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1

GFP Tagging of Sieve Element Occlusion (SEO) Proteins Results in Green Fluorescent Forisomes  

PubMed Central

Forisomes are Ca2+-driven, ATP-independent contractile protein bodies that reversibly occlude sieve elements in faboid legumes. They apparently consist of at least three proteins; potential candidates have been described previously as ‘FOR’ proteins. We isolated three genes from Medicago truncatula that correspond to the putative forisome proteins and expressed their green fluorescent protein (GFP) fusion products in Vicia faba and Glycine max using the composite plant methodology. In both species, expression of any of the constructs resulted in homogenously fluorescent forisomes that formed sieve tube plugs upon stimulation; no GFP fluorescence occurred elsewhere. Isolated fluorescent forisomes reacted to Ca2+ and chelators by contraction and expansion, respectively, and did not lose fluorescence in the process. Wild-type forisomes showed no affinity for free GFP in vitro. The three proteins shared numerous conserved motifs between themselves and with hypothetical proteins derived from the genomes of M. truncatula, Vitis vinifera and Arabidopsis thaliana. However, they showed neither significant similarities to proteins of known function nor canonical metal-binding motifs. We conclude that ‘FOR’-like proteins are components of forisomes that are encoded by a well-defined gene family with relatives in taxa that lack forisomes. Since the mnemonic FOR is already registered and in use for unrelated genes, we suggest the acronym SEO (sieve element occlusion) for this family. The absence of binding sites for divalent cations suggests that the Ca2+ binding responsible for forisome contraction is achieved either by as yet unidentified additional proteins, or by SEO proteins through a novel, uncharacterized mechanism.

Pelissier, Helene C.; Peters, Winfried S.; Collier, Ray; van Bel, Aart J. E.; Knoblauch, Michael

2008-01-01

2

Sieve element occlusion (SEO) genes encode structural phloem proteins involved in wound sealing of the phloem.  

PubMed

The sieve element occlusion (SEO) gene family originally was delimited to genes encoding structural components of forisomes, which are specialized crystalloid phloem proteins found solely in the Fabaceae. More recently, SEO genes discovered in various non-Fabaceae plants were proposed to encode the common phloem proteins (P-proteins) that plug sieve plates after wounding. We carried out a comprehensive characterization of two tobacco (Nicotiana tabacum) SEO genes (NtSEO). Reporter genes controlled by the NtSEO promoters were expressed specifically in immature sieve elements, and GFP-SEO fusion proteins formed parietal agglomerates in intact sieve elements as well as sieve plate plugs after wounding. NtSEO proteins with and without fluorescent protein tags formed agglomerates similar in structure to native P-protein bodies when transiently coexpressed in Nicotiana benthamiana, and the analysis of these protein complexes by electron microscopy revealed ultrastructural features resembling those of native P-proteins. NtSEO-RNA interference lines were essentially devoid of P-protein structures and lost photoassimilates more rapidly after injury than control plants, thus confirming the role of P-proteins in sieve tube sealing. We therefore provide direct evidence that SEO genes in tobacco encode P-protein subunits that affect translocation. We also found that peptides recently identified in fascicular phloem P-protein plugs from squash (Cucurbita maxima) represent cucurbit members of the SEO family. Our results therefore suggest a common evolutionary origin for P-proteins found in the sieve elements of all dicotyledonous plants and demonstrate the exceptional status of extrafascicular P-proteins in cucurbits. PMID:22733783

Ernst, Antonia M; Jekat, Stephan B; Zielonka, Sascia; Müller, Boje; Neumann, Ulla; Rüping, Boris; Twyman, Richard M; Krzyzanek, Vladislav; Prüfer, Dirk; Noll, Gundula A

2012-06-25

3

Interactions among tobacco sieve element occlusion (SEO) proteins  

PubMed Central

Angiosperms transport their photoassimilates through sieve tubes, which comprise longitudinally-connected sieve elements. In dicots and also some monocots, the sieve elements contain parietal structural proteins known as phloem proteins or P-proteins. Following injury, P proteins disperse and accumulate as viscous plugs at the sieve plates to prevent the loss of valuable transport sugars. Tobacco (Nicotiana tabacum) P-proteins are multimeric complexes comprising subunits encoded by members of the SEO (sieve element occlusion) gene family. The existence of multiple subunits suggests that P-protein assembly involves interactions between SEO proteins, but this process is largely uncharacterized and it is unclear whether the different subunits perform unique roles or are redundant. We therefore extended our analysis of the tobacco P-proteins NtSEO1 and NtSEO2 to investigate potential interactions between them, and found that both proteins can form homomeric and heteromeric complexes in planta.

Jekat, Stephan B.; Ernst, Antonia M.; Zielonka, Sascia; Noll, Gundula A.; Prufer, Dirk

2012-01-01

4

75 Se-Binding by Rat Plasma Proteins after Injection of 75SeO2-3.  

National Technical Information Service (NTIS)

That selenium circulates in the plasma bound to proteins has long been known. Studies of these selenium-containing proteins have not identified pure species but rather have suggested that selenium was bound to many proteins. Supraphysiologic amounts of se...

R. F. Burk

1973-01-01

5

Capital Structures in an Emerging Market: A Duration Analysis of the Time Interval Between IPO and SEO in China  

Microsoft Academic Search

We model the durations between firms’ “Initial Public Offerings” (IPOs) and their subsequent “Seasoned Equity Offerings” (SEOs) in China during the period from 1 January 2001 to 1 July 2006. Duration analysis is applied by using the nonparametric Kaplan-Meier estimator of the hazard function, and parametric accelerated failure time models with time-varying covariates. The results of this analysis have important

Yang Ni; Shasha Guo; David E. Giles

2009-01-01

6

Capital structures in an emerging market: a duration analysis of the time interval between IPO and SEO in China  

Microsoft Academic Search

We model the durations between firms’ ‘Initial Public Offerings’ (IPOs) and their subsequent ‘Seasoned Equity Offerings’ (SEOs) in China between 2001 and 2006. Our results have important implications for the capital structure in emerging markets. Our evidence on financing decisions in China contradicts the predictions of both the trade-off and pecking order theories. Firms do not issue equity after debt

Yang Ni; Shasha Guo; David E. Giles

2010-01-01

7

Rapid, room-temperature synthesis of amorphous selenium/protein composites using Capsicum annuum L extract  

NASA Astrophysics Data System (ADS)

We describe the formation of amorphous selenium (?-Se)/protein composites using Capsicum annuum L extract to reduce selenium ions (SeO32-) at room temperature. The reaction occurs rapidly and the process is simple and easy to handle. A protein with a molecular weight of 30 kDa extracted from Capsicum annuum L not only reduces the SeO32- ions to Se0, but also controls the nucleation and growth of Se0, and even participates in the formation of ?-Se/protein composites. The size and shell thickness of the ?-Se/protein composites increases with high Capsicum annuum L extract concentration, and decreases with low reaction solution pH. The results suggest that this eco-friendly, biogenic synthesis strategy could be widely used for preparing inorganic/organic biocomposites. In addition, we also discuss the possible mechanism of the reduction of SeO32- ions by Capsicum annuum L extract.

Li, Shikuo; Shen, Yuhua; Xie, Anjian; Yu, Xuerong; Zhang, Xiuzhen; Yang, Liangbao; Li, Chuanhao

2007-10-01

8

Investigation of local symmetry in LiH3(SeO3)2 single crystals by 1H and 7Li nuclear magnetic resonance  

NASA Astrophysics Data System (ADS)

The local environments of 1H and 7Li nuclei in LiH3(SeO3)2 crystals were investigated using FT NMR. The 7Li spectrum does changes from three resonance lines to one resonance line near Tm (=383 K). The variation in the splitting of the 7Li resonance lines with temperature indicates that the EFG at the Li sites produced by the (SeO3)2? groups varies with temperature. The changes in the temperature dependence of the intensity, line width, and spin–lattice relaxation time T1 near Tm for the 1H and 7Li nuclei coincide with the distortion of the structural framework surrounding each 1H and 7Li ion. Finally, the NMR results obtained here are compared to MH3(SeO3)2 (M = Na, K, and Cs) crystals previously reported.

Lim, Ae Ran

2013-10-01

9

Syntheses, structures, and properties of Ag4(Mo2O5)(SeO4)2(SeO3) and Ag2(MoO3)3SeO3  

NASA Astrophysics Data System (ADS)

Ag4(Mo2O5)(SeO4)2(SeO3) has been synthesized by reacting AgNO3, MoO3, and selenic acid under mild hydrothermal conditions. The structure of this compound consists of cis-MoO22+ molybdenyl units that are bridged to neighboring molybdenyl moieties by selenate anions and by a bridging oxo anion. These dimeric units are joined by selenite anions to yield zigzag one-dimensional chains that extended down the c-axis. Individual chains are polar with the C2 distortion of the Mo(VI) octahedra aligning on one side of each chain. However, the overall structure is centrosymmetric because neighboring chains have opposite alignment of the C2 distortion. Upon heating Ag4(Mo2O5)(SeO4)2(SeO3) looses SeO2 in two distinct steps to yield Ag2MoO4. Crystallographic data: (193 K; MoK?, ?=0.71073 Å): orthorhombic, space group Pbcm, a=5.6557(3), b=15.8904(7), c=15.7938(7) Å, V=1419.41(12), Z=4, R(F)=2.72% for 121 parameters with 1829 reflections with I>2?(I). Ag2(MoO3)3SeO3 was synthesized by reacting AgNO3 with MoO3, SeO2, and HF under hydrothermal conditions. The structure of Ag2(MoO3)3SeO3 consists of three crystallographically unique Mo(VI) centers that are in 2+2+2 coordination environments with two long, two intermediate, and two short bonds. These MoO6 units are connected to form a molybdenyl ribbon that extends along the c-axis. These ribbons are further connected together through tridentate selenite anions to form two-dimensional layers in the [bc] plane. Crystallographic data: (193 K; MoK?, ?=0.71073 Å): monoclinic, space group P21/n, a=7.7034(5), b=11.1485(8), c=12.7500(9) Å, ?=105.018(1) V=1002.7(2), Z=4, R(F)=3.45% for 164 parameters with 2454 reflections with I>2?(I). Ag2(MoO3)3SeO3 decomposes to Ag2Mo3O10 on heating above 550 °C.

Ling, Jie; Albrecht-Schmitt, Thomas E.

2007-05-01

10

Isotope effects in the crystal symmetry and nature of the phase transitions in NaH3(SeO3)2 and NaD3(SeO3)2  

Microsoft Academic Search

NMR data show that the triclinic ferroelectric phase which exists in NaH3(SeO3)2 between -79°C and -173°C does not appear in NaD3(SeO3)2. The transition from 2\\/m -->1 in NaH3(SeO3)2 is connected with a doubling of the unit cell dimensions both along the a and b axes, whereas in the low temperatures phases of symmetry m in NaH3(SeO3)2 and NaD3(SeO3)2 the unit

R. Blinc; A. Levstik; J. Stepisnik; Z. Trontelj; I. Zupancic

1968-01-01

11

Detection of calcium by a confocal laser scanning microscope in Na2SeO3-treated SW480 human colonic carcinoma cells  

NASA Astrophysics Data System (ADS)

A number of studies have demonstrated that perturbed cellular calcium homeostasis has been implicated in apoptosis. Some studies showed that selenium compounds were able to induce cell apoptosis. The main objective of this study is to evaluate effect of Na2SeO3 on intracellular Ca2+ levels in SW480 human colonic carcinoma cells. When SW480 cells were exposed to 25 to 100 micrometers ol/L Na2SeO3, we also found that Na2SeO3 was able to induce [Ca2+]i, disruption of mitochondrial membrane potential ((Delta) (psi) m) in SW480 cells by using a confocal laser scanning microscope. Ca2+ channel inhibitor CoCl2 and an intracellular Ca2+ chelator BAPTA completely inhibited [Ca2+]i increase. CoCl2, BAPTA and ruthenium red also inhibited disruption of (Delta) (psi) m. The results suggest that Na2SeO3 is able to increase [Ca2+]i mitochondria permeability transition and Ca2+ is from extracellular Ca2+.

Wang, Haitao; Liu, Yafeng; Zhang, Zhihong; Yang, Xiangliang; Xu, Hui-Bie F.

2002-04-01

12

Hydrothermal syntheses and characterization of two layered molybdenum selenites, Rb 2(MoO 3) 3SeO 3 and Tl 2MoO 3) 3SeO 3  

Microsoft Academic Search

The hydrothermal syntheses of Rb2(MoO3)3SeO3 and Tl2(MoO3)3SeO3 are described. These compounds have structures built up from hexagonal-WO3-type sheets and are isostructural with the previously reported Cs2(MoO3)3SeO3 and (NH4)2(MoO3)3SeO3. Powder X-ray, thermogravimetric, and spectroscopic data are presented and discussed.

Laurie L. Dussack; William T. A. Harrison; Allan J. Jacobson

1996-01-01

13

Synthesis, structure, and physicochemical properties of K[VO 2 (SeO 4 )(H 2 O)] and K[VO 2 (SeO 4 )(H 2 O) 2 ] · H 2 O  

Microsoft Academic Search

The vanadium(V) complexes K[VO2(SeO4)(H2O)] and K[VO2(SeO4)(H2O)2] · H2O were synthesized using original procedures; their physicochemical properties were studied, and the crystal structure was\\u000a determined on the basis of X-ray diffraction and neutron diffraction data. The structure of K[VO2(SeO4)(H2O)2] · H2O is composed of VO6 octahedra connected to form infinite chains by bridging SeO4 tetrahedra. Each VO6 tetrahedron has short terminal

A. P. Tyutyunnik; V. N. Krasil’nikov; I. F. Berger; V. G. Zubkov; L. A. Perelyaeva; I. V. Baklanova

2011-01-01

14

Behavior of 77Se Hyperfine Components of SeO43- Radicals in Highly Deuterated NH4H2PO4  

NASA Astrophysics Data System (ADS)

The authors observed the 77Se hyperfine (hf) components of ESR spectrum of SeO43- radicals doped in 94%-deuterated NH4H2PO4 (D0.94ADP) and compared the result with those for DxADP (0{?q}x{?q}0.70) crystals. In the paraelectric phase no remarkable deuteration effect was observed. In the antiferroelectric (AFE) phase, on the other hand, a new type of angular dependence of the hf line-position was found between about 185 K and Tc (236 K). The results mean that the crystal field of the AFE host crystal which distorts the SeO43- into the AFE configuration depends on temperature remarkably in the AFE D0.94ADP.

Fukami, Takanori; Akahoshi, Shin; Hukuda, Kenzi

1988-01-01

15

Crystal chemistry of selenates with mineral-like structures: VII. The structure of (H3O)[(UO2)(SeO4)(SeO2OH)] and some structural features of selenite-selenates  

NASA Astrophysics Data System (ADS)

The crystal structure of a new compound, (H3O)[(UO2)(SeO4)(SeO2OH)] (monoclinic, P21/ n, a = 8.6682(19), b = 10.6545(16), c = 9.846(2) Å, ? = 97.881(17)°, V = 900.7(3) Å3), was solved by direct methods and refined to R 1 = 0.050. The structure contains two symmetrically different Se atoms. The Se1 site is coordinated by three O atoms as is characteristic of Se4+ cations. The Se2 site is coordinated by four O atoms and forms selenate anion SeO{4/2-}. The structure is based on selenite-selenate sheets [(UO2)(SeO4)(SeO2OH)]- linked by the interlayer H3O- ions. The sheets are parallel to (101). The structure is compared to that of schmiederite, Pb2Cu2(SeO3)(SeO4)(OH)4.

Krivovichev, S. V.

2009-12-01

16

New vanadium selenites: centrosymmetric Ca2(VO2)2(SeO3)3(H2O)2, Sr2(VO2)2(SeO3)3, and Ba(V2O5)(SeO3), and noncentrosymmetric and polar A4(VO2)2(SeO3)4(Se2O5) (A = Sr2+ or Pb2+).  

PubMed

Five new vanadium selenites, Ca(2)(VO(2))(2)(SeO(3))(3)(H(2)O)(2), Sr(2)(VO(2))(2)(SeO(3))(3), Ba(V(2)O(5))(SeO(3)), Sr(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)), and Pb(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)), have been synthesized and characterized. Their crystal structures were determined by single crystal X-ray diffraction. The compounds exhibit one- or two-dimensional structures consisting of corner- and edge-shared VO(4), VO(5), VO(6), and SeO(3) polyhedra. Of the reported materials, A(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)) (A = Sr(2+) or Pb(2+)) are noncentrosymmetric (NCS) and polar. Powder second-harmonic generation (SHG) measurements revealed SHG efficiencies of approximately 130 and 150 × ?-SiO(2) for Sr(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)) and Pb(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)), respectively. Piezoelectric charge constants of 43 and 53 pm/V, and pyroelectric coefficients of -27 and -42 ?C/m(2)·K at 70 °C were obtained for Sr(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)) and Pb(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)), respectively. Frequency dependent polarization measurements confirmed that the materials are not ferroelectric, that is, the observed polarization cannot be reversed. In addition, the lone-pair on the Se(4+) cation may be considered as stereo-active consistent with calculations. For all of the reported materials, infrared, UV-vis, thermogravimetric, and differential thermal analysis measurements were performed. Crystal data: Ca(2)(VO(2))(2)(SeO(3))(3)(H(2)O)(2), orthorhombic, space group Pnma (No. 62), a = 7.827(4) Å, b = 16.764(5) Å, c = 9.679(5) Å, V = 1270.1(9) Å(3), and Z = 4; Sr(2)(VO(2))(2)(SeO(3))(3), monoclinic, space group P2(1)/c (No. 12), a = 14.739(13) Å, b = 9.788(8) Å, c = 8.440(7) Å, ? = 96.881(11)°, V = 1208.8(18) Å(3), and Z = 4; Ba(V(2)O(5))(SeO(3)), orthorhombic, space group Pnma (No. 62), a = 13.9287(7) Å, b = 5.3787(3) Å, c = 8.9853(5) Å, V = 673.16(6) Å(3), and Z = 4; Sr(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)), orthorhombic, space group Fdd2 (No. 43), a = 25.161(3) Å, b = 12.1579(15) Å, c = 12.8592(16) Å, V = 3933.7(8) Å(3), and Z = 8; Pb(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)), orthorhombic, space group Fdd2 (No. 43), a = 25.029(2) Å, b = 12.2147(10) Å, c = 13.0154(10) Å, V = 3979.1(6) Å(3), and Z = 8. PMID:22145697

Yeon, Jeongho; Kim, Sang-Hwan; Nguyen, Sau Doan; Lee, Hana; Halasyamani, P Shiv

2011-12-06

17

Hydrothermal synthesis and structural characterization of a new layered vanadium selenite: (C 4N 2H 12) 0.5[(VO) 2(H 2O) 2(SeO 3) 2(HSeO 3)  

Microsoft Academic Search

A layered vanadium selenite, (C4N2H12)0.5[(VO)2(H2O)2(SeO3)2(HSeO3)], has been hydrothermally synthesized and structurally characterized. Its structure is layered and can be described as vanadium selenite oxide layers with diprotonated piperazine occupying the interlayer space. The result of magnetic measurement for the title compound shows a typical antiferromagnetic interaction at low temperature.

Zhimin Dai; Guanghua Li; Zhan Shi; Xiaomin Liu; Shouhua Feng

2005-01-01

18

TiO2-SEO Block Copolymer Nanocomposites as Solid-State Electrolytes for Lithium Metal Batteries  

NASA Astrophysics Data System (ADS)

Replacing the liquid electrolyte in lithium batteries by a solid has been a long-standing goal of the battery industry due to the promise of better safety and the potential to produce batteries with higher energy densities. Recently, symmetric polystyrene-block-poly(ethylene oxide) (SEO) copolymers/LiX salt mixtures with high ionic conductivity and high shear modulus were developed as solid electrolytes. For an enhancement in mechanical properties and its effect on the dendrite growth from lithium metal electrodes, we study the effect of adding TiO2 nanoparticles to the SEO/LiX mixtures. We find that TiO2/SEO/LiX nanocomposite electrolytes have stable performance against the lithium metal electrodes. There appears to be a correlation between the stability of the electrolytes, morphology, and mechanical properties.

Gurevitch, Inna; Buonsanti, Raffaella; Teran, Alexander; Cabana, Jordi; Balsara, Nitash

2013-03-01

19

Toxicity of selenium (Na2SeO3) and mercury (HgCl2) on the planarian Dugesia gonocephala.  

PubMed

The toxicity of selenium (Na2SeO3) and mercury (HgCl2) was determined by using a freshwater planarian which is particularly sensitive to pollution, and belongs to a fissiparous breed of Dugesia gonocephala. The mortality and fissiparity frequency of the subjects were studied. They were exposed to intense treatments (48 hours) or for medium to long periods of time (21 days) to either the single compounds or a combination of both, and were fed or fasting. The lethal effect of sodium selenite is correlated to the food intake, whereas the toxicity of mercurous chloride is probably the result of a fixative effect which does not depend on feeding. The 21-day treatment with the first compound has a non-negligible lethal effect which is probably due to an accumulation phenomenon. At doses where an antioxidant effect prevails, fissiparity is stimulated. On the other hand, the second compound reduces reproduction frequency to half the base values. Compared to the Paracentrotus lividus, the Dugesia gonocephala offers various advantages concerning toxicological experiments; besides being easier to handle in the laboratory, it is available all year round and is not subject to seasonal cycles. It is also more susceptible to the toxic effect of mercury, which is a common and highly toxic pollutant, than the sea urchin. PMID:2616901

Congiu, A M; Casu, S; Ugazio, G

1989-10-01

20

Success in Mathematics within a Challenged Minority: The Case of Students of Ethiopian Origin in Israel (SEO)  

ERIC Educational Resources Information Center

|Many studies have reported on the economical, social, and educational difficulties encountered by Ethiopian Jews since their immigration to Israel. Furthermore, the overall academic underachievement and poor representation of students of Ethiopian origin (SEO) in the advanced mathematics and science classes were highlighted and described. Yet,…

Mulat, Tiruwork; Arcavi, Abraham

2009-01-01

21

Vapor Pressure and Thermodynamics of Selenium Dioxide. The Enthalpy of Atomization of SeO2(g).  

National Technical Information Service (NTIS)

The equilibrium vapor pressures and thermochemical properties of selenium dioxide are of practical importance to the non-ferrous metals industry since a major portion of the world's supply of metallic selenium is obtained as SeO2 in the oxidative roasting...

R. G. Behrens R. S. Lemons G. M. Rosenblatt

1973-01-01

22

High-pressure single-crystal X-ray diffraction of Tl2SeO4  

NASA Astrophysics Data System (ADS)

The effect of pressure on the crystal structure of thallium selenate (Tl2SeO4) (Pmcn, Z=4), containing the Tl+ cations with electron lone pairs, has been studied with single-crystal X-ray diffraction in a diamond anvil cell up to 3.64 GPa at room temperature. No phase transition has been observed. The compressibility data are fitted by a Murnaghan equation of state with the zero-pressure bulk modulus B0=29(1) GPa and the unit-cell volume at ambient pressure V0=529.6(8) Å3 (B?=4.00). Tl2SeO4 is the least compressible in the c direction, while the pressure-induced changes of the a and b lattice parameters are quite similar. These observations can be explained by different pressure effects on the nine- and 11-fold coordination polyhedra around the two non-equivalent Tl atoms. The SeO42- tetrahedra are not rigid units and become more distorted. Their contribution to the compressibility is small. The effect of pressure on the isotypical oxide materials A2TO4 with the ?-K2SO4 structure is discussed. It appears that the presence of electron lone pairs on the Tl+ cation does not seem to influence the compressibility of Tl2SeO4.

Grzechnik, Andrzej; Breczewski, Tomasz; Friese, Karen

2008-11-01

23

P-proteins in Arabidopsis are heteromeric structures involved in rapid sieve tube sealing  

PubMed Central

Structural phloem proteins (P-proteins) are characteristic components of the sieve elements in all dicotyledonous and many monocotyledonous angiosperms. Tobacco P-proteins were recently confirmed to be encoded by the widespread sieve element occlusion (SEO) gene family, and tobacco SEO proteins were shown to be directly involved in sieve tube sealing thus preventing the loss of photosynthate. Analysis of the two Arabidopsis SEO proteins (AtSEOa and AtSEOb) indicated that the corresponding P-protein subunits do not act in a redundant manner. However, there are still pending questions regarding the interaction properties and specific functions of AtSEOa and AtSEOb as well as the general function of structural P-proteins in Arabidopsis. In this study, we characterized the Arabidopsis P-proteins in more detail. We used in planta bimolecular fluorescence complementation assays to confirm the predicted heteromeric interactions between AtSEOa and AtSEOb. Arabidopsis mutants depleted for one or both AtSEO proteins lacked the typical P-protein structures normally found in sieve elements, underlining the identity of AtSEO proteins as P-proteins and furthermore providing the means to determine the role of Arabidopsis P-proteins in sieve tube sealing. We therefore developed an assay based on phloem exudation. Mutants with reduced AtSEO expression levels lost twice as much photosynthate following injury as comparable wild-type plants, confirming that Arabidopsis P-proteins are indeed involved in sieve tube sealing.

Jekat, Stephan B.; Ernst, Antonia M.; von Bohl, Andreas; Zielonka, Sascia; Twyman, Richard M.; Noll, Gundula A.; Prufer, Dirk

2013-01-01

24

Rapid, room-temperature synthesis of amorphous selenium\\/protein composites using Capsicum annuum L extract  

Microsoft Academic Search

We describe the formation of amorphous selenium (alpha-Se)\\/protein composites using Capsicum annuum L extract to reduce selenium ions (SeO32-) at room temperature. The reaction occurs rapidly and the process is simple and easy to handle. A protein with a molecular weight of 30 kDa extracted from Capsicum annuum L not only reduces the SeO32- ions to Se0, but also controls

Shikuo Li; Yuhua Shen; Anjian Xie; Xuerong Yu; Xiuzhen Zhang; Liangbao Yang; Chuanhao Li

2007-01-01

25

Synthesis, characterization, and structure-property relationships in two new polar oxides: Zn2(MoO4)(SeO3) and Zn2(MoO4)(TeO3).  

PubMed

Two new noncentrosymmetric (NCS) polar oxide materials, Zn(2)(MoO(4))(AO(3)) (A = Se(4+) or Te(4+)), have been synthesized by hydrothermal and solid-state techniques. Their crystal structures have been determined, and characterization of their functional properties (second-harmonic generation, piezoelectricity, and polarization) has been performed. The isostructural materials exhibit a three-dimensional network consisting of ZnO(4), ZnO(6), MoO(4), and AO(3) polyhedra that share edges and corners. Powder second-harmonic generation (SHG) measurements using 1064 nm radiation indicate the materials exhibit moderate SHG efficiencies of 100 × and 80 × ?-SiO(2) for Zn(2)(MoO(4))(SeO(3)) and Zn(2)(MoO(4))(TeO(3)), respectively. Particle size vs SHG efficiency measurements indicate the materials are type 1 non-phase-matchable. Converse piezoelectric measurements resulted in d(33) values of ?14 and ?30 pm/V for Zn(2)(MoO(4))(SeO(3)) and Zn(2)(MoO(4))(TeO(3)), respectively, whereas pyroelectric measurements revealed coefficients of -0.31 and -0.64 ?C/m(2) K at 55 °C for Zn(2)(MoO(4))(SeO(3)) and Zn(2)(MoO(4))(TeO(3)), respectively. Frequency-dependent polarization measurements confirmed that all of the materials are nonferroelectric; that is, the macroscopic polarization is not reversible, or "switchable". Infrared, UV-vis, thermogravimetric, and differential thermal analysis measurements were also performed. First-principles density functional theory (DFT) electronic structure calculations were also done. Crystal data: Zn(2)(MoO(4))(SeO(3)), monoclinic, space group P2(1) (No. 4), a = 5.1809(4) Å, b = 8.3238(7) Å, c = 7.1541(6) Å, ? = 99.413(1)°, V = 305.2(1) Å(3), Z = 2; Zn(2)(MoO(4))(TeO(3)), monoclinic, space group P2(1) (No. 4), a = 5.178(4) Å, b = 8.409(6) Å, c = 7.241(5) Å, ? = 99.351(8)°, V = 311.1(4) Å(3), Z = 2. PMID:21557565

Nguyen, Sau Doan; Kim, Sang-Hwan; Halasyamani, P Shiv

2011-05-10

26

Conserved thioredoxin fold is present in Pisum sativum L. sieve element occlusion-1 protein  

PubMed Central

Homology-based three-dimensional model for Pisum sativum sieve element occlusion 1 (Ps.SEO1) (forisomes) protein was constructed. A stretch of amino acids (residues 320 to 456) which is well conserved in all known members of forisomes proteins was used to model the 3D structure of Ps.SEO1. The structural prediction was done using Protein Homology/analogY Recognition Engine (PHYRE) web server. Based on studies of local sequence alignment, the thioredoxin-fold containing protein [Structural Classification of Proteins (SCOP) code d1o73a_], a member of the glutathione peroxidase family was selected as a template for modeling the spatial structure of Ps.SEO1. Selection was based on comparison of primary sequence, higher match quality and alignment accuracy. Motif 1 (EVF) is conserved in Ps.SEO1, Vicia faba (Vf.For1) and Medicago truncatula (MT.SEO3); motif 2 (KKED) is well conserved across all forisomes proteins and motif 3 (IGYIGNP) is conserved in Ps.SEO1 and Vf.For1.

Umate, Pavan; Tuteja, Renu

2010-01-01

27

The low-temperature structure of Tl2SeO4 at 30K  

NASA Astrophysics Data System (ADS)

The structure of Tl2SeO4 at 293, 100 and 30K has been determined. Space group at 293 and 100K is Pmcn, Z=4, lattice parameters at 293K are a=6.0838(12)(100K: 6.0336(19)), b=10.965(3) (100K: 10.903(5)) and c=7.9385(15)Å(100K: 7.921(2)). At 30K space group is P212121, Z=4, with lattice parameters a=6.2333(17), b=10.533(3) and c=7.828(2). Measurement was carried out with a Stoe IPDS (293K) and a Nonius CCD using an Oxford He-cryostat for cooling (100 and 30K). Final agreement factors at 293K after refinement with the program SHELXL97 are R(F)=0.061 (100K: 0.097), wR(F**2)=0.051 (100K: 0.156) for 566(100K: 678) unique reflections and R(F)=0.039, wR(F**2)=0.097 for 1162 unique reflections at 30K. The high-temperature phase is isotypical to the ?-K2SO4 structure, characterized by isolated selenate tetrahedra and two different cation sites with coordination number 9 and 11. In the low-temperature phase, the tetrahedra are rotated and the coordination numbers of the Tl+ ions are reduced to 8 and 10, respectively. Structural changes are similar to the ones observed in high- and low-temperature phases of Tl2MoO4. A comparison to other Tl2TX4 compounds shows that the structural instabilities are closely connected to shortest Tl-O distances.

Friese, K.; Goeta, A. E.; Leech, M. A.; Howard, J. A. K.; Madariaga, G.; Pérez-Mato, J. M.; Breczewski, T.

2004-04-01

28

Switching kinetics of the ferroelectric transition in K2SeO4 studied by stroboscopic ?-ray diffraction  

NASA Astrophysics Data System (ADS)

The kinetics of the ferroelectric lock-in transition in potassium selenate (K2SeO4) was studied on a millisecond timescale using high-resolution ?-ray diffraction. A large change of the line width and wavevector of the first order satellite is observed during the switching process. This is attributed to a loss of long-range order under the influence of the electric field. In addition, the incommensurate phase is stabilized by the pulsed field and the transition to the pure commensurate phase is shifted to lower temperatures. Strains that may build up during the rapid switching process are supposed to be the reason for this behaviour.

Leist, J.; Gibhardt, H.; Eckold, G.

2013-11-01

29

Switching kinetics of the ferroelectric transition in K2SeO4 studied by stroboscopic ?-ray diffraction.  

PubMed

The kinetics of the ferroelectric lock-in transition in potassium selenate (K2SeO4) was studied on a millisecond timescale using high-resolution ?-ray diffraction. A large change of the line width and wavevector of the first order satellite is observed during the switching process. This is attributed to a loss of long-range order under the influence of the electric field. In addition, the incommensurate phase is stabilized by the pulsed field and the transition to the pure commensurate phase is shifted to lower temperatures. Strains that may build up during the rapid switching process are supposed to be the reason for this behaviour. PMID:24132071

Leist, J; Gibhardt, H; Eckold, G

2013-10-17

30

Analyses of the Raman Spectra of the Incommensurate Ferroelectrices RB2ZnCl4 and K2SeO4.  

National Technical Information Service (NTIS)

Previously, a study (1) of the Raman spectrum of the incommensurate ferroelectric, potassium selenate (K2SeO4) was reported. A qualitative model was proposed in that work to explain the universal observation, that in its paraelectric phase, there is a hig...

V. Katkanant F. G. Ullman P. J. Edwardson J. R. Hardy

1986-01-01

31

Applications of synchrotron radiation to protein crystallography: preliminary results.  

PubMed Central

X-ray diffraction photographs of protein single crystals have been obtained using synchrotron radiation produced by an electron-positron storage ring. The diffracted intensities observed with this unconventional source are a factor of at least 60 greater than those obtained with a sealed x-ray tube using the same crystal and instrumental parameters. Diffraction data have been collected by the precession method to higher resolution and using smaller protein crystals than would have been possible with a conventional source. The crystal decay rate in the synchrotron beam for several proteins appears to be substantially less than that observed with Ni-filtered Cu radiation. The tunable nature of the source (which allows selective optimization of anomalous contributions to the scattering factors) and the low angular divergence of the beam make the source very useful for single crystal protein diffraction studies. Images

Phillips, J C; Wlodawer, A; Yevitz, M M; Hodgson, K O

1976-01-01

32

Protein C Mutation (A267T) Results in ER Retention and Unfolded Protein Response Activation  

PubMed Central

Background Protein C (PC) deficiency is associated with a high risk of venous thrombosis. Recently, we identified the PC-A267T mutation in a patient with PC deficiency and revealed by in vitro studies decreased intracellular and secreted levels of the mutant. The aim of the present study was to characterize the underlying mechanism(s). Methodology/Principal Findings CHO-K1 cells stably expressing the wild-type (PC-wt) or the PC mutant were generated. In order to examine whether the PC mutant was subjected to increased intracellular degradation, the cells were treated with several inhibitors of various degradation pathways and pulse-chase experiments were performed. Protein-chaperone complexes were analyzed by treating the cells with a cross-linker followed by Western blotting (WB). Expression levels of the immunoglobulin-binding protein (BiP) and the phosphorylated eukaryotic initiation factor 2? (P-eIF2?), both common ER stress markers, were determined by WB to examine if the mutation induced ER stress and unfolded protein response (UPR) activation. We found no major differences in the intracellular degradation between the PC variants. The PC mutant was retained in the endoplasmic reticulum (ER) and had increased association with the Grp-94 and calreticulin chaperones. Retention of the PC-A267T in ER resulted in UPR activation demonstrated by increased expression levels of the ER stress markers BiP and P-eIF2? and caused also increased apoptotic activity in CHO-K1 cells as evidenced by elevated levels of DNA fragmentation. Conclusions/Significance The reduced intracellular level and impaired secretion of the PC mutant were due to retention in ER. In contrast to other PC mutations, retention of the PC-A267T in ER resulted in minor increased proteasomal degradation, rather it induced ER stress, UPR activation and apoptosis.

Tjeldhorn, Lena; Iversen, Nina; Sandvig, Kirsten; Bergan, Jonas; Sandset, Per Morten; Skretting, Grethe

2011-01-01

33

Syntheses, crystal structures and SHG properties of a series of polar alkali-metal molybdenum(VI) selenites based on strandberg-type [Mo5O15(SeO3)2]4- polyanion.  

PubMed

Four new quaternary molybdenum selenites, namely, HRb(3)(Mo(5)O(15))(SeO(3))(2)(H(2)O)(2)1, ?-Rb(4)Mo(5)O(15)(SeO(3))(2)(H(2)O)(2)2, ?-Rb(4)Mo(5)O(15)(SeO(3))(2)(H(2)O)(2)3 and K(4)Mo(5)O(15)(SeO(3))(2)(H(2)O)(2)4 were synthesized by hydrothermal reactions. All of the four compounds feature a zero-dimensional (0D) [(Mo(5)O(15))(SeO(3))(2)](4-) anionic unit composed of a five-member MoO(6) octahedral ring capped by two SeO(3)(2-) trigonal pyramids, with the Rb(+)/K(+) or/and H(+) cations and water molecules acting as spacers and keeping charge balance. Although these compounds exhibit similar chemical formula, their structures are slightly different. HRb(3)(Mo(5)O(15))(SeO(3))(2)(H(2)O)(2)1 crystallizes in a polar space group (Pca2(1)). ?-Rb(4)Mo(5)O(15)(SeO(3))(2)(H(2)O)(2)2 crystallizes in a centrosymmetric (CS) space group (P2(1)/n) whereas ?-Rb(4)Mo(5)O(15)(SeO(3))(2)(H(2)O)(2)3 and K(4)Mo(5)O(15)(SeO(3))(2)(H(2)O)(2)4 are isomorphous, crystallize in a chiral space group (C2). The chiral structures of 3 and 4 contain two similar polyanions of [Mo(5)O(15)(SeO(3))(2)](4-) with opposite handedness. Second-harmonic-generation (SHG) measurements indicate that 1, 3 and 4 are all SHG-active. Compound 1 displays a weak SHG response of about 20% of that of KDP (KH(2)PO(4)) and is phase-matchable whereas the SHG responses of 3 and 4 are very weak (less than 5% of that of KDP). Thermal analyses and optical property measurements have also been performed. PMID:22437648

Kong, Fang; Hu, Chun-Li; Xu, Xiang; Zhou, Tian-Hua; Mao, Jiang-Gao

2012-03-22

34

Hydrogen-Bond Network in Ferroelectric Lithium Trihydrogen Selenite, LiD3(SeO3)2 by Deuteron Magnetic Resonance  

Microsoft Academic Search

Deuteron magnetic resonance study is made of single crystals of LiD3(SeO3)2 between -143°C and 110°C. The electric quadrupole coupling constant, eQq\\/h, the asymmetry parameter, eta, and the directions of the principal axes of the field-gradient tensor are determined for each deuteron at room temperature. Three non-equivalent tensors are obtained corresponding to the three non-equivalent fairly strong hydrogen bonds determined by

Gen Soda; Takehiko Chiba

1969-01-01

35

Use of bone morphogenetic proteins in arthrodesis: clinical results.  

PubMed

Bone grafting is not routinely required in primary arthrodesis in the absence of infection, avascular necrosis, bone defect or previous non-union; when any of the above factors is present, autograft is the gold-standard method. However, donor site morbidity and the quantitative and qualitative limitations of autograft have led to the development of alternatives. This study documents the use of the bone morphogenetic protein BMP-7 in a total of 19 joint fusions (ankle, subtalar, talonavicular, pubic and sacroiliac). Healing rates of 90% and satisfactory subjective functional outcome in 70% of cases were recorded over a minimum follow-up of 15 months. These data should provide a sound foundation for future clinical trials evaluating the application of BMP-7 in the fusion of joints. PMID:20082794

Kanakaris, Nikolaos K; Mallina, Ravi; Calori, Giorgio M; Kontakis, George; Giannoudis, Peter V

2009-12-01

36

Constricting force of filamentary protein rings evaluated from experimental results  

NASA Astrophysics Data System (ADS)

We present a model of Z -ring constriction in bacteria based on different experimental in vitro results. The forces produced by the Z ring due to lateral attraction of its constituent parts, estimated in previous studies that were based on FtsZ filaments observed by atomic force microscopy, are in good agreement with an estimation of the force required for recently found deformations in liposomes caused by FtsZ. These forces are calculated within the usual Helfrich energy formalism. In this context, we also explain the apparent attraction of multiple Z rings in the liposomes initially separated by small distances, as well as the stable distribution of rings separated by distances greater than approximately twice the diameter of the cylindrical liposomes. We adapted the model to the in vivo conditions imposed by the bacterial cell wall, concluding that the proposed mechanism gives a qualitative explanation for the force generation during bacterial division.

Hörger, I.; Campelo, F.; Hernández-Machado, A.; Tarazona, P.

2010-03-01

37

Synthesis of rare-earth selenate and selenite materials under "sol-gel" hydrothermal conditions: crystal structures and characterizations of La(HSeO3)(SeO4) and KNd(SeO4)2  

NASA Astrophysics Data System (ADS)

Two rare-earth compounds containing selenium atoms, La(HSeO3)(SeO4) with a new open framework structure and KNd(SeO4)2 with a layered structure, have been synthesized under "sol-gel" hydrothermal conditions for the first time. Single-crystals of La(HSeO3)(SeO4) crystallize in the monoclinic system (P21, a=8.5905(17)Å, b=7.2459(14)Å, c=9.5691(19)Å, ?=104.91(3)°, Z=2, RAll=0.032). The structure contains puckered polyhedral layers made of LaOx (x=9,10) and SeO4 groups, which are connected via SeO3-uints to the 3D structure. The crytal structure of KNd(SeO4)2 (monoclinc, P21/c, a=8.7182(17)Å, b=7.3225(15)Å, c=11.045(2)Å, ?=91.38(3)°, Z=4, RAll=0.051) contains honeycomb-like six-ring NdO9 polyhedra forming layers which are further decorated with SeO4 tetrahedra. The K+ ions occupy the interspaces of these layers and provide the charge balance.

Liu, Wei; Chen, Hao-Hong; Yang, Xin-Xin; Li, Mang-Rong; Zhao, Jing-Tai

2004-12-01

38

Physical properties of the novel Jarosite-type compound NaFe3(SeO4)2(OH)6  

NASA Astrophysics Data System (ADS)

A selenate analogue of sodium Jarosite NaFe3(SeO4)2(OH)6 has been synthesized by precipitation from aqueous solution. We have newly determined the structural parameters by powder X-ray diffraction refinement. The structure is similar to that of sulfate Jarosite analogues, while the unit cell volume is larger. The temperature dependence of the magnetic susceptibility shows a cusp-like anomaly at 45 K, and the spontaneous magnetization appears below 33 K. We have measured the Mössbauer spectra of 57Fe3+(S=2/5) ions, and revealed an anomalous fluctuation of the hyperfine field.

Oba, Noriaki; Michioka, Chishiro; Kato, Masaki; Yoshimura, Kazuyoshi; Mibu, Ko

2005-08-01

39

Silencing of Soybean Seed Storage Proteins Results in a Rebalanced Protein Composition Preserving Seed Protein Content without Major Collateral Changes in the Metabolome and Transcriptome[W][OA  

PubMed Central

The ontogeny of seed structure and the accumulation of seed storage substances is the result of a determinant genetic program. Using RNA interference, the synthesis of soybean (Glycine max) glycinin and conglycinin storage proteins has been suppressed. The storage protein knockdown (SP?) seeds are overtly identical to the wild type, maturing to similar size and weight, and in developmental ontogeny. The SP? seeds rebalance the proteome, maintaining wild-type levels of protein and storage triglycerides. The SP? soybeans were evaluated with systems biology techniques of proteomics, metabolomics, and transcriptomics using both microarray and next-generation sequencing transcript sequencing (RNA-Seq). Proteomic analysis shows that rebalancing of protein content largely results from the selective increase in the accumulation of only a few proteins. The rebalancing of protein composition occurs with small alterations to the seed’s transcriptome and metabolome. The selectivity of the rebalancing was further tested by introgressing into the SP? line a green fluorescent protein (GFP) glycinin allele mimic and quantifying the resulting accumulation of GFP. The GFP accumulation was similar to the parental GFP-expressing line, showing that the GFP glycinin gene mimic does not participate in proteome rebalancing. The results show that soybeans make large adjustments to the proteome during seed filling and compensate for the shortage of major proteins with the increased selective accumulation of other proteins that maintains a normal protein content.

Schmidt, Monica A.; Barbazuk, W. Brad; Sandford, Michael; May, Greg; Song, Zhihong; Zhou, Wenxu; Nikolau, Basil J.; Herman, Eliot M.

2011-01-01

40

Characterization of potential selenium-binding proteins in the selenophosphate synthetase system.  

PubMed

Selenophosphate, an activated form of selenium that can serve as a selenium donor, is generated by the selD gene product, selenophosphate synthetase (SPS). Selenophosphate is required by several bacteria and by mammals for the specific synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. Although free selenide can be used in vitro for synthesis of selenophosphate, the physiological system that donates selenium to SPS is incompletely characterized. To detect potential selenium-delivery proteins, two known sulfurtransferases and glyceraldehyde-3-phosphate dehydrogenase (GAPDH; EC 1.2.1.12) were analyzed for ability to bind and transfer selenium. Rhodanese (EC 2.8.1.1) was shown to bind selenium tightly, with only part of the selenium being available as substrate for SPS in the presence of added reductant. 3-Mercaptopyruvate sulfurtransferase (3-MST; EC 2.8.1.2) and GAPDH also bound selenium supplied as selenodiglutathione formed from SeO3(2-) and glutathione. Selenium bound to 3-MST and GAPDH was released more readily than that from rhodanese and also was more available as a substrate for SPS. Although rhodanese retained tightly bound selenium under aerobic conditions, the protein gradually became insoluble, whereas GAPDH containing bound selenium was stable at neutral pH for a long period. These results indicate that 3-MST and GAPDH have more suitable potentials as a physiological selenium-delivery protein than rhodanese. In the presence of a selenium-binding protein, a low level of selenodiglutathione formed from SeO3(2-) and glutathione could effectively replace the high concentrations of selenide routinely used as substrate in the SPS in vitro assays. PMID:15653770

Ogasawara, Yuki; Lacourciere, Gerard M; Ishii, Kazuyuki; Stadtman, Thressa C

2005-01-14

41

Infrared, Single Crystal Raman, and SERS Spectra of CH3NH3NaSeO4 . 6X2O and NaNH4SeO4 . 2X2O (X = H,D)  

NASA Astrophysics Data System (ADS)

IR and polarized Raman spectra of CH3NH3NaSeO4 . 6H2O (MASS), NaNH4SeO4 . 2H2O (SAS), and their deuterated analogues are recorded and analyzed. In both the crystal symmetry of SeO2-4 is lower than Td. The symmetry of CH3NH+3 is lower than C3v and hydrogen bonding is strong in MASS. NH+4 is not rotating freely in the crystal lattice of SAS. SERS spectra are recorded in two types of silver colloids. Colloid 1 adsorbs MASS through the nitrogen atom of CH3NH3 group. There are two different adsorption sites for MASS in colloid 2. SAS is chemisorbed by colloid 2 through the oxygen atom of SeO2-4. Shifting and splitting observed for the internal modes of SeO2-4 on adsorption are due to the reduced local symmetry of the ion.

Philip, Daizy; Aruldhas, G.; Osaka, T.; Miyazaki, A.

1994-05-01

42

Rational modification of protein stability by targeting surface sites leads to complicated results.  

PubMed

The rational modification of protein stability is an important goal of protein design. Protein surface electrostatic interactions are not evolutionarily optimized for stability and are an attractive target for the rational redesign of proteins. We show that surface charge mutants can exert stabilizing effects in distinct and unanticipated ways, including ones that are not predicted by existing methods, even when only solvent-exposed sites are targeted. Individual mutation of three solvent-exposed lysines in the villin headpiece subdomain significantly stabilizes the protein, but the mechanism of stabilization is very different in each case. One mutation destabilizes native-state electrostatic interactions but has a larger destabilizing effect on the denatured state, a second removes the desolvation penalty paid by the charged residue, whereas the third introduces unanticipated native-state interactions but does not alter electrostatics. Our results show that even seemingly intuitive mutations can exert their effects through unforeseen and complex interactions. PMID:23798426

Xiao, Shifeng; Patsalo, Vadim; Shan, Bing; Bi, Yuan; Green, David F; Raleigh, Daniel P

2013-06-24

43

Extended networks, porous sheets, and chiral frameworks. Thorium materials containing mixed geometry anions: Structures and properties of Th(SeO3)(SeO4), Th(IO3)2(SeO4)(H2O)3·H2O, and Th(CrO4)(IO3)2  

NASA Astrophysics Data System (ADS)

Three novel Th(IV) compounds containing heavy oxoanions, Th(SeO3)(SeO4) (1), Th(IO3)2(SeO4)(H2O)3·H2O (2), and Th(CrO4)(IO3)2 (3), have been synthesized under mild hydrothermal conditions. Each of these three distinct structures contain trigonal pyramidal and tetrahedral oxoanions. Compound 1 adopts a three-dimensional structure formed from ThO9 tricapped trigonal prisms, trigonal pyramidal selenite, SeO32 , anions containing Se(IV), and tetrahedral selenate, SeO42 , anions containing Se(VI). The structure of 2 contains two-dimensional porous sheets and occluded water molecules. The Th centers are found as isolated ThO9 tricapped trigonal prisms and are bound by four trigonal pyramidal iodate anions, two tetrahedral selenate anions, and three coordinating water molecules. In the structure of 3, the Th(IV) cations are found as ThO9 tricapped trigonal prisms. Each Th center is bound by six IO31 anions and three CrO42 anions forming a chiral three-dimensional structure. Second-harmonic generation of 532 nm light from 1064 nm radiation by a polycrystalline sample of 3 was observed. Crystallographic data (193 K, MoK?, ?=0.71073): 1; monoclinic, P21/c; a=7.0351(5)Å, b=9.5259(7)Å, c=9.0266(7)Å, ?=103.128(1), Z=4, R(F)=2.47% for 91 parameters with 1462 reflections with I>2?(I); 2, monoclinic, P21/n, a=7.4889(9)Å, b=8.002(1)Å, c=20.165(3)Å, ?=100.142(2), Z=4, R(F)=4.71% for 158 parameters with 2934 reflections with I>2?(I); 3, orthorhombic, P212121, a=7.3672(5)Å, b=9.3617(6)Å, c=11.9201(7)Å, Z=4, R(F)=2.04% for 129 parameters with 2035 reflections with I>2?(I).

Sullens, Tyler A.; Almond, Philip M.; Byrd, Jessica A.; Beitz, James V.; Bray, Travis H.; Albrecht-Schmitt, Thomas E.

2006-04-01

44

Dynamics of Nanoparticle-Protein Corona Complex Formation: Analytical Results from Population Balance Equations  

PubMed Central

Background Nanoparticle-protein corona complex formation involves absorption of protein molecules onto nanoparticle surfaces in a physiological environment. Understanding the corona formation process is crucial in predicting nanoparticle behavior in biological systems, including applications of nanotoxicology and development of nano drug delivery platforms. Method This paper extends the modeling work in to derive a mathematical model describing the dynamics of nanoparticle corona complex formation from population balance equations. We apply nonlinear dynamics techniques to derive analytical results for the composition of nanoparticle-protein corona complex, and validate our results through numerical simulations. Results The model presented in this paper exhibits two phases of corona complex dynamics. In the first phase, proteins rapidly bind to the free surface of nanoparticles, leading to a metastable composition. During the second phase, continuous association and dissociation of protein molecules with nanoparticles slowly changes the composition of the corona complex. Given sufficient time, composition of the corona complex reaches an equilibrium state of stable composition. We find analytical approximate formulae for metastable and stable compositions of corona complex. Our formulae are very well-structured to clearly identify important parameters determining corona composition. Conclusion The dynamics of biocorona formation constitute vital aspect of interactions between nanoparticles and living organisms. Our results further understanding of these dynamics through quantitation of experimental conditions, modeling results for in vitro systems to better predict behavior for in vivo systems. One potential application would involve a single cell culture medium related to a complex protein medium, such as blood or tissue fluid.

Darabi Sahneh, Faryad; Scoglio, Caterina; Riviere, Jim

2013-01-01

45

Casein protein results in higher prandial and exercise induced whole body protein anabolism than whey protein in chronic obstructive pulmonary disease.  

PubMed

Exercise is known to improve physical functioning and health status in Chronic Obstructive Pulmonary Disease (COPD). Recently, disturbances in protein turnover and amino acid kinetics have been observed after exercise in COPD. The objective was to investigate which dairy protein is able to positively influence the protein metabolic response to exercise in COPD. 8 COPD patients and 8 healthy subjects performed a cycle test on two days while ingesting casein or whey protein. Whole body protein breakdown (WbPB), synthesis (WbPS), splanchnic amino acid extraction (SPE), and NetWbPS (=WbPS-WbPB) were measured using stable isotope methodology during 20 min of exercise (at 50% peak work load of COPD group). The controls performed a second exercise test at the same relative workload. Exercise was followed by 1 h of recovery. In the healthy group, WbPS, SPE, and NetPS were higher during casein than during whey feeding (P<.01). WbPS and NetPS were higher during exercise, independent of exercise intensity (P<.01). NetPS was higher during casein feeding in COPD due to lower WbPB (P<.05). Higher SPE was found during exercise during casein and whey feeding in COPD (P<.05). Lactate levels during exercise were higher in COPD (P<.05) independent of the protein. Post-exercise, lower NetPS values were found independent of protein type in both groups. Casein resulted in more protein anabolism than whey protein which was maintained during and following exercise in COPD. Optimizing protein intake might be of importance for muscle maintenance during daily physical activities in COPD. PMID:22512824

Engelen, Mariëlle P K J; Rutten, Erica P A; De Castro, Carmen L N; Wouters, Emiel F M; Schols, Annemie M W J; Deutz, Nicolaas E P

2012-04-17

46

Protein Radical Formation Resulting from Eosinophil Peroxidase-catalyzed Oxidation of Sulfite.  

