-mediated proton transport mechanisms of the enzyme in different electronic states have been studied using the multistate empirical valence bond reactive molecular dynamics method, in order to understand any role WC2 may have in facilitating the residue pathway in bringing an additional proton to the enzyme active site. In a single electronic state A2-, a water wire was formed through which protons can be transported with a low free energy barrier. The remaining electronic states were shown, however, to be highly unfavorable to proton transport in WC2. A double amino acid substitution is predicted to obstruct proton transport in electronic state A2- by closing a cavity that could otherwise fill with water near the proximal Fe of the active site.

Sode, Olaseni; Voth, Gregory A.

2014-12-01

350

Low level water vapor fields from the VISSR Atmospheric Sounder (VAS) 'split window' channels  

NASA Technical Reports Server (NTRS)

The use of the 11 and 12-micron IR-radiometer channels of the VISSR Atmosphere Sounder (VAS) on the GOES to detect water vapor in the lowest 300-400 mb of the troposphere is reported. An algorithm is developed to eliminate the background temperature, allowing the calculation of precipitable water (PW) over both land and water via a single-layer radiative model. This 'split-window' method is demonstrated in a case study, covering the US on July 13, 1981. PW values were calculated from five VAS images and compared with those from radiosonde data and surface measurements. It is shown that the VAS PW images have good resolution (15 km), reveal vivid, continuously evolving details, and differentiate deep, convection-supporting layers from shallow ones. PW ranged from 1.7 to 5.5 g/sq cm (+ or - 1.0 g/sq cm), in good agreement with other measurements. Since this method can detect mesoscale water-vapor fields in relatively clear air, it is considered of great potential value for numerical forecasting.

Robinson, W. D.; Chesters, D.; Uccellini, L. W.

1983-01-01

351

Flow field simulation of gas-water two phase flow in annular channel  

NASA Astrophysics Data System (ADS)

The gas-water two-phase flow is very common in the industrial processes. the deep understanding of the two-phase flow state is to achieve the production equipment design and safe operation. In the measurement of gas-water two-phase flow, the differential pressure sensor is widely used, and some measurement model of multiphase flow have been concluded. The differential pressure is generated when fluid flowing through the throttling components to calculate flow rate. This paper mainly focuses on two points: 1. The change rule of the parameters include velocity, pressure, phase fraction as the change of time, when the phase inlet velocity is given. 2. Analysis the distribution of the parameters above-mentioned at a certain moment under the condition of different water inlet velocity. Three-dimensional computational fluid dynamics (CFD) approach was used to simulate gas-water two-phase flow fluid in the annular channel, which is composed of horizontal pipe and long- waist cone sensor. The simulation results were obtained from FLUENT software.

Ji, Pengcheng; Dong, Feng

2014-04-01

352

The channels of Mars  

NASA Technical Reports Server (NTRS)

The geomorphology of Mars is discussed, focusing on the Martian channels. The great flood channels of Mars, the processes of channel erosion, and dendritic channel networks, are examined. The topography of the Channeled Scabland region of the northwestern U.S. is described and compared to the Martian channels. The importance of water in the evolution of the channel systems is considered.

Baker, Victor R.

1988-01-01

353

Evidence for Recent Liquid Water on Mars: Channels and Aprons in East Gorgonum Crater  

NASA Technical Reports Server (NTRS)

[figure removed for brevity, see original site] Warning!This link leads to a very large image that may be too long for some web browsers (in these cases, you must save the link to your desktop and view with other software) [figure removed for brevity, see original site]

This suite of Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) pictures provides a vista of martian gullies on the northern wall of a 12 kilometer-(7.4 mile)-wide meteor impact crater east of the Gorgonum Chaos region on the red planet.

The first picture (above left) is a composite of three different high resolution MOC views obtained in 1999 and 2000. The second picture (above right)shows the location of the high resolution views relative to the whole crater as it appeared in the highest resolution image previously acquired of the area, taken by the Viking 1 orbiter in 1978. The release image (top) shows a close-up of one of the channels and debris aprons found in the northwestern quarter of the impact crater.

Some of the channels in this crater are deeply-entrenched and cut into lighter-toned deposits. The numerous channels and apron deposits indicate that many tens to hundreds of individual events involving the flow of water and debris have occurred here. The channels and aprons have very crisp, sharp relief and there are no small meteor impact craters on them, suggesting that these features are extremely young relative to the 4.5 billion year history of Mars. It is possible that these landforms are still being created by water seeping from the layered rock in the crater wall today.

