WorldWideScience

Sample records for gel protein database

  1. Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database

    KAUST Repository

    Komatsu, Setsuko

    2017-05-10

    The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max ‘Enrei’). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. Biological significanceThe Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all

  2. Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database.

    Science.gov (United States)

    Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

    2017-06-23

    The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max 'Enrei'). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. The Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all predicted proteins from

  3. Identifying Gel-Separated Proteins Using In-Gel Digestion, Mass Spectrometry, and Database Searching: Consider the Chemistry

    Science.gov (United States)

    Albright, Jessica C.; Dassenko, David J.; Mohamed, Essa A.; Beussman, Douglas J.

    2009-01-01

    Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is an important bioanalytical technique in drug discovery, proteomics, and research at the biology-chemistry interface. This is an especially powerful tool when combined with gel separation of proteins and database mining using the mass spectral data. Currently, few hands-on…

  4. Identifying Gel-Separated Proteins Using In-Gel Digestion, Mass Spectrometry, and Database Searching: Consider the Chemistry

    Science.gov (United States)

    Albright, Jessica C.; Dassenko, David J.; Mohamed, Essa A.; Beussman, Douglas J.

    2009-01-01

    Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is an important bioanalytical technique in drug discovery, proteomics, and research at the biology-chemistry interface. This is an especially powerful tool when combined with gel separation of proteins and database mining using the mass spectral data. Currently, few hands-on…

  5. Two dimensional gel human protein databases offer a systematic approach to the study of cell proliferation and differentiation

    DEFF Research Database (Denmark)

    Celis, J E; Gesser, B; Dejgaard, K;

    1989-01-01

    Human cellular protein databases have been established using computer-analyzed 2D gel electrophoresis. These databases, which include information on various properties of proteins, offer a global approach to the study of regulation of cell proliferation and differentiation. Furthermore, thanks...

  6. The human keratinocyte two-dimensional gel protein database (update 1995): mapping components of signal transduction pathways

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Gromov, P

    1995-01-01

    The master two-dimensional (2-D) gel database of human keratinocytes currently lists 3154 cellular proteins (2224 isoelectric focusing, IEF; and 930 nonequilibrium pH gradient electrophoresis, NEPHGE), many of which correspond to post-translational modifications. 1082 polypeptides have been ident...

  7. New algorithmic approaches to protein spot detection and pattern matching in two-dimensional electrophoresis gel databases.

    Science.gov (United States)

    Pleissner, K P; Hoffmann, F; Kriegel, K; Wenk, C; Wegner, S; Sahlström, A; Oswald, H; Alt, H; Fleck, E

    1999-01-01

    Protein spot identification in two-dimensional electrophoresis gels can be supported by the comparison of gel images accessible in different World Wide Web two-dimensional electrophoresis (2-DE) gel protein databases. The comparison may be performed either by visual cross-matching between gel images or by automatic recognition of similar protein spot patterns. A prerequisite for the automatic point pattern matching approach is the detection of protein spots yielding the x(s),y(s) coordinates and integrated spot intensities i(s). For this purpose an algorithm is developed based on a combination of hierarchical watershed transformation and feature extraction methods. This approach reduces the strong over-segmentation of spot regions normally produced by watershed transformation. Measures for the ellipticity and curvature are determined as features of spot regions. The resulting spot lists containing x(s),y(s),i(s)-triplets are calculated for a source as well as for a target gel image accessible in 2-DE gel protein databases. After spot detection a matching procedure is applied. Both the matching of a local pattern vs. a full 2-DE gel image and the global matching between full images are discussed. Preset slope and length tolerances of pattern edges serve as matching criteria. The local matching algorithm relies on a data structure derived from the incremental Delaunay triangulation of a point set and a two-step hashing technique. For the incremental construction of triangles the spot intensities are considered in decreasing order. The algorithm needs neither landmarks nor an a priori image alignment. A graphical user interface for spot detection and gel matching is written in the Java programming language for the Internet. The software package called CAROL (http://gelmatching.inf.fu-berlin.de) is realized in a client-server architecture.

