Note: This page contains sample records for the topic seo proteins results from Science.gov.
While these samples are representative of the content of Science.gov,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of Science.gov
to obtain the most current and comprehensive results.
Last update: August 15, 2014.
1

Synchronous Earth Observatory Satellite /SEOS/  

NASA Technical Reports Server (NTRS)

NASA/GSFC is currently studying the applications and technical requirements for a Synchronous Earth Observations Satellite (SEOS). Such a satellite would combine the relatively high resolution and multi-spectral capability of the Earth Resources Technology Satellite (ERTS) with the on-station continuous monitoring of the Synchronous Meteorological Satellite (SMS). SEOS capability is geared to perform disaster warning of tornadoes and floods as well as to monitor transient phenomena affecting earth resources (e.g., green waves and algae blooms). The heart of the system is a Large Earth Survey Telescope (LEST) which has a designed 1.5 meter diameter. Spectral bands in the visible, near- and far-infrared have been selected to optimize SEOS utility. A microwave sounder will be used in conjunction with the LEST for meteorological applications.

Walter, L. S.

1974-01-01

2

CEOS SEO and GISS Meeting  

NASA Technical Reports Server (NTRS)

The Committee on Earth Observation Satellites (CEOS) provides a brief to the Goddard Institute for Space Studies (GISS) regarding the CEOS Systems Engineering Office (SEO) and current work on climate requirements and analysis. A "system framework" is provided for the Global Earth Observation System of Systems (GEOSS). SEO climate-related tasks are outlined including the assessment of essential climate variable (ECV) parameters, use of the "systems framework" to determine relevant informational products and science models and the performance of assessments and gap analyses of measurements and missions for each ECV. Climate requirements, including instruments and missions, measurements, knowledge and models, and decision makers, are also outlined. These requirements would establish traceability from instruments to products and services allowing for benefit evaluation of instruments and measurements. Additionally, traceable climate requirements would provide a better understanding of global climate models.

Killough, Brian; Stover, Shelley

2008-01-01

3

Multiple cis-regulatory elements are involved in the complex regulation of the sieve element-specific MtSEO-F1 promoter from Medicago truncatula.  

PubMed

The sieve element occlusion (SEO) gene family includes several members that are expressed specifically in immature sieve elements (SEs) in the developing phloem of dicotyledonous plants. To determine how this restricted expression profile is achieved, we analysed the SE-specific Medicago truncatula SEO-F1 promoter (PMtSEO-F1) by constructing deletion, substitution and hybrid constructs and testing them in transgenic tobacco plants using green fluorescent protein as a reporter. This revealed four promoter regions, each containing cis-regulatory elements that activate transcription in SEs. One of these segments also contained sufficient information to suppress PMtSEO-F1 transcription in the phloem companion cells (CCs). Subsequent in silico analysis revealed several candidate cis-regulatory elements that PMtSEO-F1 shares with other SEO promoters. These putative sieve element boxes (PSE boxes) are promising candidates for cis-regulatory elements controlling the SE-specific expression of PMtSEO-F1. PMID:22404711

Bucsenez, M; Rüping, B; Behrens, S; Twyman, R M; Noll, G A; Prüfer, D

2012-03-01

4

Preparation and characterization of novel SeO 2/TiO 2 nanocomposite  

NASA Astrophysics Data System (ADS)

Aiming to enhance the use of solar energy, novel SeO 2/TiO 2 nanocomposite was prepared by water bathing and calcining. Based on the characteristic of SeO 2 and TiO 2, the work mechanism of the nanocomposite was discussed. The products as obtained were characterized by SEM, HRTEM, EDX, XRD, XPS, LRS and UV-vis. The results shown that the SeO 2/TiO 2 nanocomposite is a hopeful form for improving the practicability of TiO 2.

Zhang, Sheng-Yi; Chen, Xiao-Jing; Tian, Yu-Peng; Jin, Bao-Kang; Yang, Jia-Xiang

2007-06-01

5

System trades for the SEOS telescope  

NASA Technical Reports Server (NTRS)

The Synchronous Earth Observation Satellite (SEOS) is a geostationary system which provides unique possibilities for earth surveillance. Questions of SEOS applications are considered, taking into account the employment of the Large Earth Survey Telescope. Aspects of performance and costs are examined. The generation of a value function in connection with a quantitative ranking of the applications is discussed along with an analysis performed to determine those parameter values which will maximize mission performance capability at given levels of system cost.

Ritter, M.

1975-01-01

6

A theoretical investigation of the diatomic dication SeO 2+ in the gas phase  

NASA Astrophysics Data System (ADS)

The present study was initiated by the recent observation of the novel molecular species SeO 2+ in the gas phase by Franzreb and Williams at Arizona State University. Here we report a very detailed theoretical investigation of the low-lying electronic states of SeO 2+. Our results show that the potential energy surfaces of the dicationic electronic states have high potential barriers with respect to dissociation, so this dication can exist in the gas phase as a long-lived metastable molecule. The potential energy curves are used to predict the double photoionization spectrum of SeO and to derive a set of spectroscopic parameters for the bound states of SeO 2+.

Ghalila, H.; Lahmar, S.; Hochlaf, M.

2011-12-01

7

Earth resources applications of the Synchronous Earth Observatory Satellite (SEOS)  

NASA Technical Reports Server (NTRS)

The results are presented of a four month study to define earth resource applications which are uniquely suited to data collection by a geosynchronous satellite. While such a satellite could also perform many of the functions of ERTS, or its low orbiting successors, those applications were considered in those situations where requirements for timely observation limit the capability of ERTS or EOS. Thus, the application presented could be used to justify a SEOS.

Lowe, D. S.; Cook, J. J.

1973-01-01

8

EPS dilution after SEOs and earnings management  

Microsoft Academic Search

Purpose – Firms are concerned about earnings per share (EPS) dilution after equity issues. The purpose of this paper is to investigate whether firms manage upward their discretionary accruals around seasoned equity offerings (SEOs) to mitigate the impact of dilution on reported earnings. Design\\/methodology\\/approach – The authors employ adjusted discretionary accruals from cash flow statements, normalized by the average common

Hui Di; Dalia Marciukaityte; Eugenie A. Goodwin

2012-01-01

9

Synthesis, structure, and characterization of two new polar sodium tungsten selenites: Na2(WO3)3(SeO3)·2H2O and Na6(W6O19)(SeO3)2.  

PubMed

Two new quaternary sodium tungsten selenites, Na2(WO3)3(SeO3)·2H2O (P31c) and Na6(W6O19)(SeO3)2 (C2), have been synthesized and characterized. The former exhibits a hexagonal tungsten oxide layered structure, whereas the latter has a one-dimensional "ribbon" structure. The layers and "ribbons" consist of distorted WO6 and asymmetric SeO3 polyhedra. The layers in Na2(WO3)3(SeO3)·2H2O and the "ribbons" in Na6(W6O19)(SeO3)2 are separated by Na(+) cations. Powder second-harmonic-generation (SHG) measurements on Na2(WO3)3(SeO3)·2H2O and Na6(W6O19)(SeO3)2 using 1064 nm radiation reveal SHG efficiencies of approximately 450× and 20× ?-SiO2, respectively. Particle size versus SHG efficiency measurements indicate that the materials are type 1 non-phase-matchable. Converse piezoelectric measurements result in d33 values of approximately 23 and 12 pm/V, whereas pyroelectric measurements reveal coefficients of -0.41 and -1.10 ?C/m(2)·K at 60 °C for Na2(WO3)3(SeO3)·2H2O and Na6(W6O19)(SeO3)2, respectively. Frequency-dependent polarization measurements confirm that the materials are nonferroelectric; i.e., the macroscopic polarization is not reversible, or "switchable". IR and UV-vis spectroscopy, thermogravimetric and differential thermal analysis measurements, and electron localization function calculations were also done for the materials. Crystal data: Na2(WO3)3(SeO3)·2H2O, trigonal, space group P31c (No. 159), a = 7.2595(6) Å, b = 7.2595(6) Å, c = 12.4867(13) Å, V = 569.89(9) Å(3), Z = 2; Na6(W6O19)(SeO3)2, monoclinic, space group C2 (No. 5), a = 42.169(8) Å, b = 7.2690(15) Å, c = 6.7494(13) Å, ? = 98.48(3)°, V = 2046.2(7) Å(3), Z = 4. PMID:23425251

Nguyen, Sau Doan; Halasyamani, P Shiv

2013-03-01

10

Pressure and Temperature Dependence of the Dielectric Properties of Hydrogen-Bonded Ferroelectrics: LiH3(SeO3)2 and LiD3(SeO3)2  

Microsoft Academic Search

The dielectric properties of LiH3(SeO3)2 (LHS) and LiD3(SeO3)2 (LDS) were investigated as functions of hydrostatic pressure to 26 kbar and temperature 20-140°C. A ferroelectric-to-paraelectric transition can be induced in both crystals at high pressure, and their Curie points decrease linearly with pressure with slopes of -6.0+\\/-0.2°K\\/kbar for LHS and -5.9+\\/-0.4°K\\/kbar for LDS. The high-pressure results indicate that LHS and LDS

G. A. Samara

1968-01-01

11

Seos - EARSEL'S Project on Science Education Through Earth Observation for High Schools  

NASA Astrophysics Data System (ADS)

SEOS is an initiative for using remote sensing in science education curricula in high schools funded under the 6th Framework Programme of the European Commission (EC). Eleven partners from several European countries, in cooperation with the European Space Agency (ESA) and teachers from European high schools, created e-learning tutorials for science students in high schools. The tutorials cover many disciplines such as physics, biology, geography, mathematics and engineering, emphasising the interdisciplinary character of remote sensing. They are the core element of the SEOS Learning Management System, allowing teachers to create their own courses, to distribute already available or new worksheets to the students for homework and to collect the results. Forums are available for teachers, students and other users to exchange information and discuss topics relevant for their study.

Reuter, R.

2011-09-01

12

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

13

Structural phase transformation in K2SeO4  

Microsoft Academic Search

Successive phase transformations in K2SeO4 at Ti=130 K and Tc=93 K were studied by the neutron-scattering technique. The superlattice reflections in the intermediate phase were found to be incommensurate with the lattice periodicity. The wave vector characterizing the reflections is q-->delta=(1-delta)a-->*3 with delta=0.07 at 122.5 K. The deviation delta decreases with decreasing temperature with an apparently discontinuous jump to zero

M. Iizumi; J. D. Axe; G. Shirane; K. Shimaoka

1977-01-01

14

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

15

Synthesis and crystal structures of two inorganic-organic hybrid vanadium selenites with layered structures: (DABCOH 2)[(VO 2)(SeO 3)] 2·1.25H 2O and (pipeH 2)[(VO) 2(C 2O 4)(SeO 3) 2  

NASA Astrophysics Data System (ADS)

The reactions of SeO 2 with V 2O 5 or VOSO 4 in the presence of different organic amine yield two novel vanadium selenites with layered structures, formulated as (DABCOH 2)[(VO 2)(SeO 3)] 2·1.25H 2O 1 (DABCO = 1,4-diazabicyclooctane) and (pipeH 2)[(VO) 2(C 2O 4)(SeO 3) 2] 2 (pipe = piperazidine). Two compounds are characterized with elemental analysis, FT-IR spectrum, TG-DTA analysis and single-crystal X-ray diffraction analysis. In compound 1, two symmetry-related VO 6 units share an edge to form a [V 2O 6] cluster. Each [V 2O 6] cluster is bridged by four SeO 3 units to generate a two-dimensional grid structure. In compound 2, VO 6 units and SeO 3 units share corners to result in a ladder motif. Adjacent chains are interlinked by the oxalate ligands, creating a 2D brick-wall structure, which is firstly observed in V/Se/O system. Diprotonated DABCO and lattice water molecules in 1 and diprotonated piperazidine molecules in 2 are located in the interlayer regions and interact with the framework oxygen atoms via hydrogen bonds, respectively.

Lian, Zhaoxun; Zhang, Jiamin; Gu, Yongqing; Wang, Tianxi; Lou, Tianjun

2009-02-01

16

Structural phase transitions of Na(DxH1-x)3(SeO3)2 single crystals studied by observation of 2H and 23Na nuclear magnetic resonance  

NASA Astrophysics Data System (ADS)

Na(DxH1-x)3(SeO3)2 single crystals were grown with a deuterium content of 37%, and the spectra and relaxation times of the 2H and 23Na nuclei in the mixed Na(D0.37H0.63)3(SeO3)2 crystals were measured as functions of temperature. The 2H and 23Na nuclear magnetic resonance (NMR) spectra undergo changes near 213 K. Our 23Na NMR results for x>=0.3 show that there is no triclinic intermediate phase; the paraelectric ?-phase and ferroelectric ?-phase arise in mixed Na(D0.37H0.63)3(SeO3)2 crystals. In addition, the 2H and 23Na relaxation times of mixed Na(D0.37H0.63)3(SeO3)2 crystals are different from the 2H and 23Na relaxation times of NaH3(SeO3)2 and NaD3(SeO3)2. The effects of partial deuteration of sodium trihydrogen selenite crystals include not only a shift in the phase transition temperature TC but also a change in the local symmetry.

Lim, Ae Ran; Jeong, Se-Young; Kim, Sun Ha

2010-12-01

17

Rich Structural Chemistry in Scandium Selenium/Tellurium Oxides: Mixed-Valent Selenite-Selenates, Sc2(SeO3)2(SeO4) and Sc2(TeO3)(SeO3)(SeO4), and Ternary Tellurite, Sc2(TeO3)3.  

PubMed

Both single crystals and pure bulk phases of three new scandium selenium/tellurium oxides, Sc2(SeO3)2(SeO4), Sc2(TeO3)(SeO3)(SeO4), and Sc2(TeO3)3, have been synthesized through hydrothermal and solid-state reactions. X-ray diffractions were used to determine the structures and confirm the phase purities of the reported materials. Isostructural Sc2(SeO3)2(SeO4) and Sc2(TeO3)(SeO3)(SeO4) reveal three-dimensional frameworks with ScO7 pentagonal bipyramids, SeO3 (and TeO3) trigonal pyramids, and SeO4 tetrahedra. A novel ternary scandium tellurite, Sc2(TeO3)3, also shows a three-dimensional framework that is composed of ScO6 octahedra, ScO7-capped octahedra, and TeO3 trigonal pyramids. All three materials accommodate local asymmetric coordination moieties owing to the lone pairs on Se(4+) and Te(4+) cations. The effect of coordination environments of constituent cations on the frameworks, dimensionalities, and centricities of products is discussed. Thorough characterizations including elemental analyses, infrared and UV-vis diffuse reflectance spectroscopies, thermal analyses, and dipole moment calculations for the reported materials are reported. Crystal data: Sc2(SeO3)2(SeO4), monoclinic, space group P21/c (No. 14), a = 6.5294(2) Å, b = 10.8557(4) Å, c = 12.6281(6) Å, ? = 103.543(3)°, V = 870.21(6) Å(3), and Z = 4; Sc2(TeO3)(SeO3)(SeO4), monoclinic, space group P21/c (No. 14), a = 6.5345(12) Å, b = 10.970(2) Å, c = 12.559(2) Å, ? = 102.699(10)°, V = 878.3(6) Å(3), and Z = 4; Sc2(TeO3)3, monoclinic, space group P21/n (No. 14), a = 5.2345(3) Å, b = 24.3958(15) Å, c = 6.8636(4) Å, ? = 106.948(2)°, V = 838.42(9) Å(3), and Z = 4. PMID:24918773

Song, Seung Yoon; Lee, Dong Woo; Ok, Kang Min

2014-07-01

18

Structure and properties of a non-traditional glass containing TeO2, SeO2 and MoO3  

NASA Astrophysics Data System (ADS)

A glass containing SeO2, TeO2, MoO3 and La2O3 was obtained at high oxygen pressure (P = 36 MPa) using pure oxides as precursors. The real bulk chemical composition of the glass according to LA-ICP-MS analysis is 17SeO2·50TeO2·32MoO3·1La2O3 (wt.%). The glass was characterized by X-ray diffraction, scanning electron microscopy (SEM), differential thermal analysis (DTA), UV-Vis, XPS, IR and EPR spectroscopy. According to DTA the glass transition temperature (Tg) is below 300 °C. By IR and X-ray photoelectron spectroscopy was determined the main building units (TeO3, TeO4, SeO3, Mo2O8) and the existing of mixed bridging bonds only, which build up the amorphous network. It was established by UV-Vis that the glass is transparent above 490 nm. As a result of a lengthy heat treatment, crystallization took place and crystals rich in SeO2 and TeO2 were found incorporated into the amorphous part containing all components.

Bachvarova-Nedelcheva, A.; Iordanova, R.; Kostov, K. L.; Yordanov, St.; Ganev, V.

2012-09-01

19

J protein mutations and resulting proteostasis collapse  

PubMed Central

Despite a century of intensive investigation the effective treatment of protein aggregation diseases remains elusive. Ordinarily, molecular chaperones ensure that proteins maintain their functional conformation. The appearance of misfolded proteins that aggregate implies the collapse of the cellular chaperone quality control network. That said, the cellular chaperone network is extensive and functional information regarding the detailed action of specific chaperones is not yet available. J proteins (DnaJ/Hsp40) are a family of chaperone cofactors that harness Hsc70 (heat shock cognate protein of 70 kDa) for diverse conformational cellular tasks and, as such, represent novel clinically relevant targets for diseases resulting from the disruption of proteostasis. Here we review incisive reports identifying mutations in individual J protein chaperones and the proteostasis collapse that ensues.

Koutras, Carolina; Braun, Janice E. A.

2014-01-01

20

Structural and Vibrational Study of K 2SeO 4·Te(OH) 6 Material  

NASA Astrophysics Data System (ADS)

At room temperature, the new compound K 2SeO 4·Te(OH) 6 was synthesized from water solutions of H 6TeO 6/K 2SeO 4. The potassium selenate tellurate (KTSe), Mm=480.81 g, possesses a monoclinic structure with Cc space group. The crystal and refinement cell parameters are: a=11.552(2) Å, b=6.432(1) Å, c=13.919(2) Å, ?=105.92(1), V=994.5(3) Å 3, Z=4, Dx= 3.011 g/cm 3, and F(000)=840. The residuals are R1=0.023 and W R2=0.069 for 1139 observed reflections (1108 with I>2? ( I)) refined with 152 parameters. The main interest of this structure is the presence of two different and independent anionic groups (TeO 6-6 and SeO 2-4) in the same crystal. Raman and IR spectra of K 2SeO 4·Te(OH) 6, recorded at room temperature in the frequency range 200-4000 cm -1, show that both SeO 2-4 and TeO 6-6 groups coexist in the crystal independently.

Dammak, M.; Khemakhem, H.; Mhiri, T.; Kolsi, A. W.; Daoud, A.

1999-07-01

21

Ferroelectric Domain Structure in RbH3(SeO3)2  

Microsoft Academic Search

Attempts to find the domain structure in RbH3(SeO3)2 have been made. A conventional polarizing microscope method of utilizing the crystal birefringence was not successful. However, by means of a dew method the clear domain structure has been found. It has been noticed that not every crystal is suitable for the observation of domain structure. Crystals grown at temperature below about

Yoshihiro Goto; Etsuro Sawaguchi

1980-01-01

22

New bismuth selenium oxides: syntheses, structures, and characterizations of centrosymmetric Bi2(SeO3)2(SeO4) and Bi2(TeO3)2(SeO4) and noncentrosymmetric Bi(SeO3)(HSeO3).  

PubMed

Three new mixed metal selenium oxides materials, Bi2(SeO3)2(SeO4), Bi2(TeO3)2(SeO4), and Bi(SeO3)(HSeO3), have been synthesized by hydrothermal and solid-state reactions using Bi(NO3)3·5H2O, SeO2 (or TeO2), H2SeO4, and Bi2O3 as reagents. The reported materials have been structurally characterized by single crystal X-ray diffraction. While Bi2(SeO3)2(SeO4) and Bi2(TeO3)2(SeO4) are crystallographically centrosymmetric (CS), Bi(SeO3)(HSeO3) crystallizes in a noncentrosymmetric (NCS) space group. The isostructural Bi2(SeO3)2(SeO4) and Bi2(TeO3)2(SeO4) exhibit three-dimensional framework structures that are composed of BiO6, Se(4+)O3 (or Te(4+)O3), and Se(6+)O4 polyhedra. However, Bi(SeO3)(HSeO3) exhibits corrugated layers that are composed of BiO5, Se(4+)O3, and Se(4+)O2(OH) polyhedra. All three materials contain local asymmetric coordination environments attributable to the lone pairs on the Bi(3+), Se(4+), and/or Te(4+) cations. Powder second-harmonic generation (SHG) measurements on NCS Bi(SeO3)(HSeO3) using 1064 nm radiation indicate that the material has a SHG efficiency of approximately 20 times that of ?-SiO2 and is not phase-matchable (type 1). The origin and magnitude of the SHG efficiency of Bi(SeO3)(HSeO3) is explained by determining the net direction of the polarizations arising from individual asymmetric polyhedra. Infrared spectroscopy, thermal analysis, elemental analysis, and dipole moment calculations for the reported materials are also presented. PMID:23506341

Lee, Eun Pyo; Song, Seung Yoon; Lee, Dong Woo; Ok, Kang Min

2013-04-01

23

A new phase in the MnII-SeIV-MoVI-O system, Mn(MoO3)(SeO3)(H2O): Hydrothermal synthesis, crystal structure and properties  

NASA Astrophysics Data System (ADS)

A new phase in the MnII-SeIV-MoVI-O system, Mn(MoO3)(SeO3)(H2O) (1), has been hydrothermally synthesized with a high yield (82%), and characterized by IR, TG-DSC, magnetism measurement and single crystal X-ray diffraction. The structure of Mn(MoO3)(SeO3)(H2O) features a complicated 3D network composed of the 1D molybdenum(VI) oxide chains and the 1D manganese(II) selenite chains interconnected via Se-O-Mo and Mn-O-Mo bridges. It is stable up to approximately 340 °C, and losses water molecule at 340 °C, then release SeO2 at about 420 °C. The result of magnetic property measurements has indicated that there exist antiferromagnetic interactions between Mn(II) centers. Photocatalysis experimental result illustrates that the compound exhibits good photocatalytic performance for degradation of RhB under visible light irradiation.

Zhen, Yanzhong; Wang, Danjun; Liu, Bin; Fu, Feng; Xue, Ganglin

2013-11-01

24

Infrared evidence for multiple structural transitions in single crystal Cu3(SeO3)2Cl  

NASA Astrophysics Data System (ADS)

Infrared reflection and transmission over a broad temperature range (10-300 K) have been measured on the anisotropic single-crystal Cu3(SeO3)2Cl. Two distinct space groups have previously been reported for Cu3(SeO3)2Cl at 300 K (monoclinic C2/m and triclinic P1bar). Comparing the number of observed infrared active phonons with group theoretical predictions points towards the existence of the triclinic structure at 300 K; however, an impurity-rich monoclinic structure cannot be ruled out. New phonon modes are observed upon cooling below 90 K, and again upon cooling below 40 K. The latter temperature range corresponds to the onset of long range magnetic order in the material. The structural and magnetic properties of Cu3(SeO3)2Cl will be discussed in terms of our infrared spectra, group theoretical predictions, and comparisons to related compounds.

Miller, Kevin H.; Berger, Helmuth; Tanner, David B.

2013-03-01

25

Comparative study of vibrational spectra of Rb4LiH3(SO4)4, K4LiH3(SO4)4, K4LiH3(SeO4)4, Na5H3(SeO4)4.2H2O and Na2SeO4.H2SeO3.H2O crystals. Polarized infrared and Raman studies.  

PubMed

Vibrational spectra of M4LiH3(XO4)4 family, where M=K, Rb, X=S, Se together with Na5H3(SeO4)4.2H2O and Na2SeO4.H2SeO3.H2O crystals were compared. Similarities and differences are described. The spectroscopic manifestation of the presence of hydrogen bonds is discussed. Position of the bands corresponding to bending type of vibrations (in-plane and out-of plane) of hydrogen bonds is analyzed in the function of temperature. Small dynamic splitting of the bands due to weak interactions between ions is noticed. PMID:14670479

Marchewka, M K; Baran, J

2004-01-01

26

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

27

A Rhizobium selenitireducens protein showing selenite reductase activity.  

PubMed

Biobarriers remove, via precipitation, the metalloid selenite (SeO??²) from groundwater; a process that involves the biological reduction of soluble SeO??² to insoluble elemental red selenium (Se?). The enzymes associated with this reduction process are poorly understood. In Rhizobium selenitireducens at least two enzymes are potentially involved; one, a nitrite reductase reduces SeO??² to Se? but another protein may also be involved which is investigated in this study. Proteins from R. selenitireducens cells were precipitated with ammonium sulfate and run on native electrophoresis gels. When these gels were incubated with NADH and SeO??² a band of precipitated Se? developed signifying the presence of a SeO??² reducing protein. Bands were cut from the gel and analyzed for peptides via LCMSMS. The amino acid sequences associated with the bands indicated the presence of an NADH:flavin oxidoreductase that resembles YP_001326930 from Sinorhizobium medicae. The protein is part of a protein family termed old-yellow-enzymes (OYE) that contain a flavin binding domain. OYE enzymes are often involved in protecting cells from oxidative stress and, due in part to an active site that has a highly accessible binding pocket, are generally active on a wide range of substrates. This report is the first of an OYE enzyme being involved in SeO??² reduction. PMID:24474405

Hunter, W J

2014-03-01

28

UV-visible and infrared spectroscopy of gamma-irradiated lithium diborate glasses containing SeO 2  

NASA Astrophysics Data System (ADS)

UV-visible spectroscopic studies of a base lithium diborate glass together with samples containing SeO 2 substituting B 2O 3 have been measured before and after successive gamma irradiation. The optical absorption spectra of the base and SeO 2-containing samples show charge transfer UV absorption bands which are related to the unavoidable contamination with trace iron impurities [mainly Fe 3+ ions] within the raw materials used for the preparation of such glasses. The progressive introduction of SeO 2 causes some changes in the intensity of the two UV bands which are identified at 235 and 285 nm instead of the three peaks already observed in the base glass at 235, 275, 310 nm. Gamma irradiation produces induced bands which are assumed to be generated from the intrinsic defects in the lithium diborate base glass together with the sharing of trace iron impurities through suggested photochemical reactions. The UV induced bands are observed to be highly intensified showing continuous growth with progressive irradiation and are identified at about 230, 285 and 310 nm together with a further induced broad visible band centered at about 550 nm. Infrared absorption measurements of the base lithium diborate glass reveal characteristic bands due to stretching and bending vibrations of both BO 3 and BO 4 units together with the far-infrared bands due to the modifier Li + ions. The introduction of SeO 2 causes some changes in the IR spectra due either to the sharing of SeO 3 units and/or the polymerization of the borate network.

ElBatal, F. H.; Marzouk, S. Y.; Ezz-ElDin, F. M.

2011-02-01

29

Theoretical study of potential energy curves, spectroscopic constants, and radiative lifetimes of low-lying states in an SeO molecule  

NASA Astrophysics Data System (ADS)

The low-lying potential energy curves of the SeO molecule are computed by means of an ab initio multireference configuration interaction technique, taking into account relativistic (scalar plus spin—orbit coupling) effects. The spectroscopic constants of ? states for X3?-, a1?, b1?+, A3?, A'3?, and A? 3?+ states are obtained, and they are in good accordance with available experimental values. The Franck—Condon factors and transition dipole moments to the ground state are computed, and the natural radiative lifetimes of low-lying ? states are theoretically obtained. Comparisons of the natural lifetimes of ? states with previous experimental results and those of isovalent TeO molecule are made.

Li, Rui; Lian, Ke-Yan; Li, Qi-Nan; Miao, Feng-Juan; Yan, Bing; Jin, Ming-Xing

2012-12-01

30

From an open framework to a layered and a hexagonal tungsten oxide structure: controlled transformation reactions of an extended solid-state material, Cs3Ga7(SeO3)12 to Ga(OH)(SeO3) and KGa3(SeO4)2(OH)6.  

PubMed

A highly symmetric open-framework gallium selenite, Cs3Ga7(SeO3)12, containing cubic superlattices has been synthesized by a standard solid-state reaction using Cs2CO3, Ga2O3, and SeO2 as reagents. Cs3Ga7(SeO3)12 exhibits a three-dimensional open-framework structure consisting of GaO4 tetrahedra, GaO6 octahedra, and SeO3 polyhedra. Step-by-step reactions of the solid-state material in aqueous KNO3 solution at different temperatures produce Ga(OH)(SeO3) with a layered structure and KGa3(SeO4)2(OH)6 having a hexagonal tungsten oxide (HTO) topology. Novel HTO layers capped by Se(6+) cations in KGa3(SeO4)2(OH)6 led us to synthesize other alkali metal gallium selenates, NaGa3(SeO4)2(OH)6 and RbGa3(SeO4)2(OH)6, using hydrothermal reactions. Thermal analyses, infrared spectroscopy, elemental analyses, and dipole moment calculations for the reported materials are also presented. PMID:24144010

Ahn, Hyun Sun; Lee, Dong Woo; Ok, Kang Min

2013-11-01

31

Brillouin-scattering study of the ferroelastic transition in KH3(SeO3)2 and KD3(SeO3)2 under uniaxial stress  

NASA Astrophysics Data System (ADS)

The c55 elastic constant of KH3(SeO3)2 and KD3(SeO3)2 has been investigated by Brillouin scattering in the vicinity of the ferroelastic transition in free crystal and under applied uniaxial stress. At zero stress, c55 exhibits remarkable softening at the transition with no departure from classical linear temperature dependence. The effect of the ?5 stress component can be very well described by a Landau-type free-energy model. On deuteration, only the temperature, at which the protons or deuterons would order without coupling to the strain, is increased; the other parameters in the free energy are not essentially affected.

?opi?, M.; Zgonik, M.; Fox, D. L.; Lavren?i?, B. B.

1981-04-01

32

Hydroxocobalamin association during cell culture results in pink therapeutic proteins.  

PubMed

Process control of protein therapeutic manufacturing is central to ensuring the product is both safe and efficacious for patients. In this work, we investigate the cause of pink color variability in development lots of monoclonal antibody (mAb) and Fc-fusion proteins. Results show pink-colored product generated during manufacturing is due to association of hydroxocobalamin (OH-Cbl), a form of vitamin B12. OH-Cbl is not part of the product manufacturing process; however we found cyanocobalamin (CN-Cbl) in cell culture media converts to OH-Cbl in the presence of light. OH-Cbl can be released from mAb and Fc-fusion proteins by conversion with potassium cyanide to CN-Cbl, which does not bind. By exploiting the differential binding of CN-Cbl and OH-Cbl, we developed a rapid and specific assay to accurately measure B12 levels in purified protein. Analysis of multiple products and lots using this technique gives insight into color variability during manufacturing. PMID:23924851

Prentice, Kenneth M; Gillespie, Ronald; Lewis, Nathan; Fujimori, Kiyoshi; McCoy, Rebecca; Bach, Julia; Connell-Crowley, Lisa; Eakin, Catherine M

2013-01-01

33

Bi6(SeO3)3O5Br2: A new bismuth oxo-selenite bromide  

NASA Astrophysics Data System (ADS)

A new bismuth oxo-selenite bromide Bi6(SeO3)3O5Br2 was synthesized and structurally characterized. The crystal structure belongs to the triclinic system (space group P1¯, Z=2, a=7.1253(7) Å, b=10.972(1) Å, c=12.117(1) Å, ?=67.765(7)°, ?=82.188(8)°, ?=78.445(7)°) and is unrelated to those of other known oxo-selenite halides. It can be considered as an open framework composed of BiOx or BiOyBrz polyhedrons forming channels running along [1 0 0] direction which contain the selenium atoms in pyramidal shape oxygen coordination (SeO3E). The spectroscopic properties and thermal stability were studied. The new compound is stable up to 400 °C.

Berdonosov, Peter S.; Olenev, Andrei V.; Kirsanova, Maria A.; Lebed, Julia B.; Dolgikh, Valery A.

2012-12-01

34

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

35

Dielectric Anomaly at the Phase Transition of RbD3(SeO3)2  

NASA Astrophysics Data System (ADS)

The dielectric constants \\varepsilona, \\varepsilonb, and \\varepsilonc along the three crystallographic axes of the deuterated rubidium trihydrogen selenite RbD3(SeO3)2 crystal have been measured in the temperature range including the ferroelectric phase transition. It has been found that \\varepsilona shows a much larger peak at the phase transition than the peak of \\varepsilonb which is believed to be the dielectric constant along the polar axis in the ferroelectric phase. Some discussion for the crystal symmetry is presented in connection with the structure of the incommensurate phase.

Yamamoto, Ken-ichi; Fukui, Minoru; Abe, Ryuji; Sakai, Akira; Yagi, Toshirou

1984-03-01

36

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

37

Lead (II) selenite halides Pb3(SeO3)2 X 2 ( X = Br, I): Synthesis and crystal structure  

NASA Astrophysics Data System (ADS)

Two lead selenite halides, Pb3(SeO3)2Br2 and Pb3(SeO3)2I2, have been prepared by solid-phase synthesis and structurally characterized. These compounds are isotypic and can be considered 3D with a microporous framework composed of lead polyhedra (distorted Archimedean antiprisms formed by oxygen and halogen atoms). The framework contains channels oriented in the [010] direction. These channels contain selenium atoms, which are bound with framework oxygen atoms belonging to different lead polyhedra.

Berdonosov, P. S.; Olenev, A. V.; Dolgikh, V. A.

2012-03-01

38

[Results of protein-sparing modified fasting in hyperlipoproteinemias].  

PubMed

We investigated the influence of a PSMF on body weight, body composition, blood lipids, physical working capacity, and nitrogen balance in obese HLP patients. During 4 weeks, 12 patients were treated by PSMF (approximately 340 kcal/d) under health resort conditions. At the same time, they daily exercised on a bicycle with an intensity of 80% of their physical working capacity estimated by an exercise load. The therapeutic regimen induced a significant weight loss (10.1 kg in the mean). Evidently, the patients diminished their body fat only as could be shown by estimations of total body water. Triglycerides, total cholesterol, and LDL-cholesterol also decreased significantly, while HDL-cholesterol remained unchanged. In spite of the weight reduction, the physical working capacity significantly increased from 57.8 to 93.2 kgm. Measurements of total nitrogen excretion with urine gave evidence of the protein saving effect of the therapy. Thus, PSMF--representing an effective therapeutic procedure--can be recommended to be used in obese HLP patients, proceeded that contraindications have been taken into consideration carefully. PMID:4085392

Fischer, S; Hanefeld, M; Weck, M; Beckert, H; Julius, U; Eichhorn, D; Rothe, G; Leonhardt, W; Graeser, K; Haller, H

1985-01-01

39

Protein crystal growth results from shuttle flight 51-F  

NASA Technical Reports Server (NTRS)

The protein crystal growth (PCG) experiments run on 51-F were analyzed. It was found that: (1) sample stability is increased over that observed during the experiments on flight 51-D; (2) the dialysis experiments produced lysozyme crystals that were significantly larger than those obtained in our identical ground-based studies; (3) temperature fluctuations apparently caused problems during the crystallization experiments on 51-F; (4) it is indicated that teflon tape stabilizes droplets on the syringe tips; (5) samples survived during the reentry and landing in glass tips that were not stoppered with plungers; (6) from the ground-based studies, it was expected that equilibration should be complete within 2 to 4 days for all of these vapor-diffusion experiments, thus it appears that the vapor diffusion rates are somewhat slower under microgravity conditions; (7) drop tethering was highly successful, all four of the tethered drops were stable, even though they contained MPD solutions; (8) the PCG experiments on 51-F were done to assess the hardware and experimental procedures that are developed for future flights, when temperature control will be available. Lysozyme crystals obtained by microdialysis are considerably larger than those obtained on the ground, using the identical apparatus and procedures.

Bugg, C. E.

1985-01-01

40

Ordering of the O(2)…D… O(2) bonds near the phase transition in KD3(SeO3)2 single crystals by D nuclear magnetic resonance  

NASA Astrophysics Data System (ADS)

Deuterium resonance investigations of KD3(SeO3)2 single crystals have been performed near the phase transition temperature T C . There are two types of deuterium bonds in these crystals with different behaviors at this phase transition. Our experimental results show that there are significant changes in the D spinlattice relaxation time T 1 at T C ; the abrupt decrease in T 1 near T C can be explained by the critical slowing down of an overdamped soft pseudospin-type deuteron mode. Further, the ordering of the O(2)…D… O(2) bonds is affected by the phase transition, whereas the ordering of the O(1)-D… O(3) bonds is unaffected. The D NMR measurements also show that the D(2) deuteron disordering above T C is dynamic and not static.

Lim, Ae Ran; Jeong, Se-Young

2013-01-01

41

Committee on Earth Observation Satellites (CEOS) Systems Engineering Office (SEO). Ocean Surface Topography (OST) Workshop, Ruedesheim an Rhein, Germany. [CEOS SEO Status Report  

NASA Technical Reports Server (NTRS)

The CEOS Systems Engineering Office will present a 2007 status report of the CEOS constellation process, present a new systems engineering framework, and analysis results from the GEO Societal Benefit Area (SBA) assessment and the OST constellation requirements assessment.

Killough, Brian D., Jr.

2008-01-01

42

Committee on Earth Observation Satellites (CEOS) Systems Engineering Office (SEO). Ocean Surface Topography (OST) Workshop, Ruedesheim an Rhein, Germany. (CEOS SEO Status Report).  

National Technical Information Service (NTIS)

The CEOS Systems Engineering Office will present a 2007 status report of the CEOS constellation process, present a new systems engineering framework, and analysis results from the GEO Societal Benefit Area (SBA) assessment and the OST constellation requir...

B. D. Killough

2008-01-01

43

Structural and conductivity studies of CsK(SO4)0.32(SeO4)0.68Te(OH)6  

NASA Astrophysics Data System (ADS)

The compound CsK(SO4)0.32(SeO4)0.68Te(OH)6 crystallizes in the monoclinic P21/n space group. It was analyzed, at room temperature, using X-ray diffractometer data. The main feature of these atomic arrangements is the coexistence of three and different anions (SO42-, SeO42- and TeO66-groups) in the unit cell, connected by hydrogen bonds which make the building of the crystal. The thermal analysis of the title compound shows three distinct endothermal peaks at 435, 460 and 475 K. Complex impedance measurements are performed on this material as a function of both temperature and frequency. The electric conduction has been studied. The temperature dependence on the conductivity indicates that the sample became an ionic conductor at high temperature.

Djemel, M.; Abdelhedi, M.; Zouari, N.; Dammak, M.; Kolsi, A. W.

2012-12-01

44

Vibrational spectroscopic study of the uranyl selenite mineral derriksite Cu4UO2(SeO3)2(OH)6?H2O  

NASA Astrophysics Data System (ADS)

Raman spectrum of the mineral derriksite Cu4UO2(SeO3)2(OH)6?H2O was studied and complemented by the infrared spectrum of this mineral. Both spectra were interpreted and partly compared with the spectra of demesmaekerite, marthozite, larisaite, haynesite and piretite. Observed Raman and infrared bands were attributed to the (UO2)2+, (SeO3)2-, (OH)- and H2O vibrations. The presence of symmetrically distinct hydrogen bonded molecule of water of crystallization and hydrogen bonded symmetrically distinct hydroxyl ions was inferred from the spectra in the derriksite unit cell. Approximate U-O bond lengths in uranyl and O-H⋯O hydrogen bond lengths were calculated from the Raman and infrared spectra of derriksite.

Frost, Ray L.; ?ejka, Ji?í; Scholz, Ricardo; López, Andrés; Theiss, Frederick L.; Xi, Yunfei

2014-01-01

45

Vibrational spectroscopic study of the uranyl selenite mineral derriksite Cu4UO2(SeO3)2(OH)6·H2O.  

PubMed

Raman spectrum of the mineral derriksite Cu4UO2(SeO3)2(OH)6?H2O was studied and complemented by the infrared spectrum of this mineral. Both spectra were interpreted and partly compared with the spectra of demesmaekerite, marthozite, larisaite, haynesite and piretite. Observed Raman and infrared bands were attributed to the (UO2)(2+), (SeO3)(2-), (OH)(-) and H2O vibrations. The presence of symmetrically distinct hydrogen bonded molecule of water of crystallization and hydrogen bonded symmetrically distinct hydroxyl ions was inferred from the spectra in the derriksite unit cell. Approximate U-O bond lengths in uranyl and O-H···O hydrogen bond lengths were calculated from the Raman and infrared spectra of derriksite. PMID:24018173

Frost, Ray L; ?ejka, Ji?í; Scholz, Ricardo; López, Andrés; Theiss, Frederick L; Xi, Yunfei

2014-01-01

46

Plumboselite, Pb3O2(SeO3), a new oxidation-zone mineral from Tsumeb, Namibia  

NASA Astrophysics Data System (ADS)

Plumboselite, ideally Pb3O2(SeO3), is a new selenite (IMA2010-028) from the Tsumeb mine, Namibia. It occurs as fibres on clausthalite and is also associated with smithsonite, mimetite and vaterite. Plumboselite occurs in subparallel to divergent clusters of thin, flattened, colourless fibres up to 0.3 mm in length, but not exceeding 5 ?m in width and 2 ?m in thickness. The fibres are elongated parallel to [001] and flattened on {010}, with {010} the only form observed. The crystals have a dull to adamantine lustre and a white streak. The tenacity is brittle and the Mohs hardness is estimated to be between 2 and 3. Plumboselite crystals are optically biaxial with parallel extinction and are length fast in all orientations. The Gladstone-Dale relationship predicts n av = 2.115. The high indices of refraction and small crystal size prevented the determination of other optical properties. The calculated density is 7.814 g/cm3. The empirical formula (based on 5 O atoms) is Pb2.92Ca0.01Se1.03O5. Plumboselite is orthorhombic, space group Cmc21, a = 10.5384(11), b = 10.7452(13), c = 5.7577(7) Å, V = 651.98(12) Å3 and Z = 4. The five strongest lines in the powder X-ray diffraction pattern are [ d obs in Å/( I)/ hkl]: 3.155/(100)/221; 1.956/(26)/042,402; 2.886/(22)/311,002; 1.713/(21)/223; 2.691/(17)/040. The crystal structure was solved from single-crystal X-ray diffraction data and refined to R 1 = 0.0371 on the basis of 200 unique reflections with F o > 4? F. The structure is based on double [O2Pb3] chains of edge-sharing oxo-centered [OPb4] tetrahedra along c, between which are sited SeO3 triangles. The two independent Pb2+ atoms and the Se4+ atom have sterochemically active lone electron pairs.

Kampf, Anthony R.; Mills, Stuart J.; Pinch, William W.

2011-01-01

47

Local structure of Rb2Li4(SeO4)3·2H2O by the modeling of X-ray diffuse scattering — from average-structure to microdomain model  

NASA Astrophysics Data System (ADS)

Local structure of dirubidium tetralithium tris(selenate(VI)) dihydrate — Rb2Li4(SeO4)3· 2H2O has been determined basing on the modeling of X-ray diffuse scattering. The origin of observed structured diffuse streaks is SeO4 tetrahedra switching between two alternative positions in two quasi-planar layers existing in each unit cell and formation of domains with specific SeO4 tetrahedra configuration locally fulfilling condition for C-centering in the 2a×2b×c superstructure cell. The local structure solution is characterized by a uniform distribution of rather large domains (ca. thousand of unit cells) in two layers, but also monodomains can be taken into account. Inside a single domain SeO4 tetrahedra are ordered along ab-diagonal forming two-string ribbons. Inside the ribbons SeO4 and LiO4 tetrahedra share the oxygen corners, whereas ribbons are bound to each other by a net of hydrogen bonds and fastened by corner sharing SeO4 tetrahedra of the neighboring layers.

Komornicka, Dorota; Wo?cyrz, Marek; Pietraszko, Adam

2012-08-01

48

Taming the Oxidative Power of SeO3 in 1,4-Dioxane, Isolation of Two New Isomers of Mixed-Valence Selenium Oxides, and Two Unprecedented Cyclic Esters of Selenic Acid.  

PubMed

The reaction of (SeO3)4 with 1,4-dioxane (diox, dioxane) with or without diluting solvent led to the isolation of the unprecedented esters of selenic acid-1,2-ethyl selenate (CH2O)2SeO2 and the glyoxal diselenate O2Se[(OCHO)2]SeO2. It was possible to isolate an unknown dimeric form of Se2O5 (Se4O10·(diox)2) and a geometrical isomer of the mixed-valence oxide trans-Se3O7, both stabilized by dioxane. The dioxane adduct of monomeric selenium trioxide SeO3·diox was obtained from the reaction of (SeO3)4 with dioxane in liquid SO2. The reaction mechanism for the formation of these compounds was elucidated, and the molecular structure of the unstable form of the selenium trioxide was determined, consisting in a trimeric arrangement (SeO3)3. PMID:24940821

Richtera, Lukas; Jancik, Vojtech; Martínez-Otero, Diego; Pokluda, Ales; Zak, Zdirad; Taraba, Jan; Touzin, Jiri

2014-07-01

49

Transiting Exoplanet Survey Satellite (TESS) Community Observer Program including the Science Enhancement Option Box (SEO Box) - 12 TB On-board Flash Memory for Serendipitous Science  

NASA Astrophysics Data System (ADS)

The Transiting Exoplanet Survey Satellite (TESS) will perform an all-sky survey in a low-inclination, low-Earth orbit. TESS's 144 GB of raw data collected each orbit will be stacked, cleaned, cut, compressed and downloaded. The Community Observer Program is a Science Enhancement Option (SEO) that takes advantage of the low-radiation environment, technology advances in flash memory, and the vast amount of astronomical data collected by TESS. The Community Observer Program requires the addition of a 12 TB "SEO Box” inside the TESS Bus. The hardware can be built using low-cost Commercial Off-The-Shelf (COTS) components and fits within TESS's margins while accommodating GSFC gold rules. The SEO Box collects and stores a duplicate of the TESS camera data at a "raw” stage ( 4.3 GB/orbit, after stacking and cleaning) and makes them available for on-board processing. The sheer amount of onboard storage provided by the SEO Box allows the stacking and storing of several months of data, allowing the investigator to probe deeper in time prior to a given event. Additionally, with computation power and data in standard formats, investigators can utilize data-mining techniques to investigate serendipitous phenomenon, including pulsating stars, eclipsing binaries, supernovae or other transient phenomena. The Community Observer Program enables ad-hoc teams of citizen scientists to propose, test, refine and rank algorithms for on-board analysis to support serendipitous science. Combining "best practices” of online collaboration, with careful moderation and community management, enables this `crowd sourced’ participatory exploration with a minimal risk and impact on the core TESS Team. This system provides a powerful and independent tool opening a wide range of opportunity for science enhancement and secondary science. Support for this work has been provided by NASA, the Kavli Foundation, Google, and the Smithsonian Institution.