The crater has no name and it is located near 37.4oS, 168.0oW. The composite view in (above left) includes a picture taken by MOC on September 10, 1999, a picture obtained April 26, 2000, and another on May 22, 2000. The scene from left to right (including the dark gap between photos) covers an area approximately 7.6 kilometers (4.7 miles) wide by 18 km (11.1 mi) long. Sunlight illuminates the scene from the upper left. MOC high resolution images are taken black-and-white (grayscale); the color seen here has been synthesized from the colors of Mars observed by the MOC wide angle cameras and by the Viking Orbiters in the late 1970s.

2000-01-01

354

Crystal structure of the soluble form of the redox-regulated chloride ion channel protein CLIC4.  

PubMed

The structure of CLIC4, a member of the CLIC family of putative intracellular chloride ion channel proteins, has been determined at 1.8 Angstroms resolution by X-ray crystallography. The protein is monomeric and it is structurally similar to CLIC1, belonging to the GST fold class. Differences between the structures of CLIC1 and CLIC4 are localized to helix 2 in the glutaredoxin-like N-terminal domain, which has previously been shown to undergo a dramatic structural change in CLIC1 upon oxidation. The structural differences in this region correlate with the sequence differences, where the CLIC1 sequence appears to be atypical of the family. Purified, recombinant, wild-type CLIC4 is shown to bind to artificial lipid bilayers, induce a chloride efflux current when associated with artificial liposomes and produce an ion channel in artificial bilayers with a conductance of 30 pS. Membrane binding is enhanced by oxidation of CLIC4 while no channels were observed via tip-dip electrophysiology in the presence of a reducing agent. Thus, recombinant CLIC4 appears to be able to form a redox-regulated ion channel in the absence of any partner proteins. PMID:16176272

Littler, Dene R; Assaad, Nagi N; Harrop, Stephen J; Brown, Louise J; Pankhurst, Greg J; Luciani, Paolo; Aguilar, Marie-Isabel; Mazzanti, Michele; Berryman, Mark A; Breit, Samuel N; Curmi, Paul M G

2005-10-01

355

Hydrolysis of whey protein isolate using subcritical water.  

PubMed

Hydrolyzed whey protein isolate (WPI) is used in the food industry for protein enrichment and modification of functional properties. The purpose of the study was to determine the feasibility of subcritical water hydrolysis (SWH) on WPI and to determine the temperature and reaction time effects on the degree of hydrolysis (DH) and the production of peptides and free amino acids (AAs). Effects of temperature (150 to 320 °C) and time (0 to 20 min) were initially studied with a central composite rotatable design followed by a completely randomized factorial design with temperature (250 and 300 °C) and time (0 to 50 min) as factors. SWH was conducted in an electrically heated, 100-mL batch, high pressure vessel. The DH was determined by a spectrophotometric method after derivatization. The peptide molecular weights (MWs) were analyzed by gel electrophoresis and mass spectrometry, and AAs were quantified by high-performance liquid chromotography. An interaction of temperature and time significantly affected the DH and AA concentration. As the DH increased, the accumulation of lower MW peptides also increased following SWH (and above 10% DH, the majority of peptides were <1000 Da). Hydrolysis at 300 °C for 40 min generated the highest total AA concentration, especially of lysine (8.894 mg/g WPI). Therefore, WPI was successfully hydrolyzed by subcritical water, and with adjustment of treatment parameters there is reasonable control of the end-products. PMID:22122092

Espinoza, Ashley D; Morawicki, Rubén O; Hager, Tiffany

2012-01-01

356

Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding  

E-print Network

Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage of denaturation of proteins by urea is explored by using all-atom microseconds molecular dynamics simulations mechanism'' whereby urea has a stronger dispersion interaction with protein than water. denaturing mechanism

Thirumalai, Devarajan

357

Stream channel surface water - groundwater interactions in a fire impacted watershed  

NASA Astrophysics Data System (ADS)