PubMed

Eosinophil peroxidase (EPO) is an abundant heme protein in eosinophils that catalyzes the formation of cytotoxic oxidants implicated in asthma, allergic inflammatory disorders, and cancer. It is known that some proteins with peroxidase activity (horseradish peroxidase and prostaglandin hydroperoxidase) can catalyze oxidation of bisulfite (hydrated sulfur dioxide), leading to the formation of sulfur trioxide anion radical ((.)SO(3)(-)). This free radical further reacts with oxygen to form peroxymonosulfate anion radical ((-)O(3)SOO(.)) and the very reactive sulfate anion radical (SO(4)()), which is nearly as strong an oxidant as the hydroxyl radical. However, the ability of EPO to generate reactive sulfur radicals has not yet been reported. Here we demonstrate that eosinophil peroxidase/H(2)O(2) is able to oxidize bisulfite, ultimately forming the sulfate anion radical (SO(4)()), and that these reactive intermediates can oxidize target proteins to protein radicals, thereby initiating protein oxidation. We used immuno-spin trapping and confocal microscopy to study protein oxidation by EPO/H(2)O(2) in the presence of bisulfite in a pure enzymatic system and in human promyelocytic leukemia HL-60 clone 15 cells, maturated to eosinophils. Polyclonal antiserum raised against the spin trap 5,5-dimethyl-1-pyrroline N-oxide (DMPO) detected the presence of DMPO covalently attached to the proteins resulting from the DMPO trapping of protein free radicals. We found that sulfite oxidation mediated by EPO/H(2)O(2) induced the formation of radical-derived DMPO spin-trapped human serum albumin and, to a lesser extent, of DMPO-EPO. These studies suggest that EPO-dependent oxidative damage may play a role in tissue injury in bisulfite-exacerbated eosinophilic inflammatory disorders. PMID:20501663

Ranguelova, Kalina; Chatterjee, Saurabh; Ehrenshaft, Marilyn; Ramirez, Dario C; Summers, Fiona A; Kadiiska, Maria B; Mason, Ronald P

2010-05-25

47

Increasing habitual protein intake results in reduced postprandial efficiency of peripheral, anabolic wheat protein nitrogen use in  

Microsoft Academic Search

Background: The postprandial retention of dietary protein de- creases when the prevailing protein intake increases. Objective: We investigated the influence of the prevailing protein intake on the regional utilization and anabolic use of wheat protein during the postprandial non-steady state in humans. Design: Healthy adults (n 8) were adapted for 7 d, first to a normal-proteindiet(NP:1g kg1 d1)andthentoahigh-protein diet(HP:2g kg1

Barbara Juillet; Hélène Fouillet; Cécile Bos; Francois Mariotti; Nicolas Gausserès; Robert Benamouzig; Daniel Tomé; Claire Gaudichon

48

A benchmark server using high resolution protein structure data, and benchmark results for membrane helix predictions  

PubMed Central

Background Helical membrane proteins are vital for the interaction of cells with their environment. Predicting the location of membrane helices in protein amino acid sequences provides substantial understanding of their structure and function and identifies membrane proteins in sequenced genomes. Currently there is no comprehensive benchmark tool for evaluating prediction methods, and there is no publication comparing all available prediction tools. Current benchmark literature is outdated, as recently determined membrane protein structures are not included. Current literature is also limited to global assessments, as specialised benchmarks for predicting specific classes of membrane proteins were not previously carried out. Description We present a benchmark server at http://sydney.edu.au/pharmacy/sbio/software/TMH_benchmark.shtml that uses recent high resolution protein structural data to provide a comprehensive assessment of the accuracy of existing membrane helix prediction methods. The server further allows a user to compare uploaded predictions generated by novel methods, permitting the comparison of these novel methods against all existing methods compared by the server. Benchmark metrics include sensitivity and specificity of predictions for membrane helix location and orientation, and many others. The server allows for customised evaluations such as assessing prediction method performances for specific helical membrane protein subtypes. We report results for custom benchmarks which illustrate how the server may be used for specialised benchmarks. Which prediction method is the best performing method depends on which measure is being benchmarked. The OCTOPUS membrane helix prediction method is consistently one of the highest performing methods across all measures in the benchmarks that we performed. Conclusions The benchmark server allows general and specialised assessment of existing and novel membrane helix prediction methods. Users can employ this benchmark server to determine the most suitable method for the type of prediction the user needs to perform, be it general whole-genome annotation or the prediction of specific types of helical membrane protein. Creators of novel prediction methods can use this benchmark server to evaluate the performance of their new methods. The benchmark server will be a valuable tool for researchers seeking to extract more sophisticated information from the large and growing protein sequence databases.

2013-01-01

49

Gene delivery to skeletal muscle results in sustained expression and systemic delivery of a therapeutic protein  

PubMed Central

Somatic gene therapy has been proposed as a means to achieve systemic delivery of therapeutic proteins. However, there is limited evidence that current methods of gene delivery can practically achieve this goal. In this study, we demonstrate that, following a single intramuscular administration of a recombinant adeno-associated virus (rAAV) vector containing the ?-galactosidase (AAV-lacZ) gene into adult BALB/c mice, protein expression was detected in myofibers for at least 32 weeks. A single intramuscular administration of an AAV vector containing a gene for human erythropoietin (AAV-Epo) into mice resulted in dose-dependent secretion of erythropoietin and corresponding increases in red blood cell production that persisted for up to 40 weeks. Primary human myotubes transduced in vitro with the AAV-Epo vector also showed dose-dependent production of Epo. These results demonstrate that rAAV vectors are able to transduce skeletal muscle and are capable of achieving sustained expression and systemic delivery of a therapeutic protein following a single intramuscular administration. Gene therapy using AAV vectors may provide a practical strategy for the treatment of inherited and acquired protein deficiencies.

Kessler, Paul D.; Podsakoff, Gregory M.; Chen, Xiaojuan; McQuiston, Susan A.; Colosi, Peter C.; Matelis, Laura A.; Kurtzman, Gary J.; Byrne, Barry J.

1996-01-01

50

Crystal chemistry of selenates with mineral-like structures: VIII. Butlerite chains in the structure of K(UO2)(SeO4)(OH)(H2O)  

NASA Astrophysics Data System (ADS)

A new potassium uranyl selenate compound K(UO2)(SeO4)(OH)(H2O) has been synthesized for the first time using the technique of evaporation from water solution. Its crystal structure has been solved by direct methods (monoclinic, P21/ c, a = 8.0413(9) Å, b = 8.0362(9) Å, c = 11.6032(14) Å, ? = 106.925(2)°, V = 717.34(14) Å3) and refined to R 1 = 0.0319 ( wR 2 = 0.0824) for 1285 reflections with | F 0| > 4? F . The structure consists of [(UO2(SeO4)(OH)(H2O)]- chains extending along axis b. In the chains, the uranyl pentagonal bipyramids are linked via bridged hydroxyl anions and tetrahedral oxoanions [SeO4]2-. Potassium ions are situated between these chains. No chains of that type have been observed in uranyl compounds earlier, but they had been detected in the structures of butlerite, parabutlerite, uklonskovite, fibroferrite, and a number of synthetic compounds.

Gurzhii, V. V.; Bessonov, A. A.; Krivovichev, S. V.; Tananaev, I. G.; Armbruster, T.; Myasoedov, B. F.

2009-12-01

51

Crystal chemistry of selenates with mineral-like structures. III. Heteropolyhedral chains in the crystal structure of [Mg(H2O)4(SeO4)]2(H2O)  

NASA Astrophysics Data System (ADS)

The crystal structure of a new compound [Mg(H2O)4(SeO4)]2(H2O) (monoclinic, P2 1/ a, a = 7.2549(12), b = 20.059(5), c = 10.3934(17) Å, ? = 101.989(13), V = 1479.5(5) Å3) has been solved by direct methods and refined to R 1 = 0.059 for 2577 observed reflections with | F hkl | ? 4?| F hkl |. The structure consists of [Mg(H2O)4(SeO4)]0 chains formed by alternating corner-sharing Mg octahedrons and (SeO4)2- tetrahedrons. O atoms of Mg octahedrons that are shared with selenate tetrahedrons are in a trans orientation. The heteropoly-hedral octahedral-tetrahedral chains are parallel to the c axis and undulate within the (010) plane. The adjacent chains are linked by hydrogen bonds involving H2O molecules not bound with M2+ cations.

Krivovichev, S. V.

2007-12-01

52

PSI protein classifier: A new program automating PSI-BLAST search results  

Microsoft Academic Search

A new program, PSI Protein Classifier, generalizing the results of both successive and independent iterations of the PSI-BLAST\\u000a program was developed. The technical opportunities of the program are described and illustrated by two examples. An iterative\\u000a screening of the amino acid sequence database detected potential evolutionary relationships between GH5, GH13, GH27, GH31,\\u000a GH36, GH66, GH101 and GH114 families of glycoside

D. G. Naumoff; M. Carreras

2009-01-01

53

Identification of IgE-Binding Egg White Proteins: Comparison of Results Obtained by Different Methods  

Microsoft Academic Search

The binding of IgE to egg white proteins was investigated for 34 sera from adults with a positive case history and\\/or positive RAST towards egg, and the impact of experimental conditions on IgE binding in commonly used methods was studied. Radioimmunoblotting after SDS-PAGE of both reduced and unreduced egg white extracts showed complex reaction patterns. The results were confirmed by

B. Aabin; L. K. Poulsen; K. Ebbehøj; A. Nørgaard; H. Frøkiœr; C. Bindslev-Jensen; V. Barkholt

1996-01-01

54

Aging results in an unusual expression of Drosophila heat shock proteins  

SciTech Connect

The authors used high-resolution two-dimensional polyacrylamide gel electrophoresis to evaluate the effect of aging on the heat shock response in Drosophila melanogaster. Although the aging process is not well understood at the molecular level, recent observations suggest that quantitative changes in gene expression occur as these fruit flies approach senescence. Such genetic alterations are in accord with our present data, which clearly show marked differences in the synthesis of heat shock proteins between young and old fruit flies. In 10-day-old flies, a heat shock of 20 min results in the expression of 14 new proteins as detectable by two-dimensional electrophoresis of ({sup 35}S)methionine-labeled polypeptides, whereas identical treatment of 45-day-old flies leads to the expression of at least 50 new or highly up-regulated proteins. In addition, there is also a concomitant increase in the rate of synthesis of a number of the normal proteins in the older animals. Microdensitometric determinations of the low molecular weight heat shock polypeptides on autoradiographs of five age groups revealed that their maximum expression occurs at 47 days for a population of flies with a mean life span of 33.7 days. Moreover, a heat shock effect similar to that observed in senescent flies occurs in young flies fed canavanine, an arginine analogue, before heat shock.

Fleming, J.E.; Walton, J.K.; Dubitsky, R.; Bensch, K.G. (Linus Pauling Institute of Science and Medicine, Palo Alto, CA (USA))

1988-06-01

55

Diurnal rhythms result in significant changes in the cellular protein complement in the cyanobacterium Cyanothece 51142.  

PubMed

Cyanothece sp. ATCC 51142 is a diazotrophic cyanobacterium notable for its ability to perform oxygenic photosynthesis and dinitrogen fixation in the same single cell. Previous transcriptional analysis revealed that the existence of these incompatible cellular processes largely depends on tightly synchronized expression programs involving ?30% of genes in the genome. To expand upon current knowledge, we have utilized sensitive proteomic approaches to examine the impact of diurnal rhythms on the protein complement in Cyanothece 51142. We found that 250 proteins accounting for ?5% of the predicted ORFs from the Cyanothece 51142 genome and 20% of proteins detected under alternating light/dark conditions exhibited periodic oscillations in their abundances. Our results suggest that altered enzyme activities at different phases during the diurnal cycle can be attributed to changes in the abundance of related proteins and key compounds. The integration of global proteomics and transcriptomic data further revealed that post-transcriptional events are important for temporal regulation of processes such as photosynthesis in Cyanothece 51142. This analysis is the first comprehensive report on global quantitative proteomics in a unicellular diazotrophic cyanobacterium and uncovers novel findings about diurnal rhythms. PMID:21364985

Stöckel, Jana; Jacobs, Jon M; Elvitigala, Thanura R; Liberton, Michelle; Welsh, Eric A; Polpitiya, Ashoka D; Gritsenko, Marina A; Nicora, Carrie D; Koppenaal, David W; Smith, Richard D; Pakrasi, Himadri B

2011-02-22

56

Enzymatic hydrolysis of soy protein isolate and effect of succinylation on the functional properties of resulting protein hydrolysates  

Microsoft Academic Search

Commercial defatted soy meal was solubilized in an aqueous solution at pH 8.5 to prepare a soy protein isolate (SPI) with 90.45% protein and 95% solubility. Soy protein hydrolysate (SPH) was obtained by enzymatic hydrolysis of the SPI using a neutral proteinase at different degrees of hydrolysis (DH=4, 6, 8 and 10). A previous heat treatment of native SPI at

Allaoua Achouri; Wang Zhang; Xu Shiying

1998-01-01

57

Abnormal Expression of Collagen IV in Lens Activates Unfolded Protein Response Resulting in Cataract*  

PubMed Central

Human diseases caused by mutations in extracellular matrix genes are often associated with an increased risk of cataract and lens capsular rupture. However, the underlying mechanisms of cataract pathogenesis in these conditions are still unknown. Using two different mouse models, we show that the accumulation of collagen chains in the secretory pathway activates the stress signaling pathway termed unfolded protein response (UPR). Transgenic mice expressing ectopic Col4a3 and Col4a4 genes in the lens exhibited activation of IRE1, ATF6, and PERK associated with expansion of the endoplasmic reticulum and attenuation of general protein translation. The expression of the transgenes had adverse effects on lens fiber cell differentiation and eventually induced cell death in a group of transgenic fiber cells. In Col4a1+/?ex40 mutant mice, the accumulation of mutant chains also caused low levels of UPR activation. However, cell death was not induced in mutant lenses, suggesting that low levels of UPR activation are not proapoptotic. Collectively, the results provide in vivo evidence for a role of UPR in cataract formation in response to accumulation of terminally unfolded proteins in the endoplasmic reticulum.

Firtina, Zeynep; Danysh, Brian P.; Bai, Xiaoyang; Gould, Douglas B.; Kobayashi, Takehiro; Duncan, Melinda K.

2009-01-01

58

Correlating labeling chemistry and in-vitro test results with the biological behavior of radiolabeled proteins  

SciTech Connect

Monoclonal antibodies possess enormous potential for delivery of therapeutic amounts of radionuclides to target antigens in vivo, in particular for tumor imaging and therapy. Translation of this concept into practice has encountered numerous problems. Specifically whereas general protein radiolabeling methods are applicable to antibodies, immunological properties of the antibodies are often compromised resulting in reduced in-vivo specificity for the target antigens. The bifunctional chelating agent approach shows the most promise, however, development of other agents will be necessary for widespread usefulness of this technique. The effects of labeling chemistry on the in-vivo behavior of several monoclonal antibodies are described. 30 refs., 4 figs., 10 tabs.

Srivastava, S.C.; Meinken, G.E.

1985-01-01

59

Whey protein ingestion in elderly results in greater muscle protein accrual than ingestion of its constituent essential amino acid content  

PubMed Central

It is recognized that both whey protein and essential amino acids (EAA) are stimuli for muscle protein anabolism. The aim of the present study was to determine if the effects of whey protein ingestion on muscle protein accrual in elderly are due solely to its constituent EAA content. Fifteen elderly humans were randomly assigned to ingest a bolus of either 15 g of whey protein (WY), 6.72 g of essential amino acids (EAA), or 7.57 g of non-essential amino acids (NEAA). We utilized the leg arterio-venous model to measure the leg phenylalanine balance (PB), which is an index of muscle protein accrual. PB (nmol·min?1·kg lean leg mass?1) during the 3.5 hours following the bolus ingestion improved in the WY (?216 ± 14 vs ?105 ± 19; P < .05) but not in the EAA (?203 ± 21 vs ?172 ± 38; P > .05) or NEAA groups (?203 ± 19 vs ?204 ± 21; P > .05). The insulin response (ulU·ml?1 210 min?1) during the same period was lower in both the NEAA (48 ± 40) and EAA (213 ± 127) when compared to the WY (1073 ± 229; P < .05). In conclusion, whey protein ingestion improves skeletal muscle protein accrual through mechanisms that are beyond those attributed to its essential amino acid content. This finding may have practical implications for the formulation of nutritional supplements to enhance muscle anabolism in older individuals.

Katsanos, Christos S.; Chinkes, David L.; Paddon-Jones, Douglas; Zhang, Xiao-jun; Aarsland, Asle; Wolfe, Robert R.

2008-01-01

60

The relationship between dietary protein intake and blood pressure: results from the PREMIER study  

Microsoft Academic Search

Observational and clinical studies suggest that high protein intake, particularly protein from plant sources, might reduce blood pressure (BP). To examine the association of dietary protein with BP, we analysed data from PREMIER, an 18-month clinical trial (n=810) that examined the effects of two multi-component lifestyle modifications on BP. We examined the association of protein intake with BP, and in

Y F Wang; WS Yancy Jr; D Yu; C Champagne; L J Appel; P-H Lin

2008-01-01

61

Postmortem measurement of C-reactive protein and interpretation of results in ketoacidosis.  

PubMed

C-reactive protein (CRP) is a widely used acute phase protein that reacts to various tissue-destroying stimuli. Its forensic applications have been established in prior studies. We show that CRP can be successfully measured even after a long postmortem period, up to 18 days, which has not previously been reported. Information on elevated CRP levels can be very valuable for the forensic pathologist in autopsy cases with scarce findings. The interpretation of results can be very challenging, as the elevation can originate from many different reasons, and due to the biochemical changes in cadavers. One less studied possible reason for elevated CRP is ketoacidosis. Here, we present a study on the effect of both alcoholic and diabetic ketoacidosis on blood CRP elevation in forensic autopsy material. Our results imply that ketoacidosis itself can cause a rise in CRP without other underlying causes, such as infection or trauma. However, more comprehensive studies are required to confirm the relationship between ketoacidosis and CRP level elevation. PMID:22366176

Lindroos-Jokinen, Katarina; Keltanen, Terhi; Vanhala, Teija; Valonen, Tiina; Sajantila, Antti

2012-02-25

62

Parvovirus B19 Nonstructural Protein-Induced Damage of Cellular DNA and Resultant Apoptosis  

PubMed Central

Parvovirus B19 is a widespread virus with diverse clinical presentations. The viral nonstructural protein, NS1, binds to and cleaves the viral genome, and induces apoptosis when transfected into nonpermissive cells, such as hepatocytes. We hypothesized that the cytotoxicity of NS1 in such cells results from chromosomal DNA damage caused by the DNA-nicking and DNA-attaching activities of NS1. Upon testing this hypothesis, we found that NS1 covalently binds to cellular DNA and is modified by PARP, an enzyme involved in repairing single-stranded DNA nicks. We furthermore discovered that the DNA nick repair pathway initiated by poly(ADPribose)polymerase and the DNA repair pathways initiated by ATM/ATR are necessary for efficient apoptosis resulting from NS1 expression.

Poole, Brian D.; Kivovich, Violetta; Gilbert, Leona; Naides, Stanley J.

2011-01-01

63

TGF-?1 conjugated to gold nanoparticles results in protein conformational changes and attenuates the biological function.  

PubMed

Gold nanoparticles (AuNPs) are widely used as carriers or therapeutic agents due to their great biocompatibility and unique physical properties. Transforming growth factor-beta 1 (TGF-?1), a member of the cysteine-knot structural superfamily, plays a pivotal role in many diseases and is known as an immunosuppressive agent that attenuates immune response resulting in tumor growth. The results reported herein reflect strong interactions between TGF-?1 and the surface of AuNPs when incubated with serum-containing medium, and demonstrate a time- and dose-dependent pattern. Compared with other serum proteins that can also bind to the AuNP surface, AuNP-TGF?1 conjugate is a thermodynamically favored compound. Epithelial cells undergo epithelial-mesenchymal transition (EMT) upon treatment with TGF-?1; however, treatment with AuNPs reverses this effect, as detected by cell morphology and expression levels of EMT markers. TGF-?1 is found to bind to AuNPs through S-Au bonds by X-ray photoelectron spectroscopy. Fourier transform infrared spectroscopy is employed to analyze the conformational changes of TGF-?1 on the surface of AuNPs. The results indicate that TGF-?1 undergoes significant conformational changes at both secondary and tertiary structural levels after conjugation to the AuNP surface, which results in the deactivation of TGF-?1 protein. An in vivo experiment also shows that addition of AuNPs attenuates the growth of TGF-?1-secreting murine bladder tumor 2 cells in syngeneic C3H/HeN mice, but not in immunocompromised NOD-SCID mice, and this is associated with an increase in the number of tumor-infiltrating CD4? and CD8? T lymphocytes and a decrease in the number of intrasplenic Foxp3(+) lymphocytes. The findings demonstrate that AuNPs may be a promising agent for modulating tumor immunity through inhibiting immunosuppressive TGF-?1 signaling. PMID:23335450

Tsai, Yuh-Shyan; Chen, Yu-Hung; Cheng, Pai-Chiao; Tsai, Hsin-Tzu; Shiau, Ai-Li; Tzai, Tzong-Shin; Wu, Chao-Liang

2013-01-20

64

First results from the PROTEIN experiment on board the International Space Station  

Microsoft Academic Search

On March 15 2009 Space Shuttle Discovery was launched, carrying the Process Unit of the Protein Crystallization Diagnostics Facility (PCDF) to the International Space Station. It contained the PROTEIN experiment, aiming at the in-situ observation of nucleation and crystal growth behaviour of proteins. After installation in the European Drawer Rack (EDR) and connection to the PCDF Electronics Unit, experiment runs

Klaas Decanniere; Lothar Potthast; Vladimir Pletser; Dominique Maes; Fermin Otalora; Jose A. Gavira; Luis David Pati; Peter Lautenschlager; Robert Bosch

2010-01-01

65

Proteins  

NSDL National Science Digital Library

Laboratory manual and supplemental resources that were developed for a college laboratory course in protein purification. The enzyme, Beta-galactosidase, is purified in two steps, with analysis and verification of results. Course materials are divided into four units: Why Proteins, Assays, The Purification Process, and Analysis and Verification. Powerpoint lectures and study guides are provided.

Seidman, Lisa A.; Mowery, Jeanette

2009-10-01

66

Altered protein prenylation in Sertoli cells is associated with adult infertility resulting from childhood mumps infection.  

PubMed

Mumps commonly affects children 5-9 yr of age, and can lead to permanent adult sterility in certain cases. However, the etiology of this long-term effect remains unclear. Mumps infection results in progressive degeneration of the seminiferous epithelium and, occasionally, Sertoli cell-only syndrome. Thus, the remaining Sertoli cells may be critical to spermatogenesis recovery after orchitis healing. Here, we report that the protein farnesylation/geranylgeranylation balance is critical for patients' fertility. The expression of geranylgeranyl diphosphate synthase 1 (GGPPS) was decreased due to elevated promoter methylation in the testes of infertile patients with mumps infection history. When we deleted GGPPS in mouse Sertoli cells, these cells remained intact, whereas the adjacent spermatogonia significantly decreased after the fifth postnatal day. The proinflammatory MAPK and NF-?B signaling pathways were constitutively activated in GGPPS(-/-) Sertoli cells due to the enhanced farnesylation of H-Ras. GGPPS(-/-) Sertoli cells secreted an array of cytokines to stimulate spermatogonia apoptosis, and chemokines to induce macrophage invasion into the seminiferous tubules. Invaded macrophages further blocked spermatogonia development, resulting in a long-term effect through to adulthood. Notably, this defect could be rescued by GGPP administration in EMCV-challenged mice. Our results suggest a novel mechanism by which mumps infection during childhood results in adult sterility. PMID:23825187

Wang, Xiu-Xing; Ying, Pu; Diao, Fan; Wang, Qiang; Ye, Dan; Jiang, Chen; Shen, Ning; Xu, Na; Chen, Wei-Bo; Lai, Shan-Shan; Jiang, Shan; Miao, Xiao-Li; Feng, Jin; Tao, Wei-Wei; Zhao, Ning-Wei; Yao, Bing; Xu, Zhi-Peng; Sun, Hai-Xiang; Li, Jian-Min; Sha, Jia-Hao; Huang, Xing-Xu; Shi, Qing-Hua; Tang, Hong; Gao, Xiang; Li, Chao-Jun

2013-07-01

67

TATA Binding Protein Discriminates between Different Lesions on DNA, Resulting in a Transcription Decrease  

PubMed Central

DNA damage recognition by basal transcription factors follows different mechanisms. Using transcription-competition, nitrocellulose filter binding, and DNase I footprinting assays, we show that, although the general transcription factor TFIIH is able to target any kind of lesion which can be repaired by the nucleotide excision repair pathway, TATA binding protein (TBP)-TFIID is more selective in damage recognition. Only genotoxic agents which are able to induce kinked DNA structures similar to the one for the TATA box in its TBP complex are recognized. Indeed, DNase I footprinting patterns reveal that TBP protects equally 4 nucleotides upstream and 6 nucleotides downstream from the A-T (at position ?29 of the noncoding strand) of the adenovirus major late promoter and from the G-G of a cisplatin-induced 1,2-d(GpG) cross-link. Together, our results may partially explain differences in transcription inhibition rates following DNA damage.

Coin, Frederic; Frit, Philippe; Viollet, Benoit; Salles, Bernard; Egly, Jean-Marc

1998-01-01

68

Human amyloidogenic light chain proteins result in cardiac dysfunction, cell death, and early mortality in zebrafish.  

PubMed

Systemic amyloid light-chain (AL) amyloidosis is associated with rapidly progressive and fatal cardiomyopathy resulting from the direct cardiotoxic effects of circulating AL light chain (AL-LC) proteins and the indirect effects of AL fibril tissue infiltration. Cardiac amyloidosis is resistant to standard heart failure therapies, and, to date, there are limited treatment options for these patients. The mechanisms underlying the development of cardiac amyloidosis and AL-LC cardiotoxicity are largely unknown, and their study has been limited by the lack of a suitable in vivo model system. Here, we establish an in vivo zebrafish model of human AL-LC-induced cardiotoxicity. AL-LC isolated from AL cardiomyopathy patients or control nonamyloidogenic LC protein isolated from multiple myeloma patients (Con-LC) was directly injected into the circulation of zebrafish at 48 h postfertilization. AL-LC injection resulted in impaired cardiac function, pericardial edema, and increased cell death relative to Con-LC, culminating in compromised survival with 100% mortality within 2 wk, independent of AL fibril deposition. Prior work has implicated noncanonical p38 MAPK activation in the pathogenesis of AL-LC-induced cardiotoxicity, and p38 MAPK inhibition via SB-203580 rescued AL-LC-induced cardiac dysfunction and cell death and attenuated mortality in zebrafish. This in vivo zebrafish model of AL-LC cardiotoxicity demonstrates that antagonism of p38 MAPK within the AL-LC cardiotoxic signaling response may serve to improve cardiac function and mortality in AL cardiomyopathy. Furthermore, this in vivo model system will allow for further study of the molecular underpinnings of AL cardiotoxicity and identification of novel therapeutic strategies. PMID:23624626

Mishra, Shikha; Guan, Jian; Plovie, Eva; Seldin, David C; Connors, Lawreen H; Merlini, Giampaolo; Falk, Rodney H; MacRae, Calum A; Liao, Ronglih

2013-04-26

69

Pb2TiOF(SeO3)2Cl and Pb2NbO2(SeO3)2Cl: small changes in structure induced a very large SHG enhancement.  

PubMed

The replacement of NbO6 octahedra in Pb2NbO2(SeO3)2Cl by the TiO5F octahedra in Pb2TiOF(SeO3)2Cl induced a very large SHG enhancement from 2.3 × to 9.6 × KDP (KH2PO4), and both materials are type-I phase matchable. Theoretical calculations based on DFT methods indicate that the inclusion of F(-) anions in the d(0)-TM octahedral coordination unit has a great impact on the band structure and the SHG enhancement of the material. PMID:24042185

Cao, Xue-Li; Hu, Chun-Li; Xu, Xiang; Kong, Fang; Mao, Jiang-Gao

2013-10-01

70

Complex impedance and structural analyses of the mixed system 40(Cu 1? x Ag x I)–30(Ag 2O)–30(SeO 2), (0.05? x?0.25)  

Microsoft Academic Search

Using complex impedance analysis, temperature-dependent electrical conductivity studies of various compositions of the mixed system 40(Cu1?xAgxI)–30(Ag2O)–30(SeO2), (0.05?x?0.25) over the temperature region 295–445 K have been carried out. All the chosen compositions of the system exhibit Arrhenius type of conductivity as a function of temperature and their activation energies for conduction lie in the range 0.27–0.42 eV. The values of ionic

S Murugesan; S. A Suthanthiraraj; P Maruthamuthu

2002-01-01

71

Disrupted Proteolipid Protein Trafficking Results in Oligodendrocyte Apoptosis in an Animal Model of Pelizaeus-Merzbacher Disease  

Microsoft Academic Search

Pelizaeus-Merzbacher disease (PMD) is a dysmyelinating disease resulting from mutations, dele- tions, or duplications of the proteolipid protein ( PLP ) gene. Distinguishing features of PMD include pleio- tropy and a range of disease severities among patients. Previously, we demonstrated that, when expressed in transfected fibroblasts, many naturally occurring mu- tant PLP alleles encode proteins that accumulate in the endoplasmic

Alexander Gow; Cherie M. Southwood; Robert A. Lazzarini

1998-01-01

72

Analysis and characterization of formalin induced DNA-protein cross-links resulting from tissue fixation  

Microsoft Academic Search

Tissue fixation involves chemically modifying cellular proteins and other constituents to stabilize the specimen for later analyses. Fixed and archived tissues are a very important resource of DNA, RNA, and proteins for molecular biological studies such as the diagnosis and study of cancer. New methods are needed for the fixation of tumor tissues from biopsies and for using biopsies from

Alexandra Gorgevska

2006-01-01

73

G protein-coupled receptor 12 deficiency results in dyslipidemia and obesity in mice.  

PubMed

Obesity has been proposed to be a result of an imbalance in the physiological system that controls and maintains the body energy homeostasis. Several G-protein coupled receptors (GPCRs) are involved in the regulation of energy homeostasis. To investigate the importance of GPCR12, mice deficient of this receptor (GPCR12 KO) were studied regarding metabolism. Expression of GPCR12 was found primarily in the limbic and sensory systems, indicating its possible involvement in motivation, emotion together with various autonomic functions, and sensory information processing. GPCR12 KO mice were found to have higher body weight, body fat mass, lower respiratory exchange ratio (RER), hepatic steatosis, and were dyslipidemic. Neither food intake nor energy in faeces was affected in the GPCR12 KO mice. However, lower energy expenditure was found in the GPCR12 KO mice, which may explain the obesity. In conclusion, GPCR12 is considered important for the energy balance since GPCR12 KO mice develop obesity and have lower energy expenditure. This may be important for future drugs that target this receptor. PMID:16887097

Bjursell, Mikael; Gerdin, Anna-Karin; Jönsson, Marie; Surve, Vikas V; Svensson, Lennart; Huang, Xu-Feng; Törnell, Jan; Bohlooly-Y, Mohammad

2006-07-28

74

The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results.  

PubMed

The 19ID undulator beamline of the Structure Biology Center has been designed and built to take full advantage of the high flux, brilliance and quality of X-ray beams delivered by the Advanced Photon Source. The beamline optics are capable of delivering monochromatic X-rays with photon energies from 3.5 to 20 keV (3.5-0.6 A wavelength) with fluxes up to 8-18 x 10(12) photons s(-1) (depending on photon energy) onto cryogenically cooled crystal samples. The size of the beam (full width at half-maximum) at the sample position can be varied from 2.2 mm x 1.0 mm (horizontal x vertical, unfocused) to 0.083 mm x 0.020 mm in its fully focused configuration. Specimen-to-detector distances of between 100 mm and 1500 mm can be used. The high flexibility, inherent in the design of the optics, coupled with a kappa-geometry goniometer and beamline control software allows optimal strategies to be adopted in protein crystallographic experiments, thus maximizing the chances of their success. A large-area mosaic 3 x 3 CCD detector allows high-quality diffraction data to be measured rapidly to the crystal diffraction limits. The beamline layout and the X-ray optical and endstation components are described in detail, and the results of representative crystallographic experiments are presented. PMID:16371706

Rosenbaum, Gerd; Alkire, Randy W; Evans, Gwyndaf; Rotella, Frank J; Lazarski, Krzystof; Zhang, Rong Guang; Ginell, Stephan L; Duke, Norma; Naday, Istvan; Lazarz, Jack; Molitsky, Michael J; Keefe, Lisa; Gonczy, John; Rock, Larry; Sanishvili, Ruslan; Walsh, Martin A; Westbrook, Edwin; Joachimiak, Andrzej

2005-12-22

75

The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results  

PubMed Central

The 19ID undulator beamline of the Structure Biology Center has been designed and built to take full advantage of the high flux, brilliance and quality of X-ray beams delivered by the Advanced Photon Source. The beamline optics are capable of delivering monochromatic X-rays with photon energies from 3.5 to 20 keV (3.5–0.6 Å wavelength) with fluxes up to 8–18 × 1012 photons s?1 (depending on photon energy) onto cryogenically cooled crystal samples. The size of the beam (full width at half-maximum) at the sample position can be varied from 2.2 mm × 1.0 mm (horizontal × vertical, unfocused) to 0.083 mm × 0.020 mm in its fully focused configuration. Specimen-to-detector distances of between 100 mm and 1500 mm can be used. The high flexibility, inherent in the design of the optics, coupled with a ?-geometry goniometer and beamline control software allows optimal strategies to be adopted in protein crystallographic experiments, thus maximizing the chances of their success. A large-area mosaic 3 × 3 CCD detector allows high-quality diffraction data to be measured rapidly to the crystal diffraction limits. The beamline layout and the X-ray optical and endstation components are described in detail, and the results of representative crystallographic experiments are presented.

Rosenbaum, Gerd; Alkire, Randy W.; Evans, Gwyndaf; Rotella, Frank J.; Lazarski, Krzystof; Zhang, Rong-Guang; Ginell, Stephan L.; Duke, Norma; Naday, Istvan; Lazarz, Jack; Molitsky, Michael J.; Keefe, Lisa; Gonczy, John; Rock, Larry; Sanishvili, Ruslan; Walsh, Martin A.; Westbrook, Edwin; Joachimiak, Andrzej

2008-01-01

76

Nonimmune thyroid destruction results from transgenic overexpression of an allogeneic major histocompatibility complex class I protein.  

PubMed Central

The overexpression of major histocompatibility complex (MHC) class I molecules in endocrine epithelial cells is an early feature of autoimmune thyroid disease and insulin-dependent diabetes mellitus, which may reflect a cellular response, e.g., to viruses or toxins. Evidence from a transgenic model in pancreatic beta cells suggests that MHC class I overexpression could play an independent role in endocrine cell destruction. We demonstrate in this study that the transgenic overexpression of an allogeneic MHC class I protein (H-2Kb) linked to the rat thyroglobulin promoter, in H-2Kk mice homozygous for the transgene, leads to thyrocyte atrophy, hypothyroidism, growth retardation, and death. Thyrocyte atrophy occurred in the absence of lymphocytic infiltration. Tolerance to allogeneic class I was revealed by the reduced ability of primed lymphocytes from transgenic mice to lyse H-2Kb target cells in vitro. This nonimmune form of thyrocyte destruction and hypothyroidism recapitulates the beta-cell destruction and diabetes that results from transgenic overexpression of MHC class I molecules in pancreatic beta cells. Thus, we conclude that overexpression of MHC class I molecules may be a general mechanism that directly impairs endocrine epithelial cell viability. Images

Frauman, A G; Chu, P; Harrison, L C

1993-01-01

77

Expression of Huntington's disease protein results in apoptotic neurons in the brains of cloned transgenic pigs  

PubMed Central

Neurodegeneration is a hallmark of many neurological diseases, including Alzheimer's, Parkinson's and the polyglutamine diseases, which are all caused by misfolded proteins that accumulate in neuronal cells of the brain. Although apoptosis is believed to contribute to neurodegeneration in these cases, genetic mouse models of these diseases often fail to replicate apoptosis and overt neurodegeneration in the brain. Using nuclear transfer, we generated transgenic Huntington's disease (HD) pigs that express N-terminal (208 amino acids) mutant huntingtin with an expanded polyglutamine tract (105Q). Postnatal death, dyskinesia and chorea-like movement were observed in some transgenic pigs that express mutant huntingtin. Importantly, the transgenic HD pigs, unlike mice expressing the same transgene, displayed typical apoptotic neurons with DNA fragmentation in their brains. Also, expression of mutant huntingtin resulted in more neurons with activated caspase-3 in transgenic pig brains than that in transgenic mouse brains. Our findings suggest that species differences determine neuropathology and underscore the importance of large mammalian animals for modeling neurological disorders.

Yang, Dongshan; Wang, Chuan-En; Zhao, Bentian; Li, Wei; Ouyang, Zhen; Liu, Zhaoming; Yang, Huaqiang; Fan, Pei; O'Neill, Ashley; Gu, Weiwang; Yi, Hong; Li, Shihua; Lai, Liangxue; Li, Xiao-Jiang

2010-01-01

78

Simultaneous removal of thiolated membrane proteins resulting in nanostructured lipid layers.  

PubMed

Self-organization of membrane-embedded peptides and proteins causes the formation of lipid mesostructures in the membranes. One example is purple membranes (PM), which consist of lipids and bacteriorhodopsin (BR) as the only protein component. The BRs form a hexagonal crystalline lattice. A complementary structure is formed by the lipids. Employing BR and PM as an example, we report a method where major parts of the mesoscopic self-assembled protein structures can be extracted from the lipid bilayer membrane. A complementary lipid nanostructure remains on the substrate. To remove such a large number of thiolated proteins simultaneously by applying a mechanical force, they are first reacted at physiological conditions with gold nanoparticles, and then a thin gold film is sputtered onto them that fuses with the gold nanoparticles forming a uniform layer, which finally can be lifted off. In this step, all of the previously gold-labeled proteins are pulled out of the membrane simultaneously. A stable lipid nanostructure is obtained on the mica substrate. Its stability is due to either binding of the lipids to the substrate through ionic bonds or to enough residual proteins to stabilize the lipid nanostructure against reorganization. This method may be applied easily and efficiently wherever thiolated proteins or peptides are employed as self-assembling and structure-inducing units in lipid membranes. PMID:16732639

Wu, Aiguo; Jia, Zhihong; Schaper, Andreas; Noll, Frank; Hampp, Norbert A

2006-06-01

79

Moderate energy restriction with high protein diet results in healthier outcome in women  

PubMed Central

Background The present study compares two different weight reduction regimens both with a moderately high protein intake on body composition, serum hormone concentration and strength performance in non-competitive female athletes. Methods Fifteen normal weighted women involved in recreational resistance training and aerobic training were recruited for the study (age 28.5 ± 6.3 yr, height 167.0 ± 7.0 cm, body mass 66.3 ± 4.2 kg, body mass index 23.8 ± 1.8, mean ± SD). They were randomized into two groups. The 1 KG group (n = 8; energy deficit 1100 kcal/day) was supervised to reduce body weight by 1 kg per week and the 0.5 KG group (n = 7; energy deficit 550 kcal/day) by 0.5 kg per week, respectively. In both groups protein intake was kept at least 1.4 g/kg body weight/day and the weight reduction lasted four weeks. At the beginning of the study the energy need was calculated using food and training diaries. The same measurements were done before and after the 4-week weight reduction period including total body composition (DXA), serum hormone concentrations, jumping ability and strength measurements Results During the 4-week weight reduction period there were no changes in lean body mass and bone mass, but total body mass, fat mass and fat percentage decreased significantly in both groups. The changes were greater in the 1 KG group than in the 0.5 KG group in total body mass (p < 0.001), fat mass (p < 0.001) and fat percentage (p < 0.01). Serum testosterone concentration decreased significantly from 1.8 ± 1.0 to 1.4 ± 0.9 nmol/l (p < 0.01) in 1 KG and the change was greater in 1 KG (30%, p < 0.001) than in 0.5 KG (3%). On the other hand, SHBG increased significantly in 1 KG from 63.4 ± 17.7 to 82.4 ± 33.0 nmol/l (p < 0.05) during the weight reducing regimen. After the 4-week period there were no changes in strength performance in 0.5 KG group, however in 1 KG maximal strength in bench press decreased (p < 0.05) while endurance strength in squat and counter movement jump improved (p < 0.05) Conclusion It is concluded that a weight reduction by 0.5 kg per week with ~1.4 g protein/kg body weight/day can be recommended to normal weighted, physically active women instead of a larger (e.g. 1 kg per week) weight reduction because the latter may lead to a catabolic state. Vertical jumping performance is improved when fat mass and body weight decrease. Thus a moderate weight reduction prior to a major event could be considered beneficial for normal built athletes in jumping events.

2010-01-01

80

The crystal structure of ilinskite, NaCu5O2(SeO3)2Cl3, and review of mixed-ligand CuOmCln coordination geometries in minerals and inorganic compounds  

NASA Astrophysics Data System (ADS)

The crystal structure of ilinskite, NaCu5O2(SeO3)2Cl3, a rare copper selenite chloride from volcanic fumaroles of the Great fissure Tolbachik eruption (Kamchatka peninsula, Russia), has been solved by direct methods and refined to R 1 = 0.044 on the basis of 2720 unique observed reflections. The mineral is orthorhombic, Pnma, a = 17.769(7), b = 6.448(3), c = 10.522(4) Å, V = 1205.6(8) Å3, Z = 4. The The CuOmCln coordination polyhedra share edges to form tetramers that have 'additional' O1 and O2 atoms as centers. The O1Cu4 and O2Cu4 tetrahedra share common Cu atoms to form [O2Cu5]6+ sheets. The SeO3 groups and Cl atoms are adjacent to the [O2Cu5]6+ sheets to form complex layers parallel to (100). The Na+ cations are located in between the layers. A review of mixed-ligand CuOmCln coordination polyhedra in minerals and inorganic compounds is given. There are in total 26 stereochemically different mixed-ligand Cu-O-Cl coordinations.

Krivovichev, Sergey V.; Filatov, Stanislav K.; Vergasova, Lidiya P.

2013-04-01

81

The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LCMS\\/MS proteomics results  

Microsoft Academic Search

BACKGROUND: Mass spectrometry (MS) based label-free protein quantitation has mainly focused on analysis of ion peak heights and peptide spectral counts. Most analyses of tandem mass spectrometry (MS\\/MS) data begin with an enzymatic digestion of a complex protein mixture to generate smaller peptides that can be separated and identified by an MS\\/MS instrument. Peptide spectral counting techniques attempt to quantify

John C. Braisted; Srilatha Kuntumalla; Christine Vogel; Edward M. Marcotte; Alan R. Rodrigues; Rong Wang; Shih-ting Huang; Erik S. Ferlanti; Alexander I. Saeed; Robert D. Fleischmann; Scott N. Peterson; Rembert Pieper

2008-01-01

82

Next-generation protein-rich potato expressing the seed protein gene AmA1 is a result of proteome rebalancing in transgenic tuber.  

PubMed

Protein deficiency is the most crucial factor that affects physical growth and development and that increases morbidity and mortality especially in developing countries. Efforts have been made to improve protein quality and quantity in crop plants but with limited success. Here, we report the development of transgenic potatoes with enhanced nutritive value by tuber-specific expression of a seed protein, AmA1 (Amaranth Albumin 1), in seven genotypic backgrounds suitable for cultivation in different agro-climatic regions. Analyses of the transgenic tubers revealed up to 60% increase in total protein content. In addition, the concentrations of several essential amino acids were increased significantly in transgenic tubers, which are otherwise limited in potato. Moreover, the transgenics also exhibited enhanced photosynthetic activity with a concomitant increase in total biomass. These results are striking because this genetic manipulation also resulted in a moderate increase in tuber yield. The comparative protein profiling suggests that the proteome rebalancing might cause increased protein content in transgenic tubers. Furthermore, the data on field performance and safety evaluation indicate that the transgenic potatoes are suitable for commercial cultivation. In vitro and in vivo studies on experimental animals demonstrate that the transgenic tubers are also safe for human consumption. Altogether, these results emphasize that the expression of AmA1 is a potential strategy for the nutritional improvement of food crops. PMID:20855595

Chakraborty, Subhra; Chakraborty, Niranjan; Agrawal, Lalit; Ghosh, Sudip; Narula, Kanika; Shekhar, Shubhendu; Naik, Prakash S; Pande, P C; Chakrborti, Swarup Kumar; Datta, Asis

2010-09-20

83

Next-generation protein-rich potato expressing the seed protein gene AmA1 is a result of proteome rebalancing in transgenic tuber  

PubMed Central

Protein deficiency is the most crucial factor that affects physical growth and development and that increases morbidity and mortality especially in developing countries. Efforts have been made to improve protein quality and quantity in crop plants but with limited success. Here, we report the development of transgenic potatoes with enhanced nutritive value by tuber-specific expression of a seed protein, AmA1 (Amaranth Albumin 1), in seven genotypic backgrounds suitable for cultivation in different agro-climatic regions. Analyses of the transgenic tubers revealed up to 60% increase in total protein content. In addition, the concentrations of several essential amino acids were increased significantly in transgenic tubers, which are otherwise limited in potato. Moreover, the transgenics also exhibited enhanced photosynthetic activity with a concomitant increase in total biomass. These results are striking because this genetic manipulation also resulted in a moderate increase in tuber yield. The comparative protein profiling suggests that the proteome rebalancing might cause increased protein content in transgenic tubers. Furthermore, the data on field performance and safety evaluation indicate that the transgenic potatoes are suitable for commercial cultivation. In vitro and in vivo studies on experimental animals demonstrate that the transgenic tubers are also safe for human consumption. Altogether, these results emphasize that the expression of AmA1 is a potential strategy for the nutritional improvement of food crops.

Chakraborty, Subhra; Chakraborty, Niranjan; Agrawal, Lalit; Ghosh, Sudip; Narula, Kanika; Shekhar, Shubhendu; Naik, Prakash S.; Pande, P. C.; Chakrborti, Swarup Kumar; Datta, Asis

2010-01-01

84

Resistance to platelet microbicidal protein results in increased severity of experimental Candida albicans endocarditis.  

PubMed Central

Thrombin-induced platelet microbicidal protein (tPMP) exerts potent in vitro microbicidal activity against pathogens commonly found in the bloodstream, including Staphylococcus aureus, Staphylococcus epidermidis, and Candida albicans. Localized platelet release of tPMP may be important in defense against infections involving the vascular endothelium caused by tPMP-susceptible organisms. In contrast, pathogens capable of surviving in the presence of tPMP could then exploit the platelet as an adhesive surface for attachment to damaged endothelium. To examine these hypotheses, we derived a tPMP-resistant (tPMP(r)) C. albicans strain from its tPMP-sensitive (tPMP(s)) parental strains were equivalent in vitro as assessed by genotyping (electrophoretic karyotype and restriction endonuclease analysis of genomic DNA), biotyping, germination, platelet aggregation, adherence to vascular endothelial cells, and growth characteristics. In addition, the tPMP(r) phenotype was stable following multiple in vitro and in vivo passages. We then investigated the in vivo relevance of tPMP susceptibility on endovascular infection using a rabbit model of endocarditis and hematogenous dissemination. Rabbits with transaortic catheters (n = 15 in each group) were challenged with either the tPMP(s) or tPMP(r) C. albicans strain. All rabbits developed C. albicans-induced endocarditis, as determined by the presence of infected vegetations. In rabbits challenged with tPMP(s) strain (P < 0.001). These results were seen in the absence of differences in either initial adherence of strains to cardiac valves or vegetation weights. Furthermore, although these C. albicans strains induced equivalent rates and extent of hematogenous renal infection, only the tPMP(r) strain disseminated hematogenously to the spleen (15 of 15 rabbits) versus 0 of 15 [tpmp(s) strain]; P < 0.0001). Thus, tPMP(r) C. albicans caused more-severe endocarditis and produced greater metastatic sequelae than the tPMP(s) counterpart.

Yeaman, M R; Soldan, S S; Ghannoum, M A; Edwards, J E; Filler, S G; Bayer, A S

1996-01-01

85

Results of a screening programme to identify plants or plant extracts that inhibit ruminal protein degradation.  

PubMed

One aim of the EC Framework V project, 'Rumen-up' (QLK5-CT-2001-00 992), was to find plants or plant extracts that would inhibit the nutritionally wasteful degradation of protein in the rumen. A total of 500 samples were screened in vitro using 14C-labelled casein in a 30-min incubation with ruminal digesta. Eight were selected for further investigation using a batch fermentation system and soya protein and bovine serum albumin as proteolysis substrates; proteolysis was monitored over 12 h by the disappearance of soluble protein and the production of branched SCFA and NH3. Freeze-dried, ground foliage of Peltiphyllum peltatum, Helianthemum canum, Arbutus unedo, Arctostaphylos uva-ursi and Knautia arvensis inhibited proteolysis (P < 0.05), while Daucus carota, Clematis vitalba and Erica arborea had little effect. Inhibition by the first four samples appeared to be caused by the formation of insoluble tannin-protein complexes. The samples were rich in phenolics and inhibition was reversed by polyethyleneglycol. In contrast, K. arvensis contained low concentrations of phenolics and no tannins, had no effect in the 30-min assay, yet inhibited the degradation rate of soluble protein (by 14 %, P < 0.0001) and the production of branched SCFA (by 17 %, P < 0.05) without precipitating protein in the 12-h batch fermentation. The effects showed some resemblance to those obtained in parallel incubations containing 3 mum-monensin, suggesting that K. arvensis may be a plant-derived feed additive that can suppress growth and activity of key proteolytic ruminal micro-organisms in a manner similar to that already well known for monensin. PMID:17445338

Selje, N; Hoffmann, E M; Muetzel, S; Ningrat, R; Wallace, R J; Becker, K

2007-04-20

86

Vaccinia Virus Penetration Requires Cholesterol and Results in Specific Viral Envelope Proteins Associated with Lipid Rafts  

Microsoft Academic Search

Vaccinia virus infects a wide variety of mammalian cells from different hosts, but the mechanism of virus entry is not clearly defined. The mature intracellular vaccinia virus contains several envelope proteins medi- ating virion adsorption to cell surface glycosaminoglycans; however, it is not known how the bound virions initiate virion penetration into cells. For this study, we investigated the importance

Che-Sheng Chung; Cheng-Yen Huang; Wen Chang

2005-01-01

87

Native-sized recombinant spider silk protein produced in metabolically engineered Escherichia coli results in a strong fiber  

PubMed Central

Spider dragline silk is a remarkably strong fiber that makes it attractive for numerous applications. Much has thus been done to make similar fibers by biomimic spinning of recombinant dragline silk proteins. However, success is limited in part due to the inability to successfully express native-sized recombinant silk proteins (250–320 kDa). Here we show that a 284.9 kDa recombinant protein of the spider Nephila clavipes is produced and spun into a fiber displaying mechanical properties comparable to those of the native silk. The native-sized protein, predominantly rich in glycine (44.9%), was favorably expressed in metabolically engineered Escherichia coli within which the glycyl-tRNA pool was elevated. We also found that the recombinant proteins of lower molecular weight versions yielded inferior fiber properties. The results provide insight into evolution of silk protein size related to mechanical performance, and also clarify why spinning lower molecular weight proteins does not recapitulate the properties of native fibers. Furthermore, the silk expression, purification, and spinning platform established here should be useful for sustainable production of natural quality dragline silk, potentially enabling broader applications.

Xia, Xiao-Xia; Qian, Zhi-Gang; Ki, Chang Seok; Park, Young Hwan; Kaplan, David L.; Lee, Sang Yup

2010-01-01

88

Native-sized recombinant spider silk protein produced in metabolically engineered Escherichia coli results in a strong fiber.  

PubMed

Spider dragline silk is a remarkably strong fiber that makes it attractive for numerous applications. Much has thus been done to make similar fibers by biomimic spinning of recombinant dragline silk proteins. However, success is limited in part due to the inability to successfully express native-sized recombinant silk proteins (250-320 kDa). Here we show that a 284.9 kDa recombinant protein of the spider Nephila clavipes is produced and spun into a fiber displaying mechanical properties comparable to those of the native silk. The native-sized protein, predominantly rich in glycine (44.9%), was favorably expressed in metabolically engineered Escherichia coli within which the glycyl-tRNA pool was elevated. We also found that the recombinant proteins of lower molecular weight versions yielded inferior fiber properties. The results provide insight into evolution of silk protein size related to mechanical performance, and also clarify why spinning lower molecular weight proteins does not recapitulate the properties of native fibers. Furthermore, the silk expression, purification, and spinning platform established here should be useful for sustainable production of natural quality dragline silk, potentially enabling broader applications. PMID:20660779

Xia, Xiao-Xia; Qian, Zhi-Gang; Ki, Chang Seok; Park, Young Hwan; Kaplan, David L; Lee, Sang Yup

2010-07-26

89

C825T G-protein ?3 subunit gene polymorphism, tilt test results and point score in syncopal patients  

Microsoft Academic Search

We evaluated C825T polymorphism of the G-protein ?3 subunit gene in syncopal patients in regard to tilting results and the diagnostic point score (PS). In a multivariate analysis,\\u000a only PS ? ?2 was associated with positive passive tilting (P < 0.05). The relationship between tilting results and this polymorphism needs further study.

Malgorzata Lelonek; Tadeusz Pietrucha; Monika Matyjaszczyk; Jan Henryk Goch

2008-01-01

90

Loss of C. elegans BBS-7 and BBS-8 protein function results in cilia defects and compromised intraflagellar transport.  

PubMed

Bardet-Biedl syndrome (BBS) is a genetically heterogeneous developmental disorder whose molecular basis is largely unknown. Here, we show that mutations in the Caenorhabditis elegans bbs-7 and bbs-8 genes cause structural and functional defects in cilia. C. elegans BBS proteins localize predominantly at the base of cilia, and like proteins involved in intraflagellar transport (IFT), a process necessary for cilia biogenesis and maintenance, move bidirectionally along the ciliary axoneme. Importantly, we demonstrate that BBS-7 and BBS-8 are required for the normal localization/motility of the IFT proteins OSM-5/Polaris and CHE-11, and to a notably lesser extent, CHE-2. We propose that BBS proteins play important, selective roles in the assembly and/or function of IFT particle components. Our findings also suggest that some of the cardinal and secondary symptoms of BBS, such as obesity, diabetes, cardiomyopathy, and learning defects may result from cilia dysfunction. PMID:15231740

Blacque, Oliver E; Reardon, Michael J; Li, Chunmei; McCarthy, Jonathan; Mahjoub, Moe R; Ansley, Stephen J; Badano, Jose L; Mah, Allan K; Beales, Philip L; Davidson, William S; Johnsen, Robert C; Audeh, Mark; Plasterk, Ronald H A; Baillie, David L; Katsanis, Nicholas; Quarmby, Lynne M; Wicks, Stephen R; Leroux, Michel R

2004-07-01

91

Moderate energy restriction with high protein diet results in healthier outcome in women  

Microsoft Academic Search

BACKGROUND: The present study compares two different weight reduction regimens both with a moderately high protein intake on body composition, serum hormone concentration and strength performance in non-competitive female athletes. METHODS: Fifteen normal weighted women involved in recreational resistance training and aerobic training were recruited for the study (age 28.5 ± 6.3 yr, height 167.0 ± 7.0 cm, body mass

Antti A Mero; Heikki Huovinen; Olle Matintupa; Juha J Hulmi; Risto Puurtinen; Hannele Hohtari; Tuomo AM Karila

2010-01-01

92

Protein High-Force Pulling Simulations Yield Low-Force Results  

PubMed Central

All-atom explicit-solvent molecular dynamics simulations are used to pull with extremely large constant force (750–3000 pN) on three small proteins. The introduction of a nondimensional timescale permits direct comparison of unfolding across all forces. A crossover force of approximately 1100 pN divides unfolding dynamics into two regimes. At higher forces, residues sequentially unfold from the pulling end while maintaining the remainder of the protein force-free. Measurements of hydrodynamic viscous stresses are made easy by the high speeds of unfolding. Using an exact low-Reynolds-number scaling, these measurements can be extrapolated to provide, for the first time, an estimate of the hydrodynamic force on low-force unfolding. Below 1100 pN, but surprisingly still at extremely large applied force, intermediate states and cooperative unfoldings as seen at much lower forces are observed. The force-insensitive persistence of these structures indicates that decomposition into unfolded fragments requires a large fluctuation. This finding suggests how proteins are constructed to resist transient high force. The progression of helix and sheet unfolding is also found to be insensitive to force. The force-insensitivity of key aspects of unfolding opens the possibility that numerical simulations can be accelerated by high applied force while still maintaining critical features of unfolding.

Lichter, Seth; Rafferty, Benjamin; Flohr, Zachary; Martini, Ashlie

2012-01-01

93

On the Evolution of Protein Folds: Are Similar Motifs in Different Protein Folds the Result of Convergence, Insertion, or Relics of an Ancient Peptide World?  

