Science.gov

Sample records for water channel proteins

  1. Membrane Proteins Aquaporin Water Channels (Nobel Lecture)**

    E-print Network

    Economou, Tassos

    Membrane Proteins Aquaporin Water Channels (Nobel Lecture)** Peter Agre* Thank you very much. I am AQP7 and AQP9 4287 Nonhuman Aquaporins 4287 Conclusion 4288 [*] Prof. Dr. P. Agre The Johns Hopkins this lecture. P. AgreReviews 4278 2004 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim DOI: 10.1002/anie.200460804

  2. Expression of Water Channel Proteins in Mesembryanthemum crystallinum1

    PubMed Central

    Kirch, Hans-Hubert; Vera-Estrella, Rosario; Golldack, Dortje; Quigley, Francoise; Michalowski, Christine B.; Barkla, Bronwyn J.; Bohnert, Hans J.

    2000-01-01

    We have characterized transcripts for nine major intrinsic proteins (MIPs), some of which function as water channels (aquaporins), from the ice plant Mesembryanthemum crystallinum. To determine the cellular distribution and expression of these MIPs, oligopeptide-based antibodies were generated against MIP-A, MIP-B, MIP-C, or MIP-F, which, according to sequence and functional characteristics, are located in the plasma membrane (PM) and tonoplast, respectively. MIPs were most abundant in cells involved in bulk water flow and solute flux. The tonoplast MIP-F was found in all cells, while signature cell types identified different PM-MIPs: MIP-A predominantly in phloem-associated cells, MIP-B in xylem parenchyma, and MIP-C in the epidermis and endodermis of immature roots. Membrane protein analysis confirmed MIP-F as tonoplast located. MIP-A and MIP-B were found in tonoplast fractions and also in fractions distinct from either the tonoplast or PM. MIP-C was most abundant but not exclusive to PM fractions, where it is expected based on its sequence signature. We suggest that within the cell, MIPs are mobile, which is similar to aquaporins cycling through animal endosomes. MIP cycling and the differential regulation of these proteins observed under conditions of salt stress may be fundamental for the control of tissue water flux. PMID:10806230

  3. Molecular Cloning, Overexpression and Characterization of a Novel Water Channel Protein from Rhodobacter sphaeroides

    PubMed Central

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

    2014-01-01

    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 cm3/s or 4.17 (±1.38)×1010 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

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

    PubMed Central

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

    2007-01-01

    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

  5. 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...

  6. The first water channel protein (later called aquaporin 1) was first discovered in Cluj-Napoca, Romania.

    PubMed

    Benga, Gheorghe

    2004-01-01

    This invited review briefly outlines the importance of membrane water permeability, highlights the landmarks leading to the discovery of water channels. After a decade of systematic studies on water channels in human RBC Benga's group discovered in 1985 the presence and location of the water channel protein among the polypeptides migrating in the region of 35-60 kDa on the electrophoretogram of RBC membrane proteins. The work was extended and reviewed in several articles. In 1988, Agre and coworkers isolated a new protein from the RBC membrane, nick-named CHIP28 (channel-forming integral membrane protein of 28 kDa). However, in addition to the 28 kDa component, this protein had a 35-60 kDa glycosylated component, the one detected by the Benga's group. Only in 1992 Agre's group suggested that "it is likely that CHIP28 is a functional unit of membrane water channels". Half of the 2003 Nobel Prize in Chemistry was awarded to Peter Agre (Johns Hopkins University, Baltimore, USA) "for the discovery of water channels", actually the first water channel protein from the human red blood cell (RBC) membrane, known today as aquaporin 1 (AQP1). The seminal contributions from 1986 of the Benga's group were grossly overlooked by Peter Agre and by the Nobel Prize Committee. Thousands of science-related professionals from hundreds of academic and research units, as well as participants in several international scientific events, have signed as supporters of Benga; his priority is also mentioned in several comments on the 2003 Nobel Prize. PMID:15984652

  7. Characterization of OsPIP2;7, a water channel protein in rice.

    PubMed

    Li, Guo-Wei; Zhang, Min-Hua; Cai, Wei-Ming; Sun, Wei-Ning; Su, Wei-Ai

    2008-12-01

    Aquaporins are water channel proteins that facilitate passage of water and other small neutral molecules across biological membranes. There are usually a large number of members of this family in higher plants, which exhibit various physiological functions and are regulated in a time-specific and particular mode. We have previously shown that a rice gene, OsPIP2;7, was generally up-regulated in roots but down-regulated in shoots at the early stage of chilling stress. Here, OsPIP2;7 was cloned and proved to be an aquaporin with high activity in Xenopus oocytes. OsPIP2;7 was localized mainly in mesophyll cells of leaves. In roots it was detected in the vascular tissues, epidermis cells and exodermis cells at the elongation zone, as well as in the epidermis cells, exodermis cells and root hair at the maturation zone. Yeast cells overexpressing OsPIP2;7 showed a higher survival rate after freeze-thaw stress. Furthermore, OsPIP2;7 enhanced the transpiration rate and tolerance to low temperature when overexpressed in rice. These results indicated that OsPIP2;7 was involved in rapid water transport and maintenance of the water balance in cells, and ultimately improves the tolerance of yeast and rice to low temperature stress. PMID:18988636

  8. Redistribution of the water channel protein aquaporin-4 and the K+ channel protein Kir4.1 differs in low- and high-grade human brain tumors.

    PubMed

    Warth, Arne; Mittelbronn, Michel; Wolburg, Hartwig

    2005-04-01

    The blood-brain barrier (BBB) regulation is characterized by an interplay between endothelial cells, subendothelial basal laminae and astrocytic cells. Astroglial cells are highly polarized by the differentiation of perivascular membrane domains. These domains are characterized by the aggregation of, among other molecules, the water channel protein aquaporin-4 (AQP4), the dystrophin-dystroglycan complex, and the inwardly rectifying potassium channel protein Kir4.1. Normally, this ion channel plays an important role in spatial buffering of extracellular K(+) in the central nervous system, which only can be performed due to the non-uniform distribution of Kir4.1 across the surface of the glial cell. In this study, we observed a mislocalization of Kir4.1 in various human brain tumors (low- and high-grade astrocytomas and oligodendrogliomas), suggesting that buffering capacity of glial cells may be compromised, leading to water influx (cytotoxic edema). Interestingly, whereas dystrophin remained regularly restricted at the endfeet membranes in all cases investigated, AQP4 was found to be redistributed only in high-grade astrocytomas, not in low-grade astrocytomas. If the mechanisms of redistribution of AQP4 and Kir4.1 are different in low- and high-grade gliomas, this may suggest that the mechanisms of clustering of AQP4 and Kir4.1 at the glial endfeet membrane domains are also different. The redistribution of AQP4 in glioblastoma cells is discussed as a reaction to the vasogenic edema, as induced by the breakdown of the BBB, to facilitate reabsorption of excess fluid. PMID:15723236

  9. The role of water channel proteins in facilitating recovery of leaf hydraulic conductance from water stress in Populus trichocarpa.

    PubMed

    Laur, Joan; Hacke, Uwe G

    2014-01-01

    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

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

    PubMed Central

    Laur, Joan; Hacke, Uwe G.

    2014-01-01

    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

  11. Water channel proteins: from their discovery in 1985 in Cluj-Napoca, Romania, to the 2003 Nobel Prize in Chemistry.

    PubMed

    Benga, Gh

    2006-01-01

    Water channel proteins, later called aquaporins, are transmembrane proteins that have as their main(specific) function the water transport across biological membranes. The first water channel protein (WCP), now called aquaporin 1, was identified or "seen" in situ (hence discovered) in the human red blood cell (RBC) membrane in 1985 by Benga's group (Cluj-Napoca, Romania). This was achieved by a very selective radiolabeling of RBC membrane proteins with the water transport inhibitor [203Hg]-p-chloromercuribenzene sulfonate (PCMBS), under conditions of specific inhibition. The presence and location of the WCP was discovered among the polypeptides migrating in the region of 35-60 kDa on the electrophoretogram of RBC membrane proteins. The work was first published in 1986 in Biochemistry and Eur. J. Cell Biol. and reviewed by Benga in several articles in 1988-2004. We have thus a world priority in the discovery of the first water channel in the RBC membrane, that was re-discovered by chance by the group of Agre (Baltimore, USA) in 1988, when they isolated a new protein from the RBC membrane, nick-named CHIP28 (channel-forming integral membrane protein of 28 kDa). However, in addition to the 28 kDa component, this protein had a 35-60 kDa glycosylated component, the one detected by Benga's group. Only in 1992 the Agre's group suggested that "it is likely that CHIP28 is a functional unit of membrane water channels". In 1993 CHIP28 was renamed aquaporin 1. Looking in retrospect, asking the crucial question, when was the first WCP, discovered, a fair and clear cut answer would be: the first WCP, now called aquaporin 1, was identified or "seen" (hence discovered) in situ in the human RBC membrane by Benga and coworkers in 1985. It was again "seen" when it was purified in 1988 and again identified when its water transport property was found byAgre's group in 1992. If we make a comparison with the discovery of New World of America, the first man who has "seen" a part, very small indeed, of The New Land was Columbus; later, others, including Amerigo Vespucci (from whom the name derived), have better "seen" and in the subsequent years many explorers discovered the complexity of the Americas. Consequently, the initial discovery of the first water channel by Benga's group must be properly credited; the omission of Gheorghe Benga from the 2003 Nobel Prize in Chemistry (half of which was awarded to Peter Agre "for the discovery of the water channels") was a new mistake in the award of Nobel Prizes. Benga's claim is presented on the web site of the Ad Astra Association (www.ad-astra.ro/benga). As can be seen on this site his recognition as a discoverer of the first water channel protein from the human RBC membrane is growing. Thousands of science-related professionals from hundreds of academic and research units, as well as participants in several international scientific events, have signed as supporters of Benga; his priority is also mentioned in several comments on the 2003 Nobel Prize as presented on the site. PMID:17543216

  12. A Simple Water Channel

    ERIC Educational Resources Information Center

    White, A. S.

    1976-01-01

    Describes a simple water channel, for use with an overhead projector. It is run from a water tap and may be used for flow visualization experiments, including the effect of streamlining and elementary building aerodynamics. (MLH)

  13. Identification and characterization of functional aquaporin water channel protein from alimentary tract of whitefly, Bemisia tabaci

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Some hemipteran xylem and phloem feeding insects have evolved specialized alimentary structures or filter chambers that rapidly transport water for excretion or osmoregulation. In the whitefly, Bemisia tabaci, mass movement of water through opposing alimentary tract tissues within the filter chamber...

  14. Proteins, channels and crowded ions.

    PubMed

    Eisenberg, Bob

    2003-01-01

    Ion channels are proteins with a hole down their middle that control a vast range of biological function in health and disease. Selectivity is an important biological function determined by the open channel, which does not change conformation on the biological time scale. The challenge is to predict the function-the current of ions of different types and concentrations through a variety of channels-from structure, given fundamental physical laws. Walls of ion channels, like active sites of enzymes, often contain several fixed charges. Those fixed charges demand counter ions nearby, and the density of those counter ions is very high, greater than 5 molar, because of the tiny volumes of the channel's pore. Physical chemists can now calculate the free energy per mole of salt solutions (e.g. the activity coefficient) from infinite dilution to saturation, even in ionic melts. Such calculations of a model of the L-type calcium channel show that the large energies needed to crowd charges into the channel can account for the substantial selectivity and complex properties found experimentally. The properties of such crowded charge are likely to be an important determinant of the properties of proteins in general because channels are nearly enzymes. PMID:12646387

  15. Aquaporins: The renal water channels

    PubMed Central

    Agarwal, S. K.; Gupta, A.

    2008-01-01

    Water is the most abundant molecule in any cell. Specialized membrane channel, proteins called aquaporins, facilitate water transport across cell membranes. At least seven aquaporins (AQP): 1, 2, 3, 4, 6, 7, and 11 are expressed in the kidneys. Aquaporins play a role in both the short-term and long-term regulation of water balance as well as in the pathophysiology of water balance disorders. Aquaporin is composed of a single peptide chain consisting of approximately 270 amino acids. Inherited central and nephrogenic diabetes insipidus are primarily due to the decreased expression of AQP2 while mutation in the AQP2 molecule is responsible for inherited central diabetes insipidus. In acquired causes of nephrogenic diabetes insipidus, there is a downregulation of AQP2 expression in the inner medulla of the kidney. Nephrotic syndrome is characterized by excessive sodium and water reabsorption, although in spite of this, patients do not develop hyponatremia. There is a marked downregulation of both AQP2 and AQP3 expression, which could be a physiologic response to extracellular water reabsorption in patients with nephrotic syndrome. There are some conditions in which aquaporin expression has been found to increase such as experimentally induced heart failure, cirrhosis, and pregnancy. Some drugs such as cisplatin and cyclosporine, also alter the expression of aquaporins. The three-pore model of peritoneal transport depicts the importance of aquaporins. Thus, the understanding of renal water channels has solved the mystery behind many water balance disorders. Further insights into the molecular structure and biology of aquaporins will help to lay a foundation for the development of future drugs. PMID:20142913

  16. Protein-fluctuation-induced water-pore formation in ion channel voltage-sensor translocation across a lipid bilayer membrane

    NASA Astrophysics Data System (ADS)

    Rajapaksha, Suneth P.; Pal, Nibedita; Zheng, Desheng; Lu, H. Peter

    2015-11-01

    We have applied a combined fluorescence microscopy and single-ion-channel electric current recording approach, correlating with molecular dynamics (MD) simulations, to study the mechanism of voltage-sensor domain translocation across a lipid bilayer. We use the colicin Ia ion channel as a model system, and our experimental and simulation results show the following: (1) The open-close activity of an activated colicin Ia is not necessarily sensitive to the amplitude of the applied cross-membrane voltage when the cross-membrane voltage is around the resting potential of excitable membranes; and (2) there is a significant probability that the activation of colicin Ia occurs by forming a transient and fluctuating water pore of ˜15 Å diameter in the lipid bilayer membrane. The location of the water-pore formation is nonrandom and highly specific, right at the insertion site of colicin Ia charged residues in the lipid bilayer membrane, and the formation is intrinsically associated with the polypeptide conformational fluctuations and solvation dynamics. Our results suggest an interesting mechanistic pathway for voltage-sensitive ion channel activation, and specifically for translocation of charged polypeptide chains across the lipid membrane under a transmembrane electric field: the charged polypeptide domain facilitates the formation of hydrophilic water pore in the membrane and diffuses through the hydrophilic pathway across the membrane; i.e., the charged polypeptide chain can cross a lipid membrane without entering into the hydrophobic core of the lipid membrane but entirely through the aqueous and hydrophilic environment to achieve a cross-membrane translocation. This mechanism sheds light on the intensive and fundamental debate on how a hydrophilic and charged peptide domain diffuses across the biologically inaccessible high-energy barrier of the hydrophobic core of a lipid bilayer: The peptide domain does not need to cross the hydrophobic core to move across a lipid bilayer.

  17. Computational optimization of synthetic water channels.

    SciTech Connect

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

    2012-12-01

    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.

  18. Water channels in peritoneal dialysis.

    PubMed

    Devuyst, Olivier

    2010-01-01

    Peritoneal dialysis involves diffusive and convective transports and osmosis through the highly vascularized peritoneal membrane. Several lines of evidence have demonstrated that the water channel aquaporin-1 (AQP1) corresponds to the ultrasmall pore predicted by the modelization of peritoneal transport. Proof-of-principle studies have shown that up-regulation of the expression of AQP1 in peritoneal capillaries is reflected by increased water permeability and ultrafiltration, without affecting the osmotic gradient and the permeability for small solutes. Inversely, studies in Aqp1 mice have shown that haploinsufficiency in AQP1 is reflected by significant attenuation of water transport. Recent studies have identified lead compounds that could act as agonists of aquaporins, as well as putative binding sites and potential mechanisms of gating the water channel. By modulating water transport, these pharmacological agents could have clinically relevant effects in targeting specific tissues or disease states. These studies on the peritoneal membrane also provide an experimental framework to investigate the role of water channels in the endothelium and various cell types. PMID:21170876

  19. Water-transporting proteins.

    PubMed

    Zeuthen, Thomas

    2010-04-01

    Transport through lipids and aquaporins is osmotic and entirely driven by the difference in osmotic pressure. Water transport in cotransporters and uniporters is different: Water can be cotransported, energized by coupling to the substrate flux by a mechanism closely associated with protein. In the K(+)/Cl(-) and the Na(+)/K(+)/2Cl(-) cotransporters, water is entirely cotransported, while water transport in glucose uniporters and Na(+)-coupled transporters of nutrients and neurotransmitters takes place by both osmosis and cotransport. The molecular mechanism behind cotransport of water is not clear. It is associated with the substrate movements in aqueous pathways within the protein; a conventional unstirred layer mechanism can be ruled out, due to high rates of diffusion in the cytoplasm. The physiological roles of the various modes of water transport are reviewed in relation to epithelial transport. Epithelial water transport is energized by the movements of ions, but how the coupling takes place is uncertain. All epithelia can transport water uphill against an osmotic gradient, which is hard to explain by simple osmosis. Furthermore, genetic removal of aquaporins has not given support to osmosis as the exclusive mode of transport. Water cotransport can explain the coupling between ion and water transport, a major fraction of transepithelial water transport and uphill water transport. Aquaporins enhance water transport by utilizing osmotic gradients and cause the osmolarity of the transportate to approach isotonicity. PMID:20091162

  20. A substrate channel in the nitrogenase MoFe protein.

    PubMed

    Barney, Brett M; Yurth, Michael G; Dos Santos, Patricia C; Dean, Dennis R; Seefeldt, Lance C

    2009-09-01

    Nitrogenase catalyzes the six electron/six proton reduction of N2 to two ammonia molecules at a complex organometallocluster called "FeMo cofactor." This cofactor is buried within the alpha-subunit of the MoFe protein, with no obvious access for substrates. Examination of high-resolution X-ray crystal structures of MoFe proteins from several organisms has revealed the existence of a water-filled channel that extends from the solvent-exposed surface to a specific face of FeMo cofactor. This channel could provide a pathway for substrate and product access to the active site. In the present work, we examine this possibility by substituting four different amino acids that line the channel with other residues and analyze the impact of these substitutions on substrate reduction kinetic parameters. Each of the MoFe protein variants was purified and kinetic parameters were established for the reduction of the substrates N2, acetylene, azide, and propyne. For each MoFe protein, V (max) values for the different substrates were found to be nearly unchanged when compared with the values for the wild-type MoFe protein, indicating that electron delivery to the active site is not compromised by the various substitutions. In contrast, the K(m) values for these substrates were found to increase significantly (up to 22-fold) in some of the MoFe protein variants compared with the wild-type MoFe protein values. Given that each of the amino acids that were substituted is remote from the active site, these results are consistent with the water-filled channel functioning as a substrate channel in the MoFe protein. PMID:19458968

  1. [Ion channels and water channels--a prerequisite for living cells and electric signals in the brain].

    PubMed

    Storm, Johan F

    2003-12-01

    Water channels and ion channels are membrane proteins that transport water and ions into and out of cells with high selectivity and efficiency. Peter Agre and Roderick MacKinnon were awarded the Nobel Prize in chemistry 2003 for their discoveries of the structure of water channels and ion channel proteins, thus explaining basal mechanisms that are fundamental to all forms of life and in particular to the electrical signalling in the brain. These scientific achievements answer questions that biophysicists and physiologists have discussed since the 19th century. PMID:14713970

  2. Molecular dynamics insights into human aquaporin 2 water channel.

    PubMed

    Binesh, A R; Kamali, R

    2015-12-01

    In this study, the first molecular dynamics simulation of the human aquaporin 2 is performed and for a better understanding of the aquaporin 2 permeability performance, the characteristics of water transport in this protein channel and key biophysical parameters of AQP2 tetramer including osmotic and diffusive permeability constants and the pore radius are investigated. For this purpose, recently recovered high resolution X-ray crystal structure of` the human aquaporin 2 is used to perform twenty nanosecond molecular dynamics simulation of fully hydrated tetramer of this protein embedded in a lipid bilayer. The resulting water permeability characteristics of this protein channel showed that the water permeability of the human AQP2 is in a mean range in comparison with other human aquaporins family. Finally, the results reported in this research demonstrate that molecular dynamics simulation of human AQP2 provided useful insights into the mechanisms of water permeation and urine concentration in the human kidney. PMID:26489820

  3. AQP1 is not only a water channel

    PubMed Central

    2010-01-01

    AQPs are water channel proteins. In particular, AQP1 was demonstrated to be involved in cell migration. According to the model proposed by Verkman and collaborators, AQP drives water influx, facilitating lamellipodia extension and cell migration. Investigating the possible connection between AQP1 and cytoskeleton, our group showed that such a water channel through Lin7/?-catenin affects the organization of the cytoskeleton and proposed a model. All together, these data appear particularly intriguing since the use of AQP1 as target might be useful to modulate angiogenesis/vasculogenic mimicry. PMID:20168076

  4. Communication channels between membrane bound proteins

    NASA Astrophysics Data System (ADS)

    Sethna, James; Machta, Benjamin; Veatch, Sarah

    2012-02-01

    Much of what might be called biological computation takes place on the plasma membrane, a 2D liquid composed of a diverse soup of lipids and embedded proteins. Motivated by the recent discovery that these membranes seem to be tuned close to a 2D liquid-liquid critical point, we set out to understand the different channels through which membrane bound proteins can communicate. Diffusing proteins can carry out reactions like phosphorylation when they come in contact with each other. Near criticality, proteins can also exert long-ranged critical Casimir forces on one another by coupling to the local composition order parameter. By modulating the growth and breakdown of the rigid cytoskeleton, they can direct forces on even more distant regions. In addition, proteins can control the release and production of second messengers that diffuse either through the bulk, or in the plane of the membrane itself. By making simple models for these processes we bound functional measures for them as communication channels. These include information theoretic measures of bandwidth, as well as physical measures of energetic efficiency and speed. Our results will likely shed light on the functional role of clustering and other collective behaviors often seen in experiments.

  5. Solubilization of membrane proteins in ethanol: new perspective method for isolation of ion channels

    NASA Astrophysics Data System (ADS)

    Mironova, Galina D.

    1997-06-01

    In spite of the successful use of detergents for the solubilization of a number of membrane proteins, this approach has some restrictions. It is mainly due to difficulties in removing detergents from the proteins which can influence the structure and function of the isolated proteins and interfere with channel activity measurements under the reconstruction of the proteins into lipid bilayers. We have developed a method using ethanol for the extraction of membrane proteins. The dielectric constant of ethanol is between those of water and carbohydrates which aids it to penetrate into the membrane between protein and lipids. This decrease the binding of lipids to proteins and promotes protein solubilization. We have applied this approach to the isolation and reconstitution in lipid bilayer of the large subunit of the (Na+, K+)- ATPase from microsomes and from mitochondria: two Ca2+-channels, thermogenin and the KATP channel. The properties of these channels remained native.

  6. Water at interface with proteins

    E-print Network

    Giancarlo Franzese; Valentino Bianco; Svilen Iskrov

    2010-12-07

    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.

  7. Desformylgramicidin: a model channel with an extremely high water permeability.

    PubMed Central

    Saparov, S M; Antonenko, Y N; Koeppe, R E; Pohl, P

    2000-01-01

    The water conductivity of desformylgramicidin exceeds the permeability of gramicidin A by two orders of magnitude. With respect to its single channel hydraulic permeability coefficient of 1.1.10(-12) cm(3) s(-1), desformylgramicidin may serve as a model for extremely permeable aquaporin water channel proteins (AQP4 and AQPZ). This osmotic permeability exceeds the conductivity that is predicted by the theory of single-file transport. It was derived from the concentration distributions of both pore-impermeable and -permeable cations that were simultaneously measured by double barreled microelectrodes in the immediate vicinity of a planar bilayer. From solvent drag experiments, approximately five water molecules were found to be transported by a single-file process along with one ion through the channel. The single channel proton, potassium, and sodium conductivities were determined to be equal to 17 pS (pH 2.5), 7 and 3 pS, respectively. Under any conditions, the desformyl-channel remains at least 10 times longer in its open state than gramicidin A. PMID:11053127

  8. Water Stress and Protein Synthesis

    PubMed Central

    Dhindsa, R. S.; Cleland, R. E.

    1975-01-01

    Water stress causes both a qualitative change in the types of proteins produced by Avena coleoptile cells as demonstrated by a double-labeling ratio technique, and a quantitative reduction in the rate of incorporation of leucine into proteins. The osmotica mannitol and Carbowax-4000 cause similar changes in the pattern of protein synthesis showing that these effects are due to water stress rather than to a particular osmoticum. PMID:16659166

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

    E-print Network

    Gerwert, Klaus

    Proton transfer via a transient linear water-molecule chain in a membrane protein Erik Freiera,1-resolution protein ground-state structures of proton pumps and channels have revealed internal protein-bound water. An illustration of the formation of a pro- tonated protein-bound water cluster that is actively involved in proton

  10. Structure of Synaptophysin: A Hexameric MARVEL-Domain Channel Protein

    E-print Network

    Pace, Norman

    Structure Article Structure of Synaptophysin: A Hexameric MARVEL-Domain Channel Protein ChristopherI) is an archetypal member of the MARVEL-domain family of integral mem- brane proteins and one of the first synaptic ves- icle proteins to be identified and cloned. Most all MARVEL-domain proteins are involved

  11. Small Water Islands in Proteins

    NASA Astrophysics Data System (ADS)

    Helms, V.; Wade, R. C.; McCammon, J. A.

    1998-03-01

    Proteins often contain water-filled cavities. Their presence may have functional reasons or may be related to protein folding. In any case, they are integral parts of the protein. Here, results from molecular dynamics simulations for two systems are presented. First, we analyzed the hydration of an empty buried enzyme active site, cytochrome P450cam. A hydration free energy landscape was obtained by calculating free energy differences for hydrating the active site with 5 to 8 water molecules. In agreement with the crystal structure and with experiments performed under high hydrostatic pressure, 6 water molecules were found to be most favourable thermodynamically [Helms & Wade, Proteins, submited]. Long-lived hydrogen bond networks exist between the water molecules in the active site and result in a significant ordering. Secondly, results are presented from 5 simulations of green fluorescent protein (GFP) of 1 ns length each. The crystal structures of different forms of GFP contain a cluster of five water molecules next to the chromophore. The water cluster seems to play a crucial part in allowing the protein to switch between a fluorescent and a dark state [Dickson et al., Nature, 388, 385-8]. In the simulations, the water molecules are again strongly ordered by a long-lived hydrogen bond network. Both scenarios are discussed in the context of bulk liquid water.

  12. Gating of the Mechanosensitive Channel Protein MscL: The Interplay of Membrane and Protein

    PubMed Central

    Jeon, Jonggu; Voth, Gregory A.

    2008-01-01

    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 Å 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

  13. 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

  14. Physiological functions of the TRPM4 channels via protein interactions

    PubMed Central

    Lee, Young-Sun; Kim, Eunju; Hwang, Eun Mi; Park, Jae-Yong

    2015-01-01

    Transient Receptor Potential, Melastatin-related, member 4 (TRPM4) channels are Ca2+-activated Ca2+-impermeable cation channels. These channels are expressed in various types of mammalian tissues including the brain and are implicated in many diverse physiological and pathophysiological conditions. In the past several years, the trafficking processes and regulatory mechanism of these channels and their interacting proteins have been uncovered. Here in this minireview, we summarize the current understanding of the trafficking mechanism of TRPM4 channels on the plasma membrane as well as heteromeric complex formation via protein interactions. We also describe physiological implications of protein-TRPM4 interactions and suggest TRPM4 channels as therapeutic targets in many related diseases. [BMB Reports 2015; 48(1): 1-5] PMID:25441424

  15. Ion channel regulation by protein S-acylation

    PubMed Central

    2014-01-01

    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

  16. Activation of maxi-anion channel by protein tyrosine dephosphorylation.

    PubMed

    Toychiev, Abduqodir H; Sabirov, Ravshan Z; Takahashi, Nobuyaki; Ando-Akatsuka, Yuhko; Liu, Hongtao; Shintani, Takafumi; Noda, Masaharu; Okada, Yasunobu

    2009-10-01

    The maxi-anion channel with a large single-channel conductance of >300 pS, and unknown molecular identity, is functionally expressed in a large variety of cell types. The channel is activated by a number of experimental maneuvers such as exposing cells to hypotonic or ischemic stress. The most effective and consistent method of activating it is patch membrane excision. However, the activation mechanism of the maxi-anion channel remains poorly understood at present. In the present study, involvement of phosphorylation/dephosphorylation in excision-induced activation was examined. In mouse mammary fibroblastic C127 cells, activity of the channel was suppressed by intracellular application of Mg-ATP, but not Mg-5'-adenylylimidodiphosphate (AMP-PNP), in a concentration-dependent manner. When a cocktail of broad-spectrum tyrosine phosphatase inhibitors was applied, channel activation was completely abolished, whereas inhibitors of serine/threonine protein phosphatases had no effect. On the other hand, protein tyrosine kinase inhibitors brought the channel out of an inactivated state. In mouse adult skin fibroblasts (MAFs) in primary culture, similar maxi-anion channels were found to be activated on membrane excision, in a manner sensitive to tyrosine phosphatase inhibitors. In MAFs isolated from animals deficient in receptor protein tyrosine phosphatase (RPTP)zeta, activation of the maxi-anion channel was significantly slower and less prominent compared with that observed in wild-type MAFs; however, channel activation was restored by transfection of the RPTPzeta gene. Thus it is concluded that activation of the maxi-anion channel involves protein dephosphorylation mediated by protein tyrosine phosphatases that include RPTPzeta in mouse fibroblasts, but not in C127 cells. PMID:19657061

  17. Regulation of voltage-dependent calcium channels by RGK proteins

    PubMed Central

    Yang, Tingting; Colecraft, Henry M.

    2013-01-01

    RGK proteins belong to the Ras superfamily of monomeric G-proteins, and currently include four members– Rad, Rem, Rem2, and Gem/Kir. RGK proteins are broadly expressed, and are the most potent known intracellular inhibitors of high-voltage-activated Ca2+ (CaV1 and CaV2) channels. Here, we review and discuss the evidence in the literature regarding the functional mechanisms, structural determinants, physiological role, and potential practical applications of RGK-mediated inhibition of CaV1/CaV2 channels. PMID:23063948

  18. Iterative Water-filling for Gaussian Vector Multiple Access Channels

    E-print Network

    Li, Tiffany Jing

    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

  19. Regulation of heartbeat by G protein-coupled ion channels.

    PubMed

    Brown, A M

    1990-12-01

    The coupling of ion channels to receptors by G proteins is the subject of this American Physiological Society Walter B. Cannon Memorial "Physiology in Perspective" Lecture. This subject is particularly appropriate because it includes a molecular explanation of a homeostatic mechanism involving the autonomic nervous system and the latter subject preoccupied Dr. Cannon during most of his career. With the use of reconstitution methods, we and others have shown that heterotrimeric guanine nucleotide-binding (G) proteins couple receptors to ion channels by both membrane-delimited, direct pathways and cytoplasmic second messenger pathways. Furthermore, one set of receptors may be coupled to as many as three different sets of ion channels to form networks. Dual G protein pathways lead to the prediction of biphasic ion current responses in cell signaling, and this prediction was confirmed. In sinoatrial pacemaker cells, the pacemaking hyperpolarization-activated inward current (If) is directly regulated by the G proteins Gs and Go, and the two can act simultaneously. This could explain the classical observation that vagal inhibition of heart rate is greater during sympathetic stimulation. Because deactivation of the muscarinic response occurs much faster than the G protein alpha-subunit hydrolyzes guanosine 5'-triphosphate, we looked for accessory cellular factors. A surprising result was that the small monomeric ras G protein blocked the muscarinic pathway. The significance of this observation is unknown, but it appears that small and large G proteins may interact in ion channel signaling pathways. PMID:1701981

  20. Water transport by the bacterial channel alpha-hemolysin

    NASA Technical Reports Server (NTRS)

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

    1999-01-01

    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.

  1. Water hardness influences Flavobacterium columnare pathogenesis in channel catfish

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Studies were conducted to determine aspects of water chemistry responsible for large differences in pathogenesis and mortality rates in challenges of channel catfish Ictalurus punctatus with Flavobacterium columnare; challenges were conducted in water supplying the Stuttgart National Aquaculture Res...

  2. Leak detection in open water channels Erik Weyer

    E-print Network

    Bastin, Georges

    parameters. Keywords: Fault detection, CUSUM algorithm, system identification, leak detection, irrigationLeak detection in open water channels Erik Weyer Georges Bastin Department of Electrical: In this paper we present a simple cumulative sum algorithm for detection of leaks in open water channels

  3. IDENTIFICATION OF RESONANCE WAVES IN OPEN WATER CHANNELS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This article presents a procedure to determine the characteristics of open water channels required for controller and filter design, with special focus on the resonance waves. Also, a new simplified model structure for open water channels is proposed. The procedure applies System Identification tool...

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

    PubMed Central

    Beurg, Maryline; Kim, Kyunghee X.

    2014-01-01

    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

  5. Protein aggregation and deposition: implications for ion channel formation and membrane damage.

    PubMed

    Kourie, J I; Henry, C L

    2001-08-01

    Protein deposition, aggregation, and formation of amyloids are associated with a wide range of pathologies, including several neurodegenerative diseases. Aggregation and deposition are a result of malfunction in protein folding, assembly, and transport, caused by protein mutation and/or changes in the cell environment. The mechanism of protein deposition and aggregation is triggered when the hydrophobic and positively charged regions of the misfolded proteins are exposed. The cells aim to regulate these misfolded and malfunctioning aggregation-prone proteins by degradation mechanisms, e.g., proteosomes, and/or by storing them in specialized compartments, e.g., Russell bodies and aggresomes. During these processes, however, some aggregation-prone protein intermediates are capable of aggregation and forming beta-sheet based channels in various negatively charged cellular membranes. Adverse cellular conditions, transitional metals, cellular proteins, and genetic mutations play an important role in the formation and function of these non-intrinsic channels. These channels, which can damage membrane function, are pathologic because they can disrupt the metabolic, ionic, and water homeostasis and distort signal transduction. We propose that different conformations of aggregation-prone proteins could alter cell regulation by modifying several ion transport systems and also by forming heterogeneous ion channels. The changes in membrane transport systems are proposed as early steps in impairing neuronal function preceding fibril formation. We conclude that these changes damage the membrane by compromising its integrity and increasing its ion permeability. This mechanism of membrane damage is a general mechanism that may explain other malfunctioning protein processing-related pathologies. PMID:11471187

  6. Innate immune responses of immune proteins in juvenile channel catfish

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Channel catfish (Ictalurus punctatus) are raised for aquaculture in the Southeast U.S. and are susceptible to many bacterial and viral infections acquired from their pond environment. The innate immune proteins mannose-binding lectin (MBL) and lysozyme were studied during two consecutive years in ch...

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

    E-print Network

    Head III, James William

    Mars outflow channels: A reappraisal of the estimation of water flow velocities from water depths channel systems on Mars have relied widely on various versions of the Manning equation. This has led to problems in allowing for the difference between the accelerations due to gravity on Mars and Earth

  8. G Protein Regulation of Ion Channels and Abscisic Acid

    E-print Network

    Jones, Alan M.

    , and hormonal signaling in mam- malian systems (2­4). In higher plants, guard cell ion-channel regulation by inwardly rectifying K chan- nels. During inhibition of stomatal opening by the plant hormone abscisic acid) promotes plant water conservation by decreasing the apertures of stomatal pores in the epidermis through

  9. Erosional processes in channelized water flows on Mars

    NASA Technical Reports Server (NTRS)

    Baker, V. R.

    1979-01-01

    A hypothesis is investigated according to which the Martian outflow channels were formed by high-velocity flows of water or dynamically similar liquid. It is suggested that the outflow channels are largely the result of several interacting erosional mechanisms, including fluvial processes involving ice covers, macroturbulence, streamlining, and cavitation.

  10. WATER TEMPERATURE DYNAMICS IN EXPERIMENTAL FIELD CHANNELS: ANALYSIS AND MODELING

    EPA Science Inventory

    This study is on water temperature dynamics in the shallow field channels of the USEPA Monticello Ecological Research Station (MERS). The hydraulic and temperature environment in the MERS channels was measured and simulated to provide some background for several biological studie...

  11. The Acoustical Channel the Transfer Function of Water Pipes

    E-print Network

    Henkel, Werner

    The Acoustical Channel the Transfer Function of Water Pipes Supervisor Prof Werner Henkel Student in impure water, the ultrasound waves are the only means of communication through water for long distance. Severe study of underwater sound propagation dates back to the first and second world war. In that age

  12. FAITH Water Channel Flow Visualization - Duration: 56 seconds.

    NASA Video Gallery

    Water channel flow visualization experiments are performed on a three dimensional model of a small hill. This experiment was part of a series of measurements of the complex fluid flow around the hi...

  13. 11. SETTLING TANK OVERFLOW CHANNEL, NORTH SIDE. Hondius Water ...

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

    11. SETTLING TANK OVERFLOW CHANNEL, NORTH SIDE. - Hondius Water Line, 1.6 miles Northwest of Park headquarters building & 1 mile Northwest of Beaver Meadows entrance station, Estes Park, Larimer County, CO

  14. Acoustic MIMO communications in a very shallow water channel

    NASA Astrophysics Data System (ADS)

    Zhou, Yuehai; Cao, Xiuling; Tong, Feng

    2015-12-01

    Underwater acoustic channels pose significant difficulty for the development of high speed communication due to highly limited band-width as well as hostile multipath interference. Enlightened by rapid progress of multiple input multiple output (MIMO) technologies in wireless communication scenarios, MIMO systems offer a potential solution by enabling multiple spatially parallel communication channels to improve communication performance as well as capacity. For MIMO acoustic communications, deep sea channels offer substantial spatial diversity among multiple channels that can be exploited to address simultaneous multipath and co-channel interference. At the same time, there are increasing requirements for high speed underwater communication in very shallow water area (for example, a depth less than 10 m). In this paper, a space-time multichannel adaptive receiver consisting of multiple decision feedback equalizers (DFE) is adopted as the receiver for a very shallow water MIMO acoustic communication system. The performance of multichannel DFE receivers with relatively small number of receiving elements are analyzed and compared with that of the multichannel time reversal receiver to evaluate the impact of limited spatial diversity on multi-channel equalization and time reversal processing. The results of sea trials in a very shallow water channel are presented to demonstrate the feasibility of very shallow water MIMO acoustic communication.

  15. Model studies of dense water overflows in the Faroese Channels

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

    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.

  16. 5. GATE 5, INTAKE CHANNEL LOOKING SOUTH; WATER FROM GATE ...

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

    5. GATE 5, INTAKE CHANNEL LOOKING SOUTH; WATER FROM GATE 5 ENTERED DITCH AND IRRIGATED HONDIUS' FIELDS. - Hondius Water Line, 1.6 miles Northwest of Park headquarters building & 1 mile Northwest of Beaver Meadows entrance station, Estes Park, Larimer County, CO

  17. High-Density Reconstitution of Functional Water Channels into Vesicular and Planar Block Copolymer Membranes

    PubMed Central

    2012-01-01

    The exquisite selectivity and unique transport properties of membrane proteins can be harnessed for a variety of engineering and biomedical applications if suitable membranes can be produced. Amphiphilic block copolymers (BCPs), developed as stable lipid analogs, form membranes that functionally incorporate membrane proteins and are ideal for such applications. While high protein density and planar membrane morphology are most desirable, BCP–membrane protein aggregates have so far been limited to low protein densities in either vesicular or bilayer morphologies. Here, we used dialysis to reproducibly form planar and vesicular BCP membranes with a high density of reconstituted aquaporin-0 (AQP0) water channels. We show that AQP0 retains its biological activity when incorporated at high density in BCP membranes, and that the morphology of the BCP–protein aggregates can be controlled by adjusting the amount of incorporated AQP0. We also show that BCPs can be used to form two-dimensional crystals of AQP0. PMID:23082933

  18. Structure of the native Sec61 protein-conducting channel

    PubMed Central

    Pfeffer, Stefan; Burbaum, Laura; Unverdorben, Pia; Pech, Markus; Chen, Yuxiang; Zimmermann, Richard; Beckmann, Roland; Förster, Friedrich

    2015-01-01

    In mammalian cells, secretory and membrane proteins are translocated across or inserted into the endoplasmic reticulum (ER) membrane by the universally conserved protein-conducting channel Sec61, which has been structurally studied in isolated, detergent-solubilized states. Here we structurally and functionally characterize native, non-solubilized ribosome-Sec61 complexes on rough ER vesicles using cryo-electron tomography and ribosome profiling. Surprisingly, the 9-Å resolution subtomogram average reveals Sec61 in a laterally open conformation, even though the channel is not in the process of inserting membrane proteins into the lipid bilayer. In contrast to recent mechanistic models for polypeptide translocation and insertion, our results indicate that the laterally open conformation of Sec61 is the only conformation present in the ribosome-bound translocon complex, independent of its functional state. Consistent with earlier functional studies, our structure suggests that the ribosome alone, even without a nascent chain, is sufficient for lateral opening of Sec61 in a lipid environment. PMID:26411746

  19. Channel character of uncoupling protein-mediated transport.

    PubMed

    Jezek, Petr; Jab?rek, Martin; Garlid, Keith D

    2010-05-17

    Mitochondrial uncoupling proteins (UCPs) are pure anion uniporters, which mediate fatty acid (FA) uniport leading to FA cycling. Protonated FAs then flip-flop back across the lipid bilayer. An existence of pure proton channel in UCPs is excluded by the equivalent flux-voltage dependencies for uniport of FAs and halide anions, which are best described by the Eyring barrier variant with a single energy well in the middle of two peaks. Experiments with FAs unable to flip and alkylsulfonates also support this view. Phylogenetically, UCPs took advantage of the common FA-uncoupling function of SLC25 family carriers and dropped their solute transport function. PMID:20206627

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

    PubMed Central

    Larsen, Esben Kjær Unmack; Larsen, Niels B.

    2014-01-01

    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

  1. Nanosecond Relaxation Dynamics of Hydrated Proteins: Water versus protein contributions

    SciTech Connect

    Khodadadi, S; Curtis, J. E.; Sokolov, Alexei P

    2011-01-01

    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.

  2. Fiber-packed channel bioreactor for microfluidic protein digestion.

    PubMed

    Fan, Huizhi; Chen, Gang

    2007-10-01

    The fabrication and performance of a fiber-packed channel bioreactor in microchip along with its application in protein analysis were reported. The feasibility and performance of the unique microfluidic bioreactor were demonstrated by the tryptic digestion of myoglobin (MYO) and BSA. The on-chip digestion was carried out at a flow rate of 2.0 microL/min and the digestion time was significantly reduced to less than 5 s. The digests were identified by MALDI-TOF MS with sequence coverages of 66% (MYO) and 40% (BSA) that were comparable to those obtained by the conventional in-solution tryptic digestion. The present fiber-based microchip bioreactor provides a promising platform for the high-throughput protein identification. PMID:17722209

  3. Dynamic regulation of aquaporin-4 water channels in neurological disorders

    PubMed Central

    Hsu, Ying; Tran, Minh; Linninger, Andreas A.

    2015-01-01

    Aquaporin-4 water channels play a central role in brain water regulation in neurological disorders. Aquaporin-4 is abundantly expressed at the astroglial endfeet facing the cerebral vasculature and the pial membrane, and both its expression level and subcellular localization significantly influence brain water transport. However, measurements of aquaporin-4 levels in animal models of brain injury often report opposite trends of change at the injury core and the penumbra. Furthermore, aquaporin-4 channels play a beneficial role in brain water clearance in vasogenic edema, but a detrimental role in cytotoxic edema and exacerbate cell swelling. In light of current evidence, we still do not have a complete understanding of the role of aquaporin-4 in brain water transport. In this review, we propose that the regulatory mechanisms of aquaporin-4 at the transcriptional, translational, and post-translational levels jointly regulate water permeability in the short and long time scale after injury. Furthermore, in order to understand why aquaporin-4 channels play opposing roles in cytotoxic and vasogenic edema, we discuss experimental evidence on the dynamically changing osmotic gradients between blood, extracellular space, and the cytosol during the formation of cytotoxic and vasogenic edema. We conclude with an emerging picture of the distinct osmotic environments in cytotoxic and vasogenic edema, and propose that the directions of aquaporin-4-mediated water clearance in these two types of edema are distinct. The difference in water clearance pathways may provide an explanation for the conflicting observations of the roles of aquaporin-4 in edema resolution. PMID:26526878

  4. Transmembrane Passage of Hydrophobic Compounds Through a Protein Channel Wall

    SciTech Connect

    Hearn, E.; Patel, D; Lepore, D; Indic, M; van den Berg, B

    2009-01-01

    Membrane proteins that transport hydrophobic compounds have important roles in multi-drug resistance and can cause a number of diseases, underscoring the importance of protein-mediated transport of hydrophobic compounds. Hydrophobic compounds readily partition into regular membrane lipid bilayers, and their transport through an aqueous protein channel is energetically unfavourable3. Alternative transport models involving acquisition from the lipid bilayer by lateral diffusion have been proposed for hydrophobic substrates. So far, all transport proteins for which a lateral diffusion mechanism has been proposed function as efflux pumps. Here we present the first example of a lateral diffusion mechanism for the uptake of hydrophobic substrates by the Escherichia coli outer membrane long-chain fatty acid transporter FadL. A FadL mutant in which a lateral opening in the barrel wall is constricted, but which is otherwise structurally identical to wild-type FadL, does not transport substrates. A crystal structure of FadL from Pseudomonas aeruginosa shows that the opening in the wall of the {beta}-barrel is conserved and delineates a long, hydrophobic tunnel that could mediate substrate passage from the extracellular environment, through the polar lipopolysaccharide layer and, by means of the lateral opening in the barrel wall, into the lipid bilayer from where the substrate can diffuse into the periplasm. Because FadL homologues are found in pathogenic and biodegrading bacteria, our results have implications for combating bacterial infections and bioremediating xenobiotics in the environment.

  5. Microfabricated Patch Clamp Electrodes for Improved Ion Channel Protein Measurements

    NASA Astrophysics Data System (ADS)

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

    2002-03-01

    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.

  6. Regulators of G protein signaling attenuate the G protein-mediated inhibition of N-type Ca channels.

    PubMed

    Melliti, K; Meza, U; Fisher, R; Adams, B

    1999-01-01

    Regulators of G protein signaling (RGS) proteins bind to the alpha subunits of certain heterotrimeric G proteins and greatly enhance their rate of GTP hydrolysis, thereby determining the time course of interactions among Galpha, Gbetagamma, and their effectors. Voltage-gated N-type Ca channels mediate neurosecretion, and these Ca channels are powerfully inhibited by G proteins. To determine whether RGS proteins could influence Ca channel function, we recorded the activity of N-type Ca channels coexpressed in human embryonic kidney (HEK293) cells with G protein-coupled muscarinic (m2) receptors and various RGS proteins. Coexpression of full-length RGS3T, RGS3, or RGS8 significantly attenuated the magnitude of receptor-mediated Ca channel inhibition. In control cells expressing alpha1B, alpha2, and beta3 Ca channel subunits and m2 receptors, carbachol (1 microM) inhibited whole-cell currents by approximately 80% compared with only approximately 55% inhibition in cells also expressing exogenous RGS protein. A similar effect was produced by expression of the conserved core domain of RGS8. The attenuation of Ca current inhibition resulted primarily from a shift in the steady state dose-response relationship to higher agonist concentrations, with the EC50 for carbachol inhibition being approximately 18 nM in control cells vs. approximately 150 nM in RGS-expressing cells. The kinetics of Ca channel inhibition were also modified by RGS. Thus, in cells expressing RGS3T, the decay of prepulse facilitation was slower, and recovery of Ca channels from inhibition after agonist removal was faster than in control cells. The effects of RGS proteins on Ca channel modulation can be explained by their ability to act as GTPase-accelerating proteins for some Galpha subunits. These results suggest that RGS proteins may play important roles in shaping the magnitude and kinetics of physiological events, such as neurosecretion, that involve G protein-modulated Ca channels. PMID:9874691

  7. Restored physiology in protein-deficient yeast by a small molecule channel

    PubMed Central

    Cioffi, Alexander G.; Hou, Jennifer; Grillo, Anthony S.; Diaz, Katrina A.; Burke, Martin D.

    2015-01-01

    Deficiencies of protein ion channels underlie many currently incurable human diseases. Robust networks of pumps and channels are usually responsible for the directional movement of specific ions in organisms ranging from microbes to humans. We thus questioned whether minimally selective small molecule mimics of missing protein channels might be capable of collaborating with the corresponding protein ion pumps to restore physiology. Here we report vigorous and sustainable restoration of yeast cell growth by replacing missing protein ion channels with imperfect small molecule mimics. We further provide evidence that this tolerance for imperfect mimicry is attributable to collaboration between the channel-forming small molecule and protein ion pumps. These results illuminate a mechanistic framework for pursuing small molecule replacements for deficient protein ion channels that underlie a range of challenging human diseases. PMID:26230309

  8. How do membrane proteins sense water stress?

    PubMed

    Poolman, Bert; Blount, Paul; Folgering, Joost H A; Friesen, Robert H E; Moe, Paul C; van der Heide, Tiemen

    2002-05-01

    Maintenance of cell turgor is a prerequisite for almost any form of life as it provides a mechanical force for the expansion of the cell envelope. As changes in extracellular osmolality will have similar physicochemical effects on cells from all biological kingdoms, the responses to osmotic stress may be alike in all organisms. The primary response of bacteria to osmotic upshifts involves the activation of transporters, to effect the rapid accumulation of osmoprotectants, and sensor kinases, to increase the transport and/or biosynthetic capacity for these solutes. Upon osmotic downshift, the excess of cytoplasmic solutes is released via mechanosensitive channel proteins. A number of breakthroughs in the last one or two years have led to tremendous advances in our understanding of the molecular mechanisms of osmosensing in bacteria. The possible mechanisms of osmosensing, and the actual evidence for a particular mechanism, are presented for well studied, osmoregulated transport systems, sensor kinases and mechanosensitive channel proteins. The emerging picture is that intracellular ionic solutes (or ionic strength) serve as a signal for the activation of the upshift-activated transporters and sensor kinases. For at least one system, there is strong evidence that the signal is transduced to the protein complex via alterations in the protein-lipid interactions rather than direct sensing of ion concentration or ionic strength by the proteins. The osmotic downshift-activated mechanosensitive channels, on the other hand, sense tension in the membrane but other factors such as hydration state of the protein may affect the equilibrium between open and closed states of the proteins. PMID:12010487

  9. Stability Analysis of a Uniformly Heated Channel with Supercritical Water

    SciTech Connect

    Ortega Gomez, T.; Class, A.; Schulenberg, T.; Lahey, R.T. Jr.

    2006-07-01

    The thermal-hydraulic stability of a uniformly heated channel at supercritical water pressure has been investigated to help understand the system instability phenomena which may occur in Supercritical Water Nuclear Reactors (SCWR). We have extended the modeling approach often used for Boiling Water Nuclear Reactor (BWR) stability analysis to supercritical pressure operation conditions. We have shown that Ledinegg excursive instabilities and pressure-drop oscillations (PDO) will not occur in supercritical water systems. The linear stability characteristics of a typical uniformly heated channel were computed by evaluating the eigenvalues of the model. An analysis of non-linear instability phenomena was also performed in the time domain and the dynamic bifurcations were evaluated. (authors)

  10. NMR Structure and Ion Channel Activity of the p7 Protein from Hepatitis C Virus*

    PubMed Central

    Montserret, Roland; Saint, Nathalie; Vanbelle, Christophe; Salvay, Andrés Gerardo; Simorre, Jean-Pierre; Ebel, Christine; Sapay, Nicolas; Renisio, Jean-Guillaume; Böckmann, Anja; Steinmann, Eike; Pietschmann, Thomas; Dubuisson, Jean; Chipot, Christophe; Penin, François

    2010-01-01

    The small membrane protein p7 of hepatitis C virus forms oligomers and exhibits ion channel activity essential for virus infectivity. These viroporin features render p7 an attractive target for antiviral drug development. In this study, p7 from strain HCV-J (genotype 1b) was chemically synthesized and purified for ion channel activity measurements and structure analyses. p7 forms cation-selective ion channels in planar lipid bilayers and at the single-channel level by the patch clamp technique. Ion channel activity was shown to be inhibited by hexamethylene amiloride but not by amantadine. Circular dichroism analyses revealed that the structure of p7 is mainly ?-helical, irrespective of the membrane mimetic medium (e.g. lysolipids, detergents, or organic solvent/water mixtures). The secondary structure elements of the monomeric form of p7 were determined by 1H and 13C NMR in trifluoroethanol/water mixtures. Molecular dynamics simulations in a model membrane were combined synergistically with structural data obtained from NMR experiments. This approach allowed us to determine the secondary structure elements of p7, which significantly differ from predictions, and to propose a three-dimensional model of the monomeric form of p7 associated with the phospholipid bilayer. These studies revealed the presence of a turn connecting an unexpected N-terminal ?-helix to the first transmembrane helix, TM1, and a long cytosolic loop bearing the dibasic motif and connecting TM1 to TM2. These results provide the first detailed experimental structural framework for a better understanding of p7 processing, oligomerization, and ion channel gating mechanism. PMID:20667830

  11. Dynamics of protein hydration water

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    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. The obtained results prove the bimodality of the hydration shell dynamics. In addition, we find indications of a fragile-to-strong transition of hydration water.

  12. Dynamics of protein hydration water.

    PubMed

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

    2015-09-01

    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. The obtained results prove the bimodality of the hydration shell dynamics. In addition, we find indications of a fragile-to-strong transition of hydration water. PMID:26465518

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

    SciTech Connect

    Kariev, Alisher M.; Green, Michael E.

    2012-02-26

    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.

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

    PubMed

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

    2013-06-25

    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

  15. Functionality and Protein-Water Interactions

    E-print Network

    J. C. Phillips

    2008-03-02

    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.

  16. Dynamics of Protein Hydration Water

    E-print Network

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

    2014-12-08

    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.

  17. Voltage-gated sodium channel (NaV) protein dissection creates a set of

    E-print Network

    Lim, Wendell

    Voltage-gated sodium channel (NaV) protein dissection creates a set of functional pore voltage- gated sodium channel (NaVSp1) PD forms a stand-alone, ion selec- tive pore (NaVSp1p) that is tetrameric, -helical, and that forms functional, sodium-selective channels when reconstituted into lipid

  18. Sodium Channel Inhibitors Reduce DMPK mRNA and Protein.

    PubMed

    Witherspoon, Luke; O'Reilly, Sean; Hadwen, Jeremiah; Tasnim, Nafisa; MacKenzie, Alex; Farooq, Faraz

    2015-08-01

    Myotonic dystrophy type 1 (DM1) is caused by an expanded trinucleotide (CTG)n tract in the 3' untranslated region (UTR) of the dystrophia myotonica protein kinase (DMPK) gene. This results in the aggregation of an expanded mRNA forming toxic intranuclear foci which sequester splicing factors. We believe down-regulation of DMPK mRNA represents a potential, and as yet unexplored, DM1 therapeutic avenue. Consequently, a computational screen for agents which down-regulate DMPK mRNA was undertaken, unexpectedly identifying the sodium channel blockers mexiletine, prilocaine, procainamide, and sparteine as effective suppressors of DMPK mRNA. Analysis of DMPK mRNA in C2C12 myoblasts following treatment with these agents revealed a reduction in the mRNA levels. In vivo analysis of CD1 mice also showed DMPK mRNA and protein down-regulation. The role of DMPK mRNA suppression in the documented efficacy of this class of compounds in DM1 is worthy of further investigation. PMID:26011798

  19. Helix-Coil Kinetics of Individual Polyadenylic Acid Molecules in a Protein Channel Jianxun Lin,1

    E-print Network

    Helix-Coil Kinetics of Individual Polyadenylic Acid Molecules in a Protein Channel Jianxun Lin,1, Boston University, Boston, Massachusetts 02215, USA 2 Department of Chemistry, Rice University, Houston of polyadenylic acid [poly(A)] inside a small protein channel is inves- tigated for the first time, at the single

  20. Ion Channel Formation by Tau Protein: Implications for Alzheimer’s Disease and Tauopathies

    PubMed Central

    2015-01-01

    Tau is a microtubule associated protein implicated in the pathogenesis of several neurodegenerative diseases. Because of the channel forming properties of other amyloid peptides, we employed planar lipid bilayers and atomic force microscopy to test tau for its ability to form ion permeable channels. Our results demonstrate that tau can form such channels, but only under acidic conditions. The channels formed are remarkably similar to amyloid peptide channels in their appearance, physical and electrical size, permanence, lack of ion selectivity, and multiple channel conductances. These channels differ from amyloid channels in their voltage dependence and resistance to blockade by zinc ion. These channels could explain tau’s pathologic role in disease by lowering membrane potential, dysregulating calcium, depolarizing mitochondria, or depleting energy stores. Tau might also combine with amyloid beta peptides to form toxic channels. PMID:26575330

  1. Ion Channel Formation by Tau Protein: Implications for Alzheimer's Disease and Tauopathies.

    PubMed

    Patel, Nirav; Ramachandran, Srinivasan; Azimov, Rustam; Kagan, Bruce L; Lal, Ratnesh

    2015-12-22

    Tau is a microtubule associated protein implicated in the pathogenesis of several neurodegenerative diseases. Because of the channel forming properties of other amyloid peptides, we employed planar lipid bilayers and atomic force microscopy to test tau for its ability to form ion permeable channels. Our results demonstrate that tau can form such channels, but only under acidic conditions. The channels formed are remarkably similar to amyloid peptide channels in their appearance, physical and electrical size, permanence, lack of ion selectivity, and multiple channel conductances. These channels differ from amyloid channels in their voltage dependence and resistance to blockade by zinc ion. These channels could explain tau's pathologic role in disease by lowering membrane potential, dysregulating calcium, depolarizing mitochondria, or depleting energy stores. Tau might also combine with amyloid beta peptides to form toxic channels. PMID:26575330

  2. The effect of water on protein dynamics.

    PubMed Central

    Zaccai, G

    2004-01-01

    Neutron diffraction and spectroscopy were applied to describe the hydration and dynamics of a soluble protein and a natural membrane from extreme halophilic Archaea. The quantitative dependence of protein motions on water activity was clearly illustrated, and it was established that a minimum hydration shell is required for the systems to access their functional resilience, i.e. a dynamics state that allows biological activity. PMID:15306381

  3. Some thermodynamical aspects of protein hydration water

    SciTech Connect

    Mallamace, Francesco; Corsaro, Carmelo; Mallamace, Domenico; Vasi, Sebastiano; Vasi, Cirino; Stanley, H. Eugene; Chen, Sow-Hsin

    2015-06-07

    We study by means of nuclear magnetic resonance the self-diffusion of protein hydration water at different hydration levels across a large temperature range that includes the deeply supercooled regime. Starting with a single hydration shell (h = 0.3), we consider different hydrations up to h = 0.65. Our experimental evidence indicates that two phenomena play a significant role in the dynamics of protein hydration water: (i) the measured fragile-to-strong dynamic crossover temperature is unaffected by the hydration level and (ii) the first hydration shell remains liquid at all hydrations, even at the lowest temperature.