  8. The master two-dimensional gel database of human AMA cell proteins: towards linking protein and genome sequence and mapping information (update 1991)

    DEFF Research Database (Denmark)

    Celis, J E; Leffers, H; Rasmussen, H H;

    1991-01-01

    The master two-dimensional gel database of human AMA cells currently lists 3801 cellular and secreted proteins, of which 371 cellular polypeptides (306 IEF; 65 NEPHGE) were added to the master images during the last 10 months. These include: (i) very basic and acidic proteins that do not focus un...

  9. Database of two-dimensional polyacrylamide gel electrophoresis of proteins labeled with CyDye DIGE Fluor saturation dye.

    Science.gov (United States)

    Fujii, Kazuyasu; Kondo, Tadashi; Yokoo, Hideki; Okano, Tetsuya; Yamada, Masayo; Yamada, Tesshi; Iwatsuki, Keiji; Hirohashi, Setsuo

    2006-03-01

    CyDye DIGE Fluor saturation dye (saturation dye, GE Healthcare Amersham Biosciences) enables highly sensitive 2-D PAGE. As the dye reacts with all reduced cysteine thiols, 2-D PAGE can be performed with a lower amount of protein, compared with CyDye DIGE Fluor minimal dye (GE Healthcare Amersham Biosciences), the sensitivity of which is equivalent to that of silver staining. We constructed a 2-D map of the saturation dye-labeled proteins of a liver cancer cell line (HepG2) and identified by MS 92 proteins corresponding to 123 protein spots. Functional classification revealed that the identified proteins had chaperone, protein binding, nucleotide binding, metal ion binding, isomerase activity, and motor activity. The functional distribution and the cysteine contents of the proteins were similar to those in the most comprehensive 2-D database of hepatoma cells (Seow et al.., Electrophoresis 2000, 21, 1787-1813), where silver staining was used for protein visualization. Hierarchical clustering on the basis of the quantitative expression profiles of the 123 characterized spots labeled with two charge- and mass-matched saturation dyes (Cy3 and Cy5) discriminated between nine hepatocellular carcinoma cell lines and primary cultured hepatocytes from five individuals, suggesting the utility of saturation dye and our database for proteomic studies of liver cancer.

  10. The human keratinocyte two-dimensional gel protein database (update 1995): mapping components of signal transduction pathways

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Gromov, P

    1995-01-01

    )vaccinia virus expression of full length cDNAs, and (vi) in vitro transcription/translation of full-length cDNAs. This year, special emphasis has been given to the identification of signal transduction components by using 2-D gel immunoblotting of crude keratinocyte lysates in combination with enhanced......--through a systematic study of ekeratinocytes--qualitative and quantitative information on proteins and their genes that may allow us to identify abnormal patterns of gene expression and to pinpoint signaling pathways and components affected in various skin diseases, cancer included. Udgivelsesdato: 1995-Dec...

  11. Comprehensive two-dimensional gel protein databases offer a global approach to the analysis of human cells: the transformed amnion cells (AMA) master database and its link to genome DNA sequence data

    DEFF Research Database (Denmark)

    Celis, J E; Gesser, B; Rasmussen, H H;

    1990-01-01

    qualitative and quantitative annotations has been established. The protein numbers in this database differ from those reported in an earlier version (Celis et al. Leukemia 1988, 2,561-602) as a result of changes in the scanning hardware. The reported information includes: percentage of total radioactivity...... recovered from the gels (based on quantitations of polypeptides labeled with a mixture of 16 14C-amino acids), protein name (including credit to investigators that aided identification), antibody against protein, cellular localization, (nuclear, 40S hnRNP, 20S snRNP U5, proteasomes, endoplasmic reticulum...

  12. A comprehensive two-dimensional gel protein database of noncultured unfractionated normal human epidermal keratinocytes: towards an integrated approach to the study of cell proliferation, differentiation and skin diseases

    DEFF Research Database (Denmark)

    Celis, J E; Madsen, Peder; Rasmussen, H H

    1991-01-01

    proteins in alphabetical order), "basal cell markers", "differentiation markers", "proteins highly up-regulated in psoriatic skin", "microsequenced proteins" and "human autoantigens". For reference, we have also included 2-D gel (isoelectric focusing) patterns of cultured normal and psoriatic keratinocytes......A two-dimensional (2-D) gel database of cellular proteins from noncultured, unfractionated normal human epidermal keratinocytes has been established. A total of 2651 [35S]methionine-labeled cellular proteins (1868 isoelectric focusing, 783 nonequilibrium pH gradient electrophoresis) were resolved...

