WorldWideScience

Sample records for archaeo-eukaryotic gins proteins

  1. Ginning

    Science.gov (United States)

    The purpose of the cotton ginning process is to separate a field crop into its salable components. It is a necessary step between the farmer and the textile manufacturer. The original gin was a simple manually operated device that took hand harvested cotton and separated fiber from the cottonseed. T...

  2. An OmpA Family Protein, a Target of the GinI/GinR Quorum-Sensing System in Gluconacetobacter intermedius, Controls Acetic Acid Fermentation▿ †

    Science.gov (United States)

    Iida, Aya; Ohnishi, Yasuo; Horinouchi, Sueharu

    2008-01-01

    Via N-acylhomoserine lactones, the GinI/GinR quorum-sensing system in Gluconacetobacter intermedius NCI1051, a gram-negative acetic acid bacterium, represses acetic acid and gluconic acid fermentation. Two-dimensional polyacrylamide gel electrophoretic analysis of protein profiles of strain NCI1051 and ginI and ginR mutants identified a protein that was produced in response to the GinI/GinR regulatory system. Cloning and nucleotide sequencing of the gene encoding this protein revealed that it encoded an OmpA family protein, named GmpA. gmpA was a member of the gene cluster containing three adjacent homologous genes, gmpA to gmpC, the organization of which appeared to be unique to vinegar producers, including “Gluconacetobacter polyoxogenes.” In addition, GmpA was unique among the OmpA family proteins in that its N-terminal membrane domain forming eight antiparallel transmembrane β-strands contained an extra sequence in one of the surface-exposed loops. Transcriptional analysis showed that only gmpA of the three adjacent gmp genes was activated by the GinI/GinR quorum-sensing system. However, gmpA was not controlled directly by GinR but was controlled by an 89-amino-acid protein, GinA, a target of this quorum-sensing system. A gmpA mutant grew more rapidly in the presence of 2% (vol/vol) ethanol and accumulated acetic acid and gluconic acid in greater final yields than strain NCI1051. Thus, GmpA plays a role in repressing oxidative fermentation, including acetic acid fermentation, which is unique to acetic acid bacteria and allows ATP synthesis via ethanol oxidation. Consistent with the involvement of gmpA in oxidative fermentation, its transcription was also enhanced by ethanol and acetic acid. PMID:18487322

  3. An OmpA family protein, a target of the GinI/GinR quorum-sensing system in Gluconacetobacter intermedius, controls acetic acid fermentation.

    Science.gov (United States)

    Iida, Aya; Ohnishi, Yasuo; Horinouchi, Sueharu

    2008-07-01

    Via N-acylhomoserine lactones, the GinI/GinR quorum-sensing system in Gluconacetobacter intermedius NCI1051, a gram-negative acetic acid bacterium, represses acetic acid and gluconic acid fermentation. Two-dimensional polyacrylamide gel electrophoretic analysis of protein profiles of strain NCI1051 and ginI and ginR mutants identified a protein that was produced in response to the GinI/GinR regulatory system. Cloning and nucleotide sequencing of the gene encoding this protein revealed that it encoded an OmpA family protein, named GmpA. gmpA was a member of the gene cluster containing three adjacent homologous genes, gmpA to gmpC, the organization of which appeared to be unique to vinegar producers, including "Gluconacetobacter polyoxogenes." In addition, GmpA was unique among the OmpA family proteins in that its N-terminal membrane domain forming eight antiparallel transmembrane beta-strands contained an extra sequence in one of the surface-exposed loops. Transcriptional analysis showed that only gmpA of the three adjacent gmp genes was activated by the GinI/GinR quorum-sensing system. However, gmpA was not controlled directly by GinR but was controlled by an 89-amino-acid protein, GinA, a target of this quorum-sensing system. A gmpA mutant grew more rapidly in the presence of 2% (vol/vol) ethanol and accumulated acetic acid and gluconic acid in greater final yields than strain NCI1051. Thus, GmpA plays a role in repressing oxidative fermentation, including acetic acid fermentation, which is unique to acetic acid bacteria and allows ATP synthesis via ethanol oxidation. Consistent with the involvement of gmpA in oxidative fermentation, its transcription was also enhanced by ethanol and acetic acid.

  4. A Gin4-Like Protein Kinase GIL1 Involvement in Hyphal Growth, Asexual Development, and Pathogenesis in Fusarium graminearum

    Science.gov (United States)

    Yu, Dan; Zhang, Shijie; Li, Xiaoping; Xu, Jin-Rong; Schultzhaus, Zachary; Jin, Qiaojun

    2017-01-01

    Fusarium graminearum is the main causal agent of Fusarium head blight (FHB) on wheat and barley. In a previous study, a GIN4-like protein kinase gene, GIL1, was found to be important for plant infection and sexual reproduction. In this study we further characterized the functions of GIL1 kinase in different developmental processes. The Δgil1 mutants were reduced in growth, conidiation, and virulence, and formed whitish and compact colonies. Although phialide formation was rarely observed in the mutants, deletion of GIL1 resulted in increased hyphal branching and increased tolerance to cell wall and cell membrane stresses. The Δgil1 mutants produced straight, elongated conidia lacking of distinct foot cells and being delayed in germination. Compared with the wild type, some compartments in the vegetative hyphae of Δgil1 mutants had longer septal distances and increased number of nuclei, suggesting GIL1 is related to cytokinesis and septation. Localization of the GIL1-GFP fusion proteins to the septum and hyphal branching and fusion sites further supported its roles in septation and branching. Overall, our results indicate that GIL1 plays a role in vegetative growth and plant infection in F. graminearum, and is involved in septation and hyphal branching. PMID:28212314

  5. A Combined Computational and Experimental Study on the Structure-Regulation Relationships of Putative Mammalian DNA Replication Initiator GINS

    Institute of Scientific and Technical Information of China (English)

    Reiko Hayashi; Takako Arauchi; Moe Tategu; Yuya Goto; Kenichi Yoshida

    2006-01-01

    GINS, a heterotetramer of SLD5, PSF1, PSF2, and PSF3 proteins, is an emerging chromatin factor recognized to be involved in the initiation and elongation step of DNA replication. Although the yeast and Xenopus GINS genes are well documented, their orthologous genes in higher eukaryotes are not fully characterized.In this study, we report the genomic structure and transcriptional regulation of mammalian GINS genes. Serum stimulation increased the GINS Mrna levels in human cells. Reporter gene assay using putative GINS promoter sequences revealed that the expression of mammalian GINS is regulated by 17β-Estradiolstimulated estrogen receptor α, and human PSF3 acts as a gene responsive to transcription factor E2F1. The goal of this study is to present the current data so as to encourage further work in the field of GINS gene regulation and functions in mammalian cells.

  6. Electricity use patterns in cotton gins

    Science.gov (United States)

    Energy costs are the second largest source of variable costs for cotton gins, with electricity accounting for 18% of variable costs. Energy use has typically not been a major consideration in gin design and previous studies of energy use have utilized instantaneous readings or aggregated season-lon...

  7. Production and characterisation of Epstein-Barr virus helicase-primase complex and its accessory protein BBLF2/3.

    Science.gov (United States)

    Thierry, Eric; Brennich, Martha; Round, Adam; Buisson, Marlyse; Burmeister, Wim P; Hutin, Stephanie

    2015-10-01

    The helicase-primase complex is part of the lytic DNA replication machinery of herpesviruses, but up to now, almost nothing is known about its structure. For Epstein-Barr virus it consists in the helicase BBLF4, the primase BSLF1 and the accessory protein BBLF2/3. The accessory protein shows only weak sequence homology within the herpesvirus family but may be related to an inactive B-family polymerase. BSLF1 belongs to the archaeo-eukaryotic primase family, whereas the helicase BBLF4 has been related either to Dda helicases of caudovirales or to Pif1 helicases. We produced the helicase-primase complex in insect cells using a baculovirus coding for all three proteins simultaneously. The soluble monomeric helicase-primase complex containing the three proteins with 1:1:1 stoichiometry showed ATPase activity, which is strongly stimulated in the presence of ssDNA oligomers. Furthermore, we expressed BBLF2/3 as soluble monomeric protein and performed small-angle X-ray scattering experiments which yielded an envelope whose shape is compatible with B-family polymerases.

  8. Interaction between GInB and the N-terminal domain of NifA in Azospirillum brasilense

    Institute of Scientific and Technical Information of China (English)

    ZHOU XiaoYu; ZOU XiaoXiao; LI JiLun

    2008-01-01

    Azospirillum brasilense is a diazotroph associated with many important agricultural crops and shows potential as a biofertilizer. NifA, the transcriptional activator of nitrogen fixation (nif) genes, and GInB, one of P,, signal transduction family protein, are key proteins in the regulation of nitrogen fixation in A. brasilense. It was previously reported that the regulation of NifA activity in A. brasilense depends on GInB. We report here that GInB was found to interact directly with the N-terminal domain of NifA in vivo under nitrogen-free conditions and the N-terminal mutant of NifA in which the Tyr residues at position 18 and 53 were replaced by Phe (NifA-N-Y18/53F) strengthened the interaction with GInB. Moreover, we also found that the amino acid residues 66-88 and 165-176 in N-terminus of NifA are responsible for the interaction with GInB.

  9. Gin-mediated DNA inversion: product structure and the mechanism of strand exchange.

    Science.gov (United States)

    Kanaar, R; van de Putte, P; Cozzarelli, N R

    1988-02-01

    Inversion of the G loop of bacteriophage Mu requires the phage-encoded Gin protein and a host factor. The topological changes in a supercoiled DNA substrate generated by the two purified proteins were analyzed. More than 99% of the inversion products were unknotted rings. This result excludes synapsis by way of a random collision of recombination sites, because the resulting entrapped supercoils would be converted into knots by recombination. Instead, the recombination sites must come together in the synaptic complex in an ordered fashion with a fixed number of supercoils between the sites. The linking number of the substrate DNA increases by four during recombination. Thus, in three successive rounds of inversion, the change in linking number was +4, +8, and +12, respectively. These results lead to a quantitative model for the mechanism of Gin recombination that includes the distribution of supercoils in the synaptic complex, their alteration by strand exchange, and specific roles for the two proteins needed for recombination.

  10. How current ginning processes affect fiber length uniformity index

    Science.gov (United States)

    There is a need to develop cotton ginning methods that improve fiber characteristics that are compatible with the newer and more efficient spinning technologies. A literature search produced recent studies that described how current ginning processes affect HVI fiber length uniformity index. Resul...

  11. Lubbock Gin Lab - Current Research and Leaf Grade Issues

    Science.gov (United States)

    This presentation was given to a group of cotton gin managers and allied industry reps. Approximately 100 attendees were in the audience. A discussion of the current research conducted at the USDA ARS CPPRU Ginning Laboratory in Lubbock, TX was given along with a discussion of leaf grade issues and ...

  12. Evaluation of a mass flow sensor at a gin

    Science.gov (United States)

    As part of a system to optimize the cotton ginning process, a custom-built mass flow sensor was evaluated at USDA-ARS Cotton Ginning Research Unit at Stoneville, Mississippi. The mass flow sensor was fabricated based on the principle of the sensor patented by Thomasson and Sui. The optical and ele...

  13. Dust cyclone technology for gins – A literature review

    Science.gov (United States)

    Dust cyclone research leading to more efficient designs has helped the cotton ginning industry to comply with increasingly stringent air quality regulations governing fine particulate emissions. Future changes in regulations may require additional improvements in dust cyclone efficacy. This inter-...

  14. Eco-friendly rubberized cotton fabric roller for ginning machines.

    Science.gov (United States)

    Iyer, G V

    2007-01-01

    This article discusses the pollution caused by chrome composite leather-clad (CCLC) rollers commonly used in cotton roller ginning mills and suggests an alternative roller material. CCLC rollers contain about 18,000 to 36,000 mg/kg (ppm) total chromium in trivalent and hexavalent forms, which are toxic to human health and carcinogenic. When seed-cotton is processed in double roller (DR) ginning machines, the lint is contaminated with chromium, and chromium particles are carried into the spun yarns and cotton by-products. Specifically, due to persistent rubbing of the leather-clad roller over the stationary knife during the ginning process, the lint is contaminated with about 140 to 1990 ppm of chromium, and the spun yarns and cotton by-products contain about 100 to 200 ppm, far in excess of the standard limit of 0.1 ppm. Gin and mill workers are directly exposed to this carcinogenic substance. To offset this problem, pollution-free rubberized cotton fabric (RCF) rollers have been fabricated and tested in roller gins. The RCF roller covering is made of multiple layers of fabric bonded together using a white rubber compound, which has a surface finish conducive to high ginning efficiency. This eliminates chromium contamination and pollution during the ginning process. On the basis of the design and development of various test rollers and subsequent evaluation studies, the performance of pollution-free RCF rollers has been demonstrated with reference to their commercial benefit and eco-friendliness in cotton ginning mills.

  15. Integrative Functional Genomics Analysis of Sustained Polyploidy Phenotypes in Breast Cancer Cells Identifies an Oncogenic Profile for GINS2

    Directory of Open Access Journals (Sweden)

    Juha K. Rantala

    2010-11-01

    Full Text Available Aneuploidy is among the most obvious differences between normal and cancer cells. However, mechanisms contributing to development and maintenance of aneuploid cell growth are diverse and incompletely understood. Functional genomics analyses have shown that aneuploidy in cancer cells is correlated with diffuse gene expression signatures and aneuploidy can arise by a variety of mechanisms, including cytokinesis failures, DNA endoreplication, and possibly through polyploid intermediate states. To identify molecular processes contributing to development of aneuploidy, we used a cell spot microarray technique to identify genes inducing polyploidy and/or allowing maintenance of polyploid cell growth in breast cancer cells. Of 5760 human genes screened, 177 were found to induce severe DNA content alterations on prolonged transient silencing. Association with response to DNA damage stimulus and DNA repair was found to be the most enriched cellular processes among the candidate genes. Functional validation analysis of these genes highlighted GINS2 as the highest ranking candidate inducing polyploidy, accumulation of endogenous DNA damage, and impairing cell proliferation on inhibition. The cell growth inhibition and induction of polyploidy by suppression of GINS2 was verified in a panel of breast cancer cell lines. Bioinformatic analysis of published gene expression and DNA copy number studies of clinical breast tumors suggested GINS2 to be associated with the aggressive characteristics of a subgroup of breast cancers in vivo. In addition, nuclear GINS2 protein levels distinguished actively proliferating cancer cells suggesting potential use of GINS2 staining as a biomarker of cell proliferation as well as a potential therapeutic target.

  16. 29 CFR 780.807 - Cotton must be ginned “for market.”

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Cotton must be ginned âfor market.â 780.807 Section 780.807... for Market § 780.807 Cotton must be ginned “for market.” As noted in § 780.804, it is ginning of seed... only where the cotton is actually ginned “for market.” (Wirtz v. Southern Pickery, Inc. (W.D....

  17. Semana de ginástica: um olhar superador

    Directory of Open Access Journals (Sweden)

    2006-11-01

    Full Text Available Este texto relata a experiência vivenciada na disciplina Ginástica I, do curso de Educação Física, UFG/CAC, com o objetivo de problematizar o desenvolvimento histórico da ginástica em suas muitas variações na atualidade e verificar as possibilidades de sua utilização no espaço escolar a partir da construção coletiva, em uma perspectiva crítico-superadora. PALAVRAS-CHAVE: Ginástica - Educação Física Escolar A week of Gymnastics I was held in order to discuss the historical background of Gymnastics, its great number os varieties, and to check the possibilities of use of the space school as far as a critical perspective is concerned. KEY WORD: Gymnastics – Scholar Physical Education.

  18. Textile processing improvements due to high speed roller ginning of upland cotton

    Science.gov (United States)

    Selective breeding has improved upland cotton fiber properties. Processing capacities of new high-speed roller ginning technology approach that of saw ginning. Spinning mills are interested in mill performance data comparing new upland cultivars processed by both saw and roller ginning. Four dive...

  19. IMPACT OF MICRONUTRIENT FORTIFIED FOOD SUPPLEMENT ON NUTRITIONAL PROFILE AMONG GINNING WOMEN WORKERS

    Directory of Open Access Journals (Sweden)

    D.Sridevi

    2013-08-01

    Full Text Available Ginning factory discharges large amount of cotton dust, which might decrease haematological indices among the selected subjects. An attempt was made to study the haematological indices of women labourers located in the urban areas of Tirupur and Erode Districts of Tamil Nadu, India. Totally 150 non-pregnant, non-lactating adult women performing varied textile tasks and aged between 20 to 60 years were identified randomly from ginning (n=150 (gin house, gutter and sorting sections industries. Socio demographic, work pattern, nutritional and health status were assessed by administering a questionnaire. Further, to correct micronutrient deficiency, iron and folic acid fortified soy biscuits were formulated. Intervention study was conducted among the selected moderate anaemic ginners (n=20. l00 g of micronutrient fortified soy biscuit containing 13.5 g of protein, 8.4 mg of iron (ferrous fumarate and 120 µg of folic acid was supplemented to experimental group of women as a midmorning and midevening snack for a period of four months. Therapeutic efficacy of food supplement was studied by assessing their anthropometric and haematological conditions at pre and post supplementation period. Anthropometric indices showed an improvement in weight (48.7 ± 4.98 to 51.5 ± 6.25 and BMI (19.02 to 23.04. Haematological indices revealed that the mean haemoglobin of experimental group improved to 11.04 ± 0.56 g/dl from 9.1 ± 0.67. Similarly increase in serum iron from 61.9 ± 3.24 to 65.0 ± 2.95 µg/dl was noticed and showed a significant difference at 1 per cent. Improvement in total protein (6.62 ± 0.49 to 8.11 ± 0.20 g/dl, albumin (3.9 ± 0.36 to 4.73 ± 0.31 g/dl and globulin (2.82 ± 0.24 to 3.8 ± 0.29 g/dl showed significant difference at 1 per cent level. Similarly, an increase in Total WBC count (7326 ± 19.5 to 9725 ± 25.5 cumm, reduction in lymphocyte (942.16 ± 3.6 to 35.2 ± 2.2 per cent seen among the ginning women workers.

  20. Seasonal Change of Steric Sea Level in the GIN Seas

    Institute of Scientific and Technical Information of China (English)

    LI Lei; WANG Huijuan; SUN Ruili

    2011-01-01

    The Greenland Sea, Iceland Sea, and Norwegian Sea (GIN seas) form the main channel connecting the Arctic Ocean with other Oceans, where significant water and energy exchange take place, and play an important role in global climate change. In this study steric sea level, associated with temperature and salinity, in the GIN seas is examined based on analysis of the monthly temperature and salinity fields from Polar science center Hydrographic Climatology (PHC3.0). A method proposed by Tabata et al. is used to calculate steric sea level, in which, steric sea level change due to thermal expansion and haline contraction is termed as the thermosteric component (TC) and the halosteric component (SC), recpectively. Total steric sea level (TSSL) change is the sum of TC and SC. The study shows that SC is making more contributions than TC to the seasonal change of TSSL in the Greenland Sea, whereas TC contributes more in the Norwegian and the Iceland Seas. Annual variation of TSSL is larger than 50ram over most regions of the GIN Seas, and can be larger than 200mm at some locations such as 308mm at 76.5°N, 12.5°E and 246mm at 77.50N, 17.5°W.

  1. Steam Explosion Pretreatment of Cotton Gin Waste for Fuel Ethanol Production

    OpenAIRE

    Jeoh, Tina

    1998-01-01

    Steam Explosion Pretreatment of Cotton Gin Waste for Ethanol Production By Tina Jeoh Foster A. Agblevor, Chair Biological Systems Engineering ABSTRACT The current research investigates the utilization of cotton gin waste as a feedstock to produce a value-added product - fuel ethanol. Cotton gin waste consists of pieces of burs, stems, motes (immature seeds) and cotton fiber, and is considered to be a lignocellulosic material. The three main chemical constituents are ce...

  2. Evaluation of an experimental mass-flow sensor of cotton-lint at the gin

    Science.gov (United States)

    As part of a system to optimize the cotton ginning process, a custom built mass-flow sensor was evaluated at USDA-ARS Cotton Ginning Research Unit at Stoneville, Mississippi. The mass-flow sensor was fabricated based on the principle of the senor patented by Thomasson and Sui (2004). The optical a...

  3. Cyclone robber system total particulate emission factors and rates for cotton gins

    Science.gov (United States)

    This manuscript is part of a series of manuscripts that characterize cotton gin emissions from the standpoint of stack sampling. The impetus behind this project was the urgent need to collect additional cotton gin emissions data to address current regulatory issues. A key component of this study was...

  4. Cyclone robber system PM10 emission factors and rates for cotton gins

    Science.gov (United States)

    This manuscript is part of a series of manuscripts that characterize cotton gin emissions from the standpoint of stack sampling. The impetus behind this project was the urgent need to collect additional cotton gin emissions data to address current regulatory issues. A key component of this study was...

  5. Mote cyclone robber system PM10 emission factors and rates for cotton gins

    Science.gov (United States)

    This manuscript is part of a series of manuscripts that characterize cotton gin emissions from the standpoint of stack sampling. The impetus behind this project was the urgent need to collect additional cotton gin emissions data to address current regulatory issues. A key component of this study was...

  6. Cyclone robber system total particulate emission factors and rates for cotton gins: Method 17

    Science.gov (United States)

    This manuscript is part of a series of manuscripts that characterize cotton gin emissions from the standpoint of stack sampling. The impetus behind this project was the urgent need to collect additional cotton gin emissions data to address current regulatory issues. A key component of this study was...

  7. Mote cyclone robber system total particulate emission factors and rates for cotton gins

    Science.gov (United States)

    This manuscript is part of a series of manuscripts that characterize cotton gin emissions from the standpoint of stack sampling. The impetus behind this project was the urgent need to collect additional cotton gin emissions data to address current regulatory issues. A key component of this study was...

  8. Mote cyclone robber system total particulate emission factors and rate for cotton gins: Method 17

    Science.gov (United States)

    This manuscript is part of a series of manuscripts that characterize cotton gin emissions from the standpoint of stack sampling. The impetus behind this project was the urgent need to collect additional cotton gin emissions data to address current regulatory issues. A key component of this study was...

  9. Physical processing and emission characteristics of cotton ginning byproducts based firelogs

    Science.gov (United States)

    A study was conducted to evaluate the suitability of cotton ginning byproducts for manufacturing firelogs. Cotton burr with stem (CBS) a byproduct from cotton ginning operation was mixed with petroleum based paraffin wax to manufacture firelogs. The impact of varying the formulation of firelogs, an...

  10. Ginástica alemã e ginástica feminina moderna: práticas destinadas às mulheres

    Directory of Open Access Journals (Sweden)

    Tuany Defaveri Begossi

    2015-10-01

    Full Text Available O estudo tem por objetivo investigar a emergência da Ginástica Feminina Moderna no contexto porto-alegrense, durante o século XX. Por meio da análise de fontes impressas, percebemos que o incentivo à realização de práticas corporais pelas mulheres teve estreita relação com a difusão da ginástica alemã pelos teuto-brasileiros no Rio Grande do Sul. Em decorrência da distinção entre as práticas aconselhadas para cada sexo, a ginástica era indicada às mulheres. Neste sentido, a partir de prescrição de novos padrões estéticos, a Ginástica Feminina Moderna emergiu enquanto um movimento renovador, visando ampliar a expressão de graciosidade da mulher.

  11. Calculation of pesticide degradation in decaying cotton gin trash.

    Science.gov (United States)

    Crossan, Angus N; Kennedy, Ivan R

    2008-10-01

    Pesticide residues were measured in stockpiled cotton gin trash (CGT) over a 2-year period. Samples were analysed by GC/MS/MS and interpretation of the results was aided by the presence of DDE residues, remnant from prior DDT use. Fourteen pesticide residues from current agricultural practice were detected in CGT. Several of these, including indoxacarb, profenofos, chlorpyrifos, propargite, bifenthrin, ethion and cyhalothrin, were more persistent than expected on the basis of published data for soil dissipation. The results showed a complex pattern of pesticide residue decay over time because of the simultaneous decomposition of the CGT matrix.

  12. Da ‘Ginástica para a juventude’ a ‘A ginástica alemã’: observações acerca dos primeiros manuais alemães de ginástica

    Directory of Open Access Journals (Sweden)

    Evelise Amgarten Quitzau

    2015-06-01

    Full Text Available A passagem do século XVIII para o XIX se apresenta como um momento importante na constituição do que hoje conhecemos como educação física, pois é nesse período que as primeiras sistematizações dos exercícios físicos começam a ser formuladas e publicadas em diferentes manuais de ginástica. Na Alemanha, dois manuais tiveram grande destaque nesse momento de consolidação dos sistemas de exercícios físicos: Ginástica para a juventude, publicado em 1793 por J.C.F. Guts Muths, e A ginástica alemã, publicado em 1816 por F.L. Jahn. Este artigo tem como objetivo estabelecer uma aproximação entre esses dois manuais e apresentar os argumentos usados pelos autores para justificar a importância da ginástica, bem como similaridades existentes entre as duas propostas.

  13. Preliminary evaluation of feeder and lint slide moisture addition on ginning, fiber quality, and textile processing of western cotton

    Science.gov (United States)

    The objective of this study was to evaluate the effects of moisture addition at the gin stand feeder conditioning hopper and/or the battery condenser slide on gin performance and Western cotton fiber quality and textile processing. The test treatments included no moisture addition, feeder hopper hum...

  14. [New aspects of efficacy of using apparatus-programming complex "andro-gin" in the treatment of chronic prostatitis].

    Science.gov (United States)

    Pereverzev, A S; Chepenko, A V

    2006-01-01

    The results of usage of Andro-Gin unit in 187 patients with chronic prostatitis have shown that in most cases prostatitis is caused by bacteria. Andro-gin unit included in combined treatment of chronic prostatitis provides good results as it turns biofil bacteria into planktonic ones.

  15. Mote cyclone robber system PM10 emission factors and rates for cotton gins: Method 201A PM10 sizing cyclones

    Science.gov (United States)

    This manuscript is part of a series of manuscripts that characterize cotton gin emissions from the standpoint of stack sampling. The impetus behind this project was the urgent need to collect additional cotton gin emissions data to address current regulatory issues. A key component of this study was...

  16. Second stage mote system PM10 emission factors and rates for cotton gins: Method 201A PM10 sizing cyclone

    Science.gov (United States)

    This manuscript is part of a series of manuscripts that characterize cotton gin emissions from the standpoint of stack sampling. The impetus behind this project was the urgent need to collect additional cotton gin emissions data to address current regulatory issues. A key component of this study was...

  17. Cyclone robber system PM10 emission factors and rates for cotton gins: Method 201A PM10 sizing cyclones

    Science.gov (United States)

    This manuscript is part of a series of manuscripts that characterize cotton gin emissions from the standpoint of stack sampling. The impetus behind this project was the urgent need to collect additional cotton gin emissions data to address current regulatory issues. A key component of this study was...

  18. [Comparative assessment of conservative treatment of chronic prostatitis with application of complex unit andro-gin].

    Science.gov (United States)

    Golubchikova, V A; Alekseev, M Ia; Sitnikov, N V; Kochetov, A G; Podgornyĭ, V F

    2000-01-01

    The Andro-Gin unit used in combined treatment of 78 patients with chronic prostatitis (CP) and 16 women with chronic interstitial cystitis with inflammation in the internal genitalia (56.5% of the patients had sexual and spermatogenesis disorders) employed effects of simultaneous exposure to local magnetic field, electrostimulation of the small pelvis organs and prostate with introduction of contact rectal electrode, neurostimulation of pathogenic zones, low-intensity laser and light-diode radiator and color impulse therapy. Control group consisted of 85 patients with CP who received conventional physiotherapy. The comparative analysis has shown high efficiency of the unit Andro-Gin in the treatment of CP and its complications. Laboratory and clinical convalescence and persistent remission was registered in 98% of the patients of the study group. Combined treatment using Andro-Gin is twice more effective than other treatments.

  19. Detection of plastic and oily contamination in seed cotton at the gin using infra-red

    Science.gov (United States)

    Plastic and oily foreign material in bales of cotton lint poses problems to spinning and textile mills in the form of decreased productivity and products with inferior quality. Detecting and removing this plastic and oily foreign material at the gin is a long term goal of the cotton industry. In t...

  20. Impact of gin saw tooth design on fiber and textile processing quality

    Science.gov (United States)

    Toothed gin saws have been used to separate cotton fiber from the seed for over 200 years. There have been many saw tooth designs developed over the years. Most of these designs were developed by trial and error. A complete and scientific analysis of tooth design has never been done. It is not k...

  1. Cyclone robber system PM2.5 emission factors and rates for cotton gins

    Science.gov (United States)

    This manuscript is part of a series of manuscripts that detail a project to characterize cotton gin emissions from the standpoint of stack and ambient sampling. The impetus behind the project was the 2006 EPA implementation of a more stringent standard for particulate matter less than or equal to 2....

  2. Mote cyclone robber system particulate emission factors for cotton gins: Particle size distribution characteristics

    Science.gov (United States)

    This report is part of a project to characterize cotton gin emissions from the standpoint of total particulate stack sampling and particle size analyses. In 2013, the U.S. Environmental Protection Agency (EPA) published a more stringent standard for particulate matter with nominal diameter less than...

  3. Cyclone robber system particulate emission factors for cotton gins: Particle size distribution characteristics

    Science.gov (United States)

    This report is part of a project to characterize cotton gin emissions from the standpoint of total particulate stack sampling and particle size analyses. In 2013, U.S. Environmental Protection Agency (EPA) published a more stringent standard for particulate matter with nominal diameter less than or ...

  4. Geosciences Information Network (GIN): A modular, distributed, interoperable data network for the geosciences

    Science.gov (United States)

    Allison, M.; Gundersen, L. C.; Richard, S. M.; Dickinson, T. L.

    2008-12-01

    A coalition of the state geological surveys (AASG), the U.S. Geological Survey (USGS), and partners will receive NSF funding over 3 years under the INTEROP solicitation to start building the Geoscience Information Network (www.geoinformatics.info/gin) a distributed, interoperable data network. The GIN project will develop standardized services to link existing and in-progress components using a few standards and protocols, and work with data providers to implement these services. The key components of this network are 1) catalog system(s) for data discovery; 2) service definitions for interfaces for searching catalogs and accessing resources; 3) shared interchange formats to encode information for transmission (e.g. various XML markup languages); 4) data providers that publish information using standardized services defined by the network; and 5) client applications adapted to use information resources provided by the network. The GIN will integrate and use catalog resources that currently exist or are in development. We are working with the USGS National Geologic Map Database's existing map catalog, with the USGS National Geological and Geophysical Data Preservation Program, which is developing a metadata catalog (National Digital Catalog) for geoscience information resource discovery, and with the GEON catalog. Existing interchange formats will be used, such as GeoSciML, ChemML, and Open Geospatial Consortium sensor, observation and measurement MLs. Client application development will be fostered by collaboration with industry and academic partners. The GIN project will focus on the remaining aspects of the system -- service definitions and assistance to data providers to implement the services and bring content online - and on system integration of the modules. Initial formal collaborators include the OneGeology-Europe consortium of 27 nations that is building a comparable network under the EU INSPIRE initiative, GEON, Earthchem, and GIS software company ESRI

  5. A study of respiratory function among the workers engaged in ginning processes

    Directory of Open Access Journals (Sweden)

    Asim Saha

    2014-01-01

    Full Text Available Background: Known respiratory health effects of exposure to cotton dust are mainly altered pulmonary function findings and symptom of chest tightness. A number of studies have been carried out all over the world to enumerate and evaluate the health effects of cotton dust exposed workers in different processes. However, such studies carried out in ginning industry especially in Indian context are scanty. Objectives: This study was initiated to explore occupational and morbidity details and respiratory functional status of the exposed workers as well as to investigate across the working shift pulmonary function changes. Materials and Methods: A cross-sectional study was conducted including workers from ginning units where principal exposure is from cotton dust. All the workers of the selected ginning units were subjected to an interview with a predesigned questionnaire to collect occupational and medical history, clinical examination and pulmonary function test. Results: In this present study, no cross-shift significant change in relation to PEFR and FEV 1 values is observed. However, chronic effect on lung function is observed in a few subjects and declining trend of values was observed with increasing job duration as well as age of workers and among smokers. Other health problems among these subjects were backache and joint pain. Conclusions: Studies on cotton textile workers have shown both cross-shift and chronic decline of values. In this study on ginning workers, chronic effect only is observed. This difference of observation may be explained by different nature of exposure in case of ginning. This study recommends regular periodic clinical examination, lung function test and monitoring of dust, gram-negative bacteria and endotoxins in such workplaces.

  6. [Advantages of the use of Andro-Gin device for treatment of secretory infertility].

    Science.gov (United States)

    Aleksandrov, V P; Koren'kov, D G; Nikolaeva, E V

    2006-01-01

    The trial included 144 patients aged from 24 to 46 years with secretory infertility in the presence of chronic prostatitis of 2 to 13 year duration. The study group consisted of 96 patients who received conventional treatment in combination with physical factors provided by the unit APK-ELM-01 Andro-Gin. The control group consisted of 48 patients on conventional treatment alone. The results were processed mathematically and statistically. The patients were examined before, 2 weeks, 1 and 6 months after the treatment. Positive response was greater in the study group: better parameters of prostatic secretion, spermogram. Normalization of all the parameters occurred in 95 and 80% patients of the study and control groups, respectively. Thus, Andro-Gin is effective for treatment of chronic prostatitis with secretory infertility.

  7. An investigation of RSN frequency spectra using ultra-fast generalized inverse imaging (GIN

    Directory of Open Access Journals (Sweden)

    Rasim eBoyacioglu

    2013-04-01

    Full Text Available With the advancements in MRI hardware, pulse sequences and reconstruction techniques, many low TR sequences are becoming more and more popular within the fMRI community. In this study, we have investigated the spectral characteristics of resting state networks (RSNs with a newly introduced ultra fast fMRI technique, called Generalized Inverse Imaging (GIN. The high temporal resolution of GIN (TR=50 ms enables to sample cardiac signals without aliasing into a separate frequency band from the BOLD fluctuations. Respiration related signal changes are, on the other hand, removed from the data without the need for external physiological recordings. We have observed that the variance over the subjects is higher than the variance over RSNs.

  8. Geosciences Information Network (GIN): A Distributed, Interoperable Data Network for the Geosciences

    Science.gov (United States)

    Allison, L.; Gundersen, L. C.; Richard, S. M.; Dickinson, T. L.

    2008-12-01

    A coalition of the state geological surveys (AASG), the U.S. Geological Survey (USGS), and other partners will receive NSF funding over the next 3 years under the INTEROP solicitation to start building a distributed, interoperable data network that will make thousands of data bases from the geological surveys and their partners available, searchable, and interoperable. This Geosciences Information Network (GIN) will focus on both spatial and analytical geologic data collected across the country for the past 150 years. Key components of the proposed network include: 1) catalog systems for data discovery; 2) service definitions that define interfaces for searching catalogs and accessing resources; 3) shared interchange formats to encode information for transmission; 4) data providers that publish information using standardized services defined by the network; and 5) client applications enabled to utilize information resources provided by the network. The GIN will integrate and utilize catalog resources that currently exist or are in development. We are working closely with the USGS National Geologic Map Database and its existing map catalog; with the USGS National Geological and Geophysical Data Preservation project, which is developing a metadata catalog for geoscience information resource discovery; and with the GEON catalog. Existing and emerging extensible mark-up languages such as GeoSciML, ChemML, and Open Geospatial Consortium sensor, observation and measurement MLs will provide the necessary interchange formats. Client application development will be fostered by collaboration with industry partners such as ESRI who's Geology Data Model for ArcGIS software is being designed to be compatible with GIN. The GIN project will focus on development of the remaining aspects of the system including: service definitions, technical assistance to data providers to implement the services and bring content online, and system integration. The Geosciences Information Network

  9. Bulímicas: elas vão à academia de ginástica?

    Directory of Open Access Journals (Sweden)

    Andréia Weis

    2013-09-01

    Full Text Available O objetivo da pesquisa foi determinar a prevalência de mulheres com sintomas de bulimia nervosa frequentadoras de academia de ginástica e verificar, dentre as praticantes que apresentam traços bulímicos, qual a frequência de utilização do exercício físico como forma compensatória. Participaram do estudo 197 mulheres matriculadas em academias de ginástica da cidade de Marechal Cândido Rondon - PR (28,7±9,9 anos. Para avaliar o quadro de bulimia utilizou-se o Teste de Investigação Bulímica de Edingurgh (BITE e uma anamnese estruturada pelos pesquisadores para atender interesses do estudo. Na análise dos dados foi utilizada a estatística descritiva e a frequência amostral pelo programa estatístico SPSS for Windows 11.5. A prevalência de sintomas de bulimia foi de 3%. A prevalência de traços bulímicos foi de 11,2%. Dos indivíduos que apresentaram traços bulímicos, 59,1% afirmaram praticar exercício físico após episódios de alimentação exagerada. Estes resultados podem indicar que esse comportamento compensatório através da prática de exercício físico pode levar as mulheres a procurar as academias de ginástica.

  10. TechnoGIN3: a generic tool for analysing cropping systems : Application of prototype for West-African conditions within the VINVAL project

    NARCIS (Netherlands)

    Wolf, J.; Ponsioen, T.C.; Hengsdijk, H.

    2004-01-01

    TechnoGIN-3 has been developed for quantifying inputs and outputs of main current and future-oriented production activities (i.e. cropping systems) in regions in the Philippines, P.R. China and Vietnam. TechnoGIN stands for Technical coefficient generator for Ilocos Norte province, Philippines, as i

  11. Biological control agent of larger black flour beetles (Coleoptera: Tenebrionidae): a nuisance pest developing in cotton gin trash piles.

    Science.gov (United States)

    Nansen, Christian; Stokes, Bryan; James, Jacob; Porter, Patrick; Shields, Eilson J; Wheeler, Terry; Meikle, William G

    2013-04-01

    The larger black flour beetles, Cynaeus angustus (LeConte) (Coleoptera: Tenebrionidae), feeds on saprophytic fungi found in gin trash piles and occasionally becomes a nuisance pest in adjacent homes and businesses. The potential of Steinernema carpocapsae 'NY 001,' as a potential control agent of larger black flour beetle under experimental conditions was examined with particular reference to the importance of soil moisture content. Without prospects of insecticides being labeled for control of larger black flour beetle in gin trash, the data presented here support further research into applications of entomopathogenic nematodes underneath gin trash piles as a way to minimize risk of larger black flour beetle populations causing nuisance to nearby homes and businesses.

  12. Ginés Pérez y su O Crux

    Directory of Open Access Journals (Sweden)

    Climent, José

    2002-12-01

    Full Text Available The exact names attributed to Ginés Pérez were never at all clear. His first appointment to the Cathedral in Valencia complicated matters even more when he was referred to with the Christian name of what appeared to be "Juan", which only added to the confusion as it lead us to believe that he was the only candidate to apply for that position. Today, however, we now know his true and full names: he was called Ginés Pérez de la Parra. We also know, for the first time, the exact date of his death. The quality of his compositions not only contributed to their popularity but gave rise to the works of other composers being attributed to him. The authorship of the majority of his compositions are considered anonymous, though they can be located in diverse archives. Even so, we cannot find a single copy of the O Crux attributed to his name, despite the numerous copies and their variants that abound in Region of Valencia.El nombre de Ginés Pérez nunca ha tenido la claridad de debía. Su primer nombramiento en la catedral de Valencia ya lo confunde añadiéndole el “Juan” lo que ya siembra confusión, además de sugerirnos que, posiblemente, fue llamado para ocupar el puesto sin oposición. Hoy conocemos toda su filiación: Ginés Pérez de la Parra, así como la fecha de su muerte, totalmente equivocada hasta ahora. La valía de sus composiciones motivó, además de la difusión de su obra, la atribución de composiciones de otros autores. La mayor parte de sus composiciones constan como "anónimos", si bien pueden encontrarse en distintos archivos. Del presente O crux, sin embargo, no hemos podido encontrar ninguna copia con su nombre, pese a las múltiples copias, con sus variantes, existentes en la Comunidad Valenciana.

  13. Múltiplos itinerários de um lente e diretor do Ginásio Paranaense

    Directory of Open Access Journals (Sweden)

    Serlei Maria Fischer Ranzi

    2012-07-01

    Full Text Available  A partir de uma documentação pertencente ao acervo pessoal do lente e diretor do Ginásio Paranaense entre os anos de 1920 e 1928, Lysímaco Ferreira da Costa, buscamos analisar enunciados escritos que expressam manifestações do diálogo entre o diretor, professores, familiares e alunos, examinando a tensão entre a gestão da escola e o controle externo sobre os procedimentos que nela se desenvolviam. Passando por vários cargos públicos, trazendo suas experiências para a rede escolar, o Diretor defendeu mudanças que geraram controvérsias como, por exemplo, a adoção da disciplina escolar, a vigilância, e o cumprimento de regras do regimento escolar como princípios de gestão. Foi nomeado o homem de sete instrumentos, termo vinculado à imagem construída que procura referenciar uma multiplicidade de cargos assumidos simultaneamente, na sua performance de homem público.Palavras-chave: ensino secundário, ginásio paranaense, gestão escolar.   Abstract Starting by personal documents of the teacher and principal of Ginásio Paranaense, between 1920 and 1928, Lysimaco Ferreira da Costa, we intend to make an analysis of the written talks that express dialogical manifestations among the principal, the teachers, the parents and the pupils, examining the tension between the school management and the external control of the procedures that happened in there. Going through many public posts, bringing experiences to the school system, the principal defended changes that generated controversies as, for example, the adoption of the school discipline, the vigilance, and the attainment of the rules of the school regiment as management principles. He was nominated the man of seven instruments, term all ached to the built image that aims to refer the multiple posts assumed simultaneously, in his performance of public man. Keywords: secundary teachings, ginásio paranaense, school management. 

  14. Eli Whitney's Patent for the Cotton Gin. The Constitution Community: Revolution and the New Nation (1754-1820s).

    Science.gov (United States)

    Schur, Joan Brodsky

    This lesson focuses on the power of the U.S. Congress to pass laws related to issuing patents. Using Eli Whitney's 1812 Congressional petition to extend the patent on his cotton gin as an example, the lesson correlates to the National History Standards and the National Standards for Civics and Government. It contains two primary source documents,…

  15. Continued work to develop a low-cost sensor to detect plastic contamination in seed cotton at the gin

    Science.gov (United States)

    Contamination of cotton from plastic trash that collects in cotton fields or introduced at the gin or due to mishandling at the warehouse is one of the most significant threats to US cotton world market share. For U.S. cotton to maintain its status as “contamination-free”, the industry must strive t...

  16. Biological control agent of larger black flour beetles (Coleoptera: Tenebrionidae): A nuisance pest developing in cotton gin trash piles.

    Science.gov (United States)

    Larger black flour beetles (LBFB), Cynaeus angustus, feed on saprophytic fungi found in gin trash piles, and become nuisance pests in homes and businesses. We examined the dose-response of three entomopathogenic nematode species (Steinernema carpocapsae, S. feltiae, and Heterorhabditis bacteriophora...

  17. Mini-Review: The Role of Saccharomyces cerevisiae in the Production of Gin and Vodka

    Directory of Open Access Journals (Sweden)

    Matthew Pauley

    2017-02-01

    Full Text Available The spirit beverages of vodka and gin are often produced from a neutral spirits base. These neutral spirits are derived from the distillation of fermented carbohydrates of agricultural origin. The fermentations in the production of these beverages are not often reported in great detail and to some extent are shrouded in mystery. The roles of fermentation and the yeast Saccharomyces cerevisiae are essential to the complete process, and without fermentation there would not be alcohol to distil. Nevertheless, it is not the yeast that is perceived to contribute to the distinctive consumer experiences, which are associated with these beverages. However, there are opportunities for the development of new strains of S. cerevisiae for the production of neutral spirits, which have a high ethanol yield, are tolerant of ethanol stress, and produce low levels of congeners.

  18. Corpo e cultura fitness: estudo etnográfico de um ginásio em Portugal

    OpenAIRE

    Cruz, Leonardo Duarte Magalhães

    2015-01-01

    Mestrado em Antropologia Num contexto ocidental crescentemente sedentário, a responsabilidade de manutenção da condição física passa a caber a cada indivíduo. A proliferação da cultura fitness tem aqui origem, tratando-se de um fenómeno global com um impacto sentido no contexto português. Este é um estudo etnográfico sobre um ginásio em Portugal, com a sua particular dimensão idiossincrática, mas cuja realidade geral é idêntica ao panorama comum dos ginásios em sociedades ocidentais. Aq...

  19. "O trabalho na forma de alegria juvenil": a ginástica segundo Johann Christoph Friedrich Guts Muths

    Directory of Open Access Journals (Sweden)

    Evelise Amgarten Quitzau

    2012-06-01

    Full Text Available Este trabalho tem como objetivo estabelecer uma aproximação com a obra de Johann Christoph Friedrich Guts Muths, pedagogo alemão que, no final do século XVIII, publicou uma das obras fundamentadoras da ginástica alemã: Gymnastik für die Jugend (Ginástica para a Juventude. Seu trabalho baseia-se principalmente nas teorias da denominada polícia médica, e apresenta um forte discurso em defesa da instituição dos exercícios físicos como instrumento de regeneração e fortalecimento da população alemã.

  20. Ginástica laboral e prevenção de dores crônicas

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    Jorge William Pedroso Silveira

    2014-07-01

    Full Text Available Objetivo: analisar a influência da ginástica laboral em trabalhadoras de um laboratório farmacêutico do município de Irati – PR em relação à percepção de dor das mesmas. Método: para tal, realizou-se um estudo de caso com 05 mulheres trabalhadoras de um laboratório de manipulação, avaliando previamente suas sensações de dor, através dos tender points; em seguida, foram realizadas, durante 03 meses, intervenções baseadas em 05 sessões semanais de ginástica de aquecimento (10-15min diários, 05 de ginástica de pausa (10-15min diários, ambas no ambiente de trabalho, bem como 03 sessões semanais de ginástica compensatória (30-60min por sessão, seguida de uma avaliação pós-intervenção. Resultados: as pacientes detinham muitas dores derivadas de sua prática e principalmente na musculatura antagonista, chegando a estar próximas ou até mesmo do estágio de fibromialgia. Contudo, após a intervenção, nenhum dos tender points foi considerado sensível, restando apenas às dores derivadas da prática mais extenuante, os punhos. Considerações finais: a atividade física dentro da empresa torna-se um forte auxiliar na manutenção da qualidade do trabalho devido à preocupação com a saúde do trabalhador.

  1. BIL&GIN: A neuroimaging, cognitive, behavioral, and genetic database for the study of human brain lateralization.

    Science.gov (United States)

    Mazoyer, B; Mellet, E; Perchey, G; Zago, L; Crivello, F; Jobard, G; Delcroix, N; Vigneau, M; Leroux, G; Petit, L; Joliot, M; Tzourio-Mazoyer, N

    2016-01-01

    We report on a database, named BIL&GIN, designed for investigating the cognitive, behavioral, genetic, and brain morphological/functional correlates of hemispheric specialization. The database contains records from a sample of 453 adult participants enriched in left-handers (45%, N=205) as compared to the general population. For each subject, socio-demographic data, hand and eye laterality, family handedness, and cognitive abilities in the language, motor, visuo-spatial, and numerical domains have been recorded. T1-MRI and DTI data were also acquired, as well as resting-state functional MRI. Task-evoked functional MRI was performed in a sub-sample of 303 subjects (157 left-handers) using a customized functional battery of 16 cognitive tasks exploring the same three cognitive domains. Performances at the tasks executed in the magnet as well as post-acquisition debriefing were recorded. A saliva sample was obtained from the subjects of this sub-sample from which DNA was extracted. The BIL&GIN contains results of imaging data processing for each subject, namely maps of tissue (GM, WM, CSF) probability, cortical thickness, cortical surface, and diffusion parameters as well as regional values of these phenotypes for regions of both AAL and FreeSurfer parcellations. For the subjects who underwent FMRI, individual SPM contrast maps for each of the 8 runs were also calculated and included in the database, as well as corresponding BOLD variations in ROIs of the AAL and AICHA atlases, and Wilke's hemispheric functional lateralization index. The BIL&GIN data sharing is based on a collaborative model.

  2. Georges Demeny e Fernando de Azevedo: uma ginástica científica e sem excessos (Brasil, França, 1900-1930

    Directory of Open Access Journals (Sweden)

    Edivaldo Góis Junior

    2015-06-01

    Full Text Available Este trabalho teve como objetivo comparar textos produzidos no Brasil e na França sobre os métodos da ginástica. Para isso, foi feita uma pesquisa histórica limitada às décadas de 1900 a 1930. As fontes analisadas foram os textos de Georges Demeny e Fernando de Azevedo. Concluiu que nas produções textuais dos dois escritores existia a defesa de uma ginástica científica por meio de uma prática controlada e moderada. Contudo, o debate com outras tradições produziu uma cultura de ginástica eclética nos dois países.

  3. Measuring whole plant CO2 exchange with the environment reveals opposing effects of the gin2-1 mutation in shoots and roots of Arabidopsis thaliana.

    Science.gov (United States)

    Brauner, Katrin; Stutz, Simon; Paul, Martin; Heyer, Arnd G

    2015-01-01

    Using a cuvette for simultaneous measurement of net photosynthesis in above ground plant organs and root respiration we investigated the effect of reduced leaf glucokinase activity on plant carbon balance. The gin2-1 mutant of Arabidopsis thaliana is characterized by a 50% reduction of glucokinase activity in the shoot, while activity in roots is about fivefold higher and similar to wild type plants. High levels of sucrose accumulating in leaves during the light period correlated with elevated root respiration in gin2-1. Despite substantial respiratory losses in roots, growth retardation was moderate, probably because photosynthetic carbon fixation was simultaneously elevated in gin2-1. Our data indicate that futile cycling of sucrose in shoots exerts a reduction on net CO2 gain, but this is over-compensated by the prevention of exaggerated root respiration resulting from high sucrose concentration in leaf tissue.

  4. [Comparative analysis of long-term results of treating chronic prostatis with the use of the Andro-Gin device].

    Science.gov (United States)

    Alekseev, M Ia; Golubchikov, V A

    2002-01-01

    Follow-up examinations covered 91 patients aged from 20 to 60 years with chronic prostatitis (CP) history 1-18 years. The primary examination has found that 79.1% examinees has CP complicated with sexual dysfunction, disturbed spermatogenesis and psychoneurological disorders. In one group of CP patients etiopathogenetic treatment of CP was combined with magneto-laser-electrostimulation of the prostate provided by the unit Andro-Gin. This combined treatment proved more effective as it induced long-term remission (two years and longer) in 60.5% patients. Unsatisfactory results were minimal. Without use of the unit unsatisfactory results were recorded in 35% patients.