  4. Ion channel activity of influenza A virus M2 protein: characterization of the amantadine block.

    PubMed Central

    Wang, C; Takeuchi, K; Pinto, L H; Lamb, R A

    1993-01-01

    The influenza A virus M2 integral membrane protein has ion channel activity which can be blocked by the antiviral drug amantadine. The M2 protein transmembrane domain is highly conserved in amino acid sequence for all the human, swine, equine, and avian strains of influenza A virus, and thus, known amino acid differences could lead to altered properties of the M2 ion channel. We have expressed in oocytes of Xenopus laevis the M2 protein of human influenza virus A/Udorn/72 and the avian virus A/chicken/Germany/34 (fowl plague virus, Rostock) and derivatives of the Rostock ion channel altered in the presumed pore region. The pH of activation of the M2 ion channels and amantadine block of the M2 ion channels were investigated. The channels were found to be activated by pH in a similar manner but differed in their apparent Kis for amantadine block. Images PMID:7688826

  5. Intact and N- or C- terminal end truncated AQP0 function as open water channels and cell-to-cell adhesion proteins: End truncation could be a prelude for adjusting the refractive index of the lens to prevent spherical aberration

    PubMed Central

    Kumari, S. Sindhu; Varadaraj, Kulandaiappan

    2014-01-01

    Purpose Investigate the impact of natural N- or C-terminal post-translational truncations of lens mature fiber cell Aquaporin 0 (AQP0) on water permeability (Pw) and cell-to-cell adhesion (CTCA) functions. Methods The following deletions/truncations were created by site-directed mutagenesis (designations in parentheses): Amino acid residues (AA) 2–6 (AQP0-N-del-2-6), AA235-263 (AQP0-1-234), AA239-263 (AQP0-1-238), AA244-263 (AQP0-1-243), AA247-263 (AQP0-1-246), AA250-263 (AQP0-1-249) and AA260-263 (AQP0-1-259). Protein expression was studied using immunostaining, fluorescent tags and organelle-specific markers. Pw was tested by expressing the respective cRNA in Xenopus oocytes and conducting osmotic swelling assay. CTCA was assessed by transfecting intact or mutant AQP0 into adhesion-deficient L-cells and performing cell aggregation and adhesion assays. Results AQP0-1-234 and AQP0-1-238 did not traffic to the plasma membrane. Trafficking of AQP0-N-del-2-6 and AQP0-1-243 was reduced causing decreased membrane Pw and CTCA. AQP0-1-246, AQP0-1-249 and AQP0-1-259 mutants trafficked properly and functioned normally. Pw and CTCA functions of the mutants were directly proportional to the respective amount of AQP0 expressed at the plasma membrane and remained comparable to those of intact AQP0 (AQP0-1-263). Conclusion Post-translational truncation of N- or C-terminal end amino acids does not alter the basal water permeability of AQP0 or its adhesive functions. AQP0 may play a role in adjusting the refractive index to prevent spherical aberration in the constantly growing lens. General significance Similar studies can be extended to other lens proteins which undergo post-translational truncations to find out how they assist the lens to maintain transparency and homeostasis for proper focusing of objects on to the retina. PMID:24821012

  6. Model generation of viral channel forming 2B protein bundles from polio and coxsackie viruses

    E-print Network

    Watts, Anthony

    Model generation of viral channel forming 2B protein bundles from polio and coxsackie viruses by enteroviruses such as polio and coxsackie viruses with two transmembrane domains. The protein is found to make this has on the in vivo activity of 2B. Keywords: 2B, polio virus, coxsackie virus, membrane proteins

  7. Trapping a translocating protein within the anthrax toxin channel: implications for the secondary structure of permeating proteins

    PubMed Central

    Jennings-Antipov, Laura D.; Jakes, Karen S.; Finkelstein, Alan

    2011-01-01

    Anthrax toxin consists of three proteins: lethal factor (LF), edema factor (EF), and protective antigen (PA). This last forms a heptameric channel, (PA63)7, in the host cell’s endosomal membrane, allowing the former two (which are enzymes) to be translocated into the cytosol. (PA63)7 incorporated into planar bilayer membranes forms a channel that translocates LF and EF, with the N terminus leading the way. The channel is mushroom-shaped with a cap containing the binding sites for EF and LF, and an ?100 Å–long, 15 Å–wide stem. For proteins to pass through the stem they clearly must unfold, but is secondary structure preserved? To answer this question, we developed a method of trapping the polypeptide chain of a translocating protein within the channel and determined the minimum number of residues that could traverse it. We attached a biotin to the N terminus of LFN (the 263-residue N-terminal portion of LF) and a molecular stopper elsewhere. If the distance from the N terminus to the stopper was long enough to traverse the channel, streptavidin added to the trans side bound the N-terminal biotin, trapping the protein within the channel; if this distance was not long enough, streptavidin did not bind the N-terminal biotin and the protein was not trapped. The trapping rate was dependent on the driving force (voltage), the length of time it was applied, and the number of residues between the N terminus and the stopper. By varying the position of the stopper, we determined the minimum number of residues required to span the channel. We conclude that LFN adopts an extended-chain configuration as it translocates; i.e., the channel unfolds the secondary structure of the protein. We also show that the channel not only can translocate LFN in the normal direction but also can, at least partially, translocate LFN in the opposite direction. PMID:21402886

  8. Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study.

    PubMed

    Roux, B; Nina, M; Pomès, R; Smith, J C

    1996-08-01

    The proton transfer activity of the light-driven proton pump, bacteriorhodopsin (bR) in the photochemical cycle might imply internal water molecules. The free energy of inserting water molecules in specific sites along the bR transmembrane channel has been calculated using molecular dynamics simulations based on a microscopic model. The existence of internal hydration is related to the free energy change on transfer of a water molecule from bulk solvent into a specific binding site. Thermodynamic integration and perturbation methods were used to calculate free energies of hydration for each hydrated model from molecular dynamics simulations of the creation of water molecules into specific protein-binding sites. A rigorous statistical mechanical formulation allowing the calculation of the free energy of transfer of water molecules from the bulk to a protein cavity is used to estimate the probabilities of occupancy in the putative bR proton channel. The channel contains a region lined primarily by nonpolar side-chains. Nevertheless, the results indicate that the transfer of four water molecules from bulk water to this apparently hydrophobic region is thermodynamically permitted. The column forms a continuous hydrogen-bonded chain over 12 A between a proton donor, Asp 96, and the retinal Schiff base acceptor. The presence of two water molecules in direct hydrogen-bonding association with the Schiff base is found to be strongly favorable thermodynamically. The implications of these results for the mechanism of proton transfer in bR are discussed. PMID:8842206

  9. Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study.

    PubMed Central

    Roux, B; Nina, M; Pomès, R; Smith, J C

    1996-01-01

    The proton transfer activity of the light-driven proton pump, bacteriorhodopsin (bR) in the photochemical cycle might imply internal water molecules. The free energy of inserting water molecules in specific sites along the bR transmembrane channel has been calculated using molecular dynamics simulations based on a microscopic model. The existence of internal hydration is related to the free energy change on transfer of a water molecule from bulk solvent into a specific binding site. Thermodynamic integration and perturbation methods were used to calculate free energies of hydration for each hydrated model from molecular dynamics simulations of the creation of water molecules into specific protein-binding sites. A rigorous statistical mechanical formulation allowing the calculation of the free energy of transfer of water molecules from the bulk to a protein cavity is used to estimate the probabilities of occupancy in the putative bR proton channel. The channel contains a region lined primarily by nonpolar side-chains. Nevertheless, the results indicate that the transfer of four water molecules from bulk water to this apparently hydrophobic region is thermodynamically permitted. The column forms a continuous hydrogen-bonded chain over 12 A between a proton donor, Asp 96, and the retinal Schiff base acceptor. The presence of two water molecules in direct hydrogen-bonding association with the Schiff base is found to be strongly favorable thermodynamically. The implications of these results for the mechanism of proton transfer in bR are discussed. PMID:8842206

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

    E-print Network

    Zhou, Shengli

    (ZP-OFDM) in shallow water communica- Permission to make digital or hard copies of all or partShort 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

  11. Multiple Scales in the Simulation of Ion Channels and Proteins

    PubMed Central

    Eisenberg, Bob

    2010-01-01

    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

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

    NASA Astrophysics Data System (ADS)

    Hinds, Bruce

    2013-03-01

    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. DOE EPSCoR (DE-FG02-07ER46375) and DARPA, W911NF-09-1-0267

  13. Fe(2+) substrate transport through ferritin protein cage ion channels influences enzyme activity and biomineralization.

    PubMed

    Behera, Rabindra K; Torres, Rodrigo; Tosha, Takehiko; Bradley, Justin M; Goulding, Celia W; Theil, Elizabeth C

    2015-09-01

    Ferritins, complex protein nanocages, form internal iron-oxy minerals (Fe2O3·H2O), by moving cytoplasmic Fe(2+) through intracage ion channels to cage-embedded enzyme (2Fe(2+)/O2 oxidoreductase) sites where ferritin biomineralization is initiated. The products of ferritin enzyme activity are diferric oxy complexes that are mineral precursors. Conserved, carboxylate amino acid side chains of D127 from each of three cage subunits project into ferritin ion channels near the interior ion channel exits and, thus, could direct Fe(2+) movement to the internal enzyme sites. Ferritin D127E was designed and analyzed to probe properties of ion channel size and carboxylate crowding near the internal ion channel opening. Glu side chains are chemically equivalent to, but longer by one -CH2 than Asp, side chains. Ferritin D127E assembled into normal protein cages, but diferric peroxo formation (enzyme activity) was not observed, when measured at 650 nm (DFP ? max). The caged biomineral formation, measured at 350 nm in the middle of the broad, nonspecific Fe(3+)-O absorption band, was slower. Structural differences (protein X-ray crystallography), between ion channels in wild type and ferritin D127E, which correlate with the inhibition of ferritin D127E enzyme activity include: (1) narrower interior ion channel openings/pores; (2) increased numbers of ion channel protein-metal binding sites, and (3) a change in ion channel electrostatics due to carboxylate crowding. The contributions of ion channel size and structure to ferritin activity reflect metal ion transport in ion channels are precisely regulated both in ferritin protein nanocages and membranes of living cells. PMID:26202907

  14. Intrinsically disordered proteins aggregate at fungal cell-to-cell channels and regulate

    E-print Network

    Wong, Limsoon

    for eukaryotic multicellular organization. Animals use cell-to-cell adhesion to maintain tissue architectureIntrinsically disordered proteins aggregate at fungal cell-to-cell channels and regulate possess cell-to-cell channels (septal pores) that allow intercellular communication and transport. Here

  15. Early innate immune response of immune proteins in juvenile channel catfish Ictalurus punctatus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Channel catfish (Ictalurus punctatus) are raised for aquaculture in the Southeast U.S. and are susceptible to bacterial and viral infections acquired from their pond environment. Innate immune proteins mannose-binding lectin (MBL) and lysozyme were studied during two consecutive years in channel cat...

  16. Morphology of rain water channelization in systematically varied model sandy soils

    E-print Network

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

    2014-03-13

    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.

  17. Morphology of Rain Water Channeling in Systematically Varied Model Sandy Soils

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    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.

  18. Immunohistochemical Localization of the Water Channels AQP4 and AQP5 in the Rat Pituitary Gland.

    PubMed

    Matsuzaki, Toshiyuki; Inahata, Yuki; Sawai, Nobuhiko; Yang, Chun-Ying; Kobayashi, Makito; Takata, Kuniaki; Ozawa, Hitoshi

    2011-12-28

    The pituitary gland is composed of the adenohypophysis and neurohypophysis. The adenohypophysis contains endocrine cells, folliculo-stellate (FS) cells, and marginal layer cells, whereas the neurohypophysis mainly comprises axons and pituicytes. To understand the molecular nature of water transfer in the pituitary gland, we examined the immunohistochemical localization of the membrane water channels aquaporin-4 (AQP4) and AQP5 in rat tissue. Double immunofluorescence analysis of AQP4 and S100 protein, a known marker for FS cells, marginal layer cells, and pituicytes, clearly revealed that FS cells and marginal layer cells in the adenohypophysis and the pituicytes in pars nervosa are positive for AQP4. AQP5 was found to be localized at the apical membrane in some marginal layer cells surrounding the Rathke's residual pouch, in which AQP4 was observed to be localized on the basolateral membranes. These results suggest the following possibilities: 1) FS cells especially require water for their functions and 2) transepithelial water transfer could occur between the lumen of Rathke's residual pouch and the interstitial fluid in the adenohypophysis through the AQP4 and AQP5 channels in the marginal layer cells. PMID:22282586

  19. Water uptake profile in a model ion-exchange membrane: Conditions for water-rich channels

    NASA Astrophysics Data System (ADS)

    Herbst, Daniel C.; Witten, Thomas A.; Tsai, Tsung-Han; Coughlin, E. Bryan; Maes, Ashley M.; Herring, Andrew M.

    2015-03-01

    Ionic conductivity in a polymeric fuel cell requires water uptake. Previous theoretical studies of water uptake used idealized parameters. We report a parameter-free prediction of the water-swelling behavior of a model fuel cell membrane. The model polymers, poly(methyl-butylene)-block-poly(vinylbenzyl-trimethylamine), form lamellar domains that absorb water in humid air. We use the Scheutjens-Fleer methodology to predict the resulting change in lamellar structure and compare with x-ray scattering. The results suggest locally uniform water distributions. However, under conditions where a PVBTMA and water mixture phase-separate, the two phases arrange into stripes with a dilute stripe sandwiched between two concentrated stripes. A small amount of water enhances conductivity most when it is partitioned into such channels, improving fuel-cell performance.

  20. Water transport across biological membranes: Overton, water channels, and peritoneal dialysis.

    PubMed

    Devuyst, O

    2010-01-01

    Peritoneal dialysis involves diffusive and convective transports and osmosis through the highly vascularized peritoneal membrane. Several lines of evidence have demonstrated that the water channel aquaporin-1 (AQP1) corresponds to the ultrasmall pore predicted by the modelization of peritoneal transport. Proof-of-principle studies have shown that upregulation of the expression of AQP1 in peritoneal capillaries is reflected by increased water permeability and ultrafiltration, without affecting the osmotic gradient and the permeability for small solutes. Inversely, studies in Aqp1 mice have shown that haplo-insufficiency in AQP1 is reflected by significant attenuation of water transport. Recent studies have identified lead compounds that could act as agonists of aquaporins, as well as putative binding sites and potential mechanisms of gating the water channel. By modulating water transport, these pharmacological agents could have clinically relevant effects in targeting specific tissues or disease states. These studies on the peritoneal membrane also provide an experimental framework to investigate the role of water channels in the endothelium and various cell types. PMID:21510484

  1. Protective role of brain water channel AQP4 in murine cerebral malaria

    PubMed Central

    Promeneur, Dominique; Lunde, Lisa Kristina; Amiry-Moghaddam, Mahmood; Agre, Peter

    2013-01-01

    Tragically common among children in sub-Saharan Africa, cerebral malaria is characterized by rapid progression to coma and death. In this study, we used a model of cerebral malaria appearing in C57BL/6 WT mice after infection with the rodent malaria parasite Plasmodium berghei ANKA. Expression and cellular localization of the brain water channel aquaporin-4 (AQP4) was investigated during the neurological syndrome. Semiquantitative real-time PCR comparing uninfected and infected mice showed a reduction of brain AQP4 transcript in cerebral malaria, and immunoblots revealed reduction of brain AQP4 protein. Reduction of brain AQP4 protein was confirmed in cerebral malaria by quantitative immunogold EM; however, polarized distribution of AQP4 at the perivascular and subpial astrocyte membranes was not altered. To further examine the role of AQP4 in cerebral malaria, WT mice and littermates genetically deficient in AQP4 were infected with P. berghei. Upon development of cerebral malaria, WT and AQP4-null mice exhibited similar increases in width of perivascular astroglial end-feet in brain. Nevertheless, the AQP4-null mice exhibited more severe signs of cerebral malaria with greater brain edema, although disruption of the blood–brain barrier was similar in both groups. In longitudinal studies, cerebral malaria appeared nearly 1 d earlier in the AQP4-null mice, and reduced survival was noted when chloroquine rescue was attempted. We conclude that the water channel AQP4 confers partial protection against cerebral malaria. PMID:23277579

  2. The ABC protein turned chloride channel whose failure causes cystic fibrosis

    NASA Astrophysics Data System (ADS)

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

    2006-03-01

    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.

  3. On the Coupling Between Channel Level and Surface Ground Water Flows

    E-print Network

    Díaz, Jesús Ildefonso

    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

  4. Split-luciferase complementation assay to detect channel-protein interactions in live cells.

    PubMed

    Shavkunov, Alexander S; Ali, Syed R; Panova-Elektronova, Neli I; Laezza, Fernanda

    2015-01-01

    The understanding of ion channel function continues to be a significant driver in molecular pharmacology. In this field of study, protein-protein interactions are emerging as fundamental molecular determinants of ion channel function and as such are becoming an attractive source of highly specific targets for drug development. The investigation of ion channel macromolecular complexes, however, still relies on conventional methods that are usually technically challenging and time-consuming, significantly hampering our ability to identify, characterize and modify ion channel function through targeted molecular approaches. As a response to the urgent need of developing rapid and albeit accurate technologies to survey ion channel molecular complexes, we describe a new application of the split-luciferase complementation assay to study the interaction of the voltage-gated Na?+?channel with the intracellular fibroblast growth factor 14 and its dynamic regulation in live cells. We envision that the flexibility and accessibility of this assay will have a broad impact in the ion channel field complementing structural and functional studies, enabling the interrogation of protein-channel dynamic interactions in complex cellular contexts and laying the basis for new frameworks in drug discovery campaigns. PMID:25859972

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

    PubMed Central

    Fairley-Grenot, K; Assmann, SM

    1991-01-01

    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 (and not the kinetics) of inward current through K+-selective ion channels in the plasma membrane. GDP[beta]S (100 to 500 [mu]M) increases inward K+ current, whereas GTP[gamma]S (500 [mu]M) has the opposite effect. The control nucleotides ADP[beta]S and ATP[gamma]S (500 [mu]M) do not affect K+ current. Reduction of inward current by GTP[gamma]S is eliminated in the presence of the Ca2+ chelator, BAPTA (1,2-bis(2-aminophenoxy)ethane-N,N,N[prime],N[prime],-tetraacetic acid) (5 mM). When applied intracellularly, the G-protein regulators, cholera toxin and pertussis toxin, both decrease inward K+ current. The entry of K+ (and anions) into guard cells increases their turgor, opening stomatal pores in the leaf epidermis that allow gas exchange with the environment. Our data suggest the involvement of a G-protein in the inhibition of K+ uptake and stomatal opening. Changes in stomatal aperture, vital to both photosynthesis and plant water status, reflect guard-cell responsiveness to a variety of known environmental signals. The results presented here indicate that, in plants as well as animals, ion channel regulation by environmental stimuli may be mediated by G-proteins. PMID:12324626

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

    E-print Network

    Mason, Andrew

    of diseases, and discovery of new and effective drugs, tBLM biosensors merit the development of newMembrane 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

  7. Probing Membrane Protein Structure Using Water Polarization Transfer Solid-State NMR

    PubMed Central

    Williams, Jonathan K.; Hong, Mei

    2014-01-01

    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 peptide 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. PMID:25228502

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

    NASA Astrophysics Data System (ADS)

    Williams, Jonathan K.; Hong, Mei

    2014-10-01

    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.

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

    PubMed

    Williams, Jonathan K; Hong, Mei

    2014-10-01

    Water plays an essential role in the structure and function of proteins, lipid membranes and other biological macromolecules. Solid-state NMR heteronuclear-detected (1)H 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. PMID:25228502

  10. Highly permeable artificial water channels that can self-assemble into two-dimensional arrays.

    PubMed

    Shen, Yue-Xiao; Si, Wen; Erbakan, Mustafa; Decker, Karl; De Zorzi, Rita; Saboe, Patrick O; Kang, You Jung; Majd, Sheereen; Butler, Peter J; Walz, Thomas; Aksimentiev, Aleksei; Hou, Jun-li; Kumar, Manish

    2015-08-11

    Bioinspired artificial water channels aim to combine the high permeability and selectivity of biological aquaporin (AQP) water channels with chemical stability. Here, we carefully characterized a class of artificial water channels, peptide-appended pillar[5]arenes (PAPs). The average single-channel osmotic water permeability for PAPs is 1.0(± 0.3) × 10(-14) cm(3)/s or 3.5(± 1.0) × 10(8) water molecules per s, which is in the range of AQPs (3.4 ? 40.3 × 10(8) water molecules per s) and their current synthetic analogs, carbon nanotubes (CNTs, 9.0 × 10(8) water molecules per s). This permeability is an order of magnitude higher than first-generation artificial water channels (20 to ? 10(7) water molecules per s). Furthermore, within lipid bilayers, PAP channels can self-assemble into 2D arrays. Relevant to permeable membrane design, the pore density of PAP channel arrays (? 2.6 × 10(5) pores per ?m(2)) is two orders of magnitude higher than that of CNT membranes (0.1 ? 2.5 × 10(3) pores per ?m(2)). PAP channels thus combine the advantages of biological channels and CNTs and improve upon them through their relatively simple synthesis, chemical stability, and propensity to form arrays. PMID:26216964

  11. Ferroelectric Hydration Shells around Proteins: Electrostatics of the Protein-Water David N. LeBard,

    E-print Network

    Matyushov, Dmitry

    Ferroelectric Hydration Shells around Proteins: Electrostatics of the Protein-Water Interface David at the protein-water interface. The linear response relation between the average electrostatic potential and its by a slow (=1 ns) component that freezes in at the temperature of the dynamical transition of proteins

  12. Concentrating Toxoplasma gondii and Cyclospora cayetanensis from Surface Water and Drinking Water by Continuous Separation Channel Centrifugation

    EPA Science Inventory

    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 a...

  13. Competing Lipid-Protein and Protein-Protein Interactions Determine Clustering and Gating Patterns in the Potassium Channel from Streptomyces lividans (KcsA).

    PubMed

    Molina, M Luisa; Giudici, A Marcela; Poveda, José A; Fernández-Ballester, Gregorio; Montoya, Estefanía; Renart, M Lourdes; Fernández, Asia M; Encinar, José A; Riquelme, Gloria; Morales, Andrés; González-Ros, José M

    2015-10-16

    There is increasing evidence to support the notion that membrane proteins, instead of being isolated components floating in a fluid lipid environment, can be assembled into supramolecular complexes that take part in a variety of cooperative cellular functions. The interplay between lipid-protein and protein-protein interactions is expected to be a determinant factor in the assembly and dynamics of such membrane complexes. Here we report on a role of anionic phospholipids in determining the extent of clustering of KcsA, a model potassium channel. Assembly/disassembly of channel clusters occurs, at least partly, as a consequence of competing lipid-protein and protein-protein interactions at nonannular lipid binding sites on the channel surface and brings about profound changes in the gating properties of the channel. Our results suggest that these latter effects of anionic lipids are mediated via the Trp(67)-Glu(71)-Asp(80) inactivation triad within the channel structure and its bearing on the selectivity filter. PMID:26336105

  14. Piezo proteins are pore-forming subunits of mechanically activated channels.

    PubMed

    Coste, Bertrand; Xiao, Bailong; Santos, Jose S; Syeda, Ruhma; Grandl, Jörg; Spencer, Kathryn S; Kim, Sung Eun; Schmidt, Manuela; Mathur, Jayanti; Dubin, Adrienne E; Montal, Mauricio; Patapoutian, Ardem

    2012-03-01

    Mechanotransduction has an important role in physiology. Biological processes including sensing touch and sound waves require as-yet-unidentified cation channels that detect pressure. Mouse Piezo1 (MmPiezo1) and MmPiezo2 (also called Fam38a and Fam38b, respectively) induce mechanically activated cationic currents in cells; however, it is unknown whether Piezo proteins are pore-forming ion channels or modulate ion channels. Here we show that Drosophila melanogaster Piezo (DmPiezo, also called CG8486) also induces mechanically activated currents in cells, but through channels with remarkably distinct pore properties including sensitivity to the pore blocker ruthenium red and single channel conductances. MmPiezo1 assembles as a ?1.2-million-dalton homo-oligomer, with no evidence of other proteins in this complex. Purified MmPiezo1 reconstituted into asymmetric lipid bilayers and liposomes forms ruthenium-red-sensitive ion channels. These data demonstrate that Piezo proteins are an evolutionarily conserved ion channel family involved in mechanotransduction. PMID:22343900

  15. Structure of synaptophysin: A hexameric MARVEL domain channel protein

    PubMed Central

    Arthur, Christopher P.; Stowell, Michael H. B.

    2007-01-01

    Synaptophysin 1 is an archetypal member of the MARVEL domain family of integral membrane proteins and one of the first synaptic vesicle proteins to be identified and cloned (Rehm et al., 1986; Sanchez-Pulido et al., 2002). Most all MARVEL domain proteins are involved in membrane apposition and vesicle trafficking events but their precise role in these processes is unclear. We have purified mammalian Syp1 and determined its three-dimensional structure using electron microscopy and single-particle 3-D reconstruction. The hexameric structure resembles an open basket with a large pore and tenuous interactions within the cytosolic domain. The structure suggests a model for synaptophysin’s role in fusion and recycling that is regulated by known interactions with the SNARE machinery. This is the first three dimensional structure of a MARVEL domain protein and provides a structural foundation for understanding the role of these important proteins in a variety of biological processes. PMID:17562317

  16. Principles Governing Metal Ion Selectivity in Ion Channel Proteins

    NASA Astrophysics Data System (ADS)

    Lim, Carmay

    2014-03-01

    Our research interests are to (i) unravel the principles governing biological processes and use them to identify novel drug targets and guide drug design, and (ii) develop new methods for studying macromolecular interactions. This talk will provide an overview of our work in these two areas and an example of how our studies have helped to unravel the principles underlying the conversion of Ca2+-selective to Na+-selective channels. Ion selectivity of four-domain voltage-gated Ca2+(Cav) and sodium (Nav) channels, which is controlled by the selectivity filter (SF, the narrowest region of an open pore), is crucial for electrical signaling. Over billions of years of evolution, mutation of the Glu from domain II/III in the EEEE/DEEA SF of Ca2+-selective Cav channels to Lys made these channels Na+-selective. This talk will delineate the physical principles why Lys is sufficient for Na+/Ca2+selectivity and why the DEKA SF is more Na+-selective than the DKEA one.

  17. Functional reconstitution and channel activity measurements of purified wildtype and mutant CFTR protein.

    PubMed

    Eckford, Paul D W; Li, Canhui; Bear, Christine E

    2015-01-01

    The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a unique channel-forming member of the ATP Binding Cassette (ABC) superfamily of transporters. The phosphorylation and nucleotide dependent chloride channel activity of CFTR has been frequently studied in whole cell systems and as single channels in excised membrane patches. Many Cystic Fibrosis-causing mutations have been shown to alter this activity. While a small number of purification protocols have been published, a fast reconstitution method that retains channel activity and a suitable method for studying population channel activity in a purified system have been lacking. Here rapid methods are described for purification and functional reconstitution of the full-length CFTR protein into proteoliposomes of defined lipid composition that retains activity as a regulated halide channel. This reconstitution method together with a novel flux-based assay of channel activity is a suitable system for studying the population channel properties of wild type CFTR and the disease-causing mutants F508del- and G551D-CFTR. Specifically, the method has utility in studying the direct effects of phosphorylation, nucleotides and small molecules such as potentiators and inhibitors on CFTR channel activity. The methods are also amenable to the study of other membrane channels/transporters for anionic substrates. PMID:25867140

  18. Identification of yeast proteins necessary for cell-surface function of a potassium channel.

    PubMed

    Haass, Friederike A; Jonikas, Martin; Walter, Peter; Weissman, Jonathan S; Jan, Yuh-Nung; Jan, Lily Y; Schuldiner, Maya

    2007-11-13

    Inwardly rectifying potassium (Kir) channels form gates in the cell membrane that regulate the flow of K(+) ions into and out of the cell, thereby influencing the membrane potential and electrical signaling of many cell types, including neurons and cardiomyocytes. Kir-channel function depends on other cellular proteins that aid in the folding of channel subunits, assembly into tetrameric complexes, trafficking of quality-controlled channels to the plasma membrane, and regulation of channel activity at the cell surface. We used the yeast Saccharomyces cerevisiae as a model system to identify proteins necessary for the functional expression of a mammalian Kir channel at the cell surface. A screen of 376 yeast strains, each lacking one nonessential protein localized to the early secretory pathway, identified seven deletion strains in which functional expression of the Kir channel at the plasma membrane was impaired. Six deletions were of genes with known functions in trafficking and lipid biosynthesis (sur4Delta, csg2Delta, erv14Delta, emp24Delta, erv25Delta, and bst1Delta), and one deletion was of an uncharacterized gene (yil039wDelta). We provide genetic and functional evidence that Yil039wp, a conserved, phosphoesterase domain-containing protein, which we named "trafficking of Emp24p/Erv25p-dependent cargo disrupted 1" (Ted1p), acts together with Emp24p/Erv25p in cargo exit from the endoplasmic reticulum (ER). The seven yeast proteins identified in our screen likely impact Kir-channel functional expression at the level of vesicle budding from the ER and/or the local lipid environment at the plasma membrane. PMID:17989219

  19. Emerging concepts for G protein-gated inwardly rectifying potassium (GIRK) channels in health and disease

    PubMed Central

    Lüscher, Christian; Slesinger, Paul A.

    2010-01-01

    G protein-gated inwardly rectifying potassium (GIRK) channels hyperpolarize neurons in response to the activation of many G-protein coupled receptors and thus control the excitability of neurons through GIRK-mediated self-inhibition, slow synaptic potentials and volume transmission. GIRK channel function and trafficking are highly dependent on their subunit composition. Pharmacological investigations of GIRK channels and studies in animal models suggest that GIRK activity has an important role in physiological responses, including pain perception and memory modulation. Moreover, abnormal GIRK function has been implicated in altering neuronal excitability and cell death that may be important in the pathophysiology of human diseases such as epilepsy, Down’s syndrome, Parkinson’s disease and drug addiction. GIRK channels may therefore prove to be a valuable new therapeutic target for treating these health problems. PMID:20389305

  20. Ion channels go to Stockholm--this time as proteins.

    PubMed

    Miller, Christopher

    2003-12-18

    The 2003 Nobel Prize in Chemistry was awarded to two structural biologists, Roderick Mackinnon of Rockefeller University and Peter Agre of Johns Hopkins University, for their groundbreaking work on the structure and function of ion channels. In recognition of the outstanding impact that MacKinnon's work has had for neuroscience, Chris Miller traces MacKinnon's scientific path to the Nobel Prize. PMID:14687537

  1. Water behavior in serpentine micro-channel for proton exchange membrane fuel cell cathode

    NASA Astrophysics Data System (ADS)

    Quan, Peng; Zhou, Biao; Sobiesiak, Andrzej; Liu, Zhongsheng

    The behavior of water in the air-water flow inside a serpentine channel for a proton exchange membrane (PEM) fuel cell was investigated using the FLUENT software package. The volume-of-fluid (VOF) model was adopted to track the dynamic air-water interface. Five cases with varying initial water phase distribution corresponding to different fuel cell operating conditions were numerically simulated to obtain a better understanding of water behavior inside a serpentine micro-channel. Results show that the bend area of a serpentine flow channel has significant effects on the flow field, which in turn affects the air-water flow and water liquid distribution inside the channel or along the interior channel surfaces. The simulation results also indicate that water flooding could occur in the "after-bend" section of a micro-channel. For the case with larger amount of water in the two-phase flow, the simulation shows that the "after-bend" water distribution might block the reactant supply to reaction sites and, in some extreme situations, might block the reactant transport inside the flow channel, thus decreasing fuel cell performance.

  2. Comparison of Space-Time Water-filling and Spatial Water-filling for MIMO Fading Channels

    E-print Network

    Evans, Brian L.

    shadowing, space-time water-filling gains This material is based in part upon work supported by the Texas Advanced Technology Program under Grant No. 003658-0380-2003. little in capacity over spatial waterComparison of Space-Time Water-filling and Spatial Water-filling for MIMO Fading Channels Zukang

  3. Stabilization of Kv1.5 channel protein by the inotropic agent olprinone.

    PubMed

    Endo, Ryo; Kurata, Yasutaka; Notsu, Tomomi; Li, Peili; Morikawa, Kumi; Kondo, Takehito; Ogura, Kazuyoshi; Miake, Junichiro; Yoshida, Akio; Shirayoshi, Yasuaki; Ninomiya, Haruaki; Higaki, Katsumi; Kuwabara, Masanari; Yamamoto, Kazuhiro; Inagaki, Yoshimi; Hisatome, Ichiro

    2015-10-15

    Olprinone is an inotropic agent that inhibits phosphodiesterase (PDE) III and causes vasodilation. Olprinone has been shown to be less proarrhythmic and possibly affect expression of functional Kv1.5 channels that confer the ultra-rapid delayed-rectifier K(+) channel current (IKur) responsible for action potential repolarization. To reveal involvement of Kv1.5 channels in the less arrhythmic effect of olprinone, we examined effects of the agent on the stability of Kv1.5 channel proteins expressed in COS7 cells. Olprinone at 30-1000nM increased the protein level of Kv1.5 channels in a concentration-dependent manner. Chase experiments showed that olprinone delayed degradation of Kv1.5 channels. Olprinone increased the immunofluorescent signal of Kv1.5 channels in the endoplasmic reticulum (ER) and Golgi apparatus as well as on the cell surface. Kv1.5-mediated membrane currents, measured as 4-aminopyridine-sensitive currents, were increased by olprinone without changes in their activation kinetics. A protein transporter inhibitor, colchicine, abolished the olprinone-induced increase of Kv.1.5-mediated currents. The action of olprinone was inhibited by 4-aminopyridine, and was not mimicked by the application of 8-Bromo-cAMP. Taken together, we conclude that olprinone stabilizes Kv1.5 proteins at the ER through an action as a chemical chaperone, and thereby increases the density of Kv1.5 channels on the cell membrane. The enhancement of Kv1.5 currents could underlie less arrhythmogenicity of olprinone. PMID:26368666

  4. Voltage-gated sodium channel (NaV) protein dissection creates a set of functional pore-only proteins.

    PubMed

    Shaya, David; Kreir, Mohamed; Robbins, Rebecca A; Wong, Stephanie; Hammon, Justus; Brüggemann, Andrea; Minor, Daniel L

    2011-07-26

    Many voltage-gated ion channel (VGIC) superfamily members contain six-transmembrane segments in which the first four form a voltage-sensing domain (VSD) and the last two form the pore domain (PD). Studies of potassium channels from the VGIC superfamily together with identification of voltage-sensor only proteins have suggested that the VSD and the PD can fold independently. Whether such transmembrane modularity is common to other VGIC superfamily members has remained untested. Here we show, using protein dissection, that the Silicibacter pomeroyi voltage-gated sodium channel (Na(V)Sp1) PD forms a stand-alone, ion selective pore (Na(V)Sp1p) that is tetrameric, ?-helical, and that forms functional, sodium-selective channels when reconstituted into lipid bilayers. Mutation of the Na(V)Sp1p selectivity filter from LESWSM to LDDWSD, a change similar to that previously shown to alter ion selectivity of the bacterial sodium channel Na(V)Bh1 (NaChBac), creates a calcium-selective pore-only channel, Ca(V)Sp1p. We further show that production of PDs can be generalized by making pore-only proteins from two other extremophile Na(V)s: one from the hydrocarbon degrader Alcanivorax borkumensis (Na(V)Ab1p), and one from the arsenite oxidizer Alkalilimnicola ehrlichei (Na(V)Ae1p). Together, our data establish a family of active pore-only ion channels that should be excellent model systems for study of the factors that govern both sodium and calcium selectivity and permeability. Further, our findings suggest that similar dissection approaches may be applicable to a wide range of VGICs and, thus, serve as a means to simplify and accelerate biophysical, structural, and drug development efforts. PMID:21746903

  5. Amyloid ion channels: A common structural link for protein-misfolding disease

    PubMed Central

    Quist, Arjan; Doudevski, Ivo; Lin, Hai; Azimova, Rushana; Ng, Douglas; Frangione, Blas; Kagan, Bruce; Ghiso, Jorge; Lal, Ratnesh

    2005-01-01

    Protein conformational diseases, including Alzheimer's, Huntington's, and Parkinson's diseases, result from protein misfolding, giving a distinct fibrillar feature termed amyloid. Recent studies show that only the globular (not fibrillar) conformation of amyloid proteins is sufficient to induce cellular pathophysiology. However, the 3D structural conformations of these globular structures, a key missing link in designing effective prevention and treatment, remain undefined as of yet. By using atomic force microscopy, circular dichroism, gel electrophoresis, and electrophysiological recordings, we show here that an array of amyloid molecules, including amyloid-?(1–40), ?-synuclein, ABri, ADan, serum amyloid A, and amylin undergo supramolecular conformational change. In reconstituted membranes, they form morphologically compatible ion-channel-like structures and elicit single ion-channel currents. These ion channels would destabilize cellular ionic homeostasis and hence induce cell pathophysiology and degeneration in amyloid diseases. PMID:16020533

  6. Ion selectivity of the anthrax toxin channel and its effect on protein translocation.

    PubMed

    Schiffmiller, Aviva; Anderson, Damon; Finkelstein, Alan

    2015-08-01

    Anthrax toxin consists of three ? 85-kD proteins: lethal factor (LF), edema factor (EF), and protective antigen (PA). PA63 (the 63-kD, C-terminal portion of PA) forms heptameric channels ((PA63)7) in planar phospholipid bilayer membranes that enable the translocation of LF and EF across the membrane. These mushroom-shaped channels consist of a globular cap domain and a 14-stranded ?-barrel stem domain, with six anionic residues lining the interior of the stem to form rings of negative charges. (PA63)7 channels are highly cation selective, and, here, we investigate the effects on both cation selectivity and protein translocation of mutating each of these anionic residues to a serine. We find that although some of these mutations reduce cation selectivity, selectivity alone does not directly predict the rate of protein translocation; local changes in electrostatic forces must be considered as well. PMID:26170174

  7. The dynamical crossover phenomenon in bulk water, confined water and protein hydration water.

    PubMed

    Mallamace, Francesco; Corsaro, Carmelo; Baglioni, Piero; Fratini, Emiliano; Chen, Sow-Hsin

    2012-02-15

    We discuss a phenomenon regarding water that was until recently a subject of scientific controversy, i.e. the dynamical crossover from fragile-to-strong glass-forming material, for both bulk and protein hydration water. Such a crossover is characterized by a temperature T(L) at which significant dynamical changes occur, such as violation of the Stokes-Einstein relation and changes of behaviour of homologous transport parameters such as the density relaxation time and the viscosity. In this respect we will consider carefully the dynamic properties of water-protein systems. More precisely, we will study proteins and their hydration water as far as bulk and confined water. In order to clarify the controversy we will discuss in a comparative way many previous and new experimental data that have emerged using different techniques and molecular dynamic simulation (MD). We point out the reasons for the different dynamical findings from the use of different experimental techniques. PMID:22277288

  8. Assembly of transmembrane proteins on oil-water interfaces

    NASA Astrophysics Data System (ADS)

    Yunker, Peter; Landry, Corey; Chong, Shaorong; Weitz, David

    2015-03-01

    Transmembrane proteins are difficult to handle by aqueous solution-based biochemical and biophysical approaches, due to the hydrophobicity of transmembrane helices. Detergents can solubilize transmembrane proteins; however, surfactant coated transmembrane proteins are not always functional, and purifying detergent coated proteins in a micellar solution can be difficult. Motivated by this problem, we study the self-assembly of transmembrane proteins on oil-water interfaces. We found that the large water-oil interface of oil drops prevents nascent transmembrane proteins from forming non-functional aggregates. The oil provides a hydrophobic environment for the transmembrane helix, allowing the ectodomain to fold into its natural structure and orientation. Further, modifying the strength or valency of hydrophobic interactions between transmembrane proteins results in the self-assembly of spatially clustered, active proteins on the oil-water interface. Thus, hydrophobic interactions can facilitate, rather than inhibit, the assembly of transmembrane proteins.

  9. Transepithelial water permeability in microperfused distal airways. Evidence for channel-mediated water transport.

    PubMed Central

    Folkesson, H G; Matthay, M A; Frigeri, A; Verkman, A S

    1996-01-01

    Water movement across the airway epithelium is important for regulation of the volume and composition of airspace fluid. A novel approach is reported here to measure osmotic and diffusional water permeability in intact airways. Small airways (100-200 microns diameter, 1-2 mm length) from guinea pig lung were microdissected and perfused in vitro using concentric glass holding and perfusion pipettes. For measurement of osmotic water permeability (Pf), the airway lumen was perfused wit PBS (300 mOsM) containing a membrane impermeable fluorophore, fluorescein sulfonate (FS), and the airway was bathed in solutions of specified osmolalities. Pf determination was based on the changes in FS fluorescence at the distal end of the airway resulting from transepithelial water transport. Pf was 4-5 x 10(-3) cm/s at 23 degrees C and independent of lumen flow rate (10-100 nl/min) and the magnitude and direction of the osmotic gradient (bath osmolality 50-600 mOsM). Temperature dependence measurements gave an activation energy of 4.4 kcal/mol (15-37 degrees C). Pf was not altered by 0.3 mM HgCl2 or 50 microM forskolin, but was increased to 31 x 10(-3) cm/s by 100 micrograms/ml amphotericin B, indicating that osmosis is not limited by unstirred layers. Diffusional water permeability (Pd) was measured by H2O/D2O (deuterium oxide) exchange using the H2O/D2O-sensitive fluorescent probe aminonapthelane trisulfonic acid in the lumen. Measured Pd was 3-6 x 10(-6) cm/s at 23 degrees C, indicating significant restriction to water diffusion by unstirred layers. Antibody localization of water channels showed strong expression of the mercurial-insensitive water channel (AQP-4) at the basolateral membrane of airway epithelial cells. These results provide functional evidence that water movement across the distal airway epithelium is mediated by water channels. PMID:8609221

  10. Structure and Energetics of Channel-Forming Protein–Polysaccharide Complexes Inferred via Computational Statistical Thermodynamics

    PubMed Central

    Mamonova, Tatyana; Kurnikova, Maria

    2007-01-01

    The ion channel protein ?-hemolysin (?HL) forms supramolecular complexes with the polysaccharide ?-cyclodextrin (?CD). This system has potential uses in nanoscale device engineering. It has been found recently that ?CD formed longer- or shorter-lived complexes with some engineered ?HL mutants then with a wild type protein (Gu et al. J. Gen. Physiol. 2001, 118, 481–493). However, how changes in the protein sequence affect complex lifetime was not completely understood in part due to the lack of knowledge of structures of these metastable complexes. In this paper, we present an extensive molecular modeling study of the ?CD–?HL and selected mutant complexes to gain insights into the ?CD–?HL interaction mechanisms and to predict possible structures and energetics of the complexes. Thermodynamic integration (TI) and umbrella sampling (US) techniques (with the weighted histogram analysis method (WHAM)) were used to calculate the relative binding affinities of the complexes formed with the wild type ?HL and the M113N, M113E, M113A, and M113V mutants. Our results are in excellent agreement with experiment. While ?CD–M113N and ?CD–M113A complexes were stable in the configuration of the wild type complex, the equilibrium configuration of the ?CD–M113V and ?CD–M113E complexes was significantly different. In these cases, TI alone was insufficient to accurately calculate the corresponding free energy differences. By utilizing a TI/US combination in a novel manner, we were able to accurately calculate free energy changes in these flexible systems. The ?CD–M113A and ?CD–M113E complexes, which exhibited shorter lifetimes than other complexes in an experiment, in simulations exhibited greater flexibility and higher water solvation of the ?CD adapter. MD simulations of the ?CD–M113N complex with ?CD in a downward orientation were also performed. PMID:17149934

  11. Clopidogrel attenuates lithium-induced alterations in renal water and sodium channels/transporters in mice.

    PubMed

    Zhang, Yue; Peti-Peterdi, János; Heiney, Kristina M; Riquier-Brison, Anne; Carlson, Noel G; Müller, Christa E; Ecelbarger, Carolyn M; Kishore, Bellamkonda K

    2015-12-01

    Lithium (Li) administration causes deranged expression and function of renal aquaporins and sodium channels/transporters resulting in nephrogenic diabetes insipidus (NDI). Extracellular nucleotides (ATP/ADP/UTP), via P2 receptors, regulate these transport functions. We tested whether clopidogrel bisulfate (CLPD), an antagonist of ADP-activated P2Y12 receptor, would affect Li-induced alterations in renal aquaporins and sodium channels/transporters. Adult mice were treated for 14 days with CLPD and/or Li and euthanized. Urine and kidneys were collected for analysis. When administered with Li, CLPD ameliorated polyuria, attenuated the rise in urine prostaglandin E2 (PGE2), and resulted in significantly higher urinary arginine vasopressin (AVP) and aldosterone levels as compared to Li treatment alone. However, urine sodium excretion remained elevated. Semi-quantitative immunoblotting revealed that CLPD alone increased renal aquaporin 2 (AQP2), Na-K-2Cl cotransporter (NKCC2), Na-Cl cotransporter (NCC), and the subunits of the epithelial Na channel (ENaC) in medulla by 25-130 %. When combined with Li, CLPD prevented downregulation of AQP2, Na-K-ATPase, and NKCC2 but was less effective against downregulation of cortical ?- or ?-ENaC (70 kDa band). Thus, CLPD primarily attenuated Li-induced downregulation of proteins involved in water conservation (AVP-sensitive), with modest effects on aldosterone-sensitive proteins potentially explaining sustained natriuresis. Confocal immunofluorescence microscopy revealed strong labeling for P2Y12-R in proximal tubule brush border and blood vessels in the cortex and less intense labeling in medullary thick ascending limb and the collecting ducts. Therefore, there is the potential for CLPD to be directly acting at the tubule sites to mediate these effects. In conclusion, P2Y12-R may represent a novel therapeutic target for Li-induced NDI. PMID:26386699

  12. The transmembrane channel-like protein family and human papillomaviruses

    PubMed Central

    Horton, Jaime S; Stokes, Alexander J

    2014-01-01

    Epidermodysplasia verruciformis (EV) is a rare genodermatosis characterized by increased sensitivity to infection by the ?-subtype of human papillomaviruses (?-HPVs), causing persistent, tinea versicolor-like dermal lesions. In a majority of affected individuals, these macular lesions progress to invasive cutaneous squamous cell carcinoma (CSCC) in sun-exposed areas. While mutations in transmembrane channel-like 6 (TMC6 / EVER1) and 8 (TMC8 / EVER2) have been causally linked to EV, their molecular functions are unclear. It is likely that their protective effects involve regulation of the ?-HPV life cycle, host keratinocyte apoptosis vs. survival balance and/or T-cell interaction with infected host cells. PMID:24800179

  13. PIP1 aquaporins: Intrinsic water channels or PIP2 aquaporin modulators?

    PubMed

    Yaneff, Agustín; Vitali, Victoria; Amodeo, Gabriela

    2015-11-30

    The highly conserved plant aquaporins, known as Plasma membrane Intrinsic Proteins (PIPs), are the main gateways for cell membrane water exchange. Years of research have described in detail the properties of the PIP2 subfamily. However, characterizing the PIP1 subfamily has been difficult due to the failure to localize to the plasma membrane. In addition, the discovery of the PIP1-PIP2 interaction suggested that PIP1 aquaporins could be regulated by a complex posttranslational mechanism that involves trafficking, heteromerization and fine-tuning of channel activity. This review not only considers the evidence and findings but also discusses the complexity of PIP aquaporins. To establish a new benchmark in PIP regulation, we propose to consider PIP1-PIP2 pairs as functional units for the purpose of future research into their physiological roles. PMID:26526614

  14. Visualizing Water Molecules in Transmembrane Proteins Using Radiolytic Labeling Methods

    SciTech Connect

    Orban, T.; Gupta, S; Palczewski, K; Chance, M

    2010-01-01

    Essential to cells and their organelles, water is both shuttled to where it is needed and trapped within cellular compartments and structures. Moreover, ordered waters within protein structures often colocalize with strategically placed polar or charged groups critical for protein function, yet it is unclear if these ordered water molecules provide structural stabilization, mediate conformational changes in signaling, neutralize charged residues, or carry out a combination of all these functions. Structures of many integral membrane proteins, including G protein-coupled receptors (GPCRs), reveal the presence of ordered water molecules that may act like prosthetic groups in a manner quite unlike bulk water. Identification of 'ordered' waters within a crystalline protein structure requires sufficient occupancy of water to enable its detection in the protein's X-ray diffraction pattern, and thus, the observed waters likely represent a subset of tightly bound functional waters. In this review, we highlight recent studies that suggest the structures of ordered waters within GPCRs are as conserved (and thus as important) as conserved side chains. In addition, methods of radiolysis, coupled to structural mass spectrometry (protein footprinting), reveal dynamic changes in water structure that mediate transmembrane signaling. The idea of water as a prosthetic group mediating chemical reaction dynamics is not new in fields such as catalysis. However, the concept of water as a mediator of conformational dynamics in signaling is just emerging, because of advances in both crystallographic structure determination and new methods of protein footprinting. Although oil and water do not mix, understanding the roles of water is essential to understanding the function of membrane proteins.

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

    SciTech Connect

    Lee, Changhee; Yoo, Dongwan . E-mail: dyoo@uoguelph.ca

    2006-11-10

    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.

  16. Investigation of water droplet dynamics in PEM fuel cell gas channels

    NASA Astrophysics Data System (ADS)

    Gopalan, Preethi

    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.

  17. Suspended marine particulate proteins in coastal and oligotrophic waters

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    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.

  18. More than one dynamic crossover in protein hydration water

    E-print Network

    Stanley, H. Eugene

    understand the structure and behavior of water. Bulk water freezes at its homogeneous nucleation temperatureMore than one dynamic crossover in protein hydration water Marco G. Mazzaa,1,2 , Kevin Stokelya for review October 23, 2010) Studies of liquid water in its supercooled region have helped us better

  19. Alternative Splicing of the Sodium Channel SCN8A Predicts a Truncated Two-domain Protein in Fetal Brain

    E-print Network

    Meisler, Miriam

    Alternative Splicing of the Sodium Channel SCN8A Predicts a Truncated Two-domain Protein in Fetal, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5 The voltage-gated sodium channel subunit SCN8A is one of the most abundant sodium channels in neurons from brain and spinal cord. We have identified two al

  20. Cell, Vol. 107, 361372, November 2, 2001, Copyright 2001 by Cell Press Architecture of the Protein-Conducting Channel

    E-print Network

    Sali, Andrej

    from the ER lumen yeast endoplasmic reticulum, the Sec61 complex. A through the channel into the tunnel-Conducting Channel Associated with the Translating 80S Ribosome serted into, the membrane of the eukaryotic endoplas with the protein-conducting channel (PCC) (Matlack etHoward Hughes Medical Institute al., 1998). The so

  1. Channel crossing: how are proteins shipped across the bacterial plasma membrane?

    PubMed Central

    Collinson, Ian; Corey, Robin A.; Allen, William J.

    2015-01-01

    The structure of the first protein-conducting channel was determined more than a decade ago. Today, we are still puzzled by the outstanding problem of protein translocation—the dynamic mechanism underlying the consignment of proteins across and into membranes. This review is an attempt to summarize and understand the energy transducing capabilities of protein-translocating machines, with emphasis on bacterial systems: how polypeptides make headway against the lipid bilayer and how the process is coupled to the free energy associated with ATP hydrolysis and the transmembrane protein motive force. In order to explore how cargo is driven across the membrane, the known structures of the protein-translocation machines are set out against the background of the historic literature, and in the light of experiments conducted in their wake. The paper will focus on the bacterial general secretory (Sec) pathway (SecY-complex), and its eukaryotic counterpart (Sec61-complex), which ferry proteins across the membrane in an unfolded state, as well as the unrelated Tat system that assembles bespoke channels for the export of folded proteins. PMID:26370937

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

    PubMed Central

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

    2014-01-01

    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

  3. NATURAL CONTENT AND PROCESSING OF ALTERNATIVE PROTEIN SOURCES: HISTOLOGIC EFFECTS IN FINGERLING CHANNEL CATFISH (ICTALURUS PUNCTATUS)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Significant effort has been made to utilize alternative protein sources like cottonseed meal (CSM) and soybean meal (SBM) to replace fishmeal in channel catfish (Ictalurus punctatus) feed. These sources are readily available and have high nutritional value, but contain anti-nutritional factors (ANF...

  4. Effects of Fasting on IGF-Binding Proteins, Glucose, and Cortisol in Channel Catfish (Ictalurus punctatus)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The effects of fasting on IGF-binding proteins, glucose, and cortisol in channel catfish were examined. Fed fish (controls) were compared to 14-, 30-, and 45-day fasted fish and 45-day fasted fish refed for 15 additional days. Body length and body weight changes, condition factor(CF), hepatosomati...

  5. 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...

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

    SciTech Connect

    Moczydlowski, Edward G.

    2013-07-01

    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.

  7. Relationship between expression of muscle-specific uncoupling protein 2 messenger RNA and genetic selection toward growth in channel catfish

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Uncoupling protein 2 is a member of the mitochondrial channel proteins that regulate the flow of hydrogen ions and ATP generation. The relationship between UCP2 and nutrient metabolism has been well-defined in humans but unclear in fish. We hypothesized that increased muscle growth in channel catf...

  8. Electron Spin-Echo Envelope Modulation (ESEEM) Reveals Water and Phosphate Interactions with the KcsA Potassium Channel

    SciTech Connect

    Cieslak, John A.; Focia, Pamela J.; Gross, Adrian

    2010-08-13

    Electron spin-echo envelope modulation (ESEEM) spectroscopy is a well-established technique for the study of naturally occurring paramagnetic metal centers. The technique has been used to study copper complexes, hemes, enzyme mechanisms, micellar water content, and water permeation profiles in membranes, among other applications. In the present study, we combine ESEEM spectroscopy with site-directed spin labeling (SDSL) and X-ray crystallography in order to evaluate the technique's potential as a structural tool to describe the native environment of membrane proteins. Using the KcsA potassium channel as a model system, we demonstrate that deuterium ESEEM can detect water permeation along the lipid-exposed surface of the KcsA outer helix. We further demonstrate that {sup 31}P ESEEM is able to identify channel residues that interact with the phosphate headgroup of the lipid bilayer. In combination with X-ray crystallography, the {sup 31}P data may be used to define the phosphate interaction surface of the protein. The results presented here establish ESEEM as a highly informative technique for SDSL studies of membrane proteins.