Schingler, Robert; Villasenor, J. N.; Ricker, G. R.; Latham, D. W.; Vanderspek, R. K.; Ennico, K. A.; Lewis, B. S.; Bakos, G.; Brown, T. M.; Burgasser, A. J.; Charbonneau, D.; Clampin, M.; Deming, L. D.; Doty, J. P.; Dunham, E. W.; Elliot, J. L.; Holman, M. J.; Ida, S.; Jenkins, J. M.; Jernigan, J. G.; Kawai, N.; Laughlin, G. P.; Lissauer, J. J.; Martel, F.; Sasselov, D. D.; Seager, S.; Torres, G.; Udry, S.; Winn, J. N.; Worden, S. P.

2010-01-01

50

Transiting Exoplanet Survey Satellite (TESS) Community Observer Program including the Science Enhancement Option Box (SEO Box) - 12 TB On-board Flash Memory for Serendipitous Science  

Microsoft Academic Search

The Transiting Exoplanet Survey Satellite (TESS) will perform an all-sky survey in a low-inclination, low-Earth orbit. TESS's 144 GB of raw data collected each orbit will be stacked, cleaned, cut, compressed and downloaded. The Community Observer Program is a Science Enhancement Option (SEO) that takes advantage of the low-radiation environment, technology advances in flash memory, and the vast amount of

Robert Schingler; J. N. Villasenor; G. R. Ricker; D. W. Latham; R. K. Vanderspek; K. A. Ennico; B. S. Lewis; G. Bakos; T. M. Brown; A. J. Burgasser; D. Charbonneau; M. Clampin; L. D. Deming; J. P. Doty; E. W. Dunham; J. L. Elliot; M. J. Holman; S. Ida; J. M. Jenkins; J. G. Jernigan; N. Kawai; G. P. Laughlin; J. J. Lissauer; F. Martel; D. D. Sasselov; S. Seager; G. Torres; S. Udry; J. N. Winn; S. P. Worden

2010-01-01

51

Crosslinking of wheat dough proteins by glucose oxidase and the resulting effects on bread and croissants  

Microsoft Academic Search

The crosslinking of wheat flour proteins results in significant improvements in the functional properties of baked products. In this research, the enzyme glucose oxidase was investigated for its crosslinking effect on the dough proteins of bread and croissants. The macroscopic effects resulting from the addition of glucose oxidase to the dough formulation were compared to changes seen at the molecular

I. A. Rasiah; K. H. Sutton; F. L. Low; H.-M. Lin; J. A. Gerrard

2005-01-01

52

Synthesis, Crystal Structure and Thermal Decomposition of the New Cadmium Selenite Chloride, Cd4(SeO3)2OCl2  

PubMed Central

A synthetic study in the Cd-Se-O-Cl system led to formation of the new oxochloride compound Cd4(SeO3)2OCl2 via solid state reactions. The compound crystallizes in the orthorhombic space group Fmmm with cell parameters a?=?7.3610(3) Å, b?=?15.4936(2) Å, c?=?17.5603(3) Å, Z?=?8, S?=?0.969, F(000)?=?2800, R?=?0.0185, Rw?=?0.0384. Single crystal X-ray data were collected at 293 K. The crystal structure can be considered as layered and the building units are distorted [Cd(1)O6] octahedra, distorted [Cd(2)O8] cubes, irregular [Cd(3)O4Cl2] polyhedra and SeO3E trigonal pyramids. There are two crystallographically unique Cl atoms that both are half occupied. Thermogravimetric studies show that the compound starts to decompose at 500°C. The crystal structure of the new compound is closely related to the previously described compound Cd4(SeO3)2Cl4(H2O).

Rabbani, Faiz; Ajaz, Humayun; Zimmermann, Iwan; Johnsson, Mats

2014-01-01

53

Evolutionary rate covariation in meiotic proteins results from fluctuating evolutionary pressure in yeasts and mammals.  

PubMed

Evolutionary rates of functionally related proteins tend to change in parallel over evolutionary time. Such evolutionary rate covariation (ERC) is a sequence-based signature of coevolution and a potentially useful signature to infer functional relationships between proteins. One major hypothesis to explain ERC is that fluctuations in evolutionary pressure acting on entire pathways cause parallel rate changes for functionally related proteins. To explore this hypothesis we analyzed ERC within DNA mismatch repair (MMR) and meiosis proteins over phylogenies of 18 yeast species and 22 mammalian species. We identified a strong signature of ERC between eight yeast proteins involved in meiotic crossing over, which seems to have resulted from relaxation of constraint specifically in Candida glabrata. These and other meiotic proteins in C. glabrata showed marked rate acceleration, likely due to its apparently clonal reproductive strategy and the resulting infrequent use of meiotic proteins. This correlation between change of reproductive mode and change in constraint supports an evolutionary pressure origin for ERC. Moreover, we present evidence for similar relaxations of constraint in additional pathogenic yeast species. Mammalian MMR and meiosis proteins also showed statistically significant ERC; however, there was not strong ERC between crossover proteins, as observed in yeasts. Rather, mammals exhibited ERC in different pathways, such as piRNA-mediated defense against transposable elements. Overall, if fluctuation in evolutionary pressure is responsible for ERC, it could reveal functional relationships within entire protein pathways, regardless of whether they physically interact or not, so long as there was variation in constraint on that pathway. PMID:23183665

Clark, Nathan L; Alani, Eric; Aquadro, Charles F

2013-02-01

54

Evolutionary Rate Covariation in Meiotic Proteins Results from Fluctuating Evolutionary Pressure in Yeasts and Mammals  

PubMed Central

Evolutionary rates of functionally related proteins tend to change in parallel over evolutionary time. Such evolutionary rate covariation (ERC) is a sequence-based signature of coevolution and a potentially useful signature to infer functional relationships between proteins. One major hypothesis to explain ERC is that fluctuations in evolutionary pressure acting on entire pathways cause parallel rate changes for functionally related proteins. To explore this hypothesis we analyzed ERC within DNA mismatch repair (MMR) and meiosis proteins over phylogenies of 18 yeast species and 22 mammalian species. We identified a strong signature of ERC between eight yeast proteins involved in meiotic crossing over, which seems to have resulted from relaxation of constraint specifically in Candida glabrata. These and other meiotic proteins in C. glabrata showed marked rate acceleration, likely due to its apparently clonal reproductive strategy and the resulting infrequent use of meiotic proteins. This correlation between change of reproductive mode and change in constraint supports an evolutionary pressure origin for ERC. Moreover, we present evidence for similar relaxations of constraint in additional pathogenic yeast species. Mammalian MMR and meiosis proteins also showed statistically significant ERC; however, there was not strong ERC between crossover proteins, as observed in yeasts. Rather, mammals exhibited ERC in different pathways, such as piRNA-mediated defense against transposable elements. Overall, if fluctuation in evolutionary pressure is responsible for ERC, it could reveal functional relationships within entire protein pathways, regardless of whether they physically interact or not, so long as there was variation in constraint on that pathway.

Clark, Nathan L.; Alani, Eric; Aquadro, Charles F.

2013-01-01

55

Protein aggregation due to nsSNP resulting in P56S VABP protein is associated with amyotrophic lateral sclerosis.  

PubMed

Mutations in the gene encoding vesicle-associated membrane protein (VAPB) cause amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disorder. The VAPB gene is mapped to chromosome number 20 and can be found at cytogenetic location 20q13.33 of the chromosome. VAPB is seen to play a significant role in the unfolded protein response (UPR), which is a process that suppresses the accumulation of unfolded proteins in the endoplasmic reticulum. Earlier studies have reported two points; which we have analyzed in our study. Firstly, the mutation P56S in the VAPB is seen to increase the stability of the protein and secondly, the mutation P56S in VAPB is seen to interrupt the functioning of the gene and loses its ability to be involved in the activation of the IRE1/XBP1 pathway which leads to ALS. With correlation on the previous research studies on the stability of this protein, we carried out Molecular dynamics (MD) simulation. We analyzed the SNP results of 17 nsSNPs obtained from dbSNP using SIFT, polyphen, I-Mutant, SNP&GO, PhDSNP and Mutpred to predict the role of nsSNPs in VAPB. MD simulation is carried out and plots for RMSD, RMSF, Rg, SASA, H-bond and PCA are obtained to check and prove the stability of the wild type and the mutant protein structure. The protein is checked for its aggregation and the results obtained show changes in the protein structure that might result in the loss of function. PMID:24681403

Vinay Kumar, Chundi; Kumar, K M; Swetha, Rayapadi; Ramaiah, Sudha; Anbarasu, Anand

2014-08-01

56

Size- and shape-controlled synthesis of ZnSe nanocrystals using SeO2 as selenium precursor.  

PubMed

Here we report a low-cost and "green" phosphine-free route for the size- and shape-controlled synthesis of high-quality zinc blende (cubic) ZnSe nanocrystals. To avoid the use of expensive and toxic solvents such as trioctylphosphine (TOP) or tributylphosphine (TBP), SeO(2) was dispersed in 1-octadecene (ODE) as a chalcogen precursor. It has been found that the temperature and the surface ligand influenced the nucleation, the reaction speed and the formation of different shapes. Absorption spectroscopy, fluorescence spectroscopy, powder X-ray diffraction (XRD) and transmission electron microscopy (TEM) were used for the characterization of the as-synthesized ZnSe nanocrystals. The size-dependent photoluminescence (PL) range of the as-prepared ZnSe nanocrystals was between 390 and 450 nm, with the PL full width at half-maximum (FWHM) well controlled between 14 and 18 nm and PL quantum yields reached up to 40% at room temperature. Moreover, this new selenium precursor can be used to form tetrapod-shaped ZnSe nanocrystals when zinc acetylacetonate was introduced as the zinc precursor with a one-pot method. PMID:20976341

Shen, Huaibin; Niu, Jin Zhong; Wang, Hongzhe; Li, Xiaomin; Li, Lin Song; Chen, Xia

2010-12-21

57

Recent results and new hardware developments for protein crystal growth in microactivity  

NASA Technical Reports Server (NTRS)

Protein crystal growth experiments have been performed on 16 space shuttle missions since April, 1985. The initial experiments utilized vapor diffusion crystallization techniques similar to those used in laboratories for earth-based experiments. More recent experiments have utilized temperature induced crystallization as an alternative method for growing high quality protein crystals in microgravity. Results from both vapor diffusion and temperature induced crystallization experiments indicate that proteins grown in microgravity may be larger, display more uniform morphologies, and yield diffraction data to significantly higher resolutions than the best crystals of these proteins grown on earth.

Delucas, L. J.; Long, M. M.; Moore, K. M.; Smith, C.; Carson, M.; Narayana, S. V. L.; Carter, D.; Clark, A. D., Jr.; Nanni, R. G.; Ding, J.

1993-01-01

58

Amino acid enrichment and compositional changes among mammalian milk proteins and the resulting nutritional consequences.  

PubMed

Milk is a hallmark of mammalian evolution: a unique food that has evolved with mammals. Despite the importance of this food, it is not known if variation in AA composition between different species is important to milk proteins or how it might affect the nutritional value of milk. As milk is the only food source for newborn mammals, it has long been speculated that milk proteins should be enriched in essential AA. However, no systematic analysis supports this assumption. Although many factors influence the overall nutritional value of milk, including total protein concentration, we focused here on the AA composition of milk proteins and investigated the possibility that selection drives compositional changes. We identified 9 major milk proteins present in 13 mammalian species and compared them with a large group of nonmilk proteins. Our results indicate heterogeneity in the AA composition of milk proteins, showing significant enrichment and depletion of certain AA in milk-specific proteins. Although high levels of particular AA appear to be consistently maintained, orthologous milk proteins display significant differences in AA composition across species, most notably among the caseins. Interspecies variation of milk composition is thought to be indicative of nutritional optimization to the requirements of the species. In accordance with this, our observations indicate that milk proteins may have adapted to the species-specific nutritional needs of the neonate. PMID:24472131

Khaldi, Nora; Holton, Thérèse A; Shields, Denis C

2014-03-01

59

Volume Changes Due to SO2-4, SeO2-4, and H2PO-4 Adsorption on Amorphous Iron(III) Hydroxide in an Aqueous Suspension.  

PubMed

Volume changes due to SO2-4, SeO2-4, and H2PO-4 adsorption on amorphous iron(III) hydroxide were determined by dilatometry in a mixture comprising an aqueous solution of Na2SO4, Na2SeO4, or NaH2PO4 and amorphous iron(III) hydroxide suspended in 0.1 mol dm-3 NaClO4 at an initial pH ranged from 4.50 to 6.50. System volumes increased during SO2-4, SeO2-4, and H2PO-4 adsorption on amorphous iron(III) hydroxide, suggesting that some hydrated water around aqueous SO2-4, SeO2-4, or H2PO-4 ions and amorphous iron(III) hydroxide were released to the bulk. The volume changes due to SO2-4, SeO2-4, and H2PO-4 adsorption at initial pH 4.50 were +18, +18, and +14 cm3 mol-1, respectively. Phosphate, which adsorbed as an inner-sphere complex, released most of its hydration water to the bulk. The volume changes due to SO2-4 and SeO2-4 adsorption indicated that they were dehydrated at the water/amorphous iron(III) hydroxide interface. The smaller changes in volume for H2PO-4 compared to SO2-4 and SeO2-4 may be explained by differences of charges and adsorption mechanisms of these oxoanions. Copyright 1999 Academic Press. PMID:9885267

Yamaguchi; Okazaki; Hashitani

1999-01-15

60

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

2013-07-01

61

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

62

Casein protein results in higher prandial and exercise induced whole body protein anabolism than whey protein in Chronic Obstructive Pulmonary Disease  

PubMed Central

Objective 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. Materials and Methods 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 minutes 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 hour of recovery. Results In the healthy group, WbPS, SPE, and NetPS were higher during casein than during whey feeding (p<0.01). WbPS and NetPS were higher during exercise, independent of exercise intensity (p<0.01). NetPS was higher during casein feeding in COPD due to lower WbPB (p<0.05). Higher SPE was found during exercise during casein and whey feeding in COPD (p<0.05). Lactate levels during exercise were higher in COPD (p<0.05) independent of the protein. Post-exercise, lower NetPS values were found independent of protein type in both groups. Conclusion 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.

Engelen, Marielle PKJ; Rutten, Erica PA; De Castro, Carmen LN; Wouters, Emiel FM; Schols, Annemie MWJ; Deutz, Nicolaas EP

2012-01-01

63

Result-driven strategies for protein identification and quantitation--a way to optimize experimental design and derive reliable results.  

PubMed

Uni- or multidimensional microcapillary liquid chromatography (microLC) matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry (MS/MS) approaches have gained significant attention for quantifying and identifying proteins in complex biological samples. The off-line coupling of microLC with MS quantitation and MS/MS identification methods makes new result-dependent workflows possible. A relational database is used to store the results from multiple high performance liquid chromatography runs, including information about MALDI plate positions, and both peptide and protein quantitations, and identifications. Unlike electrospray methodology, where all the decisions about which peptide to fragment, must be made during peptide fractionations, in the MALDI experiments the samples are effectively "frozen in time". Therefore, additional MS and MS/MS spectra can be acquired, to promote more accurate quantitation or additional identifications until reliable results are derived that meet experimental design criteria. In the case of what can be designated the expression-dependent workflow, quantitation can be detached from identification and only peak pairs with biological relevant expression changes can be selected for further MS/MS analyses. Alternatively, additional MS/MS data can be acquired to confirm tentative peptide mass fingerprint hits in what is designated a search result-dependent workflow. In the MS data-dependent workflow, the goal is to collect as many meaningful spectra as possible by judiciously adjusting the acquisition parameters based on characteristics of the parent masses. This level of sophistication requires the development of innovative algorithms for these three result-dependent workflows that make MS and MS/MS analysis more efficient and also add confidence to experimental results. PMID:14760720

Graber, Armin; Juhasz, Peter S; Khainovski, Nikita; Parker, Kenneth C; Patterson, Dale H; Martin, Stephen A

2004-02-01

64

Modeling how reproductive ecology can drive protein diversification and result in linkage disequilibrium between sperm and egg proteins.  

PubMed

Gamete-recognition proteins determine whether sperm and eggs are compatible at fertilization, and they often evolve rapidly. The source of selection driving the evolution of these proteins is still debated. It has been suggested that sexual conflict can result in proliferation of genetic variation and possibly linkage disequilibrium between sperm and egg proteins. Empirical evidence suggests that both male and female reproductive success can be predicted by their sperm ligand genotype, but why female success can be predicted by a protein expressed only in males is unknown. Here we use mathematical modeling to investigate the interaction between reproductive behavior and sperm availability on the evolution of sperm ligands and egg receptors. We consider haploid and diploid expression in gametes in two possible ecological scenarios, monogamous spawning and competitive spawning. Reproductive behavior plays an important role in determining possible outcomes resulting from sexual conflict. Sperm limitation selects for common genotypes regardless of mating behavior. Under conditions of sperm abundance, competitive spawning provides conditions for the persistence of allelic variation and gametic disequilibrium. With monogamous spawning, such conditions are more restrictive. PMID:20455709

Tomaiuolo, Maurizio; Levitan, Don R

2010-07-01

65

Dysregulation of protein modification by ISG15 results in brain cell injury  

PubMed Central

UBP43 (USP18) is a protease that removes the ubiquitin-like modifier ISG15 from conjugated proteins. Here we present the first report of dysregulation of protein ISG15 modification by the generation of UBP43 knockout mice. In the absence of UBP43, brain tissue showed an elevated level of ISG15 conjugates, and cellular necrosis was evident in the ependyma. Such disruption of the blood–brain barrier resulted in severe neurologic disorders. These results demonstrate that UBP43 plays a critical role in maintaining the homeostatic balance of ISG15-conjugated protein, and that regulation of cellular levels of ISG15 protein modification is essential for brain cell function.

Ritchie, Kenneth J.; Malakhov, Michael P.; Hetherington, Christopher J.; Zhou, Liming; Little, Marie-Terese; Malakhova, Oxana A.; Sipe, Jack C.; Orkin, Stuart H.; Zhang, Dong-Er

2002-01-01

66

Crystal and magnetic structures and magnetic properties of selenate containing natrochalcite, A(I)M(II)2(H3O2)(SeO4)2 where A = Na or K and M = Mn, Co, or Ni.  

PubMed

The synthesis of a series of selenate containing natrochalcite, A(I)M(II)(2)(H(3)O(2))(SeO(4))(2) where A = Na or K and M = Mn, Co, or Ni (here labeled as AMH and AMD for the hydrogenated and deuterated compounds, respectively), the X-ray crystal structure determinations from single crystals (Ni) and powder (Mn), magnetic properties, and magnetic structures of the cobalt analogues are reported. The nuclear crystal structures for NaNiH, KNiH, and KMnH are similar to those reported for the cobalt analogues (NaCoH and KCoH) and consist of chains of edge-sharing octahedra (MO(6)) which are connected by H(3)O(2) and SeO(4) to form layers which are in turn bridged by the alkali, in an octahedral coordination site, to form the 3D-framework. The magnetic properties are characterized by antiferromagnetic interaction at high temperatures and antiferromagnetic ordering at low temperatures (NaCoH, 3.5 K; KCoH, 5.9 K; KNiH, 8.5 K; and KMnH, 16 K), except for KNi(2)(H(3)O(2))(SeO(4))(2) which displays a weak ferromagnetic interaction and no long-range ordering above 2 K. The neutron magnetic structures of the cobalt analogues, studied as a function of temperature, are different for the two cobalt salts and also different from all the known magnetic structures of the natrochalcite family. Whereas the magnetic structure of NaCoD has a k = (0, 0, 0), that of KCoD has one consisting of a doubled nuclear cell, k = (0, 0, 1/2). Both compounds have four magnetic sublattices related to the four cobalt atoms of the nuclear unit cell. In NaCoD the moments are in the bc-plane, M(y) = 2.51(2) ?(B) and M(z) = 1.29(4) ?(B), with the major component along the cobalt chain and the resultant moment, 2.83(3) ?(B), making an angle of 27° with the b-axis. The sum of the moments within the cell is zero. For KCoD the moment at each cobalt site has a component along each crystallographic axis, M(x) = 2.40(3), M(y) = 1.03(3), M(z) = 1.59(8) giving a total M = 2.49(3) ?(B). Within one nuclear cell the moments are fully compensated. The moments corresponding to the cobalt atoms of the second nuclear cell comprising the magnetic unit cell are oriented in opposite directions. PMID:22263636

Maalej, Wassim; Vilminot, Serge; André, Gilles; Elaoud, Zakaria; Mhiri, Tahar; Kurmoo, Mohamedally

2012-02-01

67

Overexpression of a Gluten Protein in Transgenic Wheat Results in Greatly Increased Dough Strength  

Microsoft Academic Search

The transgenic wheat line B73-6-1 contains additional genes encoding a gluten protein called HMW subunit 1Dx5, resulting in a four-fold increase in the proportion of this component in the seed proteins and corresponding increases in the proportions of total HMW subunits and total glutenins. This is associated with a dramatic increase in dough strength, as measured using a small scale

L Rooke; F Békés; R Fido; F Barro; P Gras; A. S Tatham; P Barcelo; P Lazzeri; P. R Shewry

1999-01-01

68

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

2012-09-01

69

Switching behaviour of modulated ferroelectrics: the kinetics of the field induced lock-in transition in K2SeO4  

NASA Astrophysics Data System (ADS)

The field induced switching process across the ferroelectric lock-in transition in K2SeO4 has been studied on a millisecond timescale using stroboscopic neutron diffraction. The time evolution of both the first and the third order satellites was examined. The time constants are found to vary with temperature between 0.2 and 1.2 ms. This is an order of magnitude faster than in the isostructural Rb2ZnCl4. Moreover, the time dependence of the satellite's linewidth provides information about the evolution of the coherence of the modulated structure.

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

2011-08-01

70

Study on the Incommensurate Nature of the Intermediate Phase of RbD3(SeO3)2 by Neutron Diffraction  

NASA Astrophysics Data System (ADS)

Search for an intermediate phase between the para- and ferro-electric phases of RbD3(SeO3)2 was carried out by neutron diffraction. The superlattice reflection at (2, 0, 0.5) in the ferroelectric phase was found to shift to an incommensurate position, (2, 0, 0.5+?), above the Curie point though the magnitude of the parameter ? is very small. It increases with increasing temperature and reaches to 0.003 at the paraelectric-to-intermediate transition point which is about 3 K above the Curie point.

Gesi, Kazuo; Iizumi, Masashi

1980-02-01

71

Targeted disruption of a G protein alpha subunit gene results in reduced pathogenicity in Fusarium oxysporum.  

PubMed

The cloning of fga1, the gene encoding a G protein alpha subunit, was performed by standard PCR techniques and by screening a Fusarium oxysporum genomic library, using the PCR product as a probe. The full-length open reading frame spanned 1,059 nucleotides and the deduced primary structure of the protein (353 amino acid residues) showed high identity to those of G protein alpha(i) family proteins from other filamentous fungi. Disruption of fga1 had no effect on vegetative growth, but reduced the conidiation and pathogenicity of the fungus. Disruptants also showed a decreased level of intracellular cAMP and increased resistance to heat shock at 45 degrees C. These results suggest that the Galpha subunit encoded by fga1 is involved in a signal transduction pathway in F. oxysporum that controls conidiation, heat resistance and pathogenicity. PMID:12228810

Jain, Sona; Akiyama, Kouichi; Mae, Kenjiro; Ohguchi, Tomizo; Takata, Renkichi

2002-09-01

72

Body Composition, Dietary Protein and Body Weight Regulation. Reconciling Conflicting Results from Intervention and Observational Studies?  

PubMed Central

Background/Objectives Physiological evidence indicates that high-protein diets reduce caloric intake and increase thermogenic response, which may prevent weight gain and regain after weight loss. Clinical trials have shown such effects, whereas observational cohort studies suggest an association between greater protein intake and weight gain. In both types of studies the results are based on average weight changes, and show considerable diversity in both directions. This study investigates whether the discrepancy in the evidence could be due to recruitment of overweight and obese individuals into clinical trials. Subjects/Methods Data were available from the European Diet, Obesity and Genes (DiOGenes) post-weight-loss weight-maintenance trial and the Danish Diet, Cancer and Health (DCH) cohort. Participants of the DCH cohort were matched with participants from the DiOGenes trial on gender, diet, and body characteristics. Different subsets of the DCH-participants, comparable with the trial participants, were analyzed for weight maintenance according to the randomization status (high or low protein) of the matched trial participants. Results Trial participants were generally heavier, had larger waist circumference and larger fat mass than the participants in the entire DCH cohort. A better weight maintenance in the high-protein group compared to the low protein group was observed in the subgroups of the DCH cohort matching body characteristics of the trial participants. Conclusion This modified observational study, minimized the differences between the RCT and observational data with regard to dietary intake, participant characteristics and statistical analysis. Compared with low protein diet the high protein diet was associated with better weight maintenance when individuals with greater body mass index and waist circumference were analyzed. Selecting subsets of large-scale observational cohort studies with similar characteristics as participants in clinical trials may reconcile the otherwise conflicting results.

Ankarfeldt, Mikkel Z.; Angquist, Lars; Stocks, Tanja; Jakobsen, Marianne U.; Overvad, Kim; Halkjaer, Jytte; Saris, Wim H. M.; Astrup, Arne; S?rensen, Thorkild I. A.

2014-01-01

73

Oxidative stress status accompanying diabetic bladder cystopathy results in the activation of protein degradation pathways  

PubMed Central

Objectives To investigate the role that oxidative stress plays in the development of diabetic cystopathy. Materials and methods Comparative gene expression in the bladder of non-diabetic and streptozotocin (STZ)-induced 2-month-old diabetic rats was carried out using microarray analysis. Evidence of oxidative stress was investigated in the bladder by analyzing glutathione S-transferase activity, lipid peroxidation, and carbonylation and nitrosylation of proteins. The activity of protein degradation pathways was assessed using western blot analysis. Results Analysis of global gene expression showed that detrusor smooth muscle tissue of STZ-induced diabetes undergoes significant enrichment in targets involved in the production or regulation of reactive oxygen species (P = 1.27 × 10?10). The microarray analysis was confirmed by showing that markers of oxidative stress were all significantly increased in the diabetic bladder. It was hypothesized that the sequelae to oxidative stress would be increased protein damage and apoptosis. This was confirmed by showing that two key proteins involved in protein degradation (Nedd4 and LC3B) were greatly up-regulated in diabetic bladders compared to controls by 12.2 ± 0.76 and 4.4 ± 1.0-fold, respectively, and the apoptosis inducing protein, BAX, was up-regulated by 6.76 ± 0.76-fold. Conclusions Overall, the findings obtained in the present study add to the growing body of evidence showing that diabetic cystopathy is associated with oxidative damage of smooth muscle cells, and results in protein damage and activation of apoptotic pathways that may contribute to a deterioration in bladder function.

Kanika, Nirmala; Chang, Jinsook; Tong, Yuehong; Tiplitsky, Scott; Lin, Juan; Yohannes, Elizabeth; Tar, Moses; Chance, Mark; Christ, George J.; Melman, Arnold; Davies, Kelvin

2010-01-01

74

Small structural differences of targeted anti-tumor toxins result in strong variation of protein expression.  

PubMed

Targeted anti-tumor toxins consist of a toxic functional moiety that is chemically linked or recombinantly fused to a cell-directing ligand. Ribosome-inactivating proteins (RIPs), especially type I RIPs such as saporin or dianthin, are commonly used as toxin components. Although expression of type I RIP-based fusion proteins is well reported, the achievement of higher protein yields in heterologous expression systems through innovative strategies is of major interest. In the present study, the targeted toxins (his)saporin-EGF (SE) and (his)dianthin-EGF (DE) were expressed as fusion proteins under identical expression conditions. However, the total amount of DE was nearly two-times higher than SE. The identity of the heterologously expressed targeted toxins was confirmed by mass spectrometric studies. Their biological specific activity, monitored in real time, was almost equal. Sequence alignment shows 84% identity and a structural comparison revealed five major differences, two of which affect the secondary structure resulting in a loop (SE) to ?-strand (DE) conversion and one introduces a gap in SE (after position 57). In conclusion, these structural variations resulted in different protein expression levels while codon usage and toxicity to bacteria were excluded as a cause. Minor structural differences identified in this study may be considered responsible for the protection of DE from bacterial proteases and therefore may serve as a lead to modify certain domains in type I RIP-based targeted toxins. PMID:23867360

Gilabert-Oriol, Roger; Thakur, Mayank; Weise, Christoph; Dernedde, Jens; von Mallinckrodt, Benedicta; Fuchs, Hendrik; Weng, Alexander

2013-09-01

75

Arenavirus budding resulting from viral-protein-associated cell membrane curvature.  

PubMed

Viral replication occurs within cells, with release (and onward infection) primarily achieved through two alternative mechanisms: lysis, in which virions emerge as the infected cell dies and bursts open; or budding, in which virions emerge gradually from a still living cell by appropriating a small part of the cell membrane. Virus budding is a poorly understood process that challenges current models of vesicle formation. Here, a plausible mechanism for arenavirus budding is presented, building on recent evidence that viral proteins embed in the inner lipid layer of the cell membrane. Experimental results confirm that viral protein is associated with increased membrane curvature, whereas a mathematical model is used to show that localized increases in curvature alone are sufficient to generate viral buds. The magnitude of the protein-induced curvature is calculated from the size of the amphipathic region hypothetically removed from the inner membrane as a result of translation, with a change in membrane stiffness estimated from observed differences in virion deformation as a result of protein depletion. Numerical results are based on experimental data and estimates for three arenaviruses, but the mechanisms described are more broadly applicable. The hypothesized mechanism is shown to be sufficient to generate spontaneous budding that matches well both qualitatively and quantitatively with experimental observations. PMID:23864502

Schley, David; Whittaker, Robert J; Neuman, Benjamin W

2013-09-01

76

Arenavirus budding resulting from viral-protein-associated cell membrane curvature  

PubMed Central

Viral replication occurs within cells, with release (and onward infection) primarily achieved through two alternative mechanisms: lysis, in which virions emerge as the infected cell dies and bursts open; or budding, in which virions emerge gradually from a still living cell by appropriating a small part of the cell membrane. Virus budding is a poorly understood process that challenges current models of vesicle formation. Here, a plausible mechanism for arenavirus budding is presented, building on recent evidence that viral proteins embed in the inner lipid layer of the cell membrane. Experimental results confirm that viral protein is associated with increased membrane curvature, whereas a mathematical model is used to show that localized increases in curvature alone are sufficient to generate viral buds. The magnitude of the protein-induced curvature is calculated from the size of the amphipathic region hypothetically removed from the inner membrane as a result of translation, with a change in membrane stiffness estimated from observed differences in virion deformation as a result of protein depletion. Numerical results are based on experimental data and estimates for three arenaviruses, but the mechanisms described are more broadly applicable. The hypothesized mechanism is shown to be sufficient to generate spontaneous budding that matches well both qualitatively and quantitatively with experimental observations.

Schley, David; Whittaker, Robert J.; Neuman, Benjamin W.

2013-01-01

77

SeO2 ?  

NASA Astrophysics Data System (ADS)

This document is part of Subvolume A11 'Structure Types. Part 11: Space Groups (135) P42/mbc - (123) P4/mmm' of Volume 43 'Crystal Structures of Inorganic Compounds' of Landolt-Börnstein - Group III 'Condensed Matter'.

Villars, P.; Cenzual, K.; Gladyshevskii, R.; Shcherban, O.; Dubenskyy, V.; Kuprysyuk, V.; Savysyuk, I.; Zaremba, R.

78

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

79

Pokeweed antiviral protein alters splicing of HIV-1 RNAs, resulting in reduced virus production.  

PubMed

Processing of HIV-1 transcripts results in three populations in the cytoplasm of infected cells: full-length RNA, singly spliced, and multiply spliced RNAs. Rev, regulator of virion expression, is an essential regulatory protein of HIV-1 required for transporting unspliced and singly spliced viral transcripts from the nucleus to the cytoplasm. Export allows these RNAs to be translated and the full-length RNA to be packaged into virus particles. In our study, we investigate the activity of pokeweed antiviral protein (PAP), a glycosidase isolated from the pokeweed plant Phytolacca americana, on the processing of viral RNAs. We show that coexpression of PAP with a proviral clone alters the splicing ratio of HIV-1 RNAs. Specifically, PAP causes the accumulation of multiply spliced 2-kb RNAs at the expense of full-length 9-kb and singly spliced 4-kb RNAs. The change in splicing ratio is due to a decrease in activity of Rev. We show that PAP depurinates the rev open reading frame and that this damage to the viral RNA inhibits its translation. By decreasing Rev expression, PAP indirectly reduces the availability of full-length 9-kb RNA for packaging and translation of the encoded structural proteins required for synthesis of viral particles. The decline we observe in virus protein expression is not due to cellular toxicity as PAP did not diminish translation rate. Our results describing the reduced activity of a regulatory protein of HIV-1, with resulting change in virus mRNA ratios, provides new insight into the antiviral mechanism of PAP. PMID:24951553

Zhabokritsky, Alice; Mansouri, Sheila; Hudak, Katalin A

2014-08-01

80

Diurnal Rhythms Result in Significant Changes in the Cellular Protein Complement in the Cyanobacterium Cyanothece 51142  

SciTech Connect

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.

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

2011-02-22

81

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

82

Cation-cation interactions: crystal structures of neptunyl(V) selenate hydrates, (NpO2)2(SeO4)(H2O)n (n=1, 2, and 4).  

PubMed

Green crystals of (NpO(2))(2)(SeO(4))(H(2)O)(4), (NpO(2))(2)(SeO(4))(H(2)O)(2), and (NpO(2))(2)(SeO(4))(H(2)O) have been prepared by hydrothermal methods. The structures of these compounds have been characterized by single-crystal X-ray diffraction. (NpO(2))(2)(SeO(4))(H(2)O)(4), isostructural with (NpO(2))(2)(SO(4))(H(2)O)(4), is constructed from layers comprised of corner-sharing neptunyl(V) pentagonal bipyramids and selenate tetrahedra that are further linked by hydrogen bonding with water molecules. Each NpO(2)(+) cation binds to four other NpO(2)(+) units through cation-cation interactions (CCIs) to form a distorted "cationic square net" decorated by SeO(4)(2-) tetrahedra above and below the layer. Each selenate anion is bound to two neptunyl(V) cations through monodentate linkages. (NpO(2))(2)(SeO(4))(H(2)O)(2) is isostructural with the corresponding sulfate analogue as well. It consists of puckered layers of neptunyl(V) pentagonal bipyramids that are further connected by selenate tetrahedra to form a three-dimensional framework. The CCI pattern in the neptunyl layers of dihydrate is very similar to that of tetrahydrate; however, each SeO(4)(2-) tetrahedron is bound to four NpO(2)(+) cations in a mondentate manner. (NpO(2))(2)(SeO(4))(H(2)O) crystallizes in the monoclinic space group P2(1)/c, which differs from the (NpO(2))(2)(SO(4))(H(2)O) orthorhombic structure due to the slightly different connectivities between NpO(2)(+) cations and anionic ligands. The structure of (NpO(2))(2)(SeO(4))(H(2)O) adopts a three-dimensional network of distort neptunyl(V) pentagonal bipyramids decorated by selenate tetrahedra. Each NpO(2)(+) cation connects to four other NpO(2)(+) units through CCIs and also shares an equatorial coordinating oxygen atom with one of the other units in addition to the CC bond to form a dimer. Each SeO(4)(2-) tetrahedron is bound to five NpO(2)(+) cations in a monodentate manner. Magnetic measurements obtained from the powdered tetrahydrate are consistent with a ferromagnetic ordering of the neptunyl(V) spins at 8(1) K, with an average low temperature saturation moment of 1.98(8) ?(B) per Np. Well above the ordering temperature, the susceptibility follows Curie-Weiss behavior, with an average effective moment of 3.4(2) ?(B) per Np and a Weiss constant of 14(4) K. Correlations between lattice dimensionality and magnetic behavior are discussed. PMID:21520896

Jin, Geng Bang; Skanthakumar, S; Soderholm, L

2011-06-01

83

Protein crystal growth results from the United States Microgravity Laboratory-1 mission  

NASA Technical Reports Server (NTRS)

Protein crystal growth experiments have been performed by this laboratory on 18 Space Shuttle missions since April, 1985. In addition, a number of microgravity experiments also have been performed and reported by other investigators. These Space Shuttle missions have been used to grow crystals of a variety of proteins using vapor diffusion, liquid diffusion, and temperature-induced crystallization techniques. The United States Microgravity Laboratory - 1 mission (USML-1, June 25 - July 9, 1992) was a Spacelab mission dedicated to experiments involved in materials processing. New protein crystal growth hardware was developed to allow in orbit examination of initial crystal growth results, the knowledge from which was used on subsequent days to prepare new crystal growth experiments. In addition, new seeding hardware and techniques were tested as well as techniques that would prepare crystals for analysis by x-ray diffraction, a capability projected for the planned Space Station. Hardware that was specifically developed for the USML-1 mission will be discussed along with the experimental results from this mission.

Delucas, Lawrence J.; Moore, K. M.; Vanderwoerd, M.; Bray, T. L.; Smith, C.; Carson, M.; Narayana, S. V. L.; Rosenblum, W. M.; Carter, D.; Clark, A. D, Jr.

1994-01-01

84

CaCu2(SeO3)2Cl2: Spin-(1)/(2) Heisenberg chain compound with complex frustrated interchain couplings  

NASA Astrophysics Data System (ADS)

We report the crystal structure, magnetization measurements, and band-structure calculations for the spin-(1)/(2) quantum magnet CaCu2(SeO3)2Cl2. The magnetic behavior of this compound is well reproduced by a uniform spin-(1)/(2) chain model with the nearest-neighbor exchange of about 133 K. Due to the peculiar crystal structure, spin chains run in the direction almost perpendicular to the structural chains. We find an exotic regime of frustrated interchain couplings owing to two inequivalent exchanges of 10 K each. Peculiar superexchange paths grant an opportunity to investigate bond-randomness effects under partial Cl-Br substitution.

Janson, Oleg; Tsirlin, Alexander A.; Osipova, Elena S.; Berdonosov, Peter S.; Olenev, Andrei V.; Dolgikh, Valery A.; Rosner, Helge

2011-04-01

85

Upregulation of elastase proteins results in aortic dilatation in mucopolysaccharidosis I mice  

PubMed Central

Mucopolysaccharidosis I (MPS I), known as Hurler syndrome in the severe form, is a lysosomal storage disease due to ?-l-iduronidase (IDUA) deficiency. It results in fragmentation of elastin fibers in the aorta and heart valves via mechanisms that are unclear, but may result from the accumulation of the glycosaminoglycans heparan and dermatan sulfate. Elastin fragmentation causes aortic dilatation and valvular insufficiency, which can result in cardiovascular disease. The pathophysiology of aortic disease was evaluated in MPS I mice. MPS I mice have normal elastic fiber structure and aortic compliance at early ages, which suggests that elastin assembly is normal. Elastin fragmentation and aortic dilatation are severe at 6 months, which is temporally associated with marked increases in mRNA and enzyme activity for two elastin-degrading proteins, matrix metalloproteinase-12 (MMP-12) and cathepsin S. Upregulation of these genes likely involves activation of STAT proteins, which may be induced by structural stress to smooth muscle cells from accumulation of glycosaminoglycans in lysosomes. Neonatal intravenous injection of a retroviral vector normalized MMP-12 and cathepsin S mRNA levels and prevented aortic disease. We conclude that aortic dilatation in MPS I mice is likely due to degradation of elastin by MMP-12 and/or cathepsin S. This aspect of disease might be ameliorated by inhibition of the signal transduction pathways that upregulate expression of elastase proteins, or by inhibition of elastase activity. This could result in a treatment for patients with MPS I, and might reduce aortic aneurism formation in other disorders.

Ma, Xiucui; Tittiger, Mindy; Knutsen, Russell H.; Kovacs, Attila; Schaller, Laura; Mecham, Robert P.; Ponder, Katherine P.

2013-01-01

86

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

87

HIV-1 Tat Protein Increases Microglial Outward K+ Current and Resultant Neurotoxic Activity  

PubMed Central

Microglia plays a crucial role in the pathogenesis of HIV-1-associated neurocognitive disorders. Increasing evidence indicates the voltage-gated potassium (Kv) channels are involved in the regulation of microglia function, prompting us to hypothesize Kv channels may also be involved in microglia-mediated neurotoxic activity in HIV-1-infected brain. To test this hypothesis, we investigated the involvement of Kv channels in the response of microglia to HIV-1 Tat protein. Treatment of rat microglia with HIV-1 Tat protein (200 ng/ml) resulted in pro-inflammatory microglial activation, as indicated by increases in TNF-?, IL-1?, reactive oxygen species, and nitric oxide, which were accompanied by enhanced outward K+ current and Kv1.3 channel expression. Suppression of microglial Kv1.3 channel activity, either with Kv1.3 channel blockers Margatoxin, 5-(4-Phenoxybutoxy)psoralen, or broad-spectrum K+ channel blocker 4-Aminopyridine, or by knockdown of Kv1.3 expression via transfection of microglia with Kv1.3 siRNA, was found to abrogate the neurotoxic activity of microglia resulting from HIV-1 Tat exposure. Furthermore, HIV-1 Tat-induced neuronal apoptosis was attenuated with the application of supernatant collected from K+ channel blocker-treated microglia. Lastly, the intracellular signaling pathways associated with Kv1.3 were investigated and enhancement of microglial Kv1.3 was found to correspond with an increase in Erk1/2 mitogen-activated protein kinase activation. These data suggest targeting microglial Kv1.3 channels may be a potential new avenue of therapy for inflammation-mediated neurological disorders.

Liu, Jianuo; Xu, Peng; Collins, Cory; Liu, Han; Zhang, Jingdong; Keblesh, James P.; Xiong, Huangui

2013-01-01

88

Desulfurization of Cysteine-Containing Peptides Resulting from Sample Preparation for Protein Characterization by MS  

PubMed Central

In this paper, we have examined two cysteine modifications resulting from sample preparation for protein characterization by MS: (1) a previously observed conversion of cysteine to dehydroalanine, now found in the case of disulfide mapping and (2) a novel modification corresponding to conversion of cysteine to alanine. Using model peptides, the conversion of cysteine to dehydroalanine via ?-elimination of a disulfide bond was seen to result from the conditions of typical tryptic digestion (37 °C, pH 7.0– 9.0) without disulfide reduction and alkylation.. Furthermore, the surprising conversion of cysteine to alanine was shown to occur by heating cysteine containing peptides in the presence of a phosphine (TCEP). The formation of alanine from cysteine, investigated by performing experiments in H2O or D2O, suggested a radical-based desulfurization mechanism unrelated to ?-elimination. Importantly, an understanding of the mechanism and conditions favorable for cysteine desulfurization provides insight for the establishment of improved sample preparation procedures of protein analysis.

Wang, Zhouxi; Rejtar, Tomas; Zhou, Zhaohui Sunny; Karger, Barry L.

2010-01-01

89

Mutations in Flavobacterium johnsoniae sprE Result in Defects in Gliding Motility and Protein Secretion?†  

PubMed Central

Cells of the gliding bacterium Flavobacterium johnsoniae move rapidly over surfaces. Transposon mutagenesis was used to identify sprE, which is involved in gliding. Mutations in sprE resulted in the formation of nonspreading colonies on agar. sprE mutant cells in wet mounts were almost completely deficient in attachment to and movement on glass, but a small percentage of cells exhibited slight movements, indicating that the motility machinery was not completely disrupted. SprE is a predicted lipoprotein with a tetratricopeptide repeat domain. SprE is similar in sequence to Porphyromonas gingivalis PorW, which is required for secretion of gingipain protease virulence factors. Disruption of F. johnsoniae sprE resulted in decreased extracellular chitinase activity and decreased secretion of the cell surface motility protein SprB. Reduced secretion of cell surface components of the gliding machinery, such as SprB, may account for the defects in gliding. Orthologs of sprE are found in many gliding and nongliding members of the phylum Bacteroidetes, suggesting that similar protein secretion systems are common among members of this large and diverse group of bacteria.

Rhodes, Ryan G.; Samarasam, Mudiarasan Napoleon; Van Groll, Eric J.; McBride, Mark J.

2011-01-01

90

Protein  

MedlinePLUS

... Reference, Release 14 . 2005. 4. Bernstein, A.M., et al., Major dietary protein sources and risk of ... 52 (11): p. 2277-87. 6. Pan, A., et al., Red meat consumption and mortality: results from ...

91

Inhibition of protein kinase C results in decreased expression of bovine leukemia virus.  

PubMed Central

The in vitro expression of bovine leukemia virus (BLV) in short-term cultured bovine peripheral blood mononuclear cells (PBMC) is associated with increased spontaneous lymphocyte blastogenesis. The purpose of this study was to determine whether intracellular pathways responsible for antigen- or mitogen-induced lymphocyte blastogenesis were also responsible for induction of BLV expression. The protein kinase C (PKC) inhibitor 1-(5-isoquinolinylsulfonyl)-3-methylpiperazine dihydrochloride (3-methyl H7) decreased blastogenesis in a dose-dependent manner, as measured by [3H]thymidine incorporation, in unstimulated, lipopolysaccharide-stimulated and phorbol ester (PMA)-stimulated BLV-infected PBMC. Similarly, 3-methyl H7 decreased BLV expression, as measured by production of gp51 envelope antigen or p24gag antigen, in BLV-infected PBMC under the same conditions. Using an RNase protection assay, the inhibition of BLV expression by 3-methyl H7 was shown to be due to decreased transcriptional activity. The cyclic GMP-dependent protein kinase and cyclic AMP-dependent protein kinase inhibitor N-(2-guanidinoethyl)-5-isoquinolinesulfonamide (HA1004) did not inhibit either BLV expression or blastogenesis of BLV-infected bovine PBMC. Additional evidence for the PKC-dependent expression of BLV was obtained by using a persistently BLV-infected B-lymphocyte cell line, NBC-13. Activation of PKC by PMA in NBC-13 cells increased BLV expression. 3-methyl H7 decreased the PMA-induced expression of BLV in NBC-13 cells in a dose-dependent manner, whereas HA1004 did not inhibit this expression. These results identify a mechanism for the induction of BLV expression through PKC activation and therefore indicate that latency and replication of BLV is controlled by normal B-lymphocyte intracellular signaling pathways. Images

Jensen, W A; Wicks-Beard, B J; Cockerell, G L

1992-01-01

92

Results.  

ERIC Educational Resources Information Center

Describes the Collegiate Results Instrument (CRI), which measures a range of collegiate outcomes for alumni 6 years after graduation. The CRI was designed to target alumni from institutions across market segments and assess their values, abilities, work skills, occupations, and pursuit of lifelong learning. (EV)

Zemsky, Robert; Shaman, Susan; Shapiro, Daniel B.