  5. Imagens da prática profissional em academias de ginástica na cidade do Rio de Janeiro

    Directory of Open Access Journals (Sweden)

    Carlos Alberto de Andrade Coelho Filho

    2010-05-01

    Full Text Available O objetivo deste estudo é fornecer subsídios aos cursos de educação física, aproximando a formação profissional do campo de atuação em academias de ginástica. Através da análise de discurso, descrevemos e interpretamos a maneira como o profissional apresenta a si mesmo e a sua prática às outras pessoas, os meios pelos quais dirige e regula a impressão que formam a seu respeito e as atividades que pode ou não realizar. Os resultados confirmam que a prática do profissional de ginástica em academia vive momentos de tensão e impasse, o que implica a urgência de reformular a formação para essa prática nos cursos de graduação e de pós-graduação em educação física

  6. ntegrated control of gastrointestinal nematodes (GIN) using sericea lespedeza (SL), FAMACHA, and copper oxide wire particles (COWP) in weaned goats in Arkansas

    Science.gov (United States)

    Lack of effective anthelmintics for control of GIN in goats has led to the need for an integrated management approach. FAMACHA is an effective tool for selective deworming of Haemonchus contortus-infected goats, while COWP and SL grazing have reduced H. contortus infection. The objective was to exam...

  7. Integrated control of gastrointestinal nematodes (GIN) using sericea lespedeza (SL), FAMACHA, and copper oxide wire particles (COWP) in weaned lambs in Arkansas

    Science.gov (United States)

    Alternatives to chemical dewormers are needed to counter anthelmintic resistance and improve organic management systems. The objective was to examine the effectiveness of grazing SL and selective use of COWP based on FAMACHA for control of GIN. Katahdin lambs (145.6 ± 2.1 d of age; 30.1 ± 0.7 kg) w...

  8. Evolución constructiva de San Ginés de la Jara y propuesta arquitectónica de recuperación.

    OpenAIRE

    Sánchez Medrano, Francisco José

    2012-01-01

    El artículo analiza las etapas constructivas del monasterio de San Ginés de la Jara (Cartagena, Murcia) desde su fundación en el siglo XIII hasta la actualidad. Asimismo, presenta una propuesta de restauración arquitectónica y las actuaciones parciales que se han realizado entre 2004 y 2012.

  9. El problema de la Nosografía en la obra psiquiátrica de J. Giné y Partagás

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    Diéguez Gómez, Antonio

    1998-06-01

    Full Text Available The most relevant characteristics of the Giné y Partagás's nosographic thinking are analyzed, and some questions about the earlier topical considerations on his work are arised. Pressed by the clinic, Giné adopts a pragmatic attitude, giving a relative importance to his positivist militancy and offering an eclectic nosographic approach. Because the unitarist attachment of some of de most important authors inspiring his work, this doctrine would remain implicitly assumed in itself.

    Se analizan las características más relevantes del pensamiento nosográfíco de Giné y Partagás y se plantean algunos interrogantes acerca de anteriores consideraciones tópicas sobre su obra. Por imperativos de la clínica Giné adopta una actitud pragmática, relativizando su militancia positivista y presentando un planteamiento nosográfico ecléctico. Debido a la adscripción unitarista de algunos de los más importantes inspiradores de su obra, esta doctrina quedaría asumida implícitamente en la misma.

  10. Environmental impact studies of Chrome rollers used by cotton roller ginning industries and design and development of pollution free chromeless RCF rollers.

    Science.gov (United States)

    Singh, Gurdeep; Iyer, G Vijayan

    2004-01-01

    This study focuses on environmental chromium contamination and pollution caused by the use of Chrome Composite Leather-Clad (CCLC) rollers commonly used in cotton roller ginning industries and attempts to eliminate this problem by providing eco-friendly chrome-less rollers.

  11. Mote cyclone robber system PM2.5 emission factors and rates for cotton gins: Method 201A combination PM10 and PM2.5 sizing cyclones

    Science.gov (United States)

    This report is part of a project to characterize cotton gin emissions from the standpoint of stack sampling. In 2006, the Environmental Protection Agency (EPA) finalized and published a more stringent standard for particulate matter with nominal diameter less than or equal to 2.5 µm (PM2.5). This cr...

  12. Protein

    Science.gov (United States)

    ... Food Service Resources Additional Resources About FAQ Contact Protein Protein is found throughout the body—in muscle, ... the heart and respiratory system, and death. All Protein Isn’t Alike Protein is built from building ...

  13. Comparative study of microbial-derived phenolic metabolites in human feces after intake of gin, red wine, and dealcoholized red wine.

    Science.gov (United States)

    Jiménez-Girón, Ana; Queipo-Ortuño, María Isabel; Boto-Ordóñez, Maria; Muñoz-González, Irene; Sánchez-Patán, Fernando; Monagas, Maria; Martín-Álvarez, Pedro J; Murri, Mora; Tinahones, Francisco J; Andrés-Lacueva, Cristina; Bartolomé, Begoña; Moreno-Arribas, M Victoria

    2013-04-24

    The analysis of microbial phenolic metabolites in fecal samples from in vivo studies is crucial to understanding the potential modulatory effects derived from polyphenol consumption and its overall health effects, particularly at the gut level. In this study, the composition of microbial phenolic metabolites in human feces collected after regular consumption of either red wine, dealcoholized red wine, or gin was analyzed by UPLC-ESI-MS/MS. Red wine interventions produce a change in the content of eight phenolic acids, which are probably derived from the catabolism of flavan-3-ols and anthocyanins, the main flavonoids in red wine. Moreover, alcohol seemed not to influence the formation of phenolic metabolites by the gut microbiota. A principal component analysis revealed large interindividual differences in the formation of microbial metabolites after each red wine polyphenol intervention, but not after the gin intervention, indicating differences in the gut microbial composition among subjects.

  14. 京族民间文艺与自然生态%The Gin Folk Literatures & Arts and Nature & Ecology

    Institute of Scientific and Technical Information of China (English)

    陈丽琴

    2012-01-01

    京族民间文艺的生成、发展与自然生态环境之间有着密切关系。京族民间文艺作品体现了人们独特的生态意识,自然环境对京族民间口承文艺、民间舞蹈、服饰艺术以及民间工艺的产生与传承具有深刻的影响,造就了京族民间文艺的独特风格,没有京族地区独特的生态环境,其民间文艺也就失去所赖以产生的土壤。%The Gin folk literatures and arts linked closely with the natural and ecological environment in both its forming and the development.They reveals the unique ecologically awareness of the Gin people,and was deeply ingrained by the environment in the forming and passing down of the oral fork literatures,dances,dresses and handicrafts.Without the unique ecological environment,the Gin folk literatures and arts would lose its foundation.

  15. A propósito de Ling, da ginástica sueca e da circulação de impressos em língua portuguesa

    Directory of Open Access Journals (Sweden)

    Moreno Andrea

    2015-06-01

    Full Text Available Este artigo analisa o sistema sueco de ginástica criado por P. H. Ling e retoma a trajetória de seu precursor e a vocação do Instituto Central de Ginástica de Estocolmo no papel de preservação e divulgação dos preceitos lingianos. Especificamente, atentamo-nos para a vulgarização e a circulação do método por meio de manuais em língua portuguesa produzidos entre fins do século XIX e início do XX. Tem como fontes os manuais escolares escritos por Pedro Borges, Antonio M. Ferreira, Paulo Lauret e Arthur Higgins. Percebemos neles forte inspiração na ginástica sueca, revelada nas lições sistematizadas e na valorização de aspectos como retidão, racionalidade, simetria, correção, educação da vontade e aperfeiçoamento físico.

  16. A ginástica artística masculina (GAM de alto rendimento: observando a cultura de treinamento desde dentro.

    Directory of Open Access Journals (Sweden)

    Marco Antonio Coelho Bortoleto

    2007-03-01

    Full Text Available Este artigo apresenta um estudo etnográfico realizado no Ginásio de treinamento de Ginástica Artística Masculina do Centro de Alto Rendimento de Sant Cugat del Vallès (Barcelona - Espanha. O objetivo principal desta pesquisa consistiu em desvelar as características principais da cultura de treinamento de uma sala de alto rendimento a partir de uma incursão de campo (de um ano e meio de duração orientada pelos fundamentos teóricos da antropologia simbólica e dentro do marco metodológico da etnografia. Neste artigo destacamos o contexto institucional, alguns condicionantes temporais da preparação dos ginastas, aspectos da estrutura social do grupo, além de indicadores do universo simbólico que caracteriza a atividade no interior da sala. Entre as observações mais relevantes podemos destacar o Ginásio como uma microcultura caracterizada por várias cerimônias rituais, onde os técnicos têm o poder da palavra e os ginastas se limitam a escutar e intervir quando são solicitados (obedecer. Desta forma o funcionamento da sala se fundamenta no respeito à hierarquia de mandos e no cumprimento da programação das atividades e das regras.

  17. A baixa adesão ao programa de ginástica laboral: buscando elementos do trabalho para entender o problema

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    Raquel Guimarães Soares

    Full Text Available Este artigo discute a implantação da ginástica laboral em uma central de teleatendimento e evidencia os efeitos da organização do trabalho sobre a atividade laborativa de atendimento. Buscou-se reunir elementos para analisar a baixa adesão ao Programa de Ginástica Laboral que foi implantado pelo Comitê de Ergonomia da empresa após a solicitação dos teleatendentes. Os dados obtidos por meio de observação da atividade, entrevistas abertas e aplicação de questionário são aparentemente contraditórios, pois, apesar do reconhecimento da importância dos objetivos do programa pela maioria deles, o comparecimento às sessões de ginástica laboral (GL sempre foi baixo. Viu-se que a implantação da GL sem reorganização do trabalho pode provocar constrangimentos aos trabalhadores. Os autores discutem as interações entre espaço físico e espaços social e organizacional no ambiente de trabalho e, ao final, apresentam parâmetros para o planejamento e seguimento dos programas de GL.

  18. Modelling and Predicting the Breaking Strength and Mass Irregularity of Cotton Rotor-Spun Yarns Containing Cotton Fiber Recovered from Ginning Process by Using Artificial Neural Network Algorithm

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    Mohsen Shanbeh

    2011-01-01

    Full Text Available One of the main methods to reduce the production costs is waste recycling which is the most important challenge for the future. Cotton wastes collected from ginning process have desirable properties which could be used during spinning process. The purpose of this study was to develop predictive models of breaking strength and mass irregularity (CV% of cotton waste rotor-spun yarns containing cotton waste collected from ginning process by using the artificial neural network trained with backpropagation algorithm. Artificial neural network models have been developed based on rotor diameter, rotor speed, navel type, opener roller speed, ginning waste proportion and yarn linear density as input parameters. The parameters of artificial neural network model, namely, learning, and momentum rate, number of hidden layers and number of hidden processing elements (neurons were optimized to get the best predictive models. The findings showed that the breaking strength and mass irregularity of rotor spun yarns could be predicted satisfactorily by artificial neural network. The maximum error in predicting the breaking strength and mass irregularity of testing data was 8.34% and 6.65%, respectively.

  19. Ginástica Laboral: efeitos de um programa de ginástica laboral sobre a flexibilidade em trabalhadores de diversos setores de um hospital de ensino da região do Vale do Rio Pardo/RS

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    Andréa Mattos de Andrade

    2015-12-01

    Full Text Available A Ginástica Laboral (GL é uma atividade física realizada durante a jornada de trabalho, com exercício de compensação aos movimentos repetitivos, à ausência de movimentos, ou a posturas desconfortáveis assumidas durante o período de trabalho. Objetivo: verificar possíveis efeitos de um programa de GL sobre a flexibilidade em trabalhadores de diversos setores de um hospital de ensino da região do Vale do Rio Pardo/RS. Método: estudo semi-experimental realizado em diversos setores de um hospital, de março de 2014 a maio 2015, em que foram avaliados 42 indivíduos, do sexo feminino, com idade entre 22 e 58 anos, que participavam do programa de GL. Para a coleta de dados, foi aplicado o teste sentar e alcançar (sit and reach e o teste do manguito rotador (ombro direito e esquerdo em três momentos: 1 (antes da intervenção com GL; 2 (logo após o término da intervenção e 3 (quatro meses, após a intervenção. Resultados: a flexibilidade diferiu na comparação entre os momentos 1 e 2 e entre os momentos 1 e 3, em todos os testes aplicados, demonstrando que o programa de GL melhorou os níveis de flexibilidade dos trabalhadores. Não foi observada diferença significativa entre os momentos 2 e 3. Considerações finais: o programa de GL melhorou os níveis de flexibilidade dos trabalhadores, mantendo esses níveis semelhantes seis meses após o término da intervenção.

  20. Different effect of glutamine on macrophage tumor necrosis factor-alpha release and heat shock protein 72 expression in vitro and in vivo

    Institute of Scientific and Technical Information of China (English)

    Mengfan Liang; Xuemin Wang; Yuan Yuan; Quanhong Zhou; Chuanyao Tong; Wei Jiang

    2009-01-01

    Macrophage plays a vital role in sepsis. However, the modulatory effect of glutamine (Gln) on macrophage/ monocyte-mediate cytokines release is still controver-sial. Thus, we investigated the effect of Gin on macro-phage tumor necrosis factor (TNF)-α release and heat shock protein (HSP) 72 expression in vivo and in vitro. Data from our study indicated that the increase of HSP72 expression was significant at 8 mM of Gln 4 h after lipopolysaccharide (LPS) stimulation and became independent of Gin concentrations at 24 h, whereas TNF-α release was dose- and time-dependent on Gln. Heat stress (HS) induced more HSP72 and less TNF-α production compared with the non-HS group. However, the production of TNF-α in cells pretreated with HS was increased with increasing concentrations of Gln. Treatment with various concentrations of Gin for 1 h and then 0.5 mM Gin for 4h led to an increase in HSP72 expression, but not in TNF-α production. In sepsis model mice, Gin treatment led to a significantly lower intracellular TNF-α level and an increase in HSP72 expression in mouse peritoneal macrophages. Our results demonstrate that Gin directly increases TNF-α release of LPS-stimulated RAW264.7 macro-phages in a dose-dependent manner, and also decreases mouse peritoneal macrophages TNF-α release in the sepsis model. Taken together, our data suggest that there may be more additional pathways by which Gln modulates cytokine production besides HSP72 expression in macrophage during sepsis.

  1. O estresse na arbitragem de ginástica rítmica: uma revisão sistemática

    OpenAIRE

    Debien,Paula Barreiros; Noce,Franco; Debien,Jurema Barreiros Prado; Costa,Varley Teoldo da

    2014-01-01

    O estresse em árbitros tem sido objeto de estudo em várias modalidades esportivas, entretanto pouco se sabe sobre as interferências deste constructo na atividade de árbitros de ginástica rítmica (GR). O objetivo deste estudo foi fazer uma revisão sistemática sobre o estresse na arbitragem de GR. Foi realizada uma busca de artigos publicados entre os anos de 1993 e 2013 nas bases de dados Scopus, SPORTDiscus, SocINDEX e Web of Science. Os resultados apontam para um número reduzido de publicaçõ...

  2. Application of split - type gin pole in transmission lines%可拆分式抱杆在输电线路上的应用

    Institute of Scientific and Technical Information of China (English)

    赵俊

    2012-01-01

    由于输电线路山区的特殊地形条件,施工建设者在搬运施工器具时将消耗大量体力及时间,而组塔所使用的抱杆重量主要集中在其标准节,当采用将标准节拆分为片时可降低抱杆的自重,从而起到减轻施工人员劳动强度的作用。%Due to special topographical conditions of the transmission lines in the mountains, construction builders handling equipments will consume a lot of physical strength and time, but gin pole's weight which used by the group tower is mainly concentrated in its standard section. Used the method of splitting standard section into tablets can reduce the weight of gin pole, playing the role of reducing the labor intensity of construction workers.

  3. Teste GIN: detecção de gap em crianças com desvio fonológico Noise test: gap detection in children with phonological deviation

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    Elaine Feltre Assis

    2013-02-01

    Full Text Available OBJETIVO: investigar a resolução temporal: detecção de gaps em crianças com desvios fonológicos por meio do teste GIN e relacionar o grau do desvio fonológico com desempenho no teste GIN. MÉTODO: 6 indivíduos, de ambos os gêneros, 5 meninos e 1 menina, com idade entre 10 e 11 anos, com diagnóstico de desvio fonológico, em atendimento na clínica-escola do curso de Fonoaudiologia da FEAD de Belo Horizonte/MG, todos com ausência de perda auditiva e problemas neurológicos e/ou cognitivos. Os participantes foram submetidos ao Teste GIN, em intensidade de 50dB acima do limiar. RESULTADOS: das 06 crianças avaliadas, 5 (83,33% encontram-se alteradas e apenas 1 (16,67% obteve valores dentro do padrão de normalidade. Apesar da pequena amostra, viu-se que 83,33% das crianças com desvio fonológico tiveram limiares do GIN aquém do esperado para faixa etária. Porém não foi possível estabelecer uma relação direta entre grau de classificação do desvio fonológico e o baixo desempenho obtido no teste GIN, no qual apenas 1 criança com desvio médio moderado apresentou pior desempenho no teste GIN. CONCLUSÃO: crianças com desvio fonológico podem apresentar alteração no processamento temporal.PURPOSE: to investigate the temporal resolution, as for: gaps detection in children with phonological deviation through noise test and related with the degree of phonological performance in noise test. METHOD: 6 patients of both genders, five boys and one girl, aged between 10 and 11 year-old with phonological disorder' diagnosis in attendance at the school clinic of the Speech Therapy course (FEAD Belo Horizonte / MG, all with no hearing loss and no neurological and / or cognitive problems. The subjects underwent the GIN test at intensity of 50dB above the threshold. RESULTS: from the 6 evaluated children, 5 (83.33% had abnormal responses at gin test and only one (16.67% had values within the normal range. Despite the small sample, it was

  4. Leyendo el sur. A propósito del libro Cantes al Amorsillega de Ginés Liébana

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    Bartolomé Delgado Cerrillo

    2011-06-01

    Full Text Available A través de los poemas del libro Cantes al Amorsillega de Ginés Liébana, haremos un recorrido por las principales coplas del cante flamenco, incidiendo en la personal interpretación que nos da el autor y aportando su relación con la significación de las formas poéticas y las imágenes con que las ilustra. Este libro es valioso para ser integrado en la educación reglada como producto cultural. Y es valioso no solo como portador de contenidos antropológicos, sociológicos, coreográficos, musicales, poéticos e históricos, sino también como compendio de los estereotipos culturales que caracterizan la identidad cultural andaluza.

  5. Consumo de suplementos por jovens freqüentadores de academias de ginástica em São Paulo

    OpenAIRE

    HIRSCHBRUCH, Marcia Daskal; Fisberg, Mauro [UNIFESP; Luis MOCHIZUKI

    2008-01-01

    A preocupação com a aparência e a estética pode levar ao consumo indiscriminado de suplementos nas academias. Os fatores relacionados ao consumo de suplementos em 201 jovens entre 15 e 25 anos freqüentadores de academias de ginástica da cidade de São Paulo foram investigados através da aplicação de formulário próprio. O uso de suplementos é relatado por 61,2% (n = 123) da amostra. Os homens usam mais suplementos que as mulheres (p < 0,001) e os adolescentes tendem a utilizar mais que os adult...

  6. Avaliação da qualidade de vida em funcionários praticantes de ginástica holística em empresa

    Directory of Open Access Journals (Sweden)

    Fernanda Fonseca dos Santos Lopes

    2012-06-01

    Full Text Available Introdução: A qualidade de vida na empresa é um importante recurso de promoção de saúde, e pode ser desenvolvida a partir da pratica de atividades físicas. O exercício físico é uma forma de lazer e de restaurar a saúde dos efeitos da rotina estressante do trabalho, proporcionando condições de melhor desempenho e produtividade. A Ginástica Holística atua através da sensibilização e da tomada de consciência, de modo a levar o sujeito a uma melhor utilização do seu potencial perceptivo, sensorial motor e a uma atitude corporal mais harmônica. No nível terapêutico atua em problemas como contraturas musculares, artroses, hipotonias, má postura entre outros. Objetivo: Analisar a qualidade de vida dos funcionários de uma empresa de transportes que praticavam Ginástica Holística durante o expediente de trabalho. Método: O estudo foi realizado em uma empresa especializada em transportes de containeres, remoção de transito aduaneiro e cargas perigosas, localizada na cidade de Santos/SP, tendo como sujeitos 16 funcionários, após seis meses de pratica de Ginástica Holística. O instrumento utilizado foi o World Health Quality of Life (WHOQOL – bref versão em português, composto por 24 questões englobando os domínios físico, psicológico, relações sociais e meio ambiente e mais 2 questões gerais. Resultados: Observou-se que 62,5% dos sujeitos eram mulheres e 37,5% homens, com idade entre 17 e 43 anos; sendo 31,25% casados, 62,5% solteiros e 6,25% divorciados. Com relação à escolaridade 56,25% tinham o ensino médio e 43,75% o ensino superior. Na analise da qualidade de vida, o domínio psicológico apresentou melhores escores (75,78, seguido pelo domínio das relações sociais (74,99 e pelo domínio físico (72,99. O domínio que apresentou piores escores foi o meio ambiente (54,69, provavelmente em decorrência do tipo de atividade profissional. Conclusão: O ambiente de trabalho neste segmento é extremamente

  7. Ginástica geral na escola: uma proposta metodológica General gymnastics at school: A methodological propositon Gimnasia general en la escuela: Una propuesta metodológica

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    2006-11-01

    Full Text Available Este trabalho tem por objetivo discutir a Ginástica como conteúdo da Educação Física escolar, por meio da Ginástica geral como proposta metodológica. Tal proposta tem como perspectiva a integração das diversas manifestações gímnicas e os outros componentes da cultura corporal, sendo sua principal característica a ausência da competição. PALAVRAS-CHAVE: ginástica – ginástica geral – educação física escolar. This study aims at discussing gym classes as a part of school physical education, using General Gymnastics as a methodological approach. Such an approach has the perspective of integrating the several gymnastic manifestations to the other components of body culture, with the lack of competition as its main feature. KEY WORDS: gym – general gymnastics – physical education in schools. Este trabajo tiene por objetivo discutir la Gimnasia como contenido de la Educación Física escolar, por medio de la Gimnasia general como propuesta metodológica. Tal propuesta tiene como perspectiva la integración de diversas manifestaciones gímnicas y los otros componentes de la cultura corporal, siendo su principal característica la ausencia de la competencia. PALABRAS-CLAVE: gimnasia – gimnasia general – educación física escolar.

  8. A recepção da ginástica sueca em Portugal nas primeiras décadas do século XX: conformidades e dissensões culturais e políticas

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    Luís Miguel Carvalho

    2015-06-01

    Full Text Available O artigo aborda a presença persistente da "ginástica sueca" como referente principal da educação física em contexto escolar em Portugal, nas primeiras décadas do século XX, e as recepções distintas de que foi alvo. Numa primeira parte, o texto centra-se na compreensão da centralidade adquirida pela "ginástica sueca", em múltiplos contextos geopolíticos, no contexto da consolidação do projeto da escola de massas. Numa segunda parte, o texto documenta e analisa algumas deslocações interpretativas ocorridas na recepção da "ginástica sueca" em Portugal, entre 1920 e 1940, bem como os realinhamentos educativos, sociais e políticos que acompanharam esses conflitos sobre a sua "correta" mobilização para o contexto escolar português.

  9. Comparação do tempo de reação entre atletas de Basquetebol, Ginástica Artística e não atletas

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    Alessandro Teodoro Bruzi

    2013-06-01

    Full Text Available O propósito deste estudo foi comparar o tempo de reação entre atletas de Basquetebol (grupo Basquetebol, Ginástica Artística (grupo Ginástica e não atletas (grupo controle. Os indivíduos foram avaliados no tempo de reação simples e de escolha através do instrumento MULTPSY 821 e Sistema de Testes de Viena, respectivamente. Os resultados indicaram somente diferença significativa entre os grupos na medida de tempo de reação simples. O grupo controle apresentou maior tempo de reação comparado aos outros grupos. Esses achados indicam que a prática de Basquetebol e Ginástica Artística pode melhorar o tempo de reação simples, que é uma capacidade perceptiva necessária em atividades diárias.

  10. El mejor pastor descalzo, san Pascual Baylón o la incursión teatral de Ginés Campillo de Bayle

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    Ramón Doménech Villa

    2016-12-01

    Full Text Available Cuando los últimos decenios del siglo XVII iban marcando el final de la Casa de Austria en España, un clérigo nacido en Elche (Alicante, Ginés Campillo de Bayle, intentó su incursión en el mundo literario de la época. Su figura y obra, por un motivo u otro, siempre han estado rodeadas por un entorno de misterio, desgraciada fortuna y escasa estimación. Valorado con precaución por unos pocos, ignorado o criticado por la mayoría, gran parte de su producción lírica, narrativa y teatral ha conseguido llegar, a pesar de todo, a nuestras manos. Un ejemplo de lo señalado es la comedia teatral, así titulada por el propio autor, El mejor pastor descalzo, san Pascual Baylón; toda una demostración de un subgénero característico del Siglo de Oro, que nuestro escritor publica durante los últimos coletazos de tan simbólico período. Las siguientes líneas quieren mostrar un breve análisis de la citada obra, señalando sus características más significativas e identificando cuáles serían las influencias y fuentes de las que el autor ilicitano se surte, sin olvidar las particularidades literarias del que llegó a ser beneficiado de la iglesia parroquial de Santa María la Mayor de su ciudad natal. During the last decades of the seventeenth century , which marked the end of the Royal House of Austria in Spain, a cleric born in Elche (Alicante, Ginés Campillo de Bayle, tried to participate in the literary world of the time. His life and work, for one reason or another, have always been linked to mystery, misfortune and low esteem. Valued cautiously by few, ignored or criticized by most, we have now in our hands, a part of his lyrical, narrative and theatrical productions. An example of a characteristic subgenere of Golden Century is , El mejor pastor descalzo, san Pascual Baylón, that our writer published during the last gasps of this symbolic period. The following article tries to be a brief analysis of that work, delving into its most

  11. El Manuscrito Cerramientos y trazas de montea de Ginés Martínez de Aranda

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    Calvo López, José

    2009-03-01

    Full Text Available Ginés Martínez de Aranda, master mason in the cathedrals of Cádiz and Santiago de Compostela during the late 16th century, wrote a manuscript, Cerramientos y trazas de montea, concerning geometrical problems in stone construction. This article deals with the copy of Cerramientos in the Servicio Histórico Militar (Madrid, its copyist, dating, the existence of an earlier version and whether or not Aranda intended to publish it. Also examined are the connections between Cerramientos and other Spanish stonecutting texts of the period, such as those by Alonso de Vandelvira, Cristóbal de Rojas, Alonso de Guardia or Juan de Portor y Castro. Finally, an assessment is made of Martínez de Aranda’s original contributions to European stonecutting literatura.

    El arquitecto y cantero baezano Ginés Martínez de Aranda, que trabajó a finales del siglo XVI y ejerció la maestría de las catedrales de Cádiz y Santiago de Compostela, compuso un manuscrito llamado Cerramientos y trazas de montea, que trata de los problemas geométricos de la construcción pétrea. El artículo analiza la copia del manuscrito conservada en el Servicio Histórico Militar de Madrid, la identidad del copista, la fecha de la primera redacción de la obra y la de la copia conservada, y el destino de la obra; a continuación, se estudia la relación del manuscrito con otras obras españolas de cantería, en especial las de Alonso de Vandelvira, Cristóbal de Rojas, Alonso de Guardia y Juan de Portor y Castro, para finalizar tratando diversas aportaciones originales de Aranda a la literatura europea de la cantería.

  12. Interação entre leptina, ginástica artística, puberdade e exercício em atletas do sexo feminino

    Directory of Open Access Journals (Sweden)

    Tatiana de Barros Meira

    2010-09-01

    Full Text Available Há evidências de que as atletas de ginástica artística (GA apresentam desregulações no sistema reprodutório em relação à média populacional. A interação entre alguns fatores pode explicar esse fato: genética, estresse do exercício, baixa porcentagem de gordura corporal, má nutrição e ação da leptina. Por meio de uma revisão de literatura, discutimos resultados de pesquisas que relacionam a ação do hormônio leptina e desregulações no sistema reprodutório durante a puberdade em atletas de GA do sexo feminino. Podemos afirmar que existe uma interação entre a seleção natural na modalidade, a baixa ingestão calórica e o estresse do treinamento, que ocasionaria a diminuição de leptina plasmática e causaria desregulações no sistema reprodutório durante a puberdade.

  13. Epifisiólise proximal do úmero em atleta de ginástica olímpica Proximal humeral epiphysiolysis in a gymnast

    Directory of Open Access Journals (Sweden)

    Benno Ejnisman

    2007-01-01

    Full Text Available CONTEXTO: Existem diversas causas de dor no ombro do atleta. Estruturas como tendões e ligamentos são freqüentemente acometidas por lesões. No atleta jovem com esqueleto imaturo, as afecções ósseas devem ser lembradas como possíveis causas de dor. RELATO DE CASO: Os autores relatam a ocorrência da epifisiólise proximal do úmero em um atleta de ginástica olímpica e discutem a literatura a respeito do assunto. CONCLUSÃO: A lesão da placa fisária proximal do úmero em atletas é pouco freqüente. O diagnóstico precoce e correto tratamento evitam que ocorra deformidades severas e déficits funcionais.CONTEXT: There are different causes for shoulder pain in athletes. Structures such as tendons and ligaments are frequently affected by injuries. In young athletes with immature skull, bone injuries must be ruled as a cause of pain. CASE REPORT: The authors present a case of proximal humeral epiphysiolysis in a gymnast and review literature addressing this topic. CONCLUSION: Injuries on proximal humeral physeal plates of athletes are uncommon. The early diagnosis and correct treatment can avoid deformity and functional deficits.

  14. Efeitos da ginástica laboral na dor nas costas e nos hábitos posturais adotados no ambiente de trabalho

    Directory of Open Access Journals (Sweden)

    Cláudia Tarragô Candotti

    2011-09-01

    Full Text Available O objetivo deste estudo foi verificar o efeito da Ginástica Laboral (GL sobre a dor nas costas e sobre os hábitos posturais de trabalhadores que ficam por longos períodos na posição sentada. Participaram 30 trabalhadores do setor administrativo, divididos em grupo controle (n=15 e grupo experimental (n=15, sendo este submetido a sessões de GL durante três meses. Ambos os grupos foram avaliados por um questionário de dor e postura, sendo as respostas codificadas, tabuladas e submetidas ao teste de Wilcoxon para verificar as diferenças entre pré e pós-experimento (α=0,05. Os resultados demonstraram que a GL proporcionou diminuição da intensidade e frequência da dor referida aos trabalhadores do grupo experimental, e mudança do hábito postural durante o trabalho, melhorando a postura sentada.

  15. Effects of Pyrolysis Temperature on Product Yields and Energy Recovery from Co-Feeding of Cotton Gin Trash, Cow Manure, and Microalgae: A Simulation Study.

    Directory of Open Access Journals (Sweden)

    Muhammad Usman Hanif

    Full Text Available The intensive search of new and cleaner energy catches interest in recent years due to huge consumption of fossil fuels coupled with the challenge of energy and environmental sustainability. Production of renewable and environmentally benign energy from locally available raw materials is coming in the frontline. In this work, conversion of the combined biomass (cotton gin trash, cow manure, and Microalgae [Nannochloropsis oculata] through batch pyrolysis has been investigated. The effect of temperature to the production of energy fuels such as bio-oil, char, and biogas have been simulated considering the yield and energy content as responses. Result of the investigation generally revealed that the proportions of the different biomass did not significantly affect the product yield and energy recovery. Significant effect of temperature is evident in the simulation result of energy recovery whereby maximum conversion was achieved at 400°C for char (91 wt%, 600°C for syngas (22 wt%, and 551°C for bio-oil (48 wt%. Overall energy conversion efficiency of 75.5% was obtained at 589°C in which 15.6 MJ/kg of mixed biomass will be elevated to pyrolysis products.

  16. Effects of Pyrolysis Temperature on Product Yields and Energy Recovery from Co-Feeding of Cotton Gin Trash, Cow Manure, and Microalgae: A Simulation Study.

    Science.gov (United States)

    Hanif, Muhammad Usman; Capareda, Sergio C; Iqbal, Hamid; Arazo, Renato Ortiz; Baig, Muhammad Anwar

    2016-01-01

    The intensive search of new and cleaner energy catches interest in recent years due to huge consumption of fossil fuels coupled with the challenge of energy and environmental sustainability. Production of renewable and environmentally benign energy from locally available raw materials is coming in the frontline. In this work, conversion of the combined biomass (cotton gin trash, cow manure, and Microalgae [Nannochloropsis oculata]) through batch pyrolysis has been investigated. The effect of temperature to the production of energy fuels such as bio-oil, char, and biogas have been simulated considering the yield and energy content as responses. Result of the investigation generally revealed that the proportions of the different biomass did not significantly affect the product yield and energy recovery. Significant effect of temperature is evident in the simulation result of energy recovery whereby maximum conversion was achieved at 400°C for char (91 wt%), 600°C for syngas (22 wt%), and 551°C for bio-oil (48 wt%). Overall energy conversion efficiency of 75.5% was obtained at 589°C in which 15.6 MJ/kg of mixed biomass will be elevated to pyrolysis products.

  17. Análise da incidência lesional na ginástica aeróbica espanhola de elite

    Directory of Open Access Journals (Sweden)

    Rocío Abalo Núñez

    2013-10-01

    Full Text Available INTRODUÇÃO: A ginástica aeróbica (GA é uma disciplina que possui exigências físicas específicas e treinamento adequado para prevenir ou minimizar a ocorrência de lesões esportivas. OBJETIVO: Analisar a incidência de lesões na GA e a sua vinculação com fatores de treinamento MÉTODO: Realizou-se um estudo em 40 desportistas valencianos com idades compreendidas entre nove e 17 anos. O procedimento de coleta de informações foi através de um questionário de morbidade. A variável dependente foram as lesões durante a temporada 2009-2010 e as variáveis independentes principais foram a carga de treinamento, o material de proteção, superfície de treinamento, gesto técnico e tipo de lesão e zona corporal lesionada. RESULTADOS: As lesões mais reincidentes foram as relacionadas a ligamentos, afetando por igual os membros superior e inferior. A metade das lesões ocorreu após a realização dos saltos, apesar do uso de algum material de proteção, além de terem ocorrido no início da temporada. Relações significativas entre o número de lesões e a experiência, os dias de treinamento e o número de competições (p < 0,05 foram encontradas. CONCLUSÕES: O número de lesões diminuiu enquanto o uso de medidas de proteção, com destaque para as munhequeiras, aumentou. Metade das lesões produziu-se durante o período de aprendizagem técnica de dificuldades.

  18. Caracterização postural da jovem praticante de ginástica olímpica Postural characterization of young participants in Olympic gymnastics

    Directory of Open Access Journals (Sweden)

    MMB Guimarães

    2007-06-01

    Full Text Available OBJETIVO: Identificar as alterações posturais em crianças praticantes de ginástica olímpica, com idade entre 8 e 12 anos. MÉTODOS: Foram avaliadas 84 estudantes, 38 praticantes de ginástica olímpica e 46 não praticantes, com idade entre 8 e 12 anos. Foram realizadas fotografias de cada criança nos planos frontal anterior e posterior e plano sagital. As fotos foram analisadas através do software Corel Draw, v. 11.0, utilizando as ferramentas linhas-guia e dimensão (dimensão angular, dimensão vertical e dimensão horizontal, visando determinar os parâmetros das 19 variáveis qualitativas e 5 variáveis quantitativas. RESULTADOS: Ao comparar os sujeitos do grupo teste (GT com os sujeitos do grupo controle (GC, observa-se diferença estatisticamente significante nas variáveis rotação medial de fêmur (GC 56,52%; GT 39,47%, antepulsão de pelve (GC 43,48%; GT 76,32% e rotação de tronco (GC 67,39%; GT 23,68%. Observa-se também diferença significante em relação às medidas de valgo de joelho (GC 4,06 ± 2,32 cm; GT 3,14 ± 1,49cm, desnível de pelve (GC 0,69 ± 0,39 cm; GT 0,53 ± 0,33cm e ângulo tíbio-társico (GC 86,93 ± 2,90 cm; GT 87,11 ± 4,17 cm. CONCLUSÃO: Ao analisar os resultados, nota-se uma tendência ao melhor alinhamento dos membros inferiores no grupo teste quando comparado ao grupo controle. Há um aumento da inclinação pélvica anterior e uma tendência ao aumento da hiperlordose lombar no grupo teste, fatores que podem predispor a praticante de ginástica olímpica a um desalinhamento sobre as estruturas esqueléticas, levando a quadros dolorosos, limitando a sua vida esportiva.OBJECTIVE: To identify the postural alterations among children aged 8 to 12 years who perform Olympic gymnastics. METHOD: Eighty-four students aged 8 to 12 years were assessed: 38 who were participating in Olympic gymnastics and 46 who were not. Each child was photographed in the anterior and posterior frontal planes and in the

  19. Desenvolvimento e validação de um novo sistema de seleção de talentos para a ginástica olímpica feminina: a Bateria PDGO

    OpenAIRE

    Albuquerque,Patrícia Arruda de; Farinatti,Paulo de Tarso Veras

    2007-01-01

    A ginástica olímpica (GO) envolve atividades motoras que exigem capacidades específicas. Todavia, há carência de testes para detectar o potencial para o desempenho na GO em idades precoces. Este estudo descreve e apresenta evidências da validade de uma bateria de testes para a seleção de talentos para GO feminina. Inicialmente, foram levantadas as atividades que vêm sendo aplicadas por especialistas em GO, na literatura e por consulta através de questionários. A partir das 30 atividades menci...

  20. Metodologia do ensino de ginástica: novos olhares, novas perspectivas Gym teaching methodology: new approaches, new perspectives Metodología de enseñanza de la gimnasia: Nuevos horizontes, nuevas perspectivas

    Directory of Open Access Journals (Sweden)

    2006-11-01

    Full Text Available Este artigo busca sistematizar uma proposta metodológica para o ensino da Ginástica escolar e comunitária, que vem sendo construída a partir de experiências realizadas junto aos projetos de ensino, pesquisa e extensão vinculados ao Grupo de Estudo, Pesquisa e Experimentação em Ginástica(GEPEGIN, da Faculdade de Educação Física da UFG. A proposta indica alguns princípios, conteúdos e estratégias de ação que possam contribuir para o processo de formação humana crítica, na tentativa de apontar uma nova perspectiva para o ensino, a prática e o conhecimento da Ginástica. PALAVRAS-CHAVE: metodologia da ginástica – formação humana – linguagem corporal. This article aims at systematizing a methodological approach for the teaching of gym in schools and communities, which is being built from the experiences held with teaching, research, and extension (community-bound projects linked to GEPEGIN - the Study, Research, and Gym Experimentation Group, from the Physical Education Department at UFG - the Federal University of Goias. This approach indicates some principles, contents, and strategies for action that might contribute to the process of human education in a critical way, in an attempt to point towards a new perspective for the teaching, the practice, and the knowledge of Gymnastics. KEY-WORDS: gymnastics methodology – human education – body language. Este artículo busca sistematizar una propuesta metodológica para la enseñanza de la Gimnasia escolar y comunitaria, que viene siendo construida a partir de experiencias realizadas junto a los proyectos de enseñanza, pesquisa y extensión vinculados al Grupo de Estudio, Pesquisa y Experimentación en Gimnasia (GEPEGIN, de la Facultad de Educación Física de la UFG. La propuesta indica algunos principios, contenidos y estrategias de acción que puedan contribuir para el proceso de formación humana crítica, intenta señalar una nueva perspectiva para la ense

  1. Dependência de exercício físico em academias de ginástica e sua interface com suplementação e imagem corporal

    OpenAIRE

    Luciana Rossi Marques

    2014-01-01

    O Brasil é o segundo país no mundo em número de academias de ginástica, contando atualmente com cerca de 30 mil unidades. Apesar da transição no modelo de gestão e filosofia das academias do fitness para o wellness, muitas ainda propagam em seus ambientes o culto ao corpo magro e atlético, dietas sem fundamentação nutricional e consumo descontrolado de suplementos. Crescem as evidências de que uma parcela significativa dos frequentadores de academias desenvolve um comprometimento exacerbado à...

  2. Impacto do beneficiamento sobre o número de neps e quantidade de impurezas da fibra do algodão Ginning impact on the number of neps and amount of cotton fiber contaminants

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    Odilon R. R. F. da Silva

    2010-01-01

    Full Text Available Objetivou-se, neste trabalho, estudar o efeito do beneficiamento sobre o conteúdo de impurezas, pó e o número de neps na pluma, em 12 algodoeiras do Estado de Mato Grosso. O experimento consistiu de uma combinação fatorial de cinco etapas de beneficiamento do algodão em 12 algodoeiras em delineamento inteiramente casualizado com quatro repetições. Amostras de algodão foram coletadas nas seguintes etapas: a no desmanche do fardão; b antes do descaroçamento; c logo após o descaroçamento; d na bica, sem o uso do limpador tipo serrilha; e na bica, após a limpeza da pluma, utilizando-se o limpador tipo serrilha. Em todas as etapas se retiraram quatro amostras padrão de pluma com massa de 350 g a fim de serem analisadas mediante o instrumento AFIS (Advanced Fiber Information System para determinação do conteúdo de impurezas e poeira e o número de neps da fibra. Os resultados indicam que os processos de prelimpeza do algodão em caroço e limpeza da pluma reduzem o conteúdo de impurezas e da poeira do algodão enquanto, juntamente com o descaroçamento, esses processos aumentaram o número de neps da fibra do algodão. A utilização do limpador de pluma tipo serrilha com manta contínua aumenta a eficiência de limpeza da pluma, porém ocasiona incrementos significativos no número de neps.The purpose of this work was to study the ginning effect on the amount of cotton contaminants, dust and neps in cotton fiber, in 12 industries in the Mato Grosso State. The experiment consisted of a factorial combination over five stages of ginning and 12 cotton industries using a randomized design with four replications. Some samples of cotton were collected in the following phases: a in the bale dismantling; b before the ginning; c right after ginning; d into the covered lint slide not using the saw lint cleaner; and e into the covered lint slide, after cleaning process using the saw lint cleaner system. Over all stages four standard samples of

  3. Avaliação do estado nutricional de atletas de ginástica olímpica do Rio de Janeiro e São Paulo Nutritional status evaluation of olympic gymnastics athletes from Rio de Janeiro and São Paulo, Brazil

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    Beatriz Gonçalves RIBEIRO

    2002-08-01

    Full Text Available Com o objetivo de avaliar o estado nutricional de atletas de ginástica olímpica, do sexo feminino, foram estudadas 46 ginastas, de 11 a 14 anos, pertencentes a clubes e academias das cidades do Rio de Janeiro e São Paulo. O estudo antropométrico envolveu medidas de massa corporal, estatura, dobras cutâneas e perímetros. Observou-se diferença significativa para as dobras cutâneas tricipital, suprailíaca, da coxa e da panturrilha e para o percentual de gordura (pThe purpose of this study was to evaluate the nutritional status of 46 female olympic gymnastics athletes, aged 11 to 14 years old, attending private gymnastics clubs of the cities of Rio de Janeiro and São Paulo. The anthropometric assessment involved measurements of height, body mass, skinfold thickness and circumferences. Significant difference was observed for the triceps, suprailiac, mid thigh and medial calf skinfolds and for the percentage of body fat (p<0.05. For the assessment of dietary intake a 24-hour recall and a 3-day self-register were used. The energy consumption and the percentage of carbohydrates (50% to 58% in the diet were low and the protein ingestion (1.5 to 1.7 g/kg of body weight was appropriate, according to values proposed for athletes. Vitamin intake was satisfactory, except for folic acid of gymnasts from Rio de Janeiro. From the minerals assessed, the intake of calcium, magnesium, zinc and iron was inadequate. No clinical signs of iron deficiency were observed.

  4. Dictionary of cotton: Picking & ginning

    Science.gov (United States)

    Cotton is an essential commodity for textiles and has long been an important item of trade in the world’s economy. Cotton is currently grown in over 100 countries by an estimated 100 producers. The basic unit of the cotton trade is the cotton bale which consists of approximately 500 pounds of raw c...

  5. Consumo de suplementos por jovens freqüentadores de academias de ginástica em São Paulo Supplement use amongst young individuals in São Paulo's fitness centers

    OpenAIRE

    Marcia Daskal Hirschbruch; Mauro Fisberg; Luis Mochizuki

    2008-01-01

    A preocupação com a aparência e a estética pode levar ao consumo indiscriminado de suplementos nas academias. Os fatores relacionados ao consumo de suplementos em 201 jovens entre 15 e 25 anos freqüentadores de academias de ginástica da cidade de São Paulo foram investigados através da aplicação de formulário próprio. O uso de suplementos é relatado por 61,2% (n = 123) da amostra. Os homens usam mais suplementos que as mulheres (p < 0,001) e os adolescentes tendem a utilizar mais que os adult...

  6. Detecção e seleção de talentos na ginástica artística feminina: a perspectiva dos técnicos brasileiros

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    Myrian Nunomura

    2014-04-01

    Full Text Available Este artigo tem por objetivo apresentar e discutir a detecção e a seleção de talentos na Ginástica Artística Feminina com enfoque para os aspectos que norteiam as condutas dos técnicos brasileiros. Entrevistamos 34 técnicos de 29 instituições distribuídas no Brasil. Observamos que os meios utilizados para detectar e selecionar os talentos na modalidade privilegiam a idade de ingresso, as características antropométricas e os testes físico-motores. Porém, sabemos que os determinantes do sucesso no esporte são multifatoriais e, por vezes, as avaliações transversais utilizadas não contemplam todos os fatores que contribuem para a obtenção de bons resultados no alto rendimento.

  7. Prática da ginástica laboral por trabalhadores das indústrias do Rio Grande do Sul, Brasil Stretching programs among industrial workers from the state of Rio Grande do Sul, Brazil

    Directory of Open Access Journals (Sweden)

    Luana Callegaro Rossato

    2013-03-01

    Full Text Available O presente estudo identificou a prevalência e os fatores associados à prática de ginástica laboral por trabalhadores da indústria no Estado do Rio Grande do Sul, Brasil. Realizou-se análise secundária dos dados de um estudo de delineamento transversal, com amostra probabilística de 2.265 trabalhadores, de ambos os sexos. O instrumento de pesquisa foi o questionário autoadministrado "Estilo de vida e hábitos de lazer dos trabalhadores das indústrias brasileiras", previamente validado. A variável dependente foi a prática de ginástica laboral, definida pela resposta positiva à questão: "Você participa do programa de ginástica na empresa (ginástica laboral?". Foram coletadas informações demográficas, socioeconômicas, comportamentais e relacionadas à saúde, como potenciais fatores associados. Na análise de dados, empregou-se o teste Qui-quadrado de Pearson e o modelo de regressão de Poisson com variância robusta, nas análises bruta e ajustada, respectivamente. A prática de ginástica laboral foi referida por 40,3% dos respondentes (IC95%: 38,2; 42,3, sendo mais prevalente nos trabalhadores do sexo feminino, com maiores níveis de escolaridade, naqueles mais ativos no lazer e que relatavam menores intensidades de esforço no trabalho. Não se observou associação da variável dependente com idade, estado civil, renda familiar bruta, tabagismo, autopercepção de saúde e autopercepção do nível de estresse. Programas de ginástica laboral devem desenvolver estratégias de promoção da saúde que priorizem subgrupos de trabalhadores menos envolvidos, em especial, indivíduos do sexo masculino e com menor escolaridade. Desse modo, será possível reduzir as disparidades, beneficiando trabalhadores, independentemente de suas características sociodemográficas, a melhores condições saúde e bem-estar no ambiente das indústrias.We evaluated the prevalence and factors associated with participation on stretching programs

  8. Estado de Nutrição, Composição Corporal e Maturação Sexual de Adolescentes Praticantes de Ginástica Rítmica de Alto-Rendimento: Estudo Comparativo entre as Selecções de Portugal e da Rússia

    OpenAIRE

    Rego, C. M.; Guerra, A. J. M.; A. Prata; Lebre, E.; Fontoura, M; Santos, N. Teixeira

    2014-01-01

    A prática de ginástica rítmica em regime de alto rendimento, condiciona perturbações do comportamento alimentar bem como adaptações hormonais e metabólicas. Quando esta prática se verifica durante a infância e adolescência, tais adaptações podem interferir no estado de nutrição e desenvolvimento pubertário.Com o objectivo de estudar tais repercussões, procedeu-se à avaliação de 29 ginastas pertencentes às Selecções de Ginástica Rítmica de Portugal (n=18) e da Rússia (n=11). De entre as 14 Sel...

  9. O livro como ferramenta pedagógica para a inserção da educação física e da ginástica no ensino público primário paranaense (fim do século XIX e início do século XX

    Directory of Open Access Journals (Sweden)

    Diogo Rodrigues Puchta

    2015-09-01

    Full Text Available ResumoNo presente trabalho procuramos analisar as motivações do autor Domingos Nascimento ao se valer da obra de Daniel Schreber Ginástica doméstica, médica e higiênica para escrever sobre a ginástica que deveria ser ensinada e praticada nas escolas paranaenses. Buscamos confrontar a perspectiva dos dois autores com relação à educação física e à ginástica pensadas nos anos iniciais do século XX, bem como contextualizar tais perspectivas com a situação em que se encontrava a instrução pública no Estado do Paraná, de grandes discussões em torno da renovação do ensino, manifestadas no início de um amplo ciclo de reformas escolares, no qual a “novidade” da educação física regular nas escolas é apenas um exemplo.