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

    PubMed Central

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

    2013-01-01

    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

  10. Engineering of an E. coli outer membrane protein FhuA with increased channel diameter

    PubMed Central

    2011-01-01

    Background Channel proteins like FhuA can be an alternative to artificial chemically synthesized nanopores. To reach such goals, channel proteins must be flexible enough to be modified in their geometry, i.e. length and diameter. As continuation of a previous study in which we addressed the lengthening of the channel, here we report the increasing of the channel diameter by genetic engineering. Results The FhuA ?1-159 diameter increase has been obtained by doubling the amino acid sequence of the first two N-terminal ?-strands, resulting in variant FhuA ?1-159 Exp. The total number of ?-strands increased from 22 to 24 and the channel surface area is expected to increase by ~16%. The secondary structure analysis by circular dichroism (CD) spectroscopy shows a high ?-sheet content, suggesting the correct folding of FhuA ?1-159 Exp. To further prove the FhuA ?1-159 Exp channel functionality, kinetic measurement using the HRP-TMB assay (HRP = Horse Radish Peroxidase, TMB = 3,3',5,5'-tetramethylbenzidine) were conducted. The results indicated a 17% faster diffusion kinetic for FhuA ?1-159 Exp as compared to FhuA ?1-159, well correlated to the expected channel surface area increase of ~16%. Conclusion In this study using a simple "semi rational" approach the FhuA ?1-159 diameter was enlarged. By combining the actual results with the previous ones on the FhuA ?1-159 lengthening a new set of synthetic nanochannels with desired lengths and diameters can be produced, broadening the FhuA ?1-159 applications. As large scale protein production is possible our approach can give a contribution to nanochannel industrial applications. PMID:21854627

  11. Microfiltration: Effect of channel diameter on limiting flux and serum protein removal.

    PubMed

    Hurt, E E; Adams, M C; Barbano, D M

    2015-06-01

    Our objective was to determine the limiting flux and serum protein (SP) removal at 8, 9 and 10% true protein (TP) in the retentate recirculation loop using 0.1-µm ceramic graded permeability (GP) microfiltration (MF) membranes with 3mm channel diameters (CD). An additional objective was to compare the limiting flux and SP removal between 0.1-µm ceramic GP membranes with 3mm CD and previous research using 4-mm CD membranes. The MF system was operated at 50°C, using a diluted milk protein concentrate with 85% protein on a total solids basis (MPC85) as the MF feed. The limiting flux for the MF of diluted MPC85 was determined at 8, 9, and 10% TP concentration in the recirculation loop. The experiment using the 3-mm CD membranes was replicated 3 times for a total of 9 runs. On the morning of each run MPC85 was diluted with reverse osmosis water to a MF feed TP concentration of 5.4%. In all runs the starting flux was 55 kg/m2 per hour, the flux was then increased in steps until the limiting flux was reached. For the 3-mm CD membranes, the limiting flux was 128±0.3, 109±4, and 97±0.5 kg/m2 per hour at recirculation loop TP concentrations of 8.1±0.07, 9.2±0.04, and 10.2±0.03%, respectively. For the 3-mm CD membranes, increasing the flux from the starting to the limiting flux decreased the SP removal factor from 0.72±0.02 to 0.67±0.01; however, no difference in SP removal factor among the target recirculation loop TP concentrations was detected. The limiting flux at each recirculation loop target TP concentration was lower for the 3- compared with the 4-mm CD membranes. The differences in limiting fluxes between the 3- and 4-mm CD membranes were explained in part by the difference in cross-flow velocity (5.5±0.03 and 7.0±0.03 m/s for the 3- and 4-mm CD membranes, respectively). The SP removal factor was also lower for the 3- compared with the 4-mm CD membranes, indicating that more membrane fouling may have occurred in the 3- versus 4-mm CD membranes. PMID:25892692

  12. Mapping energy transfer channels in fucoxanthin-chlorophyll protein complex.

    PubMed

    Gelzinis, Andrius; Butkus, Vytautas; Songaila, Egidijus; Augulis, Ram?nas; Gall, Andrew; Büchel, Claudia; Robert, Bruno; Abramavicius, Darius; Zigmantas, Donatas; Valkunas, Leonas

    2015-02-01

    Fucoxanthin-chlorophyll protein (FCP) is the key molecular complex performing the light-harvesting function in diatoms, which, being a major group of algae, are responsible for up to one quarter of the total primary production on Earth. These photosynthetic organisms contain an unusually large amount of the carotenoid fucoxanthin, which absorbs the light in the blue-green spectral region and transfers the captured excitation energy to the FCP-bound chlorophylls. Due to the large number of fucoxanthins, the excitation energy transfer cascades in these complexes are particularly tangled. In this work we present the two-color two-dimensional electronic spectroscopy experiments on FCP. Analysis of the data using the modified decay associated spectra permits a detailed mapping of the excitation frequency dependent energy transfer flow with a femtosecond time resolution. PMID:25445318

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

    E-print Network

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

    2011-01-01

    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.

  14. Hydrogen peroxide treatments for channel catfish eggs infected with water molds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fungi, or water molds Saprolegnia spp., on channel catfish Ictalurus punctatus eggs can lower fry production. This requires the producer to spawn more catfish or face fingerling shortages. Few treatments have been tested against channel catfish eggs infested with an identified fungus. Hydrogen pe...

  15. The Structure of the Aquaporin-1 Water Channel: A Comparison between Cryo-electron Microscopy and

    E-print Network

    de Groot, Bert

    The Structure of the Aquaporin-1 Water Channel: A Comparison between Cryo-electron Microscopy and X been solved by cryo-electron microscopy (cryo- EM) during the last two years. Recently, the structure for the channel structure, when three groups independently presented low resolution (electron microscopy

  16. Chemical synthesis approaches to the engineering of ion channels.

    PubMed

    Kochendoerfer, Gerd G; Clayton, Daniel; Becker, Christian

    2005-11-01

    Chemoselective ligation strategies have previously provided synthetic access to water-soluble proteins with novel properties, and more recently these strategies have been used to prepare ion channels. Examples of ion channels prepared by total chemical synthesis include bacterial mechanosensitive channels, and viral ion channels. Chemical protein synthesis allows for the generation of ion channel proteins with both native, and engineered structural or conductance properties. PMID:16305542

  17. Proteins modification of poly(dimethylsiloxane) microfluidic channels for the enhanced microchip electrophoresis.

    PubMed

    Wang, Ai-Jun; Xu, Jing-Juan; Chen, Hong-Yuan

    2006-02-24

    This report described proteins modification of poly(dimethylsiloxane) (PDMS) microfluidic chip based on layer-by-layer (LBL) assembly technique for enhancing separation efficiency. Two kinds of protein-coated films were prepared. One was obtained by successively immobilizing the cationic polyelectrolyte (chitosan, Chit), gold nanoparticles (GNPs), and protein (albumin, Albu) to the PDMS microfluidic channels surface. The other was achieved by sequentially coating lysozyme (Lys) and Albu. Neurotransmitters (dopamine, DA; epinephrine, EP) and environmental pollutants (p-phenylenediamine, p-PDA; 4-aminophenol, 4-AP; hydroquinone, HQ) as two groups of separation models were studied to evaluate the effect of the functional PDMS microfluidic chips. The results clearly showed these analytes were efficiently separated within 140 s in a 3.7 cm long separation channel and successfully detected with in-channel amperometric detection mode. Experimental parameters in two protocols were optimized in detail. The detection limits of DA, EP, p-PDA, 4-AP, and HQ were 2.0, 4.7, 8.1, 12.3, and 14.8 microM (S/N=3) on the Chit-GNPs-Albu coated PDMS/PDMS microchip, and 1.2, 2.7, 7.2, 9.8, and 12.2 microM (S/N=3) on the Lys-Albu coated one, respectively. In addition, through modification, the more homogenous channel surface displayed higher reproducibility and better stability. PMID:16387312

  18. From GTP and G proteins to TRPC channels: a personal account.

    PubMed

    Birnbaumer, Lutz

    2015-09-01

    By serendipity and good fortune, as a postdoctoral fellow in 1967, I landed at the right place at the right time, as I was allowed to investigate the mechanism by which hormones activate the enzyme adenylyl cyclase (then adenyl cyclase) in Martin Rodbell's Laboratory at the NIH in Bethesda, Maryland. The work uncovered first, the existence of receptors separate from the enzyme and then, the existence of transduction mechanisms requiring guanosine-5'-triphosphate (GTP) and Mg(2+). With my laboratory colleagues first and postdoctoral fellows after leaving NIH, I participated in the development of the field "signal transduction by G proteins," uncovered by molecular cloning several G-protein-coupled receptors (GPCRs) and became interested in both the molecular makeup of voltage-gated Ca channels and Ca2+ homeostasis downstream of activation of phospholipase C (PLC) by the Gq/11 signaling pathway. We were able to confirm the hypothesis that there would be mammalian homologues of the Drosophila "transient receptor potential" channel and discovered the existence of six of the seven mammalian genes, now called transient receptor potential canonical (TRPC) channels. In the present article, I summarize from a bird's eye view of what I feel were key findings along this path, not only from my laboratory but also from many others, that allowed for the present knowledge of cell signaling involving G proteins to evolve. Towards the end, I summarize roles of TRPC channels in health and disease. PMID:26377676

  19. Building the water edge : a public event for art and artists at Fort Point Channel

    E-print Network

    Godwin, Audrey

    1996-01-01

    The thesis deals with building the water edge at Fort Point Channel, between Congress Street and Summer Street Bridges. It serves as a public event that intends to establish continuity of movement along the waterfront. The ...

  20. Ordinary High Water Mark in ephemeral and intermittent channels in the arid southwestern United States

    NASA Astrophysics Data System (ADS)

    Curtis, K. E.; Lichvar, R.; Dixon, L.

    2010-12-01

    The Ordinary High Water Mark (OHWM) is important for regulating stream channels, as it defines the lateral extent of non-wetland waters, as defined under Waters of the United States in the Clean Water Act (33 CFR Part 328.3). Prior to this study, little was known about the OHWM and geomorphically effective events in arid southwest ephemeral and intermittent channels. The hydrogeomorphic floodplain features and flow dynamics are challenging to identify in these channels because of the unstable channel morphology, flashy flood events, and lack of gage data. Through field surveys, LiDAR high-resolution topography data collection, HEC-RAS flow modeling, analysis of aerial photography, and determination of recurrence intervals using gage data, we have developed a methodology to identify the hydrogeomorphic floodplain units and delineate the OHWM. The hydrogeomorphic floodplain units include a migratory low-flow channel, an active floodplain associated with low to moderate discharge events, and a low terrace inundated by moderate to high floods. We identified primary OHWM indicators such as a break in slope, a change in sediment texture, and a change in vegetation characteristics that create a repeatable and reliable signature in the channel morphology that is associated with the OHW boundary between the active floodplain and the low terrace. Secondary indicators such as drift, ripples, and silt deposits are randomly distributed throughout the channel and cannot be linked to a particular inundation extent. In an analysis of 14 gaged ephemeral and intermittent channels, we determined that the recurrence intervals varied from <1 to 15.5 yr. Lower recurrence intervals were typically associated with more stable channels, while channels with a sandy, erodable substrate had higher recurrence intervals. A more complete understanding of the channel morphology and the highly variable OHW recurrence intervals allows more reliable and repeatable delineations in southwest ephemeral and intermittent streams.

  1. How water contributes to pressure and cold denaturation of proteins

    E-print Network

    Bianco, Valentino

    2015-01-01

    The mechanisms of cold- and pressure-denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here we study several cases of proteins, with or without a unique native state, with or without hydrophilic residues, by means of a coarse-grain protein model in explicit solvent. We show, using Monte Carlo simulations, that taking into account how water at the protein interface changes its hydrogen bond properties and its density fluctuations is enough to predict protein stability regions with elliptic shapes in the temperature-pressure plane, consistent with previous theories. Our results clearly identify the different mechanisms with which water participates to denaturation and open the perspective to develop advanced computational design tools for protein engineering.

  2. Contribution of Water to Pressure and Cold Denaturation of Proteins

    NASA Astrophysics Data System (ADS)

    Bianco, Valentino; Franzese, Giancarlo

    2015-09-01

    The mechanisms of cold and pressure denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here, we study several cases of proteins, with or without a unique native state, with or without hydrophilic residues, by means of a coarse-grain protein model in explicit solvent. We show, using Monte Carlo simulations, that taking into account how water at the protein interface changes its hydrogen bond properties and its density fluctuations is enough to predict protein stability regions with elliptic shapes in the temperature-pressure plane, consistent with previous theories. Our results clearly identify the different mechanisms with which water participates to denaturation and open the perspective to develop advanced computational design tools for protein engineering.

  3. How water contributes to pressure and cold denaturation of proteins

    E-print Network

    Valentino Bianco; Giancarlo Franzese

    2015-07-14

    The mechanisms of cold- and pressure-denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here we study several cases of proteins, with or without a unique native state, with or without hydrophilic residues, by means of a coarse-grain protein model in explicit solvent. We show, using Monte Carlo simulations, that taking into account how water at the protein interface changes its hydrogen bond properties and its density fluctuations is enough to predict protein stability regions with elliptic shapes in the temperature-pressure plane, consistent with previous theories. Our results clearly identify the different mechanisms with which water participates to denaturation and open the perspective to develop advanced computational design tools for protein engineering.

  4. Establishing homology between mitochondrial calcium uniporters, prokaryotic magnesium channels and chlamydial IncA proteins.

    PubMed

    Lee, Andre; Vastermark, Ake; Saier, Milton H

    2014-08-01

    Mitochondrial calcium uniporters (MCUs) (TC no. 1.A.77) are oligomeric channel proteins found in the mitochondrial inner membrane. MCUs have two well-conserved transmembrane segments (TMSs), connected by a linker, similar to bacterial MCU homologues. These proteins and chlamydial IncA proteins (of unknown function; TC no. 9.B.159) are homologous to prokaryotic Mg(2+) transporters, AtpI and AtpZ, based on comparison scores of up to 14.5 sds. A phylogenetic tree containing all of these proteins showed that the AtpZ proteins cluster coherently as a subset within the large and diverse AtpI cluster, which branches separately from the MCUs and IncAs, both of which cluster coherently. The MCUs and AtpZs share the same two TMS topology, but the AtpIs have four TMSs, and IncAs can have either two (most frequent) or four (less frequent) TMSs. Binary alignments, comparison scores and motif analyses showed that TMSs 1 and 2 align with TMSs 3 and 4 of the AtpIs, suggesting that the four TMS AtpI proteins arose via an intragenic duplication event. These findings establish an evolutionary link interconnecting eukaryotic and prokaryotic Ca(2+) and Mg(2+) transporters with chlamydial IncAs, and lead us to suggest that all members of the MCU superfamily, including IncAs, function as divalent cation channels. PMID:24869855

  5. Software tools for identification, visualization and analysis of protein tunnels and channels.

    PubMed

    Brezovsky, Jan; Chovancova, Eva; Gora, Artur; Pavelka, Antonin; Biedermannova, Lada; Damborsky, Jiri

    2013-01-01

    Protein structures contain highly complex systems of voids, making up specific features such as surface clefts or grooves, pockets, protrusions, cavities, pores or channels, and tunnels. Many of them are essential for the migration of solvents, ions and small molecules through proteins, and their binding to the functional sites. Analysis of these structural features is very important for understanding of structure-function relationships, for the design of potential inhibitors or proteins with improved functional properties. Here we critically review existing software tools specialized in rapid identification, visualization, analysis and design of protein tunnels and channels. The strengths and weaknesses of individual tools are reported together with examples of their applications for the analysis and engineering of various biological systems. This review can assist users with selecting a proper software tool for study of their biological problem as well as highlighting possible avenues for further development of existing tools. Development of novel descriptors representing not only geometry, but also electrostatics, hydrophobicity or dynamics, is needed for reliable identification of biologically relevant tunnels and channels. PMID:22349130

  6. The use of optical biosensors to detect modulation of Slack potassium channels by G-protein coupled receptors

    PubMed Central

    Fleming, Matthew R.; Kaczmarek, Leonard K.

    2013-01-01

    Ion channels control the electrical properties of neurons and other excitable cell types by selectively allowing ion to flow through the plasma membrane. In order to regulate neuronal excitability, the biophysical properties of ion channels are modified by signaling proteins and molecules, which often bind to the channels themselves to form a heteromeric channel complex. Traditional assays examining the interaction between channels and regulatory proteins generally provide little information on the time course of interactions in living cells. We have now used a novel label-free technology to detect changes in the distribution of mass close to the plasma membrane following modulation of potassium channels by G-protein coupled receptors (GPCRs). This technology uses optical sensors embedded in microplates to detect changes in the refractive index at the surface of cells. Although the activation of GPCRs has been studied with this system, protein-protein interactions due to modulation of ion channels have not yet been characterized. Here we present data that the characteristic pattern of mass distribution following GPCR activation is significantly modified by the presence of a sodium-activated potassium channel, Slack-B, a channel that is known to be potently modulated by activation of these receptors. PMID:19640220

  7. Phospholipase C not protein kinase C is required for the activation of TRPC5 channels by cholecystokinin.

    PubMed

    Grisanti, Laurel A; Kurada, Lalitha; Cilz, Nicholas I; Porter, James E; Lei, Saobo

    2012-08-15

    Cholecystokinin (CCK) is one of the most abundant neuropeptides in the brain where it interacts with two G protein-coupled receptors (CCK1 and CCK2). Both types of CCK receptors are coupled to G(q/11) proteins resulting in increased function of phospholipase C (PLC) pathway. Whereas CCK has been suggested to increase neuronal excitability in the brain via activation of cationic channels, the types of cationic channels have not yet been identified. Here, we co-expressed CCK2 receptors and TRPC5 channels in human embryonic kidney (HEK) 293 cells and studied the effects of CCK on TRPC5 channels using patch-clamp techniques. Our results demonstrate that activation of CCK2 receptors robustly potentiates the function of TRPC5 channels. CCK-induced activation of TRPC5 channels requires the functions of G-proteins and PLC and depends on extracellular Ca(2+). The activation of TRPC5 channels mediated by CCK2 receptors is independent of IP(3) receptors and protein kinase C. CCK-induced opening of TRPC5 channels is not store-operated because application of thapsigargin to deplete intracellular Ca(2+) stores failed to alter CCK-induced TRPC5 channel currents significantly. Bath application of CCK also significantly increased the open probability of TRPC5 single channel currents in cell-attached patches. Because CCK exerts extensive effects in the brain, our results may provide a novel mechanism to explain its roles in modulating neuronal excitability. PMID:22683873

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

    PubMed Central

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

    2010-01-01

    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

  9. Identification and characterisation of a functional aquaporin water channel (Anomala cuprea DRIP) in a coleopteran insect.

    PubMed

    Nagae, Tomone; Miyake, Seiji; Kosaki, Shiho; Azuma, Masaaki

    2013-07-15

    Water transport across the plasma membrane depends on the presence of the water channel aquaporin (AQP), which mediates the bulk movement of water through osmotic and pressure gradients. In terrestrial insects, which are solid and/or plant feeders, the entrance and exit of water is primarily executed along the alimentary tract, where the hindgut, particularly the rectum, is the major site of water conservation. A cDNA encoding the homologue of the water-specific Drosophila AQP [Drosophila integral protein (DRIP)] was identified through the RT-PCR of RNA isolated from the rectum of the cupreous chafer larvae, Anomala cuprea, a humus and plant root feeder. This gene (Anocu AQP1) has a predicted molecular mass of 26.471 kDa, similar to the DRIP clade of insect AQPs characterised from caterpillars, flies and several liquid-feeding insects. When expressed in Xenopus laevis oocytes, Anocu AQP1 showed the hallmarks of aquaporin-mediated water transport but no glycerol or urea permeability, and the reversible inhibition of elevated water transport through 1 mmol l(-1) HgCl2. This is the first experimental demonstration of the presence of a water-specific AQP, namely DRIP, in the Coleoptera. The genome of the model beetle Tribolium castaneum contains six putative AQP sequences, one of which (Trica-1a, XP_972862) showed the highest similarity to Anocu AQP1 (~60% amino acid identity). Anocu AQP1 is predominantly expressed in the rectum. Using a specific antibody raised against DRIP in the silkworm Bombyx mori (AQP-Bom1), Anocu AQP1 was localised to the apical plasma membrane of rectal epithelial cells, and lacking in the midgut and gastric caecal epithelia. Based on the BeetleBase prediction, there are three putative AQPs (Trica-3a, 3b, 3c: XP_970728, 970912, 970791) that are homologous to B. mori aquaglyceroporin [AQP-Bom2 (GLP)]. The immunocytochemical studies using the specific anti-peptide antibody against AQP-Bom2 revealed the presence of the GLP homologue at the apical plasma membrane of enterocytes in the midgut and gastric caeca. Thus, DRIP (Anocu AQP1) and the putative GLP share epithelial fluid-transporting roles along the alimentary tract in cupreous chafer larvae. PMID:23531819

  10. Dependences of water permeation through cyclic octa-peptide nanotubes on channel length and membrane thickness.

    PubMed

    Liu, Jian; Fan, Jianfen; Cen, Min; Song, Xuezeng; Liu, Dongyan; Zhou, Weiqun; Liu, Zhao; Yan, Jianfeng

    2012-08-27

    Effects of the channel length and membrane thickness on the water permeation through the transmembrane cyclic octa-peptide nanotubes (octa-PNTs) have been studied by molecular dynamics (MD) simulations. The water osmotic permeability (p(f)) through the PNTs of k × (WL)(4)/POPE (1-palmitoyl-2-oleoyl-glycerophosphoethanolamine; k = 6, 7, 8, 9, and 10) was found to decay with the channel length (L) along the axis (~L(-2.0)). Energetic analysis showed that a series of water binding sites exist in these transmembrane PNTs, with the barriers of ~3k(B)T, which elucidates the tendency of p(f) well. Water diffusion permeability (p(d)) exhibits a relationship of ~L(-1.8), which results from the novel 1-2-1-2 structure of water chain in such confined nanolumens. In the range of simulation accuracy, the ratio (p(f)/p(d)) of the water osmotic and diffusion permeability is approximately a constant. MD simulations of water permeation through the transmembrane PNTs of 8 × (WL)(4)/octane with the different octane membrane thickness revealed that the water osmotic and diffusion permeability (p(f) and p(d)) are both independent of the octane membrane thickness, confirmed by the weak and nearly same interactions between the channel water and octane membranes with the different thickness. The results may be helpful for revealing the permeation mechanisms of biological water channels and designing artificial nanochannels. PMID:22834559

  11. Liquid Water Transport in the Reactant Channels of Proton Exchange Membrane Fuel Cells

    NASA Astrophysics Data System (ADS)

    Banerjee, Rupak

    Water management has been identified as a critical issue in the development of PEM fuel cells for automotive applications. Water is present inside the PEM fuel cell in three phases, i.e. liquid phase, vapor phase and mist phase. Liquid water in the reactant channels causes flooding of the cell and blocks the transport of reactants to the reaction sites at the catalyst layer. Understanding the behavior of liquid water in the reactant channels would allow us to devise improved strategies for removing liquid water from the reactant channels. In situ fuel cell tests have been performed to identify and diagnose operating conditions which result in the flooding of the fuel cell. A relationship has been identified between the liquid water present in the reactant channels and the cell performance. A novel diagnostic technique has been established which utilizes the pressure drop multiplier in the reactant channels to predict the flooding of the cell or the drying-out of the membrane. An ex-situ study has been undertaken to quantify the liquid water present in the reactant channels. A new parameter, the Area Coverage Ratio (ACR), has been defined to identify the interfacial area of the reactant channel which is blocked for reactant transport by the presence of liquid water. A parametric study has been conducted to study the effect of changing temperature and the inlet relative humidity on the ACR. The ACR decreases with increase in current density as the gas flow rates increase, removing water more efficiently. With increase in temperature, the ACR decreases rapidly, such that by 60°C, there is no significant ACR to be reported. Inlet relative humidity of the gases does change the saturation of the gases in the channel, but did not show any significant effect on the ACR. Automotive powertrains, which is the target for this work, are continuously faced with transient changes. Water management under transient operating conditions is significantly more challenging and has not been investigated in detail. This study begins to investigate the effects of changing operating conditions on liquid water transport through the reactant channels. It has been identified that rapidly increasing temperature leads to the dry-out of the membrane and rapidly cooling the cell below 55°C results in the start of cell flooding. In changing the operating load of the PEMFC, overshoot in the pressure drop in the reactant channel has been identified for the first time as part of this investigation. A parametric study has been conducted to identify the factors which influence this overshoot behavior.

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

    PubMed

    Xu, Yao; Leitner, David M

    2014-07-17

    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

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

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

    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.

  14. Steered molecular dynamics approach for promising drugs for influenza A virus targeting M2 channel proteins.

    PubMed

    Nguyen, Hung; Le, Ly

    2015-09-01

    We have used steered molecular dynamics simulation to investigate the molecular interactions between four M2 inhibitors (amantadine, rimantadine, and two other amantadine derivatives) and the M2 protein channels of influenza A virus H5N1, including the wild type (WT) and three previously identified drug-resistant variants (G34A, S31N, and V27A). The binding free energies between these four inhibitors and the M2 channel of the WT and the three mutants were also determined by use of the molecular mechanics-Poisson-Boltzmann surface area method. Our study provides important insight into binding affinity, including detailed energy components and interactions at the molecular level of four potential inhibitors with the M2 channel of drug-resistant strains; this may assist further experimental study and strategies for rational design of new inhibitors. PMID:26033540

  15. Regulation of ROMK1 channels by protein-tyrosine kinase and -tyrosine phosphatase.

    PubMed

    Moral, Z; Dong, K; Wei, Y; Sterling, H; Deng, H; Ali, S; Gu, R; Huang, X Y; Hebert, S C; Giebisch, G; Wang, W H

    2001-03-01

    We have used the two-electrode voltage clamp technique and the patch clamp technique to investigate the regulation of ROMK1 channels by protein-tyrosine phosphatase (PTP) and protein-tyrosine kinase (PTK) in oocytes coexpressing ROMK1 and cSrc. Western blot analysis detected the presence of the endogenous PTP-1D isoform in the oocytes. Addition of phenylarsine oxide (PAO), an inhibitor of PTP, reversibly reduced K(+) current by 55% in oocytes coinjected with ROMK1 and cSrc. In contrast, PAO had no significant effect on K(+) current in oocytes injected with ROMK1 alone. Moreover, application of herbimycin A, an inhibitor of PTK, increased K(+) current by 120% and completely abolished the effect of PAO in oocytes coexpressing ROMK1 and cSrc. The effects of herbimycin A and PAO were absent in oocytes expressing the ROMK1 mutant R1Y337A in which the tyrosine residue at position 337 was mutated to alanine. However, addition of exogenous cSrc had no significant effect on the activity of ROMK1 channels in inside-out patches. Moreover, the effect of PAO was completely abolished by treatment of oocytes with 20% sucrose and 250 microg/ml concanavalin A, agents that inhibit the endocytosis of ROMK1 channels. Furthermore, the effect of herbimycin A is absent in the oocytes pretreated with either colchicine, an inhibitor of microtubules, or taxol, an agent that freezes microtubules. We conclude that PTP and PTK play an important role in regulating ROMK1 channels. Inhibiting PTP increases the internalization of ROMK1 channels, whereas blocking PTK stimulates the insertion of ROMK1 channels. PMID:11114300

  16. Protein tyrosine kinase regulates the number of renal secretory K channels.

    PubMed

    Wang, W; Lerea, K M; Chan, M; Giebisch, G

    2000-01-01

    The apical small conductance (SK) channel plays a key role in K secretion in the cortical collecting duct (CCD). A high-K intake stimulates renal K secretion and involves a significant increase in the number of SK channels in the apical membrane of the CCD. We used the patch-clamp technique to examine the role of protein tyrosine kinase (PTK) in regulating the activity of SK channels in the CCD. The application of 100 microM genistein stimulated SK channels in 11 of 12 patches in CCDs from rats on a K-deficient diet, and the mean increase in NP(o), a product of channel number (N) and open probability (P(o)), was 2.5. In contrast, inhibition of PTK had no effect in tubules from animals on a high-K diet in all 10 experiments. Western blot analysis further shows that the level of cSrc, a nonreceptor type of PTK, is 261% higher in the kidneys from rats on a K-deficient diet than those on a high-K diet. However, the effect of cSrc was not the result of direct inhibition of channel itself, because addition of exogenous cSrc had no effect on SK channels in inside-out patches. In cell-attached patches, application of herbimycin A increased channel activity in 14 of 16 patches, and the mean increase in NP(o) was 2.4 in tubules from rats on a K-deficient diet. In contrast, herbimycin A had no effect on channel activity in any of 15 tubules from rats on a high-K diet. Furthermore, herbimycin A pretreatment increased NP(o) per patch from the control value (0.4) to 2.25 in CCDs from rats on a K-deficient diet, whereas herbimycin failed to increase channel activity (NP(o): control, 3.10; herbimycin A, 3.25) in the CCDs from animals on a high-K diet. We conclude that PTK is involved in regulating the number of apical SK channels in the kidney. PMID:10644668

  17. An efficient method for modeling kinetic behavior of channel proteins in cardiomyocytes.

    PubMed

    Wang, Chong; Beyerlein, Peter; Pospisil, Heike; Krause, Antje; Nugent, Chris; Dubitzky, Werner

    2012-01-01

    Characterization of the kinetic and conformational properties of channel proteins is a crucial element in the integrative study of congenital cardiac diseases. The proteins of the ion channels of cardiomyocytes represent an important family of biological components determining the physiology of the heart. Some computational studies aiming to understand the mechanisms of the ion channels of cardiomyocytes have concentrated on Markovian stochastic approaches. Mathematically, these approaches employ Chapman-Kolmogorov equations coupled with partial differential equations. As the scale and complexity of such subcellular and cellular models increases, the balance between efficiency and accuracy of algorithms becomes critical. We have developed a novel two-stage splitting algorithm to address efficiency and accuracy issues arising in such modeling and simulation scenarios. Numerical experiments were performed based on the incorporation of our newly developed conformational kinetic model for the rapid delayed rectifier potassium channel into the dynamic models of human ventricular myocytes. Our results show that the new algorithm significantly outperforms commonly adopted adaptive Runge-Kutta methods. Furthermore, our parallel simulations with coupled algorithms for multicellular cardiac tissue demonstrate a high linearity in the speedup of large-scale cardiac simulations. PMID:21576757

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

    PubMed Central

    Hill, Adrian E.

    2013-01-01

    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

  19. Cephalopod consumption by trawl caught sh in Scottish and English Channel waters

    E-print Network

    Pierce, Graham

    Cephalopod consumption by trawl caught ®sh in Scottish and English Channel waters H.I. Dalya , G waters, they are often of limited use for estimating the impact of ®sh predation on cephalopod resources. This is due to either the origin of the ®sh sampled, e.g. from areas with a relatively low cephalopod

  20. Modeling Meandering Channel by Two-Dimensional Shallow Water Equations

    NASA Astrophysics Data System (ADS)

    Yu, C.; Duan, J. G.

    2014-12-01

    This research is to simulate the process of channel meandering using a two-dimensional depth-averaged hydrodynamic model. The multiple interactions between unsteady flow, turbulence, secondary flow, nonequilibrium sediment transport and bank erosion are considered by the model. The governing equations are the 2D depth-averaged Reynolds-averaged Navier-Stokes (2D-RANS) equations and the Exner equation for bed elevation evolution. The Reynolds stresses are calculated by the k-? turbulence model. The secondary flow, is modeled by the dispersion terms in momentum equations. The spatial lag between the instantaneous flow properties and the rate of sediment transport is simulated by the nonequilibrium sediment transport model. During the process of adaptation, the sediment transport rate gradually develops into the transport capacity of a given flow condition. The evolution of channel bed and bank is modeled by the general Exner equation that accounts for both vertical deformation of bed elevation as well as lateral migration of bank. The system of governing equations is solved by a semi-implicit finite volume method over the Cartesian mesh. The advective fluxes across each cell interface are simultaneously calculated by the extended HLL Riemann solver. At each time step, the diffusion terms in the governing equations are solved by the implicit Euler scheme. The source terms are discretized in a well-balanced way to retain the C-property of the proposed model. Application of the model to different test cases indicates that the model can correctly simulate different phases of meandering channel evolution which include streamwise migration, transverse migration and rotation of channel bends.

  1. 33 CFR 207.640 - Sacramento Deep Water Ship Channel Barge Lock and Approach Canals; use, administration, and...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    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...

  2. 33 CFR 207.640 - Sacramento Deep Water Ship Channel Barge Lock and Approach Canals; use, administration, and...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    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...

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    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.

  4. Water polygons in high-resolution protein crystal structures

    PubMed Central

    Lee, Jonas; Kim, Sung-Hou

    2009-01-01

    We have analyzed the interstitial water (ISW) structures in 1500 protein crystal structures deposited in the Protein Data Bank that have greater than 1.5 Å resolution with less than 90% sequence similarity with each other. We observed varieties of polygonal water structures composed of three to eight water molecules. These polygons may represent the time- and space-averaged structures of “stable” water oligomers present in liquid water, and their presence as well as relative population may be relevant in understanding physical properties of liquid water at a given temperature. On an average, 13% of ISWs are localized enough to be visible by X-ray diffraction. Of those, averages of 78% are water molecules in the first water layer on the protein surface. Of the localized ISWs beyond the first layer, almost half of them form water polygons such as trigons, tetragons, as well as expected pentagons, hexagons, higher polygons, partial dodecahedrons, and disordered networks. Most of the octagons and nanogons are formed by fusion of smaller polygons. The trigons are most commonly observed. We suggest that our observation provides an experimental basis for including these water polygon structures in correlating and predicting various water properties in liquid state. PMID:19551896

  5. Remote Sensing of Water Vapor and Thin Cirrus Clouds using MODIS Near-IR Channels

    NASA Technical Reports Server (NTRS)

    Gao, Bo-Cai; Kaufman, Yoram J.

    2001-01-01

    The Moderate Resolution Imaging Spectroradiometer (MODIS), a major facility instrument on board the Terra Spacecraft, was successfully launched into space in December of 1999. MODIS has several near-IR channels within and around the 0.94 micrometer water vapor bands for remote sensing of integrated atmospheric water vapor over land and above clouds. MODIS also has a special near-IR channel centered at 1.375-micron with a width of 30 nm for remote sensing of cirrus clouds. In this paper, we describe briefly the physical principles on remote sensing of water vapor and cirrus clouds using these channels. We also present sample water vapor images and cirrus cloud images obtained from MODIS data.

  6. Evaluation of coastal Bermuda grass protein extract as a substitute for fishmeal in practical diets for channel catfish (Ictalurus punctatus) 

    E-print Network

    Buentello, J. Alejandro

    1995-01-01

    In response to concerns over availability and cost of fishmeal for aquaculture feeds, a study was conducted to evaluate the suitability of a protein extract from coastal Bermuda grass for channel catfish (Ictalurus punctatus). The coastal Bermuda...

  7. Mechanosensitive channels of Escherichia coli: the MscL gene, protein, and activities

    NASA Technical Reports Server (NTRS)

    Sukharev, S. I.; Blount, P.; Martinac, B.; Kung, C.

    1997-01-01

    Although mechanosensory responses are ubiquitous and diverse, the molecular bases of mechanosensation in most cases remain mysterious MscL, a mechanosensitive channel of large conductance of Escherichia coli and its bacterial homologues are the first and currently only channel molecules shown to directly sense mechanical stretch of the membrane. In response to the tension conveyed via the lipid bilayer, MscL increases its open probability by several orders of magnitude. In the present review we describe the identification, cloning, and first sets of biophysical and structural data on this simplest mechanosensory molecule. We discovered a 2.5-ns mechanosensitive conductance in giant E. coli spheroplasts. Using chromatographies to enrich the target and patch clamp to assay the channel activity in liposome-reconstituted fractions, we identified the MscL protein and cloned the mscL gene. MscL comprises 136 amino acid residues (15 kDa), with two highly hydrophobic regions, and resides in the inner membrane of the bacterium. PhoA-fusion experiments indicate that the protein spans the membrane twice with both termini in the cytoplasm. Spectroscopic techniques show that it is highly helical. Expression of MscL tandems and covalent cross-linking suggest that the active channel complex is a homo-hexamer. We have identified several residues, which when deleted or substituted, affect channel kinetics or mechanosensitivity. Although unique when discovered, highly conserved MscL homologues in both gram-negative and gram-positive bacteria have been found, suggesting their ubiquitous importance among bacteria.

  8. Structural Waters Define a Functional Channel Mediating Activation of the GPCR, rhodopsin

    SciTech Connect

    Angel, T.; Gupta, S; Jastrzebska, B; Palczewski, K; Chance, M

    2009-01-01

    Structural water molecules may act as prosthetic groups indispensable for proper protein function. In the case of allosteric activation of G protein-coupled receptors (GPCRs), water likely imparts structural plasticity required for agonist-induced signal transmission. Inspection of structures of GPCR superfamily members reveals the presence of conserved embedded water molecules likely important to GPCR function. Coupling radiolytic hydroxyl radical labeling with rapid H2O18 solvent mixing, we observed no exchange of these structural waters with bulk solvent in either ground state or for the Meta II or opsin states. However, the radiolysis approach permitted labeling of selected side chain residues within the transmembrane helices and revealed activation-induced changes in local structural constraints likely mediated by dynamics of both water and protein. These results suggest both a possible general mechanism for water-dependent communication in family A GPCRs based on structural conservation, and a strategy for probing membrane protein structure.

  9. Revealing Surface Waters on an Antifreeze Protein by Fusion Protein Crystallography Combined with Molecular Dynamic Simulations.

    PubMed

    Sun, Tianjun; Gauthier, Sherry Y; Campbell, Robert L; Davies, Peter L

    2015-10-01

    Antifreeze proteins (AFPs) adsorb to ice through an extensive, flat, relatively hydrophobic surface. It has been suggested that this ice-binding site (IBS) organizes surface waters into an ice-like clathrate arrangement that matches and fuses to the quasi-liquid layer on the ice surface. On cooling, these waters join the ice lattice and freeze the AFP to its ligand. Evidence for the generality of this binding mechanism is limited because AFPs tend to crystallize with their IBS as a preferred protein-protein contact surface, which displaces some bound waters. Type III AFP is a 7 kDa globular protein with an IBS made up two adjacent surfaces. In the crystal structure of the most active isoform (QAE1), the part of the IBS that docks to the primary prism plane of ice is partially exposed to solvent and has clathrate waters present that match this plane of ice. The adjacent IBS, which matches the pyramidal plane of ice, is involved in protein-protein crystal contacts with few surface waters. Here we have changed the protein-protein contacts in the ice-binding region by crystallizing a fusion of QAE1 to maltose-binding protein. In this 1.9 Å structure, the IBS that fits the pyramidal plane of ice is exposed to solvent. By combining crystallography data with MD simulations, the surface waters on both sides of the IBS were revealed and match well with the target ice planes. The waters on the pyramidal plane IBS were loosely constrained, which might explain why other isoforms of type III AFP that lack the prism plane IBS are less active than QAE1. The AFP fusion crystallization method can potentially be used to force the exposure to solvent of the IBS on other AFPs to reveal the locations of key surface waters. PMID:26371748

  10. More than one dynamic crossover in protein hydration water

    E-print Network

    Marco G. Mazza; Kevin Stokely; Sara E. Pagnotta; Fabio Bruni; H. Eugene Stanley; Giancarlo Franzese

    2011-08-06

    Studies of liquid water in its supercooled region have led to many insights into the structure and behavior of water. While bulk water freezes at its homogeneous nucleation temperature of approximately 235 K, for protein hydration water, the binding of water molecules to the protein avoids crystallization. Here we study the dynamics of the hydrogen bond (HB) network of a percolating layer of water molecules, comparing measurements of a hydrated globular protein with the results of a coarse-grained model that has been shown to successfully reproduce the properties of hydration water. With dielectric spectroscopy we measure the temperature dependence of the relaxation time of protons charge fluctuations. These fluctuations are associated to the dynamics of the HB network of water molecules adsorbed on the protein surface. With Monte Carlo (MC) simulations and mean--field (MF) calculations we study the dynamics and thermodynamics of the model. In both experimental and model analyses we find two dynamic crossovers: (i) one at about 252 K, and (ii) one at about 181 K. The agreement of the experiments with the model allows us to relate the two crossovers to the presence of two specific heat maxima at ambient pressure. The first is due to fluctuations in the HB formation, and the second, at lower temperature, is due to the cooperative reordering of the HB network.

  11. More than one dynamic crossover in protein hydration water.

    PubMed

    Mazza, Marco G; Stokely, Kevin; Pagnotta, Sara E; Bruni, Fabio; Stanley, H Eugene; Franzese, Giancarlo

    2011-12-13

    Studies of liquid water in its supercooled region have helped us better understand the structure and behavior of water. Bulk water freezes at its homogeneous nucleation temperature (approximately 235 K), but protein hydration water avoids this crystallization because each water molecule binds to a protein. Here, we study the dynamics of the hydrogen bond (HB) network of a percolating layer of water molecules and compare the measurements of a hydrated globular protein with the results of a coarse-grained model that successfully reproduces the properties of hydration water. Using dielectric spectroscopy, we measure the temperature dependence of the relaxation time of proton charge fluctuations. These fluctuations are associated with the dynamics of the HB network of water molecules adsorbed on the protein surface. Using Monte Carlo simulations and mean-field calculations, we study the dynamics and thermodynamics of the model. Both experimental and model analyses are consistent with the interesting possibility of two dynamic crossovers, (i) at approximately 252 K and (ii) at approximately 181 K. Because the experiments agree with the model, we can relate the two crossovers to the presence at ambient pressure of two specific heat maxima. The first is caused by fluctuations in the HB formation, and the second, at a lower temperature, is due to the cooperative reordering of the HB network. PMID:22135473

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

    E-print Network

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

    2005-05-13

    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.

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

    PubMed

    Kondolf

    1997-07-01

    / 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

  14. A high-frequency warm shallow water acoustic communications channel model and measurements.

    PubMed

    Chitre, Mandar

    2007-11-01

    Underwater acoustic communication is a core enabling technology with applications in ocean monitoring using remote sensors and autonomous underwater vehicles. One of the more challenging underwater acoustic communication channels is the medium-range very shallow warm-water channel, common in tropical coastal regions. This channel exhibits two key features-extensive time-varying multipath and high levels of non-Gaussian ambient noise due to snapping shrimp-both of which limit the performance of traditional communication techniques. A good understanding of the communications channel is key to the design of communication systems. It aids in the development of signal processing techniques as well as in the testing of the techniques via simulation. In this article, a physics-based channel model for the very shallow warm-water acoustic channel at high frequencies is developed, which are of interest to medium-range communication system developers. The model is based on ray acoustics and includes time-varying statistical effects as well as non-Gaussian ambient noise statistics observed during channel studies. The model is calibrated and its accuracy validated using measurements made at sea. PMID:18189549

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

    SciTech Connect

    Kondolf, G.M.

    1997-07-01

    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.

  16. Unidirectionally migrating deep-water channels: Architectural styles and flow processes

    NASA Astrophysics Data System (ADS)

    Gong, C.; Steel, R. J.; Wang, Y.; Xu, Q.

    2014-12-01

    3D seismic data are used to investigate flow processes and sedimentation in deep-water slope channels of an alternate type characterized by short and straight channel courses, a lack of levees, and absence of any coeval fans. The study allows a picture of unusual flow processes in submarine channels. The studied channels can be divided into two discrete segments: (1) Upper segments are characterized by low aspect ratio(W/T), little lateral offset (Lm), and low migration/aggradation ratios (Lm/Va). These upper segment channels build vertically-stacked channel-complex sets (CCSs), each of which is characterized by a facies transition from fine-grained sands in the lower part overlain by debris flow deposits and then shale drapes. Energetic sediment density flows triggered by fluid escape and/or strong wave action were well able to bypass sediment and to mask relatively weak bottom currents, yielding deep-water channels characterized by little lateral offset and dominantly aggradational stacking patterns. (2) Lower segments are characterized by higher W/T, wide lateral offset (Lm), and high Lm/Va. They consist of laterally-migrated CCSs, each of which consists of fine-grained reworked sands in the lower part overlain by debris flow deposits and, finally, shale drapes. Bottom currents restricted within the channels would have induced a tilt of the interface between turbidity currents and the overriding bottom currents (Wedderburn number > 1). This would have deflected turbidity currents downward and back toward the gentle channel bank, thus causing channel migration (the steep bank) by ~2° to 15°, and yielding a helical flow circulation composed of a high-velocity zone along the steep bank and a low-velocity zone along the gentle bank. This bottom current-induced helical flow circulation promoted deposition on the gentle bank, but it favored erosion on the steep banke, yielding deep-water channels exhibiting wide lateral offset and dominantly laterally-offset stacking patterns. Sediment supplied to the studied channels was therefore sorted, winnowed and swept along the steep bank by the high-velocity zone along this bank, yielding bottom current-reworked sands that that are preferentially disturbed along the steep bank of the studied channels.

  17. The Dynamic Transition of Protein Hydration Water

    E-print Network

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

    2010-02-12

    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.

  18. Pentameric Assembly of Potassium Channel Tetramerization Domain-Containing Protein 5

    SciTech Connect

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

    2009-07-22

    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 BTB (bric-a-brac, tramtrack, broad complex) domain surface mediates the assembly of five KCTD5 and four voltage-gated K(+) (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 by approximately 30 degrees; the C-module shows a new fold and is required to bind Golgi reassembly stacking protein 55 with approximately 1 microM affinity, as judged by surface plasmon resonance and ultracentrifugation. Fourth, despite the homology reflected in its name, KCTD5 does not impact the operation of Kv4.2, Kv3.4, Kv2.1, or Kv1.2 channels.

  19. Generation, comparison, and merging of pathways between protein conformations: gating in K-channels.

    PubMed

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

    2008-10-01

    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

  20. Long-range protein-water dynamics in hyperactive insect antifreeze proteins.

    PubMed

    Meister, Konrad; Ebbinghaus, Simon; Xu, Yao; Duman, John G; DeVries, Arthur; Gruebele, Martin; Leitner, David M; Havenith, Martina

    2013-01-29

    Antifreeze proteins (AFPs) are specific proteins that are able to lower the freezing point of aqueous solutions relative to the melting point. Hyperactive AFPs, identified in insects, have an especially high ability to depress the freezing point by far exceeding the abilities of other AFPs. In previous studies, we postulated that the activity of AFPs can be attributed to two distinct molecular mechanisms: (i) short-range direct interaction of the protein surface with the growing ice face and (ii) long-range interaction by protein-induced water dynamics extending up to 20 Å from the protein surface. In the present paper, we combine terahertz spectroscopy and molecular simulations to prove that long-range protein-water interactions make essential contributions to the high antifreeze activity of insect AFPs from the beetle Dendroides canadensis. We also support our hypothesis by studying the effect of the addition of the osmolyte sodium citrate. PMID:23277543

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

    PubMed Central

    Neely, Alan; Hidalgo, Patricia

    2014-01-01

    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

  2. Aquaporin water channel AgAQP1 in the malaria vector mosquito Anopheles gambiae during blood feeding and humidity adaptation

    PubMed Central

    Liu, Kun; Tsujimoto, Hitoshi; Cha, Sung-Jae; Agre, Peter; Rasgon, Jason L.

    2011-01-01

    Altered patterns of malaria endemicity reflect, in part, changes in feeding behavior and climate adaptation of mosquito vectors. Aquaporin (AQP) water channels are found throughout nature and confer high-capacity water flow through cell membranes. The genome of the major malaria vector mosquito Anopheles gambiae contains at least seven putative AQP sequences. Anticipating that transmembrane water movements are important during the life cycle of A. gambiae, we identified and characterized the A. gambiae aquaporin 1 (AgAQP1) protein that is homologous to AQPs known in humans, Drosophila, and sap-sucking insects. When expressed in Xenopus laevis oocytes, AgAQP1 transports water but not glycerol. Similar to mammalian AQPs, water permeation of AgAQP1 is inhibited by HgCl2 and tetraethylammonium, with Tyr185 conferring tetraethylammonium sensitivity. AgAQP1 is more highly expressed in adult female A. gambiae mosquitoes than in males. Expression is high in gut, ovaries, and Malpighian tubules where immunofluorescence microscopy reveals that AgAQP1 resides in stellate cells but not principal cells. AgAQP1 expression is up-regulated in fat body and ovary by blood feeding but not by sugar feeding, and it is reduced by exposure to a dehydrating environment (42% relative humidity). RNA interference reduces AgAQP1 mRNA and protein levels. In a desiccating environment (<20% relative humidity), mosquitoes with reduced AgAQP1 protein survive significantly longer than controls. These studies support a role for AgAQP1 in water homeostasis during blood feeding and humidity adaptation of A. gambiae, a major mosquito vector of human malaria in sub-Saharan Africa. PMID:21444767

  3. The p7 Protein of Hepatitis C Virus Forms Structurally Plastic, Minimalist Ion Channels

    PubMed Central

    Chandler, Danielle E.; Penin, François; Schulten, Klaus; Chipot, Christophe

    2012-01-01

    Hepatitis C virus (HCV) p7 is a membrane-associated oligomeric protein harboring ion channel activity. It is essential for effective assembly and release of infectious HCV particles and an attractive target for antiviral intervention. Yet, the self-assembly and molecular mechanism of p7 ion channelling are currently only partially understood. Using molecular dynamics simulations (aggregate time 1.2 µs), we show that p7 can form stable oligomers of four to seven subunits, with a bias towards six or seven subunits, and suggest that p7 self-assembles in a sequential manner, with tetrameric and pentameric complexes forming as intermediate states leading to the final hexameric or heptameric assembly. We describe a model of a hexameric p7 complex, which forms a transiently-open channel capable of conducting ions in simulation. We investigate the ability of the hexameric model to flexibly rearrange to adapt to the local lipid environment, and demonstrate how this model can be reconciled with low-resolution electron microscopy data. In the light of these results, a view of p7 oligomerization is proposed, wherein hexameric and heptameric complexes may coexist, forming minimalist, yet robust functional ion channels. In the absence of a high-resolution p7 structure, the models presented in this paper can prove valuable as a substitute structure in future studies of p7 function, or in the search for p7-inhibiting drugs. PMID:23028296

  4. Evaluation of a cathode gas channel with a water absorption layer/waste channel in a PEFC by using visualization technique

    NASA Astrophysics Data System (ADS)

    Sugiura, Kimihiko; Nakata, Motoki; Yodo, Tadakatsu; Nishiguchi, Yusuke; Yamauchi, Makoto; Itoh, Yasuhiko

    The polymer electrolyte fuel cell (PEFC) cathode is a performance-limiting component due to the slower oxygen reduction kinetics and mass transport limitations imposed by water generated in an electrochemical reaction. This water assists the performance of the PEFC by preventing drying of the polymer electrolyte. Conversely, the water hinders the transport of the reactant species by blocking the pores in the gas diffusion layer. Moreover, the effective electrode area is decreased, causing the cathode channel to become clogged with supersaturated water from the gas diffusion layer. This problem is overcome by separating the gas channel and the waste channel, and installing a water absorption layer (WAL). The new "WAL type" gas channel has an installed WAL in which the designed waste channel is compared with the gas flow characteristics of a conventional cathode gas channel by using the visualization technique. Gas flowing into the WAL type separator is barely blocked before the WAL absorbs water condensed in the cathode gas channel. Therefore, the WAL type separator effectively improves the PEFC performance.

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

    PubMed

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

    2009-01-01

    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

  6. Protein-Protein Interactions: Modeling the Hepatitis C Virus Ion Channel p7 George Patargias, Nicole Zitzmann, Raymond Dwek, and Wolfgang B. Fischer*,,

    E-print Network

    . Introduction Hepatitis C virus is the major cause of chronic viral hepatitis which can lead eventuallyProtein-Protein Interactions: Modeling the Hepatitis C Virus Ion Channel p7 George Patargias, Nicole Zitzmann, Raymond Dwek, and Wolfgang B. Fischer*,,§ Biomembrane Structure Unit and Oxford

  7. Channels Formed by Botulinum, Tetanus, and Diphtheria Toxins in Planar Lipid Bilayers: Relevance to Translocation of Proteins across Membranes

    NASA Astrophysics Data System (ADS)

    Hoch, David H.; Romero-Mira, Miryam; Ehrlich, Barbara E.; Finkelstein, Alan; Dasgupta, Bibhuti R.; Simpson, Lance L.

    1985-03-01

    The heavy chains of both botulinum neurotoxin type B and tetanus toxin form channels in planar bilayer membranes. These channels have pH-dependent and voltage-dependent properties that are remarkably similar to those previously described for diphtheria toxin. Selectivity experiments with anions and cations show that the channels formed by the heavy chains of all three toxins are large; thus, these channels could serve as ``tunnel proteins'' for translocation of active peptide fragments. These findings support the hypothesis that the active fragments of botulinum neurotoxin and tetanus toxin, like that of diphtheria toxin, are translocated across the membranes of acidic vesicles.

  8. Protein-associated water and secondary structure effect removal of blood proteins from metallic substrates.

    PubMed

    Anand, Gaurav; Zhang, Fuming; Linhardt, Robert J; Belfort, Georges

    2011-03-01

    Removing adsorbed protein from metals has significant health and industrial consequences. There are numerous protein-adsorption studies using model self-assembled monolayers or polymeric substrates but hardly any high-resolution measurements of adsorption and removal of proteins on industrially relevant transition metals. Surgeons and ship owners desire clean metal surfaces to reduce transmission of disease via surgical instruments and minimize surface fouling (to reduce friction and corrosion), respectively. A major finding of this work is that, besides hydrophobic interaction adhesion energy, water content in an adsorbed protein layer and secondary structure of proteins determined the access and hence ability to remove adsorbed proteins from metal surfaces with a strong alkaline-surfactant solution (NaOH and 5 mg/mL SDS in PBS at pH 11). This is demonstrated with three blood proteins (bovine serum albumin, immunoglobulin, and fibrinogen) and four transition metal substrates and stainless steel (platinum (Pt), gold (Au), tungsten (W), titanium (Ti), and 316 grade stainless steel (SS)). All the metallic substrates were checked for chemical contaminations like carbon and sulfur and were characterized using X-ray photoelectron spectroscopy (XPS). While Pt and Au surfaces were oxide-free (fairly inert elements), W, Ti, and SS substrates were associated with native oxide. Difference measurements between a quartz crystal microbalance with dissipation (QCM-D) and surface plasmon resonance spectroscopy (SPR) provided a measure of the water content in the protein-adsorbed layers. Hydrophobic adhesion forces, obtained with atomic force microscopy, between the proteins and the metals correlated with the amount of the adsorbed protein-water complex. Thus, the amount of protein adsorbed decreased with Pt, Au, W, Ti and SS, in this order. Neither sessile contact angle nor surface roughness of the metal substrates was useful as predictors here. All three globular proteins behaved similarly on addition of the alkaline-surfactant cleaning solution, in that platinum and gold exhibited an increase, while tungsten, titanium, and stainless steel showed a decrease in weight. According to dissipation measurements with the QCM-D, the adsorbed layer for platinum and gold was rigid, while that for the tungsten, titanium, and stainless steel was much more flexible. The removal efficiency of adsorbed-protein by alkaline solution of SDS depended on the water content of the adsorbed layers for W, Ti, and SS, while for Pt and Au, it depended on secondary structural content. When protein adsorption was high (Pt, Au), protein-protein interactions and protein-surface interactions were dominant and the removal of protein layers was limited. Water content of the adsorbed protein layer was the determining factor for how efficiently the layer was removed by alkaline SDS when protein adsorption was low. Hence, protein-protein and protein-surface interactions were minimal and protein structure was less perturbed in comparison with those for high protein adsorption. Secondary structural content determined the efficient removal of adsorbed protein for high adsorbed amount. PMID:21182242

  9. Molecular characterization, phylogenetic analysis and expression patterns of five protein arginine methyltransferase genes of channel catfish, Ictalurus punctatus (Rafinesque)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  10. 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)

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

    2014-06-01

    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.

  11. 2D IR spectroscopy reveals the role of water in the binding of channel-blocking drugs to the influenza M2 channel

    SciTech Connect

    Ghosh, Ayanjeet E-mail: gai@sas.upenn.edu; Gai, Feng E-mail: gai@sas.upenn.edu; Hochstrasser, Robin M.; Wang, Jun; DeGrado, William F.; Moroz, Yurii S.; Korendovych, Ivan V.; Zanni, Martin

    2014-06-21

    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.