Microsoft Academic Search

Thispaper presents and discusses evidence suggesting how the diversity of domain folds in existence today might have evolved from peptide ancestors. We apply a structure similarity detection method to detect instances where localized regions of different protein folds contain highly similar sequences and structures. Results of performing an all-on-all comparison of known structures are described and compared with other recently

Andrei N. Lupas; Chris P. Ponting; Robert B. Russell

2001-01-01

94

A deep intronic mutation in the ankyrin-1 gene causes diminished protein expression resulting in hemolytic anemia in mice.  

PubMed

Linkage between transmembrane proteins and the spectrin-based cytoskeleton is necessary for membrane elasticity of red blood cells. Mutations of the proteins that mediate this linkage result in various types of hemolytic anemia. Here we report a novel N-ethyl-N-nitrosourea-induced mutation of ankyrin-1, named hema6, which causes hereditary spherocytosis in mice through a mild reduction of protein expression. The causal mutation was traced to a single nucleotide transition located deep into intron 13 of gene Ank1. In vitro minigene splicing assay revealed two abnormally spliced transcripts containing cryptic exons from fragments of Ank1 intron 13. The inclusion of cryptic exons introduced a premature termination codon, which leads to nonsense-mediated decay of the mutant transcripts in vivo. Hence, in homozygous mice, only wild-type ankyrin-1 is expressed, albeit at 70% of the level in wild-type mice. Heterozygotes display a similar hereditary spherocytosis phenotype stemming from intermediate protein expression level, indicating the haploinsufficiency of the mutation. Weakened linkage between integral transmembrane protein, band 3, and underlying cytoskeleton was observed in mutant mice as the result of reduced high-affinity binding sites provided by ankyrin-1. Hema6 is the only known mouse mutant of Ank1 allelic series that expresses full-length canonical ankyrin-1 at a reduced level, a fact that makes it particularly useful to study the functional impact of ankyrin-1 quantitative deficiency. PMID:23934996

Huang, Hua; Zhao, Pengxiang; Arimatsu, Kei; Tabeta, Koichi; Yamazaki, Kazuhisa; Krieg, Lara; Fu, Emily; Zhang, Tian; Du, Xin

2013-10-03

95

A Deep Intronic Mutation in the Ankyrin-1 Gene Causes Diminished Protein Expression Resulting in Hemolytic Anemia in Mice  

PubMed Central

Linkage between transmembrane proteins and the spectrin-based cytoskeleton is necessary for membrane elasticity of red blood cells. Mutations of the proteins that mediate this linkage result in various types of hemolytic anemia. Here we report a novel N-ethyl-N-nitrosourea?induced mutation of ankyrin-1, named hema6, which causes hereditary spherocytosis in mice through a mild reduction of protein expression. The causal mutation was traced to a single nucleotide transition located deep into intron 13 of gene Ank1. In vitro minigene splicing assay revealed two abnormally spliced transcripts containing cryptic exons from fragments of Ank1 intron 13. The inclusion of cryptic exons introduced a premature termination codon, which leads to nonsense-mediated decay of the mutant transcripts in vivo. Hence, in homozygous mice, only wild-type ankyrin-1 is expressed, albeit at 70% of the level in wild-type mice. Heterozygotes display a similar hereditary spherocytosis phenotype stemming from intermediate protein expression level, indicating the haploinsufficiency of the mutation. Weakened linkage between integral transmembrane protein, band 3, and underlying cytoskeleton was observed in mutant mice as the result of reduced high-affinity binding sites provided by ankyrin-1. Hema6 is the only known mouse mutant of Ank1 allelic series that expresses full-length canonical ankyrin-1 at a reduced level, a fact that makes it particularly useful to study the functional impact of ankyrin-1 quantitative deficiency.

Huang, Hua; Zhao, PengXiang; Arimatsu, Kei; Tabeta, Koichi; Yamazaki, Kazuhisa; Krieg, Lara; Fu, Emily; Zhang, Tian; Du, Xin

2013-01-01

96

Allelic variants of the amylose extender mutation of maize demonstrate phenotypic variation in starch structure resulting from modified protein-protein interactions.  

PubMed

Amylose extender (ae(-)) starches characteristically have modified starch granule morphology resulting from amylopectin with reduced branch frequency and longer glucan chains in clusters, caused by the loss of activity of the major starch branching enzyme (SBE), which in maize endosperm is SBEIIb. A recent study with ae(-) maize lacking the SBEIIb protein (termed ae1.1 herein) showed that novel protein-protein interactions between enzymes of starch biosynthesis in the amyloplast could explain the starch phenotype of the ae1.1 mutant. The present study examined an allelic variant of the ae(-) mutation, ae1.2, which expresses a catalytically inactive form of SBEIIb. The catalytically inactive SBEIIb in ae1.2 lacks a 28 amino acid peptide (Val272-Pro299) and is unable to bind to amylopectin. Analysis of starch from ae1.2 revealed altered granule morphology and physicochemical characteristics distinct from those of the ae1.1 mutant as well as the wild-type, including altered apparent amylose content and gelatinization properties. Starch from ae1.2 had fewer intermediate length glucan chains (degree of polymerization 16-20) than ae1.1. Biochemical analysis of ae1.2 showed that there were differences in the organization and assembly of protein complexes of starch biosynthetic enzymes in comparison with ae1.1 (and wild-type) amyloplasts, which were also reflected in the composition of starch granule-bound proteins. The formation of stromal protein complexes in the wild-type and ae1.2 was strongly enhanced by ATP, and broken by phosphatase treatment, indicating a role for protein phosphorylation in their assembly. Labelling experiments with [?-(32)P]ATP showed that the inactive form of SBEIIb in ae1.2 was phosphorylated, both in the monomeric form and in association with starch synthase isoforms. Although the inactive SBEIIb was unable to bind starch directly, it was strongly associated with the starch granule, reinforcing the conclusion that its presence in the granules is a result of physical association with other enzymes of starch synthesis. In addition, an Mn(2+)-based affinity ligand, specific for phosphoproteins, was used to show that the granule-bound forms of SBEIIb in the wild-type and ae1.2 were phosphorylated, as was the granule-bound form of SBEI found in ae1.2 starch. The data strongly support the hypothesis that the complement of heteromeric complexes of proteins involved in amylopectin synthesis contributes to the fine structure and architecture of the starch granule. PMID:22121198

Liu, Fushan; Ahmed, Zaheer; Lee, Elizabeth A; Donner, Elizabeth; Liu, Qiang; Ahmed, Regina; Morell, Matthew K; Emes, Michael J; Tetlow, Ian J

2011-11-25

97

Analysis of proteins in bronchoalveolar lavage fluids during pulmonary edema resulting from nitrogen dioxide and cadmium exposure  

SciTech Connect

We have developed a new HPLC method by which quantitative measurements can be made on the biochemical constituents of the extracellular fluid lining of the lung as sampled by bronchoalveolar lavage. Nine of the fractions are proteins, two are phospholipids, and two fractions remained unidentified. Rats were subjected to the intrapulmonary deposition of cadmium, a treatment model known to induce pulmonary edema and cause a translocation of blood compartment proteins into the lung's alveolar space compartment. Resulting pulmonary edema was hallmarked by /approximately/25-fold increases in three major blood compartment-derived HPLC protein fractions, two of which have been identified as albumin and immunoglobulin(s). Analysis of lavage fluid from rats exposed to 100 ppM NO/sub 2/ for 15 min, an exposure regimen which also produces pulmonary edema, indicated that the three blood compartment proteins in the lavage fluids were elevated 35- to 72-fold over controls 24 h after exposure. These results demonstrate that HPLC can be used to provide a highly sensitive method for detection and quantitation of pulmonary edema that can occur in acute lung injuries resulting from environmental insults.

Gurley, L.R.; London, J.E.; Dethloff, L.A.; Lehnert, B.E.

1988-01-01

98

Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications  

PubMed Central

Correct codon-anticodon pairing promotes translational fidelity, with these interactions greatly facilitated by modified nucleosides found in tRNA. We hypothesized that wobble uridine modifications catalyzed by tRNA methyltransferase 9 (Trm9) are essential for translational fidelity. In support, we have used phenotypic, reporter and protein-based assays to demonstrate increased translational infidelity in trm9? Saccharomyces cerevisiae cells. Codon reengineering studies suggest that Trm9-catalyzed tRNA modifications promote fidelity during the translation of specific genes, those rich in arginine and glutamic acid codons from mixed boxes. Using quantitative tRNA modification analysis, we determined that trm9? cells are only deficient in 2 of 23 tRNA modifications, with those 2, 5-methoxycarbonylmethyluridine (mcm5U) and 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U), classified as key determinants of translational fidelity. We also show that in the absence of mcm5U and mcm5s2U, the resulting translational infidelity promotes protein errors and activation of unfolded protein and heat shock responses. These data support a model in which Trm9-catalyzed tRNA modifications promote fidelity during the translation of specific transcripts, with decreased wobble base modification leading to translational infidelity, protein errors and activation of protein stress response pathways.

Patil, Ashish; Chan, Clement T.Y.; Dyavaiah, Madhu; Rooney, John P.; Dedon, Peter C.; Begley, Thomas J.

2012-01-01

99

Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications.  

PubMed

Correct codon-anticodon pairing promotes translational fidelity, with these interactions greatly facilitated by modified nucleosides found in tRNA. We hypothesized that wobble uridine modifications catalyzed by tRNA methyltransferase 9 (Trm9) are essential for translational fidelity. In support, we have used phenotypic, reporter and protein-based assays to demonstrate increased translational infidelity in trm9? Saccharomyces cerevisiae cells. Codon reengineering studies suggest that Trm9-catalyzed tRNA modifications promote fidelity during the translation of specific genes, those rich in arginine and glutamic acid codons from mixed boxes. Using quantitative tRNA modification analysis, we determined that trm9? cells are only deficient in 2 of 23 tRNA modifications, with those 2, 5-methoxycarbonylmethyluridine (mcm ( 5) U) and 5-methoxycarbonylmethyl-2-thiouridine (mcm ( 5) s ( 2) U), classified as key determinants of translational fidelity. We also show that in the absence of mcm ( 5) U and mcm ( 5) s ( 2) U, the resulting translational infidelity promotes protein errors and activation of unfolded protein and heat shock responses. These data support a model in which Trm9-catalyzed tRNA modifications promote fidelity during the translation of specific transcripts, with decreased wobble base modification leading to translational infidelity, protein errors and activation of protein stress response pathways. PMID:22832247

Patil, Ashish; Chan, Clement T Y; Dyavaiah, Madhu; Rooney, John P; Dedon, Peter C; Begley, Thomas J

2012-07-01

100

Absence of the DNA-/RNA-binding protein MSY2 results in male and female infertility  

PubMed Central

MSY2, a germ-cell-specific member of the Y-box family of DNA-/RNA-binding proteins, is proposed to function as a coactivator of transcription in the nucleus and to stabilize and store maternal and paternal mRNAs in the cytoplasm. In mice lacking Msy2, a normal Mendelian ratio is observed after matings between heterozygotes with equal numbers of phenotypically normal but sterile male and female homozygotes (Msy2–/–). Spermatogenesis is disrupted in postmeiotic null germ cells with many misshapen and multinucleated spermatids, and no spermatozoa are detected in the epididymis. Apoptosis is increased in the testes of homozygotes, and real-time RT-PCR assays reveal large reductions in the mRNA levels of postmeiotic male germ cell mRNAs and smaller reductions of meiotic germ cell transcripts. In females, there is no apparent decrease in either the number of follicles or their morphology in ovaries obtained from 2- and 8-day-old Msy2–/– mice. In contrast, follicle number and progression are reduced in 21-day-old Msy2–/– ovaries. In adult Msy2–/– females, oocyte loss increases, anovulation is observed, and multiple oocyte and follicle defects are seen. Thus, Msy2 represents one of a small number of germ-cell-specific genes whose deletion leads to the disruption of both spermatogenesis and oogenesis.

Yang, Juxiang; Medvedev, Sergey; Yu, Junying; Tang, Linda C.; Agno, Julio E.; Matzuk, Martin M.; Schultz, Richard M.; Hecht, Norman B.

2005-01-01

101

In vitro membrane assembly of a polytopic, transmembrane protein results in an enzymatically active conformation  

PubMed Central

In vitro integration of the polytopic, transmembrane lactose permease into membrane vesicles from Escherichia coli is demonstrated. To this end the enzyme was synthesized in a homologous, cell-free transcription- translation system. In this system, synthesis occurred in an essentially membrane-free environment leading to the formation of lactose permease aggregates, which were resistant to protease digestion and detergent solubilization. However, if inverted membrane vesicles from E. coli were included in the synthesis reaction, most de novo- synthesized lactose permease could be recovered from a membrane- containing subfraction (enriched in leader [signal] peptidase activity). This membrane association of lactose permease was Na2CO3 resistant, detergent sensitive, and yielded a distinct pattern of proteolytic cleavage peptides. Moreover, membrane vesicles when present cotranslationally during synthesis of lactose permease, acquired the capability to accumulate lactose, strongly suggesting a correct in vitro assembly of the enzyme. Because of the extensive aggregation of lactose permease synthesized in the absence of membranes, only low amounts originating from the soluble enzyme pool integrated posttranslationally into the membrane vesicles. Unlike the translocation of the outer membrane protein LamB into membrane vesicles, integration of lactose permease was found to be independent of the H+-motive force.

1989-01-01

102

Loss of the homotypic fusion and vacuole protein sorting or golgi-associated retrograde protein vesicle tethering complexes results in gentamicin sensitivity in the yeast Saccharomyces cerevisiae.  

PubMed

Gentamicin continues to be a primary antibiotic against gram-negative infections. Unfortunately, associated nephro- and ototoxicity limit its use. Our previous mammalian studies showed that gentamicin is trafficked to the endoplasmic reticulum in a retrograde manner and subsequently released into the cytosol. To better dissect the mechanism through which gentamicin induces toxicity, we have chosen to study its toxicity using the simple eukaryote Saccharomyces cerevisiae. A recent screen of the yeast deletion library identified multiple gentamicin-sensitive strains, many of which participate in intracellular trafficking. Our approach was to evaluate gentamicin sensitivity under logarithmic growth conditions. By quantifying growth inhibition in the presence of gentamicin, we determined that several of the sensitive strains were part of the Golgi-associated retrograde protein (GARP) and homotypic fusion and vacuole protein sorting (HOPS) complexes. Further evaluation of their other components showed that the deletion of any GARP member resulted in gentamicin-hypersensitive strains, while the deletion of other HOPS members resulted in less gentamicin sensitivity. Other genes whose deletion resulted in gentamicin hypersensitivity included ZUO1, SAC1, and NHX1. Finally, we utilized a Texas Red gentamicin conjugate to characterize gentamicin uptake and localization in both gentamicin-sensitive and -insensitive strains. These studies were consistent with our mammalian studies, suggesting that gentamicin toxicity in yeast results from alterations to intracellular trafficking pathways. The identification of genes whose absence results in gentamicin toxicity will help target specific pathways and mechanisms that contribute to gentamicin toxicity. PMID:16436714

Wagner, Mark C; Molnar, Elizabeth E; Molitoris, Bruce A; Goebl, Mark G

2006-02-01

103

RNA editing in wheat mitochondria results in the conservation of protein sequences  

Microsoft Academic Search

RNA editing is a process that results in the production of a messenger RNA with nucleotide sequences that differ from those of the template DNA1, and provides another mechanism for modulating gene expression. The phenomenon was initially described in the mitochondria of protozoa2, 3. Here we report that RNA editing is also required for the correct expression of plant mitochondria!

José M. Gualberto; Lorenzo Lamattina; Géraldine Bonnard; Jacques-Henry Weil; Jean-Michel Grienenberger

1989-01-01

104

Unexpected random urinary protein:creatinine ratio results-limitations of the pyrocatechol violet-dye method  

PubMed Central

Background For clinicians, it is important to rely on accurate laboratory results for patient care and optimal use of health care resources. We sought to explore our observations that urine protein:creatinine ratios (PrCr) ?30 mg/mmol are seen not infrequently associated with normal pregnancy outcome. Methods Urine samples were collected prospectively from 160 pregnant women attending high-risk maternity clinics at a tertiary care facility. Urinary protein was measured using a pyrocatechol violet assay and urinary creatinine by an enzymatic method on Vitros analysers. Maternal/perinatal outcomes were abstracted from hospital records. Results 91/233 (39.1%) samples had a PrCr ?30 mg/mmol, especially when urinary creatinine concentration was <3 mM (94.1%) vs. ?3 mM (16.4%) (p?results were also more frequent among the 32 (20.0%) women with known normal pregnancy outcome (90.9% vs. 0) (p?protein was ‘detected’ in deionised water. Re-analysis of data from two cohorts revealed substantially less inflation of PrCr in dilute urine using a pyrogallol red assay. Conclusions Random urinary PrCr was overestimated in dilute urine when tested using a common pyrocatechol violet dye-based method. This effect was reduced in cohorts when pyrogallol red assays were used. False positive results can impact on diagnosis and patient care. This highlights the need for both clinical and laboratory quality improvement projects and standardization of laboratory protein measurement.

2013-01-01

105

Loss of the Tg737 protein results in skeletal patterning defects  

Microsoft Academic Search

Tg737 mutant mice exhibit pathologic conditions in numerous tissues along with skeletal patterning defects. Herein, we characterize the skeletal pathologic conditions and confirm a role for Tg737 in skeletal patterning through transgenic rescue. Analyses were conducted in both the hypomorphic Tg737(orpk) allele that results in duplication of digit one and in the null Tg737(Delta2-3betaGal) allele that is an embryonic lethal

Qihong Zhang; Noel S. Murcia; Laura R. Chittenden; William G. Richards; Edward J. Michaud; Richard P. Woychik; Bradley K. Yoder

2003-01-01

106

Knockdown of Pnpla6 protein results in motor neuron defects in zebrafish  

PubMed Central

SUMMARY Mutations in patatin-like phospholipase domain containing 6 (PNPLA6), also known as neuropathy target esterase (NTE) or SPG39, cause hereditary spastic paraplegia (HSP). Although studies on animal models, including mice and Drosophila, have extended our understanding of PNPLA6, its roles in neural development and in HSP are not clearly understood. Here, we describe the generation of a vertebrate model of PNPLA6 insufficiency using morpholino oligonucleotide knockdown in zebrafish (Danio rerio). Pnpla6 knockdown resulted in developmental abnormalities and motor neuron defects, including axon truncation and branching. The phenotypes in pnpla6 knockdown morphants were rescued by the introduction of wild-type, but not mutant, human PNPLA6 mRNA. Our results also revealed the involvement of BMP signaling in pnpla6 knockdown phenotypes. Taken together, these results demonstrate an important role of PNPLA6 in motor neuron development and implicate overexpression of BMP signaling as a possible mechanism underlying the developmental defects in pnpla6 morphants.

Song, Yang; Wang, Molin; Mao, Fei; Shao, Ming; Zhao, Baochang; Song, Zhen; Shao, Changshun; Gong, Yaoqin

2013-01-01

107

Polyoxopalladates encapsulating 8-coordinated metal ions, [MO8Pd(II)12L8]n- (M = Sc3+, Mn2+, Fe3+, Co2+, Ni2+, Cu2+, Zn2+, Lu3+; L = PhAsO3(2-), PhPO3(2-), SeO3(2-)).  

PubMed

A total of 16 discrete polyoxopalladates(II) [MO(8)Pd(II)(12)L(8)](n-), with a metal ion M encapsulated in a cuboid-shaped {Pd(12)O(8)L(8)} cage, have been synthesized: the phenylarsonate-capped series (1) L = PhAsO(3)(2-), M = Sc(3+) (ScPhAs), Mn(2+) (MnPhAs), Fe(3+) (FePhAs), Co(2+) (CoPhAs), Ni(2+) (NiPhAs), Cu(2+) (CuPhAs), Zn(2+) (ZnPhAs); the phenylphosphonate-capped series: (2) L = PhPO(3)(2-), M = Cu(2+) (CuPhP), Zn(2+) (ZnPhP); and the selenite-capped series (3) L = SeO(3)(2-), M = Mn(2+) (MnSe), Fe(3+) (FeSe), Co(2+) (CoSe), Ni(2+) (NiSe), Cu(2+), (CuSe), Zn(2+) (ZnSe), Lu(3+) (LuSe)). The polyanions were prepared in one-pot reactions in aqueous solution of [Pd(3)(CH(3)COO)(6)] with an appropriate salt of the metal ion M, as well as PhAsO(3)H(2), PhPO(3)H(2), and SeO(2), respectively, and then isolated as hydrated sodium salts Na(n)[MO(8)Pd(II)(12)L(8)]·yH(2)O (y = 10-37). The compounds were characterized in the solid state by IR spectroscopy, single-crystal XRD, elemental and thermogravimetric analyses. The solution stability of the diamagnetic polyanions ScPhAs, ZnPhAs, ZnPhP, ZnSe, and LuSe was confirmed by multinuclear ((77)Se, (31)P, (13)C, and (1)H) NMR spectroscopy. The polyoxopalladates ScPhAs, MnPhAs, CoPhAs, and CuPhAs were investigated by electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS). Electrochemical studies on the manganese- and iron-containing derivatives demonstrated that the redox properties of the Mn(2+), Fe(3+), and Pd(2+) centers in the polyanions are strikingly influenced by the nature of the capping group. These results have subsequently been verified by density functional theory (DFT) calculations. Interestingly, electron paramagnetic resonance (EPR) measurements suggest that the coordination geometry around Mn(2+) is dynamically distorted on the EPR time scale (?10(-11) s), whereas it appears as a static ensemble with cubic symmetry on the X-ray diffraction (XRD) time-scale (10(-15) s). The octacoordinated Cu(2+) cuboid is similarly distorted, in good agreement with DFT calculations. Interestingly, g(?) is smaller than g(?), which is quite unusual, needing further theoretical development. PMID:23194400

Barsukova-Stuckart, Maria; Izarova, Natalya V; Barrett, Ryan A; Wang, Zhenxing; van Tol, Johan; Kroto, Harold W; Dalal, Naresh S; Jiménez-Lozano, Pablo; Carbó, Jorge J; Poblet, Josep M; von Gernler, Marc S; Drewello, Thomas; de Oliveira, Pedro; Keita, Bineta; Kortz, Ulrich

2012-11-29

108

Oxidative stress induced by potassium bromate exposure results in altered tight junction protein expression in renal proximal tubule cells.  

PubMed

Potassium bromate (KBrO(3)) is an oxidising agent that has been widely used in the food and cosmetic industries. It has shown to be both a nephrotoxin and a renal carcinogen in in vivo and in vitro models. Here, we investigated the effects of KBrO(3) in the human and rat proximal tubular cell lines RPTEC/TERT1 and NRK-52E. A genome-wide transcriptomic screen was carried out from cells exposed to a sub-lethal concentration of KBrO(3) for 6, 24 and 72 h. Pathway analysis identified "glutathione metabolism", "Nrf2-mediated oxidative stress" and "tight junction (TJ) signalling" as the most enriched pathways. TJ signalling was less impacted in the rat model, and further studies revealed low transepithelial electrical resistance (TEER) and an absence of several TJ proteins in NRK-52E cells. In RPTEC/TERT1 cells, KBrO(3) exposure caused a decrease in TEER and resulted in altered expression of several TJ proteins. N-Acetylcysteine co-incubation prevented these effects. These results demonstrate that oxidative stress has, in conjunction with the activation of the cytoprotective Nrf2 pathway, a dramatic effect on the expression of tight junction proteins. The further understanding of the cross-talk between these two pathways could have major implications for epithelial repair, carcinogenesis and metastasis. PMID:22760423

Limonciel, Alice; Wilmes, Anja; Aschauer, Lydia; Radford, Robert; Bloch, Katarzyna M; McMorrow, Tara; Pfaller, Walter; van Delft, Joost H; Slattery, Craig; Ryan, Michael P; Lock, Edward A; Jennings, Paul

2012-07-04

109

Loss of the Tg737 protein results in skeletal patterning defects.  

PubMed

Tg737 mutant mice exhibit pathologic conditions in numerous tissues along with skeletal patterning defects. Herein, we characterize the skeletal pathologic conditions and confirm a role for Tg737 in skeletal patterning through transgenic rescue. Analyses were conducted in both the hypomorphic Tg737(orpk) allele that results in duplication of digit one and in the null Tg737(delta2-3betaGal) allele that is an embryonic lethal mutation exhibiting eight digits per limb. In early limb buds, Tg737 expression is detected throughout the mesenchyme becoming concentrated in precartilage condensations at later stages. In situ analyses indicate that the Tg737(orpk) mutant limb defects are not associated with changes in expression of Shh, Ihh, HoxD11-13, Patched, BMPs, or Glis. Likewise, in Tg737(delta2-3betaGal) mutant embryos, there was no change in Shh expression. However, in both alleles, Fgf4 was ectopically expressed on the anterior apical ectodermal ridge. Collectively, the data argue for a dosage effect of Tg737 on the limb phenotypes and that the polydactyly is independent of Shh misexpression. PMID:12701101

Zhang, Qihong; Murcia, Noel S; Chittenden, Laura R; Richards, William G; Michaud, Edward J; Woychik, Richard P; Yoder, Bradley K

2003-05-01

110

In vivo introduction of unpreferred synonymous codons into the Drosophila Adh gene results in reduced levels of ADH protein.  

PubMed Central

The evolution of codon bias, the unequal usage of synonymous codons, is thought to be due to natural selection for the use of preferred codons that match the most abundant species of isoaccepting tRNA, resulting in increased translational efficiency and accuracy. We examined this hypothesis by introducing 1, 6, and 10 unpreferred codons into the Drosophila alcohol dehydrogenase gene (Adh). We observed a significant decrease in ADH protein production with number of unpreferred codons, confirming the importance of natural selection as a mechanism leading to codon bias. We then used this empirical relationship to estimate the selection coefficient (s) against unpreferred synonymous mutations and found the value (s >or= 10(-5)) to be approximately one order of magnitude greater than previous estimates from population genetics theory. The observed differences in protein production appear to be too large to be consistent with current estimates of the strength of selection on synonymous sites in D. melanogaster.

Carlini, David B; Stephan, Wolfgang

2003-01-01

111

Replacement of Tyr62 by Trp in the designer protein Milk Bundle1 results in significant improvement of conformational stability  

Microsoft Academic Search

Protein design is currently used for the creation of new proteins with desirable traits. In our lab, we focus on the synthesis of proteins with high essential amino acid content, having potential application in animal nutrition. One of the limitations we face in this endeavor is the achievement of stable proteins in spite of a highly biased amino acid content.

M. C Gagnon; M Williams; A Doucet; M Beauregard

2000-01-01

112

Interactive intoxicating and ameliorating effects of tannic acid, aluminum (Al3+), copper (Cu2+), and selenate (SeO42-) in wheat roots. A descriptive and mathematical assessment  

Technology Transfer Automated Retrieval System (TEKTRAN)

Tannic acids and tannins are polyphenolic compounds produced by plants and are important components of soil and water organic matter. Tannic acids and tannins form complexes with proteins, metals, and soil particulate matter and perform several physiological and ecological functions. The tannic ac...

113

FEEDING DIETS CONTAINING SOY PROTEIN ISOLATE (SPI) AT WEANING RESULTS IN ACTIVATION OF PPAR AND LXR-MEDIATED PATHWAYS AS A RESULT OF UPREGULATION OF TRANSCRIPTION FACTOR EXPRESSION  

Technology Transfer Automated Retrieval System (TEKTRAN)

The current study examined the effects of feeding soy protein isolate (SPI) on expression of genes and transcription factors involved in fatty acid (FA) and cholesterol metabolism and transport in weanling rats. Sprague-Dawley rats were weaned onto AIN-93G diets containing SPI or casein (CAS) as th...

114

Proteins  

PubMed Central

An overwhelming array of structural variants has evolved from a comparatively small number of protein structural domains; which has in turn facilitated an expanse of functional derivatives. Herein, I review the primary mechanisms which have contributed to the vastness of our existing, and expanding, protein repertoires. Protein function prediction strategies, both sequence and structure based, are also discussed and their associated strengths and weaknesses assessed.

Sleator, Roy D.

2012-01-01

115

Vaccine Platforms Combining Circumsporozoite Protein and Potent Immune Modulators, rEA or EAT-2, Paradoxically Result in Opposing Immune Responses  

PubMed Central

Background Malaria greatly impacts the health and wellbeing of over half of the world's population. Promising malaria vaccine candidates have attempted to induce adaptive immune responses to Circumsporozoite (CS) protein. Despite the inclusion of potent adjuvants, these vaccines have limited protective efficacy. Conventional recombinant adenovirus (rAd) based vaccines expressing CS protein can induce CS protein specific immune responses, but these are essentially equivalent to those generated after use of the CS protein subunit based vaccines. In this study we combined the use of rAds expressing CS protein along with rAds expressing novel innate immune response modulating proteins in an attempt to significantly improve the induction of CS protein specific cell mediated immune (CMI) responses. Methods and Findings BALB/cJ mice were co-vaccinated with a rAd vectors expressing CS protein simultaneous with a rAd expressing either TLR agonist (rEA) or SLAM receptors adaptor protein (EAT-2). Paradoxically, expression of the TLR agonist uncovered a potent immunosuppressive activity inherent to the combined expression of the CS protein and rEA. Fortunately, use of the rAd vaccine expressing EAT-2 circumvented CS protein's suppressive activity, and generated a fivefold increase in the number of CS protein responsive, IFN? secreting splenocytes, as well as increased the breadth of T cells responsive to peptides present in the CS protein. These improvements were positively correlated with the induction of a fourfold improvement in CS protein specific CTL functional activity in vivo. Conclusion Our results emphasize the need for caution when incorporating CS protein into malaria vaccine platforms expressing or containing other immunostimulatory compounds, as the immunological outcomes may be unanticipated and/or counter-productive. However, expressing the SLAM receptors derived signaling adaptor EAT-2 at the same time of vaccination with CS protein can overcome these concerns, as well as significantly improve the induction of malaria antigen specific adaptive immune responses in vivo.

Appledorn, Daniel M.; Seregin, Sergey S.; Kousa, Youssef; Godbehere, Sarah; Amalfitano, Andrea

2011-01-01

116

Bone Dysplasia Sclerosteosis Results from Loss of the SOST Gene Product, a Novel Cystine Knot-Containing Protein  

PubMed Central

Sclerosteosis is an autosomal recessive sclerosing bone dysplasia characterized by progressive skeletal overgrowth. The majority of affected individuals have been reported in the Afrikaner population of South Africa, where a high incidence of the disorder occurs as a result of a founder effect. Homozygosity mapping in Afrikaner families along with analysis of historical recombinants localized sclerosteosis to an interval of ?2 cM between the loci D17S1787 and D17S930 on chromosome 17q12-q21. Here we report two independent mutations in a novel gene, termed “SOST.” Affected Afrikaners carry a nonsense mutation near the amino terminus of the encoded protein, whereas an unrelated affected person of Senegalese origin carries a splicing mutation within the single intron of the gene. The SOST gene encodes a protein that shares similarity with a class of cystine knot–containing factors including dan, cerberus, gremlin, prdc, and caronte. The specific and progressive effect on bone formation observed in individuals affected with sclerosteosis, along with the data presented in this study, together suggest that the SOST gene encodes an important new regulator of bone homeostasis.

Brunkow, Mary E.; Gardner, Jessica C.; Van Ness, Jeff; Paeper, Bryan W.; Kovacevich, Brian R.; Proll, Sean; Skonier, John E.; Zhao, L.; Sabo, P. J.; Fu, Ying-Hui; Alisch, Reid S.; Gillett, Lucille; Colbert, Trenton; Tacconi, Paolo; Galas, David; Hamersma, Herman; Beighton, Peter; Mulligan, John T.

2001-01-01

117

Inhibition of SIRT1 by HIV-1 viral protein Tat results in activation of p53 pathway.  

PubMed

Human immunodeficiency virus-1 (HIV-1) disease is characterized by a relentless decline in CD4(+) T cells, resulting in the development of AIDS. Extracellular Tat secreted from the HIV-1 infected cells, enters non-infected T cells to induce apoptosis. A number of mechanisms, none of which is mutually exclusive, have been attributed to the cell depletion property of Tat protein. In the present communication, we provide evidence that the cell-killing effect of Tat is mediated by the activation of p53 pathway via inhibition of SIRT1, an NAD(+)-dependent deacetylase belonging to class III histone deacetylases. This evidence is based on the following experimental facts reported herein: (1) Overexpression of Tat protein decreases both the deacetylase and promoter activity of SIRT1, (2) SIRT1 inhibition by Tat involves increased levels of acetylated p53 and (3) The activation of p53 leads to subsequent increases in the expression of p53 target genes, p21 and BAX. PMID:22732402

Thakur, Basant Kumar; Chandra, Angelika; Dittrich, Tino; Welte, Karl; Chandra, Prakash

2012-06-23

118

Accumulation of a Brazil nut albumin in seeds of transgenic canola results in enhanced levels of seed protein methionine  

Microsoft Academic Search

We have increased the methionine content of the seed proteins of a commercial winter variety of canola by expressing a chimeric gene encoding a methionine-rich seed protein from Brazil nut in the seeds of transgenic plants. Transgenic canola seeds accumulate the heterologous methionine-rich protein at levels which range from 1.7% to 4.0% of the total seed protein and contain up

Susan B. Altenbach; Chiung-Chi Kuo; Lisa C. Staraci; Karen W. Pearson; Connie Wainwright; Anca Georgescu; Jeffrey Townsend

1992-01-01

119

Stable expression of promyelocytic leukaemia (PML) protein in telomerase positive MCF7 cells results in alternative lengthening of telomeres phenotype  

PubMed Central

Background Cancer cells can employ telomerase or the alternative lengthening of telomeres (ALT) pathway for telomere maintenance. Cancer cells that use the ALT pathway exhibit distinct phenotypes such as heterogeneous telomeres and specialised Promyelocytic leukaemia (PML) nuclear foci called APBs. In our study, we used wild-type PML and a PML mutant, in which the coiled-coil domain is deleted (PML C/C-), to investigate how these proteins can affect telomere maintenance pathways in cancer cells that use either the telomerase or ALT pathway. Results Stable over-expression of both types of PML does not affect the telomere maintenance in the ALT cells. We report novel observations in PML over-expressed telomerase-positive MCF7 cells: 1) APBs are detected in telomerase-positive MCF7 cells following over-expression of wild-type PML and 2) rapid telomere elongation is observed in MCF7 cells that stably express either wild-type PML or PML C/C-. We also show that the telomerase activity in MCF7 cells can be affected depending on the type of PML protein over-expressed. Conclusion Our data suggests that APBs might not be essential for the ALT pathway as MCF7 cells that do not contain APBs exhibit long telomeres. We propose that wild-type PML can either definitively dominate over telomerase or enhance the activity of telomerase, and PML C/C- can allow for the co-existence of both telomerase and ALT pathways. Our findings add another dimension in the study of telomere maintenance as the expression of PML alone (wild-type or otherwise) is able to change the dynamics of the telomerase pathway.

2012-01-01

120

Reduced Sweetness of a Monellin (MNEI) Mutant Results from Increased Protein Flexibility and Disruption of a Distant Poly-(L-Proline) II Helix  

PubMed Central

Monellin is a highly potent sweet-tasting protein but relatively little is known about how it interacts with the sweet taste receptor. We determined X-ray crystal structures of 3 single-chain monellin (MNEI) proteins with alterations at 2 core residues (G16A, V37A, and G16A/V37A) that induce 2- to 10-fold reductions in sweetness relative to the wild-type protein. Surprisingly, no changes were observed in the global protein fold or the positions of surface amino acids important for MNEI sweetness that could explain these differences in protein activity. Differential scanning calorimetry showed that while the thermal stability of each mutant MNEI was reduced, the least sweet mutant, G16A-MNEI, was not the least stable protein. In contrast, solution spectroscopic measurements revealed that changes in protein flexibility and the C-terminal structure correlate directly with protein activity. G16A mutation-induced disorder in the protein core is propagated via changes to hydrophobic interactions that disrupt the formation and/or position of a critical C-terminal poly-(L-proline) II helix. These findings suggest that MNEI interaction with the sweet taste receptor is highly sensitive to the relative positions of key residues across its protein surface and that loss of sweetness in G16A-MNEI may result from an increased entropic cost of binding.

Templeton, Catherine M.; Ostovar pour, Saeideh; Hobbs, Jeanette R.; Blanch, Ewan W.; Munger, Steven D.

2011-01-01

121

Suppression of RICE TELOMERE BINDING PROTEIN1 Results in Severe and Gradual Developmental Defects Accompanied by Genome Instability in Rice  

Microsoft Academic Search

Although several potential telomere binding proteins have been identified in higher plants, their in vivo functions are still unknown at the plant level. Both knockout and antisense mutants of RICE TELOMERE BINDING PROTEIN1 (RTBP1) exhibited markedly longer telomeres relative to those of the wild type, indicating that the amount of functional RTBP1 is inversely correlated with telomere length. rtbp1 plants

Jong-Pil Hong; M. Y. Byun; D.-H. Koo; K. An; J.-W. Bang; I. K. Chung; G. An; W. T. Kim

2007-01-01

122

RECENT RESULTS WITH A PLANT-BASED TROUT FEED AND REVIEW OF WORK ON NOVEL PROTEIN SOURCES FOR TROUT.  

Technology Transfer Automated Retrieval System (TEKTRAN)

A study was conducted to evaluate the effect of protein source and nutrient density on fish growth, feed efficiency, digestibility and plasma amino acid concentrations. A four by two factorial treatment arrangement with four protein sources (fishmeal/barley, plant concentrates, plant meals, animal ...

123

The Relation between Dietary Protein, Calcium and Bone Health in Women: Results from the EPIC-Potsdam Cohort  

Microsoft Academic Search

Background\\/Aims: The role of dietary protein in bone health is controversial. The objective of the present study was to examine the association between protein intake, dietary calcium, and bone structure measured by broadband ultrasound attenuation (BUA). Methods: Our analysis includes 8,178 female study participants of the European Prospective Investigation into Cancer and Nutrition (EPIC) Potsdam Study. Ultrasound bone measurements were

Cornelia Weikert; Dietmar Walter; Kurt Hoffmann; Anja Kroke; Manuela M. Bergmann; Heiner Boeing

2005-01-01

124

Targeted overexpression of a golli–myelin basic protein isoform to oligodendrocytes results in aberrant oligodendrocyte maturation and myelination  

Microsoft Academic Search

Recently, several in vitro studies have shown that the golli- myelin basic proteins regulate Ca2+ homoeostasis in OPCs (oligodendrocyte precursor cells) and immature OLs (oligodendrocytes), and that a number of the functions of these cells are affected by cellular levels of the golli proteins. To determine the influence of golli in vivo on OL development and myelination, a transgenic mouse

Erin C Jacobs; Samuel D Reyes; Celia W Campagnoni; M Irene Givogri; Kathy Kampf; Vance Handley; Vilma Spreuer; Robin Fisher; Wendy Macklin; Anthony T Campagnoni

2009-01-01

125

Normal ranges and genetic variants of antithrombin, protein C and protein S in the general Chinese population. Results of the Chinese Hemostasis Investigation on Natural Anticoagulants Study I Group  

PubMed Central

Background Inherited deficiency of antithrombin, protein C and protein S, three important, naturally occurring coagulation inhibitors, might play a major role in the occurrence of venous thromboembolism in Chinese. The establishment of age- and gender-related normal ranges of these inhibitors is crucial for an accurate diagnosis of these deficiencies. Design and Methods We designed a prospective cross-sectional study recruiting healthy adults from four university–affiliated hospitals in China. Antithrombin, protein C and protein S were studied by measuring their activity. Gene analysis was performed when natural anticoagulant deficiency was suspected. Polymorphisms of the factor V gene were searched for among subjects who were positive for activated protein C resistance. Results In 3493 healthy Chinese adults (1734 men, 1759 women; age 17–83 years), we found higher age-adjusted activities for protein C and protein S in men than in women but no sex difference for antithrombin. In women, mean protein C and protein S activities increased with age. In men, mean protein C levels increased with age up to the age of 49 but decreased after 50 years old; mean protein S levels decreased after 50 years of age. Antithrombin levels remained stable over time in women but decreased significantly after 50 years of age in men. Reference values according to age and sex allowed the identification of 15 genetic variants (protein C: 10, antithrombin: 3, protein S: 2) in subjects with protein activity below the 1st percentile. Conclusions This is the largest survey ever conducted in the healthy general Chinese population. These normal ranges provide the essential basis for the diagnosis and treatment of thrombosis in Chinese.

Zhu, Tienan; Ding, Qiulan; Bai, Xia; Wang, Xiaoyan; Kaguelidou, Florentia; Alberti, Corinne; Wei, Xuqian; Hua, Baolai; Yang, Renchi; Wang, Xuefeng; Wang, Zhaoyue; Ruan, Changgeng; Schlegel, Nicole; Zhao, Yongqiang

2011-01-01

126

Trisomy-21 gene dosage overexpression of miRNAs results in the haploinsufficiency of specific target proteins  

PubMed Central

Down syndrome (DS) or Trisomy 21 (Ts21) is caused by the presence of an extra copy of all or part of human chromosome 21 (Hsa21) and is the most frequent survivable congenital chromosomal abnormality. Bioinformatic annotation has established that Hsa21 harbors more than 400 genes, including five microRNA (miRNA) genes (miR-99a, let-7c, miR-125b-2, miR-155 and miR-802). MiRNAs are endogenous, single-stranded, small non-coding RNA molecules that regulate gene expression by interacting with specific recognition elements harbored within the 3?-untranslated region (3?-UTR) of mRNAs and subsequently target these mRNAs for translational repression or destabilization. MiRNA expression profiling, miRNA RT-PCR and miRNA in situ hybridization experiments have demonstrated that Hsa21-derived miRNAs were overexpressed in fetal brain and heart specimens isolated from individuals with DS. We now propose that Ts21 gene dosage overexpression of Hsa21-derived miRNAs in DS individuals result in the decreased expression of specific target proteins (i.e., haploinsufficiency) that contribute, in part, to the DS phenotype.

Sansom, Sarah E; Martin, Mickey M

2010-01-01

127

Brain-derived protein concentrations in the cerebrospinal fluid: contribution of trauma resulting from ventricular drain insertion.  

PubMed

In recent years, the measurement of biomarkers following neurotrauma assisted in improving outcome prediction and guiding therapy. The use of neuroproteins as diagnostic parameters requires a detailed knowledge of their dynamics in biological fluids for an appropriate interpretation. S100B is the most widely studied neuromarker, and its concentration in serum and cerebrospinal fluid (CSF) reflects the extent of brain damage. Neuron-specific enolase (NSE) is considered reflecting neuronal damage, while Beta-Trace is a lepto-meningeal protein used to diagnose CSF leakage. In five patients treated with an external ventricular drain (EVD) because of aneurysmal subarachnoid hemorrhage (SAH, n=3) or postinfectious hydrocephalus (n=2), an EVD exchange was performed 8 to 12 days after initial insertion. S100B and NSE were measured with the Cobas e411(®) electrochemiluminescence assay (Roche Diagnostics, Mannheim, Germany) and Beta-Trace with the BN Pro Spec(®) nephelometer (Dade Behring/Siemens, Germany) 1?h before EVD exchange, upon the insertion of the new drain, and 1, 3, 6, 12, 18, 24 and 48?h after EVD exchange. Before EVD exchange, S100B CSF concentrations were within the normal range in all patients (1.48 ± 0.37??g/L), while NSE CSF concentrations were normal in four of five patients (6.51 ± 2.98??g/L). Following EVD exchange, S100B and NSE CSF levels peaked significantly at 3?h after insertion of the new drain (S100B 39.02 ± 9.17??g/L; NSE 54.80 ± 43.34??g/L). S100B serum levels were slightly increased 6 to 24?h after EVD exchange. Beta-Trace concentrations in the CSF were not altered by EVD insertion. Our data demonstrate that EVD insertion results in a distinct increase of S100B and NSE concentrations in the CSF. Thus, the tampering of brain-derived protein concentrations in the CSF by diagnostic or therapeutic procedures has to be considered in the interpretation of neuromarker levels. PMID:23390981

Brandner, Sebastian; Thaler, Christian; Buchfelder, Michael; Kleindienst, Andrea

2013-06-25

128

Attenuation of bone morphogenetic protein signaling during amphibian limb development results in the generation of stage-specific defects.  

PubMed

The vertebrate limb is one of the most intensively studied organs in the field of developmental biology. Limb development in tetrapod vertebrates is highly conserved and dependent on the interaction of several important molecular pathways. The bone morphogenetic protein (BMP) signaling cascade is one of these pathways and has been shown to be crucial for several aspects of limb development. Here, we have used a Xenopus laevis transgenic line, in which expression of the inhibitor Noggin is under the control of the heat-shock promoter hsp70 to examine the effects of attenuation of BMP signaling at different stages of limb development. Remarkably different phenotypes were produced at different stages, illustrating the varied roles of BMP in development of the limb. Very early limb buds appeared to be refractory to the effects of BMP attenuation, developing normally in most cases. Ectopic limbs were produced by overexpression of Noggin corresponding to a brief window of limb development at about stage 49/50, as recently described by Christen et al. (2012). Attenuation of BMP signaling in stage 51 or 52 tadpoles lead to a reduction in the number of digits formed, resulting in hypodactyly or ectrodactyly, as well as occasional defects in the more proximal tibia-fibula. Finally, inhibition at stage 54 (paddle stage) led to the formation of dramatically shortened digits resulting from loss of distal phalanges. Transcriptome analysis has revealed the possibility that more Noggin-sensitive members of the BMP family could be involved in limb development than previously suspected. Our analysis demonstrates the usefulness of heat-shock-driven gene expression as an effective method for inhibiting a developmental pathway at different times during limb development. PMID:23981117

Jones, Tamsin E M; Day, Robert C; Beck, Caroline W

2013-08-28

129

On the relation between experimental results for SASD type crystals and the two-sublattice model  

NASA Astrophysics Data System (ADS)

The mechanism of ferroelectric phase transitions taking place in sodium ammonium sulphate dihydrate and sodium ammonium selenate dihydrate is suggested. It is found that SO4 (SeO4) groups contribute predominantly to the phase transitions taking place in these crystals. The modified Mitsui-type model, which includes both long- and short-range correlations is tested. The cluster form of the hamiltonian is formulated and its two-sublattice variant is analysed. It is shown that the assumed approach yields the results, which are quantitatively in very good agreement with experiment data.

Lipi?ski, I. E.; Korynevskii, N. A.; Kuriata, J.; Pastusiak, W.

2003-03-01

130

Spaceflight results in increase of thick filament but not thin filament proteins in the paramyosin mutant of Caenorhabditis elegans  

NASA Astrophysics Data System (ADS)

We have investigated the effect of microgravity during spaceflight on body-wall muscle fiber size and muscle proteins in the paramyosin mutant of Caenorhabditis elegans. Both mutant and wild-type strains were subjected to 10 days of microgravity during spaceflight and compared to ground control groups. No significant change in muscle fiber size or quantity of the protein was observed in wild-type worms; where as atrophy of body-wall muscle and an increase in thick filament proteins were observed in the paramyosin mutant unc-15(e73) animals after spaceflight. We conclude that the mutant with abnormal muscle responded to microgravity by increasing the total amount of muscle protein in order to compensate for the loss of muscle function.

Adachi, R.; Takaya, T.; Kuriyama, K.; Higashibata, A.; Ishioka, N.; Kagawa, H.

131

Alterations in c-Myc phenotypes resulting from dynamin-related protein 1 (Drp1)-mediated mitochondrial fission.  

PubMed

The c-Myc (Myc) oncoprotein regulates numerous phenotypes pertaining to cell mass, survival and metabolism. Glycolysis, oxidative phosphorylation (OXPHOS) and mitochondrial biogenesis are positively controlled by Myc, with myc-/- rat fibroblasts displaying atrophic mitochondria, structural and functional defects in electron transport chain (ETC) components, compromised OXPHOS and ATP depletion. However, while Myc influences mitochondrial structure and function, it is not clear to what extent the reverse is true. To test this, we induced a state of mitochondrial hyper-fission in rat fibroblasts by de-regulating Drp1, a dynamin-like GTPase that participates in the terminal fission process. The mitochondria from these cells showed reduced mass and interconnectivity, a paucity of cristae, a marked reduction in OXPHOS and structural and functional defects in ETC Complexes I and V. High rates of abortive mitochondrial fusion were observed, likely reflecting ongoing, but ultimately futile, attempts to normalize mitochondrial mass. Cellular consequences included reduction of cell volume, ATP depletion and activation of AMP-dependent protein kinase. In response to Myc deregulation, apoptosis was significantly impaired both in the absence and presence of serum, although this could be reversed by increasing ATP levels by pharmacologic means. The current work demonstrates that enforced mitochondrial fission closely recapitulates a state of Myc deficiency and that mitochondrial integrity and function can affect Myc-regulated cellular behaviors. The low intracellular ATP levels that are frequently seen in some tumors as a result of inadequate vascular perfusion could favor tumor survival by countering the pro-apoptotic tendencies of Myc overexpression. PMID:23764851

Sarin, M; Wang, Y; Zhang, F; Rothermund, K; Zhang, Y; Lu, J; Sims-Lucas, S; Beer-Stolz, D; Van Houten, B E; Vockley, J; Goetzman, E S; Graves, J Anthony; Prochownik, E V

2013-06-13

132

Mechanisms of cross-talk between G-protein-coupled receptors resulting in enhanced release of intracellular Ca2+.  

PubMed Central

Alteration in [Ca(2+)](i) (the intracellular concentration of Ca(2+)) is a key regulator of many cellular processes. To allow precise regulation of [Ca(2+)](i) and a diversity of signalling by this ion, cells possess many mechanisms by which they are able to control [Ca(2+)](i) both globally and at the subcellular level. Among these are many members of the superfamily of GPCRs (G-protein-coupled receptors), which are characterized by the presence of seven transmembrane domains. Typically, those receptors able to activate PLC (phospholipase C) enzymes cause release of Ca(2+) from intracellular stores and influence Ca(2+) entry across the plasma membrane. It has been well documented that Ca(2+) signalling by one type of GPCR can be influenced by stimulation of a different type of GPCR. Indeed, many studies have demonstrated heterologous desensitization between two different PLC-coupled GPCRs. This is not surprising, given our current understanding of negative-feedback regulation and the likely shared components of the signalling pathway. However, there are also many documented examples of interactions between GPCRs, often coupling preferentially to different signalling pathways, which result in a potentiation of Ca(2+) signalling. Such interactions have important implications for both the control of cell function and the interpretation of in vitro cell-based assays. However, there is currently no single mechanism that adequately accounts for all examples of this type of cross-talk. Indeed, many studies either have not addressed this issue or have been unable to determine the mechanism(s) involved. This review seeks to explore a range of possible mechanisms to convey their potential diversity and to provide a basis for further experimental investigation.

Werry, Tim D; Wilkinson, Graeme F; Willars, Gary B

2003-01-01

133

High temperature redox reactions with uranium: Synthesis and characterization of Cs(UO2)Cl(SeO3), Rb2(UO2)3O2(SeO3)2, and RbNa5U2(SO4)7  

NASA Astrophysics Data System (ADS)

Cs(UO2)Cl(SeO3) (1), Rb2(UO2)3O2(SeO3)3 (2), and RbNa5U2(SO4)7 (3) single crystals were synthesized using CsCl, RbCl, and a CuCl/NaCl eutectic mixture as fluxes, respectively. Their lattice parameters and space groups are as follows: P21/n (a=6.548(1) Å, b=11.052(2) Å, c=10.666(2) Å and ?=93.897(3)°), P1¯ (a=7.051(2) Å, b=7.198(2) Å, c=8.314(2) Å, ?=107.897(3)°, ?=102.687(3)° and ?=100.564(3)°) and C2/c (a=17.862(4) Å, b=6.931(1) Å, c=20.133(4) Å and ?=109.737(6)°. The small anionic building units found in these compounds are SeO32- and SO42- tetrahedra, oxide, and chloride. The crystal structure of the first compound is composed of [(UO2)2Cl2(SeO3)2]2- chains separated by Cs+ cations. The structure of (2) is constructed from [(UO2)3O11]16- chains further connected through selenite units into layers stacked perpendicularly to the [0 1 0] direction, with Rb+ cations intercalating between them. The structure of compound (3) is made of uranyl sulfate layers formed by edge and vertex connections between dimeric [U2O16] and [SO4] polyhedra. These layers contain unusual sulfate-metal connectivity as well as large voids.

Babo, Jean-Marie; Albrecht-Schmitt, Thomas E.

2013-10-01

134

The loss of RGS protein-G?(i2) interactions results in markedly impaired mouse neutrophil trafficking to inflammatory sites.  

PubMed

Neutrophils are first responders rapidly mobilized to inflammatory sites by a tightly regulated, nonredundant hierarchy of chemoattractants. These chemoattractants engage neutrophil cell surface receptors triggering heterotrimeric G-protein G?(i) subunits to exchange GDP for GTP. By limiting the duration that G?(i) subunits remain GTP bound, RGS proteins modulate chemoattractant receptor signaling. Here, we show that neutrophils with a genomic knock in of a mutation that disables regulator of G-protein signaling (RGS)-G?(i2) interactions accumulate in the bone marrow and mobilize poorly to inflammatory sites. These defects are attributable to enhanced sensitivity to background signals, prolonged chemoattractant receptor signaling, and inappropriate CXCR2 downregulation. Intravital imaging revealed a failure of the mutant neutrophils to accumulate at and stabilize sites of sterile inflammation. Furthermore, these mice could not control a nonlethal Staphylococcus aureus infection. Neutrophil RGS proteins establish a threshold for G?(i) activation, helping to coordinate desensitization mechanisms. Their loss renders neutrophils functionally incompetent. PMID:22966200

Cho, Hyeseon; Kamenyeva, Olena; Yung, Sunny; Gao, Ji-Liang; Hwang, Il-Young; Park, Chung; Murphy, Philip M; Neubig, Richard R; Kehrl, John H

2012-09-10

135

Helicobacter pylori Infection Targets Adherens Junction Regulatory Proteins and Results in Increased Rates of Migration in Human Gastric Epithelial Cells  

Microsoft Academic Search

The human gastric pathogen Helicobacter pylori attaches to antral epithelial cells in vivo. Cultured human antral epithelial cells, AGS and NCI-N87 cell lines, were grown in the absence or presence of H. pylori and compared with respect to gene transcript levels, protein expression, organization of the actin cytoskeleton, and the regulation of cell migration. The Clontech Neurobiology array detected differentially

Victoria S. Conlin; Susan B. Curtis; Ying Zhao; Edwin D. W. Moore; Valerie C. Smith; R. Mark Meloche; B. Brett Finlay; Alison M. J. Buchan

2004-01-01

136

How maltose influences structural changes to bind to maltose-binding protein: results from umbrella sampling simulation.  