  10. Desenvolvimento e avaliação de um descaroçador e prensa enfardadeira itinerantes para o beneficiamento do algodão Development of a mobile gin and baler press for cotton

    Directory of Open Access Journals (Sweden)

    Jeane F. Jerônimo

    2013-03-01

    Full Text Available Novas tecnologias vêm sendo incorporadas ao sistema produtivo da cotonicultura brasileira, visando verticalizar a produção por meio do beneficiamento do algodão em caroço possibilitando, aos produtores ou associações, a agregação de valor à sua produção. Objetivou-se então, com o presente trabalho, desenvolver e avaliar um equipamento de beneficiamento composto de descaroçador e prensa enfardadeira itinerantes. O descaroçador se compõe de: limpador, cilindro de serras, cilindro de escovas, condensador e rolo. A prensa enfardadeira é constituída de chapas de prensagem, cilindros hidráulicos, bomba hidráulica, válvula de controle de acionamento, dispositivos de filtragem do óleo hidráulico e manômetro. Esses equipamentos são montados sobre um reboque composto por chassi de cantoneiras em U, quatro rodas de aro 13, pontas de eixo, dois feixes de cinco molas, lastro em chapa de ferro e sistema de frenagem. Na avaliação e validação do conjunto pelos cotonicultores, este conjunto recebeu o conceito "muito bom" quanto ao rendimento do descaroçador, o peso do fardo e em relação à qualidade da fibra obtida. A qualidade da fibra obtida com o conjunto descaroçador e prensa enfardadeira atendeu aos padrões da indústria têxtil.New technologies have been incorporated into the Brazilian cotton production system, in order to verticalize the production through processing, allowing the producers or associations to add value to their production. Thus, the present study aimed to develop and evaluate processing equipment composed of mobile gin and baler press. The ginner consists of cleaner, saw cylinder, cylinder brushes, condenser and coil. The baler press is constituted of pressing sheets, hydraulic cylinders, hydraulic pump, control valve actuation, devices for filtering hydraulic oil and manometer. These devices are mounted on a trailer chassis composed of U-shaped angle iron chassis, four wheels (rim 13, shaft ends, two

  11. Centro de excelência e ginástica artística feminina: a perspectiva dos técnicos brasileiros Centre of excellence for women artistic gymnastics: the Brazilian coaches' perspective

    Directory of Open Access Journals (Sweden)

    Myrian Nunomura

    2012-06-01

    Full Text Available Durante o período de 2001-2008, a Confederação Brasileira de Ginástica implementou o sistema de seleção permanente concentrada no Centro de Treinamento (CT de Curitiba. Através de um formato semelhante às escolas-internato esportivas da antiga União Soviética, as ginastas passaram a treinar juntas sob o comando de um renomado técnico estrangeiro. Este artigo visa apresentar e discutir o contexto deste CT e o sistema de seleção permanente da ginástica artística feminina (GAF brasileira, a partir da opinião dos técnicos que desenvolvem a modalidade no país. Procedemos a um estudo de campo e entrevistamos 34 treinadores de 29 instituições. Dentre os aspectos positivos da seleção permanente, os sujeitos relacionaram principalmente a infraestrutura disponível às ginastas. Sobre os aspectos negativos, foram citados problemas relacionados ao rigor do treinamento, à polarização e a consequente monopolização das atletas, o que revela que, provavelmente, não houve uma adaptação do modelo soviético às características da GAF desenvolvida no Brasil.During the period of 2001 and 2008, the Brazilian Gymnastics Confederation implemented the gymnasts training boarding center system at the Curitiba Training Center (TC. Using the former Soviet Union model of sports boarding schools, the Brazilian gymnasts started to train together under the supervision of a technical team led by a renowned foreign coach. This article aims to discuss the context of the TC and the system of centralized preparation of the Brazilian women artistic gymnastics (WAG showing the point of view of the coaches. We conducted a field survey and we interviewed 34 coaches of 29 sport institutions. Among the positive aspects, the coaches reported about the better infrastructure available to the gymnasts. The negative aspects refer to the problems regarding rigorous training, the polarization and the consequent monopolization of athletes showing lack of

  12. As possibilidades da ginástica na sua relação com o lazer e com a sociedade Possibilities of gymnastics in its relation with leisure and society Las posibilidades de la gimnasia en su relación con el ocio y con la sociedad

    Directory of Open Access Journals (Sweden)

    2006-11-01

    Full Text Available Este trabalho apresenta discussão preliminar, tendo como foco as possibilidades da ginástica como vivência no lazer e sua relação com a sociedade e aborda, também, a forma como a ginástica conquistou o espaço das academias, expandindo-se enquanto produto de consumo. O texto aponta a necessidade de se buscar uma excitação agradável na ginástica, necessária para que ela se torne prazerosa, alegre, localizando nela o componente lúdico. Assim, espera-se facilitar a inserção da ginástica no campo do lazer, embora a ludicidade não seja o seu único componente. PALAVRAS-CHAVE: ginástica – lazer – sociedade This research work presents a preliminary discussion focussing on the possibilites of gymnastics as a leisure experience and its relation to society. It also addresses the way through which gymnastics has gained ground in gyms, expanding as a consumption product. This text points to the need of searching for a pleasant excitemente in gymnastics, which is necessary for it to be pleasing and fun, by locating the playful component in it. As such, this text hopes to aid in the implementation of gymnastics in the field of leisure, although playfulness is not its only component. KEYWORDS: gymnastics – leisure – society Este trabajo presenta discusión preliminar, teniendo como foco las posibilidades de la gimnasia como vivencia en el ocio y su relación con la sociedad y aborda, también, la forma como la gimnasia conquistó el espacio de las academias, expandiéndose como producto de consumo. El texto señala la necesidad de buscar una excitación agradable en la gimnasia, necesaria para que ella se torne placentera, alegre, localizando en ella el componente lúdico. Así, se espera facilitar la inserción de la gimnasia en el campo del ocio, aunque la ludicidad no sea su único componente. PALABRAS-CLAVE: gimnasia – ocio – sociedad

  13. Controle postural e uso de informação visual em crianças praticantes e não praticantes de ginástica artística

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    André Rocha Viana

    2011-09-01

    Full Text Available O objetivo deste estudo foi investigar o desempenho e a contribuição da informação visual no controle postural de crianças praticantes e não praticantes de ginástica artística (GA. Quarenta e três meninas, 23 praticantes de GA e 20 não praticantes de GA, idade 5 a 7 e 9 a 11 anos, permaneceram em pé sobre uma plataforma de força em três bases de apoio: bipodal, semi-tandem stance e base reduzida, com olhos abertos e com olhos fechados. A área de deslocamento do centro de pressão e o índice de contribuição visual foram calculados. Os resultados indicaram que a prática de GA melhora o controle postural de crianças nos anos iniciais de desenvolvimento. Ainda, crianças praticantes de GA utilizam melhor informação visual que crianças não praticantes de GA para manter a postura ereta mais estável.

  14. Glucose elevates NITRATE TRANSPORTER2.1 protein levels and nitrate transport activity independently of its HEXOKINASE1-mediated stimulation of NITRATE TRANSPORTER2.1 expression.

    Science.gov (United States)

    de Jong, Femke; Thodey, Kate; Lejay, Laurence V; Bevan, Michael W

    2014-01-01

    Mineral nutrient uptake and assimilation is closely coordinated with the production of photosynthate to supply nutrients for growth. In Arabidopsis (Arabidopsis thaliana), nitrate uptake from the soil is mediated by genes encoding high- and low-affinity transporters that are transcriptionally regulated by both nitrate and photosynthate availability. In this study, we have studied the interactions of nitrate and glucose (Glc) on gene expression, nitrate transport, and growth using glucose-insensitive2-1 (gin2-1), which is defective in sugar responses. We confirm and extend previous work by showing that HEXOKINASE1-mediated oxidative pentose phosphate pathway (OPPP) metabolism is required for Glc-mediated NITRATE TRANSPORTER2.1 (NRT2.1) expression. Treatment with pyruvate and shikimate, two products derived from intermediates of the OPPP that are destined for amino acid production, restores wild-type levels of NRT2.1 expression, suggesting that metabolites derived from OPPP metabolism can, together with Glc, directly stimulate high levels of NRT2.1 expression. Nitrate-mediated NRT2.1 expression is not influenced by gin2-1, showing that Glc does not influence NRT2.1 expression through nitrate-mediated mechanisms. We also show that Glc stimulates NRT2.1 protein levels and transport activity independently of its HEXOKINASE1-mediated stimulation of NRT2.1 expression, demonstrating another possible posttranscriptional mechanism influencing nitrate uptake. In gin2-1 plants, nitrate-responsive biomass growth was strongly reduced, showing that the supply of OPPP metabolites is essential for assimilating nitrate for growth.

  15. Consumo de suplementos por alunos de academias de ginástica em São Paulo Supplement consumption among fitness center users in São Paulo, Brazil

    Directory of Open Access Journals (Sweden)

    Raquel Franzini Pereira

    2003-09-01

    Full Text Available O aumento do número de academias de ginástica na cidade de São Paulo, em conjunto com o aumento da oferta de diferentes suplementos no mercado, despertou interesse para o estudo do consumo de suplementos entre seus alunos. O uso de suplementos pelo público em geral não é bem quantificado e pouca informação sobre este assunto está publicada na literatura. O seu aparecimento no mercado tem sido mais rápido do que a elaboração de regulamentações e a realização de pesquisas científicas que comprovem seus efeitos na saúde dos consumidores e determinem a segurança de seu uso a longo prazo. Em uma amostra de 309 freqüentadores de sete academias de ginástica de São Paulo em 1999, 74 (23,9% consumiam algum tipo de suplemento, dos quais 77,0% eram do sexo masculino e 23,0% do sexo feminino. Os suplementos mais consumidos foram aminoácidos ou outros concentrados protéicos (38,9% e o consumo maior foi o diário (90,3%. A correlação entre gasto com suplemento e renda individual foi de 27,5% (p = 0,0483; n=52, sendo o gasto com suplementos maior entre homens do que entre mulheres; a correlação com renda familiar foi de 36,1% (p = 0,0137; n = 46 e com Índice de Massa Corporal foi de 17,1% (p = 0,1564; n = 70. Conclui-se que o uso de suplementos é significante no grupo analisado, ficando clara a necessidade de novos estudos sobre o consumo desses produtos e seus efeitos, enfocando aspectos de educação nutricional do consumidor de suplementos para aumentar o nível de informação sobre os mesmos e garantir segurança na sua utilização.The increase in the number of fitness centers in the city of São Paulo, together with the increase in the offering of different supplements, has raised interest in the study of the consumption of supplements among fitness center users. The consumption of supplements by the general public has not been well quantified yet, and little information has been published about this subject. The arrival of

  16. Caracterização dos níveis de pressão sonora em academias de ginástica e queixas apresentadas por seus professores Characterization of sound pressure levels in fitness centers and complaints from instructors

    Directory of Open Access Journals (Sweden)

    Adriana B. M. de Lacerda

    2001-09-01

    Full Text Available Objetivo: Este estudo objetiva identificar as queixas auditivas e orgânicas dos professores de ginástica e avaliar os níveis de pressão sonora (NPS produzidos nas aulas de ginástica com música. A medição dos NPS foi realizada seguindo as condições sugeridas pela Associação Brasileira de Normas Técnicas (ABNT, na Norma 10151. Forma de estudo: Prospectivo clínico randomizado. Material e método: 32 professores de ginástica responderam a um questionário com questões referentes às queixas relacionadas aos NPS. Resultados: As queixas mais freqüentes foram: zumbidos (24%, sensação de ouvido tampado (15% e baixa concentração (15%. As modalidades de ginástica nas quais foi realizada a avaliação dos níveis de pressão sonora foram: Step, Body Pump e Aerofitness. Conclusão: Os resultados desta avaliação revelaram intensidades que variaram de 73,9 a 94,2 dBA e sugerem presença de elevados níveis de pressão sonora em 66% das aulas avaliadas.Aim: The present study aims at identifying auditory and health complaints of fitness instructors in fitness centers in Curitiba, and to evaluate the sound pressure levels (SPL produced in fitness classes. SPL measurements were made following ABNT recommendations (Brazilian Technical Norms and Regulations Association - Norm 10151 and revealed levels that ranged from 73.9 to 94.2 dBA. Study design: Prospective clinical randomized. Material and method: 32 fitness instructors answered a questionnaire about their most frequent complaints related to SPL. Results: The most frequent complaints were: tinnitus (24%; ear fullness (15% and poor concentration (15%. The classes in which sound pressure levels were investigated were: Step, Body Pump and Aerofitness. Conclusion: The results of the present research suggested the presence of high sound pressure levels in 66% of the evaluated classes.

  17. Assembling the archaeal ribosome: roles for translation-factor-related GTPases.

    Science.gov (United States)

    Blombach, Fabian; Brouns, Stan J J; van der Oost, John

    2011-01-01

    The assembly of ribosomal subunits from their individual components (rRNA and ribosomal proteins) requires the assistance of a multitude of factors in order to control and increase the efficiency of the assembly process. GTPases of the TRAFAC (translation-factor-related) class constitute a major type of ribosome-assembly factor in Eukaryota and Bacteria. They are thought to aid the stepwise assembly of ribosomal subunits through a 'molecular switch' mechanism that involves conformational changes in response to GTP hydrolysis. Most conserved TRAFAC GTPases are involved in ribosome assembly or other translation-associated processes. They typically interact with ribosomal subunits, but in many cases, the exact role that these GTPases play remains unclear. Previous studies almost exclusively focused on the systems of Bacteria and Eukaryota. Archaea possess several conserved TRAFAC GTPases as well, with some GTPase families being present only in the archaeo-eukaryotic lineage. In the present paper, we review the occurrence of TRAFAC GTPases with translation-associated functions in Archaea.

  18. Primase-polymerases are a functionally diverse superfamily of replication and repair enzymes.

    Science.gov (United States)

    Guilliam, Thomas A; Keen, Benjamin A; Brissett, Nigel C; Doherty, Aidan J

    2015-08-18

    Until relatively recently, DNA primases were viewed simply as a class of proteins that synthesize short RNA primers requisite for the initiation of DNA replication. However, recent studies have shown that this perception of the limited activities associated with these diverse enzymes can no longer be justified. Numerous examples can now be cited demonstrating how the term 'DNA primase' only describes a very narrow subset of these nucleotidyltransferases, with the vast majority fulfilling multifunctional roles from DNA replication to damage tolerance and repair. This article focuses on the archaeo-eukaryotic primase (AEP) superfamily, drawing on recently characterized examples from all domains of life to highlight the functionally diverse pathways in which these enzymes are employed. The broad origins, functionalities and enzymatic capabilities of AEPs emphasizes their previous functional misannotation and supports the necessity for a reclassification of these enzymes under a category called primase-polymerases within the wider functional grouping of polymerases. Importantly, the repositioning of AEPs in this way better recognizes their broader roles in DNA metabolism and encourages the discovery of additional functions for these enzymes, aside from those highlighted here.

  19. Prevalência do uso e conhecimento de esteroides anabolizantes androgênicos por estudantes e professores de educação física que atuam em academias de ginástica

    Directory of Open Access Journals (Sweden)

    Odilon Salim Costa Abrahin

    2013-02-01

    Full Text Available INTRODUÇÃO: Os esteroides anabólicos androgênicos (EAA são substâncias, quimicamente semelhantes à testosterona, utilizadas para o tratamento/controle de diversas doenças. Contudo, tais substâncias estão sendo empregadas de forma não terapêutica e indiscriminada com finalidades de melhora da performance esportiva e principalmente estética. OBJETIVO: analisar a prevalência do uso e o conhecimento de EAA por estudantes e professores de educação física que atuam em academias de ginástica de Belém, PA. Utilizou-se para a coleta de dados um questionário fechado e anônimo, aplicado a 117 pesquisados. A comparação da prevalência do uso e o grau de conhecimento dos pesquisados sobre EAA foi realizada através de estatística não paramétrica, prova de X² (Qui-quadrado, considerando o intervalo de confiança de 95% e p < 0,05. A média de idade dos participantes da pesquisa foi de 28,0 ± 6,3 anos e a prevalência do uso de EAA foi de 31,6% do total de sujeitos pesquisados. A prevalência maior foi entre os profissionais especialistas (39,3%, tendo como principal motivação para o uso de EAA a estética com 75,6%. Em relação ao conhecimento, verificou-se que as drogas classificadas como EAA foram: Durateston®, Deca-Durabolin®, oxandrolona/Winstrol®. Entretanto, estes profissionais confundiram-se ao apontar outras substâncias como sendo EAA, entre elas: hormônio do crescimento e óleos localizados. Entre os efeitos colaterais, os mais citados foram: acne, engrossamento da voz e agressividade; contudo, efeitos colaterais mais prejudiciais como câncer e aromatização foram menos assinalados. RESULTADOS: Demonstraram que a prevalência de uso de EAA foi significativa (p < 0,03 entre os estudantes e professores de educação física que atuam em academias de Belém, PA, revelando assim prováveis desconhecimentos destes sobre alguns dos efeitos colaterais, podendo implicar no uso indiscriminado destas drogas.

  20. Uma análise exploratória do processo de orçamento de capital em empresas algodoeiras A qualitative analysis of the capital budgeting process in cotton ginning companies

    Directory of Open Access Journals (Sweden)

    Afonso Carneiro Lima

    2013-06-01

    targeted towards attempting to ensure satisfactory operating results in the short term. Hence, most of the gins investigated seem to be more susceptible to the uncertainties of the environment in which they operate since there is a limited consideration of the possibilities that investments might bring to them, as well as an inherent risk management approach; behavioral aspects such latency were verified in investment decisions performed by the managers interviewed.

  1. Protein-protein interactions

    DEFF Research Database (Denmark)

    Byron, Olwyn; Vestergaard, Bente

    2015-01-01

    Responsive formation of protein:protein interaction (PPI) upon diverse stimuli is a fundament of cellular function. As a consequence, PPIs are complex, adaptive entities, and exist in structurally heterogeneous interplays defined by the energetic states of the free and complexed protomers......, are reported. The aim is to depict how the elucidation of the interplay of structures requires the interplay of methods....

  2. Protein Condensation

    Science.gov (United States)

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

    2014-07-01

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

  3. 添加rhGH与Gln的肠外营养对短肠大鼠小肠代偿作用的研究%Simultaneous treatment with rhGH and Gin additively improves intestinal adaptation in parenteral fed, short bowel rats

    Institute of Scientific and Technical Information of China (English)

    顾岩; 昊肇汉; 靳大勇; 谢建新; 左焕琛; 付晓颍

    2000-01-01

    Objective To understand the potential synergisite effects of rhGH and Gln on postresectional adaptation of the remnant small intestine in parentera fed, short bowel rats. Methods Four PN treatment groups of SBS rat were randomized arranged in a 2 × 2 factorial design as follows: STD group (-rhGH,-Gln),Gin group (-rhGH, +Gln), rhGH group (+rhGH, -Gln) and GG group (+rhGH, +Gin). The morphological changes of the intestinal mucosal epithelia were determined; The expression of PCNA and the occurrence of the apoptosis were observed by immunohistochemical staining and TUNEL methods. The intestinal mucosal bcl-2 and bax mRNA were determined by RT-PCR methods; Intestinal IGF-1 mRNA were determined by Northern blot assays. Results Mucosal thickness, villous height, crypt depth and villous surface of the remnant small intestine in GG group were increased significantly compared to other 3 groups; The expression of PCNA was increased but the rate of apoptosis was decreased significantly; The expression of bcl-2 mRNA was increased accordingly, and bax mRNA was just on the contrary, P<0.01. There are synergistic effects between rhGH and Gin statiticaUy. The expression of the intestinal IGF-1 mRNA was higher in rhGH and Gin groups than STE) group, and was highest in GG group, P<0.05. Conelasions The combination of rhGH and Gin can significantly improve the adaptation of the remnant small intestine in parenterally fed, SBS rats, there are synergistic effects between them; The increase of proliferation and the decrease of apoptosis in the remnant intestinal epithelial cells are involved in this process; The intestinal IGF-I p; ays an important role in the intestinal adaptation. Our findings support the concept that specific gut-trophic nutrients and growth factors may combined to enhance the intestinal adaptation and reduce the severity of short bowel syndrome.%目的研究添加生长激素(rhGH)及谷氨酰胺(Gln)的肠外营养(PN),对短肠大鼠残存小肠代偿的作用

  4. Yeast Interacting Proteins Database: YML034W, YDR489W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available Psf3p), which is localized to DNA replication origins and implicated in assembly of the DNA replication mac...it of the GINS complex (Sld5p, Psf1p, Psf2p, Psf3p), which is localized to DNA replication origins and impli

  5. Ginástica rítmica – análise dos fatores competitivos motivadores e estressantes da Seleção Brasileira Juvenil =Rhythmical gymnastics – analysis of competitive, motivating and stress factors of the teenager Brazilian National Football Team

    Directory of Open Access Journals (Sweden)

    Lenamar Fiorese Vieira

    2005-07-01

    Full Text Available Este estudo objetivou investigar a trajetória de desenvolvimento das atletas de ginástica rítmica da Seleção Brasileira Juvenil, com foco na identificação dos fatores competitivos (motivadores e estressantes que ocorrem em diferentes fases da carreira esportiva. A população alvo foi de dez atletas. Como instrumentos de medida foramutilizados o Teste de Carga Psíquica de Frester e entrevista semi-estruturada. Para análise utilizou-se estatística descritiva e a análise de conteúdo do tipo categorial. Os resultados demonstraram que na ginástica rítmica o processo de especialização motora das atletas inicia aos 12 anos; os fatores motivadores evidenciados foram o gosto pelo esporte e ser o favorito; os fatores estressantes foram ser prejudicado pelos juizes e falta de tempo para divertimento.Concluindo em uma análise geral, as atletas perceberam o contexto esportivo competitivo como mais estressante do que motivador; esta afirmação acentuou-se a partir da fase de prática motora em que o estresse competitivo para o rendimento se intensificou.This study aimed to investigate the developmental trajectory of the Brazilian Rhythmic Gymnastics Youth Team, focusing on the identification of competitive factors (motivator and stressful thatoccurs in different sport’s career phases. The sample was composed ten athletes. As measure instruments were used the Frester’s Test Psychic Load and a semi-structured interview. The data were analyzed through the descriptive statistics and categorical type of content’s analysis. The results demonstrated that in the rhythmic gymnastics the process of the athletes’ motor specialization begins at 12 years; the motivator factors evidenced were fun for sport and being the favorite; the stressful factors were being harmed by the judges and not time for fun. Concluding in a general analysis the athletes perceived the competitive sporting context as more stressful than motivator; this affirmation

  6. STATISTICAL PROPERTIES OF LONG-RANGE CONTACTS IN GLOBULAR PROTEINS

    Institute of Scientific and Technical Information of China (English)

    Xiang-hong Wang; Jian-hong Ke; Mang-xiao Hu

    2004-01-01

    The analysis of residue-residue contacts in protein structures can shed some light on our understanding of the folding and stability of proteins. In this paper, we study the statistical properties of long-range and short-range residueresidue contacts of 91 globular proteins using CSU software and analyze the importance of long-range contacts in globular protein structure. There are many short-range and long-range contacts in globular proteins, and it is found that the average number of long-range contacts per residue is 5.63 and the percentage of residue-residue contacts which are involved in longrange ones is 59.4%. In more detail, the distribution of long-range contacts in different residue intervals is investigated and it is found that the residues occurring in the interval range of 4-10 residues apart in the sequence contribute more long-range contacts to the stability of globular protein. The number of long-range contacts per residue, which is a measure of ability to form residue-residue contacts, is also calculated for 20 different amino acid residues. It is shown that hydrophobic residues (including Leu, Val, Ile, Met, Phc, Tyr, Cys and Trp) having a large number of long-range contacts easily form long-range contacts, while the hydrophilic amino acids (including Ala, Gly, Thr, His, Glu, Gin, Asp, Asn, Lys, Ser, Arg, and Pro) form long-range contacts with more difficulty. The relationship between the Fauchere-Pliska hydrophobicity scale (FPH) and the number of short-range and long-range contacts per residue for 20 amino acid residues is also studied. An approximately linear relationship between the Fauchere-Pliska hydrophobicity scale (FPH) and the number of long-range contacts per residue CL is found and can be expressed as CiL= a + b x FPHwhere a = 5.04 and b = 1.23. These results can help us to understand the role of residue-residue contacts in globular protein structure.

  7. Total protein

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003483.htm Total protein To use the sharing features on this page, please enable JavaScript. The total protein test measures the total amount of two classes ...

  8. Protein Structure

    Science.gov (United States)

    Asmus, Elaine Garbarino

    2007-01-01

    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…

  9. Whey Protein

    Science.gov (United States)

    ... Fraction de Lactosérum, Fraction de Petit-Lait, Goat Milk Whey, Goat Whey, Isolat de Protéine de Lactosérum, Isolat ... Lactosérum de Lait de Chèvre, MBP, Milk Protein, Milk Protein Isolate, Mineral Whey Concentrate, Proteínas del Suero de la Leche, Protéine ...

  10. Tau protein

    DEFF Research Database (Denmark)

    Frederiksen, Jette Lautrup Battistini; Kristensen, Kim; Bahl, Jmc

    2011-01-01

    Background: Tau protein has been proposed as biomarker of axonal damage leading to irreversible neurological impairment in MS. CSF concentrations may be useful when determining risk of progression from ON to MS. Objective: To investigate the association between tau protein concentration and 14......-3-3 protein in the cerebrospinal fluid (CSF) of patients with monosymptomatic optic neuritis (ON) versus patients with monosymptomatic onset who progressed to multiple sclerosis (MS). To evaluate results against data found in a complete literature review. Methods: A total of 66 patients with MS and/or ON from...... the Department of Neurology of Glostrup Hospital, University of Copenhagen, Denmark, were included. CSF samples were analysed for tau protein and 14-3-3 protein, and clinical and paraclinical information was obtained from medical records. Results: The study shows a significantly increased concentration of tau...

  11. Yeast Interacting Proteins Database: YJL072C, YDR489W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available alized to DNA replication origins and implicated in assembly of the DNA replication machinery Rows with this...f2p, Psf3p), which is localized to DNA replication origins and implicated in asse...the GINS complex (Sld5p, Psf1p, Psf2p, Psf3p), which is localized to DNA replication origins...sf3p), which is localized to DNA replication origins and implicated in assembly of the DNA replication machi

  12. Yeast Interacting Proteins Database: YDR013W, YDR489W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available alized to DNA replication origins and implicated in assembly of the DNA replication machinery Rows with this...f2p, Psf3p), which is localized to DNA replication origins and implicated in asse... the GINS complex (Sld5p, Psf1p, Psf2p, Psf3p), which is localized to DNA replication origins...Psf3p), which is localized to DNA replication origins and implicated in assembly of the DNA replication mach

  13. Estudo dos componentes físicos implicados no ângulo de aterrissagem no movimento do rodante, executado no aparelho solo da ginástica artística Estudio de las componentes físicas implicadas con el ángulo de aterrizaje en el movimiento de rodamiento, ejecutado en el aparato solo de gimnasia artística Study of the physical components implied with the angle of landing in the rolling movement executed at the floor apparatus in artistic gymnastic

    OpenAIRE

    Edward Rasquinha; Carlos Alberto Kelencz; Marcio Magini

    2006-01-01

    INTRODUÇÃO: A biomecânica pode ser considerada uma subárea da física responsável pelo estudo do movimento humano. No contexto do estudo do movimento, a ginástica artística é uma modalidade esportiva que intriga muito dos pesquisadores dessa área do conhecimento pela sua complexidade. Este trabalho analisa um dos movimentos mais importantes dessa modalidade, o rodante. OBJETIVO: Analisar os componentes físicos implicados na execução do movimento do rodante no aparelho solo, procurando estabele...

  14. Protein-Protein Interaction Databases

    DEFF Research Database (Denmark)

    Szklarczyk, Damian; Jensen, Lars Juhl

    2015-01-01

    of research are explored. Here we present an overview of the most widely used protein-protein interaction databases and the methods they employ to gather, combine, and predict interactions. We also point out the trade-off between comprehensiveness and accuracy and the main pitfall scientists have to be aware......Years of meticulous curation of scientific literature and increasingly reliable computational predictions have resulted in creation of vast databases of protein interaction data. Over the years, these repositories have become a basic framework in which experiments are analyzed and new directions...

  15. Protein Crystallization

    Science.gov (United States)

    Chernov, Alexander A.

    2005-01-01

    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.

  16. As práticas escolares e a formação cívico-patriótica no ginásio mineiro de Uberlândia, em Minas Gerais, Brasil (1920-1970 - School practices and civic and patriotic education in lower secondary school in Uberlândia, Minas Gerais, Brazil (1920/1970

    Directory of Open Access Journals (Sweden)

    Giseli Cristina do Vale Gatti, Geraldo Inácio Filho

    2011-03-01

    Full Text Available Resumo Trata-se do exame  das  práticas  escolares efetivadas no Ginásio Mineiro de  Uberlândia,  em  Minas Gerais, Brasil, no período compreendido entre as décadas de 1920  e de 1970.  Depreende-se do cotejamento das evidências (manuscritas, impressas, orais e iconográficas com  o  contexto  sócio-histórico  da   época   que:  a metodologia de ensino no período era tradicional; a consolidação de uma representação social da  qualidade do ensino do antigo Ginásio (com  caráter   humanístico  e  com  preocupação  com  a  moral,  a disciplina e  os  bons  costumes; o  entendimento  da  escola como centro social, esportivo e cultural da  cidade,  sendo as datas cívicas muito comemoradas. Desse modo, ao conteúdo humanístico, ligado à disseminação de princípios morais aceitos socialmente, somava-se a ênfase no civismo e no patriotismo. Palavras-chave: escola; civismo; patriotismo; currículo; práticas.   SCHOOL PRACTICES AND CIVIC AND PATRIOTIC EDUCATION IN LOWER SECONDARY SCHOOL  IN UBERLANDIA, MINAS GERAIS, BRAZIL (1920/1970 Abstract This  study  is  an  examination  of  school  practices in  the  Lower Secondary  School  in  Uberlandia,  Minas  Gerais,  Brazil,  in  the decades from the 1920s  to 1970s. Conclusions are drawn from the collating of  evidence (manuscript,  printed,  oral and  iconographic with the social historical context of the time in which: the teaching methodology was traditional, consolidation of a social representation of  the  quality  of  teaching  of  the   ancient  Gymnasium  (with  a humanistic  character  and  concern  with morals,  discipline e  good habits; the  school as the social, sporting and cultural center of the city with the civic dates being highly commemorated. In this way, the emphasis  on   civic  education  and   patriotism   was  added  to   a humanistic  content  connected  with  the

  17. Formulação de Estratégia Competitiva pelo Modelo de Campos e Armas da Competição: Verificação da Aplicabilidade e Adequação a uma Rede de Academias de Ginástica

    Directory of Open Access Journals (Sweden)

    Renato Zanuto Pereira

    2013-12-01

    Full Text Available Porter e os teóricos da RBV, apesar de exporem com clareza seus conceitos sobre estratégia competitiva, não mostram claramente como empregá-los para a formulação da estratégia competitiva empresarial, o que dificulta a aplicação prática. Isso motivou os autores deste artigo a pesquisarem como outros teóricos contornam essa dificuldade e encontraram o modelo de campos e armas da competição (CAC de Contador. O CAC, modelo simultaneamente analógico e simbólico, qualitativo e quantitativo, consistentemente estruturado e cientificamente validado por meio de muitas pesquisas realizadas em empresas, serve primordialmente para entender, explicar e aumentar a competitividade empresarial. A validação do CAC consistiu em verificar epistemologicamente a aderência à realidade das empresas dos seus conceitos e constructos. Para suprir a lacuna nas obras dos citados autores, Contador propôs um processo de formulação da estratégia competitiva. Como esse processo ainda foi testado poucas vezes, os autores resolveram realizar o estudo ora relatado, cujo objetivo era verificar se esse processo é suficiente para propor estratégias competitivas que aumentassem a competitividade de uma rede de academias de ginástica. Por meio de uma pesquisa exploratória de natureza qualiquantitativa e, com base no método popperiano hipotético-dedutivo, constatou-se a suficiência do processo, pois todas as estratégias de negócio propostas foram aceitas pelo diretor proprietário da rede de academias e apenas 4,5% das ações estratégicas operacionais sugeridas não foram, o que levou à aceitação da hipótese. DOI:10.5585/riae.v12i3.1967

  18. Estado emocional de alunos da primeira série de um Grupo Escolar - Ginásio da cidade de São Paulo, Brasil: problemática de saúde pública? Emotional disturbances of 1st grade school children: a Public Health Problem?

    Directory of Open Access Journals (Sweden)

    Helena Savastano

    1977-12-01

    Full Text Available Estudou-se uma amostra representativa de alunos da 1.ª série de um Grupo Escolar-Ginásio da rede estadual da cidade de São Paulo, com o objetivo de compreender a dinâmica emocional dessas crianças. Os alunos foram estratificados em fracos e não fracos quanto à aprendizagem e disciplinamento. Utilizou-se o teste de apercepção temática de Bellak e Bellak e os resultados demonstraram, que 43% das crianças não estão emocionalmente ajustadas para enfrentar o ambiente escolar, onde a figura do adulto (professor é visualizada como agressiva e os castigos são vistos, pelas crianças, como ameaçadores; os alunos fracos revelaram maior atraso no desenvolvimento psicossocial em relação aos não fracos. Estes dados, possivelmente, esclarecem parte das dificuldades de adaptação dessas crianças �� situação escolar e sugerem: 1º maior atenção dos técnicos de educação, de saúde e áreas correlatas, para esses problemas; 2º maiores conhecimentos pelos educadores, dos aspectos do desenvolvimento psicossocial da criança.Psychological and epidemiological aspects of emotional dynamics of children enroled in the first grade of a state school of the city of São Paulo, Brazil, were studied based on results of Children's Tematic Test (CAT, of Bellak and Bellak. The mentioned test showed that the group is made up of emotionally immature children, lacking affection, especially those considered of low learning capacity. The figure of the adult, as seen by the students, is inadequate, punitive, indiferent and agressive. The results suggest that teachers should have a greater understanding reference to such problems and should give attention to these students, thus leading to the conclusion that first grade classes should not have so many students. The results also suggest that parents should have more knowledge and understanding as regards child development from conception, as well as better family struture as to more adequate

  19. Protein inference: A protein quantification perspective.

    Science.gov (United States)

    He, Zengyou; Huang, Ting; Liu, Xiaoqing; Zhu, Peijun; Teng, Ben; Deng, Shengchun

    2016-08-01

    In mass spectrometry-based shotgun proteomics, protein quantification and protein identification are two major computational problems. To quantify the protein abundance, a list of proteins must be firstly inferred from the raw data. Then the relative or absolute protein abundance is estimated with quantification methods, such as spectral counting. Until now, most researchers have been dealing with these two processes separately. In fact, the protein inference problem can be regarded as a special protein quantification problem in the sense that truly present proteins are those proteins whose abundance values are not zero. Some recent published papers have conceptually discussed this possibility. However, there is still a lack of rigorous experimental studies to test this hypothesis. In this paper, we investigate the feasibility of using protein quantification methods to solve the protein inference problem. Protein inference methods aim to determine whether each candidate protein is present in the sample or not. Protein quantification methods estimate the abundance value of each inferred protein. Naturally, the abundance value of an absent protein should be zero. Thus, we argue that the protein inference problem can be viewed as a special protein quantification problem in which one protein is considered to be present if its abundance is not zero. Based on this idea, our paper tries to use three simple protein quantification methods to solve the protein inference problem effectively. The experimental results on six data sets show that these three methods are competitive with previous protein inference algorithms. This demonstrates that it is plausible to model the protein inference problem as a special protein quantification task, which opens the door of devising more effective protein inference algorithms from a quantification perspective. The source codes of our methods are available at: http://code.google.com/p/protein-inference/.

  20. 'But Yet and Still the Cotton Gin Kept on Working...'

    Science.gov (United States)

    Walker, Alice

    1983-01-01

    Describes the work of Friends of the Children of Mississippi, a Head Start program which began in the late 1960s and for which the author was hired to develop Black history materials for teacher training. Presents excerpts from the autobiographies of several Black women trainees in the program. (GC)

  1. Salience and Blindness: A Haptic Hike on Gins Mountain

    OpenAIRE

    Garnier, Marie-Dominique

    2016-01-01

    This paper attempts to follow an improbable ridge line between architecture, geography and linguistics, between the optic and haptic ends of the concept of salience, through a reading of Helen Keller Or Arakawa, Madeline Gins’s 1994 essay-cum-joint-biography partly devoted to “salience” approached through the blind figure of Helen Keller (1880-1968). In a chapter titled “Or Mountains Or Lines”, prominent features envisaged from a sighted perception give way, under the condition of blindness, ...

  2. Ma räägin sulle loo / Margit Tõnson

    Index Scriptorium Estoniae

    Tõnson, Margit, 1978-

    2011-01-01

    Urmas Vadi (autor ja lavastaja) lavastusest "Minu isa 20 aastat hiljem" Ugala teatri kohvikus ja Norra näitekirjaniku Jon Fosse näidendi „Üks suvepäev” lavastusest Theatrumis, lavastaja Lembit Peterson

  3. Grafting of protein-protein binding sites

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A strategy for grafting protein-protein binding sites is described. Firstly, key interaction residues at the interface of ligand protein to be grafted are identified and suitable positions in scaffold protein for grafting these key residues are sought. Secondly, the scaffold proteins are superposed onto the ligand protein based on the corresponding Ca and Cb atoms. The complementarity between the scaffold protein and the receptor protein is evaluated and only matches with high score are accepted. The relative position between scaffold and receptor proteins is adjusted so that the interface has a reasonable packing density. Then the scaffold protein is mutated to corresponding residues in ligand protein at each candidate position. And the residues having bad steric contacts with the receptor proteins, or buried charged residues not involved in the formation of any salt bridge are mutated. Finally, the mutated scaffold protein in complex with receptor protein is co-minimized by Charmm. In addition, we deduce a scoring function to evaluate the affinity between mutated scaffold protein and receptor protein by statistical analysis of rigid binding data sets.

  4. Prevalência do uso e conhecimento de esteroides anabolizantes androgênicos por estudantes e professores de educação física que atuam em academias de ginástica Prevalence of the use of anabolic androgenic steroids by physical education students and teachers who work in health clubs

    Directory of Open Access Journals (Sweden)

    Odilon Salim Costa Abrahin

    2013-02-01

    Full Text Available INTRODUÇÃO: Os esteroides anabólicos androgênicos (EAA são substâncias, quimicamente semelhantes à testosterona, utilizadas para o tratamento/controle de diversas doenças. Contudo, tais substâncias estão sendo empregadas de forma não terapêutica e indiscriminada com finalidades de melhora da performance esportiva e principalmente estética. OBJETIVO: analisar a prevalência do uso e o conhecimento de EAA por estudantes e professores de educação física que atuam em academias de ginástica de Belém, PA. Utilizou-se para a coleta de dados um questionário fechado e anônimo, aplicado a 117 pesquisados. A comparação da prevalência do uso e o grau de conhecimento dos pesquisados sobre EAA foi realizada através de estatística não paramétrica, prova de X² (Qui-quadrado, considerando o intervalo de confiança de 95% e p Anabolic androgenic steroids (AAS are chemically similar to testosterone, used for the treatment/control of various diseases. However, these substances are being used in non-therapeutic and indiscriminate purposes to improve sports performance and mainly esthetics. This study aimed to analyze the prevalence of AAS use and information of undergraduates and physical education teachers working in fitness centers in Belém-PA. A closed anonymous questionnaire was applied to 117 volunteers as an instrument. Comparison of the prevalence of use and degree of information of the respondents about AAS was performed using statistical non-parametric test X² (chi-square, considering the range of 95%, significant when p<0.05. The average age of the participants was 28.0 ± 6.3 years and the prevalence of AAS use was of 31.6%. The highest prevalence found was among specialist professionals (39.3%, the main motivation for the use of AAS was 75.6% to esthetics. Regarding the information, it was found that the drugs were classified as AAS: Durateston, Deca-Durabolin, Oxandrolona/Winstrol. However, these professionals took other

  5. A influência do ciclo menstrual na flexibilidade em praticantes de ginástica de academia La influencia del ciclo menstrual sobre la flexibilidad en practicantes de gimnasia de academia The influence of the menstrual cycle on the flexibility in practitioners of gymnastics at fitness centers

    Directory of Open Access Journals (Sweden)

    Solange Mattos Melegario

    2006-06-01

    Full Text Available Este estudo teve por objetivo investigar se existem diferenças no grau de flexibilidade nas fases do ciclo menstrual de mulheres adultas jovens praticantes de ginástica de academia. A amostra intencional foi composta de 20 mulheres, com idade de 18 a 35 anos (25,8 ± 6,06, com o ciclo menstrual regular (28 até 32 dias e que não faziam uso de anticoncepcional oral. Dados referentes ao ciclo menstrual e atividade física habitual foram obtidos através da aplicação de um questionário. A flexibilidade foi aferida através da goniometria, utilizando-se oito movimentos, em três fases do ciclo menstrual. Os sujeitos foram submetidos a um teste hormonal, em que foram verificadas as taxas de estrona, estradiol e progesterona. O tratamento estatístico foi feito através de análise descritiva e inferencial (teste de Kolmogorov-Smirnov e ANOVA. Os resultados encontrados demonstraram que não houve diferença significativa (p Este estudio ha tenido por objetivo investigar si existen diferencias en el grado de flexibilidad en las fases del ciclo menstrual de mujeres adultas jóvenes practicantes de gimnasia de academia. La muestra intencional fue compuesta de 20 mujeres, con edades entre 18 a 35 años (25,8 ± 6,06, con ciclo menstrual regular (28 a 32 días y que no hacían uso de anticonceptivo oral. Datos referentes al ciclo menstrual y actividad física habitual fueron obtenidos a través de una encuesta. La flexibilidad fue medida a través de la goniometría, utilizándose ocho movimientos, en tres fases del ciclo menstrual. Los individuos fueron sometidos a un test hormonal, en donde se verificaron la tasa de estrona, estradiol y progesterona. El tratamiento estadístico fue hecho a través del análisis descriptivo y de inferencia (test de Kolmogorov-Smirnov y ANOVA. Los resultados encontrados mostraron que no hubo diferencia significativa (p This study aims to verify if there are differences in the degree of flexibility in the phases of

  6. Confiabilidade intra e interexaminadores da fotogrametria na classificação do grau de lipodistrofia ginóide em mulheres assintomáticas Intra and inter-examiner reliability of photogrammetry in the classification of the degree of gynoid lypodystrophy in asymptomatic women

    Directory of Open Access Journals (Sweden)

    Ana Maria da Silva Mendonça

    2009-06-01

    Full Text Available A lipodistrofia ginóide (celulite é uma afecção dermatológica comum entre as mulheres. Uma de suas formas de avaliação é a inspeção visual por meio da fotogrametria. Entretanto, não foram encontrados estudos que verifiquem a repetibilidade e reprodutibilidade dessa avaliação. O objetivo deste estudo foi verificar a confiabilidade intra e interexaminadores da avaliação da celulite por meio da fotogrametria. Foram fotografadas e avaliadas as regiões glúteas de 50 mulheres (26,14±4,45 anos. A reprodutibilidade foi testada pela avaliação da mesma fotografia por dois examinadores em duas ocasiões diferentes, com intervalo de um ano; a repetibilidade por um mesmo examinador, com intervalo de uma semana. Os dados foram analisados estatisticamente e utilizado o índice Kappa ponderado. Os resultados indicaram substancial correlação (κ=0,70 entre os avaliadores para o grau de celulite no glúteo superior e moderada correlação (κ=0,50 para o grau de celulite no glúteo inferior. Nas análises de repetibilidade, os dados demonstraram excelente correlação (κ=0,81 para o grau de celulite no glúteo superior e substancial correlação (κ=0,75 para os graus no glúteo inferior. O método proposto para qualificação dos diferentes graus de celulite pela fotogrametria apresentou confiabilidade aceitável intra e interexaminadores para a maioria das regiões avaliadas, com exceção da região do glúteo inferior.Gynoid lypodystrophy (cellulitis is a common condition among women. One of its forms of evaluation is the visual inspection by photogrammetry. However, no studies could be found in literature on the repeatability and reproducibility of such evaluation. The purpose of this study was to assess reliability intra and inter-examiner of cellulitis evaluation by photogrammetry. The gluteal regions of 50 women (mean age 26.14±4.45 years were photographed and evaluated. Reproducibility was tested by evaluation of the same

  7. Novas Tecnologias e Novas Formas de Organização do Trabalho do Professor nas Academias de Ginástica New Technologies and New Ways of Organizing the Work of the Teacher at Sports Centers Nuevas Tecnologías y Nuevas Formas en Organizacion de Trabajo de Profesor en Gimnasios de Gimnasia

    Directory of Open Access Journals (Sweden)

    2007-09-01

    Full Text Available A partir de um estudo de caso realizado em uma grande academia de Goiânia, trago este recorte com o objetivo de compreender como as transformações tecnológicas nas academias de ginástica têm influenciado a organização do trabalho neste espaço. A pesquisa foi desenvolvida no primeiro semestre de 2004. Para coleta de dados foram realizadas entrevistas semi-estruturadas com professores da academia pesquisada. A academia escolhida, cujo nome fictício será Academia X, foi a que representa o que há e mais avançado nesse ramo de atividade em Goiânia. Assim, poderão ser apontadas algumas tendências para as demais academias de acordo com os resultados obtidos. Isso só é possível porque a tendência das academias menos desenvolvidas é acompanhar as mais desenvolvidas. PALAVRAS-CHAVE: academia – tecnologia – trabalho. Based on a case study undertaken in a large gym in the city of Goiânia, Brazil, I present this paper that aims at understanding how technological changes in gyms have infl uenced the organization of work in such spaces. This research was developed in the first quarter of 2004. Semi-structured interviews with teachers from the investigated gym were done for data collection. The chosen gym, herein renamed as Academia X, was the one that had the most advanced technology available for this business sector in the city of Goiânia. The achieved results may point to future trends for the other gyms. This is only possible because lesser developed gyms tend to match their more developed counterparts. KEYWORDS: gym – technology – work. A partir de un estudio de caso realizado en una gran academia de la ciudad de Goiânia, traigo este resumen con el objetivo de compreender cómo las transformaciones tecnológicas en las academias de gimnasia han infl uenciado la organización del trabajo en este espacio. La investigación fue desarrollada en el primer semestre de 2004. Para adquirir datos fueron realizadas entrevistas semi

  8. EDITORIAL: Precision proteins Precision proteins

    Science.gov (United States)

    Demming, Anna

    2010-06-01

    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

  9. Scaffolds for blocking protein-protein interactions.

    Science.gov (United States)

    Hershberger, Stefan J; Lee, Song-Gil; Chmielewski, Jean

    2007-01-01

    Due to the pivotal roles that protein-protein interactions play in a plethora of biological processes, the design of therapeutic agents targeting these interactions has become an attractive and important area of research. The development of such agents is faced with a variety of challenges. Nevertheless, considerable progress has been made in the design of proteomimetics capable of disrupting protein-protein interactions. Those inhibitors based on molecular scaffold designs hold considerable interest because of the ease of variation in regard to their displayed functionality. In particular, protein surface mimetics, alpha-helical mimetics, beta-sheet/beta-strand mimetics, as well as beta-turn mimetics have successfully modulated protein-protein interactions involved in such diseases as cancer and HIV. In this review, current progress in the development of molecular scaffolds designed for the disruption of protein-protein interactions will be discussed with an emphasis on those active against biological targets.

  10. Fusion-protein-assisted protein crystallization.

    Science.gov (United States)

    Kobe, Bostjan; Ve, Thomas; Williams, Simon J

    2015-07-01

    Fusion proteins can be used directly in protein crystallization to assist crystallization in at least two different ways. In one approach, the `heterologous fusion-protein approach', the fusion partner can provide additional surface area to promote crystal contact formation. In another approach, the `fusion of interacting proteins approach', protein assemblies can be stabilized by covalently linking the interacting partners. The linker connecting the proteins plays different roles in the two applications: in the first approach a rigid linker is required to reduce conformational heterogeneity; in the second, conversely, a flexible linker is required that allows the native interaction between the fused proteins. The two approaches can also be combined. The recent applications of fusion-protein technology in protein crystallization from the work of our own and other laboratories are briefly reviewed.

  11. Protein docking prediction using predicted protein-protein interface

    Directory of Open Access Journals (Sweden)

    Li Bin

    2012-01-01

    Full Text Available Abstract 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.

  12. Protein Crystal Based Nanomaterials

    Science.gov (United States)

    Bell, Jeffrey A.; VanRoey, Patrick

    2001-01-01

    This is the final report on a NASA Grant. It concerns a description of work done, which includes: (1) Protein crystals cross-linked to form fibers; (2) Engineering of protein to favor crystallization; (3) Better knowledge-based potentials for protein-protein contacts; (4) Simulation of protein crystallization.

  13. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  14. Avaliação do conhecimento quanto a prevenção do câncer da pele e sua relação com exposição solar em freqüentadores de academia de ginástica, em Recife Evaluation about knowledge of skin cancer prevention and its relation with sun exposure among gym members in the city of Recife

    Directory of Open Access Journals (Sweden)

    Clarissa da Hora

    2003-12-01

    Full Text Available FUNDAMENTOS: O câncer da pele tem aumentado sua prevalência mundial. É importante saber o nível de conhecimento da população recifense. OBJETIVOS: Diante da carência de dados estatísticos referentes ao conhecimento e prevenção relativos à exposição solar e seus danos, sendo o principal o câncer da pele; conduziu-se um estudo epidemiológico nas principais academias de ginástica da cidade de Recife, PE. O estudo teve como objetivo avaliar o conhecimento dos freqüentadores das academias de ginástica daquela cidade sobre a prevenção e conhecimento relativo ao câncer da pele. MÉTODOS: Foram aplicados 500 questionários com 22 itens referentes à caracterização individual por meio de dados como idade, sexo, renda familiar, grau de instrução, hábitos relativos à exposição solar. Para análise estatística foi aplicado o teste Qui- quadrado de Pearson. As freqüências das respostas foram agrupadas em gráficos e tabelas que permitiram discutir os resultados e compará-los com a literatura. RESULTADOS: Verificou-se o predomínio do sexo feminino e da faixa etária abaixo dos 40 anos na amostra. A cor branca prevaleceu em relação à negra. A renda familiar modal ficou acima dos 10 salários mínimos. CONCLUSÃO: A maioria dos indivíduos conhece os riscos e danos relacionados à exposição solar, assim como também os meios de proteção. Porém os entrevistados expunham-se a esses riscos valendo-se de variadas medidas de proteção.BACKGROUND: The prevalence of skin cancer is rising worldwide. It is important to know the level of understanding of the population in the city of Recife. OBJECTIVE: Faced with the lack of statistical data on the knowledge and prevention of negative effects of sun exposure and especially skin cancer, an epidemiological study was carried out on members attending the main gyms located in the city of Recife. The study aimed at assessing their knowledge about skin cancer and its prevention. METHOD

  15. Protein folding, protein homeostasis, and cancer

    Institute of Scientific and Technical Information of China (English)

    John H. Van Drie

    2011-01-01

    Proteins fold into their functional 3-dimensional structures from a linear amino acid sequence. In vitro this process is spontaneous; while in vivo it is orchestrated by a specialized set of proteins, called chaperones. Protein folding is an ongoing cellular process, as cellular proteins constantly undergo synthesis and degradation. Here emerging links between this process and cancer are reviewed. This perspective both yields insights into the current struggle to develop novel cancer chemotherapeutics and has implications for future chemotherapy discovery.

  16. Oligomeric protein structure networks: insights into protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Brinda KV

    2005-12-01

    Full Text Available Abstract Background Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In this study, oligomeric protein structures are viewed from a network perspective to obtain new insights into protein association. Structure graphs of proteins have been constructed from a non-redundant set of protein oligomer crystal structures by considering amino acid residues as nodes and the edges are based on the strength of the non-covalent interactions between the residues. The analysis of such networks has been carried out in terms of amino acid clusters and hubs (highly connected residues with special emphasis to protein interfaces. Results A variety of interactions such as hydrogen bond, salt bridges, aromatic and hydrophobic interactions, which occur at the interfaces are identified in a consolidated manner as amino acid clusters at the interface, from this study. Moreover, the characterization of the highly connected hub-forming residues at the interfaces and their comparison with the hubs from the non-interface regions and the non-hubs in the interface regions show that there is a predominance of charged interactions at the interfaces. Further, strong and weak interfaces are identified on the basis of the interaction strength between amino acid residues and the sizes of the interface clusters, which also show that many protein interfaces are stronger than their monomeric protein cores. The interface strengths evaluated based on the interface clusters and hubs also correlate well with experimentally determined dissociation constants for known complexes. Finally, the interface hubs identified using the present method correlate very well with experimentally determined hotspots in the interfaces of protein complexes obtained from the Alanine Scanning Energetics database (ASEdb. A few predictions of interface hot

  17. Protein-losing enteropathy

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/007338.htm Protein-losing enteropathy To use the sharing features on this page, please enable JavaScript. Protein-losing enteropathy is an abnormal loss of protein ...