We are conducting a study of surface water - groundwater interactions within the Scott Creek watershed, a 4th order catchment of 76.6 km2 in central coastal California, to assess the impacts of fire on channel and riparian conditions. Scott Creek and its tributaries are valuable spawning habitat for Coho salmon and Steelhead trout. The Scott Creek watershed is located on the western (windward) side of the Santa Cruz Mountains, where the most intense precipitation falls from November to April, and includes a mixture of protected land and areas used for agriculture, grazing, and selective timber harvesting. 37% of the watershed was burned in a fire in August 2009, and we hypothesize that this could result in enhanced delivery of fine grained hill slope sediments to stream channels for several years post fire, reducing the extent of hyporheic exchange downstream of burned areas. This could reduce the survival rates of Coho and Steelhead redds (egg nests), which are dependent on surface water - groundwater exchange for regulation of water nutrient content and temperature. We are monitoring streambed seepage rates and hydraulic conductivity, and performing repeated tracer discharge experiments at three sites on Scott Creek, two within and one upstream of the area burned in the 2009 fire. Streambed seepage rates are calculated using a time series method applied to heat as a tracer, using naturally occurring diurnal changes in stream temperature, and extended to calculations of streambed hydraulic conductivity based on measured head gradients. Hyporheic exchange parameters are assessed using tracer breakthrough data, as fit by an optimized model of one-dimensional advection, dispersion and transient storage. Variations in hydrologic characteristics (e.g., transient storage area, exchange coefficient) over time at each site are being used to assess the magnitude and timing of channel modifications independent to, and associated with, the burning of catchment hill slopes. Preliminary data suggest that there is more variability in both streambed seepage rates and streambed hydraulic conductivity in burned areas relative to the unburned reach. Fires in undeveloped and urbanized areas seem likely to become more common throughout the western U.S., and other parts of the world, as a result of land use practices and climate change. Studies such as ours are important for understanding, anticipating, and mitigating the hydrologic response of critical habitat to fires and other events.

Russo, T. A.; Fisher, A. T.

2010-12-01

358

Interaction with the surrounding water plays a key role in determining the aggregation propensity of proteins.  

PubMed

Understanding the molecular determinants of the relative propensities of proteins to aggregate in a cellular environment is a central issue for treating protein-aggregation diseases and developing peptide-based therapeutics. Despite the expectation that protein aggregation can largely be attributed to direct protein-protein interactions, a crucial role the surrounding water in determining the aggregation propensity of proteins both in?vitro and in?vivo was identified. The overall protein hydrophobicity, defined solely by the hydration free energy of a protein in its monomeric state sampling its equilibrium structures, was shown to be the predominant determinant of protein aggregation propensity in aqueous solution. Striking discrimination of positively and negatively charged residues by the surrounding water was also found. This effect depends on the protein net charge and plays a crucial role in regulating the solubility of the protein. These results pave the way for the design of aggregation-resistant proteins as biotherapeutics. PMID:24615814

Chong, Song-Ho; Ham, Sihyun

2014-04-01

359

Water in the Polar and Nonpolar Cavities of the Protein Interleukin-1 Guogang Feng,  

E-print Network

Water in the Polar and Nonpolar Cavities of the Protein Interleukin-1 Hao Yin, Guogang Feng, G ReceiVed: September 13, 2010; ReVised Manuscript ReceiVed: October 19, 2010 Water in the protein by water on the basis of some experiments and simulations and to be empty on the basis of others. Here we

Clore, G. Marius

360

Effects of glycyrrhizin on renal functions in association with the regulation of water channels.  

PubMed

It is well-known that the mineralocorticoid action of glycyrrhizin, which is the major component of Glycyrrhiza uralensis, is caused by a defect in the conversion of cortisol to cortisone by the inhibition of 11-beta-hydroxysteroid dehydrogenase enzyme activity. In the present study, we investigated the mechanisms of salt and water retention in the kidney of rats administered excess amounts of glycyrrhizin (200 mg/kg/day, p.o.). Up-regulation of aquaporin (AQP) 2 and 3 water channels was detected in the renal inner and outer medulla by Western blot analysis in rats treated with glycyrrhizin for 0.5, 1 and 2 consecutive weeks. Our results show that urine flow rates and sodium excretion rates in glycyrrhizin-treated rats were decreased significantly, but creatinine clearance (Ccr) was not altered. The decreases of urine volume and urinary sodium excretion in glycyrrhizin-treated rats were reversed by a 2-week injection of spironolactone, which is a well-known mineralocorticoid receptor (MR) blocker. These results suggest that the retention of water and salt in glycyrrhizin-treated rats is, at least in part, accounted for by the increased expression of AQP 2 and 3 in the kidney, which may be causally related to the MR. PMID:12943171

Kang, Dae Gill; Sohn, Eun Jin; Lee, Ho Sub

2003-01-01

361

Identifying and tracking proteins through the marine water column: insights into the inputs and preservation mechanisms of protein in sediments  