PubMed

A well-studied periplasmic-binding protein involved in the abstraction of maltose is maltose-binding protein (MBP), which undergoes a ligand-induced conformational transition from an open (ligand-free) to a closed (ligand-bound) state. Umbrella sampling simulations have been us to estimate the free energy of binding of maltose to MBP and to trace the potential of mean force of the unbinding event using the center-of-mass distance between the protein and ligand as the reaction coordinate. The free energy thus obtained compares nicely with the experimentally measured value justifying our theoretical basis. Measurement of the domain angle (N-terminal-domain - hinge - C-terminal-domain) along the unbinding pathway established the existence of three different states. Starting from a closed state, the protein shifts to an open conformation during the initial unbinding event of the ligand then resides in a semi-open conformation and later resides predominantly in an open-state. These transitions along the ligand unbinding pathway have been captured in greater depth using principal component analysis. It is proposed that in mixed-model, both conformational selection and an induced-fit mechanism combine to the ligand recognition process in MBP. PMID:22933379

Mascarenhas, Nahren Manuel; Kästner, Johannes

2012-09-29

137

Inclusion of Many-Body Effects in the Additive CHARMM Protein CMAP Potential Results in Enhanced Cooperativity of ?-Helix and ?-Hairpin Formation  

PubMed Central

Folding simulations on peptides and proteins using empirical force fields have demonstrated the sensitivity of the results to details of the backbone potential. A recently revised version of the additive CHARMM protein force field, which includes optimization of the backbone CMAP potential to achieve good balance between different types of secondary structure, correcting the ?-helical bias present in the former CHARMM22/CMAP energy function, is shown to result in improved cooperativity for the helix-coil transition. This is due to retention of the empirical corrections introduced in the original CMAP to reproduce folded protein structures—corrections that capture many-body effects missing from an energy surface fitted to gas phase calculations on dipeptides. The experimental temperature dependence of helix formation in (AAQAA)3 and parameters for helix nucleation and elongation are in much better agreement with experiment than those obtained with other recent force fields. In contrast, CMAP parameters derived by fitting to a vacuum quantum mechanical surface for the alanine dipeptide do not reproduce the enhanced cooperativity, showing that the empirical backbone corrections, and not some other feature of the force field, are responsible. We also find that the cooperativity of ?-hairpin formation is much improved relative to other force fields we have studied. Comparison with (?,?) distributions from the Protein Data Bank further justifies the inclusion of many-body effects in the CMAP. These results suggest that the revised energy function will be suitable for both simulations of unfolded or intrinsically disordered proteins and for investigating protein-folding mechanisms.

Best, Robert B.; Mittal, Jeetain; Feig, Michael; MacKerell, Alexander D.

2012-01-01

138

Cationization of immunoglobulin G results in enhanced organ uptake of the protein after intravenous administration in rats and primate  

SciTech Connect

Cationization of proteins in general enhances the cellular uptake of these macromolecules, and cationized antibodies are known to retain antigen binding properties. Therefore, cationized antibodies may be therapeutic and allow for intracellular immunization. The present studies test the hypothesis that the tissue uptake of cationized immunoglobulin G (IgG) after intravenous administration may be greatly increased relative to the uptake of native proteins. The pharmacokinetics of cationized immunoglobulin G clearance from blood, and the volume of distribution of the cationized or native protein (albumin, IgG) for 10 organs was measured both in anesthetized rats and in an anesthetized adult Macaca irus cynomologous monkey. Initial studies on brain showed that serum factors inhibited uptake of 125I-cationized IgG, but not 3H-cationized IgG. The blood-brain barrier permeability surface area product for 3H-cationized IgG was 0.57 {plus minus} 0.04 microliters min-1 g-1. The ratio of the volume of distribution of the 3-H-cationized IgG compared to 3H-labeled native albumin ranged from 0.9 (testis) to 15.7 (spleen) in the rat at 3 hr after injection, and a similarly enhanced organ uptake was observed in the primate. In conclusion, these studies demonstrate that cationization of immunoglobulin greatly increases organ uptake of the plasma protein compared to native immunoglobulins, and suggest that cationization of monoclonal antibodies may represent a potential new strategy for enhancing the intracellular delivery of these proteins.

Triguero, D.; Buciak, J.L.; Pardridge, W.M. (Department of Medicine, University of California, Los Angeles School of Medicine (USA))

1991-07-01

139

Bombyx mori midgut membrane protein P252, which binds to Bacillus thuringiensis Cry1A, is a chlorophyllide-binding protein, and the resulting complex has antimicrobial activity.  

PubMed

The epithelial cell membrane 252-kDa protein (P252) isolated in our laboratory from Bombyx mori midgut was shown to bind strongly with Cry1Aa, Cry1Ab, and Cry1Ac toxins of Bacillus thuringiensis (15). In the current paper, P252 was shown to bind with chlorophyllide (Chlide) to form red fluorescent protein (RFP) complex, termed Bm252RFP, with absorbance and fluorescence emission peaks at 600 nm and 620 nm, respectively. P252 at a concentration of 1 microM is shown to bind with about 50 microM Chlide in a positively cooperative reaction to form Bm252RFP under aerobic conditions and in the presence of light at 37 degrees C. Various parameters influencing this reaction have been optimized for efficient in vitro chemical synthesis of Bm252RFP. Circular dichroism spectra revealed that P252 is composed of a beta-structure (39.8% +/- 2.2%, based on 5 samples) with negligible contribution of alpha-helix structure. When bound to Chlide, the beta-structure content in the complex is reduced to 21.6% +/- 3.1% (n = 5). Since Chlide had no secondary structure, the observed reduction suggests significant conformational changes of P252 during the formation of Bm252RFP complex. Bm252RFP had antimicrobial activity against Escherichia coli, Serratia marcescens, B. thuringiensis, and Saccharomyces cerevisiae with 50% effective concentrations of 2.82, 2.94, 5.88 microM, and 21.6 microM, respectively. This is the first report ever to show clear, concrete binding characteristics of the midgut protein to form an RFP having significant antimicrobial activity. PMID:18192432

Pandian, Ganesh N; Ishikawa, Toshiki; Togashi, Makoto; Shitomi, Yasuyuki; Haginoya, Kohsuke; Yamamoto, Shuhei; Nishiumi, Tadayuki; Hori, Hidetaka

2008-01-11

140

A Heuristic Method for Assigning a False-discovery Rate for Protein Identifications from Mascot Database Search Results  

Microsoft Academic Search

MS\\/MS and database searching has emerged as a valua- ble technology for rapidly analyzing protein expression, localization, and post-translational modifications. The probability-based search engine Mascot has found wide- spread use as a tool to correlate tandem mass spectra with peptides in a sequence database. Although the Mas- cot scoring algorithm provides a probability-based model for peptide identification, the independent peptide

D. Brent Weatherly; James A. Atwood; Todd A. Minning; Cameron Cavola; Rick L. Tarleton; Ron Orlando

2005-01-01

141

Decreases in valosin-containing protein result in increased levels of tau phosphorylated at Ser 262\\/356  

Microsoft Academic Search

VCP\\/p97 is a multifunctional AAA+-ATPase involved in vesicle fusion, proteasomal degradation, and autophagy. Reported dysfunctions of these processes in Alzheimer disease (AD), along with the linkage of VCP\\/p97 to inclusion body myopathy with Paget’s disease and frontotemporal dementia (IBMPFD) led us to examine the possible linkage of VCP to the AD-relevant protein, tau. VCP levels were reduced in AD brains,

Philip J. Dolan; Youngnam N. Jin; Woong Hwang; Gail V. W. Johnson

2011-01-01

142

Multicopy Suppressors of Phenotypes Resulting from the Absence of Yeast VDAC Encode a VDAC-Like Protein  

Microsoft Academic Search

The permeability of the outer mitochondrial membrane to most metabolites is believed to be based in an outer membrane, channel-forming protein known as VDAC (voltage-dependent anion channel). Although multiple isoforms of VDAC have been identified in multicellular organisms, the yeast Saccharomyces cerevisiae has been thought to contain a single VDAC gene, designated POR1. However, cells missing the POR1 gene (Dpor1)

ELIZABETH BLACHLY-DYSON; JINMING SONG; WILLIAM J. WOLFGANG; MARCO COLOMBINI

1997-01-01

143

Single amino acid exchange in bacteriophage HK620 tailspike protein results in thousand-fold increase of its oligosaccharide affinity.  

PubMed

Bacteriophage HK620 recognizes and cleaves the O-antigen polysaccharide of Escherichia coli serogroup O18A1 with its tailspike protein (TSP). HK620TSP binds hexasaccharide fragments with low affinity, but single amino acid exchanges generated a set of high-affinity mutants with submicromolar dissociation constants. Isothermal titration calorimetry showed that only small amounts of heat were released upon complex formation via a large number of direct and solvent-mediated hydrogen bonds between carbohydrate and protein. At room temperature, association was both enthalpy- and entropy-driven emphasizing major solvent rearrangements upon complex formation. Crystal structure analysis showed identical protein and sugar conformers in the TSP complexes regardless of their hexasaccharide affinity. Only in one case, a TSP mutant bound a different hexasaccharide conformer. The extended sugar binding site could be dissected in two regions: first, a hydrophobic pocket at the reducing end with minor affinity contributions. Access to this site could be blocked by a single aspartate to asparagine exchange without major loss in hexasaccharide affinity. Second, a region where the specific exchange of glutamate for glutamine created a site for an additional water molecule. Side-chain rearrangements upon sugar binding led to desolvation and additional hydrogen bonding which define this region of the binding site as the high-affinity scaffold. PMID:22923442

Broeker, Nina K; Gohlke, Ulrich; Müller, Jürgen J; Uetrecht, Charlotte; Heinemann, Udo; Seckler, Robert; Barbirz, Stefanie

2012-08-24

144

Mutations of RNA and protein sequences involved in human immunodeficiency virus type 1 packaging result in production of noninfectious virus.  

PubMed Central

To identify RNA and protein sequences involved in packaging of human immunodeficiency virus type 1 (HIV-1), various mutations were introduced into the viral genome. Portions of the human immunodeficiency virus type 1 genome between the first splice donor site and the gag initiation codon were deleted to investigate the RNA packaging site (psi). Point mutations that alter cysteine residues in one or both zinc finger motifs of p7, a cleavage product of the gag precursor, were created to study the role of the gag zinc fingers in packaging. The psi site mutants and the gag mutants exhibited similar phenotypes. Cells transfected with the mutant genomes, while expressing normal levels of human immunodeficiency virus type 1 RNA and proteins, produced viral particles that were normal in protein content but lacked detectable viral RNA. These mutant virions were unable to productively infect cells. The combination of human immunodeficiency virus type 1 packaging mutations should minimize fortuitous assembly of infectious virus and may provide a means to produce noninfectious particles for candidate vaccines. Images

Aldovini, A; Young, R A

1990-01-01

145

An insecticidal protein from Xenorhabdus budapestensis that results in prophenoloxidase activation in the wax moth, Galleria mellonella.  

PubMed

Xenorhabdus budapestensis can produce a variety of proteins that help this bacterium and its mutualistic nematode vector kill the host insect. In this report, we purified one protein fraction from the intracellular extract of X. budapestensis D43, which was designated HIP57. By injection, HIP57 caused Galleria mellonella larval bodies to blacken and die with an LD(50) of 206.81 ng/larva. Analyzes of HIP57 by two-dimensional gel electrophoresis showed that this protein was a single spot on the gel with a molecular weight of 57 kDa and a pI of ?5. Sequencing and bioinformatic analysis suggested that the HIP57 toxin was homologous to GroEL. GroEL has been accepted as molecule chaperon; however, our research revealed that HIP57 (GroEL) possesses another novel function as an insecticide. A GroEL phylogenetic tree defined the relationship among the related species of mutualistic bacteria (Xenorhabdus and Photorhabdus) from the entomopathogenic nematodes and the evolution within the family Enterobacteriaceae. Thus, GroEL could be a complement to 16S rDNA for studying the molecular phylogenies of the family Enterobacteriaceae. Phenoloxidase (PO) activity analysis of G. mellonella larvae injected with HIP57 suggested that the toxin activates the PO cascade, which provides an extensive defense reaction that potentially responsible for G. mellonella larval death. PMID:22387345

Yang, Jun; Zeng, Hong-Mei; Lin, Hua-Feng; Yang, Xiu-Fen; Liu, Zheng; Guo, Li-Hua; Yuan, Jing-Jing; Qiu, De-Wen

2012-02-23

146

Activator protein-1 (AP-1) signalling in human atherosclerosis: results of a systematic evaluation and intervention study  

PubMed Central

Animal studies implicate the AP-1 (activator protein-1) pro-inflammatory pathway as a promising target in the treatment of atherosclerotic disease. It is, however, unclear whether these observations apply to human atherosclerosis. Therefore we evaluated the profile of AP-1 activation through histological analysis and tested the potential benefit of AP-1 inhibition in a clinical trial. AP-1 activation was quantified by phospho-c-Jun nuclear translocation (immunohistochemistry) on a biobank of aortic wall samples from organ donors. The effect of AP-1 inhibition on vascular parameters was tested through a double blind placebo-controlled cross-over study of 28 days doxycycline or placebo in patients with symptomatic peripheral artery disease. Vascular function was assessed by brachial dilation as well as by plasma samples analysed for hs-CRP (high-sensitivity C-reactive protein), IL-6 (interleukin-6), IL-8, ICAM-1 (intercellular adhesion molecule-1), vWF (von Willebrand factor), MCP-1 (monocyte chemoattractant protein-1), PAI-1 (plasminogen activator inhibitor-1) and fibrinogen. Histological evaluation of human atherosclerosis showed minimal AP-1 activation in non-diseased arterial wall (i.e. vessel wall without any signs of atherosclerotic disease). A gradual increase of AP-1 activation was found in non-progressive and progressive phases of atherosclerosis respectively (P<0.044). No significant difference was found between progressive and vulnerable lesions. The expression of phospho-c-Jun diminished as the lesion stabilized (P<0.016) and does not significantly differ from the normal aortic wall (P<0.33). Evaluation of the doxycycline intervention only revealed a borderline-significant reduction of circulating hs-CRP levels (?0.51 ?g/ml, P=0.05) and did not affect any of the other markers of systemic inflammation and vascular function. Our studies do not characterize AP-1 as a therapeutic target for progressive human atherosclerotic disease.

Meijer, C. Arnoud; Le Haen, Pum A. A.; van Dijk, Rogier A.; Hira, Mitsuhisa; Hamming, Jaap F.; van Bockel, J. Hajo; Lindeman, Jan H.

2011-01-01

147

Sensitivity of antiproteases, complement factors and C-reactive protein in detecting pancreatic necrosis. Results of a prospective clinical study  

Microsoft Academic Search

Summary  Thirty-five patients with acute pancreatitis underwent serum monitoring of ?-1-protease inhibitor, ?-2-macroglobulin, complement\\u000a factors C3+C4, and C-reactive protein (CRP). Edematous interstitial pancreatitis was shown to be present in 13 patients by\\u000a contrast-enhanced computed tomography (CT) and laparotomy (n=3). Necrotizing pancreatitis was confirmed by laparotomy (n=21) and contrast-enhanced CT. There were significant differences between the serum values of all measured parameters

Markus Bfichler; Peter Malfertheiner; Cornelia Schoetensack; Waldemar Uhl; Hans G. Beger

1986-01-01

148

Human C4b-binding protein selectively interacts with Neisseria gonorrhoeae and results in species-specific infection  

PubMed Central

Neisseria gonorrhoeae is the causative agent of gonorrhea, a disease that is restricted to humans. Complement forms a key arm of the innate immune system that combats gonococcal infections. N. gonorrhoeae uses its outer membrane porin (Por) molecules to bind the classical pathway of complement down-regulatory protein C4b-binding protein (C4bp) to evade killing by human complement. Strains of N. gonorrhoeae that resisted killing by human serum complement were killed by serum from rodent, lagomorph, and primate species, which cannot be readily infected experimentally with this organism and whose C4bp molecules did not bind to N. gonorrhoeae. In contrast, we found that Yersinia pestis, an organism that can infect virtually all mammals, bound species-specific C4bp and uniformly resisted serum complement-mediated killing by these species. Serum resistance of gonococci was restored in these sera by human C4bp. An exception was serotype Por1B-bearing gonococcal strains that previously had been used successfully in a chimpanzee model of gonorrhea that simulates human disease. Por1B gonococci bound chimpanzee C4bp and resisted killing by chimpanzee serum, providing insight into the host restriction of gonorrhea and addressing why Por1B strains, but not Por1A strains, have been successful in experimental chimpanzee infection. Our findings may lead to the development of better animal models for gonorrhea and may also have implications in the choice of complement sources to evaluate neisserial vaccine candidates.

Ngampasutadol, Jutamas; Ram, Sanjay; Blom, Anna M.; Jarva, Hanna; Jerse, Ann E.; Lien, Egil; Goguen, Jon; Gulati, Sunita; Rice, Peter A.

2005-01-01

149

Human C4b-binding protein selectively interacts with Neisseria gonorrhoeae and results in species-specific infection.  

PubMed

Neisseria gonorrhoeae is the causative agent of gonorrhea, a disease that is restricted to humans. Complement forms a key arm of the innate immune system that combats gonococcal infections. N. gonorrhoeae uses its outer membrane porin (Por) molecules to bind the classical pathway of complement down-regulatory protein C4b-binding protein (C4bp) to evade killing by human complement. Strains of N. gonorrhoeae that resisted killing by human serum complement were killed by serum from rodent, lagomorph, and primate species, which cannot be readily infected experimentally with this organism and whose C4bp molecules did not bind to N. gonorrhoeae. In contrast, we found that Yersinia pestis, an organism that can infect virtually all mammals, bound species-specific C4bp and uniformly resisted serum complement-mediated killing by these species. Serum resistance of gonococci was restored in these sera by human C4bp. An exception was serotype Por1B-bearing gonococcal strains that previously had been used successfully in a chimpanzee model of gonorrhea that simulates human disease. Por1B gonococci bound chimpanzee C4bp and resisted killing by chimpanzee serum, providing insight into the host restriction of gonorrhea and addressing why Por1B strains, but not Por1A strains, have been successful in experimental chimpanzee infection. Our findings may lead to the development of better animal models for gonorrhea and may also have implications in the choice of complement sources to evaluate neisserial vaccine candidates. PMID:16275906

Ngampasutadol, Jutamas; Ram, Sanjay; Blom, Anna M; Jarva, Hanna; Jerse, Ann E; Lien, Egil; Goguen, Jon; Gulati, Sunita; Rice, Peter A

2005-11-07

150

Experience and acceptability of diets of varying protein content and glycemic index in an obese cohort: results from the Diogenes trial.  

PubMed

Background/Objectives:To investigate acceptability and tolerability of diets of different protein and glycemic index (GI) content aimed at weight maintenance following a phase of rapid weight loss, as part of a large pan-European dietary intervention trial.Subjects/Methods:The Diogenes study (www.diogenes-eu.org) consisted of an initial 8-week rapid weight-loss phase (800-1000?kcal/day), followed by a 6-month weight maintenance intervention with five different diets varying in protein and GI content. Measurement of a range of outcomes relating to experience of the Diogenes diets in terms of acceptability, experience and mood were recorded via end of day questionnaires throughout the study.Results:Weight change during the initial weight loss phase weakly, but positively correlated with acceptability of the programme (r range=-0.08 to 0.2, P?0.05, n=685 on four of five dimensions). Success at weight maintenance positively correlated with acceptance of the programme (r range=-0.21 to -0.34, P<0.001, n=540 for all five dimensions). The diets with higher protein content were more acceptable than the low protein (LP) diets, however, no differences between the high vs low GI diets were found concerning acceptability and tolerability.Conclusions:Results suggest that moderately high protein diets, compared with LP diets, are more acceptable diets for weight control in overweight individuals. PMID:23778783

McConnon, A; Horgan, G W; Lawton, C; Stubbs, J; Shepherd, R; Astrup, A; Handjieva-Darlenska, T; Kunešová, M; Larsen, T M; Lindroos, A K; Martinez, J A; Papadaki, A; Pfeiffer, A F H; van Baak, M A; Raats, M M

2013-06-19

151

[Posttranslational reactions resulting in a long-wavelength shift in the spectra of asFP595 protein from Anemonia sulcata].  

PubMed

In most fluorescent proteins characterized by light absorption and emission in the red and the far-red spectral region (550-650 nm), the chromophore pi system is extended at the expense of the additional oxidation of the GFP-like structure and the formation of an acylimine substituent. As distinct from these proteins, the photoactivateable protein asFP595 contains a chromophore with the keto group substituted for an acylimine substituent. In this work, we studied the reactions that result in a bathochromic shift in the spectrum of asFP595. Maturation kinetics analysis has shown the generation of the immature form containing a protonated chromophore (absorption at 420 nm) at the intermediate step, as in the case of other red fluorescent proteins, which then is isobestically converted into the final mature form (568 nm). Mass spectrometric analysis of the chromopeptide isolated from immature asFP595 has demonstrated that the intermediate form contains a GFP-type chromophore. It has also been found that the oxidation of the GFP chromophore is accompanied by the generation of an equimolar amount of hydro gen peroxide. The intermediate products of oxidation have been analyzed by the mutagenesis of the first chromophore-generating amino acid residue. It has been demonstrated that in the case of all mutants studied, chromophore synthesis does not terminate at the stage of the acylimine derivative, but immediately results in the fragmentation of the main chain of the protein and in the formation of the keto form. PMID:20386585

Pakhomov, A A; Tret'iakova, Iu A; Martynov, V I

152

Disruption of the midkine gene (Mdk) resulted in altered expression of a calcium binding protein in the hippocampus of infant mice and their abnormal behaviour  

Microsoft Academic Search

Background: Midkine (MK) is a growth factor implicated in the development and repair of various tissues, especially neural tissues. However, its in vivo function has not been clarified. Results: Knockout mice lacking the MK gene (Mdk) showed no gross abnormalities. We closely analysed postnatal brain development in Mdk(-\\/-) mice using calcium binding proteins as markers to distinguish neuronal subpopulations. Intense

Eishin Nakamura; Kenji Kadomatsu; Shigeki Yuasa; Hisako Muramatsu; Takayoshi Mamiya; Toshitaka Nabeshima; Qi-Wen Fan; Kazuhiro Ishiguro; Tadahiko Igakura; Shuichiro Matsubara; Tadashi Kaname; Mitsuru Horiba; Hidehiko Saito; Takashi Muramatsu

1998-01-01

153

Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of ?-helix and ?-hairpin formation.  

PubMed

Folding simulations on peptides and proteins using empirical force fields have demonstrated the sensitivity of the results to details of the backbone potential. A recently revised version of the additive CHARMM protein force field, which includes optimization of the backbone CMAP potential to achieve good balance between different types of secondary structure, correcting the ?-helical bias present in the former CHARMM22/CMAP energy function, is shown to result in improved cooperativity for the helix-coil transition. This is due to retention of the empirical corrections introduced in the original CMAP to reproduce folded protein structures-corrections that capture many-body effects missing from an energy surface fitted to gas phase calculations on dipeptides. The experimental temperature dependence of helix formation in (AAQAA)(3) and parameters for helix nucleation and elongation are in much better agreement with experiment than those obtained with other recent force fields. In contrast, CMAP parameters derived by fitting to a vacuum quantum mechanical surface for the alanine dipeptide do not reproduce the enhanced cooperativity, showing that the empirical backbone corrections, and not some other feature of the force field, are responsible. We also find that the cooperativity of ?-hairpin formation is much improved relative to other force fields we have studied. Comparison with (?,?) distributions from the Protein Data Bank further justifies the inclusion of many-body effects in the CMAP. These results suggest that the revised energy function will be suitable for both simulations of unfolded or intrinsically disordered proteins and for investigating protein-folding mechanisms. PMID:23009854

Best, Robert B; Mittal, Jeetain; Feig, Michael; MacKerell, Alexander D

2012-09-01

154

Modulation of Chaperone Gene Expression in Mutagenized Saccharomyces cerevisiae Strains Developed for Recombinant Human Albumin Production Results in Increased Production of Multiple Heterologous Proteins?  

PubMed Central

The yeast Saccharomyces cerevisiae has been successfully established as a commercially viable system for the production of recombinant proteins. Manipulation of chaperone gene expression has been utilized extensively to increase recombinant protein production from S. cerevisiae, focusing predominantly on the products of the protein disulfide isomerase gene PDI1 and the hsp70 gene KAR2. Here we show that the expression of the genes SIL1, LHS1, JEM1, and SCJ1, all of which are involved in regulating the ATPase cycle of Kar2p, is increased in a proprietary yeast strain, developed by several rounds of random mutagenesis and screening for increased production of recombinant human albumin (rHA). To establish whether this expression contributes to the enhanced-production phenotype, these genes were overexpressed both individually and in combination. The resultant strains showed significantly increased shake-flask production levels of rHA, granulocyte-macrophage colony-stimulating factor, and recombinant human transferrin.

Payne, T.; Finnis, C.; Evans, L. R.; Mead, D. J.; Avery, S. V.; Archer, D. B.; Sleep, D.

2008-01-01

155

Depletion of stromal cells expressing fibroblast activation protein-? from skeletal muscle and bone marrow results in cachexia and anemia.  

PubMed

Fibroblast activation protein-? (FAP) identifies stromal cells of mesenchymal origin in human cancers and chronic inflammatory lesions. In mouse models of cancer, they have been shown to be immune suppressive, but studies of their occurrence and function in normal tissues have been limited. With a transgenic mouse line permitting the bioluminescent imaging of FAP(+) cells, we find that they reside in most tissues of the adult mouse. FAP(+) cells from three sites, skeletal muscle, adipose tissue, and pancreas, have highly similar transcriptomes, suggesting a shared lineage. FAP(+) cells of skeletal muscle are the major local source of follistatin, and in bone marrow they express Cxcl12 and KitL. Experimental ablation of these cells causes loss of muscle mass and a reduction of B-lymphopoiesis and erythropoiesis, revealing their essential functions in maintaining normal muscle mass and hematopoiesis, respectively. Remarkably, these cells are altered at these sites in transplantable and spontaneous mouse models of cancer-induced cachexia and anemia. Thus, the FAP(+) stromal cell may have roles in two adverse consequences of cancer: their acquisition by tumors may cause failure of immunosurveillance, and their alteration in normal tissues contributes to the paraneoplastic syndromes of cachexia and anemia. PMID:23712428

Roberts, Edward W; Deonarine, Andrew; Jones, James O; Denton, Alice E; Feig, Christine; Lyons, Scott K; Espeli, Marion; Kraman, Matthew; McKenna, Brendan; Wells, Richard J B; Zhao, Qi; Caballero, Otavia L; Larder, Rachel; Coll, Anthony P; O'Rahilly, Stephen; Brindle, Kevin M; Teichmann, Sarah A; Tuveson, David A; Fearon, Douglas T

2013-05-27

156

Positive selection results in frequent reversible amino acid replacements in the G protein gene of human respiratory syncytial virus.  

PubMed

Human respiratory syncytial virus (HRSV) is the major cause of lower respiratory tract infections in children under 5 years of age and the elderly, causing annual disease outbreaks during the fall and winter. Multiple lineages of the HRSVA and HRSVB serotypes co-circulate within a single outbreak and display a strongly temporal pattern of genetic variation, with a replacement of dominant genotypes occurring during consecutive years. In the present study we utilized phylogenetic methods to detect and map sites subject to adaptive evolution in the G protein of HRSVA and HRSVB. A total of 29 and 23 amino acid sites were found to be putatively positively selected in HRSVA and HRSVB, respectively. Several of these sites defined genotypes and lineages within genotypes in both groups, and correlated well with epitopes previously described in group A. Remarkably, 18 of these positively selected tended to revert in time to a previous codon state, producing a "flip-flop" phylogenetic pattern. Such frequent evolutionary reversals in HRSV are indicative of a combination of frequent positive selection, reflecting the changing immune status of the human population, and a limited repertoire of functionally viable amino acids at specific amino acid sites. PMID:19119418

Botosso, Viviane F; Zanotto, Paolo M de A; Ueda, Mirthes; Arruda, Eurico; Gilio, Alfredo E; Vieira, Sandra E; Stewien, Klaus E; Peret, Teresa C T; Jamal, Leda F; Pardini, Maria I de M C; Pinho, João R R; Massad, Eduardo; Sant'anna, Osvaldo A; Holmes, Eddie C; Durigon, Edison L

2009-01-02

157

Positive Selection Results in Frequent Reversible Amino Acid Replacements in the G Protein Gene of Human Respiratory Syncytial Virus  

PubMed Central

Human respiratory syncytial virus (HRSV) is the major cause of lower respiratory tract infections in children under 5 years of age and the elderly, causing annual disease outbreaks during the fall and winter. Multiple lineages of the HRSVA and HRSVB serotypes co-circulate within a single outbreak and display a strongly temporal pattern of genetic variation, with a replacement of dominant genotypes occurring during consecutive years. In the present study we utilized phylogenetic methods to detect and map sites subject to adaptive evolution in the G protein of HRSVA and HRSVB. A total of 29 and 23 amino acid sites were found to be putatively positively selected in HRSVA and HRSVB, respectively. Several of these sites defined genotypes and lineages within genotypes in both groups, and correlated well with epitopes previously described in group A. Remarkably, 18 of these positively selected tended to revert in time to a previous codon state, producing a “flip-flop” phylogenetic pattern. Such frequent evolutionary reversals in HRSV are indicative of a combination of frequent positive selection, reflecting the changing immune status of the human population, and a limited repertoire of functionally viable amino acids at specific amino acid sites.

Botosso, Viviane F.; de A. Zanotto, Paolo M.; Ueda, Mirthes; Arruda, Eurico; Gilio, Alfredo E.; Vieira, Sandra E.; Stewien, Klaus E.; Peret, Teresa C. T.; Jamal, Leda F.; Pardini, Maria I. de M. C.; Pinho, Joao R. R.; Massad, Eduardo; Sant'Anna, Osvaldo A.; Holmes, Eddie C.; Durigon, Edison L.

2009-01-01

158

Post-natal knockout of prion protein alters hippocampal CA1 properties, but does not result in neurodegeneration  

PubMed Central

Prion protein (PrP) plays a crucial role in prion disease, but its physiological function remains unclear. Mice with gene deletions restricted to the coding region of PrP have only minor phenotypic deficits, but are resistant to prion disease. We generated double transgenic mice using the Cre–loxP system to examine the effects of PrP depletion on neuronal survival and function in adult brain. Cre-mediated ablation of PrP in neurons occurred after 9 weeks. We found that the mice remained healthy without evidence of neurodegeneration or other histopathological changes for up to 15 months post-knockout. However, on neurophysiological evaluation, they showed significant reduction of afterhyperpolarization potentials (AHPs) in hippocampal CA1 cells, suggesting a direct role for PrP in the modulation of neuronal excitability. These data provide new insights into PrP function. Furthermore, they show that acute depletion of PrP does not affect neuronal survival in this model, ruling out loss of PrP function as a pathogenic mechanism in prion disease and validating therapeutic approaches targeting PrP.

Mallucci, G.R.; Ratte, S.; Asante, E.A.; Linehan, J.; Gowland, I.; Jefferys, J.G.R.; Collinge, J.

2002-01-01

159

COOH-terminal truncated cardiac myosin-binding protein C mutants resulting from familial hypertrophic cardiomyopathy mutations exhibit altered expression and/or incorporation in fetal rat cardiomyocytes.  

PubMed

Mutations in human cardiac myosin-binding protein C (cMyBP-C) gene are associated with familial hypertrophic cardiomyopathy (FHC), and most of them are predicted to produce COOH-truncated proteins. To understand the molecular mechanism(s) by which such mutations cause FHC, we analyzed (i) the accumulation of human cMyBP-C mutants in fetal rat cardiomyocytes, and (ii) the protein sequence of the human wild-type (wt) cMyBP-C by hydrophobic cluster analysis with the aim of identifying new putative myosin-binding site(s). Accumulation and sarcomeric localization of the wt protein and of four FHC-mutant cMyBP-Cs (E542Q and three COOH-truncated proteins) were studied in cardiomyocytes by immunostaining and confocal microscopy after transfection with myc-tagged constructs. We found that: (i) 10 % of the cells expressing COOH-truncated mutants exhibit an incorporation into the A-band of the sarcomere without any alteration of the myofibrillar architecture versus 76 % of those expressing the wt or E542Q mutant cMyBP-Cs (p<0.001); (ii) 90 % of the cells expressing the truncated mutants show a diffuse localization of these proteins in the cardiomyocytes, out of which 45 % exhibit a significant alteration of the sarcomeric structure (p<0.0001 versus wt); and (iii) the two shortest mutant cMyBP-Cs accumulate at very low levels in fetal rat cardiomyocytes as compared to the wt (p<0.008). Protein sequence analysis indicated that a 45-residue sequence in the NH2-terminal C0 domain of cMyBP-C exhibits a consistent homology (sequence similarity score of 42 %) with a segment of the NH2-terminal domain of myomesin, another myosin-binding protein. This result suggests that the C0 domain of human cMyBP-C contains a novel putative myosin-binding site that could account for the A-band incorporation of the truncated mutants. In addition, the faint accumulation and the diffuse localization of truncated mutants could probably be explained by a low affinity of the C0 domain for myosin. We conclude that COOH-truncated cMyBP-Cs may act as poison polypeptides that disrupt the myofibrillar architecture and result in the defects observed in FHC. PMID:10610770

Flavigny, J; Souchet, M; Sébillon, P; Berrebi-Bertrand, I; Hainque, B; Mallet, A; Bril, A; Schwartz, K; Carrier, L

1999-11-26

160

Lack of the ApbC or ApbE Protein Results in a Defect in Fe-S Cluster Metabolism in Salmonella enterica Serovar Typhimurium  

PubMed Central

The isc genes function in the assembly of Fe-S clusters and are conserved in many prokaryotic and eukaryotic organisms. In most bacteria studied, the isc operon can be deleted without loss of cell viability, indicating that additional systems for Fe-S cluster assembly must exist. Several laboratories have described nutritional and biochemical defects resulting from mutations in the isc operon. Here we demonstrate that null mutations in two genes of unknown function, apbC and apbE, result in similar cellular deficiencies. Exogenous ferric chloride suppressed these deficiencies in the apbC and apbE mutants, distinguishing them from previously described isc mutants. The deficiencies caused by the apbC and isc mutations were additive, which is consistent with Isc and ApbC's having redundant functions or with Isc and ApbC's functioning in different areas of Fe-S cluster metabolism (e.g., Fe-S cluster assembly and Fe-S cluster repair). Both the ApbC and ApbE proteins are similar in sequence to proteins that function in metal cofactor assembly. Like the enzymes with sequence similarity to ApbC, purified ApbC protein was able to hydrolyze ATP. The data herein are consistent with the hypothesis that the ApbC and ApbE proteins function in Fe-S cluster metabolism in vivo.

Skovran, Elizabeth; Downs, Diana M.

2003-01-01

161

Lack of the ApbC or ApbE protein results in a defect in Fe-S cluster metabolism in Salmonella enterica serovar Typhimurium.  

PubMed

The isc genes function in the assembly of Fe-S clusters and are conserved in many prokaryotic and eukaryotic organisms. In most bacteria studied, the isc operon can be deleted without loss of cell viability, indicating that additional systems for Fe-S cluster assembly must exist. Several laboratories have described nutritional and biochemical defects resulting from mutations in the isc operon. Here we demonstrate that null mutations in two genes of unknown function, apbC and apbE, result in similar cellular deficiencies. Exogenous ferric chloride suppressed these deficiencies in the apbC and apbE mutants, distinguishing them from previously described isc mutants. The deficiencies caused by the apbC and isc mutations were additive, which is consistent with Isc and ApbC's having redundant functions or with Isc and ApbC's functioning in different areas of Fe-S cluster metabolism (e.g., Fe-S cluster assembly and Fe-S cluster repair). Both the ApbC and ApbE proteins are similar in sequence to proteins that function in metal cofactor assembly. Like the enzymes with sequence similarity to ApbC, purified ApbC protein was able to hydrolyze ATP. The data herein are consistent with the hypothesis that the ApbC and ApbE proteins function in Fe-S cluster metabolism in vivo. PMID:12486045

Skovran, Elizabeth; Downs, Diana M

2003-01-01

162

Anti-depressant medication use and C-reactive protein: results from two population-based studies.  

PubMed

The use of anti-depressant medication has been linked to cardiovascular disease (CVD). We examined the association between anti-depressant medication use and a marker of low grade systemic inflammation as a potential pathway linking anti-depressant use and CVD in two population based studies. Data were collected in a representative sample of 8131 community dwelling adults (aged 47.4±15.9 years, 46.7% male) from the Scottish Health Surveys (SHS). The use of anti-depressant medication was coded according to the British National Formulary and blood was drawn for the measurement of C-reactive protein (CRP). In a second study, we attempted to replicate our findings using longitudinal data from the Whitehall II study (n=4584, aged 55.5±5.9 years, mean follow-up 5.5 years). Antidepressants were used in 5.6% of the SHS sample, with selective serotonin reuptake inhibitors (SSRIs) being the most common. There was a higher risk of elevated CRP (>3 mg/L) in users of tricyclic antidepressant (TCA) medication (multivariate adjusted odds ratio (OR)=1.52, 95% CI, 1.07-2.15), but not in SSRI users (multivariate adjusted OR=1.07, 95% CI, 0.81-1.42). A longitudinal association between any antidepressant use and subsequent CRP was confirmed in the Whitehall cohort. In summary, the use of anti-depressants was associated with elevated levels of systemic inflammation independently from the symptoms of mental illness and cardiovascular co-morbidity. This might be a potential mechanism through which antidepressant medication increases CVD risk. Further data are required to explore the effects of dosage and duration of antidepressant treatment. PMID:20863880

Hamer, Mark; Batty, G D; Marmot, Michael G; Singh-Manoux, Archana; Kivimäki, Mika

2010-09-21

163

Genetic Divergence of Rotavirus Nonstructural Protein 4 Results in Distinct Serogroup-Specific Viroporin Activity and Intracellular Punctate Structure Morphologies  

PubMed Central

Nonstructural protein 4 (NSP4) viroporin activity is critical for the replication and assembly of serogroup A rotavirus (RVA); however, the dramatic primary sequence divergence of NSP4s across serogroups raises the possibility that viroporin activity is not a common feature among RVs. We tested for NSP4 viroporin activity from divergent strains, including RVA (EC and Ty-1), RVB (IDIR), and RVC (Cowden). Canonical viroporin motifs were identified in RVA, RVB, and RVC NSP4s, but the arrangement of basic residues and the amphipathic ?-helices was substantially different between serogroups. Using Escherichia coli and mammalian cell expression, we showed that each NSP4 tested had viroporin activity, but serogroup-specific viroporin phenotypes were identified. Only mammalian RVA and RVC NSP4s induced BL21-pLysS E. coli cell lysis, a classical viroporin activity assay. In contrast, RVA, RVB, and RVC NSP4 expression was universally cytotoxic to E. coli and disrupted reduction-oxidation activities, as measured by a new redox dye assay. In mammalian cells, RVB and RVC NSP4s were initially localized in the endoplasmic reticulum (ER) and trafficked into punctate structures that were mutually exclusive with RVA NSP4. The punctate structures partially localized to the ER-Golgi intermediate compartment (ERGIC) but primarily colocalized with punctate LC3, a marker for autophagosomes. Similar to RVA NSP4, expression of RVB and RVC NSP4s significantly elevated cytosolic calcium levels, demonstrating that despite strong primary sequence divergence, RV NSP4 has maintained viroporin activity across serogroups A to C. These data suggest that elevated cytosolic calcium is a common critical process for all rotavirus strains.

Hyser, Joseph M.; Utama, Budi; Crawford, Sue E.

2012-01-01

164

Study of recombinant antibody fragments and PAI-1 complexes combining protein-protein docking and results from site-directed mutagenesis.  

PubMed

Elevated plasma levels of plasminogen activator inhibitor-1 (PAI-1) have been correlated with cardiovascular diseases such as myocardial infarction and venous thrombosis. PAI-1 has also been shown to play an important role in tumor development, diabetes, and obesitas. Monoclonal antibodies MA-8H9D4 and MA-56A7C10, and their single-chain variable fragments (scFv), exhibit PAI-1-neutralizing properties. In this study, a rigid-body docking approach is used to predict the binding geometry of two distinct conformations of PAI-1 (active and latent) in complex with these antibody fragments. Resulting models were initially refined by using the dead-end elimination algorithm. Different filtering criteria based on the mutagenesis studies and structural considerations were applied to select the final models. These were refined by using the slow-cooling torsion-angle dynamic annealing protocol. The docked structures reveal the respective epitopes and paratopes and their potential interactions. This study provides crucial information that is necessary for the rational development of low-molecular weight PAI-1 inhibitors. PMID:17850750

Novoa de Armas, Hector; Dewilde, Maarten; Verbeke, Koen; De Maeyer, Marc; Declerck, Paul J

2007-09-01

165

Copper deficiency in the young bovine results in dramatic decreases in brain copper concentration but does not alter brain prion protein biology  

Microsoft Academic Search

An Mn for Cu substitution on cellular prion proteins (PrPc) in the brain that results in bio- chemical changes to PrPc has been implicated in the pathogenesis of transmissible spongiform encephal- opathies. Recent research in the mature bovine does not support this theory. The present study tested this hypothesis by using progeny from gestating cows re- ceiving Cu-deficient diets or

L. R. Legleiter; J. W. Spears; H. C. Liu

2008-01-01

166

Accumulation of radium in ferruginous protein bodies formed in lung tissue: association of resulting radiation hotspots with malignant mesothelioma and other malignancies  

PubMed Central

While exposure to fibers and particles has been proposed to be associated with several different lung malignancies including mesothelioma, the mechanism for the carcinogenesis is not fully understood. Along with mineralogical observation, we have analyzed forty-four major and trace elements in extracted asbestos bodies (fibers and proteins attached to them) with coexisting fiber-free ferruginous protein bodies from extirpative lungs of individuals with malignant mesothelioma. These observations together with patients’ characteristics suggest that inhaled iron-rich asbestos fibers and dust particles, and excess iron deposited by continuous cigarette smoking would induce ferruginous protein body formation resulting in ferritin aggregates in lung tissue. Chemical analysis of ferruginous protein bodies extracted from lung tissues reveals anomalously high concentrations of radioactive radium, reaching millions of times higher concentration than that of seawater. Continuous and prolonged internal exposure to hotspot ionizing radiation from radium and its daughter nuclides could cause strong and frequent DNA damage in lung tissue, initiate different types of tumour cells, including malignant mesothelioma cells, and may cause cancers.

Nakamura, Eizo; Makishima, Akio; Hagino, Kyoko; Okabe, Kazunori

2009-01-01

167

Over-expression of rice leucine-rich repeat protein results in activation of defense response, thereby enhancing resistance to bacterial soft rot in Chinese cabbage.  

PubMed

Pectobacterium carotovorum subsp. carotovorum causes soft rot disease in various plants, including Chinese cabbage. The simple extracellular leucine-rich repeat (eLRR) domain proteins have been implicated in disease resistance. Rice leucine-rich repeat protein (OsLRP), a rice simple eLRR domain protein, is induced by pathogens, phytohormones, and salt. To see whether OsLRP enhances disease resistance to bacterial soft rot, OsLRP was introduced into Chinese cabbage by Agrobacterium-mediated transformation. Two independent transgenic lines over-expressing OsLRP were generated and further analyzed. Transgenic lines over-expressing OsLRP showed enhanced disease resistance to bacterial soft rot compared to non-transgenic control. Bacterial growth was retarded in transgenic lines over-expressing OsLRP compared to non-transgenic controls. We propose that OsLRP confers enhanced resistance to bacterial soft rot. Monitoring expression of defense-associated genes in transgenic lines over-expressing OsLRP, two different glucanases and Brassica rapa polygalacturonase inhibiting protein 2, PDF1 were constitutively activated in transgenic lines compared to non-transgenic control. Taken together, heterologous expression of OsLRP results in the activation of defense response and enhanced resistance to bacterial soft rot. PMID:22717673

Park, Young Ho; Choi, Changhyun; Park, Eun Mi; Kim, Hyo Sun; Park, Hong Jae; Bae, Shin Cheol; Ahn, Ilpyung; Kim, Min Gab; Park, Sang Ryeol; Hwang, Duk-Ju

2012-06-21

168

17-Allylamino-17-demethoxygeldanamycin induces downregulation of critical Hsp90 protein clients and results in cell cycle arrest and apoptosis of human urinary bladder cancer cells  

PubMed Central

Background 17-Allylamino-17-demethoxygeldanamycin (17-AAG), a benzoquinone ansamycin antibiotic, specifically targets heat shock protein 90 (Hsp90) and interferes with its function as a molecular chaperone that maintains the structural and functional integrity of various protein clients involved in cellular signaling. In this study, we have investigated the effect of 17-AAG on the regulation of Hsp90-dependent signaling pathways directly implicated in cell cycle progression, survival and motility of human urinary bladder cancer cell lines. Methods We have used MTT-based assays, FACS analysis, Western blotting, semi-quantitative RT-PCR, immunocytochemistry and scratch-wound assay in RT4, RT112 and T24 human urinary bladder cancer cell lines. Results We have demonstrated that, upon 17-AAG treatment, bladder cancer cells are arrested in the G1 phase of the cell cycle and eventually undergo apoptotic cell death in a dose-dependent manner. Furthermore, 17-AAG administration was shown to induce a pronounced downregulation of multiple Hsp90 protein clients and other downstream effectors, such as IGF-IR, Akt, IKK-?, IKK-?, FOXO1, ERK1/2 and c-Met, resulting in sequestration-mediated inactivation of NF-?B, reduced cell proliferation and decline of cell motility. Conclusions In total, we have clearly evinced a dose-dependent and cell type-specific effect of 17-AAG on cell cycle progression, survival and motility of human bladder cancer cells, due to downregulation of multiple Hsp90 clients and subsequent disruption of signaling integrity.

2010-01-01

169

Acute leukemias of different lineages have similar MLL gene fusions encoding related chimeric proteins resulting from chromosomal translocation.  

PubMed Central

The MLL gene, on human chromosome 11q23, undergoes chromosomal translocation in acute leukemias, resulting in gene fusion with AF4 (chromosome 4) and ENL (chromosome 19). We report here translocation of MLL with nine different chromosomes and two paracentric chromosome 11 deletions in early B cell, B- or T-cell lineage, or nonlymphocytic acute leukemias. The mRNA translocation junction from 22 t(4;11) patients, including six adult leukemias, and nine t(11;19) tumors reveals a remarkable conservation of breakpoints within MLL, AF4, or ENL genes, irrespective of tumor phenotype. Typically, the breakpoints are upstream of the zinc-finger region of MLL, and deletion of this region can accompany translocation, supporting the der(11) chromosome as the important component in leukemogenesis. Partial sequence of a fusion between MLL and the AFX1 gene from chromosome X shows the latter to be rich in Ser/Pro codons, like the ENL mRNA. These data suggest that the heterogeneous 11q23 abnormalities might cause attachment of Ser/Pro-rich segments to the NH2 terminus of MLL, lacking the zinc-finger region, and that translocations occur in early hematopoietic cells, before commitment to distinct lineages. Images Fig. 1

Corral, J; Forster, A; Thompson, S; Lampert, F; Kaneko, Y; Slater, R; Kroes, W G; van der Schoot, C E; Ludwig, W D; Karpas, A

1993-01-01

170

Acute leukemias of different lineages have similar MLL gene fusions encoding related chimeric proteins resulting from chromosomal translocation  

SciTech Connect

The MLL gene, on human chromosome 11q23, undergoes chromosomal translocation in acute leukemias, resulting in gene fusion with AF4 (chromosome 4) and ENL (chromosome 19). The authors report here translocation of MLL with nine different chromosomes and two paracentric chromosome 11 deletions in early B cell, B- or T-cell lineage, or nonlymphocytic acute leukemias. The mRNA translocation junction from 22t(4;11) patients, including six adult leukemias, and nine t(11;19) tumors reveals a remarkable conservation of breakpoints within MLL, AF4, or ENL genes, irrespective of tumor phenotype. Typically, the breakpoints are upstream of the zinc-finger region of MLL, and deletion of this region can accompany translocation, supporting the der(11) chromosome as the important component in leukemogenesis. Partial sequence of a fusion between MLL and the AFX1 gene from chromosome X shows the latter to be rich in Ser/Pro codons, like the ENL mRNA. These data suggest that the heterogeneous 11q23 abnormalities might cause attachment of Ser/Pro-rich segments to the NH[sub 2] terminus of MLL, lacking the zinc-finger region, and that translocation occurs in early hematopoietic cells, before commitment to distinct lineages. 36 refs., 2 figs.

Corral, J.; Forster, A.; Thompson, S.; Rabbitts, T.H. (Medical Research Council Laboratory of Molecular Biology, Cambridge (United Kingdom)); Lampert, F. (Kinderklinik-Universitaet Giessen (Germany)); Kaneko, Y. (Saitama Cancer Centre, Saitama (Japan)); Slater, R.; Kroes, W.G. (Univ. of Amsterdam (Netherlands)); Van Der Schoot, C.E. (Central Laboratory of the Netherlands Red Cross, Amsterdam (Netherlands)); Ludwig, W.D. (Institut fur Humangenetik und Antrhopologie, Heidelberg (Germany)); Karpas, A. (Univ. of Cambridge (United Kingdom)); Pocock, C.; Cotter, F. (Institute of Child Health, London (United Kingdom))

1993-09-15

171

An HLA-A2-restricted tyrosinase antigen on melanoma cells results from posttranslational modification and suggests a novel pathway for processing of membrane proteins  

PubMed Central

T lymphocytes recognize antigens consisting of peptides presented by class I and II major histocompatibility complex (MHC) molecules. The peptides identified so far have been predictable from the amino acid sequences of proteins. We have identified the natural peptide target of a CTL clone that recognizes the tyrosinase gene product on melanoma cells. The peptide results from posttranslational conversion of asparagine to aspartic acid. This change is of central importance for peptide recognition by melanoma-specific T cells, but has no impact on peptide binding to the MHC molecule. This posttranslational modification has not been previously described for any MHC-associated peptide and represents the first demonstration of posttranslational modification of a naturally processed class I-associated peptide. This observation is relevant to the identification and prediction of potential peptide antigens. The most likely mechanism for production of this peptide leads to the suggestion that antigenic peptides can be derived from proteins that are translated into the endoplasmic reticulum.

1996-01-01

172

Disruption of the A-Kinase Anchoring Domain in Flagellar Radial Spoke Protein 3 Results in Unregulated Axonemal cAMP-dependent Protein Kinase Activity and Abnormal Flagellar Motility  

PubMed Central

Biochemical studies of Chlamydomonas flagellar axonemes revealed that radial spoke protein (RSP) 3 is an A-kinase anchoring protein (AKAP). To determine the physiological role of PKA anchoring in the axoneme, an RSP3 mutant, pf14, was transformed with an RSP3 gene containing a mutation in the PKA-binding domain. Analysis of several independent transformants revealed that the transformed cells exhibit an unusual phenotype: a fraction of the cells swim normally; the remainder of the cells twitch feebly or are paralyzed. The abnormal/paralyzed motility is not due to an obvious deficiency of radial spoke assembly, and the phenotype cosegregates with the mutant RSP3. We postulated that paralysis was due to failure in targeting and regulation of axonemal cAMP-dependent protein kinase (PKA). To test this, reactivation experiments of demembranated cells were performed in the absence or presence of PKA inhibitors. Importantly, motility in reactivated cell models mimicked the live cell phenotype with nearly equal fractions of motile and paralyzed cells. PKA inhibitors resulted in a twofold increase in the number of motile cells, rescuing paralysis. These results confirm that flagellar RSP3 is an AKAP and reveal that a mutation in the PKA binding domain results in unregulated axonemal PKA activity and inhibition of normal motility.

Gaillard, Anne R.; Fox, Laura A.; Rhea, Jeanne M.; Craige, Branch

2006-01-01

173

Basal activation of p70S6K results in adipose-specific insulin resistance in protein-tyrosine phosphatase 1B -/- mice.  

PubMed

Although protein-tyrosine phosphatase 1B (PTP-1B) is a negative regulator of insulin action, adipose tissue from PTP-1B-/- mice does not show enhanced insulin-stimulated insulin receptor phosphorylation. Investigation of glucose uptake in isolated adipocytes revealed that the adipocytes from PTP-1B-/- mice have a significantly attenuated insulin response as compared with PTP-1B+/+ adipocytes. This insulin resistance manifests in PTP-1B-/- animals older than 16 weeks of age and could be partially rescued by adenoviral expression of PTP-1B in null adipocytes. Examination of adipose signaling pathways found that the basal p70S6K activity was at least 50% higher in adipose from PTP-1B-/- mice compared with wild type animals. The increased basal activity of p70S6K in PTP-1B-/- adipose correlated with decreases in IR substrate-1 protein levels and insulin-stimulated Akt/protein kinase B activity, explaining the decrease in insulin sensitivity even as insulin receptor phosphorylation was unaffected. The insulin resistance of the of the PTP-1B-/- adipocytes could also be rescued by treatment with rapamycin, suggesting that in adipose the loss of PTP-1B results in basal activation of mTOR (mammalian target of rapamycin) complex 1 leading to a tissue-specific insulin resistance. PMID:17664276

Ruffolo, Salvatore C; Forsell, Pontus K A; Yuan, Xiling; Desmarais, Sylvie; Himms-Hagen, Jean; Cromlish, Wanda; Wong, Kenny K; Kennedy, Brian P

2007-07-30

174

Differences in folate?protein interactions result in differing inhibition of native rat liver and recombinant glycine N-methyltransferase by 5-methyltetrahydrofolate  

SciTech Connect

Glycine N-methyltransferase (GNMT) is a key regulatory enzyme in methyl group metabolism. In mammalian liver it reduces S-adenosylmethionine levels by using it to methylate glycine, producing N-methylglycine (sarcosine) and S-adenosylhomocysteine. GNMT is inhibited by binding two molecules of 5-methyltetrahydrofolate (mono- or polyglutamate forms) per tetramer of the active enzyme. Inhibition is sensitive to the status of the N-terminal valine of GNMT and to polyglutamation of the folate inhibitor. It is inhibited by pentaglutamate form more efficiently compared to monoglutamate form. The native rat liver GNMT contains an acetylated N-terminal valine and is inhibited much more efficiently compared to the recombinant protein expressed in E. coli where the N-terminus is not acetylated. In this work we used a protein crystallography approach to evaluate the structural basis for these differences. We show that in the folate-GNMT complexes with the native enzyme, two folate molecules establish three and four hydrogen bonds with the protein. In the folate-recombinant GNMT complex only one hydrogen bond is established. This difference results in more effective inhibition by folate of the native liver GNMT activity compared to the recombinant enzyme.

Luka, Zigmund; Pakhomova, Svetlana; Loukachevitch, Lioudmila V.; Newcomer, Marcia E.; Wagner, Conrad (Vanderbilt); (LSU)

2012-06-27

175

Reduced Susceptibility of Haemophilus influenzae to the Peptide Deformylase Inhibitor LBM415 Can Result from Target Protein Overexpression Due to Amplified Chromosomal def Gene Copy Number?  

PubMed Central

Previous genetic analysis of Haemophilus influenzae revealed two mechanisms associated with decreased susceptibility to the novel peptide deformylase inhibitor LBM415: AcrAB-TolC-mediated efflux and Fmt bypass, resulting from mutations in the pump repressor gene acrR and in the fmt gene, respectively. We have isolated an additional mutant, CDS23 (LBM415 MIC, 64 ?g/ml versus 4 ?g/ml against the parent strain NB65044) that lacks mutations in the acrR or fmt structural genes or in the gene encoding Def, the intracellular target of LBM415. Western immunoblot analysis, two-dimensional gel electrophoresis, and tryptic digestion combined with mass spectrometric identification showed that the Def protein was highly overexpressed in the mutant strain. Consistent with this, real-time reverse transcription-PCR revealed a significant increase in def transcript titer. No mutations were found in the region upstream of def that might account for altered expression; however, pulsed-field gel electrophoresis suggested that a genetic rearrangement of the region containing def had occurred. Using a combination of PCR, sequencing, and Southern blot analyses, it was determined that the def gene had undergone copy number amplification, explaining the high level of target protein expression. Inactivation of the AcrAB-TolC efflux pump in this mutant increased susceptibility 16-fold, highlighting the role of efflux in exacerbating the overall reduced susceptibility resulting from target overexpression.