2001-01-01

93

Compromised Mitochondrial Fatty Acid Synthesis in Transgenic Mice Results in Defective Protein Lipoylation and Energy Disequilibrium  

PubMed Central

A mouse model with compromised mitochondrial fatty acid synthesis has been engineered in order to assess the role of this pathway in mitochondrial function and overall health. Reduction in the expression of mitochondrial malonyl CoA-acyl carrier protein transacylase, a key enzyme in the pathway encoded by the nuclear Mcat gene, was achieved to varying extents in all examined tissues employing tamoxifen-inducible Cre-lox technology. Although affected mice consumed more food than control animals, they failed to gain weight, were less physically active, suffered from loss of white adipose tissue, reduced muscle strength, kyphosis, alopecia, hypothermia and shortened lifespan. The Mcat-deficient phenotype is attributed primarily to reduced synthesis, in several tissues, of the octanoyl precursors required for the posttranslational lipoylation of pyruvate and ?-ketoglutarate dehydrogenase complexes, resulting in diminished capacity of the citric acid cycle and disruption of energy metabolism. The presence of an alternative lipoylation pathway that utilizes exogenous free lipoate appears restricted to liver and alone is insufficient for preservation of normal energy metabolism. Thus, de novo synthesis of precursors for the protein lipoylation pathway plays a vital role in maintenance of mitochondrial function and overall vigor.

Smith, Stuart; Witkowski, Andrzej; Moghul, Ayesha; Yoshinaga, Yuko; Nefedov, Michael; de Jong, Pieter; Feng, Dejiang; Fong, Loren; Tu, Yiping; Hu, Yan; Young, Stephen G.; Pham, Thomas; Cheung, Carling; Katzman, Shana M.; Brand, Martin D.; Quinlan, Casey L.; Fens, Marcel; Kuypers, Frans; Misquitta, Stephanie; Griffey, Stephen M.; Tran, Son; Gharib, Afshin; Knudsen, Jens; Hannibal-Bach, Hans Kristian; Wang, Grace; Larkin, Sandra; Thweatt, Jennifer; Pasta, Saloni

2012-01-01

94

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

95

SANS study of interaction of silica nanoparticles with BSA protein and their resultant structure  

NASA Astrophysics Data System (ADS)

Small angle neutron scattering (SANS) has been carried out to study the interaction of anionic silica nanoparticles (88 Å) with globular protein Bovine Serum Albumin (BSA) (M.W. 66.4 kD) in aqueous solution. The measurements have been carried out on fixed concentration (1 wt %) of Ludox silica nanoparticles with varying concentration of BSA (0-5 wt %) at pH7. Results show that silica nanoparticles and BSA coexist as individual entities at low concentration of BSA where electrostatic repulsive interactions between them prevent their aggregation. However, as the concentration of BSA increases (? 0.5 wt %), it induces the attractive depletion interaction among nanoparticles leading to finally their aggregation at higher BSA concentration (2 wt %). The aggregates are found to be governed by the diffusion limited aggregation (DLA) morphology of fractal nature having fractal dimension about 2.4.

Yadav, Indresh; Aswal, V. K.; Kohlbrecher, J.

2014-04-01

96

Crystallisation of alpha-crustacyanin, the lobster carapace astaxanthin-protein: results from EURECA  

NASA Astrophysics Data System (ADS)

Crystallisation of alpha-crustacyanin, the lobster carapace astaxanthin-protein was attempted under microgravity conditions in EURECA satellite using liquid-liquid diffusion with polyethyleneglycol (PEG) as precipitant; in a second reaction chamber phenol and dioxan were used as additives to prevent composite crystal growth. Crystals of alpha-crustacyanin grown under microgravity from PEG were larger than those grown terrestrially in the same apparatus under otherwise identical conditions. On retrieval, the crystals from PEG were shown to be composite and gave a powder diffraction pattern. The second reaction chamber showed leakage on retrieval and had also been subjected to rapid temperature variation during flight. Crystal fragments were nevertheless recovered but showed a powder diffraction pattern. It is concluded, certainly for liquid-liquid diffusion using PEG alone, that, for crustacyanin, although microgravity conditions resulted in an increase in dimensions of crystals, a measurable improvement in molecular ordering was not achieved.

Zagalsky, P. F.; Wright, C. E.; Parsons, M.

1995-08-01

97

Loss of Niemann-Pick C1 or C2 Protein Results in Similar Biochemical Changes Suggesting That These Proteins Function in a Common Lysosomal Pathway  

PubMed Central

Niemann-Pick Type C (NPC) disease is a lysosomal storage disorder characterized by accumulation of unesterified cholesterol and other lipids in the endolysosomal system. NPC disease results from a defect in either of two distinct cholesterol-binding proteins: a transmembrane protein, NPC1, and a small soluble protein, NPC2. NPC1 and NPC2 are thought to function closely in the export of lysosomal cholesterol with both proteins binding cholesterol in vitro but they may have unrelated lysosomal roles. To investigate this possibility, we compared biochemical consequences of the loss of either protein. Analyses of lysosome-enriched subcellular fractions from brain and liver revealed similar decreases in buoyant densities of lysosomes from NPC1 or NPC2 deficient mice compared to controls. The subcellular distribution of both proteins was similar and paralleled a lysosomal marker. In liver, absence of either NPC1 or NPC2 resulted in similar alterations in the carbohydrate processing of the lysosomal protease, tripeptidyl peptidase I. These results highlight biochemical alterations in the lysosomal system of the NPC-mutant mice that appear secondary to lipid storage. In addition, the similarity in biochemical phenotypes resulting from either NPC1 or NPC2 deficiency supports models in which the function of these two proteins within lysosomes are linked closely.

Dixit, Sayali S.; Jadot, Michel; Sohar, Istvan; Sleat, David E.; Stock, Ann M.; Lobel, Peter

2011-01-01

98

Th(VO3)2(SeO3) and Ln(VO3)2(IO3) (Ln = Ce, Pr, Nd, Sm, and Eu): unusual cases of aliovalent substitution.  

PubMed

Th(VO3)2(SeO3) and Ln(VO3)2(IO3) (Ln = Ce, Pr, Nd, Sm, and Eu) have been prepared and characterized. Surprisingly, these compounds are isotypic and rather extreme examples of aliovalent substitution (Th(IV)vs. Ln(III); Se(IV)O3(2-)vs. I(V)O3(-)) are possible in this structure type. PMID:24590373

Eaton, Teresa; Lin, Jian; Cross, Justin N; Stritzinger, Jared T; Albrecht-Schmitt, Thomas E

2014-04-11

99

Experimental validation of FINDSITEcomb virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders  

PubMed Central

Background Identification of ligand-protein binding interactions is a critical step in drug discovery. Experimental screening of large chemical libraries, in spite of their specific role and importance in drug discovery, suffer from the disadvantages of being random, time-consuming and expensive. To accelerate the process, traditional structure- or ligand-based VLS approaches are combined with experimental high-throughput screening, HTS. Often a single protein or, at most, a protein family is considered. Large scale VLS benchmarking across diverse protein families is rarely done, and the reported success rate is very low. Here, we demonstrate the experimental HTS validation of a novel VLS approach, FINDSITEcomb, across a diverse set of medically-relevant proteins. Results For eight different proteins belonging to different fold-classes and from diverse organisms, the top 1% of FINDSITEcomb’s VLS predictions were tested, and depending on the protein target, 4%-47% of the predicted ligands were shown to bind with ?M or better affinities. In total, 47 small molecule binders were identified. Low nanomolar (nM) binders for dihydrofolate reductase and protein tyrosine phosphatases (PTPs) and micromolar binders for the other proteins were identified. Six novel molecules had cytotoxic activity (<10 ?g/ml) against the HCT-116 colon carcinoma cell line and one novel molecule had potent antibacterial activity. Conclusions We show that FINDSITEcomb is a promising new VLS approach that can assist drug discovery.

2014-01-01

100

Vascular endothelial dysfunction resulting from l-arginine deficiency in a patient with lysinuric protein intolerance  

PubMed Central

Although L-arginine is the only substrate for nitric oxide (NO) production, no studies have yet been reported on the effect of an L-arginine deficiency on vascular function in humans. Lysinuric protein intolerance (LPI) is a rare autosomal recessive defect of dibasic amino acid transport caused by mutations in the SLC7A7 gene, resulting in an L-arginine deficiency. Vascular endothelial function was examined in an LPI patient who was shown to be a compound heterozygote for two mutations in the gene (5.3-kbp Alu-mediated deletion, IVS3+1G??). The lumen diameter of the brachial artery was measured in this patient and in healthy controls at rest, during reactive hyperemia (endothelium-dependent vasodilation [EDV]), and after sublingual nitroglycerin administration (endothelium-independent vasodilation [EIV]) using ultrasonography. Both EDV and NOx concentrations were markedly reduced in the patient compared with those for the controls. They became normal after an L-arginine infusion. EIV was not significantly different between the patient and controls. Positron emission tomography of the heart and a treadmill test revealed ischemic changes in the patient, which were improved by the L-arginine infusion. Thus, in the LPI patient, L-arginine deficiency caused vascular endothelial dysfunction via a decrease in NO production.

Kamada, Yoshihiro; Nagaretani, Hiroyuki; Tamura, Shinji; Ohama, Tohru; Maruyama, Takao; Hiraoka, Hisatoyo; Yamashita, Shizuya; Yamada, Akira; Kiso, Shinichi; Inui, Yoshiaki; Ito, Nobuyuki; Kayanoki, Yoshiro; Kawata, Sumio; Matsuzawa, Yuji

2001-01-01

101

The antibody against a nuclear autoantigenic sperm protein can result in reproductive failure.  

PubMed

To study whether the antibody against the testis form of the nuclear autoantigenic sperm protein (tNASP) could result in reproductive failure, we successfully cloned and expressed a 339-bp cDNA fragment of mouse tNASP (mtNASP). Using mouse as a model, recombinant mtNASP (rmtNASP) and a synthetic peptide, human tNASP(393-408) (htNASP(393-408)), were investigated for their antifertility effect. Active immunization with rmtNASP or the synthesized peptide raised high antibody titers in the immunized mice. Sperm-egg binding and fusion assay were carried out in 8-10-week-old BALB/c mice. Sperm-egg binding and in vitro fertilization of mouse oocytes were inhibited by co-incubation of zona-free mouse oocytes with capacitated mouse spermatozoa in the presence of varying concentrations of the antisera against rmtNASP. There was a significant antifertility effect in animals immunized with rmtNASP or the synthesized peptide. The effect on fertility in the mice immunized with the synthesized peptide was reversible. Our data indicate that active immunization with rmtNASP antigen may induce a strong antibody response that causes an inhibition of fertility. PMID:19219058

Wang, Min; Shi, Jian-Li; Cheng, Guo-Yan; Hu, Yan-Qing; Xu, Chen

2009-03-01

102

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

2006-01-01

103

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

104

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

105

Cow's milk protein-sensitive enteropathy. Clinical and histological results of the cow's milk provocation test.  

PubMed

Nineteen infants suspected of having cow's milk protein-sensitive enteropathy were studied. They all showed failure to thrive, diarrhoea and/or vomiting when fed a diet of cow's milk, and improved when their diet was changed to casein hydrolysate. Jejunal biopsy was done before and 18--23 hours after a milk challenge. Of the 19 infants, 12 presented histological evidence of cow's milk protein intolerance. Eight suffered from vomiting and diarrhoea within 9 days of the milk challenge, but in 4 cases the histological abnormalities were not accompanied by clinical symptoms. In one case a chicken meat intolerance was documented. The histological appearance of the intestinal mucosa after chicken challenge was identical to that observed after milk challenge. In our opinion, repeated intestinal biopsies before and after an acute challenge is the best method to establish the diagnosis not only of cow's milk protein intolerance but also of intolerance to other alimentary proteins. PMID:521297

Vitoria, J C; Camarero, C; Solaguren, R; Aranjuelo, M; Oliveros, R; Navajas, A; Rodríguez-Soriano, J

1979-09-01

106

Pooled results from 5 validation studies of dietary self-report instruments using recovery biomarkers for energy and protein intake.  

PubMed

We pooled data from 5 large validation studies of dietary self-report instruments that used recovery biomarkers as references to clarify the measurement properties of food frequency questionnaires (FFQs) and 24-hour recalls. The studies were conducted in widely differing US adult populations from 1999 to 2009. We report on total energy, protein, and protein density intakes. Results were similar across sexes, but there was heterogeneity across studies. Using a FFQ, the average correlation coefficients for reported versus true intakes for energy, protein, and protein density were 0.21, 0.29, and 0.41, respectively. Using a single 24-hour recall, the coefficients were 0.26, 0.40, and 0.36, respectively, for the same nutrients and rose to 0.31, 0.49, and 0.46 when three 24-hour recalls were averaged. The average rate of under-reporting of energy intake was 28% with a FFQ and 15% with a single 24-hour recall, but the percentages were lower for protein. Personal characteristics related to under-reporting were body mass index, educational level, and age. Calibration equations for true intake that included personal characteristics provided improved prediction. This project establishes that FFQs have stronger correlations with truth for protein density than for absolute protein intake, that the use of multiple 24-hour recalls substantially increases the correlations when compared with a single 24-hour recall, and that body mass index strongly predicts under-reporting of energy and protein intakes. PMID:24918187

Freedman, Laurence S; Commins, John M; Moler, James E; Arab, Lenore; Baer, David J; Kipnis, Victor; Midthune, Douglas; Moshfegh, Alanna J; Neuhouser, Marian L; Prentice, Ross L; Schatzkin, Arthur; Spiegelman, Donna; Subar, Amy F; Tinker, Lesley F; Willett, Walter

2014-07-15

107

Diminished Self-Chaperoning Activity of the ?F508 Mutant of CFTR Results in Protein Misfolding  

PubMed Central

The absence of a functional ATP Binding Cassette (ABC) protein called the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) from apical membranes of epithelial cells is responsible for cystic fibrosis (CF). Over 90% of CF patients carry at least one mutant allele with deletion of phenylalanine at position 508 located in the N-terminal nucleotide binding domain (NBD1). Biochemical and cell biological studies show that the ?F508 mutant exhibits inefficient biosynthetic maturation and susceptibility to degradation probably due to misfolding of NBD1 and the resultant misassembly of other domains. However, little is known about the direct effect of the Phe508 deletion on the NBD1 folding, which is essential for rational design strategies of cystic fibrosis treatment. Here we show that the deletion of Phe508 alters the folding dynamics and kinetics of NBD1, thus possibly affecting the assembly of the complete CFTR. Using molecular dynamics simulations, we find that meta-stable intermediate states appearing on wild type and mutant folding pathways are populated differently and that their kinetic accessibilities are distinct. The structural basis of the increased misfolding propensity of the ?F508 NBD1 mutant is the perturbation of interactions in residue pairs Q493/P574 and F575/F578 found in loop S7-H6. As a proof-of-principle that the S7-H6 loop conformation can modulate the folding kinetics of NBD1, we virtually design rescue mutations in the identified critical interactions to force the S7-H6 loop into the wild type conformation. Two redesigned NBD1-?F508 variants exhibited significantly higher folding probabilities than the original NBD1-?F508, thereby partially rescuing folding ability of the NBD1-?F508 mutant. We propose that these observed defects in folding kinetics of mutant NBD1 may also be modulated by structures separate from the 508 site. The identified structural determinants of increased misfolding propensity of NBD1-?F508 are essential information in correcting this pathogenic mutant.

Riordan, John R.; Dokholyan, Nikolay V.

2008-01-01

108

Deletion of potD, encoding a putative spermidine-binding protein, results in a complex phenotype in Legionella pneumophila.  

PubMed

L. pneumophila is an intracellular pathogen that replicates in a membrane-bound compartment known as the Legionella-containing vacuole (LCV). We previously observed that the polyamine spermidine, produced by host cells or added exogenously, enhances the intracellular growth of L. pneumophila. To study this enhancing effect and determine whether polyamines are used as nutrients, we deleted potD from L. pneumophila strain JR32. The gene potD encodes a spermidine-binding protein that in other bacteria is essential for the function of the PotABCD polyamine transporter. Deletion of potD did not affect L. pneumophila growth in vitro in the presence or absence of spermidine and putrescine, suggesting that PotD plays a redundant or no role in polyamine uptake. However, deletion of potD resulted in a puzzlingly complex phenotype that included defects in L. pneumophila's ability to form filaments, tolerate Na(+), associate with macrophages and amoeba, recruit host vesicles to the LCV, and initiate intracellular growth. Moreover, the ?potD mutant was completely unable to grow in L929 cells treated with a pharmacological inhibitor of spermidine synthesis. These complex and disparate effects suggest that the L. pneumophila potD encodes either: (i) a multifunctional protein, (ii) a protein that interacts with, or regulates a, multifunctional protein, or (iii) a protein that contributes (directly or indirectly) to a regulatory network. Protein function studies with the L. pneumophila PotD protein are thus warranted. PMID:24928741

Nasrallah, Gheyath K; Abdelhady, Hany; Tompkins, Nicholas P; Carson, Kaitlyn R; Garduño, Rafael A

2014-07-01

109

Protein  

NSDL National Science Digital Library

Protein structure: Primary protein structure is a sequence of amino acids. Secondary protein structure occurs when the amino acids in the sequence are linked by hydrogen bonds. Tertiary protein structure occurs when certain attractions are present between alpha helices and pleated sheets. Quaternary protein structure is a protein consisting of more than one amino acid chain.

BEGIN:VCARD VERSION:2.1 FN:Darryl Leja N:Leja;Darryl ORG:National Human Genome Research Institute REV:2005-04-04 END:VCARD

2005-04-04

110

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

111

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

112

Inactivation of the protein phosphatase 2A regulatory subunit A results in morphological and transcriptional defects in Saccharomyces cerevisiae.  

PubMed Central

We have determined that TPD3, a gene previously identified in a screen for mutants defective in tRNA biosynthesis, most likely encodes the A regulatory subunit of the major protein phosphatase 2A species in the yeast Saccharomyces cerevisiae. The predicted amino acid sequence of the product of TPD3 is highly homologous to the sequence of the mammalian A subunit of protein phosphatase 2A. In addition, antibodies raised against Tpd3p specifically precipitate a significant fraction of the protein phosphatase 2A activity in the cell, and extracts of tpd3 strains yield a different chromatographic profile of protein phosphatase 2A than do extracts of isogenic TPD3 strains. tpd3 deletion strains generally grow poorly and have at least two distinct phenotypes. At reduced temperatures, tpd3 strains appear to be defective in cytokinesis, since most cells become multibudded and multinucleate following a shift to 13 degrees C. This is similar to the phenotype obtained by overexpression of the protein phosphatase 2A catalytic subunit or by loss of CDC55, a gene that encodes a protein with homology to a second regulatory subunit of protein phosphatase 2A. At elevated temperatures, tpd3 strains are defective in transcription by RNA polymerase III. Consistent with this in vivo phenotype, extracts of tpd3 strains fail to support in vitro transcription of tRNA genes, a defect that can be reversed by addition of either purified RNA polymerase III or TFIIIB. These results reinforce the notion that protein phosphatase 2A affects a variety of biological processes in the cell and provide an initial identification of critical substrates for this phosphatase. Images

van Zyl, W; Huang, W; Sneddon, A A; Stark, M; Camier, S; Werner, M; Marck, C; Sentenac, A; Broach, J R

1992-01-01

113

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

PubMed Central

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 [?-32P]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 Mn2+-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.

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

2012-01-01

114

Recombinant PNPLA3 protein shows triglyceride hydrolase activity and its I148M mutation results in loss of function.  

PubMed

The patatin-like phospholipase domain containing 3 (PNPLA3, also called adiponutrin, ADPN) is a membrane-bound protein highly expressed in the liver. The genetic variant I148M (rs738409) was found to be associated with progression of chronic liver disease. We aimed to establish a protein purification protocol in a yeast system (Pichia pastoris) and to examine the human PNPLA3 enzymatic activity, substrate specificity and the I148M mutation effect. hPNPLA3 148I wild type and 148M mutant cDNA were cloned into P. pastoris expression vectors. Yeast cells were grown in 3L fermentors. PNPLA3 protein was purified from membrane fractions by Ni-affinity chromatography. Enzymatic activity was assessed using radiolabeled substrates. Both 148I wild type and 148M mutant proteins are localized to the membrane. The wild type protein shows a predominant lipase activity with mild lysophosphatidic acid acyl transferase activity (LPAAT) and the I148M mutation results in a loss of function of both these activities. Our data show that PNPLA3 has a predominant lipase activity and I148M mutation results in a loss of function. PMID:24369119

Pingitore, Piero; Pirazzi, Carlo; Mancina, Rosellina M; Motta, Benedetta M; Indiveri, Cesare; Pujia, Arturo; Montalcini, Tiziana; Hedfalk, Kristina; Romeo, Stefano

2014-04-01

115

Morbid Obesity Resulting from Inactivation of the Ciliary Protein CEP19 in Humans and Mice  

PubMed Central

Obesity is a major public health concern, and complementary research strategies have been directed toward the identification of the underlying causative gene mutations that affect the normal pathways and networks that regulate energy balance. Here, we describe an autosomal-recessive morbid-obesity syndrome and identify the disease-causing gene defect. The average body mass index of affected family members was 48.7 (range = 36.7–61.0), and all had features of the metabolic syndrome. Homozygosity mapping localized the disease locus to a region in 3q29; we designated this region the morbid obesity 1 (MO1) locus. Sequence analysis identified a homozygous nonsense mutation in CEP19, the gene encoding the ciliary protein CEP19, in all affected family members. CEP19 is highly conserved in vertebrates and invertebrates, is expressed in multiple tissues, and localizes to the centrosome and primary cilia. Homozygous Cep19-knockout mice were morbidly obese, hyperphagic, glucose intolerant, and insulin resistant. Thus, loss of the ciliary protein CEP19 in humans and mice causes morbid obesity and defines a target for investigating the molecular pathogenesis of this disease and potential treatments for obesity and malnutrition.

Shalata, Adel; Ramirez, Maria C.; Desnick, Robert J.; Priedigkeit, Nolan; Buettner, Christoph; Lindtner, Claudia; Mahroum, Mohammed; Abdul-Ghani, Muhammad; Dong, Feng; Arar, Nazik; Camacho-Vanegas, Olga; Zhang, Rui; Camacho, Sandra C.; Chen, Ying; Ibdah, Mwafaq; DeFronzo, Ralph; Gillespie, Virginia; Kelley, Kevin; Dynlacht, Brian D.; Kim, Sehyun; Glucksman, Marc J.; Borochowitz, Zvi U.; Martignetti, John A.

2013-01-01

116

Engagement of glycosylphosphatidylinositol-anchored proteins results in enhanced mouse and human invariant natural killer T cell responses  

PubMed Central

Invariant natural killer T (iNKT) cells are a small subset of lymphocytes that recognize glycolipid antigens in the context of CD1d and consequently produce large quantities of pro-inflammatory and/or anti-inflammatory cytokines. Several transmembrane glycoproteins have been implicated in the co-stimulation of iNKT cell responses. However, whether glycosylphosphatidylinositol (GPI)-anchored proteins can function in this capacity is not known. Here, we demonstrate that antibody-mediated cross-linking of the prototype mouse GPI-anchored protein Thy-1 (CD90) on the surface of a double-negative (CD4?CD8?) iNKT cell line leads to cytokine production at both the mRNA and protein levels. In addition, Thy-1 triggering enhanced cytokine secretion by iNKT cells that were concomitantly stimulated with ?-galactosylceramide (?GC), consistent with a co-stimulatory role for Thy-1 in iNKT cell activation. This was also evident when a CD4+ mouse iNKT cell line or primary hepatic NKT cells were stimulated with ?GC and/or anti-Thy-1 antibody. Cross-linking Ly-6A/E, another GPI-anchored protein, could also boost cytokine secretion by ?GC-stimulated iNKT cells, suggesting that the observed effects reflect a general property of GPI-anchored proteins. To extend these results from mouse to human cells, we focused on CD55, a GPI-anchored protein that, unlike Thy-1, is expressed on human iNKT cells. Cross-linking CD55 augmented ?GC-induced iNKT cell responses as judged by more vigorous proliferation and higher CD69 expression. Collectively, these findings demonstrate for the first time that GPI-anchored proteins are able to co-stimulate CD1d-restricted, glycolipid-reactive iNKT cells in both mice and humans.

Mannik, Lisa A; Chin-Yee, Ian; Sharif, Shayan; Van Kaer, Luc; Delovitch, Terry L; Haeryfar, S M Mansour

2011-01-01

117

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

118

Phospholipase C regulatory mutation of Pseudomonas aeruginosa that results in constitutive synthesis of several phosphate-repressible proteins.  

PubMed Central

We describe here a new mutant of Pseudomonas aeruginosa PAO, strain D10C (genotype plcB), which produces phospholipase C and alkaline phosphatase constitutively. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the extracellular proteins produced by this mutant in high- and low-Pi media revealed that the mutation resulted in a marked deficiency of one major Pi-regulated protein of 41,000 molecular weight and constitutive synthesis of all other major extracellular Pi-regulated proteins. Furthermore, the plcB mutant was deficient in phosphate transport. A plcA mutation, which also led to a loss of the 41,000-molecular-weight protein, was similarly deficient in Pi transport. The genetic loci, plcA and plcB, located at 22 to 23 min on the PAO chromosome, were indistinguishable by conjugational and transductional mapping, and may therefore be in the same gene or in a cluster of genes which regulate the synthesis of Pi-repressible proteins. Images

Gray, G L; Berka, R M; Vasil, M L

1982-01-01

119

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

120

MyopicMarketing Management: Evidenc e of the Phenomenon and Its Long-Term Performance Consequences in the SEO Context  

Microsoft Academic Search

anagers often have incentives to artificially inflate current-term earnings by cutting marketing expendi- tures, even if it comes at the expense of long-term profits. Because investors rely on current-term account- ing measures to form expectations of future-term profits, inflating current-term results can lead to enhanced current-term stock price. We present evidence that some firms engage in this type of \\

Natalie Mizik

2007-01-01

121

Natriuretic Peptide Receptor-3 Gene (NPR3) Nonsynonymous Polymorphism Results in Significant Reduction in Protein Expression Because of Accelerated Degradation  

PubMed Central

Background The primary role of natriuretic peptide receptor-3 (NPR3) or NPR-C is in the clearance of natriuretic peptides that play an important role in modulating intravascular volume and vascular tone. Genetic variation in NPR3 has been associated with variation in blood pressure and obesity. Despite the importance of NPR3, sequence variation in the gene has not been addressed using DNA from different ethnic populations. We set out to identify and functionally characterize genetic variation in NPR3 in 3 ethnic groups. Methods and Results DNA samples from 96 European American, 96 African American, and 96 Han Chinese American healthy subjects were used to resequence NPR3 exons, splice junctions, and flanking regions. We identified 105 polymorphisms, 50 of which were novel, including 8 nonsynonymous single-nucleotide polymorphisms, 7 were novel. Expression constructs were created for the nonsynonymous single-nucleotide polymorphisms. HEK293 cells were transfected with constructs for wild type and variant allozymes; and recombinant proteins were measured by quantitative Western blot analysis. The most significant change in NPR3 protein was observed for the Arg146 variant allozyme, with 20% of wild-type protein, primarily because of autophagy-dependent degradation. NPR3 structural modeling confirmed that the Arg146 variant protein was not compatible with wild-type conformation and could result in protein misfolding or instability. Conclusions Multiple novel NPR3 genetic polymorphisms were identified in 3 ethnic groups. The Arg146 allozyme displayed a significant decrease in protein quantity because of degradation mediated predominantly by autophagy. This genetic variation could have a significant effect on the metabolism of natriuretic peptides with potential clinical implications.

Pereira, Naveen L.; Lin, Dong; Pelleymounter, Linda; Moon, Irene; Stilling, Gail; Eckloff, Bruce W.; Wieben, Eric D.; Redfield, Margaret M.; Burnett, John C.; Yee, Vivien C.; Weinshilboum, Richard M.

2013-01-01

122

Natriuretic peptide receptor-3 gene (NPR3): nonsynonymous polymorphism results in significant reduction in protein expression because of accelerated degradation.  

PubMed

BACKGROUND- The primary role of natriuretic peptide receptor-3 (NPR3) or NPR-C is in the clearance of natriuretic peptides that play an important role in modulating intravascular volume and vascular tone. Genetic variation in NPR3 has been associated with variation in blood pressure and obesity. Despite the importance of NPR3, sequence variation in the gene has not been addressed using DNA from different ethnic populations. We set out to identify and functionally characterize genetic variation in NPR3 in 3 ethnic groups. METHODS AND RESULTS- DNA samples from 96 European American, 96 African American, and 96 Han Chinese American healthy subjects were used to resequence NPR3 exons, splice junctions, and flanking regions. We identified 105 polymorphisms, 50 of which were novel, including 8 nonsynonymous single-nucleotide polymorphisms, 7 were novel. Expression constructs were created for the nonsynonymous single-nucleotide polymorphisms. HEK293 cells were transfected with constructs for wild type and variant allozymes; and recombinant proteins were measured by quantitative Western blot analysis. The most significant change in NPR3 protein was observed for the Arg146 variant allozyme, with 20% of wild-type protein, primarily because of autophagy-dependent degradation. NPR3 structural modeling confirmed that the Arg146 variant protein was not compatible with wild-type conformation and could result in protein misfolding or instability. CONCLUSIONS- Multiple novel NPR3 genetic polymorphisms were identified in 3 ethnic groups. The Arg146 allozyme displayed a significant decrease in protein quantity because of degradation mediated predominantly by autophagy. This genetic variation could have a significant effect on the metabolism of natriuretic peptides with potential clinical implications. PMID:23493048

Pereira, Naveen L; Lin, Dong; Pelleymounter, Linda; Moon, Irene; Stilling, Gail; Eckloff, Bruce W; Wieben, Eric D; Redfield, Margaret M; Burnett, John C; Yee, Vivien C; Weinshilboum, Richard M

2013-04-01

123

Loss of signaling through the G protein, Gz, results in abnormal platelet activation and altered responses to psychoactive drugs  

PubMed Central

Heterotrimeric G proteins mediate the earliest step in cell responses to external events by linking cell surface receptors to intracellular signaling pathways. Gz is a member of the Gi family of G proteins that is prominently expressed in platelets and brain. Here, we show that deletion of the ? subunit of Gz in mice: (i) impairs platelet aggregation by preventing the inhibition of cAMP formation normally seen at physiologic concentrations of epinephrine, and (ii) causes the mice to be more resistant to fatal thromboembolism. Loss of Gz? also results in greatly exaggerated responses to cocaine, reduces the analgesic effects of morphine, and abolishes the effects of widely used antidepressant drugs that act as catecholamine reuptake inhibitors. These changes occur despite the presence of other Gi? family members in the same cells and are not accompanied by detectable compensatory changes in the level of expression of other G protein subunits. Therefore, these results provide insights into receptor selectivity among G proteins and a model for understanding platelet function and the effects of psychoactive drugs.

Yang, Jing; Wu, Jie; Kowalska, M. Anna; Dalvi, Ashutosh; Prevost, Nicolas; O'Brien, Peter J.; Manning, David; Poncz, Mortimer; Lucki, Irwin; Blendy, Julie A.; Brass, Lawrence F.

2000-01-01

124

Interaction of Zyxin, a Focal Adhesion Protein, with the E6 Protein from Human Papillomavirus Type 6 Results in Its Nuclear Translocation  

PubMed Central

Zyxin, a focal adhesion molecule, interacts specifically with the E6 protein from human papillomavirus (HPV) type 6 in a yeast two-hybrid screen of a cDNA library prepared from human keratinocytes. Zyxin does not interact significantly with E6 proteins from HPV types 11, 16, or 18. The interaction was confirmed by in vitro and in vivo analyses and it requires the LIM domains (Lin-11, Isl-1, and Mec-3 [G. Freyd, S. K. Kim, and H. R. Horvitz, Nature 344:876–879, 1990]) found at the carboxyl terminus of zyxin. Cotransfection of E6 from HPV (6E6) and zyxin results in the accumulation of zyxin in the nucleus where it can function as a transcriptional activator. 6E6 can also mobilize endogenous zyxin to the nucleus.

Degenhardt, Yan Yan; Silverstein, Saul

2001-01-01

125

Reciprocal regulation of protein kinase C isoforms results in differential cellular responsiveness.  

PubMed

Immunological homeostasis is often maintained by counteractive functions of two different cell types or two different receptors signaling through different intermediates in the same cell. One of these signaling intermediates is protein kinase C (PKC). Ten differentially regulated PKC isoforms are integral to receptor-triggered responses in different cells. So far, eight PKC isoforms are reported to be expressed in macrophages. Whether a single receptor differentially uses PKC isoforms to regulate counteractive effector functions has never been addressed. As CD40 is the only receptor characterized to trigger counteractive functions, we examined the relative role of PKC isoforms in the CD40-induced macrophage functions. We report that in BALB/c mouse macrophages, higher doses of CD40 stimulation induce optimum phosphorylation and translocation of PKC?, ?I, ?II, and ? whereas lower doses of CD40 stimulation activates PKC?, ?, and ?. Infection of macrophages with the protozoan parasite Leishmania major impairs PKC?, ?I, ?II, and ? isoforms but enhances PKC?, ?, and ? isoforms, suggesting a reciprocity among these PKC isoforms. Indeed, PKC?, ?I, ?II, and ? isoforms mediate CD40-induced p38MAPK phosphorylation, IL-12 expression, and Leishmania killing; PKC? and ?/? mediate ERK1/2 phosphorylation, IL-10 production, and parasite growth. Treatment of the susceptible BALB/c mice with the lentivirally expressed PKC?- or ?-specific short hairpin RNA significantly reduces the infection and reinstates host-protective IFN-?-dominated T cell response, defining the differential roles for PKC isoforms in immune homeostasis and novel PKC-targeted immunotherapeutic and parasite-derived immune evasion strategies. PMID:22271653

Sudan, Raki; Srivastava, Neetu; Pandey, Surya Prakash; Majumdar, Subrata; Saha, Bhaskar

2012-03-01

126

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

127

Compid: a new software tool to integrate and compare MS/MS based protein identification results from Mascot and Paragon.  

PubMed

Tandem mass spectrometry-based proteomics experiments produce large amounts of raw data, and different database search engines are needed to reliably identify all the proteins from this data. Here, we present Compid, an easy-to-use software tool that can be used to integrate and compare protein identification results from two search engines, Mascot and Paragon. Additionally, Compid enables extraction of information from large Mascot result files that cannot be opened via the Web interface and calculation of general statistical information about peptide and protein identifications in a data set. To demonstrate the usefulness of this tool, we used Compid to compare Mascot and Paragon database search results for mitochondrial proteome sample of human keratinocytes. The reports generated by Compid can be exported and opened as Excel documents or as text files using configurable delimiters, allowing the analysis and further processing of Compid output with a multitude of programs. Compid is freely available and can be downloaded from http://users.utu.fi/lanatr/compid. It is released under an open source license (GPL), enabling modification of the source code. Its modular architecture allows for creation of supplementary software components e.g. to enable support for additional input formats and report categories. PMID:20973569

Lietzén, Niina; Natri, Lari; Nevalainen, Olli S; Salmi, Jussi; Nyman, Tuula A

2010-12-01

128

Search Engine Optimization: SEO Book  

NSDL National Science Digital Library

The strange and wondrous ways in which search engines gather their indexes is made a little clearer in this tutorial. Written by a web designer disappointed with how difficult his pages were to find with the standard search engines, this page gives insight into how Infoseek, Lycos, Alta Vista, Excite, Web Crawler, and Open Text catalog web pages. The search strategy of each engine is described, along with tips for how web designers can increase their site's chances of being among the hits returned when users enter relevant search criteria. Although indexing algorithms are constantly being updated, this site presents common-sense guidelines that web designers interested in reaching a wider audience will find useful.

Wall, Aaron

2007-07-14

129

Multiple interactions between polyphenols and a salivary proline-rich protein repeat result in complexation and precipitation.  

PubMed

Polyphenols (tannins) in the diet not only precipitate oral proteins, producing an astringent sensation, but also interact with dietary proteins and digestive enzymes in the gut, resulting in a variety of antinutritive and toxic effects. Salivary proline-rich proteins (PRPs), which are secreted into the oral cavity, form complexes with and precipitate dietary polyphenols, and thus, they constitute the primary mammalian defense directed against ingested tannins. In order to characterize the interaction, NMR studies were performed which involved titrating a series of polyphenols into a synthetic 19-residue PRP fragment. The results show that the predominant mode of association is a hydrophobic stacking of the polyphenol ring against the pro-S face of proline and that the first proline residue of a Pro-Pro sequence is a particularly favored binding site. Measurement of dissociation constants indicates that the larger and more complex polyphenols interact more strongly with the PRP fragment; the order of binding affinity was determined as procyanidin dimer B-2 > pentagalloylglucose > trigalloylglucose > proanthocyanidin monomer (-)-epicatechin approximately propyl gallate. Smaller polyphenols can bind with one phenolic ring stacked against each proline residue, whereas larger polyphenols occupy two or three consecutive prolines. The more complex polyphenols interact with the PRP fragment in a multidentate fashion; moreover, they self-associate or stack when bound. Thus, a model is proposed in which multiple polyphenol/polyphenol and polyphenol/PRP interactions act cooperatively to achieve precipitation. PMID:9154941

Baxter, N J; Lilley, T H; Haslam, E; Williamson, M P

1997-05-01

130

Genetic properties of medium (M) and small (S) genomic RNA segments of Seoul hantavirus isolated from Rattus norvegicus and antigenicity analysis of recombinant nucleocapsid protein  

Microsoft Academic Search

A novel isolate of Seoul (SEO) hantaviruses was detected and identified in Rattus norvegicus in Shandong Province, China and designated as JUN5-14. The partial M segment and the coding region of nucleocapsid protein\\u000a (NP) in the S segment of JUN5-14 were PCR-amplified and sequenced. Nucleotide sequence analysis of the partial M segment (300 bp)\\u000a revealed that JUN5-14 isolate was closely related

Zexin Tao; Zhiyu Wang; Shaoxia Song; Hongling Wen; Guijie Ren; Guiting Wang

2007-01-01

131

Coupled continual screening super producers molecular efforts improve efficacy hydrolytic proteins known genes generation Optimist xylanolytic enzyme cocktail result increase current yields bioethanol  

EPA Pesticide Factsheets

Did you mean: Coupled continual screening super producers molecular efforts improve efficacy hydrolytic proteins known genes generation Optimist xylanolytic enzyme cocktail result increase current yields bioethanol ?

132

Protein Dynamics Physically Characterized Using Molecular Monolayers as Protein Models: Experimental Results Obtained Through Acoustic Shear and Electrical Double Layer Measurements  

Microsoft Academic Search

A thorough explanation of protein adsorption will lead to understanding the interaction of body fluids with medical implants, to more efficient separation and purification of complex media, to the production of high quality filters for water treatment, and to the precise characterization of biosensors. One important aspect of protein adsorption is the conformation the protein assumes upon adsorbing. Few if

Steven Ross Clark

1992-01-01

133

Proteins.  

ERIC Educational Resources Information Center

Examines proteins which give rise to structure and, by virtue of selective binding to other molecules, make genes. Binding sites, amino acids, protein evolution, and molecular paleontology are discussed. Work with encoding segments of deoxyribonucleic acid (exons) and noncoding stretches (introns) provides new information for hypotheses. (DH)

Doolittle, Russell F.

1985-01-01

134

Proteins  

NSDL National Science Digital Library

Paul Anderson explains the structure and importance of proteins. He describes how proteins are created from amino acids connected by dehydration synthesis. He shows the importance of chemical properties in the R-groups of individual amino acids in the polypeptide.

Anderson, Paul

2013-03-12

135

Protein  

MedlinePLUS

... for Everyone Introduction Nutrition Basics Food Groups Water Dietary Fat Trans Fat Saturated Fat Cholesterol Polyunsaturated Fats and Monounsaturated Fats Carbohydrates Protein Vitamins and Minerals Fruits and Vegetables Nutrition Information How Many Fruits ...

136

Genetic deletion of murine SPRY domain-containing SOCS box protein 2 (SSB-2) results in very mild thrombocytopenia.  

PubMed

The SSB family is comprised of four highly homologous proteins containing a C-terminal SOCS box motif and a central SPRY domain. No function has yet been ascribed to any member of this family in mammalian species despite a clear role for other SOCS proteins in negative regulation of cytokine signaling. To investigate its physiological role, the murine Ssb-2 gene was deleted by homologous recombination. SSB-2-deficient mice were shown to have a reduced rate of platelet production, resulting in very mild thrombocytopenia (25% decrease in circulating platelets). Tissue histology and other hematological parameters were normal, as was the majority of serum biochemistry, with the exception that blood urea nitrogen (BUN) levels were decreased in mice lacking SSB-2. Quantitative analysis of SSB mRNA levels indicated that SSB-1, -2, and -3 were ubiquitously expressed; however, SSB-4 was only expressed at very low levels. SSB-2 expression was observed in the kidney and in megakaryocytes, a finding consistent with the phenotype of mice lacking this gene. Deletion of SSB-2 thus perturbs the steady-state level of two tightly controlled homeostatic parameters and identifies a critical role for SSB-2 in regulating platelet production and BUN levels. PMID:15964819

Masters, S L; Palmer, K R; Stevenson, W S; Metcalf, D; Viney, E M; Sprigg, N S; Alexander, W S; Nicola, N A; Nicholson, S E

2005-07-01

137

The failure to express a protein disulphide isomerase-like protein results in a floury endosperm and an endoplasmic reticulum stress response in rice  

PubMed Central

The rice somaclonal mutant T3612 produces small grains with a floury endosperm, caused by the loose packing of starch granules. The positional cloning of the mutation revealed a deletion in a gene encoding a protein disulphide isomerase-like enzyme (PDIL1-1). In the wild type, PDIL1-1 was expressed throughout the plant, but most intensely in the developing grain. In T3612, its expression was abolished, resulting in a decrease in the activity of plastidial phosphorylase and pullulanase, and an increase in that of soluble starch synthase I and ADP-glucose pyrophosphorylase. The amylopectin in the T3612 endosperm showed an increase in chains with a degree of polymerization 8–13 compared with the wild type. The expression in the mutant's endosperm of certain endoplasmic reticulum stress-responsive genes was noticeably elevated. PDIL1-1 appears to play an important role in starch synthesis. Its absence is associated with endoplasmic reticulum stress in the endosperm, which is likely to underlie the formation of the floury endosperm in the T3612 mutant.

Han, Xiaohua; Wang, Yihua; Liu, Xi; Jiang, Ling; Ren, Yulong; Liu, Feng; Peng, Cheng; Li, Jingjing; Jin, Ximing; Wu, Fuqing; Wang, Jiulin; Guo, Xiuping; Zhang, Xin; Cheng, Zhijun; Wan, Jianmin

2012-01-01

138

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

139

Association of overactive bladder and C-reactive protein levels. Results from the Boston Area Community Health (BACH) Survey  

PubMed Central

OBJECTIVE To investigate the association between overactive bladder (OAB) and C-reactive protein (CRP) in a population-based sample of men and women. SUBJECTS AND METHODS Epidemiological survey of urological symptoms among men and women aged 30–79 years. A multi-stage stratified cluster design was used to randomly sample 5503 adults from the city of Boston. Analyses were conducted on 1898 men and 1854 women with available CRP levels. The International Continence Society defines OAB as ‘Urgency with or without urge incontinence, usually with frequency and nocturia.’ OAB was defined as: (1) urgency, (2) urgency with frequency, and (3) urgency with frequency and nocturia. Odds ratios (OR) and 95% confidence intervals (95% CI) of the CRP and OAB association were estimated using logistic regression. RESULTS Prevalence of OAB increased with CRP levels in both men and women. In men, adjusted ORs (95% CI) per log10(CRP) levels were 1.90 (1.26–2.86) with OAB defined as urgency, 1.65 (1.06–2.58) with OAB defined as urgency and frequency, and 1.92 (1.13–3.28) with OAB defined as urgency, frequency and nocturia. The association was more modest in women with ORs (95% CI) of 1.53 (1.07–2.18) for OAB as defined urgency, 1.51 (1.02–2.23) for OAB defined as urgency and frequency, and 1.34 (0.85–2.12) for OAB defined as urgency, frequency and nocturia. CONCLUSIONS Results show a consistent association of increasing CRP levels and OAB among both men and women. These results support our hypothesis for the role of inflammation in the development of OAB and a possible role for anti-inflammatory agents in its treatment.

Kupelian, Varant; Rosen, Raymond C.; Roehrborn, Claus G.; Tyagi, Pradeep; Chancellor, Michael B.; McKinlay, John B.

2011-01-01

140

Protein Dynamics Physically Characterized Using Molecular Monolayers as Protein Models: Experimental Results Obtained Through Acoustic Shear and Electrical Double Layer Measurements.  

NASA Astrophysics Data System (ADS)

A thorough explanation of protein adsorption will lead to understanding the interaction of body fluids with medical implants, to more efficient separation and purification of complex media, to the production of high quality filters for water treatment, and to the precise characterization of biosensors. One important aspect of protein adsorption is the conformation the protein assumes upon adsorbing. Few if any techniques currently exist to study protein conformations on a solid surface. In this dissertation a new method for studying large molecules (i.e. proteins) adsorbed to a metallic interface in solution is described. The approach has been to study the conformational changes of large molecules adsorbed to surfaces using double layer capacitance, solution resistance, and the frequency of a QCM (quartz crystal microbalance). The design, development and calibration of the inexpensive double layer capacitance meter, and its interfacing to the oscillator circuitry controlling a QCM is also described. The use of the QCM in liquids has developed to where many examples can be found for their use, but the types of surface interactions that generate a sensor response in the liquid phase has been elusive. Many investigations have shown that the macroscopic structure of the solution/sensor interface dominates the sensor's response. Even though the theory of the sensor's operation in liquids is becoming more sophisticated, the experimental data supporting these theories are still scarce. Interfacing a double layer capacitance meter developed in our lab to the QCM's electrode has provided additional information about dynamic changes occurring near the electrodes surface when large molecules adsorb. Apparently the relationship that exists between the measured for gold electrodes chemically modified by long hydrocarbon chain thiols is Delta F~Delta C~ (Delta R)^{-1}. Relationships between these three variables do also exist for adsorbed proteins, but the relationship depends on the time at which the variables are compared and the solution environment at those times.

Clark, Steven Ross

141

Crowding Induces Differences in the Diffusion of Thermophilic and Mesophilic Proteins: A New Look at Neutron Scattering Results  

PubMed Central

The dynamical basis underlying the increased thermal stability of thermophilic proteins remains uncertain. Here, we challenge the new paradigm established by neutron scattering experiments in solution, in which the adaptation of thermophilic proteins to high temperatures lies in the lower sensitivity of their flexibility to temperature changes. By means of a combination of molecular dynamics and Brownian dynamics simulations, we report a reinterpretation of those experiments and show evidence that under crowding conditions, such as in vivo, thermophilic and homolog mesophilic proteins have diffusional properties with different thermal behavior.