PubMed Central

Proteins generated during primary production represent an important fraction of marine organic nitrogen and carbon, and have the potential to provide organism-specific information in the environment. The Bering Sea is a highly productive system dominated by seasonal blooms and was used as a model system for algal proteins to be tracked through the water column and incorporated into detrital sedimentary material. Samples of suspended and sinking particles were collected at multiple depths along with surface sediments on the continental shelf and deeper basin of the Bering Sea. Modified standard proteomic preparations were used in conjunction with high pressure liquid chromatography-tandem mass spectrometry to identify the suite of proteins present and monitor changes in their distribution. In surface waters 207 proteins were identified, decreasing through the water column to 52 proteins identified in post-bloom shelf surface sediments and 24 proteins in deeper (3490 m) basin sediments. The vast majority of identified proteins in all samples were diatom in origin, reflecting their dominant contribution of biomass during the spring bloom. Identified proteins were predominantly from metabolic, binding/structural, and transport-related protein groups. Significant linear correlations were observed between the number of proteins identified and the concentration of total hydrolysable amino acids normalized to carbon and nitrogen. Organelle-bound, transmembrane, photosynthetic, and other proteins involved in light harvesting were preferentially retained during recycling. These findings suggest that organelle and membrane protection represent important mechanisms that enhance the preservation of protein during transport and incorporation into sediments. PMID:22711915

Moore, Eli K.; Nunn, Brook L.; Goodlett, David R.; Harvey, H. Rodger

2012-01-01

362

Identifying and tracking proteins through the marine water column: Insights into the inputs and preservation mechanisms of protein in sediments  

NASA Astrophysics Data System (ADS)

Proteins generated during primary production represent an important fraction of marine organic nitrogen and carbon, and have the potential to provide organism-specific information in the environment. The Bering Sea is a highly productive system dominated by seasonal blooms and was used as a model system for algal proteins to be tracked through the water column and incorporated into detrital sedimentary material. Samples of suspended and sinking particles were collected at multiple depths along with surface sediments on the continental shelf and deeper basin of the Bering Sea. Modified standard proteomic preparations were used in conjunction with high pressure liquid chromatography-tandem mass spectrometry to identify the suite of proteins present and monitor changes in their distribution. In surface waters 207 proteins were identified, decreasing through the water column to 52 proteins identified in post-bloom shelf surface sediments and 24 proteins in deeper (3490 m) basin sediments. The vast majority of identified proteins in all samples were diatom in origin, reflecting their dominant contribution of biomass during the spring bloom. Identified proteins were predominantly from metabolic, binding/structural, and transport-related protein groups. Significant linear correlations were observed between the number of proteins identified and the concentration of total hydrolysable amino acids normalized to carbon and nitrogen. Organelle-bound, transmembrane, photosynthetic, and other proteins involved in light harvesting were preferentially retained during recycling. These findings suggest that organelle and membrane protection represent important mechanisms that enhance the preservation of protein during transport and incorporation into sediments.

Moore, Eli K.; Nunn, Brook L.; Goodlett, David R.; Harvey, H. Rodger

2012-04-01

363

The effect of ultrasonic salting on protein and water-protein interactions in meat.  

PubMed

The aim of this study was to assess the effect of power ultrasound (US) treatment (4.2, 11 or 19 W cm(-2) for 10, 25 or 40 min) on water-protein interactions during the salting of pork. All US treatments increased the protein extraction above that of the control (p<0.001), with the exception of 4.2 W cm(-2) for 10 and 25 min. Differential scanning calorimetry indicated myosin denaturation at the surface of the sample treated with the highest power (19 W cm(-2), 40 min). There was no effect on water binding capacity assessed by centrifuge, however, low-field nuclear magnetic resonance T21 relaxation was increased by 19 W cm(-2) (p<0.05). No changes to the meat matrix were evident by light microscopy. Findings indicate that US salting could be a surface phenomenon which can accelerate mass transfer and extract protein but denature myosin at high power inputs. Potential could exist for US to enhance conventional curing techniques. PMID:24206713

McDonnell, C K; Allen, P; Morin, C; Lyng, J G

2014-03-15

364

A conceptual model for river water and sediment dispersal in the Santa Barbara Channel, California  

USGS Publications Warehouse

The ephemeral Santa Clara River delivers large amounts of freshwater and sediment to the eastern Santa Barbara Channel during brief, episodic discharge events. This discharge into the channel was characterized here with shipboard measurements during floods of 1997 and 1998. Within approximately 1-km of the river mouth, the river discharge quickly stratifies into a freshened, turbid surface plume and a bottom nephloid layer. Observations immediately off the Santa Clara River mouth on a peak day of river discharge revealed that sediment rapidly settled from the freshened surface waters, as suspended sediment in the freshened surface plume contained only ???6% of the sediment mass expected if the sediment mixed conservatively. On the two subsequent days the reduction of sediment mass in the surface plume continued at ???50% per day. These observations suggest that river sediment undergoes rapid initial settling within ???1-km of the river mouth, followed by somewhat slower rates of settling. Although we did not measure sedimentation or bottom boundary layer processes, our mass balance results suggest that almost all of the river sediment either escapes along or deposits upon the inner shelf seabed.