Dean, Charles R.; Narayan, Shubha; Richards, Joel; Daigle, Denis M.; Esterow, Stacy; Leeds, Jennifer A.; Kamp, Heather; Puyang, Xiaoling; Wiedmann, Brigitte; Mueller, Dieter; Voshol, Hans; van Oostrum, Jan; Wall, Daniel; Koehn, James; Dzink-Fox, JoAnn; Ryder, Neil S.

2007-01-01

176

TNF receptor I on human keratinocytes is a binding partner for staphylococcal protein A resulting in the activation of NF kappa B, AP-1, and downstream gene transcription.  

PubMed

Primary human keratinocytes and immortalized HaCaT cells were analysed for their capacity to bind purified staphylococcal protein A (SpA). Co-incubation with FITC-labelled SpA led to a dose-depending attachment. Pull-down experiments with cellular extracts revealed the TNF? receptor I (TNF RI) as binding partner on keratinocytes. Thus, we next looked for expression of this receptor in human epidermis and cultured keratinocytes. TNF RI is strongly expressed on all keratinocytes analysed, both at the mRNA and protein level and activation by SpA at optimal doses of 50-100 ?g/ml resulted in the phosphorylation of the TNF RI downstream kinases MEK1/2, JNK1/2, and p38 subsequently leading to translocation of the p65 NF kappa B subunit and AP-1 into the nucleus. This translocation was then followed by increased expression of IL-8 and COX-2, two known NF kappa B-induced pro-inflammatory genes. To further test the relevance of our findings, we analysed in vitro production of over 100 strains isolated from atopic eczema showing that more than 85% of the tested strains produced extracellular SpA in substantial amounts. Thus, besides superantigens, haemolysins, and other cell wall components, Staphylococcus aureus exerts pro-inflammatory stimuli on human keratinocytes through the production of SpA signalling through TNF RI. PMID:20955203

Classen, Anna; Kalali, Behnam N; Schnopp, Christina; Andres, Christian; Aguilar-Pimentel, Juan A; Ring, Johannes; Ollert, Markus; Mempel, Martin

2010-10-18

177

SILENCING OF SUBFAMILY I OF PROTEIN PHOSPHATASE 2A CATALYTIC SUBUNITS RESULTS IN ACTIVATION OF PLANT DEFENSE RESPONSES AND LOCALIZED CELL DEATH.  

Technology Transfer Automated Retrieval System (TEKTRAN)

The central importance of protein phosphorylation in plant defense responses has been demonstrated by the isolation of several disease resistance genes that encode protein kinase. In addition, there are many reports of changes in protein phosphorylation accompanying plant response to pathogens. In ...

178

Modulation of Chaperone Gene Expression in Mutagenized Saccharomyces cerevisiae Strains Developed for Recombinant Human Albumin Production Results in Increased Production of Multiple Heterologous Proteins  

Microsoft Academic Search

The yeast Saccharomyces cerevisiae has been successfully established as a commercially viable system for the production of recombinant proteins. Manipulation of chaperone gene expression has been utilized extensively to increase recombinant protein production from S. cerevisiae, focusing predominantly on the products of the protein disulfide isomerase gene PDI1 and the hsp70 gene KAR2. Here we show that the expression of

T. Payne; C. Finnis; L. R. Evans; D. J. Mead; S. V. Avery; D. B. Archer; D. Sleep

2008-01-01

179

Antigenic complementarity between HIV and other AIDS-associated infections results in idiotype-antiidiotype antibody complexes that cross react with lymphocyte proteins.  

PubMed

HIV proteins mimic HLA proteins, and the proteins of cofactor infections (cytomegalovirus, hepatitis viruses, mycobacteria, mycoplasmas) mimic CD4 proteins, making some HIV antigens molecularly complementary to cofactor antigens. Antibodies to HIV and its cofactors should therefore act like idiotype-antiidiotype pairs. Over 2000 combinations of antibodies were tested for such complementarity using modified forms of Ouchterlony immunodiffusion and ELISA. HIV antibodies do precipitate some antibodies against cofactor infections including CMV, HBV, mycobacteria and mycoplasmas. These antibodies also mimic antibodies against HLA and CD4 proteins. Thus, some combinations of HIV with cofactor infections may induce lymphocytotoxic antibodies (LCTA), a risk that must be addressed in vaccine development. PMID:15755587

Root-Bernstein, Robert

2005-03-18

180

Characterization of the Arabidopsis Lysine-Rich Arabinogalactan-Protein AtAGP17 Mutant (rat1) That Results in a Decreased Efficiency of Agrobacterium Transformation1[w  

PubMed Central

Arabinogalactan-proteins (AGPs) are a family of complex proteoglycans widely distributed in plants. The Arabidopsis rat1 mutant, previously characterized as resistant to Agrobacterium tumefaciens root transformation, is due to a mutation in the gene for the Lys-rich AGP, AtAGP17. We show that the phenotype of rat1 correlates with down-regulation of AGP17 in the root as a result of a T-DNA insertion into the promoter of AGP17. Complementation of rat1 plants by a floral dip method with either the wild-type AGP17 gene or cDNA can restore the plant to a wild-type phenotype in several independent transformants. Based on changes in PR1 gene expression and a decrease in free salicylic acid levels upon Agrobacterium infection, we suggest mechanisms by which AGP17 allows Agrobacterium rapidly to reduce the systemic acquired resistance response during the infection process.

Gaspar, Yolanda Maria; Nam, Jaesung; Schultz, Carolyn Jane; Lee, Lan-Ying; Gilson, Paul R.; Gelvin, Stanton B.; Bacic, Antony

2004-01-01

181

Analysis of protein adducts as biomarkers of short-term exposure to ethylene oxide and results of follow-up biomonitoring.  

PubMed

An accidental exposure of six workers to ethylene oxide (EO) provided the rationale for a biomonitoring and follow-up study, whose aim was to analyse protein adduct kinetics and examine the differentiation between accidental and environmental exposure, e.g., from tobacco smoke. For this purpose, the decrease in the concentration of the haemoglobin adduct N-2-hydroxyethylvaline (HEV) was followed during a five-month period after the accident, together with N-2-cyanoethylvaline (CEV) and urinary cotinine, two well-established biomarkers for smoking. The follow-up study showed that EO adduct concentrations significantly increased after a short but presumably high exposure. Initial biomonitoring revealed HEV levels above 500 pmol g(-1) globin in all cases, with a maximum of about 2,400 pmol g(-1) globin. This compares to a German EKA value (exposure equivalent for carcinogenic substances) for a daily 8-h-exposure to 1 ppm EO of 90 ?g L(-1) blood (~3,900 pmol g(-1) globin). The adduct levels dropped in accordance with the expected zero-order kinetics for a single exposure. After the five-month observation interval, the HEV concentrations in blood reflected the individual background from tobacco smoking. The results of this study show that even a short exposure to ethylene oxide may result in a significant rise in haemoglobin adduct levels. Although protein adducts and their occupational-medical assessment values are considered for long-term exposure surveillance, they can also be used for monitoring accidental exposures. In these cases, the calculation of daily 'ppm-equivalents' may provide a means for a comparison with the existing assessment values. PMID:22728792

Bader, Michael; Will, Wolfgang; Frey, Gunild; Nasterlack, Michael

2012-06-01

182

Toxicity of human adenovirus E4orf4 protein in Saccharomyces cerevisiae results from interactions with the Cdc55 regulatory B subunit of PP2A.  

PubMed

The E4orf4 protein of human adenovirus induces p53-independent apoptosis, a process that may promote cell death and viral spread. When expressed alone, E4orf4 kills transformed cells but not normal human cells. The only clear target of E4orf4 in mammalian cells is the Balpha (B55) subunit of protein phosphatase 2A (PP2A), a member of one of three classes of regulatory B subunits. Here we report the effects of E4orf4 in Saccharomyces cerevisiae, which encodes two PP2A regulatory B subunits, CDC55 and RTS1, that share homology with mammalian B and B' subunits, respectively. E4orf4 expression was found to be toxic in yeast, resulting in the accumulation of cells in G2/M phase that failed to grow upon removal of E4orf4. E4orf4-expressing yeast also displayed an elongated cell morphology similar to cdc55 deletion strains. E4orf4 required CDC55 to elicit its effect, whereas RTS1 was dispensable. The recruitment of the PP2A holoenzyme by E4orf4 was entirely dependent on Cdc55. These studies indicate that E4orf4-induced apoptosis in mammalian cells and cell death in yeast require functional interactions with B-type subunits of PP2A. However, some inhibition of growth by E4orf4 was observed in the cdc55 strain and with an E4orf4 mutant that fails to interact with Cdc55, indicating that E4orf4 may possess a second Cdc55-independent function affecting cell growth. PMID:11536041

Roopchand, D E; Lee, J M; Shahinian, S; Paquette, D; Bussey, H; Branton, P E

2001-08-30

183

Hydrothermal syntheses, crystal structures, and magnetic properties of inorganic-organic hybrid vanadium selenites with zero- to three-dimensional structures: (1,10-phenanthroline)(2)V(2)SeO(7), (2,2'-bipyridine)VSeO(4), (4,4'-bipyridine)V(2)Se(2)O(8), and (4,4'-bipyridine)(2)V(4)Se(3)O(15).H(2)O.  

PubMed

A family of inorganic-organic hybrid vanadium selenites with zero-, one-, two-, and three-dimensional structures, (1,10-phen)(2)V(2)SeO(7), (2,2'-bipy)VSeO(4), (4,4'-bipy)V(2)Se(2)O(8), and (4,4'-bipy)(2)V(4)Se(3)O(15).H(2)O (where phen = phenanthroline and bipy = bipyridine), were hydrothermally synthesized and characterized by single-crystal X-ray diffraction. Different bidentate organodiamine ligands and reactant concentrations were used in the four reaction systems, which are responsible for the variety of structural dimensions of the compounds. (1,10-phen)(2)V(2)SeO(7) crystallizes in a monoclinic system with space group P2(1)/n and cell parameters a = 8.6509(3) A,( )b = 7.8379(2) A, c = 34.0998(13) A, beta = 91.503(2) degrees, and Z = 4. (2,2'-bipy)VSeO(4) crystallizes in a monoclinic system with space group C2/c and cell parameters a = 17.0895(12) A, b = 14.7707(10) A, c = 11.7657(8) A, beta = 131.354(3) degrees, and Z = 8. (4,4'-bipy)V(2)Se(2)O(8) crystallizes in a triclinic system with space group Ponemacr; and cell parameters a = 7.1810(10) A, b = 10.8937(13) A, c = 11.1811(15) A, alpha = 115.455(3) degrees, beta = 107.582(3) degrees, gamma = 91.957(4) degrees, and Z = 2. (4,4'-bipy)(2)V(4)Se(3)O(15).H(2)O crystallizes in a monoclinic system with space group Pc and cell parameters a = 7.9889(9) A, b = 7.8448 A, c = 23.048(3) A, beta = 99.389(4) degrees, and Z = 2. (1,10-phen)(2)V(2)SeO(7) has an isolated structure, (2,2'-bipy)VSeO(4) has a chain structure, (4,4'-bipy)V(2)Se(2)O(8) has a layered structure, and (4,4'-bipy)(2)V(4)Se(3)O(15).H(2)O has a framework structure. The chains are constructed from VO(4)N(2) octahedra and SeO(3) pyramids, laced by organic ligands (2,2'-bipy). The layers consist of vanadium selenite chains [(VO)(2)(SeO(3))(2)]( infinity ), linked by 4,4'-bipy molecules. The framework is composed of vanadium selenite sheets [V(4)Se(3)O(16)]( infinity ), pillared by 4,4'-bipy molecules. All of the compounds are thermally stable to 300 degrees C, and the magnetic susceptibilities confirm the existence of tetravalent V atoms in the antiferromagnetic (4,4'-bipy)V(2)Se(2)O(8) complex and mixed tetravalent and pentavalent V atoms in the paramagnetic complex (4,4'-bipy)(2)V(4)Se(3)O(15).H(2)O. PMID:14606834

Dai, Zhimin; Shi, Zhan; Li, Guanghua; Zhang, Dong; Fu, Wensheng; Jin, Haiying; Xu, Wei; Feng, Shouhua

2003-11-17

184

Gene transfer of master autophagy regulator TFEB results in clearance of toxic protein and correction of hepatic disease in alpha-1-anti-trypsin deficiency  

PubMed Central

Alpha-1-anti-trypsin deficiency is the most common genetic cause of liver disease in children and liver transplantation is currently the only available treatment. Enhancement of liver autophagy increases degradation of mutant, hepatotoxic alpha-1-anti-trypsin (ATZ). We investigated the therapeutic potential of liver-directed gene transfer of transcription factor EB (TFEB), a master gene that regulates lysosomal function and autophagy, in PiZ transgenic mice, recapitulating the human hepatic disease. Hepatocyte TFEB gene transfer resulted in dramatic reduction of hepatic ATZ, liver apoptosis and fibrosis, which are key features of alpha-1-anti-trypsin deficiency. Correction of the liver phenotype resulted from increased ATZ polymer degradation mediated by enhancement of autophagy flux and reduced ATZ monomer by decreased hepatic NF?B activation and IL-6 that drives ATZ gene expression. In conclusion, TFEB gene transfer is a novel strategy for treatment of liver disease of alpha-1-anti-trypsin deficiency. This study may pave the way towards applications of TFEB gene transfer for treatment of a wide spectrum of human disorders due to intracellular accumulation of toxic proteins.

Pastore, Nunzia; Blomenkamp, Keith; Annunziata, Fabio; Piccolo, Pasquale; Mithbaokar, Pratibha; Maria Sepe, Rosa; Vetrini, Francesco; Palmer, Donna; Ng, Philip; Polishchuk, Elena; Iacobacci, Simona; Polishchuk, Roman; Teckman, Jeffrey; Ballabio, Andrea; Brunetti-Pierri, Nicola

2013-01-01

185

Growth impairment resulting from expression of influenza virus M2 protein in Saccharomyces cerevisiae: identification of a novel inhibitor of influenza virus.  

PubMed Central

The gene encoding M2, the ion channel-forming protein of influenza virus A, was expressed under the control of an inducible promoter in Saccharomyces cerevisiae. By using single and multicopy plasmids containing GAL promoter-M2 fusions, a correlation was observed between plasmid copy number and growth in medium inducing M2 expression. Cells expressing M2 from multicopy plasmids have reduced growth rates, suggesting that high levels of M2 are toxic to growth. The addition of amantadine, a compound known to block the ion channel activity of certain M2 alleles, restores the growth rates to wild-type levels in cells expressing an amantadine-susceptible allele of M2 but not an amantadine-resistant allele of M2, suggesting that M2 expression in S. cerevisiae results in the formation of functional M2 ion channels. Measurements of extracellular acidification by microphysiometry suggest that proton efflux in M2-expressing cells is altered and that the addition of amantadine permits the reestablishment of the proton gradient. The growth impairment phenotype resulting from M2 expression was used to develop a high-capacity screening assay which identified a novel inhibitor possessing an antiviral profile similar to that of amantadine.

Kurtz, S; Luo, G; Hahnenberger, K M; Brooks, C; Gecha, O; Ingalls, K; Numata, K; Krystal, M

1995-01-01

186

PPAR?/RXR?-induced and CD36-mediated microglial amyloid-? phagocytosis results in cognitive improvement in amyloid precursor protein/presenilin 1 mice.  

PubMed

Alzheimer's disease (AD) is characterized by the extracellular deposition of amyloid-? (A?), neurofibrillary tangle formation, and a microglial-driven inflammatory response. Chronic inflammatory activation compromises microglial clearance functions. Because peroxisome proliferator-activated receptor ? (PPAR?) agonists suppress inflammatory gene expression, we tested whether activation of PPAR? would also result in improved microglial A? phagocytosis. The PPAR? agonist pioglitazone and a novel selective PPAR?/? modulator, DSP-8658, currently in clinical development for the treatment of type 2 diabetes, enhanced the microglial uptake of A? in a PPAR?-dependent manner. This PPAR?-stimulated increase of A? phagocytosis was mediated by the upregulation of scavenger receptor CD36 expression. In addition, combined treatment with agonists for the heterodimeric binding partners of PPAR?, the retinoid X receptors (RXRs), showed additive enhancement of the A? uptake that was mediated by RXR? activation. Evaluation of DSP-8658 in the amyloid precursor protein/presenilin 1 mouse model confirmed an increased microglial A? phagocytosis in vivo, which subsequently resulted in a reduction of cortical and hippocampal A? levels. Furthermore, DSP-8658-treated mice showed improved spatial memory performance. Therefore, stimulation of microglial clearance by simultaneous activation of the PPAR?/RXR? heterodimer may prove beneficial in prevention of AD. PMID:23197723

Yamanaka, Mitsugu; Ishikawa, Taizo; Griep, Angelika; Axt, Daisy; Kummer, Markus P; Heneka, Michael T

2012-11-28

187

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: NDR2 protein kinase Serine/threonine-protein kinase 38-like Cellular Function: Cytoskeleton Producer Cell Type: Epithelial line, Lymphoid line Modifications: Protein fragment Molecules/virion: Viral Partner: Undetermined Cellular

188

Gene trap mutation of murine Outer dense fiber protein-2 gene can result in sperm tail abnormalities in mice with high percentage chimaerism  

PubMed Central

Background Outer dense fiber protein 2, Odf2, is a major component of the outer dense fibers, ODF, in the flagellum of spermatozoa. ODF are associated with microtubule doublets that form the axoneme. We recently demonstrated that tyrosine phosphorylation of Odf2 is important for sperm motility. In the course of a study of Odf2 using Odf2 mouse knockout lines we observed that males of a high percentage chimaerism, made using XL169 embryonic stem cells, were infertile, whereas mice of low-medium percentage chimaerism were fertile. Results XL169 ES cells have a ?-geo gene trap cassette inserted in the Odf2 gene. To determine possible underlying mechanisms resulting in infertility we analyzed epididymal sperm and observed that >50% displayed bent tails. We next performed ultrastructural analyses on testis of high percentage XL169 chimaeric mice. This analysis showed that high percentage XL169 chimaeric mice produce elongating spermatids that miss one or more entire outer dense fibers in their midpiece and principal piece. In addition, we observed elongating spermatids that show thinning of outer dense fibers. No other obvious abnormalities or defects are present in elongating spermatids. Spermatozoa from the caput and cauda epididymis of XL169 mice of high percentage chimaerism show additional tail defects, including absence of one or more axonemal microtubule doublets and bent tails. Sperm with bent tails display abnormal motility. Conclusions Our results document the possible impact of loss of one Odf2 allele on sperm tail structure and function, resulting in a novel sperm tail phenotype.

2010-01-01

189

Substitution of Critical Isoleucines in the KH Domains of Drosophila Fragile X Protein Results in Partial Loss-of-Function Phenotypes  

Microsoft Academic Search

Fragile X mental retardation proteins (FMRP) are RNA-binding proteins that interact with a subset of cellular RNAs. Several RNA-binding domains have been identified in FMRP, but the contribution of these individual domains to FMRP function in an animal model is not well understood. In this study, we have generated flies with point mutations in the KH domains of the Drosophila

Paromita Banerjee; Shweta Nayar; Sarita Hebbar; Catherine F. Fox; Michele C. Jacobs; Jae H. Park; Joyce J. Fernandes; Thomas C. Dockendorff

2006-01-01

190

Sustained Release of Bone Morphogenetic Protein-4 in Adult Rabbit Extraocular Muscle Results in Decreased Force and Muscle Size: Potential for Strabismus Treatment  

PubMed Central

Purpose. To assess the effect of a sustained-release preparation of bone morphogenetic protein-4 (BMP-4) on EOM force generation and muscle size. Methods. Sustained-release pellets, releasing 500 nanograms/day of BMP-4 for a maximum of 3 months, were implanted beneath the superior rectus muscle (SR) belly in anesthetized adult rabbits. The contralateral side received a placebo pellet as a control. After 1, 3, and 6 months, SRs were removed, and force generation at twitch and tetanic frequencies as well as fatigue resistance were determined in vitro. Myofiber size, myosin heavy chain isoform expression, and satellite cell density were assessed histologically. Results. SR force generation was significantly decreased by BMP-4 compared with the contralateral controls. Force generation was decreased by 25–30% by 1 month, 31–50% by 3 months, and at 6 months, after 3 BMP-4–free months, force was still decreased by 20–31%. No change in fatigue was seen. Significant decreases in muscle size were seen, greatest at 3 months. At all time points Pax7- and MyoD-positive satellite cell densities were significantly decreased. Conclusions. The decreased force generation and muscle size caused by sustained release of BMP-4 suggests that myogenic signaling factors may provide a more biological method of decreasing muscle strength in vivo than exogenously administered toxins. Treating antagonist-agonist pairs of EOM with titratable, naturally occurring myogenic signaling and growth factors may provide safe, efficacious, nonsurgical treatment options for patients with strabismus.

Anderson, Brian C.; Daniel, Mark L.; Kendall, Jeffrey D.; Christiansen, Stephen P.

2011-01-01

191

Rhizobium selenitireducens proteins involved in the reduction of selenite to elemental selenium  

Technology Transfer Automated Retrieval System (TEKTRAN)

Microbial based bioremediation barriers can remove the metalloid selenite (SeO3–2) from flowing groundwater. The organisms associated with the process include microorganisms from within the bacterial and archaeal domains that can reduce soluble SeO3–2 to the insoluble and reddish-colored elemental ...

192

Hypertension resulting from overexpression of translationally controlled tumor protein increases the severity of atherosclerosis in apolipoprotein E knock-out mice.  

PubMed

Hypertension is a well-established etiological factor for atherogenesis. We previously showed that transgenic mice overexpressing translationally controlled tumor protein (TCTP) develop systemic arterial hypertension. In this study we explored the cardiovascular effects of TCTP overexpression and possibly of the resultant hypertension on the severity of atherosclerosis in apolipoprotein E-deficient mice. Through multiple mating of TCTP-overexpressing transgenic mice (TCTP-TG) with apolipoprotein E knock-out mice (ApoE KO), we generated non-transgenic (nTG), TCTP-TG, nTG/ApoE KO and TCTP-TG/ApoE KO mice with similar genetic background. Male mice, 7-week old, were fed a lipid-enriched Western diet for 16 weeks, and blood pressure and body weight change were monitored every 2 weeks. Plasma lipid profiles and atherosclerotic lesions in aorta were quantified at the end of study. We found that blood pressure levels of TCTP-TG and TCTP-TG/ApoE KO, were similarly elevated while nTG and nTG/ApoE KO mice were normotensive. TCTP overexpression in ApoE KO mice led to significant exacerbation of atherosclerotic lesions. Feeding Western diet resulted in increases in total cholesterol, triglyceride (TG) and low density lipoprotein, and decreased high density lipoprotein (HDL) in ApoE KO mice. No significant differences were found in plasma lipid profiles of nTG/ApoE KO and TCTP-TG/ApoE KO. This study suggests that overexpression of TCTP, which induces hypertension, also accelerates the development of atherosclerotic lesion caused by high-fat and high-cholesterol diet without significantly altering plasma lipid profiles. We conclude that TCTP-induced hypertension could increase the severity of atherosclerotic lesion and suggest that inhibition of TCTP or its signaling pathways may be a potential approach to the therapy of both diseases, hypertension and atherosclerosis. PMID:22415346

Cho, Yujeong; Maeng, Jeehye; Ryu, Jungmin; Shin, Hyekyoung; Kim, Miyoung; Oh, Goo Taeg; Lee, Moo-Yeol; Lee, Kyunglim

2012-03-14

193

CDKN2A mutation in a non-FAMMM kindred with cancers at multiple sites results in a functionally abnormal protein.  

PubMed

The CDKN2A gene encodes p16 (CDKN2A), a cell-cycle inhibitor protein which prevents inappropriate cell cycling and, hence, proliferation. Germ-line mutations in CDKN2A predispose to the familial atypical multiple-mole melanoma (FAMMM) syndrome but also have been seen in rare families in which only 1 or 2 individuals are affected by cutaneous malignant melanoma (CMM). We therefore sequenced exons 1alpha and 2 of CDKN2A using lymphocyte DNA isolated from index cases from 67 families with cancers at multiple sites, where the patterns of cancer did not resemble those attributable to known genes such as hMLH1, hMLH2, BRCA1, BRCA2, TP53 or other cancer susceptibility genes. We found one mutation, a mis-sense mutation resulting in a methionine to isoleucine change at codon 53 (M531) of exon 2. The individual tested had developed 2 CMMs but had no dysplastic nevi and lacked a family history of dysplastic nevi or CMM. Other family members had been diagnosed with oral cancer (2 persons), bladder cancer (1 person) and possibly gall-bladder cancer. While this mutation has been reported in Australian and North American melanoma kindreds, we did not observe it in 618 chromosomes from Scottish and Canadian controls. Functional studies revealed that the CDKN2A variant carrying the M531 change was unable to bind effectively to CDK4, showing that this mutation is of pathological significance. Our results have confirmed that CDKN2A mutations are not limited to FAMMM kindreds but also demonstrate that multi-site cancer families without melanoma are very unlikely to contain CDKN2A mutations. PMID:9389568

Sun, S; Pollock, P M; Liu, L; Karimi, S; Jothy, S; Milner, B J; Renwick, A; Lassam, N J; Hayward, N K; Hogg, D; Narod, S A; Foulkes, W D

1997-11-14

194

Inhibition of protein kinase C results in a switch from a non-motile to a motile phenotype in diverse human lymphocyte populations.  

PubMed Central

Circulating lymphocytes are rounded, non-motile cells which on contact with cytokines, specialized or activated endothelium, acquire a constantly shape-changing, polarized morphology which enables migration into appropriate sites. The biochemical mechanisms which regulate this switch are not understood but the various stimuli may have a common final pathway. In this study we show that protein kinase C (PKC) inhibitors of the bisindolylmaleimide type (GF 109203X, Ro 31-8220, CGP 41,251) induce resting, spherical lymphocytes to change rapidly (< 30 min) into polarized, locomotory cells. This phenomenon was seen with diverse populations of blood T lymphocytes, tonsillar B cells and Jurkat and Molt4 T-cell lines. Consistent with this, down-regulation of PKC by chronic treatment (44 hr) with bryostatin also induced the polarized phenotype in blood lymphocytes and non-motile Molt4 cells. Conversely, treatment of a spontaneously motile subline of Molt4 cells with various PKC activators caused a reversion to the non-motile phenotype within minutes. PKC activation must be sufficient to overcome the effects of a constitutively active phosphatase because bisindolylmaleimide induction of motility could be prevented by pretreatment of the cells with a phosphatase inhibitor, calyculin A. It is concluded that, in resting lymphocytes, chronic activation of a PKC offsets the action of a constitutively active phosphatase and the net result is maintenance of the non-motile state. Agents which alter the kinase/phosphatase balance in favour of dephosphorylation result in induction of the locomotory phenotype. Images Figure 3 Figure 4

Southern, C; Wilkinson, P C; Thorp, K M; Henderson, L K; Nemec, M; Matthews, N

1995-01-01

195

Homozygosity for a Missense Mutation in SERPINH1, which Encodes the Collagen Chaperone Protein HSP47, Results in Severe Recessive Osteogenesis Imperfecta  

PubMed Central

Osteogenesis imperfecta (OI) is characterized by bone fragility and fractures that may be accompanied by bone deformity, dentinogenesis imperfecta, short stature, and shortened life span. About 90% of individuals with OI have dominant mutations in the type I collagen genes COL1A1 and COL1A2. Recessive forms of OI resulting from mutations in collagen-modifying enzymes and chaperones CRTAP, LEPRE1, PPIB, and FKBP10 have recently been identified. We have identified an autosomal-recessive missense mutation (c.233T>C, p.Leu78Pro) in SERPINH1, which encodes the collagen chaperone-like protein HSP47, that leads to a severe OI phenotype. The mutation results in degradation of the endoplasmic reticulum resident HSP47 via the proteasome. Type I procollagen accumulates in the Golgi of fibroblasts from the affected individual and a population of the secreted type I procollagen is protease sensitive. These findings suggest that HSP47 monitors the integrity of the triple helix of type I procollagen at the ER/cis-Golgi boundary and, when absent, the rate of transit from the ER to the Golgi is increased and helical structure is compromised. The normal 3-hydroxylation of the prolyl residue at position 986 of the triple helical domain of pro?1(I) chains places the role of HSP47 downstream from the CRTAP/P3H1/CyPB complex that is involved in prolyl 3-hydroxylation. Identification of this mutation in SERPINH1 gives further insight into critical steps of the collagen biosynthetic pathway and the molecular pathogenesis of OI.

Christiansen, Helena E.; Schwarze, Ulrike; Pyott, Shawna M.; AlSwaid, Abdulrahman; Al Balwi, Mohammed; Alrasheed, Shatha; Pepin, Melanie G.; Weis, Mary Ann; Eyre, David R.; Byers, Peter H.

2010-01-01

196

Elevated Levels of Synthesis of over 20 Proteins Results after Mutation of the Rhizobium leguminosarum Exopolysaccharide Synthesis Gene pssA  

PubMed Central

The protein expression profiles of Rhizobium leguminosarum strains in response to specific genetic perturbations in exopolysaccharide (EPS) biosynthesis genes were examined using two-dimensional gel electrophoresis. Lesions in either pssA, pssD, or pssE of R. leguminosarum bv. viciae VF39 or in pssA of R. leguminosarum bv. trifolii ANU794 not only abolished the capacity of these strains to synthesize EPS but also had a pleiotropic effect on protein synthesis levels. A minimum of 22 protein differences were observed for the two pssA mutant strains. The differences identified in the pssD and pssE mutants of strain VF39 were a distinct subset of the same protein synthesis changes that occurred in the pssA mutant. The pssD and pssE mutant strains shared identical alterations in the proteins synthesized, suggesting that they share a common function in the biosynthesis of EPS. In contrast, a pssC mutant that produces 38% of the EPS level of the parental strain showed no differences in its protein synthesis patterns, suggesting that the absence of EPS itself was contributing to the changes in protein synthesis and that there may be a complex interconnection of the EPS biosynthetic pathway with other metabolic pathways. Genetic complementation of pssA can restore wild-type protein synthesis levels, indicating that many of the observed differences in protein synthesis are also a specific response to a dysfunctional PssA. The relevance of these proteins, which are grouped as members of the pssA mutant stimulon, remains unclear, as the majority lacked a homologue in the current sequence databases and therefore possibly represent a novel functional network(s). These findings have illustrated the potential of proteomics to reveal unexpected higher-order processes of protein function and regulation that arise from mutation. In addition, it is evident that enzymatic pathways and regulatory networks are more interconnected and more sensitive to structural changes in the cell than is often appreciated. In these cases, linking the observed phenotype directly to the mutated gene can be misleading, as the phenotype could be attributable to downstream effects of the mutation.

Guerreiro, Nelson; Ksenzenko, Vladimir N.; Djordjevic, Michael A.; Ivashina, Tanya V.; Rolfe, Barry G.

2000-01-01

197

From The Cover: Human C4b-binding protein selectively interacts with Neisseria gonorrhoeae and results in species-specific infection  

Microsoft Academic Search

Neisseria gonorrhoeae is the causative agent of gonorrhea, a disease that is restricted to humans. Complement forms a key arm of the innate immune system that combats gonococcal infections. N. gonorrhoeae uses its outer membrane porin (Por) molecules to bind the classical pathway of complement down-regulatory protein C4b-binding protein (C4bp) to evade killing by human complement. Strains of N. gonorrhoeae

Jutamas Ngampasutadol; Sanjay Ram; Anna M. Blom; Hanna Jarva; Ann E. Jerse; Egil Lien; Jon Goguen; Sunita Gulati; Peter A. Rice

2005-01-01

198

Intracellular accumulation of a 46 kDa species of mouse prion protein as a result of loss of glycosylation in cultured mammalian cells  

Microsoft Academic Search

Prion diseases are fatal neurodegenerative disorders characterized by the accumulation of an abnormal isoform (PrPSc) of the normal cellular prion protein (PrPC) in the brain. Reportedly, abnormal N-linked glycosylation patterns in PrPC are associated with disease susceptibility; thus, we compared the glycosylation status of normal and several mutant forms of the murine prion protein (MuPrP) in cultured mammalian cells. Substitution

Subhabrata Biswas; Jan P. M. Langeveld; Donald Tipper; Shan Lu

2006-01-01

199

Immunization with A2 protein results in a mixed Th1\\/Th2 and a humoral response which protects mice against Leishmania donovani infections  

Microsoft Academic Search

The A2 genes of Leishmania donovani encode amastigote-specific A2 proteins, which are considered to be virulence factors required for the survival of this protozoan parasite in the mammalian host. The A2 genes are present within a multigene family and corresponding A2 proteins are composed predominantly of multiple copies of a 10 amino acid repeat sequences. A2-specific antibodies have been detected

Anirban Ghosh; Wen Wei Zhang; Greg Matlashewski

2001-01-01

200

Folate deprivation results in the loss of breast cancer resistance protein (BCRP\\/ABCG2) expression. A role for BCRP in cellular folate homeostasis  

Microsoft Academic Search

Breast cancer resistance protein (BCRP\\/ABCG2) is currently the only ABC transporter that exports mono- and polyglutamates of folates and methotrexate (MTX). Here we explored the relationship between cellular folate status and BCRP expression. Toward this end, MCF-7 breast cancer cells, with low BCRP and moderate multidrug resistance protein 1 (MRP1\\/ABCC1) levels, and their mitoxantrone (MR)-resistant MCF-7\\/MR subline, with BCRP overexpression

I. Ifergan; A Shafran; G. Jansen; J. H. Hooijberg; G. L. Scheffer; Y. G. Assaraf

2004-01-01

201

The influence of habitual protein intake in early childhood on BMI and age at adiposity rebound: results from the DONALD Study  

Microsoft Academic Search

Objective:To analyse the influence of habitual protein intake in early childhood on age and body mass index (BMI) at adiposity rebound (AR), a potential critical period for the development of obesity.Subjects:A total of 313 children (161 boys, 152 girls) participating in the Dortmund Nutritional and Anthropometric Longitudinally Designed Study.Methods:Weighted summary indices were created reflecting habitual, energy-adjusted protein intake (expressed as

A L B Günther; A E Buyken; A Kroke; ALB Günther

2006-01-01

202

Identification of precursor to cytomegalovirus capsid assembly protein and evidence that processing results in loss of its carboxy-terminal end.  

PubMed Central

The 37-kilodalton (kDa) assembly protein of cytomegalovirus (strain Colburn) B capsids is shown to have a 40-kDa precursor. Pulse-chase radiolabeling experiments revealed that conversion of the precursor to the product was slow, requiring over 6 h for completion, and correlated with movement from the cytoplasmic to the nuclear fraction of Nonidet P-40-disrupted cells. Of these two proteins, only the 40-kDa precursor was synthesized in vitro from infected-cell RNA, consistent with its being the primary translation product. Amino acid sequence data obtained from CNBr-treated, high-performance liquid chromatography-purified assembly protein indicated that precursor translation begins at the first of two closely spaced potential initiation sites and that precursor maturation involves the loss of at least 32 amino acids from its carboxy-terminal end. It is also shown by immunological cross-reactivity and peptide similarity that three low-abundance B-capsid proteins (i.e., the 45-kilodalton [45K], 39K, and 38K proteins) are closely related to the assembly protein; the nature of this relatedness is discussed. Images

Gibson, W; Marcy, A I; Comolli, J C; Lee, J

1990-01-01

203

BBS7 is required for BBSome formation and its absence in mice results in Bardet-Biedl syndrome phenotypes and selective abnormalities in membrane protein trafficking.  

PubMed

Bardet-Biedl Syndrome (BBS) is a pleiotropic and genetically heterozygous disorder caused independently by numerous genes (BBS1-BBS17). Seven highly conserved BBS proteins (BBS1, 2, 4, 5, 7, 8 and 9) form a complex known as the BBSome, which functions in ciliary membrane biogenesis. BBS7 is both a unique subunit of the BBSome and displays direct physical interaction with a second BBS complex, the BBS chaperonin complex. To examine the in vivo function of BBS7, we generated Bbs7 knockout mice. Bbs7(-/-) mice show similar phenotypes to other BBS gene mutant mice including retinal degeneration, obesity, ventriculomegaly and male infertility characterized by abnormal spermatozoa flagellar axonemes. Using tissues from Bbs7(-/-) mice, we show that BBS7 is required for BBSome formation, and that BBS7 and BBS2 depend on each other for protein stability. Although the BBSome serves as a coat complex for ciliary membrane proteins, BBS7 is not required for the localization of ciliary membrane proteins polycystin-1, polycystin-2, or bitter taste receptors, but absence of BBS7 leads to abnormal accumulation of the dopamine D1 receptor to the ciliary membrane, indicating that BBS7 is involved in specific membrane protein localization to cilia. PMID:23572516

Zhang, Qihong; Nishimura, Darryl; Vogel, Tim; Shao, Jianqiang; Swiderski, Ruth; Yin, Terry; Searby, Charles; Carter, Calvin S; Kim, Gunhee; Bugge, Kevin; Stone, Edwin M; Sheffield, Val C

2013-04-09

204

The RecBC enzyme loads RecA protein onto ssDNA asymmetrically and independently of ?, resulting in constitutive recombination activation  

PubMed Central

Double-strand DNA break repair and homologous recombination in Escherichia coli proceed by the RecBCD pathway, which is regulated by cis-acting elements known as ? sites. A crucial feature of this regulation is the RecBCD enzyme-directed loading of RecA protein specifically onto the 3?-terminal, ?-containing DNA strand. Here we show that RecBC enzyme (lacking the RecD subunit) loads RecA protein constitutively onto the 3?-terminal DNA strand, with no requirement for ?. This strand is preferentially utilized in homologous pairing reactions. We propose that RecA protein loading is a latent property of the RecBCD holoenzyme, which is normally blocked by the RecD subunit and is revealed following interaction with ?.

Churchill, Jason J.; Anderson, Daniel G.; Kowalczykowski, Stephen C.

1999-01-01

205

Biological Determinants of and Reference Values for Plasma Interleukin8, Monocyte Chemoattractant Protein1, Epidermal Growth Factor, and Vascular Endothelial Growth Factor: Results from the STANISLAS Cohort  

Microsoft Academic Search

Background: Interleukin-8 (IL-8), monocyte chemoat- tractant protein-1 (MCP-1), epidermal growth factor (EGF), and vascular endothelial growth factor (VEGF) are known to be involved in various diseases related to inflammation, vascular remodeling, or growth deregu- lation. In addition, increases in plasma concentrations of these cytokines appear to provide useful diagnostic and prognostic information. We therefore investigated which factors most strongly influence

Hind Berrahmoune; John V. Lamont; Bernard Herbeth; Peter S. FitzGerald; Sophie Visvikis-Siest

206

Formation of high-molecular-weight angiotensinogen during pregnancy is a result of competing redox reactions with the proform of eosinophil major basic protein.  

PubMed

The plasma concentration of the placentally derived proMBP (proform of eosinophil major basic protein) increases in pregnancy, and three different complexes containing proMBP have been isolated from pregnancy plasma and serum: a 2:2 complex with the metalloproteinase, PAPP-A (pregnancy-associated plasma protein-A), a 2:2 complex with AGT (angiotensinogen) and a 2:2:2 complex with AGT and complement C3dg. In the present study we show that during human pregnancy, all of the circulating proMBP exists in covalent complexes, bound to either PAPP-A or AGT. We also show that the proMBP-AGT complex constitutes the major fraction of circulating HMW (high-molecular weight) AGT in late pregnancy, and that this complex is able to further associate with complement C3 derivatives post-sampling. Clearance experiments in mice suggest that complement C3-based complexes are removed faster from the circulation compared to monomeric AGT and the proMBP-AGT complex. Furthermore, we have used recombinant proteins to analyse the formation of the proMBP-PAPP-A and the proMBP-AGT complexes, and we demonstrate that they are competing reactions, depending on the same cysteine residue of proMBP, but differentially on the redox potential, potentially important for the relative amounts of the complexes in vivo. These findings may be important physiologically, since the biochemical properties of the proteins change as a consequence of complex formation. PMID:23033876

Kløverpris, Søren; Skov, Louise L; Glerup, Simon; Pihl, Kasper; Christiansen, Michael; Oxvig, Claus

2013-01-01

207

Feeding soy protein isolate (SPI) does not result in an estrogenic gene expression profile in the mammary of ovariectomized (OVX) female rats  

Technology Transfer Automated Retrieval System (TEKTRAN)

Concerns of increased breast cancer risk in women consuming soy exist because of the perceived estrogenicity of soy isoflavones. Female Sprague-Dawley rats (N equals 20/group) were fed AIN-93G diets with casein or SPI as the protein from PND30. On PND50 rats were OVX and 10/group infused s.c. with 5...

208

TAT-Mediated Transduction of MafA Protein In Utero Results in Enhanced Pancreatic Insulin Expression and Changes in Islet Morphology  

PubMed Central

Alongside Pdx1 and Beta2/NeuroD, the transcription factor MafA has been shown to be instrumental in the maintenance of the beta cell phenotype. Indeed, a combination of MafA, Pdx1 and Ngn3 (an upstream regulator of Beta2/NeuroD) was recently reported to lead to the effective reprogramming of acinar cells into insulin-producing beta cells. These experiments set the stage for the development of new strategies to address the impairment of glycemic control in diabetic patients. However, the clinical applicability of reprogramming in this context is deemed to be poor due to the need to use viral vehicles for the delivery of the above factors. Here we describe a recombinant transducible version of the MafA protein (TAT-MafA) that penetrates across cell membranes with an efficiency of 100% and binds to the insulin promoter in vitro. When injected in utero into living mouse embryos, TAT-MafA significantly up-regulates target genes and induces enhanced insulin production as well as cytoarchitectural changes consistent with faster islet maturation. As the latest addition to our armamentarium of transducible proteins (which already includes Pdx1 and Ngn3), the purification and characterization of a functional TAT-MafA protein opens the door to prospective therapeutic uses that circumvent the use of viral delivery. To our knowledge, this is also the first report on the use of protein transduction in utero.

Vargas, Nancy; Fort, Nicholas M.; Cechin, Sirlene; Garcia, Enrique; Espino-Grosso, Pedro; Fraker, Christopher A.; Ricordi, Camillo; Inverardi, Luca; Pastori, Ricardo L.; Dominguez-Bendala, Juan

2011-01-01

209

TAT-mediated transduction of MafA protein in utero results in enhanced pancreatic insulin expression and changes in islet morphology.  

PubMed

Alongside Pdx1 and Beta2/NeuroD, the transcription factor MafA has been shown to be instrumental in the maintenance of the beta cell phenotype. Indeed, a combination of MafA, Pdx1 and Ngn3 (an upstream regulator of Beta2/NeuroD) was recently reported to lead to the effective reprogramming of acinar cells into insulin-producing beta cells. These experiments set the stage for the development of new strategies to address the impairment of glycemic control in diabetic patients. However, the clinical applicability of reprogramming in this context is deemed to be poor due to the need to use viral vehicles for the delivery of the above factors. Here we describe a recombinant transducible version of the MafA protein (TAT-MafA) that penetrates across cell membranes with an efficiency of 100% and binds to the insulin promoter in vitro. When injected in utero into living mouse embryos, TAT-MafA significantly up-regulates target genes and induces enhanced insulin production as well as cytoarchitectural changes consistent with faster islet maturation. As the latest addition to our armamentarium of transducible proteins (which already includes Pdx1 and Ngn3), the purification and characterization of a functional TAT-MafA protein opens the door to prospective therapeutic uses that circumvent the use of viral delivery. To our knowledge, this is also the first report on the use of protein transduction in utero. PMID:21857924

Vargas, Nancy; Álvarez-Cubela, Silvia; Giraldo, Jaime A; Nieto, Margarita; Fort, Nicholas M; Cechin, Sirlene; García, Enrique; Espino-Grosso, Pedro; Fraker, Christopher A; Ricordi, Camillo; Inverardi, Luca; Pastori, Ricardo L; Domínguez-Bendala, Juan

2011-08-04

210

Receptor-mediated Uptake of Antigen\\/Heat Shock Protein Complexes Results in Major Histocompatibility Complex Class I Antigen Presentation via Two Distinct Processing Pathways  

Microsoft Academic Search

Heat shock proteins (HSPs) derived from tumors or virally infected cells can stimulate antigen- specific CD8 1 T cell responses in vitro and in vivo. Although this antigenicity is known to arise from HSP-associated peptides presented to the immune system by major histocompatibility complex (MHC) class I molecules, the cell biology underlying this presentation process remains poorly understood. Here we

Flora Castellino; Philip E. Boucher; Katrin Eichelberg; Mark Mayhew; James E. Rothman; Alan N. Houghton; Ronald N. Germain

211

An assembly defect as a result of an attenuating mutation in the capsid proteins of the poliovirus type 3 vaccine strain.  

PubMed Central

The molecular basis of the temperature-sensitive (ts) phenotype of P3/Sabin, the type 3 vaccine strain of poliovirus, was investigated in light of the known correlation between ts and attenuation phenotypes. A phenylalanine at residue 91 of the capsid protein VP3 was a major determinant of both phenotypes, and attenuation and ts could be reverted by the same second-site mutations. The ts phenotype was due to a defect early in the assembly process that inhibited the formation of 14S pentamers, empty capsids, and virions. It was further shown that capsid proteins that were not incorporated into higher-order structures had short half-lives at the nonpermissive temperature. Images

Macadam, A J; Ferguson, G; Arnold, C; Minor, P D

1991-01-01

212

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Ubiquitin Cellular Function: ER, Protein turnover, Protein-targeting Producer Cell Type: Lymphoid line Modifications: None detected Molecules/virion: 200-500 (10 percent of Gag) Viral Partner: Undetermined Cellular

213

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Protein kinase C and casein kinase substrate in neurons protein 2 Cellular Function: Vesicular Trafficking Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular

214

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Protein kinase C inhibitor protein 1 beta/alpha Cellular Function: Cellular Signalling Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular

215

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Protein kinase C inhibitor protein 1 zeta/delta Cellular Function: Cellular Signalling Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular

216

Proteolysis of Japanese quail and chicken plasma apolipoprotein B and vitellogenin by cathepsin D: Similarity of the resulting protein fragments with egg yolk polypeptides  

Microsoft Academic Search

Plasma very-low density lipoprotein (VLDL) and vitellogenin (VTG) from mature female Japanese quail (Coturnix coturnix japonica) and chickens (Gallus domesticus) were isolated and digested in vitro with cathepsin D (EC3.4.23.5). The incubation mixtures were then reduced and subjected to gradient (4.5-18%) SDS-polyacrylamide gel electrophoresis. Protein fragments were stained with either Coomassie Brilliant Blue R-250 (VLDL digests) or Coomassie Brilliant Blue

Robert G. Elkin; Marisue B. Freed; Stephanie A. H. Danetz; Christopher A. Bidwell

1995-01-01

217

Mitogen-Activated Protein Kinase Activation Resulting from Selective Oncogene Expression in NIH 3T3 and Rat 1a Cells  

Microsoft Academic Search

Mitogen-activated protein kinases (MAPKs) are serine\\/threonine kinases that are rapidly activated in response to a variety of growth factors in many cell types. MAPKs are activated by phosphorylation of both tyrosine and threonine residues. They are proposed to be key integrators of growth factor receptor transduction systems involving conversion of tyrosine kinase signals to serine\\/threonine kinase activation. We have studied

Carme Gallego; Sunil K. Gupta; Lynn E. Heasley; Nan-Xin Qian; Gary L. Johnson

1992-01-01

218

Increased Atherosclerosis in ApoE and LDL Receptor Gene Knock-Out Mice as a Result of Human Cholesteryl Ester Transfer Protein Transgene Expression  

Microsoft Academic Search

Abstract—The plasma cholesteryl ester transfer protein (CETP) plays a major role in the catabolism of HDL cholesteryl ester (CE). CETP transgenic mice have decreased HDL cholesterol levels and have been reported to have either increased or decreased early atherosclerotic lesions. To evaluate the impact of CETP expression on more,advanced forms of atherosclerosis, we have cross-bred the human CETP transgene into

Andrew S. Plump; Lori Masucci-Magoulas; Can Bruce; Charles L. Bisgaier; Jan L. Breslow; Alan R. Tall

2010-01-01

219

Exon 10 skipping caused by intron 10 splice donor site mutation in cholesteryl ester transfer protein gene results in abnormal downstream splice site selection  

Microsoft Academic Search

Cholesteryl ester transfer protein (CETP) defi- ciency is the most common cause of hyperalphalipoprote- inemia in Japan. However, the genetic basis of this disorder has not been fully characterized. We have studied a 49-year- old Japanese male presenting with total cholesterol, HDL- cholesterol, and apolipoprotein A-I levels of 300, 236, and 233 mg\\/dl, respectively, and total absence of CETP activity

Naohiko Sakai; Silvia Santamarina-Fojo; Shizuya Yamashita; Yuji Matsuzawa

220

Development of a novel compression-resistant carrier for recombinant human bone morphogenetic protein-2 (rhBMP-2) and preliminary clinical results  

Microsoft Academic Search

Recombinant human bone morphogenetic protein-2 (rhBMP-2) has been commercially available in the United States since July 2002\\u000a (INFUSE® Bone Graft\\/LTCAGE ®Lumbar Tapered Fusion Device, Medtronic, Inc., Memphis, TN). It was initially approved for use\\u000a in interbody spinal fusions inside a threaded titanium interbody fusion device. Since then, it has been approved for two additional\\u000a clinical indications: fresh tibial fractures and

William F. McKay; Steven M. Peckham; Jeffrey M. Badura

221

Influence of Insulin-Like Growth Factor Binding Protein (IGFBP)-1 and IGFBP-3 on Bone Health: Results from the European Male Ageing Study  

Microsoft Academic Search

The aim of this study was to determine the influence of insulin-like growth factor binding protein (IGFBP)-1, IGFBP-3, and\\u000a IGF-I on calcaneal ultrasound parameters in middle-aged and elderly European men. Men aged 40–79 years were recruited from\\u000a population registers for participation in the European Male Ageing Study (EMAS). Subjects were invited by letter to complete\\u000a a postal questionnaire and to attend

Stephen R. Pye; Bader Almusalam; Steven Boonen; Dirk Vanderschueren; Herman Borghs; Evelien Gielen; Judith E. Adams; Kate A. Ward; Gyorgy Bartfai; Felipe F. Casanueva; Joseph D. Finn; Gianni Forti; Aleksander Giwercman; Thang S. Han; Ilpo T. Huhtaniemi; Krzysztof Kula; Fernand Labrie; Michael E. J. Lean; Neil Pendleton; Margus Punab; Alan J. Silman; Frederick C. W. Wu; Terence W. O’Neill

2011-01-01

222

Expression of human amyloid precursor protein in the skeletal muscles of Drosophila results in age- and activity-dependent muscle weakness  

Microsoft Academic Search

Background  One of the hallmarks of Alzheimer's disease, and several other degenerative disorders such as Inclusion Body Myositis, is\\u000a the abnormal accumulation of amyloid precursor protein (APP) and its proteolytic amyloid peptides. To better understand the\\u000a pathological consequences of inappropriate APP expression on developing tissues, we generated transgenic flies that express\\u000a wild-type human APP in the skeletal muscles, and then performed

Chul Kim; Sapeckshita Srivastava; Marian Rice; Tanja A Godenschwege; Brooke Bentley; Saranya Ravi; Shuang Shao; Craig T Woodard; Lawrence M Schwartz

2011-01-01

223

Overexpression of the Gene Encoding the Multidrug Resistance-Associated Protein Results in Increased ATP-Dependent Glutathione S-Conjugate Transport  

Microsoft Academic Search

The multidrug resistance-associated protein (MRP) is a 180- to 195-kDa glycoprotein associated with multidrug resistance of human tumor cells. MRP is mainly located in the plasma membrane and it confers resistance by exporting natural product drugs out of the cell. Here we demonstrate that overexpression of the MRP gene in human cancer cells increases the ATP-dependent glutathione S-conjugate carrier activity

Michael Muller; Coby Meijer; Guido J. R. Zaman; Piet Borst; Rik J. Scheper; Nanno H. Mulder; Elisabeth G. E. de Vries; Peter L. M. Jansen

1994-01-01

224

Increased Pregnancy-Associated Plasma Protein-A as a Marker for Peripheral Atherosclerosis: Results from the Linz Peripheral Arterial Disease Study  

Microsoft Academic Search

Background: The aim of the present investigation was to test the hypothesis that pregnancy-associated plasma protein-A (PAPP-A), a zinc-binding metalloproteinase implicated in acute coronary syndrome, is associated with atherosclerotic peripheral arterial disease (PAD). Methods: The study comprised 433 patients with symp- tomatic atherosclerotic PAD (i.e., chronic limb ischemia) and 433 controls matched to the patients with PAD in a 1:1

Thomas Mueller; Benjamin Dieplinger; Werner Poelz; Meinhard Haltmayer

225

Complement factor H is a serum-binding protein for adrenomedullin, and the resulting complex modulates the bioactivities of both partners.  

PubMed

Adrenomedullin (AM) is an important regulatory peptide involved in both physiological and pathological states. We have previously demonstrated the existence of a specific AM-binding protein (AMBP-1) in human plasma. In the present study, we developed a nonradioactive ligand blotting assay, which, together with high pressure liquid chromatography/SDS-polyacrylamide gel electrophoresis purification techniques, allowed us to isolate AMBP-1 to homogeneity. The purified protein was identified as human complement factor H. We show that AM/factor H interaction interferes with the established methodology for quantification of circulating AM. Our data suggest that this routine procedure does not take into account the AM bound to its binding protein. In addition, we show that factor H affects AM in vitro functions. It enhances AM-mediated induction of cAMP in fibroblasts, augments the AM-mediated growth of a cancer cell line, and suppresses the bactericidal capability of AM on Escherichia coli. Reciprocally, AM influences the complement regulatory function of factor H by enhancing the cleavage of C3b via factor I. In summary, we report on a potentially new regulatory mechanism of AM biology, the influence of factor H on radioimmunoassay quantification of AM, and the possible involvement of AM as a regulator of the complement cascade. PMID:11116141

Pio, R; Martinez, A; Unsworth, E J; Kowalak, J A; Bengoechea, J A; Zipfel, P F; Elsasser, T H; Cuttitta, F

2000-12-14

226

Rats fed soy protein isolate (SPI) have impaired hepatic CYP1A1 induction by polycyclic aromatic hydrocarbons as a result of interference with aryl hydrocarbon receptor signaling.  