  12. 4D photogrammetric technique to study free surface water in open channels

    NASA Astrophysics Data System (ADS)

    Aubé, Damien; Berkaoui, Amine; Vinatier, Fabrice; Bailly, Jean-Stéphane; Belaud, Gilles

    2015-04-01

    Characteristics of three-dimensional surface water are considered as the most valuable information to understand hydrodynamic phenomena in open channel flow. An accurate and coherent description of the free water surface morphology improves the accuracy of hydraulic models which study river processes. However, amongst existing techniques to measure three-dimensional surface, stereo-photogrammetry is clearly the most effective technique to obtain an instantaneous and high accurate 3D free water surface and it's suitable to both flume and field condition. Our study aims at developing this technique in two controlled channels, one in interior with glass borders (length: 6 m, width: 0.3 m and depth: 0.5 m) and one outside with cement borders (length: 13 m, width: 0.7 m and depth: 0.4 m). A system consisting in three NIKON-D3200 cameras, mounted to an adjustable tripod head, which is fixed to an inverted aluminium T-bar with the center camera higher than the two side cameras. Each camera is fitted with a 28 mm lens and cameras are synchronized using a Phottix(R) system. The system was mounted at a downstream position from the channel with an oblique configuration. A series of pictures taken at a 3 s interval during the water weight bearing were reported and analyzed using the Photoscan Pro(R) software for image matching. Validation procedure of the technique was realized using an orthophotography of the lateral border of the interior channel to delimit the line of water surface, and using a video capture of a slide fixed inside the outside channel. A high resolution and dynamic elevation map of the surface water was constructed. Our study give encouraging results, with a good capture of water surface morphology and a limited occlusion issues. The confrontation of the results with the validation dataset highlight limitations that need to be discussed with the audience.

  13. Estimating Small Scale River Channel Roughness Using a Through-water Photo-based technique

    NASA Astrophysics Data System (ADS)

    James, M. R.; Scarborough, F.; Folkard, A. M.

    2014-12-01

    Channel roughness is critical to the understanding of fluvial geomorphology and hydrology due to its connection with the transportation of sediment and effect on flow discharge. Due to manual measurement methods being costly and time consuming, and traditional visual observation methods being subjective, we have explored the use of a close-range remote sensing approach, based on through-water photography to estimate channel characteristics. Previous similar photo-based measurements have focused on estimating water depth by correcting data from stereo image pairs for refraction at the water surface. Here, we extend this approach to multi-image data sets, and implement refraction correction for data from commonly used 'structure from motion' based software. The accuracy of applied corrections is assessed in a laboratory setting using a gravel surface submerged at a range of water depths. We demonstrate the approach in the field by photographing cross sections to produce high density point clouds and hence digital elevation models of the stream bed. Correcting submerged regions for refraction effects allows channel characteristics such as wetted perimeter and water depth to be estimated. We explore the use of parameters thus estimated for deriving coefficients of channel flow resistance such as Manning's coefficient.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    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.

  15. Microfiltration: Effect of retentate protein concentration on limiting flux and serum protein removal with 4-mm-channel ceramic microfiltration membranes.

    PubMed

    Hurt, E E; Adams, M C; Barbano, D M

    2015-04-01

    The objective of our study was to determine if the limiting flux and serum protein (SP) removal were different at 8, 9, or 10% true protein (TP) in the microfiltration (MF) retentate recirculation loop using 0.1-µm ceramic graded permeability membranes with 4-mm-channel diameters operated at 50 °C using a diluted milk protein concentrate with 85% protein on a total solids basis (MPC85) as the MF feed. The limiting flux for the MF of diluted MPC85 was determined at 3 TP concentrations in the recirculation loop (8, 9, and 10%). The experiment was replicated 3 times for a total of 9 runs. On the morning of each run, MPC85 was diluted with reverse osmosis water to an MF feed TP concentration of 5.4%. In all runs, the starting flux was 55 kg/m(2) per hour, the flux was increased in steps until the limiting flux was reached. The minimum flux increase was 10 kg/m(2) per hour. The limiting flux decreased as TP concentration in the recirculation loop increased. The limiting flux was 154 ± 0.3, 133 ± 0.7, and 117 ± 3.3 kg/m(2) per hour at recirculation loop TP concentrations of 8.2 ± 0.07, 9.2 ± 0.04, and 10.2 ± 0.09%, respectively. No effect of recirculation loop TP concentration on the SP removal factor was detected. However, the SP removal factor decreased from 0.80 ± 0.02 to 0.75 ± 0.02 as flux was increased from the starting flux of 55 kg/m(2) per hour to the limiting flux, with a similar decrease seen at all recirculation loop TP concentrations. PMID:25682139

  16. Hydration water and bulk water in proteins have distinct properties in radial distributions calculated from 105 atomic resolution crystal structures

    PubMed Central

    Chen, Xianfeng; Weber, Irene; Harrison, Robert W.

    2009-01-01

    Water plays a critical role in the structure and function of proteins, although the experimental properties of water around protein structures are not well understood. The water can be classified by the separation from the protein surface into bulk water and hydration water. Hydration water interacts closely with the protein and contributes to protein folding, stability and dynamics, as well as interacting with the bulk water. Water potential functions are often parameterized to fit bulk water properties because of the limited experimental data for hydration water. Therefore, the structural and energetic properties of the hydration water were assessed for 105 atomic resolution (?1.0 Å) protein crystal structures with a high level of hydration water by calculating the experimental water-protein radial distribution function or surface distribution function (SDF) and water radial distribution function (RDF). Two maxima are observed in SDF: the first maximum at a radius of 2.75 Å reflects first shell and hydrogen bond interactions between protein and water, the second maximum at 3.65 Å reflects second shell and van der Waals interactions between water and non-polar atoms of protein forming clathrate-hydrate-like structures. Thus, the two shells do not overlap. The RDF showed the features of liquid water rather than solid ice. The first and second maxima of RDF at 2.75 and 4.5 Å, respectively, are the same as for bulk water, but the peaks are sharper indicating hydration water is more stable than bulk water. Both distribution functions are inversely correlated with the distribution of B factors (atomic thermal factors) for the waters, suggesting that the maxima reflect stable positions. Therefore, the average water structure near the protein surface has experimentally observable differences from bulk water. This analysis will help improve the accuracy for models of water on the protein surface by providing rigorous data for the effects of the apparent chemical potential of the water near a protein surface. PMID:18754631

  17. Imaging ROMK1 inwardly rectifying ATP-sensitive K+ channel protein using atomic force microscopy.

    PubMed Central

    Henderson, R M; Schneider, S; Li, Q; Hornby, D; White, S J; Oberleithner, H

    1996-01-01

    The inwardly rectifying K+ channel ROMK1 has been implicated as being significant in K+ secretion in the distal nephron. ROMK1 has been shown by immunocytochemistry to be expressed in relevant nephron segments. The development of the atomic force microscope has made possible the production of high resolution images of small particles, including a variety of biological macromolecules. Recently, a fusion protein of glutathione S-transferase (GST) and ROMK1 (ROMK1-GST) has been used to produce a polyclonal antibody for immunolocalization of ROMK1. We have used atomic force microscopy to examine ROMK1-GST and the native ROMK1 polypeptide cleaved from GST. Imaging was conducted with the proteins in physiological solutions attached to mica. ROMK1-GST appears in images as a particle composed of two units of similar size. Analyses of images indicate that the two units have volumes of approximately 118 nm3, which is close to the theoretical volume of a globular protein of approximately 65 kDa (the molecular mass of ROMK1-GST). Native GST exists as a dimer, and the images obtained here are consistent with the ROMK1-GST fusion protein's existence as a heterodimer. In experiments on ROMK1 in aqueous solution, single molecules appear to aggregate, but contact to the mica was maintained. Addition of ATP to the solution produced a change in height of the aggregates. This change (which was reversible) suggests that ATP induces a structural change in the ROMK1 protein. The data show that atomic force microscopy is a useful tool for examination of purified protein molecules under near-physiological conditions, and furthermore, that structural alterations in the proteins may be continuously investigated. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:8710944

  18. Ferroelectric hydration shells around proteins: Electrostatics of the protein/water interface

    E-print Network

    LeBard, David N

    2010-01-01

    Numerical simulations of hydrated proteins show that protein hydration shells are polarized into a ferroelectric cluster with a large magnitude of its average dipole moment. The emergence of this new mesophase dramatically alters the statistics of electrostatic fluctuations at the protein/water interface. The linear-response relation between the average electrostatic potential and its variance breaks down, with the breadth of the electrostatic noise far exceeding the expectations of the linear response theories. The dynamics of these non-Gaussian electrostatic fluctuations are dominated by a slow (~ 1 ns) component which freezes in at the temperature of dynamical transition of proteins.

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

    PubMed

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

    2014-01-01

    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

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

    PubMed Central

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

    2014-01-01

    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

  1. Dynamics of energy distribution in three channel alpha helix protein based on Davydov's ansatz

    NASA Astrophysics Data System (ADS)

    Ahmad, Faozan; Alatas, Husin

    2015-04-01

    An important aspect of many biological processes at molecular level is the transfer and storage mechanism of bioenergy released in the reaction of the hydrolysis of Adenosinetriphosphate (ATP) by biomacromolecule especially protein. Model of Soliton Davydov is a new break-through that could describe that mechanism. Here we have reformulated quantum mechanical the Davydov theory, using least action principle. Dynamical aspect of the model is analyzed by numerical calculation. We found two dynamical cases: the traveling and pinning soliton that we suggest they are related to the energy transfer and storage mechanism in the protein. Traveling and pinning soliton can be controlled by strength of coupling. In 3- channel approach, we found the breather phenomena in which its frequency is determined by interchannel coupling parameter.

  2. Dynamics of energy distribution in three channel alpha helix protein based on Davydov’s ansatz

    SciTech Connect

    Ahmad, Faozan; Alatas, Husin

    2015-04-16

    An important aspect of many biological processes at molecular level is the transfer and storage mechanism of bioenergy released in the reaction of the hydrolysis of Adenosinetriphosphate (ATP) by biomacromolecule especially protein. Model of Soliton Davydov is a new break-through that could describe that mechanism. Here we have reformulated quantum mechanical the Davydov theory, using least action principle. Dynamical aspect of the model is analyzed by numerical calculation. We found two dynamical cases: the traveling and pinning soliton that we suggest they are related to the energy transfer and storage mechanism in the protein. Traveling and pinning soliton can be controlled by strength of coupling. In 3- channel approach, we found the breather phenomena in which its frequency is determined by interchannel coupling parameter.

  3. A new view of water dynamics in immobilized proteins.

    PubMed Central

    Halle, B; Denisov, V P

    1995-01-01

    The inflection frequency of the deuteron magnetic relaxation dispersion from water in rotationally immobilized protein samples has recently been found to be essentially independent of temperature and protein structure. This remarkable invariance has been interpreted in terms of a universal residence time of 1 microseconds for protein-associated water molecules. We demonstrate here that this interpretation is an artifact of the conventional perturbation theory of spin relaxation, which is not valid for rotationally immobile proteins. Using a newly developed non-perturbative, stochastic theory of spin relaxation, we identify the apparent correlation time of 1 microseconds with the inverse of the nuclear quadrupole frequency, thus explaining its invariance. The observed dispersion profiles are consistent with a broad distribution of residence times, spanning the microseconds range. Furthermore, we argue that the deuteron dispersion is due to buried water molecules rather than to the traditional surface hydration previously invoked, and that the contribution from rapidly exchanging protein hydrogens cannot be neglected. The conclusions of the present work are also relevant to proton relaxation in immobilized protein samples and to magnetic resonance imaging of soft tissue. PMID:7669901

  4. Adaptive resolution simulation of an atomistic protein in MARTINI water

    SciTech Connect

    Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J.; Praprotnik, Matej; Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000 Ljubljana

    2014-02-07

    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.

  5. Predicting grain protein content of winter wheat using remote sensing data based on nitrogen status and water stress

    NASA Astrophysics Data System (ADS)

    Zhao, Chunjiang; Liu, Liangyun; Wang, Jihua; Huang, Wenjiang; Song, Xiaoyu; Li, Cunjun

    2005-05-01

    Advanced site-specific knowledge of grain protein content of winter wheat from remote sensing data would provide opportunities to manage grain harvest differently, and to maximize output by adjusting input in fields. In this study, remote sensing data were utilized to predict grain protein content. Firstly, the leaf nitrogen content at winter wheat anthesis stage was proved to be significantly correlated with grain protein content ( R2 = 0.36), and spectral indices significantly correlated to leaf nitrogen content at anthesis stage were potential indicators for grain protein content. The vegetation index, VI green, derived from the canopy spectral reflectance at green and red bands, was significantly correlated to the leaf nitrogen content at anthesis stage, and also highly significantly correlated to the final grain protein content ( R2 = 0.46). Secondly, the external conditions, such as irrigation, fertilization and temperature, had important influence on grain quality. Water stress at grain filling stage can increase grain protein content, and leaf water content is closely related to irrigation levels, therefore, the spectral indices correlated to leaf water content can be potential indicators for grain protein content. The spectral reflectance of TM channel 5 derived from canopy spectra or image data at grain filling stage was all significantly correlated to grain protein content ( R2 = 0.31 and 0.37, respectively). Finally, not only this study proved the feasibility of using remote sensing data to predict grain protein content, but it also provided a tentative prediction of the grain protein content in Beijing area using the reflectance image of TM channel 5.

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

    PubMed

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

    2013-03-01

    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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    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.

  8. Computation of water-surface profiles in open channels

    USGS Publications Warehouse

    Davidian, Jacob

    1984-01-01

    The standard step-backwater method of computing water-surface profiles is described in this chapter. The hydraulic principles and assumptions are reviewed, and the field data requirements are described. Certain special cases of backwater curves and certain special field conditions are discussed in detail. The technique is used to establish or extend stage-discharge ratings; to define areas which will be innundated by flood flows of a given frequency; and to compute profiles through various reaches, including multichannel flows, and past control structures such as bridges, culverts, and road embankments. A brief description of analysis of floodways and effects of encroachments is also presented.

  9. Phylogenetic conservation of protein-lipid motifs in pentameric ligand-gated ion channels.

    PubMed

    Barrantes, Francisco J

    2015-09-01

    Using the crosstalk between the nicotinic acetylcholine receptor (nAChR) and its lipid microenvironment as a paradigm, this short overview analyzes the occurrence of structural motifs which appear not only to be conserved within the nAChR family and contemporary eukaryotic members of the pentameric ligand-gated ion channel (pLGIC) superfamily, but also extend to prokaryotic homologues found in bacteria. The evolutionarily conserved design is manifested in: 1) the concentric three-ring architecture of the transmembrane region, 2) the occurrence in this region of distinct lipid consensus motifs in prokaryotic and eukaryotic pLGIC and 3) the key participation of the outer TM4 ring in conveying the influence of the lipid membrane environment to the middle TM1-TM3 ring and this, in turn, to the inner TM2 channel-lining ring, which determines the ion selectivity of the channel. The preservation of these constant structural-functional features throughout such a long phylogenetic span likely points to the successful gain-of-function conferred by their early acquisition. This article is part of a Special Issue entitled: Lipid-protein interactions. PMID:25839355

  10. Tip-link protein protocadherin 15 interacts with transmembrane channel-like proteins TMC1 and TMC2

    PubMed Central

    Maeda, Reo; Kindt, Katie S.; Mo, Weike; Morgan, Clive P.; Erickson, Timothy; Zhao, Hongyu; Clemens-Grisham, Rachel; Barr-Gillespie, Peter G.; Nicolson, Teresa

    2014-01-01

    The tip link protein protocadherin 15 (PCDH15) is a central component of the mechanotransduction complex in auditory and vestibular hair cells. PCDH15 is hypothesized to relay external forces to the mechanically gated channel located near its cytoplasmic C terminus. How PCDH15 is coupled to the transduction machinery is not clear. Using a membrane-based two-hybrid screen to identify proteins that bind to PCDH15, we detected an interaction between zebrafish Pcdh15a and an N-terminal fragment of transmembrane channel-like 2a (Tmc2a). Tmc2a is an ortholog of mammalian TMC2, which along with TMC1 has been implicated in mechanotransduction in mammalian hair cells. Using the above-mentioned two-hybrid assay, we found that zebrafish Tmc1 and Tmc2a can interact with the CD1 or CD3 cytoplasmic domain isoforms of Pcdh15a, and this interaction depends on the common region shared between the two Pcdh15 isoforms. Moreover, an interaction between mouse PCDH15-CD3 and TMC1 or TMC2 was observed in both yeast two-hybrid assays and coimmunoprecipitation experiments. To determine whether the Pcdh15–Tmc interaction is relevant to mechanotransduction in vivo, we overexpressed N-terminal fragments of Tmc2a in zebrafish hair cells. Overexpression of the Tmc2a N terminus results in mislocalization of Pcdh15a within hair bundles, together with a significant decrease in mechanosensitive responses, suggesting that a Pcdh15a–Tmc complex is critical for mechanotransduction. Together, these results identify an evolutionarily conserved association between the fish and mouse orthologs of PCDH15 and TMC1 and TMC2, supporting the notion that TMCs are key components of the transduction complex in hair cells. PMID:25114259

  11. Tip-link protein protocadherin 15 interacts with transmembrane channel-like proteins TMC1 and TMC2.

    PubMed

    Maeda, Reo; Kindt, Katie S; Mo, Weike; Morgan, Clive P; Erickson, Timothy; Zhao, Hongyu; Clemens-Grisham, Rachel; Barr-Gillespie, Peter G; Nicolson, Teresa

    2014-09-01

    The tip link protein protocadherin 15 (PCDH15) is a central component of the mechanotransduction complex in auditory and vestibular hair cells. PCDH15 is hypothesized to relay external forces to the mechanically gated channel located near its cytoplasmic C terminus. How PCDH15 is coupled to the transduction machinery is not clear. Using a membrane-based two-hybrid screen to identify proteins that bind to PCDH15, we detected an interaction between zebrafish Pcdh15a and an N-terminal fragment of transmembrane channel-like 2a (Tmc2a). Tmc2a is an ortholog of mammalian TMC2, which along with TMC1 has been implicated in mechanotransduction in mammalian hair cells. Using the above-mentioned two-hybrid assay, we found that zebrafish Tmc1 and Tmc2a can interact with the CD1 or CD3 cytoplasmic domain isoforms of Pcdh15a, and this interaction depends on the common region shared between the two Pcdh15 isoforms. Moreover, an interaction between mouse PCDH15-CD3 and TMC1 or TMC2 was observed in both yeast two-hybrid assays and coimmunoprecipitation experiments. To determine whether the Pcdh15-Tmc interaction is relevant to mechanotransduction in vivo, we overexpressed N-terminal fragments of Tmc2a in zebrafish hair cells. Overexpression of the Tmc2a N terminus results in mislocalization of Pcdh15a within hair bundles, together with a significant decrease in mechanosensitive responses, suggesting that a Pcdh15a-Tmc complex is critical for mechanotransduction. Together, these results identify an evolutionarily conserved association between the fish and mouse orthologs of PCDH15 and TMC1 and TMC2, supporting the notion that TMCs are key components of the transduction complex in hair cells. PMID:25114259

  12. EFFECT OF WATER VELOCITY ON PASSAGE OF SALMONIDS IN A TRANSPORTATION CHANNEL

    E-print Network

    provided at. some dams to pass fish from a single major entrance to a distant fishway. The Dalles Dam in a transportation channel is important from t.he st.andpoint of fish passage as well as wat.er use. Clay (1961, Fishery Biologist (Research) BUREAU OF COMMERCIAL FISHERIES FISH-PASSAGE RESEARCH PROGRAM, SEATTLE, WASH

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

    PubMed

    Behera, Rabindra K; Theil, Elizabeth C

    2014-06-01

    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

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

    PubMed

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

    2000-05-24

    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

  15. Design of Peptide-Membrane Interactions to Modulate Single-File Water Transport through Modified Gramicidin Channels

    PubMed Central

    Portella, Guillem; Polupanow, Tanja; Zocher, Florian; Boytsov, Danila A.; Pohl, Peter; Diederichsen, Ulf; de Groot, Bert L.

    2012-01-01

    Water permeability through single-file channels is affected by intrinsic factors such as their size and polarity and by external determinants like their lipid environment in the membrane. Previous computational studies revealed that the obstruction of the channel by lipid headgroups can be long-lived, in the range of nanoseconds, and that pore-length-matching membrane mimetics could speed up water permeability. To test the hypothesis of lipid-channel interactions modulating channel permeability, we designed different gramicidin A derivatives with attached acyl chains. By combining extensive molecular-dynamics simulations and single-channel water permeation measurements, we show that by tuning lipid-channel interactions, these modifications reduce the presence of lipid headgroups in the pore, which leads to a clear and selective increase in their water permeability. PMID:23083713

  16. Design of peptide-membrane interactions to modulate single-file water transport through modified gramicidin channels.

    PubMed

    Portella, Guillem; Polupanow, Tanja; Zocher, Florian; Boytsov, Danila A; Pohl, Peter; Diederichsen, Ulf; de Groot, Bert L

    2012-10-17

    Water permeability through single-file channels is affected by intrinsic factors such as their size and polarity and by external determinants like their lipid environment in the membrane. Previous computational studies revealed that the obstruction of the channel by lipid headgroups can be long-lived, in the range of nanoseconds, and that pore-length-matching membrane mimetics could speed up water permeability. To test the hypothesis of lipid-channel interactions modulating channel permeability, we designed different gramicidin A derivatives with attached acyl chains. By combining extensive molecular-dynamics simulations and single-channel water permeation measurements, we show that by tuning lipid-channel interactions, these modifications reduce the presence of lipid headgroups in the pore, which leads to a clear and selective increase in their water permeability. PMID:23083713

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

    PubMed Central

    Johnson, Alan Kim

    2013-01-01

    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

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

    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.

  19. Bassoon specifically controls presynaptic P/Q-type Ca(2+) channels via RIM-binding protein.

    PubMed

    Davydova, Daria; Marini, Claudia; King, Claire; Klueva, Julia; Bischof, Ferdinand; Romorini, Stefano; Montenegro-Venegas, Carolina; Heine, Martin; Schneider, Romy; Schröder, Markus S; Altrock, Wilko D; Henneberger, Christian; Rusakov, Dmitri A; Gundelfinger, Eckart D; Fejtova, Anna

    2014-04-01

    Voltage-dependent Ca(2+) channels (CaVs) represent the principal source of Ca(2+) ions that trigger evoked neurotransmitter release from presynaptic boutons. Ca(2+) influx is mediated mainly via CaV2.1 (P/Q-type) and CaV2.2 (N-type) channels, which differ in their properties. Their relative contribution to synaptic transmission changes during development and tunes neurotransmission during synaptic plasticity. The mechanism of differential recruitment of CaV2.1 and CaV2.2 to release sites is largely unknown. Here, we show that the presynaptic scaffolding protein Bassoon localizes specifically CaV2.1 to active zones via molecular interaction with the RIM-binding proteins (RBPs). A genetic deletion of Bassoon or an acute interference with Bassoon-RBP interaction reduces synaptic abundance of CaV2.1, weakens P/Q-type Ca(2+) current-driven synaptic transmission, and results in higher relative contribution of neurotransmission dependent on CaV2.2. These data establish Bassoon as a major regulator of the molecular composition of the presynaptic neurotransmitter release sites. PMID:24698275

  20. EXPERIMENTAL STUDY OF TURBULENT SUPERCRITICAL OPEN CHANNEL WATER FLOW AS APPLIED TO THE CLiFF CONCEPT

    E-print Network

    California at Los Angeles, University of

    EXPERIMENTAL STUDY OF TURBULENT SUPERCRITICAL OPEN CHANNEL WATER FLOW AS APPLIED TO THE CLi Angeles, CA 90095-1597 ABSTRACT. An experimental study of turbulent open channel water flows was conducted that simulated basic features of the flow of molten salt in the CLiFF (Convective Liquid Flow First-Wall) concept

  1. Experimental study of turbulent supercritical open channel water flow as applied to the CLiFF concept

    E-print Network

    Abdou, Mohamed

    Experimental study of turbulent supercritical open channel water flow as applied to the CLi Angeles, CA 90095-1597, USA Abstract An experimental study of turbulent open channel water flows was conducted that simulated basic features of the flow of molten salt in the convective liquid flow first

  2. Unintended consequences? Water molecules at biological and crystallographic protein-protein interfaces.

    PubMed

    Ahmed, Mostafa H; Habtemariam, Mesay; Safo, Martin K; Scarsdale, J Neel; Spyrakis, Francesca; Cozzini, Pietro; Mozzarelli, Andrea; Kellogg, Glen E

    2013-12-01

    The importance of protein-protein interactions (PPIs) is becoming increasingly appreciated, as these interactions lie at the core of virtually every biological process. Small molecule modulators that target PPIs are under exploration as new therapies. One of the greatest obstacles faced in crystallographically determining the 3D structures of proteins is coaxing the proteins to form "artificial" PPIs that lead to uniform crystals suitable for X-ray diffraction. This work compares interactions formed naturally, i.e., "biological", with those artificially formed under crystallization conditions or "non-biological". In particular, a detailed analysis of water molecules at the interfaces of high-resolution (?2.30 Å) X-ray crystal structures of protein-protein complexes, where 140 are biological protein-protein complex structures and 112 include non-biological protein-protein interfaces, was carried out using modeling tools based on the HINT forcefield. Surprisingly few and relatively subtle differences were observed between the two types of interfaces: (i) non-biological interfaces are more polar than biological interfaces, yet there is better organized hydrogen bonding at the latter; (ii) biological associations rely more on water-mediated interactions with backbone atoms compared to non-biological associations; (iii) aromatic/planar residues play a larger role in biological associations with respect to water, and (iv) Lys has a particularly large role at non-biological interfaces. A support vector machines (SVMs) classifier using descriptors from this study was devised that was able to correctly classify 84% of the two interface types. PMID:24076743

  3. Selective modulation of neuronal nicotinic acetylcholine receptor channel subunits by Go-protein subunits.

    PubMed

    Fischer, Harald; Liu, Dong-Mei; Lee, Aven; Harries, Janet C; Adams, David J

    2005-04-01

    G-protein modulation of neuronal nicotinic acetylcholine receptor (nAChR) channels in rat intrinsic cardiac ganglia was examined using dialyzed whole-cell and excised membrane patch-recording configurations. Cell dialysis with GTPgammaS increased the agonist affinity of nAChRs, resulting in a potentiation of nicotine-evoked whole-cell currents at low concentrations. ACh- and nicotine-evoked current amplitudes were increased approximately twofold in the presence of GTPgammaS. In inside-out membrane patches, the open probability (NP(o)) of nAChR-mediated unitary currents was reversibly increased fourfold after bath application of 0.2 mm GTPgammaS relative to control but was unchanged in the presence of GDPbetaS. The modulation of nAChR-mediated whole-cell currents was agonist specific; currents evoked by the cholinergic agonists ACh, nicotine, and 1,1-dimethyl-4-phenylpiperazinium iodide, but not cytisine or choline, were potentiated in the presence of GTPgammaS. The direct interaction between G-protein subunits and nAChRs was examined by bath application of either G(o)alpha or Gbetagamma subunits to inside-out membrane patches and in glutathione S-transferase pull-down and coimmunoprecipitation experiments. Bath application of 50 nm Gbetagamma increased the open probability of ACh-activated single-channel currents fivefold, whereas G(o)alpha (50 nm) produced no significant increase in NP(o). Neuronal nAChR subunits alpha3-alpha5 and beta2 exhibited a positive interaction with G(o)alpha and Gbetagamma, whereas beta4 and alpha7 failed to interact with either of the G-protein subunits. These results provide evidence for a direct interaction between nAChR and G-protein subunits, underlying the increased open probability of ACh-activated single-channel currents and potentiation of nAChR-mediated whole-cell currents in parasympathetic neurons of rat intrinsic cardiac ganglia. PMID:15814787

  4. The Outer Membrane Protein OmpW Forms an Eight-Stranded beta-Barrel with a Hydrophobic Channel

    SciTech Connect

    Hong,H.; Patel, D.; Tamm, L.; van den Berg, B.

    2006-01-01

    Escherichia coli OmpW belongs to a family of small outer membrane (OM) proteins that are widespread in Gram-negative bacteria. Their functions are unknown, but recent data suggest that they may be involved in the protection of bacteria against various forms of environmental stress. In order to gain insight into the function of these proteins we have determined the crystal structure of Escherichia coli OmpW to 2.7 Angstroms resolution. The structure shows that OmpW forms an eight-stranded beta-barrel with a long and narrow hydrophobic channel that contains a bound LDAO detergent molecule. Single channel conductance experiments show that OmpW functions as an ion channel in planar lipid bilayers. The channel activity can be blocked by the addition of LDAO. Taken together, the data suggest that members of the OmpW family could be involved in the transport of small hydrophobic molecules across the bacterial OM.

  5. Ferroelectric hydration shells around proteins: electrostatics of the protein-water interface.

    PubMed

    LeBard, David N; Matyushov, Dmitry V

    2010-07-22

    Numerical simulations of hydrated proteins show that protein hydration shells are polarized into a ferroelectric layer with large values of the average dipole moment magnitude and the dipole moment variance. The emergence of the new polarized mesophase dramatically alters the statistics of electrostatic fluctuations at the protein-water interface. The linear response relation between the average electrostatic potential and its variance breaks down, with the breadth of the electrostatic fluctuations far exceeding the expectations of the linear response theories. The dynamics of these non-Gaussian electrostatic fluctuations are dominated by a slow (approximately = 1 ns) component that freezes in at the temperature of the dynamical transition of proteins. The ferroelectric shell propagates 3-5 water diameters into the bulk. PMID:20578769

  6. Expression of the Astrocyte Water Channel Aquaporin-4 in the Mouse Brain

    PubMed Central

    Hubbard, Jacqueline A.; Hsu, Mike S.; Seldin, Marcus M.

    2015-01-01

    Aquaporin-4 (AQP4) is a bidirectional water channel that is found on astrocytes throughout the central nervous system. Expression is particularly high around areas in contact with cerebrospinal fluid, suggesting that AQP4 plays a role in fluid exchange between the cerebrospinal fluid compartments and the brain. Despite its significant role in the brain, the overall spatial and region-specific distribution of AQP4 has yet to be fully characterized. In this study, we used Western blotting and immunohistochemical techniques to characterize AQP4 expression and localization throughout the mouse brain. We observed AQP4 expression throughout the forebrain, subcortical areas, and brainstem. AQP4 protein levels were highest in the cerebellum with lower expression in the cortex and hippocampus. We found that AQP4 immunoreactivity was profuse on glial cells bordering ventricles, blood vessels, and subarachnoid space. Throughout the brain, AQP4 was expressed on astrocytic end-feet surrounding blood vessels but was also heterogeneously expressed in brain tissue parenchyma and neuropil, often with striking laminar specificity. In the cerebellum, we showed that AQP4 colocalized with the proteoglycan brevican, which is synthesized by and expressed on cerebellar astrocytes. Despite the high abundance of AQP4 in the cerebellum, its functional significance has yet to be investigated. Given the known role of AQP4 in synaptic plasticity in the hippocampus, the widespread and region-specific expression pattern of AQP4 suggests involvement not only in fluid balance and ion homeostasis but also local synaptic plasticity and function in distinct brain circuits. PMID:26489685

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

    SciTech Connect

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

    2009-06-15

    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.

  8. ABA signaling in guard cells entails a dynamic protein-protein interaction relay from the PYL-RCAR family receptors to ion channels.

    PubMed

    Lee, Sung Chul; Lim, Chae Woo; Lan, Wenzhi; He, Kai; Luan, Sheng

    2013-03-01

    Plant hormone abscisic acid (ABA) serves as an integrator of environmental stresses such as drought to trigger stomatal closure by regulating specific ion channels in guard cells. We previously reported that SLAC1, an outward anion channel required for stomatal closure, was regulated via reversible protein phosphorylation events involving ABA signaling components, including protein phosphatase 2C members and a SnRK2-type kinase (OST1). In this study, we reconstituted the ABA signaling pathway as a protein-protein interaction relay from the PYL/RCAR-type receptors, to the PP2C-SnRK2 phosphatase-kinase pairs, to the ion channel SLAC1. The ABA receptors interacted with and inhibited PP2C phosphatase activity against the SnRK2-type kinase, releasing active SnRK2 kinase to phosphorylate, and activate the SLAC1 channel, leading to reduced guard cell turgor and stomatal closure. Both yeast two-hybrid and bimolecular fluorescence complementation assays were used to verify the interactions among the components in the pathway. These biochemical assays demonstrated activity modifications of phosphatases and kinases by their interaction partners. The SLAC1 channel activity was used as an endpoint readout for the strength of the signaling pathway, depending on the presence of different combinations of signaling components. Further study using transgenic plants overexpressing one of the ABA receptors demonstrated that changing the relative level of interacting partners would change ABA sensitivity. PMID:22935148

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

    USGS Publications Warehouse

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

    2006-01-01

    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.

  10. Engineering the gramicidin channel.

    PubMed

    Koeppe, R E; Anderson, O S

    1996-01-01

    The chemical design or redesign of proteins with significant biological activity presents formidable challenges. Ion channels offer advantages for such design studies because one can examine the function of single molecular entities in real time. Gramicidin channels are attractive for study because of their known structure and exceptionally well-defined function. This article focuses on amino acid sequence changes that redesign the structure or function of gramicidin channels. New, and functional, folded states have been achieved. In some cases, a single amino acid sequence can give rise to several (up to three) functional conformations. Single amino acid substitutions confer voltage-dependent channel gating. The findings provide insight into the folding of integral membrane proteins, the importance of tryptophan residues at the membrane/water interface, and the mechanism of channel gating. PMID:8800470

  11. Discrete cage form of water hexamer in the hydrophilic channels assembled by heterocyclic azopyrrole

    NASA Astrophysics Data System (ADS)

    Zhang, Hongwei; Yin, Zhenming

    2015-07-01

    A heterocyclic azopyrrole compound, meso-diethyl-5,5?-bis(thiazolyldiazo)-dipyrromethane (1), has been synthesized and its two crystals have been characterized by X-ray crystallography. The molecules of compound 1 self-assembled into channel structure in the crystal of 1·3H2O, whereas interlocked type dimer in the crystal of 1·CHCl3. In the 1-D hydrophilic channels of 1·3H2O, six water molecules were held together by eight O-H…O hydrogen bonds and formed discrete cage hexameric clusters. The dehydration/rehydration processes of the compound 1 are also studied.

  12. The Protein-Water Energy Seascape Protein molecules and liquid water are very different systems both

    E-print Network

    Doster, Wolfgang

    -range ordered, but long range diffusion allows it to flow, the essence of the liquid state. The energy landscape the properties of both systems. The protein landscape is modulated in time by density fluctuations in the liquid can be super- cooled until a glass transition interferes at 170 K. In such hydrated protein powders

  13. Soy protein polymers: Enhancing the water stability property

    NASA Astrophysics Data System (ADS)

    Srinivasan, Gowrishankar

    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.

  14. Convergent regulation of skeletal muscle Ca2+ channels by dystrophin, the actin cytoskeleton, and cAMP-dependent protein kinase

    NASA Astrophysics Data System (ADS)

    Johnson, Barry D.; Scheuer, Todd; Catterall, William A.

    2005-03-01

    The skeletal muscle L-type Ca2+ channel (CaV1.1), which is responsible for initiating muscle contraction, is regulated by phosphorylation by cAMP-dependent protein kinase (PKA) in a voltage-dependent manner that requires direct physical association between the channel and the kinase mediated through A-kinase anchoring proteins (AKAPs). The role of the actin cytoskeleton in channel regulation was investigated in skeletal myocytes cultured from wild-type mice, mdx mice that lack the cytoskeletal linkage protein dystrophin, and a skeletal muscle cell line, 129 CB3. Voltage dependence of channel activation was shifted positively, and potentiation was greatly diminished in mdx myocytes and in 129 CB3 cells treated with the microfilament stabilizer phalloidin. Voltage-dependent potentiation by strong depolarizing prepulses was reduced in mdx myocytes but could be restored by positively shifting the stimulus potentials to compensate for the positive shift in the voltage dependence of gating. Inclusion of PKA in the pipette caused a negative shift in the voltage dependence of activation and restored voltage-dependent potentiation in mdx myocytes. These results show that skeletal muscle Ca2+ channel activity and voltage-dependent potentiation are controlled by PKA and microfilaments in a convergent manner. Regulation of Ca2+ channel activity by hormones and neurotransmitters that use the PKA signal transduction pathway may interact in a critical way with the cytoskeleton and may be impaired by deletion of dystrophin, contributing to abnormal regulation of intracellular calcium concentrations in dystrophic muscle.

  15. Effect of channelization of Rio Puerto Nuevo on ground-water levels in the San Juan metropolitan area, Puerto Rico

    USGS Publications Warehouse

    Padilla, Ingrid

    1991-01-01

    Channelization and concrete lining of the Rio Puerto Nuevo and its tributaries in the San Juan Metropolitan area has been proposed to control flooding in low lying areas adjacent to the stream. Concern about the effect of these channel modifications on the ground-water system prompted the U.S. Geological Survey in cooperation with the U.S. Army Corps of Engineers to conduct an investigation of surface-water and ground-water interactions in the Rio Puerto Nuevo basin in 1988. A principal objective of this investigation was to determine the potential effect of channelization of the Rio Puerto Nuevo on ground-water levels.

  16. Patients with autosomal nephrogenic diabetes insipidus homozygous for mutations in the aquaporin 2 water-channel gene

    SciTech Connect

    Lieburg, A.F. van; Verdijk, M.A.J.; Knoers, V.V.A.M.; Monnens, L.A.H.; Oost, B.A. van; Os, C.H. van; Deen, P.M.T.; Essen, A.J. van; Proesmans, W.; Mallmann, R.

    1994-10-01

    Mutations in the X-chromosomal V2 receptor gene are known to cause nephrogenic diabetes insipidus (NDI). Besides the X-linked form, an autosomal mode of inheritance has been described. Recently, mutations in the autosomal gene coding for water-channel aquaporin 2 (AQP2) of the renal collecting duct were reported in an NDI patient. In the present study, missense mutations and a single nucleotide deletion in the aquaporin 2 gene of three NDI patients from consanquineous matings are described. Expression studies in Xenopus oocytes showed that the missense AQP2 proteins are nonfunctional. These results prove that mutations in the AQP2 gene cause autosomal recessive NDI. 32 refs., 4 figs.

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

    SciTech Connect

    M Whorton; R MacKinnon

    2011-12-31

    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.

  18. Cytocompatible and water stable ultrafine protein fibers for tissue engineering

    NASA Astrophysics Data System (ADS)

    Jiang, Qiuran

    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.

  19. Experimental Measurements of Skin Friction in Air and Water Micro-Channels

    NASA Astrophysics Data System (ADS)

    Crafton, Jim; Fonov, Sergey; Jones, Grant; Forlines, Alan

    2008-11-01

    Surface Stress Sensitive Film (S3F), is a relatively new experimental sensor that provides continuous measurements of skin friction and pressure on aerodynamic and hydrodynamic surfaces. This sensor is based on the distortions of an elastic polymer film which deforms under the action of the applied normal and tangential loads. Skin friction and pressure gradients are determined by monitoring these distortions and applying a finite element model to the elastic film. This technique has been demonstrated by performing quantitative measurements of pressure and skin friction in several wind tunnels, water tunnel, and channel flows. This paper will focus on experimental measurements in fully developed micro-channels that have been used to validate the S3F measurements. Comparisons between S3F, theoretical relations based on Reynolds number and Poiseuille Flow, and experimental measurements of skin friction based on monitoring the pressure gradient in the channel indicate agreement of better than 5%.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    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.

  1. Hydrocolloid interaction with water, protein, and starch in wheat dough.

    PubMed

    Linlaud, Natalia; Ferrer, Evelina; Puppo, María Cecilia; Ferrero, Cristina

    2011-01-26

    Interaction of hydrocolloids (xanthan gum, locust bean gum, guar gum, and high-methoxyl pectin) with macrocomponents of dough (water, starch, and protein) was evaluated by different techniques. (1)H spin-spin NMR relaxation assays were applied to study the mobility of the gluten-hydrocolloid-water matrix, and the amount of freezable water was determined by differential scanning calorimetry (DSC). Starch gelatinization parameters (T, enthalpy) were also analyzed by DSC. The influence of additives on the protein matrix was studied by Fourier transform (FT) Raman assays; analysis of the extracted gliadins and glutenins was performed by electrophoresis (SDS-PAGE). A significantly higher molecular mobility was found in matrices containing xanthan gum, whereas pectin led to the lowest molecular mobility. Freezable water showed a trend of increasing in the presence of hydrocolloids, particularly under conditions of water restriction. Starch gelatinization final temperature was decreased when hydrocolloids were added in the presence of enough water. In general, FT-Raman and SDS-PAGE indicated that hydrocolloid addition promoted a more disordered and labile network, particularly in the case of pectin addition. On the other hand, results obtained for dough with guar gum would indicate a good compatibility between this hydrocolloid and the gluten network. PMID:21175189

  2. Subunit composition of G(o) proteins functionally coupling galanin receptors to voltage-gated calcium channels.

    PubMed Central

    Kalkbrenner, F; Degtiar, V E; Schenker, M; Brendel, S; Zobel, A; Heschler, J; Wittig, B; Schultz, G

    1995-01-01

    The neuropeptide galanin is widely expressed in the central nervous system and other tissues and induces different cellular reactions, e.g. hormone release from pituitary and inhibition of insulin release from pancreatic B cells. By microinjection of antisense oligonucleotides we studied the question as to which G proteins mediate the galanin-induced inhibition of voltage-gated Ca2+ channels in the rat pancreatic B-cell line RINm5F and in the rat pituitary cell line GH3. Injection of antisense oligonucleotides directed against alpha 01, beta 2, beta 3, gamma 2 and gamma 4 G protein subunits reduced the inhibition of Ca2+ channel current which was induced by galanin, whereas no change was seen after injection of cells with antisense oligonucleotides directed against alpha i, alpha q, alpha 11, alpha 14, alpha 15, beta 1, beta 4, gamma 1, gamma 3, gamma 5, or gamma 7 G protein subunits or with sense control oligonucleotides. In view of these data and of previous results, we conclude that the galanin receptors in GH3 and in RINm5F cells couple mainly to the G(0) protein consisting of alpha 01 beta 2 gamma 2 to inhibit Ca2+ channels and use alpha 01beta 3 gamma 4 less efficiently. The latter G protein composition was previously shown to be used by muscarinic M4 receptors to inhibit Ca2+ channels. Images PMID:7588602

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

    PubMed Central

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

    1986-01-01

    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

  4. Regulation of cardiac CFTR Cl(-) channel activity by a Mg(2+)-dependent protein phosphatase.

    PubMed

    Zhou, S -S; Takai, A; Okada, Y

    2002-06-01

    Dephosphorylation of the CFTR Cl(-) channel is known to be induced by both okadaic-acid- (OA-) sensitive and -insensitive protein phosphatases (PPs). In the present study, the effects of cytosolic free Mg(2+) on the cardiac CFTR Cl(-) current were examined in relation to the latter PP activity in guinea pig ventricular myocytes. Even when maintaining intracellular Mg-ATP at millimolar concentrations under whole-cell patch-clamp mode, cAMP-activated Cl(-) conductance was reversibly suppressed by cytosolic free Mg(2+), with an IC(50) of around 2.5 mmol/l. In contrast, changes in the cytosolic concentration of free Mg(2+) ([Mg(2+)](i)) had no effect on genistein-activated CFTR Cl(-) currents. The Mg(2+) effect on cAMP-activated CFTR Cl(-) conductance was completely reversed by application of anthracene-9-carboxylic acid (9-AC), which was previously shown to inhibit an OA-insensitive PP in cardiac myocytes. A 9-AC-sensitive fraction of endogenous PP activity in the extract of guinea pig ventricle was found to be activated by free Mg(2+) at millimolar concentrations but to be inactive at micromolar concentrations. The intracellular application of OA failed to activate basal Cl(-) conductance at millimolar [Mg(2+)](i). In the presence of OA, however, basal Cl(-) conductance became activated either by reducing [Mg(2+)](i) to micromolar concentrations or by applying 9-AC. Thus, we conclude that a Mg(2+)-dependent PP sensitive to 9-AC plays a key role in the cAMP-mediated regulation of cardiac CFTR Cl(-) channel at physiological [Mg(2+)](i)under both basal and cAMP-activated conditions. Also, it appears that the genistein-activated conformation of the cardiac CFTR channel is not sensitive to the Mg(2+)-dependent PP. PMID:12111240

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

    PubMed Central

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

    2011-01-01

    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

  6. SWELL1, a plasma membrane protein, is an essential component of volume-regulated anion channel

    PubMed Central

    Qiu, Zhaozhu; Dubin, Adrienne E.; Mathur, Jayanti; Tu, Buu; Reddy, Kritika; Miraglia, Loren J.; Reinhardt, Jürgen; Orth, Anthony P.; Patapoutian, Ardem

    2014-01-01

    Summary Maintenance of a constant cell volume in response to extracellular or intracellular osmotic changes is critical for cellular homeostasis. Activation of a ubiquitous volume-regulated anion channel (VRAC) plays a key role in this process; however, its molecular identity in vertebrates remains unknown. Here, we used a cell-based fluorescence assay and performed a genome-wide RNAi screen to find components of VRAC. We identified SWELL1 (LRRC8A), a member of a four-transmembrane protein family with unknown function, as essential for hypotonicity-induced iodide influx. SWELL1 is localized to the plasma membrane, and its knockdown dramatically reduces endogenous VRAC currents and regulatory cell volume decrease in various cell types. Furthermore, point mutations in SWELL1 cause a significant change in VRAC anion selectivity, demonstrating that SWELL1 is an essential VRAC component. These findings enable further molecular characterization of the VRAC channel complex and genetic studies for understanding the function of VRAC in normal physiology and disease. PMID:24725410

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

    PubMed

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

    2014-01-01

    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

  8. AG Channel Measurement and Modeling Results for Over-Water and Hilly Terrain Conditions

    NASA Technical Reports Server (NTRS)

    Matolak, David W.; Sun, Ruoyu

    2015-01-01

    This report describes work completed over the past year on our project, entitled "Unmanned Aircraft Systems (UAS) Research: The AG Channel, Robust Waveforms, and Aeronautical Network Simulations." This project is funded under the NASA project "Unmanned Aircraft Systems (UAS) in the National Airspace System (NAS)." In this report we provide the following: an update on project progress; a description of the over-freshwater and hilly terrain initial results on path loss, delay spread, small-scale fading, and correlations; complete path loss models for the over-water AG channels; analysis for obtaining parameter statistics required for development of accurate wideband AG channel models; and analysis of an atypical AG channel in which the aircraft flies out of the ground site antenna main beam. We have modeled the small-scale fading of these channels with Ricean statistics, and have quantified the behavior of the Ricean K-factor. We also provide some results for correlations of signal components, both intra-band and inter-band. An updated literature review, and a summary that also describes future work, are also included.

  9. Relief of G-protein inhibition of calcium channels and short-term synaptic facilitation in cultured hippocampal neurons.

    PubMed

    Brody, D L; Yue, D T

    2000-02-01

    G-protein inhibition of voltage-gated calcium channels can be transiently relieved by repetitive physiological stimuli. Here, we provide evidence that such relief of inhibition contributes to short-term synaptic plasticity in microisland-cultured hippocampal neurons. With G-protein inhibition induced by the GABA(B) receptor agonist baclofen or the adenosine A1 receptor agonist 2-chloroadenosine, short-term synaptic facilitation emerged during action potential trains. The facilitation decayed with a time constant of approximately 100 msec. However, addition of the calcium channel inhibitor Cd(2+) at 2-3 microM had no such effect and did not alter baseline synaptic depression. As expected of facilitation from relief of channel inhibition, analysis of miniature EPSCs implicated presynaptic modulation, and elevating presynaptic Ca(2+) entry blunted the facilitation. Most telling was the near occlusion of synaptic facilitation after selective blockade of P/Q- but not N-type calcium channels. This was as predicted from experiments using recombinant calcium channels expressed in human embryonic kidney (HEK) 293 cells; we found significantly stronger relief of G-protein inhibition in recombinant P/Q- versus N-type channels during action potential trains. G-protein inhibition in HEK 293 cells was induced via recombinant M2 muscarinic acetylcholine receptors activated by carbachol, an acetylcholine analog. Thus, relief of G-protein inhibition appears to produce a novel form of short-term synaptic facilitation in cultured neurons. Similar short-term synaptic plasticity may be present at a wide variety of synapses, as it could occur during autoreceptor inhibition by glutamate or GABA, heterosynaptic inhibition by GABA, tonic adenosine inhibition, and in many other instances. PMID:10648693

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

    PubMed Central

    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

    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

  11. Vpr Protein of Human Immunodeficiency Virus Type 1 Forms Cation-Selective Channels in Planar Lipid Bilayers

    NASA Astrophysics Data System (ADS)

    Piller, S. C.; Ewart, G. D.; Premkumar, A.; Cox, G. B.; Gage, P. W.

    1996-01-01

    A small (96-aa) protein, virus protein R (Vpr), of human immunodeficiency virus type 1 contains one hydrophobic segment that could form a membrane-spanning helix. Recombinant Vpr, expressed in Escherichia coli and purified by affinity chromatography, formed ion channels in planar lipid bilayers when it was added to the cis chamber and when the trans chamber was held at a negative potential. The channels were more permeable to Na+ than to Cl- ions and were inhibited when the trans potential was made positive. Similar channel activity was caused by Vpr that had a truncated C terminus, but the potential dependence of channel activity was no longer seen. Antibody raised to a peptide mimicking part of the C terminus of Vpr (AbC) inhibited channel activity when added to the trans chamber but had no effect when added to the cis chamber. Antibody to the N terminus of Vpr (AbN) increased channel activity when added to the cis chamber but had no effect when added to the trans chamber. The effects of potential and antibodies on channel activity are consistent with a model in which the positive C-terminal end of dipolar Vpr is induced to traverse the bilayer membrane when the opposite (trans) side of the membrane is at a negative potential. The C terminus of Vpr would then be available for interaction with AbC in the trans chamber, and the N terminus would be available for interaction with AbN in the cis chamber. The ability of Vpr to form ion channels in vitro suggests that channel formation by Vpr in vivo is possible and may be important in the life cycle of human immunodeficiency virus type 1 and/or may cause changes in cells that contribute to AIDS-related pathologies.

  12. Ship interaction in narrow water channels: A two-lane cellular automata approach

    NASA Astrophysics Data System (ADS)

    Sun, Zhuo; Chen, Zhonglong; Hu, Hongtao; Zheng, Jianfeng

    2015-08-01

    In narrow waterways, closed ships might interact due to hydrodynamic forces. To avoid clashes, different lane-changing rules are required. In this paper, a two-lane cellular automata model is proposed to investigate the traffic flow patterns in narrow water channels. Numerical experiments show that ship interaction can form "lumps" in traffic flow which will significantly depress the flux. We suggest that the lane-changing frequency of fast ships should be limited.

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

    NASA Astrophysics Data System (ADS)

    Dufresne, Christiane; Duffa, Céline; Rey, Vincent

    2014-01-01

    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.

  14. Quantifying the Entropy of Binding for Water Molecules in Protein Cavities by Computing Correlations

    E-print Network

    Huggins, David J.

    2014-12-17

    Protein structural analysis demonstrates that water molecules are commonly found in the internal cavities of proteins. Analysis of experimental data on the entropies of inorganic crystals suggests that the entropic cost of transferring such a water...

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

    SciTech Connect

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

    2009-10-02

    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.

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

    PubMed Central

    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.; Pla, Alessandra Fiorio; Prevarskaya, Natalia

    2015-01-01

    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

  17. 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)

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

    2014-12-01

    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.

  18. Water surface and channel bed morphology change before and after a laboratory meander neck cutoff

    NASA Astrophysics Data System (ADS)

    Han, B.; Endreny, T. A.

    2012-12-01

    Meander evolution of narrowing point bars ultimately forms a straight reach and an associated oxbow lake after meand bend cutoff. Observing the water surface and bed topography change during the meander cutoff process allows scientists and engineers to better understand flow mechanisms in meandering rivers, predict river behavior following cutoff, and minimize damage to life and property. Theoretical river evolution model indicates that head loss between the upstream and downstream meander neck increases during meander evolution, and this leads to an increasing hydraulic gradient and intensification of the cutoff. Yet no detailed observations are available to support the theory. In this research, we establish a physical model of a meander cutoff in a 1.8 m * 3.7 m laboratory river table using 0.18 mm median diameter sand and river discharge of 100 mL/s. The initial meander is a highly curved meander with a sinuosity of 5.6. Erosion is initiated by stream flow and the meander goes through the cutoff process. Water surface elevation along the river, river bed topography, and groundwater head in the intra-meander zone are precisely measured with an accuracy of up to 0.4 mm using a close range photogrammetry technique and ultrasonic sensors. The measurements are taken every 5 hours before the cutoff, immediately after the cutoff, and 1 hour, 5 hours after the cutoff respectively. Our results show that hydraulic gradient gradually steepens crossing the meander neck before the cutoff. River bed elevation gradients crossing the meander neck are enlarged due to the continuous deposition at the upstream neck and erosion at the downstream neck. However, the river bed elevation differences is counter balanced by the water depth which is smaller at the upstream and larger at the downstream, and the head loss across the neck remains nearly the same during cutoff. Immediately after the meander cutoff, a cascade emerges, and then rapidly dissipates into the new channel during rapid headwater erosion. After 1 hour of the cutoff the oxbow lake has separated from the main river channel, and the water surface in the oxbow lake is flat but higher than that in the main river channel. After 5 hours of the cutoff, water surface at the oxbow lake is regulated to that in the main river channel. Some of the abandoned channel morphology in the oxbow lake forms islands due to the decreased water depth.

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

    NASA Technical Reports Server (NTRS)

    Komar, P. D.

    1979-01-01

    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.

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

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

    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.

  1. Early Fluid and Protein Shifts in Men During Water Immersion

    NASA Technical Reports Server (NTRS)

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

    1987-01-01

    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.

  2. Influence of antifreeze proteins on the ice/water interface.

    PubMed

    Todde, Guido; Hovmöller, Sven; Laaksonen, Aatto

    2015-02-26

    Antifreeze proteins (AFP) are responsible for the survival of several species, ranging from bacteria to fish, that encounter subzero temperatures in their living environment. AFPs have been divided into two main families, moderately and hyperactive, depending on their thermal hysteresis activity. We have studied one protein from both families, the AFP from the snow flea (sfAFP) and from the winter flounder (wfAFP), which belong to the hyperactive and moderately active family, respectively. On the basis of molecular dynamics simulations, we have estimated the thickness of the water/ice interface for systems both with and without the AFPs attached onto the ice surface. The calculation of the diffusion profiles along the simulation box allowed us to measure the interface width for different ice planes. The obtained widths clearly show a different influence of the two AFPs on the ice/water interface. The different impact of the AFPs here studied on the interface thickness can be related to two AFPs properties: the protein hydrophobic surface and the number of hydrogen bonds that the two AFPs faces form with water molecules. PMID:25611783

  3. A structural model for facultative anion channels in an oligomeric membrane protein: the yeast TRK (K(+)) system.

    PubMed

    Pardo, Juan Pablo; González-Andrade, Martin; Allen, Kenneth; Kuroda, Teruo; Slayman, Clifford L; Rivetta, Alberto

    2015-12-01

    TRK transporters, a class of proteins which generally carry out the bulk of K(+) accumulation in plants, fungi, and bacteria, mediate ion currents driven by the large membrane voltages (-150 to -250 mV) common to non-animal cells. Bacterial TRK proteins resemble K(+) channels in their primary sequence, crystallize as membrane dimers having intramolecular K(+)-channel-like folding, and complex with a cytoplasmic collar formed of four RCK domains (Nature 471:336, 2011; Ibid 496:324, 2013). Fungal TRK proteins appear simpler in form than the bacterial members, but do possess two special features: a large built-in regulatory domain, and a highly conserved pair of transmembrane helices (TM7 and TM8, ahead of the C-terminus), which were postulated to facilitate intramembranal oligomerization (Biophys. J. 77:789, 1999; FEMS Yeast Res. 9:278, 2009). A surprising associated functional process in the fungal proteins which have been explored (Saccharomyces, Candida, and Neurospora) is facilitation of channel-like chloride efflux. That process is suppressed by osmoprotective agents, appears to involve hydrophobic gating, and strongly resembles conduction by Cys-loop ligand-gated anion channels. And it leads to a rather general hypothesis: that the thermodynamic tendency for hydrophobic or amphipathic transmembrane helices to self-organize into oligomers can create novel ionic pathways through biological membranes: fundamental hydrophobic nanopores, pathways of low selectivity governed by the chaotropic behavior of individual ionic species and under the strong influence of membrane voltage. PMID:26100673

  4. Students' Understanding of External Representations of the Potassium Ion Channel Protein Part II: Structure-Function Relationships and Fragmented Knowledge

    ERIC Educational Resources Information Center

    Harle, Marissa; Towns, Marcy H.