  18. Conductometric monitoring of protein-protein interactions.

    Science.gov (United States)

    Spera, Rosanna; Festa, Fernanda; Bragazzi, Nicola L; Pechkova, Eugenia; LaBaer, Joshua; Nicolini, Claudio

    2013-12-06

    Conductometric monitoring of protein-protein and protein-sterol interactions is here proved feasible by coupling quartz crystal microbalance with dissipation monitoring (QCM_D) to nucleic acid programmable protein arrays (NAPPA). The conductance curves measured in NAPPA microarrays printed on quartz surface allowed the identification of binding events between the immobilized proteins and the query. NAPPA allows the immobilization on the quartz surface of a wide range of proteins and can be easily adapted to generate innumerous types of biosensors. Indeed multiple proteins on the same quartz crystal have been tested and envisaged proving the possibility of analyzing the same array for several distinct interactions. Two examples of NAPPA-based conductometer applications with clinical relevance are presented herein, the interaction between the transcription factors Jun and ATF2 and the interaction between Cytochrome P540scc and cholesterol.

  19. Relação entre os achados audiométricos e as queixas auditivas e extra-auditivas dos professores de uma academia de ginástica Relationship between audiometric findings and auditory and extra-auditory complaints of physical education teachers

    Directory of Open Access Journals (Sweden)

    Isabela Freixo Côrtes de Andrade

    2010-01-01

    Full Text Available OBJETIVOS: Estudar as queixas auditivas e extra-auditivas de professores de uma academia de ginástica expostos à música eletronicamente amplificada, descrever os achados audiométricos e investigar a influência das variáveis, tempo de profissão, carga horária de trabalho e presença de entalhe audiométrico. MÉTODOS: Inicialmente, foi realizada a medida dos níveis de pressão sonora das seis salas de aula da academia (média 101,4 dB(A. Em seguida, 32 professores foram avaliados por meio de anamnese e pesquisa dos limiares tonais por via aérea, e a presença de entalhe audiométrico foi investigada. RESULTADOS: Foi encontrada uma elevada porcentagem de professores (87,5% com exposições extra-ocupacionais. As queixas mais frequentes foram: intolerância aos sons intensos (43,8%, tontura (12,5%; irritabilidade e nervosismo (28,1%; insônia (31,3%; dor de cabeça (37,5%; zumbido (12,5%; plenitude auricular (12,5% e dificuldade de escutar às vezes (43,8%. Em relação aos achados audiométricos, 9,37% apresentaram alteração: 3,12% por perda neurossensorial bilateral e 6,25% queda nas frequências de 3000 Hz ou 4000 Hz. A frequência mais acometida pelo entalhe audiométrico foi 6000 Hz, sendo que 50% o apresentaram em, pelo menos, uma orelha. Não houve diferença estatisticamente significante na comparação entre o tempo de profissão, horas trabalhadas e queixas com os resultados do entalhe audiométrico. CONCLUSÃO: 68,75% dos professores apresentaram queixas extra-auditivas. Os resultados mostraram que apesar de ocorrer uma porcentagem pequena (9,37% de perda auditiva na população estudada, já existe na metade dos professores entalhe audiométrico em pelo menos uma orelha.PURPOSE: To study auditory and extra-auditory complaints of physical education teachers exposed to electronically amplified music, to describe their audiometric findings, and to investigate the importance of the variables time of profession, work-journey, and

  20. Protein sequence comparison and protein evolution

    Energy Technology Data Exchange (ETDEWEB)

    Pearson, W.R. [Univ. of Virginia, Charlottesville, VA (United States). Dept. of Biochemistry

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. This tutorial examines how the information conserved during the evolution of a protein molecule can be used to infer reliably homology, and thus a shared proteinfold and possibly a shared active site or function. The authors start by reviewing a geological/evolutionary time scale. Next they look at the evolution of several protein families. During the tutorial, these families will be used to demonstrate that homologous protein ancestry can be inferred with confidence. They also examine different modes of protein evolution and consider some hypotheses that have been presented to explain the very earliest events in protein evolution. The next part of the tutorial will examine the technical aspects of protein sequence comparison. Both optimal and heuristic algorithms and their associated parameters that are used to characterize protein sequence similarities are discussed. Perhaps more importantly, they survey the statistics of local similarity scores, and how these statistics can both be used to improve the selectivity of a search and to evaluate the significance of a match. They them examine distantly related members of three protein families, the serine proteases, the glutathione transferases, and the G-protein-coupled receptors (GCRs). Finally, the discuss how sequence similarity can be used to examine internal repeated or mosaic structures in proteins.

  1. Prediction of Protein-Protein Interactions Using Protein Signature Profiling

    Institute of Scientific and Technical Information of China (English)

    Mahmood A. Mahdavi; Yen-Han Lin

    2007-01-01

    Protein domains are conserved and functionally independent structures that play an important role in interactions among related proteins. Domain-domain inter- actions have been recently used to predict protein-protein interactions (PPI). In general, the interaction probability of a pair of domains is scored using a trained scoring function. Satisfying a threshold, the protein pairs carrying those domains are regarded as "interacting". In this study, the signature contents of proteins were utilized to predict PPI pairs in Saccharomyces cerevisiae, Caenorhabditis ele- gans, and Homo sapiens. Similarity between protein signature patterns was scored and PPI predictions were drawn based on the binary similarity scoring function. Results show that the true positive rate of prediction by the proposed approach is approximately 32% higher than that using the maximum likelihood estimation method when compared with a test set, resulting in 22% increase in the area un- der the receiver operating characteristic (ROC) curve. When proteins containing one or two signatures were removed, the sensitivity of the predicted PPI pairs in- creased significantly. The predicted PPI pairs are on average 11 times more likely to interact than the random selection at a confidence level of 0.95, and on aver- age 4 times better than those predicted by either phylogenetic profiling or gene expression profiling.

  2. Inferring Protein Associations Using Protein Pulldown Assays

    Energy Technology Data Exchange (ETDEWEB)

    Sharp, Julia L.; Anderson, Kevin K.; Daly, Don S.; Auberry, Deanna L.; Borkowski, John J.; Cannon, William R.

    2007-02-01

    Background: One method to infer protein-protein associations is through a “bait-prey pulldown” assay using a protein affinity agent and an LC-MS (liquid chromatography-mass spectrometry)-based protein identification method. False positive and negative protein identifications are not uncommon, however, leading to incorrect inferences. Methods: A pulldown experiment generates a protein association matrix wherein each column represents a sample from one bait protein, each row represents one prey protein and each cell contains a presence/absence association indicator. Our method evaluates the presence/absence pattern across a prey protein (row) with a Likelihood Ratio Test (LRT), computing its p-value with simulated LRT test statistic distributions after a check with simulated binomial random variates disqualified the large sample 2 test. A pulldown experiment often involves hundreds of tests so we apply the false discovery rate method to control the false positive rate. Based on the p-value, each prey protein is assigned a category (specific association, non-specific association, or not associated) and appraised with respect to the pulldown experiment’s goal and design. The method is illustrated using a pulldown experiment investigating the protein complexes of Shewanella oneidensis MR-1. Results: The Monte Carlo simulated LRT p-values objectively reveal specific and ubiquitous prey, as well as potential systematic errors. The example analysis shows the results to be biologically sensible and more realistic than the ad hoc screening methods previously utilized. Conclusions: The method presented appears to be informative for screening for protein-protein associations.

  3. Polymer Directed Protein Assemblies

    NARCIS (Netherlands)

    van Rijn, Patrick

    2013-01-01

    Protein aggregation and protein self-assembly is an important occurrence in natural systems, and is in some form or other dictated by biopolymers. Very obvious influences of biopolymers on protein assemblies are, e. g., virus particles. Viruses are a multi-protein assembly of which the morphology is

  4. Mirror image proteins.

    Science.gov (United States)

    Zhao, Le; Lu, Wuyuan

    2014-10-01

    Proteins composed entirely of unnatural d-amino acids and the achiral amino acid glycine are mirror image forms of their native l-protein counterparts. Recent advances in chemical protein synthesis afford unique and facile synthetic access to domain-sized mirror image d-proteins, enabling protein research to be conducted through 'the looking glass' and in a way previously unattainable. d-Proteins can facilitate structure determination of their native l-forms that are difficult to crystallize (racemic X-ray crystallography); d-proteins can serve as the bait for library screening to ultimately yield pharmacologically superior d-peptide/d-protein therapeutics (mirror-image phage display); d-proteins can also be used as a powerful mechanistic tool for probing molecular events in biology. This review examines recent progress in the application of mirror image proteins to structural biology, drug discovery, and immunology.

  5. Protein- protein interaction detection system using fluorescent protein microdomains

    Science.gov (United States)

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2010-02-23

    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.

  6. Urine Protein and Urine Protein to Creatinine Ratio

    Science.gov (United States)

    ... limited. Home Visit Global Sites Search Help? Urine Protein and Urine Protein to Creatinine Ratio Share this page: Was this page helpful? Also known as: 24-Hour Urine Protein; Urine Total Protein; Urine Protein to Creatinine Ratio; ...

  7. IGSF9 Family Proteins

    DEFF Research Database (Denmark)

    Hansen, Maria; Walmod, Peter Schledermann

    2013-01-01

    The Drosophila protein Turtle and the vertebrate proteins immunoglobulin superfamily (IgSF), member 9 (IGSF9/Dasm1) and IGSF9B are members of an evolutionarily ancient protein family. A bioinformatics analysis of the protein family revealed that invertebrates contain only a single IGSF9 family gene......, the longest isoforms of the proteins have the same general organization as the neural cell adhesion molecule family of cell adhesion molecule proteins, and like this family of proteins, IGSF9 family members are expressed in the nervous system. A review of the literature revealed that Drosophila Turtle...... facilitates homophilic cell adhesion. Moreover, IGSF9 family proteins have been implicated in the outgrowth and branching of neurites, axon guidance, synapse maturation, self-avoidance, and tiling. However, despite the few published studies on IGSF9 family proteins, reports on the functions of both Turtle...

  8. Physics of protein motility and motor proteins

    Science.gov (United States)

    Kolomeisky, Anatoly B.

    2013-09-01

    Motor proteins are enzymatic molecules that transform chemical energy into mechanical motion and work. They are critically important for supporting various cellular activities and functions. In the last 15 years significant progress in understanding the functioning of motor proteins has been achieved due to revolutionary breakthroughs in single-molecule experimental techniques and strong advances in theoretical modelling. However, microscopic mechanisms of protein motility are still not well explained, and the collective efforts of many scientists are needed in order to solve these complex problems. In this special section the reader will find the latest advances on the difficult road to mapping motor proteins dynamics in various systems. Recent experimental developments have allowed researchers to monitor and to influence the activity of single motor proteins with a high spatial and temporal resolution. It has stimulated significant theoretical efforts to understand the non-equilibrium nature of protein motility phenomena. The latest results from all these advances are presented and discussed in this special section. We would like to thank the scientists from all over the world who have reported their latest research results for this special section. We are also grateful to the staff and editors of Journal of Physics: Condensed Matter for their invaluable help in handling all the administrative and refereeing activities. The field of motor proteins and protein motility is fast moving, and we hope that this collection of articles will be a useful source of information in this highly interdisciplinary area. Physics of protein motility and motor proteins contents Physics of protein motility and motor proteinsAnatoly B Kolomeisky Identification of unique interactions between the flexible linker and the RecA-like domains of DEAD-box helicase Mss116 Yuan Zhang, Mirkó Palla, Andrew Sun and Jung-Chi Liao The load dependence of the physical properties of a molecular motor

  9. Polymer Directed Protein Assemblies

    Directory of Open Access Journals (Sweden)

    Patrick van Rijn

    2013-05-01

    Full Text Available Protein aggregation and protein self-assembly is an important occurrence in natural systems, and is in some form or other dictated by biopolymers. Very obvious influences of biopolymers on protein assemblies are, e.g., virus particles. Viruses are a multi-protein assembly of which the morphology is dictated by poly-nucleotides namely RNA or DNA. This “biopolymer” directs the proteins and imposes limitations on the structure like the length or diameter of the particle. Not only do these bionanoparticles use polymer-directed self-assembly, also processes like amyloid formation are in a way a result of directed protein assembly by partial unfolded/misfolded biopolymers namely, polypeptides. The combination of proteins and synthetic polymers, inspired by the natural processes, are therefore regarded as a highly promising area of research. Directed protein assembly is versatile with respect to the possible interactions which brings together the protein and polymer, e.g., electrostatic, v.d. Waals forces or covalent conjugation, and possible combinations are numerous due to the large amounts of different polymers and proteins available. The protein-polymer interacting behavior and overall morphology is envisioned to aid in clarifying protein-protein interactions and are thought to entail some interesting new functions and properties which will ultimately lead to novel bio-hybrid materials.

  10. Protein and protein hydrolysates in sports nutrition.

    Science.gov (United States)

    van Loon, Luc J C; Kies, Arie K; Saris, Wim H M

    2007-08-01

    With the increasing knowledge about the role of nutrition in increasing exercise performance, it has become clear over the last 2 decades that amino acids, protein, and protein hydrolysates can play an important role. Most of the attention has been focused on their effects at a muscular level. As these nutrients are ingested, however, it also means that gastrointestinal digestibility and absorption can modulate their efficacy significantly. Therefore, discussing the role of amino acids, protein, and protein hydrolysates in sports nutrition entails holding a discussion on all levels of the metabolic route. On May 28-29, 2007, a small group of researchers active in the field of exercise science and protein metabolism presented an overview of the different aspects of the application of protein and protein hydrolysates in sports nutrition. In addition, they were asked to share their opinions on the future progress in their fields of research. In this overview, an introduction to the workshop and a short summary of its outcome is provided.

  11. Protein electrophoresis - serum

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/003540.htm Protein electrophoresis - serum To use the sharing features on ... JavaScript. This lab test measures the types of protein in the fluid (serum) part of a blood ...

  12. Protein Data Bank (PDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and...

  13. Abnormal protein aggregationand neurodegenerativediseases

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Abnormal protein aggregation or amyloid is the major cause ofmany neurodegenerative disorders. The present review focuses on the correlation between sequence and structure features of proteins related to the diseases and abnormal protein aggregation. Recent progress has improved our knowledge on understand-ing the mechanism of amyloid formation. We suggest a nucleation model for ordered protein aggregation, which can also explain pathogenesis mechanisms of these neurodegenerative diseases in vivo.

  14. CSF total protein

    Science.gov (United States)

    CSF total protein is a test to determine the amount of protein in your spinal fluid, also called cerebrospinal fluid (CSF). ... The normal protein range varies from lab to lab, but is typically about 15 to 60 milligrams per deciliter (mg/dL) ...

  15. Protein domain prediction

    NARCIS (Netherlands)

    Ingolfsson, Helgi; Yona, Golan

    2008-01-01

    Domains are considered to be the building blocks of protein structures. A protein can contain a single domain or multiple domains, each one typically associated with a specific function. The combination of domains determines the function of the protein, its subcellular localization and the interacti

  16. Destabilized bioluminescent proteins

    Science.gov (United States)

    Allen, Michael S.; Rakesh, Gupta; Gary, Sayler S.

    2007-07-31

    Purified nucleic acids, vectors and cells containing a gene cassette encoding at least one modified bioluminescent protein, wherein the modification includes the addition of a peptide sequence. The duration of bioluminescence emitted by the modified bioluminescent protein is shorter than the duration of bioluminescence emitted by an unmodified form of the bioluminescent protein.

  17. Protein Frustratometer 2

    DEFF Research Database (Denmark)

    Gonzalo Parra, R.; Schafer, Nicholas P.; Radusky, Leandro G.

    2016-01-01

    The protein frustratometer is an energy landscape theory-inspired algorithm that aims at localizing and quantifying the energetic frustration present in protein molecules. Frustration is a useful concept for analyzing proteins' biological behavior. It compares the energy distributions of the nati...... a user-friendly interface. The webserver is freely available at URL: http://frustratometer.qb.fcen.uba.ar....

  18. Protopia: a protein-protein interaction tool

    Science.gov (United States)

    Real-Chicharro, Alejandro; Ruiz-Mostazo, Iván; Navas-Delgado, Ismael; Kerzazi, Amine; Chniber, Othmane; Sánchez-Jiménez, Francisca; Medina, Miguel Ángel; Aldana-Montes, José F

    2009-01-01

    Background Protein-protein interactions can be considered the basic skeleton for living organism self-organization and homeostasis. Impressive quantities of experimental data are being obtained and computational tools are essential to integrate and to organize this information. This paper presents Protopia, a biological tool that offers a way of searching for proteins and their interactions in different Protein Interaction Web Databases, as a part of a multidisciplinary initiative of our institution for the integration of biological data . Results The tool accesses the different Databases (at present, the free version of Transfac, DIP, Hprd, Int-Act and iHop), and results are expressed with biological protein names or databases codes and can be depicted as a vector or a matrix. They can be represented and handled interactively as an organic graph. Comparison among databases is carried out using the Uniprot codes annotated for each protein. Conclusion The tool locates and integrates the current information stored in the aforementioned databases, and redundancies among them are detected. Results are compatible with the most important network analysers, so that they can be compared and analysed by other world-wide known tools and platforms. The visualization possibilities help to attain this goal and they are especially interesting for handling multiple-step or complex networks. PMID:19828077

  19. Protein crystallization with paper

    Science.gov (United States)

    Matsuoka, Miki; Kakinouchi, Keisuke; Adachi, Hiroaki; Maruyama, Mihoko; Sugiyama, Shigeru; Sano, Satoshi; Yoshikawa, Hiroshi Y.; Takahashi, Yoshinori; Yoshimura, Masashi; Matsumura, Hiroyoshi; Murakami, Satoshi; Inoue, Tsuyoshi; Mori, Yusuke; Takano, Kazufumi

    2016-05-01

    We developed a new protein crystallization method that incorporates paper. A small piece of paper, such as facial tissue or KimWipes, was added to a drop of protein solution in the traditional sitting drop vapor diffusion technique, and protein crystals grew by incorporating paper. By this method, we achieved the growth of protein crystals with reducing osmotic shock. Because the technique is very simple and the materials are easy to obtain, this method will come into wide use for protein crystallization. In the future, it could be applied to nanoliter-scale crystallization screening on a paper sheet such as in inkjet printing.

  20. Highly thermostable fluorescent proteins

    Science.gov (United States)

    Bradbury, Andrew M.; Waldo, Geoffrey S.; Kiss, Csaba

    2011-03-22

    Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

  1. Protein oxidation and peroxidation

    DEFF Research Database (Denmark)

    Davies, Michael Jonathan

    2016-01-01

    and chain reactions with alcohols and carbonyls as major products; the latter are commonly used markers of protein damage. Direct oxidation of cysteine (and less commonly) methionine residues is a major reaction; this is typically faster than with H2O2, and results in altered protein activity and function....... Unlike H2O2, which is rapidly removed by protective enzymes, protein peroxides are only slowly removed, and catabolism is a major fate. Although turnover of modified proteins by proteasomal and lysosomal enzymes, and other proteases (e.g. mitochondrial Lon), can be efficient, protein hydroperoxides...

  2. Protein aggregate myopathies

    Directory of Open Access Journals (Sweden)

    Sharma M

    2005-01-01

    Full Text Available Protein aggregate myopathies (PAM are an emerging group of muscle diseases characterized by structural abnormalities. Protein aggregate myopathies are marked by the aggregation of intrinsic proteins within muscle fibers and fall into four major groups or conditions: (1 desmin-related myopathies (DRM that include desminopathies, a-B crystallinopathies, selenoproteinopathies caused by mutations in the, a-B crystallin and selenoprotein N1 genes, (2 hereditary inclusion body myopathies, several of which have been linked to different chromosomal gene loci, but with as yet unidentified protein product, (3 actinopathies marked by mutations in the sarcomeric ACTA1 gene, and (4 myosinopathy marked by a mutation in the MYH-7 gene. While PAM forms 1 and 2 are probably based on impaired extralysosomal protein degradation, resulting in the accumulation of numerous and diverse proteins (in familial types in addition to respective mutant proteins, PAM forms 3 and 4 may represent anabolic or developmental defects because of preservation of sarcomeres outside of the actin and myosin aggregates and dearth or absence of other proteins in these actin or myosin aggregates, respectively. The pathogenetic principles governing protein aggregation within muscle fibers and subsequent structural sarcomeres are still largely unknown in both the putative catabolic and anabolic forms of PAM. Presence of inclusions and their protein composition in other congenital myopathies such as reducing bodies, cylindrical spirals, tubular aggregates and others await clarification. The hitherto described PAMs were first identified by immunohistochemistry of proteins and subsequently by molecular analysis of their genes.

  3. Racemic protein crystallography.

    Science.gov (United States)

    Yeates, Todd O; Kent, Stephen B H

    2012-01-01

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

  4. Toxic proteins in plants.

    Science.gov (United States)

    Dang, Liuyi; Van Damme, Els J M

    2015-09-01

    Plants have evolved to synthesize a variety of noxious compounds to cope with unfavorable circumstances, among which a large group of toxic proteins that play a critical role in plant defense against predators and microbes. Up to now, a wide range of harmful proteins have been discovered in different plants, including lectins, ribosome-inactivating proteins, protease inhibitors, ureases, arcelins, antimicrobial peptides and pore-forming toxins. To fulfill their role in plant defense, these proteins exhibit various degrees of toxicity towards animals, insects, bacteria or fungi. Numerous studies have been carried out to investigate the toxic effects and mode of action of these plant proteins in order to explore their possible applications. Indeed, because of their biological activities, toxic plant proteins are also considered as potentially useful tools in crop protection and in biomedical applications, such as cancer treatment. Genes encoding toxic plant proteins have been introduced into crop genomes using genetic engineering technology in order to increase the plant's resistance against pathogens and diseases. Despite the availability of ample information on toxic plant proteins, very few publications have attempted to summarize the research progress made during the last decades. This review focuses on the diversity of toxic plant proteins in view of their toxicity as well as their mode of action. Furthermore, an outlook towards the biological role(s) of these proteins and their potential applications is discussed.

  5. PROTEIN - WHICH IS BEST?

    Directory of Open Access Journals (Sweden)

    Michael J. Falvo

    2004-09-01

    Full Text Available Protein intake that exceeds the recommended daily allowance is widely accepted for both endurance and power athletes. However, considering the variety of proteins that are available much less is known concerning the benefits of consuming one protein versus another. The purpose of this paper is to identify and analyze key factors in order to make responsible recommendations to both the general and athletic populations. Evaluation of a protein is fundamental in determining its appropriateness in the human diet. Proteins that are of inferior content and digestibility are important to recognize and restrict or limit in the diet. Similarly, such knowledge will provide an ability to identify proteins that provide the greatest benefit and should be consumed. The various techniques utilized to rate protein will be discussed. Traditionally, sources of dietary protein are seen as either being of animal or vegetable origin. Animal sources provide a complete source of protein (i.e. containing all essential amino acids, whereas vegetable sources generally lack one or more of the essential amino acids. Animal sources of dietary protein, despite providing a complete protein and numerous vitamins and minerals, have some health professionals concerned about the amount of saturated fat common in these foods compared to vegetable sources. The advent of processing techniques has shifted some of this attention and ignited the sports supplement marketplace with derivative products such as whey, casein and soy. Individually, these products vary in quality and applicability to certain populations. The benefits that these particular proteins possess are discussed. In addition, the impact that elevated protein consumption has on health and safety issues (i.e. bone health, renal function are also reviewed

  6. Protein kinesis: The dynamics of protein trafficking and stability

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-12-31

    The purpose of this conference is to provide a multidisciplinary forum for exchange of state-of-the-art information on protein kinesis. This volume contains abstracts of papers in the following areas: protein folding and modification in the endoplasmic reticulum; protein trafficking; protein translocation and folding; protein degradation; polarity; nuclear trafficking; membrane dynamics; and protein import into organelles.

  7. Protein Electrophoresis/Immunofixation Electrophoresis

    Science.gov (United States)

    ... be limited. Home Visit Global Sites Search Help? Protein Electrophoresis Immunofixation Electrophoresis Share this page: Was this page helpful? Also known as: Serum Protein Electrophoresis; Protein ELP; SPE; SPEP; Urine Protein Electrophoresis; ...

  8. Protein: FEA4 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FEA4 Proteins in gibberellin signaling GID2 F-box protein GID2 Gibberellin-insensitive dwarf protein 2, Prot...ein GIBBERELLIN INSENSITIVE DWARF2 39947 Oryza sativa subsp. japonica Q7XAK4 ...

  9. NMR of unfolded proteins

    Indian Academy of Sciences (India)

    Amarnath Chtterjee; Ashutosh Kumar; Jeetender Chugh; Sudha Srivastava; Neel S Bhavesh; Ramakrishna V Hosur

    2005-01-01

    In the post-genomic era, as more and more genome sequences are becoming known and hectic efforts are underway to decode the information content in them, it is becoming increasingly evident that flexibility in proteins plays a crucial role in many of the biological functions. Many proteins have intrinsic disorder either wholly or in specific regions. It appears that this disorder may be important for regulatory functions of the proteins, on the one hand, and may help in directing the folding process to reach the compact native state, on the other. Nuclear magnetic resonance (NMR) has over the last two decades emerged as the sole, most powerful technique to help characterize these disordered protein systems. In this review, we first discuss the significance of disorder in proteins and then describe the recent developments in NMR methods for their characterization. A brief description of the results obtained on several disordered proteins is presented at the end.

  10. Computational Protein Design

    DEFF Research Database (Denmark)

    Johansson, Kristoffer Enøe

    Proteins are the major functional group of molecules in biology. The impact of protein science on medicine and chemical productions is rapidly increasing. However, the greatest potential remains to be realized. The fi eld of protein design has advanced computational modeling from a tool of support...... to a central method that enables new developments. For example, novel enzymes with functions not found in natural proteins have been de novo designed to give enough activity for experimental optimization. This thesis presents the current state-of-the-art within computational design methods together...... with a novel method based on probability theory. With the aim of assembling a complete pipeline for protein design, this work touches upon several aspects of protein design. The presented work is the computational half of a design project where the other half is dedicated to the experimental part...

  11. Protein Models Comparator

    CERN Document Server

    Widera, Paweł

    2011-01-01

    The process of comparison of computer generated protein structural models is an important element of protein structure prediction. It has many uses including model quality evaluation, selection of the final models from a large set of candidates or optimisation of parameters of energy functions used in template free modelling and refinement. Although many protein comparison methods are available online on numerous web servers, their ability to handle a large scale model comparison is often very limited. Most of the servers offer only a single pairwise structural comparison, and they usually do not provide a model-specific comparison with a fixed alignment between the models. To bridge the gap between the protein and model structure comparison we have developed the Protein Models Comparator (pm-cmp). To be able to deliver the scalability on demand and handle large comparison experiments the pm-cmp was implemented "in the cloud". Protein Models Comparator is a scalable web application for a fast distributed comp...

  12. Mayaro virus proteins.

    Science.gov (United States)

    Mezencio, J M; Rebello, M A

    1993-01-01

    Mayaro virus was grown in BHK-21 cells and purified by centrifugation in a potassium-tartrate gradient (5-50%). The electron microscopy analyses of the purified virus showed an homogeneous population of enveloped particles with 69 +/- 2.3 nm in diameter. Three structural virus proteins were identified and designated p1, p2 and p3. Their average molecular weight were p1, 54 KDa; p2, 50 KDa and p3, 34 KDa. In Mayaro virus infected Aedes albopictus cells and in BHK-21 infected cells we detected six viral proteins, in which three of them are the structural virus proteins and the other three were products from processing of precursors of viral proteins, whose molecular weights are 62 KDa, 64 KDa and 110 KDa. The 34 KDa protein was the first viral protein synthesized at 5 hours post-infection in both cell lines studied.

  13. Mayaro virus proteins

    Directory of Open Access Journals (Sweden)

    J. M. S. Mezencio

    1993-06-01

    Full Text Available Mayaro virus was grown in BHK-21 cells and purified by centrifugation in a potassium-tartrate gradient (5-50%. The electron microscopy analyses of the purified virus showed an homogeneous population of enveloped particles with 69 ñ 2.3 nm in diameter. Three structural virus proteins were identified and designated pl, p2 and p3. Their average molecular weight were p1, 54 KDa; p2, 50 KDa and p3, 34 KDa. In Mayaro virus infected. Aedes albopictus cells and in BHK-21 infected cells we detected six viral proteins, in wich three of them are the structural virus proteins and the other three were products from processing of precursors of viral proteins, whose molecular weights are 62 KDa, 64 KDa and 110 KDa. The 34 KDa protein was the first viral protein sinthesized at 5 hours post-infection in both cell lines studied.

  14. Proteins: Form and function

    OpenAIRE

    Roy D Sleator

    2012-01-01

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

  15. Pressure cryocooling protein crystals

    Science.gov (United States)

    Kim, Chae Un; Gruner, Sol M.

    2011-10-04

    Preparation of cryocooled protein crystal is provided by use of helium pressurizing and cryocooling to obtain cryocooled protein crystal allowing collection of high resolution data and by heavier noble gas (krypton or xenon) binding followed by helium pressurizing and cryocooling to obtain cryocooled protein crystal for collection of high resolution data and SAD phasing simultaneously. The helium pressurizing is carried out on crystal coated to prevent dehydration or on crystal grown in aqueous solution in a capillary.

  16. Acanthamoeba castellanii STAT Protein

    OpenAIRE

    Anna Kicinska; Jacek Leluk; Wieslawa Jarmuszkiewicz

    2014-01-01

    STAT (signal transducers and activators of transcription) proteins are one of the important mediators of phosphotyrosine-regulated signaling in metazoan cells. We described the presence of STAT protein in a unicellular, free-living amoebae with a simple life cycle, Acanthamoeba castellanii. A. castellanii is the only, studied to date, Amoebozoan that does not belong to Mycetozoa but possesses STATs. A sequence of the A. castellanii STAT protein includes domains similar to those of the Dictyos...

  17. Moonlighting proteins in cancer.

    Science.gov (United States)

    Min, Kyung-Won; Lee, Seong-Ho; Baek, Seung Joon

    2016-01-01

    Since the 1980s, growing evidence suggested that the cellular localization of proteins determined their activity and biological functions. In a classical view, a protein is characterized by the single cellular compartment where it primarily resides and functions. It is now believed that when proteins appear in different subcellular locations, the cells surpass the expected activity of proteins given the same genomic information to fulfill complex biological behavior. Many proteins are recognized for having the potential to exist in multiple locations in cells. Dysregulation of translocation may cause cancer or contribute to poorer cancer prognosis. Thus, quantitative and comprehensive assessment of dynamic proteins and associated protein movements could be a promising indicator in determining cancer prognosis and efficiency of cancer treatment and therapy. This review will summarize these so-called moonlighting proteins, in terms of a coupled intracellular cancer signaling pathway. Determination of the detailed biological intracellular and extracellular transit and regulatory activity of moonlighting proteins permits a better understanding of cancer and identification of potential means of molecular intervention.

  18. Self assembling proteins

    Science.gov (United States)

    Yeates, Todd O.; Padilla, Jennifer; Colovos, Chris

    2004-06-29

    Novel fusion proteins capable of self-assembling into regular structures, as well as nucleic acids encoding the same, are provided. The subject fusion proteins comprise at least two oligomerization domains rigidly linked together, e.g. through an alpha helical linking group. Also provided are regular structures comprising a plurality of self-assembled fusion proteins of the subject invention, and methods for producing the same. The subject fusion proteins find use in the preparation of a variety of nanostructures, where such structures include: cages, shells, double-layer rings, two-dimensional layers, three-dimensional crystals, filaments, and tubes.

  19. Acanthamoeba castellanii STAT protein.

    Directory of Open Access Journals (Sweden)

    Anna Kicinska

    Full Text Available STAT (signal transducers and activators of transcription proteins are one of the important mediators of phosphotyrosine-regulated signaling in metazoan cells. We described the presence of STAT protein in a unicellular, free-living amoebae with a simple life cycle, Acanthamoeba castellanii. A. castellanii is the only, studied to date, Amoebozoan that does not belong to Mycetozoa but possesses STATs. A sequence of the A. castellanii STAT protein includes domains similar to those of the Dictyostelium STAT proteins: a coiled coil (characteristic for Dictyostelium STAT coiled coil, a STAT DNA-binding domain and a Src-homology domain. The search for protein sequences homologous to A. castellanii STAT revealed 17 additional sequences from lower eukaryotes. Interestingly, all of these sequences come from Amoebozoa organisms that belong to either Mycetozoa (slime molds or Centramoebida. We showed that there are four separated clades within the slime mold STAT proteins. The A. castellanii STAT protein branches next to a group of STATc proteins from Mycetozoa. We also demonstrate that Amoebozoa form a distinct monophyletic lineage within the STAT protein world that is well separated from the other groups.

  20. Acanthamoeba castellanii STAT protein.

    Science.gov (United States)

    Kicinska, Anna; Leluk, Jacek; Jarmuszkiewicz, Wieslawa

    2014-01-01

    STAT (signal transducers and activators of transcription) proteins are one of the important mediators of phosphotyrosine-regulated signaling in metazoan cells. We described the presence of STAT protein in a unicellular, free-living amoebae with a simple life cycle, Acanthamoeba castellanii. A. castellanii is the only, studied to date, Amoebozoan that does not belong to Mycetozoa but possesses STATs. A sequence of the A. castellanii STAT protein includes domains similar to those of the Dictyostelium STAT proteins: a coiled coil (characteristic for Dictyostelium STAT coiled coil), a STAT DNA-binding domain and a Src-homology domain. The search for protein sequences homologous to A. castellanii STAT revealed 17 additional sequences from lower eukaryotes. Interestingly, all of these sequences come from Amoebozoa organisms that belong to either Mycetozoa (slime molds) or Centramoebida. We showed that there are four separated clades within the slime mold STAT proteins. The A. castellanii STAT protein branches next to a group of STATc proteins from Mycetozoa. We also demonstrate that Amoebozoa form a distinct monophyletic lineage within the STAT protein world that is well separated from the other groups.

  1. PIC: Protein Interactions Calculator.

    Science.gov (United States)

    Tina, K G; Bhadra, R; Srinivasan, N

    2007-07-01

    Interactions within a protein structure and interactions between proteins in an assembly are essential considerations in understanding molecular basis of stability and functions of proteins and their complexes. There are several weak and strong interactions that render stability to a protein structure or an assembly. Protein Interactions Calculator (PIC) is a server which, given the coordinate set of 3D structure of a protein or an assembly, computes various interactions such as disulphide bonds, interactions between hydrophobic residues, ionic interactions, hydrogen bonds, aromatic-aromatic interactions, aromatic-sulphur interactions and cation-pi interactions within a protein or between proteins in a complex. Interactions are calculated on the basis of standard, published criteria. The identified interactions between residues can be visualized using a RasMol and Jmol interface. The advantage with PIC server is the easy availability of inter-residue interaction calculations in a single site. It also determines the accessible surface area and residue-depth, which is the distance of a residue from the surface of the protein. User can also recognize specific kind of interactions, such as apolar-apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near the surface or deep inside.

  2. Characterization of Metal Proteins

    Science.gov (United States)

    Unno, Masaki; Ikeda-Saito, Masao

    Some metals are essential for life. Most of these metals are associated with biological macromolecule like DNA (deoxyribonucleic acid), RNA (ribonucleic acid), and more often with proteins: metals bind or interact with them. A number of protein molecules intrinsically contain metals in their structure. Some of these proteins catalyze unique chemical reactions and perform specific physiological functions. In this chapter, we will shed light on the several metalcontaining proteins, termed metalloproteins, and other proteins interacting metals. We will also introduce several key techniques which have been used to characterize these proteins. Characterizing these proteins and to understand the relationships between their structures and functions shall continue to be one of the major avenues to solve the mysteries of life. At first, we introduce what are the protein structures and how these proteins interact with metals. In the next section, we discuss the physiological roles of some representative metals. Next, we show two examples of special metal cofactors those help the biological macromolecules to carry out their functions. Then we describe some functions of metalloproteins. Finally, we introduce some physical methods to characterize metalloproteins.

  3. Dietary proteins and angiogenesis.

    Science.gov (United States)

    Medina, Miguel Ángel; Quesada, Ana R

    2014-01-17

    Both defective and persistent angiogenesis are linked to pathological situations in the adult. Compounds able to modulate angiogenesis have a potential value for the treatment of such pathologies. Several small molecules present in the diet have been shown to have modulatory effects on angiogenesis. This review presents the current state of knowledge on the potential modulatory roles of dietary proteins on angiogenesis. There is currently limited available information on the topic. Milk contains at least three proteins for which modulatory effects on angiogenesis have been previously demonstrated. On the other hand, there is some scarce information on the potential of dietary lectins, edible plant proteins and high protein diets to modulate angiogenesis.

  4. [Alternative scaffold proteins].

    Science.gov (United States)

    Petrovskaia, L E; Shingarova, L N; Dolgikh, D A; Kirpichnikov, M P

    2011-01-01

    Review is devoted to the challenging direction in modem molecular biology and bioengineering - the properties of alternative scaffold proteins (ASP) and methods for obtaining ASP binding molecules. ASP molecules incorporate conservative protein core and hypervariable regions, providing for the binding function. Structural classification of ASP includes several types which differ also in their molecular targets and potential applications. Construction of artificial binding proteins on the ASP basis implies a combinatorial library design with subsequent selection of specific binders with the use of phage display or the modem cell-free systems. Alternative binding proteins on non-immunoglobulin scaffolds find broad applications in different fields ofbiotechnology and molecular medicine.

  5. Ultrafiltration of pegylated proteins

    Science.gov (United States)

    Molek, Jessica R.

    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

  6. Protein oxidation in aquatic foods

    DEFF Research Database (Denmark)

    Baron, Caroline P.

    2014-01-01

    The chapter discusses general considerations about protein oxidation and reviews the mechanisms involved in protein oxidation and consequences of protein oxidation on fish proteins. It presents two case studies, the first deals with protein and lipid oxidation in frozen rainbow trout, and the sec......The chapter discusses general considerations about protein oxidation and reviews the mechanisms involved in protein oxidation and consequences of protein oxidation on fish proteins. It presents two case studies, the first deals with protein and lipid oxidation in frozen rainbow trout...... oxidation. The protein carbonyl group measurement is the widely used method for estimating protein oxidation in foods and has been used in fish muscle. The chapter also talks about the impact of protein oxidation on protein functionality, fish muscle texture, and food nutritional value. Protein oxidation...... may not only induce quality losses but may be desirable in some type of foods, such as salted herring....

  7. Protein and Heart Health

    Science.gov (United States)

    ... of food? Drink an 8-ounce glass of milk, and you’ll log 8 grams of protein. Add a cup of yogurt for another 11 ... low-fat options, such as lean meats, skim milk or other foods with high levels of protein. Legumes, for example, can pack about 16 grams ...

  8. Brushes and proteins

    NARCIS (Netherlands)

    Bosker, W.T.E.

    2011-01-01

      Brushes and Proteins   Wouter T. E. Bosker         Protein adsorption at solid surfaces can be prevented by applying a polymer brush at the surface. A polymer brush consists of polymer chains end-grafted to the surface at such a grafting density that th

  9. Poxviral Ankyrin Proteins

    Directory of Open Access Journals (Sweden)

    Michael H. Herbert

    2015-02-01

    Full Text Available Multiple repeats of the ankyrin motif (ANK are ubiquitous throughout the kingdoms of life but are absent from most viruses. The main exception to this is the poxvirus family, and specifically the chordopoxviruses, with ANK repeat proteins present in all but three species from separate genera. The poxviral ANK repeat proteins belong to distinct orthologue groups spread over different species, and align well with the phylogeny of their genera. This distribution throughout the chordopoxviruses indicates these proteins were present in an ancestral vertebrate poxvirus, and have since undergone numerous duplication events. Most poxviral ANK repeat proteins contain an unusual topology of multiple ANK motifs starting at the N-terminus with a C-terminal poxviral homologue of the cellular F-box enabling interaction with the cellular SCF ubiquitin ligase complex. The subtle variations between ANK repeat proteins of individual poxviruses suggest an array of different substrates may be bound by these protein-protein interaction domains and, via the F-box, potentially directed to cellular ubiquitination pathways and possible degradation. Known interaction partners of several of these proteins indicate that the NF-κB coordinated anti-viral response is a key target, whilst some poxviral ANK repeat domains also have an F-box independent affect on viral host-range.

  10. Learning about Proteins

    Science.gov (United States)

    ... Emergency Room? What Happens in the Operating Room? Learning About Proteins KidsHealth > For Kids > Learning About Proteins A A A What's in this ... Nutrition & Fitness Center Minerals Vitamins Eating for Sports Learning About Fats MyPlate Food Guide Word! Nutrition Contact ...

  11. Protein Attachment on Nanodiamonds.

    Science.gov (United States)

    Lin, Chung-Lun; Lin, Cheng-Huang; Chang, Huan-Cheng; Su, Meng-Chih

    2015-07-16

    A recent advance in nanotechnology is the scale-up production of small and nonaggregated diamond nanoparticles suitable for biological applications. Using detonation nanodiamonds (NDs) with an average diameter of ∼4 nm as the adsorbents, we have studied the static attachment of three proteins (myoglobin, bovine serum albumin, and insulin) onto the nanoparticles by optical spectroscopy, mass spectrometry, and dynamic light scattering, and electrophoretic zeta potential measurements. Results show that the protein surface coverage is predominantly determined by the competition between protein-protein and protein-ND interactions, giving each protein a unique and characteristic structural configuration in its own complex. Specifically, both myoglobin and bovine serum albumin show a Langmuir-type adsorption behavior, forming 1:1 complexes at saturation, whereas insulin folds into a tightly bound multimer before adsorption. The markedly different adsorption patterns appear to be independent of the protein concentration and are closely related to the affinity of the individual proteins for the NDs. The present study provides a fundamental understanding for the use of NDs as a platform for nanomedical drug delivery.

  12. Engineered Protein Polymers

    Science.gov (United States)

    2010-05-31

    of each pure polymer, we plan to combine the various polymer solutions in different ratios to tune the composition and physico-chemical properties...protein materials as vehicles for storage and delivery of small molecules. Each protein polymer under concentrations for particle formation ( vida

  13. Sensitizing properties of proteins

    DEFF Research Database (Denmark)

    Poulsen, Lars K.; Ladics, Gregory S; McClain, Scott;

    2014-01-01

    The scope of allergy risk is diverse considering the myriad ways in which protein allergenicity is affected by physiochemical characteristics of proteins. The complexity created by the matrices of foods and the variability of the human immune system add additional challenges to understanding...... the relationship between sensitization potential and allergy disease. To address these and other issues, an April 2012 international symposium was held in Prague, Czech Republic, to review and discuss the state-of-the-science of sensitizing properties of protein allergens. The symposium, organized by the Protein...... Allergenicity Technical Committee of the International Life Sciences Institute's Health and Environmental Sciences Institute, featured presentations on current methods, test systems, research trends, and unanswered questions in the field of protein sensitization. A diverse group of over 70 interdisciplinary...

  14. Unconventional protein secretion.

    Science.gov (United States)

    Ding, Yu; Wang, Juan; Wang, Junqi; Stierhof, York-Dieter; Robinson, David G; Jiang, Liwen

    2012-10-01

    It is generally believed that protein secretion or exocytosis is achieved via a conventional ER (endoplasmic reticulum)-Golgi-TGN (trans-Golgi network)-PM (plasma membrane) pathway in the plant endomembrane system. However, such signal peptide (SP)-dependent protein secretion cannot explain the increasing number of SP-lacking proteins which are found outside of the PM in plant cells. The process by which such leaderless secretory proteins (LSPs) gain access to the cell exterior is termed unconventional protein secretion (UPS) and has been well-studied in animal and yeast cells, but largely ignored by the plant community. Here, we review the evidence for UPS in plants especially in regard to the recently discovered EXPO (exocyst-positive-organelle).

  15. Protein Unfolding and Alzheimer's

    Science.gov (United States)

    Cheng, Kelvin

    2012-10-01

    Early interaction events of beta-amyloid (Aβ) 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 Aβ 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 Aβ 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 Aβ 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 Aβ proteins.

  16. Manipulating and Visualizing Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Simon, Horst D.

    2003-12-05

    ProteinShop Gives Researchers a Hands-On Tool for Manipulating, Visualizing Protein Structures. The Human Genome Project and other biological research efforts are creating an avalanche of new data about the chemical makeup and genetic codes of living organisms. But in order to make sense of this raw data, researchers need software tools which let them explore and model data in a more intuitive fashion. With this in mind, researchers at Lawrence Berkeley National Laboratory and the University of California, Davis, have developed ProteinShop, a visualization and modeling program which allows researchers to manipulate protein structures with pinpoint control, guided in large part by their own biological and experimental instincts. Biologists have spent the last half century trying to unravel the ''protein folding problem,'' which refers to the way chains of amino acids physically fold themselves into three-dimensional proteins. This final shape, which resembles a crumpled ribbon or piece of origami, is what determines how the protein functions and translates genetic information. Understanding and modeling this geometrically complex formation is no easy matter. ProteinShop takes a given sequence of amino acids and uses visualization guides to help generate predictions about the secondary structures, identifying alpha helices and flat beta strands, and the coil regions that bind them. Once secondary structures are in place, researchers can twist and turn these pre-configurations until they come up with a number of possible tertiary structure conformations. In turn, these are fed into a computationally intensive optimization procedure that tries to find the final, three-dimensional protein structure. Most importantly, ProteinShop allows users to add human knowledge and intuition to the protein structure prediction process, thus bypassing bad configurations that would otherwise be fruitless for optimization. This saves compute cycles and accelerates

  17. Transdermal delivery of proteins.

    Science.gov (United States)

    Kalluri, Haripriya; Banga, Ajay K

    2011-03-01

    Transdermal delivery of peptides and proteins avoids the disadvantages associated with the invasive parenteral route of administration and other alternative routes such as the pulmonary and nasal routes. Since proteins have a large size and are hydrophilic in nature, they cannot permeate passively across the skin due to the stratum corneum which allows the transport of only small lipophilic drug molecules. Enhancement techniques such as chemical enhancers, iontophoresis, microneedles, electroporation, sonophoresis, thermal ablation, laser ablation, radiofrequency ablation and noninvasive jet injectors aid in the delivery of proteins by overcoming the skin barrier in different ways. In this review, these enhancement techniques that can enable the transdermal delivery of proteins are discussed, including a discussion of mechanisms, sterility requirements, and commercial development of products. Combination of enhancement techniques may result in a synergistic effect allowing increased protein delivery and these are also discussed.

  18. Coarse-grain modelling of protein-protein interactions

    NARCIS (Netherlands)

    Baaden, Marc; Marrink, Siewert J.

    2013-01-01

    Here, we review recent advances towards the modelling of protein-protein interactions (PPI) at the coarse-grained (CG) level, a technique that is now widely used to understand protein affinity, aggregation and self-assembly behaviour. PPI models of soluble proteins and membrane proteins are separate

  19. Protein Binding Pocket Dynamics.

    Science.gov (United States)

    Stank, Antonia; Kokh, Daria B; Fuller, Jonathan C; Wade, Rebecca C

    2016-05-17

    The dynamics of protein binding pockets are crucial for their interaction specificity. Structural flexibility allows proteins to adapt to their individual molecular binding partners and facilitates the binding process. This implies the necessity to consider protein internal motion in determining and predicting binding properties and in designing new binders. Although accounting for protein dynamics presents a challenge for computational approaches, it expands the structural and physicochemical space for compound design and thus offers the prospect of improved binding specificity and selectivity. A cavity on the surface or in the interior of a protein that possesses suitable properties for binding a ligand is usually referred to as a binding pocket. The set of amino acid residues around a binding pocket determines its physicochemical characteristics and, together with its shape and location in a protein, defines its functionality. Residues outside the binding site can also have a long-range effect on the properties of the binding pocket. Cavities with similar functionalities are often conserved across protein families. For example, enzyme active sites are usually concave surfaces that present amino acid residues in a suitable configuration for binding low molecular weight compounds. Macromolecular binding pockets, on the other hand, are located on the protein surface and are often shallower. The mobility of proteins allows the opening, closing, and adaptation of binding pockets to regulate binding processes and specific protein functionalities. For example, channels and tunnels can exist permanently or transiently to transport compounds to and from a binding site. The influence of protein flexibility on binding pockets can vary from small changes to an already existent pocket to the formation of a completely new pocket. Here, we review recent developments in computational methods to detect and define binding pockets and to study pocket dynamics. We introduce five

  20. Anchored design of protein-protein interfaces.

    Directory of Open Access Journals (Sweden)

    Steven M Lewis

    Full Text Available BACKGROUND: Few existing protein-protein interface design methods allow for extensive backbone rearrangements during the design process. There is also a dichotomy between redesign methods, which take advantage of the native interface, and de novo methods, which produce novel binders. METHODOLOGY: Here, we propose a new method for designing novel protein reagents that combines advantages of redesign and de novo methods and allows for extensive backbone motion. This method requires a bound structure of a target and one of its natural binding partners. A key interaction in this interface, the anchor, is computationally grafted out of the partner and into a surface loop on the design scaffold. The design scaffold's surface is then redesigned with backbone flexibility to create a new binding partner for the target. Careful choice of a scaffold will bring experimentally desirable characteristics into the new complex. The use of an anchor both expedites the design process and ensures that binding proceeds against a known location on the target. The use of surface loops on the scaffold allows for flexible-backbone redesign to properly search conformational space. CONCLUSIONS AND SIGNIFICANCE: This protocol was implemented within the Rosetta3 software suite. To demonstrate and evaluate this protocol, we have developed a benchmarking set of structures from the PDB with loop-mediated interfaces. This protocol can recover the correct loop-mediated interface in 15 out of 16 tested structures, using only a single residue as an anchor.

  1. PSC: protein surface classification.

    Science.gov (United States)

    Tseng, Yan Yuan; Li, Wen-Hsiung

    2012-07-01

    We recently proposed to classify proteins by their functional surfaces. Using the structural attributes of functional surfaces, we inferred the pairwise relationships of proteins and constructed an expandable database of protein surface classification (PSC). As the functional surface(s) of a protein is the local region where the protein performs its function, our classification may reflect the functional relationships among proteins. Currently, PSC contains a library of 1974 surface types that include 25,857 functional surfaces identified from 24,170 bound structures. The search tool in PSC empowers users to explore related surfaces that share similar local structures and core functions. Each functional surface is characterized by structural attributes, which are geometric, physicochemical or evolutionary features. The attributes have been normalized as descriptors and integrated to produce a profile for each functional surface in PSC. In addition, binding ligands are recorded for comparisons among homologs. PSC allows users to exploit related binding surfaces to reveal the changes in functionally important residues on homologs that have led to functional divergence during evolution. The substitutions at the key residues of a spatial pattern may determine the functional evolution of a protein. In PSC (http://pocket.uchicago.edu/psc/), a pool of changes in residues on similar functional surfaces is provided.