PubMed

Consumption of soy diets has been found to reduce cancer incidence in animals and is associated with reduced cancer risk in humans. Previously, we have demonstrated that female Sprague-Dawley rats fed purified AIN-93G diets with soy protein isolate (SPI) as the sole protein source had reduced CYP1A1 induction and basal aryl hydrocarbon receptor (AhR) levels relative to those fed the same diet containing casein (CAS). In the present study, the molecular mechanisms underlying reduced AhR expression have been studied. The SPI-effect on AhR was not observed after feeding diets containing the purified soy isoflavones genistein or daidzein. Rat hepatoma FGC-4 cells were treated with the serum obtained from rats fed CAS- or SPI-containing diets. Reduced AhR levels (P<0.05) were observed after 24 h exposure to SPI-serum without any changes in the overall expression of chaperone proteins--HSP90 and XAP2. SPI-serum-stimulated AhR degradation was inhibited by treating the cells with the proteasome inhibitor, MG132, and was observed to be preceded by ubiquitination of the receptor. A reduced association of XAP2 with the immunoprecipitated AhR complex was observed. SPI-serum-mediated AhR degradation was preceded by nuclear translocation of the receptor. However, the translocated receptor was found to be unable to heterodimerize with ARNT or to bind to XRE elements on the CYP1A1 enhancer. These data suggest that feeding SPI-containing diets antagonizes AhR signaling by a novel mechanism which differs from those established for known AhR antagonists. PMID:18078967

Singhal, Rohit; Badger, Thomas M; Ronis, Martin J

2007-11-21

227

Adenovirus E3 protein causes constitutively internalized epidermal growth factor receptors to accumulate in a prelysosomal compartment, resulting in enhanced degradation.  

PubMed Central

We have previously identified and characterized an integral membrane protein coded for by the early transcription region 3 (E3) of human group C adenoviruses that down-regulates the epidermal growth factor receptor (EGFR). The goal of this study was to characterize the early receptor trafficking events leading to enhanced EGFR degradation in adenovirus-infected cells. Specifically, we wished to determine whether adenovirus increases the rate of EGFR internalization or alters the subcellular compartmentalization of internalized EGFRs. Once the optimal time for measuring early trafficking events was determined, surface EGFRs were labeled with a cleavable biotin reagent to measure internalization rates and with a receptor-specific monoclonal antibody (MAb) conjugated to colloidal gold for intracellular localization studies. We first showed that the rate of EGFR internalization in adenovirus-infected cells is indistinguishable from the constitutive internalization rate for unoccupied EGFRs. The possibility that the E3 protein can affect trafficking of EGFRs internalized at a low constitutive rate was further supported by studies showing that adenovirus-mediated down-regulation occurs independently of EGFR oligomerization and intrinsic EGFR tyrosine kinase activity, which are required for efficient ligand-induced internalization. Other tyrosine kinases inhibited by genistein are also not required for adenovirus-induced down-regulation. When the intracellular localization of EGFRs during adenovirus-mediated down-regulation was examined by electron microscopy, there was a threefold increase in the number of EGFRs localized to multivesicular bodies. The multivesicular body has been proposed to be important for regulating intracellular membrane protein sorting, since trafficking patterns for receptors that recycle and receptors that are degraded diverge in this organelle. These data therefore suggest that adenovirus may enhance EGFR degradation by causing constitutively internalized EGFRs to accumulate in a prelysosomal compartment. This is the first example of a mechanism that efficiently down-regulates EGFR without significantly increasing the rate of internalization or that does not require EGFR tyrosine kinase activity. Since viral proteins often mimic or modify a host counterpart, this suggests that there are normal physiological conditions when receptor destruction without tyrosine signalling is beneficial. Images

Hoffman, P; Carlin, C

1994-01-01

228

Probing local environments of tryptophan residues in proteins: comparison of 19F nuclear magnetic resonance results with the intrinsic fluorescence of soluble human tissue factor.  

PubMed

19F nuclear magnetic resonance (19F NMR) of 5-fluorotryptophan (5F-Trp) and tryptophan (Trp) fluorescence both provide information about local environment and solvent exposure of Trp residues. To compare the information provided by these spectroscopies, the four Trp residues in recombinant soluble human tissue factor (sTF) were replaced with 5F-Trp. 19F NMR assignments for the 5F-Trp residues (14, 25, 45, and 158) were based on comparison of the wild-type protein spectrum with the spectra of three single Trp-to-Phe replacement mutants. Previously we showed from fluorescence and absorption difference spectra of mutant versus wild-type sTF that the side chains of Trpl4 and Trp25 are buried, whereas those of Trp45 and Trp158 are partially exposed to bulk solvent (Hasselbacher et al., Biophys J 1995;69:20-29). 19F NMR paramagnetic broadening and solvent-induced isotope-shift experiments show that position 5 of the indole ring of 5F-Trp158 is exposed, whereas that of 5F-Trp45 is essentially inaccessible. Although 5F-Trp incorporation had no discernable effect on the procoagulant cofactor activity of either the wild-type or mutant proteins, 19F NMR chemical shifts showed that the single-Trp mutations are accompanied by subtle changes in the local environments of 5F-Trp residues residing in the same structural domain. PMID:10651284

Zemsky, J; Rusinova, E; Nemerson, Y; Luck, L A; Ross, J B

1999-12-01

229

Selection for low or high primary dormancy in Lolium rigidum Gaud seeds results in constitutive differences in stress protein expression and peroxidase activity  

PubMed Central

Seed dormancy in wild Lolium rigidum Gaud (annual ryegrass) populations is highly variable and not well characterized at the biochemical level. To identify some of the determinants of dormancy level in these seeds, the proteomes of subpopulations selected for low and high levels of primary dormancy were compared by two-dimensional polyacrylamide gel electrophoresis of extracts from mature, dry seeds. High-dormancy seeds showed higher expression of small heat shock proteins, enolase, and glyoxalase I than the low-dormancy seeds. The functional relevance of these differences in protein expression was confirmed by the fact that high-dormancy seeds were more tolerant to high temperatures imposed at imbibition and had consistently higher glyoxalase I activity over 0–42?d dark stratification. Higher expression of a putative glutathione peroxidase in low-dormancy seeds was not accompanied by higher activity, but these seeds had a slightly more oxidized glutathione pool and higher total peroxidase activity. Overall, these biochemical and physiological differences suggest that L. rigidum seeds selected for low dormancy are more prepared for rapid germination via peroxidase-mediated cell wall weakening, whilst seeds selected for high dormancy are constitutively prepared to survive environmental stresses, even in the absence of stress during seed development.

Goggin, Danica E.; Powles, Stephen B.; Steadman, Kathryn J.

2011-01-01

230

Enterovirus 71 VP1 Activates Calmodulin-Dependent Protein Kinase II and Results in the Rearrangement of Vimentin in Human Astrocyte Cells.  

PubMed

Enterovirus 71 (EV71) is one of the main causative agents of foot, hand and mouth disease. Its infection usually causes severe central nervous system diseases and complications in infected infants and young children. In the present study, we demonstrated that EV71 infection caused the rearrangement of vimentin in human astrocytoma cells. The rearranged vimentin, together with various EV71 components, formed aggresomes-like structures in the perinuclear region. Electron microscopy and viral RNA labeling indicated that the aggresomes were virus replication sites since most of the EV71 particles and the newly synthesized viral RNA were concentrated here. Further analysis revealed that the vimentin in the virus factories was serine-82 phosphorylated. More importantly, EV71 VP1 protein is responsible for the activation of calmodulin-dependent protein kinase II (CaMK-II) which phosphorylated the N-terminal domain of vimentin on serine 82. Phosphorylation of vimentin and the formation of aggresomes were required for the replication of EV71 since the latter was decreased markedly after phosphorylation was blocked by KN93, a CaMK-II inhibitor. Thus, as one of the consequences of CaMK-II activation, vimentin phosphorylation and rearrangement may support virus replication by playing a structural role for the formation of the replication factories. Collectively, this study identified the replication centers of EV71 in human astrocyte cells. This may help us understand the replication mechanism and pathogenesis of EV71 in human. PMID:24073199

Haolong, Cong; Du, Ning; Hongchao, Tian; Yang, Yang; Wei, Zhang; Hua, Zhang; Wenliang, Zhang; Lei, Song; Po, Tien

2013-09-20

231

Enterovirus 71 VP1 Activates Calmodulin-Dependent Protein Kinase II and Results in the Rearrangement of Vimentin in Human Astrocyte Cells  

PubMed Central

Enterovirus 71 (EV71) is one of the main causative agents of foot, hand and mouth disease. Its infection usually causes severe central nervous system diseases and complications in infected infants and young children. In the present study, we demonstrated that EV71 infection caused the rearrangement of vimentin in human astrocytoma cells. The rearranged vimentin, together with various EV71 components, formed aggresomes-like structures in the perinuclear region. Electron microscopy and viral RNA labeling indicated that the aggresomes were virus replication sites since most of the EV71 particles and the newly synthesized viral RNA were concentrated here. Further analysis revealed that the vimentin in the virus factories was serine-82 phosphorylated. More importantly, EV71 VP1 protein is responsible for the activation of calmodulin-dependent protein kinase II (CaMK-II) which phosphorylated the N-terminal domain of vimentin on serine 82. Phosphorylation of vimentin and the formation of aggresomes were required for the replication of EV71 since the latter was decreased markedly after phosphorylation was blocked by KN93, a CaMK-II inhibitor. Thus, as one of the consequences of CaMK-II activation, vimentin phosphorylation and rearrangement may support virus replication by playing a structural role for the formation of the replication factories. Collectively, this study identified the replication centers of EV71 in human astrocyte cells. This may help us understand the replication mechanism and pathogenesis of EV71 in human.

Haolong, Cong; Du, Ning; Hongchao, Tian; Yang, Yang; Wei, Zhang; Hua, Zhang; Wenliang, Zhang; Lei, Song; Po, Tien

2013-01-01

232

Binding of selenium-75 to blood and liver cytosolic proteins in the preruminant calf  

SciTech Connect

Labeled selenite (75Se) administered to calves in milk replacer, containing .2 or 5 ppm Se, was rapidly absorbed with peak blood 75Se at 6 h. Gel filtration and dialysis treatment of plasma and erythrocyte hemolysates showed that initially 75Se was transported in blood as 75SeO3= or loosely bound to plasma and erythrocyte proteins. At high Se intake, albumin became a transport protein for some of the plasma 75Se, and proportionately more blood radioactivity was carried in the erythrocytes. At 72 h after dosing, most plasma 75Se was tightly bound to protein in glutathione peroxidase fraction with low peroxidase activity, possibly Se transport protein. At 72 h, distribution of 75Se in erythrocyte was 35 to 40% in glutathione peroxidase, 50% in hemoglobin, and 5% in a selenite plus selenopolypeptide fraction. Erythrocyte peroxidase activity was mostly in the glutathione peroxidase fraction (57%) and hemoglobin (38%). Molecular weight estimate for erythrocyte glutathione peroxidase was 84,200 daltons; about 90% of blood peroxidase activity was in erythrocytes. High Se intake had no marked effect on distribution of 75Se among liver cytosolic proteins. About 35% of 75Se was in glutathione peroxidase fraction, having most of the peroxidase activity, 25% in void volume, 11 to 18% in a selenite plus selenopolypeptide fraction, and small amounts in selenoproteins of about 12,000 and 50,000 daltons.

Jenkins, K.J.; Hidiroglou, M.

1988-02-01

233

Night-time consumption of protein or carbohydrate results in increased morning resting energy expenditure in active college-aged men.  

PubMed

The purpose of the present study was to investigate whether whey protein (WP), casein protein (CP), carbohydrate (CHO) or a non-energy-containing placebo (PLA) consumed before sleep alters morning appetite and resting energy expenditure (REE) in active men. A total of eleven men (age: 23·6 (sem 1·0) years; body fat: 16·3 (sem 2·5) %) participated in this randomised, double-blind, cross-over study. A single dose of WP (30 g), CP (30 g), CHO (33 g) or PLA was consumed 30 min before sleep, and each trial was separated by 48-72 h. The next morning (05.00-08.00 hours), measurements of satiety, hunger and desire to eat and REE were taken. After a 30 min equilibration period, REE in the supine position was measured for 60 min. An analysis of 10 min mean intervals over the final 50 min of the measurement period was conducted. Statistical analyses were conducted using repeated-measures ANOVA for metabolic variables, and a one-way ANOVA was used for measuring changes in appetite markers. Group differences were examined by Tukey's post hoc analysis. There were no significant differences in appetite measures among the groups. There was a main group effect for REE. The predicted REE was significantly greater after consumption of the WP (8151 (sem 67) kJ/d), CP (8126 (sem 67) kJ/d) and CHO (7988 (sem 67) kJ/d) than after that of the PLA (7716 (sem 67) kJ/d, P <0·0001). There were no significant differences between the WP and CP groups in any metabolic measurements. Night-time consumption of WP, CP or CHO, in the hours close to sleep, elicits favourable effects on the next-morning metabolism when compared with that of a PLA in active young men. PMID:23768612

Madzima, Takudzwa A; Panton, Lynn B; Fretti, Sarah K; Kinsey, Amber W; Ormsbee, Michael J

2013-06-17

234

Programmed necrosis induced by asbestos in human mesothelial cells causes high-mobility group box 1 protein release and resultant inflammation  

PubMed Central

Asbestos carcinogenesis has been linked to the release of cytokines and mutagenic reactive oxygen species (ROS) from inflammatory cells. Asbestos is cytotoxic to human mesothelial cells (HM), which appears counterintuitive for a carcinogen. We show that asbestos-induced HM cell death is a regulated form of necrosis that links to carcinogenesis. Asbestos-exposed HM activate poly(ADP-ribose) polymerase, secrete H2O2, deplete ATP, and translocate high-mobility group box 1 protein (HMGB1) from the nucleus to the cytoplasm, and into the extracellular space. The release of HMGB1 induces macrophages to secrete TNF-?, which protects HM from asbestos-induced cell death and triggers a chronic inflammatory response; both favor HM transformation. In both mice and hamsters injected with asbestos, HMGB1 was specifically detected in the nuclei, cytoplasm, and extracellular space of mesothelial and inflammatory cells around asbestos deposits. TNF-? was coexpressed in the same areas. HMGB1 levels in asbestos-exposed individuals were significantly higher than in nonexposed controls (P < 0.0001). Our findings identify the release of HMGB1 as a critical initial step in the pathogenesis of asbestos-related disease, and provide mechanistic links between asbestos-induced cell death, chronic inflammation, and carcinogenesis. Chemopreventive approaches aimed at inhibiting the chronic inflammatory response, and especially blocking HMGB1, may decrease the risk of malignant mesothelioma among asbestos-exposed cohorts.

Yang, Haining; Rivera, Zeyana; Jube, Sandro; Nasu, Masaki; Bertino, Pietro; Goparaju, Chandra; Franzoso, Guido; Lotze, Michael T.; Krausz, Thomas; Pass, Harvey I.; Bianchi, Marco E.; Carbone, Michele

2010-01-01

235

Receptor-Mediated Uptake of Antigen/Heat Shock Protein Complexes Results in Major Histocompatibility Complex Class I Antigen Presentation via Two Distinct Processing Pathways  

PubMed Central

Heat shock proteins (HSPs) derived from tumors or virally infected cells can stimulate antigen-specific CD8+ T cell responses in vitro and in vivo. Although this antigenicity is known to arise from HSP-associated peptides presented to the immune system by major histocompatibility complex (MHC) class I molecules, the cell biology underlying this presentation process remains poorly understood. Here we show that HSP 70 binds to the surface of antigen presenting cells by a mechanism with the characteristics of a saturable receptor system. After this membrane interaction, processing and MHC class I presentation of the HSP-associated antigen can occur via either a cytosolic (transporter associated with antigen processing [TAP] and proteasome–dependent) or an endosomal (TAP and proteasome–independent) route, with the preferred pathway determined by the sequence context of the optimal antigenic peptide within the HSP-associated material. These findings not only characterize two highly efficient, specific pathways leading to the conversion of HSP-associated antigens into ligands for CD8+ T cells, they also imply the existence of a mechanism for receptor-facilitated transmembrane transport of HSP or HSP-associated ligands from the plasma membrane or lumen of endosomes into the cytosol.

Castellino, Flora; Boucher, Philip E.; Eichelberg, Katrin; Mayhew, Mark; Rothman, James E.; Houghton, Alan N.; Germain, Ronald N.

2000-01-01

236

Absence of the transcription factor CCAAT enhancer binding protein ? results in loss of myeloid identity in bcr/abl-induced malignancy  

PubMed Central

The lineage-determining transcription factor CCAAT enhancer binding protein ? (C/EBP?) is required for myeloid differentiation. Decreased function or expression of C/EBP? is often found in human acute myeloid leukemia. However, the precise impact of C/EBP? deficiency on the maturation arrest in leukemogenesis is not well understood. To address this question, we used a murine transplantation model of a bcr/abl-induced myeloproliferative disease. The expression of bcr/abl in C/EBP?pos fetal liver cells led to a chronic myeloid leukemia-like disease. Surprisingly, bcr/abl-expressing C/EBP??/? fetal liver cells failed to induce a myeloid disease in transplanted mice, but caused a fatal, transplantable erythroleukemia instead. Accordingly, increased expression of the transcription factors SCL and GATA-1 in hematopoietic precursor cells of C/EBP??/? fetal livers was found. The mechanism for the lineage shift from myeloid to erythroid leukemia was studied in a bcr/abl-positive cell line. Consistent with findings of the transplant model, expression of C/EBP? and GATA-1 was inversely correlated. Id1, an inhibitor of erythroid differentiation, was identified as a critical direct target of C/EBP?. Down-regulation of Id1 by RNA interference impaired C/EBP?-induced granulocytic differentiation. Taken together, our study provides evidence that myeloid lineage identity of malignant hematopoietic progenitor cells requires the residual expression of C/EBP?.

Wagner, Katharina; Zhang, Pu; Rosenbauer, Frank; Drescher, Bettina; Kobayashi, Susumu; Radomska, Hanna S.; Kutok, Jeffery L.; Gilliland, D. Gary; Krauter, Jurgen; Tenen, Daniel G.

2006-01-01

237

Cancer immunotherapy targeting the HMW-MAA protein results in a broad antitumor response and reduction of pericytes in the tumor vasculature  

PubMed Central

The high molecular weight melanoma-associated antigen (HMW-MAA), also known as melanoma chondroitin sulfate proteoglycan, has been used as a target for the immunotherapy of melanoma. This antigen is expressed on the cell surface and has a restricted distribution in normal tissues. Besides its expression in a broad range of transformed cells, this antigen is also found in pericytes, which are important for tumor angiogenesis. We generated a recombinant Listeria monocytogenes (Lm-LLO-HMW-MAA-C) that expresses and secretes a fragment of HMW-MAA (residues 2,160–2,258) fused to the first 441 residues of the listeriolysin O (LLO) protein. Immunization with Lm-LLO-HMW-MAA-C was able to impede the tumor growth of early established B16F10-HMW-MAA tumors in mice and both CD4+ and CD8+ T cells were required for therapeutic efficacy. Immune responses to a known HLA-A2 epitope present in the HMW-MAA2160–2258 fragment was detected in the HLA-A2/Kb transgenic mice immunized with Lm-LLO-HMW-MAA-C. Surprisingly, this vaccine also significantly impaired the in vivo growth of other tumorigenic cell lines, such as melanoma, renal carcinoma, and breast tumors, which were not engineered to express HMW-MAA. One hypothesis is that the vaccine could be targeting pericytes, which are important for tumor angiogenesis. In a breast tumor model, immunization with Lm-LLO-HMW-MAA-C caused CD8+ T-cell infiltration in the tumor stroma and a significant decrease in the number of pericytes in the tumor blood vessels. In conclusion, a Lm-based vaccine against HMW-MAA can trigger cell-mediated immune responses to this antigen that can target not only tumor cells but also pericytes in the tumor vasculature.

Maciag, Paulo Cesar; Seavey, Matthew; Pan, Zhen-Kun; Ferrone, Soldano; Paterson, Yvonne

2009-01-01

238

Lack of CD47 Impairs Bone Cell Differentiation and Results in an Osteopenic Phenotype in Vivo due to Impaired Signal Regulatory Protein ? (SIRP?) Signaling.  

PubMed

Here, we investigated whether the cell surface glycoprotein CD47 was required for normal formation of osteoblasts and osteoclasts and to maintain normal bone formation activity in vitro and in vivo. In parathyroid hormone or 1?,25(OH)2-vitamin D3 (D3)-stimulated bone marrow cultures (BMC) from CD47(-/-) mice, we found a strongly reduced formation of multinuclear tartrate-resistant acid phosphatase (TRAP)(+) osteoclasts, associated with reduced expression of osteoclastogenic genes (nfatc1, Oscar, Trap/Acp, ctr, catK, and dc-stamp). The production of M-CSF and RANKL (receptor activator of nuclear factor ?? ligand) was reduced in CD47(-/-) BMC, as compared with CD47(+/+) BMC. The stromal cell phenotype in CD47(-/-) BMC involved a blunted expression of the osteoblast-associated genes osterix, Alp/Akp1, and ?-1-collagen, and reduced mineral deposition, as compared with that in CD47(+/+) BMC. CD47 is a ligand for SIRP? (signal regulatory protein ?), which showed strongly reduced tyrosine phosphorylation in CD47(-/-) bone marrow stromal cells. In addition, stromal cells lacking the signaling SIRP? cytoplasmic domain also had a defect in osteogenic differentiation, and both CD47(-/-) and non-signaling SIRP? mutant stromal cells showed a markedly reduced ability to support osteoclastogenesis in wild-type bone marrow macrophages, demonstrating that CD47-induced SIRP? signaling is critical for stromal cell support of osteoclast formation. In vivo, femoral bones of 18- or 28-week-old CD47(-/-) mice showed significantly reduced osteoclast and osteoblast numbers and exhibited an osteopenic bone phenotype. In conclusion, lack of CD47 strongly impairs SIRP?-dependent osteoblast differentiation, deteriorate bone formation, and cause reduced formation of osteoclasts. PMID:23990469

Koskinen, Cecilia; Persson, Emelie; Baldock, Paul; Stenberg, Asa; Boström, Ingrid; Matozaki, Takashi; Oldenborg, Per-Arne; Lundberg, Pernilla

2013-08-29

239

A bivalent Neisseria meningitidis recombinant lipidated factor H binding protein vaccine in young adults: results of a randomised, controlled, dose-escalation phase 1 trial.  

PubMed

Neisseria meningitidis is a leading cause of meningitis and septicaemia, but a broadly-protective vaccine against endemic serogroup B disease is not licensed and available. The conserved, outer-membrane lipoprotein factor H binding protein (fHBP, also known as LP2086) is expressed as one of two subfamily variants in virtually all meningococci. This study investigated the safety, tolerability, and immunogenicity of a recombinant-expressed bivalent fHBP (r-fHBP) vaccine in healthy adults. Participants (N=103) aged 18-25 years were recruited into three ascending dose level cohorts of 20, 60, and 200?g of a bivalent r-fHBP vaccine formulation and randomised to receive vaccine or placebo at 0, 1, and 6 months. The vaccine was well tolerated. Geometric mean titres (GMTs) for r-fHBP subfamily-specific IgG antibodies increased 19-168-fold from pre-vaccination to post-dose 2 in a dose level-dependent manner. In addition, robust serum bactericidal assay using human complement (hSBA) responses for strains expressing both homologous and heterologous fHBP variants were observed. After three vaccinations, 16-52% of the placebo group and 47-90%, 75-100%, and 88-100%, of the 20, 60, and 200?g dose levels, respectively, had seroprotective (? 1:4) hSBA titres against six serogroup B strains. The bivalent r-fHBP vaccine was well tolerated and induced robust bactericidal activity against six diverse serogroup B strains in young adults at the 60 and 200?g dose levels. PMID:22871351

Richmond, P C; Nissen, M D; Marshall, H S; Lambert, S B; Roberton, D; Gruber, W C; Jones, T R; Arora, A

2012-08-05

240

Minor Nucleotide Substitutions in the omp31 Gene of Brucella ovis Result in Antigenic Differences in the Major Outer Membrane Protein That It Encodes Compared to Those of the Other Brucella Species  

PubMed Central

The gene coding for the major outer membrane protein Omp31 was sequenced in five Brucella species and their biovars. Although the omp31 genes appeared to be highly conserved in the genus Brucella, nine nucleotide substitutions were detected in the gene of Brucella ovis compared to that of Brucella melitensis. As shown by differential binding properties of monoclonal antibodies (MAbs) to the two Brucella species, these nucleotide substitutions result in different antigenic properties of Omp31. The antigenic differences were also evidenced when sera from B. ovis-infected rams were tested by Western blotting with the recombinant B. melitensis or B. ovis Omp31 proteins. Twelve available sera reacted with recombinant B. ovis Omp31, but only four of them reacted with recombinant B. melitensis Omp31. These results validate previous evidence for the potential of Omp31 as a diagnostic antigen for B. ovis infection in rams and demonstrate that B. ovis Omp31, instead of B. melitensis Omp31, should be used to evaluate this point. The antigenic differences between the B. melitensis and B. ovis Omp31 proteins should also be taken into account when Omp31 is evaluated as a candidate for the development of subcellular vaccines against B. ovis infection. No reactivity against recombinant B. melitensis Omp31 was detected, by Western blotting, with sera from B. melitensis-infected sheep. Accordingly, Omp31 does not seem to be a good diagnostic antigen for B. melitensis infections in sheep. Two immunodominant regions were identified on the B. ovis Omp31 protein by using recombinant DNA techniques and specific MAbs. Sera from B. ovis-infected rams that reacted with the recombinant protein were tested by Western blotting against one of these immunodominant regions shown to be exposed at the bacterial surface. Only 4 of the 12 sera reacted, but with strong intensity.

Vizcaino, Nieves; Kittelberger, Reinhold; Cloeckaert, Axel; Marin, Clara M.; Fernandez-Lago, Luis

2001-01-01

241

Lack of the ApbC or ApbE Protein Results in a Defect in Fe-S Cluster Metabolism in Salmonella enterica Serovar Typhimurium  

Microsoft Academic Search

The isc genes function in the assembly of Fe-S clusters and are conserved in many prokaryotic and eukaryotic organisms. In most bacteria studied, the isc operon can be deleted without loss of cell viability, indicating that additional systems for Fe-S cluster assembly must exist. Several laboratories have described nutritional and biochemical defects resulting from mutations in the isc operon. Here

Elizabeth Skovran; Diana M. Downs

2003-01-01

242

Expression of Chinese Hamster cAMP-Dependent Protein Kinase in Escherichia coli Results in Growth Inhibition of Bacterial Cells: A Model System for the Rapid Screening of Mutant Type I Regulatory Subunits  

Microsoft Academic Search

The regulatory and catalytic subunits of cAMP-dependent protein kinase (PKA) were coexpressed within the same bacterial cell using a polycistronic bacterial T7 expression vector encoding Chinese hamster cDNAs for the type I regulatory (RI) and catalytic alpha (Calpha) subunits of PKA. Basal expression of active RI\\/Calpha holoenzyme in the BL21(DE3) strain of Escherichia coli caused severe growth inhibition resulting in

Marilyn E. Gosse; Anita Padmanabhan; Robert D. Fleischmann; Michael M. Gottesman

1993-01-01

243

A missense mutation in the transmembrane domain of CESA4 affects protein abundance in the plasma membrane and results in abnormal cell wall biosynthesis in rice  

Microsoft Academic Search

Cellulose synthase (CESA) is a critical catalytic subunit of the cellulose synthase complex responsible for glucan chain elongation.\\u000a Our knowledge about how CESA functions is still very limited. Here, we report the functional characterization of a rice mutant,\\u000a brittle culm11, that shows growth retardation and dramatically reduced plant strength. Map-based cloning revealed that all the mutant phenotypes\\u000a result from a

Baocai Zhang; Lingwei Deng; Qian Qian; Guangyan Xiong; Dali Zeng; Rui Li; Longbiao Guo; Jiayang Li; Yihua Zhou

2009-01-01

244

Asp1424Asn MYH9 mutation results in an unstable protein responsible for the phenotypes in May-Hegglin anomaly\\/Fechtner syndrome  

Microsoft Academic Search

May-Hegglin anomaly (MHA), Fechtner syndrome (FTNS), Sebastian syndrome (SBS), and Epstein syndrome (EPS) are a group of rare, autosomal dominant disor- ders characterized by thrombocytopenia, giant platelets, and Dohle-like inclusion bodies, together with variable manifesta- tions of Alport-like symptoms that in- clude high-tone sensorineural deafness, cataracts, and nephritis. These disorders result from mutations in the MYH9 gene, which encodes for

Samuel Deutsch; Alexandra Rideau; Marie-Luce Bochaton-Piallat; Giuseppe Merla; Antoine Geinoz; Giulio Gabbiani; Torsten Schwede; Thomas Matthes; Stylianos E. Antonarakis; Photis Beris

2003-01-01

245

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: HS1 (Hematopoietic cell-specific LYN substrate 1) Cellular Function: Cellular Signalling Producer Cell Type: Lymphoid line Modifications: Protein fragment Molecules/virion: 20-50 (1 precent of Gag) Viral Partner: Cellular

246

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Actin alpha smooth muscle Cellular Function: Cytoskeleton, RNA-binding Producer Cell Type: Lymphoid line Modifications: Protein fragment Molecules/virion: 2 percent of Gag (20-50) Viral Partner: NC Cellular

247

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: CD43 Cellular Function: Cellular Signalling Producer Cell Type: Lymphoid line, Primary macrophage Modifications: Protein fragment Molecules/virion: 20-50 (1 percent of Gag) Viral Partner: Undetermined Cellular

248

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: eEF1A Elongation factor 1 alpha Cellular Function: Translation Producer Cell Type: Epithelial line, Lymphoid line, Macrophage line Modifications: Protein fragment Molecules/virion: >120-30 6% of Gag Viral

249

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Rho-GTPase-activating protein 1 Cellular Function: Producer Cell Type: Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Uniprot Accession #: Q07960 Sequence/Peptide

250

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Rho GTPase activating protein 18 Cellular Function: ??? Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Biochemical:

251

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Rho-related GTP-binding protein RhoG Cellular Function: Cellular Signalling Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method

252

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Rho-GTPase-activating protein 1 Cellular Function: Cellular Signalling Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method

253

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Transcriptional activator protein PUR-alpha Cellular Function: Transcription Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method

254

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Signal transducer and activator of transcription 1 (STAT1) Cellular Function: Cellular Signalling Producer Cell Type: Primary macrophage Modifications: Protein fragment Molecules/virion: Viral Partner: Undetermined Cellular

255

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: GDP dissociation inhibitor beta (Rab GDI b) Cellular Function: Protein-targeting Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Rab Method

256

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Rap-1A (Ras-related protein) Cellular Function: Cellular Signalling Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method

257

Predicting protein-protein binding sites in membrane proteins  

Microsoft Academic Search

BACKGROUND: Many integral membrane proteins, like their non-membrane counterparts, form either transient or permanent multi-subunit complexes in order to carry out their biochemical function. Computational methods that provide structural details of these interactions are needed since, despite their importance, relatively few structures of membrane protein complexes are available. RESULTS: We present a method for predicting which residues are in protein-protein

Andrew J. Bordner

2009-01-01

258

Protein N -glycosylation, protein folding, and protein quality control  

Microsoft Academic Search

Quality control of protein folding represents a fundamental cellular activity. Early steps of protein N-glycosylation involving the removal of three glucose and some specific mannose residues in the endoplasmic reticulum have\\u000a been recognized as being of importance for protein quality control. Specific oligosaccharide structures resulting from the\\u000a oligosaccharide processing may represent a glycocode promoting productive protein folding, whereas others may

Jürgen Roth; Christian Zuber; Sujin Park; Insook Jang; Yangsin Lee; Katarina Gaplovska Kysela; Valérie Le Fourn; Roger Santimaria; Bruno Guhl; Jin Won Cho

2010-01-01

259

Effects of 4 weight-loss diets differing in fat, protein, and carbohydrate on fat mass, lean mass, visceral adipose tissue, and hepatic fat: results from the POUNDS LOST trial123  

PubMed Central

Background: Weight loss reduces body fat and lean mass, but whether these changes are influenced by macronutrient composition of the diet is unclear. Objective: We determined whether energy-reduced diets that emphasize fat, protein, or carbohydrate differentially reduce total, visceral, or hepatic fat or preserve lean mass. Design: In a subset of participants in a randomized trial of 4 weight-loss diets, body fat and lean mass (n = 424; by using dual-energy X-ray absorptiometry) and abdominal and hepatic fat (n = 165; by using computed tomography) were measured after 6 mo and 2 y. Changes from baseline were compared between assigned amounts of protein (25% compared with 15%) and fat (40% compared with 20%) and across 4 carbohydrate amounts (35% through 65%). Results: At 6 mo, participants lost a mean (±SEM) of 4.2 ± 0.3 kg (12.4%) fat and 2.1 ± 0.3 kg (3.5%) lean mass (both P < 0.0001 compared with baseline values), with no differences between 25% and 15% protein (P ? 0.10), 40% and 20% fat (P ? 0.34), or 65% and 35% carbohydrate (P ? 0.27). Participants lost 2.3 ± 0.2 kg (13.8%) abdominal fat: 1.5 ± 0.2 kg (13.6%) subcutaneous fat and 0.9 ± 0.1 kg (16.1%) visceral fat (all P < 0.0001 compared with baseline values), with no differences between the diets (P ? 0.29). Women lost more visceral fat than did men relative to total-body fat loss. Participants regained ?40% of these losses by 2 y, with no differences between diets (P ? 0.23). Weight loss reduced hepatic fat, but there were no differences between groups (P ? 0.28). Dietary goals were not fully met; self-reported contrasts were closer to 2% protein, 8% fat, and 14% carbohydrate at 6 mo and 1%, 7%, and 10%, respectively, at 2 y. Conclusion: Participants lost more fat than lean mass after consumption of all diets, with no differences in changes in body composition, abdominal fat, or hepatic fat between assigned macronutrient amounts. This trial was registered at clinicaltrials.gov as NCT00072995.

de Souza, Russell J; Carey, Vincent J; Hall, Kevin D; LeBoff, Meryl S; Loria, Catherine M; Laranjo, Nancy M; Sacks, Frank M; Smith, Steven R

2012-01-01

260

Extrusion Texturized Dairy Proteins  

Microsoft Academic Search

The primary proteins in milk, casein and the whey proteins ?-lactalbumin and ?-lactoglobulin, have a number of health benefits and desirable functional properties. In a twin-screw extruder, mechanical shear forces, heat, and pressure cause considerable changes in the molecular structures of the dairy proteins, a process known as texturization. These changes further impart unique functional properties to dairy proteins, resulting

Charles I. Onwulata; Michael H. Tunick; Phoebe X. Qi

2011-01-01

261

Diets containing soy or rice protein isolate increase insulin sensitivity and improve lipid homeostasis in weanling rats fed high fat, high cholesterol Western diets as a result of activation of PPAR and LXR-mediated pathways  

Technology Transfer Automated Retrieval System (TEKTRAN)

The current study examined the effects of feeding soy protein isolate (SPI) and rice protein isolate (RPI) on insulin sensitivity and fat breakdown in weanling rats consuming high fat/high cholesterol diets. Male Sprague-Dawley rats were placed on semi-purified diets containing the milk protein case...

262

ITT results  

Center for Biologics Evaluation and Research (CBER)

Text Version... 0 Baseline Infra-renal inflation Supra- renal inflation 30 min treatment Supra- renal deflation ... aorta, balloon inflation results in diversion of cardiac ... More results from www.fda.gov/downloads/advisorycommittees/committeesmeetingmaterials

263

Detection of IgM responses to bovine respiratory syncytial virus by indirect ELISA following experimental infection and reinfection of calves: abolition of false positive and false negative results by pre-treatment of sera with protein-G agarose.  

PubMed

The IgM responses in three panels of sera generated by infection and reinfection of calves with bovine respiratory syncytial virus (BRSV) were measured by indirect ELISA (I-ELISA). The effect of depleting serum IgG by pre-treatment with protein G agarose (PGA) was evaluated. Following primary infection a weak IgM response was detected in the untreated sera of 3 out of 4 calves with maternally derived antibody (MDA). Both the magnitude and duration of the specific IgM responses in these calves were increased by pre-treatment with PGA. In addition, the fourth infected calf tested gave a single positive IgM result following PGA treatment. Transient or persistent IgM responses which were abolished by pre-treatment of sera with PGA were detected in 4/8 calves following reinfection. These were considered to be false positive results, consistent with the influence of IgM rheumatoid factor (IgM-RF). One of these calves and two additional calves showed transient increases in IgM which were resistant to PGA treatment. These were considered to represent specific IgM responses to reinfection. The results indicate the ability of PGA treatment to eliminate both false positive and false negative results and emphasise the necessity for controlling the influence of IgM-RF in IgM-specific indirect ELISAs. PMID:10522785

Graham, D A; Foster, J C; Mawhinney, K A; Elvander, M; Adair, B M; Merza, M

1999-10-01

264

Altered affinity of insulin-like growth factor II (IGF-II) for receptors and IGF-binding proteins, resulting from limited modifications of the IGF-II molecule.  

PubMed Central

The binding affinities of seven analogues of recombinant human insulin-like growth factor II (hIGF-II) were characterized for the IGF type-I and type-II receptors and insulin receptors, as well as for IGF-binding protein (IGFBP)-1, IGFBP-2, IGFPB-3 and human serum IGFBPs. A switch of two of the three cysteine bridges in hIGF-II, 9-47 and 46-51 to 9-46 and 47-51, severely impaired the binding of this analogue to all receptors and to the IGFBPs. The affinities for the IGF type-I receptor and the IGFBPs were decreased over 100-fold, while the binding to the insulin receptor and the IGF type-II receptor was less affected, with a 6-10-fold decrease in affinity. Slight modifications of the N-terminus had only minor effects upon the binding of hIGF-II to the IGFBPs or to the receptors. Deletion of both the N-terminal amino acid and the two C-terminal amino acids resulted in moderate decreases in affinity, with a 60% decrease in affinity for IGFBP-1 and the IGF type-I receptor. Acetylation of the N-terminus of Ala1 and the epsilon-nitrogen of Lys65 decreased the affinity, by 60-90%, of hIGF-II for all of the IGFBPs and receptors. The experiments involving acetylation of IGF-II or switching of its cysteine bridges indicated that these modifications (no substitution, deletion or addition of any of the 67 amino acids of hIGF-II) may lead to a severe impairment of the binding affinity of IGF-II for both the IGFBPs and the receptors. Acetylation of the epsilon-nitrogen of Lys65, which causes a charge change, or alteration of the three-dimensional structure, as shown by the cysteine bridge switch, lead to a severe impairment of the binding affinity for the binding proteins and for the receptors. In general, care should be taken with the synthesis of analogues and the interpretation of resulting binding data, since affinity alterations ascribed to amino acid changes may instead be caused by alterations of the charge or the three-dimensional structure of the protein.

Oh, Y; Beukers, M W; Pham, H M; Smanik, P A; Smith, M C; Rosenfeld, R G

1991-01-01

265

Reconstruction of the alveolar cleft: can growth factor-aided tissue engineering replace autologous bone grafting? A literature review and systematic review of results obtained with bone morphogenetic protein-2.  

PubMed

The alveolar cleft in patients with clefts of lip, alveolus and palate (CLAP) is usually reconstructed with an autologous bone graft. Harvesting of autologous bone grafts is associated with more or less donor site morbidity. Donor site morbidity could be eliminated if bone is fabricated by growth factor-aided tissue engineering. The objective of this review was to provide an oversight on the current state of the art in growth factor-aided tissue engineering with regard to reconstruction of the alveolar cleft in CLAP. Medline, Embase and Central databases were searched for articles on bone morphogenetic protein 2 (BMP-2), bone morphogenetic protein 7, transforming growth factor beta, platelet-derived growth factor, insulin-like growth factor, fibroblast growth factor, vascular endothelial growth factor and platelet-rich plasma for the reconstruction of the alveolar cleft in CLAP. Two-hundred ninety-one unique search results were found. Three articles met our selection criteria. These three selected articles compared BMP-2-aided bone tissue engineering with iliac crest bone grafting by clinical and radiographic examinations. Bone quantity appeared comparable between the two methods in patients treated during the stage of mixed dentition, whereas bone quantity appeared superior in the BMP-2 group in skeletally mature patients. Favourable results with BMP-2-aided bone tissue engineering have been reported for the reconstruction of the alveolar cleft in CLAP. More studies are necessary to assess the quality of bone. Advantages are shortening of the operation time, absence of donor site morbidity, shorter hospital stay and reduction of overall cost. PMID:21465220

van Hout, Wouter M M T; Mink van der Molen, Aebele B; Breugem, Corstiaan C; Koole, Ronald; Van Cann, Ellen M

2011-04-05

266

ZEUS Results  

SciTech Connect

Several results from the ZEUS Collaboration were presented at this Workshop. The highlights are presented in this summary, and include results from NLO QCD fits and determination of {alpha}S, from forward jets and diffractive final states, from pentaquarks and searches and from heavy flavour production. Also the first results from the analysis of the HERA II e+p/e-p data are shown.

Gallo, Elisabetta [INFN Florence (Italy)

2005-10-06

267

API2-MALT1 fusion protein induces transcriptional activation of the API2 gene through NF-{kappa}B binding elements: Evidence for a positive feed-back loop pathway resulting in unremitting NF-{kappa}B activation  

SciTech Connect

t(11;18)(q21;q21) is a characteristic as well as the most frequent chromosomal translocation in mucosa-associated lymphoid tissue (MALT) type lymphoma, and this translocation results in a fusion transcript, API2-MALT1. Although API2-MALT1 has been shown to enforce activation of NF-{kappa}B signaling, the transcriptional target genes of this fusion protein remains to be identified. Our analyses of the API2-MALT transfectants suggested that one of the target genes may be the apoptotic inhibitor API2 gene. Luciferase reporter assays with deletion and mutational constructs of the API2 promoter and electrophoretic mobility shift assays established that API2-MALT1 induces transcriptional activation of the API2 gene through two NF-{kappa}B binding elements. Moreover, supershift experiments indicated that these elements are recognized by the NF-{kappa}B p50/p65 heterodimer. Taken together, our results strongly indicated that API2-MALT1 possesses a novel mechanism of self-activation by up-regulating its own expression in t(11;18)(q21;q21)-carrying MALT lymphomas, highlighting a positive feedback-loop pathway resulting in unremitting NF-{kappa}B activation.

Hosokawa, Yoshitaka [Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya 464-8681 (Japan)]. E-mail: yhosokaw@aichi-cc.jp; Suzuki, Hiroko [Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya 464-8681 (Japan); Nakagawa, Masao [Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya 464-8681 (Japan); Japan Biological Informatics Consortium, Tokyo 104-0032 (Japan); Lee, Tae H. [Department of Biology, College of Science, Yonsei University, Seoul 120-749 (Korea, Republic of); Seto, Masao [Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya 464-8681 (Japan)

2005-08-19

268

Bacteriophage Protein-Protein Interactions  

PubMed Central

Bacteriophages T7, ?, P22, and P2/P4 (from Escherichia coli), as well as ?29 (from Bacillus subtilis), are among the best-studied bacterial viruses. This chapter summarizes published protein interaction data of intraviral protein interactions, as well as known phage–host protein interactions of these phages retrieved from the literature. We also review the published results of comprehensive protein interaction analyses of Pneumococcus phages Dp-1 and Cp-1, as well as coliphages ? and T7. For example, the ?55 proteins encoded by the T7 genome are connected by ?43 interactions with another ?15 between the phage and its host. The chapter compiles published interactions for the well-studied phages ? (33 intra-phage/22 phage-host), P22 (38/9), P2/P4 (14/3), and ?29 (20/2). We discuss whether different interaction patterns reflect different phage lifestyles or whether they may be artifacts of sampling. Phages that infect the same host can interact with different host target proteins, as exemplified by E. coli phage ? and T7. Despite decades of intensive investigation, only a fraction of these phage interactomes are known. Technical limitations and a lack of depth in many studies explain the gaps in our knowledge. Strategies to complete current interactome maps are described. Although limited space precludes detailed overviews of phage molecular biology, this compilation will allow future studies to put interaction data into the context of phage biology.

Hauser, Roman; Blasche, Sonja; Dokland, Terje; Haggard-Ljungquist, Elisabeth; von Brunn, Albrecht; Salas, Margarita; Casjens, Sherwood; Molineux, Ian

2012-01-01

269

Mutations in genes patA and patL of Anabaena sp. strain PCC 7120 result in similar phenotypes, and the proteins encoded by those genes may interact.  

PubMed

PatA resembles a response regulator protein with a defective DNA-binding domain, and PatL (All3305) is a pentapeptide repeat protein. A yeast two-hybrid library identified PatL as a protein with which PatA may interact. Heterocysts of patA and patL Anabaena sp. form nearly exclusively terminally in long filaments, further linking the genes. PMID:21890704

Liu, Jinjie; Wolk, C Peter

2011-09-02

270

COOH-terminal truncated cardiac myosin-binding protein C mutants resulting from familial hypertrophic cardiomyopathy mutations exhibit altered expression and\\/or incorporation in fetal rat cardiomyocytes 1 1 Edited by J. Karn  

Microsoft Academic Search

Mutations in human cardiac myosin-binding protein C (cMyBP-C) gene are associated with familial hypertrophic cardiomyopathy (FHC), and most of them are predicted to produce COOH-truncated proteins. To understand the molecular mechanism(s) by which such mutations cause FHC, we analyzed (i) the accumulation of human cMyBP-C mutants in fetal rat cardiomyocytes, and (ii) the protein sequence of the human wild-type (wt)

Jeanne Flavigny; Michel Souchet; Pascale Sébillon; Isabelle Berrebi-Bertrand; Bernard Hainque; Alain Mallet; Antoine Bril; Ketty Schwartz; Lucie Carrier

1999-01-01

271

Mobility of photosynthetic proteins.  

PubMed

The mobility of photosynthetic proteins represents an important factor that affects light-energy conversion in photosynthesis. The specific feature of photosynthetic proteins mobility can be currently measured in vivo using advanced microscopic methods, such as fluorescence recovery after photobleaching which allows the direct observation of photosynthetic proteins mobility on a single cell level. The heterogeneous organization of thylakoid membrane proteins results in heterogeneity in protein mobility. The thylakoid membrane contains both, protein-crowded compartments with immobile proteins and fluid areas (less crowded by proteins), allowing restricted diffusion of proteins. This heterogeneity represents an optimal balance as protein crowding is necessary for efficient light-energy conversion, and protein mobility plays an important role in the regulation of photosynthesis. The mobility is required for an optimal light-harvesting process (e.g., during state transitions), and also for transport of proteins during their synthesis or repair. Protein crowding is then a key limiting factor of thylakoid membrane protein mobility; the less thylakoid membranes are crowded by proteins, the higher protein mobility is observed. Mobility of photosynthetic proteins outside the thylakoid membrane (lumen and stroma/cytosol) is less understood. Cyanobacterial phycobilisomes attached to the stromal side of the thylakoid can move relatively fast. Therefore, it seems that stroma with their active enzymes of the Calvin-Benson cycle, are a more fluid compartment in comparison to the rather rigid thylakoid lumen. In conclusion, photosynthetic protein diffusion is generally slower in comparison to similarly sized proteins from other eukaryotic membranes or organelles. Mobility of photosynthetic proteins resembles restricted protein diffusion in bacteria, and has been rationalized by high protein crowding similar to that of thylakoids. PMID:23955784

Ka?a, Radek

2013-08-17

272

Protein docking prediction using predicted protein-protein interface  

PubMed Central

Background Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. Results We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm), is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. Conclusion We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

2012-01-01

273

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: ATP synthase beta chain Cellular Function: Producer Cell Type: Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Uniprot Accession #: P06576 Sequence/Peptide

274

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Syndecan-2 Cellular Function: Adhesion Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Biochemical: CD45-depletion Uniprot

275

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Cofilin Cellular Function: Cytoskeleton Producer Cell Type: Lymphoid line Modifications: Molecules/virion: 20-500 (2-10 percent of Gag) Viral Partner: Undetermined Cellular Partners: Actin Method of Detection: Biochemical:

276

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Actin Beta Cellular Function: Cytoskeleton, RNA-binding Producer Cell Type: Lymphoid line Modifications: None detected Molecules/virion: 200-500 (10 percent of Gag) Viral Partner: NC Cellular Partners: Cofilin,

277

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Glyceraldehyde-3-phosphate dehydrogenase Cellular Function: Cytoskeleton, Glycolysis, RNA-binding Producer Cell Type: Lymphoid line Modifications: None detected Molecules/virion: 20-30 (1% of Gag) Viral Partner: Undetermined Cellular

278

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Ezrin Cellular Function: Cytoskeleton Producer Cell Type: Lymphoid line Modifications: None detected Molecules/virion: 20-50(2% of Gag) Viral Partner: Undetermined Cellular Partners: Actin Method of Detection: Biochemical:

279

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Alpha-2-HS-glycoprotein (Fetuin-A) Cellular Function: Endocytosis Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method

280

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Clathrin heavy chain 1 Cellular Function: Endocytosis Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: AP-1, AP-2, AP-3 Method

281

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Vacuolar proton pump subunit 1 Cellular Function: Endocytosis Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of

282

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Vacuolar ATP synthase subunit D Cellular Function: Endocytosis Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Biochemical:

283

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: CD205 Cellular Function: Endocytosis Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Biochemical: CD45-depletion Uniprot

284

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Vacuolar ATP synthase subunit B Cellular Function: Endocytosis Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of

285

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Clathrin light chain B Cellular Function: Endocytosis Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Clathrin heavy chain Method

286

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Rab 5A Cellular Function: Endocytosis Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Biochemical: CD45-depletion Uniprot

287

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Vacuolar ATP synthase subunit G 1 Cellular Function: Endocytosis Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of

288

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: LAMP-1 (CD107a) Cellular Function: Endocytosis Producer Cell Type: Primary macrophage Modifications: Other Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Biochemical:

289

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Peroxiredoxin 6 Cellular Function: Red-Ox control Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Biochemical:

290

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Peroxiredoxin 1 Cellular Function: Red-Ox control Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Biochemical:

291

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Helicase MOV-10 Cellular Function: ??? Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Biochemical:

292

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Alpha-enolase Cellular Function: multiple Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Biochemical:

293

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: 2',3'-cyclic nucleotide 3'-phosphodiesterase Cellular Function: Cellular Signalling Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method

294

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Beta-glucan receptor isoform E Cellular Function: Immunoregulation Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of

295

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Glutathione S-transferase P Cellular Function: Red-Ox control Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Biochemical:

296

PURPOSE RESULTS BACKGROUND METHODS RESULTS ...  

Center for Drug Evaluation (CDER)

Text Version... KETOCONAZOLE IN SUBJECTS WITH RENAL IMPAIRMENT (RI) TAKING RIVAROXABAN Ping Zhao, Joseph A. Grillo, Young-Moon Choi, Brian P ... More results from www.fda.gov/downloads/drugs/developmentapprovalprocess

297

Neutralization of Transthyretin Reverses the Neuroprotective Effects of Secreted Amyloid Precursor Protein (APP) in APPSw Mice Resulting in Tau Phosphorylation and Loss of Hippocampal Neurons: Support for the Amyloid Hypothesis  

Microsoft Academic Search

Alzheimer's disease (AD) may be caused by the abnormal processing of the amyloid precursor protein (APP) and the accumulation of -amyloid (A). The amyloid precursor protein can be proteolytically cleaved into multiple fragments, many of which have distinct biological actions. Although a high level of A can be toxic, the -secretase cleaved APP (sAPP) is neuroprotective. However, the mechanism of

Thor D. Stein; Nicholas J. Anders; Charles DeCarli; Sic L. Chan; Mark P. Mattson; Jeffrey A. Johnson

2004-01-01

298

Lipid-transfer protein is the major maize allergen maintaining IgE-binding activity after cooking at 100°C, as demonstrated in anaphylactic patients and patients with positive double-blind, placebo-controlled food challenge results  

Microsoft Academic Search

BackgroundIn a previous study a 9-kd lipid-transfer protein (LTP) was identified as the major allergen of raw maize in a population of 22 anaphylactic patients. However, the stability of this protein in cooked maize is unknown.

Elide A. Pastorello; Carlo Pompei; Valerio Pravettoni; Laura Farioli; Ambra Marianna Calamari; Joseph Scibilia; Anna Maria Robino; Amedeo Conti; Stefania Iametti; Donatella Fortunato; Simona Bonomi; Claudio Ortolani

2003-01-01

299

Tevatron results  

SciTech Connect

Recent results obtained by the CDF and D0 experiments at the Tevatron Run II are presented. A first part is dedicated to QCD physics where inclusive jet production, dijet azimuthal decorrelations and jet shapes measurements are reported. Electroweak physics is then discussed relating measurements of the W and Z bosons productions, of the forward-backward charge asymmetry in W production, of the W width and of the top quarks mass. The extensive Run II exploration program is finally approached reporting about searches for neutral supersymmetric Higgs bosons in multijet events and for sbottom quark from gluino decays.

Lefevre, R.; /Barcelona, Autonoma U.

2005-01-01

300

Predicting protein crystallization propensity from protein sequence  

PubMed Central

The high-throughput structure determination pipelines developed by structural genomics programs offer a unique opportunity for data mining. One important question is how protein properties derived from a primary sequence correlate with the protein’s propensity to yield X-ray quality crystals (crystallizability) and 3D X-ray structures. A set of protein properties were computed for over 1,300 proteins that expressed well but were insoluble, and for ~720 unique proteins that resulted in X-ray structures. The correlation of the protein’s iso-electric point and grand average hydropathy (GRAVY) with crystallizability was analyzed for full length and domain constructs of protein targets. In a second step, several additional properties that can be calculated from the protein sequence were added and evaluated. Using statistical analyses we have identified a set of the attributes correlating with a protein’s propensity to crystallize and implemented a Support Vector Machine (SVM) classifier based on these. We have created applications to analyze and provide optimal boundary information for query sequences and to visualize the data. These tools are available via the web site http://bioinformatics.anl.gov/cgi-bin/tools/pdpredictor.

2011-01-01

301

Combined Results from Solution Studies on Intact Influenza Virus M1 Protein and from a New Crystal Form of Its N-Terminal Domain Show That M1 Is an Elongated Monomer  

Microsoft Academic Search

The amino-terminal domain of influenza A virus matrix protein (residues 1–164) was crystallized at pH 7 into a new crystal form in space group P1. This packing of the protein implies that M1(1–164) was monomeric in solution when it crystallized. Otherwise, the structure of the M1 fragment in the pH 7 crystals was the same as the monomers in crystals

Steffi Arzt; Florence Baudin; Annie Barge; Peter Timmins; Wim P. Burmeister; Rob W. H. Ruigrok

2001-01-01

302

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Ubiquitin-p6 complex Cellular Function: ESCRT targeting, Protein-targeting Producer Cell Type: Lymphoid line Modifications: Ubiquitinated Molecules/virion: 40-100 (2 percent of Gag) Viral Partner: p6Gag Cellular

303

Positive anti-citrullinated protein antibody status and small joint arthritis are consistent predictors of chronic disease in patients with very early arthritis: results from the NOR-VEAC cohort  

PubMed Central

Introduction The current 1987 American College of Rheumatology (ACR) classification criteria for rheumatoid arthritis (RA) have proven less useful in early arthritis. The objective of this study was to identify and compare predictors of three relevant outcomes of chronic arthritis in a cohort of very early arthritis patients. Methods The Norwegian Very Early Arthritis Cohort (NOR-VEAC) includes adult patients with at least one swollen joint of ?16 weeks' duration. Patients are followed for 2 years with comprehensive clinical and laboratory examinations. Logistic regression analyses were performed to determine independent predictors of three outcomes: persistent synovitis, prescription of disease-modifying anti-rheumatic drugs (DMARDs), and established clinical RA diagnosis within one year. Results Of 384 patients eligible for one year follow-up (56.3% females, mean (SD) age 45.8 (14.7) years, median (IQR) duration of arthritis 31 (10-62) days), 14.4% were anti-CCP2 positive, and 11.2% were IgM RF positive. 98 patients (25.5%) had persistent synovitis, 106 (27.6%) had received DMARD treatment during follow-up, while 68 (17.7%) were diagnosed with RA. Consistent independent predictors across all three outcomes were positive anti-citrullinated protein antibody (ACPA) status (odds ratio (OR) 3.2, 5.6 and 19.3), respectively, and small joint arthritis (proximal interphalangeal joint (PIP), metacarpo-phalangeal joint (MCP), and/or metatarso-phalangeal joint (MTP) joint swelling) (OR 1.9, 3.5, and 3.5, respectively). Conclusions Positive ACPA status and small joint arthritis were consistent predictors of three relevant outcomes of chronic arthritis in very early arthritis patients. This consistency supports DMARD prescription as a valid surrogate endpoint for chronic arthritis. Importantly, this surrogate is used in ongoing efforts to develop new diagnostic criteria for early RA.