    2012-01-01

    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…

  5. Cloud area determination from AVIRIS data using water vapor channels near 1. mu. m

    SciTech Connect

    Gao, B.C.; Goetz, A.F.H. )

    1991-02-20

    Fractional cloud area is derived from spectral images collected by the airborne visible-infrared imaging spectrometer (AVIRIS). AVIRIS covers the spectral region from 0.4 to 2.5 {mu}m with 224 channels and has a ground instantaneous field of view of 20 {times} 20 m from an altitude of 20 km. The derivation is made by ratioing radiances near the 0.94- and the 1.14-{mu}m water vapor band centers against those in the intermediate atmospheric window regions. The derivation makes use of the facts that (1) the reflectances of most ground targets vary approximately linearly with wavelength in the 0.94- and the 1.14-{mu}m water vapor band absorption regions, and (2) the peak absorptions of the water vapor band over cloudy areas are smaller than those over nearby clear surface areas because of the rapidly decreasing atmospheric water vapor concentration with height. The band ratioing technique effectively discriminates among clouds and surface areas having similar reflectance values. Such discrimination is not possible using standard radiance thresholding techniques. It is expected that the use of water vapor channels in the near-infrared region in future satellites will improve the ability to determine cloud cover over the land.

  6. Dynamical coupling of intrinsically disordered proteins and their hydration water: comparison with folded soluble and membrane proteins.

    PubMed

    Gallat, F-X; Laganowsky, A; Wood, K; Gabel, F; van Eijck, L; Wuttke, J; Moulin, M; Härtlein, M; Eisenberg, D; Colletier, J-P; Zaccai, G; Weik, M

    2012-07-01

    Hydration water is vital for various macromolecular biological activities, such as specific ligand recognition, enzyme activity, response to receptor binding, and energy transduction. Without hydration water, proteins would not fold correctly and would lack the conformational flexibility that animates their three-dimensional structures. Motions in globular, soluble proteins are thought to be governed to a certain extent by hydration-water dynamics, yet it is not known whether this relationship holds true for other protein classes in general and whether, in turn, the structural nature of a protein also influences water motions. Here, we provide insight into the coupling between hydration-water dynamics and atomic motions in intrinsically disordered proteins (IDP), a largely unexplored class of proteins that, in contrast to folded proteins, lack a well-defined three-dimensional structure. We investigated the human IDP tau, which is involved in the pathogenic processes accompanying Alzheimer disease. Combining neutron scattering and protein perdeuteration, we found similar atomic mean-square displacements over a large temperature range for the tau protein and its hydration water, indicating intimate coupling between them. This is in contrast to the behavior of folded proteins of similar molecular weight, such as the globular, soluble maltose-binding protein and the membrane protein bacteriorhodopsin, which display moderate to weak coupling, respectively. The extracted mean square displacements also reveal a greater motional flexibility of IDP compared with globular, folded proteins and more restricted water motions on the IDP surface. The results provide evidence that protein and hydration-water motions mutually affect and shape each other, and that there is a gradient of coupling across different protein classes that may play a functional role in macromolecular activity in a cellular context. PMID:22828339

  7. Do Water Molecules Mediate Protein-DNA Recognition? Ch. Koti Reddy, Achintya Das and B. Jayaram*

    E-print Network

    Jayaram, Bhyravabotla

    Do Water Molecules Mediate Protein-DNA Recognition? Ch. Koti Reddy, Achintya Das and B. Jayaram analysis of interfacial water molecules in the structures of 109 unique protein-DNA complexes is presented together with a new view on their role in protein-DNA recognition. Location of interfacial water molecules

  8. Activation of Mitochondrial Uncoupling Protein 4 and ATP-Sensitive Potassium Channel Cumulatively Decreases Superoxide Production in Insect Mitochondria.

    PubMed

    Sloci?ska, Malgorzata; Rosinski, Grzegorz; Jarmuszkiewicz, Wieslawa

    2016-01-01

    It has been evidenced that mitochondrial uncoupling protein 4 (UCP4) and ATP-regulated potassium channel (mKATP channel) of insect Gromphadorhina coqereliana mitochondria decrease superoxide anion production. We elucidated whether the two energy-dissipating systems work together on a modulation of superoxide level in cockroach mitochondria. Our data show that the simultaneous activation of UCP4 by palmitic acid and mKATP channel by pinacidil revealed a cumulative effect on weakening mitochondrial superoxide formation. The inhibition of UCP4 by GTP (and/or ATP) and mKATP channel by ATP elevated superoxide production. These results suggest a functional cooperation of both energy-dissipating systems in protection against oxidative stress in insects. PMID:26548865

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

    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.

  10. Activation of the epithelial Na+ channel in the collecting duct by vasopressin contributes to water reabsorption.

    PubMed

    Bugaj, Vladislav; Pochynyuk, Oleh; Stockand, James D

    2009-11-01

    We used patch-clamp electrophysiology on isolated, split-open murine collecting ducts (CD) to test the hypothesis that regulation of epithelial sodium channel (ENaC) activity is a physiologically important effect of vasopressin. Surprisingly, this has not been tested directly before. We ask whether vasopressin affects ENaC activity distinguishing between acute and chronic effects, as well as, parsing the cellular signaling pathway and molecular mechanism of regulation. In addition, we quantified possible synergistic regulation of ENaC by vasopressin and aldosterone associating this with a requirement for distal nephron Na+ reabsorption during water conservation vs. maintenance of Na+ balance. We find that vasopressin significantly increases ENaC activity within 2-3 min by increasing open probability (P(o)). This activation was dependent on adenylyl cyclase (AC) and PKA. Water restriction (18-24 h) and pretreatment of isolated CD with vasopressin (approximately 30 min) resulted in a similar increase in P(o). In addition, this also increased the number (N) of active ENaC in the apical membrane. Similar to P(o), increases in N were sensitive to inhibitors of AC. Stressing animals with water and salt restriction separately and jointly revealed an important effect of vasopressin: conservation of water and Na+ each independently increased ENaC activity and jointly had a synergistic effect on channel activity. These results demonstrate a quantitatively important action of vasopressin on ENaC suggesting that distal nephron Na+ reabsorption mediated by this channel contributes to maintenance of water reabsorption. In addition, our results support that the combined actions of vasopressin and aldosterone are required to achieve maximally activated ENaC. PMID:19692483

  11. The DEG/ENaC protein MEC-10 regulates the transduction channel complex in Caenorhabditis elegans touch receptor neurons.

    PubMed

    Arnadóttir, Jóhanna; O'Hagan, Robert; Chen, Yushu; Goodman, Miriam B; Chalfie, Martin

    2011-08-31

    Gentle touch sensation in Caenorhabditis elegans is mediated by the MEC-4/MEC-10 channel complex, which is expressed exclusively in six touch receptor neurons (TRNs). The complex contains two pore-forming subunits, MEC-4 and MEC-10, as well as the accessory subunits MEC-2, MEC-6, and UNC-24. MEC-4 is essential for channel function, but beyond its role as a pore-forming subunit, the functional contribution of MEC-10 to the channel complex and to touch sensation is unclear. We addressed this question using behavioral assays, in vivo electrophysiological recordings from TRNs, and heterologous expression of mutant MEC-10 isoforms. Animals with a deletion in mec-10 showed only a partial loss of touch sensitivity and a modest decrease in the size of the mechanoreceptor current (MRC). In contrast, five previously identified mec-10 alleles acted as recessive gain-of-function alleles that resulted in complete touch insensitivity. Each of these alleles produced a substantial decrease in MRC size and a shift in the reversal potential in vivo. The latter finding indicates that these mec-10 mutations alter the ionic selectivity of the transduction channel in vivo. All mec-10 mutant animals had properly localized channel complexes, indicating that the loss of MRCs was not attributable to a dramatic mislocalization of transduction channels. Finally, electrophysiological examination of heterologously expressed complexes suggests that mutant MEC-10 proteins may affect channel current via MEC-2. PMID:21880930

  12. Effects of fluoxetine on protein expression of potassium ion channels in the brain of chronic mild stress rats

    PubMed Central

    Chen, Chunlin; Wang, Ling; Rong, Xianfang; Wang, Weiping; Wang, Xiaoliang

    2014-01-01

    The purpose of this study is to investigate the expression of major potassium channel subtypes in the brain of chronical mild stress (CMS) rats and reveal the effects of fluoxetine on the expression of these channels. Rats were exposed to a variety of unpredictable stress for three weeks and induced anhedonia, lower sucrose preference, locomotor activity and lower body weight. The protein expressions were determined by Western blot. CMS significantly increased the expression of Kv2.1 channel in frontal cortex but not in hippocampus, and the expression level was normalized after fluoxetine treatment. The expression of TREK-1 channel was also obviously increased in frontal cortex in CMS rats. Fluoxetine treatment might prevent this increase. However, the expression of Kv3.1 and Kv4.2 channels was considerably decreased in hippocampus after CMS, and was not affected by fluoxetine. These results suggest that different subtypes of potassium channels are associated with the pathophysiology of depression and that the therapeutical effects of fluoxetine may relate to Kv2.1 and TREK-1 potassium channels. PMID:26579425

  13. Chryse Planitia region, Mars: Channeling history, flood-volume estimates, and scenarios for bodies of water in the northern plains

    NASA Technical Reports Server (NTRS)

    Rotto, Susan L.; Tanaka, Kenneth L.

    1992-01-01

    The Chryse Planitia region of Mars includes several outflow channels that debouched into a single basin. Here we evaluate possible volumes and areal extents of standing bodies of water that collected in the northern lowland plains, based on evidence provided by topography, fluvial relations, and channel chronology and geomorphology.

  14. Cytoplasmic Domain of MscS Interacts with Cell Division Protein FtsZ: A Possible Non-Channel Function of the Mechanosensitive Channel in Escherichia Coli

    PubMed Central

    Koprowski, Piotr; Grajkowski, Wojciech; Balcerzak, Marcin; Filipiuk, Iwona; Fabczak, Hanna; Kubalski, Andrzej

    2015-01-01

    Bacterial mechano-sensitive (MS) channels reside in the inner membrane and are considered to act as emergency valves whose role is to lower cell turgor when bacteria enter hypo-osmotic environments. However, there is emerging evidence that members of the Mechano-sensitive channel Small (MscS) family play additional roles in bacterial and plant cell physiology. MscS has a large cytoplasmic C-terminal region that changes its shape upon activation and inactivation of the channel. Our pull-down and co-sedimentation assays show that this domain interacts with FtsZ, a bacterial tubulin-like protein. We identify point mutations in the MscS C-terminal domain that reduce binding to FtsZ and show that bacteria expressing these mutants are compromised in growth on sublethal concentrations of ?-lactam antibiotics. Our results suggest that interaction between MscS and FtsZ could occur upon inactivation and/or opening of the channel and could be important for the bacterial cell response against sustained stress upon stationary phase and in the presence of ?-lactam antibiotics. PMID:25996836

  15. Proton transfer and water exchange in the green fluorescent protein

    NASA Astrophysics Data System (ADS)

    Agmon, Noam

    2014-03-01

    The green fluorescent protein (GFP) is the only naturally occurring protein in which excited-state proton-transfer has been identified. Upon excitation, a proton is ejected from its chromophore, travelling through the ``privileged water molecule'' (PWM) and Ser205 to Glu222, on a 10 ps timescale or faster. However, time-resolved fluorescence from the chromophore exhibits a t-? power-law decay extending into the ns regime. With increasing temperature, ? switches from 1/2 (below 230 K) to 3/2 (above it). This has been interpreted as pseudo one-dimensional proton hopping along an internal ``proton wire,'' with an activated process that opens a ``doorway'' for proton escape to solution at the higher temperatures. To identify such putative pathways, we have developed a computer code mapping all ``proton wires'' within a protein structure. Applying it to a X-ray GFP structure of 0.9 Angstrom resolution, a proton wire indeed continues from Glu222 along the axis of the GFP ``barrel,'' connecting to a negatively charged surface patch (a ``proton collecting antenna''?). This might explain the t- 1 / 2 behavior. However, a direct escape pathway opening from the chromophore to solution is not readily identified in the X-ray structure. Here we report molecular dynamics results showing that the PWM escapes to solution on the 100 ps timescale. This occurs by fluctuations of the beta-sheet, creating an opening through which water molecules can leave and enter the protein. The exact pathway of the PWM on its way in and out has been identified, as well as the water-exchange kinetics that follows a stretched-exponential time behavior. This research was supported by the ISRAEL SCIENCE FOUNDATION grant No. 766/12.

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

    PubMed

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

    2014-05-01

    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

  17. Water Channel of Horseradish Peroxidase Studied by the Charge-Transfer Absorption Band of Ferric Heme

    E-print Network

    Sharp, Kim

    , the protein was incorporated into trehalose/sucrose glasses and the hydration of the sugar glasses was varied. Absorption spectra of HRP in sugar glasses and in glycerol/water were taken in the range 10-300 K. The CT absorption band shows vibronic fine structure. The peak positions are the same in hydrated sugar and glycerol

  18. Estradiol activates epithelial sodium channels in rat alveolar cells through the G protein-coupled estrogen receptor

    PubMed Central

    Mitzelfelt, Jeremiah D.; Yu, Ling; Yue, Qiang; Duke, Billie Jeanne; Harrell, Constance S.; Neigh, Gretchen N.; Eaton, Douglas C.

    2013-01-01

    Female sex predisposes individuals to poorer outcomes during respiratory disorders like cystic fibrosis and influenza-associated pneumonia. A common link between these disorders is dysregulation of alveolar fluid clearance via disruption of epithelial sodium channel (ENaC) activity. Recent evidence suggests that female sex hormones directly regulate expression and activity of alveolar ENaC. In our study, we identified the mechanism by which estradiol (E2) or progesterone (P4) independently regulates alveolar ENaC. Using cell-attached patch clamp, we measured ENaC single-channel activity in a rat alveolar cell line (L2) in response to overnight exposure to either E2 or P4. In contrast to P4, E2 increased ENaC channel activity (NPo) through an increase in channel open probability (Po) and an increased number of patches with observable channel activity. Apical plasma membrane abundance of the ENaC ?-subunit (?ENaC) more than doubled in response to E2 as determined by cell surface biotinylation. ?ENaC membrane abundance was approximately threefold greater in lungs from female rats in proestrus, when serum E2 is greatest, compared with diestrus, when it is lowest. Our results also revealed a significant role for the G protein-coupled estrogen receptor (Gper) to mediate E2's effects on ENaC. Overall, our results demonstrate that E2 signaling through Gper selectively activates alveolar ENaC through an effect on channel gating and channel density, the latter via greater trafficking of channels to the plasma membrane. The results presented herein implicate E2-mediated regulation of alveolar sodium channels in the sex differences observed in the pathogenesis of several pulmonary diseases. PMID:24097558

  19. Estradiol activates epithelial sodium channels in rat alveolar cells through the G protein-coupled estrogen receptor.

    PubMed

    Greenlee, Megan M; Mitzelfelt, Jeremiah D; Yu, Ling; Yue, Qiang; Duke, Billie Jeanne; Harrell, Constance S; Neigh, Gretchen N; Eaton, Douglas C

    2013-12-01

    Female sex predisposes individuals to poorer outcomes during respiratory disorders like cystic fibrosis and influenza-associated pneumonia. A common link between these disorders is dysregulation of alveolar fluid clearance via disruption of epithelial sodium channel (ENaC) activity. Recent evidence suggests that female sex hormones directly regulate expression and activity of alveolar ENaC. In our study, we identified the mechanism by which estradiol (E2) or progesterone (P4) independently regulates alveolar ENaC. Using cell-attached patch clamp, we measured ENaC single-channel activity in a rat alveolar cell line (L2) in response to overnight exposure to either E2 or P4. In contrast to P4, E2 increased ENaC channel activity (NPo) through an increase in channel open probability (Po) and an increased number of patches with observable channel activity. Apical plasma membrane abundance of the ENaC ?-subunit (?ENaC) more than doubled in response to E2 as determined by cell surface biotinylation. ?ENaC membrane abundance was approximately threefold greater in lungs from female rats in proestrus, when serum E2 is greatest, compared with diestrus, when it is lowest. Our results also revealed a significant role for the G protein-coupled estrogen receptor (Gper) to mediate E2's effects on ENaC. Overall, our results demonstrate that E2 signaling through Gper selectively activates alveolar ENaC through an effect on channel gating and channel density, the latter via greater trafficking of channels to the plasma membrane. The results presented herein implicate E2-mediated regulation of alveolar sodium channels in the sex differences observed in the pathogenesis of several pulmonary diseases. PMID:24097558

  20. Phase separation predicted to induce water-rich channels in fuel cell membranes

    NASA Astrophysics Data System (ADS)

    Herbst, Daniel; Witten, Thomas; Tsai, Tsung-Han; Coughlin, Bryan; Maes, Ashley; Herring, Andrew

    2015-03-01

    Fuel cells are a promising alternative energy technology that convert chemical fuel directly into electric power. One important fundamental property is exactly how and where water is absorbed in the polyelectrolyte membrane. Previous theoretical studies have used idealized parameters. In this talk, I show how we made a rigorous connection to experiment to make parameter-free predictions of the water-swelling behavior, using self-consistent field theory. The model block co-polymers we studied form alternating hydrophilic/hydrophobic lamellar domains that absorb water in humid air. I will show how simple measurements of the hydrophilic portion in solution lead to predictions of non-uniform water distribution in the membrane, and compare the results to x-ray scattering. The results suggest locally near-uniform water distributions. In special cases, however, each hydrophilic lamella phase-separates, forming an additional water-rich lamella down the center, a beneficial arrangement for ion conductivity. A small amount of water enhances conductivity most when it is partitioned into such channels, improving fuel-cell performance. MURI #W911NF-10-1-0520.

  1. A Water-Explicit Lattice Model of Heat-, Cold-, and Pressure-Induced Protein Unfolding

    E-print Network

    A Water-Explicit Lattice Model of Heat-, Cold-, and Pressure-Induced Protein Unfolding Bryan A captures many aspects of water ther- modynamics, including the existence of density anomalies, and we exposure to water (6). Second, natural water-soluble proteins are unable to fold into their native states

  2. Protein phosphatases modulate the apparent agonist affinity of the light-regulated ion channel in retinal rods.

    PubMed

    Gordon, S E; Brautigan, D L; Zimmerman, A L

    1992-10-01

    Ion channels directly activated by cGMP mediate the light response in retinal rods. Several components of the enzyme cascade controlling cGMP concentration are regulated, but there are no accepted mechanisms for modulation of the response of the channel to cGMP. Here we report evidence that in excised patches an endogenous protein phosphatase converts the channel from a state with low cGMP sensitivity to a state with almost 3 orders of magnitude higher sensitivity in the predicted physiological range of cGMP concentration. The action of this endogenous phosphatase was blocked by specific serine/threonine phosphatase inhibitors (microcystin-LR, okadaic acid, and calyculin A). An increase in apparent agonist affinity also was produced by addition of purified protein phosphatase 1. In contrast, protein phosphatase 2A decreased apparent agonist affinity, suggesting that two phosphorylation sites may regulate the agonist sensitivity of the channel in a reciprocal manner. This regulation may be involved in fine-tuning the light response or in light or dark adaptation. PMID:1382474

  3. The English Channel: Contamination status of its transitional and coastal waters.

    PubMed

    Tappin, A D; Millward, G E

    2015-06-30

    The chemical contamination (organic compounds, metals, radionuclides, microplastics, nutrients) of English Channel waters has been reviewed, focussing on the sources, concentrations and impacts. River loads were only reliable for Pb, whereas atmospheric loads appeared robust for Cd, Pb, Hg, PCB-153 and ?-HCH. Temporal trends in atmospheric inputs were decreasing. Contaminant concentrations in biota were relatively constant or decreasing, but not for Cd, Hg and HBCDD, and deleterious impacts on fish and copepods were reported. However, data on ecotoxicological effects were generally sparse for legacy and emerging contaminants. Intercomparison of activity concentrations of artificial radionuclides in sediments and biota on both Channel coasts was hindered by differences in methodological approaches. Riverine phosphate loads decreased with time, while nitrate loads remained uniform. Increased biomass of algae, attributable to terrestrial inputs of nutrients, has affected benthic production and shellfisheries. A strategic approach to the identification of contaminant impacts on marine biota is recommended. PMID:25649837

  4. Schlieren visualization of water natural convection in a vertical ribbed channel

    NASA Astrophysics Data System (ADS)

    Fossa, M.; Misale, M.; Tanda, G.

    2015-11-01

    Schlieren techniques are valuable tools for the qualitative and quantitative visualizations of flows in a wide range of scientific and engineering disciplines. A large number of schlieren systems have been developed and documented in the literature; majority of applications involve flows of gases, typically air. In this work, a schlieren technique is applied to visualize the buoyancy-induced flow inside vertical ribbed channels using water as convective fluid. The test section consists of a vertical plate made of two thin sheets of chrome-plated copper with a foil heater sandwiched between them; the external sides of the plate are roughened with transverse, square-cross-sectioned ribs. Two parallel vertical walls, smooth and unheated, form with the heated ribbed plate two adjacent, identical and asymmetrically heated, vertical channels. Results include flow schlieren visualizations with colour-band filters, reconstructions of the local heat transfer coefficient distributions along the ribbed surfaces and comparisons with past experiments performed using air as working fluid.

  5. Interlayer Water Regulates the Bio-nano Interface of a ?-sheet Protein stacking on Graphene

    PubMed Central

    Lv, Wenping; Xu, Guiju; Zhang, Hongyan; Li, Xin; Liu, Shengju; Niu, Huan; Xu, Dongsheng; Wu, Ren'an

    2015-01-01

    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. PMID:25557857

  6. Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins

    PubMed Central

    Schirò, Giorgio; Fichou, Yann; Gallat, Francois-Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Härtlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J.; Weik, Martin

    2015-01-01

    Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300?K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240?K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity. PMID:25774711

  7. Seismic patterns and migration history of submarine fan channels in deep-water area, Niger Delta, West Africa

    NASA Astrophysics Data System (ADS)

    Zhang, Guotao; Zhang, Shangfeng; Li, Yuan

    2015-04-01

    The channels of deep-water submarine fan under Niger delta slope are characterized by large dimensions special deposition positions and complex formation processes, its geographical location and sedimentary environment also hinder the research and exploration development. According to the strata slicing, RMS amplitude attribute and other techniques, we exhibit the platforms patterns of channels at different period, and based on the analysis of internal architecture and deformation history of channel-leveed systems, migration and evolution process of channel systems could be understood accurately. A great quantity of isolated channels develop in middle Miocene and aggrading streams in late Miocene, which generating because of large scale of turbidity caused by the drop of second order sea-level, which characterized by vertical accretion at smooth channel, while vertical accretion and lateral migration at bend. Evolution of channel systems can be divided into three stages: the initial erosion, erosion and filling alternately, and abandoned stage. With these three stages, the sinuosity of channel change from moderate to high, then decrease. Incision and filling of channels, being during the three development phases, is the driving force of meander-loops migration, which promote three kinds of migration patterns: lateral, down-system and combination migration. The research provides theoretical basis for high-precision prediction and evaluation of deep-water reservoir.

  8. Protein Solvation in Membranes and at Water-Membrane Interfaces

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Chipot, Christophe; Wilson, Michael A.

    2002-01-01

    Different salvation properties of water and membranes mediate a host of biologically important processes, such as folding, insertion into a lipid bilayer, associations and functions of membrane proteins. These processes will be discussed in several examples involving synthetic and natural peptides. In particular, a mechanism by which a helical peptide becomes inserted into a model membrane will be described. Further, the molecular mechanism of recognition and association of protein helical segments in membranes will be discussed. These processes are crucial for proper functioning of a cell. A membrane-spanning domain of glycophorin A, which exists as a helical dimer, serves as the model system. For this system, the free energy of dissociation of the helices is being determined for both the wild type and a mutant, in which dimerization is disrupted.

  9. 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

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

    1994-01-01

    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.

  10. Infiltration and quality of water for two arroyo channels, Albuquerque, New Mexico, 1988-92

    USGS Publications Warehouse

    Thomas, Carole L.

    1995-01-01

    Selected reaches of Grant Line Arroyo and Tijeras Arroyo in Albuquerque, New Mexico, were studied to collect information about the amount and quality of infiltration through arroyo channels. Infiltration rate was calculated for selected reaches of Grant Line Arroyo and Tijeras Arroyo based on instantaneous streamflow-loss volumes, wetted channel area, and instantaneous evaporation rates measured during 1988-92. Infiltration rates at Grant Line Arroyo ranged from 0.0 to 0.6 foot per day, and at Tijeras Arroyo from 2.28 to 30 feet per day. The evaporation rate ranged from one-tenth of 1 percent to 2 percent of the infiltration rate. Infiltration rates differed with the location of the reach isolated for measurement and with the time of day of the infiltration-rate measurement. Differences in intrinsic permeability of the sediments may be the most important factor affecting spatial variations in infiltration. The most important factor affecting temporal variations in infiltration may be the temperature of the water and sediment where infiltration occurs. Annual evaporation rates were greatest over saturated stream sediments and ranged from 802 to 1,025 millimeters per year or from 31.57 to 40.35 inches per year. Annual evaporation rates were least over unsaturated, unvegetated soil and ranged from 174 to 291 millimeters per year or from 6.85 to 11.46 inches per year. Annual evapotranspiration rates over grasses or shrubs or both were about one-half the rates over saturated stream sediments. Rates were similar for Grant Line and Tijeras Arroyos. The land- surface vegetation, availability of water at the land surface, availability of energy to enable a change of state from water to vapor, existence of a vapor concentration gradient, and a turbulent atmosphere to carry the vapor away may be the factors that determine the amount of evaporation and evapotranspiration. Water in Grant Line Arroyo and Tijeras Arroyo met U. S. Environmental Protection Agency drinking-water regulations for nitrate, volatile organic compounds, dissolved lead, and dissolved and total arsenic, barium, cadmium, chromium, copper, iron, silver, zinc, selenium, chloride, and sulfate concentrations. Total lead concentration in one sample from Tramway Floodway Channel, a tributary to Tijeras Arroyo, was 55 micrograms per liter, exceeding the Environmental Protection Agency drinking-water regulation of 50 micrograms per liter. Dissolved-solids concentrations calculated from the sum of cations and anions usually exceeded the Environmental Protection Agency drinking-water dissolved-solids regulation of 500 milligrams per liter at Tijeras Arroyo above Four Hills Bridge.

  11. Influenza virus M2 protein ion channel activity stabilizes the native form of fowl plague virus hemagglutinin during intracellular transport.

    PubMed Central

    Takeuchi, K; Lamb, R A

    1994-01-01

    The influenza A/fowl plague virus/Rostock/34 hemagglutinin (HA), which is cleaved intracellularly and has a high pH threshold (pH 5.9) for undergoing its conformational change to the low-pH form, was expressed from cDNA in CV-1 and HeLa T4 cells in the absence of other influenza virus proteins. It was found, by biochemical assays, that the majority of the HA molecules were in a form indistinguishable from the low-pH form of HA. The acidotropic agent, ammonium chloride, stabilized the accumulation of HA in its native form. Coexpression of HA and the homotypic influenza virus M2 protein, which has ion channel activity, stabilized the accumulation of HA in its pH neutral (native) form, and the M2 protein ion channel blocker, amantadine, prevented the rescue of HA in its native form. These data provide direct evidence that the influenza virus M2 protein ion channel activity can affect the status of the conformational form of cleaved HA during intracellular transport. Images PMID:7507186

  12. The nodulation-signaling protein NodO from Rhizobium leguminosarum biovar viciae forms ion channels in membranes.

    PubMed Central

    Sutton, J M; Lea, E J; Downie, J A

    1994-01-01

    The secreted nodulation-signaling protein NodO was purified from the supernatant of cultures of Rhizobium leguminosarum biovar viciae. The native protein has a M(r) of approximately 67,000, suggesting that it exists as a dimer since the DNA sequence predicts a M(r) of 30,002. Pure NodO protein had no protease, pectinase, or cellulase activity, and no binding was observed to lipooligosaccharide nodulation factors. Although NodO is relatively hydrophilic, it appeared to insert into liposomes and was protected by liposomes from proteolytic cleavage. When added to planar lipid bilayers, NodO formed cation-selective channels that allowed the movement of monovalent cations (K+ and Na+) across the membrane. NodO is a Ca(2+)-binding protein; in the presence of high concentrations of Ca2+, channel activity was reduced. We hypothesize that NodO plays a role in nodulation signaling by stimulating uptake of nodulation factors or by forming cation-specific channels that function synergistically with the proposed lipooligosaccharide-induced depolarization of the plasma membrane of leguminous plants. Images PMID:7524090

  13. Evidence for Recent Liquid Water on Mars: Channeled Aprons in a Small Crater within Newton Crater

    NASA Technical Reports Server (NTRS)

    2000-01-01

    [figure removed for brevity, see original site]

    Newton Crater is a large basin formed by an asteroid impact that probably occurred more than 3 billion years ago. It is approximately 287 kilometers (178 miles) across. The picture shown here (top) highlights the north wall of a specific, smaller crater located in the southwestern quarter of Newton Crater (above). The crater of interest was also formed by an impact; it is about 7 km (4.4 mi) across, which is about 7 times bigger than the famous Meteor Crater in northern Arizona in North America.

    The north wall of the small crater has many narrow gullies eroded into it. These are hypothesized to have been formed by flowing water and debris flows. Debris transported with the water created lobed and finger-like deposits at the base of the crater wall where it intersects the floor (bottom center top image). Many of the finger-like deposits have small channels indicating that a liquid--most likely water--flowed in these areas. Hundreds of individual water and debris flow events might have occurred to create the scene shown here. Each outburst of water from higher upon the crater slopes would have constituted a competition between evaporation, freezing, and gravity.

    The individual deposits at the ends of channels in this MOC image mosaic were used to get a rough estimate of the minimum amount of water that might be involved in each flow event. This is done first by assuming that the deposits are like debris flows on Earth. In a debris flow, no less than about 10% (and no more than 30%) of their volume is water. Second, the volume of an apron deposit is estimated by measuring the area covered in the MOC image and multiplying it by a conservative estimate of thickness, 2 meters (6.5 feet). For a flow containing only 10% water, these estimates conservatively suggest that about 2.5 million liters (660,000 gallons) of water are involved in each event; this is enough to fill about 7 community-sized swimming pools or enough to supply 20 people with their water needs for a year.

    The MOC high resolution view is located near 41.1oS, 159.8oW and is a mosaic of three different pictures acquired between January and May 2000. The MOC scene is illuminated from the left; north is up. The context picture was acquired in 1977 by the Viking 1 orbiter and is illuminated from the upper right.

  14. On the behavior of water at subfreezing temperatures in a protein crystal: evidence of higher mobility than in bulk water.

    PubMed

    Wang, Dongqi; Böckmann, Anja; Dolenc, Jožica; Meier, Beat H; van Gunsteren, Wilfred F

    2013-10-01

    NMR experiments have shown that water molecules in the crystal of the protein Crh are still mobile at temperatures well below 273 K. In order to investigate this water anomaly, a molecular dynamics (MD) simulation study of crystalline Crh was carried out to determine the mobility of water in this crystal. The simulations were carried out at three temperatures, 150, 200, and 291 K. Simulations of bulk water at these temperatures were also done to obtain the properties of the simple point charge (SPC) water model used at these temperatures and to allow a comparison of the properties of water in the Crh crystal with those of bulk water at the same temperatures. According to the simulations, water is immobilized at 150 K both in crystal and in bulk water. As expected, at 291 K it diffuses and rotates more slowly in the protein crystal than in bulk water. However, at 200 K, the translational and rotational mobility of the water molecules is larger in the crystal than in bulk water. The enhancement of water mobility in the crystal at 200 K was further investigated by MD simulations in which the backbone or all protein atoms were positionally restrained, and in which additionally the electrostatic protein-water interactions were removed. Of these changes in the environment of the water molecules, rigidifying the protein backbones slightly enhanced water diffusion, while it slowed down rotation. In contrast, removal of electrostatic protein-water interactions did not change water diffusion but enhanced rotational motion significantly. Further investigations are required to delineate particular features of the protein crystal that induce the anomalous behavior of water at 200 K. PMID:23998392

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

    NASA Technical Reports Server (NTRS)

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

    2003-01-01

    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.

  16. CRMP2 protein SUMOylation modulates NaV1.7 channel trafficking.

    PubMed

    Dustrude, Erik T; Wilson, Sarah M; Ju, Weina; Xiao, Yucheng; Khanna, Rajesh

    2013-08-23

    Voltage-gated sodium channel (NaV) trafficking is incompletely understood. Post-translational modifications of NaVs and/or auxiliary subunits and protein-protein interactions have been posited as NaV-trafficking mechanisms. Here, we tested if modification of the axonal collapsin response mediator protein 2 (CRMP2) by a small ubiquitin-like modifier (SUMO) could affect NaV trafficking; CRMP2 alters the extent of NaV slow inactivation conferred by the anti-epileptic (R)-lacosamide, implying NaV-CRMP2 functional coupling. Expression of a CRMP2 SUMOylation-incompetent mutant (CRMP2-K374A) in neuronal model catecholamine A differentiated (CAD) cells did not alter lacosamide-induced NaV slow inactivation compared with CAD cells expressing wild type CRMP2. Like wild type CRMP2, CRMP2-K374A expressed robustly in CAD cells. Neurite outgrowth, a canonical CRMP2 function, was moderately reduced by the mutation but was still significantly higher than enhanced GFP-transfected cortical neurons. Notably, huwentoxin-IV-sensitive NaV1.7 currents, which predominate in CAD cells, were significantly reduced in CAD cells expressing CRMP2-K374A. Increasing deSUMOylation with sentrin/SUMO-specific protease SENP1 or SENP2 in wild type CRMP2-expressing CAD cells decreased NaV1.7 currents. Consistent with a reduction in current density, biotinylation revealed a significant reduction in surface NaV1.7 levels in CAD cells expressing CRMP2-K374A; surface NaV1.7 expression was also decreased by SENP1 + SENP2 overexpression. Currents in HEK293 cells stably expressing NaV1.7 were reduced by CRMP2-K374A in a manner dependent on the E2-conjugating enzyme Ubc9. No decrement in current density was observed in HEK293 cells co-expressing CRMP2-K374A and NaV1.1 or NaV1.3. Diminution of sodium currents, largely NaV1.7, was recapitulated in sensory neurons expressing CRMP2-K374A. Our study elucidates a novel regulatory mechanism that utilizes CRMP2 SUMOylation to choreograph NaV1.7 trafficking. PMID:23836888

  17. The NOAA Water Instrument: A Two-Channel, Tunable Diode Laser-Based Hygrometer for Measurement of Water Vapor and Cirrus Cloud Ice Water Content

    NASA Astrophysics Data System (ADS)

    Fahey, D. W.; Thornberry, T. D.; Rollins, A. W.; Gao, R. S.; Watts, L. A.; Ciciora, S. J.; McLaughlin, R. J.

    2014-12-01

    The recently developed NOAA Water instrument is a two-channel, closed-path, tunable diode laser absorption spectrometer designed for the measurement of water vapor and enhanced total water (vapor + inertially enhanced condensed-phase) from the NASA Global Hawk unmanned aircraft system (UAS) or other high-altitude research aircraft. Combining the measurements from the two channels allows the determination of cloud ice water content (IWC), an important metric for evaluating the radiative properties of cirrus clouds. The instrument utilizes wavelength-modulated spectroscopy with second harmonic detection near 2694 nm to achieve high precision with a 79 cm double-pass optical path. The detection cells are operated under constant temperature, pressure and flow conditions to maintain a constant sensitivity to H2O independent of the ambient sampling environment. An on-board calibration system is used to perform periodic in situ calibrations to verify the stability of the instrument sensitivity during flight. For the water vapor channel, ambient air is sampled perpendicular to the flow past the aircraft in order to reject cloud particles, while the total water channel uses a heated, forward-facing inlet to sample both water vapor and cloud particles. The total water inlet operates subisokinetically, thereby inertially enhancing cloud particle number in the sample flow and affording increased cirrus IWC sensitivity. The NOAA Water instrument was flown for the first time during the second deployment of the Airborne Tropical TRopopause EXperiment (ATTREX) in February-March 2013 on board the Global Hawk UAS. The instrument demonstrated a typical in-flight precision (1 s, 1 ?) of better than 0.17 parts per million (ppm, 10-6 mol/mol), with an overall H2O vapor measurement uncertainty of 5% ± 0.23 ppm. The inertial enhancement for cirrus cloud particle sampling under ATTREX flight conditions ranged from 33-48 for ice particles larger than 8 µm in diameter, depending primarily on aircraft altitude. The resulting IWC detection limit (2 ?) was 0.023-0.013 ppm, corresponding to approximately 2 µg m-3, with an estimated overall uncertainty of 20%.

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

    NASA Astrophysics Data System (ADS)

    Liu, J. B.; Bao, Y.

    2011-09-01

    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.

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

    NASA Astrophysics Data System (ADS)

    Chung Yang, Han; Xue Yang, Jia

    2014-05-01

    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.

  20. 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)

    Moore, Eli K.; Nunn, Brook L.; Goodlett, David R.; Harvey, H. Rodger

    2012-04-01

    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.

  1. Identifying and tracking proteins through the marine water column: insights into the inputs and preservation mechanisms of protein in sediments

    PubMed Central

    Moore, Eli K.; Nunn, Brook L.; Goodlett, David R.; Harvey, H. Rodger

    2012-01-01

    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

  2. Experimental study of Cu-water nanofluid forced convective flow inside a louvered channel

    NASA Astrophysics Data System (ADS)

    Khoshvaght-Aliabadi, M.; Hormozi, F.; Zamzamian, A.

    2015-03-01

    Heat transfer enhancement plays a very important role for energy saving in plate-fin heat exchangers. In the present study, the influences of simultaneous utilization of a louvered plate-fin channel and copper-base deionized water nanofluid on performance of these exchangers are experimentally explored. The effects of flow rate (2-5 l/min) and nanoparticles weight fraction (0-0.4 %) on heat transfer and pressure drop characteristics are determined. Experimental results indicate that the use of louvered channel instead of the plain one can improve the heat transfer performance. Likewise, addition of small amounts of copper nanoparticles to the base fluid augments the convective heat transfer coefficient remarkably. The maximum rise of 21.7 % in the convective heat transfer coefficient is observed for the 0.4 % wt nanofluid compared to the base fluid. Also, pumping power for the base fluid and nanofluids are calculated based on the measured pressure drop in the louvered channel. The average increase in pumping power is 11.8 % for the nanofluid with 0.4 % wt compared to the base fluid. Applied performance criterion shows a maximum performance index of 1.167 for the nanofluid with 0.1 % wt Finally, two correlations are proposed for Nusselt number and friction factor which fit the experimental data with in ±10 %.

  3. Experimental study of Cu-water nanofluid forced convective flow inside a louvered channel

    NASA Astrophysics Data System (ADS)

    Khoshvaght-Aliabadi, M.; Hormozi, F.; Zamzamian, A.

    2014-09-01

    Heat transfer enhancement plays a very important role for energy saving in plate-fin heat exchangers. In the present study, the influences of simultaneous utilization of a louvered plate-fin channel and copper-base deionized water nanofluid on performance of these exchangers are experimentally explored. The effects of flow rate (2-5 l/min) and nanoparticles weight fraction (0-0.4 %) on heat transfer and pressure drop characteristics are determined. Experimental results indicate that the use of louvered channel instead of the plain one can improve the heat transfer performance. Likewise, addition of small amounts of copper nanoparticles to the base fluid augments the convective heat transfer coefficient remarkably. The maximum rise of 21.7 % in the convective heat transfer coefficient is observed for the 0.4 % wt nanofluid compared to the base fluid. Also, pumping power for the base fluid and nanofluids are calculated based on the measured pressure drop in the louvered channel. The average increase in pumping power is 11.8 % for the nanofluid with 0.4 % wt compared to the base fluid. Applied performance criterion shows a maximum performance index of 1.167 for the nanofluid with 0.1 % wt Finally, two correlations are proposed for Nusselt number and friction factor which fit the experimental data with in ±10 %.

  4. Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding

    E-print Network

    Thirumalai, Devarajan

    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

  5. Does oxidation affect the water functionality of myofibrillar proteins?

    PubMed

    Bertram, Hanne Christine; Kristensen, Mette; Østdal, Henrik; Baron, Caroline P; Young, Jette F; Andersen, Henrik Jørgen

    2007-03-21

    Water-binding properties of myofibrils extracted from porcine muscle, and added hemoglobin with and without exposure to H2O2, were characterized using low-field proton NMR T2 relaxometry. The effects of pH and ionic strength in the samples were investigated as pH was adjusted to 5.4, 6.2, and 7.0 and ionic strength was adjusted to 0.29, 0.46, and 0.71 M, respectively. The formation of dityrosine as a measure of oxidative protein cross-linking revealed a significant increase in dityrosine concentrations upon H2O2 activation. The formation of dityrosine was strongly pH-dependent and increased with decreasing pH. In addition, increased levels of thiobarbituric acid reactive substances were observed upon addition of H2O2, implying that lipid oxidation was enhanced, however, with a different oxidation pattern as compared to the myofibrillar proteins. Low-field NMR relaxation measurements revealed reduced T2 relaxation times upon H2O2 activation, which corresponds to reduced water-holding capacity upon oxidation. However, a direct relationship between degree of oxidation and T2 relaxation time was not observed with various pH values and ionic strengths, and further studies are needed for a complete understanding of the effect of oxidation on myofibrillar functionality. PMID:17316016

  6. Dynamics of Protein and its Hydration Water: Neutron Scattering Studies on Fully Deuterated GFP

    PubMed Central

    Nickels, Jonathan D.; O’Neill, Hugh; Hong, Liang; Tyagi, Madhusudan; Ehlers, Georg; Weiss, Kevin L.; Zhang, Qiu; Yi, Zheng; Mamontov, Eugene; Smith, Jeremy C.; Sokolov, Alexei P.

    2012-01-01

    We present a detailed analysis of the picosecond-to-nanosecond motions of green fluorescent protein (GFP) and its hydration water using neutron scattering spectroscopy and hydrogen/deuterium contrast. The analysis reveals that hydration water suppresses protein motions at lower temperatures (protein dynamics at high temperatures. Experimental data demonstrate that the hydration water is harmonic at temperatures proteins’ methyl group rotations. The dynamics of the hydration water exhibits changes at ?180–190 K that we ascribe to the glass transition in the hydrated protein. Our results confirm significant differences in the dynamics of protein and its hydration water at high temperatures: on the picosecond-to-nanosecond timescale, the hydration water exhibits diffusive dynamics, while the protein motions are localized to water is similar to the behavior of hydration water previously observed for other proteins. Comparison with other globular proteins (e.g., lysozyme) reveals that on the timescale of 1 ns and at equivalent hydration level, GFP dynamics (mean-square displacements and quasielastic intensity) are of much smaller amplitude. Moreover, the suppression of the protein dynamics by the hydration water at low temperatures appears to be stronger in GFP than in other globular proteins. We ascribe this observation to the barrellike structure of GFP. PMID:23062349

  7. Copper accumulation in channel catfish (Ictalurus punctatus) exposed to water borne copper sulfate

    SciTech Connect

    Hobbs, M.; Griffin, B.; Schlenk, D.; Kadlubar, F.; Brand, C.D.

    1995-12-31

    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.

  8. Channel water balance and exchange with subsurface flow along a mountain headwater stream in Montana, United States

    USGS Publications Warehouse

    Payn, R.A.; Gooseff, M.N.; McGlynn, B.L.; Bencala, K.E.; Wondzell, S.M.

    2009-01-01

    Channel water balances of contiguous reaches along streams represent a poorly understood scale of stream-subsurface interaction. We measured reach water balances along a headwater stream in Montana, United States, during summer base flow recessions. Reach water balances were estimated from series of tracer tests in 13 consecutive reaches delineated evenly along a 2.6 km valley segment. For each reach, we estimated net change in discharge, gross hydrologic loss, and gross hydrologic gain from tracer dilution and mass recovery. Four series of tracer tests were performed during relatively high, intermediate, and low base flow conditions. The relative distribution of channel water along the stream was strongly related to a transition in valley structure, with a general increase in gross losses through the recession. During tracer tests at intermediate and low flows, there were frequent substantial losses of tracer mass (>10%) that could not be explained by net loss in flow over the reach, indicating that many of the study reaches were concurrently losing and gaining water. For example, one reach with little net change in discharge exchanged nearly 20% of upstream flow with gains and losses along the reach. These substantial bidirectional exchanges suggest that some channel interactions with subsurface flow paths were not measurable by net change in flow or transient storage of recovered tracer. Understanding bidirectional channel water balances in stream reaches along valleys is critical to an accurate assessment of stream solute fate and transport and to a full assessment of exchanges between the stream channel and surrounding subsurface.

  9. The effect of ultrasonic salting on protein and water-protein interactions in meat.

    PubMed

    McDonnell, C K; Allen, P; Morin, C; Lyng, J G

    2014-03-15

    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

  10. Modulation by protein kinase C activation of rat brain delayed-rectifier K+ channel expressed in Xenopus oocytes.

    PubMed

    Peretz, T; Levin, G; Moran, O; Thornhill, W B; Chikvashvili, D; Lotan, I

    1996-02-26

    The modulation by protein kinase C (PKC) of the RCK1 K+ channel was investigated in Xenopus oocytes by integration of two-electrode voltage clamp, site-directed mutagenesis and SDS-PAGE analysis techniques. Upon application of beta-phorbol 12-myristate 13-acetate (PMA) the current was inhibited by 50-90%. No changes in the voltage sensitivity of the channel, changes in membrane surface area or selective elimination of RCK1 protein from the plasma membrane could be detected. The inhibition was mimicked by 1-oleoyl-2-acetyl-rac-glycerol (OAG) but not by alphaPMA, and was blocked by staurosporine and calphostin C. Upon deletion of most of the N-terminus a preceding enhancement of about 40% of the current was prominent in response to PKC activation. Its physiological significance is discussed. The N-terminus deletion eliminated 50% of the inhibition. However, phosphorylation of none of the ten classical PKC phosphorylation sites on the channel molecule could account, by itself or in combination with others, for the inhibition. Thus, our results show that PKC activation can modulate the channel conductance in a bimodal fashion. The N-terminus is involved in the inhibition, however, not via its direct phosphorylation. PMID:8641443

  11. Response of the distributary channel of the Huanghe River estuary to water and sediment discharge regulation in 2007

    NASA Astrophysics Data System (ADS)

    Ma, Yanyan; Li, Guangxue; Ye, Siyuan; Zhang, Zhiheng; Zhao, Guangming; Li, Jingyang; Zhou, Chunyan; Ding, Wenjie; Yang, Xin

    2010-11-01

    The water and sediment discharge regulation (WSDR) project, which has been performed since 2002 before flood season every year, is of great significance to the river management in China. Until 2007, six experiments have been fulfilled to evaluate the effect of the project on the natural environment. To fill the gap of investigations, a study on flood and suspended sediment transportation and channel changing along the distributary channel of the Huanghe (Yellow) River was conducted during the WSDR project period in 2007. The lower channel was scoured rapidly and the channel became unobstructed gradually several days after the flood peak water was discharged from the Xiaolangdi Reservoir. Within four days after the flood peak at 3 000 m3/s entered the distributary, the channel in the river mouth area was eroded quickly. Both the mean values of area and depth of the main channel were tripled, and the maximum flood carrying capacity increased to 5 500 m3/s or more. Then, the river channel was silted anew in a very short time after completion of the WSDR. Favored by the WSDR project, the river status in April 2008 became better than that of the year before. The adjustment ranges of main channel parameters were about 30%, 10%, and 10% at sections C2, Q4, and Q7, respectively. The process of rapid erosion-deposition was more active 15 km away in the channel from the river mouth due to the marine influence. It is reasonable for discharging sediment at concentration peak from Xiaolangdi Reservoir at the end of the flood peak. As a result, the sediment peak reached the river mouth about two days later than that of the water current. In addition, the WSDR project has improved the development of the estuarine wetland. Wetland vegetation planted along the river banks restrained the water flow as a strainer and improved the main channel stability. It is suggested to draw water at mean rate of 150 m3/s from the Huanghe River during flood periods, because at the rate the water in the wetland would be stored and replenished in balance. Moreover, we believe that cropland on the river shoal of the lower Huanghe River should be replaced by wetland. These activities should achieve the Huanghe River management strategy of “To concentrate flow to scour sediment, stabilize the main channel, and regulate water and sediment”.

  12. Suprachiasmatic nucleus function and circadian entrainment are modulated by G protein-coupled inwardly rectifying (GIRK) channels

    PubMed Central

    Hablitz, L M; Molzof, H E; Paul, J R; Johnson, R L; Gamble, K L

    2014-01-01

    Abstract G protein signalling within the central circadian oscillator, the suprachiasmatic nucleus (SCN), is essential for conveying time-of-day information. We sought to determine whether G protein-coupled inwardly rectifying potassium channels (GIRKs) modulate SCN physiology and circadian behaviour. We show that GIRK current and GIRK2 protein expression are greater during the day. Pharmacological inhibition of GIRKs and genetic loss of GIRK2 depolarized the day-time resting membrane potential of SCN neurons compared to controls. Behaviourally, GIRK2 knockout (KO) mice failed to shorten free running period in response to wheel access in constant darkness and entrained more rapidly to a 6 h advance of a 12 h:12 h light–dark (LD) cycle than wild-type (WT) littermate controls. We next examined whether these effects were due to disrupted signalling of neuropeptide Y (NPY), which is known to mediate non-photic phase shifts, attenuate photic phase shifts and activate GIRKs. Indeed, GIRK2 KO SCN slices had significantly fewer silent cells in response to NPY, likely contributing to the absence of NPY-induced phase advances of PER2::LUC rhythms in organotypic SCN cultures from GIRK2 KO mice. Finally, GIRK channel activation is sufficient to cause a non-photic-like phase advance of PER2::LUC rhythms on a Per2Luc+/? background. These results suggest that rhythmic regulation of GIRK2 protein and channel function in the SCN contributes to day-time resting membrane potential, providing a mechanism for the fine tuning responses to non-photic and photic stimuli. Further investigation could provide insight into disorders with circadian disruption comorbidities such as epilepsy and addiction, in which GIRK channels have been implicated. PMID:25217379

  13. Transverse slope of bed and turbid-clear water interface of channelized turbidity currents flowing around bends

    E-print Network

    Parker, Gary

    ," in that they are created by the interaction water flow and sediment transport in rivers under air (i.e. the atmosphere1 Transverse slope of bed and turbid-clear water interface of channelized turbidity currents flowing around bends G Parkera , Jasim Imranb , Carlos Pirmezc a St. Anthony Falls Laboratory University

  14. Wetting and dewetting of narrow hydrophobic channels by orthogonal electric fields: Structure, free energy, and dynamics for different water models.

    PubMed

    Kayal, Abhijit; Chandra, Amalendu

    2015-12-14

    Wetting and dewetting of a (6,6) carbon nanotube in presence of an orthogonal electric field of varying strengths are studied by means of molecular dynamics simulations using seven different models of water. We have looked at filling of the channel, occupancy and structure of water inside it, associated free energy profiles, and also dynamical properties like the time scales of collective dipole flipping and residence dynamics. For the current systems where the entire simulation box is under the electric field, the nanotube is found to undergo electrodrying, i.e., transition from filled to empty states on increase of the electric field. The free energy calculations show that the empty state is the most stable one at higher electric field as it raptures the hydrogen bond environment inside the carbon nanotube by reorienting water molecules to its direction leading to a depletion of water molecules inside the channel. We investigated the collective flipping of water dipoles inside the channel and found that it follows a fast stepwise mechanism. On the dynamical side, the dipole flipping is found to occur at a faster rate with increase of the electric field. Also, the rate of water flow is found to decrease dramatically as the field strength is increased. The residence time of water molecules inside the channel is also found to decrease with increasing electric field. Although the effects of electric field on different water models are found to be qualitatively similar, the quantitative details can be different for different models. In particular, the dynamics of water molecules inside the channel can vary significantly for different water models. However, the general behavior of wetting and dewetting transitions, enhanced dipole flips, and shorter residence times on application of an orthogonal electric field hold true for all water models considered in the current work. PMID:26671397

  15. The channels of Mars

    NASA Technical Reports Server (NTRS)

    Baker, Victor R.

    1988-01-01

    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.

  16. Water Permeability of Aquaporin-4 Channel Depends on Bilayer Composition, Thickness, and Elasticity

    PubMed Central

    Tong, Jihong; Briggs, Margaret M.; McIntosh, Thomas J.

    2012-01-01

    Aquaporin-4 (AQP4) is the primary water channel in the mammalian brain, particularly abundant in astrocytes, whose plasma membranes normally contain high concentrations of cholesterol. Here we test the hypothesis that the water permeabilities of two naturally occurring isoforms (AQP4-M1 and AQP4-M23) depend on bilayer mechanical/structural properties modulated by cholesterol and phospholipid composition. Osmotic stress measurements were performed with proteoliposomes containing AQP4 and three different lipid mixtures: 1), phosphatidylcholine (PC) and phosphatidylglycerol (PG); 2), PC, PG, with 40 mol % cholesterol; and 3), sphingomyelin (SM), PG, with 40 mol % cholesterol. The unit permeabilities of AQP4-M1 were 3.3 ± 0.4 × 10?13 cm3/s (mean ± SE), 1.2 ± 0.1 × 10?13 cm3/s, and 0.4 ± 0.1 × 10?13 cm3/s in PC:PG, PC:PG:cholesterol, and SM:PG:cholesterol, respectively. The unit permeabilities of AQP4-M23 were 2.1 ± 0.2 × 10?13 cm3/s, 0.8 ± 0.1 × 10?13 cm3/s, and 0.3 ± 0.1 × 10?13 cm3/s in PC:PG, PC:PG:cholesterol, and SM:PG:cholesterol, respectively. Thus, for each isoform the unit permeabilities strongly depended on bilayer composition and systematically decreased with increasing bilayer compressibility modulus and bilayer thickness. These observations suggest that altering lipid environment provides a means of regulating water channel permeability. Such permeability changes could have physiological consequences, because AQP4 water permeability would be reduced by its sequestration into SM:cholesterol-enriched raft microdomains. Conversely, under ischemic conditions astrocyte membrane cholesterol content decreases, which could increase AQP4 permeability. PMID:23199918

  17. Progesterone effect mediated by the voltage-dependent calcium channel and protein kinase C on noncapacitated cryopreserved bovine spermatozoa.

    PubMed

    Córdoba, M; Beconi, M T

    2001-03-01

    An increase in intracellular calcium is essential to trigger capacitation and the acrosome reaction. The aim of this study was to determine the progesterone effect mediated by the voltage-dependent calcium channel and protein kinase C on heparin-capacitated and noncapacitated spermatozoa. Protein kinase C was activated by 1-oleoyl-2-acetyl glycerol, a membrane-permeant diacyl-glycerol, and inhibited by GF-109203X. The percentage of true acrosome reaction was evaluated using differential-interferential optical contrast microscopy and trypan blue stain. The calcium concentration was evaluated by FURA-2AM and methoxyverapamil was used as a voltage-dependent calcium channel inhibitor. A rapid calcium increase and acrosome reaction were induced by progesterone in capacitated and noncapacitated spermatozoa, a higher intracellular calcium increase being observed in capacitated than in noncapacitated samples (P < 0.05). The calcium increase and acrosome reaction were blocked significantly by GF-109203X in noncapacitated and capacitated spermatozoa by the addition of progesterone and/or 1-oleoyl-2-acetylglycerol. Methoxyverapamil blocked calcium influx in samples treated with progesterone and heparin/progesterone, but not in those treated with 1-oleoyl-2-acetyl glycerol. Progesterone induces the acrosome reaction in noncapacitated cryopreserved bovine spermatozoa through intracellular mechanisms dependent on protein kinase C and the voltage-dependent calcium channel. PMID:11350374

  18. Fragile X mental retardation protein controls synaptic vesicle exocytosis by modulating N-type calcium channel density

    PubMed Central

    Ferron, Laurent; Nieto-Rostro, Manuela; Cassidy, John S.; Dolphin, Annette C.