  13. 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...

  14. Rheology and structure of milk protein gels

    NARCIS (Netherlands)

    Vliet, van T.; Lakemond, C.M.M.; Visschers, R.W.

    2004-01-01

    Recent studies on gel formation and rheology of milk gels are reviewed. A distinction is made between gels formed by aggregated casein, gels of `pure` whey proteins and gels in which both casein and whey proteins contribute to their properties. For casein' whey protein mixtures, it has been shown th

  15. Rheology and structure of milk protein gels

    NARCIS (Netherlands)

    Vliet, van T.; Lakemond, C.M.M.; Visschers, R.W.

    2004-01-01

    Recent studies on gel formation and rheology of milk gels are reviewed. A distinction is made between gels formed by aggregated casein, gels of `pure` whey proteins and gels in which both casein and whey proteins contribute to their properties. For casein' whey protein mixtures, it has been shown

  16. 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.

  17. Mapping and identification of HeLa cell proteins separated by immobilized pH-gradient two-dimensional gel electrophoresis and construction of a two-dimensional polyacrylamide gel electrophoresis database

    DEFF Research Database (Denmark)

    Shaw, AC; Rossel Larsen, M; Roepstorff, P

    1999-01-01

    improvements of two-dimensional gel electrophoresis with immobilized pH gradients (IPG) compared to isoelectric focusing with carrier ampholytes, a highly reproducible method for examining global changes in HeLa cell protein expression due to different stimuli is now available. Therefore, we have initiated...

  18. Mapping and identification of HeLa cell proteins separated by immobilized pH-gradient two-dimensional gel electrophoresis and construction of a two-dimensional polyacrylamide gel electrophoresis database

    DEFF Research Database (Denmark)

    Shaw, AC; Rossel Larsen, M; Roepstorff, P

    1999-01-01

    improvements of two-dimensional gel electrophoresis with immobilized pH gradients (IPG) compared to isoelectric focusing with carrier ampholytes, a highly reproducible method for examining global changes in HeLa cell protein expression due to different stimuli is now available. Therefore, we have initiated...

  19. Stiffening in gels containing whey protein isolate

    NARCIS (Netherlands)

    Purwanti, N.; Veen, van der E.; Goot, van der A.J.; Boom, R.M.

    2013-01-01

    Gels made only from whey protein isolate (WPI) stiffened over the first few days of storage, after which the textural properties remained nearly constant. However, protein gels containing WPI microparticles, at the same total protein content, stiffened over a longer period than those without micropa

  20. Database of Interacting Proteins (DIP)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent...

  1. Database Description - Yeast Interacting Proteins Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Yeast Interacting Proteins Database Database Description General information of database Database name Yeast... Interacting Proteins Database Alternative name - Creator Creator Name: Takashi Ito* Creator Affiliation: Di...-4-7136-3989 FAX: +81-4-7136-3979 E-mail : Database classification Metabolic and Signaling Pathways - Protei...n-protein interactions Organism Taxonomy Name: Saccharomyces cerevisiae Taxonomy ID: 4932 Database descripti...ive yeast two-hybrid analysis of budding yeast proteins. Features and manner of utilization of database Prot

  2. Maize Arabinoxylan Gels as Protein Delivery Matrices

    Directory of Open Access Journals (Sweden)

    Ana Luisa Martínez-López

    2009-04-01

    Full Text Available The laccase induced gelation of maize bran arabinoxylans at 2.5% (w/v in the presence of insulin or β-lactoglobulin at 0.1% (w/v was investigated. Insulin and β-lacto-globulin did not modify either the gel elasticity (9 Pa or the cross-links content (0.03 and 0.015 mg di- and triferulic acids/mg arabinoxylan, respectively. The protein release capability of the gel was also investigated. The rate of protein release from gels was dependent on the protein molecular weight. The apparent diffusion coefficient was 0.99 × 10-7 and 0.79 × 10-7 cm2/s for insulin (5 kDa and β-lactoglobulin (18 kDa, respectively. The results suggest that maize bran arabinoxylan gels can be potential candidates for the controlled release of proteins.