Marcos, Enrique; Mestres, Pau; Crehuet, Ramon

2011-01-01

142

Loss of the Synaptic Vesicle Protein SV2B Results in Reduced Neurotransmission and Altered Synaptic Vesicle Protein Expression in the Retina  

PubMed Central

The Synaptic Vesicle Protein 2 (SV2) family of transporter-like proteins is expressed exclusively in vesicles that undergo calcium-regulated exocytosis. Of the three isoforms expressed in mammals, SV2B is the most divergent. Here we report studies of SV2B location and function in the retina. Immunolabeling studies revealed that SV2B is detected in rod photoreceptor synaptic terminals where it is the primary isoform. In mice lacking SV2B, synaptic transmission at the synapse between photoreceptors and bipolar neurons was decreased, as evidenced by a significant reduction in the amplitude of the b-wave in electroretinogram recordings. Quantitative immunoblot analyses of whole eyes revealed that loss of SV2B was associated with reduced levels of synaptic vesicle proteins including synaptotagmin, VAMP, synaptophysin and the vesicular glutamate transporter V-GLUT1. Immunolabeling studies revealed that SV2B is detected in rod photoreceptor synaptic terminals where it is the primary isoform. Thus, SV2B contributes to the modulation of synaptic vesicle exocytosis and plays a significant role in regulating synaptic protein content.

Burton, Kimberly; Idzerda, Rejean; McKnight, G. Stanley; Bajjalieh, Sandra M.

2009-01-01

143

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.

144

Mapping antibody binding sites on cytochrome c with synthetic peptides: are results representative of the antigenic structure of proteins?  

PubMed Central

Crystallographic work on antigen-antibody complexes has revealed that extensive surface areas of proteins may interact with antibodies. On the other hand, most experimental approaches to locate and define antigenic determinants of protein antigens rely on the linear sequence of the polypeptide chain. Hence the question arises whether mapping of antibody binding sites by analysis of the reactivity of anti-protein antibodies with synthetic peptides can provide a representative picture of the antigenic structure of a protein antigen. We have addressed this question using yeast iso-1 cytochrome c as a protein antigen against which antisera were raised in rabbits. The reaction of the antisera with 103 synthetic hexapeptides covering the entire sequence of cytochrome c was tested by the pepscan procedure in which peptides are coupled to polyethylene rods and tested by ELISA. For the assay, anti-cytochrome c antibodies were fractionated by affinity chromatography on native yeast iso-1 cytochrome c and on apo-cytochrome c; the latter is a random coil. It was found that only antibodies retained by the apo-cytochrome c affinity column react with synthetic peptides. These antibodies comprise a small fraction, probably less than 2%, of all cytochrome c-specific antibodies. The majority of antigenic determinants, which seem to consist of strongly conformation-dependent topographic epitopes, could not be uncovered by the peptide approach. Epitope mapping with short peptides seems of limited usefulness in the case of small, globular, and conformationally stable proteins like cytochrome c.

Schwab, C.; Twardek, A.; Lo, T. P.; Brayer, G. D.; Bosshard, H. R.

1993-01-01

145

Two New Barium-Vanadium(IV) Phases: Ba(VO) 2(SeO 3) 2(HSeO 3) 2, the First Barium Vanadium Selenite, and Ba 8(VO) 6(PO 4) 2(HPO 4) 11 · 3H 2O, a Compound Built Up from Two Types of One-Dimensional Chains  

Microsoft Academic Search

The hydrothermal syntheses, X-ray single-crystal structures, and some properties of Ba(VO)2(SeO3)2(HSeO3)2 and Ba8(VO)6 (Po4)2(HPO4)11 · 3H2O are described. Ba(VO)2(SeO3)2(HSeO3)2 contains a three-dimensional network of VO6 and (H)SeO3 polyhedra, linked via V-O-Se bonds. The Ba cation is 10-coordinate, the VO6 group contains a short vanadyl V[?]O bond typical of VIV, and the (H)SeO3 groups are pyramidal. Magnetic susceptibility data are consistent

William T. A. Harrison; J. T. Vaughey; Allan J. Jacobson; David P. Goshorn; Jack W. Johnson

1995-01-01

146

Sex differences in the phosphorylation of mitochondrial proteins result in reduced production of reactive oxygen species and cardioprotection in females  

PubMed Central

Rationale Although pre-menopausal females have a lower risk for cardiovascular disease, the mechanism(s) are poorly understood. Objective We tested the hypothesis that cardioprotection in females is mediated by altered mitochondrial protein levels and/or post-translational modifications. Methods and Results Using both an in vivo and an isolated heart model of ischemia and reperfusion (I/R), we found that females had less injury than males. Using proteomic methods we found that female hearts had increased phosphorylation and activity of aldehyde dehydrogenase-2 (ALDH2), an enzyme that detoxifies ROS generated aldehyde adducts, and that an activator of ALDH2 reduced I/R injury in males but had no significant effect in females. Wortmannin, an inhibitor of PI3K, blocked the protection and the increased phosphorylation of ALDH2 in females, but had no effect in males. Furthermore, we found an increase in phosphorylation of ?-ketoglutarate dehydrogenase (?KGDH) in female hearts. ?KGDH is a major source of ROS generation particularly with a high NADH/NAD ratio which occurs during I/R. We found decreased ROS generation in permeabilized female mitochondria given ?KGDH substrates and NADH, suggesting that increased phosphorylation of ?KGDH might reduce ROS generation by ?KGDH. In support of this hypothesis, we found that PKC dependent phosphorylation of purified ?KGDH reduced ROS generation. Additionally, myocytes from female hearts had less ROS generation following I/R than males and addition of wortmannin increased ROS generation in females to the same levels as in males. Conclusion These data suggest that post-translational modifications can modify ROS handling and play an important role in female cardioprotection.

Lagranha, Claudia J; Deschamps, Anne; Aponte, Angel; Steenbergen, Charles; Murphy, Elizabeth

2010-01-01

147

The Loss of RGS Protein-G?i2 Interactions Results in Markedly Impaired Mouse Neutrophil Trafficking to Inflammatory Sites  

PubMed Central

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.

Kamenyeva, Olena; Yung, Sunny; Gao, Ji-Liang; Hwang, Il-Young; Park, Chung; Murphy, Philip M.; Neubig, Richard R.

2012-01-01

148

Ultraviolet radiation, but not ? radiation or etoposide-induced DNA damage, results in the phosphorylation of the murine p53 protein at serine-389  

PubMed Central

Polyclonal antibodies were produced and purified that selectively react with a p53 epitope containing the murine phosphoserine-389 or the human phosphoserine-392 residue, but not the unphosphorylated epitope. These antibodies, termed alpha-392, were employed to demonstrate that the phosphorylation of this serine-389 residue in the p53 protein occurs in vivo in response to ultraviolet radiation of cells containing the p53 protein. After ultraviolet radiation of cells in culture, p53 levels increase and concomitantly serine-389 is phosphorylated in these cells. By contrast, the serine-389 phosphorylation of the p53 protein was not detected by these antibodies in the increased levels of p53 protein made in response to ? radiation or the treatment of cells with etoposide. These results demonstrate an ultraviolet responsive and specific phosphorylation site at serine-389 of the mouse or serine-392 of the human p53 protein. Previous studies have demonstrated that this phosphorylation of p53 activates the protein for specific DNA binding. This study demonstrates in vivo a unique phosphorylation site in the p53 protein that responds to a specific type of DNA damage.

Lu, Hua; Taya, Yoichi; Ikeda, Masako; Levine, Arnold J.

1998-01-01

149

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

150

Solid-state synthesis, structure and properties of a novel open-framework cadmium selenite bromide: [Cd10(SeO3)8Br4]·HBr·H2O  

NASA Astrophysics Data System (ADS)

A novel open-framework cadmium selenite bromide, [Cd10(SeO3)8Br4]·HBr·H2O (1), has been obtained by a solid-state reaction at 450 °C, and the structure has been determined by single-crystal X-ray diffraction analysis. Compound 1 crystallizes in Pbcm of the orthorhombic system: a=10.882(3), b=16.275(5), c=18.728(6) Å, V=3317(2) Å3, R1/wR2=0.0411/0.0659. Compound 1 is characteristic of a novel 3-D open-framework structure, composing ?2[CdSeO3] layers and the pillars of edge-shared CdO3Br2 square pyramids. The lattice water molecules and the HBr molecules locate in the voids of the framework. Optical absorption spectrum of 1 reveals the presence of an optical gap of 1.65 eV. Solid-state photoluminescent study indicates that compound 1 exhibits strong violet emission. TG-DSC measurement shows that compound 1 is thermally stable up to 200 °C.

Chen, Wen-Tong; Wang, Ming-Sheng; Wang, Guan-E.; Chen, Hui-Fen; Guo, Guo-Cong

2013-08-01

151

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

152

Pigment protein complexes and functional properties of tetratype resulting from crosses between CP 1 and CP 2 less Chlamydomonas mutants  

Microsoft Academic Search

A chlorophyll b-less mutant of Chlamydomonas reinhardtii (Pg27) was isolated after UV irradiation of the wild type cells. This photosynthetically competent mutant totally lacks chlorophyll b and the CP2 chlorophyll-protein complex. However, SDS-PAGE, proteolytic digestions and immunodetections demonstrated that the 24–25 Kd apoproteins of the lacking CP2 complex are still present in thylakoids of the Pg27 mutant. It is concluded

A. Picaud; G. Dubertret

1986-01-01

153

N488I Mutation of the 2Subunit Results in Bidirectional Changes in AMP-Activated Protein Kinase Activity  

Microsoft Academic Search

Mutations in the human gene encoding the nucleotide-binding region in the -subunit of AMP-activated protein kinase (AMPK) cause cardiomyopathy with preexcitation syndrome. Mutant AMPK showed reduced binding affinity to nucleotides in vitro raising the possibility that altered regulation of AMPK activity by AMP\\/ATP could contribute to the disease phenotype. In this study, we determined the sensitivity of AMPK activity to

Liqun Zou; Mei Shen; Michael Arad; Huamei He; Bo Løfgren; Joanne S. Ingwall; Christine E. Seidman; Jon G. Seidman; Rong Tian

154

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

2012-05-01

155

Cyclophilin A Binds to the Viral RNA and Replication Proteins, Resulting in Inhibition of Tombusviral Replicase Assembly  

PubMed Central

Replication of plus-stranded RNA viruses is greatly affected by numerous host-encoded proteins that act as restriction factors. Cyclophilins, which are a large family of cellular prolyl isomerases, have been found to inhibit Tomato bushy stunt tombusvirus (TBSV) replication in a Saccharomyces cerevisiae model based on genome-wide screens and global proteomics approaches. In this report, we further characterize single-domain cyclophilins, including the mammalian cyclophilin A and plant Roc1 and Roc2, which are orthologs of the yeast Cpr1p cyclophilin, a known inhibitor of TBSV replication in yeast. We found that recombinant CypA, Roc1, and Roc2 strongly inhibited TBSV replication in a cell-free replication assay. Additional in vitro studies revealed that CypA, Roc1, and Roc2 cyclophilins bound to the viral replication proteins, and CypA and Roc1 also bound to the viral RNA. These interactions led to inhibition of viral RNA recruitment, the assembly of the viral replicase complex, and viral RNA synthesis. A catalytically inactive mutant of CypA was also able to inhibit TBSV replication in vitro due to binding to the replication proteins and the viral RNA. Overexpression of CypA and its mutant in yeast or plant leaves led to inhibition of tombusvirus replication, confirming that CypA is a restriction factor for TBSV. Overall, the current work has revealed a regulatory role for the cytosolic single-domain Cpr1-like cyclophilins in RNA virus replication.

Kovalev, Nikolay

2013-01-01

156

Knockout of STriatal Enriched Protein Tyrosine Phosphatase in Mice Results in Increased ERK1/2 Phosphorylation  

PubMed Central

STriatal Enriched protein tyrosine Phosphatase (STEP) is a brain-specific protein that is thought to play a role in synaptic plasticity. This hypothesis is based on previous findings demonstrating a role for STEP in the regulation of the extracellular signal-regulated kinase1/2 (ERK1/2). We have now generated a STEP knockout mouse and investigated the effect of knocking out STEP in the regulation of ERK1/2 activity. Here, we show that the STEP knockout mice are viable and fertile and have no detectable cytoarchitectural abnormalities in the brain. The homozygous knockout mice lack the expression of all STEP isoforms, whereas the heterozygous mice have reduced STEP protein levels when compared with the wild-type mice. The STEP knockout mice show enhanced phosphorylation of ERK1/2 in the striatum, CA2 region of the hippocampus, as well as central and lateral nuclei of the amygdala. In addition, the cultured neurons from KO mice showed significantly higher levels of pERK1/2 following synaptic stimulation when compared with wild-type controls. These data demonstrate more conclusively the role of STEP in the regulation of ERK1/2 activity.

VENKITARAMANI, DEEPA V.; PAUL, SUROJIT; ZHANG, YONGFANG; KURUP, PRADEEP; DING, LI; TRESSLER, LYAL; ALLEN, MELANIE; SACCA, ROSALBA; PICCIOTTO, MARINA R.; LOMBROSO, PAUL J.

2009-01-01

157

Life-long protein malnutrition in the rat (Rattus norvegicus) results in altered patterns of craniofacial growth and smaller individuals  

PubMed Central

Dietary protein is a limiting factor in mammalian growth, significantly affecting the non-linear trajectories of skeletal growth. Young females may be particularly vulnerable to protein malnutrition if the restriction is not lifted before they become reproductive. With such early malnutrition, limited amino acids would be partitioned between two physiological objectives, successful reproduction vs. continued growth. Thus, the consequences of protein malnutrition could affect more than one generation. However, few studies have quantified these cross-generational effects. Our objective was to test for differences in skeletal growth in a second generation of malnourished rats compared with rats malnourished only post-weaning, the first generation and with controls. In this longitudinal study we modelled the growth of 22 craniofacial measurements with the logistic Gompertz equation, and tested for differences in the equation's parameters among the diet groups. The female offspring of post-weaning malnourished dams did not catch up in size to the first generation or to controls, although certain aspects of their craniofacial skeleton were less affected than others. The second generation's growth trajectories resembled the longer and slower growth of the first malnourished generation. There was a complex interaction between developmental processes and early nutritional environment, which affected variation of adult size.

Lobe, Shannon L; Bernstein, Marica C; German, Rebecca Z

2006-01-01

158

Pseudomonas seleniipraecipitans Proteins Potentially Involved in Selenite Reduction.  

PubMed

Pseudomonas seleniipraecipitans grows in the presence of high levels of selenite and selenate and reduces both oxyanions to elemental selenium (Se(0)), a property that may make P. seleniipraecipitans useful as an inoculant for biobarriers designed to remove selenite or selenate from ground or surface waters. An earlier study showed that P. seleniipraecipitans nitrate reductase reduced selenate to Se(0), but failed to identify the protein(s) involved in selenite reduction. This study used ammonium sulfate precipitation, hydrophobic interaction chromatography, and native PAGE to isolate two electrophoretic gel regions, identified as bands A and B that showed selenite-reductase-activity. Proteomics was used to identify the proteins present in those regions. Glutathione reductase (GR) was detected in the A-band; based on this information, Saccharomyces cerevisiae GR, obtained from a commercial source, was evaluated and found to have selenite-reductase-activity, confirming that GR can reduce selenite to Se(0). Proteomics was also used to detect the proteins present in the B-band and thioredoxin reductase (ThxR) was detected as a B-band protein; based on this information, E. coli ThxR, obtained from a commercial source, was evaluated and found to have selenite-reductase-activity, confirming that ThxR can reduce selenite to elemental selenium. Thus, evidence presented in this study shows that S. cerevisiae GR and E. coli ThxR can reduce SeO3 (2-) to Se(0) and strongly suggests that P. seleniipraecipitans GR and ThxR can also reduce SeO3 (2-) to Se(0). PMID:24604150

Hunter, William J

2014-07-01

159

Ultrasonic energy as a new tool for fast isotopic 18O labeling of proteins for mass spectrometry-based techniques: preliminary results.  

PubMed

Preliminary results regarding fast isotopic labeling of proteins with (18)O in conjunction with matrix assisted laser desorption ionization time of flight mass spectrometry technique are presented. Similar (16)O/(18)O isotopic labeling ratios were found for the overnight procedure (12h) and the new fast ultrasonic one (30 min) for the BSA, ovalbumin and alpha-lactalbumin proteins. The procedure, however, failed to promote double (18)O isotopic labeling for the proteins, ovalbumin and alpha-lactalbumin. Two different sonication frequencies, 35 and 130 kHz, were studied at two different sonication times of 15 and 30 min, being best results obtained with the procedure at 130 kHz of sonication frequency and 30 min of sonication time. For comparative purposes the overnight isotopic (18)O labeling procedure was done. In addition, the new fast isotopic labeling procedure was also studied without ultrasonication, in a water bath at 60 degrees C. PMID:18585297

Carreira, R J; Rial-Otero, R; López-Ferrer, D; Lodeiro, C; Capelo, J L

2008-07-15

160

Ultrasonic Energy as a New Tool for Fast Isotopic 18O Labeling of Proteins for Mass Spectrometry-Based Techniques: Preliminary Results  

SciTech Connect

Preliminary results regarding fast isotopic labeling of proteins with 18O in conjunction with matrix assisted laser desorption ionization time of flight mass spectrometry technique are presented. Similar 16O/18O isotopic labeling ratios were found for the overnight procedure (12 h) and the new fast ultrasonic one (30 min) for the BSA, ovalbumin and ?-lactalbumin proteins. The procedure, however, failed to promote double 18O isotopic labeling for the proteins ovalbumin and ?-lactalbumin. Two different sonication frequencies, 35 kHz and 130 kHz, were studied at two different sonication times of 15 min and 30 min, being best results obtained with the procedure at 130 kHz of sonication frequency and 30 min of sonication time. For comparative purposes the overnight isotopic 18O labeling procedure was done. In addition, the new fast isotopic labeling procedure was also studied without ultrasonication, in a water bath at 60 ºC.

Carreira, R.J.; Rial-Otero, R.; Lopez-Ferrer, Dani; Lodeiro, C.; Capelo, J.L.

2008-07-15

161

Knockdown of piRNA pathway proteins results in enhanced Semliki Forest virus production in mosquito cells  

PubMed Central

The exogenous siRNA pathway is important in restricting arbovirus infection in mosquitoes. Less is known about the role of the PIWI-interacting RNA pathway, or piRNA pathway, in antiviral responses. Viral piRNA-like molecules have recently been described following infection of mosquitoes and derived cell lines with several arboviruses. The piRNA pathway has thus been suggested to function as an additional small RNA-mediated antiviral response to the known infection-induced siRNA response. Here we show that piRNA-like molecules are produced following infection with the naturally mosquito-borne Semliki Forest virus in mosquito cell lines. We show that knockdown of piRNA pathway proteins enhances the replication of this arbovirus and defines the contribution of piRNA pathway effectors, thus characterizing the antiviral properties of the piRNA pathway. In conclusion, arbovirus infection can trigger the piRNA pathway in mosquito cells, and knockdown of piRNA proteins enhances virus production.

Donald, Claire L.; Human, Stacey; Watson, Mick; Siu, Ricky W. C.; McFarlane, Melanie; Fazakerley, John K.; Kohl, Alain

2013-01-01

162

Introduction of Caveolae Structural Proteins into the Protozoan Toxoplasma Results in the Formation of Heterologous Caveolae but Not Caveolar Endocytosis  

PubMed Central

Present on the plasma membrane of most metazoans, caveolae are specialized microdomains implicated in several endocytic and trafficking mechanisms. Caveolins and the more recently discovered cavins are the major protein components of caveolae. Previous studies reported that caveolar invaginations can be induced de novo on the surface of caveolae-negative mammalian cells upon heterologous expression of caveolin-1. However, it remains undocumented whether other components in the transfected cells participate in caveolae formation. To address this issue, we have exploited the protozoan Toxoplasma as a heterologous expression system to provide insights into the minimal requirements for caveogenesis and caveolar endocytosis. Upon expression of caveolin-1, Toxoplasma accumulates prototypical exocytic caveolae ‘precursors’ in the cytoplasm. Toxoplasma expressing caveolin-1 alone, or in conjunction with cavin-1, neither develops surface-located caveolae nor internalizes caveolar ligands. These data suggest that the formation of functional caveolae at the plasma membrane in Toxoplasma and, by inference in all non-mammalian cells, requires effectors other than caveolin-1 and cavin-1. Interestingly, Toxoplasma co-expressing caveolin-1 and cavin-1 displays an impressive spiraled network of membranes containing the two proteins, in the cytoplasm. This suggests a synergistic activity of caveolin-1 and cavin-1 in the morphogenesis and remodeling of membranes, as illustrated for Toxoplasma.

Lige, Bao; Sonda, Sabrina; Joiner, Keith A.; Coppens, Isabelle

2012-01-01

163

Absence of iron-regulatory protein Hfe results in hyperproliferation of retinal pigment epithelium: role of cystine/glutamate exchanger.  

PubMed

Haemochromatosis is an iron-overload disorder with age-dependent oxidative stress and dysfunction in a variety of tissues. Mutations in HFE (histocompatability leucocyte antigen class I-like protein involved in iron homoeostasis) are responsible for most cases of haemochromatosis. We demonstrated recently that HFE is expressed exclusively in the basal membrane of RPE (retinal pigment epithelium). In the present study, we used Hfe-/- mice to examine ferritin levels (an indirect readout for iron levels) and morphological changes in retina. We found increased ferritin accumulation in retina in 18-month-old, but not in 2-month-old, mice with considerable morphological damage compared with age-matched controls. The retinal phenotype included hypertrophy and hyperplasia of RPE. RPE cells isolated from Hfe-/- mice exhibited a hyperproliferative phenotype. We also compared the gene expression profile between wild-type and Hfe-/- RPE cells by microarray analysis. These studies showed that many cell cycle-related genes were differentially regulated in Hfe-/- RPE cells. One of the genes up-regulated in Hfe-/- RPE cells was Slc7a11 (where Slc is solute carrier) which codes for the 'transporter proper' xCT in the heterodimeric cystine/glutamate exchanger (xCT/4F2hc). This transporter plays a critical role in cellular glutathione status and cell-cycle progression. We confirmed the microarrray data by monitoring xCT mRNA levels by RT (reverse transcription)-PCR and also by measuring transport function. We also found increased levels of glutathione and the transcription factor/cell-cycle promoter AP1 (activator protein 1) in Hfe-/- RPE cells. Wild-type mouse RPE cells and human RPE cell lines, when loaded with iron by exposure to ferric ammonium citrate, showed increased expression and activity of xCT, reproducing the biochemical phenotype observed with Hfe-/- RPE cells. PMID:19715555

Gnana-Prakasam, Jaya P; Thangaraju, Muthusamy; Liu, Kebin; Ha, Yonju; Martin, Pamela M; Smith, Sylvia B; Ganapathy, Vadivel

2009-12-01

164

Proteomic profiling reveals that rabies virus infection results in differential expression of host proteins involved in ion homeostasis and synaptic physiology in the central nervous system  

Microsoft Academic Search

To understand how rabies virus (RV) infection results in neuronal dysfunction, the authors employed proteomics technology\\u000a to profile host responses to RV infection. In mice infected with wild-type (wt) RV, the expression of proteins involved in\\u000a ion homeostasis was altered. H+ ATPase and Na+\\/K+ ATPase were up-regulated whereas Ca2+ ATPase was down-regulated, which resulted in reduction of the intracellular Na+

Vikas Dhingra; Xiaqing Li; Yuru Liu; Zhen F. Fu

2007-01-01

165

Mutation of the surface-exposed amino acid Trp to Ala in the FVIII C2 domain results in defective secretion of the otherwise functional protein.  

PubMed

The C2 domain of factor VIII (FVIII) is important for FVIII-phospholipid (PL) and FVIII-von Willebrand factor (VWF) interactions. A FVIII structural model, derived by electron crystallography, suggests four hydrophobic loops at the FVIII C2 domain-PL interface. Within loop four, the solvent-exposed amino acid, Trp(2313), is believed to contribute to FVIII-PL binding. To analyse this interaction, the amino-acid exchange Trp(2313) to Ala (W2313A) was introduced into the C2 domain of B-domain-deleted FVIII (dBFVIII). Both proteins, dBFVIII and W2313A, were expressed in a mammalian expression system. Labelling experiments showed that the mutation W2313A resulted in reduced secretion but did not affect intracellular synthesis of the protein. Specific activity, kinetic parameters, binding to VWF and haemostatic potential in a murine model of haemophilia A were found to be similar for both proteins. Binding studies to synthetic 4% phosphatidyl-l-serine vesicles showed, however, a 28-fold higher K(D) for W2313A, indicating the important role of Trp(2313) in the FVIII-PL interaction. In conclusion, the C2-domain-surface-exposed residue Trp(2313), is critical for secretion of the protein. The W2313A mutation weakens binding to phosphatidyl-l-serine vesicles but the mutant protein has the same effector function as dBFVIII in vitro and in vivo. PMID:15147379

Schatz, Simone M; Zimmermann, Klaus; Hasslacher, Meinhard; Kerschbaumer, Randolf; Dockal, Michael; Gritsch, Herbert; Turecek, Peter L; Schwarz, Hans P; Dorner, Friedrich; Scheiflinger, Friedrich

2004-06-01

166

Loss of lysosomal membrane protein NCU-G1 in mice results in spontaneous liver fibrosis with accumulation of lipofuscin and iron in Kupffer cells.  

PubMed

Human kidney predominant protein, NCU-G1, is a highly conserved protein with an unknown biological function. Initially described as a nuclear protein, it was later shown to be a bona fide lysosomal integral membrane protein. To gain insight into the physiological function of NCU-G1, mice with no detectable expression of this gene were created using a gene-trap strategy, and Ncu-g1(gt/gt) mice were successfully characterized. Lysosomal disorders are mainly caused by lack of or malfunctioning of proteins in the endosomal-lysosomal pathway. The clinical symptoms vary, but often include liver dysfunction. Persistent liver damage activates fibrogenesis and, if unremedied, eventually leads to liver fibrosis/cirrhosis and death. We demonstrate that the disruption of Ncu-g1 results in spontaneous liver fibrosis in mice as the predominant phenotype. Evidence for an increased rate of hepatic cell death, oxidative stress and active fibrogenesis were detected in Ncu-g1(gt/gt) liver. In addition to collagen deposition, microscopic examination of liver sections revealed accumulation of autofluorescent lipofuscin and iron in Ncu-g1(gt/gt) Kupffer cells. Because only a few transgenic mouse models have been identified with chronic liver injury and spontaneous liver fibrosis development, we propose that the Ncu-g1(gt/gt) mouse could be a valuable new tool in the development of novel treatments for the attenuation of fibrosis due to chronic liver damage. PMID:24487409

Kong, Xiang Y; Nesset, Cecilie Kasi; Damme, Markus; Løberg, Else-Marit; Lübke, Torben; Mæhlen, Jan; Andersson, Kristin B; Lorenzo, Petra I; Roos, Norbert; Thoresen, G Hege; Rustan, Arild C; Kase, Eili T; Eskild, Winnie

2014-03-01

167

Loss of lysosomal membrane protein NCU-G1 in mice results in spontaneous liver fibrosis with accumulation of lipofuscin and iron in Kupffer cells  

PubMed Central

Human kidney predominant protein, NCU-G1, is a highly conserved protein with an unknown biological function. Initially described as a nuclear protein, it was later shown to be a bona fide lysosomal integral membrane protein. To gain insight into the physiological function of NCU-G1, mice with no detectable expression of this gene were created using a gene-trap strategy, and Ncu-g1gt/gt mice were successfully characterized. Lysosomal disorders are mainly caused by lack of or malfunctioning of proteins in the endosomal-lysosomal pathway. The clinical symptoms vary, but often include liver dysfunction. Persistent liver damage activates fibrogenesis and, if unremedied, eventually leads to liver fibrosis/cirrhosis and death. We demonstrate that the disruption of Ncu-g1 results in spontaneous liver fibrosis in mice as the predominant phenotype. Evidence for an increased rate of hepatic cell death, oxidative stress and active fibrogenesis were detected in Ncu-g1gt/gt liver. In addition to collagen deposition, microscopic examination of liver sections revealed accumulation of autofluorescent lipofuscin and iron in Ncu-g1gt/gt Kupffer cells. Because only a few transgenic mouse models have been identified with chronic liver injury and spontaneous liver fibrosis development, we propose that the Ncu-g1gt/gt mouse could be a valuable new tool in the development of novel treatments for the attenuation of fibrosis due to chronic liver damage.

Kong, Xiang Y.; Nesset, Cecilie Kasi; Damme, Markus; L?berg, Else-Marit; Lubke, Torben; Maehlen, Jan; Andersson, Kristin B.; Lorenzo, Petra I.; Roos, Norbert; Thoresen, G. Hege; Rustan, Arild C.; Kase, Eili T.; Eskild, Winnie

2014-01-01

168

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

169

Extreme hyperopia is the result of null mutations in MFRP, which encodes a Frizzled-related protein.  

PubMed

Nanophthalmos is a rare disorder of eye development characterized by extreme hyperopia (farsightedness), with refractive error in the range of +8.00 to +25.00 diopters. Because the cornea and lens are normal in size and shape, hyperopia occurs because insufficient growth along the visual axis places these lensing components too close to the retina. Nanophthalmic eyes show considerable thickening of both the choroidal vascular bed and scleral coat, which provide nutritive and structural support for the retina. Thickening of these tissues is a general feature of axial hyperopia, whereas the opposite occurs in myopia. We have mapped recessive nanophthalmos to a unique locus at 11q23.3 and identified four independent mutations in MFRP, a gene that is selectively expressed in the eye and encodes a protein with homology to Tolloid proteases and the Wnt-binding domain of the Frizzled transmembrane receptors. This gene is not critical for retinal function, as patients entirely lacking MFRP can still have good refraction-corrected vision, produce clinically normal electro-retinograms, and show only modest anomalies in the dark adaptation of photoreceptors. MFRP appears primarily devoted to regulating axial length of the eye. It remains to be determined whether natural variation in its activity plays a role in common refractive errors. PMID:15976030

Sundin, Olof H; Leppert, Gregory S; Silva, Eduardo D; Yang, Jun-Ming; Dharmaraj, Sharola; Maumenee, Irene H; Santos, Luisa Coutinho; Parsa, Cameron F; Traboulsi, Elias I; Broman, Karl W; Dibernardo, Cathy; Sunness, Janet S; Toy, Jeffrey; Weinberg, Ethan M

2005-07-01

170

Mutation of ribosomal protein RPS24 in Diamond-Blackfan anemia results in a ribosome biogenesis disorder.  

PubMed

Diamond-Blackfan anemia (DBA) is a rare congenital disease affecting erythroid precursor differentiation. DBA is emerging as a paradigm for a new class of pathologies potentially linked to disorders in ribosome biogenesis. Three genes encoding ribosomal proteins have been associated to DBA: after RPS19, mutations in genes RPS24 and RPS17 were recently identified in a fraction of the patients. Here, we show that cells from patients carrying mutations in RPS24 have defective pre-rRNA maturation, as in the case of RPS19 mutations. However, in contrast to RPS19 involvement in the maturation of the internal transcribed spacer 1, RPS24 is required for processing of the 5' external transcribed spacer. Remarkably, epistasis experiments with small interfering RNAs indicate that the functions of RPS19 and RPS24 in pre-rRNA processing are connected. Resolution of the crystal structure of RPS24e from the archeon Pyroccocus abyssi reveals domains of RPS24 potentially involved in interactions with pre-ribosomes. Based on these data, we discuss the impact of RPS24 mutations and speculate that RPS19 and RPS24 cooperate at a particular stage of ribosome biogenesis connected to a cell cycle checkpoint, thus affecting differentiation of erythroid precursors as well as developmental processes. PMID:18230666

Choesmel, Valérie; Fribourg, Sébastien; Aguissa-Touré, Almass-Houd; Pinaud, Noël; Legrand, Pierre; Gazda, Hanna T; Gleizes, Pierre-Emmanuel

2008-05-01

171

Forkhead box protein C2 contributes to invasion and metastasis of extrahepatic cholangiocarcinoma, resulting in a poor prognosis.  

PubMed

Extrahepatic cholangiocarcinoma (EHCC) is a cancer with a poor prognosis, and the postoperative survival of patients depends on the existence of invasion and metastasis. The epithelial-to-mesenchymal transition (EMT) is an important step in EHCC invasion and metastasis. Forkhead box protein C2 (FOXC2) is a transcription factor that has been reported to induce the EMT. Therefore we examined the correlation between FOXC2 expression and clinical pathological factors, and analysed the function of FOXC2. The expression of FOXC2 in 77 EHCC cases was investigated by immunohistochemical staining, and the relationship between FOXC2 expression and clinicopathological factor was assessed. Knockdown by small interfering RNA (siRNA) was performed to determine the roles of FOXC2 in EHCC cell line. FOXC2 expression correlated with lymph node metastasis (P = 0.0205). Patients in the high FOXC2 expression group had a poorer prognosis than the patients in the low FOXC2 expression group. Moreover, FOXC2 knockdown inhibited cell motility and invasion, and decreased the expression of EMT markers (N-cadherin, and matrix metalloproteinase (MMP) -2) and Angiopietin-2 (Ang-2). The EMT inducer FOXC2 contributes to a poor prognosis and cancer progression. FOXC2 may be a promising molecular target for regulating EHCC metastasis. PMID:23919841

Watanabe, Akira; Suzuki, Hideki; Yokobori, Takehiko; Altan, Bolag; Kubo, Norio; Araki, Kenichiro; Wada, Satoshi; Mochida, Yasushi; Sasaki, Shigeru; Kashiwabara, Kenji; Hosouchi, Yasuo; Kuwano, Hiroyuki

2013-11-01

172

The Human Cytomegalovirus UL11 Protein Interacts with the Receptor Tyrosine Phosphatase CD45, Resulting in Functional Paralysis of T Cells  

PubMed Central

Human cytomegalovirus (CMV) exerts diverse and complex effects on the immune system, not all of which have been attributed to viral genes. Acute CMV infection results in transient restrictions in T cell proliferative ability, which can impair the control of the virus and increase the risk of secondary infections in patients with weakened or immature immune systems. In a search for new immunomodulatory proteins, we investigated the UL11 protein, a member of the CMV RL11 family. This protein family is defined by the RL11 domain, which has homology to immunoglobulin domains and adenoviral immunomodulatory proteins. We show that pUL11 is expressed on the cell surface and induces intercellular interactions with leukocytes. This was demonstrated to be due to the interaction of pUL11 with the receptor tyrosine phosphatase CD45, identified by mass spectrometry analysis of pUL11-associated proteins. CD45 expression is sufficient to mediate the interaction with pUL11 and is required for pUL11 binding to T cells, indicating that pUL11 is a specific CD45 ligand. CD45 has a pivotal function regulating T cell signaling thresholds; in its absence, the Src family kinase Lck is inactive and signaling through the T cell receptor (TCR) is therefore shut off. In the presence of pUL11, several CD45-mediated functions were inhibited. The induction of tyrosine phosphorylation of multiple signaling proteins upon TCR stimulation was reduced and T cell proliferation was impaired. We therefore conclude that pUL11 has immunosuppressive properties, and that disruption of T cell function via inhibition of CD45 is a previously unknown immunomodulatory strategy of CMV.

Gabaev, Ildar; Steinbruck, Lars; Pokoyski, Claudia; Pich, Andreas; Stanton, Richard J.; Schwinzer, Reinhard; Schulz, Thomas F.; Jacobs, Roland; Messerle, Martin; Kay-Fedorov, Penelope C.

2011-01-01

173

Herbicide resistance in Chlamydomonas reinhardtii results from a mutation in the chloroplast gene for the 32-kilodalton protein of photosystem II  

PubMed Central

We report the isolation and characterization of a uniparental mutant of Chlamydomonas reinhardtii that is resistant to 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) and 2-chloro-4-ethylamino-6-isopropylamino-s-triazine (atrazine). Such herbicides inhibit photosynthesis by preventing transfer of electrons in photosystem II from the primary stable electron acceptor Q to the secondary stable electron acceptor complex B, which is thought to contain a protein of 32 kDa and a bound quinone. It has been proposed that herbicide binding to the 32-kDa protein alters the B complex so that electron transfer from Q is prohibited. Both whole and broken-cell preparations of the mutant alga show a resistance to the effects of herbicide on electron transfer from Q to B, as measured by fluorescence-induction kinetics. In the absence of herbicide, mutant cells exhibit a slower rate of Q to B electron transfer than do wild-type cells. The 32-kDa protein from wild-type cells, but not mutant cells, binds azido[14C]atrazine at 0.1 ?M. We have isolated psbA, the chloroplast gene for the 32-kDa protein, from both wild-type and herbicide-resistant algae and sequenced the coding regions of the gene that are contained in five exons. The only difference between the exon nucleotide sequences of the wild-type and mutant psbA is a single T-A to G-C transversion. This mutation results in a predicted amino acid change of serine in the wild-type protein to alanine in the mutant. We suggest that this alteration in the 32-kDa protein is the molecular basis for herbicide resistance in the C. reinhardtii mutant. Images

Erickson, Jeanne M.; Rahire, Michele; Bennoun, Pierre; Delepelaire, Philippe; Diner, Bruce; Rochaix, Jean-David

1984-01-01

174

Intermolecular protein interactions in solutions of calf lens alpha-crystallin. Results from 1/T1 nuclear magnetic relaxation dispersion profiles.  

PubMed Central

From analyses of the magnetic field dependence of 1/T1 (NMRD profiles) of water protons in solutions of calf lens alpha-crystallin at several concentrations, we find two regimes of solute behavior in both cortical and nuclear preparations. Below approximately 15% vol/vol protein concentration, the solute molecules appear as compact globular proteins of approximately 1,350 (cortical) and approximately 1,700 (nuclear) kD. At higher concentrations, the effective solute particle size increases, reversibly, as evidenced by the appearance of spectra-like 14N peaks in the NMRD profiles and a change in the field and temperature dependence of 1/T1. At these higher concentrations, the profiles are very similar to those of calf gamma II-crystallin, a crystallin that undergoes an analogous transition near approximately 15% protein (Koenig, S. H., C.F. Beaulieu, R. D. Brown III, and M. Spiller, 1990. Biophys. J. 57:461-469). By comparison with recent analyses of NMRD results for solutions of immobilized proteins as models for the transition from protein solutions to tissue (Koenig, S. H., and R. D. Brown III. 1991. Prog. NMR Spectr. 22:487-567), we argue that alpha-crystallin solute behaves as aggregates approximately greater than 50,000 kD as protein concentration is progressively increased above 15%. Finally, the concentration dependence of the NMRD profiles of alpha- and gamma II-crystallin can readily explain recent osmotic pressure data, in particular the intersection of the respective pressure curves at approximately 23% vol/vol (Vérétout, F., and A. Tardieu. 1989. Eur. Biophys. J. 17:61-68). Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 7

Koenig, S H; Brown, R D; Spiller, M; Chakrabarti, B; Pande, A

1992-01-01

175

Exposure to vehicle emissions results in altered blood brain barrier permeability and expression of matrix metalloproteinases and tight junction proteins in mice  

PubMed Central

Background Traffic-generated air pollution-exposure is associated with adverse effects in the central nervous system (CNS) in both human exposures and animal models, including neuroinflammation and neurodegeneration. While alterations in the blood brain barrier (BBB) have been implicated as a potential mechanism of air pollution-induced CNS pathologies, pathways involved have not been elucidated. Objectives To determine whether inhalation exposure to mixed vehicle exhaust (MVE) mediates alterations in BBB permeability, activation of matrix metalloproteinases (MMP) -2 and ?9, and altered tight junction (TJ) protein expression. Methods Apolipoprotein (Apo) E?/? and C57Bl6 mice were exposed to either MVE (100 ?g/m3 PM) or filtered air (FA) for 6 hr/day for 30 days and resulting BBB permeability, expression of ROS, TJ proteins, markers of neuroinflammation, and MMP activity were assessed. Serum from study mice was applied to an in vitro BBB co-culture model and resulting alterations in transport and permeability were quantified. Results MVE-exposed Apo E?/? mice showed increased BBB permeability, elevated ROS and increased MMP-2 and ?9 activity, compared to FA controls. Additionally, cerebral vessels from MVE-exposed mice expressed decreased levels of TJ proteins, occludin and claudin-5, and increased levels of inducible nitric oxide synthase (iNOS) and interleukin (IL)-1? in the parenchyma. Serum from MVE-exposed animals also resulted in increased in vitro BBB permeability and altered P-glycoprotein transport activity. Conclusions These data indicate that inhalation exposure to traffic-generated air pollutants promotes increased MMP activity and degradation of TJ proteins in the cerebral vasculature, resulting in altered BBB permeability and expression of neuroinflammatory markers.

2013-01-01

176

Prenatal and neonatal exposure to perfluorooctane sulfonic acid results in changes in miRNA expression profiles and synapse associated proteins in developing rat brains.  

PubMed

We previously identified a number of perfluorooctane sulfonic acid (PFOS)-responsive transcripts in developing rat brains using microarray analysis. However, the underlying mechanisms and functional consequences remain unclear. We hypothesized that microRNAs (miRNAs), which have emerged as powerful negative regulators of mRNA and protein levels, might be responsible for PFOS-induced mRNA changes and consequent neural dysfunctions. We used eight miRNA arrays to profile the expression of brain miRNAs in neonatal rats on postnatal days (PND) 1 and 7 with maternal treatment of 0 (Control) and 3.2 mg/kg of PFOS feed from gestational day 1 to PND 7, and subsequently examined six potentially altered synapse-associated proteins to evaluate presumptive PFOS-responsive functions. Twenty-four brain miRNAs on PND 1 and 17 on PND 7 were significantly altered with PFOS exposure (P < 0.05), with miR-466b, -672, and -297, which are critical in neurodevelopment and synapse transmission, showing a more than 5-fold reduction. Levels of three synapse-involved proteins, NGFR, TrkC, and VGLUT2, were significantly decreased with no protein up-regulated on PND 1 or 7. Perfluorooctane sulfonic acid might affect calcium actions during synapse transmission in the nervous system by interfering with SYNJ1, ITPR1, and CALM1 via their targeting miRNAs. Our results indicated that miRNA had little direct regulatory effect on the expression of mRNAs and synapse-associated proteins tested in the developing rat brain exposed to PFOS, and it seems that the PFOS-induced synaptic dysfunctions and changes in transcripts resulted from a combinatory action of biological controllers and processes, rather than directed by one single factor. PMID:22594572

Wang, Faqi; Liu, Wei; Ma, Junsheng; Yu, Mingxi; Jin, Yihe; Dai, Jiayin

2012-06-19

177

The end-product method of measuring whole-body protein turnover: a review of published results and a comparison with those obtained by leucine infusion.  

PubMed

The present review summarizes the results of all published papers on whole-body protein turnover in man measured by [15N]glycine and the end-product method using both urea and ammonia. It begins with a short account of the underlying assumptions and the justification for the use of [15N]glycine. The results are then compared with those of a large sample of measurements by the 'gold standard' precursor method with continuous infusion of [13C]leucine. The pros and cons of the two methods are compared and it is suggested that there is a place for further work by the less invasive end-product method, particularly for population studies of the genetic, environmental and functional determinants of whole-body rates of protein synthesis. PMID:16115347

Duggleby, S L; Waterlow, J C

2005-08-01

178

Nonablative skin rejuvenation devices and the role of heat shock protein 70: results of a human skin explant model  

NASA Astrophysics Data System (ADS)

Nonablative thermal laser therapy with a 1540-nm laser induces controlled, spatially determined thermal damage, allowing subsequent collagen remodeling while preserving the epidermis. A photorejuvenation effect using nonthermal nonablative stimulation of cells with low energy and narrow band light has been termed photomodulation. Light emitting diodes (LEDs) are narrow band emitters that lead to photomodulation via stimulation of mitochondrial cell organelles. In a previous study, we demonstrated in a human skin explant model that heat shock protein 70 (HSP70) plays a pivotal role in the initiation of skin remodeling after ablative fractional photothermolysis. To test its importance in nonablative laser therapy and photomodulation, the spatio-temporal expression of HSP70 is investigated in response to a 1540-nm laser treatment and six different LED therapies. An Er:glass laser is used with a 1-Hz repetition rate, 30-J/cm2 fluence, and a hand piece with a 2-mm spot size. Nonthermal nonablative treatment is performed using two LED (LEDA SCR red light: 635 nm, 40 to 120 W/cm2, 40 to 120 J/cm2 LEDA SCR yellow light: 585 nm, 16 to 35 W/cm2, 20 to 100 J/cm2 spot size 16×10 cm). Immediate responses as well as responses 1, 3, or 7 days postprocedure are studied; untreated skin explants serve as control. Immunohistochemical investigation (HSP70) is performed in all native, nontreated, and Er:glass laser- or LED-treated samples (n=175). Nonablative laser therapy leads to a clear time-dependent induction of epidermally expressed HSP70, peaking between one to three days post-treatment. In contrast, none of the various LED treatments up-regulated the HSP70 expression in our skin explant model. HSP70 is up-regulated by nonablative but thermal laser devices, but does not seem to play a significant role in the induction of skin remodeling induced by photomodulation. The maximum of HSP70 expression is reached later after Er:glass laser intervention compared to ablative fractional (AFP) treatment.

Helbig, Doris; Moebius, Anne; Simon, Jan C.; Paasch, Uwe

2010-05-01

179

Nonablative skin rejuvenation devices and the role of heat shock protein 70: results of a human skin explant model.  

PubMed

Nonablative thermal laser therapy with a 1,540-nm laser induces controlled, spatially determined thermal damage, allowing subsequent collagen remodeling while preserving the epidermis. A photorejuvenation effect using nonthermal nonablative stimulation of cells with low energy and narrow band light has been termed photomodulation. Light emitting diodes (LEDs) are narrow band emitters that lead to photomodulation via stimulation of mitochondrial cell organelles. In a previous study, we demonstrated in a human skin explant model that heat shock protein 70 (HSP70) plays a pivotal role in the initiation of skin remodeling after ablative fractional photothermolysis. To test its importance in nonablative laser therapy and photomodulation, the spatio-temporal expression of HSP70 is investigated in response to a 1540-nm laser treatment and six different LED therapies. An Er:glass laser is used with a 1-Hz repetition rate, 30-J/cm(2) fluence, and a hand piece with a 2-mm spot size. Nonthermal nonablative treatment is performed using two LED (LEDA SCR red light: 635 nm, 40 to 120 W/cm(2), 40 to 120 J/cm(2); LEDA SCR yellow light: 585 nm, 16 to 35 W/cm(2), 20 to 100 J/cm(2); spot size 16 x 10 cm). Immediate responses as well as responses 1, 3, or 7 days postprocedure are studied; untreated skin explants serve as control. Immunohistochemical investigation (HSP70) is performed in all native, nontreated, and Er:glass laser- or LED-treated samples (n=175). Nonablative laser therapy leads to a clear time-dependent induction of epidermally expressed HSP70, peaking between one to three days post-treatment. In contrast, none of the various LED treatments up-regulated the HSP70 expression in our skin explant model. HSP70 is up-regulated by nonablative but thermal laser devices, but does not seem to play a significant role in the induction of skin remodeling induced by photomodulation. The maximum of HSP70 expression is reached later after Er:glass laser intervention compared to ablative fractional (AFP) treatment. PMID:20615048

Helbig, Doris; Moebius, Anne; Simon, Jan C; Paasch, Uwe

2010-01-01

180

Beta-scission of side-chain alkoxyl radicals on peptides and proteins results in the loss of side-chains as aldehydes and ketones  

Microsoft Academic Search

Exposure of proteins to radicals in the presence of O2 results in side-chain oxidation and backbone fragmentation; the interrelationship between these processes is not fully understood. Recently, initial attack on Ala side-chains was shown to give ?-carbon radicals (and hence backbone cleavage) and formaldehyde, via the formation and subsequent ?-scission, of C-3 alkoxyl radicals. We now show that this side-chain

Henrietta A. Headlam; Michael J. Davies

2002-01-01

181

Elongation studies of the human agouti-related protein (AGRP) core decapeptide (Yc[CRFFNAFC]Y) results in antagonism at the mouse melanocortin-3 receptor  

Microsoft Academic Search

The agouti-related protein (AGRP) is an endogenous antagonist of the brain melanocortin receptors (MC3R and MC4R) and is believed to be involved in feeding behavior and energy homeostasis. Previous results identified that the human AGRP decapeptide Yc[CRFFNAFC]Y binds to the MC3R and MC4R and acts as an antagonist at the MC4R but not at the MC3R. We have synthesized the

Christine G Joseph; Rayna M Bauzo; Zhimin Xiang; Amanda M Shaw; William J Millard; Carrie Haskell-Luevano

2003-01-01

182

Boron deficiency results in induction of pathogenesis-related proteins from the PR-10 family during the legume-rhizobia interaction.  