Warrick, J.A.; Mertes, L.A.K.; Washburn, L.; Siegel, D.A.

2004-01-01

365

The role of water exchange between a stream channel and its hyporheic zone in nitrogen cycling at the terrestrial-aquatic interface  

USGS Publications Warehouse

The subsurface riparian zone was examined as an ecotone with two interfaces. Inland is a terrestrial boundary, where transport of water and dissolved solutes is toward the channel and controlled by watershed hydrology. Streamside is an aquatic boundary, where exchange of surface water and dissolved solutes is bi-directional and flux is strongly influenced by channel hydraulics. Streamside, bi-directional exchange of water was qualitatively defined using biologically conservative tracers in a third order stream. In several experiments, penetration of surface water extended 18 m inland. Travel time of water from the channel to bankside sediments was highly variable. Subsurface chemical gradients were indirectly related to the travel time. Sites with long travel times tended to be low in nitrate and DO (dissolved oxygen) but high in ammonium and DOC (dissolved organic carbon). Sites with short travel times tended to be high in nitrate and DO but low in ammonium and DOC. Ammonium concentration of interstitial water also was influenced by sorption-desorption processes that involved clay minerals in hyporheic sediments. Denitrification potential in subsurface sediments increased with distance from the channel, and was limited by nitrate at inland sites and by DO in the channel sediments. Conversely, nitrification potential decreased with distance from the channel, and was limited by DO at inland sites and by ammonium at channel locations. Advection of water and dissolved oxygen away from the channel resulted in an oxidized subsurface habitat equivalent to that previously defined as the hyporheic zone. The hyporheic zone is viewed as stream habitat because of its high proportion of surface water and the occurrence of channel organisms. Beyond the channel's hydrologic exchange zone, interstitial water is often chemically reduced. Interstitial water that has not previously entered the channel, groundwater, is viewed as a terrestrial component of the riparian ecotone. Thus, surface water habitats may extend under riparian vegetation, and terrestrial groundwater habitats may be found beneath the stream channel. ?? 1993 Kluwer Academic Publishers.

Triska, F.J.; Duff, J.H.; Avanzino, R.J.

1993-01-01

366

The water channels, new druggable targets to combat cancer cell survival, invasiveness and metastasis.  

PubMed

Cell viability and motility are critical for cancer progression. Among a plethora of mechanisms that regulate these phenotypes, the balance of water and monovalent metal cations plays a pivotal role in the dynamics of focal contacts and cytoskeletal rearrangements at the cell's leading edge. Furthermore, cell survival requires the optimal concentration of water and solutes. This balance is largely maintained by aquaporins (AQPs), a family of 13 small integral plasma membrane proteins whose major function is the transport of water and small solutes across the plasma membrane. We review the recent knowledge about the role of AQPs in cell migration, survival, tumor angiogenesis and metastasis with the focus on therapeutic possibilities to prevent these clinically unfavourable events. The review discusses the inhibition of AQP expression and/or AQP-mediated water influx by acetazolamide, cyclophosphamide, topiramate, thiopental, phenobarbital and propofol. Down-regulation of water transport by these drugs affects cancer cell migration and metastasis. We conclude that AQPs can be considered a point where the mechanisms of survival and motility converge. Therapeutic targeting of AQPs may thus be advantageous for blocking the mechanism common for a number of key cancer phenotypes. PMID:17979673

Monzani, Elena; Shtil, Alexander A; La Porta, Caterina A M

2007-10-01

367

A computational study of water and CO migration sites and channels inside myoglobin.  

PubMed

Pathways are computed for transport of H2O and CO in myoglobin (Mb), using the single sweep and zero-temperature string methods in a fully atomistic, explicitly solvated model system. Our predictions of sites and barriers in the pathways for CO transport agree with previous studies. For H2O, we predict a binding site in the distal pocket (DP), in agreement with crystallographic observations, and another one close to Leu 29 which explains the importance of this residue in controlling the pocket's hydrophobicity, as well as disordered minima in the largely apolar xenon cavities. In particular, H2O can occupy and transition among the xenon cavities, Xe4, Xe2, and Xe3. Our results support the hypothesis that the thermodynamically most favorable entry/exit portal for H2O is the so-called histidine gate (HG), the same as for CO. This result, along with the observation of water occupation of both DP and apolar Xe cavities, suggest that water and small gas molecules like CO compete for access to the protein interior, and therefore models of gas molecule transport within proteins should also explicitly consider water transport. PMID:23505344

Lapelosa, Mauro; Abrams, Cameron F

2013-02-12

368

A computational study of water and CO migration sites and channels inside myoglobin  