    2014-01-01

    Fragile X syndrome (FXS), the most common heritable form of mental retardation, is characterized by synaptic dysfunction. Synaptic transmission depends critically on presynaptic calcium entry via voltage-gated calcium (CaV) channels. Here we show that the functional expression of neuronal N-type CaV channels (CaV2.2) is regulated by fragile X mental retardation protein (FMRP). We find that FMRP knockdown in dorsal root ganglion neurons increases CaV channel density in somata and in presynaptic terminals. We then show that FMRP controls CaV2.2 surface expression by targeting the channels to the proteasome for degradation. The interaction between FMRP and CaV2.2 occurs between the carboxy-terminal domain of FMRP and domains of CaV2.2 known to interact with the neurotransmitter release machinery. Finally, we show that FMRP controls synaptic exocytosis via CaV2.2 channels. Our data indicate that FMRP is a potent regulator of presynaptic activity, and its loss is likely to contribute to synaptic dysfunction in FXS. PMID:24709664

  19. Water in the Polar and Nonpolar Cavities of the Protein Interleukin-1 Guogang Feng,

    E-print Network

    Clore, G. Marius

    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

  20. Hydration shell of the TS-Kappa protein: higher density than bulk water

    E-print Network

    Barbosa, Marcia C. B.

    Hydration shell of the TS-Kappa protein: higher density than bulk water Rafael de C. Barbosaa, 91501-970, Porto Alegre, RS, Brazil Abstract The density of the water molecules in the presence the behavior of hydrated TS Kappa protein in SPC/E and TIP4P-2005 water models. The simulations were performed

  1. Mechanism of Interaction between the General Anesthetic Halothane and a Model Ion Channel Protein, II: Fluorescence and Vibrational Spectroscopy Using a Cyanophenylalanine Probe

    SciTech Connect

    Liu, J.; Strzalka, J; Tronin, A; Johansson, J; Blasie, J

    2009-01-01

    We demonstrate that cyano-phenylalanine (PheCN) can be utilized to probe the binding of the inhalational anesthetic halothane to an anesthetic-binding, model ion channel protein hbAP-PheCN. The Trp to PheCN mutation alters neither the a-helical conformation nor the 4-helix bundle structure. The halothane binding properties of this PheCN mutant hbAP-PheCN, based on fluorescence quenching, are consistent with those of the prototype, hbAP1. The dependence of fluorescence lifetime as a function of halothane concentration implies that the diffusion of halothane in the nonpolar core of the protein bundle is one-dimensional. As a consequence, at low halothane concentrations, the quenching of the fluorescence is dynamic, whereas at high concentrations the quenching becomes static. The 4-helix bundle structure present in aqueous detergent solution and at the air-water interface, is preserved in multilayer films of hbAP-PheCN, enabling vibrational spectroscopy of both the protein and its nitrile label (-CN). The nitrile groups' stretching vibration band shifts to higher frequency in the presence of halothane, and this blue-shift is largely reversible. Due to the complexity of this amphiphilic 4-helix bundle model membrane protein, where four PheCN probes are present adjacent to the designed cavity forming the binding site within each bundle, all contributing to the infrared absorption, molecular dynamics (MD) simulation is required to interpret the infrared results. The MD simulations indicate that the blue-shift of -CN stretching vibration induced by halothane arises from an indirect effect, namely an induced change in the electrostatic protein environment averaged over the four probe oscillators, rather than a direct interaction with the oscillators. hbAP-PheCN therefore provides a successful template for extending these investigations of the interactions of halothane with the model membrane protein via vibrational spectroscopy, using cyano-alanine residues to form the anesthetic binding cavity.

  2. Tentative Study on Performance of Darriues-Type Hydroturbine Operated in Small Open Water Channel

    NASA Astrophysics Data System (ADS)

    Matsushita, D.; Moriyama, R.; Nakashima, K.; Watanabe, S.; Okuma, K.; Furukawa, A.

    2014-03-01

    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.

  3. Electron transfer activation of a second water channel for proton transport in [FeFe]-hydrogenase

    SciTech Connect

    Sode, Olaseni; Voth, Gregory A.

    2014-12-14

    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 A{sup 2?}, 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 A{sup 2-} by closing a cavity that could otherwise fill with water near the proximal Fe of the active site.

  4. Dynamical deductions from nuclear magnetic resonance relaxation measurements at the water-protein interface.

    PubMed Central

    Bryant, R G; Shirley, W M

    1980-01-01

    Nuclear magnetic resonance (NMR) measurements provide both structural and dynamical information about the molecules in which nuclear resonances are observed. This manuscript addresses NMR relaxation of water protons in protein powder systems. Inclusion of magnetic communication between the water proton spins and protein proton spins leads to a clearer view of water molecule dynamics at the protein surface than has been previously available. We conclude that water molecule motion at the protein surface is somewhat slower than in the solute free solvent, but it is orders of magnitude faster than motions in a rigid ice lattice even in samples hydrated to levels well below what is generally thought to be the full hydration complement of the protein. The NMR relaxation data on lysozyme powders support a model that leaves adsorbed water very fluid at the protein surface with reorientational correlation times for the water shorter than nanoseconds. PMID:7248450

  5. Monitoring water masses properties by Glider in Sardinia Channel during summer 2014

    NASA Astrophysics Data System (ADS)

    Gana, Slim; Iudicone, Daniele; Ghenim, Leila; Mortier, Laurent; Testor, Pierre; Tintoré, Joaquin; Olita, Antonio

    2015-04-01

    1. Summary In the framework of the EC funded project, PERSEUS (WP3, Subtask 3.3.1: Repeated glider sections in key channels and sub-basin) and with the support of JERICO TNA (EU-FP7), a deep water glider (up to 1000m) was deployed from the R/V Tethys in the Sardinia Channel and has carried out 3 return trips during the period spanning from the 16th of August 2014 to the 19th of September 2014. The Gilder was equipped with CTD, O2 sensors, Fluorometers (ChlA), back scattering from 470 to 880 nm and was programmed to follow a path close to SARAL satellite track #887. During this experiment, a significant dataset, as never obtained before for this area, has been collected. The innovation stands in the high spatial resolution, in the temporal repetitivity and in the number of parameters sampled simultaneously. The first step of the work will focuses on the analysis of the hydrological properties of the existing water masses in the area. 2. Frame and aim of the experiment The Sardinia Channel is a zonally oriented passage connecting the Algerian and the Tyrrhenian basins, with a sill depth of about 1900 m. In spite of the considerable amount of work achieved and accurate results obtained about the circulation in the Western Mediterranean Sea, during the last 20 years, the Sardinia Channel is still one of the region where the dynamical processes and water exchanges are not clearly identified. Previous studies (Garzoli S. and C. Maillard, 1979, and Ozturgut Erdogan, 1975) pointed out the complexity of the processes in the region and the role of the bottom topography in sustaining them, and provided a first estimation of the involved fluxes. The main knowledge about the water masses crossing this region mostly concerns the AW (Atlantic Water) and the LIW (Levantine Intermediate Water). Along the Algerian coast, the AW is transported mainly by the Algerian current (AC Millot, 1985) from which the anticyclonic Algerian eddies (AEs, Puillat et al., 2002; Taupier-Letage et al., 2003), often involving surface and intermediate waters, are generated by baroclinic instabilities of the AC itself. The AEs generally remain more or less included in the main AC flow. The AEs alongslope-downstream propagation usually ends in the Channel of Sardinia, where AEs dramatically interact with the bathymetry and can remain almost blocked in the Sardinia Channel area for several months before collapsing (Puillat et al., 2002). In order to clarify some of these processes, including the behavior of the Algerian current and associated eddies, our methodology is based on a combined approach using glider observations and sea surface features observed by satellite. By autonomously collecting high-quality observations in three dimensions, gliders allow high-resolution oceanographic monitoring and provide useful contributions for the understanding of mesoscale dynamics and multidisciplinary interactions (e.g., Hodges and Fratantoni, 2009). On top of that, the glider route follows the ground track of the satellite SARAL, equipped with a Ka band altimeter (AltiKa), with the view to implement a methodology of analysis as performed by Bouffard et al. (2010). The main objectives of the project are : • identification of the physical properties of the surface and intermediate water masses between Northern Tunisian Coast and Sardinia and evaluation of the transport of water, salt and heat through the area • study of the variability of the physical properties of surface and intermediate water masses through the use of in-situ and satellite data. • understanding exchanges through sub-basins and the complex interactions through eddies • validation of the operational hydrodynamic numerical model of the western Mediterranean (http://www.seaforecast.cnr.it/en/fl/wmed.php) through the use of in-situ and satellite data. 3. Preliminary results of the experiment The glider carried out 6 legs during the period spanning from the 16th of August 2014 to the 19th of September 2014: Leg#1 (16 to 23 August 2014), Leg#2 (23 to 28 August 2014), Leg#3 (28 Aug. to 03 Sept. 2014)

  6. Brain-derived neurotrophic factor modulation of Kv1.3 channel is disregulated by adaptor proteins Grb10 and nShc

    PubMed Central

    Colley, Beverly S; Cavallin, Melissa A; Biju, KC; Marks, David R; Fadool, Debra A

    2009-01-01

    Background Neurotrophins are important regulators of growth and regeneration, and acutely, they can modulate the activity of voltage-gated ion channels. Previously we have shown that acute brain-derived neurotrophic factor (BDNF) activation of neurotrophin receptor tyrosine kinase B (TrkB) suppresses the Shaker voltage-gated potassium channel (Kv1.3) via phosphorylation of multiple tyrosine residues in the N and C terminal aspects of the channel protein. It is not known how adaptor proteins, which lack catalytic activity, but interact with members of the neurotrophic signaling pathway, might scaffold with ion channels or modulate channel activity. Results We report the co-localization of two adaptor proteins, neuronal Src homology and collagen (nShc) and growth factor receptor-binding protein 10 (Grb10), with Kv1.3 channel as demonstrated through immunocytochemical approaches in the olfactory bulb (OB) neural lamina. To further explore the specificity and functional ramification of adaptor/channel co-localization, we performed immunoprecipitation and Western analysis of channel, kinase, and adaptor transfected human embryonic kidney 293 cells (HEK 293). nShc formed a direct protein-protein interaction with Kv1.3 that was independent of BDNF-induced phosphorylation of Kv1.3, whereas Grb10 did not complex with Kv1.3 in HEK 293 cells. Both adaptors, however, co-immunoprecipitated with Kv1.3 in native OB. Grb10 was interestingly able to decrease the total expression of Kv1.3, particularly at the membrane surface, and subsequently eliminated the BDNF-induced phosphorylation of Kv1.3. To examine the possibility that the Src homology 2 (SH2) domains of Grb10 were directly binding to basally phosphorylated tyrosines in Kv1.3, we utilized point mutations to substitute multiple tyrosine residues with phenylalanine. Removal of the tyrosines 111–113 and 449 prevented Grb10 from decreasing Kv1.3 expression. In the absence of either adaptor protein, channel co-expression reciprocally down-regulated expression and tyrosine phosphorylation of TrkB kinase and related insulin receptor kinase. Finally, through patch-clamp electrophysiology, we found that the BDNF-induced current suppression of the channel was prevented by both nShc and Grb10. Conclusion We report that adaptor protein alteration of kinase-induced Kv1.3 channel modulation is related to the degree of direct protein-protein association and that the channel itself can reciprocally modulate receptor-linked tyrosine kinase expression and activity. PMID:19166614

  7. Evidence for Recent Liquid Water on Mars: Channels and Aprons in East Gorgonum Crater

    NASA Technical Reports Server (NTRS)

    2000-01-01

    [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.

  8. Center for Nanostructured Biomimetic Interfaces Integrated Electrochemical and Optical Methods for Studying TRPV Channel Proteins

    E-print Network

    leading to increase in blood pressure in rats fed a high salt diet ·VR1 shows preference for Ca2+ ions a significant role in salt induced increases in blood pressure ·A protagonist (capsaicin) can open up this VR1 channel leading to decrease in blood pressure ·An antagonist (capsazepine) was found to close this channel

  9. Osmotic properties of auditory hair cells in the leopard frog: evidence for water-permeable channels.

    PubMed

    Farahbakhsh, Nasser A; Zelaya, Jaime E; Narins, Peter M

    2011-02-01

    When amphibian papillar hair cells (APHCs) of the leopard frog, Rana pipiens pipiens, are osmotically challenged, they exhibit a characteristically asymmetric (rectifying) response: small decreases (5%, or less) in the extracellular solution's osmolarity do not significantly affect the cells' volume; larger decreases produce a relatively slow volume increase in APHCs, while exposure to a hyperosmotic medium leads to rapid shrinking of these cells. Furthermore, the rate of volume change appears to be a function of the rate of extracellular osmotic change. These characteristics make the application of methods devised for the estimation of the osmotic permeability coefficient (P(f)) for semipermeable membranes - i.e., those with significant permeability only to water - to APHC membrane rather futile. We have, therefore, devised a method that takes both the permeability to solutes as well as the kinetics of the osmolarity change into consideration, in order to obtain estimates of P(f) that are to a large degree independent of these factors. We have compared the new and earlier methods. Using the new method, we have estimated the P(f) of APHCs' plasma membrane to be in the 10(-2)-cm/s range, and thus significantly larger than those reported for lipid bilayers. APHC's membrane P(f) appears to be cell-size independent and insensitive to extracellular mercury. These results suggest that APHCs express water-permeable channels in their plasma membrane. Furthermore, we suggest that asymmetric and rate dependent shape changes produced by osmolarity changes in APHCs imply the presence of significant permeability to solutes. The significance of transmembrane solute transport and water channel expression in amphibian auditory hair cells is discussed. PMID:21044674

  10. Coastal water circulation patterns around the Northern Channel Islands and Point Conception, California

    NASA Astrophysics Data System (ADS)

    Fewings, Melanie R.; Washburn, Libe; Ohlmann, J. Carter

    2015-11-01

    The Northern Channel Islands in California host multiple Marine Protected Areas containing kelp forest ecosystems. Little is known about the water circulation onshore of the 20-m isobath. We use water velocity recorded at 21 sites near the 15-m isobath at the Islands and mainland during 1999-2012 to describe the water circulation on time scales of days to months. The mean circulation is eastward or weak at the Islands but poleward along the mainland (speeds 0-10 cm s-1). The subinertial-frequency along-shelf flow is surface-intensified and reverses direction on time scales of days. In summer, the flow becomes more poleward throughout the region. The mean cross-shelf flow profiles are strikingly similar at most sites, with flow speeds 1-2 cm s-1. The mean flow near bottom in the vicinity of the kelp forests is offshore. The time-varying, two-layered response to wind is stronger, up to 6 cm s-1. The flushing time of the shelf onshore of the 15-m isobath is short, at most ?2 dy. At a few sites exposed to the prevailing wind, up to 60% of the velocity variance is predictable from wind measured in the Santa Barbara Channel. In the lee of Point Conception or at the Islands, however, regional wind explains little of the velocity variance. During weak winds, the velocity at some mainland, but not Island, sites responds to pressure gradients measured along the mainland coast. These pressure gradients are associated with local wind relaxations at Pt. Conception, not with remotely-generated coastal-trapped waves.

  11. AQP1 Is Not Only a Water Channel: It Contributes to Cell Migration through Lin7/Beta-Catenin

    E-print Network

    Elena Monzani; Riccardo Bazzotti; Carla Perego; Caterina A. M. La Porta

    2013-08-28

    Background: AQP1 belongs to aquaporins family, water-specific, membrane-channel proteins expressed in diverse tissues. Recent papers showed that during angiogenesis, AQP1 is expressed preferentially by microvessels, favoring angiogenesis via the increase of permeability In particular, in AQP1 null mice, endothelial cell migration is impaired without altering their proliferation or adhesion. Therefore, AQP1 has been proposed as a novel promoter of tumor angiogenesis. Methods/Findings: Using targeted silencing of AQP1 gene expression, an impairment in the organization of F-actin and a reduced migration capacity was demonstrated in human endothelial and melanoma cell lines. Interestingly, we showed, for the first time, that AQP1 co-immunoprecipitated with Lin-7. Lin7-GFP experiments confirmed co-immunoprecipitation. In addition, the knock down of AQP1 decreased the level of expression of Lin-7 and b-catenin and the inhibition of proteasome contrasted partially such a decrease. Conclusions/Significance: All together, our findings show that AQP1 plays a role inside the cells through Lin-7/b-catenin interaction. Such a role of AQP1 is the same in human melanoma and endothelial cells, suggesting that AQP1 plays a global physiological role. A model is presented.

  12. An atypical role for collapsin response mediator protein 2 (CRMP-2) in neurotransmitter release via interaction with presynaptic voltage-gated calcium channels.

    PubMed

    Brittain, Joel M; Piekarz, Andrew D; Wang, Yuying; Kondo, Takako; Cummins, Theodore R; Khanna, Rajesh

    2009-11-01

    Collapsin response mediator proteins (CRMPs) specify axon/dendrite fate and axonal growth of neurons through protein-protein interactions. Their functions in presynaptic biology remain unknown. Here, we identify the presynaptic N-type Ca(2+) channel (CaV2.2) as a CRMP-2-interacting protein. CRMP-2 binds directly to CaV2.2 in two regions: the channel domain I-II intracellular loop and the distal C terminus. Both proteins co-localize within presynaptic sites in hippocampal neurons. Overexpression in hippocampal neurons of a CRMP-2 protein fused to enhanced green fluorescent protein caused a significant increase in Ca(2+) channel current density, whereas lentivirus-mediated CRMP-2 knockdown abolished this effect. Interestingly, the increase in Ca(2+) current density was not due to a change in channel gating. Rather, cell surface biotinylation studies showed an increased number of CaV2.2 at the cell surface in CRMP-2-overexpressing neurons. These neurons also exhibited a significant increase in vesicular release in response to a depolarizing stimulus. Depolarization of CRMP-2-enhanced green fluorescent protein-overexpressing neurons elicited a significant increase in release of glutamate compared with control neurons. Toxin block of Ca(2+) entry via CaV2.2 abolished this stimulated release. Thus, the CRMP-2-Ca(2+) channel interaction represents a novel mechanism for modulation of Ca(2+) influx into nerve terminals and, hence, of synaptic strength. PMID:19755421

  13. A Geophysical Investigation along a Fractured Bedrock River Channel: Implications to Groundwater-Surface Water Interaction

    NASA Astrophysics Data System (ADS)

    Steelman, C. M.; Kennedy, C.; Parker, B. L.; Cherry, J.

    2012-12-01

    Fractured sedimentary rock aquifers represent an important source of water for many communities around the world. The Eramosa River - a major tributary of the Speed River within the Grand River Watershed, Ontario, Canada - resides upon a bedrock aquifer of densely fractured dolostone with dissolution-enhanced channels and karst features. While this aquifer represents a major component of the total water supply for the surrounding region, the potential effects of increased groundwater extraction on the overlying river and surrounding environment are not yet fully understood. A comprehensive assessment of groundwater-surface water interaction over a 12 km reach of the river has been initiated using a discrete fracture network framework, i.e., based on the idea that groundwater flow occurs in networks of discrete fractures or channels that are interconnected. Preliminary measurements using airborne infrared thermography and surface-water temperature have been collected in an attempt to delineate hydraulically-active fracture zones; however, these measurements do not provide any information about the physical geometry of features potentially controlling hydraulic interactions. A nest of small-diameter vertical coreholes have been drilled through the upper 15 m to characterize the geology and hydrogeology at a single location along the river. While these coreholes provide the typical information used to understand flow systems, well installation can be improved using prior knowledge of the shallow subsurface and river flow system. Geophysical techniques such as ground-penetrating radar (GPR) and frequency-domain electromagnetics (FDEM) can provide detailed information about and shallow rock environment, thereby increasing the likelihood of identifying hydraulically-active zones along a river channel. To examine the suitability of GPR and FDEM for the characterization of bedrock river environments, a geophysical investigation has been initiated along a 0.5 km reach of the river in close proximity to the vertical coreholes. The study area contains outcrops along the riverbank which enable direct imaging into the upper 15-20 m rock. GPR reflection profiles and common-midpoint (CMP) soundings were collected using 50 MHz and 100 MHz antennas along two main transects situated on either side of the river to examine the nature of the formation. FDEM measurements using an EM-34, -31 and -38 were concurrently collected along the GPR transects to identify variations in depth to rock and riverbed sedimentation. In addition, a 3D GPR reflection grid and azimuthal CMP and EM-31 measurements were collected over a 10 × 25 m plot immediately adjacent to the river to better understand fracture orientation and karst development within the formations. These geophysical data provide valuable insight into the nature of the structurally-controlled features expected to strongly influence groundwater discharge and surface water recharge along the bedrock river channel. This information will guide the site-selection process and placement of future coreholes, ultimately minimizing the invasiveness of small-diameter drilling activities.

  14. Multi-scaled normal mode analysis method for dynamics simulation of protein-membrane complexes: A case study of potassium channel gating motion correlations

    NASA Astrophysics Data System (ADS)

    Wu, Xiaokun; Han, Min; Ming, Dengming

    2015-10-01

    Membrane proteins play critically important roles in many cellular activities such as ions and small molecule transportation, signal recognition, and transduction. In order to fulfill their functions, these proteins must be placed in different membrane environments and a variety of protein-lipid interactions may affect the behavior of these proteins. One of the key effects of protein-lipid interactions is their ability to change the dynamics status of membrane proteins, thus adjusting their functions. Here, we present a multi-scaled normal mode analysis (mNMA) method to study the dynamics perturbation to the membrane proteins imposed by lipid bi-layer membrane fluctuations. In mNMA, channel proteins are simulated at all-atom level while the membrane is described with a coarse-grained model. mNMA calculations clearly show that channel gating motion can tightly couple with a variety of membrane deformations, including bending and twisting. We then examined bi-channel systems where two channels were separated with different distances. From mNMA calculations, we observed both positive and negative gating correlations between two neighboring channels, and the correlation has a maximum as the channel center-to-center distance is close to 2.5 times of their diameter. This distance is larger than recently found maximum attraction distance between two proteins embedded in membrane which is 1.5 times of the protein size, indicating that membrane fluctuation might impose collective motions among proteins within a larger area. The hybrid resolution feature in mNMA provides atomic dynamics information for key components in the system without costing much computer resource. We expect it to be a conventional simulation tool for ordinary laboratories to study the dynamics of very complicated biological assemblies. The source code is available upon request to the authors.

  15. Viruses infecting marine picoplancton encode functional potassium ion channels.

    PubMed

    Siotto, Fenja; Martin, Corinna; Rauh, Oliver; Van Etten, James L; Schroeder, Indra; Moroni, Anna; Thiel, Gerhard

    2014-10-01

    Phycodnaviruses are dsDNA viruses, which infect algae. Their large genomes encode many gene products, like small K(+) channels, with homologs in prokaryotes and eukaryotes. Screening for K(+) channels revealed their abundance in viruses from fresh-water habitats. Recent sequencing of viruses from marine algae or from salt water in Antarctica revealed sequences with the predicted characteristics of K(+) channels but with some unexpected features. Two genes encode either 78 or 79 amino acid proteins, which are the smallest known K(+) channels. Also of interest is an unusual sequence in the canonical ?-helixes in K(+) channels. Structural prediction algorithms indicate that the new channels have the conserved ?-helix folds but the algorithms failed to identify the expected transmembrane domains flanking the K(+) channel pores. In spite of these unexpected properties electophysiological studies confirmed that the new proteins are functional K(+) channels. PMID:25441713

  16. Definitive Assignment of Proton Selectivity and Attoampere Unitary Current to the M2 Ion Channel Protein of Influenza A Virus

    PubMed Central

    Lin, Tse-I; Schroeder, Cornelia

    2001-01-01

    The viral ion channel protein M2 supports the transit of influenza virus and its glycoproteins through acidic compartments of the cell. M2 conducts endosomal protons into the virion to initiate uncoating and, by equilibrating the pH at trans-Golgi membranes, preserves the native conformation of acid-sensitive viral hemagglutinin. The exceptionally low conductance of the M2 channel thwarted resolution of single channels by electrophysiological techniques. Assays of liposome-reconstituted M2 yielded the average unitary channel current of the M2 tetramer—1.2 aA (1.2 × 10?18 A) at neutral pH and 2.7 to 4.1 aA at pH 5.7—which activates the channel. Extrapolation to physiological temperature predicts 4.8 and 40 aA, respectively, and a unitary conductance of 0.03 versus 0.4 fS. This minute activity, below previous estimates, appears sufficient for virus reproduction, but low enough to avert abortive cytotoxicity. The unitary permeability of M2 was within the range reported for other proton channels. To address the ion selectivity of M2, we exploited the coupling of ionic influx and efflux in sealed liposomes. Metal ion fluxes were monitored by proton counterflow, employing a pH probe 1,000 times more sensitive than available Na+ or K+ probes. Even low-pH-activated M2 did not conduct Na+ and K+. The proton selectivity of M2 was estimated to be at least 3 × 106 (over sodium or potassium ions), in agreement with electrophysiological studies. The stringent proton selectivity of M2 suggests that the cytopathology of influenza virus does not involve direct perturbation of cellular sodium or potassium gradients. PMID:11264354

  17. A computational study of water and CO migration sites and channels inside myoglobin.

    PubMed

    Lapelosa, Mauro; Abrams, Cameron F

    2013-02-12

    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

  18. Expression and isotopic labelling of the potassium channel blocker ShK toxin as a thioredoxin fusion protein in bacteria.

    PubMed

    Chang, Shih Chieh; Galea, Charles A; Leung, Eleanor W W; Tajhya, Rajeev B; Beeton, Christine; Pennington, Michael W; Norton, Raymond S

    2012-10-01

    The polypeptide toxin ShK is a potent blocker of Kv1.3 potassium channels, which play a crucial role in the activation of human effector memory T-cells (T(EM)). Selective blockers constitute valuable therapeutic leads for the treatment of autoimmune diseases mediated by T(EM) cells, such as multiple sclerosis, rheumatoid arthritis, and type-1 diabetes. We have established a recombinant peptide expression system in order to generate isotopically-labelled ShK and various ShK analogues for in-depth biophysical and pharmacological studies. ShK was expressed as a thioredoxin fusion protein in Escherichia coli BL21 (DE3) cells and purified initially by Ni²? iminodiacetic acid affinity chromatography. The fusion protein was cleaved with enterokinase and purified to homogeneity by reverse-phase HPLC. NMR spectra of ¹?N-labelled ShK were similar to those reported previously for the unlabelled synthetic peptide, confirming that recombinant ShK was correctly folded. Recombinant ShK blocked Kv1.3 channels with a K(d) of 25 pM and inhibited the proliferation of human and rat T lymphocytes with a preference for T(EM) cells, with similar potency to synthetic ShK in all assays. This expression system also enables the efficient production of ¹?N-labelled ShK for NMR studies of peptide dynamics and of the interaction of ShK with Kv1.3 channels. PMID:22659540

  19. Anchored Clathrate Waters Bind Antifreeze Proteins to Ice

    SciTech Connect

    C Garnham; R Campbell; P Davies

    2011-12-31

    The mechanism by which antifreeze proteins (AFPs) irreversibly bind to ice has not yet been resolved. The ice-binding site of an AFP is relatively hydrophobic, but also contains many potential hydrogen bond donors/acceptors. The extent to which hydrogen bonding and the hydrophobic effect contribute to ice binding has been debated for over 30 years. Here we have elucidated the ice-binding mechanism through solving the first crystal structure of an Antarctic bacterial AFP. This 34-kDa domain, the largest AFP structure determined to date, folds as a Ca{sup 2+}-bound parallel beta-helix with an extensive array of ice-like surface waters that are anchored via hydrogen bonds directly to the polypeptide backbone and adjacent side chains. These bound waters make an excellent three-dimensional match to both the primary prism and basal planes of ice and in effect provide an extensive X-ray crystallographic picture of the AFP{vert_ellipsis}ice interaction. This unobstructed view, free from crystal-packing artefacts, shows the contributions of both the hydrophobic effect and hydrogen bonding during AFP adsorption to ice. We term this mode of binding the 'anchored clathrate' mechanism of AFP action.

  20. A conceptual model for river water and sediment dispersal in the Santa Barbara Channel, California

    USGS Publications Warehouse

    Warrick, J.A.; Mertes, L.A.K.; Washburn, L.; Siegel, D.A.

    2004-01-01

    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.

  1. Regulation of the human ether-a-go-go-related gene (hERG) potassium channel by Nedd4 family interacting proteins (Ndfips).

    PubMed

    Kang, Yudi; Guo, Jun; Yang, Tonghua; Li, Wentao; Zhang, Shetuan

    2015-11-15

    The cardiac electrical disorder long QT syndrome (LQTS) pre-disposes affected individuals to ventricular arrhythmias and sudden death. Dysfunction of the human ether-a-go-go-related gene (hERG)-encoded rapidly activating delayed rectifier K(+) channel (IKr) is a major cause of LQTS. The expression of hERG channels is controlled by anterograde trafficking of newly synthesized channels to and retrograde degradation of existing channels from the plasma membrane. We have previously shown that the E3 ubiquitin (Ub) ligase Nedd4-2 (neural precursor cell expressed developmentally down-regulated protein 4-2) targets the PY motif of hERG channels to initiate channel degradation. Although both immature and mature hERG channels contain the PY motif, Nedd4-2 selectively mediates the degradation of mature hERG channels. In the present study, we demonstrate that Nedd4-2 is directed to specific cellular compartments by the Nedd4 family interacting proteins, Nedd4 family-interacting protein 1 (Ndfip1) and Ndfip2. Ndfip1 is primarily localized in the Golgi apparatus where it recruits Nedd4-2 to mediate the degradation of mature hERG proteins during channel trafficking to the plasma membrane. Although Ndfip2 directs Nedd4-2 to the Golgi apparatus, it also recruits Nedd4-2 to the multivesicular bodies (MVBs), which may impair MVB function and impede the degradation of mature hERG proteins mediated by Nedd4-2. These findings extend our understanding of hERG channel regulation and provide information which may be useful for the rescue of impaired hERG function in LQTS. PMID:26363003

  2. Protein extraction and 2-DE of water- and lipid-soluble proteins from bovine pericardium, a low-cellularity tissue

    PubMed Central

    Griffiths, Leigh G.; Choe, Leila; Lee, Kelvin H.; Reardon, Kenneth F.; Orton, E. Christopher

    2009-01-01

    Bovine pericardium (BP) is an important biomaterial used in the production of glutaraldehyde-fixed heart valves and tissue-engineering applications. The ability to perform proteomic analysis on BP is useful for a range of studies, including investigation of immune rejection after implantation. However, proteomic analysis of fibrous tissues such as BP is challenging due to their relative low-cellularity and abundance of extracellular matrix. A variety of methods for tissue treatment, protein extraction, and ;fractionation were investigated with the aim of producing high-quality 2-DE gels for both water- and lipid-soluble BP proteins. Extraction of water-soluble proteins with 3-(benzyldimethylammonio)-propanesulfonate followed by n-dodecyl ?-d-maltoside extraction and ethanol precipitation for lipid-soluble proteins provided the best combination of yield, spot number, and resolution on 2-DE gels (Protocol E2). ESI-quadrupole/ion trap or MALDI-TOF/TOF MS protein identifications were performed to confirm bovine origin and appropriate subcellular prefractionation of resolved proteins. Twenty-five unique, predominantly cytoplasmic bovine proteins were identified from the water-soluble fraction. Thirty-two unique, predominantly membrane bovine proteins were identified from the lipid-soluble fraction. These results demonstrated that the final protocol produced high-quality proteomic data from this important tissue for both cytoplasmic and membrane proteins. PMID:18985661

  3. The role of water exchange between a stream channel and its hyporheic zone in nitrogen cycling at the terrestrial-aquatic interface

    USGS Publications Warehouse

    Triska, F.J.; Duff, J.H.; Avanzino, R.J.

    1993-01-01

    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.

  4. From sequence to antibody: genetic immunisation is suitable to generate antibodies against a rare plant membrane protein, the KAT 1 channel.

    PubMed

    Gehwolf, Renate; Weiss, Richard; Gabler, Maximilian; Hurst, Annette C; Bertl, Adam; Thalhamer, Josef; Obermeyer, Gerhard

    2007-02-01

    Monoclonal antibodies against the K(+) channel KAT1 of Arabidopsis thaliana, a low abundance, plant plasma membrane protein, were generated by genetic immunisation to avoid the time and labour consuming purification of native or recombinant proteins and peptides usually necessary for conventional immunisation techniques. The resulting polyclonal and monoclonal antibody sera recognised a single protein band in a microsomal fraction of wild-type A. thaliana leaves and in membrane fractions of transgenic yeast cells and tobacco plants expressing the KAT1 protein. Therefore, genetic immunisation is suitable for generating monoclonal antibodies against plant proteins and particularly, against plant membrane proteins of low abundance. PMID:17239865

  5. From sequence to antibody: Genetic immunisation is suitable to generate antibodies against a rare plant membrane protein, the KAT 1 channel

    PubMed Central

    Gehwolf, Renate; Weiss, Richard; Gabler, Maximilian; Hurst, Annette C.; Bertl, Adam; Thalhamer, Josef; Obermeyer, Gerhard

    2010-01-01

    Monoclonal antibodies against the K+ channel KAT1 of Arabidopsis thaliana, a low abundance, plant plasma membrane protein, were generated by genetic immunisation to avoid the time and labour consuming purification of native or recombinant proteins and peptides usually necessary for conventional immunisation techniques. The resulting polyclonal and monoclonal antibody sera recognised a single protein band in a microsomal fraction of wild-type A. thaliana leaves and in membrane fractions of transgenic yeast cells and tobacco plants expressing the KAT1 protein. Therefore, genetic immunisation is suitable for generating monoclonal antibodies against plant proteins and particularly, against plant membrane proteins of low abundance. PMID:17239865

  6. Water channel in the binding site of a high affinity anti-methotrexate antibody.

    PubMed

    Gayda, Susan; Longenecker, Kenton L; Manoj, Sharmila; Judge, Russell A; Saldana, Sylvia C; Ruan, Qiaoqiao; Swift, Kerry M; Tetin, Sergey Y

    2014-06-17

    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

  7. Golgi Anti-apoptotic Proteins Are Highly Conserved Ion Channels That Affect Apoptosis and Cell Migration

    E-print Network

    Carrara, Guia; Saraiva, Nuno; Parsons, Maddy; Byrne, Bernadette; Prole, David L.; Taylor, Colin W.; Smith, Geoffrey L.

    2015-02-24

    . Within eukaryotes, GAAPs regulate the Ca2+ content of intracellular stores, inhibit apoptosis, and promote cell adhesion and migration. Data presented here demonstrate that purified viral GAAPs (vGAAPs) and human Bax inhibitor 1 form ion channels...

  8. Influence of protein type on oxidation and digestibility of fish oil-in-water emulsions: gliadin, caseinate, and whey protein.

    PubMed

    Qiu, Chaoying; Zhao, Mouming; Decker, Eric Andrew; McClements, David Julian

    2015-05-15

    The influence of three surface-active proteins on the oxidative stability and lipase digestibility of emulsified ?-3 oils was examined: deamidated wheat gliadin (gliadin); sodium caseinate (CN); whey protein isolate (WPI). Gliadin and WPI were more effective at inhibiting lipid oxidation (hydroperoxides and TBARS) of fish oil-in-water emulsions than CN. Protein oxidation during storage was determined by measuring the loss of tryptophan fluorescence. The CN-emulsions exhibited the highest loss of tryptophan fluorescence during aging, as well as the highest amount of lipid oxidation. Potential reasons for the differences in oxidative stability of the emulsions with different proteins include differences in interfacial film thickness, protein chelating ability, and antioxidant amino acids profiles. During in vitro digestion, gliadin-stabilized emulsions had the lowest digestion rate of the three proteins. These results have important implications for using proteins to fabricate emulsion-based delivery systems for ?-3 oils. PMID:25577077

  9. Role of protein dynamics in ion selectivity and allosteric coupling in the NaK channel.

    PubMed

    Brettmann, Joshua B; Urusova, Darya; Tonelli, Marco; Silva, Jonathan R; Henzler-Wildman, Katherine A

    2015-12-15

    Flux-dependent inactivation that arises from functional coupling between the inner gate and the selectivity filter is widespread in ion channels. The structural basis of this coupling has only been well characterized in KcsA. Here we present NMR data demonstrating structural and dynamic coupling between the selectivity filter and intracellular constriction point in the bacterial nonselective cation channel, NaK. This transmembrane allosteric communication must be structurally different from KcsA because the NaK selectivity filter does not collapse under low-cation conditions. Comparison of NMR spectra of the nonselective NaK and potassium-selective NaK2K indicates that the number of ion binding sites in the selectivity filter shifts the equilibrium distribution of structural states throughout the channel. This finding was unexpected given the nearly identical crystal structure of NaK and NaK2K outside the immediate vicinity of the selectivity filter. Our results highlight the tight structural and dynamic coupling between the selectivity filter and the channel scaffold, which has significant implications for channel function. NaK offers a distinct model to study the physiologically essential connection between ion conduction and channel gating. PMID:26621745

  10. Channel catfish (Ictalurus punctatus) muscle protein isolate performance processed under different acid and alkali pH values.

    PubMed

    Davenport, M P; Kristinsson, H G

    2011-04-01

    Channel catfish (Ictalurus punctatus) muscle was subjected to 6 protein extraction and precipitation techniques using acid solubilization (pH 2.0, 2.5, and 3.0) or alkaline solubilization (pH 10.5, 11.0, 11.5) followed by precipitation at pH 5.5. The catfish protein isolate was compared with ground defatted white muscle. Alkali-processed catfish showed increased gel rigidity, gel strength, and gel flexibility compared to acid-processed catfish, which exhibited inconsistent functional performance, increasing and decreasing gel rigidity, gel strength, and gel flexibility. The gel rigidity (G') at pH 3.0 in the absence of salt had the highest?G' of the acid treatments and was not significantly different from the alkaline-treated catfish muscle (P>0.05). However in the presence of added salt pH treatment it had the lowest?G' and was different from alkaline treatments (P<0.05) during break force testing. These results show that pH-shift processing of channel catfish muscle provides highly functional isolates with a potentially broad range of applications. This range of applications is possible due to the modification of the textural properties of catfish muscle protein produced using different acidic or alkaline pH solubility treatments. PMID:21535823

  11. Silver nanoparticle exposure induces rat motor dysfunction through decrease in expression of calcium channel protein in cerebellum.

    PubMed

    Yin, Nuoya; Zhang, Yang; Yun, Zhaojun; Liu, Qian; Qu, Guangbo; Zhou, Qunfang; Hu, Ligang; Jiang, Guibin

    2015-09-01

    Silver nanoparticles (AgNPs) are currently used widely, however, their impact on central nervous system still remains ambiguous and needs to be elucidated. This study is performed to investigate the neurotoxicity of AgNPs and illustrate the potential molecular mechanism. Neonatal Sprague-Dawley (SD) rats are exposed to AgNPs by intranasal instillation for 14 weeks. It is demonstrated that AgNPs exposure causes cerebellar ataxia like symptom in rats, evidenced by dysfunction of motor coordination and impairment of locomotor activity. Observation of cerebellum section reveals that AgNPs can provoke destruction of cerebellum granular layer with concomitant activation of glial cells. AgNPs treatment decreases calcium channel protein (CACNA1A) levels in cerebellum without changing potassium channel protein (KCNA1) levels. The levels of silver in rat cerebellum tissue are correlated with exposure doses. In vitro experiments reveal that AgNPs treatment significantly reduces the protein and mRNA levels of CACNA1A in primary cultured cerebellum granule cells (CGCs). These findings suggest that AgNPs-induced rat motor dysfunction is associated with CACNA1A expression decrease, which reveals the underlying molecular mechanism for the neurotoxicity of AgNPs. Possible counteractions may accordingly be suggested to attenuate the unexpected harmful effects in biological applications of AgNPs. PMID:26068065

  12. Nifedipine represses ion channels, transporters and Ca{sup 2+}-binding proteins in hearts of spontaneously hypertensive rats

    SciTech Connect

    Zwadlo, Carolin; Borlak, Juergen . E-mail: borlak@item.fraunhofer.de

    2006-06-15

    The Ca{sup 2+} antagonists nifedipine has been used for more than three decades to treat hypertension, but its effects on the transcriptional regulation of cardiac genes are basically unknown. We therefore studied expression of genes coding for ion channels, ion transporters and associated partners as well as Ca{sup 2+}-binding proteins in ventricular tissue of normotensive and spontaneously hypertensive (SH) rats after repeated intraperitoneally (i.p.) dosing of nifedipine. Notably, we observed significant (P < 0.05) repression in transcript levels of most of the genes investigated, including cardiac Na{sup +}, K{sup +}, Ca{sup 2+}-channels (L-type Ca{sup 2+}-channel, K{sub ir}3.4, K{sub ir}6.1, Na{sub v}1.5), ATP-driven ion exchangers (Na{sup +}-K{sup +}-ATPase, NCX-1, PMCA 2 and 4, SERCA 2a and 2b) and their associated partners (phospholamban, RyR-2) as well as cytoskeletal proteins ({alpha} and {beta}-MHC, {alpha} cardiac and {alpha} skeletal actin, troponin T and I). Repression in transcript levels was, however, only seen in ventricular tissue of hypertensive animals. This points to fundamental differences in the mode of action of nifedipine in diseased and healthy animals. Indeed, this preponderance of repressed genes will promote disturbed ion homeostasis to result in contractile dysfunction. It is of considerable importance that repressed gene expression was also seen in end-stage human heart failure [Borlak, J., Thum, T., 2003. Hallmarks of ion channel gene expression in end-stage heart failure. FASEB J. 17, 1592-1608]. We propose repression of cardiac-specific gene expression as a hallmark of nifedipine treatment in hypertrophic hearts.

  13. Protein interactions central to stabilizing the K[superscript +] channel selectivity filter in a four-sited configuration for selective K[superscript +] permeation

    SciTech Connect

    Sauer, David B.; Zeng, Weizhong; Raghunathan, Srinivasan; Jiang, Youxing

    2011-11-18

    The structural and functional conversion of the nonselective NaK channel to a K{sup +} selective channel (NaK2K) allows us to identify two key residues, Tyr and Asp in the filter sequence of TVGYGD, that participate in interactions central to stabilizing the K{sup +} channel selectivity filter. By using protein crystallography and channel electrophysiology, we demonstrate that the K{sup +} channel filter exists as an energetically strained structure and requires these key protein interactions working in concert to hold the filter in the precisely defined four-sited configuration that is essential for selective K{sup +} permeation. Disruption of either interaction, as tested on both the NaK2K and eukaryotic K{sub v}1.6 channels, can reduce or completely abolish K{sup +} selectivity and in some cases may also lead to channel inactivation due to conformational changes at the filter. Additionally, on the scaffold of NaK we recapitulate the protein interactions found in the filter of the Kir channel family, which uses a distinct interaction network to achieve similar stabilization of the filter.

  14. Hydration shell of the TS-Kappa protein: Higher density than bulk water

    NASA Astrophysics Data System (ADS)

    Barbosa, Rafael de C.; Barbosa, Marcia C.

    2015-12-01

    The density of the water molecules in the presence of hydrophobic and hydrophilic amino acids was studied. Molecular dynamic simulation were employed to analyze the behavior of hydrated TS Kappa protein in SPC/E and TIP4P-2005 water models. The simulations were performed in the NPT ensemble with the Nosé-Hoover thermostat and the Parrinello-Rahman barostat. The density profile of these systems were obtained for different temperatures at constant pressure. Two complementary phenomena were observed. The protein-water system exhibits a temperature of maximum density lower than the temperature observed in the pure water system. The densities of the water in vicinity of the hydrophobic and hydrophilic sites are higher than the density of the water in the bulk. Our results suggest that interactions between protein and water and the water-water Hydrogen bonds are essential to the understanding of these phenomena.

  15. Effect of dietary K intake on apical small-conductance K channel in CCD: role of protein tyrosine kinase.

    PubMed

    Wei, Y; Bloom, P; Lin, D; Gu, R; Wang, W H

    2001-08-01

    We have used Western blot to examine the expression of cSrc protein tyrosine kinase (PTK) and protein tyrosine phosphatase (PTP)-1D in the renal cortex, and the patch-clamp technique to determine the role of PTK in mediating the effect of dietary K intake on the small-conductance K (SK) channel in the cortical collecting duct (CCD). When rats were on a K-deficient (KD) diet for 1, 3, 5, and 7 days, the expression of cSrc increased by 40, 90, 140, and 135%, respectively. In contrast, the expression of cSrc in the renal cortex from rats on a high-K (HK) diet for 1, 2, and 3 days decreased by 40, 60, and 75%, respectively. However, the protein level of PTP-1D was not significantly changed by dietary K intake. The addition of 1 microM herbimycin A increased NP(o), a product of channel number (N) and open probability (P(o)) in the CCD from rats on a normal diet or on a KD diet. The increase in NP(o) was 0.30 (normal), 0.45 (1-day KD), 0.65 (3-day KD), 1.55 (5-day KD), and 1.85 (7-day KD), respectively. Treatment of the CCD with herbimycin A from rats on a KD diet increased NP(o) per patch from the control value (0.7) to 1.4 (1-day KD), 1.6 (3-day KD), 2.6 (5-day KD), and 3.5 (7-day KD), respectively. In contrast, HK intake for as short as 1 day abolished the effect of herbimycin A. Furthermore, the expression of ROMK channels in the renal cortex was the same between rats on a KD diet or on a HK diet. Moreover, treatment with herbimycin A did not further increase NP(o) in the CCDs from rats on a HK diet. We conclude that dietary K intake plays a key role in regulating the activity of the SK channels and that PTK is involved in mediating the effect of the K intake on channel activity in the CCD. PMID:11457712

  16. Protein isoform-specific validation defines multiple chloride intracellular channel and tropomyosin isoforms as serological biomarkers of ovarian cancer

    PubMed Central

    Tang, Hsin-Yao; Beer, Lynn A.; Tanyi, Janos L.; Zhang, Rugang; Liu, Qin; Speicher, David W.

    2013-01-01

    New serological biomarkers for early detection and clinical management of ovarian cancer are urgently needed, and many candidates have been reported. A major challenge frequently encountered when validating candidates in patients is establishing quantitative assays that distinguish between highly homologous proteins. The current study tested whether multiple members of two recently discovered ovarian cancer biomarker protein families, chloride intracellular channel (CLIC) proteins and tropomyosins (TPM), were detectable in ovarian cancer patient sera. A multiplexed, label-free multiple reaction monitoring (MRM) assay was established to target peptides specific to all detected CLIC and TPM family members, and their serum levels were quantitated for ovarian cancer patients and non-cancer controls. In addition to CLIC1 and TPM1, which were the proteins initially discovered in a xenograft mouse model, CLIC4, TPM2, TPM3, and TPM4 were present in ovarian cancer patient sera at significantly elevated levels compared with controls. Some of the additional biomarkers identified in this homolog-centric verification and validation approach may be superior to the previously identified biomarkers at discriminating between ovarian cancer and non-cancer patients. This demonstrates the importance of considering all potential protein homologs and using quantitative assays for cancer biomarker validation with well-defined isoform specificity. PMID:23792823

  17. Inspection Head Design for the In-Service Inspection of Fuel Channels of Pressurized Heavy Water Reactors

    SciTech Connect

    Haruray, Amit Kumar; Veerapur, R.D.; Puri, R.K.; Singh, Manjit

    2006-07-01

    This paper discusses the challenges associated with the mechanical design of Inspection Head for the in-service inspection (ISI) of fuel channels of Indian Pressurized Heavy Water Reactors (PHWRs). ISI is carried out during shut down period in the reactor. Non Destructive Examination (NDE) of fuel channels is a mandatory requirement to acquire knowledge about the structural condition. A typical 220 MWe Reactor-core consists of 306 horizontal fuel channel assemblies (tubular in shape). There are typical design challenges due to their horizontal nature, long length (each assembly is around 9 meters long), and high radiation. Because of combined effect of above mentioned factors, these fuel channels develop permanent downward sag during service. This sag has to be negotiated by the Inspection Head. The Inspection Head houses all the NDE sensors and is deployed in the fuel channel with the help of reactor fuelling machine. It is driven inside the fuel channel by a separate external drive-system, which is capable of linearly advancing, retracting as well as rotating it all-round to achieve full-volumetric inspection. The paper also discusses an important design feature in the Inspection Head, which helps in maintaining a fixed distance between NDE sensors and the internal surface (ID) of the fuel channel, to enable us to obtain reliable and consistent inspection results. This objective is achieved with the help of two specially designed leaf-spring loaded roller modules, which are assembled in the Inspection Head at its front and rear, with NDE Sensor Module sandwiched between them. Another very important design feature in the Inspection Head helps the Spring-Loaded Roller Modules in carrying out their intended function of maintaining fixed distance despite the weight of the long drive extension links attached at the rear of Inspection Head or deviations due to any other reason. There are multiple drive extension links attached at the rear of the Inspection Head as the fuel channel assembly is very long and the external drive system can accommodate a limited length drive extension link. Issues related to the sealing in Inspection Head and drive extension links are also discussed, as this system is driven inside the heavy water filled fuel channel from a drive system, which is installed just outside in front of the fuel channel in dry ambience. The Inspection Head is a part of BARCIS (Bhabha Atomic Research Centre Channel Inspection System), which is used for the inspection of fuel channels in Indian PHWRs. (authors)

  18. Water Molecule Contributions to Proton Spin-Lattice Relaxation in Rotationally Immobilized Proteins

    PubMed Central

    Goddard, Yanina A.; Korb, Jean-Pierre; Bryant, Robert G.

    2009-01-01

    Spin-lattice relaxation rates of protein and water protons in dry and hydrated immobilized bovine serum albumin were measured in the range of 1H Larmor frequency from 10 kHz to 30 MHz at temperatures from 154 to 302 K. The water proton spin-lattice relaxation reports on that of protein protons, which causes the characteristic power law dependence on the magnetic field strength. Isotope substitution of deuterium for hydrogen in water and studies at different temperatures expose three classes of water molecule dynamics that contribute to the spin-lattice relaxation dispersion profile. At 185 K, a water 1H relaxation contribution derives from reorientation of protein-bound molecules that are dynamically uncoupled from the protein backbone and is characterized by a Lorentzian function. Bound water molecule motions that can be dynamically uncoupled or coupled to the protein fluctuations make dominant contributions at higher temperatures as well. Surface water translational diffusion that is magnetically two-dimensional makes relaxation contributions at frequencies above 10 MHz. It is shown using isotope substitution that the exponent of the power law of the water signal in hydrated immobilized protein systems is the same as that for protons in lyophilized proteins over four orders of magnitude in the Larmor frequency, which implies that changes in the protein structure associated with hydration do not affect the 1H spin relaxation. PMID:19394883

  19. Contribution of Water to Pressure and Cold Denaturation of Proteins Valentino Bianco and Giancarlo Franzese*

    E-print Network

    Franzese, Giancarlo

    Contribution of Water to Pressure and Cold Denaturation of Proteins Valentino Bianco and Giancarlo) The mechanisms of cold and pressure denaturation of proteins are matter of debate and are commonly understood. Our results clearly identify the different mechanisms with which water participates to denaturation

  20. Communication: Nanoscale electrostatic theory of epistructural fields at the protein-water interface

    NASA Astrophysics Data System (ADS)

    Fernández, Ariel

    2012-12-01

    Nanoscale solvent confinement at the protein-water interface promotes dipole orientations that are not aligned with the internal electrostatic field of a protein, yielding what we term epistructural polarization. To quantify this effect, an equation is derived from first principles relating epistructural polarization with the magnitude of local distortions in water coordination causative of interfacial tension. The equation defines a nanoscale electrostatic model of water and enables an estimation of protein denaturation free energies and the inference of hot spots for protein associations. The theoretical results are validated vis-à-vis calorimetric data, revealing the destabilizing effect of epistructural polarization and its molecular origin.

  1. Making water-soluble integral membrane proteins in vivo using an amphipathic protein fusion strategy.

    PubMed

    Mizrachi, Dario; Chen, Yujie; Liu, Jiayan; Peng, Hwei-Ming; Ke, Ailong; Pollack, Lois; Turner, Raymond J; Auchus, Richard J; DeLisa, Matthew P

    2015-01-01

    Integral membrane proteins (IMPs) play crucial roles in all cells and represent attractive pharmacological targets. However, functional and structural studies of IMPs are hindered by their hydrophobic nature and the fact that they are generally unstable following extraction from their native membrane environment using detergents. Here we devise a general strategy for in vivo solubilization of IMPs in structurally relevant conformations without the need for detergents or mutations to the IMP itself, as an alternative to extraction and in vitro solubilization. This technique, called SIMPLEx (solubilization of IMPs with high levels of expression), allows the direct expression of soluble products in living cells by simply fusing an IMP target with truncated apolipoprotein A-I, which serves as an amphipathic proteic 'shield' that sequesters the IMP from water and promotes its solubilization. PMID:25851941

  2. Making water-soluble integral membrane proteins in vivo using an amphipathic protein fusion strategy

    PubMed Central

    Mizrachi, Dario; Chen, Yujie; Liu, Jiayan; Peng, Hwei-Ming; Ke, Ailong; Pollack, Lois; Turner, Raymond J.; Auchus, Richard J.; DeLisa, Matthew P.

    2015-01-01

    Integral membrane proteins (IMPs) play crucial roles in all cells and represent attractive pharmacological targets. However, functional and structural studies of IMPs are hindered by their hydrophobic nature and the fact that they are generally unstable following extraction from their native membrane environment using detergents. Here we devise a general strategy for in vivo solubilization of IMPs in structurally relevant conformations without the need for detergents or mutations to the IMP itself, as an alternative to extraction and in vitro solubilization. This technique, called SIMPLEx (solubilization of IMPs with high levels of expression), allows the direct expression of soluble products in living cells by simply fusing an IMP target with truncated apolipoprotein A-I, which serves as an amphipathic proteic ‘shield' that sequesters the IMP from water and promotes its solubilization. PMID:25851941

  3. Neutron scattering evidence of a boson peak in protein hydration water Alessandro Paciaroni,1

    E-print Network

    Tuscia, Università Degli Studi Della

    around plas- tocyanin PC 1 , a copper containing protein involved in the photosynthetic processNeutron scattering evidence of a boson peak in protein hydration water Alessandro Paciaroni,1 Anna of H2O-hydrated plastocyanin relative to D2O-hydrated protein allowed us to reveal the presence

  4. SEPARATION OF WATER SOLUBLE PROTEINS FROM CEREALS BY FREE ZONE CAPILLARY ELECTROPHORESIS (FZCE)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Most research concerning grain proteins has concentrated upon the gluten storage proteins. The albumins and globulins are the water and salt soluble proteins that contain biologically active enzymes and enzyme inhibitors. A Free Zone Capillary electrophoresis method was developed to separate these p...

  5. Channel water balance and exchange with subsurface flow along a mountain headwater stream in Montana, United States

    USGS Publications Warehouse

    Payn, R.A.; Gooseff, M.N.; McGlynn, B.L.; Bencala, K.E.; Wondzell, S.M.

    2009-01-01

    Channel water balances of contiguous reaches along streams represent a poorly understood scale of stream-subsurface interaction. We measured reach water balances along a headwater stream in Montana, United States, during summer base flow recessions. Reach water balances were estimated from series of tracer tests in 13 consecutive reaches delineated evenly along a 2.6 km valley segment. For each reach, we estimated net change in discharge, gross hydrologic loss, and gross hydrologic gain from tracer dilution and mass recovery. Four series of tracer tests were performed during relatively high, intermediate, and low base flow conditions. The relative distribution of channel water along the stream was strongly related to a transition in valley structure, with a general increase in gross losses through the recession. During tracer tests at intermediate and low flows, there were frequent substantial losses of tracer mass (>10%) that could not be explained by net loss in flow over the reach, indicating that many of the study reaches were concurrently losing and gaining water. For example, one reach with little net change in discharge exchanged nearly 20% of upstream flow with gains and losses along the reach. These substantial bidirectional exchanges suggest that some channel interactions with subsurface flow paths were not measurable by net change in flow or transient storage of recovered tracer. Understanding bidirectional channel water balances in stream reaches along valleys is critical to an accurate assessment of stream solute fate and transport and to a full assessment of exchanges between the stream channel and surrounding subsurface. Copyright 2009 by the American Geophysical Union.