PubMed

Boron (B) deficiency has a strong effect on molecular and cellular plant-bacteria interactions during the development of the legume-rhizobia symbiosis, leading to reduced infection and early necrosis of nodules, resembling a pathogenic-like rather than a symbiotic interaction. Therefore, induction of pathogenesis-related (PRs) proteins was investigated here in legume root nodules. Following two-dimensional electrophoresis and MALDI-TOF spectrometry analysis of proteins extracted from Pisum sativum B-sufficient (+B) or B-deficient (-B) root nodules, two proteins from the family PR10, ABR17 and PR10.1, were identified as highly induced in -B nodules. Analysis of gene expression and the use of anti-ABR17 confirmed that induction occurred in B-deficient young nodules and increased during nodule development. ABR17 was also induced in -B nodules of Phaseolus vulgaris. Boron deficiency did not significantly increase the expression of these PR10 in uninfected plant tissues. Moreover, independent of B, induction was detected in senescent tissues, although at a level weaker than in -B nodules. The immunochemical study of ABR17 antigen distribution showed that it was localized in all tissues of poorly invaded B-deficient nodules and accumulated around bacteria, which showed advanced degradation. These results suggest that, under B deficiency, the rhizobia-legume dialogue fails and the bacterium is recognized as a pathogen by the plant, which reacts to prevent infection by inducing at least these two identified PR10 proteins. PMID:20138685

Reguera, María; Bonilla, Ildefonso; Bolaños, Luis

2010-05-15

183

Altered levels of the Taraxacum kok-saghyz (Russian dandelion) small rubber particle protein, TkSRPP3, result in qualitative and quantitative changes in rubber metabolism.  

PubMed

Several proteins have been identified and implicated in natural rubber biosynthesis, one of which, the small rubber particle protein (SRPP), was originally identified in Hevea brasiliensis as an abundant protein associated with cytosolic vesicles known as rubber particles. While previous in vitro studies suggest that SRPP plays a role in rubber biosynthesis, in vivo evidence is lacking to support this hypothesis. To address this issue, a transgene approach was taken in Taraxacum kok-saghyz (Russian dandelion or Tk) to determine if altered SRPP levels would influence rubber biosynthesis. Three dandelion SRPPs were found to be highly abundant on dandelion rubber particles. The most abundant particle associated SRPP, TkSRPP3, showed temporal and spatial patterns of expression consistent with patterns of natural rubber accumulation in dandelion. To confirm its role in rubber biosynthesis, TkSRPP3 expression was altered in Russian dandelion using over-expression and RNAi methods. While TkSRPP3 over-expressing lines had slightly higher levels of rubber in their roots, relative to the control, TkSRPP3 RNAi lines showed significant decreases in root rubber content and produced dramatically lower molecular weight rubber than the control line. Not only do results here provide in vivo evidence of TkSRPP proteins affecting the amount of rubber in dandelion root, but they also suggest a function in regulating the molecular weight of the cis-1, 4-polyisoprene polymer. PMID:22609069

Collins-Silva, Jillian; Nural, Aise Taban; Skaggs, Amanda; Scott, Deborah; Hathwaik, Upul; Woolsey, Rebekah; Schegg, Kathleen; McMahan, Colleen; Whalen, Maureen; Cornish, Katrina; Shintani, David

2012-07-01

184

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

PubMed

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. PMID:19644223

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

2009-01-01

185

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

186

All-solid-state cells based on solid electrolyte systems Cu 1? x Ag x I–Ag 2O–Y, where x = 0.05–0.25; Y = MoO 3, B 2O 3, SeO 2, V 2O 5 and CrO 3  

Microsoft Academic Search

All-solid-state cells of the configuration (?)Ag+SE\\/\\/SE\\/\\/I2-phenothiazine+C(+) using the best conducting compositions of the solid electrolyte systems, namely, Cu1?xAgxI–Ag2O–Y where x=0.05, 0.1, 0.15, 0.2 and 0.25, Y=MoO3, B2O3, SeO2, V2O5 and CrO3, as the electrolytes were fabricated. Discharge, polarization and power characteristics of these cells were also evaluated. The open circuit voltage values of these cells were in the range 620–635mV.

S. Murugesan; S. A. Suthanthiraraj; P. Maruthamuthu

2007-01-01

187

Methotrexate treatment of FraX fibroblasts results in FMR1 transcription but not in detectable FMR1 protein levels  

PubMed Central

Background Fragile X syndrome is caused by the loss of FMRP expression due to methylation of the FMR1 promoter. Treatment of fragile X syndrome patients’ lymphoblastoid cells with 5-azadeoxycytidine results in demethylation of the promoter and reactivation of the gene. The aim of the study was to analyze if methotrexate, an agent which also reduces DNA methylation but with less toxicity than 5-azadeoxycytidine, has therapeutic potential in fragile X syndrome. Methods Fibroblasts of fragile X syndrome patients were treated with methotrexate in concentrations ranging from 1 to 4 ?g/ml for up to 14 days. FMR1 and FMRP expression were analyzed by quantitative PCR and western blotting. Results FMR1 mRNA was detected and levels correlated positively with methotrexate concentrations and time of treatment, but western blotting did not show detectable FMRP levels. Conclusions We show that it is possible to reactivate FMR1 transcription in fibroblasts of fragile X syndrome patients by treatment with methotrexate. However, we were not able to show FMRP expression, possibly due to the reduced translation efficacy caused by the triplet repeat extension. Unless FMR1 reactivation is more effective in vivo our results indicate that methotrexate has no role in the treatment of fragile X syndrome.

2013-01-01

188

A graphical display useful for meta-analysis F. JAVIER JIMENEZ, EL1SEO GUALLAR, JOSE M. MARTfN-MORENO  

Microsoft Academic Search

Graphical methods are frequently used in meta-analysis to summarize their results and to explore potential sources of heterogeneity across studies. In this paper, we illustrate a graphical method for meta-analysis of studies with dichotomous exposures and outcomes that complements other graphical and analytical approaches to meta-analysis. In prospective studies, the proportion of cases among the unexposed is plotted on the

F. Javier Jimenez; E. Guallar; J. M. Martin-Moreno; Carlos HI

2010-01-01

189

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

190

Association between Sleep Quality and C-Reactive Protein: Results from National Health and Nutrition Examination Survey, 2005-2008  

PubMed Central

Objective Our objective was to explore the association between poor sleep quality and hs_CRP in an adult U.S. population. Methods This study focused on 9,317 participants in the National Health and Nutrition Examination Survey (NHANES) from 2005–2008 who were aged 20–85 years, completed a sleep disorder questionnaire, and had available information on serum hs_CRP. Sleep quality was classified into three categories (good, moderate, poor) based on the responses of participants to the NHANES sleep disorder questionnaire. High CRP was defined as hs-CRP >1 md/dL. Linear regression model was applied to investigate the association between poor sleep quality and log-transformed hs_CRP. And logistic regression model was fitted to evaluate the association between sleep quality and the risk of high CRP. Results Females were more likely to report poor sleep quality than males (26% vs. 19%, p<0.0001). Each sleep disorder was significantly associated with increased hs_CRP and correlative to other sleep disorders. In fully-adjusted linear regression model, poor sleep quality was significantly associated with elevated hs_CRP (log transformed) among the overall sample and in females only (??=?0.10, se?=?0.03, p<0.01 and ??=?0.13, se?=?0.04, p<0.01, respectively). In fully-adjusted logistics regression model, poor sleep quality was linked with risk of high CRP(OR: 1.42, 95%CI: 1.15–1.76 in overall sample and OR: 1.59, 95%CI: 1.18–2.14 in females, respectively). Conclusion We found that poor sleep quality was independently associated with elevated hs_CRP in females but not in males in a U.S. adult population.

Liu, Rong; Liu, Xin; Zee, Phyllis C.; Hou, Lifang; Zheng, Zheng; Wei, Yongxiang; Du, Jie

2014-01-01

191

Polyphenols can inhibit furin in vitro as a result of the reactivity of their auto-oxidation products to proteins.  

PubMed

Methods using fluorogenic peptide substrates have been proposed for screening of proprotein convertase (PC) inhibitors and they are attractive since they offer the advantage of being sensitive, cost-effective and susceptible to miniaturization. Several polyphenols, including epigallocatechin gallate ((-)EGCG), the main component of green tea, and quercetin, widely distributed in fruit and vegetables, however, led to false positive results when fluorogenic peptide substrates were used. Processing of genuine furin substrates was not inhibited by these polyphenols. In the present study, these discordant effects of (-)EGCG on the PC furin were studied. While quercetin can form aggregates in solution, aggregate-based promiscuous inhibition could be ruled out as underlying mechanism for (-)EGCG. Hydrogen peroxide production, from auto-oxidation, was too low to be a major factor but appeared associated to furin inhibition, suggesting a role for other auto-oxidation products. Since the instability of catechins is related to their electrophilic character, we tested the nucleophilic substance glutathione for stabilization. Indeed glutathione reduced furin inhibition and (-)EGCG binding to furin and serum albumin as shown by redox-cycling staining. Catechins, therefore, seem to form reactive compounds and this should be taken into account in screening assays. Adding glutathione to the detergent-based assay, as used in these studies to measure furin processing activity, strongly reduced inhibition by a number of polyphenols (catechins, gallic acid and quercetin), while the effect on the genuine inhibitor nona-D-arginine remained unchanged. In conclusion: the combined use of detergent and glutathione in the screening assay for furin inhibitors improves the predictive value. PMID:23231348

Zhu, J; Van de Ven, W J M; Verbiest, T; Koeckelberghs, G; Chen, C; Cui, Y; Vermorken, A J M

2013-02-01

192

ICGA-PSO-ELM approach for accurate multiclass cancer classification resulting in reduced gene sets in which genes encoding secreted proteins are highly represented.  

PubMed

A combination of Integer-Coded Genetic Algorithm (ICGA) and Particle Swarm Optimization (PSO), coupled with the neural-network-based Extreme Learning Machine (ELM), is used for gene selection and cancer classification. ICGA is used with PSO-ELM to select an optimal set of genes, which is then used to build a classifier to develop an algorithm (ICGA_PSO_ELM) that can handle sparse data and sample imbalance. We evaluate the performance of ICGA-PSO-ELM and compare our results with existing methods in the literature. An investigation into the functions of the selected genes, using a systems biology approach, revealed that many of the identified genes are involved in cell signaling and proliferation. An analysis of these gene sets shows a larger representation of genes that encode secreted proteins than found in randomly selected gene sets. Secreted proteins constitute a major means by which cells interact with their surroundings. Mounting biological evidence has identified the tumor microenvironment as a critical factor that determines tumor survival and growth. Thus, the genes identified by this study that encode secreted proteins might provide important insights to the nature of the critical biological features in the microenvironment of each tumor type that allow these cells to thrive and proliferate. PMID:21233525

Saraswathi, Saras; Sundaram, Suresh; Sundararajan, Narasimhan; Zimmermann, Michael; Nilsen-Hamilton, Marit

2011-01-01

193

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

194

In vivo particle polymorphism results from deletion of a N-terminal peptide molecular switch in brome mosaic virus capsid protein.  

PubMed

The interaction between brome mosaic virus (BMV) coat protein (CP) and viral RNA is a carefully orchestrated process resulting in the formation of homogeneous population of infectious virions with T=3 symmetry. Expression in vivo of either wild type or mutant BMV CP through homologous replication never results in the assembly of aberrant particles. In this study, we report that deletion of amino acid residues 41-47 from the N-proximal region of BMV CP resulted in the assembly of polymorphic virions in vivo. Purified virions from symptomatic leaves remain non-infectious and Northern blot analysis of virion RNA displayed packaging defects. Biochemical characterization of variant CP by circular dichroism and MALDI-TOF, respectively, revealed that the engineered deletion affected the protein structure and capsid dynamics. Most significantly, CP subunits dissociated from polymorphic virions are incompetent for in vitro reassembly. Based on these observations, we propose a chaperon-mediated mechanism for the assembly of variant CP in vivo and also hypothesize that (41)KAIKAIA(47) N-proximal peptide functions as a molecular switch in regulating T=3 virion symmetry. PMID:17449079

Calhoun, Shauni L; Speir, Jeffrey A; Rao, A L N

2007-08-01

195

Should the Amounts of Fat and Protein Be Taken into Consideration to Calculate the Lunch Prandial Insulin Bolus? Results from a Randomized Crossover Trial  

PubMed Central

Abstract Background Concerning continuous subcutaneous insulin infusion (CSII), there are controversial results related to changes in glycemic response according to the meal composition and bolus design. Our aim is to determine whether the presence of protein and fat in a meal could involve a different postprandial glycemic response than that obtained with only carbohydrates (CHs). Subjects and Methods This was a crossover, randomized clinical trial. Seventeen type 1 diabetes (T1D) patients on CSII wore a blinded continuous glucose monitoring system sensor for 3 days. They ingested two meals (meal 1 vs. meal 2) with the same CH content (50?g) but different fat (8.9?g vs. 37.4?g) and protein (3.3?g vs. 28.9?g) contents. A single-wave insulin bolus was used, and the interstitial glucose values were measured every 30?min for 3?h. We evaluated the different postprandial glycemic response between meal 1 and meal 2 by using mixed-effects models. Results The postmeal glucose increase was 22?mg/dL for meal 1 and 31?mg/dL for meal 2. In univariate analysis, at different times not statistically significant differences in glucose levels between meals occurred. In mixed-model analysis, a time×meal interaction was found, indicating a different response between treatments along the time. However, most of the patients remained in the normoglycemic range (70–180?mg/dL) during the 3-h postmeal period (84.4% for meal 1 and 93.1% for meal 2). Conclusions The presence of balanced amounts of protein and fat determined a different glycemic response from that obtained with only CH up to 3?h after eating. The clinical relevance of this finding remains to be elucidated.

Gonzalez-Rodriguez, Maria; Pazos-Couselo, Marcos; Gude, Francisco; Prieto-Tenreiro, Alma; Casanueva, Felipe

2013-01-01

196

Overexpression of the cellular retinoic acid binding protein-I (CRABP-I) results in a reduction in differentiation-specific gene expression in F9 teratocarcinoma cells.  

PubMed

Treatment of F9 teratocarcinoma stem cells with retinoic acid (RA) causes their irreversible differentiation into extraembryonic endoderm. To elucidate the role of the cellular retinoic acid binding protein-I (CRABP-I) in this differentiation process, we have generated several different stably transfected F9 stem cell lines expressing either elevated or reduced levels of functional CRABP-I protein. Stably transfected lines expressing elevated levels of CRABP-I exhibit an 80-90% reduction in the RA induced expression of retinoic acid receptor (RAR) beta, laminin B1, and collagen type IV (alpha 1) mRNAs at low exogenous RA concentrations, but this reduction is eliminated at higher RA concentrations. Thus, greater expression of CRABP-I reduces the potency of RA in this differentiation system. Moreover, transfection of a CRABP-I expression vector into F9 cells resulted in five- and threefold decreases in the activation of the laminin B1 RARE (retinoic acid response element) and the RAR beta RARE, respectively, as measured from RARE/CAT expression vectors in transient transfection assays. These results support the idea that CRABP-I sequesters RA within the cell and thereby prevents RA from acting to regulate differentiation specific gene expression. Our data suggest a mechanism whereby the level of CRABP-I can regulate responsiveness to RA during development. PMID:1847931

Boylan, J F; Gudas, L J

1991-03-01

197

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

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 microg/ml versus 4 microg/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. PMID:17220413

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

2007-03-01

198

Surfactant protein D binds to Mycobacterium tuberculosis bacilli and lipoarabinomannan via carbohydrate-lectin interactions resulting in reduced phagocytosis of the bacteria by macrophages.  

PubMed

Surfactant protein-D (SP-D) is a collectin produced in the distal lung airspaces that is believed to play an important role in innate pulmonary immunity. Naive immunologic responses to Mycobacterium tuberculosis (M.tb) are especially important in the lung, since entry of this inhaled pathogen into the alveolar macrophage is a pivotal event in disease pathogenesis. Here we investigated SP-D binding to M.tb and the effect of this binding on the adherence of M. tb to human macrophages. These studies demonstrate specific binding of SP-D to M.tb that is saturable, calcium dependent, and carbohydrate inhibitable. In addition to purified SP-D, SP-D in bronchoalveolar lavage fluids from healthy donors and patients with alveolar proteinosis also binds to M.tb. Incubation of M.tb with SP-D results in agglutination of the bacteria. In contrast to its binding to M.tb, SP-D binds minimally to the avirulent Mycobacterium smegmatis. SP-D binds predominantly to lipoarabinomannan from the virulent Erdman strain of M.tb, but not the lipoarabinomannan from M. smegmatis. The binding of SP-D to Erdman lipoarabinomannan is mediated by the terminal mannosyl oligosaccharides of this lipoglycan. Incubation of M.tb with subagglutinating concentrations of SP-D leads to reduced adherence of the bacteria to macrophages (62.7% of control adherence +/- 3.3% SEM, n = 8), whereas incubation of bacteria with surfactant protein A leads to significantly increased adherence to monocyte-derived macrophages. These data provide evidence for specific binding of SP-D to M. tuberculosis and indicate that SP-D and surfactant protein A serve different roles in the innate host response to this pathogen in the lung. PMID:10384130

Ferguson, J S; Voelker, D R; McCormack, F X; Schlesinger, L S

1999-07-01

199

Sugared water consumption by adult offspring of mothers fed a protein-restricted diet during pregnancy results in increased offspring adiposity: the second hit effect.  

PubMed

Poor maternal nutrition predisposes offspring to metabolic disease. This predisposition is modified by various postnatal factors. We hypothesised that coupled to the initial effects of developmental programming due to a maternal low-protein diet, a second hit resulting from increased offspring postnatal sugar consumption would lead to additional changes in metabolism and adipose tissue function. The objective of the present study was to determine the effects of sugared water consumption (5% sucrose in the drinking-water) on adult offspring adiposity as a 'second hit' following exposure to maternal protein restriction during pregnancy. We studied four offspring groups: (1) offspring of mothers fed the control diet (C); (2) offspring of mothers fed the restricted protein diet (R); (3) offspring of control mothers that drank sugared water (C-S); (4) offspring of restricted mothers that drank sugared water (R-S). Maternal diet in pregnancy was considered the first factor and sugared water consumption as the second factor - the second hit. Body weight and total energy consumption, before and after sugared water consumption, were similar in all the groups. Sugared water consumption increased TAG, insulin and cholesterol concentrations in both the sexes of the C-S and R-S offspring. Sugared water consumption increased leptin concentrations in the R-S females and males but not in the R offspring. There was also an interaction between sugared water and maternal diet in males. Sugared water consumption increased adipocyte size and adiposity index in both females and males, but the interaction with maternal diet was observed only in females. Adiposity index and plasma leptin concentrations were positively correlated in both the sexes. The present study shows that a second hit during adulthood can amplify the effects of higher adiposity arising due to poor maternal pregnancy diet in an offspring sex dependent fashion. PMID:24124655

Cervantes-Rodríguez, M; Martínez-Gómez, M; Cuevas, E; Nicolás, L; Castelán, F; Nathanielsz, P W; Zambrano, E; Rodríguez-Antolín, J

2014-02-01

200

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

PubMed Central

Background One of the hallmarks of Alzheimer's disease, and several other degenerative disorders such as Inclusion Body Myositis, is the abnormal accumulation of amyloid precursor protein (APP) and its proteolytic amyloid peptides. To better understand the pathological consequences of inappropriate APP expression on developing tissues, we generated transgenic flies that express wild-type human APP in the skeletal muscles, and then performed anatomical, electrophysiological, and behavioral analysis of the adults. Results We observed that neither muscle development nor animal longevity was compromised in these transgenic animals. However, human APP expressing adults developed age-dependent defects in both climbing and flying. We could advance or retard the onset of symptoms by rearing animals in vials with different surface properties, suggesting that human APP expression-mediated behavioral defects are influenced by muscle activity. Muscles from transgenic animals did not display protein aggregates or structural abnormalities at the light or transmission electron microscopic levels. In agreement with genetic studies performed with developing mammalian myoblasts, we observed that co-expression of the ubiquitin E3 ligase Parkin could ameliorate human APP-induced defects. Conclusions These data suggest that: 1) ectopic expression of human APP in fruit flies leads to age- and activity-dependent behavioral defects without overt changes to muscle development or structure; 2) environmental influences can greatly alter the phenotypic consequences of human APP toxicity; and 3) genetic modifiers of APP-induced pathology can be identified and analyzed in this model.

2011-01-01

201

Mutations in the TIR1 Auxin Receptor That Increase Affinity for Auxin/Indole-3-Acetic Acid Proteins Result in Auxin Hypersensitivity1[W][OA  

PubMed Central

The phytohormone auxin regulates virtually every aspect of plant development. The hormone directly mediates the interaction between the two members of the auxin coreceptor complex, a TRANSPORT INHIBITOR RESPONSE (TIR1)/AUXIN SIGNALING F-BOX protein and an AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) transcriptional repressor. To learn more about the interaction between these proteins, a mutant screen was performed using the yeast (Saccharomyces cerevisiae) two-hybrid system in Arabidopsis (Arabidopsis thaliana). Two tir1 mutations were identified that increased interaction with Aux/IAAs. The D170E and M473L mutations increase affinity between TIR1 and the degron motif of Aux/IAAs and enhance the activity of the SCFTIR1 complex. This resulted in faster degradation of Aux/IAAs and increased transcription of auxin-responsive genes in the plant. Plants carrying the pTIR1:tir1 D170E/M473L-Myc transgene exhibit diverse developmental defects during plant growth and display an auxin-hypersensitive phenotype. This work demonstrates that changes in the leucine-rich repeat domain of the TIR1 auxin coreceptor can alter the properties of SCFTIR1.

Yu, Hong; Moss, Britney L.; Jang, Seunghee S.; Prigge, Michael; Klavins, Eric; Nemhauser, Jennifer L.; Estelle, Mark

2013-01-01

202

Activation of macrophage peroxisome proliferator-activated receptor-gamma by diclofenac results in the induction of cyclooxygenase-2 protein and the synthesis of anti-inflammatory cytokines.  

PubMed

Cyclooxygenase-2 (COX-2) is an inducible isoform of the COX family of enzymes central to the synthesis of pro-inflammatory prostaglandins. Induction of COX-2 is mediated by many endogenous and exogenous molecules that include pro-inflammatory cytokines and bacterial lipopolysaccharide (LPS). It has been demonstrated that COX-2 can also be induced by diclofenac in cultured J774.2 macrophages. This induction was delayed compared to COX-2 induced by LPS and paracetamol selectively inhibited activity of this protein. The aim of the present study was to determine the transcription factor involved in the production of COX-2 after treatment of J774.2 cells with 500 microM diclofenac. Pre-treatment of cells with the peroxisome proliferator-activated receptor-gamma (PPAR-gamma) antagonists GW9662 (0.1-1 microM) or biphenol A Diglycidyl Ether (100-200 microM) resulted in reduction of the induction of COX-2 by diclofenac, but not by LPS. Induction of COX-2 by the PPAR-gamma agonist 15deoxyDelta(12,14)prostaglandin J(2) was also reduced when the cells were pre-treated with the PPAR-gamma antagonists BADGE or GW9662. On the other hand, pre-treatment of cells with the nuclear factor-kappa-B (NF-kappaB) Super-repressor IkappaBalpha (150-600 nM) reduced the induction of COX-2 by LPS, but not by diclofenac. We, therefore, have identified that PPAR-gamma activation is a requirement for COX-2 induction after diclofenac stimulation of J774.2 cells. These results along with the finding that treatment of J774.2 macrophages with diclofenac resulted in the release of the anti-inflammatory cytokines, interleukin-10 and transforming growth factor-beta suggest that the diclofenac-induced COX-2 protein may possess anti-inflammatory actions. PMID:19219624

Ayoub, Samir S; Botting, Regina M; Joshi, Amrish N; Seed, Michael P; Colville-Nash, Paul R

2009-07-01

203

Disruption of the protein kinase N gene of Drosophila melanogaster Results in the Recessive delorean Allele (pkndln) With a Negative Impact on Wing Morphogenesis.  

PubMed

We describe the delorean mutation of the Drosophila melanogaster protein kinase N gene (pkn(dln)) with defects in wing morphology. Flies homozygous for the recessive pkn(dln) allele have a composite wing phenotype that exhibits changes in relative position and shape of the wing blade as well as loss of specific vein and bristle structures. The pkn(dln) allele is the result of a P-element insertion in the first intron of the pkn locus, and the delorean wing phenotype is contingent upon the interaction of insertion-bearing alleles in trans. The presence of the insertion results in production of a novel transcript that initiates from within the 3' end of the P-element. The delorean-specific transcript is predicted to produce a wild-type PKN protein. The delorean phenotype is not the result of a reduction in pkn expression, as it could not be recreated using a variety of wing-specific drivers of pkn-RNAi expression. Rather, it is the presence of the delorean-specific transcript that correlates with the mutant phenotype. We consider the delorean wing phenotype to be due to a pairing-dependent, recessive mutation that behaves as a dosage-sensitive, gain of function. Our analysis of genetic interactions with basket and nemo reflects an involvement of pkn and Jun-terminal kinase signaling in common processes during wing differentiation and places PKN as a potential effector of Rho1's involvement in the Jun-terminal kinase pathway. The delorean phenotype, with its associated defects in wing morphology, provides evidence of a role for PKN in adult morphogenetic processes. PMID:24531729

Sass, Georgette L; Ostrow, Bruce D

2014-01-01

204

Disruption of the protein kinase N gene of Drosophila melanogaster Results in the Recessive delorean Allele (pkndln) With a Negative Impact on Wing Morphogenesis  

PubMed Central

We describe the delorean mutation of the Drosophila melanogaster protein kinase N gene (pkndln) with defects in wing morphology. Flies homozygous for the recessive pkndln allele have a composite wing phenotype that exhibits changes in relative position and shape of the wing blade as well as loss of specific vein and bristle structures. The pkndln allele is the result of a P-element insertion in the first intron of the pkn locus, and the delorean wing phenotype is contingent upon the interaction of insertion-bearing alleles in trans. The presence of the insertion results in production of a novel transcript that initiates from within the 3? end of the P-element. The delorean-specific transcript is predicted to produce a wild-type PKN protein. The delorean phenotype is not the result of a reduction in pkn expression, as it could not be recreated using a variety of wing-specific drivers of pkn-RNAi expression. Rather, it is the presence of the delorean-specific transcript that correlates with the mutant phenotype. We consider the delorean wing phenotype to be due to a pairing-dependent, recessive mutation that behaves as a dosage-sensitive, gain of function. Our analysis of genetic interactions with basket and nemo reflects an involvement of pkn and Jun-terminal kinase signaling in common processes during wing differentiation and places PKN as a potential effector of Rho1’s involvement in the Jun-terminal kinase pathway. The delorean phenotype, with its associated defects in wing morphology, provides evidence of a role for PKN in adult morphogenetic processes.

Sass, Georgette L.; Ostrow, Bruce D.

2014-01-01

205

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Heat shock 40 kDa protein 4 DnaJ protein homolog 2 Cellular Function: Protein Folding Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular

206

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

207

Immune sensitization to methylene diphenyl diisocyanate (MDI) resulting from skin exposure: albumin as a carrier protein connecting skin exposure to subsequent respiratory responses  

PubMed Central

Background Methylene diphenyl diisocyanate (MDI), a reactive chemical used for commercial polyurethane production, is a well-recognized cause of occupational asthma. The major focus of disease prevention efforts to date has been respiratory tract exposure; however, skin exposure may also be an important route for inducing immune sensitization, which may promote subsequent airway inflammatory responses. We developed a murine model to investigate pathogenic mechanisms by which MDI skin exposure might promote subsequent immune responses, including respiratory tract inflammation. Methods Mice exposed via the skin to varying doses (0.1-10% w/v) of MDI diluted in acetone/olive oil were subsequently evaluated for MDI immune sensitization. Serum levels of MDI-specific IgG and IgE were measured by enzyme-linked immunosorbant assay (ELISA), while respiratory tract inflammation, induced by intranasal delivery of MDI-mouse albumin conjugates, was evaluated based on bronchoalveolar lavage (BAL). Autologous serum IgG from "skin only" exposed mice was used to detect and guide the purification/identification of skin proteins antigenically modified by MDI exposure in vivo. Results Skin exposure to MDI resulted in specific antibody production and promoted subsequent respiratory tract inflammation in animals challenged intranasally with MDI-mouse albumin conjugates. The degree of (secondary) respiratory tract inflammation and eosinophilia depended upon the (primary) skin exposure dose, and was maximal in mice exposed to 1% MDI, but paradoxically limited in mice receiving 10-fold higher doses (e.g. 10% MDI). The major antigenically-modified protein at the local MDI skin exposure site was identified as albumin, and demonstrated biophysical changes consistent with MDI conjugation. Conclusions MDI skin exposure can induce MDI-specific immune sensitivity and promote subsequent respiratory tract inflammatory responses and thus, may play an important role in MDI asthma pathogenesis. MDI conjugation and antigenic modification of albumin at local (skin/respiratory tract) exposure sites may represent the common antigenic link connecting skin exposure to subsequent respiratory tract inflammation.

2011-01-01

208

Lipid raft- and protein kinase C-mediated synergism between glucocorticoid- and gonadotropin-releasing hormone signaling results in decreased cell proliferation.  

PubMed

Cross-talk between the glucocorticoid receptor (GR) and other receptors is emerging as a mechanism for fine-tuning cellular responses. We have previously shown that gonadotropin-releasing hormone (GnRH) ligand-independently activates the GR and synergistically modulates glucocorticoid-induced transcription of an endogenous gene in L?T2 pituitary gonadotrope precursor cells. Here, we investigated GR and GnRH receptor (GnRHR) cross-talk that involves co-localization with lipid rafts in L?T2 cells. We report that the GnRHR and a small population of the GR co-localize with the lipid raft protein flotillin-1 (Flot-1) at the plasma membrane and that the GR is present in a complex with Flot-1, independent of the presence of ligands. We found that the SGK-1 gene is up-regulated by Dex and GnRH alone, whereas a combination of both ligands resulted in a synergistic increase in SGK-1 mRNA levels. Using siRNA-mediated knockdown and antagonist strategies, we show that the gene-specific synergistic transcriptional response requires the GR, GnRHR, and Flot-1 as well as the protein kinase C pathway. Interestingly, although several GR cofactors are differentially recruited to the SGK-1 promoter in the presence of Dex and GnRH, GR levels remain unchanged compared with Dex treatment alone, suggesting that lipid raft association of the GR has a role in enhancing its transcriptional output in the nucleus. Finally, we show that Dex plus GnRH synergistically inhibit cell proliferation in a manner dependent on SGK-1 and Flot-1. Collectively the results support a mechanism whereby GR and GnRHR cross-talk within Flot-1-containing lipid rafts modulates cell proliferation via PKC activation and SGK-1 up-regulation. PMID:24558046

Wehmeyer, Lancelot; Du Toit, Andrea; Lang, Dirk M; Hapgood, Janet P

2014-04-01

209

Measurement of multisite oxidation kinetics reveals an active site conformational change in Spo0F as a result of protein oxidation.  

PubMed

When most proteins undergo oxidative damage, they yield a variety of products containing oxidative damage at a large number of sites, most of which are modified substoichiometrically. The resulting complex mixture of products is not amenable to high-resolution structural analyses. The previous methods of structural analysis have relied upon either very generalized structural analyses such as circular dichroism or the creation of a battery of mutants to try to isolate single-residue damage effects. We present a methodology using mass spectrometry to measure the kinetics of oxidation at many sites simultaneously. Previous studies have shown that these kinetics are determined by the chemical nature of the damage site and by the accessibility of that site to the radical. By measuring deviations in the rate of oxidation from the expected pseudo-zero-order kinetics, we can detect and characterize local structural changes due to the oxidative damage. We demonstrate the application of this new technique to the Spo0F protein, a regulator of sporulation in Bacillus subtilis. Circular dichroism studies suggest a partial loss of helical structure of Spo0F as a result of oxidative damage. We report that oxidation causes a three-stage conformational change in Spo0F. Furthermore, we find the dramatic structural changes affect only the region surrounding the active site, while the remainder of the structure remains relatively unperturbed. Finally, we are able to determine that the specific oxidation event that triggers the conformational change at the active site of Spo0F occurs at Met81, a partially conserved methionine in the CheY superfamily. PMID:16700537

Sharp, Joshua S; Sullivan, Daniel M; Cavanagh, John; Tomer, Kenneth B

2006-05-23

210

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database  

SciTech Connect

HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics. med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.

Omenn, Gilbert; States, David J.; Adamski, Marcin; Blackwell, Thomas W.; Menon, Rajasree; Hermjakob, Henning; Apweiler, Rolf; Haab, Brian B.; Simpson, Richard; Eddes, James; Kapp, Eugene; Moritz, Rod; Chan, Daniel W.; Rai, Alex J.; Admon, Arie; Aebersold, Ruedi; Eng, Jimmy K.; Hancock, William S.; Hefta, Stanley A.; Meyer, Helmut; Paik, Young-Ki; Yoo, Jong-Shin; Ping, Peipei; Pounds, Joel G.; Adkins, Joshua N.; Qian, Xiaohong; Wang, Rong; Wasinger, Valerie; Wu, Chi Yue; Zhao, Xiaohang; Zeng, Rong; Archakov, Alexander; Tsugita, Akira; Beer, Ilan; Pandey, Akhilesh; Pisano, Michael; Andrews, Philip; Tammen, Harald; Speicher, David W.; Hanash, Samir M.

2005-08-13

211

Association of C-Reactive Protein and Lower Urinary Tract Symptoms in Men and Women. Results from the Boston Area Community Health (BACH) Survey  

PubMed Central

Objectives The objectives of this study were: 1) to determine whether there is an association between C-reactive protein (CRP) levels and lower urinary tract symptoms (LUTS) as assessed by the American Urological Association Symptom Index (AUA-SI) among both men and women, 2) to determine the association of CRP levels with individual urologic symptoms comprising the AUA-SI among both men and women. Methods The Boston Area Community Health (BACH) Survey used a multistage stratified design to recruit a random sample of 5,502 adults age 30–79. Blood samples were obtained on 3,752 participants. Analyses were conducted on 1,898 men and 1,854 women with complete data on C-Reactive Protein (CRP) levels. Overall LUTS was defined as an AUA-SI?8 (moderate to severe LUTS). Urologic symptoms comprising the AUA-SI were included in the analysis as reports of fairly often to almost always vs. non/rarely/a few times. Results A statistically significant association was observed between CRP levels and overall LUTS among both men and women. The pattern of associations between individual symptoms and CRP levels varied by gender. Nocturia and straining were associated with higher CRP levels among men, while incomplete emptying and weak stream were associated with higher CRP levels among women. Conclusions This study demonstrates an association between CRP levels and LUTS in both men and women. The dose-response relationship between increased CRP levels and increased odds of LUTS supports the hypothesized role of inflammatory processes in the etiology of LUTS.

Kupelian, Varant; McVary, Kevin T.; Barry, Michael J.; Link, Carol L.; Rosen, Raymond C.; Aiyer, Lalitha Padmanabhan; Mollon, Patrick; McKinlay, John B.

2012-01-01

212

Moderate Hypoxia Followed by Reoxygenation Results in Blood-Brain Barrier Breakdown via Oxidative Stress-Dependent Tight-Junction Protein Disruption  

PubMed Central

Re-canalization of cerebral vessels in ischemic stroke is pivotal to rescue dysfunctional brain areas that are exposed to moderate hypoxia within the penumbra from irreversible cell death. Goal of the present study was to evaluate the effect of moderate hypoxia followed by reoxygenation (MHR) on the evolution of reactive oxygen species (ROS) and blood-brain barrier (BBB) integrity in brain endothelial cells (BEC). BBB integrity was assessed in BEC in vitro and in microvessels of the guinea pig whole brain in situ preparation. Probes were exposed to MHR (2 hours 67-70 mmHg O2, 3 hours reoxygenation, BEC) or towards occlusion of the arteria cerebri media (MCAO) with or without subsequent reperfusion in the whole brain preparation. In vitro BBB integrity was evaluated using trans-endothelial electrical resistance (TEER) and transwell permeability assays. ROS in BEC were evaluated using 2?,7?-dichlorodihydrofluorescein diacetate (DCF), MitoSox and immunostaining for nitrotyrosine. Tight-junction protein (TJ) integrity in BEC, stainings for nitrotyrosine and FITC-albumin extravasation in the guinea pig brain preparation were assessed by confocal microscopy. Diphenyleneiodonium (DPI) was used to investigate NADPH oxidase dependent ROS evolution and its effect on BBB parameters in BEC. MHR impaired TJ proteins zonula occludens 1 (ZO-1) and claudin 5 (Cl5), decreased TEER, and significantly increased cytosolic ROS in BEC. These events were blocked by the NADPH oxidase inhibitor DPI. MCAO with or without subsequent reoxygenation resulted in extravasation of FITC-albumin and ROS generation in the penumbra region of the guinea pig brain preparation and confirmed BBB damage. BEC integrity may be impaired through ROS in MHR on the level of TJ and the BBB is also functionally impaired in moderate hypoxic conditions followed by reperfusion in a complex guinea pig brain preparation. These findings suggest that the BBB is susceptible towards MHR and that ROS play a key role in this process.

Zehendner, Christoph M.; Librizzi, Laura; Hedrich, Jana; Bauer, Nina M.; Angamo, Eskedar A.; de Curtis, Marco; Luhmann, Heiko J.

2013-01-01

213

Moderate hypoxia followed by reoxygenation results in blood-brain barrier breakdown via oxidative stress-dependent tight-junction protein disruption.  

PubMed

Re-canalization of cerebral vessels in ischemic stroke is pivotal to rescue dysfunctional brain areas that are exposed to moderate hypoxia within the penumbra from irreversible cell death. Goal of the present study was to evaluate the effect of moderate hypoxia followed by reoxygenation (MHR) on the evolution of reactive oxygen species (ROS) and blood-brain barrier (BBB) integrity in brain endothelial cells (BEC). BBB integrity was assessed in BEC in vitro and in microvessels of the guinea pig whole brain in situ preparation. Probes were exposed to MHR (2 hours 67-70 mmHg O2, 3 hours reoxygenation, BEC) or towards occlusion of the arteria cerebri media (MCAO) with or without subsequent reperfusion in the whole brain preparation. In vitro BBB integrity was evaluated using trans-endothelial electrical resistance (TEER) and transwell permeability assays. ROS in BEC were evaluated using 2',7'-dichlorodihydrofluorescein diacetate (DCF), MitoSox and immunostaining for nitrotyrosine. Tight-junction protein (TJ) integrity in BEC, stainings for nitrotyrosine and FITC-albumin extravasation in the guinea pig brain preparation were assessed by confocal microscopy. Diphenyleneiodonium (DPI) was used to investigate NADPH oxidase dependent ROS evolution and its effect on BBB parameters in BEC. MHR impaired TJ proteins zonula occludens 1 (ZO-1) and claudin 5 (Cl5), decreased TEER, and significantly increased cytosolic ROS in BEC. These events were blocked by the NADPH oxidase inhibitor DPI. MCAO with or without subsequent reoxygenation resulted in extravasation of FITC-albumin and ROS generation in the penumbra region of the guinea pig brain preparation and confirmed BBB damage. BEC integrity may be impaired through ROS in MHR on the level of TJ and the BBB is also functionally impaired in moderate hypoxic conditions followed by reperfusion in a complex guinea pig brain preparation. These findings suggest that the BBB is susceptible towards MHR and that ROS play a key role in this process. PMID:24324834

Zehendner, Christoph M; Librizzi, Laura; Hedrich, Jana; Bauer, Nina M; Angamo, Eskedar A; de Curtis, Marco; Luhmann, Heiko J

2013-01-01

214

Multi-megabase silencing in nucleolar dominance results from siRNA-directed de novo DNA methylation recognized by specific methylcytosine binding proteins  

PubMed Central

In genetic hybrids, the silencing of nucleolar rRNA genes inherited from one progenitor is the epigenetic phenomenon known as nucleolar dominance. An RNAi knockdown screen identified the Arabidopsis de novo cytosine methyltransferase, DRM2 and the methylcytosine binding domain proteins, MBD6 and MBD10 as activities required for nucleolar dominance. MBD10 localizes throughout the nucleus, but MBD6 preferentially associates with silenced rRNA genes, and does so in a DRM2-dependent manner. DRM2 methylation is thought to be guided by siRNAs whose biogenesis requires RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3). Consistent with this hypothesis, knockdown of DCL3 or RDR2 disrupts nucleolar dominance. In genetic hybrids, the silencing of nucleolar rRNA genes inherited from one progenitor is the epigenetic phenomenon known as nucleolar dominance. An RNAi knockdown screen identified the Arabidopsis de novo cytosine methyltransferase, DRM2 and the methylcytosine binding domain proteins, MBD6 and MBD10 as activities required for nucleolar dominance. MBD10 localizes throughout the nucleus, but MBD6 preferentially associates with silenced rRNA genes, and does so in a DRM2-dependent manner. DRM2 methylation is thought to be guided by siRNAs whose biogenesis requires RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3). Consistent with this hypothesis, knockdown of DCL3 or RDR2 disrupts nucleolar dominance. Collectively, these results indicate that in addition to directing the silencing of retrotransposons and noncoding repeats, siRNAs specify de novo cytosine methylation patterns that are recognized by MBD6 and MBD10 in the large-scale silencing of rRNA gene loci.

Preuss, Sasha B.; Costa-Nunes, Pedro; Tucker, Sarah; Pontes, Olga; Lawrence, Richard J.; Mosher, Rebecca; Kasschau, Kristin D.; Carrington, James C.; Baulcombe, David C.; Viegas, Wanda; Pikaard, Craig S.

2008-01-01

215

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

216

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

PubMed

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. PMID:7751011

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

1995-02-01

217

Do insulin-like growth factor associated proteins qualify as a tumor marker? Results of a prospective study in 163 cancer patients  

PubMed Central

Objective Insulin-like growth factor (IGF)-1, -2 and Insulin like growth factor binding proteins (IGFBP) are involved in the proliferation and differentiation of cells. It has never been evaluated, if the IGF-system can serve as a tumor marker in neoplasms. Methods In our prospective study 163 patients with colorectal cancer (22), prostate cancer (21), head and neck tumors (17), lymphomas (20), lung cancer (34) and other entities (49) were analysed for their IGF and IGFBP serum levels at the beginning and the end of radiotherapy and compared to 13 healthy people. Subgroups of patients with local tumor disease versus metastatic disease, primary and recurrent therapy and curative versus palliative therapy were compared. Results The serum levels of IGF-2 were significantly elevated in patients with prostate and colorectal cancer. However, sensitivity and specificity were only 70%. IGFBP-2 serum levels were elevated in patients with head and neck tumors. Again sensitivity and specificity were only 73%. A difference between local disease and metastatic disease could not be found. A difference between IGF serum levels before and after radiotherapy could not be detected. Conclusion The IGF-system cannot serve as a new tumor marker. The detected differences are very small, sensitivity and specificity are too low. IGF measurement is not useful for the evaluation of the success of radiotherapy in malignancies.

2011-01-01

218

Inactivation of the Streptococcus mutans wall-associated protein A gene (wapA) results in a decrease in sucrose-dependent adherence and aggregation.  

PubMed Central

A 0.8-kb HindIII-BamHI internal fragment of the Streptococcus mutans wall-associated protein A gene (wapA) was ligated to the 5.1-kb HindIII-BamHI fragment of the chimeric Streptococcus-Escherichia coli plasmid pVA891 (Emr Cmr). The resulting construct was used to transform S. mutans GS-5, and erythromycin-resistant mutants were isolated and analyzed. Directed mutagenesis of the wapA gene by plasmid insertion through homologous recombination was demonstrated by Southern blot hybridization with the wapA and pVA891 probes. Stable mutants were obtained, and the alteration of the wapA gene by insertional inactivation was associated with a significant decrease in S. mutans sucrose-dependent aggregation and binding to smooth surfaces. Thus, WapA may play an important role in the colonization of the tooth surface by S. mutans and in the buildup of dental plaque. These findings provided an explanation for previous studies which indicated that WapA was effective in the prevention of dental caries in animal models. Thus, the use of recombinant WapA in the preparation of a safe and effective human dental vaccine should be investigated further. Images

Qian, H; Dao, M L

1993-01-01

219

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

220

Absence of myotonic dystrophy protein kinase (DMPK) mRNA as a result of a triplet repeat expansion in myotonic dystrophy  

SciTech Connect

Myotonic dystrophy is an autosomally dominant inherited disease in which system-wide abnormalities are caused by a triplet repeat expansion within the 3[prime] untranslated region of the myotonic dystrophy protein kinase (DMPK) gene. To determine the effect an expanded repeat region has on DMPK expression, the authors have separated the chromosome 19 homologues from a 36-year-old woman with myotonic dystrophy into different cell lines by way of somatic cell hybridization. Hybrid DM9101 contains the normal DMPK allele (13 repeats), whereas hybrid DM1115 harbors the mutant allele ([approximately]133 repeats). Reverse transcription/polymerase chain reaction (RT/PCR) amplification of coding sequences from the DMPK gene has shown both reduced levels of primary DMPK transcripts and impaired processing of these transcripts in hybrid cell line DM1115. These findings suggest that the presence of a large number of repeats in the 3[prime] untranslated region of the DMPK gene reduces both the synthesis and the processing of DMPK mRNA, resulting in undetectable levels of processed DMPK mRNA from the mutant allele. 41 refs., 6 figs., 1 tab.