  2. Bacterial Ice Crystal Controlling Proteins

    Directory of Open Access Journals (Sweden)

    Janet S. H. Lorv

    2014-01-01

    Full Text Available Across the world, many ice active bacteria utilize ice crystal controlling proteins for aid in freezing tolerance at subzero temperatures. Ice crystal controlling proteins include both antifreeze and ice nucleation proteins. Antifreeze proteins minimize freezing damage by inhibiting growth of large ice crystals, while ice nucleation proteins induce formation of embryonic ice crystals. Although both protein classes have differing functions, these proteins use the same ice binding mechanisms. Rather than direct binding, it is probable that these protein classes create an ice surface prior to ice crystal surface adsorption. Function is differentiated by molecular size of the protein. This paper reviews the similar and different aspects of bacterial antifreeze and ice nucleation proteins, the role of these proteins in freezing tolerance, prevalence of these proteins in psychrophiles, and current mechanisms of protein-ice interactions.

  3. Alpha Shapes and Proteins

    DEFF Research Database (Denmark)

    Winter, Pawel; Sterner, Henrik; Sterner, Peter

    2009-01-01

    We provide a unified description of (weighted) alpha shapes, beta shapes and the corresponding simplicialcomplexes. We discuss their applicability to various protein-related problems. We also discuss filtrations of alpha shapes and touch upon related persistence issues.We claim that the full...... potential of alpha-shapes and related geometrical constructs in protein-related problems yet remains to be realized and verified. We suggest parallel algorithms for (weighted) alpha shapes, and we argue that future use of filtrations and kinetic variants for larger proteins will need such implementation....

  4. Protein oxidation and ageing

    DEFF Research Database (Denmark)

    Linton, S; Davies, Michael Jonathan; Dean, R T

    2001-01-01

    of redox-active metal ions that could catalyse oxidant formation. As a result of this decrease in antioxidant defences, and increased rate of ROS formation, it is possible that the impact of ROS increases with age. ROS are known to oxidise biological macromolecules, with proteins an important target....... If the argument that the impact of ROS increases with age is true, then proteins would be expected to accumulate oxidised materials with age, and the rate of such accumulation should increase with time, reflecting impaired inefficiency of homeostasis. Here we review the evidence for the accumulation of oxidised......, or modified, extra- and intra-cellular proteins in vivo....

  5. Piezoelectric allostery of protein

    Science.gov (United States)

    Ohnuki, Jun; Sato, Takato; Takano, Mitsunori

    2016-07-01

    Allostery is indispensable for a protein to work, where a locally applied stimulus is transmitted to a distant part of the molecule. While the allostery due to chemical stimuli such as ligand binding has long been studied, the growing interest in mechanobiology prompts the study of the mechanically stimulated allostery, the physical mechanism of which has not been established. By molecular dynamics simulation of a motor protein myosin, we found that a locally applied mechanical stimulus induces electrostatic potential change at distant regions, just like the piezoelectricity. This novel allosteric mechanism, "piezoelectric allostery", should be of particularly high value for mechanosensor/transducer proteins.

  6. Protein crystallography prescreen kit

    Science.gov (United States)

    Segelke, Brent W.; Krupka, Heike I.; Rupp, Bernhard

    2005-07-12

    A kit for prescreening protein concentration for crystallization includes a multiplicity of vials, a multiplicity of pre-selected reagents, and a multiplicity of sample plates. The reagents and a corresponding multiplicity of samples of the protein in solutions of varying concentrations are placed on sample plates. The sample plates containing the reagents and samples are incubated. After incubation the sample plates are examined to determine which of the sample concentrations are too low and which the sample concentrations are too high. The sample concentrations that are optimal for protein crystallization are selected and used.

  7. Protein: MPA6 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available in 30 kDa adipocyte complement-related protein, Adipocyte complement-related 30 kDa protein, Adipocyte, C1q ...and collagen domain-containing protein, Adipose most abundant gene transcript 1 protein, Gelatin-binding protein 9606 Homo sapiens Q15848 9370 9370 Q15848 18054335, 19646806 ...

  8. Protein: FEB6 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FEB6 Photoresponse regulatory proteins HD1 SE1 Zinc finger protein HD1 Protein CONSTANS-like, Prot...ein HEADING DATE 1, Protein PHOTOPERIOD SENSITIVITY 1 39947 Oryza sativa subsp. japonica 4340746 Q9FDX8 21952207, 19246394 #shimamoto ...

  9. New approach for predicting protein-protein interactions

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    @@ Protein-protein interactions (PPIs) are of vital importance for virtually all processes of a living cell. The study of these associations of protein molecules could improve people's understanding of diseases and provide basis for therapeutic approaches.

  10. Analysis of correlations between protein complex and protein-protein interaction and mRNA expression

    Institute of Scientific and Technical Information of China (English)

    CAI Lun; XUE Hong; LU Hongchao; ZHAO Yi; ZHU Xiaopeng; BU Dongbo; LING Lunjiang; CHEN Runsheng

    2003-01-01

    Protein-protein interaction is a physical interaction of two proteins in living cells. In budding yeast Saccharomyces cerevisiae, large-scale protein-protein interaction data have been obtained through high-throughput yeast two-hybrid systems (Y2H) and protein complex purification techniques based on mass-spectrometry. Here, we collect 11855 interactions between total 2617 proteins. Through seriate genome-wide mRNA expression data, similarity between two genes could be measured. Protein complex data can also be obtained publicly and can be translated to pair relationship that any two proteins can only exist in the same complex or not. Analysis of protein complex data, protein-protein interaction data and mRNA expression data can elucidate correlations between them. The results show that proteins that have interactions or similar expression patterns have a higher possibility to be in the same protein complex than randomized selected proteins, and proteins which have interactions and similar expression patterns are even more possible to exist in the same protein complex. The work indicates that comprehensive integration and analysis of public large-scale bioinformatical data, such as protein complex data, protein-protein interaction data and mRNA expression data, may help to uncover their relationships and common biological information underlying these data. The strategies described here may help to integrate and analyze other functional genomic and proteomic data, such as gene expression profiling, protein-localization mapping and large-scale phenotypic data, both in yeast and in other organisms.

  11. A Bayesian Estimator of Protein-Protein Association Probabilities

    Energy Technology Data Exchange (ETDEWEB)

    Gilmore, Jason M.; Auberry, Deanna L.; Sharp, Julia L.; White, Amanda M.; Anderson, Kevin K.; Daly, Don S.

    2008-07-01

    The Bayesian Estimator of Protein-Protein Association Probabilities (BEPro3) is a software tool for estimating probabilities of protein-protein association between bait and prey protein pairs using data from multiple-bait, multiple-replicate, protein pull-down LC-MS assay experiments. BEPro3 is open source software that runs on both Windows XP and Mac OS 10.4 or newer versions, and is freely available from http://www.pnl.gov/statistics/BEPro3.

  12. Protein in diet

    Science.gov (United States)

    ... Dietary Reference Intakes for Energy, Carbohydrate, Fiber, Fat, Fatty Acids, Cholesterol, Protein, and Amino Acids . National Academy Press. Washington, DC, 2005. US Department of Health and Human Services and US Department of Agriculture. ...

  13. Protein Colloidal Aggregation Project

    Science.gov (United States)

    Oliva-Buisson, Yvette J. (Compiler)

    2014-01-01

    To investigate the pathways and kinetics of protein aggregation to allow accurate predictive modeling of the process and evaluation of potential inhibitors to prevalent diseases including cataract formation, chronic traumatic encephalopathy, Alzheimer's Disease, Parkinson's Disease and others.

  14. Protein Model Database

    Energy Technology Data Exchange (ETDEWEB)

    Fidelis, K; Adzhubej, A; Kryshtafovych, A; Daniluk, P

    2005-02-23

    The phenomenal success of the genome sequencing projects reveals the power of completeness in revolutionizing biological science. Currently it is possible to sequence entire organisms at a time, allowing for a systemic rather than fractional view of their organization and the various genome-encoded functions. There is an international plan to move towards a similar goal in the area of protein structure. This will not be achieved by experiment alone, but rather by a combination of efforts in crystallography, NMR spectroscopy, and computational modeling. Only a small fraction of structures are expected to be identified experimentally, the remainder to be modeled. Presently there is no organized infrastructure to critically evaluate and present these data to the biological community. The goal of the Protein Model Database project is to create such infrastructure, including (1) public database of theoretically derived protein structures; (2) reliable annotation of protein model quality, (3) novel structure analysis tools, and (4) access to the highest quality modeling techniques available.

  15. Plant protein glycosylation

    Science.gov (United States)

    Strasser, Richard

    2016-01-01

    Protein glycosylation is an essential co- and post-translational modification of secretory and membrane proteins in all eukaryotes. The initial steps of N-glycosylation and N-glycan processing are highly conserved between plants, mammals and yeast. In contrast, late N-glycan maturation steps in the Golgi differ significantly in plants giving rise to complex N-glycans with β1,2-linked xylose, core α1,3-linked fucose and Lewis A-type structures. While the essential role of N-glycan modifications on distinct mammalian glycoproteins is already well documented, we have only begun to decipher the biological function of this ubiquitous protein modification in different plant species. In this review, I focus on the biosynthesis and function of different protein N-linked glycans in plants. Special emphasis is given on glycan-mediated quality control processes in the ER and on the biological role of characteristic complex N-glycan structures. PMID:26911286

  16. Interactive protein manipulation

    Energy Technology Data Exchange (ETDEWEB)

    SNCrivelli@lbl.gov

    2003-07-01

    We describe an interactive visualization and modeling program for the creation of protein structures ''from scratch''. The input to our program is an amino acid sequence -decoded from a gene- and a sequence of predicted secondary structure types for each amino acid-provided by external structure prediction programs. Our program can be used in the set-up phase of a protein structure prediction process; the structures created with it serve as input for a subsequent global internal energy minimization, or another method of protein structure prediction. Our program supports basic visualization methods for protein structures, interactive manipulation based on inverse kinematics, and visualization guides to aid a user in creating ''good'' initial structures.

  17. MicroProteins

    DEFF Research Database (Denmark)

    Eguen, Teinai Ebimienere; Straub, Daniel; Graeff, Moritz;

    2015-01-01

    MicroProteins (miPs) are short, usually single-domain proteins that, in analogy to miRNAs, heterodimerize with their targets and exert a dominant-negative effect. Recent bioinformatic attempts to identify miPs have resulted in a list of potential miPs, many of which lack the defining...... characteristics of a miP. In this opinion article, we clearly state the characteristics of a miP as evidenced by known proteins that fit the definition; we explain why modulatory proteins misrepresented as miPs do not qualify as true miPs. We also discuss the evolutionary history of miPs, and how the miP concept...

  18. Polymers for Protein Conjugation

    Directory of Open Access Journals (Sweden)

    Gianfranco Pasut

    2014-01-01

    Full Text Available Polyethylene glycol (PEG at the moment is considered the leading polymer for protein conjugation in view of its unique properties, as well as to its low toxicity in humans, qualities which have been confirmed by its extensive use in clinical practice. Other polymers that are safe, biodegradable and custom-designed have, nevertheless, also been investigated as potential candidates for protein conjugation. This review will focus on natural polymers and synthetic linear polymers that have been used for protein delivery and the results associated with their use. Genetic fusion approaches for the preparation of protein-polypeptide conjugates will be also reviewed and compared with the best known chemical conjugation ones.

  19. Electron transfer in proteins

    DEFF Research Database (Denmark)

    Farver, O; Pecht, I

    1991-01-01

    Electron migration between and within proteins is one of the most prevalent forms of biological energy conversion processes. Electron transfer reactions take place between active centers such as transition metal ions or organic cofactors over considerable distances at fast rates and with remarkable...... specificity. The electron transfer is attained through weak electronic interaction between the active sites, so that considerable research efforts are centered on resolving the factors that control the rates of long-distance electron transfer reactions in proteins. These factors include (in addition......-containing proteins. These proteins serve almost exclusively in electron transfer reactions, and as it turns out, their metal coordination sites are endowed with properties uniquely optimized for their function....

  20. Recombinant Collagenlike Proteins

    Science.gov (United States)

    Fertala, Andzej

    2007-01-01

    A group of collagenlike recombinant proteins containing high densities of biologically active sites has been invented. The method used to express these proteins is similar to a method of expressing recombinant procollagens and collagens described in U. S. Patent 5,593,859, "Synthesis of human procollagens and collagens in recombinant DNA systems." Customized collagenous proteins are needed for biomedical applications. In particular, fibrillar collagens are attractive for production of matrices needed for tissue engineering and drug delivery. Prior to this invention, there was no way of producing customized collagenous proteins for these and other applications. Heretofore, collagenous proteins have been produced by use of such biological systems as yeasts, bacteria, and transgenic animals and plants. These products are normal collagens that can also be extracted from such sources as tendons, bones, and hides. These products cannot be made to consist only of biologically active, specific amino acid sequences that may be needed for specific applications. Prior to this invention, it had been established that fibrillar collagens consist of domains that are responsible for such processes as interaction with cells, binding of growth factors, and interaction with a number of structural proteins present in the extracellular matrix. A normal collagen consists of a sequence of domains that can be represented by a corresponding sequence of labels, e.g., D1D2D3D4. A collagenlike protein of the present invention contains regions of collagen II that contain multiples of a single domain (e.g., D1D1D1D1 or D4D4D4D4) chosen for its specific biological activity. By virtue of the multiplicity of the chosen domain, the density of sites having that specific biological activity is greater than it is in a normal collagen. A collagenlike protein according to this invention can thus be made to have properties that are necessary for tissue engineering.

  1. Occupational protein contact dermatitis.

    Science.gov (United States)

    Barbaud, Annick; Poreaux, Claire; Penven, Emmanuelle; Waton, Julie

    2015-01-01

    Occupational contact dermatitis is generally caused by haptens but can also be induced by proteins causing mainly immunological contact urticaria (ICU); chronic hand eczema in the context of protein contact dermatitis (PCD). In a monocentric retrospective study, from our database, only 31 (0.41%) of patients with contact dermatitis had positive skin tests with proteins: 22 had occupational PCD, 3 had non-occupational PCD, 5 occupational ICU and 1 cook had a neutrophilic fixed food eruption (NFFE) due to fish. From these results and analysis of literature, the characteristics of PCD can be summarized as follows. It is a chronic eczematous dermatitis, possibly exacerbated by work, suggestive if associated with inflammatory perionyxix and immediate erythema with pruritis, to be investigated when the patient resumes work after a period of interruption. Prick tests with the suspected protein-containing material are essential, as patch tests have negative results. In case of multisensitisation revealed by prick tests, it is advisable to analyse IgE against recombinant allergens. A history of atopy, found in 56 to 68% of the patients, has to be checked for. Most of the cases are observed among food-handlers but PCD can also be due to non-edible plants, latex, hydrolysed proteins or animal proteins. Occupational exposure to proteins can thus lead to the development of ICU. Reflecting hypersensitivity to very low concentrations of allergens, investigating ICU therefore requires caution and prick tests should be performed with a diluted form of the causative protein-containing product. Causes are food, especially fruit peel, non-edible plants, cosmetic products, latex, animals.

  2. Colorimetric protein assay techniques.

    Science.gov (United States)

    Sapan, C V; Lundblad, R L; Price, N C

    1999-04-01

    There has been an increase in the number of colorimetric assay techniques for the determination of protein concentration over the past 20 years. This has resulted in a perceived increase in sensitivity and accuracy with the advent of new techniques. The present review considers these advances with emphasis on the potential use of such technologies in the assay of biopharmaceuticals. The techniques reviewed include Coomassie Blue G-250 dye binding (the Bradford assay), the Lowry assay, the bicinchoninic acid assay and the biuret assay. It is shown that each assay has advantages and disadvantages relative to sensitivity, ease of performance, acceptance in the literature, accuracy and reproducibility/coefficient of variation/laboratory-to-laboratory variation. A comparison of the use of several assays with the same sample population is presented. It is suggested that the most critical issue in the use of a chromogenic protein assay for the characterization of a biopharmaceutical is the selection of a standard for the calibration of the assay; it is crucial that the standard be representative of the sample. If it is not possible to match the standard with the sample from the perspective of protein composition, then it is preferable to use an assay that is not sensitive to the composition of the protein such as a micro-Kjeldahl technique, quantitative amino acid analysis or the biuret assay. In a complex mixture it might be inappropriate to focus on a general method of protein determination and much more informative to use specific methods relating to the protein(s) of particular interest, using either specific assays or antibody-based methods. The key point is that whatever method is adopted as the 'gold standard' for a given protein, this method needs to be used routinely for calibration.

  3. Protein Nitrogen Determination

    Science.gov (United States)

    Nielsen, S. Suzanne

    The protein content of foods can be determined by numerous methods. The Kjeldahl method and the nitrogen combustion (Dumas) method for protein analysis are based on nitrogen determination. Both methods are official for the purposes of nutrition labeling of foods. While the Kjeldahl method has been used widely for over a hundred years, the recent availability of automated instrumentation for the Dumas method in many cases is replacing use of the Kjeldahl method.

  4. Transdermal Delivery of Proteins

    OpenAIRE

    Kalluri, Haripriya; Banga, Ajay K.

    2011-01-01

    Transdermal delivery of peptides and proteins avoids the disadvantages associated with the invasive parenteral route of administration and other alternative routes such as the pulmonary and nasal routes. Since proteins have a large size and are hydrophilic in nature, they cannot permeate passively across the skin due to the stratum corneum which allows the transport of only small lipophilic drug molecules. Enhancement techniques such as chemical enhancers, iontophoresis, microneedles, electro...

  5. Protein phosphorylation and photorespiration.

    Science.gov (United States)

    Hodges, M; Jossier, M; Boex-Fontvieille, E; Tcherkez, G

    2013-07-01

    Photorespiration allows the recycling of carbon atoms of 2-phosphoglycolate produced by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) oxygenase activity, as well as the removal of potentially toxic metabolites. The photorespiratory pathway takes place in the light, encompasses four cellular compartments and interacts with several other metabolic pathways and functions. Therefore, the regulation of this cycle is probably of paramount importance to plant metabolism, however, our current knowledge is poor. To rapidly respond to changing conditions, proteins undergo a number of different post-translational modifications that include acetylation, methylation and ubiquitylation, but protein phosphorylation is probably the most common. The reversible covalent addition of a phosphate group to a specific amino acid residue allows the modulation of protein function, such as activity, subcellular localisation, capacity to interact with other proteins and stability. Recent data indicate that many photorespiratory enzymes can be phosphorylated, and thus it seems that the photorespiratory cycle is, in part, regulated by protein phosphorylation. In this review, the known phosphorylation sites of each Arabidopsis thaliana photorespiratory enzyme and several photorespiratory-associated proteins are described and discussed. A brief account of phosphoproteomic protocols is also given since the published data compiled in this review are the fruit of this approach.

  6. Hepatitis C virus proteins

    Institute of Scientific and Technical Information of China (English)

    Jean Dubuisson

    2007-01-01

    Hepatitis C virus (HCV) encodes a single polyprotein,which is processed by cellular and viral proteases to generate 10 polypeptides. The HCV genome also contains an overlapping +1 reading frame that may lead to the synthesis of an additional protein. Until recently,studies of HCV have been hampered by the lack of a productive cell culture system. Since the identification of HCV genome approximately 17 years ago, structural,biochemical and biological information on HCV proteins has mainly been obtained with proteins produced by heterologous expression systems. In addition, some functional studies have also been confirmed with replicon systems or with retroviral particles pseudotyped with HCV envelope glycoproteins. The data that have accumulated on HCV proteins begin to provide a framework for understanding the molecular mechanisms involved in the major steps of HCV life cycle. Moreover,the knowledge accumulated on HCV proteins is also leading to the development of antiviral drugs among which some are showing promising results in early-phase clinical trials. This review summarizes the current knowledge on the functions and biochemical features of HCV proteins.

  7. Cardiolipin Interactions with Proteins.

    Science.gov (United States)

    Planas-Iglesias, Joan; Dwarakanath, Himal; Mohammadyani, Dariush; Yanamala, Naveena; Kagan, Valerian E; Klein-Seetharaman, Judith

    2015-09-15

    Cardiolipins (CL) represent unique phospholipids of bacteria and eukaryotic mitochondria with four acyl chains and two phosphate groups that have been implicated in numerous functions from energy metabolism to apoptosis. Many proteins are known to interact with CL, and several cocrystal structures of protein-CL complexes exist. In this work, we describe the collection of the first systematic and, to the best of our knowledge, the comprehensive gold standard data set of all known CL-binding proteins. There are 62 proteins in this data set, 21 of which have nonredundant crystal structures with bound CL molecules available. Using binding patch analysis of amino acid frequencies, secondary structures and loop supersecondary structures considering phosphate and acyl chain binding regions together and separately, we gained a detailed understanding of the general structural and dynamic features involved in CL binding to proteins. Exhaustive docking of CL to all known structures of proteins experimentally shown to interact with CL demonstrated the validity of the docking approach, and provides a rich source of information for experimentalists who may wish to validate predictions.

  8. Disease specific protein corona

    Science.gov (United States)

    Rahman, M.; Mahmoudi, M.

    2015-03-01

    It is now well accepted that upon their entrance into the biological environments, the surface of nanomaterials would be covered by various biomacromolecules (e.g., proteins and lipids). The absorption of these biomolecules, so called `protein corona', onto the surface of (nano)biomaterials confers them a new `biological identity'. Although the formation of protein coronas on the surface of nanoparticles has been widely investigated, there are few reports on the effect of various diseases on the biological identity of nanoparticles. As the type of diseases may tremendously changes the composition of the protein source (e.g., human plasma/serum), one can expect that amount and composition of associated proteins in the corona composition may be varied, in disease type manner. Here, we show that corona coated silica and polystyrene nanoparticles (after interaction with in the plasma of the healthy individuals) could induce unfolding of fibrinogen, which promotes release of the inflammatory cytokines. However, no considerable releases of inflammatory cytokines were observed for corona coated graphene sheets. In contrast, the obtained corona coated silica and polystyrene nanoparticles from the hypofibrinogenemia patients could not induce inflammatory cytokine release where graphene sheets do. Therefore, one can expect that disease-specific protein coronas can provide a novel approach for applying nanomedicine to personalized medicine, improving diagnosis and treatment of different diseases tailored to the specific conditions and circumstances.

  9. The effect of protein-protein and protein-membrane interactions on membrane fouling in ultrafiltration

    NARCIS (Netherlands)

    Huisman, I.H.; Prádanos, P.; Hernández, A.

    2000-01-01

    It was studied how protein-protein and protein-membrane interactions influence the filtration performance during the ultrafiltration of protein solutions over polymeric membranes. This was done by measuring flux, streaming potential, and protein transmission during filtration of bovine serum albumin

  10. Similarity measures for protein ensembles

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper

    2009-01-01

    Analyses of similarities and changes in protein conformation can provide important information regarding protein function and evolution. Many scores, including the commonly used root mean square deviation, have therefore been developed to quantify the similarities of different protein conformatio...

  11. Controllability in protein interaction networks.

    Science.gov (United States)

    Wuchty, Stefan

    2014-05-13

    Recently, the focus of network research shifted to network controllability, prompting us to determine proteins that are important for the control of the underlying interaction webs. In particular, we determined minimum dominating sets of proteins (MDSets) in human and yeast protein interaction networks. Such groups of proteins were defined as optimized subsets where each non-MDSet protein can be reached by an interaction from an MDSet protein. Notably, we found that MDSet proteins were enriched with essential, cancer-related, and virus-targeted genes. Their central position allowed MDSet proteins to connect protein complexes and to have a higher impact on network resilience than hub proteins. As for their involvement in regulatory functions, MDSet proteins were enriched with transcription factors and protein kinases and were significantly involved in bottleneck interactions, regulatory links, phosphorylation events, and genetic interactions.

  12. Protein hydrolysates in sports nutrition

    Directory of Open Access Journals (Sweden)

    Manninen Anssi H

    2009-09-01

    Full Text Available Abstract It has been suggested that protein hydrolysates providing mainly di- and tripeptides are superior to intact (whole proteins and free amino acids in terms of skeletal muscle protein anabolism. This review provides a critical examination of protein hydrolysate studies conducted in healthy humans with special reference to sports nutrition. The effects of protein hydrolysate ingestion on blood amino acid levels, muscle protein anabolism, body composition, exercise performance and muscle glycogen resynthesis are discussed.

  13. Protein Functionality in Food Systems

    Institute of Scientific and Technical Information of China (English)

    WANG Panpan

    2010-01-01

    The structure,shape,color,smell and taste of food were decided by protein functionality.The utilization of protein will improve by changing the protein functionality.Protein functionality is also advantage to maintain and utilize the nutrition of food.This paper summarized the nature,classification,factors and prospect of protein functionality.It ccn provide a theoretical basis for application of protein in food industry.

  14. The cullin protein family.

    Science.gov (United States)

    Sarikas, Antonio; Hartmann, Thomas; Pan, Zhen-Qiang

    2011-01-01

    Cullin proteins are molecular scaffolds that have crucial roles in the post-translational modification of cellular proteins involving ubiquitin. The mammalian cullin protein family comprises eight members (CUL1 to CUL7 and PARC), which are characterized by a cullin homology domain. CUL1 to CUL7 assemble multi-subunit Cullin-RING E3 ubiquitin ligase (CRL) complexes, the largest family of E3 ligases with more than 200 members. Although CUL7 and PARC are present only in chordates, other members of the cullin protein family are found in Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and yeast. A cullin protein tethers both a substrate-targeting unit, often through an adaptor protein, and the RING finger component in a CRL. The cullin-organized CRL thus positions a substrate close to the RING-bound E2 ubiquitin-conjugating enzyme, which catalyzes the transfer of ubiquitin to the substrate. In addition, conjugation of cullins with the ubiquitin-like molecule Nedd8 modulates activation of the corresponding CRL complex, probably through conformational regulation of the interactions between cullin's carboxy-terminal tail and CRL's RING subunit. Genetic studies in several model organisms have helped to unravel a multitude of physiological functions associated with cullin proteins and their respective CRLs. CRLs target numerous substrates and thus have an impact on a range of biological processes, including cell growth, development, signal transduction, transcriptional control, genomic integrity and tumor suppression. Moreover, mutations in CUL7 and CUL4B genes have been linked to hereditary human diseases.

  15. PROTEIN SYNTHESIS GAME

    Directory of Open Access Journals (Sweden)

    J.C.Q. Carvalho

    2004-05-01

    Full Text Available The theoretical explanation of biological concepts, associated with the use of teaching games andmodels, intensify the comprehension and increase students interest, stimulating them to participateactively on the teaching-learning process. The sta of dissemination from Centro de BiotecnologiaMolecular Estrutural (CBME, in partnership with the Centro de Divulgac~ao Cientca e Cultural(CDCC, presents, in this work, a new educational resource denoted: Protein Synthesis Game. Theapproach of the game involves the cytological aspects of protein synthesis, directed to high schoolstudents. Students are presented to day-by-day facts related to the function of a given protein in thehuman body. Such task leads players to the goal of solving out a problem through synthesizing aspecied protein. The game comprises: (1 a board illustrated with the transversal section of animalcell, with its main structures and organelles and sequences of hypothetical genes; (2 cards with thedescription of steps and other structures required for protein synthesis in eukaryotic cells; (3 piecesrepresenting nucleotides, polynucleotides, ribosome, amino acids, and polypeptide chains. In order toplay the game, students take cards that sequentially permit them to acquire the necessary pieces forproduction of the protein described in each objective. Players must move the pieces on the board andsimulate the steps of protein synthesis. The dynamic of the game allows students to easily comprehendprocesses of transcription and translation. This game was presented to dierent groups of high schoolteachers and students. Their judgments have been heard and indicated points to be improved, whichhelped us with the game development. Furthermore, the opinions colleted were always favorable forthe application of this game as a teaching resource in classrooms.

  16. Bioinformatics and moonlighting proteins

    Directory of Open Access Journals (Sweden)

    Sergio eHernández

    2015-06-01

    Full Text Available Multitasking or moonlighting is the capability of some proteins to execute two or more biochemical functions. Usually, moonlighting proteins are experimentally revealed by serendipity. For this reason, it would be helpful that Bioinformatics could predict this multifunctionality, especially because of the large amounts of sequences from genome projects. In the present work, we analyse and describe several approaches that use sequences, structures, interactomics and current bioinformatics algorithms and programs to try to overcome this problem. Among these approaches are: a remote homology searches using Psi-Blast, b detection of functional motifs and domains, c analysis of data from protein-protein interaction databases (PPIs, d match the query protein sequence to 3D databases (i.e., algorithms as PISITE, e mutation correlation analysis between amino acids by algorithms as MISTIC. Programs designed to identify functional motif/domains detect mainly the canonical function but usually fail in the detection of the moonlighting one, Pfam and ProDom being the best methods. Remote homology search by Psi-Blast combined with data from interactomics databases (PPIs have the best performance. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can only be used in very specific situations –it requires the existence of multialigned family protein sequences - but can suggest how the evolutionary process of second function acquisition took place. The multitasking protein database MultitaskProtDB (http://wallace.uab.es/multitask/, previously published by our group, has been used as a benchmark for the all of the analyses.

  17. Modeling Mercury in Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Jeremy C [ORNL; Parks, Jerry M [ORNL

    2016-01-01

    Mercury (Hg) is a naturally occurring element that is released into the biosphere both by natural processes and anthropogenic activities. Although its reduced, elemental form Hg(0) is relatively non-toxic, other forms such as Hg2+ and, in particular, its methylated form, methylmercury, are toxic, with deleterious effects on both ecosystems and humans. Microorganisms play important roles in the transformation of mercury in the environment. Inorganic Hg2+ can be methylated by certain bacteria and archaea to form methylmercury. Conversely, bacteria also demethylate methylmercury and reduce Hg2+ to relatively inert Hg(0). Transformations and toxicity occur as a result of mercury interacting with various proteins. Clearly, then, understanding the toxic effects of mercury and its cycling in the environment requires characterization of these interactions. Computational approaches are ideally suited to studies of mercury in proteins because they can provide a detailed picture and circumvent issues associated with toxicity. Here we describe computational methods for investigating and characterizing how mercury binds to proteins, how inter- and intra-protein transfer of mercury is orchestrated in biological systems, and how chemical reactions in proteins transform the metal. We describe quantum chemical analyses of aqueous Hg(II), which reveal critical factors that determine ligand binding propensities. We then provide a perspective on how we used chemical reasoning to discover how microorganisms methylate mercury. We also highlight our combined computational and experimental studies of the proteins and enzymes of the mer operon, a suite of genes that confers mercury resistance in many bacteria. Lastly, we place work on mercury in proteins in the context of what is needed for a comprehensive multi-scale model of environmental mercury cycling.

  18. A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction

    OpenAIRE

    Meijing Li; Tsendsuren Munkhdalai; Xiuming Yu; Keun Ho Ryu

    2015-01-01

    Many researchers focus on developing protein-named entity recognition (Protein-NER) or PPI extraction systems. However, the studies about these two topics cannot be merged well; then existing PPI extraction systems’ Protein-NER still needs to improve. In this paper, we developed the protein-protein interaction extraction system named PPIMiner based on Support Vector Machine (SVM) and parsing tree. PPIMiner consists of three main models: natural language processing (NLP) model, Protein-NER mod...

  19. ADSORPTION OF PROTEIN ON NANOPARTICLES

    Institute of Scientific and Technical Information of China (English)

    WU Qi

    1994-01-01

    The adsorption of protein on nanoparticles was studied by using dynamic light scattering to measure the hydrodynamic size of both pure protein and nanoparticles adsorbed with different amounts of protein. The thickness of the adsorbed protein layer increases as protein concentration, but decreases as the initial size of nanoparticles. After properly scaling the thickness with the initial diameter, we are able to fit all experimental data with a single master curve. Our experimental results suggest that the adsorbed proteins form a monolayeron the nanoparticle surface and the adsorbed protein molecules are attached to the particle surface at many points through a possible hydrogen-bonding. Our results also indicate that as protein concentration increases, the overall shape of the adsorbed protein molecule continuously changes from a flat layer on the particle surface to a stretched coil extended into water. During the change, the hydrodynamic volume of the adsorbed protein increases linearly with protein concentration.

  20. Benchtop Detection of Proteins

    Science.gov (United States)

    Scardelletti, Maximilian C.; Varaljay, Vanessa

    2007-01-01

    A process, and a benchtop-scale apparatus for implementing the process, have been developed to detect proteins associated with specific microbes in water. The process and apparatus may also be useful for detection of proteins in other, more complex liquids. There may be numerous potential applications, including monitoring lakes and streams for contamination, testing of blood and other bodily fluids in medical laboratories, and testing for microbial contamination of liquids in restaurants and industrial food-processing facilities. A sample can be prepared and analyzed by use of this process and apparatus within minutes, whereas an equivalent analysis performed by use of other processes and equipment can often take hours to days. The process begins with the conjugation of near-infrared-fluorescent dyes to antibodies that are specific to a particular protein. Initially, the research has focused on using near-infrared dyes to detect antigens or associated proteins in solution, which has proven successful vs. microbial cells, and streamlining the technique in use for surface protein detection on microbes would theoretically render similar results. However, it is noted that additional work is needed to transition protein-based techniques to microbial cell detection. Consequently, multiple such dye/antibody pairs could be prepared to enable detection of multiple selected microbial species, using a different dye for each species. When excited by near-infrared light of a suitable wavelength, each dye fluoresces at a unique longer wavelength that differs from those of the other dyes, enabling discrimination among the various species. In initial tests, the dye/antibody pairs are mixed into a solution suspected of containing the selected proteins, causing the binding of the dye/antibody pairs to such suspect proteins that may be present. The solution is then run through a microcentrifuge that includes a membrane that acts as a filter in that it retains the dye/antibody/protein

  1. Purine inhibitors of protein kinases, G proteins and polymerases

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Nathanael S. (Berkeley, CA); Schultz, Peter (Oakland, CA); Kim, Sung-Hou (Moraga, CA); Meijer, Laurent (Roscoff, FR)

    2001-07-03

    The present invention relates to purine analogs that inhibit, inter alia, protein kinases, G-proteins and polymerases. In addition, the present invention relates to methods of using such purine analogs to inhibit protein kinases, G-proteins, polymerases and other cellular processes and to treat cellular proliferative diseases.

  2. Integral UBL domain proteins: a family of proteasome interacting proteins

    DEFF Research Database (Denmark)

    Hartmann-Petersen, Rasmus; Gordon, Colin

    2004-01-01

    The family of ubiquitin-like (UBL) domain proteins (UDPs) comprises a conserved group of proteins involved in a multitude of different cellular activities. However, recent studies on UBL-domain proteins indicate that these proteins appear to share a common property in their ability to interact wi...

  3. Electrochemical nanomoulding through proteins

    Science.gov (United States)

    Allred, Daniel B.

    The continued improvements in performance of modern electronic devices are directly related to the manufacturing of smaller, denser features on surfaces. Electrochemical fabrication has played a large role in continuing this trend due to its low cost and ease of scaleability toward ever smaller dimensions. This work introduces the concept of using proteins, essentially monodisperse complex polymers whose three-dimensional structures are fixed by their encoded amino acid sequences, as "moulds" around which nanostructures can be built by electrochemical fabrication. Bacterial cell-surface layer proteins, or "S-layer" proteins, from two organisms---Deinococcus radiodurans and Sporosarcina ureae---were used as the "moulds" for electrochemical fabrication. The proteins are easily purified as micron-sized sheets of periodic molecular complexes with 18-nm hexagonal and 13-nm square unit cell lattices, respectively. Direct imaging by transmission electron microscopy on ultrathin noble metal films without sample preparation eliminates potential artifacts to the high surface energy substrates necessary for high nucleation densities. Characterization involved imaging, electron diffraction, spectroscopy, and three-dimensional reconstruction. The S-layer protein of D. radiodurans was further subjected to an atomic force microscope based assay to determine the integrity of its structure and long-range order and was found to be useful for fabrication from around pH 3 to 12.

  4. Protein Dynamics in Enzymology

    Science.gov (United States)

    Brooks, , III

    2001-03-01

    Enzymes carry-out the chemical activity essential for living processes by providing particular structural arrangements of chemically functional moieties through the structure of their constituent proteins. They are suggested to be optimized through evolution to specifically bind the transition state for the chemical processes they participate in, thereby enhancing the rate of these chemical events by 6-12 orders of magnitude. However, proteins are malleable and fluctuating many-body systems and may also utilize coupling between motional processes with catalysis to regulate or promote these processes. Our studies are aimed at exploring the hypothesis that motions of the protein couple distant regions of the molecule to assist catalytic processes. We demonstrate, through the use of molecular simulations, that strongly coupled motions occur in regions of protein molecules distant in sequence and space from each other, and the enzyme’s active site, when the protein is in a reactant state. Further, we find that the presence of this coupling disappears in complexes no longer reactive-competent, i.e., for product configurations and mutant sequences. The implications of these findings and aspects of evolutionary relationships and mutational studies which support the coupling hypothesis will be discussed in the context of our work on dihydrofolate reductase.

  5. Heat Capacity in Proteins

    Science.gov (United States)

    Prabhu, Ninad V.; Sharp, Kim A.

    2005-05-01

    Heat capacity (Cp) is one of several major thermodynamic quantities commonly measured in proteins. With more than half a dozen definitions, it is the hardest of these quantities to understand in physical terms, but the richest in insight. There are many ramifications of observed Cp changes: The sign distinguishes apolar from polar solvation. It imparts a temperature (T) dependence to entropy and enthalpy that may change their signs and which of them dominate. Protein unfolding usually has a positive ΔCp, producing a maximum in stability and sometimes cold denaturation. There are two heat capacity contributions, from hydration and protein-protein interactions; which dominates in folding and binding is an open question. Theoretical work to date has dealt mostly with the hydration term and can account, at least semiquantitatively, for the major Cp-related features: the positive and negative Cp of hydration for apolar and polar groups, respectively; the convergence of apolar group hydration entropy at T ≈ 112°C; the decrease in apolar hydration Cp with increasing T; and the T-maximum in protein stability and cold denaturation.

  6. Protein Crystal Serum Albumin

    Science.gov (United States)

    1998-01-01

    As the most abundant protein in the circulatory system albumin contributes 80% to colloid osmotic blood pressure. Albumin is also chiefly responsible for the maintenance of blood pH. It is located in every tissue and bodily secretion, with extracellular protein comprising 60% of total albumin. Perhaps the most outstanding property of albumin is its ability to bind reversibly to an incredible variety of ligands. It is widely accepted in the pharmaceutical industry that the overall distribution, metabolism, and efficiency of many drugs are rendered ineffective because of their unusually high affinity for this abundant protein. An understanding of the chemistry of the various classes of pharmaceutical interactions with albumin can suggest new approaches to drug therapy and design. Principal Investigator: Dan Carter/New Century Pharmaceuticals

  7. Polarizable protein packing

    KAUST Repository

    Ng, Albert H.

    2011-01-24

    To incorporate protein polarization effects within a protein combinatorial optimization framework, we decompose the polarizable force field AMOEBA into low order terms. Including terms up to the third-order provides a fair approximation to the full energy while maintaining tractability. We represent the polarizable packing problem for protein G as a hypergraph and solve for optimal rotamers with the FASTER combinatorial optimization algorithm. These approximate energy models can be improved to high accuracy [root mean square deviation (rmsd) < 1 kJ mol -1] via ridge regression. The resulting trained approximations are used to efficiently identify new, low-energy solutions. The approach is general and should allow combinatorial optimization of other many-body problems. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011 Copyright © 2011 Wiley Periodicals, Inc.

  8. Discovery of binding proteins for a protein target using protein-protein docking-based virtual screening.

    Science.gov (United States)

    Zhang, Changsheng; Tang, Bo; Wang, Qian; Lai, Luhua

    2014-10-01

    Target structure-based virtual screening, which employs protein-small molecule docking to identify potential ligands, has been widely used in small-molecule drug discovery. In the present study, we used a protein-protein docking program to identify proteins that bind to a specific target protein. In the testing phase, an all-to-all protein-protein docking run on a large dataset was performed. The three-dimensional rigid docking program SDOCK was used to examine protein-protein docking on all protein pairs in the dataset. Both the binding affinity and features of the binding energy landscape were considered in the scoring function in order to distinguish positive binding pairs from negative binding pairs. Thus, the lowest docking score, the average Z-score, and convergency of the low-score solutions were incorporated in the analysis. The hybrid scoring function was optimized in the all-to-all docking test. The docking method and the hybrid scoring function were then used to screen for proteins that bind to tumor necrosis factor-α (TNFα), which is a well-known therapeutic target for rheumatoid arthritis and other autoimmune diseases. A protein library containing 677 proteins was used for the screen. Proteins with scores among the top 20% were further examined. Sixteen proteins from the top-ranking 67 proteins were selected for experimental study. Two of these proteins showed significant binding to TNFα in an in vitro binding study. The results of the present study demonstrate the power and potential application of protein-protein docking for the discovery of novel binding proteins for specific protein targets.

  9. The representation of protein complexes in the Protein Ontology (PRO

    Directory of Open Access Journals (Sweden)

    Smith Barry

    2011-09-01

    Full Text Available Abstract Background Representing species-specific proteins and protein complexes in ontologies that are both human- and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. Description We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. Conclusion PRO is a unique database resource for species-specific protein complexes. PRO facilitates robust annotation of variations in composition and function contexts for protein complexes within and between species.

  10. Stress proteins in CNS inflammation

    NARCIS (Netherlands)

    Noort, J.M. van

    2008-01-01

    Stress proteins or heat shock proteins (HSPs) are ubiquitous cellular components that have long been known to act as molecular chaperones. By assisting proper folding and transport of proteins, and by assisting in the degradation of aberrant proteins, they play key roles in cellular metabolism. The

  11. Protein: FBA3 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA3 Atg1 kinase complex ATG1 APG1, AUT3, CVT10 Serine/threonine-protein kinase ATG1 Autophagy prot...ein 3, Autophagy-related protein 1, Cytoplasm to vacuole targeting protein 10 559292 Sacchar

  12. Protein: FEA3 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FEA3 AREB pathway: Signaling proteins SRK2E OST1, SNRK2.6 Serine/threonine-protein kinase SRK2E Prot...ein OPEN STOMATA 1, SNF1-related kinase 2.6, Serine/threonine-protein kinase OST1 3702 Arabidopsis thaliana 829541 Q940H6 3UC4, 3ZUT, 3ZUU, 3UDB 19805022 ...

  13. Protein: FEA3 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FEA3 AREB pathway: Signaling proteins AZF1 OZAKGYO, ZF1 At5g67450, Cys2/His2-type zinc finger prot...ein 1, Zinc finger protein OZAKGYO, Zinc-finger protein 1 3702 Arabidopsis thaliana 836881 Q9SSW1 21852415 ...

  14. Ubiquitin domain proteins in disease

    DEFF Research Database (Denmark)

    Klausen, Louise Kjær; Schulze, Andrea; Seeger, Michael;

    2007-01-01

    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...... and cancer. Publication history: Republished from Current BioData's Targeted Proteins database (TPdb; http://www.targetedproteinsdb.com)....

  15. The Formation of Protein Structure

    DEFF Research Database (Denmark)

    Bohr, Jakob; Bohr, Henrik; Brunak, Søren

    1996-01-01

    Dynamically induced curvature owing to long-range excitations along the backbones of protein molecules with non-linear elastic properties may control the folding of proteins.......Dynamically induced curvature owing to long-range excitations along the backbones of protein molecules with non-linear elastic properties may control the folding of proteins....

  16. Protein: FBB5 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBB5 RNA silencing TNRC6A CAGH26, KIAA1460, TNRC6 TNRC6A Trinucleotide repeat-containing gene 6A protein... CAG repeat protein 26, EMSY interactor protein, GW182 autoantigen, Glycine-tryptophan protein of 182 kDa 9606 Homo sapiens Q8NDV7 27327 27327 19398495 ...

  17. Cold gelation of globular proteins

    NARCIS (Netherlands)

    Alting, A.C.

    2003-01-01

    Keywords : globular proteins, whey protein, ovalbumin, cold gelation, disulfide bonds, texture, gel hardnessProtein gelation in food products is important to obtain desirable sensory and textural properties. Cold gelation is a novel method to produce protein-based gels. It is a two step process in w

  18. Protein: FBA7 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA7 claudin-zona occluden TJP3 ZO3 TJP3 Tight junction protein ZO-3 Tight junction protein 3, Zona occlude...ns protein 3, Zonula occludens protein 3 9606 Homo sapiens O95049 27134 3KFV 27134 O95049 ...

  19. Protein: FBA7 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA7 claudin-zona occluden TJP2 X104, ZO2 TJP2 Tight junction protein ZO-2 Tight ju...nction protein 2, Zona occludens protein 2, Zonula occludens protein 2 9606 Homo sapiens Q9UDY2 9414 3E17, 2OSG 9414 ...

  20. Protein: FBA7 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA7 claudin-zona occluden Tjp1 Zo1 Tight junction protein ZO-1 Tight junction protein 1, Zona occlude...ns protein 1, Zonula occludens protein 1 10090 Mus musculus 21872 P39447 2RRM P39447 21431884 ...

  1. A simple dependence between protein evolution rate and the number of protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Hirsh Aaron E

    2003-05-01

    Full Text Available Abstract Background It has been shown for an evolutionarily distant genomic comparison that the number of protein-protein interactions a protein has correlates negatively with their rates of evolution. However, the generality of this observation has recently been challenged. Here we examine the problem using protein-protein interaction data from the yeast Saccharomyces cerevisiae and genome sequences from two other yeast species. Results In contrast to a previous study that used an incomplete set of protein-protein interactions, we observed a highly significant correlation between number of interactions and evolutionary distance to either Candida albicans or Schizosaccharomyces pombe. This study differs from the previous one in that it includes all known protein interactions from S. cerevisiae, and a larger set of protein evolutionary rates. In both evolutionary comparisons, a simple monotonic relationship was found across the entire range of the number of protein-protein interactions. In agreement with our earlier findings, this relationship cannot be explained by the fact that proteins with many interactions tend to be important to yeast. The generality of these correlations in other kingdoms of life unfortunately cannot be addressed at this time, due to the incompleteness of protein-protein interaction data from organisms other than S. cerevisiae. Conclusions Protein-protein interactions tend to slow the rate at which proteins evolve. This may be due to structural constraints that must be met to maintain interactions, but more work is needed to definitively establish the mechanism(s behind the correlations we have observed.

  2. The Development and Characterization of Protein-Based Stationary Phases for Studying Drug-Protein and Protein-Protein Interactions

    OpenAIRE

    Sanghvi, Mitesh; Moaddel, Ruin; Wainer, Irving W.

    2011-01-01

    Protein-based liquid chromatography stationary phases are used in bioaffinity chromatography for studying drug-protein interactions, the determination of binding affinities, competitive and allosteric interactions, as well as for studying protein-protein interactions. This review addresses the development and characterization of protein-based stationary phase, and the application of these phases using frontal and zonal chromatography techniques. The approach will be illustrated using immobili...

  3. Laboratory and outside the laboratory measurements of ginned and ot ginned cotton for fiber micronaire and maturity by portable Near Infrared (NIR) Instruments

    Science.gov (United States)

    Micronaire is a key cotton quality assessment property, impacting downstream fiber processing and dye consistency. A component of micronaire is fiber maturity (degree of secondary wall development). Historically, micronaire and maturity are measured in a laboratory under tight environmental condit...

  4. Sound of proteins

    DEFF Research Database (Denmark)

    2007-01-01

    and statistical analysis of the resulting molecular trajectories (as everybody else!). However, recently I started assigning a particular sound frequency to each amino acid in the protein, and by setting the amplitude of each frequency according to the movement amplitude we can "hear" whenever two aminoacids...

  5. Protein Requirements during Aging

    Directory of Open Access Journals (Sweden)

    Glenda Courtney-Martin

    2016-08-01

    Full Text Available Protein recommendations for elderly, both men and women, are based on nitrogen balance studies. They are set at 0.66 and 0.8 g/kg/day as the estimated average requirement (EAR and recommended dietary allowance (RDA, respectively, similar to young adults. This recommendation is based on single linear regression of available nitrogen balance data obtained at test protein intakes close to or below zero balance. Using the indicator amino acid oxidation (IAAO method, we estimated the protein requirement in young adults and in both elderly men and women to be 0.9 and 1.2 g/kg/day as the EAR and RDA, respectively. This suggests that there is no difference in requirement on a gender basis or on a per kg body weight basis between younger and older adults. The requirement estimates however are ~40% higher than the current protein recommendations on a body weight basis. They are also 40% higher than our estimates in young men when calculated on the basis of fat free mass. Thus, current recommendations may need to be re-assessed. Potential rationale for this difference includes a decreased sensitivity to dietary amino acids and increased insulin resistance in the elderly compared with younger individuals.

  6. Markers of protein oxidation

    DEFF Research Database (Denmark)

    Headlam, Henrietta A; Davies, Michael Jonathan

    2004-01-01

    Exposure of proteins to radicals in the presence of O2 gives both side-chain oxidation and backbone fragmentation. These processes can be interrelated, with initial side-chain oxidation giving rise to backbone damage via transfer reactions. We have shown previously that alkoxyl radicals formed on...

  7. Protein oxidation and peroxidation

    DEFF Research Database (Denmark)

    Davies, Michael Jonathan

    2016-01-01

    to the residues targeted and their spatial location. Modification can result in increased side-chain hydrophilicity, side-chain and backbone fragmentation, aggregation via covalent cross-linking or hydrophobic interactions, protein unfolding and altered conformation, altered interactions with biological partners...

  8. Cellulose binding domain proteins

    Science.gov (United States)

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  9. Tuber storage proteins.

    Science.gov (United States)

    Shewry, Peter R

    2003-06-01

    A wide range of plants are grown for their edible tubers, but five species together account for almost 90 % of the total world production. These are potato (Solanum tuberosum), cassava (Manihot esculenta), sweet potato (Ipomoea batatus), yams (Dioscorea spp.) and taro (Colocasia, Cyrtosperma and Xanthosoma spp.). All of these, except cassava, contain groups of storage proteins, but these differ in the biological properties and evolutionary relationships. Thus, patatin from potato exhibits activity as an acylhydrolase and esterase, sporamin from sweet potato is an inhibitor of trypsin, and dioscorin from yam is a carbonic anhydrase. Both sporamin and dioscorin also exhibit antioxidant and radical scavenging activity. Taro differs from the other three crops in that it contains two major types of storage protein: a trypsin inhibitor related to sporamin and a mannose-binding lectin. These characteristics indicate that tuber storage proteins have evolved independently in different species, which contrasts with the highly conserved families of storage proteins present in seeds. Furthermore, all exhibit biological activities which could contribute to resistance to pests, pathogens or abiotic stresses, indicating that they may have dual roles in the tubers.

  10. Predicting where small molecules bind at protein-protein interfaces.

    Directory of Open Access Journals (Sweden)

    Peter Walter

    Full Text Available Small molecules that bind at protein-protein interfaces may either block or stabilize protein-protein interactions in cells. Thus, some of these binding interfaces may turn into prospective targets for drug design. Here, we collected 175 pairs of protein-protein (PP complexes and protein-ligand (PL complexes with known three-dimensional structures for which (1 one protein from the PP complex shares at least 40% sequence identity with the protein from the PL complex, and (2 the interface regions of these proteins overlap at least partially with each other. We found that those residues of the interfaces that may bind the other protein as well as the small molecule are evolutionary more conserved on average, have a higher tendency of being located in pockets and expose a smaller fraction of their surface area to the solvent than the remaining protein-protein interface region. Based on these findings we derived a statistical classifier that predicts patches at binding interfaces that have a higher tendency to bind small molecules. We applied this new prediction method to more than 10,000 interfaces from the protein data bank. For several complexes related to apoptosis the predicted binding patches were in direct contact to co-crystallized small molecules.