PubMed Central

Pathways are computed for transport of H2O and CO in myoglobin (Mb), using the single sweep and zero-temperature string methods in a fully atomistic, explicitly solvated model system. Our predictions of sites and barriers in the pathways for CO transport agree with previous studies. For H2O, we predict a binding site in the distal pocket (DP), in agreement with crystallographic observations, and another one close to Leu 29 which explains the importance of this residue in controlling the pocket’s hydrophobicity, as well as disordered minima in the largely apolar xenon cavities. In particular, H2O can occupy and transition among the xenon cavities, Xe4, Xe2, and Xe3. Our results support the hypothesis that the thermodynamically most favorable entry/exit portal for H2O is the so-called histidine gate (HG), the same as for CO. This result, along with the observation of water occupation of both DP and apolar Xe cavities, suggest that water and small gas molecules like CO compete for access to the protein interior, and therefore models of gas molecule transport within proteins should also explicitly consider water transport. PMID:23505344

Lapelosa, Mauro

2013-01-01

369

Water channel in the binding site of a high affinity anti-methotrexate antibody.  

PubMed

In the present study, we report the structure of the free and drug-bound Fab fragment of a high affinity anti-methotrexate antibody and perform a thermodynamic analysis of the binding process. The anti-methotrexate Fab fragment features a remarkably rigid tunnel-like binding site that extends into a water channel serving as a specialized route to move solvent out and into the site upon ligand binding and dissociation. This new finding in antibody structure-function relationships directly relates to the fast association (1 × 10? M?¹ s?¹) and slow dissociation (4 × 10?? s?¹) rates determined for mAb ADD056, resulting in a very strong binding with a K(D) ~ 3.6 pM at 20 °C. As follows from the X-ray data analysis, the methotrexate-antibody complex is stabilized by an extended network of hydrogen bonds and stacking interactions. The analysis also shows structural involvement of the CDR H3 in formation of the water channel revealing another important role of this hypervariable region. This suggests a new direction in natural affinity maturation and opens a new possibility in antibody engineering. Methotrexate is a widely used therapeutic agent for many malignant diseases and inflammatory disorders. Unfortunately, it may also interfere with central aspects of metabolism and thereby cause inevitable side effects. Therefore, methotrexate therapy requires careful monitoring of drug blood levels, which is traditionally done by immunoassays. An understanding of the structure-function properties of antibodies selected for drug monitoring substantiates the performance and robustness of such tests. PMID:24832237

Gayda, Susan; Longenecker, Kenton L; Manoj, Sharmila; Judge, Russell A; Saldana, Sylvia C; Ruan, Qiaoqiao; Swift, Kerry M; Tetin, Sergey Y

2014-06-17

370

Multiple pharmacological actions of centrally acting antitussives--Do they target G protein-coupled inwardly rectifying K? (GIRK) channels?  

PubMed

Antitussive drugs have been used for decades and their modes of action are well elucidated. However, recent studies on the mechanism of their antitussive action seem to be opening a new way for discovery or development of novel drugs for intractable brain diseases including psychiatric disorders. Antitussives inhibit the currents caused by activation of G protein-coupled inwardly rectifying K? (GIRK) channels in neurons. In our own studies carried out so far, we found that antitussives possessing an inhibitory action on GIRK channels, similar to the effects of an enriched environment, ameliorate symptoms of intractable brain diseases in various animal models. In this review, the multiple pharmacological actions of the antitussives are described, and their mechanisms are discussed addressing GIRK channels as a possible molecular target. PMID:23059953

Takahama, Kazuo

2012-01-01

371

Transport of Small Molecules Across Cell Membranes: Water Channels and Urea Transporters  

NSDL National Science Digital Library

How do small hydrophilic nonelectrolytes cross cell membranes? Which pathways are most important for small lipid insoluble molecules to cross cell membranes? These are questions that have been basic to membrane transport physiology for decades. More importantly, these are questions whose answers have changed significantly within the last 10 years. This review discusses the evidence that pathways other than the lipid bilayer itself exist for the transport across cell membranes of specific small hydrophilic nonelectrolytes. The description begins with briefly analyzing the relevance of well accepted basic mathematical models for transport for understanding the permeability of representative physiologically important molecules across actual cell membranes. Particular emphasis is placed on describing recently discovered proteins that facilitate the transport of some of the smallest physiologically important lipid-insoluble molecules, water, and urea. Evidence also exists for transport proteins that selectively enhance the transmembrane transport of other small lipid-insoluble molecules. Do nonselective pores for small molecules exist in cell membranes?