Carango, P.; Noble, J.E.; Funanage, V.L.; Marks, H.G. (Alfred I. duPont Institute, Wilmington, DE (United States))

1993-11-01

221

Slow Proton Transfer Coupled to Unfolding Explains the Puzzling Results of Single-Molecule Experiments on BBL, a Paradigmatic Downhill Folding Protein  

PubMed Central

A battery of thermodynamic, kinetic, and structural approaches has indicated that the small ?-helical protein BBL folds-unfolds via the one-state downhill scenario. Yet, single-molecule fluorescence spectroscopy offers a more conflicting view. Single-molecule experiments at pH 6 show a unique half-unfolded conformational ensemble at mid denaturation, whereas other experiments performed at higher pH show a bimodal distribution, as expected for two-state folding. Here we use thermodynamic and laser T-jump kinetic experiments combined with theoretical modeling to investigate the pH dependence of BBL stability, folding kinetics and mechanism within the pH 6–11 range. We find that BBL unfolding is tightly coupled to the protonation of one of its residues with an apparent pKa of ?7. Therefore, in chemical denaturation experiments around neutral pH BBL unfolds gradually, and also converts in binary fashion to the protonated species. Moreover, under the single-molecule experimental conditions (denaturant midpoint and 279 K), we observe that proton transfer is much slower than the ?15 microseconds folding-unfolding kinetics of BBL. The relaxation kinetics is distinctly biphasic, and the overall relaxation time (i.e. 0.2–0.5 ms) becomes controlled by the proton transfer step. We then show that a simple theoretical model of protein folding coupled to proton transfer explains quantitatively all these results as well as the two sets of single-molecule experiments, including their more puzzling features. Interestingly, this analysis suggests that BBL unfolds following a one-state downhill folding mechanism at all conditions. Accordingly, the source of the bimodal distributions observed during denaturation at pH 7–8 is the splitting of the unique conformational ensemble of BBL onto two slowly inter-converting protonation species. Both, the unprotonated and protonated species unfold gradually (one-state downhill), but they exhibit different degree of unfolding at any given condition because the native structure is less stable for the protonated form.

Cerminara, Michele; Campos, Luis A.; Ramanathan, Ravishankar; Munoz, Victor

2013-01-01

222

Perturbations in the spi1p GTPase cycle of Schizosaccharomyces pombe through its GTPase-activating protein and guanine nucleotide exchange factor components result in similar phenotypic consequences.  

PubMed Central

spi1p of Schizosaccharomyces pombe is a structural homolog of the mammalian GTPase Ran. The distribution between the GTP- and GDP-bound forms of the protein is regulated by evolutionarily conserved gene products, rna1p and pim1p, functioning as GTPase-activating protein (GAP) and guanine nucleotide exchange factor (GEF), respectively. Antibodies to spi1p, pim1p, and rna1p were generated and used to demonstrate that pim1p is exclusively nuclear, while rna1p is cytoplasmic. A loss of pim1p GEF activity or an increase in the rna1p GAP activity correlates with a change in the localization of the GTPase from predominantly nuclear to uniformly distributed, suggesting that the two forms are topologically segregated and that the nucleotide-bound state of spi1p may dictate its intracellular localization. We demonstrate that the phenotype of cells overproducing the GAP resembles the previously reported phenotype of mutants with alterations in the GEF: the cells are arrested in the cell cycle as septated, binucleated cells with highly condensed chromatin, fragmented nuclear envelopes, and abnormally wide septa. Consistent with the expectation that either an increased dosage of the GAP or a mutation in the GEF would lead to an increase of the spi1p-GDP/spi1p-GTP ratio relative to that of wild-type cells, overexpression of the GAP together with a mutation in the GEF is synthetically lethal. The similar phenotypic consequences of altering the functioning of the nuclear GEF or the cytoplasmic GAP suggest that there is a single pool of the spi1p GTPase that shuttles between the nucleus and the cytoplasm. Phenotypically, rna1 null mutants, in which spi1p-GTP would be expected to accumulate, resemble pim1(ts) and rna1p-overproducing cells, in which spi1p-GDP would be expected to accumulate. Taken together, these results support the hypothesis that the balance between the GDP- and GTP-bound forms of spi1p mediates the host of nuclear processes that are adversely affected when the functioning of different components of this system is perturbed in various organisms.

Matynia, A; Dimitrov, K; Mueller, U; He, X; Sazer, S

1996-01-01

223

Sequential extraction results in improved proteome profiling of medicinal plant Pinellia ternata tubers, which contain large amounts of high-abundance proteins.  

PubMed

Pinellia ternata tuber is one of the well-known Chinese traditional medicines. In order to understand the pharmacological properties of tuber proteins, it is necessary to perform proteome analysis of P. ternata tubers. However, a few high-abundance proteins (HAPs), mainly mannose-binding lectin (agglutinin), exist in aggregates of various sizes in the tubers and seriously interfere with proteome profiling by two-dimensional electrophoresis (2-DE). Therefore, selective depletion of these HAPs is a prerequisite for enhanced proteome analysis of P. ternata tubers. Based on differential protein solubility, we developed a novel protocol involving two sequential extractions for depletion of some HAPs and prefractionation of tuber proteins prior to 2-DE. The first extraction using 10% acetic acid selectively extracted acid-soluble HAPs and the second extraction using the SDS-containing buffer extracted remaining acid-insoluble proteins. After application of the protocol, 2-DE profiles of P. ternata tuber proteins were greatly improved and more protein spots were detected, especially low-abundance proteins. Moreover, the subunit composition of P. ternata lectin was analyzed by electrophoresis. Native lectin consists of two hydrogen-bonded subunits (11 kDa and 25 kDa) and the 11 kDa subunit was a glycoprotein. Subsequently, major HAPs in the tubers were analyzed by mass spectrometry, with nine protein spots being identified as lectin isoforms. The methodology was easy to perform and required no specialized apparatus. It would be useful for proteome analysis of other tuber plants of Araceae. PMID:23185632

Wu, Xiaolin; Xiong, Erhui; An, Sufang; Gong, Fangping; Wang, Wei

2012-01-01

224

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

225

N-Octanoyl Dopamine Treatment of Endothelial Cells Induces the Unfolded Protein Response and Results in Hypometabolism and Tolerance to Hypothermia  

PubMed Central

Aim N-acyl dopamines (NADD) are gaining attention in the field of inflammatory and neurological disorders. Due to their hydrophobicity, NADD may have access to the endoplasmic reticulum (ER). We therefore investigated if NADD induce the unfolded protein response (UPR) and if this in turn influences cell behaviour. Methods Genome wide gene expression profiling, confirmatory qPCR and reporter assays were employed on human umbilical vein endothelial cells (HUVEC) to validate induction of UPR target genes and UPR sensor activation by N-octanoyl dopamine (NOD). Intracellular ATP, apoptosis and induction of thermotolerance were used as functional parameters to assess adaptation of HUVEC. Results NOD, but not dopamine dose dependently induces the UPR. This was also found for other synthetic NADD. Induction of the UPR was dependent on the redox activity of NADD and was not caused by selective activation of a particular UPR sensor. UPR induction did not result in cell apoptosis, yet NOD strongly impaired cell proliferation by attenuation of cells in the S-G2/M phase. Long-term treatment of HUVEC with low NOD concentration showed decreased intracellular ATP concentration paralleled with activation of AMPK. These cells were significantly more resistant to cold inflicted injury. Conclusions We provide for the first time evidence that NADD induce the UPR in vitro. It remains to be assessed if UPR induction is causally associated with hypometabolism and thermotolerance. Further pharmacokinetic studies are warranted to address if the NADD concentrations used in vitro can be obtained in vivo and if this in turn shows therapeutic efficacy.

Stamellou, Eleni; Fontana, Johann; Wedel, Johannes; Ntasis, Emmanouil; Sticht, Carsten; Becker, Anja; Pallavi, Prama; Wolf, Kerstin; Kramer, Bernhard K.; Hafner, Mathias; van Son, Willem J.; Yard, Benito A.

2014-01-01

226

Forebrain-Specific Inactivation of Gq\\/G11 Family G Proteins Results in Age-Dependent Epilepsy and Impaired Endocannabinoid Formation  

Microsoft Academic Search

Received 7 March 2006\\/Returned for modification 28 April 2006\\/Accepted 11 May 2006 Metabotropic receptors coupled to Gq\\/G11 family G proteins critically contribute to nervous system functions by modulating synaptic transmission, often facilitating excitation. We investigated the role of Gq\\/G11 family G proteins in the regulation of neuronal excitability in mice that selectively lack the -subunits of Gq and G11, Gq

Nina Wettschureck; Mario van der Stelt; Hiroshi Tsubokawa; Heinz Krestel; Alexandra Moers; Stefania Petrosino; Gunther Schutz; V. Di Marzo; S. Offermanns

2006-01-01

227

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  

Microsoft Academic Search

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

Panagiotis K Karkoulis; Dimitrios J Stravopodis; Lukas H Margaritis; Gerassimos E Voutsinas

2010-01-01

228

Absence of IE1 p72 Protein Function during Low-Multiplicity Infection by Human Cytomegalovirus Results in a Broad Block to Viral Delayed-Early Gene Expression  

Microsoft Academic Search

Human cytomegalovirus (HCMV) ie1 deletion mutant CR208 is profoundly growth deficient after low- multiplicity infection of primary fibroblasts. Previously, we showed that many fewer cells infected with CR208 at low multiplicity accumulated the delayed-early (DE) protein ppUL44 than accumulated the immediate-early 2 (IE2) p86 protein, indicating a high frequency of abortive infections. We now demonstrate that accumulation of all DE

Jonathan M. Gawn; Richard F. Greaves

2002-01-01

229

Association Between Combined Interleukin-6 and C-Reactive Protein Levels and Pulmonary Function in Older Women: Results from the Women's Health and Aging Studies I and II  

PubMed Central

OBJECTIVES To determine whether combined higher interleukin-6 (IL-6) and C-reactive protein (CRP) levels are associated with lower pulmonary function levels in older women, accounting for chronic inflammatory diseases, physical function, and other factors associated with inflammation. DESIGN Cross-sectional study using data from two prospective cohorts. SETTING Baltimore, Maryland. PARTICIPANTS Eight hundred forty disabled and 332 higher-functioning community-dwelling women aged 65 and older from the Women’s Health and Aging Studies (WHAS) I and II, respectively. MEASUREMENTS IL-6 and CRP, combined according to their tertile concentrations, and pulmonary function measures, assessed according to forced expiratory volume in 1 second (FEV1) and forced vital capacity (FVC). RESULTS In WHAS I and II, similar dose-response trends were observed between combined higher IL-6 and CRP levels and lower pulmonary function levels. In WHAS I (disabled women), the combined highest IL-6 and CRP levels were associated with the lowest levels of FEV1 (mean 137.0 mL, 95% confidence interval (CI) = 128.4–145.7 mL) and FVC (mean 191.7 mL, 95% CI = 180.4–202.9 mL). Similarly, in WHAS II (higher-functioning women), the combined highest IL-6 and CRP levels were associated with the lowest levels of FEV1 (mean 158.3 mL, 95% CI = 146.3–170.4 mL) and FVC (mean 224.2 mL, 95% CI = 209.9–238.5 mL). CONCLUSION Combined elevations in IL-6 and CRP were associated with the lowest pulmonary function levels in older women. These findings suggest that high IL-6 and CRP levels may be an indication of prevalent impaired pulmonary function. Future studies should determine whether measurement of IL-6 and CRP could enhance current methods of monitoring respiratory diseases beyond that provided by pulmonary function measures.

Chang, Sandy S.; Fragoso, Carlos A. Vaz; Van Ness, Peter H.; Fried, Linda P.; Tinetti, Mary E.

2014-01-01

230

F box protein FBXL2 exerts human lung tumor suppressor-like activity by ubiquitin-mediated degradation of cyclin D3 resulting in cell cycle arrest  

PubMed Central

Dyregulated behavior of cell cycle proteins and their control by ubiquitin E3 ligases is an emerging theme in human lung cancer. Here we identified and characterized the activity of a novel F box protein, termed FBXL2, belonging to the SCF (Skip-Cullin1-F-box protein) E3 ligase family. Ectopically expressed FBXL2 triggered G2/M phase arrest, induced chromosomal anomalies, and increased apoptosis of transformed lung epithelia by mediating polyubiquitination and degradation of the mitotic regulator, cyclin D3. Unlike other F box proteins that target phosphodegrons within substrates, FBXL2 uniquely recognizes a canonical calmodulin-binding motif within cyclin D3 to facilitate its polyubiquitination. Calmodulin bound and protected cyclin D3 from FBXL2 by direct intermolecular competition with the F box protein for access within this motif. The chemotherapeutic agent vinorelbine increased apoptosis of human lung carcinoma cells by inducing FBXL2 expression and cyclin D3 degradation, an effect accentuated by calmodulin knockdown. Depletion of endogenous FBXL2 stabilized cyclin D3 levels, accellerated cancer cell growth, and increased cell viability after vinorelbine treatment. Last, ectopic expression of FBXL2 significantly inhibited the growth and migration of tumorogenic cells and tumor formation in athymic nude mice. These observations implicate SCFFBXL2 as an indispensible regulator of mitosis that serves as a tumor suppressor.

Chen, Bill B.; Glasser, Jennifer R.; Coon, Tiffany A.; Mallampalli, Rama K.

2011-01-01

231

The Insertion of Fluorescent Proteins in a Variable Region of Respiratory Syncytial Virus L Polymerase Results in Fluorescent and Functional Enzymes But with Reduced Activities  

PubMed Central

The respiratory syncytial virus (RSV) Large protein L is the catalytic subunit of the RNA-dependent RNA polymerase complex. Currently, no structural information is available for RSV L. Sequence alignments of L protein from human and bovine strains of RSV revealed the existence of two variable regions, VR1 and VR2. Following comparison with morbillivirus and rhabdovirus L genes, VR2, which is located between domains V and VI, was chosen as an insertion site for sequences encoding the epitope tag HA or the fluorescent proteins eGFP and mCherry. Recombinant tagged-L proteins co-localized with RSV N and P proteins in transfected cells. These recombinant polymerases were shown to be functional using a viral minigenome system assay, their activities being reduced by ~70% compared to the unmodified L polymerase. We have also shown by site-directed mutagenesis that the GDNQ motif (residues 810-813 for the Long strain of HRSV) is essential for L activity.

Fix, Jenna; Galloux, Marie; Blondot, Marie-Lise; Eleouet, Jean-Francois

2011-01-01

232

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 Central

Summary 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.

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.

2013-01-01

233

Microsomal triglyceride transfer protein -164 T > C gene polymorphism and risk of cardiovascular disease: results from the EPIC-Potsdam case-cohort study  

PubMed Central

Background The microsomal triglyceride transfer protein (MTTP) is encoded by the MTTP gene that is regulated by cholesterol in humans. Previous studies investigating the effect of MTTP on ischemic heart disease have produced inconsistent results. Therefore, we have tested the hypothesis that the rare allele of the -164T?>?C polymorphism in MTTP alters the risk of cardiovascular disease (CVD), depending on the cholesterol levels. Methods The -164T > C polymorphism was genotyped in a case-cohort study (193 incident myocardial infarction (MI) and 131 incident ischemic stroke (IS) cases and 1 978 non-cases) nested within the European Prospective Investigation into Cancer and Nutrition (EPIC)–Potsdam study, comprising 27 548 middle-aged subjects. The Heinz Nixdorf Recall study (30 CVD cases and 1 188 controls) was used to replicate our findings. Results Genotype frequencies were not different between CVD and CVD free subjects (P = 0.79). We observed an interaction between the -164T > C polymorphism and total cholesterol levels in relation to future CVD. Corresponding stratified analyses showed a significant increased risk of CVD (HRadditve = 1.38, 95% CI: 1.07 to 1.78) for individuals with cholesterol levels <200 mg/dL in the EPIC-Potsdam study. HRadditive was 1.06, 95% CI: 0.33 to 3.40 for individuals in the Heinz Nixdorf Recall study. A borderline significant decrease in CVD risk was observed in subjects with cholesterol levels ?200 mg/dL (HRadditve = 0.77, 95% CI: 0.58 to 1.03) in the EPIC-Potsdam study. A similar trend was observed in the independent cohort (HRadditve = 0.60, 95% CI: 0.29 to 1.25). Conclusions Our study suggests an interaction between MTTP -164T > C functional polymorphism with total cholesterol levels. Thereby risk allele carriers with low cholesterol levels may be predisposed to an increased risk of developing CVD, which seems to be abolished among risk allele carriers with high cholesterol levels.

2013-01-01

234

Unraveling the binding interaction and kinetics of a prospective anti-HIV drug with a model transport protein: results and challenges.  

PubMed

The present contribution reports a detailed characterization of the binding interaction of a potential anticancer, anti-HIV drug 1-phenylisatin (1-PI) with a model transport protein Bovine Serum Albumin (BSA) using fluorescence spectroscopic techniques. The thermodynamic parameters e.g., ?H, ?S and ?G for the binding phenomenon have been evaluated on the basis of the van't Hoff equation to reveal that the binding process is principally driven by ionic interactions mediated by charge transfer interaction. This line of argument has been substantiated by frontier molecular orbital analysis of 1-PI. However, the drug-induced quenching of the intrinsic tryptophanyl fluorescence of the protein is found not to abide by a linear Stern-Volmer regression (displaying an upward curvature) when an extensive time-resolved fluorescence spectroscopic characterization of the quenching process has been undertaken to unveil the actuating quenching mechanism. Based on the constancy of the fluorescence lifetime of the protein as a function of drug concentration the observed quenching is inferred to proceed through a static mechanism between the quenching partners. Constant wavelength synchronous fluorescence, excitation-emission matrix fluorescence and circular dichroic (CD) spectroscopic techniques have been exploited to unravel the tertiary and secondary conformational changes in the protein (BSA) induced by drug (1-PI)-binding. The probable binding location of the drug molecule within the protein cavity (hydrophilic subdomain I) has been explored by AutoDock-based blind docking simulation and the inference is further substantiated by site-competitive replacement experiments with specific site-markers. Light is also cast on the drug-protein binding kinetics using the stopped-flow fluorescence technique which reveals an association rate constant of k(a) (± 5%) = 1.471 × 10(-3) s(-1) for the interaction of 1-PI with BSA. PMID:23232916

Paul, Bijan Kumar; Ray, Debarati; Guchhait, Nikhil

2013-01-28

235

Muscle Uncoupling Protein 3 Expression Is Unchanged by Chronic Ephedrine/Caffeine Treatment: Results of a Double Blind, Randomised Clinical Trial in Morbidly Obese Females  

PubMed Central

Ephedrine/caffeine combination (EC) has been shown to induce a small-to-moderate weight loss in obese patients. Several mechanisms have been proposed, among which an increased thermogenic capacity of skeletal muscle consequent to the EC-induced up-regulation of uncoupling protein 3 (UCP3) gene expression. We did a parallel group double-blind, placebo-controlled, 4-week trial to investigate this hypothesis. Thirteen morbidly obese women (25–52 years of age, body-mass index 48.0±4.0 kg/m2, range 41.1–57.6) were randomly assigned to EC (200/20 mg, n?=?6) or to placebo (n?=?7) administered three times a day orally, before undergoing bariatric surgery. All individuals had an energy-deficit diet equal to about 70% of resting metabolic rate (RMR) diet (mean 5769±1105 kJ/day). The RMR analysed by intention to treat and the UCP3 (long and short isoform) mRNA levels in rectus abdominis were the primary outcomes. Body weight, plasma levels of adrenaline, noradrenaline, triglycerides, free fatty acids, glycerol, TSH, fT4, and fT3 were assessed, as well as fasting glucose, insulin and HOMA index, at baseline and at the end of treatments. Body weight loss was evident in both groups when compared to baseline values (overall ?5.2±3.2%, p<0.0001) without significant differences between the treated groups. EC treatment increased the RMR (+9.2±6.8%, p?=?0.020), differently from placebo which was linked to a reduction of RMR (?7.6±6.5%, p?=?0.029). No significant differences were seen in other metabolic parameters. Notably, no changes of either UCP3 short or UCP3 long isoform mRNA levels were evident between EC and placebo group. Our study provides evidence that 4-week EC administration resulted in a pronounced thermogenic effect not related to muscle UCP3 gene expression and weight loss in morbidly obese females under controlled conditions. Trial Registration ClinicalTrials.gov NCT02048215

Bracale, Renata; Petroni, Maria Letizia; Davinelli, Sergio; Bracale, Umberto; Scapagnini, Giovanni; Carruba, Michele O.; Nisoli, Enzo

2014-01-01

236

MART-1 peptide vaccination plus IMP321 (LAG-3Ig fusion protein) in patients receiving autologous PBMCs after lymphodepletion: results of a Phase I trial  

PubMed Central

Background Immunotherapy offers a promising novel approach for the treatment of cancer and both adoptive T-cell transfer and immune modulation lead to regression of advanced melanoma. However, the potential synergy between these two strategies remains unclear. Methods We investigated in 12 patients with advanced stage IV melanoma the effect of multiple MART-1 analog peptide vaccinations with (n?=?6) or without (n?=?6) IMP321 (LAG-3Ig fusion protein) as an adjuvant in combination with lymphodepleting chemotherapy and adoptive transfer of autologous PBMCs at day (D) 0 (Trial registration No: NCT00324623). All patients were selected on the basis of ex vivo detectable MART-1-specific CD8 T-cell responses and immunized at D0, 8, 15, 22, 28, 52, and 74 post-reinfusion. Results After immunization, a significant expansion of MART-1-specific CD8 T cells was measured in 83% (n?=?5/6) and 17% (n?=?1/6) of patients from the IMP321 and control groups, respectively (P?2-, >4- and >6-fold higher at D15, D30 and D60 (P?

2014-01-01

237

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

2011-01-01

238

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

239

A serine-to-threonine substitution in the triazine herbicide-binding protein in potato cells results in atrazine resistance without impairing productivity.  

PubMed Central

A mutation of the psbA gene was identified in photoautotrophic potato (Solanum tuberosum L. cv Superior x U.S. Department of Agriculture line 66-142) cells selected for resistance to 6-chloro-N-ethyl-N'-(1-methylethyl)-1,3,5-triazine-2,4-diamine (atrazine). Photoaffinity labeling with 6-azido-N-ethyl-N'-(1-methylethyl)-1,3,5-triazine-2,4-diamine detected a thylakoid membrane protein with a M(r) of 32,000 in susceptible, but not in resistant, cells. This protein was identified as the secondary quinone acceptor of photosystem II (QB) protein. Atrazine resistance in selected cells was attributable to a mutation from AGT (serine) to ACT (threonine) in codon 264 of the psbA gene that encodes the QB protein. Although the mutant cells exhibited extreme levels of resistance to atrazine, no concomitant reductions in photosynthetic electron transport or cell growth rates compared to the unselected cells were detected. This is in contrast with the losses in productivity observed in atrazine-resistant mutants that contain a glycine-264 alteration.

Smeda, R J; Hasegawa, P M; Goldsbrough, P B; Singh, N K; Weller, S C

1993-01-01

240

Absence of asparagine-linked oligosaccharides from glycoprotein D of herpes simplex virus type 1 results in a structurally altered but biologically active protein.  

PubMed Central

Glycoprotein D (gD) of herpes simplex virus contains three utilized sites (Asn-X-Ser/Thr) for addition of asparagine-linked carbohydrates (N-CHO). Previously, we used oligonucleotide-directed mutagenesis to alter serine or threonine residues to alanine at each N-CHO addition site. Studies with monoclonal antibodies showed that a mutant protein lacking all three sites (now designated AAA) was structurally altered because of the amino acid change at residue 96 as well as the absence of the N-CHO. In this study, we constructed additional single mutations at site 1 (residues 94 and 96) and found that in most cases, the amino acid change itself adversely affected the conformation of gD. However, changing asparagine 94 to glutamine (Q) at site 1 had the least effect on gD. We constructed a second triple mutant, QAA, which lacked all three N-CHO signals. The antigenic conformation of QAA was similar to that of gD produced in the presence of tunicamycin (TM-gD). However, binding of MAbs to the AAA protein or to single mutants altered at site 1 was reduced compared with TM-gD. Wild-type gD and QAA proteins were equally susceptible to digestion by trypsin or Staphylococcus aureus V8 protease. In contrast, the AAA protein was more sensitive to trypsin but less sensitive to V8, again suggesting conformational alterations of the AAA protein. Despite what appeared to be large changes in structure, each mutant complemented the infectivity of a virus lacking gD (F-gD beta). We conclude that the N-CHO and amino acids at N-CHO site 1 play an important role in forming and/or maintaining gD structure, but none of the N-CHO are required for gD to function in the complementation assay. Images

Sodora, D L; Cohen, G H; Muggeridge, M I; Eisenberg, R J

1991-01-01

241

Introduction of silent mutations in a codon-optimized xylanase (xynB) results in enhanced protein expression in HEK293A cells.  

PubMed

Xylanase is used extensively to improve feed conversion rates to enhance the performance of poultry and pigs. By expressing xylanase in simple-stomached animals, new breeds of genetically modified animals with enhanced feed conversion rates may be obtained. However, expression of heterologous proteins derived from lower organisms in mammalian cells is usually inefficient. When common codons of a ''one amino acid-one codon"-optimized xylanase from Streptomyces olivaceoviridis were replaced with rare codons, xylanase expression in human embryonic kidney 293A cells increased by 1.4- to 2.3-fold as determined by flow cytometry, western blot and enzymatic activity assay. Quantitative RT-PCR assay indicated that the enhanced expression could not be attributed to altered mRNA levels. This study provides an alternative strategy for improving expression levels of heterologous proteins in mammalian cells, which is potentially helpful for generating genetically modified animals with enhanced feed conversion ability. PMID:23974494

Liu, Zhiguo; Feng, Tao; Ji, Qianqian; Cong, Peiqing; Chen, Yaosheng; He, Zuyong

2013-12-01

242

Perinatal Oxygen Restriction Does Not Result in Reduced Rat Frontal Cortex Synaptophysin Protein Levels at Adulthood as Opposed to Postmortem Findings in Schizophrenia  

Microsoft Academic Search

Synaptophysin, a synaptic vesicle protein and a marker for synaptic density has been found to be reduced in postmortem prefrontal\\u000a cortex of schizophrenia patients, consistent with evidence for synaptic deficits in schizophrenia. The contribution of both\\u000a genetic and environmental factors to the etiology of schizophrenia is well established, and obstetric complications have been\\u000a suggested as a non-genetic risk factor of

Carmit Nadri; Galila Agam

2009-01-01

243

Nonaqueous encapsulation of excipient-stabilized spray-freeze dried BSA into poly(lactide- co-glycolide) microspheres results in release of native protein  

Microsoft Academic Search

Encapsulation of the model protein bovine serum albumin (BSA) into poly(d,l lactide-co-glycolide) (PLG) microspheres was performed by a non-aqueous oil-in-oil (o\\/o) methodology. Powder formulations of BSA obtained by spray-freeze drying were first suspended in methylene chloride containing PLG followed by coacervation by adding silicon oil and microsphere hardening in heptane. The secondary structure of BSA was determined at relevant steps

Karen G Carrasquillo; Ann M Stanley; Juan C Aponte-Carro; Patricia De Jésus; Henry R Costantino; Carlos J Bosques; Kai Griebenow

2001-01-01

244

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

245

Novel ENU-Induced Point Mutation in Scavenger Receptor Class B, Member 1, Results in Liver Specific Loss of SCARB1 Protein  

PubMed Central

Cardiovascular disease (CVD) is the largest cause of premature death in human populations throughout the world. Circulating plasma lipid levels, specifically high levels of LDL or low levels of HDL, are predictive of susceptibility to CVD. The scavenger receptor class B member 1 (SCARB1) is the primary receptor for the selective uptake of HDL cholesterol by liver and steroidogenic tissues. Hepatic SCARB1 influences plasma HDL-cholesterol levels and is vital for reverse cholesterol transport. Here we describe the mapping of a novel N-ethyl-N-nitrosourea (ENU) induced point mutation in the Scarb1 gene identified in a C57BL/6J background. The mutation is located in a highly conserved amino acid in the extracellular loop and leads to the conversion of an isoleucine to an asparagine (I179N). Homozygous mutant mice express normal Scarb1 mRNA levels and are fertile. SCARB1 protein levels are markedly reduced in liver (?90%), but not in steroidogenic tissues. This leads to ?70% increased plasma HDL levels due to reduced HDL cholesteryl ester selective uptake. Pdzk1 knockout mice have liver-specific reduction of SCARB1 protein as does this mutant; however, in vitro analysis of the mutation indicates that the regulation of SCARB1 protein in this mutant is independent of PDZK1. This new Scarb1 model may help further our understanding of post-translational and tissue-specific regulation of SCARB1 that may aid the important clinical goal of raising functional HDL.

Stylianou, Ioannis M.; Svenson, Karen L.; VanOrman, Sara K.; Langle, Yanina; Millar, John S.; Paigen, Beverly; Rader, Daniel J.

2009-01-01

246

Predicting Protein Phenotypes Based on Protein-Protein Interaction Network  

Microsoft Academic Search

BackgroundIdentifying associated phenotypes of proteins is a challenge of the modern genetics since the multifactorial trait often results from contributions of many proteins. Besides the high-through phenotype assays, the computational methods are alternative ways to identify the phenotypes of proteins.Methodology\\/Principal FindingsHere, we proposed a new method for predicting protein phenotypes in yeast based on protein-protein interaction network. Instead of only

Lele Hu; Tao Huang; Xiao-Jun Liu; Yu-Dong Cai; Hitoshi Okazawa

2011-01-01

247

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  

SciTech Connect

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.

Singhal, Rohit [Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Badger, Thomas M. [Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Arkansas Children's Nutrition Center, Little Rock, AR 72202 (United States); Ronis, Martin J. [Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Arkansas Children's Nutrition Center, Little Rock, AR 72202 (United States)], E-mail: RonisMartinJ@uams.edu

2008-03-01

248

Mutations in the yeast Myb-like protein Bas1p resulting in discrimination between promoters in vivo but notin vitro.  

PubMed Central

Bas1p is a yeast transcription factor that activates expression of purine and histidine biosynthesis genes in response to extracellular purine limitation. The N-terminal part of Bas1p contains an Myb-like DNA binding domain composed of three tryptophan-rich imperfect repeats. We show that mutating the conserved tryptophan residues in the DNA binding domain of Bas1p severely impairs in vivo activation of target genes and in vitro DNA binding of Bas1p. We also found that two mutations (H34L and W42A) in the first repeat make Bas1p discriminate between promoters in vivo . These two BAS1 mutants are able to activate expression of an HIS4-lacZ fusion but not that of ADE1-lacZ or ADE17-lacZ fusions. Surprisingly, these mutant proteins bind equally well to the three promoters in vitro , suggesting that the mutations affect the interaction of Bas1p with some promoter-specific factor(s) in vivo . By mutating a potential nucleotide binding site in the DNA binding domain of Bas1p, we also show that this motif does not play a major role in purine regulation of Bas1p activity. Finally, using a green fluorescence protein (GFP)-Bas1p fusion, we establish the strict nuclear localization of Bas1p and show that it is not affected by extracellular adenine.

Pinson, B; Sagot, I; Borne, F; Gabrielsen, O S; Daignan-Fornier, B

1998-01-01

249

Agents that stabilize mutated von Hippel-Lindau (VHL) protein: results of a high-throughput screen to identify compounds that modulate VHL proteostasis.  

PubMed

Von Hippel-Lindau (VHL) disease is an autosomal dominant disorder that affects multiple organs. Treatment is mainly surgical, and effective systemic therapies are needed. We developed a cell-based screening tool to identify compounds that stabilize or upregulate full-length, point-mutated VHL protein. The 786-0 cell line was infected with full-length W117A-mutated VHL linked to a C-terminal Venus fluorescent protein. This VHL-W117A-Venus line was used to screen the Prestwick drug library and was tested against proteasome inhibitors MG132 and bortezomib. Western blot validation and evaluation of functional readouts, including hypoxia-inducible factor 2? (HIF2?) and glucose transporter 1 (Glut1) levels, were performed. We found that bortezomib, MG132, and the Prestwick compounds 8-azaguanine, thiostrepton, and thioguanosine upregulated VHL-W117A-Venus in 786-0 cells. 8-Azaguanine downregulated HIF2? levels and was augmented by the presence of VHL W117A. VHL p30 band intensities varied as a function of compound used, suggesting alternate posttranslational processing. Nuclear-cytoplasmic localization of VHL-W117A-Venus varied among the different compounds. In conclusion, a 786-0 cell line containing VHL-W117A-Venus was successfully used to identify compounds that upregulate VHL levels, with differential effect on VHL intracellular localization and posttranslational processing. Further screening efforts will broaden the number of pharmacophores available to develop therapeutic agents that will upregulate and refunctionalize mutated VHL. PMID:22357874

Ding, Zhiyong; German, Peter; Bai, Shanshan; Feng, Zhehui; Gao, Meng; Si, Wendy; Sobieski, Mary M; Stephan, Clifford C; Mills, Gordon B; Jonasch, Eric

2012-06-01

250

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

2014-01-14

251

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

252

Recurrent miscarriage syndrome due to blood coagulation protein/platelet defects: prevalence, treatment and outcome results. DRW Metroplex Recurrent Miscarriage Syndrome Cooperative Group.  

PubMed

Although first-time miscarriages are usually caused by chromosomal defects, about 55% of recurrent miscarriages are caused by procoagulant defects that induce thrombosis and infarction of placental vessels. Of recurrent miscarriages, about 7% are caused by chromosome defects, 15% to hormonal defects, and 10% to 15% to anatomical defects. Recurrent miscarriage involves more than 500,000 women in the United States each year. During the past 4 years, 179 patients, prescreened for chromosomal, hormonal, and anatomical defects, and found to harbor none, underwent hemostasis defect evaluation. A total of 160 of these have been analyzed. A hemostasis defect was found in 150 of 160 women (n = 94% of screened women). The mean age was 33 years; the mean number of miscarriages before referral was three. All women with a procoagulant defect (149) were treated with preconception ASA at 81 mg/d, and unfractionated porcine heparin at 5000 U every 12 hours was added immediately postconception; both agents were used to term delivery. Only two of 149 patients failed therapy. The defects found were as follows: antiphospholipid syndrome, 67%; sticky platelet syndrome, 21%; tissue plasminogen activator (TPA) deficiency, 9%; factor V Leiden, 7%; high PAI-1, 6%; protein S, 5%; high LP(a), 3%; AT, 2%; protein C, 1%. Thirty-eight patients had more than one defect. In the group with antiphospholipid syndrome, 24% only had a subgroup antibody (antiphosphatidyl-serine, -inositol, -ethanolamine, -choline, -glycerol) or antiphosphatidic acid antibody, in the absence of anticardiolipin antibody or lupus anticoagulant. This finding is similar to that recently reported in early age ischemic stroke patients (<50 years old). In summary, about 55% of patients with recurrent miscarriage harbor a procoagulant defect to account for placental vascular occlusion. More than 98% will have a normal term delivery with preconception aspirin (ASA) and addition of postconception heparin to term. Patients should be screened by an obstetrician or by reproductive specialists for hormonal and anatomic defects before initiating a procoagulant evaluation; if such prescreening is done, the yield of a defect is high and appropriate therapy leads to an excellent outcome. PMID:10898270

Bick, R L

2000-07-01

253

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

254

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: gp91-phox Cellular Function: ion transport Producer Cell Type: Primary macrophage Modifications: Protein fragment Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Biochemical:

255

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Matriptase (MT-SP1) Cellular Function: Proteolysis Producer Cell Type: Primary macrophage Modifications: Protein fragment Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Biochemical:

256

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: C-PKA/ cAMP-dependent protein kinase Cellular Function: Cellular Signalling Producer Cell Type: Lymphoid line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method

257

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: L-plastin (lymphocyte cytosolic protein 1) Cellular Function: Cytoskeleton Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Actin Method

258

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: HEM-1, Nck-associated protein 1-like Cellular Function: Cytoskeleton Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Actin Method

259

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: PEBP-1 Phosphitylethanolamine binding protein Cellular Function: Lipid organization Producer Cell Type: Lymphoid line Modifications: Molecules/virion: Undetermined Viral Partner: Cellular Partners: Phospatitylethanolamine

260

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

261

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Epiderm. fatty acid-bind. protein (E-FABP) Cellular Function: Lipid organization Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method

262

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

263

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: TCP-1-beta Cellular Function: Protein Folding Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Biochemical:

264

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: SNARE protein Ykt6 Cellular Function: ER Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Biochemical:

265

Vaccination with a fusion protein that introduces HIV-1 gag antigen into a multitrimer CD40L construct results in enhanced CD8+ T cell responses and protection from viral challenge by vaccinia-gag.  

PubMed

CD40 ligand (CD40L, CD154) is a membrane protein that is important for the activation of dendritic cells (DCs) and DC-induced CD8(+) T cell responses. To be active, CD40L must cluster CD40 receptors on responding cells. To produce a soluble form of CD40L that clusters CD40 receptors necessitates the use of a multitrimer construct. With this in mind, a tripartite fusion protein was made from surfactant protein D (SPD), HIV-1 Gag as a test antigen, and CD40L, where SPD serves as a scaffold for the multitrimer protein complex. This SPD-Gag-CD40L protein activated CD40-bearing cells and bone marrow-derived DCs in vitro. Compared to a plasmid for Gag antigen alone (pGag), DNA vaccination of mice with pSPD-Gag-CD40L induced an increased number of Gag-specific CD8(+) T cells with increased avidity for major histocompatibility complex class I-restricted Gag peptide and improved vaccine-induced protection from challenge by vaccinia-Gag virus. The importance of the multitrimeric nature of the complex was shown using a plasmid lacking the N terminus of SPD that produced a single trimer fusion protein. This plasmid, pTrimer-Gag-CD40L, was only weakly active on CD40-bearing cells and did not elicit strong CD8(+) T cell responses or improve protection from vaccinia-Gag challenge. An adenovirus 5 (Ad5) vaccine incorporating SPD-Gag-CD40L was much stronger than Ad5 expressing Gag alone (Ad5-Gag) and induced complete protection (i.e., sterilizing immunity) from vaccinia-Gag challenge. Overall, these results show the potential of a new vaccine design in which antigen is introduced into a construct that expresses a multitrimer soluble form of CD40L, leading to strongly protective CD8(+) T cell responses. PMID:24227853

Gupta, Sachin; Termini, James M; Raffa, Francesca N; Williams, Cindi-Ann; Kornbluth, Richard S; Stone, Geoffrey W

2014-02-01

266

Influence of insulin-like growth factor binding protein (IGFBP)-1 and IGFBP-3 on bone health: results from the European Male Ageing Study.  

PubMed

The aim of this study was to determine the influence of insulin-like growth factor binding protein (IGFBP)-1, IGFBP-3, and IGF-I on calcaneal ultrasound parameters in middle-aged and elderly European men. Men aged 40-79 years were recruited from population registers for participation in the European Male Ageing Study (EMAS). Subjects were invited by letter to complete a postal questionnaire and to attend for an interviewer-assisted questionnaire, quantitative ultrasound (QUS) of the calcaneus, and a fasting blood sample from which serum levels of IGFBP-1, IGFBP-3, IGF-I, estradiol (E(2)), and SHBG were assayed. The questionnaires included the Physical Activity Scale for the Elderly (PASE) and questions about smoking and alcohol consumption. Estimated bone mineral density (eBMD) was derived as a function of the QUS parameters speed of sound and broadband ultrasound attenuation. Height and weight were measured in all subjects. 3057 men, mean age 59.7 years (standard deviation 11.0) were included in the analysis. After adjusting for age, center, and BMI, higher levels of IGFBP-1 were associated with lower eBMD. Higher levels of both IGFBP-3 and IGF-I were associated with higher eBMD. After further adjustment for PASE score, current smoking, alcohol consumption, free E(2), and SHBG, IGFBP-3 and IGF-I, though not IGFBP-1, remained significantly associated with eBMD. IGFBP-1 was associated with bone health, though the effect could be explained by other factors. IGFBP-3 and IGF-I were independent determinants of bone health in middle-aged and elderly European men. PMID:21503646

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

2011-06-01

267

Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1  

PubMed Central

Background Shewanella oneidensis MR-1 is a facultative, gram-negative bacterium capable of coupling the oxidation of organic carbon to a wide range of electron acceptors such as oxygen, nitrate and metals, and has potential for bioremediation of heavy metal contaminated sites. The complete 5-Mb genome of S. oneidensis MR-1 was sequenced and standard sequence-comparison methods revealed approximately 42% of the MR-1 genome encodes proteins of unknown function. Defining the functions of hypothetical proteins is a great challenge and may need a systems approach. In this study, by using integrated approaches including whole genomic microarray and proteomics, we examined knockout effects of the gene encoding SO1377 (gi24372955), a member of the conserved, hypothetical, bacterial protein family COG2268 (Clusters of Orthologous Group) in bacterium Shewanella oneidensis MR-1, under various physiological conditions. Results Compared with the wild-type strain, growth assays showed that the deletion mutant had a decreased growth rate when cultured aerobically, but not affected under anaerobic conditions. Whole-genome expression (RNA and protein) profiles revealed numerous gene and protein expression changes relative to the wild-type control, including some involved in iron metabolism, oxidative damage protection and respiratory electron transfer, e. g. complex IV of the respiration chain. Although total intracellular iron levels remained unchanged, whole-cell electron paramagnetic resonance (EPR) demonstrated that the level of free iron in mutant cells was 3 times less than that of the wild-type strain. Siderophore excretion in the mutant also decreased in iron-depleted medium. The mutant was more sensitive to hydrogen peroxide and gave rise to 100 times more colonies resistant to gentamicin or kanamycin. Conclusion Our results showed that the knock-out of SO1377 gene had pleiotropic effects and suggested that SO1377 may play a role in iron homeostasis and oxidative damage protection in S. oneidensis MR-1.

Gao, Weimin; Liu, Yongqing; Giometti, Carol S; Tollaksen, Sandra L; Khare, Tripti; Wu, Liyou; Klingeman, Dawn M; Fields, Matthew W; Zhou, Jizhong

2006-01-01

268

Deletion of RTS1, Encoding a Regulatory Subunit of Protein Phosphatase 2A, Results in Constitutive Amino Acid Signaling via Increased Stp1p Processing  

Microsoft Academic Search

In Saccharomyces cerevisiae, extracellular amino acids are sensed at the plasma membrane by the SPS sensor, consisting of the transporter homologue Ssy1p, Ptr3p, and the endoprotease Ssy5p. Amino acid sensing results in proteolytic truncation of the transcription factors Stp1p and Stp2p, followed by their relocation from the cytoplasm to the nucleus, where they activate transcription of amino acid permease genes.

Nadine Eckert-Boulet; Katrin Larsson; Boqian Wu; Peter Poulsen; Birgitte Regenberg; Jens Nielsen; Morten C. Kielland-Brandt

2006-01-01

269

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  

Microsoft Academic Search

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

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

2007-01-01

270

A single amino acid change in AngR, a protein encoded by pJM1-like virulence plasmids, results in hyperproduction of anguibactin.  

PubMed Central

The siderophore anguibactin is produced in vivo in a diffusible form and is an important factor in the virulence of Vibrio anguillarum. The natural isolate V. anguillarum 531A is a hyperproducer of anguibactin when compared with the prototype strain V. anguillarum 775. The angR gene was found to be responsible for this difference in levels of anguibactin produced. Nucleotide sequence analysis showed that the angR531A differed in a single nucleotide from the angR775 present in the prototype plasmid pJM1. This nucleotide substitution resulted in a change in amino acid 267 from His in strain 775 to Asn in strain 531A. This amino acid is located in a region between one of the two helix-turn-helix domains and the neighboring leucine zipper. Mutations to replace His with either Leu or Gln, generated by site-directed mutagenesis, in amino acid 267 resulted in strains for which the MIC of the iron chelator ethylenediamine di(o-hydroxyphenyl) acetic acid were lower than for the proptotype 775 but higher than for iron uptake-deficient strains. In addition to its transcriptional activating function, AngR also complemented a mutation in the Escherichia coli entE gene, which encodes the enterobactin biosynthetic enzyme 2,3-dihydroxybenzoate-AMP ligase. Therefore, AngR may also function in V. anguillarum as an EntE-like enzyme for the biosynthesis of anguibactin. Images

Tolmasky, M E; Actis, L A; Crosa, J H

1993-01-01

271

Detecting overlapping protein complexes in protein-protein interaction networks  

PubMed Central

We introduce clustering with overlapping neighborhood expansion (ClusterONE), a method for detecting potentially overlapping protein complexes from protein-protein interaction data. ClusterONE-derived complexes for several yeast data sets showed better correspondence with reference complexes in the Munich Information Center for Protein Sequence (MIPS) catalog and complexes derived from the Saccharomyces Genome Database (SGD) than the results of seven popular methods. The results also showed a high extent of functional homogeneity.

Nepusz, Tamas; Yu, Haiyuan; Paccanaro, Alberto

2012-01-01

272

INSULIN-LIKE GROWTH FACTORS AND INSULIN-LIKE GROWTH FACTOR BINDING PROTEINS AND PROSTATE CANCER RISK: RESULTS FROM THE PROSTATE CANCER PREVENTION TRIAL  

PubMed Central

The role of the insulin-like growth factor (IGF) axis and whether IGFs interact with androgen-suppressing agents in relation to prostate carcinogenesis is unclear. This nested case-control study (n=1652 cases/1543 controls) examined whether serum IGF1, IGF2, IGFBP2, IGFBP3 and the IGF1:IGFBP3 ratio were associated with prostate cancer in the Prostate Cancer Prevention Trial, a randomized, placebo-controlled trial of finasteride for prostate cancer prevention. Presence or absence of cancer was determined by prostate biopsy. Baseline serum was assayed for IGF-axis analytes using ELISA. Logistic regression estimated odds ratios and 95% confidence intervals for risk of total, low-grade (Gleason 2–6) and high-grade (Gleason 7–10) cancers. Results were stratified by intervention assignment. In both the placebo and finasteride arms, serum IGF1, IGF2, IGFBP3 and the IGF1:IGFBP3 ratio were not associated with prostate cancer. However men in the highest vs. lowest quartile of serum IGFBP2 had a 48% (P-trend =0.02) and 55% (P-trend=0.01) increased risk for total and low-grade cancers respectively. These IGFBP2 associations were attenuated and no longer statistically significant in the finasteride arm. Our results suggest that in general, serum IGF-axis analytes were not associated with prostate cancer risk in the PCPT where presence or absence of all cancers was biopsy-determined. The exception was the finding that high serum IGFBP2 is a risk factor for low-grade disease, which was attenuated for men on finasteride. Further research is needed to understand better the risk incurred by high IGFBP2 and whether androgen-suppressing agents such as finasteride influence aspects of IGFBP2 physiology relevant to prostate carcinogenesis.