  11. Interaction between plate make and protein in protein crystallisation screening.

    Directory of Open Access Journals (Sweden)

    Gordon J King

    Full Text Available BACKGROUND: Protein crystallisation screening involves the parallel testing of large numbers of candidate conditions with the aim of identifying conditions suitable as a starting point for the production of diffraction quality crystals. Generally, condition screening is performed in 96-well plates. While previous studies have examined the effects of protein construct, protein purity, or crystallisation condition ingredients on protein crystallisation, few have examined the effect of the crystallisation plate. METHODOLOGY/PRINCIPAL FINDINGS: We performed a statistically rigorous examination of protein crystallisation, and evaluated interactions between crystallisation success and plate row/column, different plates of same make, different plate makes and different proteins. From our analysis of protein crystallisation, we found a significant interaction between plate make and the specific protein being crystallised. CONCLUSIONS/SIGNIFICANCE: Protein crystal structure determination is the principal method for determining protein structure but is limited by the need to produce crystals of the protein under study. Many important proteins are difficult to crystallize, so that identification of factors that assist crystallisation could open up the structure determination of these more challenging targets. Our findings suggest that protein crystallisation success may be improved by matching a protein with its optimal plate make.

  12. An evaluation of in vitro protein-protein interaction techniques: assessing contaminating background proteins.

    Science.gov (United States)

    Howell, Jenika M; Winstone, Tara L; Coorssen, Jens R; Turner, Raymond J

    2006-04-01

    Determination of protein-protein interactions is an important component in assigning function and discerning the biological relevance of proteins within a broader cellular context. In vitro protein-protein interaction methodologies, including affinity chromatography, coimmunoprecipitation, and newer approaches such as protein chip arrays, hold much promise in the detection of protein interactions, particularly in well-characterized organisms with sequenced genomes. However, each of these approaches attracts certain background proteins that can thwart detection and identification of true interactors. In addition, recombinant proteins expressed in Escherichia coli are also extensively used to assess protein-protein interactions, and background proteins in these isolates can thus contaminate interaction studies. Rigorous validation of a true interaction thus requires not only that an interaction be found by alternate techniques, but more importantly that researchers be aware of and control for matrix/support dependence. Here, we evaluate these methods for proteins interacting with DmsD (an E. coli redox enzyme maturation protein chaperone), in vitro, using E. coli subcellular fractions as prey sources. We compare and contrast the various in vitro interaction methods to identify some of the background proteins and protein profiles that are inherent to each of the methods in an E. coli system.

  13. Exploring NMR ensembles of calcium binding proteins: Perspectives to design inhibitors of protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Craescu Constantin T

    2011-05-01

    Full Text Available Abstract Background Disrupting protein-protein interactions by small organic molecules is nowadays a promising strategy employed to block protein targets involved in different pathologies. However, structural changes occurring at the binding interfaces make difficult drug discovery processes using structure-based drug design/virtual screening approaches. Here we focused on two homologous calcium binding proteins, calmodulin and human centrin 2, involved in different cellular functions via protein-protein interactions, and known to undergo important conformational changes upon ligand binding. Results In order to find suitable protein conformations of calmodulin and centrin for further structure-based drug design/virtual screening, we performed in silico structural/energetic analysis and molecular docking of terphenyl (a mimicking alpha-helical molecule known to inhibit protein-protein interactions of calmodulin into X-ray and NMR ensembles of calmodulin and centrin. We employed several scoring methods in order to find the best protein conformations. Our results show that docking on NMR structures of calmodulin and centrin can be very helpful to take into account conformational changes occurring at protein-protein interfaces. Conclusions NMR structures of protein-protein complexes nowadays available could efficiently be exploited for further structure-based drug design/virtual screening processes employed to design small molecule inhibitors of protein-protein interactions.

  14. Bayesian Estimator of Protein-Protein Association Probabilities

    Energy Technology Data Exchange (ETDEWEB)

    2008-05-28

    The Bayesian Estimator of Protein-Protein Association Probabilities (BEPro3) is a software tool for estimating probabilities of protein-protein association between bait and prey protein pairs using data from multiple-bait, multiple-replicate, protein LC-MS/MS affinity isolation experiments. BEPro3 is public domain software, has been tested on Windows XP and version 10.4 or newer of the Mac OS 10.4, and is freely available. A user guide, example dataset with analysis and additional documentation are included with the BEPro3 download.

  15. High quality protein microarray using in situ protein purification

    Directory of Open Access Journals (Sweden)

    Fleischmann Robert D

    2009-08-01

    Full Text Available Abstract Background In the postgenomic era, high throughput protein expression and protein microarray technologies have progressed markedly permitting screening of therapeutic reagents and discovery of novel protein functions. Hexa-histidine is one of the most commonly used fusion tags for protein expression due to its small size and convenient purification via immobilized metal ion affinity chromatography (IMAC. This purification process has been adapted to the protein microarray format, but the quality of in situ His-tagged protein purification on slides has not been systematically evaluated. We established methods to determine the level of purification of such proteins on metal chelate-modified slide surfaces. Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays. Results Two slide surfaces were examined, chelated Cu2+ slides suspended on a polyethylene glycol (PEG coating and chelated Ni2+ slides immobilized on a support without PEG coating. Using PEG-coated chelated Cu2+ slides, consistently higher purities of recombinant proteins were measured. An optimized wash buffer (PBST composed of 10 mM phosphate buffer, 2.7 mM KCl, 140 mM NaCl and 0.05% Tween 20, pH 7.4, further improved protein purity levels. Using Escherichia coli cell lysates expressing 90 recombinant Streptococcus pneumoniae proteins, 73 proteins were successfully immobilized, and 66 proteins were in situ purified with greater than 90% purity. We identified several antigens among the in situ-purified proteins via assays with anti-S. pneumoniae rabbit antibodies and a human patient antiserum, as a demonstration project of large scale microarray-based immunoproteomics profiling. The methodology is compatible with higher throughput formats of in vivo protein expression, eliminates the need for resin-based purification and circumvents

  16. Metabolism of minor isoforms of prion proteins: Cytosolic prion protein and transmembrane prion protein

    OpenAIRE

    Song, Zhiqi; Zhao, Deming; Yang, Lifeng

    2013-01-01

    Transmissible spongiform encephalopathy or prion disease is triggered by the conversion from cellular prion protein to pathogenic prion protein. Growing evidence has concentrated on prion protein configuration changes and their correlation with prion disease transmissibility and pathogenicity. In vivo and in vitro studies have shown that several cytosolic forms of prion protein with specific topological structure can destroy intracellular stability and contribute to prion protein pathogenicit...

  17. Dairy Proteins and Energy Balance

    DEFF Research Database (Denmark)

    Bendtsen, Line Quist

    High protein diets affect energy balance beneficially through decreased hunger, enhanced satiety and increased energy expenditure. Dairy products are a major source of protein. Dairy proteins are comprised of two classes, casein (80%) and whey proteins (20%), which are both of high quality......, but casein is absorbed slowly and whey is absorbed rapidly. The present PhD study investigated the effects of total dairy proteins, whey, and casein, on energy balance and the mechanisms behind any differences in the effects of the specific proteins. The results do not support the hypothesis that dairy...... proteins, whey or casein are more beneficial than other protein sources in the regulation of energy balance, and suggest that dairy proteins, whey or casein seem to play only a minor role, if any, in the prevention and treatment of obesity....

  18. The quality of microparticulated protein.

    Science.gov (United States)

    Erdman, J W

    1990-08-01

    The purpose of this paper is to describe the effects of microparticulation upon the quality of microparticulated protein products and to confirm that microparticulation does not result in changes in protein structure or quality different from those that occur with cooking. Two products were tested: microparticulated egg white and skim milk proteins and microparticulated whey protein concentrate. Three approaches were used to monitor for changes in amino acid and protein value: amino acid analysis, protein efficiency ratio (PER) bioassay, and both one- and two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis. Evaluation of the results of these tests indicates that no significant differences were found when comparing the premix before and after microparticulation. Significant differences also did not occur when the premix was cooked using conventional methods. Collectively, the data provide strong evidence that the protein microparticulation process used to prepare microparticulated protein products (e.g., Simplesse) does not alter the quality or nutritional value of protein in the final products.

  19. Coevolution study of mitochondria respiratory chain proteins:Toward the understanding of protein-protein interaction

    Institute of Scientific and Technical Information of China (English)

    Ming Yang; Yan Ge; Jiayan Wu; Jingfa Xiao; Jun Yu

    2011-01-01

    Coevolution can be seen as the interdependency between evolutionary histories. In the context of protein evolution, functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity. As to complex system, there are two forms of protein-protein interactions in vivo, which refer to inter-complex interaction and intra-complex interaction. In this paper, we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using "Mirror tree" method on the respiratory chain (RC) proteins. We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein-protein interaction in intra-complex and the binary protein-protein interaction in inter-complex, respectively. A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions (Wilcoxon test, p-value = 4.4 x 10-6). Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein-protein interaction.Furthermore, the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane. More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study.

  20. Mapping the human protein interactome

    Institute of Scientific and Technical Information of China (English)

    Daniel Figeys

    2008-01-01

    Interactions are the essence of all biomolecules because they cannot fulfill their roles without interacting with other molecules. Hence, mapping the interactions of biomolecules can be useful for understanding their roles and functions. Furthermore, the development of molecular based systems biology requires an understanding of the biomolecular interactions. In recent years, the mapping of protein-protein interactions in different species has been reported, but few reports have focused on the large-scale mapping of protein-protein interactions in human. Here, we review the developments in protein interaction mapping and we discuss issues and strategies for the mapping of the human protein interactome.

  1. Hydrogels Constructed from Engineered Proteins.

    Science.gov (United States)

    Li, Hongbin; Kong, Na; Laver, Bryce; Liu, Junqiu

    2016-02-24

    Due to their various potential biomedical applications, hydrogels based on engineered proteins have attracted considerable interest. Benefitting from significant progress in recombinant DNA technology and protein engineering/design techniques, the field of protein hydrogels has made amazing progress. The latest progress of hydrogels constructed from engineered recombinant proteins are presented, mainly focused on biorecognition-driven physical hydrogels as well as chemically crosslinked hydrogels. The various bio-recognition based physical crosslinking strategies are discussed, as well as chemical crosslinking chemistries used to engineer protein hydrogels, and protein hydrogels' various biomedical applications. The future perspectives of this fast evolving field of biomaterials are also discussed.

  2. Competitive Protein Adsorption - Multilayer Adsorption and Surface Induced Protein Aggregation

    DEFF Research Database (Denmark)

    Holmberg, Maria; Hou, Xiaolin

    2009-01-01

    In this study, competitive adsorption of albumin and IgG (immunoglobulin G) from human serum solutions and protein mixtures onto polymer surfaces is studied by means of radioactive labeling. By using two different radiolabels (125I and 131I), albumin and IgG adsorption to polymer surfaces...... is monitored simultaneously and the influence from the presence of other human serum proteins on albumin and IgG adsorption, as well as their mutual influence during adsorption processes, is investigated. Exploring protein adsorption by combining analysis of competitive adsorption from complex solutions...... of high concentration with investigation of single protein adsorption and interdependent adsorption between two specific proteins enables us to map protein adsorption sequences during competitive protein adsorption. Our study shows that proteins can adsorb in a multilayer fashion onto the polymer surfaces...

  3. Inferring protein-protein interaction complexes from immunoprecipitation data

    NARCIS (Netherlands)

    Kutzera, J.; Hoefsloot, H.C.J.; Malovannaya, A.; Smit, A.B.; Van Mechelen, I.; Smilde, A.K.

    2013-01-01

    BACKGROUND: Protein inverted question markprotein interactions in cells are widely explored using small inverted question markscale experiments. However, the search for protein complexes and their interactions in data from high throughput experiments such as immunoprecipitation is still a challenge.

  4. Cow's Milk Protein Allergy.

    Science.gov (United States)

    Mousan, Grace; Kamat, Deepak

    2016-10-01

    Cow's milk protein allergy (CMPA) is a common condition encountered in children with incidence estimated as 2% to 7.5% in the first year of life. Formula and breast-fed babies can present with symptoms of CMPA. It is important to accurately diagnose CMPA to avoid the consequences of either under- or overdiagnosis. CMPA is classically categorized into immunoglobulin E (IgE)- or non-IgE-mediated reaction that vary in clinical manifestations, diagnostic evaluation, and prognosis. The most commonly involved systems in patients with CMPA are gastrointestinal, skin, and respiratory. Evaluation of CMPA starts with good data gathering followed by testing if indicated. Treatment is simply by avoidance of cow's milk protein (CMP) in the child's or mother's diet, if exclusively breast-feeding. This article reviews the definition, epidemiology, risk factors, pathogenesis, clinical presentation, evaluation, management, and prognosis of CMPA and provides an overview of different options for formulas and their indication in the treatment of CMPA.

  5. Water-transporting proteins

    DEFF Research Database (Denmark)

    Zeuthen, Thomas

    2010-01-01

    . In the K(+)/Cl(-) and the Na(+)/K(+)/2Cl(-) cotransporters, water is entirely cotransported, while water transport in glucose uniporters and Na(+)-coupled transporters of nutrients and neurotransmitters takes place by both osmosis and cotransport. The molecular mechanism behind cotransport of water......Transport through lipids and aquaporins is osmotic and entirely driven by the difference in osmotic pressure. Water transport in cotransporters and uniporters is different: Water can be cotransported, energized by coupling to the substrate flux by a mechanism closely associated with protein...... is not clear. It is associated with the substrate movements in aqueous pathways within the protein; a conventional unstirred layer mechanism can be ruled out, due to high rates of diffusion in the cytoplasm. The physiological roles of the various modes of water transport are reviewed in relation to epithelial...

  6. Protein Functionalized Nanodiamond Arrays

    Directory of Open Access Journals (Sweden)

    Liu YL

    2010-01-01

    Full Text Available Abstract Various nanoscale elements are currently being explored for bio-applications, such as in bio-images, bio-detection, and bio-sensors. Among them, nanodiamonds possess remarkable features such as low bio-cytotoxicity, good optical property in fluorescent and Raman spectra, and good photostability for bio-applications. In this work, we devise techniques to position functionalized nanodiamonds on self-assembled monolayer (SAMs arrays adsorbed on silicon and ITO substrates surface using electron beam lithography techniques. The nanodiamond arrays were functionalized with lysozyme to target a certain biomolecule or protein specifically. The optical properties of the nanodiamond-protein complex arrays were characterized by a high throughput confocal microscope. The synthesized nanodiamond-lysozyme complex arrays were found to still retain their functionality in interacting with E. coli.

  7. Neurocognitive derivation of protein surface property from protein aggregate parameters

    OpenAIRE

    Mishra, Hrishikesh; Lahiri, Tapobrata

    2011-01-01

    Current work targeted to predicate parametric relationship between aggregate and individual property of a protein. In this approach, we considered individual property of a protein as its Surface Roughness Index (SRI) which was shown to have potential to classify SCOP protein families. The bulk property was however considered as Intensity Level based Multi-fractal Dimension (ILMFD) of ordinary microscopic images of heat denatured protein aggregates which was known to have potential to serve as...

  8. Purine inhibitors of protein kinases, G proteins and polymerases

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Nathanael S.; Schultz, Peter; Kim, Sung-Hou; Meijer, Laurent

    2004-10-12

    The present invention relates to 2-N-substituted 6-(4-methoxybenzylamino)-9-isopropylpurines that inhibit, inter alia, protein kinases, G-proteins and polymerases. In addition, the present invention relates to methods of using such 2-N-substituted 6-(4-methoxybenzylamino)-9-isopropylpurines to inhibit protein kinases, G-proteins, polymerases and other cellular processes and to treat cellular proliferative diseases.

  9. Protein-protein fusion catalyzed by sortase A.

    Science.gov (United States)

    Levary, David A; Parthasarathy, Ranganath; Boder, Eric T; Ackerman, Margaret E

    2011-04-06

    Chimeric proteins boast widespread use in areas ranging from cell biology to drug delivery. Post-translational protein fusion using the bacterial transpeptidase sortase A provides an attractive alternative when traditional gene fusion fails. We describe use of this enzyme for in vitro protein ligation and report the successful fusion of 10 pairs of protein domains with preserved functionality--demonstrating the robust and facile nature of this reaction.

  10. Protein-protein fusion catalyzed by sortase A.

    Directory of Open Access Journals (Sweden)

    David A Levary

    Full Text Available Chimeric proteins boast widespread use in areas ranging from cell biology to drug delivery. Post-translational protein fusion using the bacterial transpeptidase sortase A provides an attractive alternative when traditional gene fusion fails. We describe use of this enzyme for in vitro protein ligation and report the successful fusion of 10 pairs of protein domains with preserved functionality--demonstrating the robust and facile nature of this reaction.

  11. Quality protein maize: QPM

    Directory of Open Access Journals (Sweden)

    Ignjatović-Micić Dragana

    2008-01-01

    Full Text Available Quality protein maize (QPM contains the opaque-2 gene along with numerous modifiers for kernel hardness. Therefore, QPM is maize with high nutritive value of endosperm protein, with substantially higher content of two essential amino acids - lysine and tryptophan, and with good agronomical performances. Although QPM was developed primarily for utilization in the regions where, because of poverty, maize is the main staple food, it has many advantages for production and consumption in other parts of the world, too. QPM can be used for production of conventional and new animal feed, as well as for human nurture. As the rate of animal weight gain is doubled with QPM and portion viability is better, a part of normal maize production could be available for other purposes, such as, for example, ethanol production. Thus, breeding QPM is set as a challenge to produce high quality protein maize with high yield and other important agronomical traits, especially with today's food and feed demands and significance of energy crisis.

  12. Process for protein PEGylation.

    Science.gov (United States)

    Pfister, David; Morbidelli, Massimo

    2014-04-28

    PEGylation is a versatile drug delivery technique that presents a particularly wide range of conjugation chemistry and polymer structure. The conjugated protein can be tuned to specifically meet the needs of the desired application. In the area of drug delivery this typically means to increase the persistency in the human body without affecting the activity profile of the original protein. On the other hand, because of the high costs associated with the production of therapeutic proteins, subsequent operations imposed by PEGylation must be optimized to minimize the costs inherent to the additional steps. The closest attention has to be given to the PEGylation reaction engineering and to the subsequent purification processes. This review article focuses on these two aspects and critically reviews the current state of the art with a clear focus on the development of industrial scale processes which can meet the market requirements in terms of quality and costs. The possibility of using continuous processes, with integration between the reaction and the separation steps is also illustrated.

  13. Hydrolyzed Proteins in Allergy.

    Science.gov (United States)

    Salvatore, Silvia; Vandenplas, Yvan

    2016-01-01

    Hydrolyzed proteins are used worldwide in the therapeutic management of infants with allergic manifestations and have long been proposed as a dietetic measure to prevent allergy in at risk infants. The degree and method of hydrolysis, protein source and non-nitrogen components characterize different hydrolyzed formulas (HFs) and may determine clinical efficacy, tolerance and nutritional effects. Cow's milk (CM)-based HFs are classified as extensively (eHF) or partially HF (pHF) based on the percentage of small peptides. One whey pHF has been shown to reduce atopic dermatitis in high-risk infants who are not exclusively breastfed. More studies are needed to determine the benefit of these formulas in the prevention of CM allergy (CMA) and in the general population. eHFs represent up to now the treatment of choice for most infants with CMA. However, new developments, such as an extensively hydrolyzed rice protein-based formula, could become alternative options if safety and nutritional and therapeutic efficacy are confirmed as this type of formula is less expensive. In some countries, an extensive soy hydrolysate is available.

  14. Neutron protein crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Niimura, Nobuo [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1998-10-01

    X-ray diffraction of single crystal has enriched the knowledge of various biological molecules such as proteins, DNA, t-RNA, viruses, etc. It is difficult to make structural analysis of hydrogen atoms in a protein using X-ray crystallography, whereas neutron diffraction seems usable to directly determine the location of those hydrogen atoms. Here, neutron diffraction method was applied to structural analysis of hen egg-white lysozyme. Since the crystal size of a protein to analyze is generally small (5 mm{sup 3} at most), the neutron beam at the sample position in monochromator system was set to less than 5 x 5 mm{sup 2} and beam divergence to 0.4 degree or less. Neutron imaging plate with {sup 6}Li or Gd mixed with photostimulated luminescence material was used and about 2500 Bragg reflections were recorded in one crystal setting. A total of 38278 reflections for 2.0 A resolution were collected in less than 10 days. Thus, stereo views of Trp-111 omit map around the indol ring of Trp-111 was presented and the three-dimensional arrangement of 696H and 264D atoms in the lysozyme molecules was determined using the omit map. (M.N.)

  15. A Bayesian Framework for Combining Protein and Network Topology Information for Predicting Protein-Protein Interactions.

    Science.gov (United States)

    Birlutiu, Adriana; d'Alché-Buc, Florence; Heskes, Tom

    2015-01-01

    Computational methods for predicting protein-protein interactions are important tools that can complement high-throughput technologies and guide biologists in designing new laboratory experiments. The proteins and the interactions between them can be described by a network which is characterized by several topological properties. Information about proteins and interactions between them, in combination with knowledge about topological properties of the network, can be used for developing computational methods that can accurately predict unknown protein-protein interactions. This paper presents a supervised learning framework based on Bayesian inference for combining two types of information: i) network topology information, and ii) information related to proteins and the interactions between them. The motivation of our model is that by combining these two types of information one can achieve a better accuracy in predicting protein-protein interactions, than by using models constructed from these two types of information independently.

  16. Metabolism of minor isoforms of prion proteins Cytosolic prion protein and transmembrane prion protein*

    Institute of Scientific and Technical Information of China (English)

    Zhiqi Song; Deming Zhao; Lifeng Yang

    2013-01-01

    Transmissible spongiform encephalopathy or prion disease is triggered by the conversion from cellular prion protein to pathogenic prion protein. Growing evidence has concentrated on prion protein configuration changes and their correlation with prion disease transmissibility and pathoge-nicity. In vivo and in vitro studies have shown that several cytosolic forms of prion protein with spe-cific topological structure can destroy intracellular stability and contribute to prion protein pathoge-nicity. In this study, the latest molecular chaperone system associated with endoplasmic reticu-lum-associated protein degradation, the endoplasmic reticulum resident protein quality-control system and the ubiquitination proteasome system, is outlined. The molecular chaperone system directly correlates with the prion protein degradation pathway. Understanding the molecular me-chanisms wil help provide a fascinating avenue for further investigations on prion disease treatment and prion protein-induced neurodegenerative diseases.

  17. Predicting disease-related proteins based on clique backbone in protein-protein interaction network.

    Science.gov (United States)

    Yang, Lei; Zhao, Xudong; Tang, Xianglong

    2014-01-01

    Network biology integrates different kinds of data, including physical or functional networks and disease gene sets, to interpret human disease. A clique (maximal complete subgraph) in a protein-protein interaction network is a topological module and possesses inherently biological significance. A disease-related clique possibly associates with complex diseases. Fully identifying disease components in a clique is conductive to uncovering disease mechanisms. This paper proposes an approach of predicting disease proteins based on cliques in a protein-protein interaction network. To tolerate false positive and negative interactions in protein networks, extending cliques and scoring predicted disease proteins with gene ontology terms are introduced to the clique-based method. Precisions of predicted disease proteins are verified by disease phenotypes and steadily keep to more than 95%. The predicted disease proteins associated with cliques can partly complement mapping between genotype and phenotype, and provide clues for understanding the pathogenesis of serious diseases.

  18. Protein engineering techniques gateways to synthetic protein universe

    CERN Document Server

    Poluri, Krishna Mohan

    2017-01-01

    This brief provides a broad overview of protein-engineering research, offering a glimpse of the most common experimental methods. It also presents various computational programs with applications that are widely used in directed evolution, computational and de novo protein design. Further, it sheds light on the advantages and pitfalls of existing methodologies and future perspectives of protein engineering techniques.

  19. Ontology integration to identify protein complex in protein interaction networks

    Directory of Open Access Journals (Sweden)

    Yang Zhihao

    2011-10-01

    Full Text Available Abstract 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.

  20. Multiscale modeling of proteins.

    Science.gov (United States)

    Tozzini, Valentina

    2010-02-16

    The activity within a living cell is based on a complex network of interactions among biomolecules, exchanging information and energy through biochemical processes. These events occur on different scales, from the nano- to the macroscale, spanning about 10 orders of magnitude in the space domain and 15 orders of magnitude in the time domain. Consequently, many different modeling techniques, each proper for a particular time or space scale, are commonly used. In addition, a single process often spans more than a single time or space scale. Thus, the necessity arises for combining the modeling techniques in multiscale approaches. In this Account, I first review the different modeling methods for bio-systems, from quantum mechanics to the coarse-grained and continuum-like descriptions, passing through the atomistic force field simulations. Special attention is devoted to their combination in different possible multiscale approaches and to the questions and problems related to their coherent matching in the space and time domains. These aspects are often considered secondary, but in fact, they have primary relevance when the aim is the coherent and complete description of bioprocesses. Subsequently, applications are illustrated by means of two paradigmatic examples: (i) the green fluorescent protein (GFP) family and (ii) the proteins involved in the human immunodeficiency virus (HIV) replication cycle. The GFPs are currently one of the most frequently used markers for monitoring protein trafficking within living cells; nanobiotechnology and cell biology strongly rely on their use in fluorescence microscopy techniques. A detailed knowledge of the actions of the virus-specific enzymes of HIV (specifically HIV protease and integrase) is necessary to study novel therapeutic strategies against this disease. Thus, the insight accumulated over years of intense study is an excellent framework for this Account. The foremost relevance of these two biomolecular systems was

  1. Chemical Protein Modification through Cysteine.

    Science.gov (United States)

    Gunnoo, Smita B; Madder, Annemieke

    2016-04-01

    The modification of proteins with non-protein entities is important for a wealth of applications, and methods for chemically modifying proteins attract considerable attention. Generally, modification is desired at a single site to maintain homogeneity and to minimise loss of function. Though protein modification can be achieved by targeting some natural amino acid side chains, this often leads to ill-defined and randomly modified proteins. Amongst the natural amino acids, cysteine combines advantageous properties contributing to its suitability for site-selective modification, including a unique nucleophilicity, and a low natural abundance--both allowing chemo- and regioselectivity. Native cysteine residues can be targeted, or Cys can be introduced at a desired site in a protein by means of reliable genetic engineering techniques. This review on chemical protein modification through cysteine should appeal to those interested in modifying proteins for a range of applications.

  2. Protein Linked to Atopic Dermatitis

    Science.gov (United States)

    ... Research Matters NIH Research Matters January 14, 2013 Protein Linked to Atopic Dermatitis Normal skin from a ... in mice suggests that lack of a certain protein may trigger atopic dermatitis, the most common type ...

  3. Protein: MPA1 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available feron stimulator, Mediator of IRF3 activation, Stimulator of interferon genes protein 9606 Homo sapiens Q86WV6 340061 ... ...MPA1 TLR signaling molecules TMEM173 ERIS, MITA, STING Transmembrane protein 173 Endoplasmic reticulum inter

  4. Protein: FBA3 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA3 Atg1 kinase complex TOR1 DRR1 Serine/threonine-protein kinase TOR1 Dominant rapamycin... resistance protein 1, Phosphatidylinositol kinase homolog TOR1, Target of rapamycin kinase 1 559292

  5. Functional aspects of protein flexibility

    DEFF Research Database (Denmark)

    Teilum, Kaare; Olsen, Johan G; Kragelund, Birthe B

    2009-01-01

    Proteins are dynamic entities, and they possess an inherent flexibility that allows them to function through molecular interactions within the cell, among cells and even between organisms. Appreciation of the non-static nature of proteins is emerging, but to describe and incorporate...... this into an intuitive perception of protein function is challenging. Flexibility is of overwhelming importance for protein function, and the changes in protein structure during interactions with binding partners can be dramatic. The present review addresses protein flexibility, focusing on protein-ligand interactions....... The thermodynamics involved are reviewed, and examples of structure-function studies involving experimentally determined flexibility descriptions are presented. While much remains to be understood about protein flexibility, it is clear that it is encoded within their amino acid sequence and should be viewed...

  6. Controlling allosteric networks in proteins

    Science.gov (United States)

    Dokholyan, Nikolay

    2013-03-01

    We present a novel methodology based on graph theory and discrete molecular dynamics simulations for delineating allosteric pathways in proteins. We use this methodology to uncover the structural mechanisms responsible for coupling of distal sites on proteins and utilize it for allosteric modulation of proteins. We will present examples where inference of allosteric networks and its rewiring allows us to ``rescue'' cystic fibrosis transmembrane conductance regulator (CFTR), a protein associated with fatal genetic disease cystic fibrosis. We also use our methodology to control protein function allosterically. We design a novel protein domain that can be inserted into identified allosteric site of target protein. Using a drug that binds to our domain, we alter the function of the target protein. We successfully tested this methodology in vitro, in living cells and in zebrafish. We further demonstrate transferability of our allosteric modulation methodology to other systems and extend it to become ligh-activatable.

  7. Protein: FBA6 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA6 transport vesicle formation SEC12 SED2 Guanine nucleotide-exchange factor SEC12 Protein... transport protein SEC12 559292 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 855760 P11655 ...

  8. Protein: MPA1 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available MPA1 TLR signaling molecules MAVS IPS1, KIAA1271, VISA VISA_(gene) Mitochondrial an...tiviral-signaling protein CARD adapter inducing interferon beta, Interferon beta promoter stimulator protein 1, Putative NF-kappa

  9. Microtubules, Tubulins and Associated Proteins.

    Science.gov (United States)

    Raxworthy, Michael J.

    1988-01-01

    Reviews much of what is known about microtubules, which are biopolymers consisting predominantly of subunits of the globular protein, tubulin. Describes the functions of microtubules, their structure and assembly, microtube associated proteins, and microtubule-disrupting agents. (TW)

  10. Protein Misfolding and Human Disease

    DEFF Research Database (Denmark)

    Gregersen, Niels; Bross, Peter Gerd; Vang, Søren

    2006-01-01

    phenylketonuria, Parkinson's disease, α-1-antitrypsin deficiency, familial neurohypophyseal diabetes insipidus, and short-chain acyl-CoA dehydrogenase deficiency. Despite the differences, an emerging paradigm suggests that the cellular effects of protein misfolding provide a common framework that may contribute......Protein misfolding is a common event in living cells. In young and healthy cells, the misfolded protein load is disposed of by protein quality control (PQC) systems. In aging cells and in cells from certain individuals with genetic diseases, the load may overwhelm the PQC capacity, resulting...... in accumulation of misfolded proteins. Dependent on the properties of the protein and the efficiency of the PQC systems, the accumulated protein may be degraded or assembled into toxic oligomers and aggregates. To illustrate this concept, we discuss a number of very different protein misfolding diseases including...

  11. Yeast Interacting Proteins Database: YJL199C, YJL199C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available d in closely related Saccharomyces species; protein detected in large-scale protein-protein interaction studies...cies; protein detected in large-scale protein-protein interaction studies Rows with this prey as prey (4) Ro...n; not conserved in closely related Saccharomyces species; protein detected in large-scale protein-protein interaction studies... species; protein detected in large-scale protein-protein interaction studies Rows with this prey as prey Ro

  12. Similarity measures for protein ensembles

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper

    2009-01-01

    Analyses of similarities and changes in protein conformation can provide important information regarding protein function and evolution. Many scores, including the commonly used root mean square deviation, have therefore been developed to quantify the similarities of different protein conformations...... a synthetic example from molecular dynamics simulations. We then apply the algorithms to revisit the problem of ensemble averaging during structure determination of proteins, and find that an ensemble refinement method is able to recover the correct distribution of conformations better than standard single...

  13. Purification of Tetrahymena cytoskeletal proteins.

    Science.gov (United States)

    Honts, Jerry E

    2012-01-01

    Like all eukaryotic cells, Tetrahymena thermophila contains a rich array of cytoskeletal proteins, some familiar and some novel. A detailed analysis of the structure, function, and interactions of these proteins requires procedures for purifying the individual protein components. Procedures for the purification of actin and tubulin from Tetrahymena are reviewed, followed by a description of a procedure that yields proteins from the epiplasmic layer and associated structures, including the tetrins. Finally, the challenges and opportunities for future advances are assessed.

  14. Protein loss during nuclear isolation

    OpenAIRE

    1983-01-01

    Cryomicrodissection makes possible the measurement of the entire in vivo protein content of the amphibian oocyte nucleus and provides a heretofore missing baseline for estimating protein loss during nuclear isolation by other methods. When oocyte nuclei are isolated into an aqueous medium, they lose 95% of their protein with a half-time of 250 s. This result implies an even more rapid loss of protein from aqueously isolated nuclei of ordinary-size cells.

  15. Understanding Protein-Protein Interactions Using Local Structural Features

    DEFF Research Database (Denmark)

    Planas-Iglesias, Joan; Bonet, Jaume; García-García, Javier;

    2013-01-01

    Protein-protein interactions (PPIs) play a relevant role among the different functions of a cell. Identifying the PPI network of a given organism (interactome) is useful to shed light on the key molecular mechanisms within a biological system. In this work, we show the role of structural features...... (loops and domains) to comprehend the molecular mechanisms of PPIs. A paradox in protein-protein binding is to explain how the unbound proteins of a binary complex recognize each other among a large population within a cell and how they find their best docking interface in a short timescale. We use...

  16. Protein: FBA4 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available tion factor complex helicase XPB subunit Basic transcription factor 2 89 kDa subunit, DNA excision repair prot...ein ERCC-3, DNA repair protein complementing XP-B cells, TFIIH basal transcription factor complex 89 kDa s...ubunit, Xeroderma pigmentosum group B-complementing protein 9606 Homo sapiens P19447 2071 2071 P19447 ...

  17. Protein: FBA4 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA4 REST-TBP TBP GTF2D1, TF2D, TFIID TATA_binding_protein TATA-box-binding protein... TATA sequence-binding protein, TATA-binding factor, TATA-box factor, Transcription initiation factor TFIID

  18. Hydrophobic patches on protein surfaces

    NARCIS (Netherlands)

    Lijnzaad, P.

    2007-01-01

    Hydrophobicity is a prime determinant of the structure and function of proteins. It is the driving force behind the folding of soluble proteins, and when exposed on the surface, it is frequently involved in recognition and binding of ligands and other proteins. The energetic cost of exposing hydroph

  19. Validation of protein carbonyl measurement

    DEFF Research Database (Denmark)

    Augustyniak, Edyta; Adam, Aisha; Wojdyla, Katarzyna;

    2015-01-01

    Protein carbonyls are widely analysed as a measure of protein oxidation. Several different methods exist for their determination. A previous study had described orders of magnitude variance that existed when protein carbonyls were analysed in a single laboratory by ELISA using different commercial...

  20. Structuring high-protein foods

    NARCIS (Netherlands)

    Purwanti, N.

    2012-01-01

    Increased protein consumption gives rise to various health benefits. High-protein intake can lead to muscle development, body weight control and suppression of sarcopenia progression. However, increasing the protein content in food products leads to textural changes over time. These changes result i

  1. The Proteins API: accessing key integrated protein and genome information.

    Science.gov (United States)

    Nightingale, Andrew; Antunes, Ricardo; Alpi, Emanuele; Bursteinas, Borisas; Gonzales, Leonardo; Liu, Wudong; Luo, Jie; Qi, Guoying; Turner, Edd; Martin, Maria

    2017-04-05

    The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics data from large scale data sources (LSS). Using the coordinates service, researchers are able to retrieve the genomic sequence coordinates for proteins in UniProtKB. This, the LSS genomics and proteomics data for UniProt proteins is programmatically only available through this service. A Swagger UI has been implemented to provide documentation, an interface for users, with little or no programming experience, to 'talk' to the services to quickly and easily formulate queries with the services and obtain dynamically generated source code for popular programming languages, such as Java, Perl, Python and Ruby. Search results are returned as standard JSON, XML or GFF data objects. The Proteins API is a scalable, reliable, fast, easy to use RESTful services that provides a broad protein information resource for users to ask questions based upon their field of expertise and allowing them to gain an integrated overview of protein annotations available to aid their knowledge gain on proteins in biological processes. The Proteins API is available at (http://www.ebi.ac.uk/proteins/api/doc).

  2. Protein stress and stress proteins: implications in aging and disease

    Indian Academy of Sciences (India)

    C Sőti; Péter Csermely

    2007-04-01

    Environmantal stress induces damage that activates an adaptive response in any organism. The cellular stress response is based on the induction of cytoprotective proteins, the so called stress or heat shock proteins. The stress response as well as stress proteins are ubiquitous, highly conserved mechanism, and genes, respectively, already present in prokaryotes. Chaperones protect the proteome against conformational damage, promoting the function of protein networks. Protein damage takes place during aging and in several degenerative diseases, and presents a threat to overload the cellular defense mechanisms. The preservation of a robust stress response and protein disposal is indispensable for health and longevity. This review summarizes the present knowledge of protein damage, turnover, and the stress response in aging and degenerative diseases.

  3. Protein subcellular localization assays using split fluorescent proteins

    Science.gov (United States)

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2009-09-08

    The invention provides protein subcellular localization assays using split fluorescent protein systems. The assays are conducted in living cells, do not require fixation and washing steps inherent in existing immunostaining and related techniques, and permit rapid, non-invasive, direct visualization of protein localization in living cells. The split fluorescent protein systems used in the practice of the invention generally comprise two or more self-complementing fragments of a fluorescent protein, such as GFP, wherein one or more of the fragments correspond to one or more beta-strand microdomains and are used to "tag" proteins of interest, and a complementary "assay" fragment of the fluorescent protein. Either or both of the fragments may be functionalized with a subcellular targeting sequence enabling it to be expressed in or directed to a particular subcellular compartment (i.e., the nucleus).

  4. Flowering Buds of Globular Proteins: Transpiring Simplicity of Protein Organization

    Science.gov (United States)

    Berezovsky, Igor N.

    2002-01-01

    Structural and functional complexity of proteins is dramatically reduced to a simple linear picture when the laws of polymer physics are considered. A basic unit of the protein structure is a nearly standard closed loop of 25–35 amino acid residues, and every globular protein is built of consecutively connected closed loops. The physical necessity of the closed loops had been apparently imposed on the early stages of protein evolution. Indeed, the most frequent prototype sequence motifs in prokaryotic proteins have the same sequence size, and their high match representatives are found as closed loops in crystallized proteins. Thus, the linear organization of the closed loop elements is a quintessence of protein evolution, structure and folding. PMID:18629251

  5. Protein enriched pasta: structure and digestibility of its protein network.

    Science.gov (United States)

    Laleg, Karima; Barron, Cécile; Santé-Lhoutellier, Véronique; Walrand, Stéphane; Micard, Valérie

    2016-02-01

    Wheat (W) pasta was enriched in 6% gluten (G), 35% faba (F) or 5% egg (E) to increase its protein content (13% to 17%). The impact of the enrichment on the multiscale structure of the pasta and on in vitro protein digestibility was studied. Increasing the protein content (W- vs. G-pasta) strengthened pasta structure at molecular and macroscopic scales but reduced its protein digestibility by 3% by forming a higher covalently linked protein network. Greater changes in the macroscopic and molecular structure of the pasta were obtained by varying the nature of protein used for enrichment. Proteins in G- and E-pasta were highly covalently linked (28-32%) resulting in a strong pasta structure. Conversely, F-protein (98% SDS-soluble) altered the pasta structure by diluting gluten and formed a weak protein network (18% covalent link). As a result, protein digestibility in F-pasta was significantly higher (46%) than in E- (44%) and G-pasta (39%). The effect of low (55 °C, LT) vs. very high temperature (90 °C, VHT) drying on the protein network structure and digestibility was shown to cause greater molecular changes than pasta formulation. Whatever the pasta, a general strengthening of its structure, a 33% to 47% increase in covalently linked proteins and a higher β-sheet structure were observed. However, these structural differences were evened out after the pasta was cooked, resulting in identical protein digestibility in LT and VHT pasta. Even after VHT drying, F-pasta had the best amino acid profile with the highest protein digestibility, proof of its nutritional interest.

  6. CPL:Detecting Protein Complexes by Propagating Labels on Protein-Protein Interaction Network

    Institute of Scientific and Technical Information of China (English)

    代启国; 郭茂祖; 刘晓燕; 滕志霞; 王春宇

    2014-01-01

    Proteins usually bind together to form complexes, which play an important role in cellular activities. Many graph clustering methods have been proposed to identify protein complexes by finding dense regions in protein-protein interaction networks. We present a novel framework (CPL) that detects protein complexes by propagating labels through interactions in a network, in which labels denote complex identifiers. With proper propagation in CPL, proteins in the same complex will be assigned with the same labels. CPL does not make any strong assumptions about the topological structures of the complexes, as in previous methods. The CPL algorithm is tested on several publicly available yeast protein-protein interaction networks and compared with several state-of-the-art methods. The results suggest that CPL performs better than the existing methods. An analysis of the functional homogeneity based on a gene ontology analysis shows that the detected complexes of CPL are highly biologically relevant.

  7. [Protein nutrition and physical activity].

    Science.gov (United States)

    Navarro, M P

    1992-09-01

    The relationship between physical exercise and diet in order to optimize performance is getting growing interest. This review examines protein needs and protein intakes as well as the role of protein in the body and the metabolic changes occurring at the synthesis and catabolic levels during exercise. Protein synthesis in muscle or liver, amino acids oxidation, glucose production via gluconeogenesis from amino acids, etc., are modified, and consequently plasma and urinary nitrogen metabolites are affected. A brief comment on the advantages, disadvantages and forms of different protein supplements for sportsmen is given.

  8. [Protein phosphatases: structure and function].

    Science.gov (United States)

    Bulanova, E G; Budagian, V M

    1994-01-01

    The process of protein and enzyme systems phosphorylation is necessary for cell growth, differentiation and preparation for division and mitosis. The conformation changes of protein as a result of phosphorylation lead to increased enzyme activity and enhanced affinity to substrates. A large group of enzymes--protein kinases--is responsible for phosphorylation process in cell, which are divided into tyrosine- and serine-threonine-kinases depending on their ability to phosphorylate appropriate amino acid residues. In this review has been considered the functional importance and structure of protein phosphatases--enzymes, which are functional antagonists of protein kinases.

  9. Protein: FBA3 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA3 Atg8 conjugation sysytem Map1lc3b Map1alc3, Map1lc3 MAP1LC3B Microtubule-associated protein...s 1A/1B light chain 3B Autophagy-related protein LC3 B, Autophagy-related ubiquitin-like modifi...er LC3 B, MAP1 light chain 3-like protein 2, MAP1A/MAP1B light chain 3 B, Microtubule-associated protein 1 l

  10. ING proteins in cellular senescence.

    Science.gov (United States)

    Menéndez, Camino; Abad, María; Gómez-Cabello, Daniel; Moreno, Alberto; Palmero, Ignacio

    2009-05-01

    Cellular senescence is an effective anti-tumor barrier that acts by restraining the uncontrolled proliferation of cells carrying potentially oncogenic alterations. ING proteins are putative tumor suppressor proteins functionally linked to the p53 pathway and to chromatin regulation. ING proteins exert their tumor-protective action through different types of responses. Here, we review the evidence on the participation of ING proteins, mainly ING1 and ING2, in the implementation of the senescent response. The currently available data support an important role of ING proteins as regulators of senescence, in connection with the p53 pathway and chromatin organization.

  11. Protein nanotechnology: what is it?

    Science.gov (United States)

    Gerrard, Juliet A

    2013-01-01

    Protein nanotechnology is an emerging field that is still defining itself. It embraces the intersection of protein science, which exists naturally at the nanoscale, and the burgeoning field of nanotechnology. In this opening chapter, a select review is given of some of the exciting nanostructures that have already been created using proteins, and the sorts of applications that protein engineers are reaching towards in the nanotechnology space. This provides an introduction to the rest of the volume, which provides inspirational case studies, along with tips and tools to manipulate proteins into new forms and architectures, beyond Nature's original intentions.

  12. Protein-protein interaction network-based detection of functionally similar proteins within species.

    Science.gov (United States)

    Song, Baoxing; Wang, Fen; Guo, Yang; Sang, Qing; Liu, Min; Li, Dengyun; Fang, Wei; Zhang, Deli

    2012-07-01

    Although functionally similar proteins across species have been widely studied, functionally similar proteins within species showing low sequence similarity have not been examined in detail. Identification of these proteins is of significant importance for understanding biological functions, evolution of protein families, progression of co-evolution, and convergent evolution and others which cannot be obtained by detection of functionally similar proteins across species. Here, we explored a method of detecting functionally similar proteins within species based on graph theory. After denoting protein-protein interaction networks using graphs, we split the graphs into subgraphs using the 1-hop method. Proteins with functional similarities in a species were detected using a method of modified shortest path to compare these subgraphs and to find the eligible optimal results. Using seven protein-protein interaction networks and this method, some functionally similar proteins with low sequence similarity that cannot detected by sequence alignment were identified. By analyzing the results, we found that, sometimes, it is difficult to separate homologous from convergent evolution. Evaluation of the performance of our method by gene ontology term overlap showed that the precision of our method was excellent.

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

    Directory of Open Access Journals (Sweden)

    Pang Chi

    2008-11-01

    Full Text Available Abstract 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.

  14. Human cancer protein-protein interaction network: a structural perspective.

    Directory of Open Access Journals (Sweden)

    Gozde Kar

    2009-12-01

    Full Text Available Protein-protein interaction networks provide a global picture of cellular function and biological processes. Some proteins act as hub proteins, highly connected to others, whereas some others have few interactions. The dysfunction of some interactions causes many diseases, including cancer. Proteins interact through their interfaces. Therefore, studying the interface properties of cancer-related proteins will help explain their role in the interaction networks. Similar or overlapping binding sites should be used repeatedly in single interface hub proteins, making them promiscuous. Alternatively, multi-interface hub proteins make use of several distinct binding sites to bind to different partners. We propose a methodology to integrate protein interfaces into cancer interaction networks (ciSPIN, cancer structural protein interface network. The interactions in the human protein interaction network are replaced by interfaces, coming from either known or predicted complexes. We provide a detailed analysis of cancer related human protein-protein interfaces and the topological properties of the cancer network. The results reveal that cancer-related proteins have smaller, more planar, more charged and less hydrophobic binding sites than non-cancer proteins, which may indicate low affinity and high specificity of the cancer-related interactions. We also classified the genes in ciSPIN according to phenotypes. Within phenotypes, for breast cancer, colorectal cancer and leukemia, interface properties were found to be discriminating from non-cancer interfaces with an accuracy of 71%, 67%, 61%, respectively. In addition, cancer-related proteins tend to interact with their partners through distinct interfaces, corresponding mostly to multi-interface hubs, which comprise 56% of cancer-related proteins, and constituting the nodes with higher essentiality in the network (76%. We illustrate the interface related affinity properties of two cancer-related hub

  15. Mathematical methods for protein science

    Energy Technology Data Exchange (ETDEWEB)

    Hart, W.; Istrail, S.; Atkins, J. [Sandia National Labs., Albuquerque, NM (United States)

    1997-12-31

    Understanding the structure and function of proteins is a fundamental endeavor in molecular biology. Currently, over 100,000 protein sequences have been determined by experimental methods. The three dimensional structure of the protein determines its function, but there are currently less than 4,000 structures known to atomic resolution. Accordingly, techniques to predict protein structure from sequence have an important role in aiding the understanding of the Genome and the effects of mutations in genetic disease. The authors describe current efforts at Sandia to better understand the structure of proteins through rigorous mathematical analyses of simple lattice models. The efforts have focused on two aspects of protein science: mathematical structure prediction, and inverse protein folding.

  16. Pentatricopeptide repeat proteins in plants.

    Science.gov (United States)

    Barkan, Alice; Small, Ian

    2014-01-01

    Pentatricopeptide repeat (PPR) proteins constitute one of the largest protein families in land plants, with more than 400 members in most species. Over the past decade, much has been learned about the molecular functions of these proteins, where they act in the cell, and what physiological roles they play during plant growth and development. A typical PPR protein is targeted to mitochondria or chloroplasts, binds one or several organellar transcripts, and influences their expression by altering RNA sequence, turnover, processing, or translation. Their combined action has profound effects on organelle biogenesis and function and, consequently, on photosynthesis, respiration, plant development, and environmental responses. Recent breakthroughs in understanding how PPR proteins recognize RNA sequences through modular base-specific contacts will help match proteins to potential binding sites and provide a pathway toward designing synthetic RNA-binding proteins aimed at desired targets.

  17. Rat myocardial protein degradation.

    Science.gov (United States)

    Steer, J H; Hopkins, B E

    1981-07-01

    1. Myocardial protein degradation rates were determined by following tyrosine release from rat isolated left hemi-atria in vitro. 2. After two 20 min preincubations the rate of tyrosine release from hemi-atria was constant for 4 h. 3. Skeletal muscle protein degradation was determined by following tyrosine release from rat isolated hemi-diaphragm (Fulks, Li & Goldberg, 1975). 4. Insulin (10(-7) M) inhibited tyrosine release from hemi-atria and hemi-diaphragm to a similar extent. A 48 h fast increased tyrosine release rate from hemi-diaphragm and decreased tyrosine release rate from hemi-atria. Hemi-diaphragm tyrosine release was inhibited by 15 mmol/l D-glucose but a variety of concentrations of D-glucose (0, 5, 15 mmol/l) had no effect on tyrosine release from hemi-atria. Five times the normal plasma levels of the branched-chain amino acids leucine, isoleucine and valine had no effect on tyrosine release from either hemi-atria or hemi-diaphragm.

  18. Introduction to protein crystallization.

    Science.gov (United States)

    McPherson, Alexander; Gavira, Jose A

    2014-01-01

    Protein crystallization was discovered by chance about 150 years ago and was developed in the late 19th century as a powerful purification tool and as a demonstration of chemical purity. The crystallization of proteins, nucleic acids and large biological complexes, such as viruses, depends on the creation of a solution that is supersaturated in the macromolecule but exhibits conditions that do not significantly perturb its natural state. Supersaturation is produced through the addition of mild precipitating agents such as neutral salts or polymers, and by the manipulation of various parameters that include temperature, ionic strength and pH. Also important in the crystallization process are factors that can affect the structural state of the macromolecule, such as metal ions, inhibitors, cofactors or other conventional small molecules. A variety of approaches have been developed that combine the spectrum of factors that effect and promote crystallization, and among the most widely used are vapor diffusion, dialysis, batch and liquid-liquid diffusion. Successes in macromolecular crystallization have multiplied rapidly in recent years owing to the advent of practical, easy-to-use screening kits and the application of laboratory robotics. A brief review will be given here of the most popular methods, some guiding principles and an overview of current technologies.