PhD Barbara E. Goodman (University of South Dakota School of Medicine Division of Basic Biomedical Sciences)

2002-09-01

372

DEFECTIVE TRAFFICKING OF CONE PHOTORECEPTOR CNG CHANNELS INDUCES THE UNFOLDED PROTEIN RESPONSE AND ER STRESS-ASSOCIATED CELL DEATH  

PubMed Central

SYNOPSIS Mutations that perturb the function of photoreceptor cyclic nucleotide-gated (CNG) channels are associated with several human retinal disorders, but the molecular and cellular mechanisms leading to photoreceptor dysfunction and degeneration remain unclear. Many loss-of-function mutations result in intracellular accumulation of CNG channel subunits. Accumulation of proteins in the endoplasmic reticulum (ER) is known to cause ER stress and trigger the unfolded protein response (UPR), an evolutionarily conserved cellular program that results in either adaptation via increased protein processing capacity or apoptotic cell death. We hypothesize that defective trafficking of cone photoreceptor CNG channels can induce UPR-mediated cell death. To test this idea, CNGA3 subunits bearing the R563H and Q655X mutations were expressed in photoreceptor-derived 661W cells with CNGB3 subunits. Compared to wild type, R563H and Q655X subunits displayed altered degradation rates and/or were retained in the ER. ER retention was associated with increased expression of UPR-related markers of ER stress and with decreased cell viability. Chemical and pharmacological chaperones (TUDCA, 4PBA, and the cGMP analog CPT-cGMP) differentially reduced degradation and/or promoted plasma-membrane localization of defective subunits. Improved subunit maturation was concordant with reduced expression of ER stress markers and improved viability of cells expressing localization-defective channels. These results indicate that ER stress can arise from expression of localization defective CNG channels, and may represent a contributing factor for photoreceptor degeneration. PMID:21992067

Duricka, Deborah L.; Brown, R. Lane; Varnum, Michael D.

2011-01-01

373

G-protein-independent modulation of P-type calcium channels by ?-opioids in Purkinje neurons of rat  

PubMed Central

P-type calcium channels play a key role in the synaptic transmission between mammalian central neurons since a major part of calcium entering pre-synaptic terminals is delivered via these channels. Using conventional whole-cell patch clamp techniques we have studied the effect of ?-opioids on P-type calcium channels in acutely isolated Purkinje neurons from rat cerebellum. The selective ?-opioid agonist DAMGO (10 nM) produced a small, but consistent facilitation of current through P-type calcium channels (10±1%, n=27, p<0.001). The effect of DAMGO was rapid (less than 10 sec) and fully reversible. This effect was both concentration and voltage-dependent. The EC50 for the effect of DAMGO was 1.3±0.4 nM and the saturating concentration was 100 nM. The endogenous selective agonist of ?-opioid receptors, endomorphin-1 demonstrated similar action. Intracellular perfusion of Purkinje neurons with GTP?S (0.5 mM) or GDP?S (0.5 mM), as well as strong depolarizing pre-pulses (+50 mV), did not eliminate facilitatory action of DAMGO on P-channels indicating that this effect is not mediated by G-proteins. Furthermore, the effect of DAMGO was preserved in the presence of a non-specific inhibitor of PKA and PKC, (H7, 10 ?M) inside the cell. DAMGO–induced facilitation of P-current was almost completely abolished by the selective ?-opioid antagonist CTOP (100 nM). These observations indicate that ?-type opioid receptors modulate P-type calcium channels in Purkinje neurons via G-protein-independent mechanism. PMID:20541588

Iegorova, Olena; Fisyunov, Alexander; Krishtal, Oleg

2010-01-01

374

Water around thermophilic proteins: the role of charged and apolar atoms  

NASA Astrophysics Data System (ADS)

The thermal response of three proteins with mesophilic, thermophilic and hyperthermophilic character hints at the essential role played in thermostability by the protein-water interface. The formation of spanning water clusters enveloping the macromolecule and their resistance to thermal stress is shown to correlate with the charge distribution at the protein surface; in particular our findings suggest an effective role of the superficial charge distribution in stabilizing the global connectivity of the hydration water.

Sterpone, Fabio; Bertonati, Claudia; Briganti, Giuseppe; Melchionna, Simone

2010-07-01

375

Molecular characterization, phylogenetic analysis and expression patterns of five protein arginine methyltransferase genes of channel catfish, Ictalurus punctatus (Rafinesque).  