Neuhouser, Marian L; Platz, Elizabeth A.; Till, Cathee; Tangen, Catherine M; Goodman, Phyllis J; Kristal, Alan; Parnes, Howard L.; Tao, Yuzhen; Figg, William D.; Lucia, M Scott; Hoque, Ashraful; Hsing, Ann W.; Thompson, Ian M.; Pollak, Michael

2012-01-01

273

Bacteriophage protein-protein interactions.  

PubMed

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. PMID:22748812

Häuser, Roman; Blasche, Sonja; Dokland, Terje; Haggård-Ljungquist, Elisabeth; von Brunn, Albrecht; Salas, Margarita; Casjens, Sherwood; Molineux, Ian; Uetz, Peter

2012-01-01

274

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

2013-10-01

275

AVP: View Protein Details  

Cancer.gov

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

276

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: CD31 PECAM-1 Cellular Function: Adhesion Producer Cell Type: Lymphoid line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: PTPN11 Method of Detection: ELISA capture Uniprot

277

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Alix (AIP-1) Cellular Function: Late Endosome Trafficking Producer Cell Type: Epithelial line, Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method

278

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Vps4b Cellular Function: ESCRT targeting Producer Cell Type: Lymphoid line Modifications: None detected Molecules/virion: 1 Viral Partner: Undetermined Cellular Partners: Alix(AIP1) Method of Detection: Biochemical:

279

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: CD62L L-selectin Cellular Function: Adhesion Producer Cell Type: Lymphoid line Modifications: None detected Molecules/virion: Viral Partner: Cellular Partners: Method of Detection: ELISA capture Uniprot Accession

280

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Plectin 1 (PLTN) Cellular Function: Cytoskeleton Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Biochemical:

281

AVP: View Protein Details  

Cancer.gov

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

282

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

283

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Nucleoside diphosphate kinase A NM23-H1 Cellular Function: Producer Cell Type: Lymphoid line Modifications: Molecules/virion: Undetermined Viral Partner: Cellular Partners: GAPDH Method of Detection: Biochemical Uniprot

284

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Prolyl endopeptidase Cellular Function: Proteolysis Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Uniprot

285

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Type 3 inositol 1,4,5-trisphosphate receptor Cellular Function: Lipid organization Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular

286

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Desmoplakin-3 (Junction plakoglobin) Cellular Function: Cytoskeleton Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method

287

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Desmoplakin (DP) Cellular Function: Cytoskeleton Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Actin Method of Detection: Biochemical:

288

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: CD84 Cellular Function: Cellular Signalling Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: SH2D1A SAP Method of Detection: Biochemical:

289

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:

290

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: CD4 Cellular Function: T cell response Producer Cell Type: Lymphoid line Modifications: None detected Molecules/virion: Viral Partner: SU Cellular Partners: HLA-II, TCR Method of Detection: Immunoelectron

291

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: COP9 signalosome complex subunit 7b Cellular Function: Cellular Signalling, Neddylation Producer Cell Type: Macrophage line Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular

292

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Thymidine phosphorylase (TdRPase) Cellular Function: Metabolism Producer Cell Type: Primary macrophage Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of

293

AVP: View Protein Details  

Cancer.gov

View Protein Details Search Results Protein: Thymidine phosphorylase (TdRPase) Cellular Function: Producer Cell Type: Modifications: None detected Molecules/virion: Viral Partner: Undetermined Cellular Partners: Method of Detection: Uniprot Accession

294

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

295

Protein Analysis  

NSDL National Science Digital Library

This workbook allows the analysis of sample or imported protein sequences. The model can analyze protein sequences up to 500 amino acids long. The program analyzes five aspects of the protein sequence: the highest potential charge along the protein sequence, the amino acid composition of the protein sequence, the isoelectric point of the protein sequence at varying pHs, the hydrophobicity to predict surface and membrane spanning regions of the protein sequence and the protein structure using the Chau and Fassman algorithm.

John Jungck (Beloit College;Biology); Annelise Myers (Beloit College;)

2007-05-22

296

Dramatic Structural Changes Resulting from the Loss of a Crucial Hydrogen Bond in the Hinge Region Involved in C-Terminal Helix Swapping in SurE: A Survival Protein from Salmonella typhimurium  

PubMed Central

Domain swapping is an interesting feature of some oligomeric proteins in which each protomer of the oligomer provides an identical surface for exclusive interaction with a segment or domain belonging to another protomer. Here we report results of mutagenesis experiments on the structure of C-terminal helix swapped dimer of a stationary phase survival protein from Salmonella typhimurium (StSurE). Wild type StSurE is a dimer in which a large helical segment at the C-terminus and a tetramerization loop comprising two ? strands are swapped between the protomers. Key residues in StSurE that might promote C-terminal helix swapping were identified by sequence and structural comparisons. Three mutants in which the helix swapping is likely to be avoided were constructed and expressed in E. coli. Three-dimensional X-ray crystal structures of the mutants H234A and D230A/H234A could be determined at 2.1 Å and 2.35 Å resolutions, respectively. Contrary to expectations, helix swapping was mostly retained in both the mutants. The loss of the crucial D230 OD2– H234 NE2 hydrogen bond (2.89 Å in the wild type structure) in the hinge region was compensated by new inter and intra-chain interactions. However, the two fold molecular symmetry was lost and there were large conformational changes throughout the polypeptide. In spite of these changes, the dimeric structure and an approximate tetrameric organization were retained, probably due to the interactions involving the tetramerization loop. Mutants were mostly functionally inactive, highlighting the importance of precise inter-subunit interactions for the symmetry and function of StSurE.

Mathiharan, Yamuna Kalyani; Pappachan, Anju; Savithri, H. S.; Murthy, Mathur R. N.

2013-01-01

297

Mutation of the f-protein cleavage site of avian paramyxovirus type 7 results in furin cleavage, fusion promotion, and increased replication in vitro but not increased replication, tissue tropism, or virulence in chickens.  

PubMed

We constructed a reverse genetics system for avian paramyxovirus serotype 7 (APMV-7) to investigate the role of the fusion F glycoprotein in tissue tropism and virulence. The AMPV-7 F protein has a single basic residue arginine (R) at position -1 in the F cleavage site sequence and also is unusual in having alanine at position +2 (LPSSR?FA) (underlining indicates the basic amino acids at the F protein cleavage site, and the arrow indicates the site of cleavage.). APMV-7 does not form syncytia or plaques in cell culture, but its replication in vitro does not depend on, and is not increased by, added protease. Two mutants were successfully recovered in which the cleavage site was modified to mimic sites that are found in virulent Newcastle disease virus isolates and to contain 4 or 5 basic residues as well as isoleucine in the +2 position: (RRQKR?FI) or (RRKKR?FI), named Fcs-4B or Fcs-5B, respectively. In cell culture, one of the mutants, Fcs-5B, formed protease-independent syncytia and grew to 10-fold-higher titers compared to the parent and Fcs-4B viruses. This indicated the importance of the single additional basic residue (K) at position -3. Syncytium formation and virus yield of the Fcs-5B virus was impaired by the furin inhibitor decanoyl-RVKR-CMK, whereas parental APMV-7 was not affected. APMV-7 is avirulent in chickens and is limited in tropism to the upper respiratory tract of 1-day-old and 2-week-old chickens, and these characteristics were unchanged for the two mutant viruses. Thus, the acquisition of furin cleavability by APMV-7 resulted in syncytium formation and increased virus yield in vitro but did not alter virus yield, tropism, or virulence in chickens. PMID:22258248

Xiao, Sa; Khattar, Sunil K; Subbiah, Madhuri; Collins, Peter L; Samal, Siba K

2012-04-01

298

Severe arrhythmia as a result of the interaction of cetirizine and pilsicainide in a patient with renal insufficiency: first case presentation showing competition for excretion via renal multidrug resistance protein 1 and organic cation transporter 2.  

PubMed

A 72-year-old woman with renal insufficiency who was taking oral pilsicainide (150 mg/d) complained of feeling faint 3 days after she was prescribed oral cetirizine (20 mg/d). She was found to have a wide QRS wave with bradycardia. Her symptoms were relieved by termination of pilsicainide. The plasma concentrations of both drugs were significantly increased during the coadministration, and the cetirizine concentration decreased on cessation of pilsicainide despite the fact that treatment with cetirizine was continued, which suggested that the fainting was induced by the pharmacokinetic drug interaction. A pharmacokinetic study in 6 healthy male volunteers after a single dose of either cetirizine (20 mg) or pilsicainide (50 mg), or both, found that the renal clearance of each drug was significantly decreased by the coadministration of the drugs (from 475 +/- 101 mL/min to 279 +/- 117 mL/min for pilsicainide and from 189 +/- 37 mL/min to 118 +/- 28 mL/min for cetirizine; P = .008 and .009, respectively). In vitro studies using Xenopus oocytes with microinjected human organic cation transporter 2 and renal cells transfected with human multidrug resistance protein 1 revealed that the transport of the substrates of these transporters was inhibited by either cetirizine or pilsicainide. Thus elevated concentrations of these drugs as a result of a pharmacokinetic drug-drug interaction via either human multidrug resistance protein 1 or human organic cation transporter 2 (or both) in the renal tubular cells might have caused the arrhythmia in our patient. Although cetirizine has less potential for causing arrhythmias than other histamine 1 blockers, such an interaction should be considered, especially in patients with renal insufficiency who are receiving pilsicainide. PMID:16580907

Tsuruoka, Shuichi; Ioka, Takashi; Wakaumi, Michi; Sakamoto, Koh-ichi; Ookami, Hitoshi; Fujimura, Akio

2006-04-01

299

Protein Crystallization  

NASA Technical Reports Server (NTRS)

Nucleation, growth and perfection of protein crystals will be overviewed along with crystal mechanical properties. The knowledge is based on experiments using optical and force crystals behave similar to inorganic crystals, though with a difference in orders of magnitude in growing parameters. For example, the low incorporation rate of large biomolecules requires up to 100 times larger supersaturation to grow protein, rather than inorganic crystals. Nucleation is often poorly reproducible, partly because of turbulence accompanying the mixing of precipitant with protein solution. Light scattering reveals fluctuations of molecular cluster size, its growth, surface energies and increased clustering as protein ages. Growth most often occurs layer-by-layer resulting in faceted crystals. New molecular layer on crystal face is terminated by a step where molecular incorporation occurs. Quantitative data on the incorporation rate will be discussed. Rounded crystals with molecularly disordered interfaces will be explained. Defects in crystals compromise the x-ray diffraction resolution crucially needed to find the 3D atomic structure of biomolecules. The defects are immobile so that birth defects stay forever. All lattice defects known for inorganics are revealed in protein crystals. Contribution of molecular conformations to lattice disorder is important, but not studied. This contribution may be enhanced by stress field from other defects. Homologous impurities (e.g., dimers, acetylated molecules) are trapped more willingly by a growing crystal than foreign protein impurities. The trapped impurities induce internal stress eliminated in crystals exceeding a critical size (part of mni for ferritin, lysozyme). Lesser impurities are trapped from stagnant, as compared to the flowing, solution. Freezing may induce much more defects unless quickly amorphysizing intracrystalline water.

Chernov, Alexander A.

2005-01-01

300

Discover protein sequence signatures from protein-protein interaction data  

Microsoft Academic Search

BACKGROUND: The development of high-throughput technologies such as yeast two-hybrid systems and mass spectrometry technologies has made it possible to generate large protein-protein interaction (PPI) datasets. Mining these datasets for underlying biological knowledge has, however, remained a challenge. RESULTS: A total of 3108 sequence signatures were found, each of which was shared by a set of guest proteins interacting with

Jianwen Fang; Ryan J. Haasl; Yinghua Dong; Gerald H. Lushington

2005-01-01

301

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

302

Results from tandem Phase 1 studies evaluating the safety, reactogenicity and immunogenicity of the vaccine candidate antigen Plasmodium falciparum FVO merozoite surface protein-1 (MSP142) administered intramuscularly with adjuvant system AS01  

PubMed Central

Background The development of an asexual blood stage vaccine against Plasmodium falciparum malaria based on the major merozoite surface protein-1 (MSP1) antigen is founded on the protective efficacy observed in preclinical studies and induction of invasion and growth inhibitory antibody responses. The 42 kDa C-terminus of MSP1 has been developed as the recombinant protein vaccine antigen, and the 3D7 allotype, formulated with the Adjuvant System AS02A, has been evaluated extensively in human clinical trials. In preclinical rabbit studies, the FVO allele of MSP142 has been shown to have improved immunogenicity over the 3D7 allele, in terms of antibody titres as well as growth inhibitory activity of antibodies against both the heterologous 3D7 and homologous FVO parasites. Methods Two Phase 1 clinical studies were conducted to examine the safety, reactogenicity and immunogenicity of the FVO allele of MSP142 in the adjuvant system AS01 administered intramuscularly at 0-, 1-, and 2-months: one in the USA and, after evaluation of safety data results, one in Western Kenya. The US study was an open-label, dose escalation study of 10 and 50 ?g doses of MSP142 in 26 adults, while the Kenya study, evaluating 30 volunteers, was a double-blind, randomized study of only the 50 ?g dose with a rabies vaccine comparator. Results In these studies it was demonstrated that this vaccine formulation has an acceptable safety profile and is immunogenic in malaria-naïve and malaria-experienced populations. High titres of anti-MSP1 antibodies were induced in both study populations, although there was a limited number of volunteers whose serum demonstrated significant inhibition of blood-stage parasites as measured by growth inhibition assay. In the US volunteers, the antibodies generated exhibited better cross-reactivity to heterologous MSP1 alleles than a MSP1-based vaccine (3D7 allele) previously tested at both study sites. Conclusions Given that the primary effector mechanism for blood stage vaccine targets is humoral, the antibody responses demonstrated to this vaccine candidate, both quantitative (total antibody titres) and qualitative (functional antibodies inhibiting parasite growth) warrant further consideration of its application in endemic settings. Trial registrations Clinical Trials NCT00666380

2013-01-01

303

Adaptation of Tick-Borne Encephalitis Virus to BHK-21 Cells Results in the Formation of Multiple Heparan Sulfate Binding Sites in the Envelope Protein and Attenuation In Vivo  

Microsoft Academic Search

Propagation of the flavivirus tick-borne encephalitis virus in BHK-21 cells selected for mutations within the large surface glycoprotein E that increased the net positive charge of the protein. In the course of 16 independent experiments, 12 different protein E mutation patterns were identified. These were located in all three of the structural domains and distributed over almost the entire upper

CHRISTIAN W. MANDL; HELGA KROSCHEWSKI; STEVEN L. ALLISON; REGINA KOFLER; HEIDEMARIE HOLZMANN; TAMARA MEIXNER; FRANZ X. HEINZ

2001-01-01

304

Lactose binding to human galectin-7 (p53-induced gene 1) induces long-range effects through the protein resulting in increased dimer stability and evidence for positive cooperativity  

PubMed Central

The product of p53-induced gene 1 is a member of the galectin family, i.e., galectin-7 (Gal-7). To move beyond structural data by X-ray diffraction, we initiated the study of the lectin by nuclear magnetic resonance (NMR) and circular dichroism spectroscopies, and molecular dynamics (MD) simulations. In concert, our results indicate that lactose binding to human Gal-7 induces long-range effects (minor conformational shifts and changes in structural dynamics) throughout the protein that result in stabilization of the dimer state, with evidence for positive cooperativity. Monte Carlo fits of 15N-Gal-7 HSQC titrations with lactose using a two-site model yield K1 = 0.9 ± 0.6 × 103 M?1 and K2 = 3.4 ± 0.8 × 103 M?1. Ligand binding-induced stabilization of the Gal-7 dimer was supported by several lines of evidence: MD-based calculations of interaction energies between ligand-loaded and ligand-free states, gel filtration data and hetero-FRET spectroscopy that indicate a highly reduced tendency for dimer dissociation in the presence of lactose, CD-based thermal denaturation showing that the transition temperature of the lectin is significantly increased in the presence of lactose, and saturation transfer difference (STD) NMR using a molecular probe of the monomer state whose presence is diminished in the presence of lactose. MD simulations with the half-loaded ligand-bound state also provided insight into how allosteric signaling may occur. Overall, our results reveal long-range effects on Gal-7 structure and dynamics, which factor into entropic contributions to ligand binding and allow further comparisons with other members of the galectin family.

Ermakova, Elena; Miller, Michelle C; Nesmelova, Irina V; Lopez-Merino, Lara; Berbis, Manuel Alvaro; Nesmelov, Yuri; Tkachev, Yaroslav V; Lagartera, Laura; Daragan, Vladimir A; Andre, Sabine; Canada, F Javier; Jimenez-Barbero, Jesus; Solis, Dolores; Gabius, Hans-Joachim; Mayo, Kevin H

2013-01-01

305

Protein-protein alternative binding modes do not overlap.  

PubMed

Proteins often bind other proteins in more than one way. Thus alternative binding modes is an essential feature of protein interactions. Such binding modes may be detected by X-ray crystallography and thus reflected in Protein Data Bank. The alternative binding is often observed not for the protein itself but for its structural homolog. The results of this study based on the analysis of a comprehensive set of co-crystallized protein-protein complexes show that the alternative binding modes generally do not overlap, but are spatially separated. This effect is based on molecular recognition characteristics of the protein structures. The results are also in excellent agreement with the intermolecular energy funnel size estimates obtained previously by an independent methodology. The results provide an important insight into the principles of protein association, as well as potential guidelines for modeling of protein complexes and the design of protein interfaces. PMID:23775945

Kundrotas, Petras J; Vakser, Ilya A

2013-08-01

306

Correlation Between Functional Annotation and Topology of Protein-Protein Interaction Network  

Microsoft Academic Search

The functional annotation of proteins was believed to be related to the topology of the protein-protein interaction network. People utilized the protein-protein interaction network to infer the protein function by various methods. Here, we select the protein interaction data of Saccharomyces cerevisia and calculated the correlation between functional annotation of proteins and the topology of protein-protein interaction network. The result

Jiun-Yan Huang

2008-01-01

307

Total protein  

MedlinePLUS

The total protein test measures the total amount of two classes of proteins found in the fluid portion of your blood. These are albumin and globulin. Proteins are important parts of all cells and tissues. ...

308

A Single Ala139-to-Glu Substitution in the Renibacterium salmoninarum Virulence-Associated Protein p57 Results in Antigenic Variation and Is Associated with Enhanced p57 Binding to Chinook Salmon Leukocytes  

Microsoft Academic Search

The gram-positive bacterium Renibacterium salmoninarum produces relatively large amounts of a 57-kDa protein (p57) implicated in the pathogenesis of salmonid bacterial kidney disease. Antigenic variation in p57 was identified by using monoclonal antibody 4C11, which exhibited severely decreased binding to R. salmoni- narum strain 684 p57 and bound robustly to the p57 proteins of seven other R. salmoninarum strains. This

Gregory D. Wiens; Ron Pascho; James R. Winton

2002-01-01

309

Genetic and Molecular Analysis of the X Chromosomal Region 14b17-14c4 in Drosophila Melanogaster: Loss of Function in Nona, a Nuclear Protein Common to Many Cell Types, Results in Specific Physiological and Behavioral Defects  

PubMed Central

We have performed a genetic analysis of the 14C region of the X chromosome of Drosophila melanogaster to isolate loss of function alleles of no-on-transient A (nonA; 14C1-2; 1-52.3). NONA is a nuclear protein common to many cell types, which is present in many puffs on polytene chromosomes. Sequence data suggest that the protein contains a pair of RNA binding motifs (RRM) found in many single-strand nucleic acid binding proteins. Hypomorphic alleles of this gene, which lead to aberrant visual and courtship song behavior, still contain normally distributed nonA RNA and NONA protein in embryos, and in all available alleles NONA protein is present in puffs of third instar larval polytene chromosomes. We find that complete loss of this general nuclear protein is semilethal in hemizygous males and homozygous cell lethal in the female germline. Surviving males show more extreme defects in nervous system function than have been described for the hypomorphic alleles. Five other essential genes that reside within this region have been partially characterized.

Stanewsky, R.; Rendahl, K. G.; Dill, M.; Saumweber, H.

1993-01-01

310

DONUT results  

SciTech Connect

The DONUT experiment succeeded in observing tau-neutrino CC interactions for the first time in 2000. The analysis using total sample is presented in this paper, based on 3.5x10{sup 17} protons on target. The number of identified {nu}{sub {tau}} CC interactions is 9 from 581 neutrino interactions located in the emulsion. The result of the first measurement of {nu}{sub {tau}} CC cross section is consistent with the expectation from the Standard Model.

Furukawa, Tomoko [Nagoya University, (Japan)

2008-02-21

311

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

312

Chronic administration of green tea extract to TRAMP mice induces the collapse of Golgi apparatus in prostate secretory cells and results in alterations of protein post-translational processing.  

PubMed

Considering its long latency, prostate cancer (PCa) represents an ideal target for chemoprevention strategies. Green tea extract (GTE) has been proved to be one of the most promising natural substances capable of inhibiting PCa progression in animal models (transgenic adenocarcinoma of mouse prostate), as well as in humans. However, the cellular targets of the GTE action are mostly unknown. The main objective of this work was to investigate whether the endoplasmic reticulum (ER) and the Golgi apparatus (GA), known to be actively involved in sensing stress stimuli and initiating and propagating cell death signalling, may represent the subcellular targets of GTE action. To this end, 42 TRAMP mice were divided into four experimental groups: groups II and IV, received GTE in tap water (0.3 g/100 ml solution) starting at 8 weeks of age and up to the time of sacrifice. Groups I and III were respective age-matched water-fed controls. The animals were sacrificed after 4 weeks (groups I and II) or 40 weeks of treatment (groups II and IV). We also treated TRAMP-C2 cells with GTE (20 µg/ml for 7 days) to check the expression profile of clusterin (CLU), a protein involved in prostate tumourigenesis, extensively processed through ER-GA before being secreted through the plasma membrane. In vivo we found that chronic administration of GTE in TRAMP mice results in collapse of ER and GA in prostate epithelial cells. Consistently, in vitro we found that the mature, fully processed form of CLU, sCLU, is strongly reduced by GTE treatment in TRAMP-C2 cells. Taking into account the sCLU biogenesis dependence on the ER-GA integrity and the proposed anti-apoptotic role of sCLU, the possibility for GTE to counteract PCa progression by interfering with sCLU biogenesis is suggested. PMID:21935569

Davalli, Pierpaola; Rizzi, Federica; Caldara, Gaetano Felice; Davoli, Serena; Corti, Arnaldo; Silva, Alessandro; Astancolle, Serenella; Vitale, Marco; Bettuzzi, Saverio; Arcari, Marialuisa; Azzali, Giacomo

2011-12-01

313

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

314

STOP proteins.  

PubMed

Microtubules assembled from purified tubulin in vitro are labile, rapidly disassembling when exposed to a variety of depolymerizing conditions such as cold temperature. In contrast, in many cell types, microtubules seem to be unaffected when the cell is exposed to the cold. This resistance of microtubules to the cold has been intriguing because the earliest and by far most studied microtubule-associated proteins such as MAP2 and tau are devoid of microtubule cold stabilizing activity. Over the past several years, it has been shown that resistance of microtubules to the cold is largely due to polymer association with a class of microtubule-associated proteins called STOPs. STOPs are calmodulin-binding and calmodulin-regulated proteins which, in mammals, are encoded by a single gene but exhibit substantial cell specific variability due to mRNA splicing and alternative promoter use. STOP microtubule stabilizing activity has been ascribed to two classes of new bifunctional calmodulin- and microtubule-binding motifs, with distinct microtubule binding properties in vivo. STOPs seem to be restricted to vertebrates and are composed of a conserved domain split by the apparent insertion of variable sequences that are completely unrelated among species. Recently, STOP suppression in mice has been found to induce synaptic defects associated with neuroleptic-sensitive behavioral disorders. Thus, STOPs are important for synaptic plasticity. Additionally, STOP-deficient mice may yield a pertinent model for the study of neuroleptics in illnesses such as schizophrenia, currently thought to result from defects in synapse function. PMID:14567673

Bosc, Christophe; Andrieux, Annie; Job, Didier

2003-10-28

315

A single immunization with a rhabdovirus-based vector expressing severe acute respiratory syndrome coronavirus (SARS-CoV) S protein results in the production of high levels of SARS-CoV-neutralizing antibodies  

PubMed Central

Foreign viral proteins expressed by rabies virus (RV) have been shown to induce potent humoral and cellular immune responses in immunized animals. In addition, highly attenuated and, therefore, very safe RV-based vectors have been constructed. Here, an RV-based vaccine vehicle was utilized as a novel vaccine against severe acute respiratory syndrome coronavirus (SARS-CoV). For this approach, the SARS-CoV nucleocapsid protein (N) or envelope spike protein (S) genes were cloned between the RV glycoprotein G and polymerase L genes. Recombinant vectors expressing SARS-CoV N or S protein were recovered and their immunogenicity was studied in mice. A single inoculation with the RV-based vaccine expressing SARS-CoV S protein induced a strong SARS-CoV-neutralizing antibody response. The ability of the RV-SARS-CoV S vector to confer immunity after a single inoculation makes this live vaccine a promising candidate for eradication of SARS-CoV in animal reservoirs, thereby reducing the risk of transmitting the infection to humans.

Faber, Milosz; Lamirande, Elaine W.; Roberts, Anjeanette; Rice, Amy B.; Koprowski, Hilary; Dietzschold, Bernhard; Schnell, Matthias J.

2005-01-01

316

Coexpression of the maize delta-zein and beta-zein genes results in stable accumulation of delta-zein in endoplasmic reticulum-derived protein bodies formed by beta-zein.  

PubMed Central

Zeins, the major seed storage proteins of maize, are of four distinct types: alpha, beta, delta, and gamma. They are synthesized on the rough endoplasmic reticulum (ER) in a sequential manner and deposited in ER-derived protein bodies. We investigated the potential for producing sulfur-rich beta-zein and delta-zein proteins in leaf and seed tissues by expressing the corresponding genes in a constitutive manner in transgenic tobacco. The delta-zein and beta-zein, when synthesized individually, were stable in the vegetative tissues and were deposited in unique, zein-specific ER-derived protein bodies. Coexpression of delta-zein and beta-zein genes, however, showed that delta-zein was colocalized in beta-zein-containing protein bodies and that the level of delta-zein was fivefold higher in delta-/beta-zein plants than in delta-zein plants. We conclude that delta-zein interacts with beta-zein and that the interaction has a stabilizing effect on delta-zein.

Bagga, S; Adams, H P; Rodriguez, F D; Kemp, J D; Sengupta-Gopalan, C

1997-01-01

317

Polymorphisms in the Low-Density Lipoprotein Receptor-Related Protein 5 (LRP5) Gene Are Associated with Peak Bone Mass in Non-sedentary Men: Results from the Odense Androgen Study  

PubMed Central

Purpose To investigate the impact of the Ala1330Val (rs3736228, exon 18) and Val667Met (rs4988321, exon 9) polymorphisms of the low-density lipoprotein receptor-related protein 5 (LRP5) gene on peak bone mass in young men. Methods The Odense Androgen Study (OAS) is a population-based study comprising 783 Caucasian men aged 20-30 years. Genotyping was performed using real-time polymerase chain reaction (PCR) or fluorescence polarization. Bone mineral density (BMD) measurements were performed using dual-energy X-ray absorptiometry. Results The CC, CT, and TT genotypes in Ala1330Val were found in 75.6%, 21.8%, and 2.6% of the participants, respectively. Similarly, the GG, GA, and AA genotypes of Val667Met were found in 89.7%, 9.8%, and 0.5%, respectively. For the Ala1330Val polymorphism, no significant differences between the genotypes were found regarding BMD in the overall study population. However, when analysis was restricted to non-sedentary men (n = 589), a significant association between the number of T-alleles and BMD in the spine and whole body were found. Each copy of the T-allele changed the Z-score of the spine by (median and 95% confidence interval) ?0.21 [95% CI: ?0.40; ?0.03] (p < 0.02). Analysis suggested an association between the AA genotype in the Val667Met polymorphism and increased body height and decreased BMD of the femoral neck; however, no significant gene-dose effect of the A-allele could be demonstrated in the whole population. When the analysis was restricted to non-sedentary subjects, however, each number of A-alleles was associated with a change in Z-score of ?0.26 [95% CI: ?0.51; ?0.01] (p = 0.04). No further significant results emerged with haplotype analysis. Conclusion The Ala1330Val and Val667Met polymorphisms in the LRP5 gene are significantly associated with peak bone mass in physically active men.

Beckers, S.; Peeters, A.; Piters, E.; Balemans, W.; Nielsen, T. L.; Wraae, K.; Bathum, L.; Brasen, C.; Hagen, C.; Andersen, M.; Van Hul, W.; Abrahamsen, B.

2007-01-01

318

Inactivation of Two Dictyostelium discoideum Genes, DdPIK1 and DdPIK2, Encoding Proteins Related to Mammalian Phosphatidylinositide 3-kinases, Results in Defects in Endocytosis, Lysosome to Postlysosome Transport, and Actin Cytoskeleton Organization  

PubMed Central

Phosphatidylinositide 3-kinases (PI 3-kinases) have been implicated in controlling cell proliferation, actin cytoskeleton organization, and the regulation of vesicle trafficking between intracellular organelles. There are at least three genes in Dictyostelium discoideum, DdPIK1, DdPIK2, and DdPIK3, encoding proteins most closely related to the mammalian 110-kD PI-3 kinase in amino acid sequence within the kinase domain. A mutant disrupted in DdPIK1 and DdPIK2 (?ddpik1/ddpik2) grows slowly in liquid medium. Using FITC-dextran (FD) as a fluid phase marker, we determined that the mutant strain was impaired in pinocytosis but normal in phagocytosis of beads or bacteria. Microscopic and biochemical approaches indicated that the transport rate of fluid-phase from acidic lysosomes to non-acidic postlysosomal vacuoles was reduced in mutant cells resulting in a reduction in efflux of fluid phase. Mutant cells were also almost completely devoid of large postlysosomal vacuoles as determined by transmission EM. However, ?ddpik1/ddpik2 cells functioned normally in the regulation of other membrane traffic. For instance, radiolabel pulse-chase experiments indicated that the transport rates along the secretory pathway and the sorting efficiency of the lysosomal enzyme ?-mannosidase were normal in the mutant strain. Furthermore, the contractile vacuole network of membranes (probably connected to the endosomal pathway by membrane traffic) was functionally and morphologically normal in mutant cells. Light microscopy revealed that ?ddpik1/ddpik2 cells appeared smaller and more irregularly shaped than wild-type cells; 1–3% of the mutant cells were also connected by a thin cytoplasmic bridge. Scanning EM indicated that the mutant cells contained numerous filopodia projecting laterally and vertically from the cell surface, and fluorescent microscopy indicated that these filopodia were enriched in F-actin which accumulated in a cortical pattern in control cells. Finally, ?ddpik1/ddpik2 cells responded and moved more rapidly towards cAMP. Together, these results suggest that Dictyostelium DdPIK1 and DdPIK2 gene products regulate multiple steps in the endosomal pathway, and function in the regulation of cell shape and movement perhaps through changes in actin organization.

Buczynski, Greg; Grove, Bryon; Nomura, Anson; Kleve, Maurice; Bush, John; Firtel, Richard A.; Cardelli, James

1997-01-01

319

Hantavirus Nucleocapsid Protein Oligomerization  

PubMed Central

Hantaviruses are enveloped, negative-strand RNA viruses which can be lethal to humans, causing either a hemorrhagic fever with renal syndrome or a hantaviral pulmonary syndrome. The viral genomes consist of three RNA segments: the L segment encodes the viral polymerase, the M segment encodes the viral surface glycoproteins G1 and G2, and the S segment encodes the nucleocapsid (N) protein. The N protein is a 420- to 430-residue, 50-kDa protein which appears to direct hantavirus assembly, although mechanisms of N protein oligomerization, RNA encapsidation, budding, and release are poorly understood. We have undertaken a biochemical and genetic analysis of N protein oligomerization. Bacterially expressed N proteins were found by gradient fractionation to associate not only as large multimers or aggregates but also as dimers or trimers. Chemical cross-linking of hantavirus particles yielded N protein cross-link products with molecular masses of 140 to 150 kDa, consistent with the size of an N trimer. We also employed a genetic, yeast two-hybrid method for monitoring N protein interactions. Analyses showed that the C-terminal half of the N protein plus the N-terminal 40 residues permitted association with a full-length N protein fusion. These N-terminal 40 residues of seven different hantavirus strains were predicted to form trimeric coiled coils. Our results suggest that coiled-coil motifs contribute to N protein trimerization and that nucleocapsid protein trimers are hantavirus particle assembly intermediates.

Alfadhli, Ayna; Love, Zac; Arvidson, Brian; Seeds, Joshua; Willey, Jessica; Barklis, Eric

2001-01-01

320

Impact of Protein Supplementation and Care and Support on Body Composition and CD4 Count among HIV-Infected Women Living in Rural India: Results from a Randomized Pilot Clinical Trial  

PubMed Central

Body composition in HIV-infected individuals is subject to many influences. We conducted a pilot six-month randomized trial of 68 WLA (women living with AIDS) from rural India. High protein intervention combined with education and supportive care delivered by HIV-trained village women (Asha [Activated Social Health Activist] Life [AL]) was compared to standard protein with usual care delivered by village community assistants (Usual Care [UC]). Measurements included CD4 counts, ART adherence, socio-demographics, disease characteristics (questionnaires); and anthropometry (bioimpedance analyzer). Repeated measures analysis of variance modeled associations. AL significantly gained in BMI, muscle mass, fat mass, ART adherence, and CD4 counts compared to UC, with higher weight and muscle mass gains among ART adherent (? 66%) participants who had healthier immunity (CD4 ? 450). BMI of WLA improved through high protein supplementation combined with education and supportive care. Future research is needed to determine which intervention aspect was most responsible.

Nyamathi, Adeline; Sinha, Sanjeev; Ganguly, Kalyan K; Ramakrishna, Padma; Suresh, P.; Carpenter, Catherine L

2013-01-01

321

Protein Analysis  

NASA Astrophysics Data System (ADS)

Proteins are an abundant component in all cells, and almost all except storage proteins are important for biological functions and cell structure. Food proteins are very complex. Many have been purified and characterized. Proteins vary in molecular mass, ranging from approximately 5000 to more than a million Daltons. They are composed of elements including hydrogen, carbon, nitrogen, oxygen, and sulfur. Twenty ?-amino acids are the building blocks of proteins; the amino acid residues in a protein are linked by peptide bonds. Nitrogen is the most distinguishing element present in proteins. However, nitrogen content in various food proteins ranges from 13.4 to 19.1% (1) due to the variation in the specific amino acid composition of proteins. Generally, proteins rich in basic amino acids contain more nitrogen.

Chang, Sam K. C.

322

Protein complex forming ability is favored over the features of interacting partners in determining the evolutionary rates of proteins in the yeast protein-protein interaction networks  

Microsoft Academic Search

BACKGROUND: Evolutionary rates of proteins in a protein-protein interaction network are primarily governed by the protein connectivity and\\/or expression level. A recent study revealed the importance of the features of the interacting protein partners, viz., the coefficient of functionality and clustering coefficient in controlling the protein evolutionary rates in a protein-protein interaction (PPI) network. RESULTS: By multivariate regression analysis we

Sandip Chakraborty; Bratati Kahali; Tapash C Ghosh

2010-01-01

323

Protein solubility modeling  

NASA Technical Reports Server (NTRS)

A thermodynamic framework (UNIQUAC model with temperature dependent parameters) is applied to model the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is modeled as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the modeled and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the model closely follows the experimental behavior. Model calculations and model parameters are reviewed to examine the model and protein crystallization process. Copyright 1999 John Wiley & Sons, Inc.

Agena, S. M.; Pusey, M. L.; Bogle, I. D.

1999-01-01

324

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

325

Smoking interacts with HLA-DRB1 shared epitope in the development of anti-citrullinated protein antibody-positive rheumatoid arthritis: results from the Malaysian Epidemiological Investigation of Rheumatoid Arthritis (MyEIRA)  

PubMed Central

Introduction Rheumatoid arthritis (RA) is a multifactorial autoimmune disease in which genetic and environmental factors interact in the etiology. In this study, we investigated whether smoking and HLA-DRB1 shared-epitope (SE) alleles interact differently in the development of the two major subgroups of rheumatoid arthritis (RA), anti-citrullinated proteins antibody (ACPA)-positive and ACPA-negative disease, in a multiethnic population of Asian descent. Methods A case-control study comprising early diagnosed RA cases was carried out in Malaysia between 2005 and 2009. In total, 1,076 cases and 1,612 matched controls participated in the study. High-resolution HLA-DRB1 genotyping was performed for shared-epitope (SE) alleles. All participants answered a questionnaire on a broad range of issues, including smoking habits. The odds ratio (OR) of developing ACPA-positive and ACPA-negative disease was calculated for smoking and the presence of any SE alleles separately. Potential interaction between smoking history (defined as "ever" and "never" smoking) and HLA-DRB1 SE alleles also was calculated. Results In our multiethnic study, both the SE alleles and smoking were associated with an increased risk of developing ACPA-positive RA (OR SE alleles, 4.7; 95% confidence interval (CI), 3.6 to 6.2; OR smoking, 4.1; 95% CI, 1.9 to 9.2). SE-positive smokers had an odds ratio of ACPA-positive RA of 25.6 (95% CI, 10.4 to 63.4), compared with SE-negative never-smokers. The interaction between smoking and SE alleles was significant (attributable proportion due to interaction (AP) was 0.7 (95% CI, 0.5 to 1.0)). The HLA-DRB1*04:05 SE allele, which is common in Asian populations, but not among Caucasians, was associated with an increased risk of ACPA-positive RA, and this allele also showed signs of interaction with smoking (AP, 0.4; 95% CI, -0.1 to 0.9). Neither smoking nor SE alleles nor their combination was associated with an increased risk of ACPA-negative RA. Conclusions The risk of developing ACPA-positive RA is associated with a strong gene-environment interaction between smoking and HLA-DRB1 SE alleles in a Malaysian multiethnic population of Asian descent. This interaction seems to apply also between smoking and the specific HLA-DRB1*04:05 SE allele, which is common in Asian populations but not in Caucasians.

2012-01-01

326

Functional clustering of yeast proteins from the protein-protein interaction network  

Microsoft Academic Search

BACKGROUND: The abundant data available for protein interaction networks have not yet been fully understood. New types of analyses are needed to reveal organizational principles of these networks to investigate the details of functional and regulatory clusters of proteins. RESULTS: In the present work, individual clusters identified by an eigenmode analysis of the connectivity matrix of the protein-protein interaction network

Taner Z. Sen; Andrzej Kloczkowski; Robert L. Jernigan

2006-01-01

327

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

328

Exposure to the Three Structurally Different PCB Congeners (PCB 118, 153, and 126) Results in Decreased Protein Expression and Altered Steroidogenesis in the Human Adrenocortical Carcinoma Cell Line H295R.  

PubMed

Polychlorinated biphenyls (PCB), synthetic, persistent organic pollutants (POP), are detected ubiquitously, in water, soil, air, and sediments, as well as in animals and humans. PCB are associated with range of adverse health effects, such as interference with the immune system and nervous system, reproductive abnormalities, fetotoxicity, carcinogenicity, and endocrine disruption. Our objective was to determine the effects of three structurally different PCB congeners, PCB118, PCB 126, and PCB 153, each at two concentrations, on the steroidogenic capacity and proteome of human adrenocortical carcinoma cell line cultures (H295R) . After 48 h of exposure, cell viability was monitored and estradiol, testosterone, cortisol and progesterone secretion measured to quantify steroidogenic capacity of the cells. Two-dimensional (2D) gel-based proteomics was used to screen for proteome alterations in H295R cells in response to the PCB. Exposure to PCB 118 increased estradiol and cortisol secretion, while exposure to PCB 153 elevated estradiol secretion. PCB 126 was the most potent congener, increasing estradiol, cortisol, and progesterone secretion in exposed H295R cells. Seventy-three of the 711 spots analyzed showed a significant difference in normalized spot volumes between controls (vehicle only) and at least one exposure group. Fourteen of these protein spots were identified by liquid chromatography with mass spectroscopy (LC-MS/MS). Exposure to three PCB congeners with different chemical structure perturbed steroidogenesis and protein expression in the H295R in vitro model. This study represents an initial analysis of the effects on proteins and hormones in the H295R cell model, and additional studies are required in order to obtain a more complete understanding of the pathways disturbed by PCB congeners in H295R cells. Overall, alterations in protein regulation and steroid hormone synthesis suggest that exposure to PCB disturbs several cellular processes, including protein synthesis, stress response, and apoptosis. PMID:24754389

Tremoen, Nina Hårdnes; Fowler, Paul A; Ropstad, Erik; Verhaegen, Steven; Krogenæs, Anette

2014-01-01

329

A comparative study of cancer proteins in the human protein-protein interaction network  

PubMed Central

Background Cancer is a complex disease. So far, many genes have been reported to involve in the development of cancer. Rather than the traditional approach to studying individual genes or loci, a systematic investigation of cancer proteins in the human protein-protein interaction network may provide important biological information for uncovering the molecular mechanisms of cancer and, potentially, other complex diseases. Results We explored global and local network characteristics of the proteins encoded by cancer genes (cancer proteins) in the human interactome. We found that the network topology of the cancer proteins was much different from that of the proteins encoded by essential genes (essential proteins) or control genes (control proteins). Relative to the essential proteins or control proteins, cancer proteins tended to have higher degree, higher betweenness, shorter shortest-path distance, and weaker clustering coefficient in the human interactome. We further separated the cancer proteins into two groups (recessive and dominant cancer proteins) and compared their topological features. Recessive cancer proteins had higher betweenness than dominant cancer proteins, while their degree distribution and characteristic shortest path distance were also significantly different. Finally, we found that cancer proteins were not randomly distributed in the human interactome and they connected strongly with each other. Conclusion Our study revealed much stronger protein-protein interaction characteristics of cancer proteins relative to the essential proteins or control proteins in the whole human interactome. We also found stronger network characteristics of recessive than dominant cancer proteins. The results are helpful for cancer candidate gene prioritization and verification, biomarker discovery, and, ultimately, understanding the etiology of cancer at the systems biological level.

2010-01-01

330

Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources  

PubMed Central

Protein interactions play an important role in the discovery of protein functions and pathways in biological processes. This is especially true in case of the diseases caused by the loss of specific protein-protein interactions in the organism. The accuracy of experimental results in finding protein-protein interactions, however, is rather dubious and high throughput experimental results have shown both high false positive beside false negative information for protein interaction. Computational methods have attracted tremendous attention among biologists because of the ability to predict protein-protein interactions and validate the obtained experimental results. In this study, we have reviewed several computational methods for protein-protein interaction prediction as well as describing major databases, which store both predicted and detected protein-protein interactions, and the tools used for analyzing protein interaction networks and improving protein-protein interaction reliability.

Zahiri, Javad; Bozorgmehr, Joseph Hannon; Masoudi-Nejad, Ali

2013-01-01

331

Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources.  

PubMed

Protein interactions play an important role in the discovery of protein functions and pathways in biological processes. This is especially true in case of the diseases caused by the loss of specific protein-protein interactions in the organism. The accuracy of experimental results in finding protein-protein interactions, however, is rather dubious and high throughput experimental results have shown both high false positive beside false negative information for protein interaction. Computational methods have attracted tremendous attention among biologists because of the ability to predict protein-protein interactions and validate the obtained experimental results. In this study, we have reviewed several computational methods for protein-protein interaction prediction as well as describing major databases, which store both predicted and detected protein-protein interactions, and the tools used for analyzing protein interaction networks and improving protein-protein interaction reliability. PMID:24396273

Zahiri, Javad; Bozorgmehr, Joseph Hannon; Masoudi-Nejad, Ali

2013-09-01

332

Naturally occurring R225W mutation of the gene encoding AMP-activated protein kinase (AMPK)? 3 results in increased oxidative capacity and glucose uptake in human primary myotubes  

Microsoft Academic Search

Aims\\/hypothesis  AMP-activated protein kinase (AMPK) has a broad role in the regulation of glucose and lipid metabolism making it a promising\\u000a target in the treatment of type 2 diabetes mellitus. We therefore sought to characterise for the first time the effects of\\u000a chronic AMPK activation on skeletal muscle carbohydrate metabolism in carriers of the rare gain-of-function mutation of the\\u000a gene encoding

S. A. Crawford; S. R. Costford; C. Aguer; S. C. Thomas; R. A. deKemp; J. N. DaSilva; D. Lafontaine; M. Kendall; R. Dent; R. S. B. Beanlands; R. McPherson; M.-E. Harper

2010-01-01

333

Environments of the four tryptophans in the extracellular domain of human tissue factor: comparison of results from absorption and fluorescence difference spectra of tryptophan replacement mutants with the crystal structure of the wild-type protein.  

PubMed Central

The local environments of the four tryptophan residues of the extracellular domain of human tissue factor (sTF) were assessed from difference absorption and fluorescence spectra. The difference spectra were derived by subtracting spectra from single Trp-to-Phe or Trp-to-Tyr replacement mutants from the corresponding spectrum of the wild-type protein. Each of the mutants was capable of enhancing the proteolytic activity of factor VIIa showing that the mutations did not introduce major structural changes, although the mutants were more susceptible to denaturation by guanidinium chloride. The difference spectra indicate that the Trp residues are buried to different extents within the protein matrix. This evaluation was compared with the x-ray crystal structure of sTF. There is excellent agreement between predictions from the difference spectra and the environments of the Trp residues observed in the x-ray crystal structure, demonstrating that difference absorption and particularly fluorescence spectra derived from functional single-Trp replacement mutants can be used to obtain information about the local environments of individual Trp residues in multi-tryptophan proteins. Images FIGURE 7 FIGURE 8

Hasselbacher, C A; Rusinova, E; Waxman, E; Rusinova, R; Kohanski, R A; Lam, W; Guha, A; Du, J; Lin, T C; Polikarpov, I

1995-01-01

334

Protein- protein interaction detection system using fluorescent protein microdomains  

DOEpatents

The invention provides a protein labeling and interaction detection system based on engineered fragments of fluorescent and chromophoric proteins that require fused interacting polypeptides to drive the association of the fragments, and further are soluble and stable, and do not change the solubility of polypeptides to which they are fused. In one embodiment, a test protein X is fused to a sixteen amino acid fragment of GFP (.beta.-strand 10, amino acids 198-214), engineered to not perturb fusion protein solubility. A second test protein Y is fused to a sixteen amino acid fragment of GFP (.beta.-strand 11, amino acids 215-230), engineered to not perturb fusion protein solubility. When X and Y interact, they bring the GFP strands into proximity, and are detected by complementation with a third GFP fragment consisting of GFP amino acids 1-198 (strands 1-9). When GFP strands 10 and 11 are held together by interaction of protein X and Y, they spontaneous association with GFP strands 1-9, resulting in structural complementation, folding, and concomitant GFP fluorescence.

Waldo, Geoffrey S. (Santa Fe, NM); Cabantous, Stephanie (Los Alamos, NM)

2010-02-23

335

Protein C  

MedlinePLUS

... to tell your doctor about all medicines and supplements you are taking before having this test. Some medicines that prevent blood clots from forming (anticoagulants), such as warfarin (Coumadin), decrease protein C and protein S levels. Your doctor may ask ...