  3. The Pfam protein families database.

    Science.gov (United States)

    Finn, Robert D; Tate, John; Mistry, Jaina; Coggill, Penny C; Sammut, Stephen John; Hotz, Hans-Rudolf; Ceric, Goran; Forslund, Kristoffer; Eddy, Sean R; Sonnhammer, Erik L L; Bateman, Alex

    2008-01-01

    Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenPept and on sequences from selected metagenomics projects. Pfam is available on the web from the consortium members using a new, consistent and improved website design in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/), as well as from mirror sites in France (http://pfam.jouy.inra.fr/) and South Korea (http://pfam.ccbb.re.kr/).

  4. Update History of This Database - Yeast Interacting Proteins Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...Yeast Interacting Proteins Database Update History of This Database Date Update contents 2010/03/29 Yeast In...t This Database Database Description Download License Update History of This Database Site Policy | Contact Us Update History

  5. Power Law Behavior of Structural Properties of Protein Gels

    NARCIS (Netherlands)

    Verheul, Marleen; Roefs, Sebastianus P.F.M.; Mellema, Jorrit; Kruif, Kees G.

    1998-01-01

    Whey proteins are globular, heat-sensitive proteins. The gel structure, the formation of this structure, and the rheological properties of particulate whey protein isolate (WPI) gels have been investigated. On increasing the NaCl concentration, the permeability of the WPI gels increased, indicating

  6. The MRC-5 human embryonal lung fibroblast two-dimensional gel cellular protein database: quantitative identification of polypeptides whose relative abundance differs between quiescent, proliferating and SV40 transformed cells

    DEFF Research Database (Denmark)

    Celis, J E; Dejgaard, K; Madsen, Peder;

    1990-01-01

    (1323 with isoelectric focusing and 572 with nonequilibrium pH gradient electrophoresis) are recorded in this database, containing quantitative and qualitative data on the relative abundance of cellular proteins synthesized by quiescent, proliferating and SV40 transformed MRC-5 fibroblasts. Of the 592...... proteins quantitated so far, the levels of 138 were up- or down-regulated (51 and 87, respectively) by two times or more in the transformed cells as compared to their normal proliferating counterparts, while only 14 behaved similarly in quiescent cells. Seven MRC-5 SV40 proteins, including plastin and two...... cells (AMA) database (Celis et al., Electrophoresis 1990, 11, 989-1071) for those polypeptides of known and unknown identity that have been matched to AMA polypeptides. As more information is gathered in this and other laboratories, including data on oncogene proteins and transcription factors...

  7. Protein electrophoretic migration data from custom and commercial gradient gels

    Directory of Open Access Journals (Sweden)

    Andrew J. Miller

    2016-12-01

    Full Text Available This paper presents data related to the article “A method for easily customizable gradient gel electrophoresis” (A.J. Miller, B. Roman, E.M. Norstrom, 2016 [1]. Data is presented on the rate of electrophoretic migration of proteins in both hand-poured and commercially acquired acrylamide gradient gels. For each gel, migration of 9 polypeptides of various masses was measured upon completion of gel electrophoresis. Data are presented on the migration of proteins within separate lanes of the same gel as well as migration rates from multiple gels.

  8. Discovering and Mining Links for Protein Databases

    Directory of Open Access Journals (Sweden)

    A.Immaculate Mercy

    2014-01-01

    Full Text Available This work introduces a link analysis procedure for discovering relationships in a protein database or a relational database generalizing simple correspondence analysis. It is based on extracting the links to the rela ted protein database and malfunctioned protein database. The datasets are trained in order to find out missing interactions and the sequences related to them. Further the analysis of links proceeds by performing a random walk defining a Markov chain. The e lements of interest are analysed through stochastic complementation which gives a reduced Markov chain. This reduced map is then analysed by projecting the elements of interest through Principal component analysis. Several Protein datasets are analysed using the proposed methodology, showing the usefulness of the technique for extracting relationships in relational databases or graphs.