  6. Nighttime Cirrus Detection using Atmospheric Infrared Sounder Window Channels and Total Column Water Vapor

    NASA Technical Reports Server (NTRS)

    Kahn, Brian H.; Liou, Kuo Nan; Lee, Sung-Yung; Fishbein, Evan F.; DeSouza-Machado, Sergio; Eldering, Annmarie; Fetzer, Eric J.; Hannon, Scott E.; Strow, L. Larrabee

    2005-01-01

    A method of cirrus detection at nighttime is presented that utilizes 3.8 and 10.4 (micro)m infrared (IR) window brightness temperature differences (dBT) and total column precipitable water (PW) measurements. This technique is applied to the Atmospheric Infrared Sounder (AIRS) and Advanced Microwave Sounding Unit A (AMSU-A) instrument suite on board EOS-Aqua, where dBT is determined from sets of carefully selected AIRS window channels, while PW is derived from the synergistic AIRS and AMSU-A water vapor retrievals. Simulated and observed dBT for a particular value of PW are not constant; several physical factors impact dBT, including the variability in temperature and relative humidity profiles, surface emissivity, instrument noise, and skin/ near-surface air temperature differences. We simulate clear-sky dBT over a realistic range of PWs using 8350 radiosondes that have varying temperature and relative humidity profiles. Thresholds between cloudy and uncertain sky conditions are derived once the scatter in the clear-sky dBT is determined. Simulations of optically thin cirrus indicate that this technique is most sensitive to cirrus optical depth in the 10 (micro)m window of 0.1-0.15 or greater over the tropical and subtropical oceans, where surface emissivity and skin/near-surface air temperature impacts on the IR radiances are minimal. The method at present is generally valid over oceanic regions only, specifically, the tropics and subtropics. The detection of thin cirrus, and other cloud types, is validated using observations at the Atmospheric Radiation Measurement (ARM) program site located at Manus Island in the tropical western Pacific for 89 coincident EOS-Aqua overpasses. Even though the emphasis of this work is on the detection of thin cirrus at nighttime, this technique is sensitive to a broad cloud morphology. The cloud detection technique agrees with ARM-detected clouds 82-84% of the time, which include thin cirrus, as well as other cloud types. Most of the disagreements are well explained by AIRS footprint-scale heterogeneity compared to ARM point measurements, cirrus overlying lower-layer water clouds, possible mixed phase microphysics in midlevel clouds, and significant IR channel noise for cold BT scenes over deep convective towers.

  7. Coupled relaxations at the protein–water interface in the picosecond time scale

    PubMed Central

    Paciaroni, A.; Cornicchi, E.; Marconi, M.; Orecchini, A.; Petrillo, C.; Haertlein, M.; Moulin, M.; Sacchetti, F.

    2009-01-01

    The spectral behaviour of a protein and its hydration water has been investigated through neutron scattering. The availability of both hydrogenated and perdeuterated samples of maltose-binding protein (MBP) allowed us to directly measure with great accuracy the signal from the protein and the hydration water alone. Both the spectra of the MBP and its hydration water show two distinct relaxations, a behaviour that is reminiscent of glassy systems. The two components have been described using a phenomenological model that includes two Cole–Davidson functions. In MBP and its hydration water, the two relaxations take place with similar average characteristic times of approximately 10 and 0.2 ps. The common time scales of these relaxations suggest that they may be a preferential route to couple the dynamics of the water hydrogen-bond network around the protein surface with that of protein fluctuations. PMID:19640876

  8. Optimizing copper sulfate treatments for fungus control on channel catfish eggs in high alkalinity/moderate hardness water

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Interest in the use of copper sulfate (CuSO4) for fungus (Saprolegnia sp.) control in catfish hatcheries has developed over the past few years. A range-finding study was designed to determine the optimum concentration needed for fungus control on channel catfish eggs in 23.5°C well water at the Stu...

  9. Monitoring Water Quality at Lake Merritt, Oakland, CA Following Improvements to the Tidal Channel to the San Francisco Bay

    NASA Astrophysics Data System (ADS)

    Bracho, H.; Martinez, J.; Johnson, M.; Turrey, A.; Avila, M.; Medina, S.; Rubio, E.; Ahumada, E.; Nguyen, S.; Guzman, Y.

    2014-12-01

    Elliot Ahumada, Esosa Oghogho, Samantha Nguyen, Humberto Bracho, Diego Quintero, Ashanti Johnson and Kevin Cuff Lake Merritt is a tidal lagoon in the center of Oakland, California, just east of Downtown. Water quality at Lake Merritt has been a major concern for community members and researchers for many years (Pham 200X). Results of past research lead to recommendations to lengthen a channel that connects Lake Merritt with the San Francisco Bay to improve water flow and quality. In 2012 the City of Oakland responded to these recommendations by initiating the creation of a 230-meter long channel. In conducting our research we use a water quality index that takes into account measurements of pH, temperature, water hardness (dissolved solids), ammonia, salinity, dissolved oxygen, and nitrate. Newly collected data is then compared with that collected by Pham using comparable parameters to assess the impact of recent changes at the Lake on its overall water quality. In addition, we measured the abundance of aquatic species at four different sites within the Lake. Preliminary results suggest that an increase in the abundance of fish and improved overall water quality have resulted from channel extension at Lake Merritt.

  10. Assembly of water-soluble chlorophyll-binding proteins with native hydrophobic chlorophylls in water-in-oil emulsions.

    PubMed

    Bednarczyk, Dominika; Takahashi, Shigekazu; Satoh, Hiroyuki; Noy, Dror

    2015-03-01

    The challenges involved in studying cofactor binding and assembly, as well as energy- and electron transfer mechanisms in the large and elaborate transmembrane protein complexes of photosynthesis and respiration have prompted considerable interest in constructing simplified model systems based on their water-soluble protein analogs. Such analogs are also promising templates and building blocks for artificial bioinspired energy conversion systems. Yet, development is limited by the challenge of introducing the essential cofactors of natural proteins that are highly water-insoluble into the water-soluble protein analogs. Here we introduce a new efficient method based on water-in-oil emulsions for overcoming this challenge. We demonstrate the effectiveness of the method in the assembly of native chlorophylls with four recombinant variants of the water-soluble chlorophyll-binding protein of Brassicaceae plants. We use the method to gain new insights into the protein-chlorophyll assembly process, and demonstrate its potential as a fast screening system for developing novel chlorophyll-protein complexes. PMID:25511505

  11. Maternal protein restriction induces alterations in insulin signaling and ATP sensitive potassium channel protein in hypothalami of intrauterine growth restriction fetal rats

    PubMed Central

    Liu, Xiaomei; Qi, Ying; Gao, Hong; Jiao, Yisheng; Gu, Hui; Miao, Jianing; Yuan, Zhengwei

    2013-01-01

    It is well recognized that intrauterine growth restriction leads to the development of insulin resistance and type 2 diabetes mellitus in adulthood. To investigate the mechanisms behind this ”metabolic imprinting” phenomenon, we examined the impact of maternal undernutrition on insulin signaling pathway and the ATP sensitive potassium channel expression in the hypothalamus of intrauterine growth restriction fetus. Intrauterine growth restriction rat model was developed through maternal low protein diet. The expression and activated levels of insulin signaling molecules and KATP protein in the hypothalami which were dissected at 20 days of gestation, were analyzed by western blot and real time PCR. The tyrosine phosphorylation levels of the insulin receptor substrate 2 and phosphatidylinositol 3'-kinase p85? in the hypothalami of intrauterine growth restriction fetus were markedly reduced. There was also a downregulation of the hypothalamic ATP sensitive potassium channel subunit, sulfonylurea receptor 1, which conveys the insulin signaling. Moreover, the abundances of gluconeogenesis enzymes were increased in the intrauterine growth restriction livers, though no correlation was observed between sulfonylurea receptor 1 and gluconeogenesis enzymes. Our data suggested that aberrant intrauterine milieu impaired insulin signaling in the hypothalamus, and these alterations early in life might contribute to the predisposition of the intrauterine growth restriction fetus toward the adult metabolic disorders. PMID:23341697

  12. ( sup 3 H)phenamil binding protein of the renal epithelium Na+ channel. Purification, affinity labeling, and functional reconstitution

    SciTech Connect

    Barbry, P.; Chassande, O.; Marsault, R.; Lazdunski, M.; Frelin, C. )

    1990-01-30

    This paper describes a large-scale purification procedure of the amiloride binding component of the epithelium Na+ channel. (3H)Phenamil was used as a labeled ligand to follow the purification. The first two steps are identical with those previously described. A third step was a hydroxyapatite column. The purified material consisted of a homodimer of two 88-kDa proteins that migrated anomalously in SDS-PAGE to give an apparent Mr of 105,000. Deglycosylation by treatment with neuraminidase and endoglycosidase F or with neuraminidase and glycopeptidase F indicated that less than 5% of the mass of the native receptor was carbohydrate. Sedimentation analysis of the purified Na+ channel in H2O and D2O sucrose gradients and gel filtration experiments led to an estimated molecular weight of the (3H)phenamil receptor protein-detergent-phospholipid complex of 288,000 and of the native (3H)phenamil receptor protein of 158,000. (3H)Br-benzamil is another labeled derivative of amiloride that recognized binding sites that had the same pharmacological properties as (3H)phenamil binding sites and that copurified with them. Upon irradiation of kidney membranes, (3H)Br-benzamil incorporated specifically into a 185-kDa polypeptide chain under nonreducing electrophoretic conditions and a 105-kDa protein under reducing conditions. The same labeling pattern was observed at the different steps of the purification. Reconstitution of the purified phenamil receptor into large unilamellar vesicles was carried out. A low but significant phenamil- and amiloride-sensitive electrogenic Na+ transport was observed.

  13. The GTP- and Phospholipid-Binding Protein TTD14 Regulates Trafficking of the TRPL Ion Channel in Drosophila Photoreceptor Cells

    PubMed Central

    Cerny, Alexander C.; Altendorfer, André; Schopf, Krystina; Baltner, Karla; Maag, Nathalie; Sehn, Elisabeth; Wolfrum, Uwe; Huber, Armin

    2015-01-01

    Recycling of signaling proteins is a common phenomenon in diverse signaling pathways. In photoreceptors of Drosophila, light absorption by rhodopsin triggers a phospholipase C?-mediated opening of the ion channels transient receptor potential (TRP) and TRP-like (TRPL) and generates the visual response. The signaling proteins are located in a plasma membrane compartment called rhabdomere. The major rhodopsin (Rh1) and TRP are predominantly localized in the rhabdomere in light and darkness. In contrast, TRPL translocates between the rhabdomeral plasma membrane in the dark and a storage compartment in the cell body in the light, from where it can be recycled to the plasma membrane upon subsequent dark adaptation. Here, we identified the gene mutated in trpl translocation defective 14 (ttd14), which is required for both TRPL internalization from the rhabdomere in the light and recycling of TRPL back to the rhabdomere in the dark. TTD14 is highly conserved in invertebrates and binds GTP in vitro. The ttd14 mutation alters a conserved proline residue (P75L) in the GTP-binding domain and abolishes binding to GTP. This indicates that GTP binding is essential for TTD14 function. TTD14 is a cytosolic protein and binds to PtdIns(3)P, a lipid enriched in early endosome membranes, and to phosphatidic acid. In contrast to TRPL, rhabdomeral localization of the membrane proteins Rh1 and TRP is not affected in the ttd14P75L mutant. The ttd14P75L mutation results in Rh1-independent photoreceptor degeneration and larval lethality suggesting that other processes are also affected by the ttd14P75L mutation. In conclusion, TTD14 is a novel regulator of TRPL trafficking, involved in internalization and subsequent sorting of TRPL into the recycling pathway that enables this ion channel to return to the plasma membrane. PMID:26509977

  14. Polymodal sensory function of the Caenorhabditis elegans OCR-2 channel arises from distinct intrinsic determinants within the protein and is selectively conserved in mammalian TRPV proteins.

    PubMed

    Sokolchik, Irina; Tanabe, Takahiro; Baldi, Pierre F; Sze, Ji Ying

    2005-01-26

    Caenorhabditis elegans OCR-2 (OSM-9 and capsaicin receptor-related) is a TRPV (vanilloid subfamily of transient receptor potential channel) protein that regulates serotonin (5-HT) biosynthesis in chemosensory neurons and also mediates olfactory and osmotic sensation. Here, we identify the molecular basis for the polymodal function of OCR-2 in its native cellular environment. We show that OCR-2 function in 5-HT production and osmotic sensing is governed by its N-terminal region upstream of the ankyrin repeats domain, but the diacetyl sensitivity is mediated by independent mechanisms. The ocr-2(yz5) mutation results in a glycine-to-glutamate substitution (G36E) within the N-terminal region. The G36E substitution causes dramatic downregulation of 5-HT synthesis in the ADF neurons, eliminates osmosensation mediated by the ASH neurons, but does not affect the response to the odorant diacetyl mediated by the AWA neurons. Conversely, wild-type sequence of the N-terminal segment confers osmotic sensitivity and upregulation of 5-HT production to a normally insensitive C. elegans homolog, OCR-4, but this chimeric channel does not respond to diacetyl stimuli. Furthermore, expression of either the mouse or human TRPV2 gene under the ocr-2 promoter can substantially restore 5-HT biosynthesis in ocr-2-null mutants but cannot improve the deficits in osmotic or olfactory sensation, suggesting that TRPV2 can substitute for the role of OCR-2 only in serotonergic neurons. Thus, different sensory functions of OCR-2 arise from separable intrinsic determinants, and specific functional properties of TRPV channel proteins may be selectively conserved across phyla. PMID:15673683

  15. Expression and Function of Water Channels (Aquaporins) in Migrating Malignant Astrocytes

    PubMed Central

    McCOY, ERIC; SONTHEIMER, HARALD

    2008-01-01

    Aquaporins (AQP) constitute the principal pathway for water movement across biological membranes. Consequently, their expression and function is important for cell volume regulation. Glioma cells quickly adjust their cell volume in response to osmotic challenges or spontaneously as they invade into the narrow and tortuous extracellular spaces of the brain. These cell volume changes are likely to engage water movements across the cell membrane through AQP. AQP expression in glioma cells is poorly understood. In this study, we examined the expression of AQP in several commonly used human glioma cell lines (D54, D65, STTG1, U87, U251) and in numerous acute patient biopsies by PCR, Western blot, and immunocytochemistry and compared them to nonmalignant astrocytes and normal brain. All glioma patient biopsies expressed AQP1, AQP4 and some expressed AQP5. However, when isolated and grown as cell lines they lose all AQP proteins except a few cell lines that maintain expression of AQP1 (D65, U251, GBM62). Reintroducing either AQP1 or AQP4 stably into glioma cell lines allowed us to show that each AQP is sufficient to restore water permeability. Yet, only the presence of AQP1, but not AQP4, enhanced cell growth and migration, typical properties of gliomas, while AQP4 enhanced cell adhesion suggesting differential biological roles for AQP1 and AQP4 in glioma cell biology. PMID:17549682

  16. Requirement of Fra proteins for communication channels between cells in the filamentous nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120.

    PubMed

    Omairi-Nasser, Amin; Mariscal, Vicente; Austin, Jotham R; Haselkorn, Robert

    2015-08-11

    The filamentous nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120 differentiates specialized cells, heterocysts, that fix atmospheric nitrogen and transfer the fixed nitrogen to adjacent vegetative cells. Reciprocally, vegetative cells transfer fixed carbon to heterocysts. Several routes have been described for metabolite exchange within the filament, one of which involves communicating channels that penetrate the septum between adjacent cells. Several fra gene mutants were isolated 25 y ago on the basis of their phenotypes: inability to fix nitrogen and fragmentation of filaments upon transfer from N+ to N- media. Cryopreservation combined with electron tomography were used to investigate the role of three fra gene products in channel formation. FraC and FraG are clearly involved in channel formation, whereas FraD has a minor part. Additionally, FraG was located close to the cytoplasmic membrane and in the heterocyst neck, using immunogold labeling with antibody raised to the N-terminal domain of the FraG protein. PMID:26216997

  17. Hydrophilic microenvironment required for the channel-independent insertase function of YidC protein.

    PubMed

    Shimokawa-Chiba, Naomi; Kumazaki, Kaoru; Tsukazaki, Tomoya; Nureki, Osamu; Ito, Koreaki; Chiba, Shinobu

    2015-04-21

    The recently solved crystal structure of YidC protein suggests that it mediates membrane protein insertion by means of an intramembrane cavity rather than a transmembrane (TM) pore. This concept of protein translocation prompted us to characterize the native, membrane-integrated state of YidC with respect to the hydropathic nature of its TM region. Here, we show that the cavity-forming region of the stage III sporulation protein J (SpoIIIJ), a YidC homolog, is indeed open to the aqueous milieu of the Bacillus subtilis cells and that the overall hydrophilicity of the cavity, along with the presence of an Arg residue on several alternative sites of the cavity surface, is functionally important. We propose that YidC functions as a proteinaceous amphiphile that interacts with newly synthesized membrane proteins and reduces energetic costs of their membrane traversal. PMID:25855636

  18. Hydrophilic microenvironment required for the channel-independent insertase function of YidC protein

    PubMed Central

    Shimokawa-Chiba, Naomi; Kumazaki, Kaoru; Tsukazaki, Tomoya; Nureki, Osamu; Ito, Koreaki; Chiba, Shinobu

    2015-01-01

    The recently solved crystal structure of YidC protein suggests that it mediates membrane protein insertion by means of an intramembrane cavity rather than a transmembrane (TM) pore. This concept of protein translocation prompted us to characterize the native, membrane-integrated state of YidC with respect to the hydropathic nature of its TM region. Here, we show that the cavity-forming region of the stage III sporulation protein J (SpoIIIJ), a YidC homolog, is indeed open to the aqueous milieu of the Bacillus subtilis cells and that the overall hydrophilicity of the cavity, along with the presence of an Arg residue on several alternative sites of the cavity surface, is functionally important. We propose that YidC functions as a proteinaceous amphiphile that interacts with newly synthesized membrane proteins and reduces energetic costs of their membrane traversal. PMID:25855636

  19. Construction, characterization, expression and immune responses of flagellar proteins of channel catfish, important pathogen Edwardsiella ictaluri

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Edwardsiella ictaluri causes enteric septicemia of catfish, which is the leading disease in channel catfish (Ictalurus punctatus)and is responsible for $50 - 60 million economic losses to catfish producers annually in the southeastern U.S. Bacterial flagella are complex polymeric structu...

  20. Purification and subunit structure of a putative K sup + -channel protein identified by its binding properties for dendrotoxin I

    SciTech Connect

    Rehm, H.; Lazdunski, M. )

    1988-07-01

    The binding protein for the K{sup +}-channel toxin dendrotoxin I was purified from a detergent extract of rat brain membranes. The purification procedure utilized chromatography on DEAE-Trisacryl, affinity chromatography on a dendrotoxin-I-Aca 22 column, and wheat germ agglutinin-Affigel 10 with a final 3,800- to 4,600-fold enrichment and a recovery of 8-16%. The high affinity (K{sub d}, 40-100 pM) and specificity of the binding site are retained throughout the purification procedure. Analysis of the purified material on silver-stained NaDodSO{sub 4}/polyacrylamide gel revealed three bands of M{sub r} 76,000-80,000, 38,000 and 35,000. Interestingly, the binding site for {sup 125}I-labeled mast cell degranulating peptide, another putative K{sup +}-channel ligand from bee venom, which induces long-term potentiation in hippocampus, seems to reside on the same protein complex, as both binding sites copurify through the entire purification protocol.

  1. A two-channel, tunable diode laser-based hygrometer for measurement of water vapor and cirrus cloud ice water content in the upper troposphere and lower stratosphere

    NASA Astrophysics Data System (ADS)

    Thornberry, T. D.; Rollins, A. W.; Gao, R. S.; Watts, L. A.; Ciciora, S. J.; McLaughlin, R. J.; Fahey, D. W.

    2015-01-01

    The recently developed NOAA Water instrument is a two-channel, closed-path, tunable diode laser absorption spectrometer designed for the measurement of upper troposphere/lower stratosphere water vapor and enhanced total water (vapor + inertially enhanced condensed phase) from the NASA Global Hawk unmanned aircraft system (UAS) or other high-altitude research aircraft. The instrument utilizes wavelength-modulated spectroscopy with second harmonic detection near 2694 nm to achieve high precision with a 79 cm double-pass optical path. The detection cells are operated under constant temperature, pressure, and flow conditions to maintain a constant sensitivity to H2O independent of the ambient sampling environment. An onboard calibration system is used to perform periodic in situ calibrations to verify the stability of the instrument sensitivity during flight. For the water vapor channel, ambient air is sampled perpendicular to the flow past the aircraft in order to reject cloud particles, while the total water channel uses a heated, forward-facing inlet to sample both water vapor and cloud particles. The total water inlet operates subisokinetically, thereby inertially enhancing cloud particle number in the sample flow and affording increased cloud water content sensitivity. The NOAA Water instrument was flown for the first time during the second deployment of the Airborne Tropical TRopopause EXperiment (ATTREX) in February-March 2013 on the NASA Global Hawk UAS. The instrument demonstrated a typical in-flight precision (1 s, 1?) of better than 0.17 parts per million (ppm, 10-6 mol mol-1), with an overall H2O vapor measurement uncertainty of 5% ± 0.23 ppm. The inertial enhancement for cirrus cloud particle sampling under ATTREX flight conditions ranged from 33 to 48 for ice particles larger than 8 ?m in diameter, depending primarily on aircraft altitude. The resulting ice water content detection limit (2?) was 0.023-0.013 ppm, corresponding to approximately 2 ?g m-3, with an estimated overall uncertainty of 20%.

  2. Polyethylenimine modified poly(ethylene terephthalate) capillary channeled-polymer fibers for anion exchange chromatography of proteins.

    PubMed

    Jiang, Liuwei; Jin, Yi; Marcus, R Kenneth

    2015-09-01

    Native poly(ethylene terephthalate) (PET) capillary-channeled polymer (C-CP) fibers have been previously studied as stationary phases for reversed phase and affinity protein separations. In this study, surface modified PET C-CP fibers were evaluated for the anion exchange separation of proteins. The native PET C-CP fibers were aminated using polyethylenimine (PEI) followed by a 1,4-butanediol diglycidyl ether (BUDGE) cross-linking step. Subsequent PEI/BUDGE treatments can be employed to further develop the polyamine layer on the fiber surfaces. The PEI densities of the modified fibers were quantified through the ninhydrin reaction, yielding values of 0.43-0.89?molg(-1). The surface modification impact on column permeability was found to be 0.66×10(-11) to 1.33×10(-11)m(2), depending on the modification time and conditions. The dynamic binding capacities of the modified fiber media were determined to be 1.99-8.54mgmL(-1) bed volume, at linear velocities of 88-438cmmin(-1) using bovine serum albumin as the model protein. It was found that increasing the mobile phase linear velocity (up to 438cmmin(-1)) had no effect on the separation quality for a synthetic protein mixture, reflecting the lack of van Deemter C-term effects for the C-CP fiber phase. The low-cost, easy modification method and the capability of fast protein separation illustrate great potential in the use of PEI/BUDGE-modified PET C-CP fibers for high-throughput protein separation and downstream processing. PMID:26253835

  3. A New Criterion to Evaluate Water Vapor Interference in Protein Secondary Structural Analysis by FTIR Spectroscopy

    PubMed Central

    Zou, Ye; Ma, Gang

    2014-01-01

    Second derivative and Fourier self-deconvolution (FSD) are two commonly used techniques to resolve the overlapped component peaks from the often featureless amide I band in Fourier transform infrared (FTIR) curve-fitting approach for protein secondary structural analysis. Yet, the reliability of these two techniques is greatly affected by the omnipresent water vapor in the atmosphere. Several criteria are currently in use as quality controls to ensure the protein absorption spectrum is negligibly affected by water vapor interference. In this study, through a second derivative study of liquid water, we first argue that the previously established criteria cannot guarantee a reliable evaluation of water vapor interference due to a phenomenon that we refer to as sample’s absorbance-dependent water vapor interference. Then, through a comparative study of protein and liquid water, we show that a protein absorption spectrum can still be significantly affected by water vapor interference even though it satisfies the established criteria. At last, we propose to use the comparison between the second derivative spectra of protein and liquid water as a new criterion to better evaluate water vapor interference for more reliable second derivative and FSD treatments on the protein amide I band. PMID:24901531

  4. Membrane channel formation by the lymphocyte pore-forming protein: comparison between susceptible and resistant target cells

    PubMed Central

    1990-01-01

    The assembly of pores by the pore-forming protein (perforin) of cytolytic T lymphocytes (CTLs) and natural killer cells on the membranes of different cell lines was studied. Using the patch clamp technique in the whole cell configuration, we measured the conductance increase induced by perforin in susceptible cell lines as well as in resistant CTL lines (CTLLs). The results showed that although the amplitudes of the first observed conductance steps produced in both cell types were comparable, CTLLs required at least 10-fold higher doses of perforin to form membrane pores. Outside-out patches excised from CTLL-R8, on the other hand, appeared to be more susceptible to channel formation by perforin than intact cells, as lower doses were able to induce conductance increases. Once channels were induced in CTL membranes, however, their conductances (greater than 1 nS) were indistinguishable from the ones obtained in susceptible cell lines. Fluorescence measurements with quin-2 showed that perforin induced rapid increases in the intracellular Ca2+ concentration in susceptible EL4 cells. In marked contrast, a perforin dose 60-120-fold higher than the minimal dose required to elicit Ca2+ changes in EL4 cells was not able to induce any measurable Ca2+ increase in CTLL-R8. The data suggest that the resistance of CTLs to lysis mediated by their own mediator perforin is at least in part due to their ability to avoid pore formation by this protein. The mechanism underlying this phenomenon is not yet understood, but the observation that outside-out patches excised from CTLL-R8 are more susceptible to channel formation by perforin than intact cells raises the possibility that an intracellular mechanism may be involved. PMID:1693622

  5. Circulation, Water Temperature, and Larval Settlement Over the Inner Continental Shelves of the Santa Barbara Channel, California

    NASA Astrophysics Data System (ADS)

    Fewings, M. R.; Washburn, L.; Ohlmann, C.; Blanchette, C.; Caselle, J.; Gotschalk, C.

    2008-12-01

    We use seven-year time series of wind stress, water velocity, and temperature in 15-18 m water depth to describe the circulation and water temperature over the inner continental shelves of the Channel Islands and California mainland in the Santa Barbara Basin. This area is strongly influenced by the California Current upwelling system. In turn, the water circulation in the Santa Barbara Basin influences the local marine ecosystem by affecting the water temperature and the supply of nutrients and larval fish and invertebrates. Larvae and nutrients traveling from the coast to the open ocean and back again must somehow pass through the inner shelf. The water circulation over the inner continental shelf of the Northern Channel Islands has not been described. Due to the shallowness of the water, an inner shelf has different physical dynamics than either the surfzone or the middle and outer continental shelf. We discuss the relative importance of upwelling- favorable along-shelf winds and of cross-shelf winds as forcing mechanisms for coastal upwelling circulations over the inner shelf; test whether the cross-shelf wind stress and surface gravity waves are important for cross-shelf circulation in the Santa Barbara Basin; and describe the subtidal patterns of water temperature, stratification, and velocity around the Channel Islands and their relation to observed larval settlement patterns. Cross-shelf circulation and the movement of water masses into and out of the Basin have implications for settlement and recruitment of many coastal species, including the economically important kelp rockfish, kelp bass, and sea urchin. Understanding the circulation of the Santa Barbara Basin and its inner shelves is a precursor to determining the source locations of the planktonic larvae. That information on source locations is essential for the design, siting, and assessment of existing and future marine protected areas in California and elsewhere.

  6. A water level relationship between consecutive gauge stations along Solim\\~oes/Amazonas main channel: a wavelet approach

    E-print Network

    Somoza, R D; Novo, E M L; Rennó, C D

    2013-01-01

    Gauge stations are distributed along the Solim\\~oes/Amazonas main channel to monitor water level changes over time. Those measurements help quantify both the water movement and its variability from one gauge station to the next downstream. The objective of this study is to detect changes in the water level relationship between consecutive gauge stations along the Solim\\~oes/Amazonas main channel, since 1980. To carry out the analyses, data spanning from 1980 to 2010 from three consecutive gauges (Tefe, Manaus and Obidos) were used to compute standardized daily anomalies. In particular for infra-annual periods it was possible to detect changes for the water level variability along the Solim\\~oes/Amazonas main channel, by applying the Morlet Wavelet Transformation (WT) and Wavelet Cross Coherence (WCC) methods. It was possible to quantify the waves amplitude for the WT infra-annual scaled-period and were quite similar to the three gauge stations denoting that the water level variability are related to the same ...

  7. Active zone protein Bassoon co-localizes with presynaptic calcium channel, modifies channel function, and recovers from aging related loss by exercise.

    PubMed

    Nishimune, Hiroshi; Numata, Tomohiro; Chen, Jie; Aoki, Yudai; Wang, Yonghong; Starr, Miranda P; Mori, Yasuo; Stanford, John A

    2012-01-01

    The P/Q-type voltage-dependent calcium channels (VDCCs) are essential for synaptic transmission at adult mammalian neuromuscular junctions (NMJs); however, the subsynaptic location of VDCCs relative to active zones in rodent NMJs, and the functional modification of VDCCs by the interaction with active zone protein Bassoon remain unknown. Here, we show that P/Q-type VDCCs distribute in a punctate pattern within the NMJ presynaptic terminals and align in three dimensions with Bassoon. This distribution pattern of P/Q-type VDCCs and Bassoon in NMJs is consistent with our previous study demonstrating the binding of VDCCs and Bassoon. In addition, we now show that the interaction between P/Q-type VDCCs and Bassoon significantly suppressed the inactivation property of P/Q-type VDCCs, suggesting that the Ca(2+) influx may be augmented by Bassoon for efficient synaptic transmission at NMJs. However, presynaptic Bassoon level was significantly attenuated in aged rat NMJs, which suggests an attenuation of VDCC function due to a lack of this interaction between VDCC and Bassoon. Importantly, the decreased Bassoon level in aged NMJs was ameliorated by isometric strength training of muscles for two months. The training increased Bassoon immunoreactivity in NMJs without affecting synapse size. These results demonstrated that the P/Q-type VDCCs preferentially accumulate at NMJ active zones and play essential role in synaptic transmission in conjunction with the active zone protein Bassoon. This molecular mechanism becomes impaired by aging, which suggests altered synaptic function in aged NMJs. However, Bassoon level in aged NMJs can be improved by muscle exercise. PMID:22701595

  8. Water promotes the sealing of nanoscale packing defects in folding proteins.

    PubMed

    Fernández, Ariel

    2014-05-21

    A net dipole moment is shown to arise from a non-Debye component of water polarization created by nanoscale packing defects on the protein surface. Accordingly, the protein electrostatic field exerts a torque on the induced dipole, locally impeding the nucleation of ice at the protein-water interface. We evaluate the solvent orientation steering (SOS) as the reversible work needed to align the induced dipoles with the Debye electrostatic field and computed the SOS for the variable interface of a folding protein. The minimization of the SOS is shown to drive protein folding as evidenced by the entrainment of the total free energy by the SOS energy along trajectories that approach a Debye limit state where no torque arises. This result suggests that the minimization of anomalous water polarization at the interface promotes the sealing of packing defects, thereby maintaining structural integrity and committing the protein chain to fold. PMID:24769440

  9. Infrared spectral marker bands characterizing a transient water wire inside a hydrophobic membrane protein

    NASA Astrophysics Data System (ADS)

    Wolf, Steffen; Freier, Erik; Cui, Qiang; Gerwert, Klaus

    2014-12-01

    Proton conduction along protein-bound "water wires" is an essential feature in membrane proteins. Here, we analyze in detail a transient water wire, which conducts protons via a hydrophobic barrier within a membrane protein to create a proton gradient. It is formed only for a millisecond out of three water molecules distributed at inactive positions in a polar environment in the ground state. The movement into a hydrophobic environment causes characteristic shifts of the water bands reflecting their different chemical properties. These band shifts are identified by time-resolved Fourier Transform Infrared difference spectroscopy and analyzed by biomolecular Quantum Mechanical/Molecular Mechanical simulations. A non-hydrogen bonded ("dangling") O-H stretching vibration band and a broad continuum absorbance caused by a combined vibration along the water wire are identified as characteristic marker bands of such water wires in a hydrophobic environment. The results provide a basic understanding of water wires in hydrophobic environments.

  10. Infrared spectral marker bands characterizing a transient water wire inside a hydrophobic membrane protein

    SciTech Connect

    Wolf, Steffen; Gerwert, Klaus; Freier, Erik; Cui, Qiang

    2014-12-14

    Proton conduction along protein-bound “water wires” is an essential feature in membrane proteins. Here, we analyze in detail a transient water wire, which conducts protons via a hydrophobic barrier within a membrane protein to create a proton gradient. It is formed only for a millisecond out of three water molecules distributed at inactive positions in a polar environment in the ground state. The movement into a hydrophobic environment causes characteristic shifts of the water bands reflecting their different chemical properties. These band shifts are identified by time-resolved Fourier Transform Infrared difference spectroscopy and analyzed by biomolecular Quantum Mechanical/Molecular Mechanical simulations. A non-hydrogen bonded (“dangling”) O–H stretching vibration band and a broad continuum absorbance caused by a combined vibration along the water wire are identified as characteristic marker bands of such water wires in a hydrophobic environment. The results provide a basic understanding of water wires in hydrophobic environments.

  11. Aquaporins comprise a family of water-transporting membrane proteins. All aquaporins are efficient water transporters, while

    E-print Network

    de Groot, Bert

    of the membrane potential and intracellular pH requires that aquaporins inhibit the passage of ions, especially509 Aquaporins comprise a family of water-transporting membrane proteins. All aquaporins are efficient water transporters, while sustaining strict selectivity, even against protons, thereby maintaining

  12. Quantifying the Entropy of Binding for Water Molecules in Protein Cavities by Computing Correlations

    PubMed Central

    Huggins, David J.

    2015-01-01

    Protein structural analysis demonstrates that water molecules are commonly found in the internal cavities of proteins. Analysis of experimental data on the entropies of inorganic crystals suggests that the entropic cost of transferring such a water molecule to a protein cavity will not typically be greater than 7.0 cal/mol/K per water molecule, corresponding to a contribution of approximately +2.0 kcal/mol to the free energy. In this study, we employ the statistical mechanical method of inhomogeneous fluid solvation theory to quantify the enthalpic and entropic contributions of individual water molecules in 19 protein cavities across five different proteins. We utilize information theory to develop a rigorous estimate of the total two-particle entropy, yielding a complete framework to calculate hydration free energies. We show that predictions from inhomogeneous fluid solvation theory are in excellent agreement with predictions from free energy perturbation (FEP) and that these predictions are consistent with experimental estimates. However, the results suggest that water molecules in protein cavities containing charged residues may be subject to entropy changes that contribute more than +2.0 kcal/mol to the free energy. In all cases, these unfavorable entropy changes are predicted to be dominated by highly favorable enthalpy changes. These findings are relevant to the study of bridging water molecules at protein-protein interfaces as well as in complexes with cognate ligands and small-molecule inhibitors. PMID:25692597

  13. Unimolecular and hydrolysis channels for the detachment of water from microsolvated alkaline earth dication (Mg2+, Ca2+, Sr2+, Ba2+) clusters

    SciTech Connect

    Miliordos, Evangelos; Xantheas, Sotiris S.

    2014-02-07

    We examine theoretically the three channels that are associated with the detachment of a single water molecule from the aqueous clusters of the alkaline earth dications, [M(H2O)n]2+, M = Mg, Ca, Sr, Ba, n ? 6. These are the unimolecular water loss (M2+(H2O)n-1 + H2O) and the two hydrolysis channels resulting to the loss of hydronium ([MOH(H2O)n-2]+ + H3O+) and Zundel ([MOH(H2O)n-3]+ + H3O+(H2O)) cations. The Potential Energy Curves (PECs) corresponding to those three channels were constructed at the Møller-Plesset second order perturbation (MP2) level of theory with basis sets of double- and triple-? quality. We furthermore investigated the water and hydronium loss channels from the mono-hydroxide water clusters with up to four water molecules, [MOH(H2O)n]+, 1 ? n ? 4. Our results indicate the preference of the hydronium loss and possibly the Zundel cation loss channels for the smallest size clusters, whereas the unimolecular water loss channel is preferred for the larger ones as well as the mono-hydroxide clusters. Although the charge separation (hydronium and Zundel cation loss) channels produce more stable products when compared to the ones for the unimolecular water loss, they also require the surmounting of high energy barriers, a fact that makes the experimental observation of fragments related to these hydrolysis channels difficult.

  14. Shut-off of a geopressured water channel behind casing via coiled tubing utilizing a dual slurry cement system: A case history

    SciTech Connect

    Nowak, T.W.; Lange, K.J.; Grant, W.H.; Patout, T.S.

    1995-12-31

    This paper presents a case history involving a unique dual cement system to shut off a geopressured water channel behind casing utilizing coiled tubing. The channeling problem was identified and documented using water flow logging techniques. Logging indicated the lower gravel packed selective could produce salt water if perforated without eliminating the suspected water channel. Reserves did not warrant a major rig workover, making a non-rig workover via coiled tubing the only viable option to repair the well. A unique dual cement system tested on a hesitation squeeze schedule pumped through coiled tubing with extremely limited thickening time was necessary to repair the primary cement job.

  15. Calibration of the 1064 nm lidar channel using water phase and cirrus clouds.

    PubMed

    Wu, Yonghua; Gan, Chuen Meei; Cordero, Lina; Gross, Barry; Moshary, Fred; Ahmed, Sam

    2011-07-20

    Calibration is essential to derive aerosol backscatter coefficients from elastic scattering lidar. Unlike the visible UV wavelengths where calibration is based on a molecular reference, calibration of the 1064 nm lidar channel requires other approaches, which depend on various assumptions. In this paper, we analyze two independent calibration methods which use (i) low-altitude water phase clouds and (ii) high cirrus clouds. In particular, we show that to achieve optimal performance, aerosol attenuation below the cloud base and cloud multiple scattering must be accounted for. When all important processes are considered, we find that these two independent methods can provide a consistent calibration constant with relative differences less than 15%. We apply these calibration techniques to demonstrate the stability of our lidar on a monthly scale, along with a natural reduction of the lidar efficiency on an annual scale. Furthermore, our calibration procedure allows us to derive consistent aerosol backscatter coefficients and angstrom coefficient profiles (532-1064 nm) along with column extinction-to-backscatter ratios which are in good agreement with sky radiometer inversions. PMID:21772382

  16. Spinocerebellar ataxia-13 Kv3.3 potassium channels: arginine-to-histidine mutations affect both functional and protein expression on the cell surface.

    PubMed

    Zhao, Jian; Zhu, Jing; Thornhill, William B

    2013-09-01

    The voltage-gated potassium channel Kv3.3 is the causative gene of SCA13 (spinocerebellar ataxia type 13), an autosomal dominant neurological disorder. The four dominant mutations identified to date cause Kv3.3 channels to be non-functional or have altered gating properties in Xenopus oocytes. In the present paper, we report that SCA13 mutations affect functional as well as protein expression of Kv3.3 channels in a mammalian cell line. The reduced protein level of SCA13 mutants is caused by a shorter protein half-life, and blocking the ubiquitin-proteasome pathway increases the total protein of SCA13 mutants more than wild-type. SCA13 mutated amino acids are highly conserved, and the side chains of these residues play a critical role in the stable expression of Kv3.3 proteins. In addition, we show that mutant Kv3.3 protein levels could be partially rescued by treatment with the chemical chaperone TMAO (trimethylamine N-oxide) and to a lesser extent with co-expression of Kv3.1b. Thus our results suggest that amino acid side chains of SCA13 positions affect the protein half-life and/or function of Kv3.3, and the adverse effect on protein expression cannot be fully rescued. PMID:23734863

  17. Modes of sediment transport in channelized water flows with ramifications to the erosion of the Martian outflow channels

    NASA Technical Reports Server (NTRS)

    Komar, P. D.

    1980-01-01

    The paper discusses application to Martian water flows of the criteria that determine which grain-size ranges are transported as bed load, suspension, and wash load. The results show nearly all sand-sized material and finer would have been transported as wash load and that basalt pebbles and even cobbles could have been transported at rapid rates of suspension. An analysis of the threshold of sediment motion on Mars further indicates that the flows would have been highly competent, the larger flows having been able to transport boulder-sized material. Comparisons with terrestrial rivers which transport hyperconcentration levels of sediments suggest that the Martian water flows could have achieved sediment concentrations up to 70% in weight. Although it is possible that flows could have picked up enough sediment to convert to pseudolaminar mud flows, they probably remained at hyperconcentration levels and fully turbulent in flow character.

  18. Pore Hydration States of KcsA Potassium Channels in Membranes.

    PubMed

    Blasic, Joseph R; Worcester, David L; Gawrisch, Klaus; Gurnev, Philip; Mihailescu, Mihaela

    2015-10-30

    Water-filled hydrophobic cavities in channel proteins serve as gateways for transfer of ions across membranes, but their properties are largely unknown. We determined water distributions along the conduction pores in two tetrameric channels embedded in lipid bilayers using neutron diffraction: potassium channel KcsA and the transmembrane domain of M2 protein of influenza A virus. For the KcsA channel in the closed state, the distribution of water is peaked in the middle of the membrane, showing water in the central cavity adjacent to the selectivity filter. This water is displaced by the channel blocker tetrabutyl-ammonium. The amount of water associated with the channel was quantified, using neutron diffraction and solid state NMR. In contrast, the M2 proton channel shows a V-shaped water profile across the membrane, with a narrow constriction at the center, like the hourglass shape of its internal surface. These two types of water distribution are therefore very different in their connectivity to the bulk water. The water and protein profiles determined here provide important evidence concerning conformation and hydration of channels in membranes and the potential role of pore hydration in channel gating. PMID:26370089

  19. Thermal performance of Al2O3 in water - ethylene glycol nanofluid mixture as cooling medium in mini channel

    NASA Astrophysics Data System (ADS)

    Zakaria, Irnie Azlin; Mohamed, Wan Ahmad Najmi Wan; Mamat, Aman Mohd Ihsan; Sainan, Khairul Imran; Talib, Siti Fatimah Abu

    2015-08-01

    Continuous need for an optimum conversion efficiency of a Proton Exchange Membrane Fuel Cell (PEMFC) operation has triggered varieties of advancements namely on the thermal management engineering scope. Nanofluids as an innovative heat transfer fluid solution are expected to be a promising candidate for alternative coolant in mini channel cooling plate of PEMFC. In this work, heat transfer performance of low concentration of 0.1, 0.3 and 0.5 % Al2O3 in water: Ethylene glycol (EG) mixtures of 100:0 and 50:50 nanofluids have been studied and compared against its base fluids at Re number ranging from 10 to 100. A steady, laminar and incompressible flow with constant heat flux is assumed in the channel of 140mm × 200mm. It was found that nanofluids have performed better than the base fluid but the demerit is on the pumping power due to the higher pressure drop across mini channel geometry as expected.

  20. EARLY SENESCENCE1 Encodes a SCAR-LIKE PROTEIN2 That Affects Water Loss in Rice.

    PubMed

    Rao, Yuchun; Yang, Yaolong; Xu, Jie; Li, Xiaojing; Leng, Yujia; Dai, Liping; Huang, Lichao; Shao, Guosheng; Ren, Deyong; Hu, Jiang; Guo, Longbiao; Pan, Jianwei; Zeng, Dali

    2015-10-01

    The global problem of drought threatens agricultural production and constrains the development of sustainable agricultural practices. In plants, excessive water loss causes drought stress and induces early senescence. In this study, we isolated a rice (Oryza sativa) mutant, designated as early senescence1 (es1), which exhibits early leaf senescence. The es1-1 leaves undergo water loss at the seedling stage (as reflected by whitening of the leaf margin and wilting) and display early senescence at the three-leaf stage. We used map-based cloning to identify ES1, which encodes a SCAR-LIKE PROTEIN2, a component of the suppressor of cAMP receptor/Wiskott-Aldrich syndrome protein family verprolin-homologous complex involved in actin polymerization and function. The es1-1 mutants exhibited significantly higher stomatal density. This resulted in excessive water loss and accelerated water flow in es1-1, also enhancing the water absorption capacity of the roots and the water transport capacity of the stems as well as promoting the in vivo enrichment of metal ions cotransported with water. The expression of ES1 is higher in the leaves and leaf sheaths than in other tissues, consistent with its role in controlling water loss from leaves. GREEN FLUORESCENT PROTEIN-ES1 fusion proteins were ubiquitously distributed in the cytoplasm of plant cells. Collectively, our data suggest that ES1 is important for regulating water loss in rice. PMID:26243619

  1. Activation of K+ channels in renal medullary vesicles by cAMP-dependent protein kinase

    SciTech Connect

    Reeves, W.B.; McDonald, G.A.; Mehta, P.; Andreoli, T.E. )

    1989-07-01

    ADH, acting through cAMP, increases the potassium conductance of apical membranes of mouse medullary thick ascending limbs of Henle. The present studies tested whether exposure of renal medullary apical membranes in vitro to the catalytic subunit of cAMP-dependent protein kinase resulted in an increase in potassium conductance. Apical membrane vesicles prepared from rabbit outer renal medulla demonstrated bumetanide- and chloride-sensitive {sup 22}Na+ uptake and barium-sensitive, voltage-dependent {sup 86}Rb+ influx. When vesicles were loaded with purified catalytic subunit of cAMP-dependent protein kinase (150 mU/ml), 1 mM ATP, and 50 mM KCl, the barium-sensitive {sup 86}Rb+ influx increased from 361 {plus minus} 138 to 528 {plus minus} 120 pM/mg prot.30 sec (P less than 0.01). This increase was inhibited completely when heat-stable protein kinase inhibitor (1 microgram/ml) was also present in the vesicle solutions. The stimulation of {sup 86}Rb+ uptake by protein kinase required ATP rather than ADP. It also required opening of the vesicles by hypotonic shock, presumably to allow the kinase free access to the cytoplasmic face of the membranes. We conclude that cAMP-dependent protein kinase-mediated phosphorylation of apical membranes from the renal medulla increases the potassium conductance of these membranes. This mechanism may account for the ADH-mediated increase in potassium conductance in the mouse mTALH.

  2. Versatile multiple protein nanopatterning within a microfluidic channel for cell recruitment studies.

    PubMed

    Andersen, A S; Zheng, W F; Sutherland, D S; Jiang, X Y

    2015-12-21

    A novel approach combining self-assembly-based colloidal lithography and polydimethylsiloxane (PDMS) micromolding to generate complex protein nanopatterns for studying the mechanisms of leukocyte extravasation within microchannels is presented. Nanostructured surfaces sealed onto PDMS-molded microchannels are chemically functionalized in situ in an all-aqueous process to generate bi-functional chemical nanopatterns. Subsequent co-immobilization with proteins makes use of common non-covalent coupling (e.g. HIS-tags, FC-tags and biotin-tags), giving nanopatterns of arbitrary combinations of oriented, functional proteins. Up to three different proteins were simultaneously co-immobilized into the microchannel with nanoscale precision, demonstrating the complex patterns. As a proof-of-principle, a mimic of an inflamed endothelium was constructed using a macro- and nanoscale pattern of intercellular adhesion molecule 1 (ICAM1) and P-selectin, and the response of leukocytes through live cell imaging was measured. A clear result on the rolling behavior of the cells was observed with rolling limited to areas where ICAM1 and P-selectin are present. This micro/nano-interface will open new doors to investigations of how spatial distributions of proteins control cellular activity. PMID:26527486

  3. Trigonellae Semen Enhances Sperm Motility and the Expression of the Cation Sperm Channel Proteins in Mouse Testes

    PubMed Central

    Kim, Do Rim; Kim, Hyu Young; Kim, Ha Young; Chang, Mun Seog; Park, Seong Kyu

    2015-01-01

    Genetic defects during spermatogenesis can lead to a reduction in sperm motility and cause male infertility. The cation channels of sperm (CatSper) play a role in the regulation of hyperactivated sperm motility in mouse testes. The effect of Trigonellae Semen (TS) on the male reproductive system and CatSper protein in mouse testes during spermatogenesis was examined. C57BL/c mice were divided into the following five groups: normal, cyclophosphamide- (CP-) only treated (control group), and three groups treated with varying concentrations of TS with CP (100, 500, and 1000?mg/kg TS and 100?mg/kg CP). Real-time PCR, western blot analysis, and a testosterone immunoassay were performed to assess CatSper protein levels in the five groups. Additionally, sperm cell counts and motility were examined. Results indicate that sperm motility and sperm counts increased in the TS treated groups in a dose-dependent manner (p < 0.01). CatSper levels were also significantly higher in the TS treated groups compared to that of the control group (p < 0.001). Therefore, TS treatment could enhance sperm function by promoting spermatogenesis and the expression of CatSper proteins in mouse testes. PMID:26539234

  4. Retrieval of Temperature and Water Vapour From Multiple Channel Lidar Systems Using an Optimal Estimation Method

    NASA Astrophysics Data System (ADS)

    Sica, Robert; Haefele, Alexander

    2015-04-01

    While the application of optimal estimation methods (OEMs) is well-known for the retrieval of atmospheric parameters from passive instruments, active instruments have typically not employed the OEM. For instance, the measurement of temperature in the middle atmosphere with Rayleigh-scatter lidars is an important technique for assessing atmospheric change. Current retrieval schemes for these temperatures have several shortcomings which can be overcome using an OEM. Forward models have been constructed that fully characterize the measurement and allow the simultaneous retrieval of temperature, dead time and background. The OEM allows a full uncertainty budget to be obtained on a per profile basis that includes, in addition to the statistical uncertainties, the smoothing error and uncertainties due to Rayleigh extinction, ozone absorption, the lidar constant, nonlinearity in the counting system, variation of the Rayleigh-scatter cross section with altitude, pressure, acceleration due to gravity and the variation of mean molecular mass with altitude. The vertical resolution of the temperature profile is found at each height, and a quantitative determination is made of the maximum height to which the retrieval is valid. A single temperature profile can be retrieved from measurements with multiple channels that cover different height ranges, vertical resolutions and even different detection methods. The OEM employed is shown to give robust estimates of temperature consistent with previous methods, while requiring minimal computational time. Retrieval of water vapour mixing ratio from vibrational Raman scattering lidar measurements is another example where an OEM offers a considerable advantage over the standard analysis technique, with the same advantages as discussed above for Rayleigh-scatter temperatures but with an additional benefit. The conversion of the lidar measurement into mixing ratio requires a calibration constant to be employed. Using OEM the calibration constant can be retrieved if additional water vapour measurements, such as those provided by a radiosonde or microwave radiometer, are included. The success of lidar temperature and composition retrievals using an OEM opens new possibilities in atmospheric science for measurement integration between active and passive remote sensing instruments. This presentation will highlight some of these possibilities, as well as show temperature and water vapour retrievals from the MétéoSuisse Raman Lidar for Meteorological Observations and The University of Western Ontario's Purple Crow Lidar.

  5. Putting proteins back into water Paolo De Los Rios1

    E-print Network

    Caldarelli, Guido

    conceptual and practical relevance, since it could lead, for example, to high specificity drugs. Proteins of globular proteins is the hydrophobicity of nonpolar amino acids 3 . Consequently, the important properties . Hydrophobicity can be described as the tendency of hy- drophobic molecules to reduce as much as possible

  6. Nonlinear concentration gradients regulated by the width of channels for observation of half maximal inhibitory concentration (IC50) of transporter proteins.

    PubMed

    Abe, Yuta; Kamiya, Koki; Osaki, Toshihisa; Sasaki, Hirotaka; Kawano, Ryuji; Miki, Norihisa; Takeuchi, Shoji

    2015-08-21

    This paper describes a simple microfluidic device that can generate nonlinear concentration gradients. We changed the "width" of channels that can drastically shorten the total microfluidic channel length and simplify the microfluidic network design rather than the "length" of channels. The logarithmic concentration gradients generated by the device were in good agreement with those obtained by simulation. Using this device, we evaluated a probable IC50 value of the ABC transporter proteins by the competitive transport assays at five different logarithmic concentrations. This probable IC50 value was in good agreement with an IC50 value (0.92 ?M) obtained at the diluted concentrations of seven points. PMID:26153566

  7. Crystal Structure of the Mammalian GIRK2 K[superscript +] Channel and Gating Regulation by G Proteins, PIP[subscript 2], and Sodium

    SciTech Connect

    Whorton, Matthew R.; MacKinnon, Roderick

    2011-11-17

    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.

  8. SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters

    PubMed Central

    Lee, Po-Hsien; Kuo, Kuei-Ling; Chu, Pei-Ying; Liu, Eric M.; Lin, Jung-Hsin

    2009-01-01

    Many proteins use a long channel to guide the substrate or ligand molecules into the well-defined active sites for catalytic reactions or for switching molecular states. In addition, substrates of membrane transporters can migrate to another side of cellular compartment by means of certain selective mechanisms. SLITHER (http://bioinfo.mc.ntu.edu.tw/slither/or http://slither.rcas.sinica.edu.tw/) is a web server that can generate contiguous conformations of a molecule along a curved tunnel inside a protein, and the binding free energy profile along the predicted channel pathway. SLITHER adopts an iterative docking scheme, which combines with a puddle-skimming procedure, i.e. repeatedly elevating the potential energies of the identified global minima, thereby determines the contiguous binding modes of substrates inside the protein. In contrast to some programs that are widely used to determine the geometric dimensions in the ion channels, SLITHER can be applied to predict whether a substrate molecule can crawl through an inner channel or a half-channel of proteins across surmountable energy barriers. Besides, SLITHER also provides the list of the pore-facing residues, which can be directly compared with many genetic diseases. Finally, the adjacent binding poses determined by SLITHER can also be used for fragment-based drug design. PMID:19433508

  9. SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters.

    PubMed

    Lee, Po-Hsien; Kuo, Kuei-Ling; Chu, Pei-Ying; Liu, Eric M; Lin, Jung-Hsin

    2009-07-01

    Many proteins use a long channel to guide the substrate or ligand molecules into the well-defined active sites for catalytic reactions or for switching molecular states. In addition, substrates of membrane transporters can migrate to another side of cellular compartment by means of certain selective mechanisms. SLITHER (http://bioinfo.mc.ntu.edu.tw/slither/or http://slither.rcas.sinica.edu.tw/) is a web server that can generate contiguous conformations of a molecule along a curved tunnel inside a protein, and the binding free energy profile along the predicted channel pathway. SLITHER adopts an iterative docking scheme, which combines with a puddle-skimming procedure, i.e. repeatedly elevating the potential energies of the identified global minima, thereby determines the contiguous binding modes of substrates inside the protein. In contrast to some programs that are widely used to determine the geometric dimensions in the ion channels, SLITHER can be applied to predict whether a substrate molecule can crawl through an inner channel or a half-channel of proteins across surmountable energy barriers. Besides, SLITHER also provides the list of the pore-facing residues, which can be directly compared with many genetic diseases. Finally, the adjacent binding poses determined by SLITHER can also be used for fragment-based drug design. PMID:19433508

  10. The decomposition of the Faroe-Shetland Channel water masses using Parametric Optimum Multi-Parameter analysis

    NASA Astrophysics Data System (ADS)

    McKenna, C.; Berx, B.; Austin, W. E. N.

    2016-01-01

    The Faroe-Shetland Channel (FSC) is an important conduit for the poleward flow of Atlantic water towards the Nordic Seas and, as such, it plays an integral part in the Atlantic's thermohaline circulation. Mixing processes in the FSC are thought to result in an exchange of properties between the channel's inflow and outflow, with wider implications for this circulation; the nature of this mixing in the FSC is, however, uncertain. To constrain this uncertainty, we used a novel empirical method known as Parametric Optimum Multi-Parameter (POMP) analysis to objectively quantify the distribution of water masses in the channel in May 2013. This was achieved by using a combination of temperature and salinity measurements, as well as recently available nutrient and ?18O measurements. The outcomes of POMP analysis are in good agreement with established literature and demonstrate the benefits of representing all five water masses in the FSC. In particular, our results show the recirculation of Modified North Atlantic Water in the surface layers, and the pathways of Norwegian Sea Arctic Intermediate Water and Norwegian Sea Deep Water from north to south for the first time. In a final step, we apply the mixing fractions from POMP analysis to decompose the volume transport through the FSC by water mass. Despite a number of caveats, our study suggests that improved estimates of the volume transport of Atlantic inflow towards the Arctic and, thus, the associated poleward fluxes of salt and heat are possible. A new prospect to more accurately monitor the strength of the FSC branch of the thermohaline circulation emerges from this study.

  11. Quantifying the effects of stream channels on storm water quality in a semi-arid urban environment

    NASA Astrophysics Data System (ADS)

    Gallo, Erika L.; Lohse, Kathleen A.; Brooks, Paul D.; McIntosh, Jennifer C.; Meixner, Thomas; McLain, Jean E. T.

    2012-11-01

    SummaryStormwater drainage systems can have a large effect on urban runoff quality, but it is unclear how ephemeral urban streams alter runoff hydrochemistry. This problem is particularly relevant in semi-arid regions, where urban storm runoff is considered a renewable water resource. Here we address the question: how do stream channels alter urban runoff hydrochemistry? We collected synoptic stormwater samples during three rainfall-runoff events from nine ephemeral streams reaches (three concrete or metal, three grass, three gravel) in Tucson, Arizona. We identified patterns of temporal and spatial (longitudinal) variability in concentrations of conservative (chloride and isotopes of water) and reactive solutes (inorganic-N, soluble reactive phosphorous, sulfate-S, dissolved organic carbon (DOC) and nitrogen, and fecal indicator bacteria). Water isotopes and chloride (Cl) concentrations indicate that solute flushing and evapoconcentration alter temporal patterns in runoff hydrochemistry, but not spatial hydrochemical responses. Solute concentrations and stream channel solute sourcing and retention during runoff were significantly more variable at the grass reaches (CV = 2.3 - 144%) than at the concrete or metal (CV = 1.6 - 107%) or gravel reaches (CV = 1.9 - 60%), which functioned like flow-through systems. Stream channel soil Cl and DOC decreased following a runoff event (Cl: 12.1-7.3 ?g g-1 soil; DOC: 87.7-30.1 ?g g-1 soil), while soil fecal indicator bacteria counts increased (55-215 CFU g-1 soil). Finding from this study suggest that the characteristics of the ephemeral stream channel substrate control biogeochemical reactions between runoff events, which alter stream channel soil solute stores and the hydrochemistry of subsequent runoff events.