336

Dietary Proteins  

MedlinePLUS

... nuts and certain grains and beans. Proteins from meat and other animal products are complete proteins. This means they supply all of the amino acids the body can't make on its own. Plant proteins are incomplete. You must combine them to ...

337

Protein Bracelets  

NSDL National Science Digital Library

In this activity, learners use beads, which represent amino acids, to create protein bracelets. Learners examine the relationship between amino acids and proteins. Learners also discover that different arrangements of amino acids create different kinds of proteins. Note: Have a bracelet already created so students can see what they are working to create.

Center, Arizona S.

2012-01-01

338

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

339

Predicting protein diffusion coefficients.  

PubMed Central

Diffusion coefficients for proteins in water are predicted. The numerical method developed is general enough to be applied to a wide range of protein surface shapes, from rodlike to globular. Results are presented for lysozyme and tobacco mosaic virus, and they are compared with actual data and with predictions made by less general methods. Images Fig. 2

Brune, D; Kim, S

1993-01-01

340

Protein Synthesis Patterns 1  

PubMed Central

The proteins synthesized during the first hours of seed imbibition were studied in axes and scutellum of maize embryos separately. Increase in fresh weight was followed in the embryonic axes through the germination period. Pulse labeling experiments with 14C-amino acids were carried out at two stages of development: 0 to 6 and 18 to 24 hours in the presence and absence of ?-amanitin. The proteins were analyzed by two-dimensional gel electrophoresis and fluorography. Results showed a major pattern of proteins common to both tissues, axes and scutellum (`house keeping' proteins), besides the specific proteins synthesized by each tissue. In the axes, the changes in proteins observed between the periods of 0 to 6 and 18 to 24 hours of development seem to be due both to newly synthesized mRNA as well as to delayed translation of stored mRNA species. Images Fig. 2 Fig. 3 Fig. 4

de Jimenez, Estela Sanchez; Aguilar, Raul

1984-01-01

341

Culex quinquefasciatus Storage Proteins  

PubMed Central

Insect storage proteins accumulate at high levels during larval development of holometabolous insects. During metamorphosis they are degraded, supplying energy and amino acids for the completion of adult development. The genome of Culex quinquefasciatus contains eleven storage protein-coding genes. Their transcripts are more abundant in larvae than in pupae and in adults. In fact, only four of these genes are transcribed in adults, two of which in blood-fed adult females but not in adult males. Transcripts corresponding to all Cx. quinquefasciatus storage proteins were detected by RT-PCR, while mass spectrometric analysis of larval and pupal proteins identified all storage proteins with the exception of one encoded by Cq LSP1.8. Our results indicate that the identified Cx. quinquefasciatus storage protein-coding genes are candidates for identifying regulatory sequences for the development of molecular tools for vector control.

Martins, Larissa A.; Fogaca, Andrea C.; Bijovsky, A. Tania; Carballar-Lejarazu, Rebeca; Marinotti, Osvaldo; Cardoso, Andre F.

2013-01-01

342

The penicillin resistance of Enterococcus faecalis JH2-2r results from an overproduction of the low-affinity penicillin-binding protein PBP4 and does not involve a psr-like gene  

Microsoft Academic Search

A penicillin-resistant mutant, JH2-2r (MIC 75 l gm lN1), was isolated from Enterococcus faecalis JH2-2 (MIC 5 l gm lN1) by successive passages on plates containing increasing concentrations of benzylpenicillin. A comparison of the penicillin-binding protein (PBP) profiles in the two strains revealed a more intensely labelled PBP4 in JH2-2r. Because the sequences of the JH2-2 and JH2-2r pbp4 genes

Colette Duez; Willy Zorzi; Iris Thamm; Jacques Coyette

343

Molecular modelling of protein-protein/protein-solvent interactions  

NASA Astrophysics Data System (ADS)

The inner workings of individual cells are based on intricate networks of protein-protein interactions. However, each of these individual protein interactions requires a complex physical interaction between proteins and their aqueous environment at the atomic scale. In this thesis, molecular dynamics simulations are used in three theoretical studies to gain insight at the atomic scale about protein hydration, protein structure and tubulin-tubulin (protein-protein) interactions, as found in microtubules. Also presented, in a fourth project, is a molecular model of solvation coupled with the Amber molecular modelling package, to facilitate further studies without the need of explicitly modelled water. Basic properties of a minimally solvated protein were calculated through an extended study of myoglobin hydration with explicit solvent, directly investigating water and protein polarization. Results indicate a close correlation between polarization of both water and protein and the onset of protein function. The methodology of explicit solvent molecular dynamics was further used to study tubulin and microtubules. Extensive conformational sampling of the carboxy-terminal tails of 8-tubulin was performed via replica exchange molecular dynamics, allowing the characterisation of the flexibility, secondary structure and binding domains of the C-terminal tails through statistical analysis methods. Mechanical properties of tubulin and microtubules were calculated with adaptive biasing force molecular dynamics. The function of the M-loop in microtubule stability was demonstrated in these simulations. The flexibility of this loop allowed constant contacts between the protofilaments to be maintained during simulations while the smooth deformation provided a spring-like restoring force. Additionally, calculating the free energy profile between the straight and bent tubulin configurations was used to test the proposed conformational change in tubulin, thought to cause microtubule destabilization. No conformational change was observed but a nucleotide dependent 'softening' of the interaction was found instead, suggesting that an entropic force in a microtubule configuration could be the mechanism of microtubule collapse. Finally, to overcome much of the computational costs associated with explicit soIvent calculations, a new combination of molecular dynamics with the 3D-reference interaction site model (3D-RISM) of solvation was integrated into the Amber molecular dynamics package. Our implementation of 3D-RISM shows excellent agreement with explicit solvent free energy calculations. Several optimisation techniques, including a new multiple time step method, provide a nearly 100 fold performance increase, giving similar computational performance to explicit solvent.

Luchko, Tyler

344

Ultrafiltration of pegylated proteins  

NASA Astrophysics Data System (ADS)

There is considerable clinical interest in the use of "second-generation" therapeutics produced by conjugation of a native protein with various polymers including polyethylene glycol (PEG). PEG--protein conjugates, so-called PEGylated proteins, can exhibit enhanced stability, half-life, and bioavailability. One of the challenges in the commercial production of PEGylated proteins is the purification required to remove unreacted polymer, native protein, and in many cases PEGylated proteins with nonoptimal degrees of conjugation. The overall objective of this thesis was to examine the use of ultrafiltration for the purification of PEGylated proteins. This included: (1) analysis of size-based separation of PEGylated proteins using conventional ultrafiltration membranes, (2) use of electrically-charged membranes to exploit differences in electrostatic interactions, and (3) examination of the effects of PEGylation on protein fouling. The experimental results were analyzed using appropriate theoretical models, with the underlying physical properties of the PEGylated proteins evaluated using size exclusion chromatography, capillary electrophoresis, dynamic light scattering, and reverse phase chromatography. PEGylated proteins were produced by covalent attachment of activated PEG to a protein via primary amines on the lysine residues. A simple model was developed for the reaction kinetics, which was used to explore the effect of reaction conditions and mode of operation on the distribution of PEGylated products. The effective size of the PEGylated proteins was evaluated using size exclusion chromatography, with appropriate correlations developed for the size in terms of the molecular weight of the native protein and attached PEG. The electrophoretic mobility of the PEGylated proteins were evaluated by capillary electrophoresis with the data in good agreement with a simple model accounting for the increase in protein size and the reduction in the number of protonated amine groups in the PEGylated proteins. Ultrafiltration experiments were performed using PEGylated alpha-lactalbumin, ovalbumin, and bovine serum albumin. In contrast to the size exclusion chromatography data, the sieving coefficient of the PEGylated proteins depended upon both the number and size of the attached PEG chains due to the elongation or deformation of the PEG associated with the filtrate flux. Sieving coefficients at low filtrate flux were in good agreement with predictions of available hydrodynamic models, with significant elongation occurring when the Deborah number for the PEG chain exceeded 0.001. The effects of electrostatic interactions on the ultrafiltration of PEGylated proteins were examined using electrically-charged membranes generated by covalent attachment of sulphonic acid groups to the base cellulosic membrane. Transmission of PEGylated proteins through charged membranes was dramatically reduced at low ionic strength due to strong electrostatic interactions, despite the presence of the neutral PEG. The experimental results were in good agreement with model calculations developed for the partitioning of charged spheres into charged cylindrical pores. The experimental and theoretical results provide the first quantitative analysis of the effects of PEGylation on transport through semipermeable ultrafiltration membranes. The results from small-scale ultrafiltration experiments were used to develop a two-stage diafiltration process to purify PEGylated alpha-lactalbumin. The first-stage used a neutral membrane to remove the unreacted protein by exploiting differences in size. The second stage used a negatively-charged membrane to remove hydrolyzed PEG, with the PEGylated product retained by strong electrostatic interactions. This process provided a purification factor greater than 1000 with respect to the unreacted protein and greater than 20-fold with respect to the PEG with an overall yield of PEGylated alpha-lactalbumin of 78%. These results provide the first demonstration of the potential of using ultrafiltration for the purificatio

Molek, Jessica R.

345

Predicting Permanent and Transient Protein-Protein Interfaces  

PubMed Central

Protein-protein interactions are involved in many diverse functions in a cell. To optimize functional roles of interactions, proteins interact with a spectrum of binding affinities. Interactions are conventionally classified into permanent and transient, where the former denotes tight binding between proteins that result in strong complexes, while the latter compose of relatively weak interactions that can dissociate after binding to regulate functional activity at specific time point. Knowing the type of interactions has significant implications for understanding the nature and function of protein-protein interactions. In this study, we constructed amino acid substitution models that capture mutation patterns at permanent and transient type of protein interfaces, which were found to be different with statistical significance. Using the substitution models, we developed a novel computational method that predicts permanent and transient protein binding interfaces in protein surfaces. Without knowledge of the interacting partner, the method employs a single query protein structure and a multiple sequence alignment of the sequence family. Using a large dataset of permanent and transient proteins, we show that our method performs very well in protein interface classification. A very high Area Under the Curve (AUC) value of 0.957 was observed when predicted protein binding sites were classified. Remarkably, near prefect accuracy was achieved with an AUC of 0.991 when actual binding sites were classified. The developed method will be also useful for protein design of permanent and transient protein binding interfaces.

La, David; Kong, Misun; Hoffman, William; Choi, Youn Im; Kihara, Daisuke

2014-01-01

346

Correlation Between Functional Annotation and Topology of Protein-Protein Interaction Network  

NASA Astrophysics Data System (ADS)

The functional annotation of proteins was believed to be related to the topology of the protein-protein interaction network. People utilized the protein-protein interaction network to infer the protein function by various methods. Here, we select the protein interaction data of Saccharomyces cerevisia and calculated the correlation between functional annotation of proteins and the topology of protein-protein interaction network. The result shows that the functional correlation decays exponentially with the distance between two proteins, and beyond the characteristic distance, it has no correlation.

Huang, Jiun-Yan

347

Protein Data Bank.  

National Technical Information Service (NTIS)

The Protein Data Bank is the international depository for the results of structural studies of biological macromolecules. At present, some 1200 biological macromolecules are reported to have been crystallized, of which approximately 350 have structures de...

E. E. Abola F. C. Bernstein T. F. Koetzle

1984-01-01

348

Protein-protein interactions: methods for detection and analysis.  

PubMed Central

The function and activity of a protein are often modulated by other proteins with which it interacts. This review is intended as a practical guide to the analysis of such protein-protein interactions. We discuss biochemical methods such as protein affinity chromatography, affinity blotting, coimmunoprecipitation, and cross-linking; molecular biological methods such as protein probing, the two-hybrid system, and phage display: and genetic methods such as the isolation of extragenic suppressors, synthetic mutants, and unlinked noncomplementing mutants. We next describe how binding affinities can be evaluated by techniques including protein affinity chromatography, sedimentation, gel filtration, fluorescence methods, solid-phase sampling of equilibrium solutions, and surface plasmon resonance. Finally, three examples of well-characterized domains involved in multiple protein-protein interactions are examined. The emphasis of the discussion is on variations in the approaches, concerns in evaluating the results, and advantages and disadvantages of the techniques.

Phizicky, E M; Fields, S

1995-01-01

349

Protein deamidation  

PubMed Central

A completely automatic computerized technique for the quantitative estimation of the deamidation rates of any protein for which the three-dimensional structure is known has been developed. Calculations of the specific deamidation rates of 170,014 asparaginyl residues in 13,335 proteins have been carried out. The calculated values have good quantitative reliability when compared with experimental measurements. These rates demonstrate that deamidation may be a biologically relevant phenomenon in a remarkably large percentage of proteins.

Robinson, Noah E.

2002-01-01

350

Protein Dynamics  

NASA Astrophysics Data System (ADS)

Proteins combine properties of solids, liquids, and glasses. Schr"odinger anticipated the main features of biomolecules long ago by stating that they had to be solid-like, but able to assume many different conformations. Indeed proteins can assume a gigantic number of conformational substates with the same primary sequence but different conformations. The different substates are described as craters in a very-high-dimensional energy landscape. The energy landscape is organized in a hierarchy of tiers, craters within craters within craters. Protein motions are pictured as transition between substates - jumps from crater to crater. Initially we assumed that these jumps were controlled by internal barriers between substates, but experiments have shown that nature selected a different approach. Proteins are surrounded by one to two layers of water and are embedded in a bulk solvent. Structural motions of the protein are controlled by the alpha fluctuations in the solvent surrounding the protein. Some internal motions most likely involving side chains are controlled electrostatically by beta fluctuations in the hydration shell. The dynamics of proteins is consequently dominated by the environment (H. Frauenfelder et al. PNAS 106, 5129 (2009). One can speculate that this organization permits exchange of information among biomolecules. The energy landscape is not just organized into two tiers, alpha and beta, but cryogenic experiments have revealed more tiers and protein more properties similar to that of glasses. While proteins function at ambient temperatures, cryogenic studies are necessary to understand the physics relevant for biology.

Frauenfelder, Hans

2011-03-01

351

Expressed protein ligation for protein semisynthesis and engineering.  

PubMed

Over the past decade, a significant methodological development in peptide ligation strategies has been elaborated that now permits the assembly of peptides and proteins. Native chemical ligation (NCL) has been introduced to join synthetic unprotected peptides by using the chemoselective reaction between a C-terminal thioester and an N-terminal cysteine residue to result in a native peptide bond. Although this method has been applied to obtain peptides, small proteins, or protein domains (up to approx 150 residues), larger proteins could not been easily received because of the limited size of the ligated fragments. Intein technologies benefit from the opportunity to participate in the production of polypeptides with the reactive groups necessary for NCL aside from the rapid isolation of highly pure recombinant proteins. Expressed protein ligation extends the scope of NCL by overcoming the size limitation of target proteins accessible to synthesis. The intein splicing and EPL have been already proven to be useful for protein semisynthesis and for various investigations, including the studies of protein-protein interactions, segmental isotopic labeling for protein structure determination, synthesis of cytotoxic proteins, protein cyclization, and site-specific incorporation of noncanonical amino acids and biophysical probes into a protein sequence. PMID:16044543

Machova, Zuzana; Beck-Sickinger, Annette G

2005-01-01

352

Ubiquitin domain proteins in disease  

Microsoft Academic Search

The human genome encodes several ubiquitin-like (UBL) domain proteins (UDPs). Members of this protein family are involved in a variety of cellular functions and many are connected to the ubiquitin proteasome system, an essential pathway for protein degradation in eukaryotic cells. Despite their structural similarity, the UBL domains appear to have a range of different targets, resulting in a considerable

Louise Madsen; Andrea Schulze; Michael Seeger; Rasmus Hartmann-Petersen

2007-01-01

353

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

ABSTRACT: 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. PMID:23039402

Plant, Darren; Ibrahim, Ibrahim; Lunt, Mark; Eyre, Stephen; Flynn, Edward; Hyrich, Kimme L; Morgan, Ann W; Wilson, Anthony G; Isaacs, John D; Barton, Anne

2012-10-01

354

Protein Unfolding and Alzheimer's  

NASA Astrophysics Data System (ADS)

Early interaction events of beta-amyloid (A?) proteins with neurons have been associated with the pathogenesis of Alzheimer's disease. Knowledge pertaining to the role of lipid molecules, particularly cholesterol, in modulating the single A? interactions with neurons at the atomic length and picosecond time resolutions, remains unclear. In our research, we have used atomistic molecular dynamics simulations to explore early molecular events including protein insertion kinetics, protein unfolding, and protein-induced membrane disruption of A? in lipid domains that mimic the nanoscopic raft and non-raft regions of the neural membrane. In this talk, I will summarize our current work on investigating the role of cholesterol in regulating the A? interaction events with membranes at the molecular level. I will also explain how our results will provide new insights into understanding the pathogenesis of Alzheimer's disease associated with the A? proteins.

Cheng, Kelvin

2012-10-01

355

New designed protein assemblies.  

PubMed

Self-assembly is an essential concept of all organisms. Polypeptides self-assemble either within a single polypeptide chain or through assembly of protein domains. Recent advances in designed protein assemblies were achieved by genetic or chemical linkage of oligomerization domains and by engineering new interaction interfaces, which resulted in formation of lattices and cage-like protein assemblies. The absence of new experimentally determined protein folds in the last few years underlines the challenge of designing new folds. Recently a new strategy for designing self-assembly of a polypeptide fold, based on the topological arrangement of coiled-coil modules as the protein origami, has been proposed. The polypeptide tetrahedron was designed from a single chain concatenating of coiled-coil forming building modules interspersed with flexible hinges. In this strategy the order of coiled-coil segments defines the fold of the polypeptide nanostructure. PMID:24183814

Boži?, Sabina; Doles, Tibor; Gradišar, Helena; Jerala, Roman

2013-12-01

356

Protein crystallizability.  

PubMed

Obtaining well-diffracting crystals remains a major challenge in protein structure research. In this chapter, we review currently available computational methods to estimate the crystallization potential of a protein, to optimize amino acid sequences toward improved crystallization likelihood, and to design optimal crystal screen conditions. PMID:20221931

Smialowski, Pawel; Frishman, Dmitrij

2010-01-01

357

The t(10;11)(p13;q14) in the U937 cell line results in the fusion of the AF10 gene and CALM, encoding a new member of the AP-3 clathrin assembly protein family.  

PubMed

The translocation t(10;11)(p13;q14) is a recurring chromosomal abnormality that has been observed in patients with acute lymphoblastic leukemia as well as acute myeloid leukemia. We have recently reported that the monocytic cell line U937 has a t(10;11)(p13;q14) translocation. Using a combination of positional cloning and candidate gene approach, we cloned the breakpoint and were able to show that AF10 is fused to a novel gene that we named CALM (Clathrin Assembly Lymphoid Myeloid leukemia gene) located at 11q14. AF10, a putative transcription factor, had recently been cloned as one of the fusion partners of MLL. CALM has a very high homology in its N-terminal third to the murine ap-3 gene which is one of the clathrin assembly proteins. The N-terminal region of ap-3 has been shown to bind to clathrin and to have a high-affinity binding site for phosphoinositols. The identification of the CALM/AF10 fusion gene in the widely used U937 cell line will contribute to our understanding of the malignant phenotype of this line. PMID:8643484

Dreyling, M H; Martinez-Climent, J A; Zheng, M; Mao, J; Rowley, J D; Bohlander, S K

1996-05-14

358

Potential Survival Benefit of Anti-Apoptosis Protein: Survivin-Derived Peptide Vaccine with and without Interferon Alpha Therapy for Patients with Advanced or Recurrent Urothelial Cancer--Results from Phase I Clinical Trials  

PubMed Central

We previously identified a human leukocyte antigen (HLA)-A24-restricted antigenic peptide, survivin-2B80–88, a member of the inhibitor of apoptosis protein family, recognized by CD8+cytotoxic T lymphocytes (CTL). In a phase I clinical trial of survivin-2B80-88 vaccination for metastatic urothelial cancer (MUC), we achieved clinical and immunological responses with safety. Moreover, our previous study indicated that interferon alpha (IFN?) enhanced the effects of the vaccine for colorectal cancer. Therefore, we started a new phase I clinical trial of survivin-2B80–88 vaccination with IFN? for MUC patients. Twenty-one patients were enrolled and no severe adverse event was observed. HLA-A24/survivin-2B80–88 tetramer analysis and ELISPOT assay revealed a significant increase in the frequency of the peptide-specific CTLs after vaccination in nine patients. Six patients had stable disease. The effects of IFN? on the vaccination were unclear for MUC. Throughout two trials, 30 MUO patients received survivin-2B80–88 vaccination. Patients receiving the vaccination had significantly better overall survival than a comparable control group of MUO patients without vaccination (P = 0.0009). Survivin-2B80–88 vaccination may be a promising therapy for selected patients with MUC refractory to standard chemotherapy. This trial was registered with UMIN00005859.

Kitamura, Hiroshi; Nishida, Sachiyo; Takahashi-Takaya, Akari; Kawami, Sachiyo; Torigoe, Toshihiko; Hirohashi, Yoshihiko; Tsukamoto, Taiji; Sato, Noriyuki; Masumori, Naoya

2013-01-01

359

Protein Complex Identification by Integrating Protein-Protein Interaction Evidence from Multiple Sources  

PubMed Central

Background Understanding protein complexes is important for understanding the science of cellular organization and function. Many computational methods have been developed to identify protein complexes from experimentally obtained protein-protein interaction (PPI) networks. However, interaction information obtained experimentally can be unreliable and incomplete. Reconstructing these PPI networks with PPI evidences from other sources can improve protein complex identification. Results We combined PPI information from 6 different sources and obtained a reconstructed PPI network for yeast through machine learning. Some popular protein complex identification methods were then applied to detect yeast protein complexes using the new PPI networks. Our evaluation indicates that protein complex identification algorithms using the reconstructed PPI network significantly outperform ones on experimentally verified PPI networks. Conclusions We conclude that incorporating PPI information from other sources can improve the effectiveness of protein complex identification.

Xu, Bo; Lin, Hongfei; Chen, Yang; Yang, Zhihao; Liu, Hongfang

2013-01-01

360

Evolutionary constraints on yeast protein size  

PubMed Central

Background Despite a strong evolutionary pressure to reduce genome size, proteins vary in length over a surprisingly wide range also in very compact genomes. Here we investigated the evolutionary forces that act on protein size in the yeast Saccharomyces cerevisiae utilizing a system-wide bioinformatics approach. Data on yeast protein size was compared to global experimental data on protein expression, phenotypic pleiotropy, protein-protein interactions, protein evolutionary rate and biochemical classification. Results Comparing the experimentally determined abundance of individual proteins, highly expressed proteins were found to be consistently smaller than lowly expressed proteins, in accordance with the biosynthetic cost minimization hypothesis. Yeast proteins able to maintain a high expression level despite a large size tended to belong to a very distinct set of protein families, notably nuclear transport and translation initiation/elongation. Large proteins have significantly more protein-protein interactions than small proteins, suggesting that a requirement for multiple interaction domains may constitute a positive selective pressure for large protein size in yeast. The higher frequency of protein-protein interactions in large proteins was not accompanied by a higher phenotypic pleiotropy. Hence, the increase in interactions may not reflect an increase in function differentiation. Proteins of different sizes also evolved at similar rates. Finally, whereas the biological process involved was found to have little influence on protein size the biochemical activity exerted by the protein represented a dominant factor. More than one third of all biochemical activity classes were enriched in one or more size intervals. Conclusion In yeast, there is an inverse relationship between protein size and protein expression such that highly expressed proteins tend to be of smaller size. Also, protein size is moderately affected by protein connectivity and strongly affected by biochemical activity. Phenotypic pleiotropy does not seem to affect protein size.

Warringer, Jonas; Blomberg, Anders

2006-01-01

361

Protein kinases and multidrug resistance  

Microsoft Academic Search

The role of protein kinases in the multidrug resistance phenotype of cancer cell lines is discussed with an emphasis on protein\\u000a kinase C and protein kinase A. Evidence that P-glycoprotein is phosphorylated by these kinases is summarised and the relationship\\u000a between P-glycoprotein phosphorylation and the multidrug-resistant phenotype discussed. Results showing that protein kinase\\u000a C, particularly the alpha subspecies, is overexpressed

Martin G. Rumsby; Lisa Drew; J. Roger Warr

1998-01-01

362

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

363

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

364

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

365

Phospholipid/protein cones.  

PubMed

The presence of protein in tubule-forming solutions of the diacetylenic phospholipid 1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphocholine results in the formation of hollow cones rather than the expected hollow cylinders. Differential phase-contrast video microscopy reveals that cones grow from proteinaceous nodules in a fashion similar to cylindrical tubule growth from spherical vesicles. Spatially resolved electron-beam energy-dispersive X-ray fluorescence spectroscopy shows the protein to be associated with the cone wall. Small-angle X-ray scattering shows that, like the protein-free cylinders, the cones are multilamellar with essentially identical interlamellar spacing. PMID:12059207

Mishra, Bijaya K; Thomas, Britt N

2002-06-19

366

Ontology integration to identify protein complex in protein interaction networks  

PubMed Central

Background Protein complexes can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of protein complexes detection algorithms. Methods We have developed novel semantic similarity method, which use Gene Ontology (GO) annotations to measure the reliability of protein-protein interactions. The protein interaction networks can be converted into a weighted graph representation by assigning the reliability values to each interaction as a weight. Following the approach of that of the previously proposed clustering algorithm IPCA which expands clusters starting from seeded vertices, we present a clustering algorithm OIIP based on the new weighted Protein-Protein interaction networks for identifying protein complexes. Results The algorithm OIIP is applied to the protein interaction network of Sacchromyces cerevisiae and identifies many well known complexes. Experimental results show that the algorithm OIIP has higher F-measure and accuracy compared to other competing approaches.

2011-01-01

367

Protein Phosphatases  

NSDL National Science Digital Library

This Teaching Resource provides lecture notes and slides for a class covering the structure and function of protein phosphatases and is part of the course "Cell Signaling Systems: A Course for Graduate Students." The lecture begins with a discussion of the importance of phosphatases in physiology, recognized by the award of a Nobel Prize in 1992, and then proceeds to describe the two types of protein phosphatases: serine/threonine and tyrosine phosphatases. The information covered includes the structure, regulation, and substrate specificity of protein phosphatases, with an emphasis on their importance in disease and clinical settings.

Stephen R. Salton (Mount Sinai School of Medicine;Department of Neuroscience REV)

2005-03-01

368

Transport Proteins  

NSDL National Science Digital Library

This Teaching Resource provides and describes two animated lessons that illustrate general properties of transport proteins. The lesson called “transport protein classes” depicts major classes and subclasses of transport proteins. The “transporters, mechanism of action” lesson explains how transporters and P class ATPase (adenosine triphosphatase) pumps function. These animations serve as valuable resources for any collegiate-level course that describes these important factors. Courses that might use them include introductory biology, biochemistry, cell biology, physiology, and biophysics.

Jack D. Thatcher (Lewisburg;West Virginia School of Osteopathic Medicine REV)

2013-04-16

369

EDITORIAL: Precision proteins Precision proteins  

NASA Astrophysics Data System (ADS)

Since the birth of modern day medicine, during the times of Hippocrates in ancient Greece, the profession has developed from the rudimentary classification of disease into a rigorous science with an inspiring capability to treat and cure. Scientific methodology has distilled clinical diagnostic tools from the early arts of prognosis, which used to rely as much on revelation and prophecy, as intuition and judgement [1]. Over the past decade, research into the interactions between proteins and nanosystems has provided some ingenious and apt techniques for delving into the intricacies of anatomical systems. In vivo biosensing has emerged as a vibrant field of research, as much of medical diagnosis relies on the detection of substances or an imbalance in the chemicals in the body. The inherent properties of nanoscale structures, such as cantilevers, make them well suited to biosensing applications that demand the detection of molecules at very low concentrations. Measurable deflections in cantilevers functionalised with antibodies provide quantitative indicators of the presence of specific antigens when the two react. Such developments have roused mounting interest in the interactions of proteins with nanostructures, such as carbon nanotubes [3], which have demonstrated great potential as generic biomarkers. Plasmonic properties are also being exploited in sensing applications, such as the molecular sentinel recently devised by researchers in the US. The device uses the plasmonic properties of a silver nanoparticle linked to a Raman labelled hairpin DNA probe to signal changes in the probe geometry resulting from interactions with substances in the environment. Success stories so far include the detection of two specific genes associated with breast cancer [4]. A greater understanding of how RNA interference regulates gene expression has highlighted the potential of using this natural process as another agent for combating disease in personalized medicine. However, the large molecular weight, net negative charge and hydrophilicity of synthetic small interfering RNAs makes it hard for the molecules to cross the plasma membrane and enter the cell cytoplasm. Immune responses can also diminish the effectiveness of this approach. In this issue, Shiri Weinstein and Dan Peer from Tel Aviv University provide an overview of the challenges and recent progress in the use of nanocarriers for delivering RNAi effector molecules into target tissues and cells more effectively [5]. Also in this issue, researchers in Korea report new results that demonstrate the potential of nanostructures in neural network engineering [6]. Min Jee Jang et al report directional growth of neurites along linear carbon nanotube patterns, demonstrating great progress in neural engineering and the scope for using nanotechnology to treat neural diseases. Modern medicine cannot claim to have abolished the pain and suffering that accompany disease. But a comparison between the ghastly and often ineffective iron implements of early medicine and the smart gadgets and treatments used in hospitals today speaks volumes for the extraordinary progress that has been made, and the motivation behind this research. References [1] Wallis F 2000 Signs and senses: diagnosis and prognosis in early medieval pulse and urine texts Soc. Hist. Med. 13 265-78 [2] Arntz Y, Seelig J D, Lang H P, Zhang J, Hunziker P, Ramseyer J P, Meyer E, Hegner M and Gerber Ch 2003 Label-free protein assay based on a nanomechanical cantiliever array Nanotechnology 14 86-90 [3] Gowtham S, Scheicher R H, Pandey R, Karna S P and Ahuja R 2008 First-principles study of physisorption of nucleic acid bases on small-diameter carbon nanotubes Nanotechnology 19 125701 [4] Wang H-N and Vo-Dinh T 2009 Multiplex detection of breast cancer biomarkers using plasmonic molecular sentinel nanoprobes Nanotechnology 20 065101 [5] Weinstein S and Peer D 2010 RNAi nanomedicines: challenges and opportunities within the immune system Nanotechnology 21 232001 [6] Jang M J, Namgung S, Hong S, and Nam Y 2010 Directional neurite gro

Demming, Anna

2010-06-01

370

Protein S  

MedlinePLUS

... including: Disseminated intravascular coagulation (DIC) HIV infection Liver disease Long-term antibiotic use Warfarin (Coumadin) use Protein S levels rise with age, but this does not cause any health problems.

371

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

372

A novel functional module detection algorithm for protein-protein interaction networks  

Microsoft Academic Search

BACKGROUND: The sparse connectivity of protein-protein interaction data sets makes identification of functional modules challenging. The purpose of this study is to critically evaluate a novel clustering technique for clustering and detecting functional modules in protein-protein interaction networks, termed STM. RESULTS: STM selects representative proteins for each cluster and iteratively refines clusters based on a combination of the signal transduced

Woochang Hwang; Young-rae Cho; Aidong Zhang; Murali Ramanathan

2006-01-01

373

An interaction between the human cholesteryl ester transfer protein (CETP) and apolipoprotein A-I genes in transgenic mice results in a profound CETP-mediated depression of high density lipoprotein cholesterol levels.  

PubMed Central

We have previously described two transgenic mouse lines, one heterozygous for the human apo A-I gene and the other heterozygous for a human cholesteryl ester transfer protein (CETP) minigene driven by the mouse metallothionein-I gene promoter. In the current study, these two lines were crossed producing control, HuCETPTg, HuAITg, and HuAICETPTg mice to study the influence of CETP on HDL cholesterol levels, particle size distribution, and metabolism in animals with mouse and human-like HDL. In the HuCETPTg and HuAICETPTg animals, zinc induction approximately doubled plasma CETP activity, with no activity in plasma from the control and HuAITg animals. The only significant effect of CETP on lipoprotein subfraction cholesterol concentrations was for HDL-C. Compared to control animals, HuCETPTg animals had lower HDL-C, 20% before and 35% after Zn induction, and compared to HuAITg animals, HuAICETPTg animals had lower HDL-C, 35% before and 66% after Zn induction. Control and HuCETPTg HDL consist primarily of a single size population with a mean diameter of 10.00 +/- 0.10 nm and 9.71 +/- 0.05 nm, respectively. HuAITg HDL consists primarily of three distinct HDL size subpopulations with peak diameters of 10.35 +/- 0.08 nm, 8.80 +/- 0.06 nm, 7.40 +/- 0.10 nm, and HuAICETPTg HDL also consists primarily of three distinct HDL size subpopulations with peak diameters of 9.87 +/- 0.05 nm, 8.60 +/- 0.10 nm, 7.30 +/- 0.15 nm before, and 9.71 +/- 0.08 nm, 8.50 +/- 0.11 nm, 7.27 +/- 0.15 nm after zinc induction, respectively. Western blotting analysis of nondenaturing gradient gels of plasma with a monoclonal antibody to CETP indicated that in HuCETPTg and HuAICETPTg mice, 22 and 100%, respectively, of the CETP was HDL associated. Turnover studies with HDL doubly labeled with 125I apo A-I and 3H cholesteryl linoleate indicated that the CETP-induced fall in HDL-C was associated with increased HDL-cholesterol ester fractional catabolic rate in both the absence and presence of human apo A-I, suggesting CETP-mediated transfer of HDL-cholesterol ester to apo B-containing lipoproteins. In summary, these studies suggest that CETP has a much more profound effect on HDL cholesterol levels in transgenic animals expressing human apo A-I. This may be due to an enhanced interaction of CETP with human compared to mouse apo A-I or to the HDL particles they produce. Images

Hayek, T; Chajek-Shaul, T; Walsh, A; Agellon, L B; Moulin, P; Tall, A R; Breslow, J L

1992-01-01

374

Do cancer proteins really interact strongly in the human protein-protein interaction network?  

PubMed Central

Protein-protein interaction (PPI) network analysis has been widely applied in the investigation of the mechanisms of diseases, especially cancer. Recent studies revealed that cancer proteins tend to interact more strongly than other categories of proteins, even essential proteins, in the human interactome. However, it remains unclear whether this observation was introduced by the bias towards more cancer studies in humans. Here, we examined this important issue by uniquely comparing network characteristics of cancer proteins with three other sets of proteins in four organisms, three of which (fly, worm, and yeast) whose interactomes are essentially not biased towards cancer or other diseases. We confirmed that cancer proteins had stronger connectivity, shorter distance, and larger betweenness centrality than non-cancer disease proteins, essential proteins, and control proteins. Our statistical evaluation indicated that such observations were overall unlikely attributed to random events. Considering the large size and high quality of the PPI data in the four organisms, the conclusion that cancer proteins interact strongly in the PPI networks is reliable and robust. This conclusion suggests that perturbation of cancer proteins might cause major changes of cellular systems and result in abnormal cell function leading to cancer.

Xia, Junfeng; Sun, Jingchun; Jia, Peilin; Zhao, Zhongming

2011-01-01

375

Predicting permanent and transient protein-protein interfaces.  

PubMed

Protein-protein interactions (PPIs) are involved in diverse functions in a cell. To optimize functional roles of interactions, proteins interact with a spectrum of binding affinities. Interactions are conventionally classified into permanent and transient, where the former denotes tight binding between proteins that result in strong complexes, whereas the latter compose of relatively weak interactions that can dissociate after binding to regulate functional activity at specific time point. Knowing the type of interactions has significant implications for understanding the nature and function of PPIs. In this study, we constructed amino acid substitution models that capture mutation patterns at permanent and transient type of protein interfaces, which were found to be different with statistical significance. Using the substitution models, we developed a novel computational method that predicts permanent and transient protein binding interfaces (PBIs) in protein surfaces. Without knowledge of the interacting partner, the method uses a single query protein structure and a multiple sequence alignment of the sequence family. Using a large dataset of permanent and transient proteins, we show that our method, BindML+, performs very well in protein interface classification. A very high area under the curve (AUC) value of 0.957 was observed when predicted protein binding sites were classified. Remarkably, near prefect accuracy was achieved with an AUC of 0.991 when actual binding sites were classified. The developed method will be also useful for protein design of permanent and transient PBIs. PMID:23239312

La, David; Kong, Misun; Hoffman, William; Choi, Youn Im; Kihara, Daisuke

2013-05-01

376

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

377

Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks  

PubMed Central

Background Identification of essential proteins plays a significant role in understanding minimal requirements for the cellular survival and development. Many computational methods have been proposed for predicting essential proteins by using the topological features of protein-protein interaction (PPI) networks. However, most of these methods ignored intrinsic biological meaning of proteins. Moreover, PPI data contains many false positives and false negatives. To overcome these limitations, recently many research groups have started to focus on identification of essential proteins by integrating PPI networks with other biological information. However, none of their methods has widely been acknowledged. Results By considering the facts that essential proteins are more evolutionarily conserved than nonessential proteins and essential proteins frequently bind each other, we propose an iteration method for predicting essential proteins by integrating the orthology with PPI networks, named by ION. Differently from other methods, ION identifies essential proteins depending on not only the connections between proteins but also their orthologous properties and features of their neighbors. ION is implemented to predict essential proteins in S. cerevisiae. Experimental results show that ION can achieve higher identification accuracy than eight other existing centrality methods in terms of area under the curve (AUC). Moreover, ION identifies a large amount of essential proteins which have been ignored by eight other existing centrality methods because of their low-connectivity. Many proteins ranked in top 100 by ION are both essential and belong to the complexes with certain biological functions. Furthermore, no matter how many reference organisms were selected, ION outperforms all eight other existing centrality methods. While using as many as possible reference organisms can improve the performance of ION. Additionally, ION also shows good prediction performance in E. coli K-12. Conclusions The accuracy of predicting essential proteins can be improved by integrating the orthology with PPI networks.

2012-01-01

378

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

379

Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein–protein interaction network  

Microsoft Academic Search

Evolutionary rates of party hub and date hub proteins of Saccharomyces cerevisiae are analyzed under the perspective of ordered\\/disordered ness of proteins and the three dimensional structural context such as the solvent accessibility of the amino acid residues. Our results suggest that the lowering of evolutionary rate of the party hub proteins than the date hub proteins is solely contributed

Bratati Kahali; Shandar Ahmad; Tapash Chandra Ghosh

2009-01-01

380

Antigen Retrieval Causes Protein Unfolding  

PubMed Central

Antigen retrieval (AR), in which formalin-fixed paraffin-embedded tissue sections are briefly heated in buffers at high temperature, often greatly improves immunohistochemical staining. An important unresolved question regarding AR is how formalin treatment affects the conformation of protein epitopes and how heating unmasks these epitopes for subsequent antibody binding. The objective of the current study was to use model proteins to determine the effect of formalin treatment on protein conformation and thermal stability in relation to the mechanism of AR. Sodium dodecyl sulfate polyacrylamide gel electrophoresis was used to identify the presence of protein formaldehyde cross-links, and circular dichroism spectropolarimetry was used to determine the effect of formalin treatment and high-temperature incubation on the secondary and tertiary structure of the model proteins. Results revealed that for some proteins, formalin treatment left the native protein conformation unaltered, whereas for others, formalin denatured tertiary structure, yielding a molten globule protein. In either case, heating to temperatures used in AR methods led to irreversible protein unfolding, which supports a linear epitope model of recovered protein immunoreactivity. Consequently, the core mechanism of AR likely centers on the restoration of normal protein chemical composition coupled with improved accessibility to linear epitopes through protein unfolding.

Fowler, Carol B.; Evers, David L.; O'Leary, Timothy J.; Mason, Jeffrey T.

2011-01-01

381

Evolution of Chloroplast J Proteins  

PubMed Central

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.

Chiu, Chi-Chou; Chen, Lih-Jen; Su, Pai-Hsiang; Li, Hsou-min

2013-01-01

382

Protein structure prediction using threading.  

PubMed

This chapter discusses the protocol for computational protein structure prediction by protein threading. First, we present a general procedure and summarize some typical ideas for each step of protein threading. Then, we describe the design and implementation of RAPTOR, a protein structure prediction program based on threading. The major focuses are three key components of RAPTOR: a linear programming approach to protein threading, two machine learning approaches (SVM and Gradient Boosting) to fold recognition, and evaluation of the statistical significance of the prediction results. The first part of this chapter is a brief review of protein threading, and the second part contains original research results. Some key ideas and results have been previously published. PMID:18075163

Xu, Jinbo; Jiao, Feng; Yu, Libo

2008-01-01

383

Peroxynitrite-mediated oxidative protein modifications  

Microsoft Academic Search

Proteins are targets of reactive species and detection of oxidatively modified proteins is often used as an index of oxidative stress. Peroxynitrite is a strong oxidant formed by reaction of nitric oxide with superoxide. Using fatty acid-free bovine serum albumin as a model we examined peroxynitrite-mediated protein modifications. The reaction of protein with peroxynitrite resulted in the oxidation of tryptophan

Harry Ischiropoulos; Abu B. Al-Mehdi

1995-01-01

384

High throughput protein-protein interaction data: clues for the architecture of protein complexes  

PubMed Central

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 quality pairwise interaction data, core-module-attachment classifications from affinity purifications of complexes and predicted domain-domain interactions. Pairwise interaction data could accurately determine the members of each complex, but was unexpectedly poor at deciphering the topology of proteins in complexes. Core and module data from affinity purification studies were less useful for accurately defining the member proteins of these complexes. However, these data gave strong information on the spatial proximity of many proteins. Predicted domain-domain interactions provided some insight into the topology of proteins within complexes, but was affected by a lack of available structural data for the co-activator complexes and the presence of shared domains in paralogous proteins. Conclusion The constituent proteins of complexes are likely to be determined with accuracy by combining data from high-throughput techniques. The topology of some proteins in the complexes will be able to be clearly inferred. We finally suggest strategies that can be employed to use high throughput interaction data to define the membership and understand the architecture of proteins in novel complexes.

Krycer, James R; Pang, Chi Nam Ignatius; Wilkins, Marc R

2008-01-01

385

Protein crystal growth in microgravity  

NASA Technical Reports Server (NTRS)

Major advances have been made in several of the experimental aspects of protein crystallography, leaving protein crystallization as one of the few remaining bottlenecks. As a result, it has become important that the science of protein crystal growth is better understood and that improved methods for protein crystallization are developed. Preliminary experiments with both small molecules and proteins indicate that microgravity may beneficially affect crystal growth. For this reason, a series of protein crystal growth experiments using the Space Shuttle was initiated. The preliminary space experiments were used to evolve prototype hardware that will form the basis for a more advanced system that can be used to evaluate effects of gravity on protein crystal growth. Various optical techniques are being utilized to monitor the crystal growth process from the incipient or nucleation stage and throughout the growth phase. The eventual goal of these studies is to develop a system which utilizes optical monitoring for dynamic control of the crystallization process.

Rosenblum, William M.; Delucas, Lawrence J.; Wilson, William W.

1989-01-01

386

Computational Design of Membrane Proteins  

PubMed Central

Summary Membrane proteins are involved in a wide variety of cellular processes, and are typically part of the first interaction a cell has with extracellular molecules. As a result, these proteins comprise a majority of known drug targets. Membrane proteins are among the most difficult proteins to obtain and characterize, and a structure-based understanding of their properties can be difficult to elucidate. Notwithstanding, the design of membrane proteins can provide stringent tests of our understanding of these crucial biological systems, as well as introduce novel or targeted functionalities. Computational design methods have been particularly helpful in addressing these issues and this review discusses recent studies that tailor membrane proteins to display specific structures or functions, and how redesigned membrane proteins are being used to facilitate structural and functional studies.

Perez-Aguilar, Jose Manuel; Saven, Jeffery G.

2014-01-01

387

Spatial propagation of protein polymerization.  

PubMed

We consider the spatial dependence of filamentous protein self-assembly. Through studying the cases where the spreading of aggregated material is dominated either by diffusion or by growth, we derive analytical results for the spatial evolution of filamentous protein aggregation, which we validate against Monte Carlo simulations. Moreover, we compare the predictions of our theory with experimental measurements of two systems for which we identify the propagation as either growth or diffusion controlled. Our results connect the macroscopic observables that characterize the spatial propagation of protein self-assembly with the underlying microscopic processes and provide physical limits on spatial propagation and prionlike behavior associated with protein aggregation. PMID:24655282

Cohen, S I A; Rajah, L; Yoon, C H; Buell, A K; White, D A; Sperling, R A; Vendruscolo, M; Terentjev, E M; Dobson, C M; Weitz, D A; Knowles, T P J

2014-03-01

388

Retinal proteins as model systems for membrane protein folding.  

PubMed

Experimental folding studies of membrane proteins are more challenging than water-soluble proteins because of the higher hydrophobicity content of membrane embedded sequences and the need to provide a hydrophobic milieu for the transmembrane regions. The first challenge is their denaturation: due to the thermodynamic instability of polar groups in the membrane, secondary structures in membrane proteins are more difficult to disrupt than in soluble proteins. The second challenge is to refold from the denatured states. Successful refolding of membrane proteins has almost always been from very subtly denatured states. Therefore, it can be useful to analyze membrane protein folding using computational methods, and we will provide results obtained with simulated unfolding of membrane protein structures using the Floppy Inclusions and Rigid Substructure Topography (FIRST) method. Computational methods have the advantage that they allow a direct comparison between diverse membrane proteins. We will review here both, experimental and FIRST studies of the retinal binding proteins bacteriorhodopsin and mammalian rhodopsin, and discuss the extension of the findings to deriving hypotheses on the mechanisms of folding of membrane proteins in general. This article is part of a Special Issue entitled: Retinal Proteins-You can teach an old dog new tricks. PMID:24333783

Tastan, Oznur; Dutta, Arpana; Booth, Paula; Klein-Seetharaman, Judith

2014-05-01

389

Active learning for human protein-protein interaction prediction  

PubMed Central

Background Biological processes in cells are carried out by means of protein-protein interactions. Determining whether a pair of proteins interacts by wet-lab experiments is resource-intensive; only about 38,000 interactions, out of a few hundred thousand expected interactions, are known today. Active machine learning can guide the selection of pairs of proteins for future experimental characterization in order to accelerate accurate prediction of the human protein interactome. Results Random forest (RF) has previously been shown to be effective for predicting protein-protein interactions. Here, four different active learning algorithms have been devised for selection of protein pairs to be used to train the RF. With labels of as few as 500 protein-pairs selected using any of the four active learning methods described here, the classifier achieved a higher F-score (harmonic mean of Precision and Recall) than with 3000 randomly chosen protein-pairs. F-score of predicted interactions is shown to increase by about 15% with active learning in comparison to that with random selection of data. Conclusion Active learning algorithms enable learning more accurate classifiers with much lesser labelled data and prove to be useful in applications where manual annotation of data is formidable. Active learning techniques demonstrated here can also be applied to other proteomics applications such as protein structure prediction and classification.

2010-01-01

390

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

391

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