2009-01-01

304

High-sensitivity C-reactive Protein is a Predictive Factor of Adiposity in Children: Results of the Identification and prevention of Dietary- and lifestyle-induced health Effects in Children and InfantS (IDEFICS) Study  

PubMed Central

Background Whereas cross?sectional studies have shown that obesity is associated with increased C?reactive protein (CRP) levels in children, little is known about the impact of low?grade inflammation on body mass changes during growth. Methods and Results We assessed cross?sectionally and longitudinally the association of high?sensitivity (hs)?CRP levels with overweight/obesity and related cardiometabolic risk factors in the Identification and prevention of Dietary? and lifestyle?induced health Effects in Children and InfantS (IDEFICS) cohort. 16 224 children from 8 European countries (2 to 9 years) were recruited during the baseline survey (T0). After the exclusion of 7187 children because of missing hs?CRP measurements and 2421 because of drug use during the previous week, the analysis was performed on 6616 children (Boys=3347; Girls=3269; age=6.3±1.7 years). Of them, 4110 were reexamined 2 years later (T1). Anthropometric variables, blood pressure, hs?CRP, blood lipids, glucose and insulin were measured. The population at T0 was divided into 3 categories, according to the baseline hs?CRP levels. Higher hs?CRP levels were associated with significantly higher prevalence of overweight/obesity, body mass index (BMI) z?score and central adiposity indices (P values all <0.0001), and with higher blood pressure and lower HDL?cholesterol levels. Over the 2?year follow?up, higher baseline hs?CRP levels were associated with a significant increase in BMI z?score (P<0.001) and significantly higher risk of incident overweight/obesity. Conclusions Higher hs?CRP levels are associated to higher body mass and overweight/obesity risk in a large population of European children. Children with higher baseline levels of hs?CRP had a greater increase in BMI z?score and central adiposity over time and were at higher risk of developing overweight/obesity during growth.

Nappo, Annunziata; Iacoviello, Licia; Fraterman, Arno; Gonzalez-Gil, Esther M.; Hadjigeorgiou, Charis; Marild, Staffan; Molnar, Denes; Moreno, Luis A.; Peplies, Jenny; Sioen, Isabel; Veidebaum, Toomas; Siani, Alfonso; Russo, Paola

2013-01-01

305

Proteins of Soybean Seeds  

PubMed Central

Soybean (Glycine max) storage proteins were characterized by sedimentation and by polyacrylamide gel electrophoresis under dissociating (8 m urea) and nondissociating conditions. Three sedimenting classes of proteins were found, with sedimentation coefficients of 2.2S, 7.5S, and 11.8S. The coefficients were related to the bands obtained by electrophoretic separation. The results support the idea that relatively few proteins make up the bulk of the seed protein.

Hill, J. E.; Breidenbach, R. W.

1974-01-01

306

Protein N-glycosylation, protein folding, and protein quality control.  

PubMed

Quality control of protein folding represents a fundamental cellular activity. Early steps of protein N-glycosylation involving the removal of three glucose and some specific mannose residues in the endoplasmic reticulum have been recognized as being of importance for protein quality control. Specific oligosaccharide structures resulting from the oligosaccharide processing may represent a glycocode promoting productive protein folding, whereas others may represent glyco-codes for routing not correctly folded proteins for dislocation from the endoplasmic reticulum to the cytosol and subsequent degradation. Although quality control of protein folding is essential for the proper functioning of cells, it is also the basis for protein folding disorders since the recognition and elimination of non-native conformers can result either in loss-of-function or pathological-gain-of-function. The machinery for protein folding control represents a prime example of an intricate interactome present in a single organelle, the endoplasmic reticulum. Here, current views of mechanisms for the recognition and retention leading to productive protein folding or the eventual elimination of misfolded glycoproteins in yeast and mammalian cells are reviewed. PMID:21340671

Roth, Jürgen; Zuber, Christian; Park, Sujin; Jang, Insook; Lee, Yangsin; Kysela, Katarina Gaplovska; Le Fourn, Valérie; Santimaria, Roger; Guhl, Bruno; Cho, Jin Won

2010-11-26

307

Protein Condensation  

NASA Astrophysics Data System (ADS)

Preface; 1. Introduction; 2. Globular protein structure; 3. Experimental methods; 4. Thermodynamics and statistical mechanics; 5. Protein-protein interactions; 6. Theoretical studies of equilibrium; 7. Nucleation theory; 8. Experimental studies of nucleation; 9. Lysozyme; 10. Some other globular proteins; 11. Membrane proteins; 12. Crystallins and cataracts; 13. Sickle hemoglobin and sickle cell anemia; 14, Alzheimer's disease; Index.

Gunton, James D.; Shiryayev, Andrey; Pagan, Daniel L.

2007-09-01

308

Interleukin 6, lipopolysaccharide-binding protein and interleukin 10 in the prediction of risk and etiologic patterns in patients with community-acquired pneumonia: results from the German competence network CAPNETZ  

PubMed Central

Background The aim of our study was to investigate the predictive value of the biomarkers interleukin 6 (IL-6), interleukin 10 (IL-10) and lipopolysaccharide-binding protein (LBP) compared with clinical CRB and CRB-65 severity scores in patients with community-acquired pneumonia (CAP). Methods Samples and data were obtained from patients enrolled into the German CAPNETZ study group. Samples (blood, sputum and urine) were collected within 24 h of first presentation and inclusion in the CAPNETZ study, and CRB and CRB-65 scores were determined for all patients at the time of enrollment. The combined end point representative of a severe course of CAP was defined as mechanical ventilation, intensive care unit treatment and/or death within 30 days. Overall, a total of 1,000 patients were enrolled in the study. A severe course of CAP was observed in 105 (10.5%) patients. Results The highest IL-6, IL-10 and LBP concentrations were found in patients with CRB-65 scores of 3-4 or CRB scores of 2-3. IL-6 and LBP levels on enrollment in the study were significantly higher for patients with a severe course of CAP than for those who did not have severe CAP. In receiver operating characteristic analyses, the area under the curve values for of IL-6 (0.689), IL-10 (0.665) and LPB (0.624) in a severe course of CAP were lower than that of CRB-65 (0.764) and similar to that of CRB (0.69). The accuracy of both CRB and CRB-65 was increased significantly by including IL-6 measurements. In addition, higher cytokine concentrations were found in patients with typical bacterial infections compared with patients with atypical or viral infections and those with infection of unknown etiology. LBP showed the highest discriminatory power with respect to the etiology of infection. Conclusions IL-6, IL-10 and LBP concentrations were increased in patients with a CRB-65 score of 3-4 and a severe course of CAP. The concentrations of IL-6 and IL-10 reflected the severity of disease in patients with CAP. The predictive power of IL-6, IL-10 and LBP for a severe course of pneumonia was lower than that of CRB-65. Typical bacterial pathogens induced the highest LBP, IL-6 and IL-10 concentrations.

2012-01-01

309

TRANSFORMATION OF ESCHERICHIA COLI K-12 WITH A HIGH COPY PLASMID ENCODING THE GREEN FLUORESCENT PROTEIN OF AEQUOREA VICTORIA RESULTS IN REDUCED FITNESS IN THE FORM OF SLOWER GROWTH  

Technology Transfer Automated Retrieval System (TEKTRAN)

The green fluorescent protein (GFP) of the jellyfish Aequorea victoria has been widely used as a biomarker in eucaryotic and prokaryotic cells and has potential for developing predictive models for behavior of single strains of bacteria in naturally contaminated food and environmental samples. Howe...

310

Gradual Soil Water Depletion Results in Reversible Changes of Gene Expression, Protein Profiles, Ecophysiology, and Growth Performance in Populus euphratica, a Poplar Growing in Arid Regions1[W][OA  

PubMed Central

The responses of Populus euphratica Oliv. plants to soil water deficit were assessed by analyzing gene expression, protein profiles, and several plant performance criteria to understand the acclimation of plants to soil water deficit. Young, vegetatively propagated plants originating from an arid, saline field site were submitted to a gradually increasing water deficit for 4 weeks in a greenhouse and were allowed to recover for 10 d after full reirrigation. Time-dependent changes and intensity of the perturbations induced in shoot and root growth, xylem anatomy, gas exchange, and water status were recorded. The expression profiles of approximately 6,340 genes and of proteins and metabolites (pigments, soluble carbohydrates, and oxidative compounds) were also recorded in mature leaves and in roots (gene expression only) at four stress levels and after recovery. Drought successively induced shoot growth cessation, stomatal closure, moderate increases in oxidative stress-related compounds, loss of CO2 assimilation, and root growth reduction. These effects were almost fully reversible, indicating that acclimation was dominant over injury. The physiological responses were paralleled by fully reversible transcriptional changes, including only 1.5% of the genes on the array. Protein profiles displayed greater changes than transcript levels. Among the identified proteins for which expressed sequence tags were present on the array, no correlation was found between transcript and protein abundance. Acclimation to water deficit involves the regulation of different networks of genes in roots and shoots. Such diverse requirements for protecting and maintaining the function of different plant organs may render plant engineering or breeding toward improved drought tolerance more complex than previously anticipated.

Bogeat-Triboulot, Marie-Beatrice; Brosche, Mikael; Renaut, Jenny; Jouve, Laurent; Le Thiec, Didier; Fayyaz, Payam; Vinocur, Basia; Witters, Erwin; Laukens, Kris; Teichmann, Thomas; Altman, Arie; Hausman, Jean-Francois; Polle, Andrea; Kangasjarvi, Jaakko; Dreyer, Erwin

2007-01-01

311

TGF-beta signaling proteins and the Protein Ontology  

Microsoft Academic Search

BACKGROUND: The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and\\/or post-translational

Cecilia N. Arighi; Hongfang Liu; Darren A. Natale; Winona C. Barker; Harold J. Drabkin; Judith A. Blake; Barry Smith; Cathy H. Wu

2009-01-01

312

Alternative Protein-Protein Interfaces Are Frequent Exceptions  

Microsoft Academic Search

The intricate molecular details of protein-protein interactions (PPIs) are crucial for function. Therefore, measuring the same interacting protein pair again, we expect the same result. This work measured the similarity in the molecular details of interaction for the same and for homologous protein pairs between different experiments. All scores analyzed suggested that different experiments often find exceptions in the interfaces

Tobias Hamp; Burkhard Rost

2012-01-01

313

The Effect of Ruboxistaurin on Visual Loss in Patients With Moderately Severe to Very Severe Nonproliferative Diabetic Retinopathy Initial Results of the Protein Kinase C Inhibitor Diabetic Retinopathy Study (PKC-DRS) Multicenter Randomized Clinical Trial  

Microsoft Academic Search

The purpose of this study was to evaluate the safety and efficacy of the orally administered protein kinase C (PKC) isoform-selective inhibitor ruboxistaurin (RBX) in sub- jects with moderately severe to very severe nonprolifera- tive diabetic retinopathy (NPDR). In this multicenter, double-masked, randomized, placebo-controlled study, 252 subjects received placebo or RBX (8, 16, or 32 mg\\/day) for 36-46 months. Patients

Paul Aiello

2005-01-01

314

The substitutions G245C and G245D in the Zn-binding pocket of the p53 protein result in differences of conformational flexibility of the DNA-binding domain  

Microsoft Academic Search

Transcription activation of the proapoptotic target genes is a means by which the p53 protein implements its function of tumor suppression. Zn is a known regulator of p53 binding to the target genes. We have previously obtained an evidence that amino acid substitutions in the p53 Zn-binding pocket can presumably exert an influence on Zn position in the Zn-p53 complex

S. S. Pintus; N. V. Ivanisenko; P. S. Demenkov; T. V. Ivanisenko; S. Ramachandran; N. A. Kolchanov; V. A. Ivanisenko

2012-01-01

315

Growth hormone deficiency in 'little' mice results in aberrant body composition, reduced insulin-like growth factor-I and insulin-like growth factor-binding protein-3 (IGFBP-3), but does not affect IGFBP-2, -1 or -4  

Microsoft Academic Search

Although GH is known to regulate somatic growth during development, its role in regulating adult body composition is less well defined. The effects of GH on individual body compartments--water, fat, protein and mineral--are achieved both by the action of GH and by a GH-induced hormone, insulin-like growth factor-I (IGF-I). We used a genetic model of GH deficiency, the 'little' (gene

L. R. Donahue; W. G. Beamer

1993-01-01

316

The roles of signaling by the p42\\/p44 mitogen-activated protein (MAP) kinase pathway; a potential route to radio- and chemo-sensitization of tumor cells resulting in the induction of apoptosis and loss of clonogenicity  

Microsoft Academic Search

During the last 10 years, multiple signal transduction pathways within cells have been discovered. These pathways have been linked to the regulation of many diverse cellular events such as proliferation, senescence, differentiation and apoptosis. This review will focus upon the many roles of signaling by the p42\\/p44 mitogen-activated protein (MAP) kinase pathway. Recent evidence suggests that signaling by the MAP

P Dent; WD Jarvis; MJ Birrer; PB Fisher; RK Schmidt-Ullrich; S Grant

1998-01-01

317

Association of the Herpes Simplex Virus Type 1 Us11 Gene Product with the Cellular Kinesin Light-Chain-Related Protein PAT1 Results in the Redistribution of Both Polypeptides  

Microsoft Academic Search

The herpes simplex virus type 1 (HSV-1) Us11 gene encodes a multifunctional double-stranded RNA (dsRNA)- binding protein that is expressed late in infection and packaged into the tegument layer of the virus particle. As a tegument component, Us11 associates with nascent capsids after its synthesis late in the infectious cycle and is delivered into newly infected cells at times prior

Louisa Benboudjema; Matthew Mulvey; Yuehua Gao; Sanjay W. Pimplikar; Ian Mohr

2003-01-01

318

Photoswitchable cyan fluorescent protein for protein tracking.  

PubMed

In recent years diverse photolabeling techniques using green fluorescent protein (GFP)-like proteins have been reported, including photoactivatable PA-GFP, photoactivatable protein Kaede, the DsRed 'greening' technique and kindling fluorescent proteins. So far, only PA-GFP, which is monomeric and gives 100-fold fluorescence contrast, could be applied for protein tracking. Here we describe a dual-color monomeric protein, photoswitchable cyan fluorescent protein (PS-CFP). PS-CFP is capable of efficient photoconversion from cyan to green, changing both its excitation and emission spectra in response to 405-nm light irradiation. Complete photoactivation of PS-CFP results in a 1,500-fold increase in the green-to-cyan fluorescence ratio, making it the highest-contrast monomeric photoactivatable fluorescent protein described to date. We used PS-CFP as a photoswitchable tag to study trafficking of human dopamine transporter in living cells. At moderate excitation intensities, PS-CFP can be used as a pH-stable cyan label for protein tagging and fluorescence resonance energy transfer applications. PMID:15502815

Chudakov, Dmitriy M; Verkhusha, Vladislav V; Staroverov, Dmitry B; Souslova, Ekaterina A; Lukyanov, Sergey; Lukyanov, Konstantin A

2004-10-24

319

Degradation of Mutant Proteins, Underlying \\  

Microsoft Academic Search

Many Mendelian monogenic disorders are caused by loss of the function of a single protein. This can result from rapid degradation of the mutant protein by cellular proteases, which reduces the steady-state concentration of the protein within the cell. The susceptibility of a protein to such proteolytic breakdown depends upon its kinetics of monomer folding and oligomer assembly and upon

Paula J. Waters

2001-01-01

320

Racemic protein crystallography.  

PubMed

Although natural proteins are chiral and are all of one "handedness," their mirror image forms can be prepared by chemical synthesis. This opens up new opportunities for protein crystallography. A racemic mixture of the enantiomeric forms of a protein molecule can crystallize in ways that natural proteins cannot. Recent experimental data support a theoretical prediction that this should make racemic protein mixtures highly amenable to crystallization. Crystals obtained from racemic mixtures also offer advantages in structure determination strategies. The relevance of these potential advantages is heightened by advances in synthetic methods, which are extending the size limit for proteins that can be prepared by chemical synthesis. Recent ideas and results in the area of racemic protein crystallography are reviewed. PMID:22443988

Yeates, Todd O; Kent, Stephen B H

2012-03-14

321

Prediction of Protein-protein Interactions Using Alpha Shape Modeling  

NASA Astrophysics Data System (ADS)

Protein-protein interactions play important roles in a lot of biological progress. Previous studies about protein-protein interactions were mainly based on sequence analysis. As more 3D structural information can be obtained from protein-protein complexes, structural analysis becomes feasible and useful. In this study, we used structural alignment to predict the protein-binding site and apply 3D alpha shape modeling to analyze the interface characteristics. We have developed a method for protein-protein interaction prediction. The result indicates good performance of our method in discriminating protein-binding structures from non-protein binding structures. Our method outperforms the previous methods based on the Matthews correlation coefficient.

Zhou, Weiqiang; Yan, Hong; Fan, Xiaodan; Hao, Quan

2011-06-01

322

Recombinant insulin-like growth factor-I (IGF-I) production in Super-CHO results in the expression of IGF-I receptor and IGF binding protein 3  

Microsoft Academic Search

Previously, we described the genetic construction Super- CHO, a cell line capable of autocrine growth under fully defined\\u000a protein-free conditions. Super-CHO cells constitutively express insulin growth factor-I (IGF-I) and transferrin in sufficient\\u000a amounts to support long-term, stable growth without the addition of exogenous growth factors, thus making it an ideal host\\u000a for the production of recombinant biopharmaceuticals. although IGF-I has

Noelle-Anne Sunstrom; Masood Baig; Louise Cheng; Derick Payet Sugyiono; Peter Gray

1998-01-01

323

Selenium adsorption on Mg–Al and Zn–Al layered double hydroxides  

Microsoft Academic Search

Layered double hydroxides (LDHs) have high anion exchange capacities that enhances their potential to remove anionic contaminants from aqueous systems. In this study, different Mg–Al and Zn–Al LDHs were synthesized by a coprecipitation method, with the products evaluated for their ability to adsorb selenite (SeO32?) and selenate (SeO42?). Results indicated the adsorption isotherm for SeO32? retention by Mg–Al and Zn–Al

Youwen You; George F Vance; Hongting Zhao

2001-01-01

324

The 3; 21 translocation in myelodysplasia results in a fusion transcript between the AML1 gene and the gene for EAP, a highly conserved protein associated with the Epstein-Barr virus small RNA EBER 1  

SciTech Connect

In the 8;21 translocation, the AML1 gene, located at chromosome band 21q22, is translocated to chromosome 8 (q22), where it is fused to the ETO gene and transcribed as a chimeric gene. AML1 is the human homolog of the recently cloned mouse gene pebp2[alpha]B, homologous to the DNA binding [alpha] subunit of the polyoma enhancer factor pebp2. AML1 is also involved in a translocation with chromosome 3 that is seen in patients with therapy-related acute myeloid leukemia and myelodysplastic syndrome and in chronic myelogenous leukemia in blast crisis. The authors have isolated a fusion cDNA clone from a t(3;21) library derived from a patient with therapy-related myelodysplastic syndrome; this clone contains sequences from AML1 and from EAP, which have now been localized to ban 3q26. EAP has previously been characterized as a highly expressed small nuclear protein of 128 residues (EBER 1) associated with Epstein-Barr virus small RNA. The fusion clone contains the DNA binding 5[prime] part of AML1 that is fused to ETO in the t(8;21) and, in addition, at least one other exon. The translocation replaces the last nine codons of AML1 with the last 96 codons of EAP. The fusion does not maintain the correct reading frame of EAP and may not lead to a functional chimeric protein. 23 refs., 6 figs.

Nucifora, G.; Begy, C.R.; Rowley, J.D. (Univ. of Chicago, IL (United States)); Erickson, P.; Drabkin, H.A. (Univ. of Colorado Health Sciences Center, Denver, CO (United States))

1993-08-15

325

Effect of intensive lifestyle intervention on C-reactive protein in subjects with impaired glucose tolerance and obesity. Results from a randomized controlled trial with 5-year follow-up.  

PubMed

C-reactive protein (CRP) is a marker of metabolic and cardiovascular disease. To study the effects of lifestyle on CRP in a high-risk population we conducted a randomized controlled trial on 200 obese subjects (BMI > 27 kg m(-2)) with impaired glucose tolerance recruited from primary care settings. They were randomized to either a 1-month stay at a wellness centre focusing on diet, exercise and stress management (intervention group) or 30-60 min of oral and written information on lifestyle intervention (control group). A significant reduction of CRP was observed after 1 month and 1 year in the intervention group. They reduced their CRP levels more than the control group 1 year after intervention (p=0.004). In conclusion lifestyle intervention can decrease CRP in obese individuals with impaired glucose tolerance for up to 1 year. Further research is needed to evaluate whether the CRP level reduction translates into a decreased risk for cardiovascular morbidity. PMID:19096961

Andersson, Jonas; Boman, Kurt; Jansson, Jan-Håkan; Nilsson, Torbjørn K; Lindahl, Bernt

2008-11-01

326

Physical Inactivity Is Correlated with Levels of Quantitative C-reactive Protein in Serum, Independent of Obesity: Results of the National Surveillance of Risk Factors of Non-communicable Diseases in Iran  

PubMed Central

Increased C-reactive protein (CRP) levels are associated with coronary heart disease, stroke, and mortality. Physical activity prevents cardiovascular disorders, which can be partly mediated through reducing inflammation, including serum CRP levels. The association of different intensities of physical activity, sedentary behaviours, and C-reactive protein (CRP) levels in serum was examined after adjustment for markers of adiposity, including waist-circumference and body mass index (BMI), in a large population-based study. Using data of the SuRFNCD-2007 study, a large national representative population-based study in Iran, the relationship between quantitative CRP concentrations in serum and physical activity was examined in a sample of 3,001 Iranian adults. The global physical activity questionnaire (GPAQ) was used for evaluating the duration and intensity of physical activity. Total physical activity (TPA) was calculated using metabolic equivalents for the intensity of physical activity. Quantitative CRP concentrations in serum were measured with high-sensitivity enzyme immunoassay. The CRP levels in serum significantly correlated with TPA (r=-0.103, p=0.021 in men and r=-0.114, p=0.017 in women), duration of vigorous-intensity activity (r=-0.122, p=0.019 in men and r=-0.109, p=0.026 in women), duration of moderate-intensity activity (r=-0.107, p=0.031 in men and r=-0.118, p=0.020 in women), and duration of sedentary behaviours (r=0.092, p=0.029 in men and r=0.101, p=0.022 in women) after multiple adjustments for age, area of residence, BMI, waist-circumference, smoking, and diabetes mellitus. Physical activity (of both moderate and vigorous intensity) is inversely associated with the quantitative CRP levels in serum, independent of diabetes and body adiposity.

Morteza, Afsaneh; Khalilzadeh, Omid; Anvari, Mehdi; Noshad, Sina; Zandieh, Ali; Nakhjavani, Manouchehr

2012-01-01

327

Physical inactivity is correlated with levels of quantitative C-reactive protein in serum, independent of obesity: results of the national surveillance of risk factors of non-communicable diseases in Iran.  

PubMed

Increased C-reactive protein (CRP) levels are associated with coronary heart disease, stroke, and mortality. Physical activity prevents cardiovascular disorders, which can be partly mediated through reducing inflammation, including serum CRP levels. The association of different intensities of physical activity, sedentary behaviours, and C-reactive protein (CRP) levels in serum was examined after adjustment for markers of adiposity, including waist-circumference and body mass index (BMI), in a large population-based study. Using data of the SuRFNCD-2007 study, a large national representative population-based study in Iran, the relationship between quantitative CRP concentrations in serum and physical activity was examined in a sample of 3,001 Iranian adults. The global physical activity questionnaire (GPAQ) was used for evaluating the duration and intensity of physical activity. Total physical activity (TPA) was calculated using metabolic equivalents for the intensity of physical activity. Quantitative CRP concentrations in serum were measured with high-sensitivity enzyme immunoassay. The CRP levels in serum significantly correlated with TPA (r=-0.103, p=0.021 in men and r=-0.114, p=0.017 in women), duration of vigorous-intensity activity (r=-0.122, p=0.019 in men and r=-0.109, p=0.026 in women), duration of moderate-intensity activity (r=-0.107, p=0.031 in men and r=-0.118, p=0.020 in women), and duration of sedentary behaviours (r=0.092, p=0.029 in men and r=0.101, p=0.022 in women) after multiple adjustments for age, area of residence, BMI, waist-circumference, smoking, and diabetes mellitus. Physical activity (of both moderate and vigorous intensity) is inversely associated with the quantitative CRP levels in serum, independent of diabetes and body adiposity. PMID:22524121

Esteghamati, Alireza; Morteza, Afsaneh; Khalilzadeh, Omid; Anvari, Mehdi; Noshad, Sina; Zandieh, Ali; Nakhjavani, Manouchehr

2012-03-01

328

Effect of sepsis on calcium uptake and content in skeletal muscle and regulation in vitro by calcium of total and myofibrillar protein breakdown in control and septic muscle: Results from a preliminary study  

SciTech Connect

Because high calcium concentration in vitro stimulates muscle proteolysis, calcium has been implicated in the pathogenesis of increased muscle breakdown in different catabolic conditions. Protein breakdown in skeletal muscle is increased during sepsis, but the effect of sepsis on muscle calcium uptake and content is not known. In this study the influence of sepsis, induced in rats by cecal ligation and puncture, on muscle calcium uptake and content was studied. Sixteen hours after cecal ligation and puncture or sham operation, calcium content of the extensor digitorum longus (EDL) and soleus (SOL) muscles was determined with an atomic absorption spectrometer. Calcium uptake was measured in intact SOL muscles incubated in the presence of calcium 45 (45Ca) for between 1 and 120 minutes. Total and myofibrillar protein breakdown was determined in SOL muscles, incubated in the presence of different calcium concentrations (0; 2.5; 5.0 mmol/L), and measured as release into the incubation medium of tyrosine and 3-methylhistidine (3-MH), respectively. Calcium content was increased by 51% (p less than 0.001) during sepsis in SOL and by 10% (p less than 0.05) in EDL muscle. There was no difference in 45Ca uptake between control and septic muscles during the early phase (1 to 5 minutes) of incubation. During more extended incubation (30 to 120 minutes), muscles from septic rats took up significantly more 45Ca than control muscles (p less than 0.05). Tyrosine release by incubated SOL muscles from control and septic rats was increased when calcium was added to the incubation medium, and at a calcium concentration of 2.5 mmol/L, the increase in tyrosine release was greater in septic than in control muscle. Addition of calcium to the incubation medium did not affect 3-MH release in control or septic muscle.

Benson, D.W.; Hasselgren, P.O.; Hiyama, D.T.; James, J.H.; Li, S.; Rigel, D.F.; Fischer, J.E.

1989-07-01

329

Protein Structure  

ERIC Educational Resources Information Center

|Individual students model specific amino acids and then, through dehydration synthesis, a class of students models a protein. The students clearly learn amino acid structure, primary, secondary, tertiary, and quaternary structure in proteins and the nature of the bonds maintaining a protein's shape. This activity is fun, concrete, inexpensive and…

Asmus, Elaine Garbarino

2007-01-01

330

Exploring NMR ensembles of calcium binding proteins: Perspectives to design inhibitors of protein-protein interactions  

PubMed Central

Background Disrupting protein-protein interactions by small organic molecules is nowadays a promising strategy employed to block protein targets involved in different pathologies. However, structural changes occurring at the binding interfaces make difficult drug discovery processes using structure-based drug design/virtual screening approaches. Here we focused on two homologous calcium binding proteins, calmodulin and human centrin 2, involved in different cellular functions via protein-protein interactions, and known to undergo important conformational changes upon ligand binding. Results In order to find suitable protein conformations of calmodulin and centrin for further structure-based drug design/virtual screening, we performed in silico structural/energetic analysis and molecular docking of terphenyl (a mimicking alpha-helical molecule known to inhibit protein-protein interactions of calmodulin) into X-ray and NMR ensembles of calmodulin and centrin. We employed several scoring methods in order to find the best protein conformations. Our results show that docking on NMR structures of calmodulin and centrin can be very helpful to take into account conformational changes occurring at protein-protein interfaces. Conclusions NMR structures of protein-protein complexes nowadays available could efficiently be exploited for further structure-based drug design/virtual screening processes employed to design small molecule inhibitors of protein-protein interactions.

2011-01-01

331

Interfacing protein lysine acetylation and protein phosphorylation: ancient modifications meet on ancient proteins.  

PubMed

Recognition that different protein covalent modifications can operate in concert to regulate a single protein has forced us to re-think the relationship between amino acid side chain modifications and protein function. Results presented by Tran et al. 2012 demonstrate the association of a protein phosphatase (PP2A) with a histone/lysine deacetylase (HDA14) on plant microtubules along with a histone/lysine acetyltransferase (ELP3). This finding reveals a regulatory interface between two prevalent covalent protein modifications, protein phosphorylation and acetylation, emphasizing the integrated complexity of post-translational protein regulation found in nature. PMID:22827947

Tran, Hue T; Uhrig, R Glen; Nimick, Mhairi; Moorhead, Greg B

2012-07-25

332

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: S100A10 (p11) Cellular Function: Producer Cell Type: Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Annexin 2A Method of Detection: Uniprot Accession #: P60903 Sequence/Peptide

333

Physics of protein motility and motor proteins  

NASA Astrophysics Data System (ADS)

Motor proteins are enzymatic molecules that transform chemical energy into mechanical motion and work. They are critically important for supporting various cellular activities and functions. In the last 15 years significant progress in understanding the functioning of motor proteins has been achieved due to revolutionary breakthroughs in single-molecule experimental techniques and strong advances in theoretical modelling. However, microscopic mechanisms of protein motility are still not well explained, and the collective efforts of many scientists are needed in order to solve these complex problems. In this special section the reader will find the latest advances on the difficult road to mapping motor proteins dynamics in various systems. Recent experimental developments have allowed researchers to monitor and to influence the activity of single motor proteins with a high spatial and temporal resolution. It has stimulated significant theoretical efforts to understand the non-equilibrium nature of protein motility phenomena. The latest results from all these advances are presented and discussed in this special section. We would like to thank the scientists from all over the world who have reported their latest research results for this special section. We are also grateful to the staff and editors of Journal of Physics: Condensed Matter for their invaluable help in handling all the administrative and refereeing activities. The field of motor proteins and protein motility is fast moving, and we hope that this collection of articles will be a useful source of information in this highly interdisciplinary area. Physics of protein motility and motor proteins contents Physics of protein motility and motor proteinsAnatoly B Kolomeisky Identification of unique interactions between the flexible linker and the RecA-like domains of DEAD-box helicase Mss116 Yuan Zhang, Mirkó Palla, Andrew Sun and Jung-Chi Liao The load dependence of the physical properties of a molecular motor Xianchao Meng, Min Yu and Yunxin Zhang Microtubule organization by kinesin motors and microtubule crosslinking protein MAP65 Joshua Pringle, Amutha Muthukumar, Amanda Tan, Laura Crankshaw, Leslie Conway and Jennifer L Ross Backtracking dynamics of RNA polymerase: pausing and error correction Mamata Sahoo and Stefan Klumpp First-passage problems in DNA replication: effects of template tension on stepping and exonuclease activities of a DNA polymerase motor Ajeet K Sharma and Debashish Chowdhury

Kolomeisky, Anatoly B.

2013-09-01

334

Protopia: a protein-protein interaction tool  

PubMed Central

Background Protein-protein interactions can be considered the basic skeleton for living organism self-organization and homeostasis. Impressive quantities of experimental data are being obtained and computational tools are essential to integrate and to organize this information. This paper presents Protopia, a biological tool that offers a way of searching for proteins and their interactions in different Protein Interaction Web Databases, as a part of a multidisciplinary initiative of our institution for the integration of biological data . Results The tool accesses the different Databases (at present, the free version of Transfac, DIP, Hprd, Int-Act and iHop), and results are expressed with biological protein names or databases codes and can be depicted as a vector or a matrix. They can be represented and handled interactively as an organic graph. Comparison among databases is carried out using the Uniprot codes annotated for each protein. Conclusion The tool locates and integrates the current information stored in the aforementioned databases, and redundancies among them are detected. Results are compatible with the most important network analysers, so that they can be compared and analysed by other world-wide known tools and platforms. The visualization possibilities help to attain this goal and they are especially interesting for handling multiple-step or complex networks.

Real-Chicharro, Alejandro; Ruiz-Mostazo, Ivan; Navas-Delgado, Ismael; Kerzazi, Amine; Chniber, Othmane; Sanchez-Jimenez, Francisca; Medina, Miguel Angel; Aldana-Montes, Jose F

2009-01-01

335

Toxic proteins inhibiting protein synthesis  

Microsoft Academic Search

Proteins which destroy various organisms are widely distributed in nature. Some of these proteins exert their toxic effect by inhibiting protein synthesis in a specific manner. Thus, Colicin E 3 kills susceptible bacteria by inhibiting ribosome function. It does this by splitting off a small fragment from the t6S ribosomal RNA thus inactivating the 30S ribosomal subunit. Diphtheria toxin inhibits

Sjur Olsnes; Norsk Hydro

1972-01-01

336

Therapeutic proteins.  

PubMed

Protein-based therapeutics are highly successful in clinic and currently enjoy unprecedented recognition of their potential. More than 100 genuine and similar number of modified therapeutic proteins are approved for clinical use in the European Union and the USA with 2010 sales of US$108 bln; monoclonal antibodies (mAbs) accounted for almost half (48%) of the sales. Based on their pharmacological activity, they can be divided into five groups: (a) replacing a protein that is deficient or abnormal; (b) augmenting an existing pathway; (c) providing a novel function or activity; (d) interfering with a molecule or organism; and (e) delivering other compounds or proteins, such as a radionuclide, cytotoxic drug, or effector proteins. Therapeutic proteins can also be grouped based on their molecular types that include antibody-based drugs, Fc fusion proteins, anticoagulants, blood factors, bone morphogenetic proteins, engineered protein scaffolds, enzymes, growth factors, hormones, interferons, interleukins, and thrombolytics. They can also be classified based on their molecular mechanism of activity as (a) binding non-covalently to target, e.g., mAbs; (b) affecting covalent bonds, e.g., enzymes; and (c) exerting activity without specific interactions, e.g., serum albumin. Most protein therapeutics currently on the market are recombinant and hundreds of them are in clinical trials for therapy of cancers, immune disorders, infections, and other diseases. New engineered proteins, including bispecific mAbs and multispecific fusion proteins, mAbs conjugated with small molecule drugs, and proteins with optimized pharmacokinetics, are currently under development. However, in the last several decades, there are no conceptually new methodological developments comparable, e.g., to genetic engineering leading to the development of recombinant therapeutic proteins. It appears that a paradigm change in methodologies and understanding of mechanisms is needed to overcome major challenges, including resistance to therapy, access to targets, complexity of biological systems, and individual variations. PMID:22735943

Dimitrov, Dimiter S

2012-01-01

337

Regulatory Submissions - Part VIII: New Protein Consultations  

Center for Food Safety and Applied Nutrition (CFSAN)

... Regulatory Submissions - Part VIII: New Protein Consultations. ... VIII. Information Specific to New Protein Consultation Submissions. ... More results from www.fda.gov/food/guidanceregulation/guidancedocumentsregulatoryinformation

338

High-Pressure Synthesis and Structure Determination of K6(SeO4)(SeO5), The First Potassium Orthoselenate(VI)  

SciTech Connect

The authors report on the first synthesis of a potassium orthoselenate(VI), K{sub 6}(SeO{sub 4})(SeO{sub 5}), and the structure determination from synchrotron powder diffraction data. The title compound crystallizes in the tetragonal space group P4{sub 1}2{sub 1}2 with a = 8.1259(1) {angstrom}, c = 17.4953(2) {angstrom}, V = 1155.21(2) {angstrom}{sup 3}, and Z = 4. Selenium displays two different complex anions, tetrahedral SeO{sub 4}{sup 2-} and trigonal-bipyramidal SeO{sub 5}{sup 4-}. When the formula is reduced to A{sub 3}B, the spatial arrangement of the constituting building units can be derived from the Li{sub 3}Bi type of structure.

Orosel,D.; Dinnebeier, R.; Jansen, M.

2006-01-01

339

Hydrophobic folding units at protein-protein interfaces: implications to protein folding and to protein-protein association.  

PubMed Central

A hydrophobic folding unit cutting algorithm, originally developed for dissecting single-chain proteins, has been applied to a dataset of dissimilar two-chain protein-protein interfaces. Rather than consider each individual chain separately, the two-chain complex has been treated as a single chain. The two-chain parsing results presented in this work show hydrophobicity to be a critical attribute of two-state versus three-state protein-protein complexes. The hydrophobic folding units at the interfaces of two-state complexes suggest that the cooperative nature of the two-chain protein folding is the outcome of the hydrophobic effect, similar to its being the driving force in a single-chain folding. In analogy to the protein-folding process, the two-chain, two-state model complex may correspond to the formation of compact, hydrophobic nuclei. On the other hand, the three-state model complex involves binding of already folded monomers, similar to the association of the hydrophobic folding units within a single chain. The similarity between folding entities in protein cores and in two-state protein-protein interfaces, despite the absence of some chain connectivities in the latter, indicates that chain linkage does not necessarily affect the native conformation. This further substantiates the notion that tertiary, non-local interactions play a critical role in protein folding. These compact, hydrophobic, two-chain folding units, derived from structurally dissimilar protein-protein interfaces, provide a rich set of data useful in investigations of the role played by chain connectivity and by tertiary interactions in studies of binding and of folding. Since they are composed of non-contiguous pieces of protein backbones, they may also aid in defining folding nuclei.

Tsai, C. J.; Nussinov, R.

1997-01-01

340

Correlation of C-reactive protein haplotypes with serum C-reactive protein level and response to anti-tumor necrosis factor therapy in UK rheumatoid arthritis patients: results from the Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate cohort  

PubMed Central

Introduction In many European countries, restrictions exist around the prescription of anti-tumor necrosis factor (anti-TNF) treatments for rheumatoid arthritis (RA). Eligibility and response to treatment is assessed by using the disease activity score 28 (DAS28) algorithm, which incorporates one of two inflammatory markers, erythrocyte sedimentation rate (ESR) or C-reactive protein (CRP). Although DAS28-CRP provides a more reliable measure of disease activity, functional variants exist within the CRP gene that affect basal CRP production. Therefore, we aimed to determine the relation between functional genetic variants at the CRP gene locus and levels of serum CRP in RA patients, and whether these variants, alone or in combination, are correlated with DAS28-CRP and change in DAS28-CRP after anti-TNF treatment. Methods DNA samples from the Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate (BRAGGSS) were genotyped for rs1205, rs1800947, and rs3091244 by using either TaqMan or the Sequenom MassARRAY iPLEX system. Estimated haplotypes were constructed for each sample by using the expectation maximization algorithm implemented in the haplo.stats package within the R statistical program. CRP values were log transformed, and the association between single nucleotide polymorphisms (SNPs), haplotypes of SNPs and baseline CRP, baseline DAS28-CRP, and change in DAS28-CRP were evaluated by using linear regression in STATA v.10. Results Baseline CRP measurements were available for 599 samples with 442 also having data 6 months after treatment with an anti-TNF. For these 442 samples, the study had > 80% power to detect a clinically meaningful difference of 0.6 DAS28 Units for an allele frequency of 5%. Estimated haplotype frequencies corresponded with previous frequencies reported in the literature. Overall, no significant association was observed between any of the markers investigated and baseline CRP levels. Further, CRP haplotypes did not correlate with baseline CRP (P = 0.593), baseline DAS28-CRP (P = 0.540), or change in DAS28-CRP after treatment with an anti-TNF over a 6-month period (P = 0.302). Conclusions Although CRP genotype may influence baseline CRP levels, in patients with very active disease, no such association was found. This suggests that genetic variation at the CRP locus does not influence DAS28-CRP, which may continue to be used in determining eligibility for and response to anti-TNF treatment, without adjusting for CRP genotype.

2012-01-01

341

Do REITs Manipulate Their Financial Results Around Seasoned Equity Offerings? Evidence from US Equity REITs  

Microsoft Academic Search

This study addresses two questions: Is there earnings management in the REIT industry around seasoned equity offerings (SEO)?\\u000a How is earnings management affected by financial and governance factors? Discretionary accruals methods are used to measure\\u000a earnings management. In addition, the difference between actual and calculated FFO is used to capture the potential FFO manipulation.\\u000a We examine how these manipulation measures

Yuan Wei Zhu; Seow Eng Ong; Wee Yong Yeo

2010-01-01

342

How Many Protein-Protein Interactions Types Exist in Nature?  

PubMed Central

Protein quaternary structure universe” refers to the ensemble of all protein-protein complexes across all organisms in nature. The number of quaternary folds thus corresponds to the number of ways proteins physically interact with other proteins. This study focuses on answering two basic questions: Whether the number of protein-protein interactions is limited and, if yes, how many different quaternary folds exist in nature. By all-to-all sequence and structure comparisons, we grouped the protein complexes in the protein data bank (PDB) into 3,629 families and 1,761 folds. A statistical model was introduced to obtain the quantitative relation between the numbers of quaternary families and quaternary folds in nature. The total number of possible protein-protein interactions was estimated around 4,000, which indicates that the current protein repository contains only 42% of quaternary folds in nature and a full coverage needs approximately a quarter century of experimental effort. The results have important implications to the protein complex structural modeling and the structure genomics of protein-protein interactions.

Mitra, Pralay; Zhang, Yang

2012-01-01

343

Principles of Protein-Protein Interactions  

Microsoft Academic Search

This review examines protein complexes in the Brookhaven Protein Databank to gain a better understanding of the principles governing the interactions involved in protein-protein recognition. The factors that influence the formation of protein-protein complexes are explored in four different types of protein-protein complexes--homodimeric proteins, heterodimeric proteins, enzyme-inhibitor complexes, and antibody-protein complexes. The comparison between the complexes highlights differences that reflect

Susan Jones; Janet M. Thornton

1996-01-01

344

Production of specific antibodies against protein A fusion proteins.  

PubMed Central

The gene for Staphylococcal protein A was fused to the coding sequence of bacterial beta-galactosidase, alkaline phosphatase and human insulin-like growth factor I (IGF-I). The fusion proteins, expressed in bacteria, were purified by affinity chromatography on IgG-Sepharose and antibodies were raised in rabbits. All three fusion proteins elicited specific antibodies against both the inserted protein sequences and the protein A moiety. In the case of IGF-I, the protein A moiety in the fusion protein may act as an adjuvant since native IGF-I alone is a poor immunogen. The results suggest that the protein A fusion system can be used for efficient antibody production against peptides or proteins expressed from cloned or synthetic genes. To facilitate such gene fusions a set of optimized vectors have been constructed. Images Fig. 2. Fig. 3. Fig. 4. Fig. 6.

Lowenadler, B; Nilsson, B; Abrahmsen, L; Moks, T; Ljungqvist, L; Holmgren, E; Paleus, S; Josephson, S; Philipson, L; Uhlen, M

1986-01-01

345

Plant proteins  

US Patent & Trademark Office Database

Adhesive proteins isolated from mature plants selected from the group consisting of macroalgae and microalgae, said proteins being characterized by the presence of at least one RGD or RGD-like or other adhesive recognition sequence, the absence of DOPA and hydroxyproline units, and by the fact that the proteins may be used by the plants in their natural state, for the purpose of adhesion to substrates.

1999-01-12

346

Human Plasma Protein C  

PubMed Central

Protein C is a vitamin K-dependent protein, which exists in bovine plasma as a precursor of a serine protease. In this study, protein C was isolated to homogeneity from human plasma by barium citrate adsorption and elution, ammonium sulfate fractionation, DEAE-Sephadex chromatography, dextran sulfate agarose chromatography, and preparative polyacrylamide gel electrophoresis. Human protein C (Mr = 62,000) contains 23% carbohydrate and is composed of a light chain (Mr = 21,000) and a heavy chain (Mr = 41,000) held together by a disulfide bond(s). The light chain has an amino-terminal sequence of Ala-Asn-Ser-Phe-Leu- and the heavy chain has an aminoterminal sequence of Asp-Pro-Glu-Asp-Gln. The residues that are identical to bovine protein C are underlined. Incubation of human protein C with human ?-thrombin at an enzyme to substrate weight ratio of 1:50 resulted in the formation of activated protein C, an enzyme with serine amidase activity. In the activation reaction, the apparent molecular weight of the heavy chain decreased from 41,000 to 40,000 as determined by gel electrophoresis in the presence of sodium dodecyl sulfate. No apparent change in the molecular weight of the light chain was observed in the activation process. The heavy chain of human activated protein C also contains the active-site serine residue as evidenced by its ability to react with radiolabeled diisopropyl fluorophosphate. Human activated protein C markedly prolongs the kaolin-cephalin clotting time of human plasma, but not that of bovine plasma. The amidolytic and anticoagulant activities of human activated protein C were completely obviated by prior incubation of the enzyme with diisopropyl fluorophosphate. These results indicate that human protein C, like its bovine counterpart, exists in plasma as a zymogen and is converted to a serine protease by limited proteolysis with attendant anticoagulant activity. Images

Kisiel, Walter

1979-01-01

347

Improved method for protein complex detection using bottleneck proteins  

PubMed Central

Background Detecting protein complexes is one of essential and fundamental tasks in understanding various biological functions or processes. Therefore accurate identification of protein complexes is indispensable. Methods For more accurate detection of protein complexes, we propose an algorithm which detects dense protein sub-networks of which proteins share closely located bottleneck proteins. The proposed algorithm is capable of finding protein complexes which allow overlapping with each other. Results We applied our algorithm to several PPI (Protein-Protein Interaction) networks of Saccharomyces cerevisiae and Homo sapiens, and validated our results using public databases of protein complexes. The prediction accuracy was even more improved over our previous work which used also bottleneck information of the PPI network, but showed limitation when predicting small-sized protein complex detection. Conclusions Our algorithm resulted in overlapping protein complexes with significantly improved F1 score over existing algorithms. This result comes from high recall due to effective network search, as well as high precision due to proper use of bottleneck information during the network search.

2013-01-01

348

Unscrambling an egg: protein disaggregation by AAA+ proteins  

Microsoft Academic Search

A protein quality control system, consisting of molecular chaperones and proteases, controls the folding status of proteins and prevents the aggregation of misfolded proteins by either refolding or degrading aggregation-prone species. During severe stress conditions this protection system can be overwhelmed by high substrate load, resulting in the formation of protein aggregates. In such emergency situations, Hsp104\\/ClpB becomes a key

Jimena Weibezahn; Bernd Bukau; Axel Mogk

2004-01-01

349

Network analysis of protein dynamics  

Microsoft Academic Search

The network paradigm is increasingly used to describe the topology and dynamics of complex systems. Here we review the results of the topological analysis of protein structures as molecular networks describing their small-world character, and the role of hubs and central network elements in governing enzyme activity, allosteric regulation, protein motor function, signal transduction and protein stability. We summarize available

Csaba Böde; István A. Kovács; Máté S. Szalayb; Robin Palotaib; Tamás Korcsmárosb; Péter Csermely

350

Terminating protein ubiquitination  

PubMed Central

Ubiquitination is a post-translational modification that generally directs proteins for degradation by the proteasome or by lysosomes. However, ubiquitination has been implicated in many other cellular processes, including transcriptional regulation, DNA repair, regulation of protein-protein interactions and association with ubiquitin-binding scaffolds. Ubiquitination is a dynamic process. Ubiquitin is added to proteins by E3 ubiquitin ligases as a covalent modification to one or multiple lysine residues as well as non-lysine amino acids. Ubiquitin itself contains seven lysines, each of which can also be ubiquitinated, leading to polyubiquitin chains that are best characterized for linkages occurring through K48 and K63. Ubiquitination can also be reversed by the action of deubiquitination enzymes (DUbs). Like E3 ligases, DUbs play diverse and critical roles in cells.1 Ubiquitin is expressed as a fusion protein, as a linear repeat or as a fusion to ribosomal subunits, and DUbs are necessary to liberate free ubiquitin, making them the first enzyme of the ubiquitin cascade. Proteins destined for degradation by the proteasome or by lysosomes are deubiquitinated prior to their degradation, which allows ubiquitin to be recycled by the cell, contributing to the steady-state pool of free ubiquitin. Proteins destined for degradation by lysosomes are also acted upon by both ligases and DUbs. Deubiquitination can also act as a means to prevent protein degradation, and many proteins are thought to undergo rounds of ubiquitination and deubiquitination, ultimately resulting in either the degradation or stabilization of those proteins. Despite years of study, examining the effects of the ubiquitination of proteins remains quite challenging. This is because the methods that are currently being employed to study ubiquitination are limiting. Here, we briefly examine current strategies to study the effects of ubiquitination and describe an additional novel approach that we have developed.

Stringer, Daniel K.; Piper, Robert C.

2011-01-01

351

Quantification of the influence of protein-protein interactions on adsorbed protein structure and bioactivity.  

PubMed

While protein-surface interactions have been widely studied, relatively little is understood at this time regarding how protein-surface interaction effects are influenced by protein-protein interactions and how these effects combine with the internal stability of a protein to influence its adsorbed-state structure and bioactivity. The objectives of this study were to develop a method to study these combined effects under widely varying protein-protein interaction conditions using hen egg-white lysozyme (HEWL) adsorbed on silica glass, poly(methyl methacrylate), and polyethylene as our model systems. In order to vary protein-protein interaction effects over a wide range, HEWL was first adsorbed to each surface type under widely varying protein solution concentrations for 2h to saturate the surface, followed by immersion in pure buffer solution for 15h to equilibrate the adsorbed protein layers in the absence of additionally adsorbing protein. Periodic measurements were made at selected time points of the areal density of the adsorbed protein layer as an indicator of the level of protein-protein interaction effects within the layer, and these values were then correlated with measurements of the adsorbed protein's secondary structure and bioactivity. The results from these studies indicate that protein-protein interaction effects help stabilize the structure of HEWL adsorbed on silica glass, have little influence on the structural behavior of HEWL on HDPE, and actually serve to destabilize HEWL's structure on PMMA. The bioactivity of HEWL on silica glass and HDPE was found to decrease in direct proportion to the degree of adsorption-induce protein unfolding. A direct correlation between bioactivity and the conformational state of adsorbed HEWL was less apparent on PMMA, thus suggesting that other factors influenced HEWL's bioactivity on this surface, such as the accessibility of HEWL's bioactive site being blocked by neighboring proteins or the surface itself. The developed methods provide an effective means to characterize the influence of protein-protein interaction effects and provide new molecular-level insights into how protein-protein interaction effects combine with protein-surface interaction and internal protein stability effects to influence the structure and bioactivity of adsorbed protein. PMID:23751416

Wei, Yang; Thyparambil, Aby A; Latour, Robert A

2013-05-13

352

Overexpression of KLF15 Transcription Factor in Adipocytes of Mice Results in Down-regulation of SCD1 Protein Expression in Adipocytes and Consequent Enhancement of Glucose-induced Insulin Secretion*  

PubMed Central

Krüppel-like factor 15 (KLF15), a member of the Krüppel-like factor family of transcription factors, has been found to play diverse roles in adipocytes in vitro. However, little is known of the function of KLF15 in adipocytes in vivo. We have now found that the expression of KLF15 in adipose tissue is down-regulated in obese mice, and we therefore generated adipose tissue-specific KLF15 transgenic (aP2-KLF15 Tg) mice to investigate the possible contribution of KLF15 to various pathological conditions associated with obesity in vivo. The aP2-KLF15 Tg mice manifest insulin resistance and are resistant to the development of obesity induced by maintenance on a high fat diet. However, they also exhibit improved glucose tolerance as a result of enhanced insulin secretion. Furthermore, this enhancement of insulin secretion was shown to result from down-regulation of the expression of stearoyl-CoA desaturase 1 (SCD1) in white adipose tissue and a consequent reduced level of oxidative stress. This is supported by the findings that restoration of SCD1 expression in white adipose tissue of aP2-KLF15 Tg mice exhibited increased oxidative stress in white adipose tissue and reduced insulin secretion with hyperglycemia. Our data thus provide an example of cross-talk between white adipose tissue and pancreatic ? cells mediated through modulation of oxidative stress.

Nagare, Tomoki; Sakaue, Hiroshi; Matsumoto, Michihiro; Cao, Yongheng; Inagaki, Kenjiro; Sakai, Mashito; Takashima, Yasuhiro; Nakamura, Kyoko; Mori, Toshiyuki; Okada, Yuko; Matsuki, Yasushi; Watanabe, Eijiro; Ikeda, Kazutaka; Taguchi, Ryo; Kamimura, Naomi; Ohta, Shigeo; Hiramatsu, Ryuji; Kasuga, Masato

2011-01-01

353

High throughput protein-protein interaction data: clues for the architecture of protein complexes  

Microsoft Academic Search

BACKGROUND: High-throughput techniques are becoming widely used to study protein-protein interactions and protein complexes on a proteome-wide scale. Here we have explored the potential of these techniques to accurately determine the constituent proteins of complexes and their architecture within the complex. RESULTS: Two-dimensional representations of the 19S and 20S proteasome, mediator, and SAGA complexes were generated and overlaid with high

James R Krycer; Chi Nam Ignatius Pang; Marc R Wilkins

2008-01-01

354

Essential Proteins Discovery from Weighted Protein Interaction Networks  

NASA Astrophysics Data System (ADS)

Identifying essential proteins is important for understanding the minimal requirements for cellular survival and development. Fast growth in the amount of available protein-protein interactions has produced unprecedented opportunities for detecting protein essentiality on network level. A series of centrality measures have been proposed to discover essential proteins based on network topology. However, most of them treat all interactions equally and are sensitive to false positives. In this paper, six standard centrality measures are redefined to be used in weighted network. A new method for weighing protein-protein interactions is proposed based on the combination of logistic regression-based model and function similarity. The experimental results on yeast network show that the weighting method can improve the performance of centrality measures considerably. More essential proteins are discovered by the weighted centrality measures than by the original centrality measures used in unweighted network. Even about 20% improvements are obtained from closeness centrality and subgraph centrality.

Li, Min; Wang, Jianxin; Wang, Huan; Pan, Yi

355

Proteins : paradigms of complexity /  

SciTech Connect

Proteins are the working machines of living systems. Directed by the DNA, of the order of a few hundred building blocks, selected from twenty different amino acids, are covalently linked into a linear polypeptide chain. In the proper environment, the chain folds into the working protein, often a globule of linear dimensions of a few nanometers. The biologist considers proteins units from which living systems are built. Many physical scientists look at them as systems in which the laws of complexity can be studied better than anywhere else. Some of the results of such studies will be sketched.