PubMed

Protein arginine methylation, catalyzed by protein arginine methyltransferases (PRMT), has recently emerged as an important modification in the regulation of gene expression. In this communication, we identified and characterized the channel catfish orthologs to human PRMT 1, 3, 4 and 5, and PRMT4 like. Each PRMT nucleic acid sequence has an open reading frame (ORF) and 3'-untranslated regions. Each ORF appears to encode 361, 587 and 458 amino acid residues for PRMT1, PRMT4 and variant, respectively. The partial ORF of PRMT3 and PRMT5 encode 292 and 563 amino acids, respectively. By comparison with the human counterparts, each channel catfish PRMT also has conserved domains. For expression profile, the channel catfish PRMT1 transcript was detected by RT-PCR in spleens, anterior kidneys, livers, intestines, skin and gills of fish examined. Except in liver, the PRMT3 transcript was detected in all catfish tissues examined. However, the PRMT4 cDNA was detected in livers from all three catfish and gills from two fish, but not other tissues. This information will enable us to further elucidate PRMT functions in channel catfish. PMID:22286871

Yeh, Hung-Yueh; Klesius, Phillip H

2012-08-01

376

5,5?-Dithio-bis(2-nitrobenzoic acid) modification of cysteine improves the crystal quality of human chloride intracellular channel protein 2  

Microsoft Academic Search

Structural studies of human chloride intracellular channel protein 2 (CLIC2) had been hampered by the problem of generating suitable crystals primarily due to the protein containing exposed cysteines. Several chemical reagents were used to react with the cysteines on CLIC2 in order to modify the redox state of the protein. We have obtained high quality crystals that diffracted to better

Wei Mi; Lanfen Li; Xiao-Dong Su

2008-01-01

377

Free lysine ( l-lysine · HCl) is utilized for growth less efficiently than protein-bound lysine (soybean meal) in practical diets by young channel catfish ( Ictalurus punctatus)  

Microsoft Academic Search

Two 10-week feeding experiments were conducted with channel catfish fingerlings in aquaria to compare the efficiency of utilization for growth of free versus protein bound lysine in practical diets. In experiment 1, a basal, 26% protein diet, deficient only in lysine, was formulated with a combination of peanut meal and corn gluten meal as the primary protein source. The diet

Dannie D. Zarate; Richard T. Lovell

1997-01-01

378

ENaC Channels in Oocytes from Xenopus laevis and their Regulation by xShroom1 Protein  

Microsoft Academic Search

Shroom is a family of related proteins linked to the actin cytoskeleton. xShroom1 is constitutively expressed in X. oocytes and is required for the expression of amiloride sensitive sodium channels (ENaC). Oocytes were injected with ?, ?, and ? mENaC and xShroom1 sense or antisense oligonucleotides. We used voltage clamp techniques to study the amiloride-sensitive Na+ currents (INa(amil)). We observed

Yanina A. Assef; Marcelo Ozu; Gabriela I. Marino; Luciano Galizia; Basilio A. Kotsias

2011-01-01

379

A Trace Component of Ginseng that Inhibits Ca2+ Channels through a Pertussis Toxin-Sensitive G Protein  

Microsoft Academic Search

A crude extract from ginseng root inhibits high-threshold, voltage-dependent Ca2+ channels through an unknown receptor linked to a pertussis toxin-sensitive G protein. We now have found the particular compound that seems responsible for the effect: it is a saponin, called ginsenoside Rf (Rf), that is present in only trace amounts within ginseng. At saturating concentrations, Rf rapidly and reversibly inhibits

Seung-Yeol Nah; Hwa-Jin Park; Edwin W. McCleskey

1995-01-01

380

Channel catfish (Ictalurus punctatus) protein disulphide isomerase, PDIA6: molecular characterization and expression regulated by bacteria and virus inoculation.  

PubMed

Protein disulfide isomerases (PDIs) are thought to aid protein folding and assembly by catalyzing formation and shuffling of cysteine disulfide bonds in the endoplasmic reticulum (ER). Currently, increasing evidence suggests PDIs play an important role in host cell invasion and they are relevant targets for the host immune response. However the roles of specific PDIs in teleosts are little known. Here, we characterized the Protein disulfide isomerase family A, member 6 (PDIA6) from channel catfish, Ictalurus punctatus (named as ccPDIA6). The catfish ccPDIA6 gene was homologous to those of other vertebrate species with 13 exons and 12 introns. The consensus full-length ccPDIA6 cDNA contained an ORF of 1320 bp encoding a putative protein of 439 amino acids. It had a 19 amino acid signal peptide and two active thioredoxin-like domains. Sequence of phylogenic analysis and multiple alignments showed that ccPDIA6 was conserved throughout vertebrate evolution. Southern blot analysis suggested the presence of one copy of the ccPDIA6 gene in the catfish genome. Tissue distribution shows that ccPDIA6 was expressed in all examined tissues at the mRNA level. When using the aquatic z