  19. Bioactive proteins from pipefishes

    Institute of Scientific and Technical Information of China (English)

    E. Rethna Priya; S. Ravichandran; R. Ezhilmathi

    2013-01-01

    Objective: To screen antimicrobial potence of some pipefish species collected from Tuticorin coastal environment.Methods:Antimicrobial activity of pipefishes in methanol extract was investigated against 10 bacterial and 10 fungal human pathogenic strains.Results:Among the tested strains, in Centriscus scutatus, pipefish showed maximum zone of inhibition against Vibrio cholerae (8 mm) and minimum in the sample of Hippichthys cyanospilos against Klebseilla pneumoniae (2 mm). In positive control, maximum zone of inhibition was recorded in Vibrio cholerae (9 mm) and minimum in Klebseilla pneumoniae, and Salmonella paratyphi (5 mm). Chemical investigation indicated the presence of peptides as evidenced by ninhydrin positive spots on thin layer chromatography and presence of peptide. In SDS PAGE, in Centriscus scutatus, four bands were detected in the gel that represented the presence of proteins in the range nearly 25.8-75 kDa. In Hippichthys cyanospilos, five bands were detected in the gel that represented the presence of proteins in the range nearly 20.5-78 kDa. The result of FT-IR spectrum revealed that the pipe fishes extracts compriseed to have peptide derivatives as their predominant chemical groups.Conclusions:It can be conclude that this present investigation suggests the tested pipe fishes will be a potential source of natural bioactive compounds.

  20. Peptides and proteins

    Energy Technology Data Exchange (ETDEWEB)

    Bachovchin, W.W.; Unkefer, C.J.

    1994-12-01

    Advances in magnetic resonance and vibrational spectroscopy make it possible to derive detailed structural information about biomolecular structures in solution. These techniques are critically dependent on the availability of labeled compounds. For example, NMR techniques used today to derive peptide and protein structures require uniformity {sup 13}C-and {sup 15}N-labeled samples that are derived biosynthetically from (U-6-{sup 13}C) glucose. These experiments are possible now because, during the 1970s, the National Stable Isotope Resource developed algal methods for producing (U-6-{sup 13}C) glucose. If NMR techniques are to be used to study larger proteins, we will need sophisticated labelling patterns in amino acids that employ a combination of {sup 2}H, {sup 13}C, and {sup 15}N labeling. The availability of these specifically labeled amino acids requires a renewed investment in new methods for chemical synthesis of labeled amino acids. The development of new magnetic resonance or vibrational techniques to elucidate biomolecular structure will be seriously impeded if we do not see rapid progress in labeling technology. Investment in labeling chemistry is as important as investment in the development of advanced spectroscopic tools.

  1. Protein Chemical Shift Prediction

    CERN Document Server

    Larsen, Anders S

    2014-01-01

    The protein chemical shifts holds a large amount of information about the 3-dimensional structure of the protein. A number of chemical shift predictors based on the relationship between structures resolved with X-ray crystallography and the corresponding experimental chemical shifts have been developed. These empirical predictors are very accurate on X-ray structures but tends to be insensitive to small structural changes. To overcome this limitation it has been suggested to make chemical shift predictors based on quantum mechanical(QM) calculations. In this thesis the development of the QM derived chemical shift predictor Procs14 is presented. Procs14 is based on 2.35 million density functional theory(DFT) calculations on tripeptides and contains corrections for hydrogen bonding, ring current and the effect of the previous and following residue. Procs14 is capable at performing predictions for the 13CA, 13CB, 13CO, 15NH, 1HN and 1HA backbone atoms. In order to benchmark Procs14, a number of QM NMR calculatio...

  2. Prion protein in milk.

    Directory of Open Access Journals (Sweden)

    Nicola Franscini

    Full Text Available BACKGROUND: Prions are known to cause transmissible spongiform encephalopathies (TSE after accumulation in the central nervous system. There is increasing evidence that prions are also present in body fluids and that prion infection by blood transmission is possible. The low concentration of the proteinaceous agent in body fluids and its long incubation time complicate epidemiologic analysis and estimation of spreading and thus the risk of human infection. This situation is particularly unsatisfactory for food and pharmaceutical industries, given the lack of sensitive tools for monitoring the infectious agent. METHODOLOGY/PRINCIPAL FINDINGS: We have developed an adsorption matrix, Alicon PrioTrap, which binds with high affinity and specificity to prion proteins. Thus we were able to identify prion protein (PrP(C--the precursor of prions (PrP(Sc--in milk from humans, cows, sheep, and goats. The absolute amount of PrP(C differs between the species (from microg/l range in sheep to ng/l range in human milk. PrP(C is also found in homogenised and pasteurised off-the-shelf milk, and even ultrahigh temperature treatment only partially diminishes endogenous PrP(C concentration. CONCLUSIONS/SIGNIFICANCE: In view of a recent study showing evidence of prion replication occurring in the mammary gland of scrapie infected sheep suffering from mastitis, the appearance of PrP(C in milk implies the possibility that milk of TSE-infected animals serves as source for PrP(Sc.

  3. Water-transporting proteins.

    Science.gov (United States)

    Zeuthen, Thomas

    2010-04-01

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

  4. An intravascular protein osmometer.

    Science.gov (United States)

    Henson, J W; Brace, R A

    1983-05-01

    Our purpose was to develop an intravascular osmometer for measuring the colloid (i.e., protein) osmotic pressure (COP) of circulating blood. A semipermeable hollow fiber from a Cordis Dow artificial kidney (C-DAK 4000) was attached to polyethylene tubing on one end, filled with saline, and sealed at the other end. This was small enough to be inserted into the vasculature of research animals. Protein osmotic pressure plus hydrostatic pressure was measured by a Statham pressure transducer attached to the hollow fiber. Simultaneously, a second catheter and transducer was used to measure hydrostatic pressure, which was subtracted from the pressure measured from the fiber with an on-line computer. The system was documented by a variety of tests. The colloid osmotic pressure vs. albumin concentration curve determined with the fiber is identical to the curve determined by standard membrane osmometry. The time constant for 2- and 8-cm fibers was 2.6 +/- 0.6 and 1.5 +/- 0.5 (+/- SD) min, respectively. The reflection coefficient (+/- SD) of the fiber for NaCl is 0.042 +/- 0.019 (n = 38); COP measured at varying temperatures (absolute scale) changed linearly as expected from COP = nCRT (i.e., van't Hoff's law). Finally, hollow-fiber osmometers were inserted into femoral veins of dogs and sheep, and blood COP was continuously recorded during osmotic manipulations. In conclusion, we attempted to develop and document a simple method for continuous measurement of intravascular colloid osmotic pressure.

  5. Protein-protein interaction based on pairwise similarity

    Directory of Open Access Journals (Sweden)

    Zaki Nazar

    2009-05-01

    Full Text Available Abstract Background Protein-protein interaction (PPI is essential to most biological processes. Abnormal interactions may have implications in a number of neurological syndromes. Given that the association and dissociation of protein molecules is crucial, computational tools capable of effectively identifying PPI are desirable. In this paper, we propose a simple yet effective method to detect PPI based on pairwise similarity and using only the primary structure of the protein. The PPI based on Pairwise Similarity (PPI-PS method consists of a representation of each protein sequence by a vector of pairwise similarities against large subsequences of amino acids created by a shifting window which passes over concatenated protein training sequences. Each coordinate of this vector is typically the E-value of the Smith-Waterman score. These vectors are then used to compute the kernel matrix which will be exploited in conjunction with support vector machines. Results To assess the ability of the proposed method to recognize the difference between "interacted" and "non-interacted" proteins pairs, we applied it on different datasets from the available yeast saccharomyces cerevisiae protein interaction. The proposed method achieved reasonable improvement over the existing state-of-the-art methods for PPI prediction. Conclusion Pairwise similarity score provides a relevant measure of similarity between protein sequences. This similarity incorporates biological knowledge about proteins and it is extremely powerful when combined with support vector machine to predict PPI.

  6. General introduction: recombinant protein production and purification of insoluble proteins.

    Science.gov (United States)

    Ferrer-Miralles, Neus; Saccardo, Paolo; Corchero, José Luis; Xu, Zhikun; García-Fruitós, Elena

    2015-01-01

    Proteins are synthesized in heterologous systems because of the impossibility to obtain satisfactory yields from natural sources. The production of soluble and functional recombinant proteins is among the main goals in the biotechnological field. In this context, it is important to point out that under stress conditions, protein folding machinery is saturated and this promotes protein misfolding and, consequently, protein aggregation. Thus, the selection of the optimal expression organism and the most appropriate growth conditions to minimize the formation of insoluble proteins should be done according to the protein characteristics and downstream requirements. Escherichia coli is the most popular recombinant protein expression system despite the great development achieved so far by eukaryotic expression systems. Besides, other prokaryotic expression systems, such as lactic acid bacteria and psychrophilic bacteria, are gaining interest in this field. However, it is worth mentioning that prokaryotic expression system poses, in many cases, severe restrictions for a successful heterologous protein production. Thus, eukaryotic systems such as mammalian cells, insect cells, yeast, filamentous fungus, and microalgae are an interesting alternative for the production of these difficult-to-express proteins.

  7. Bioinformatic Prediction of WSSV-Host Protein-Protein Interaction

    Directory of Open Access Journals (Sweden)

    Zheng Sun

    2014-01-01

    Full Text Available WSSV is one of the most dangerous pathogens in shrimp aquaculture. However, the molecular mechanism of how WSSV interacts with shrimp is still not very clear. In the present study, bioinformatic approaches were used to predict interactions between proteins from WSSV and shrimp. The genome data of WSSV (NC_003225.1 and the constructed transcriptome data of F. chinensis were used to screen potentially interacting proteins by searching in protein interaction databases, including STRING, Reactome, and DIP. Forty-four pairs of proteins were suggested to have interactions between WSSV and the shrimp. Gene ontology analysis revealed that 6 pairs of these interacting proteins were classified into “extracellular region” or “receptor complex” GO-terms. KEGG pathway analysis showed that they were involved in the “ECM-receptor interaction pathway.” In the 6 pairs of interacting proteins, an envelope protein called “collagen-like protein” (WSSV-CLP encoded by an early virus gene “wsv001” in WSSV interacted with 6 deduced proteins from the shrimp, including three integrin alpha (ITGA, two integrin beta (ITGB, and one syndecan (SDC. Sequence analysis on WSSV-CLP, ITGA, ITGB, and SDC revealed that they possessed the sequence features for protein-protein interactions. This study might provide new insights into the interaction mechanisms between WSSV and shrimp.

  8. Protein-protein interaction network of celiac disease

    Science.gov (United States)

    Zamanian Azodi, Mona; Peyvandi, Hassan; Rostami-Nejad, Mohammad; Safaei, Akram; Rostami, Kamran; Vafaee, Reza; Heidari, Mohammadhossein; Hosseini, Mostafa; Zali, Mohammad Reza

    2016-01-01

    Aim: The aim of this study is to investigate the Protein-Protein Interaction Network of Celiac Disease. Background: Celiac disease (CD) is an autoimmune disease with susceptibility of individuals to gluten of wheat, rye and barley. Understanding the molecular mechanisms and involved pathway may lead to the development of drug target discovery. The protein interaction network is one of the supportive fields to discover the pathogenesis biomarkers for celiac disease. Material and methods: In the present study, we collected the articles that focused on the proteomic data in celiac disease. According to the gene expression investigations of these articles, 31 candidate proteins were selected for this study. The networks of related differentially expressed protein were explored using Cytoscape 3.3 and the PPI analysis methods such as MCODE and ClueGO. Results: According to the network analysis Ubiquitin C, Heat shock protein 90kDa alpha (cytosolic and Grp94); class A, B and 1 member, Heat shock 70kDa protein, and protein 5 (glucose-regulated protein, 78kDa), T-complex, Chaperon in containing TCP1; subunit 7 (beta) and subunit 4 (delta) and subunit 2 (beta), have been introduced as hub-bottlnecks proteins. HSP90AA1, MKKS, EZR, HSPA14, APOB and CAD have been determined as seed proteins. Conclusion: Chaperons have a bold presentation in curtail area in network therefore these key proteins beside the other hub-bottlneck proteins may be a suitable candidates biomarker panel for diagnosis, prognosis and treatment processes in celiac disease. PMID:27895852

  9. THE CLINICAL EXPRESSION OF HEREDITARY PROTEIN-C AND PROTEIN-S DEFICIENCY - A RELATION TO CLINICAL THROMBOTIC RISK-FACTORS AND TO LEVELS OF PROTEIN-C AND PROTEIN-S

    NARCIS (Netherlands)

    HENKENS, CMA; VANDERMEER, J; HILLEGE, JL; BOM, VJJ; HALIE, MR; van der Schaaf, W

    1993-01-01

    We investigated 103 first-degree relatives of 13 unrelated protein C or protein S deficient patients to assess the role of additional thrombotic risk factors and of protein C and protein S levels in the clinical expression of hereditary protein C and protein S deficiency. Fifty-seven relatives were

  10. Protein-water dynamics in antifreeze protein III activity

    Science.gov (United States)

    Xu, Yao; Bäumer, Alexander; Meister, Konrad; Bischak, Connor G.; DeVries, Arthur L.; Leitner, David M.; Havenith, Martina

    2016-03-01

    We combine Terahertz absorption spectroscopy (THz) and molecular dynamics (MD) simulations to investigate the underlying molecular mechanism for the antifreeze activity of one class of antifreeze protein, antifreeze protein type III (AFP-III) with a focus on the collective water hydrogen bond dynamics near the protein. After summarizing our previous work on AFPs, we present a new investigation of the effects of cosolutes on protein antifreeze activity by adding sodium citrate to the protein solution of AFP-III. Our results reveal that for AFP-III, unlike some other AFPs, the addition of the osmolyte sodium citrate does not affect the hydrogen bond dynamics at the protein surface significantly, as indicated by concentration dependent THz measurements. The present data, in combination with our previous THz measurements and molecular simulations, confirm that while long-range solvent perturbation is a necessary condition for the antifreeze activity of AFP-III, the local binding affinity determines the size of the hysteresis.

  11. Expanding coordination chemistry from protein to protein assembly.

    Science.gov (United States)

    Sanghamitra, Nusrat J M; Ueno, Takafumi

    2013-05-14

    Bioinorganic chemistry is of growing importance in the fields of nanomaterial science and biotechnology. Coordination of metals by biological systems is a crucial step in intricate enzymatic reactions such as photosynthesis, nitrogen fixation and biomineralization. Although such systems employ protein assemblies as molecular scaffolds, the important roles of protein assemblies in coordination chemistry have not been systematically investigated and characterized. Many researchers are joining the field of bioinorganic chemistry to investigate the inorganic chemistry of protein assemblies. This area is emerging as an important next-generation research field in bioinorganic chemistry. This article reviews recent progress in rational design of protein assemblies in coordination chemistry for integration of catalytic reactions using metal complexes, preparation of mineral biomimetics, and mechanistic investigations of biomineralization processes with protein assemblies. The unique chemical properties of protein assemblies in the form of cages, tubes, and crystals are described in this review.

  12. Neurocognitive derivation of protein surface property from protein aggregate parameters

    Science.gov (United States)

    Mishra, Hrishikesh; Lahiri, Tapobrata

    2011-01-01

    Current work targeted to predicate parametric relationship between aggregate and individual property of a protein. In this approach, we considered individual property of a protein as its Surface Roughness Index (SRI) which was shown to have potential to classify SCOP protein families. The bulk property was however considered as Intensity Level based Multi-fractal Dimension (ILMFD) of ordinary microscopic images of heat denatured protein aggregates which was known to have potential to serve as protein marker. The protocol used multiple ILMFD inputs obtained for a protein to produce a set of mapped outputs as possible SRI candidates. The outputs were further clustered and largest cluster centre after normalization was found to be a close approximation of expected SRI that was calculated from known PDB structure. The outcome showed that faster derivation of individual protein’s surface property might be possible using its bulk form, heat denatured aggregates. PMID:21572883

  13. Mitochondrial nucleoid interacting proteins support mitochondrial protein synthesis.

    Science.gov (United States)

    He, J; Cooper, H M; Reyes, A; Di Re, M; Sembongi, H; Litwin, T R; Gao, J; Neuman, K C; Fearnley, I M; Spinazzola, A; Walker, J E; Holt, I J

    2012-07-01

    Mitochondrial ribosomes and translation factors co-purify with mitochondrial nucleoids of human cells, based on affinity protein purification of tagged mitochondrial DNA binding proteins. Among the most frequently identified proteins were ATAD3 and prohibitin, which have been identified previously as nucleoid components, using a variety of methods. Both proteins are demonstrated to be required for mitochondrial protein synthesis in human cultured cells, and the major binding partner of ATAD3 is the mitochondrial ribosome. Altered ATAD3 expression also perturbs mtDNA maintenance and replication. These findings suggest an intimate association between nucleoids and the machinery of protein synthesis in mitochondria. ATAD3 and prohibitin are tightly associated with the mitochondrial membranes and so we propose that they support nucleic acid complexes at the inner membrane of the mitochondrion.

  14. Enhanced protein production by engineered zinc finger proteins.

    Science.gov (United States)

    Reik, Andreas; Zhou, Yuanyue; Collingwood, Trevor N; Warfe, Lyndon; Bartsevich, Victor; Kong, Yanhong; Henning, Karla A; Fallentine, Barrett K; Zhang, Lei; Zhong, Xiaohong; Jouvenot, Yann; Jamieson, Andrew C; Rebar, Edward J; Case, Casey C; Korman, Alan; Li, Xiao-Yong; Black, Amelia; King, David J; Gregory, Philip D

    2007-08-01

    Increasing the yield of therapeutic proteins from mammalian production cell lines reduces costs and decreases the time to market. To this end, we engineered a zinc finger protein transcription factor (ZFP TF) that binds a DNA sequence within the promoter driving transgene expression. This ZFP TF enabled >100% increase in protein yield from CHO cells in transient, stable, and fermentor production run settings. Expression vectors engineered to carry up to 10 ZFP binding sites further enhanced ZFP-mediated increases in protein production up to approximately 500%. The multimerized ZFP binding sites function independently of the promoter, and therefore across vector platforms. CHO cell lines stably expressing ZFP TFs demonstrated growth characteristics similar to parental cell lines. ZFP TF expression and gains in protein production were stable over >30 generations in the absence of antibiotic selection. Our results demonstrate that ZFP TFs can rapidly and stably increase protein production in mammalian cells.

  15. Proteins interacting with cloning scars: a source of false positive protein-protein interactions.

    Science.gov (United States)

    Banks, Charles A S; Boanca, Gina; Lee, Zachary T; Florens, Laurence; Washburn, Michael P

    2015-01-01

    A common approach for exploring the interactome, the network of protein-protein interactions in cells, uses a commercially available ORF library to express affinity tagged bait proteins; these can be expressed in cells and endogenous cellular proteins that copurify with the bait can be identified as putative interacting proteins using mass spectrometry. Control experiments can be used to limit false-positive results, but in many cases, there are still a surprising number of prey proteins that appear to copurify specifically with the bait. Here, we have identified one source of false-positive interactions in such studies. We have found that a combination of: 1) the variable sequence of the C-terminus of the bait with 2) a C-terminal valine "cloning scar" present in a commercially available ORF library, can in some cases create a peptide motif that results in the aberrant co-purification of endogenous cellular proteins. Control experiments may not identify false positives resulting from such artificial motifs, as aberrant binding depends on sequences that vary from one bait to another. It is possible that such cryptic protein binding might occur in other systems using affinity tagged proteins; this study highlights the importance of conducting careful follow-up studies where novel protein-protein interactions are suspected.

  16. Information assessment on predicting protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Gerstein Mark

    2004-10-01

    Full Text Available Abstract Background Identifying protein-protein interactions is fundamental for understanding the molecular machinery of the cell. Proteome-wide studies of protein-protein interactions are of significant value, but the high-throughput experimental technologies suffer from high rates of both false positive and false negative predictions. In addition to high-throughput experimental data, many diverse types of genomic data can help predict protein-protein interactions, such as mRNA expression, localization, essentiality, and functional annotation. Evaluations of the information contributions from different evidences help to establish more parsimonious models with comparable or better prediction accuracy, and to obtain biological insights of the relationships between protein-protein interactions and other genomic information. Results Our assessment is based on the genomic features used in a Bayesian network approach to predict protein-protein interactions genome-wide in yeast. In the special case, when one does not have any missing information about any of the features, our analysis shows that there is a larger information contribution from the functional-classification than from expression correlations or essentiality. We also show that in this case alternative models, such as logistic regression and random forest, may be more effective than Bayesian networks for predicting interactions. Conclusions In the restricted problem posed by the complete-information subset, we identified that the MIPS and Gene Ontology (GO functional similarity datasets as the dominating information contributors for predicting the protein-protein interactions under the framework proposed by Jansen et al. Random forests based on the MIPS and GO information alone can give highly accurate classifications. In this particular subset of complete information, adding other genomic data does little for improving predictions. We also found that the data discretizations used in the

  17. Proteins, exons and molecular evolution.

    Science.gov (United States)

    Holland, S K; Blake, C C

    1987-01-01

    The discovery of the eukaryotic gene structure has prompted research into the potential relationship between protein structure and function and the corresponding exon/intron patterns. The exon shuffling hypothesis put forward by Gilbert and Blake suggests the encodement of structural and functional protein elements by exons which can recombine to create novel proteins. This provides an explanation for the relatively rapid evolution of proteins from a few primordial molecules. As the number of gene and protein structures increases, evidence of exon shuffling is becoming more apparent and examples are presented both from modern multi-domain proteins and ancient proteins. Recent work into the chemical properties and catalytic functions of RNA have led to hypotheses based upon the early existence of RNA. These theories suggest that the split gene structure originated in the primordial soup as a result of random RNA synthesis. Stable regions of RNA, or exons, were utilised as primitive enzymes. In response to selective pressures for information storage, the activity was directly transferred from the RNA enzymes or ribozymes, to proteins. These short polypeptides fused together to create larger proteins with a wide range of functions. Recent research into RNA processing and exon size, discussed in this review, provides a clearer insight into the evolutionary development of the gene and protein structure.

  18. Protein Adaptations in Archaeal Extremophiles

    Directory of Open Access Journals (Sweden)

    Christopher J. Reed

    2013-01-01

    Full Text Available Extremophiles, especially those in Archaea, have a myriad of adaptations that keep their cellular proteins stable and active under the extreme conditions in which they live. Rather than having one basic set of adaptations that works for all environments, Archaea have evolved separate protein features that are customized for each environment. We categorized the Archaea into three general groups to describe what is known about their protein adaptations: thermophilic, psychrophilic, and halophilic. Thermophilic proteins tend to have a prominent hydrophobic core and increased electrostatic interactions to maintain activity at high temperatures. Psychrophilic proteins have a reduced hydrophobic core and a less charged protein surface to maintain flexibility and activity under cold temperatures. Halophilic proteins are characterized by increased negative surface charge due to increased acidic amino acid content and peptide insertions, which compensates for the extreme ionic conditions. While acidophiles, alkaliphiles, and piezophiles are their own class of Archaea, their protein adaptations toward pH and pressure are less discernible. By understanding the protein adaptations used by archaeal extremophiles, we hope to be able to engineer and utilize proteins for industrial, environmental, and biotechnological applications where function in extreme conditions is required for activity.

  19. Protein stability, flexibility and function

    DEFF Research Database (Denmark)

    Teilum, Kaare; Olsen, Johan G; Kragelund, Birthe B

    2011-01-01

    Proteins rely on flexibility to respond to environmental changes, ligand binding and chemical modifications. Potentially, a perturbation that changes the flexibility of a protein may interfere with its function. Millions of mutations have been performed on thousands of proteins in quests for a de......Proteins rely on flexibility to respond to environmental changes, ligand binding and chemical modifications. Potentially, a perturbation that changes the flexibility of a protein may interfere with its function. Millions of mutations have been performed on thousands of proteins in quests...... for a delineation of the molecular details of their function. Several of these mutations interfered with the binding of a specific ligand with a concomitant effect on the stability of the protein scaffold. It has been ambiguous and not straightforward to recognize if any relationships exist between the stability...... of a protein and the affinity for its ligand. In this review, we present examples of proteins where changes in stability results in changes in affinity and of proteins where stability and affinity are uncorrelated. We discuss the possibility for a relationship between stability and binding. From the data...

  20. Protein Polymers and Amyloids

    DEFF Research Database (Denmark)

    Risør, Michael Wulff

    2014-01-01

    , underlining the importance of understanding this relationship. The monomeric C-36 peptide was investigated by liquid-state NMR spectroscopy and found to be intrinsically disordered with minor propensities towards β-sheet structure. The plasticity of such a peptide makes it suitable for a whole range......, is a general hallmark. They also include the α1-antitrypsin deficiency, where disease-causing mutations in the serine protease inhibitor, α1-antitrypsin (α1AT), leads to accumulation of the aberrant protein in the liver of these patients. The native metastable structure of α1AT constitutes a molecular trap...... of this mechanism were investigated through a series of interaction experiments. Despite a very buried location in the native structure, evidence here suggest that the C-terminal tail is labile under slightly destabilizing conditions, providing new detail to this matter. A small infectious polymer unit was also...

  1. Exploring the repeat protein universe through computational protein design.

    Science.gov (United States)

    Brunette, T J; Parmeggiani, Fabio; Huang, Po-Ssu; Bhabha, Gira; Ekiert, Damian C; Tsutakawa, Susan E; Hura, Greg L; Tainer, John A; Baker, David

    2015-12-24

    A central question in protein evolution is the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain. Repeat proteins composed of multiple tandem copies of a modular structure unit are widespread in nature and have critical roles in molecular recognition, signalling, and other essential biological processes. Naturally occurring repeat proteins have been re-engineered for molecular recognition and modular scaffolding applications. Here we use computational protein design to investigate the space of folded structures that can be generated by tandem repeating a simple helix-loop-helix-loop structural motif. Eighty-three designs with sequences unrelated to known repeat proteins were experimentally characterized. Of these, 53 are monomeric and stable at 95 °C, and 43 have solution X-ray scattering spectra consistent with the design models. Crystal structures of 15 designs spanning a broad range of curvatures are in close agreement with the design models with root mean square deviations ranging from 0.7 to 2.5 Å. Our results show that existing repeat proteins occupy only a small fraction of the possible repeat protein sequence and structure space and that it is possible to design novel repeat proteins with precisely specified geometries, opening up a wide array of new possibilities for biomolecular engineering.

  2. Hydration of proteins: excess partial volumes of water and proteins.

    Science.gov (United States)

    Sirotkin, Vladimir A; Komissarov, Igor A; Khadiullina, Aigul V

    2012-04-05

    High precision densitometry was applied to study the hydration of proteins. The hydration process was analyzed by the simultaneous monitoring of the excess partial volumes of water and the proteins in the entire range of water content. Five unrelated proteins (lysozyme, chymotrypsinogen A, ovalbumin, human serum albumin, and β-lactoglobulin) were used as models. The obtained data were compared with the excess partial enthalpies of water and the proteins. It was shown that the excess partial quantities are very sensitive to the changes in the state of water and proteins. At the lowest water weight fractions (w(1)), the changes of the excess functions can mainly be attributed to water addition. A transition from the glassy to the flexible state of the proteins is accompanied by significant changes in the excess partial quantities of water and the proteins. This transition appears at a water weight fraction of 0.06 when charged groups of proteins are covered. Excess partial quantities reach their fully hydrated values at w(1) > 0.5 when coverage of both polar and weakly interacting surface elements is complete. At the highest water contents, water addition has no significant effect on the excess quantities. At w(1) > 0.5, changes in the excess functions can solely be attributed to changes in the state of the proteins.

  3. Versatile protein tagging in cells with split fluorescent protein

    OpenAIRE

    Kamiyama, Daichi; Sekine, Sayaka; Barsi-Rhyne, Benjamin; Hu, Jeffrey; Chen, Baohui; Gilbert, Luke A.; Ishikawa, Hiroaki; Leonetti, Manuel D.; Marshall, Wallace F.; Weissman, Jonathan S.; Huang, Bo

    2016-01-01

    In addition to the popular method of fluorescent protein fusion, live cell protein imaging has now seen more and more application of epitope tags. The small size of these tags may reduce functional perturbation and enable signal amplification. To address their background issue, we adapt self-complementing split fluorescent proteins as epitope tags for live cell protein labelling. The two tags, GFP11 and sfCherry11 are derived from the eleventh β-strand of super-folder GFP and sfCherry, respec...

  4. Noninvasive imaging of protein-protein interactions in living animals

    Science.gov (United States)

    Luker, Gary D.; Sharma, Vijay; Pica, Christina M.; Dahlheimer, Julie L.; Li, Wei; Ochesky, Joseph; Ryan, Christine E.; Piwnica-Worms, Helen; Piwnica-Worms, David

    2002-05-01

    Protein-protein interactions control transcription, cell division, and cell proliferation as well as mediate signal transduction, oncogenic transformation, and regulation of cell death. Although a variety of methods have been used to investigate protein interactions in vitro and in cultured cells, none can analyze these interactions in intact, living animals. To enable noninvasive molecular imaging of protein-protein interactions in vivo by positron-emission tomography and fluorescence imaging, we engineered a fusion reporter gene comprising a mutant herpes simplex virus 1 thymidine kinase and green fluorescent protein for readout of a tetracycline-inducible, two-hybrid system in vivo. By using micro-positron-emission tomography, interactions between p53 tumor suppressor and the large T antigen of simian virus 40 were visualized in tumor xenografts of HeLa cells stably transfected with the imaging constructs. Imaging protein-binding partners in vivo will enable functional proteomics in whole animals and provide a tool for screening compounds targeted to specific protein-protein interactions in living animals.

  5. High throughput recombinant protein production of fungal secreted proteins

    DEFF Research Database (Denmark)

    Vala, Andrea Lages Lino; Roth, Doris; Grell, Morten Nedergaard

    2011-01-01

    a high-throughput protein production system with a special focus on fungal secreted proteins. We use a ligation independent cloning to clone target genes into expression vectors for E. coli and P. pastoris and a small scale test expression to identify constructs producing soluble protein. Expressed...... interaction), between fungi of the order Entomophthorales and aphids (pathogenic interaction), and in the mycoparasitic interaction between the oomycetes Pythium oligandrum and P. ultimum. In general, the high-throughput protein production system can lead to a better understanding of fungal/host interactions...

  6. Protein Hormones and Immunity‡

    Science.gov (United States)

    Kelley, Keith W.; Weigent, Douglas A.; Kooijman, Ron

    2007-01-01

    A number of observations and discoveries over the past 20 years support the concept of important physiological interactions between the endocrine and immune systems. The best known pathway for transmission of information from the immune system to the neuroendocrine system is humoral in the form of cytokines, although neural transmission via the afferent vagus is well documented also. In the other direction, efferent signals from the nervous system to the immune system are conveyed by both the neuroendocrine and autonomic nervous systems. Communication is possible because the nervous and immune systems share a common biochemical language involving shared ligands and receptors, including neurotransmitters, neuropeptides, growth factors, neuroendocrine hormones and cytokines. This means that the brain functions as an immune-regulating organ participating in immune responses. A great deal of evidence has accumulated and confirmed that hormones secreted by the neuroendocrine system play an important role in communication and regulation of the cells of the immune system. Among protein hormones, this has been most clearly documented for prolactin (PRL), growth hormone (GH), and insulin-like growth factor-1 (IGF-I), but significant influences on immunity by thyroid stimulating hormone (TSH) have also been demonstrated. Here we review evidence obtained during the past 20 years to clearly demonstrate that neuroendocrine protein hormones influence immunity and that immune processes affect the neuroendocrine system. New findings highlight a previously undiscovered route of communication between the immune and endocrine systems that is now known to occur at the cellular level. This communication system is activated when inflammatory processes induced by proinflammatory cytokines antagonize the function of a variety of hormones, which then causes endocrine resistance in both the periphery and brain. Homeostasis during inflammation is achieved by a balance between cytokines and

  7. Protein (Cyanobacteria): 210308 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ike protein Stanieria cyanosphaera PCC 7437 MSEPKAEAKRILETKDNLANVLPTAPEQQKPVSSAQALKERLDWGEPAFTIADARDRDSFNTERILGAVPIDSEETLGRLMNSLSTRRELYIYGDNDEQAQSAVEQFVSAGFENVSRLQGGLAGWKAISGPTEGRVA ...

  8. Protein (Viridiplantae): 159465487 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 84 predicted protein Chlamydomonas reinhardtii MPPIHLLRLLFASALLFATWHVSRADDIASQASITTSDNIPQMKYFFLNEVTGATQLTDPGNTPYEDEQTGELYWLAEDGVTRLAQDPNRLRFAWIETYSPEAKRSFYFNQVTRESTWERPADLAWRRLRAEE ...

  9. Protein (Viridiplantae): 255083394 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available predicted protein Micromonas sp. RCC299 MKVLRKVKGKSRILIFVAVVALLSLALRKLKQDTKKHREILPWHQGGYEDHHGDLDGGFVPDRGVLGAVGAMRGGGGRDVGGESTSTSKVLDDGGVRDAPGGNRNIDDISHLVDDDDEDVLGVKDEAFAGMRDSREKASR ...

  10. Protein (Cyanobacteria): 118077 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ical protein Microcystis aeruginosa PCC 9432 MNPNRVVIDTNVFISALLNPLGTPKKVINITVSQFTILQSEATYQELATRISKKKFDKYLEKDDRLDFLSSLRNRSLFVDISHETRVCSDLDDNKFLELAVSGMAQYIITGDNALLILNTYQGIPIITPAEFLVIF ...

  11. Protein (Cyanobacteria): 118035 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ical protein Microcystis aeruginosa PCC 7941 MNPNRVVIDTNVFISALLNPLGTPKKVINITVSQFTILQSEATYQELATRISKKKFDKYLEKDDRLDFLSSLRNRSLFVDISHETRVCSDLDDNKFLELAVSGMAQYIITGDKDLLILNTYQGIPIITPAEFLVIF ...

  12. Protein (Cyanobacteria): 118042 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tical protein Microcystis aeruginosa PCC 9809 MNPNRVVIDTNVFISALLNPLGTPKKVINIAVSQFTILQSEATYQELATRISKKKFDKYLEKDDRLDFLSSLRNRSLFVDISHETRVCSDLDDNKFLELAVSGMAQYIITGDKDLLILNTYQGIPIITPAEFLAIF ...

  13. Protein (Viridiplantae): 226491436 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rized protein LOC100275991 Zea mays MSATLCFMGVARESLSLDAPVAAPKLGRERRSALASANSGPQCWRWRRGLAMRCQTGSTAAPFLRTEEAPAAASGARNAQAGFTIVMKFDGSSLASVERMREVAGLILSAGERTRLPLDRTEGKIHTTADRVRRKMAITEPI ...

  14. Protein (Viridiplantae): 308804025 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available unnamed protein product Ostreococcus tauri MACAGRGVLRLGALEGGSDVVFAATVRRDLNGTLAPLRGQREDVAIVVGDDAARLETNAARVTQSLRTRRAHAHVTPASGLGESSSSSSSTDFRTPSPRGPPPSCVVWSLSTLPCRSFRRDTCACASACASASA ...

  15. Protein (Viridiplantae): 308812394 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available unnamed protein product Ostreococcus tauri MGRHHTEYERAPPTRRVNARTWDDITQSTTPGCPAPRNIPRRPHPRASVTPPSHVDASTPRPNARTSARARGRERERERERASARSGGRSRAWRCKRGRGRGGGDRDRAHLFHRRRRRANERAIEANVEARCRC ...

  16. Protein (Viridiplantae): 255083122 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available predicted protein Micromonas sp. RCC299 MYASPALHRAVAFPKATKPAEASKAGRVATRAAAPEDKPAAAARPTGRRSFSVATLAAVVAAASAPDAALAFGSGIPGYDINEKARDAQRKAINDELAEQRELARKEKERRRLLKEAEEAEECARNPESCPAPAES ...

  17. Protein (Viridiplantae): 15227263 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 93 putative protein kinase Arabidopsis thaliana MKLVLEGVDSFETLRVVGTFNCIDPDYVGSKRVTKKADVYAFEVILMELITGRKANYETLSVDEQNLVMWLRPKIKISTFLNLVDGTIATDKETIKRIKKIAKLAEYCTSQEVESRPLRASRTKSGNEVTSED ...

  18. Protein (Cyanobacteria): 77417 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ntaining protein Acaryochloris marina MBIC11017 MRALLDTHTFLWWNTNDAQLSAAARQFIENSDHILLLSVVSVWEIVIKYKLGKLPLPESPEIYIPKRLEYYQFQILPVHLPHVLRIAHLAPHHNDSFDRLLIAQSQMEKLAIITVDKKIQQYSVEIIW ...

  19. Vegetarian Choices in the Protein Foods Group

    Science.gov (United States)

    ... choices Print Share Vegetarian choices in the Protein Foods Group Vegetarians get enough protein from this group as ... selected are adequate. Protein sources from the Protein Foods Group for vegetarians include eggs (for ovo-vegetarians), beans ...

  20. Protein (Viridiplantae): 159470013 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available KHMSEHGVLTEPYVVTFEASKDDCCLIMASDGVWDVMDGQEAVNRVMEVASEGKTAAQAAKMLVEEAVELGVKSPCGEADNTSAIVVFFA ... ...66 predicted protein Chlamydomonas reinhardtii MPHGARSAAGLAHAVCRLPQPQEGFSGTVNLKDAAHEDGYLQVVTGPWQGYELSVTRALGH

  1. Protein (Cyanobacteria): 176329 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available etical protein Microcystis aeruginosa PCC 9432 MNNQVIRTDKAPAPVGPYNQAIAAPGPFLFVAGQIPLDPVTGEIVSGEISAQTEQVMANLEGILTAAGANWSNVVKTTVFLSDLANFGAMNQVYARYFPPETAPARACVEVARLPKDVLVEIECIAALA ...

  2. Protein (Cyanobacteria): 426260 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available aining protein Nostoc sp. PCC 7524 MKAAEYLSSAAKSVNEIPGITEATILEYFATLNAGEFLATAALFAEDGVMYPPFESGIVGPDAIANYLQQEAQDIKADTHQGIVEPLDNQHIQVQVTGKAQTSWCSVNVLWIFILNQHKEIIDAKIKLLASPQELLALRRE ...

  3. Protein (Cyanobacteria): 409390 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available protein Oscillatoria sp. PCC 6506 MESLNGFIALIGGILIGLSATLLLAFNGRIAGISGIVNGAIAFSKQEVWRWIFIVGMLLGGVIYEYGLAPQPTPTPALTPWAMTIGGFLVGFGTRMGGGCTSGHGVCGLGRLSMRSLVAVLTFMITAILTVFVVRHVLQLSI ...

  4. Protein (Cyanobacteria): 426188 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available protein Microcoleus sp. PCC 7113 MTIAEDKSTTTPSATGVDWTIEGIDESVVWRYFQTMNAADYEGTAALFAPTGALHPPFEEPIEGKEAIATYLKAEAKGMQLFPREGIAEALEEDQIQIQVKGKVQTSLFGVNVAWIFILNPEREILYAQIKLLASPQELLNLRR ...

  5. Protein (Cyanobacteria): 187027 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available domain protein Stanieria cyanosphaera PCC 7437 MRSQFITSIVFISAFIVLTLAGVKPVKTQLKQNSLQGCTTVYSFPVGGNLISKESESQINVREEPTVSAKVSDFGNQGEPIYVTQVFENNADGYCWYKVSFQSGAKGWVRGDFVSIFLASLAEAPLCSL ...

  6. Protein (Viridiplantae): 159472102 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 4474 predicted protein, partial Chlamydomonas reinhardtii PPSPAPPSPEPGSPPPSPAPPSPQPPSPAPPSPEPGSPPPSPAPPSPKPPSPAPPSPEQPGSPPPSPPPPRPQPPSPAPPSPEPGSPPPSPAPPSPQPPSPAPPSPEPGSPPPSPAPTQP ...

  7. Protein (Cyanobacteria): 301492 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available g protein Thermosynechococcus elongatus BP-1 MPTPTYPKASLIIRERGLPKREVLLSPDRQWTIGRQLDCSIRLTDAYVSRLHAVINAFLFRGQPLYFIRDAHSRNGTFLNGFPLQHSTLLHHEDVIGVGTTLLVFYYPDMFREISLDECPELTKGSTDSLPWRS ...

  8. Protein (Viridiplantae): 15238919 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ve protein Arabidopsis thaliana MAGGIGKCSKIRHIVKLRQMLRQWRNKARMSSVRRSVPSDVPSGHVAVYVGRSCRRFVVLATYLNHPILMNLLVKAEEEFGFANQGPLVIPCEESVFEESIRFITRSSRFTCTDDLKKNRHGGIRSKLDLLMESRPLLHGVSEKAIIW ...

  9. Protein (Cyanobacteria): 129527 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ing protein Oscillatoriales cyanobacterium JSC-12 MLLIDTSVWISVFRDRTGQVRQKLETLIDARDIFLTRFTQLKLLQGSLNEKEWTLLSTYLETQDYVEPVGNSWRAAARIYYDLRRRGLTVRSPIDCCIAQAALENDLLLIHNDRDFETIAQVRSLQHFRFQP ...

  10. Protein (Cyanobacteria): 518319094 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available hypothetical protein Calothrix sp. PCC 7103 MKSGYPKNNNAYIELLKGFPPRPITSHEEFVATQKVIDSLIDKKGQLTRDEQDYLNILGTIVYEYEEKQVKIPDIYGIDLLKALLSELNLSTKDLIPIFKTESHVSNVLNGKIDLTVEDISKLANFFKISPAAFVKK

  11. Protein (Viridiplantae): 224138986 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available icted protein Populus trichocarpa MALDIKTFETIIPSCFLSFTIPNPVLPTHLLRVAVLDSSIQFTESPQIATLLVSQTREPDWIFSTESGHLQLLLSSPEISQLILIGNNRINGSDSSLLTYHKRDNTQYVKSLENSLKPLFFALSPKVSVKDGIFDCSVLDDALIHLH ...

  12. Protein (Cyanobacteria): 16889 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available mily protein Acaryochloris marina MBIC11017 MVDGQAAHLGTGWTFPIGVNTQGNLRFSAHAIRNIEESIAIVLGTKLGERVYRPEFGSRLSELTFAPMNTQTLLLIRLYVTEALQRWEPRIVLDGVYTEPDPIEGRVDITLEYHPKQTHDYRSLVYPFYLTPIT ...

  13. Protein (Viridiplantae): 159485290 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available predicted protein Chlamydomonas reinhardtii MADAGPASGAMAAGVAAAPAVAGETVVGARAGPSGSGGVAGVDMADAGPASGAMAAGVAAAAAV...AGETVVGARAGPSGSGGVAGVDMADAGPASGAMAAGVAAAAAVAGETVVGARAGPSGSGGVAGVDMADAGPAGGAMAAATVAMLGAAAVASAWLLTACSPEGSGPGPS

  14. Protein (Viridiplantae): 159474930 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 5155 predicted protein Chlamydomonas reinhardtii MGYVCSSVRFGGLLCNTKCGSRIPATSAPCKGAWCQPPVHTATARWTVATIHMMIPVAMHEAWAVTASLTTERYHQPPVDANGSQGNATKLQRPKLDVVPRLTRYTLSPQEWPPLCGPVKASGSSQVPLPFHN ...

  15. Protein (Viridiplantae): 159468866 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available predicted protein Chlamydomonas reinhardtii MVVSAAWRRPTGGGRCRLLAAVLLGAVVVMAAHGGPLGASAQEEKLGGTDAAVQFGAAPPSPAPPSPSYPPSPAPPSPSYPPSPAPPS...PSYPPSPAPPSPSYPPSPAPPSPSYPPSPAPPSPAAHRPGAAHLLPVSAERKPCFKVFAWRKTLLYVQSEDRFTYNEAQEFCSD

  16. Protein (Cyanobacteria): 24305 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ing protein Anabaena sp. 90 MNKLIFLDTNILGMVTNPKSSNSNCQECKEWLDELPLKSYQIILPEIADYEVRRELLRAGKTKGIKRLDQLKQAITYLPITTATMLLAAQFWAEIRNTGKPTADPKSLDGDVILAAQAKIEELNGDQVIVATTNVKHLSLFVDAREWQMIN ...

  17. Protein (Viridiplantae): 224129758 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available predicted protein Populus trichocarpa MAKEMPAMKRALCEWMIVEEFPSWFKADNEWKAELCRLCNLESTEDLELGWRDMVNKFELVWKGEPRKKYKKPRPKVRVGLPKKICQYFDDRIGREENEVIVVLGSRGDSFCLALRFLNSNWVQKPGKHNQGQQQKLK ...

  18. Protein (Viridiplantae): 255073899 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available cted protein Micromonas sp. RCC299 MTQGSRVIFCDREPLAIHCALSSAQLNGLEVHSVEDISKSSQGVAGAVLDWASPLHTLAQSADVVLGADCLYDPATAAMLAKTCKHVLGEDGVVVICEPELERAKGTYSKFLEAAKMLGAASAEILPHPDSDEPRSILLRVSWKSL ...

  19. Protein (Cyanobacteria): 60937 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available cal protein Microcystis aeruginosa PCC 9443 MSNETVTYSLEAVLTRIEGKIDSLEKRLDEKIDSLEKRIDEKIDSLEKRIDEKIDSLEKRIDERFDKIEDRLTKVEIGQAELKGEIKALDERVSTKIEGLTARVAYQEFTNRGILIALVVAILGGAAKLFGFFPNP ...

  20. Protein (Cyanobacteria): 60897 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available cal protein Microcystis aeruginosa PCC 9717 MSNETVTYSLEAVLTRIEGKIDSLEKRLDEKIDSLEKRIDEKIDSLEKRIDEKIDSLEKRIDERFDKIEDRLTKVEIGQAELKGEIKALDERVSTKIEGLTARVAYQEFTNRGILIALVVAILGGAAKLFGFFPNP ...

  1. Protein (Cyanobacteria): 60829 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available cal protein Microcystis aeruginosa PCC 9806 MSNETVTYSLEAVLTRIEGKIDSLEKRIDEKIDSLEKRIDEKIDSLEKRIDEKIDSLENRIDERFDKVEDRLTKVEIGQAELKGDIKALDEKINGLTARVAYQEFTNRGILIALVVAILGGAAKLFGFFPNP ...

  2. Protein (Cyanobacteria): 444805 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available pothetical protein Arthrospira maxima CS-328 MNSNHKILAVTRPNKPPEPSSESPTTNTQEHSRSTGTVKHIPSRTVKPSKPIKHKPKVAVKLPQADNSEGEVFVVGDHILVRAPWGLWARAEIKTFYQSSPDTVMAHFIPKEERTNWTWMGGLIRSDLLKRANPDS ...

  3. Protein (Cyanobacteria): 448175 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ining protein Cyanothece sp. PCC 7424 MKKAQLVLTFFFSFLLAVFVSFNLVVDSAMAFSGPVSESCIDLELSGSILSANCETANGYYEKASINLDEVIGNLDGMLSWDSQNFSQTCEDISLEKRYSITFPILMATCQEAIGGENYMATEVYLDDHIFNVNGTLFYN ...

  4. Role of Dietary Soy Protein in Obesity

    OpenAIRE

    Manuel T. Velasquez, Sam J. Bhathena

    2007-01-01

    Soy protein is an important component of soybeans and provides an abundant source of dietary protein. Among the dietary proteins, soy protein is considered a complete protein in that it contains ample amounts of all the essential amino acids plus several other macronutrients with a nutritional value roughly equivalent to that of animal protein of high biological value. Soy protein is unique among the plant-based proteins because it is associated with isoflavones, a group of compounds with a v...

  5. Phase retrieval in protein crystallography.

    Science.gov (United States)

    Liu, Zhong Chuan; Xu, Rui; Dong, Yu Hui

    2012-03-01

    Solution of the phase problem is central to crystallographic structure determination. An oversampling method is proposed, based on the hybrid input-output algorithm (HIO) [Fienup (1982). Appl. Opt. 21, 2758-2769], to retrieve the phases of reflections in crystallography. This method can extend low-resolution structures to higher resolution for structure determination of proteins without additional sample preparation. The method requires an envelope of the protein which divides a unit cell into the density region where the proteins are located and the non-density region occupied by solvents. After a few hundred to a few thousand iterations, the correct phases and density maps are recovered. The method has been used successfully in several cases to retrieve the phases from the experimental X-ray diffraction data and the envelopes of proteins constructed from structure files downloaded from the Protein Data Bank. It is hoped that this method will greatly facilitate the ab initio structure determination of proteins.

  6. Validation of protein carbonyl measurement

    DEFF Research Database (Denmark)

    Augustyniak, Edyta; Adam, Aisha; Wojdyla, Katarzyna

    2015-01-01

    Protein carbonyls are widely analysed as a measure of protein oxidation. Several different methods exist for their determination. A previous study had described orders of magnitude variance that existed when protein carbonyls were analysed in a single laboratory by ELISA using different commercial...... kits. We have further explored the potential causes of variance in carbonyl analysis in a ring study. A soluble protein fraction was prepared from rat liver and exposed to 0, 5 and 15min of UV irradiation. Lyophilised preparations were distributed to six different laboratories that routinely undertook...... protein carbonyl analysis across Europe. ELISA and Western blotting techniques detected an increase in protein carbonyl formation between 0 and 5min of UV irradiation irrespective of method used. After irradiation for 15min, less oxidation was detected by half of the laboratories than after 5min...

  7. Posttranslational protein modification in Archaea.

    Science.gov (United States)

    Eichler, Jerry; Adams, Michael W W

    2005-09-01

    One of the first hurdles to be negotiated in the postgenomic era involves the description of the entire protein content of the cell, the proteome. Such efforts are presently complicated by the various posttranslational modifications that proteins can experience, including glycosylation, lipid attachment, phosphorylation, methylation, disulfide bond formation, and proteolytic cleavage. Whereas these and other posttranslational protein modifications have been well characterized in Eucarya and Bacteria, posttranslational modification in Archaea has received far less attention. Although archaeal proteins can undergo posttranslational modifications reminiscent of what their eucaryal and bacterial counterparts experience, examination of archaeal posttranslational modification often reveals aspects not previously observed in the other two domains of life. In some cases, posttranslational modification allows a protein to survive the extreme conditions often encountered by Archaea. The various posttranslational modifications experienced by archaeal proteins, the molecular steps leading to these modifications, and the role played by posttranslational modification in Archaea form the focus of this review.

  8. Protein microarrays for systems biology

    Institute of Scientific and Technical Information of China (English)

    Lina Yang; Shujuan Guo; Yang Li; Shumin Zhou; Shengce Tao

    2011-01-01

    Systems biology holds the key for understanding biological systems on a system level. It eventually holds the key for the treatment and cure of complex diseases such as cancer,diabetes, obesity, mental disorders, and many others. The '-omics' technologies, such as genomics, transcriptomics,proteomics, and metabonomics, are among the major driving forces of systems biology. Featured as highthroughput, miniaturized, and capable of parallel analysis,protein microarrays have already become an important technology platform for systems biology, In this review, we will focus on the system level or global analysis of biological systems using protein microarrays. Four major types of protein microarrays will be discussed: proteome microarrays, antibody microarrays, reverse-phase protein arrays,and lectin microarrays. We will also discuss the challenges and future directions of protein microarray technologies and their applications for systems biology. We strongly believe that protein microarrays will soon become an indispensable and invaluable tool for systems biology.