  12. Experimental and numerical characterization of the water flow in spacer-filled channels of spiral-wound membranes.

    PubMed

    Bucs, Szilard S; Valladares Linares, Rodrigo; Marston, Jeremy O; Radu, Andrea I; Vrouwenvelder, Johannes S; Picioreanu, Cristian

    2015-12-15

    Micro-scale flow distribution in spacer-filled flow channels of spiral-wound membrane modules was determined with a particle image velocimetry system (PIV), aiming to elucidate the flow behaviour in spacer-filled flow channels. Two-dimensional water velocity fields were measured in a flow cell (representing the feed spacer-filled flow channel of a spiral wound reverse osmosis membrane module without permeate production) at several planes throughout the channel height. At linear flow velocities (volumetric flow rate per cross-section of the flow channel considering the channel porosity, also described as crossflow velocities) used in practice (0.074 and 0.163 m·s(-1)) the recorded flow was laminar with only slight unsteadiness in the upper velocity limit. At higher linear flow velocity (0.3 m·s(-1)) the flow was observed to be unsteady and with recirculation zones. Measurements made at different locations in the flow cell exhibited very similar flow patterns within all feed spacer mesh elements, thus revealing the same hydrodynamic conditions along the length of the flow channel. Three-dimensional (3-D) computational fluid dynamics simulations were performed using the same geometries and flow parameters as the experiments, based on steady laminar flow assumption. The numerical results were in good agreement (0.85-0.95 Bray-Curtis similarity) with the measured flow fields at linear velocities of 0.074 and 0.163 m·s(-1), thus supporting the use of model-based studies in the optimization of feed spacer geometries and operational conditions of spiral wound membrane systems. PMID:26433778

  13. Dipole Moment and Binding Energy of Water in Proteins from Crystallographic Analysis

    PubMed Central

    2015-01-01

    The energetics of water molecules in proteins is studied using the water placement software Dowser. We compared the water position predictions for 14 high-resolution crystal structures of oligopeptide-binding protein (OppA) containing a large number of resolved internal water molecules. From the analysis of the outputs of Dowser with variable parameters and comparison with experimental X-ray data, we derived an estimate of the average dipole moment of water molecules located in the internal cavities of the protein and their binding energies. The water parameters thus obtained from the experimental data are then analyzed within the framework of charge-scaling theory developed recently by this group; the parameters are shown to be in good agreement with the predictions that the theory makes for the dipole moment in a protein environment. The water dipole in the protein environment is found to be much different from that in the bulk and in such models as SPC or TIPnP. The role of charge scaling due to electronic polarizability of the protein is discussed. PMID:25328496

  14. Estimation of uncertainties in the spectral response function of the water vapor channel of a meteorological imager

    NASA Astrophysics Data System (ADS)

    Ahn, Myoung-Hwan; Lee, Su Jeong; Kim, Dohyeong

    2015-06-01

    The five channel meteorological imager (MI) on-board the geostationary Communication, Ocean, and Meteorological Satellite (COMS) of Korea has been operationally used since April 2011. For a better utilization of the MI data, a rigorous characterization of the four infrared channel data has been conducted using the GSICS (Global Space-based Inter-Calibration System) approach with the IASI (Infrared Atmospheric Sounding Interferometer) on-board the European Metop satellite as the reference instrument. Although all four channels show the uncertainty characteristics that are in line with the results from both the ground tests and the in-orbit-test, there shows an unexpected systematic bias in the water vapor channel of MI, showing a cold bias at the warm target temperature and a warm bias with the cold target temperature. It has been shown that this kind of systematic bias could be introduced by the uncertainties in the spectral response function (SRF) of the specific channel which is similar to the heritage instruments on-board GOES series satellite. An extensive radiative transfer simulation using a radiative transfer model has confirmed that the SRF uncertainty could indeed introduce such a systematic bias. By using the collocated data set consisting of the MI data and the hyperspectral IASI data, the first order correction value for the SRF uncertainty is estimated to be about 2.79 cm-1 shift of the central position of the current SRF.

  15. Detection of differential fetal and adult expression of chloride intracellular channel 4 (CLIC4) protein by analysis of a green fluorescent protein knock-in mouse line

    PubMed Central

    2014-01-01

    Background Chloride Intracellular Channel 4 (CLIC4) is one of seven members in the closely related CLIC protein family. CLIC4 is involved in multiple cellular processes including apoptosis, cellular differentiation, inflammation and endothelial tubulogenesis. Despite over a decade of research, no comprehensive in situ expression analysis of CLIC4 in a living organism has been reported. In order to fulfill this goal, we generated a knock-in mouse to express Green Fluorescent Protein (GFP) from the CLIC4 locus, thus substituting the GFP coding region for CLIC4. We used GFP protein expression to eliminate cross reaction with other CLIC family members. Results We analyzed CLIC4 expression during embryonic development and adult organs. During mid and late gestation, CLIC4 expression is modulated particularly in fetal brain, heart, thymus, liver and kidney as well as in developing brown adipose tissue and stratifying epidermis. In the adult mouse, CLIC4 is highly expressed globally in vascular endothelial cells as well as in liver, lung alveolar septae, pancreatic acini, spermatogonia, renal proximal tubules, cardiomyocytes and thymic epithelial cells. Neural expression included axonal tracks, olfactory bulb, Purkinje cell layer and dentate gyrus. Renal CLIC4 expression was most pronounced in proximal tubules, although altered renal function was not detected in the absence of CLIC4. Myeloid cells and B cells of the spleen are rich in CLIC4 expression as are CD4 and CD8 positive T cells. Conclusions In a comprehensive study detailing CLIC4 expression in situ in a mouse model that excludes cross reaction with other family members, we were able to document previously unreported expression for CLIC4 in developing fetus, particularly the brain. In addition, compartmentalized expression of CLIC4 in specific adult tissues and cells provides a focus to explore potential functions of this protein not addressed previously. PMID:24886590

  16. Calcium Channels

    NASA Astrophysics Data System (ADS)

    Corry, Ben; Hool, Livia

    Ion channels underlie the electrical activity of cells. Calcium channels have a unique functional role, because not only do they participate in this activity, they form the means bywhich electrical signals are converted to responses within the cell. Calcium concentrations in the cytoplasm of cells are maintained at a low level, and calcium channels activate quickly such that the opening of ion channels can rapidly change the cytoplasmic environment. Once inside the cell, calcium acts as a "second messenger" prompting responses by binding to a variety of calcium sensitive proteins. Calcium channels are known to play an important role in stimulating muscle contraction, in neurotransmitter secretion, gene regulation, activating other ion channels, controlling the shape and duration of action potentials and many other processes. Since calcium plays an integral role in cell function, and since excessive quantities can be toxic, its movement is tightly regulated and controlled through a large variety of mechanisms.

  17. Numerical investigation of the Sicily Channel dynamics: density currents and water mass advection

    E-print Network

    Ozgökmen, Tamay M.

    strength of the Tyrrhenian and Sicilian MAW branches. The transport across the Channel is found to increase Channel and Ionian Sea), while the highest values correspond to more remote density values, i and West- ern Mediterranean Sea, playing an important role in the dynamics of the Mediterranean general

  18. Copper-based micro-channel cooler reliably operated using solutions of distilled-water and ethanol as a coolant

    NASA Astrophysics Data System (ADS)

    Chin, A. K.; Nelson, A.; Chin, R. H.; Bertaska, R.; Jacob, J. H.

    2015-03-01

    Copper-based micro-channel coolers (Cu-MCC) are the lowest thermal-resistance heat-sinks for high-power laserdiode (LD) bars. Presently, the resistivity, pH and oxygen content of the de-ionized water coolant, must be actively controlled to minimize cooler failure by corrosion and electro-corrosion. Additionally, the water must be constantly exposed to ultraviolet radiation to limit the growth of micro-organisms that may clog the micro-channels. In this study, we report the reliable, care-free operation of LD-bars attached to Cu-MCCs, using a solution of distilledwater and ethanol as the coolant. This coolant meets the storage requirements of Mil-Std 810G, e.g. exposure to a storage temperature as low as -51°C and no growth of micro-organisms during passive storage.

  19. Observation of ice-like water layers at an aqueous protein surface

    PubMed Central

    Meister, Konrad; Strazdaite, Simona; DeVries, Arthur L.; Lotze, Stephan; Olijve, Luuk L. C.; Voets, Ilja K.; Bakker, Huib J.

    2014-01-01

    We study the properties of water at the surface of an antifreeze protein with femtosecond surface sum frequency generation spectroscopy. We find clear evidence for the presence of ice-like water layers at the ice-binding site of the protein in aqueous solution at temperatures above the freezing point. Decreasing the temperature to the biological working temperature of the protein (0 °C to ?2 °C) increases the amount of ice-like water, while a single point mutation in the ice-binding site is observed to completely disrupt the ice-like character and to eliminate antifreeze activity. Our observations indicate that not the protein itself but ordered ice-like water layers are responsible for the recognition and binding to ice. PMID:25468976

  20. Bidirectional Transformation of a Metamorphic Protein between the Water-Soluble and Transmembrane Native States.

    PubMed

    Tanaka, Koji; Caaveiro, Jose M M; Tsumoto, Kouhei

    2015-11-24

    The bidirectional transformation of a protein between its native water-soluble and integral transmembrane conformations is demonstrated for FraC, a hemolytic protein of the family of pore-forming toxins. In the presence of biological membranes, the water-soluble conformation of FraC undergoes a remarkable structural reorganization generating cytolytic transmembrane nanopores conducive to cell death. So far, the reverse transformation from the native transmembrane conformation to the native water-soluble conformation has not been reported. We describe the use of detergents with different physicochemical properties to achieve the spontaneous conversion of transmembrane pores of FraC back into the initial water-soluble state. Thermodynamic and kinetic stability data suggest that specific detergents cause an asymmetric change in the energy landscape of the protein, allowing the bidirectional transformation of a membrane protein. PMID:26544760

  1. Observation of ice-like water layers at an aqueous protein surface.

    PubMed

    Meister, Konrad; Strazdaite, Simona; DeVries, Arthur L; Lotze, Stephan; Olijve, Luuk L C; Voets, Ilja K; Bakker, Huib J

    2014-12-16

    We study the properties of water at the surface of an antifreeze protein with femtosecond surface sum frequency generation spectroscopy. We find clear evidence for the presence of ice-like water layers at the ice-binding site of the protein in aqueous solution at temperatures above the freezing point. Decreasing the temperature to the biological working temperature of the protein (0 °C to -2 °C) increases the amount of ice-like water, while a single point mutation in the ice-binding site is observed to completely disrupt the ice-like character and to eliminate antifreeze activity. Our observations indicate that not the protein itself but ordered ice-like water layers are responsible for the recognition and binding to ice. PMID:25468976

  2. Rab27a negatively regulates CFTR chloride channel function in colonic epithelia: Involvement of the effector proteins in the regulatory mechanism

    SciTech Connect

    Saxena, Sunil K. . E-mail: ssaxena@stevens.edu; Kaur, Simarna

    2006-07-21

    Cystic fibrosis, an autosomal recessive disorder, is caused by the disruption of biosynthesis or function of CFTR. CFTR regulatory mechanisms include channel transport to plasma membrane and protein-protein interactions. Rab proteins are small GTPases involved in vesicle transport, docking, and fusion. The colorectal epithelial HT-29 cells natively express CFTR and respond to cAMP with an increase in CFTR-mediated currents. DPC-inhibited currents could be completely eliminated with CFTR-specific SiRNA. Over-expression of Rab27a inhibited, while isoform specific SiRNA and Rab27a antibody stimulated CFTR-mediated currents in HT-29 cells. CFTR activity is inhibited both by Rab27a (Q78L) (constitutive active GTP-bound form of Rab27a) and Rab27a (T23N) (constitutive negative form that mimics the GDP-bound form). Rab27a mediated effects could be reversed by Rab27a-binding proteins, the synaptotagmin-like protein (SLP-5) and Munc13-4 accessory protein (a putative priming factor for exocytosis). The SLP reversal of Rab27a effect was restricted to C2A/C2B domains while the SHD motif imparted little more inhibition. The CFTR-mediated currents remain unaffected by Rab3 though SLP-5 appears to weakly bind it. The immunoprecipitation experiments suggest protein-protein interactions between Rab27a and CFTR. Rab27a appears to impair CFTR appearance at the cell surface by trapping CFTR in the intracellular compartments. Munc13-4 and SLP-5, on the other hand, limit Rab27a availability to CFTR, thus minimizing its effect on channel function. These observations decisively prove that Rab27a is involved in CFTR channel regulation through protein-protein interactions involving Munc13-4 and SLP-5 effector proteins, and thus could be a potential target for cystic fibrosis therapy.

  3. Channel catfish

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This book chapter provides a comprehensive overview of channel catfish aquaculture. Sections include fish biology; commercial culture; culture facilities; production practices; water quality management; nutrition, feeding and feed formulation; infectious diseases; harvesting and processing; and the...

  4. Molecular Determinants within N Terminus of Orai3 Protein That Control Channel Activation and Gating*

    PubMed Central

    Bergsmann, Judith; Derler, Isabella; Muik, Martin; Frischauf, Irene; Fahrner, Marc; Pollheimer, Philipp; Schwarzinger, Clemens; Gruber, Hermann J.; Groschner, Klaus; Romanin, Christoph

    2011-01-01

    STIM1 and Orai represent the key components of Ca2+ release-activated Ca2+ channels. Activation of Orai channels requires coupling of the C terminus of STIM1 to the N and C termini of Orai. Although the latter appears to be central in the interaction with STIM1, the role of the N terminus and particularly of the conserved region close to the first transmembrane sequence is less well understood. Here, we investigated in detail the functional role of this conserved region in Orai3 by stepwise deletions. Molecular determinants were mapped for the two modes of Orai3 activation via STIM1 or 2-aminoethoxydiphenyl borate (2-APB) and for current gating characteristics. Increasing N-terminal truncations revealed a progressive decrease of the specific fast inactivation of Orai3 concomitant with diminished binding to calmodulin. STIM1-dependent activation of Orai3 was maintained as long as the second half of this conserved N-terminal domain was present. Further truncations abolished it, whereas Orai3 stimulation via 2-APB was partially retained. In aggregate, the N-terminal conserved region plays a multifaceted role in Orai3 current gating with distinct structural requirements for STIM1- and 2-APB-stimulated activation. PMID:21724845

  5. Modulation of firing and synaptic transmission of serotonergic neurons by intrinsic G protein-coupled receptors and ion channels

    PubMed Central

    Maejima, Takashi; Masseck, Olivia A.; Mark, Melanie D.; Herlitze, Stefan

    2013-01-01

    Serotonergic neurons project to virtually all regions of the central nervous system and are consequently involved in many critical physiological functions such as mood, sexual behavior, feeding, sleep/wake cycle, memory, cognition, blood pressure regulation, breathing, and reproductive success. Therefore, serotonin release and serotonergic neuronal activity have to be precisely controlled and modulated by interacting brain circuits to adapt to specific emotional and environmental states. We will review the current knowledge about G protein-coupled receptors and ion channels involved in the regulation of serotonergic system, how their regulation is modulating the intrinsic activity of serotonergic neurons and its transmitter release and will discuss the latest methods for controlling the modulation of serotonin release and intracellular signaling in serotonergic neurons in vitro and in vivo. PMID:23734105

  6. The involvement of actin, calcium channels and exocytosis proteins in somato-dendritic oxytocin and vasopressin release

    PubMed Central

    Tobin, Vicky; Leng, Gareth; Ludwig, Mike

    2012-01-01

    Hypothalamic magnocellular neurons release vasopressin and oxytocin not only from their axon terminals into the blood, but also from their somata and dendrites into the extracellular space of the brain, and this can be regulated independently. Differential release of neurotransmitters from different compartments of a single neuron requires subtle regulatory mechanisms. Somato-dendritic, but not axon terminal release can be modulated by changes in intracellular calcium concentration [(Ca2+)] by release of calcium from intracellular stores, resulting in priming of dendritic pools for activity-dependent release. This review focuses on our current understanding of the mechanisms of priming and the roles of actin remodeling, voltage-operated calcium channels (VOCCs) and SNARE proteins in the regulation somato-dendritic and axon terminal peptide release. PMID:22934017

  7. Protein kinase C regulates the activity of voltage-sensitive calcium channels of the rat chromaffin cells

    SciTech Connect

    Wakade, A.R.; Malhotra, R.K.; Wakade, T.D.

    1986-03-05

    Phorbol dibutyrate (PB), an activator of protein kinase C was used as a tool to study the role of protein kinase C in the secretion of catecholamines (CA) from the perfused adrenal gland of rat. Secretion of CA evoked by splanchnic nerve stimulation, nicotine (N), carbamylcholine (C) and 35 mM K (K) was enhanced (about 2-fold) by 30 nM PB, but that evoked by muscarine (M) was not. In Ca-free and 1 mM EGTA Krebs solution, N and M did not evoke secretion, and PB also had no effect. If Ca concentration of the perfusion medium was maintained at 0.1 mM, N-evoked secretion was reduced over 80% but M-evoked secretion was still about 60% of the control value. Addition of PB to this medium did not modify secretion evoked by M, but N-evoked secretion was facilitated by 3-fold. Ca/sup 45/ flux data showed that N-, C-, and K-evoked secretion of CA was associated with 2- to 3-fold increase in Ca/sup 45/ uptake. However, M-evoked secretion did not cause Ca/sup 45/ uptake. These results suggest that N utilizes extracellular whereas M utilizes mostly intracellular Ca ions for the secretion of CA. PB alone did not affect Ca/sup 45/ uptake, but after stimulation with N, C and K, Ca/sup 45/ uptake was further enhanced by PB. It is concluded that protein kinase C phosphorylates membrane proteins that control opening and closing of Ca channels regulated by nicotine receptors and changes in membrane potentials.

  8. Evidence of Distinct Channel Conformations and Substrate Binding Affinities for the Mitochondrial Outer Membrane Protein Translocase Pore Tom40.

    PubMed

    Kuszak, Adam J; Jacobs, Daniel; Gurnev, Philip A; Shiota, Takuya; Louis, John M; Lithgow, Trevor; Bezrukov, Sergey M; Rostovtseva, Tatiana K; Buchanan, Susan K

    2015-10-23

    Nearly all mitochondrial proteins are coded by the nuclear genome and must be transported into mitochondria by the translocase of the outer membrane complex. Tom40 is the central subunit of the translocase complex and forms a pore in the mitochondrial outer membrane. To date, the mechanism it utilizes for protein transport remains unclear. Tom40 is predicted to comprise a membrane-spanning ?-barrel domain with conserved ?-helical domains at both the N and C termini. To investigate Tom40 function, including the role of the N- and C-terminal domains, recombinant forms of the Tom40 protein from the yeast Candida glabrata, and truncated constructs lacking the N- and/or C-terminal domains, were functionally characterized in planar lipid membranes. Our results demonstrate that each of these Tom40 constructs exhibits at least four distinct conductive levels and that full-length and truncated Tom40 constructs specifically interact with a presequence peptide in a concentration- and voltage-dependent manner. Therefore, neither the first 51 amino acids of the N terminus nor the last 13 amino acids of the C terminus are required for Tom40 channel formation or for the interaction with a presequence peptide. Unexpectedly, substrate binding affinity was dependent upon the Tom40 state corresponding to a particular conductive level. A model where two Tom40 pores act in concert as a dimeric protein complex best accounts for the observed biochemical and electrophysiological data. These results provide the first evidence for structurally distinct Tom40 conformations playing a role in substrate recognition and therefore in transport function. PMID:26336107

  9. Extended-gate field-effect transistor packed in micro channel for glucose, urea and protein biomarker detection.

    PubMed

    Lin, Yen-Heng; Chu, Chih-Pin; Lin, Chen-Fu; Liao, Hsin-Hao; Tsai, Hann-Huei; Juang, Ying-Zong

    2015-12-01

    This study developed a packaging method to integrate the extended-gate field-effect transistor (EGFET) into a microfluidic chip as a biological sensor. In addition, we present two immobilization approaches for the bio-recognition that are appropriate to this chip, allowing it to measure the concentrations of hydrogen ions, glucose, urea, and specific proteins in a solution. Alginate-calcium microcubes were used to embed the enzymes and magnetic powder (enzyme carrier). When the sensing chip needs the enzyme for the catalytic reaction, the alginate microcubes containing the corresponding enzymes enter through the flow channel and are immobilized on the EGFET surface with an external magnet. High sensing performance of the chip is achieved, with 37.45 mV/mM for measuring hydrogen ions at pH 6-8 with a linearity of 0.9939, 7.00 mV/mM for measuring glucose with a linearity of 0.9962, and 8.01 mV/mM for measuring urea with a linearity of 0.9809. In addition, based on the principle of the immunoassay, the magnetic beads with the specific antibody were used to capture the target protein in the sample. Then, negatively charged DNA fragments bound to a secondary antibody were used to amplify the signal for EGFET measurement. The magnetic beads with completed immune response bonding were then fixed on the surface of the sensor by an external magnetic field. Therefore, the measured object can directly contact the sensor surface, and quantitative detection of the protein concentration can be achieved. Apolipoprotein A1 (APOA1) was detected as a target protein, with a minimum detection limit of approximately 12.5 ng/mL. PMID:26553100

  10. Voltage-Gated R-Type Calcium Channel Inhibition via Human ?-, ?-, and ?-opioid Receptors Is Voltage-Independently Mediated by G?? Protein Subunits.

    PubMed

    Berecki, Géza; Motin, Leonid; Adams, David J

    2016-01-01

    Elucidating the mechanisms that modulate calcium channels via opioid receptor activation is fundamental to our understanding of both pain perception and how opioids modulate pain. Neuronal voltage-gated N-type calcium channels (Cav2.2) are inhibited by activation of G protein-coupled opioid receptors (ORs). However, inhibition of R-type (Cav2.3) channels by ?- or ?-ORs is poorly defined and has not been reported for ?-ORs. To investigate such interactions, we coexpressed human ?-, ?-, or ?-ORs with human Cav2.3 or Cav2.2 in human embryonic kidney 293 cells and measured depolarization-activated Ba(2+) currents (IBa). Selective agonists of ?-, ?-, and ?-ORs inhibited IBa through Cav2.3 channels by 35%. Cav2.2 channels were inhibited to a similar extent by ?-ORs, but more potently (60%) via ?- and ?-ORs. Antagonists of ?- and ?-ORs potentiated IBa amplitude mediated by Cav2.3 and Cav2.2 channels. Consistent with G protein ?? (G??) interaction, modulation of Cav2.2 was primarily voltage-dependent and transiently relieved by depolarizing prepulses. In contrast, Cav2.3 modulation was voltage-independent and unaffected by depolarizing prepulses. However, Cav2.3 inhibition was sensitive to pertussis toxin and to intracellular application of guanosine 5'-[?-thio]diphosphate trilithium salt and guanosine 5'-[?-thio]triphosphate tetralithium salt. Coexpression of G??-specific scavengers-namely, the carboxyl terminus of the G protein-coupled receptor kinase 2 or membrane-targeted myristoylated-phosducin-attenuated or abolished Cav2.3 modulation. Our study reveals the diversity of OR-mediated signaling at Cav2 channels and identifies neuronal Cav2.3 channels as potential targets for opioid analgesics. Their novel modulation is dependent on pre-existing OR activity and mediated by membrane-delimited G?? subunits in a voltage-independent manner. PMID:26490245

  11. Regulation of neuronal voltage-gated sodium channels by the ubiquitin-protein ligases Nedd4 and Nedd4-2.

    PubMed

    Fotia, Andrew B; Ekberg, Jenny; Adams, David J; Cook, David I; Poronnik, Philip; Kumar, Sharad

    2004-07-01

    Nedd4 and Nedd4-2 are ubiquitin-protein ligases known to regulate a number of membrane proteins including receptors and ion transporters. Regulation of the epithelial Na(+) channel by Nedd4 and Nedd4-2 is mediated via interactions between the PY motifs of the epithelial sodium channel subunits and the Nedd4/Nedd4-2 WW domains. This example serves as a model for the regulation of other PY motif-containing ion channels by Nedd4 and Nedd4-2. We found that the carboxyl termini of the six voltage-gated Na(+) (Na(v)) channels contain typical PY motifs (PPXY), and a further Na(v) contains a PY motif variant (LPXY). Not only did we demonstrate by Far-Western analysis that Nedd4 and Nedd4-2 interact with the PY motif-containing Na(v) channels, but we also showed that these channels have conserved WW domain binding specificity. We further showed that the carboxyl termini fusion proteins of one central nervous system and one peripheral nervous system-derived Na(+) channel (Na(v)1.2 and Na(v)1.7, respectively) are readily ubiquitinated by Nedd4-2. In Xenopus oocytes, Nedd4-2 strongly inhibited the activities of all three Na(v)s (Na(v)1.2, Na(v)1.7, and Na(v)1.8) tested. Interestingly, Nedd4 suppressed the activity of Na(v)1.2 and Na(v)1.7 but was a poor inhibitor of Na(v)1.8. Our results provide evidence that Nedd4 and Nedd4-2 are likely to be key regulators of specific neuronal Na(v) channels in vivo. PMID:15123669

  12. Molecular Dynamics Analysis of Lysozyme Protein in Ethanol-Water Mixed Solvent Environment

    NASA Astrophysics Data System (ADS)

    Ochije, Henry Ikechukwu

    Effect of protein-solvent interaction on the protein structure is widely studied using both experimental and computational techniques. Despite such extensive studies molecular level understanding of proteins and some simple solvents is still not fully understood. This work focuses on detailed molecular dynamics simulations to study of solvent effect on lysozyme protein, using water, alcohol and different concentrations of water-alcohol mixtures as solvents. The lysozyme protein structure in water, alcohol and alcohol-water mixture (0-12% alcohol) was studied using GROMACS molecular dynamics simulation code. Compared to water environment, the lysozome structure showed remarkable changes in solvents with increasing alcohol concentration. In particular, significant changes were observed in the protein secondary structure involving alpha helices. The influence of alcohol on the lysozyme protein was investigated by studying thermodynamic and structural properties. With increasing ethanol concentration we observed a systematic increase in total energy, enthalpy, root mean square deviation (RMSD), and radius of gyration. a polynomial interpolation approach. Using the resulting polynomial equation, we could determine above quantities for any intermediate alcohol percentage. In order to validate this approach, we selected an intermediate ethanol percentage and carried out full MD simulation. The results from MD simulation were in reasonably good agreement with that obtained using polynomial approach. Hence, the polynomial approach based method proposed here eliminates the need for computationally intensive full MD analysis for the concentrations within the range (0-12%) studied in this work.

  13. The Origins of Transmembrane Ion Channels

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Wilson, Michael A.

    2012-01-01

    Even though membrane proteins that mediate transport of ions and small molecules across cell walls are among the largest and least understood biopolymers in contemporary cells, it is still possible to shed light on their origins and early evolution. The central observation is that transmembrane portions of most ion channels are simply bundles of -helices. By combining results of experimental and computer simulation studies on synthetic models and natural channels, mostly of non-genomic origin, we show that the emergence of -helical channels was protobiologically plausible, and did not require highly specific amino acid sequences. Despite their simple structure, such channels could possess properties that, at the first sight, appear to require markedly larger complexity. Specifically, we explain how the antiamoebin channels, which are made of identical helices, 16 amino acids in length, achieve efficiency comparable to that of highly evolved channels. We further show that antiamoebin channels are extremely flexible, compared to modern, genetically coded channels. On the basis of our results, we propose that channels evolved further towards high structural complexity because they needed to acquire stable rigid structures and mechanisms for precise regulation rather than improve efficiency. In general, even though architectures of membrane proteins are not nearly as diverse as those of water-soluble proteins, they are sufficiently flexible to adapt readily to the functional demands arising during evolution.

  14. The kappa opioid receptor agonist U-50488 blocks Ca2+ channels in a voltage-and G protein-independent manner in sensory neurons

    PubMed Central

    Hassan, Bassil; Ruiz-Velasco, Victor

    2012-01-01

    Background and Objectives Kappa opioid receptor (?-OR) activation is known to play a role in analgesia and central sedation. The purpose of the present study was to examine the effect of the ?-OR agonist, U-50488 (an arylacetamide), on Ca2+ channel currents and the signaling proteins involved in acutely isolated rat dorsal root ganglia (DRG) neurons expressing the putative promoter region of the tetrodotoxin (TTX)-resistant Na+ channel (NaV 1.8) that is known to be involved in pain transmission. Methods Acutely isolated rat DRG neurons were transfected with cDNA coding for enhanced green fluorescent protein (EGFP), whose expression is driven by the Nav 1.8 promoter region. Thereafter, the whole-cell variant of the patch-clamp technique was employed to record Ca2+ channel currents in neurons expressing EGFP. Results Exposure of EGFP-expressing DRG neurons to U-50488 (0.3 to 40 ?M) led to voltage-independent inhibition of the Ca2+ channel currents. The modulation of the Ca2+ currents did not appear to be mediated by the G? protein subfamilies: G?i/o, G?s, G?q/11, G?14 and G?z. Furthermore, dialysis of the hydrolysis-resistant GDP analog, GDP-?-S (1 mM), did not affect the U-50488-mediated blocking effect, ruling out involvement of other G protein subunits. Finally, U-50488 (20 ?M) blocked Ca2+ channels heterologously expressed in HeLa cells that do not express ?-OR. Conclusion These results suggest that the antinociceptive actions mediated by U-50488 are likely due to both a direct block of Ca2+ channels in sensory neurons as well as G protein modulation of Ca2+ currents via ?-OR-expressing neurons. PMID:23222359

  15. Water organization between oppositely charged surfaces: Implications for protein sliding along DNA a)

    NASA Astrophysics Data System (ADS)

    Marcovitz, Amir; Naftaly, Aviv; Levy, Yaakov

    2015-02-01

    Water molecules are abundant in protein-DNA interfaces, especially in their nonspecific complexes. In this study, we investigated the organization and energetics of the interfacial water by simplifying the geometries of the proteins and the DNA to represent them as two equally and oppositely charged planar surfaces immersed in water. We found that the potential of mean force for bringing the two parallel surfaces into close proximity comprises energetic barriers whose properties strongly depend on the charge density of the surfaces. We demonstrated how the organization of the water molecules into discretized layers and the corresponding energetic barriers to dehydration can be modulated by the charge density on the surfaces, salt, and the structure of the surfaces. The 1-2 layers of ordered water are tightly bound to the charged surfaces representing the nonspecific protein-DNA complex. This suggests that water might mediate one-dimensional diffusion of proteins along DNA (sliding) by screening attractive electrostatic interactions between the positively charged molecular surface on the protein and the negatively charged DNA backbone and, in doing so, reduce intermolecular friction in a manner that smoothens the energetic landscape for sliding, and facilitates the 1D diffusion of the protein.

  16. Interlayer Water Regulates the Bio-nano Interface of a \\b{eta}-sheet Protein stacking on Graphene

    E-print Network

    Wenping Lv; Guiju Xu; Hongyan Zhang; Xin Li; Shengju Liu; Huan Niu; Dongsheng Xu; Renan Wu

    2014-12-03

    Using molecular dynamics simulations, we investigated an integrated bio-nano interface consisting of a \\b{eta}-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...{\\pi} 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.

  17. Molecular Dynamics Study of Hydration Water Behavior in Blue Copper Protein

    NASA Astrophysics Data System (ADS)

    Sugiyama, Ayumu; Takamatsu, Yuichiro; Purqon, Acep; Mizukami, Taku; Nagao, Hidemi; Nishikawa, Kiyoshi

    2006-05-01

    We carry out the molecular dynamics(MD) simulation of type 1 blue copper protein azurin in room and some lower temperatures to investigate the behavior of hydration water molecules in the protein surface. In this study, we find the anomalous behavior of the water molecules , which depend on the system temperatures. These water molecules have hydrogen bond to the protein surface residues. We specify the residues type, being classified as the hydration donor and the hydration acceptor of water molecules. We analyze the residue type, and the bond length and bond strength between solvent water molecules in each temperature. Moreover, we estimate the B-factor of these residues which indicates the fluctuation of hydration residues in each temperature. B-factor values depend on the system temperatue althought the number of hydration residue do not depend on the temperature.

  18. Analysis of ocean color components within stratified and well-mixed waters of the western English Channel

    NASA Technical Reports Server (NTRS)

    Hochmann, Herschel T.; Walsh, John J.; Carder, Kendall L.; Sournia, A.; Muller-Karger, Frank E.

    1995-01-01

    In situ pigment and dissolved organic carbon (DOC) data from two distinct hydrographic regions of the western English Channel are used to explore the possible marine DOC contamination of the past satellite estimates of phytoplankton biomass. To compare with field measurements, the individual spectral contributions of DOC, pigments, and water to the total diffuse attenuation coefficient, K(sub par), are summed on a quantum basis within stratified waters near Plymouth, England; and for the spectrally averaged diffuse attenuation coefficient, K(sub d), on an energy basis within tidally mixed waters near Roscoff, France. In addition, coastal zone color scanner (CZCS) images from 1979 to 1986 were used to compute DOC concentrations for comparison with in situ values. Our analysis suggests that almost 50% of the color signal of satellite-sensed pigments may be attributed to absorption by marine colored DOC (CDOC) within the English Channel. These results compare favorably to the in situ DOC measurements off Plymouth, but not to off-Roscoff measurements, suggesting that there may be more CDOC in the stratified waters and more nonabsorbing DOC in the tidally mixed waters.

  19. Electron crystallography of PhoE porin, an outer membrane, channel- forming protein from E. coli

    SciTech Connect

    Walian, P.J.

    1989-11-01

    One approach to studying the structure of membrane proteins is the use of electron crystallography. Dr. Bing Jap has crystallized PhoE pore-forming protein (porin) from the outer membrane of escherichia coli (E. coli) into monolayer crystals. The findings of this research and those of Jap (1988, 1989) have determined these crystals to be highly ordered, yielding structural information to a resolution of better than 2.8 angstroms. The task of this thesis has been to collect and process the electron diffraction patterns necessary to generate a complete three-dimensional set of high resolution structure factor amplitudes of PhoE porin. Fourier processing of these amplitudes when combined with the corresponding phase data is expected to yield the three-dimensional structure of PhoE porin at better than 3.5 angstroms resolution. 92 refs., 33 figs., 3 tabs. (CBS)

  20. Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein.

    PubMed

    Kuffel, Anna; Czapiewski, Dariusz; Zielkiewicz, Jan

    2015-10-01

    The dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties of solvation water of ice around its two crystallographic planes: basal and prism. Three main conclusions are inferred from our investigations. The first one is that the solvation shell of CfAFP does not seem to be particularly far-ranged, at least not beyond what is usually observed for proteins that do not interact with ice. Therefore, it does not appear to us that the antifreeze activity is enhanced by a long-ranged retardation of water mobility. Also the correlation between the collective mobility of water and the collective mobility of protein atoms highly resembles the one measured for the protein that does not interact with ice. Our second conclusion is that the dynamical properties of solvation water of CfAFP are non-uniform. The dynamics of solvation water of ice-binding plane is, in some respects, different from the dynamics of solvation water of the two remaining planes. The feature that distinguishes the dynamics of solvation water of the three planes is the activation energy of diffusion process. The third conclusion is that-from the three analyzed solvation shells of CfAFP-the dynamical properties of solvation water of the ice-binding plane resemble the most the properties of solvation water of ice; note, however, that these properties still clearly differ from the dynamic properties of solvation water of ice. PMID:26450333

  1. Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein

    NASA Astrophysics Data System (ADS)

    Kuffel, Anna; Czapiewski, Dariusz; Zielkiewicz, Jan

    2015-10-01

    The dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties of solvation water of ice around its two crystallographic planes: basal and prism. Three main conclusions are inferred from our investigations. The first one is that the solvation shell of CfAFP does not seem to be particularly far-ranged, at least not beyond what is usually observed for proteins that do not interact with ice. Therefore, it does not appear to us that the antifreeze activity is enhanced by a long-ranged retardation of water mobility. Also the correlation between the collective mobility of water and the collective mobility of protein atoms highly resembles the one measured for the protein that does not interact with ice. Our second conclusion is that the dynamical properties of solvation water of CfAFP are non-uniform. The dynamics of solvation water of ice-binding plane is, in some respects, different from the dynamics of solvation water of the two remaining planes. The feature that distinguishes the dynamics of solvation water of the three planes is the activation energy of diffusion process. The third conclusion is that—from the three analyzed solvation shells of CfAFP—the dynamical properties of solvation water of the ice-binding plane resemble the most the properties of solvation water of ice; note, however, that these properties still clearly differ from the dynamic properties of solvation water of ice.

  2. Liquid water quantification in the cathode side gas channels of a proton exchange membrane fuel cell through two-phase flow visualization

    NASA Astrophysics Data System (ADS)

    Banerjee, Rupak; Kandlikar, Satish G.

    2014-02-01

    Water management is crucial to the performance of PEM fuel cells. Water is generated as part of the electrochemical reaction, and is removed through the reactant channels. This results in two-phase flow in the reactant channels. Increased understanding of the behavior of the liquid water in the channels allows us to devise better strategies for managing the water content inside the fuel cell. Most previous work has been focused on qualitative information regarding flow pattern maps. The current work presents new algorithms developed in MATLAB® to quantify the liquid water and to identify the flow patterns in the cathode side reactant channels. Parallel channels with dimensions matching those of commercial stacks have been used in this study. The liquid water present in the reactant channels is quantified for different temperature, inlet RH and current density conditions, and the results are presented in terms of area coverage ratio. The dominant flow patterns for the different conditions have been mapped, and trends interpreted on the basis of air flow velocities and saturation conditions within the channels.

  3. The effects of channel diameter on flow pattern, void fraction and pressure drop of two-phase air-water flow in circular micro-channels

    SciTech Connect

    Saisorn, Sira; Wongwises, Somchai

    2010-05-15

    Two-phase air-water flow characteristics are experimentally investigated in horizontal circular micro-channels. Test sections are made of fused silica. The experiments are conducted based on three different inner diameters of 0.53, 0.22 and 0.15 mm with the corresponding lengths of 320, 120 and 104 mm, respectively. The test runs are done at superficial velocities of gas and liquid ranging between 0.37-42.36 and 0.005-3.04 m/s, respectively. The flow visualisation is facilitated by systems mainly including stereozoom microscope and high-speed camera. The flow regime maps developed from the observed flow patterns are presented. The void fractions are determined based on image analysis. New correlation for two-phase frictional multiplier is also proposed for practical applications. (author)

  4. Coupling of protein and hydration-water dynamics in biological membranes

    PubMed Central

    Wood, K.; Plazanet, M.; Gabel, F.; Kessler, B.; Oesterhelt, D.; Tobias, D. J.; Zaccai, G.; Weik, M.

    2007-01-01

    The dynamical coupling between proteins and their hydration water is important for the understanding of macromolecular function in a cellular context. In the case of membrane proteins, the environment is heterogeneous, composed of lipids and hydration water, and the dynamical coupling might be more complex than in the case of the extensively studied soluble proteins. Here, we examine the dynamical coupling between a biological membrane, the purple membrane (PM), and its hydration water by a combination of elastic incoherent neutron scattering, specific deuteration, and molecular dynamics simulations. Examining completely deuterated PM, hydrated in H2O, allowed the direct experimental exploration of water dynamics. The study of natural abundance PM in D2O focused on membrane dynamics. The temperature-dependence of atomic mean-square displacements shows inflections at 120 K and 260 K for the membrane and at 200 K and 260 K for the hydration water. Because transition temperatures are different for PM and hydration water, we conclude that ps–ns hydration water dynamics are not directly coupled to membrane motions on the same time scale at temperatures <260 K. Molecular-dynamics simulations of hydrated PM in the temperature range from 100 to 296 K revealed an onset of hydration-water translational diffusion at ?200 K, but no transition in the PM at the same temperature. Our results suggest that, in contrast to soluble proteins, the dynamics of the membrane protein is not controlled by that of hydration water at temperatures <260 K. Lipid dynamics may have a stronger impact on membrane protein dynamics than hydration water. PMID:17986611

  5. In silico studies of the properties of water hydrating a small protein

    SciTech Connect

    Sinha, Sudipta Kumar; Chakraborty, Kausik; Bandyopadhyay, Sanjoy; Jana, Madhurima

    2014-12-14

    Atomistic molecular dynamics simulation of an aqueous solution of the small protein HP-36 has been carried out with explicit solvent at room temperature. Efforts have been made to explore the influence of the protein on the relative packing and ordering of water molecules around its secondary structures, namely, three ?-helices. The calculations reveal that the inhomogeneous water ordering and density distributions around the helices are correlated with their relative hydrophobicity. Importantly, we have identified the existence of a narrow relatively dehydrated region containing randomly organized “quasi-free” water molecules beyond the first layer of “bound” waters at the protein surface. These water molecules with relatively weaker binding energies form the transition state separating the “bound” and “free” water molecules at the interface. Further, increased contribution of solid-like caging motions of water molecules around the protein is found to be responsible for reduced fluidity of the hydration layer. Interestingly, we notice that the hydration layer of helix-3 is more fluidic with relatively higher entropy as compared to the hydration layers of the other two helical segments. Such characteristics of helix-3 hydration layer correlate well with the activity of HP-36, as helix-3 contains the active site of the protein.

  6. Structural and Thermodynamic Characteristics That Seed Aggregation of Amyloid-? Protein in Water.

    PubMed

    Chong, Song-Ho; Park, Mirae; Ham, Sihyun

    2012-02-14

    Amyloid-? (A?) proteins undergo conformational transitions leading to aggregation-prone structures, which can initiate self-assembly to form soluble oligomers and eventually insoluble amyloid fibrils when transferred from the transmembrane phase to the physiological aqueous phase. Yet, how A? proteins acquire an aggregation-prone nature during the conformational transitions in water remains elusive. Here, we investigate key structural and thermodynamic features of a 42-residue A? (A?42) protein that seed aggregation based on the fully atomistic, explicit-water molecular dynamics simulations as well as on the integral-equation theory of liquids for solvation thermodynamic analysis. We performed a structure-based analysis on the solvation free energy, a major determinant of the protein hydrophobicity/solubility that influences the aggregation propensity of A?42 protein in water. In addition, the Gibbs free energy and its constituents including protein internal energy, protein configurational entropy, solvation enthalpy, and solvation entropy were computed to elucidate thermodynamic driving forces for the conformational transitions of A?42 protein in water. On the basis of the atomic-decomposition analysis of these thermodynamic functions, we demonstrate how N-terminal (residues 1-11) and C-terminal (39-42) regions as well as the central region (16-18) contribute significantly to decreasing the solubility of A?42 protein upon its conformational transitions in water. These results are consistent with the recent experimental and computational implications and further provide the molecular origin for why the C terminus may serve as an "internal seed" for aggregation and the N-terminal segment may act as a "catalyst" in inducing the A?42 self-assembly. This work takes a step forward toward the identification of structural and thermodynamic features of the A?42 monomer that seed the aggregation process in water. PMID:26596619

  7. Protein fouling behavior of carbon nanotube/polyethersulfone composite membranes during water filtration.

    PubMed

    Celik, Evrim; Liu, Lei; Choi, Heechul

    2011-10-15

    The protein fouling of membranes can be related to the hydrophobic and electrostatic interactions between proteins and the membrane material; i.e., protein fouling can be reduced by changing the membrane properties. In this study, multi-walled carbon nanotube/polyethersulfone (C/P) composite membranes were prepared via the phase inversion method in order to investigate protein fouling, with bovine serum albumin (BSA) and ovalbumin (OVA) used as the model protein for assessing the protein fouling behavior. The results show that the C/P composite membranes were fouled less compared to the bare polyethersulfone (PES) membrane at 4 h of static protein adsorption at neutral pH. Moreover, the irreversible fouling ratio of the C/P composite membranes was less than the bare PES membrane after 1 h of protein ultrafiltration, and the flux recovery ratio of the C/P composite membranes was higher than the bare PES membrane after 20 min of DI water filtration. Based on these results, C/P composite membranes were shown to have the potential to alleviate the effects of protein fouling, thereby enabling C/P composite membranes to be used for several runs of protein filtration after simple washing with water. PMID:21862096

  8. The G protein-coupled receptor-transient receptor potential channel axis: molecular insights for targeting disorders of sensation and inflammation.

    PubMed

    Veldhuis, Nicholas A; Poole, Daniel P; Grace, Megan; McIntyre, Peter; Bunnett, Nigel W

    2015-01-01

    Sensory nerves are equipped with receptors and ion channels that allow them to detect and respond to diverse chemical, mechanical, and thermal stimuli. These sensory proteins include G protein-coupled receptors (GPCRs) and transient receptor potential (TRP) ion channels. A subclass of peptidergic sensory nerves express GPCRs and TRP channels that detect noxious, irritant, and inflammatory stimuli. Activation of these nerves triggers protective mechanisms that lead to withdrawal from danger (pain), removal of irritants (itch, cough), and resolution of infection (neurogenic inflammation). The GPCR-TRP axis is central to these mechanisms. Signals that emanate from the GPCR superfamily converge on the small TRP family, leading to channel sensitization and activation, which amplify pain, itch, cough, and neurogenic inflammation. Herein we discuss how GPCRs and TRP channels function independently and synergistically to excite sensory nerves that mediate noxious and irritant responses and inflammation in the skin and the gastrointestinal and respiratory systems. We discuss the signaling mechanisms that underlie the GPCR-TRP axis and evaluate how new information about the structure of GPCRs and TRP channels provides insights into their functional interactions. We propose that a deeper understanding of the GPCR-TRP axis may facilitate the development of more selective and effective therapies to treat dysregulated processes that underlie chronic pain, itch, cough, and inflammation. PMID:25361914

  9. Modulation of Plasmon-Enhanced Resonance Energy Transfer to Gold Nanoparticles by Protein Survivin Channeled-Shell Gating.

    PubMed

    Stobiecka, Magdalena; Chalupa, Agata

    2015-10-15

    The resonance energy transfer (RET) from excited fluorescent probe molecules to plasmonic gold nanoparticles (AuNPs) can be gated by modulating the width of channels (gates) in submonolayer protein shells surrounding AuNPs. We have explored the gated-RET (gRET) processes using an antiapoptotic protein survivin (Sur) as the gating material, citrate-capped gold nanoparticles (AuNP@Cit), and fluorescein isothiocyanate as the fluorescent probe. Despite the electrostatic repulsive forces between these components, a strong modulation of RET efficiency by Sur down to 240 pM (S/N = 3) is possible. Using piezometric measurements, we have confirmed the Sur adsorbability on Cit-coated Au surfaces with monolayer coverage: ?Sur = 5.4 pmol/cm(2) and Langmuirian adsorption constant KL,Sur = 1.09 × 10(9) M(-1). The AuNP@Cit/Sur stability has been corroborated using resonance elastic light scattering. The quantum mechanical calculations indicate that multiple hydrogen bonding between Cit ligands and -NH3(+), =NH2(+), and -NH2 groups of lysines and arginines of Sur have likely facilitated Sur bonding to nanoparticles. A theoretical model of gated-RET has been developed, enabling predictions of the system behavior. In contrast to the positive slope of the Stern-Volmer quenching dependence (F0/F) = f(QA), a negative slope has been obtained for gRET relationship (F0/F) = f(cP), attributed to the dequenching. PMID:26389984

  10. Grouper voltage-dependent anion selective channel protein 2 is required for nervous necrosis virus infection.

    PubMed

    Chang, Jui-Shin; Chi, Shau-Chi

    2015-10-01

    Nervous necrosis virus (NNV) is a non-enveloped virus with 2 segmented positive-sense single-stranded RNAs. NNV-induced mass mortality has occurred worldwide in many species of cultured marine fish and resulted in substantial economic losses. In our previous study, we cloned the gene of voltage-dependent anion selective channel protein 2 (GVDAC2), and the NNV RNA2 expression level decreased in GVDAC2-knockdown GF-1 cells 24 h after infection. Here, we investigated the role of GVDAC2 in the NNV infection in GF-1 cells. NNV infection did not considerably affect GVDAC2 gene expression. After performing immunostaining, we detected GVDAC2 at the mitochondria and GVDAC2 was colocalized with NNV-RNA-dependent RNA polymerase. However, these 2 proteins did not interact with each other in immunoprecipitation assay. The cellular ATP level in GVDAC2-downregulated cells was lower than that in control cells, and NNV-induced apoptosis was delayed in GVDAC2-siRNA-transfected cells. Therefore, we suggest that GVDAC2 is required for NNV infection for maintaining the cellular ATP level and has positive impact on virus-induced apoptosis. PMID:26052016

  11. IgG from Amyotrophic Lateral Sclerosis Patients Increases Current Through P-Type Calcium Channels in Mammalian Cerebellar Purkinje Cells and in Isolated Channel Protein in Lipid Bilayer

    NASA Astrophysics Data System (ADS)

    Llinas, R.; Sugimori, M.; Cherksey, B. D.; Smith, R. Glenn; Delbono, O.; Stefani, E.; Appel, S.

    1993-12-01

    The effect of the IgG from amyotrophic lateral sclerosis (ALS) patients was tested on the voltage-dependent barium currents (IBa) in mammalian dissociated Purkinje cells and in isolated P-type calcium channels in lipid bilayers. Whole cell clamp of Purkinje cells demonstrates that ALS IgG increases the amplitude of IBa without modifying their voltage kinetics. This increased IBa could be blocked by a purified nonpeptide toxin from Agelenopsis aperta venom (purified funnel-web spider toxin) or by a synthetic polyamine analog (synthetic funnel-web spider toxin) and by a peptide toxin from the same spider venom, ?-Aga-IVA. Similar results were obtained on single-channel recordings from purified P channel protein. The addition of ALS IgG increased single-channel IBa open time without affecting slope conductance. The results described above were not seen with normal human IgG nor with boiled ALS IgG. It is concluded that ALS IgG enhances inward current through P-type calcium channels. Since P-type Ca2+ channels are present in motoneuron axon terminals, we propose that the enhanced calcium current triggered by ALS IgG may contribute to neuronal damage in ALS.

  12. The channel domain of colicin A is inhibited by its immunity protein through direct interaction in the Escherichia coli inner membrane.

    PubMed Central

    Espesset, D; Duché, D; Baty, D; Géli, V

    1996-01-01

    A bacterial signal sequence was fused to the colicin A pore-forming domain: the exported pore-forming domain was highly cytotoxic. We thus introduced a cysteine-residue pair in the fusion protein which has been shown to form a disulfide bond in the natural colicin A pore-forming domain between alpha-helices 5 and 6. Formation of the disulfide bond prevented the cytotoxic activity of the fusion protein, presumably by preventing the membrane insertion of helices 5 and 6. However, the cytotoxicity of the disulfide-linked pore-forming domain was reactivated by adding dithiothreitol into the culture medium. We were then able to co-produce the immunity protein with the disulfide linked pore-forming domain, by using a co-immunoprecipitation procedure, in order to show that they interact. We showed both proteins to be co-localized in the Escherichia coli inner membrane and subsequently co-immunoprecipitated them. The interaction required a functional immunity protein. The immunity protein also interacted with a mutant form of the pore-forming domain carrying a mutation located in the voltage-gated region: this mutant was devoid of pore-forming activity but still inserted into the membrane. Our results indicate that the immunity protein interacts with the membrane-anchored channel domain; the interaction requires a functional membrane-inserted immunity protein but does not require the channel to be in the open state. Images PMID:8665842

  13. WATER RESOURCES RESEARCH, VOL. 33, NO. 3, PAGES 485-490, MARCH 1997 Channel incision on the lower American River, California,

    E-print Network

    James, L. Allan

    WATER RESOURCES RESEARCH, VOL. 33, NO. 3, PAGES 485-490, MARCH 1997 Channel incision on the lower,Universityof SouthCarolina,Columbia Abstract. Channelincisionalongthe lowerAmericanRiver from 1905to 1995is stageslowered2 m from 1924to 1970.Channelincisionwasthe resultof channel recoveryfrom aggradationdue

  14. Liquid water quantification in the cathode side gas channels of a proton exchange membrane fuel cell through two-phase flow

    E-print Network

    Kandlikar, Satish

    to quantify liquid water in two-phase flow. Dominant flow patterns detected and quantified for each condition electrolyte membrane fuel cell Two-phase flow visualization Gas channels Area coverage ratio Water exchange membrane fuel cells (PEMFCs) [1e8]. Understanding the two- phase flow of water and reactants

  15. Effects of Dietary Protein Concentration and L-carnitine on Growth, Processing Yield, and Body Composition of Channel X Blue Catfish Hybrids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A study was conducted in earthen ponds to evaluate effects of dietary protein concentration and L-carnitine supplementation on production and processing traits of channel catfish × blue catfish hybrids. Hybrid fingerlings, mean initial weight = 66 g, were stocked into 20, 0.04-ha earthen ponds at a...

  16. Label-free study of the function of ion channel protein on a microfluidic optical sensor integrated with artificial cell membrane.

    PubMed

    Li, Zhen; Tang, Yanyan; Zhang, Ling; Wu, Jianmin

    2014-01-21

    A label-free optical sensor was constructed by integrating pH sensing material and supported phospholipid bilayers (SPBs) in a microfluidic chip. The pH sensing material was composed of a double layer structure consisting of chitosan hydrogel and electrochemically etched porous silicon. The pH change in the microchip could induce a reversible swelling of the chitosan hydrogel layer and consequently caused a shift in effective optical thickness (EOT) of the double layer, which could be observed by Fourier transformed reflectometric interference spectroscopy (FT-RIS). After phospholipid bilayers (PLBs) were self-assembled on the sensing layer, the EOT almost remained constant during the cycling of pH from 7.4 to 6.2, indicating the blockage of H(+) translocation by the PLBs. For studying the behavior of ion channel protein, gramicidin A, a typical ion channel protein, was inserted in the SPBs for mimicking the ion transportation function of cell membrane. Due to the H(+) transportation capability of gramicidin A, the optical response to pH change could partially recover. In the presence of Ca(2+), the pore of the ion channel protein was blocked, causing a significant decrease in the EOT response upon pH change. The bio-functionalized microfluidic sensor fabricated in this work will provide a reliable platform for studying the function of ion channel protein, which is an important class of drug targets. PMID:24232219

  17. G-protein coupled receptor 18 (GPR18) in channel catfish: Expression analysis and efficacy as immunostimulant against Aeromonas hydrophila infection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objectives of this study were: 1) to determine the transcriptional profiles of G-protein coupled receptor 18 (GPR18) in channel catfish after infection with A. hydrophila compared to that in healthy catfish; 2) to determine whether over-expression of GPR18 in catfish gill cells will offer protec...

  18. Students' Understanding of External Representations of the Potassium Ion Channel Protein, Part I: Affordances and Limitations of Ribbon Diagrams, Vines, and Hydrophobic/Polar Representations

    ERIC Educational Resources Information Center

    Harle, Marissa; Towns, Marcy H.

    2012-01-01

    Research on external representations in biochemistry has uncovered student difficulties in comprehending and interpreting external representations. This project focuses on students' understanding of three external representations of the potassium ion channel protein. This is part I of a two-part study, which focuses on the affordances and…

  19. A two-channel, tunable diode laser-based hygrometer for measurement of water vapor and cirrus cloud ice water content in the upper troposphere and lower stratosphere

    NASA Astrophysics Data System (ADS)

    Thornberry, T. D.; Rollins, A. W.; Gao, R. S.; Watts, L. A.; Ciciora, S. J.; McLaughlin, R. J.; Fahey, D. W.

    2014-08-01

    The recently developed NOAA Water instrument is a two-channel, closed-path, tunable diode laser absorption spectrometer designed for the measurement of water vapor and enhanced total water (vapor + inertially enhanced condensed-phase) in the upper troposphere/lower stratosphere from the NASA Global Hawk unmanned aircraft system (UAS) or other high-altitude research aircraft. The instrument utilizes wavelength-modulated spectroscopy with second harmonic detection near 2694 nm to achieve high precision with a 79 cm double-pass optical path. The detection cells are operated under constant temperature, pressure and flow conditions to maintain a constant sensitivity to H2O independent of the ambient sampling environment. An on-board calibration system is used to perform periodic in situ calibrations to verify the stability of the instrument sensitivity during flight. For the water vapor