Frauenfelder, Hans,

2001-01-01

356

Protein based Block Copolymers  

PubMed Central

Advances in genetic engineering have led to the synthesis of protein-based block copolymers with control of chemistry and molecular weight, resulting in unique physical and biological properties. The benefits from incorporating peptide blocks into copolymer designs arise from the fundamental properties of proteins to adopt ordered conformations and to undergo self-assembly, providing control over structure formation at various length scales when compared to conventional block copolymers. This review covers the synthesis, structure, assembly, properties, and applications of protein-based block copolymers.

Rabotyagova, Olena S.; Cebe, Peggy; Kaplan, David L.

2011-01-01

357

High quality protein microarray using in situ protein purification  

PubMed Central

Background In the postgenomic era, high throughput protein expression and protein microarray technologies have progressed markedly permitting screening of therapeutic reagents and discovery of novel protein functions. Hexa-histidine is one of the most commonly used fusion tags for protein expression due to its small size and convenient purification via immobilized metal ion affinity chromatography (IMAC). This purification process has been adapted to the protein microarray format, but the quality of in situ His-tagged protein purification on slides has not been systematically evaluated. We established methods to determine the level of purification of such proteins on metal chelate-modified slide surfaces. Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays. Results Two slide surfaces were examined, chelated Cu2+ slides suspended on a polyethylene glycol (PEG) coating and chelated Ni2+ slides immobilized on a support without PEG coating. Using PEG-coated chelated Cu2+ slides, consistently higher purities of recombinant proteins were measured. An optimized wash buffer (PBST) composed of 10 mM phosphate buffer, 2.7 mM KCl, 140 mM NaCl and 0.05% Tween 20, pH 7.4, further improved protein purity levels. Using Escherichia coli cell lysates expressing 90 recombinant Streptococcus pneumoniae proteins, 73 proteins were successfully immobilized, and 66 proteins were in situ purified with greater than 90% purity. We identified several antigens among the in situ-purified proteins via assays with anti-S. pneumoniae rabbit antibodies and a human patient antiserum, as a demonstration project of large scale microarray-based immunoproteomics profiling. The methodology is compatible with higher throughput formats of in vivo protein expression, eliminates the need for resin-based purification and circumvents protein solubility and denaturation problems caused by buffer exchange steps and freeze-thaw cycles, which are associated with resin-based purification, intermittent protein storage and deposition on microarrays. Conclusion An optimized platform for in situ protein purification on microarray slides using His-tagged recombinant proteins is a desirable tool for the screening of novel protein functions and protein-protein interactions. In the context of immunoproteomics, such protein microarrays are complimentary to approaches using non-recombinant methods to discover and characterize bacterial antigens.

Kwon, Keehwan; Grose, Carissa; Pieper, Rembert; Pandya, Gagan A; Fleischmann, Robert D; Peterson, Scott N

2009-01-01

358

Protein Purification  

NSDL National Science Digital Library

This animation produced by WGBH and Digizyme, Inc. demonstrates how a protein of interest is isolated from other contents in a transformed bacterial cell—a process called purification—using a lab technique called hydrophobic interaction chromatography.

Foundation, Wgbh E.

2011-12-30

359

Protein kinase substrate identification on functional protein arrays  

PubMed Central

Background Over the last decade, kinases have emerged as attractive therapeutic targets for a number of different diseases, and numerous high throughput screening efforts in the pharmaceutical community are directed towards discovery of compounds that regulate kinase function. The emerging utility of systems biology approaches has necessitated the development of multiplex tools suitable for proteomic-scale experiments to replace lower throughput technologies such as mass spectroscopy for the study of protein phosphorylation. Recently, a new approach for identifying substrates of protein kinases has applied the miniaturized format of functional protein arrays to characterize phosphorylation for thousands of candidate protein substrates in a single experiment. This method involves the addition of protein kinases in solution to arrays of immobilized proteins to identify substrates using highly sensitive radioactive detection and hit identification algorithms. Results To date, the factors required for optimal performance of protein array-based kinase substrate identification have not been described. In the current study, we have carried out a detailed characterization of the protein array-based method for kinase substrate identification, including an examination of the effects of time, buffer compositions, and protein concentration on the results. The protein array approach was compared to standard solution-based assays for assessing substrate phosphorylation, and a correlation of greater than 80% was observed. The results presented here demonstrate how novel substrates for protein kinases can be quickly identified from arrays containing thousands of human proteins to provide new clues to protein kinase function. In addition, a pooling-deconvolution strategy was developed and applied that enhances characterization of specific kinase-substrate relationships and decreases reagent consumption. Conclusion Functional protein microarrays are an important new tool that enables multiplex analysis of protein phosphorylation, and thus can be utilized to identify novel kinase substrates. Integrating this technology with a systems biology approach to cell signalling will help uncover new layers in our understanding of this essential class of enzymes.

Meng, Lihao; Michaud, Gregory A; Merkel, Janie S; Zhou, Fang; Huang, Jing; Mattoon, Dawn R; Schweitzer, Barry

2008-01-01

360

Protein chainmail: catenated protein in viral capsids.  

PubMed

The capsid shells of bacteriophage HK97 and several other phages contain polypeptides that are covalently linked into complexes so large that they do not enter polyacrylamide gels after denaturation. The enormous apparent size of these protein complexes in HK97 derives from a novel protein topology. HK97 subunits cross-link via isopeptide bonds into oligomers that are closed rings of five or six members. However, polypeptides from neighboring pentamer and hexamer rings intertwine before the covalent cross-links form. As a result, adjacent protein rings catenate into a network similar to chainmail armor. In vitro linking and unlinking experiments provide strong support for the chainmail model, which explains the unusual properties of these bacteriophages and may apply to other macromolecular structures. PMID:9674427

Duda, R L

1998-07-10

361

Fullerene sorting proteins  

NASA Astrophysics Data System (ADS)

Proteins bind fullerenes. Hydrophobic pockets can accommodate a carbon cage either in full or in part. However, the identification of proteins able to discriminate between different cages is an open issue. Prediction of candidates able to perform this function is desirable and is achieved with an inverse docking procedure that accurately accounts for (i) van der Waals interactions between the cage and the protein surface, (ii) desolvation free energy, (iii) shape complementarity, and (iv) minimization of the number of steric clashes through conformational variations. A set of more than 1000 protein structures is divided into four categories that either select C60 or C70 (p-C60 or p-C70) and either accommodate the cages in the same pocket (homosaccic proteins, from ????o? meaning pocket) or in different pockets (heterosaccic proteins). In agreement with the experiments, the KcsA Potassium Channel is predicted to have one of the best performances for both cages. Possible ways to exploit the results and efficiently separate the two cages with proteins are also discussed.

Calvaresi, Matteo; Zerbetto, Francesco

2011-07-01

362

Heat shock proteins: molecular chaperones of protein biogenesis.  

PubMed Central

Heat shock proteins (Hsps) were first identified as proteins whose synthesis was enhanced by stresses such as an increase in temperature. Recently, several of the major Hsps have been shown to be intimately involved in protein biogenesis through a direct interaction with a wide variety of proteins. As a reflection of this role, these Hsps have been referred to as molecular chaperones. Hsp70s interact with incompletely folded proteins, such as nascent chains on ribosomes and proteins in the process of translocation from the cytosol into mitochondria and the endoplasmic reticulum. Hsp60 also binds to unfolded proteins, preventing aggregation and facilitating protein folding. Although less well defined, other Hsps such as Hsp90 also play important roles in modulating the activity of a number of proteins. The function of the proteolytic system is intertwined with that of molecular chaperones. Several components of this system, encoded by heat-inducible genes, are responsible for the degradation of abnormal or misfolded proteins. The budding yeast Saccharomyces cerevisiae has proven very useful in the analysis of the role of molecular chaperones in protein maturation, translocation, and degradation. In this review, results of experiments are discussed within the context of experiments with other organisms in an attempt to describe the current state of understanding of these ubiquitous and important proteins.

Craig, E A; Gambill, B D; Nelson, R J

1993-01-01

363

Protein Identification from Protein Product Ion Spectra.  

National Technical Information Service (NTIS)

Mass spectrometry is used to identify a protein of interest. The protein is first ionized then fragmented into protein product ion. Masses of the observed product ions are compared to product ion masses calculated in silico for database protein sequences ...

G. E. Reid J. M. Hogan S. A. McLuckey

2003-01-01

364

Macrophage inflammatory protein-1.  

PubMed

Macrophage inflammatory protein (MIP)-1alpha was identified 15 years ago as the first of now four members of the MIP-1 CC chemokine subfamily. These proteins termed CCL3 (MIP-1alpha), CCL4 (MIP-1beta), CCL9/10 (MIP-1delta), and CCL15 (MIP-1gamma) according to the revised nomenclature for chemokines are produced by many cells, particularly macrophages, dendritic cells, and lymphocytes. MIP-1 proteins, which act via G-protein-coupled cell surface receptors (CCR1, 3, 5), e.g. expressed by lymphocytes and monocytes/macrophages (MPhi), are best known for their chemotactic and proinflammatory effects but can also promote homoeostasis. The encouraging results of preclinical studies in murine models of inflammation, i.e. asthma, arthritis, or multiple sclerosis, have led to the development of potent CCR3 and 5 antagonists, some of which are currently being tested in first clinical trials. PMID:15203102

Maurer, M; von Stebut, E

2004-10-01

365

Dietary protein for muscle hypertrophy.  

PubMed

Skeletal muscle hypertrophy is a beneficial adaptation for many individuals. The metabolic basis for muscle hypertrophy is the balance between the rates of muscle protein synthesis (MPS) and muscle protein breakdown (MPB), i.e. net muscle protein balance (NMPB = MPS - MPB). Resistance exercise potentiates the response of muscle to protein ingestion for up to 24 h following the exercise bout. Ingestion of many protein sources in temporal proximity (immediately before and at least within 24 h after) to resistance exercise increases MPS resulting in positive NMPB. Moreover, it seems that not all protein sources are equal in their capacity to stimulate MPS. Studies suggest that ?20-25 g of a high-quality protein maximizes the response of MPS following resistance exercise, at least in young, resistance-trained males. However, more protein may be required to maximize the response of MPS with less than optimal protein sources and/or with older individuals. Ingestion of carbohydrate with protein does not seem to increase the response of MPS following exercise. The response of inactive muscle to protein ingestion is impaired. Ingestion of a high-quality protein within close temporal proximity of exercise is recommended to maximize the potential for muscle growth. PMID:23899756

Tipton, Kevin D; Phillips, Stuart M

2013-07-25

366

Evolution of chloroplast J proteins.  

PubMed

Hsp70 chaperones are involved in multiple biological processes and are recruited to specific processes by designated J domain-containing cochaperones, or J proteins. To understand the evolution and functions of chloroplast Hsp70s and J proteins, we identified the Arabidopsis chloroplast J protein constituency using a combination of genomic and proteomic database searches and individual protein import assays. We show that Arabidopsis chloroplasts have at least 19 J proteins, the highest number of confirmed J proteins for any organelle. These 19 J proteins are classified into 11 clades, for which cyanobacteria and glaucophytes only have homologs for one clade, green algae have an additional three clades, and all the other 7 clades are specific to land plants. Each clade also possesses a clade-specific novel motif that is likely used to interact with different client proteins. Gene expression analyses indicate that most land plant-specific J proteins show highly variable expression in different tissues and are down regulated by low temperatures. These results show that duplication of chloroplast Hsp70 in land plants is accompanied by more than doubling of the number of its J protein cochaperones through adding new J proteins with novel motifs, not through duplications within existing families. These new J proteins likely recruit chloroplast Hsp70 to perform tissue specific functions related to biosynthesis rather than to stress resistance. PMID:23894646

Chiu, Chi-Chou; Chen, Lih-Jen; Su, Pai-Hsiang; Li, Hsou-min

2013-07-23

367

Dielectric response of hydrated proteins  

NASA Astrophysics Data System (ADS)

We study dipolar susceptibility of hydrated proteins, representing the average dipole moment induced at the hydrated protein by a uniform external field. This parameter shows remarkable variation among proteins. We find a negative value of the dipolar susceptibility for some proteins, which implies a dia-electric dipolar response and negative dielectrophoresis. Such proteins, even though carrying significant permanent dipole moments, repel from the electric field. This outcome is the result of a negative cross-correlation between the protein and water dipoles, compensating for the positive variance of the intrinsic protein dipole in the overall dipolar susceptibility. We therefore suggest that the dipolar response of proteins in solution is strongly affected by the coupling of the protein surface charge to the hydration water. The protein-water dipolar cross-correlations are long-ranged, extending approximately 2 nm from the protein surface into the bulk. A similar correlation length of about 1 nm is found for the electrostatic potential. The model is applied to the analysis of light absorption by protein solutions in the THz window of radiation. Here we also find significant deviations of the absorption coefficient from the predictions of traditional theories.

Matyushov, Dmitry

2013-03-01

368

Subchronic toxicity evaluation of potato protein isolates  

Microsoft Academic Search

The protein content of potatoes has a high nutritional value on par with eggs and soybeans. As a result, processed potato protein isolates may have commercial value for addition to other food products to increase protein content A manufacturing process to produce total potato (TP), as well as low (LMW) and high molecular (HMW) weight, protein isolates as food ingredients.

B. Lynch; R. R. Simon; F. M. van Otterdijk; H. H. Emmen; M. L. F. Giuseppin; C. Kemme-Kroonsberg

369

Modelling of proteins in membranes.  

PubMed

This review describes some recent theories and simulations of mesoscopic and microscopic models of lipid membranes with embedded or attached proteins. We summarize results supporting our understanding of phenomena for which the activities of proteins in membranes are expected to be significantly affected by the lipid environment. Theoretical predictions are pointed out, and compared to experimental findings, if available. Among others, the following phenomena are discussed: interactions of interfacially adsorbed peptides, pore-forming amphipathic peptides, adsorption of charged proteins onto oppositely charged lipid membranes, lipid-induced tilting of proteins embedded in lipid bilayers, protein-induced bilayer deformations, protein insertion and assembly, and lipid-controlled functioning of membrane proteins. PMID:16620797

Sperotto, Maria Maddalena; May, Sylvio; Baumgaertner, Artur

2006-03-27

370

Does Asymmetric Information Affect SEOs and M&A Activity? Evidence from Corporate Pension Plans  

Microsoft Academic Search

We present evidence of the impact of asymmetric information on firms' likelihood to issue equity and to be acquired. We argue that the existence of corporate sponsored defined benefit pension liabilities, and their magnitude, are a source of risk for buyers of the firm's shares. We show that firms that sponsor DB pension plans and have a large pension deficit

João F. Cocco; Paolo F. Volpin

371

Ab initio Studies of the Phase Transitions in K2SeO4.  

National Technical Information Service (NTIS)

An ab initio model is developed for the potentials in ionic molecular solids in which the electron covalenc within the molecular ions substantially affects the interionic interactions. By treating the intermolecular and intramolecular interactions on the ...

H. M. Lu J. R. Hardy

1990-01-01

372

Unscrambling an egg: protein disaggregation by AAA+ proteins  

PubMed Central

A protein quality control system, consisting of molecular chaperones and proteases, controls the folding status of proteins and prevents the aggregation of misfolded proteins by either refolding or degrading aggregation-prone species. During severe stress conditions this protection system can be overwhelmed by high substrate load, resulting in the formation of protein aggregates. In such emergency situations, Hsp104/ClpB becomes a key player for cell survival, as it has the extraordinary capacity to rescue proteins from an aggregated state in cooperation with an Hsp70 chaperone system. The ring-forming Hsp104/ClpB chaperone belongs to the AAA+ protein superfamily, which in general drives the assembly and disassembly of protein complexes by ATP-dependent remodelling of protein substrates. A disaggregation activity was also recently attributed to other eubacterial AAA+ proteins, while such an activity has not yet been identified in mammalian cells. In this review, we report on new insights into the mechanism of protein disaggregation by AAA+ proteins, suggesting that these chaperones act as molecular crowbars or ratchets.

Weibezahn, Jimena; Bukau, Bernd; Mogk, Axel

2004-01-01

373

Protein intrinsic disorder toolbox for comparative analysis of viral proteins  

PubMed Central

To examine the usefulness of protein disorder predictions as a tool for the comparative analysis of viral proteins, a relational database has been constructed. The database includes proteins from influenza A and HIV-related viruses. Annotations include viral protein sequence, disorder prediction, structure, and function. Location of each protein within a virion, if known, is also denoted. Our analysis reveals a clear relationship between proximity to the RNA core and the percentage of predicted disordered residues for a set of influenza A virus proteins. Neuraminidases (NA) and hemagglutinin (HA) of major influenza A pandemics tend to pair in such a way that both proteins tend to be either ordered-ordered or disordered-disordered by prediction. This may be the result of these proteins evolving from being lipid-associated. High abundance of intrinsic disorder in envelope and matrix proteins from HIV-related viruses likely represents a mechanism where HIV virions can escape immune response despite the availability of antibodies for the HIV-related proteins. This exercise provides an example showing how the combined use of intrinsic disorder predictions and relational databases provides an improved understanding of the functional and structural behaviour of viral proteins.

Goh, Gerard Kian-Meng; Dunker, A Keith; Uversky, Vladimir N

2008-01-01

374

LEA proteins prevent protein aggregation due to water stress.  

PubMed

LEA (late embryogenesis abundant) proteins in both plants and animals are associated with tolerance to water stress resulting from desiccation and cold shock. However, although various functions of LEA proteins have been proposed, their precise role has not been defined. Recent bioinformatics studies suggest that LEA proteins might behave as molecular chaperones, and the current study was undertaken to test this hypothesis. Recombinant forms of AavLEA1, a group 3 LEA protein from the anhydrobiotic nematode Aphelenchus avenae, and Em, a group 1 LEA protein from wheat, have been subjected to functional analysis. Heat-stress experiments with citrate synthase, which is susceptible to aggregation at high temperatures, suggest that LEA proteins do not behave as classical molecular chaperones, but they do exhibit a protective, synergistic effect in the presence of the so-called chemical chaperone, trehalose. In contrast, both LEA proteins can independently protect citrate synthase from aggregation due to desiccation and freezing, in keeping with a role in water-stress tolerance; similar results were obtained with lactate dehydrogenase. This is the first evidence of anti-aggregation activity of LEA proteins due to water stress. Again, a synergistic effect of LEA and trehalose was observed, which is significant given that non-reducing disaccharides are known to accumulate during dehydration in plants and nematodes. A model is proposed whereby LEA proteins might act as a novel form of molecular chaperone, or 'molecular shield', to help prevent the formation of damaging protein aggregates during water stress. PMID:15631617

Goyal, Kshamata; Walton, Laura J; Tunnacliffe, Alan

2005-05-15

375

Cotton and Protein Interactions  

SciTech Connect

The adsorbent properties of important wound fluid proteins and cotton cellulose are reviewed. This review focuses on the adsorption of albumin to cotton-based wound dressings and some chemically modified derivatives targeted for chronic wounds. Adsorption of elastase in the presence of albumin was examined as a model to understand the interactive properties of these wound fluid components with cotton fibers. In the chronic non-healing wound, elastase appears to be over-expressed, and it digests tissue and growth factors, interfering with the normal healing process. Albumin is the most prevalent protein in wound fluid, and in highly to moderately exudative wounds, it may bind significantly to the fibers of wound dressings. Thus, the relative binding properties of both elastase and albumin to wound dressing fibers are of interest in the design of more effective wound dressings. The present work examines the binding of albumin to two different derivatives of cotton, and quantifies the elastase binding to the same derivatives following exposure of albumin to the fiber surface. An HPLC adsorption technique was employed coupled with a colorimetric enzyme assay to quantify the relative binding properties of albumin and elastase to cotton. The results of wound protein binding are discussed in relation to the porosity and surface chemistry interactions of cotton and wound proteins. Studies are directed to understanding the implications of protein adsorption phenomena in terms of fiber-protein models that have implications for rationally designing dressings for chronic wounds.

Goheen, Steven C.; Edwards, J. V.; Rayburn, Alfred R.; Gaither, Kari A.; Castro, Nathan J.

2006-06-30

376

Identifying Protein-Protein interactions in Biomedical publications  

Microsoft Academic Search

The paper describes the approaches and the results of our participation in the protein-protein interaction (PPI) extraction task (sub-tasks 1 to 3) of the BioCreative II challenge.1 The core of our approach is to analyse the logical forms of those sentences which contain the mentioning of relevant protein names, and to rank the sentences from which the relations where extracted

Alejandro Figueroa; Gunter Neumann

377

Protein constituents of the eggshell: eggshell-specific matrix proteins  

Microsoft Academic Search

In this article, we review the results of recent proteomic and genomic analyses of eggshell matrix proteins and draw attention\\u000a to the impact of these data on current understanding of eggshell formation and function. Eggshell-specific matrix proteins\\u000a from avian (ovocleidins and ovocalyxins) and non-avian (paleovaterin) shells are discussed. Two possible roles for eggshell-specific\\u000a matrix proteins have been proposed; both reflect

Megan L. H. Rose; Maxwell T. Hincke

2009-01-01

378

Intercomparison of streamflow postprocessing techniques: first results of a HEPEX community experiment  

NASA Astrophysics Data System (ADS)

Hydrological ensemble forecasts comprise uncertainties originating from multiple sources. Often, they are characterized by biases in the mean, spread or higher moments of their associated probability distributions. These biases may be unconditional or conditional upon several factors, such as the magnitude of the observed or forecast variable, season, or forecast lead time, and may be manifest in either the volume or timing of streamflow. The different biases may be more or less critical for practical applications ranging from flood prediction to reservoir regulation, which often require (or assume) unbiasedness. To some degree, statistical post-processors can correct for these biases. They include a broad range of statistical techniques that may target particular types of bias or a range of unconditional and conditional biases. For example, when viewed conditionally upon the forecast variable, a common aim is to produce sharp forecasts that are also reliable, i.e. have an appropriate amount of spread to accommodate forecast errors. Post-processing techniques also vary in whether they lump together all sources of bias and uncertainty or address the meteorological and hydrologic uncertainties separately. In the last couple of decades, several postprocessing techniques have been developed and tested for hydrological prediction. Applied to single-valued (deterministic) predictions as well as to multi-scenario (ensemble or multi-model) predictions for short- to long-term forecasts, they have however rarely been examined together, within an extensive and coherent inter-comparison framework. In order to promote a better understanding of the strengths and weaknesses of several of those techniques, and whether the choice of technique really matters, an inter-comparison was initiated in June 2012 under the auspices of the Hydrologic Ensemble Prediction Experiment HEPEX (van Andel et al., 2013). This experiment is fully described at http://www.hepex.org/. The inter-comparison comprises several phases. The first phase is concerned with estimating the hydrologic uncertainties separately from the forcing uncertainties. Verification of the first results submitted by several participants is performed with the Ensemble Verification System (EVS; Brown et al., 2010) and the scope for assessing the strengths and weaknesses of different post-processors with multiple verification metrics is discussed. Brown J.D., J. Demargne, D-J. Seo, and Y. Liu (2010) The Ensemble Verification System (EVS): a software tool for verifying ensemble forecasts of hydrometeorological and hydrologic variables at discrete locations. Environmental Modelling and Software, 25(7): 854-872. van Andel, S. J., A. Weerts, J. Schaake, and K. Bogner (2013) Post-processing hydrological ensemble predictions intercomparison experiment. Hydrological Processes, Special Issue: Hydrological Ensemble Prediction Systems (HEPS), 27(1): 158-161.

Brown, James; Ramos, Maria-Helena; Voisin, Nathalie

2013-04-01

379

Colorimetric protein assay techniques.  

PubMed

There has been an increase in the number of colorimetric assay techniques for the determination of protein concentration over the past 20 years. This has resulted in a perceived increase in sensitivity and accuracy with the advent of new techniques. The present review considers these advances with emphasis on the potential use of such technologies in the assay of biopharmaceuticals. The techniques reviewed include Coomassie Blue G-250 dye binding (the Bradford assay), the Lowry assay, the bicinchoninic acid assay and the biuret assay. It is shown that each assay has advantages and disadvantages relative to sensitivity, ease of performance, acceptance in the literature, accuracy and reproducibility/coefficient of variation/laboratory-to-laboratory variation. A comparison of the use of several assays with the same sample population is presented. It is suggested that the most critical issue in the use of a chromogenic protein assay for the characterization of a biopharmaceutical is the selection of a standard for the calibration of the assay; it is crucial that the standard be representative of the sample. If it is not possible to match the standard with the sample from the perspective of protein composition, then it is preferable to use an assay that is not sensitive to the composition of the protein such as a micro-Kjeldahl technique, quantitative amino acid analysis or the biuret assay. In a complex mixture it might be inappropriate to focus on a general method of protein determination and much more informative to use specific methods relating to the protein(s) of particular interest, using either specific assays or antibody-based methods. The key point is that whatever method is adopted as the 'gold standard' for a given protein, this method needs to be used routinely for calibration. PMID:10075906

Sapan, C V; Lundblad, R L; Price, N C

1999-04-01

380

The comparative genomics of protein interactions.  

PubMed

The detection of gene fusion events across genomes can be used for the prediction of functional associations of proteins, including physical interactions or complex formation. These predictions are obtained by the detection of similarity for pairs of 'component' proteins to 'composite' proteins. Since the amount of composite proteins is limited in nature, we augment this set by creating artificial fusion proteins from experimentally determined protein interacting pairs. The goal is to study the extent of protein interaction partners with increasing phylogenetic distance, using an automated method. We have thus detected component pairs within seven entire genome sequences of similar size, using artificially generated composite proteins that have been shown to interact experimentally. Our results indicate that protein interactions are not conserved over large phylogenetic distances. In addition, we provide a set of predictions for functionally associated proteins across seven species using experimental information and demonstrate the applicability of fusion analysis for the comparative genomics of protein interactions. PMID:18546511

Peregrín-Alvarez, José M; Ouzounis, Christos A

2007-01-01

381

Utilizing protein networks to determine novel annotations  

NASA Astrophysics Data System (ADS)

Proteins are a key element of life because they are involved in every metabolic process, yet a majority of proteins remain unannotated. Current chemical and physical annotation methods are inaccurate, inefficient, or expensive. Without proper annotation, understanding of organisms' metabolic pathways is limited. Based on the hypothesis that proteins with similar primary structures have similar characteristics, we theorize that a method for protein annotation can be developed using protein networking, which was previously thought to be useful in determining the evolutionary paths of proteins. A large, diverse database of proteins is used to connect protein fragments by using a preset identity threshold. With this method, unknown proteins are connected to known ones. By observing the number of links to proteins with annotated functions, a likely annotation candidate will be reached. This procedure can potentially facilitate the process of finding more accurate annotations. We have used and validated this approach to annotate putative uncharacterized proteins. Results will be presented at the conference.

Shiao, Kenneth; Feng, Jerry; Doan, Tina; Gorin, Andrey

2011-10-01

382

Predicting Protein Interactions by Brownian Dynamics Simulations  

PubMed Central

We present a newly adapted Brownian-Dynamics (BD)-based protein docking method for predicting native protein complexes. The approach includes global BD conformational sampling, compact complex selection, and local energy minimization. In order to reduce the computational costs for energy evaluations, a shell-based grid force field was developed to represent the receptor protein and solvation effects. The performance of this BD protein docking approach has been evaluated on a test set of 24 crystal protein complexes. Reproduction of experimental structures in the test set indicates the adequate conformational sampling and accurate scoring of this BD protein docking approach. Furthermore, we have developed an approach to account for the flexibility of proteins, which has been successfully applied to reproduce the experimental complex structure from the structure of two unbounded proteins. These results indicate that this adapted BD protein docking approach can be useful for the prediction of protein-protein interactions.

Meng, Xuan-Yu; Xu, Yu; Zhang, Hong-Xing; Mezei, Mihaly; Cui, Meng

2012-01-01

383

Interactions between geminivirus replication proteins.  

PubMed

Geminiviruses are small DNA viruses that replicate in the nuclei of infected plant cells. The closely related geminiviruses tomato golden mosaic virus and bean golden mosaic virus each encode a protein, AL1, that catalyzes the initiation of rolling-circle replication. Both viruses also specify a second replication protein, AL3, that greatly enhances the level of viral DNA accumulation. Using recombinant proteins produced in a baculovirus expression system, we showed that AL1 copurifies with a protein fusion of glutathione S-transferase (GST) and AL1, independent of the GST domain. Similarly, authentic AL3 cofractionates with a GST-AL3 fusion protein. These results demonstrated that both AL1 and AL3 form oligomers. Immunoprecipitation of protein extracts from insect cells expressing both AL1 and AL3 showed that the two proteins also complex with each other. None of the protein interactions displayed virus specificity; the tomato and bean golden mosaic virus proteins complexed with each other. The addition of heterologous replication proteins had no effect on the efficiency of geminivirus replication in transient-replication assays, suggesting that heteroprotein complexes might be functional. The significance of these protein interactions is discussed with respect to geminivirus replication in plant cells. PMID:8794317

Settlage, S B; Miller, A B; Hanley-Bowdoin, L

1996-10-01

384

Interactions between geminivirus replication proteins.  

PubMed Central

Geminiviruses are small DNA viruses that replicate in the nuclei of infected plant cells. The closely related geminiviruses tomato golden mosaic virus and bean golden mosaic virus each encode a protein, AL1, that catalyzes the initiation of rolling-circle replication. Both viruses also specify a second replication protein, AL3, that greatly enhances the level of viral DNA accumulation. Using recombinant proteins produced in a baculovirus expression system, we showed that AL1 copurifies with a protein fusion of glutathione S-transferase (GST) and AL1, independent of the GST domain. Similarly, authentic AL3 cofractionates with a GST-AL3 fusion protein. These results demonstrated that both AL1 and AL3 form oligomers. Immunoprecipitation of protein extracts from insect cells expressing both AL1 and AL3 showed that the two proteins also complex with each other. None of the protein interactions displayed virus specificity; the tomato and bean golden mosaic virus proteins complexed with each other. The addition of heterologous replication proteins had no effect on the efficiency of geminivirus replication in transient-replication assays, suggesting that heteroprotein complexes might be functional. The significance of these protein interactions is discussed with respect to geminivirus replication in plant cells.

Settlage, S B; Miller, A B; Hanley-Bowdoin, L

1996-01-01

385

Quantification of Protein Solutions with Trinitrobenzenesulfonic Acid  

Microsoft Academic Search

solutions of protein. The trinitrophenyl protein-sulfite corn plexes resulting from reaction of TNBS with protein in the presence of sulfite are highly colored and exhibit maximum spectral absorbance at 420 nm. The TNBS protein-sulfite complex is formed by a simple two.stage condensation and complexation reaction. Protein in concentrations as low as 20 JLgmay be detected by the reaction. The method

Jesse F. Goodwin; Siu-Ying Choi

386

Arbitrary protein-protein docking targets biologically relevant interfaces  

PubMed Central

Background Protein-protein recognition is of fundamental importance in the vast majority of biological processes. However, it has already been demonstrated that it is very hard to distinguish true complexes from false complexes in so-called cross-docking experiments, where binary protein complexes are separated and the isolated proteins are all docked against each other and scored. Does this result, at least in part, reflect a physical reality? False complexes could reflect possible nonspecific or weak associations. Results In this paper, we investigate the twilight zone of protein-protein interactions, building on an interesting outcome of cross-docking experiments: false complexes seem to favor residues from the true interaction site, suggesting that randomly chosen partners dock in a non-random fashion on protein surfaces. Here, we carry out arbitrary docking of a non-redundant data set of 198 proteins, with more than 300 randomly chosen "probe" proteins. We investigate the tendency of arbitrary partners to aggregate at localized regions of the protein surfaces, the shape and compositional bias of the generated interfaces, and the potential of this property to predict biologically relevant binding sites. We show that the non-random localization of arbitrary partners after protein-protein docking is a generic feature of protein structures. The interfaces generated in this way are not systematically planar or curved, but tend to be closer than average to the center of the proteins. These results can be used to predict biological interfaces with an AUC value up to 0.69 alone, and 0.72 when used in combination with evolutionary information. An appropriate choice of random partners and number of docking models make this method computationally practical. It is also noted that nonspecific interfaces can point to alternate interaction sites in the case of proteins with multiple interfaces. We illustrate the usefulness of arbitrary docking using PEBP (Phosphatidylethanolamine binding protein), a kinase inhibitor with multiple partners. Conclusions An approach using arbitrary docking, and based solely on physical properties, can successfully identify biologically pertinent protein interfaces.

2012-01-01

387

Protein Kinases  

NSDL National Science Digital Library

This Teaching Resource provides lecture notes and slides for a class covering the structure and function of protein kinases and is part of the course "Cell Signaling Systems: A Course for Graduate Students." The lecture begins with a discussion of the genomics and evolutionary relationships among kinases and then proceeds to describe the structure-function relationships of specific kinases, the molecular mechanisms underlying substrate specificity, and selected issues in regulation of kinase activity.

Avrom Caplan (Mount Sinai School of Medicine;Department of Pharmacology and Biological Chemistry REV)

2005-02-22

388

Breakfast Proteins  

NSDL National Science Digital Library

In this activity, learners construct a cereal chain as a model of how proteins are made in the cell. Learners build their chain off of an initial template which represents a single copy of DNA and hand-written notes, replicating the process of transcription and translation. In this model, the letters of the chain correspond to the colors of the cereal (not the amino acids).

Yu, Julie

2009-01-01

389

Protein damage, repair and proteolysis.  

PubMed

Proteins are continuously affected by various intrinsic and extrinsic factors. Damaged proteins influence several intracellular pathways and result in different disorders and diseases. Aggregation of damaged proteins depends on the balance between their generation and their reversal or elimination by protein repair systems and degradation, respectively. With regard to protein repair, only few repair mechanisms have been evidenced including the reduction of methionine sulfoxide residues by the methionine sulfoxide reductases, the conversion of isoaspartyl residues to L-aspartate by L-isoaspartate methyl transferase and deglycation by phosphorylation of protein-bound fructosamine by fructosamine-3-kinase. Protein degradation is orchestrated by two major proteolytic systems, namely the lysosome and the proteasome. Alteration of the function for both systems has been involved in all aspects of cellular metabolic networks linked to either normal or pathological processes. Given the importance of protein repair and degradation, great effort has recently been made regarding the modulation of these systems in various physiological conditions such as aging, as well as in diseases. Genetic modulation has produced promising results in the area of protein repair enzymes but there are not yet any identified potent inhibitors, and, to our knowledge, only one activating compound has been reported so far. In contrast, different drugs as well as natural compounds that interfere with proteolysis have been identified and/or developed resulting in homeostatic maintenance and/or the delay of disease progression. PMID:23107776

Chondrogianni, Niki; Petropoulos, Isabelle; Grimm, Stefanie; Georgila, Konstantina; Catalgol, Betul; Friguet, Bertrand; Grune, Tilman; Gonos, Efstathios S

2012-10-26

390

Protein Stability in Ice  

Microsoft Academic Search

This study presents an experimental approach, based on the change of Trp fluorescence between native and denatured states of proteins, which permits to monitor unfolding equilibria and the thermodynamic stability (?G°) of these macromolecules in frozen aqueous solutions. The results obtained by guanidinium chloride denaturation of the azurin mutant C112S from Pseudomonas aeruginosa, in the temperature range from ?8 to

Giovanni B. Strambini; Margherita Gonnelli

2007-01-01

391

Predicting multiplex subcellular localization of proteins using protein-protein interaction network: a comparative study  

PubMed Central

Background Proteins that interact in vivo tend to reside within the same or "adjacent" subcellular compartments. This observation provides opportunities to reveal protein subcellular localization in the context of the protein-protein interaction (PPI) network. However, so far, only a few efforts based on heuristic rules have been made in this regard. Results We systematically and quantitatively validate the hypothesis that proteins physically interacting with each other probably share at least one common subcellular localization. With the result, for the first time, four graph-based semi-supervised learning algorithms, Majority, ?2-score, GenMultiCut and FunFlow originally proposed for protein function prediction, are introduced to assign "multiplex localization" to proteins. We analyze these approaches by performing a large-scale cross validation on a Saccharomyces cerevisiae proteome compiled from BioGRID and comparing their predictions for 22 protein subcellular localizations. Furthermore, we build an ensemble classifier to associate 529 unlabeled and 137 ambiguously-annotated proteins with subcellular localizations, most of which have been verified in the previous experimental studies. Conclusions Physical interaction of proteins has actually provided an essential clue for their co-localization. Compared to the local approaches, the global algorithms consistently achieve a superior performance.

2012-01-01

392

Protein quality of chickpea ( Cicer arietinum L.) protein hydrolysates  

Microsoft Academic Search

Chickpea protein isolate (CPI) was used as the starting material in the production of chickpea protein hydrolysates (CPHs). To obtain a highly extensive hydrolysate with a degree of hydrolysis higher than 50%, a sequential utilisation of endoprotease (Alcalase) and exoprotease (Flavourzyme) was necessary. Molecular weight patterns of CPHs were determined by gel filtration chromatography. As a result of the enzymatic

Alfonso Clemente; Javier Vioque; Raúl Sánchez-Vioque; Justo Pedroche; Juan Bautista; Francisco Millán

1999-01-01

393

On the role of electrostatics on protein-protein interactions  

PubMed Central

The role of electrostatics on protein-protein interactions and binding is reviewed in this article. A brief outline of the computational modeling, in the framework of continuum electrostatics, is presented and basic electrostatic effects occurring upon the formation of the complex are discussed. The role of the salt concentration and pH of the water phase on protein-protein binding free energy is demonstrated and indicates that the increase of the salt concentration tends to weaken the binding, an observation that is attributed to the optimization of the charge-charge interactions across the interface. It is pointed out that the pH-optimum (pH of optimal binding affinity) varies among the protein-protein complexes, and perhaps is a result of their adaptation to particular subcellular compartment. At the end, the similarities and differences between hetero- and homo-complexes are outlined and discussed with respect to the binding mode and charge complementarity.

Zhang, Zhe; Witham, Shawn; Alexov, Emil

2011-01-01

394

Dipolar response of hydrated proteins  

NASA Astrophysics Data System (ADS)

The paper presents an analytical theory and numerical simulations of the dipolar response of hydrated proteins in solution. We calculate the effective dielectric constant representing the average dipole moment induced at the protein by a uniform external field. The dielectric constant shows a remarkable variation among the proteins, changing from 0.5 for ubiquitin to 640 for cytochrome c. The former value implies a negative dipolar susceptibility, that is a dia-electric dipolar response and negative dielectrophoresis. It means that ubiquitin, carrying an average dipole of ~=240 D, is expected to repel from the region of a stronger electric field. This outcome is the result of a negative cross-correlation between the protein and water dipoles, compensating for the positive variance of the intrinsic protein dipole in the overall dipolar susceptibility. In contrast to the neutral ubiquitin, charged proteins studied here show para-electric dipolar response and positive dielectrophoresis. The study suggests that the dipolar response of proteins in solution is strongly affected by the coupling of the protein surface charge to the hydration water. The protein-water dipolar cross-correlations are long-ranged, extending ~2 nm from the protein surface into the bulk. A similar correlation length of about 1 nm is seen for the electrostatic potential produced by the hydration water inside the protein. The analysis of numerical simulations suggests that the polarization of the protein-water interface is highly heterogeneous and does not follow the standard dielectric results for cavities carved in dielectrics. The polarization of the water shell gains in importance, relative to the intrinsic protein dipole, at high frequencies, above the protein Debye peak. The induced interfacial dipole can be either parallel or antiparallel to the protein dipole, depending on the distribution of the protein surface charge. As a result, the high-frequency absorption of the protein solution can be either higher or lower than the absorption of water. Both scenarios have been experimentally observed in the THz window of radiation.

Matyushov, Dmitry V.

2012-02-01

395

Improving the prediction of yeast protein function using weighted protein-protein interactions  

PubMed Central

Background Bioinformatics can be used to predict protein function, leading to an understanding of cellular activities, and equally-weighted protein-protein interactions (PPI) are normally used to predict such protein functions. The present study provides a weighting strategy for PPI to improve the prediction of protein functions. The weights are dependent on the local and global network topologies and the number of experimental verification methods. The proposed methods were applied to the yeast proteome and integrated with the neighbour counting method to predict the functions of unknown proteins. Results A new technique to weight interactions in the yeast proteome is presented. The weights are related to the network topology (local and global) and the number of identified methods, and the results revealed improvement in the sensitivity and specificity of prediction in terms of cellular role and cellular locations. This method (new weights) was compared with a method that utilises interactions with the same weight and it was shown to be superior. Conclusions A new method for weighting the interactions in protein-protein interaction networks is presented. Experimental results concerning yeast proteins demonstrated that weighting interactions integrated with the neighbor counting method improved the sensitivity and specificity of prediction in terms of two functional categories: cellular role and cell locations.

2011-01-01

396

Protein Adsorption in Three Dimensions  

PubMed Central

Recent experimental and theoretical work clarifying the physical chemistry of blood-protein adsorption from aqueous-buffer solution to various kinds of surfaces is reviewed and interpreted within the context of biomaterial applications, especially toward development of cardiovascular biomaterials. The importance of this subject in biomaterials surface science is emphasized by reducing the “protein-adsorption problem” to three core questions that require quantitative answer. An overview of the protein-adsorption literature identifies some of the sources of inconsistency among many investigators participating in more than five decades of focused research. A tutorial on the fundamental biophysical chemistry of protein adsorption sets the stage for a detailed discussion of the kinetics and thermodynamics of protein adsorption, including adsorption competition between two proteins for the same adsorbent immersed in a binary-protein mixture. Both kinetics and steady-state adsorption can be rationalized using a single interpretive paradigm asserting that protein molecules partition from solution into a three-dimensional (3D) interphase separating bulk solution from the physical-adsorbent surface. Adsorbed protein collects in one-or-more adsorbed layers, depending on protein size, solution concentration, and adsorbent surface energy (water wettability). The adsorption process begins with the hydration of an adsorbent surface brought into contact with an aqueous-protein solution. Surface hydration reactions instantaneously form a thin, pseudo-2D interface between the adsorbent and protein solution. Protein molecules rapidly diffuse into this newly-formed interface, creating a truly 3D interphase that inflates with arriving proteins and fills to capacity within milliseconds at mg/mL bulk-solution concentrations CB. This inflated interphase subsequently undergoes time-dependent (minutes-to-hours) decrease in volume VI by expulsion of either-or-both interphase water and initially-adsorbed protein. Interphase protein concentration CI increases as VI decreases, resulting in slow reduction in interfacial energetics. Steady-state is governed by a net partition coefficient P=(/CBCI). In the process of occupying space within the interphase, adsorbing protein molecules must displace an equivalent volume of interphase water. Interphase water is itself associated with surface-bound water through a network of transient hydrogen bonds. Displacement of interphase water thus requires an amount of energy that depends on the adsorbent surface chemistry/energy. This “adsorption-dehydration” step is the significant free-energy cost of adsorption that controls the maximum amount of protein that can be adsorbed at steady state to a unit adsorbent-surface area (the adsorbent capacity). As adsorbent hydrophilicity increases, protein adsorption monotonically decreases because the energetic cost of surface dehydration increases, ultimately leading to no protein adsorption near an adsorbent water wettability (surface energy) characterized by a water contact angle ? ? 65°. Consequently, protein does not adsorb (accumulate at interphase concentrations greater than bulk solution) to more hydrophilic adsorbents exhibiting ? < 65° . For adsorbents bearing strong Lewis acid/base chemistry such as ion-exchange resins, protein/surface interactions can be highly favorable, causing protein to adsorb in multilayers in a relatively thick interphase. A straightforward, three-component free energy relationship captures salient features of protein adsorption to all surfaces predicting that the overall free energy of protein adsorption ?Gadso is a relatively small multiple of thermal energy for any surface chemistry (except perhaps for bioengineered surfaces bearing specific ligands for adsorbing protein) because a surface chemistry that interacts chemically with proteins must also interact with water through hydrogen bonding. In this way, water moderates protein adsorption to any surface by competing with

Vogler, Erwin A.

2011-01-01

397

Modelling of proteins in membranes  

Microsoft Academic Search

This review describes some recent theories and simulations of mesoscopic and microscopic models of lipid membranes with embedded or attached proteins. We summarize results supporting our understanding of phenomena for which the activities of proteins in membranes are expected to be significantly affected by the lipid environment. Theoretical predictions are pointed out, and compared to experimental findings, if available. Among

Maria Maddalena Sperotto; Sylvio May; Artur Baumgaertner

2006-01-01

398

Discrete breathers in protein structures  

Microsoft Academic Search

Recently, using a numerical surface cooling approach, we have shown that highly energetic discrete breathers (DBs) can form in the stiffest parts of nonlinear network models of large protein structures. In the present study, using an analytical approach, we extend our previous results to low-energy discrete breathers as well as to smaller proteins. We confirm and further scrutinize the striking

Francesco Piazza; Yves-Henri Sanejouand

2008-01-01

399

Phylogenomics of Prokaryotic Ribosomal Proteins  

PubMed Central

Archaeal and bacterial ribosomes contain more than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes). Despite the high sequence conservation, annotation of ribosomal (r-) protein genes is often difficult because of their short lengths and biased sequence composition. We developed an automated computational pipeline for identification of r-protein genes and applied it to 995 completely sequenced bacterial and 87 archaeal genomes available in the RefSeq database. The pipeline employs curated seed alignments of r-proteins to run position-specific scoring matrix (PSSM)-based BLAST searches against six-frame genome translations, mitigating possible gene annotation errors. As a result of this analysis, we performed a census of prokaryotic r-protein complements, enumerated missing and paralogous r-proteins, and analyzed the distributions of ribosomal protein genes among chromosomal partitions. Phyletic patterns of bacterial and archaeal r-protein genes were mapped to phylogenetic trees reconstructed from concatenated alignments of r-proteins to reveal the history of likely multiple independent gains and losses. These alignments, available for download, can be used as search profiles to improve genome annotation of r-proteins and for further comparative genomics studies.

Yutin, Natalya; Puigbo, Pere; Koonin, Eugene V.; Wolf, Yuri I.

2012-01-01

400

PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure  

PubMed Central

PocketQuery (http://pocketquery.csb.pitt.edu) is a web interface for exploring the properties of protein–protein interaction (PPI) interfaces with a focus on the discovery of promising starting points for small-molecule design. PocketQuery rapidly focuses attention on the key interacting residues of an interaction using a ‘druggability’ score that provides an estimate of how likely the chemical mimicry of a cluster of interface residues would result in a small-molecule inhibitor of an interaction. These residue clusters are chemical starting points that can be seamlessly exported to a pharmacophore-based drug discovery workflow. PocketQuery is updated on a weekly basis to contain all applicable PPI structures deposited in the Protein Data Bank and allows users to upload their own custom structures for analysis.

Koes, David Ryan; Camacho, Carlos J.

2012-01-01

401

NOXclass: prediction of protein-protein interaction types  

PubMed Central

Background Structural models determined by X-ray crystallography play a central role in understanding protein-protein interactions at the molecular level. Interpretation of these models requires the distinction between non-specific crystal packing contacts and biologically relevant interactions. This has been investigated previously and classification approaches have been proposed. However, less attention has been devoted to distinguishing different types of biological interactions. These interactions are classified as obligate and non-obligate according to the effect of the complex formation on the stability of the protomers. So far no automatic classification methods for distinguishing obligate, non-obligate and crystal packing interactions have been made available. Results Six interface properties have been investigated on a dataset of 243 protein interactions. The six properties have been combined using a support vector machine algorithm, resulting in NOXclass, a classifier for distinguishing obligate, non-obligate and crystal packing interactions. We achieve an accuracy of 91.8% for the classification of these three types of interactions using a leave-one-out cross-validation procedure. Conclusion NOXclass allows the interpretation and analysis of protein quaternary structures. In particular, it generates testable hypotheses regarding the nature of protein-protein interactions, when experimental results are not available. We expect this server will benefit the users of protein structural models, as well as protein crystallographers and NMR spectroscopists. A web server based on the method and the datasets used in this study are available at .

Zhu, Hongbo; Domingues, Francisco S; Sommer, lngolf; Lengauer, Thomas

2006-01-01

402

MI-98-1: Protein Feed Rules  

Center for Food Safety and Applied Nutrition (CFSAN)

... MI-98-1: Protein Feed Rules. HHS:PHS:FDA:CFSAN:OC:DCP:MSB. 200 C Street, SW Washington DC. MI-98-1. ... SUBJECT: PROTEIN FEED RULES. ... More results from www.fda.gov/food/guidanceregulation/guidancedocumentsregulatoryinformation

403

Protein engineering with unnatural amino acids.  

PubMed

Protein engineering has become an extensively used tool in many fields, allowing us to probe protein function, characterize proteins using a range of biophysical techniques, chemically modify proteins and improve protein function for medical and industrial applications. It is now possible to site-specifically incorporate unnatural, or non-canonical, amino acids (uAAs) into proteins, which has had a major impact on protein engineering. In this review, we discuss the recent technical developments in the field and how uAA-protein engineering is becoming an increasingly valuable molecular tool, with the unique chemical functionalities of some uAAs allowing a range of otherwise impossible experiments to be performed. Finally, the impediments that have resulted in a relatively small number of recent studies in which uAA-protein engineering has been used to improve protein function are discussed, alongside some of the recent technical developments that may serve to overcome these obstacles. PMID:23835227

Zhang, William H; Otting, Gottfried; Jackson, Colin J

2013-07-05

404

RINGdb: An integrated database for G protein-coupled receptors and regulators of G protein signaling  

Microsoft Academic Search

BACKGROUND: Many marketed therapeutic agents have been developed to modulate the function of G protein-coupled receptors (GPCRs). The regulators of G-protein signaling (RGS proteins) are also being examined as potential drug targets. To facilitate clinical and pharmacological research, we have developed a novel integrated biological database called RINGdb to provide comprehensive and organized RGS protein and GPCR information. RESULTS: RINGdb

Yu-Ching Fang; Wei-Hsin Sun; Li-Cheng Wu; Hsien-Da Huang; Hsueh-Fen Juan; Jorng-Tzong Horng

2006-01-01

405

Brassica carinata protein isolates: chemical composition, protein characterization and improvement of functional properties by protein hydrolysis  

Microsoft Academic Search

Brassica carinata defatted flour has been used to prepare protein isolates by alkaline extraction and precipitation at low pH. Different extraction parameters have been tested, and the chemical composition and functional properties of the resulting isolates have been analyzed. All the isolates had a protein content above 90% and a well balanced amino acid composition according to FAO standards except

J Pedroche; M. M Yust; H Lqari; J Girón-Calle; M Alaiz; J Vioque; F Millán

2004-01-01

406

Water-protein interactions from high-resolution protein crystallography.  

PubMed Central

To understand the role of water in life at molecular and atomic levels, structures and interactions at the protein-water interface have been investigated by cryogenic X-ray crystallography. The method enabled a much clearer visualization of definite hydration sites on the protein surface than at ambient temperature. Using the structural models of proteins, including several hydration water molecules, the characteristics in hydration structures were systematically analysed for the amount, the interaction geometries between water molecules and proteins, and the local and global distribution of water molecules on the surface of proteins. The tetrahedral hydrogen-bond geometry of water molecules in bulk solvent was retained at the interface and enabled the extension of a three-dimensional chain connection of a hydrogen-bond network among hydration water molecules and polar protein atoms over the entire surface of proteins. Networks of hydrogen bonds were quite flexible to accommodate and/or to regulate the conformational changes of proteins such as domain motions. The present experimental results may have profound implications in the understanding of the physico-chemical principles governing the dynamics of proteins in an aqueous environment and a discussion of why water is essential to life at a molecular level.

Nakasako, Masayoshi

2004-01-01

407

Water-protein interactions from high-resolution protein crystallography.  

PubMed

To understand the role of water in life at molecular and atomic levels, structures and interactions at the protein-water interface have been investigated by cryogenic X-ray crystallography. The method enabled a much clearer visualization of definite hydration sites on the protein surface than at ambient temperature. Using the structural models of proteins, including several hydration water molecules, the characteristics in hydration structures were systematically analysed for the amount, the interaction geometries between water molecules and proteins, and the local and global distribution of water molecules on the surface of proteins. The tetrahedral hydrogen-bond geometry of water molecules in bulk solvent was retained at the interface and enabled the extension of a three-dimensional chain connection of a hydrogen-bond network among hydration water molecules and polar protein atoms over the entire surface of proteins. Networks of hydrogen bonds were quite flexible to accommodate and/or to regulate the conformational changes of proteins such as domain motions. The present experimental results may have profound implications in the understanding of the physico-chemical principles governing the dynamics of proteins in an aqueous environment and a discussion of why water is essential to life at a molecular level. PMID:15306376

Nakasako, Masayoshi

2004-08-29

408

Lipid demixing and protein-protein interactions in the adsorption of charged proteins on mixed membranes.  

PubMed Central

The adsorption free energy of charged proteins on mixed membranes, containing varying amounts of (oppositely) charged lipids, is calculated based on a mean-field free energy expression that accounts explicitly for the ability of the lipids to demix locally, and for lateral interactions between the adsorbed proteins. Minimization of this free energy functional yields the familiar nonlinear Poisson-Boltzmann equation and the boundary condition at the membrane surface that allows for lipid charge rearrangement. These two self-consistent equations are solved simultaneously. The proteins are modeled as uniformly charged spheres and the (bare) membrane as an ideal two-dimensional binary mixture of charged and neutral lipids. Substantial variations in the lipid charge density profiles are found when highly charged proteins adsorb on weakly charged membranes; the lipids, at a certain demixing entropy penalty, adjust their concentration in the vicinity of the adsorbed protein to achieve optimal charge matching. Lateral repulsive interactions between the adsorbed proteins affect the lipid modulation profile and, at high densities, result in substantial lowering of the binding energy. Adsorption isotherms demonstrating the importance of lipid mobility and protein-protein interactions are calculated using an adsorption equation with a coverage-dependent binding constant. Typically, at bulk-surface equilibrium (i.e., when the membrane surface is "saturated" by adsorbed proteins), the membrane charges are "overcompensated" by the protein charges, because only about half of the protein charges (those on the hemispheres facing the membrane) are involved in charge neutralization. Finally, it is argued that the formation of lipid-protein domains may be enhanced by electrostatic adsorption of proteins, but its origin (e.g., elastic deformations associated with lipid demixing) is not purely electrostatic.

May, S; Harries, D; Ben-Shaul, A

2000-01-01

409

Protein denaturing on Nanospheres  

NASA Astrophysics Data System (ADS)

We have used localized surface plasmon resonance (LSPR) to monitor the structural changes that accompany thermal denaturing of Bovine Serum Albumin(BSA) adsorbed onto gold nanospheres of size 5nm-60nm. The effect of the protein on the LSPR was monitored by visible extinction spectroscopy. The position of the resonance is affected by the conformation of the adsorbed protein layer, and as such can be used as a very sensitive probe of thermal denaturing that is specific to the adsorbed protein. The results are compared to detailed calculations and show that full calculations can lead to significant increases in knowledge where gold nanospheres are used as biosensors. Thermal denaturing on spheres with diameter > 20 nm show strong similarity to bulk calorimetric studies of BSA in solution. BSA adsorbed on nanospheres with d<= 15 nm shows a qualitative difference in behavior, suggesting a sensitivity of denaturing characteristics on local surface curvature. Studies of isothermal denaturing kinetics were used to obtain an activatiuon barrier for thermal denaturing. This activation barrier also exhibited a strong dependence on nanoparticle size. These