  9. Monitoring protein stability in vivo

    Directory of Open Access Journals (Sweden)

    Ignatova Zoya

    2005-08-01

    Full Text Available Abstract Reduced protein stability in vivo is a prerequisite to aggregation. While this is merely a nuisance factor in recombinant protein production, it holds a serious impact for man. This review focuses on specific approaches to selectively determine the solubility and/or stability of a target protein within the complex cellular environment using different detection techniques. Noninvasive techniques mapping folding/misfolding events on a fast time scale can be used to unravel the complexity and dynamics of the protein aggregation process and factors altering protein solubility in vivo. The development of approaches to screen for folding and solubility in vivo should facilitate the identification of potential components that improve protein solubility and/or modulate misfolding and aggregation and may provide a therapeutic benefit.

  10. Monitoring protein stability in vivo.

    Science.gov (United States)

    Ignatova, Zoya

    2005-08-24

    Reduced protein stability in vivo is a prerequisite to aggregation. While this is merely a nuisance factor in recombinant protein production, it holds a serious impact for man. This review focuses on specific approaches to selectively determine the solubility and/or stability of a target protein within the complex cellular environment using different detection techniques. Noninvasive techniques mapping folding/misfolding events on a fast time scale can be used to unravel the complexity and dynamics of the protein aggregation process and factors altering protein solubility in vivo. The development of approaches to screen for folding and solubility in vivo should facilitate the identification of potential components that improve protein solubility and/or modulate misfolding and aggregation and may provide a therapeutic benefit.

  11. Theoretical studies of protein-protein and protein-DNA binding rates

    Science.gov (United States)

    Alsallaq, Ramzi A.

    Proteins are folded chains of amino acids. Some of the amino acids (e.g. Lys, Arg, His, Asp, and Glu) carry charges under physiological conditions. Proteins almost always function through binding to other proteins or ligands, for example barnase is a ribonuclease protein, found in the bacterium Bacillus amyloliquefaceus. Barnase degrades RNA by hydrolysis. For the bacterium to inhibit the potentially lethal action of Barnase within its own cell it co-produces another protein called barstar which binds quickly, and tightly, to barnase. The biological function of this binding is to block the active site of barnase. The speeds (rates) at which proteins associate are vital to many biological processes. They span a wide range (from less than 103 to 108 M-1s-1 ). Rates greater than ˜ 106 M -1s-1 are typically found to be manifestations of enhancements by long-range electrostatic interactions between the associating proteins. A different paradigm appears in the case of protein binding to DNA. The rate in this case is enhanced through attractive surface potential that effectively reduces the dimensionality of the available search space for the diffusing protein. This thesis presents computational and theoretical models on the rate of association of ligands/proteins to other proteins or DNA. For protein-protein association we present a general strategy for computing protein-protein rates of association. The main achievements of this strategy is the ability to obtain a stringent reaction criteria based on the landscape of short-range interactions between the associating proteins, and the ability to compute the effect of the electrostatic interactions on the rates of association accurately using the best known solvers for Poisson-Boltzmann equation presently available. For protein-DNA association we present a mathematical model for proteins targeting specific sites on a circular DNA topology. The main achievements are the realization that a linear DNA with reflecting ends

  12. FLUORESCENCE LIFETIME DISTRIBUTIONS IN PROTEINS

    OpenAIRE

    ALCALA, JR; Gratton, E; PRENDERGAST, FG

    1987-01-01

    The fluorescence lifetime value of tryptophan residues varies by more than a factor of 100 in different proteins and is determined by several factors, which include solvent exposure and interactions with other elements of the protein matrix. Because of the variety of different elements that can alter the lifetime value and the sensitivity to the particular environment of the tryptophan residue, it is likely that non-unique lifetime values result in protein systems. The emission decay of most ...

  13. Protein mixtures: interactions and gelation

    OpenAIRE

    Ersch, C.

    2015-01-01

    Gelation is a ubiquitous process in the preparation of foods. As most foods are multi constituent mixtures, understanding gelation in mixtures is an important goal in food science. Here we presented a systematic investigation on the influence of molecular interactions on the gelation in protein mixtures. Gelatin gels with added globular protein and globular protein gels with added gelatin were analyzed for their gel microstructure and rheological properties. Mixed gels with altered microstruc...

  14. Posttranslational Protein Modification in Archaea

    OpenAIRE

    Eichler, Jerry; Adams, Michael W. W.

    2005-01-01

    One of the first hurdles to be negotiated in the postgenomic era involves the description of the entire protein content of the cell, the proteome. Such efforts are presently complicated by the various posttranslational modifications that proteins can experience, including glycosylation, lipid attachment, phosphorylation, methylation, disulfide bond formation, and proteolytic cleavage. Whereas these and other posttranslational protein modifications have been well characterized in Eucarya and B...

  15. Vegetable proteins and milk puddings

    OpenAIRE

    2003-01-01

    In recent years, interest in animal free foods has increased tremendously due to factors like BSE crisis, rise of nutritionally dependent illnesses, like diabetes type II, cardiovascular and digestive diseases, along with ethic orientations of denying animal intakes of any kind. The use of proteins from leguminous seeds as an alternative to the animal proteins in dairy desserts was studied. Lupin, pea and soya protein isolates were used in combination with k- carrageenan, gellan a...

  16. Developing algorithms for predicting protein-protein interactions of homology modeled proteins.

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Shawn Bryan; Sale, Kenneth L.; Faulon, Jean-Loup Michel; Roe, Diana C.

    2006-01-01

    The goal of this project was to examine the protein-protein docking problem, especially as it relates to homology-based structures, identify the key bottlenecks in current software tools, and evaluate and prototype new algorithms that may be developed to improve these bottlenecks. This report describes the current challenges in the protein-protein docking problem: correctly predicting the binding site for the protein-protein interaction and correctly placing the sidechains. Two different and complementary approaches are taken that can help with the protein-protein docking problem. The first approach is to predict interaction sites prior to docking, and uses bioinformatics studies of protein-protein interactions to predict theses interaction site. The second approach is to improve validation of predicted complexes after docking, and uses an improved scoring function for evaluating proposed docked poses, incorporating a solvation term. This scoring function demonstrates significant improvement over current state-of-the art functions. Initial studies on both these approaches are promising, and argue for full development of these algorithms.

  17. Novel protein-protein interaction family proteins involved in chloroplast movement response.

    Science.gov (United States)

    Kodama, Yutaka; Suetsugu, Noriyuki; Wada, Masamitsu

    2011-04-01

    To optimize photosynthetic activity, chloroplasts change their intracellular location in response to ambient light conditions; chloroplasts move toward low intensity light to maximize light capture, and away from high intensity light to avoid photodamage. Although several proteins have been reported to be involved in the chloroplast photorelocation movement response, any physical interaction among them was not found so far. We recently found a physical interaction between two plant-specific coiled-coil proteins, WEB1 (Weak Chloroplast Movement under Blue Light 1) and PMI2 (Plastid Movement Impaired 2), that were identified to regulate chloroplast movement velocity. Since the both coiled-coil regions of WEB1 and PMI2 were classified into an uncharacterized protein family having DUF827 (DUF: Domain of Unknown Function) domain, it was the first report that DUF827 proteins could mediate protein-protein interaction. In this mini-review article, we discuss regarding molecular function of WEB1 and PMI2, and also define a novel protein family composed of WEB1, PMI2 and WEB1/PMI2-like proteins for protein-protein interaction in land plants.

  18. Protein function prediction using neighbor relativity in protein-protein interaction network.

    Science.gov (United States)

    Moosavi, Sobhan; Rahgozar, Masoud; Rahimi, Amir

    2013-04-01

    There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interaction information to predict function for un-annotated proteins. In this paper, we propose a novel approach called "Neighbor Relativity Coefficient" (NRC) based on interaction network topology which estimates the functional similarity between two proteins. NRC is calculated for each pair of proteins based on their graph-based features including distance, common neighbors and the number of paths between them. In order to ascribe function to an un-annotated protein, NRC estimates a weight for each neighbor to transfer its annotation to the unknown protein. Finally, the unknown protein will be annotated by the top score transferred functions. We also investigate the effect of using different coefficients for various types of functions. The proposed method has been evaluated on Saccharomyces cerevisiae and Homo sapiens interaction networks. The performance analysis demonstrates that NRC yields better results in comparison with previous protein function prediction approaches that utilize interaction network.

  19. Recovery of protein from green leaves

    NARCIS (Netherlands)

    Tamayo Tenorio, Angelica; Gieteling, Jarno; Jong, De Govardus A.H.; Boom, Remko M.; Goot, Van Der Atze J.

    2016-01-01

    Plant leaves are a major potential source of novel food proteins. Till now, leaf protein extraction methods mainly focus on the extraction of soluble proteins, like rubisco protein, leaving more than half of all protein unextracted. Here, we report on the total protein extraction from sugar beet

  20. Protein-stabilized magnetic fluids

    Science.gov (United States)

    Soenen, S. J. H.; Hodenius, M.; Schmitz-Rode, T.; De Cuyper, M.

    The adsorption of bovine serum albumin (BSA) and egg yolk phosvitin on magnetic fluid particles was investigated. Incubation mixtures were prepared by mixing an alkaline suspension of tetramethylammonium-coated magnetite cores with protein solutions at various protein/Fe 3O 4 ratios, followed by dialysis against a 5 mM TES buffer (pH 7.0), after which separation of bound and non-bound protein by high-gradient magnetophoresis was executed. Both the kinetic profiles as well as the isotherms of adsorption strongly differed for both proteins. In case of the spherical BSA, initially, abundant adsorption occurred, then it decreased and—at high protein concentrations—it slowly raised again. In contrast, with the highly phosphorylated phosvitin, binding slowly started and the extent of protein adsorption remained unchanged both as a function of time and phosvitin concentration. Competition binding studies, using binary protein mixtures composed of equal weight amounts of BSA and phosvitin, showed that binding of the latter protein is 'unrealistically' high. Based on the geometry of the two proteins, putative pictures on their orientation on the particle's surface in the various experimental conditions were deduced.

  1. Recombinant protein expression in Nicotiana.

    Science.gov (United States)

    Matoba, Nobuyuki; Davis, Keith R; Palmer, Kenneth E

    2011-01-01

    Recombinant protein pharmaceuticals are now widely used in treatment of chronic diseases, and several recombinant protein subunit vaccines are approved for human and veterinary use. With growing demand for complex protein pharmaceuticals, such as monoclonal antibodies, manufacturing capacity is becoming limited. There is increasing need for safe, scalable, and economical alternatives to mammalian cell culture-based manufacturing systems, which require substantial capital investment for new manufacturing facilities. Since a seminal paper reporting immunoglobulin expression in transgenic plants was published in 1989, there have been many technological advances in plant expression systems to the present time where production of proteins in leaf tissues of nonfood crops such as Nicotiana species is considered a viable alternative. In particular, transient expression systems derived from recombinant plant viral vectors offer opportunities for rapid expression screening, construct optimization, and expression scale-up. Extraction of recombinant proteins from Nicotiana leaf tissues can be achieved by collection of secreted protein fractions, or from a total protein extract after grinding the leaves with buffer. After separation from solids, the major purification challenge is contamination with elements of the photosynthetic complex, which can be solved by application of a variety of facile and proven strategies. In conclusion, the technologies required for safe, efficient, scalable manufacture of recombinant proteins in Nicotiana leaf tissues have matured to the point where several products have already been tested in phase I clinical trials and will soon be followed by a rich pipeline of recombinant vaccines, microbicides, and therapeutic proteins.

  2. Protein leverage and energy intake.

    Science.gov (United States)

    Gosby, A K; Conigrave, A D; Raubenheimer, D; Simpson, S J

    2014-03-01

    Increased energy intakes are contributing to overweight and obesity. Growing evidence supports the role of protein appetite in driving excess intake when dietary protein is diluted (the protein leverage hypothesis). Understanding the interactions between dietary macronutrient balance and nutrient-specific appetite systems will be required for designing dietary interventions that work with, rather than against, basic regulatory physiology. Data were collected from 38 published experimental trials measuring ad libitum intake in subjects confined to menus differing in macronutrient composition. Collectively, these trials encompassed considerable variation in percent protein (spanning 8-54% of total energy), carbohydrate (1.6-72%) and fat (11-66%). The data provide an opportunity to describe the individual and interactive effects of dietary protein, carbohydrate and fat on the control of total energy intake. Percent dietary protein was negatively associated with total energy intake (F = 6.9, P protein. The analysis strongly supports a role for protein leverage in lean, overweight and obese humans. A better appreciation of the targets and regulatory priorities for protein, carbohydrate and fat intake will inform the design of effective and health-promoting weight loss diets, food labelling policies, food production systems and regulatory frameworks.

  3. Computational protein design: a review

    Science.gov (United States)

    Coluzza, Ivan

    2017-04-01

    Proteins are one of the most versatile modular assembling systems in nature. Experimentally, more than 110 000 protein structures have been identified and more are deposited every day in the Protein Data Bank. Such an enormous structural variety is to a first approximation controlled by the sequence of amino acids along the peptide chain of each protein. Understanding how the structural and functional properties of the target can be encoded in this sequence is the main objective of protein design. Unfortunately, rational protein design remains one of the major challenges across the disciplines of biology, physics and chemistry. The implications of solving this problem are enormous and branch into materials science, drug design, evolution and even cryptography. For instance, in the field of drug design an effective computational method to design protein-based ligands for biological targets such as viruses, bacteria or tumour cells, could give a significant boost to the development of new therapies with reduced side effects. In materials science, self-assembly is a highly desired property and soon artificial proteins could represent a new class of designable self-assembling materials. The scope of this review is to describe the state of the art in computational protein design methods and give the reader an outline of what developments could be expected in the near future.

  4. [Protein toxins of Staphylococcus aureus].

    Science.gov (United States)

    Shamsutdinov, A F; Tiurin, Iu A

    2014-01-01

    Main scientific-research studies regarding protein bacterial toxins of the most widespread bacteria that belong to Staphylococcus spp. genus and in particular the most pathogenic species for humans--Staphylococcus aureus, are analyzed. Structural and biological properties of protein toxins that have received the name of staphylococcus pyrogenic toxins (PTSAg) are presented. Data regarding genetic regulation of secretion and synthesis of these toxins and 3 main regulatory genetic systems (agr--accessory gene regulator, xpr--extracellular protein regulator, sar--staphylococcal accessory regulator) that coordinate synthesis of the most important protein toxins and enzymes for virulence of S. aureus, are presented.

  5. Pathogen mimicry of host protein-protein interfaces modulates immunity.

    Science.gov (United States)

    Guven-Maiorov, Emine; Tsai, Chung-Jung; Nussinov, Ruth

    2016-10-01

    Signaling pathways shape and transmit the cell's reaction to its changing environment; however, pathogens can circumvent this response by manipulating host signaling. To subvert host defense, they beat it at its own game: they hijack host pathways by mimicking the binding surfaces of host-encoded proteins. For this, it is not necessary to achieve global protein homology; imitating merely the interaction surface is sufficient. Different protein folds often interact via similar protein-protein interface architectures. This similarity in binding surfaces permits the pathogenic protein to compete with a host target protein. Thus, rather than binding a host-encoded partner, the host protein hub binds the pathogenic surrogate. The outcome can be dire: rewiring or repurposing the host pathways, shifting the cell signaling landscape and consequently the immune response. They can also cause persistent infections as well as cancer by modulating key signaling pathways, such as those involving Ras. Mapping the rewired host-pathogen 'superorganism' interaction network - along with its structural details - is critical for in-depth understanding of pathogenic mechanisms and developing efficient therapeutics. Here, we overview the role of molecular mimicry in pathogen host evasion as well as types of molecular mimicry mechanisms that emerged during evolution.

  6. Detecting protein-protein interactions in living cells

    DEFF Research Database (Denmark)

    Gottschalk, Marie; Bach, Anders; Hansen, Jakob Lerche

    2009-01-01

    to the endogenous C-terminal peptide of the NMDA receptor, as evaluated by a cell-free protein-protein interaction assay. However, it is important to address both membrane permeability and effect in living cells. Therefore a bioluminescence resonance energy transfer (BRET) assay was established, where the C...

  7. Protein-protein interaction networks in the spinocerebellar ataxias

    OpenAIRE

    David C Rubinsztein

    2006-01-01

    A large yeast two-hybrid study investigating whether the proteins mutated in different forms of spinocerebellar ataxia have interacting protein partners in common suggests that some forms do share common pathways, and will provide a valuable resource for future work on these diseases.

  8. Protein-Protein Interactions (PPI) reagents: | Office of Cancer Genomics

    Science.gov (United States)

    The CTD2 Center at Emory University has a library of genes used to study protein-protein interactions in mammalian cells. These genes are cloned in different mammalian expression vectors. A list of available cancer-associated genes can be accessed below.

  9. Protein-Protein Interaction Reagents | Office of Cancer Genomics

    Science.gov (United States)

    The CTD2 Center at Emory University has a library of genes used to study protein-protein interactions in mammalian cells. These genes are cloned in different mammalian expression vectors. A list of available cancer-associated genes can be accessed below. Emory_CTD^2_PPI_Reagents.xlsx Contact: Haian Fu

  10. Hydration of proteins: excess partial enthalpies of water and proteins.

    Science.gov (United States)

    Sirotkin, Vladimir A; Khadiullina, Aigul V

    2011-12-22

    Isothermal batch calorimetry was applied to study the hydration of proteins. The hydration process was analyzed by the simultaneous monitoring of the excess partial enthalpies of water and the proteins in the entire range of water content. Four unrelated proteins (lysozyme, chymotrypsinogen A, human serum albumin, and β-lactoglobulin) were used as models. The excess partial quantities are very sensitive to the changes in the state of water and proteins. At the lowest water weight fractions (w(1)), the changes of the excess thermochemical functions can mainly be attributed to water addition. A transition from the glassy to the flexible state of the proteins is accompanied by significant changes in the excess partial quantities of water and the proteins. This transition appears at a water weight fraction of 0.06 when charged groups of proteins are covered. Excess partial quantities reach their fully hydrated values at w(1) > 0.5 when coverage of both polar and weakly interacting surface elements is complete. At the highest water contents, water addition has no significant effect on the excess thermochemical quantities. At w(1) > 0.5, changes in the excess functions can solely be attributed to changes in the state of the proteins.

  11. Mapping Protein-Protein Interactions by Quantitative Proteomics

    DEFF Research Database (Denmark)

    Dengjel, Joern; Kratchmarova, Irina; Blagoev, Blagoy

    2010-01-01

    spectrometry (MS)-based proteomics in combination with affinity purification protocols has become the method of choice to map and track the dynamic changes in protein-protein interactions, including the ones occurring during cellular signaling events. Different quantitative MS strategies have been used...

  12. Website on Protein Interaction and Protein Structure Related Work

    Science.gov (United States)

    Samanta, Manoj; Liang, Shoudan; Biegel, Bryan (Technical Monitor)

    2003-01-01

    In today's world, three seemingly diverse fields - computer information technology, nanotechnology and biotechnology are joining forces to enlarge our scientific knowledge and solve complex technological problems. Our group is dedicated to conduct theoretical research exploring the challenges in this area. The major areas of research include: 1) Yeast Protein Interactions; 2) Protein Structures; and 3) Current Transport through Small Molecules.

  13. Protein folding and the organization of the protein topology universe

    DEFF Research Database (Denmark)

    Lindorff-Larsen,, Kresten; Røgen, Peter; Paci, Emanuele

    2005-01-01

    of protein folds that is based on the topological features of the polypeptide backbone, rather than the conventional view that depends on the arrangement of different types of secondary-structure elements. By linking the folding process to the organization of the protein structure universe, we propose...

  14. Characterization of protein-protein interactions by isothermal titration calorimetry.

    Science.gov (United States)

    Velazquez-Campoy, Adrian; Leavitt, Stephanie A; Freire, Ernesto

    2015-01-01

    The analysis of protein-protein interactions has attracted the attention of many researchers from both a fundamental point of view and a practical point of view. From a fundamental point of view, the development of an understanding of the signaling events triggered by the interaction of two or more proteins provides key information to elucidate the functioning of many cell processes. From a practical point of view, understanding protein-protein interactions at a quantitative level provides the foundation for the development of antagonists or agonists of those interactions. Isothermal Titration Calorimetry (ITC) is the only technique with the capability of measuring not only binding affinity but the enthalpic and entropic components that define affinity. Over the years, isothermal titration calorimeters have evolved in sensitivity and accuracy. Today, TA Instruments and MicroCal market instruments with the performance required to evaluate protein-protein interactions. In this methods paper, we describe general procedures to analyze heterodimeric (porcine pancreatic trypsin binding to soybean trypsin inhibitor) and homodimeric (bovine pancreatic α-chymotrypsin) protein associations by ITC.

  15. Protein linguistics - a grammar for modular protein assembly?

    Science.gov (United States)

    Gimona, Mario

    2006-01-01

    The correspondence between biology and linguistics at the level of sequence and lexical inventories, and of structure and syntax, has fuelled attempts to describe genome structure by the rules of formal linguistics. But how can we define protein linguistic rules? And how could compositional semantics improve our understanding of protein organization and functional plasticity?

  16. Protein stability: a crystallographer’s perspective

    Energy Technology Data Exchange (ETDEWEB)

    Deller, Marc C., E-mail: mdeller@stanford.edu [Stanford University, Shriram Center, 443 Via Ortega, Room 097, MC5082, Stanford, CA 94305-4125 (United States); Kong, Leopold [National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Building 8, Room 1A03, 8 Center Drive, Bethesda, MD 20814 (United States); Rupp, Bernhard [k.-k. Hofkristallamt, 91 Audrey Place, Vista, CA 92084 (United States); Medical University of Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck (Austria)

    2016-01-26

    An understanding of protein stability is essential for optimizing the expression, purification and crystallization of proteins. In this review, discussion will focus on factors affecting protein stability on a somewhat practical level, particularly from the view of a protein crystallographer. Protein stability is a topic of major interest for the biotechnology, pharmaceutical and food industries, in addition to being a daily consideration for academic researchers studying proteins. An understanding of protein stability is essential for optimizing the expression, purification, formulation, storage and structural studies of proteins. In this review, discussion will focus on factors affecting protein stability, on a somewhat practical level, particularly from the view of a protein crystallographer. The differences between protein conformational stability and protein compositional stability will be discussed, along with a brief introduction to key methods useful for analyzing protein stability. Finally, tactics for addressing protein-stability issues during protein expression, purification and crystallization will be discussed.

  17. Information-driven structural modelling of protein-protein interactions.

    Science.gov (United States)

    Rodrigues, João P G L M; Karaca, Ezgi; Bonvin, Alexandre M J J

    2015-01-01

    Protein-protein docking aims at predicting the three-dimensional structure of a protein complex starting from the free forms of the individual partners. As assessed in the CAPRI community-wide experiment, the most successful docking algorithms combine pure laws of physics with information derived from various experimental or bioinformatics sources. Of these so-called "information-driven" approaches, HADDOCK stands out as one of the most successful representatives. In this chapter, we briefly summarize which experimental information can be used to drive the docking prediction in HADDOCK, and then focus on the docking protocol itself. We discuss and illustrate with a tutorial example a "classical" protein-protein docking prediction, as well as more recent developments for modelling multi-body systems and large conformational changes.

  18. Protein-protein interaction predictions using text mining methods.

    Science.gov (United States)

    Papanikolaou, Nikolas; Pavlopoulos, Georgios A; Theodosiou, Theodosios; Iliopoulos, Ioannis

    2015-03-01

    It is beyond any doubt that proteins and their interactions play an essential role in most complex biological processes. The understanding of their function individually, but also in the form of protein complexes is of a great importance. Nowadays, despite the plethora of various high-throughput experimental approaches for detecting protein-protein interactions, many computational methods aiming to predict new interactions have appeared and gained interest. In this review, we focus on text-mining based computational methodologies, aiming to extract information for proteins and their interactions from public repositories such as literature and various biological databases. We discuss their strengths, their weaknesses and how they complement existing experimental techniques by simultaneously commenting on the biological databases which hold such information and the benchmark datasets that can be used for evaluating new tools.

  19. Understanding protein evolution: from protein physics to Darwinian selection.

    Science.gov (United States)

    Zeldovich, Konstantin B; Shakhnovich, Eugene I

    2008-01-01

    Efforts in whole-genome sequencing and structural proteomics start to provide a global view of the protein universe, the set of existing protein structures and sequences. However, approaches based on the selection of individual sequences have not been entirely successful at the quantitative description of the distribution of structures and sequences in the protein universe because evolutionary pressure acts on the entire organism, rather than on a particular molecule. In parallel to this line of study, studies in population genetics and phenomenological molecular evolution established a mathematical framework to describe the changes in genome sequences in populations of organisms over time. Here, we review both microscopic (physics-based) and macroscopic (organism-level) models of protein-sequence evolution and demonstrate that bridging the two scales provides the most complete description of the protein universe starting from clearly defined, testable, and physiologically relevant assumptions.

  20. Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces.

    Directory of Open Access Journals (Sweden)

    Ruzianisra Mohamed

    Full Text Available Protein-protein interactions (PPIs play a major role in many biological processes and they represent an important class of targets for therapeutic intervention. However, targeting PPIs is challenging because often no convenient natural substrates are available as starting point for small-molecule design. Here, we explored the characteristics of protein interfaces in five non-redundant datasets of 174 protein-protein (PP complexes, and 161 protein-ligand (PL complexes from the ABC database, 436 PP complexes, and 196 PL complexes from the PIBASE database and a dataset of 89 PL complexes from the Timbal database. In all cases, the small molecule ligands must bind at the respective PP interface. We observed similar amino acid frequencies in all three datasets. Remarkably, also the characteristics of PP contacts and overlapping PL contacts are highly similar.

  1. Studies on ternary silver sulfides; Fukugo gin ryukabutsu ni kansuru kenkyu

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-10-31

    Some sulfides containing silver show high ion mobility based on movability of silver, whose application is expected. Studies have been carried out centrally on synthesis of new compounds of ternary silver sulfides by elucidating the relationship among their compositions, structures and properties by means of crystal chemical studies mainly on their phase relationship. A few new compounds have been synthesized, such as the ones having the argyrodite family compound structure including transition metals. The synthesizing process takes a kind of turbulent liquid state structure at elevated temperatures because of movability of silver, but silver is fixed at low temperatures in different sites between skeleton structures made by other atoms. These studies on phase transfer, structures, and silver movability have been based on X-ray diffraction, infrared and Raman spectroscopic measurements, NMR, measurements of electric and thermal characteristics. For the studies related to compositions and structures of ternary metal sulfides which take compound crystalline structure, a structure analyzing method based on multi-dimensional hyperspatial groups was used. This paper reports the summary of the studies in seven chapters, and dwells on the remaining problems and future prospects. 158 refs., 114 figs., 65 tabs.

  2. 29 CFR 1928.57 - Guarding of farm field equipment, farmstead equipment, and cotton gins.

    Science.gov (United States)

    2010-07-01

    ... in place. (2) Other power transmission components. (i) The mesh or nip-points of all power driven.... (2) Other power transmission components. (i) The mesh or nip-points of all power driven gears, belts... deposits of lint, only the face section of nip-point and pulley guards is required. The guard shall...

  3. Development of a prototype sensor to detect plastic contamination in seed cotton at the gin

    Science.gov (United States)

    US cotton is considered to have some of the lowest levels of contamination in the world. That reputation is expected by foreign and domestic mills. Despite this reputation, U.S. spinners have recently experienced some serious contamination issues with US cotton. Of particular concern are plastic con...

  4. Text Mining for Protein Docking.

    Directory of Open Access Journals (Sweden)

    Varsha D Badal

    2015-12-01

    Full Text Available The rapidly growing amount of publicly available information from biomedical research is readily accessible on the Internet, providing a powerful resource for predictive biomolecular modeling. The accumulated data on experimentally determined structures transformed structure prediction of proteins and protein complexes. Instead of exploring the enormous search space, predictive tools can simply proceed to the solution based on similarity to the existing, previously determined structures. A similar major paradigm shift is emerging due to the rapidly expanding amount of information, other than experimentally determined structures, which still can be used as constraints in biomolecular structure prediction. Automated text mining has been widely used in recreating protein interaction networks, as well as in detecting small ligand binding sites on protein structures. Combining and expanding these two well-developed areas of research, we applied the text mining to structural modeling of protein-protein complexes (protein docking. Protein docking can be significantly improved when constraints on the docking mode are available. We developed a procedure that retrieves published abstracts on a specific protein-protein interaction and extracts information relevant to docking. The procedure was assessed on protein complexes from Dockground (http://dockground.compbio.ku.edu. The results show that correct information on binding residues can be extracted for about half of the complexes. The amount of irrelevant information was reduced by conceptual analysis of a subset of the retrieved abstracts, based on the bag-of-words (features approach. Support Vector Machine models were trained and validated on the subset. The remaining abstracts were filtered by the best-performing models, which decreased the irrelevant information for ~ 25% complexes in the dataset. The extracted constraints were incorporated in the docking protocol and tested on the Dockground unbound

  5. Protein-protein interactions within late pre-40S ribosomes.

    Directory of Open Access Journals (Sweden)

    Melody G Campbell

    Full Text Available Ribosome assembly in eukaryotic organisms requires more than 200 assembly factors to facilitate and coordinate rRNA transcription, processing, and folding with the binding of the ribosomal proteins. Many of these assembly factors bind and dissociate at defined times giving rise to discrete assembly intermediates, some of which have been partially characterized with regards to their protein and RNA composition. Here, we have analyzed the protein-protein interactions between the seven assembly factors bound to late cytoplasmic pre-40S ribosomes using recombinant proteins in binding assays. Our data show that these factors form two modules: one comprising Enp1 and the export adaptor Ltv1 near the beak structure, and the second comprising the kinase Rio2, the nuclease Nob1, and a regulatory RNA binding protein Dim2/Pno1 on the front of the head. The GTPase-like Tsr1 and the universally conserved methylase Dim1 are also peripherally connected to this second module. Additionally, in an effort to further define the locations for these essential proteins, we have analyzed the interactions between these assembly factors and six ribosomal proteins: Rps0, Rps3, Rps5, Rps14, Rps15 and Rps29. Together, these results and previous RNA-protein crosslinking data allow us to propose a model for the binding sites of these seven assembly factors. Furthermore, our data show that the essential kinase Rio2 is located at the center of the pre-ribosomal particle and interacts, directly or indirectly, with every other assembly factor, as well as three ribosomal proteins required for cytoplasmic 40S maturation. These data suggest that Rio2 could play a central role in regulating cytoplasmic maturation steps.

  6. Porcine prion protein amyloid.

    Science.gov (United States)

    Hammarström, Per; Nyström, Sofie

    2015-01-01

    Mammalian prions are composed of misfolded aggregated prion protein (PrP) with amyloid-like features. Prions are zoonotic disease agents that infect a wide variety of mammalian species including humans. Mammals and by-products thereof which are frequently encountered in daily life are most important for human health. It is established that bovine prions (BSE) can infect humans while there is no such evidence for any other prion susceptible species in the human food chain (sheep, goat, elk, deer) and largely prion resistant species (pig) or susceptible and resistant pets (cat and dogs, respectively). PrPs from these species have been characterized using biochemistry, biophysics and neurobiology. Recently we studied PrPs from several mammals in vitro and found evidence for generic amyloidogenicity as well as cross-seeding fibril formation activity of all PrPs on the human PrP sequence regardless if the original species was resistant or susceptible to prion disease. Porcine PrP amyloidogenicity was among the studied. Experimentally inoculated pigs as well as transgenic mouse lines overexpressing porcine PrP have, in the past, been used to investigate the possibility of prion transmission in pigs. The pig is a species with extraordinarily wide use within human daily life with over a billion pigs harvested for human consumption each year. Here we discuss the possibility that the largely prion disease resistant pig can be a clinically silent carrier of replicating prions.

  7. Genome-wide protein-protein interactions and protein function exploration in cyanobacteria.

    Science.gov (United States)

    Lv, Qi; Ma, Weimin; Liu, Hui; Li, Jiang; Wang, Huan; Lu, Fang; Zhao, Chen; Shi, Tieliu

    2015-10-22

    Genome-wide network analysis is well implemented to study proteins of unknown function. Here, we effectively explored protein functions and the biological mechanism based on inferred high confident protein-protein interaction (PPI) network in cyanobacteria. We integrated data from seven different sources and predicted 1,997 PPIs, which were evaluated by experiments in molecular mechanism, text mining of literatures in proved direct/indirect evidences, and "interologs" in conservation. Combined the predicted PPIs with known PPIs, we obtained 4,715 no-redundant PPIs (involving 3,231 proteins covering over 90% of genome) to generate the PPI network. Based on the PPI network, terms in Gene ontology (GO) were assigned to function-unknown proteins. Functional modules were identified by dissecting the PPI network into sub-networks and analyzing pathway enrichment, with which we investigated novel function of underlying proteins in protein complexes and pathways. Examples of photosynthesis and DNA repair indicate that the network approach is a powerful tool in protein function analysis. Overall, this systems biology approach provides a new insight into posterior functional analysis of PPIs in cyanobacteria.

  8. Assessing protein-protein interactions based on the semantic similarity of interacting proteins.

    Science.gov (United States)

    Cui, Guangyu; Kim, Byungmin; Alguwaizani, Saud; Han, Kyungsook

    2015-01-01

    The Gene Ontology (GO) has been used in estimating the semantic similarity of proteins since it has the largest and reliable vocabulary of gene products and characteristics. We developed a new method which can assess Protein-Protein Interactions (PPI) using the branching factor and information content of the common ancestor of interacting proteins in the GO hierarchy. We performed a comparative evaluation of the measure with other GO-based similarity measures and evaluation results showed that our method outperformed others in most GO domains.

  9. Modelling of proteins in membranes

    DEFF Research Database (Denmark)

    Sperotto, Maria Maddalena; May, S.; Baumgaertner, A.

    2006-01-01

    This review describes some recent theories and simulations of mesoscopic and microscopic models of lipid membranes with embedded or attached proteins. We summarize results supporting our understanding of phenomena for which the activities of proteins in membranes are expected to be significantly...

  10. Protein and amino acid nutrition

    Science.gov (United States)

    Dairy cow protein and amino acid nutrition have a significant role in sustainable dairying. Protein, amino acids, and nitrogen are inextricably linked through effects in the rumen, metabolism of the cow, and environmental nutrient management. Feeding systems have been making progress toward emphasiz...

  11. Small Molecules Target Carcinogenic Proteins

    Science.gov (United States)

    Gradinaru, Claudiu

    2009-03-01

    An ingenious cellular mechanism of effecting protein localization is prenylation: the covalent attachment of a hydrophobic prenyl group to a protein that facilitates protein association with cell membranes. Fluorescence microscopy was used to investigate whether the oncogenic Stat3 protein can undergo artificial prenylation via high-affinity prenylated small-molecule binding agents and thus be rendered inactive by localization at the plasma membrane instead of nucleus. The measurements were performed on a home-built instrument capable of recording simultaneously several optical parameters (lifetime, polarization, color, etc) and with single-molecule sensitivity. A pH-invariant fluorescein derivative with double moiety was designed to bridge a prenyl group and a small peptide that binds Stat3 with high affinity. Confocal fluorescence images show effective localization of the ligand to the membrane of liposomes. Stat3 predominantly localizes at the membrane only in the presence of the prenylated ligand. Single-molecule FRET (fluorescence resonance energy transfer) between donor-labeled prenylated agents and acceptor-labeled, surface tethered Stat3 protein is used to determine the dynamic heterogeneity of the protein-ligand interaction and follow individual binding-unbinding events in real time. The data indicates that molecules can effect protein localization, validating a therapeutic design that influences protein activity via induced localization.

  12. Protein: MPB4 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available ABP-280 homolog, Actin-binding-like protein, Beta-filamin, Filamin homolog 1, Filamin-3, Thyroid autoantige...n, Truncated actin-binding protein 9606 Homo sapiens O75369 2317 2EED, 3FER, 2DIA, 2DLG, 2EE6, 2WA5, 2EE9, 2

  13. Protein: MPA6 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available MPA6 SREBBP1c SREBF1 BHLHD1, SREBP1 Sterol regulatory element-binding protein 1 Cla...ss D basic helix-loop-helix protein 1, Sterol regulatory element-binding transcription factor 1 9606 Homo sapiens P36956 6720 1AM9 6720 P36956 ...

  14. Protein: FBB5 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBB5 RNA silencing EIF2C1 AGO1 EIF2C1 Protein argonaute-1 Eukaryotic translation in...itiation factor 2C 1, Putative RNA-binding protein Q99 9606 Homo sapiens Q9UL18 26523 1SI3, 1SI2 26523 Q9UL18 ...

  15. Protein: FBA3 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA3 PtdIns 3-kinase complex ATG14 APG14, CVT12 Autophagy-related protein 14 Cytopl...asm to vacuole targeting protein 12 559292 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 852425 P38270 22013444 ...

  16. Targeting Protein Prenylation in Progeria

    Science.gov (United States)

    Young, Stephen G.; Yang, Shao H.; Davies, Brandon S. J.; Jung, Hea-Jin; Fong, Loren G.

    2013-01-01

    A clinical trial of a protein farnesyltransferase inhibitor (lonafarnib) for the treatment of Hutchinson-Gilford progeria syndrome (HGPS) was recently completed. Here, we discuss the mutation that causes HGPS, the rationale for inhibiting protein farnesyltransferase, the potential limitations of this therapeutic approach, and new potential strategies for treating the disease. PMID:23390246

  17. Targeting Protein Prenylation in Progeria

    OpenAIRE

    Young, Stephen G.; Yang, Shao H.; Davies, Brandon S.J.; Jung, Hea-Jin; Fong, Loren G.

    2013-01-01

    A clinical trial of a protein farnesyltransferase inhibitor (lonafarnib) for the treatment of Hutchinson-Gilford progeria syndrome (HGPS) was recently completed. Here, we discuss the mutation that causes HGPS, the rationale for inhibiting protein farnesyltransferase, the potential limitations of this therapeutic approach, and new potential strategies for treating the disease.

  18. Protein-ECE MEtallopincer Hybrids

    NARCIS (Netherlands)

    Kruithof, C.A.

    2007-01-01

    Modification of proteins with metal complexes is a promising and a relatively new field which conceals many challenges and potential applications. The field is a balance of contributions from the biological (protein engineering, bioconjugation) and chemical sciences (organic, inorganic and organomet

  19. Separating proteins with activated carbon.

    Science.gov (United States)

    Stone, Matthew T; Kozlov, Mikhail

    2014-07-15

    Activated carbon is applied to separate proteins based on differences in their size and effective charge. Three guidelines are suggested for the efficient separation of proteins with activated carbon. (1) Activated carbon can be used to efficiently remove smaller proteinaceous impurities from larger proteins. (2) Smaller proteinaceous impurities are most efficiently removed at a solution pH close to the impurity's isoelectric point, where they have a minimal effective charge. (3) The most efficient recovery of a small protein from activated carbon occurs at a solution pH further away from the protein's isoelectric point, where it is strongly charged. Studies measuring the binding capacities of individual polymers and proteins were used to develop these three guidelines, and they were then applied to the separation of several different protein mixtures. The ability of activated carbon to separate proteins was demonstrated to be broadly applicable with three different types of activated carbon by both static treatment and by flowing through a packed column of activated carbon.

  20. Protein palmitoylation in protozoan parasites.

    Science.gov (United States)

    Corvi, Maria Martha; Berthiaume, Luc Gerard; De Napoli, Maximiliano Gabriel

    2011-06-01

    Palmitoylation plays an important role in the regulation of the localization and function of the modified protein. Although many aspects of protein palmitoylation have been identified in mammalian and yeast cells, little information is available of this modification in protozoan parasites. Protein palmitoylation has been described for a few set of proteins in E.tenella, P. falciparum, T. gondii, G. lamblia and T. cruzi. Interestingly, in all these parasites palmitoylated proteins appears to be involved in vital processes such as invasion and motility. In addition, most of these parasites contain in their genomes genes that encode for putative palmitoyl-acyl transferases, the enzymes catalyzing the palmitoylation reaction. Although protein palmitoylation could be playing key roles in invasion and motility in a variety of parasites, little is known about this important reversible modification of proteins that typically plays a role in membrane tethering. As such, this review will focus on the main features of protein palmitoylation as well as provide an overview of the state of knowledge of this modification in protozoan parasites.

  1. Protein folding on a chip

    CERN Multimedia

    2004-01-01

    "Scientists at the U.S. Department of Energy's Brookhaven National Laboratory are proposing to use a super- computer originally developed to simulate elementary particles in high- energy physics to help determine the structures and functions of proteins, including, for example, the 30,000 or so proteins encoded by the human genome" (1 page)

  2. Protein folding and wring resonances

    DEFF Research Database (Denmark)

    Bohr, Jakob; Bohr, Henrik; Brunak, Søren

    1997-01-01

    that protein folding takes place when the amplitude of a wring excitation becomes so large that it is energetically favorable to bend the protein backbone. The condition under which such structural transformations can occur is found, and it is shown that both cold and hot denaturation (the unfolding...

  3. Prions: Beyond a Single Protein.

    Science.gov (United States)

    Das, Alvin S; Zou, Wen-Quan

    2016-07-01

    Since the term protein was first coined in 1838 and protein was discovered to be the essential component of fibrin and albumin, all cellular proteins were presumed to play beneficial roles in plants and mammals. However, in 1967, Griffith proposed that proteins could be infectious pathogens and postulated their involvement in scrapie, a universally fatal transmissible spongiform encephalopathy in goats and sheep. Nevertheless, this novel hypothesis had not been evidenced until 1982, when Prusiner and coworkers purified infectious particles from scrapie-infected hamster brains and demonstrated that they consisted of a specific protein that he called a "prion." Unprecedentedly, the infectious prion pathogen is actually derived from its endogenous cellular form in the central nervous system. Unlike other infectious agents, such as bacteria, viruses, and fungi, prions do not contain genetic materials such as DNA or RNA. The unique traits and genetic information of prions are believed to be encoded within the conformational structure and posttranslational modifications of the proteins. Remarkably, prion-like behavior has been recently observed in other cellular proteins-not only in pathogenic roles but also serving physiological functions. The significance of these fascinating developments in prion biology is far beyond the scope of a single cellular protein and its related disease.

  4. Illustrating Chromatography with Colorful Proteins

    Science.gov (United States)

    Lefebvre, Brian G.; Farrell, Stephanie; Dominiak, Richard S.

    2007-01-01

    Advances in biology are prompting new discoveries in the biotechnology, pharmaceutical, medical technology, and chemical industries. This paper presents a detailed description of an anion exchange chromatography experiment using a pair of colorful proteins and summarizes the effect of operating parameters on protein separation. This experiment…

  5. Protein: FBA5 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA5 VSOP(voltage sensor-only protein1) HVCN1 VSOP, VSX1 Voltage-gated hydrogen cha...nnel 1 Hydrogen voltage-gated channel 1, Voltage sensor domain-only protein 7719 Ciona intestinalis 778897 Q1JV40 ...

  6. Protein: FBA5 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA5 VSOP(voltage sensor-only protein1) HVCN1 VSOP Voltage-gated hydrogen channel 1... Hydrogen voltage-gated channel 1, Voltage sensor domain-only protein 9606 Homo sapiens Q96D96 84329 3A2A 18583477, 19285483 ...

  7. Protein: FBB5 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBB5 RNA silencing TARBP2 TRBP TARBP2 RISC-loading complex subunit TARBP2 TAR RNA-binding protein... 2, Trans-activation-responsive RNA-binding protein 9606 Homo sapiens Q15633 6895 3ADL 2CPN 3LLH 6895 21080422 ...

  8. Protein: FBA5 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA5 VSP(voltage-sensor containing phosphatase) ptenb pten Novel protein similar to...og B (Mutated in multiple advanced cancers 1), Phosphatase and tensin-like protein B short splice variant 7955 Danio rerio Q7ZZ56 ...

  9. Simple rheology of mixed proteins

    Science.gov (United States)

    Mixing different proteins to form strong gel networks for food applications may create synergistic increases in viscoelasticity that cannot be achieved with a single protein. In this study, small amplitude oscillatory shear analyses were used to investigate the rheology of calcium caseinate (CC), e...

  10. Teaching computers to fold proteins

    DEFF Research Database (Denmark)

    Winther, Ole; Krogh, Anders Stærmose

    2004-01-01

    A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic average...

  11. Twin-Arginine Protein Translocation

    NARCIS (Netherlands)

    Goosens, Vivianne J; van Dijl, Jan Maarten

    2016-01-01

    Twin-arginine protein translocation systems (Tat) translocate fully folded and co-factor-containing proteins across biological membranes. In this review, we focus on the Tat pathway of Gram-positive bacteria. The minimal Tat pathway is composed of two components, namely a TatA and TatC pair, which a

  12. Update on protein structure prediction

    DEFF Research Database (Denmark)

    Hubbard, T; Tramontano, A; Barton, G

    1996-01-01

    Computational tools for protein structure prediction are of great interest to molecular, structural and theoretical biologists due to a rapidly increasing number of protein sequences with no known structure. In October 1995, a workshop was held at IRBM to predict as much as possible about a numbe...

  13. Protein Crystal Growth in Microgravity

    Institute of Scientific and Technical Information of China (English)

    毕汝昌; 桂璐璐; 师珂; 王耀萍; 陈世芝; 韩青; 胡永林; 沈福苓; 牛秀田; 华子谦; 卢光莹; 张健; 李松林; 龚为民; 牛立文; 黄其辰

    1994-01-01

    Protein crystal growth is quite important for the determination of protein structureswhich are essential to the understanding of life at molecular level as well as to the development of molecu-lar biotechnology.The microgravity environment of space is an ideal place to study the complicated pro-tein crystallization and to grow good-quality protein crystals.A number of crystal-growth experiments of10 different proteins were carried out in August,1992 on the Chinese re-entry satellite FSW-2 in spaceusing a tube crystallization equipment made in China.A total of 25 samples from 6 proteins producedcrystals,and the effects of microgravity on protein crystal growth were observed,especially for an acidicphospholipase A2 and henegg-white lysozyme which gave better crystals in space than earth-grown crys-tals in ground control experiments.The results have shown that the microgravity in space favors the im-provement of the size,perfection,morphology and internal order of the grown protein crytals.

  14. Characterization of carrot arabinogalactan proteins

    NARCIS (Netherlands)

    Immerzeel, P.

    2005-01-01

    Arabinogalactan proteins (AGPs) are highly glycosylated proteins. Besides galactose and arabinose the carbohydrate part of AGPs contains other neutral sugars and uronic acids. AGPs are widely distributed in the plant kingdom, probably occurring in all tissues of every plant. Yariv phenylglycoside is

  15. Protein: MPA1 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available MPA1 TLR signaling molecules Nlrp3 Cias1, Mmig1, Nalp3, Pypaf1 NACHT, LRR and PYD d...n-associated-inducible protein 1, PYRIN-containing APAF1-like protein 1 10090 Mus musculus 216799 Q8R4B8 Q8R4B8 20007575 ...

  16. Targeting protein prenylation in progeria.

    Science.gov (United States)

    Young, Stephen G; Yang, Shao H; Davies, Brandon S J; Jung, Hea-Jin; Fong, Loren G

    2013-02-06

    A clinical trial of a protein farnesyltransferase inhibitor (lonafarnib) for the treatment of Hutchinson-Gilford progeria syndrome (HGPS) was recently completed. Here, we discuss the mutation that causes HGPS, the rationale for inhibiting protein farnesyltransferase, the potential limitations of this therapeutic approach, and new potential strategies for treating the disease.

  17. Dual targeting of peroxisomal proteins

    Directory of Open Access Journals (Sweden)

    Julia eAst

    2013-10-01

    Full Text Available Cellular compartmentalization into organelles serves to separate biological processes within the environment of a single cell. While some metabolic reactions are specific to a single organelle, others occur in more than one cellular compartment. Specific targeting of proteins to compartments inside of eukaryotic cells is mediated by defined sequence motifs. To achieve multiple targeting to different compartments cells use a variety of strategies. Here, we focus on mechanisms leading to dual targeting of peroxisomal proteins. In many instances, isoforms of peroxisomal proteins with distinct intracellular localization are encoded by separate genes. But also single genes can give rise to differentially localized proteins. Different isoforms can be generated by use of alternative transcriptional start sites, by differential splicing or ribosomal read-through of stop codons. In all these cases different peptide variants are produced, of which only one carries a peroxisomal targeting signal. Alternatively, peroxisomal proteins contain additional signals that compete for intracellular targeting. Dual localization of proteins residing in both the cytoplasm and in peroxisomes may also result from use of inefficient targeting signals. The recent observation that some bona fide cytoplasmic enzymes were also found in peroxisomes indicates that dual targeting of proteins to both the cytoplasm and the peroxisome might be more widespread. Although current knowledge of proteins exhibiting only partial peroxisomal targeting is far from being complete, we speculate that the metabolic capacity of peroxisomes might be larger than previously assumed.

  18. Direct electrochemistry of redox proteins.

    NARCIS (Netherlands)

    Heering, H.A.

    1995-01-01

    The goal of the project was to obtain more detailed insight in interactions between redox proteins and solid electrodes and the mechanisms of electron transfer. In addition to this, the influence of the protein environment on the redox properties of the active site and the possible influence of the

  19. Soy protein modification: A review

    Directory of Open Access Journals (Sweden)

    Barać Miroljub B.

    2004-01-01

    Full Text Available Soy protein products such as flour, concentrates and isolates are used in food formulation because of their functionality, nutritional value and low cost. To obtain their optimal nutritive and functional properties as well as desirable flavor different treatments are used. Soybean proteins can be modified by physical, chemical and enzymatic treatments. Different thermal treatments are most commonly used, while the most appropriate way of modifying soy proteins from the standpoint of safety is their limited proteolysis. These treatments cause physical and chemical changes that affect their functional properties. This review discusses three principal methods used for modification of soy protein products, their effects on dominant soy protein properties and some biologically active compounds.

  20. Structural Genomics of Protein Phosphatases

    Energy Technology Data Exchange (ETDEWEB)

    Almo,S.; Bonanno, J.; Sauder, J.; Emtage, S.; Dilorenzo, T.; Malashkevich, V.; Wasserman, S.; Swaminathan, S.; Eswaramoorthy, S.; et al

    2007-01-01

    The New York SGX Research Center for Structural Genomics (NYSGXRC) of the NIGMS Protein Structure Initiative (PSI) has applied its high-throughput X-ray crystallographic structure determination platform to systematic studies of all human protein phosphatases and protein phosphatases from biomedically-relevant pathogens. To date, the NYSGXRC has determined structures of 21 distinct protein phosphatases: 14 from human, 2 from mouse, 2 from the pathogen Toxoplasma gondii, 1 from Trypanosoma brucei, the parasite responsible for African sleeping sickness, and 2 from the principal mosquito vector of malaria in Africa, Anopheles gambiae. These structures provide insights into both normal and pathophysiologic processes, including transcriptional regulation, regulation of major signaling pathways, neural development, and type 1 diabetes. In conjunction with the contributions of other international structural genomics consortia, these efforts promise to provide an unprecedented database and materials repository for structure-guided experimental and computational discovery of inhibitors for all classes of protein phosphatases.