  9. Discovering and Mining Links for Protein Databases

    Directory of Open Access Journals (Sweden)

    A. Immaculate Mercy

    2015-10-01

    Full Text Available protein database or a relational database generalizing simple correspondence analysis. It is based on extracting the links to the related protein database and malfunctioned protein database. The datasets are trained in order to find out missing interactions and the sequences related to them. Further the analysis of links proceeds by performing a random walk defining a Markov chain. The elements of interest are analysed through stochastic complementation which gives a reduced Markov chain. This reduced map is then analysed by projecting the elements of interest through Principal component analysis. Several Protein datasets are analysed using the proposed methodology, showing the usefulness of the technique for extracting relationships in relational databases or graphs.

  10. Gelatin increases the coarseness of whey protein gels and impairs water exudation from the mixed gel at low temperatures

    NARCIS (Netherlands)

    Martin, A.H.; Bakhuizen, E.; Ersch, C.; Urbonaite, V.; Jongh, H.H.J. de; Pouvreau, L.

    2016-01-01

    To understand the origin of water holding of mixed protein gels, a study was performed on water exudation from mixed whey protein (WP)-gelatin gels upon applied pressure. Mixed gels were prepared with varying WP and gelatin concentration and gelatin type to obtain gels with a wide range of gel

  11. Gel and gel-free approaches for the quantitative characterisation of complex protein mixtures

    CSIR Research Space (South Africa)

    Buthelezi, S

    2012-10-01

    Full Text Available -dimensional gel electrophoresis (2DE gels), solution phase isoelectric focusing (IEF), offline strong cation exchange (SCX) chromatography and offline high pH reverse phase (RP) chromatography. All fractions collected from the solution-based methods were... which fractionation method between 2DE gels, solution phase IEF, SCX-RP and RP-RP results in the highest number of protein identities RESULTS When the number of protein identities in the different fractionation techniques was compared (Figure 2...

  12. Fibril Formation from Pea Protein and Sesequent Gel Formation

    NARCIS (Netherlands)

    Munialo, C.D.; Martin, A.H.; Linden, van der E.; Jongh, de H.H.J.

    2014-01-01

    The objective of this study was to characterize fibrillar aggregates made using pea proteins, to assemble formed fibrils into protein-based gels, and to study the rheological behavior of these gels. Micrometer-long fibrillar aggregates were observed after pea protein solutions had been heated for 20

  13. Fibril Formation from Pea Protein and Subsequent Gel Formation

    NARCIS (Netherlands)

    Munialo, XC.D.; Martin, A.H.; Linden, E. van der; Jongh, H.H.J de

    2014-01-01

    The objective of this study was to characterize fibrillar aggregates made using pea proteins, to assemble formed fibrils into protein-based gels, and to study the rheological behavior of these gels. Micrometer-long fibrillar aggregates were observed after pea protein solutions had been heated for 20

  14. SENTRA, a database of signal transduction proteins.

    Energy Technology Data Exchange (ETDEWEB)

    D' Souza, M.; Romine, M. F.; Maltsev, N.; Mathematics and Computer Science; PNNL

    2000-01-01

    SENTRA, available via URL http://wit.mcs.anl.gov/WIT2/Sentra/, is a database of proteins associated with microbial signal transduction. The database currently includes the classical two-component signal transduction pathway proteins and methyl-accepting chemotaxis proteins, but will be expanded to also include other classes of signal transduction systems that are modulated by phosphorylation or methylation reactions. Although the majority of database entries are from prokaryotic systems, eukaroytic proteins with bacterial-like signal transduction domains are also included. Currently SENTRA contains signal transduction proteins in 34 complete and almost completely sequenced prokaryotic genomes, as well as sequences from 243 organisms available in public databases (SWISS-PROT and EMBL). The analysis was carried out within the framework of the WIT2 system, which is designed and implemented to support genetic sequence analysis and comparative analysis of sequenced genomes.

  15. Fibril formation from pea protein and subsequent gel formation.

    Science.gov (United States)

    Munialo, Claire Darizu; Martin, Anneke H; van der Linden, Erik; de Jongh, Harmen H J

    2014-03-19

    The objective of this study was to characterize fibrillar aggregates made using pea proteins, to assemble formed fibrils into protein-based gels, and to study the rheological behavior of these gels. Micrometer-long fibrillar aggregates were observed after pea protein solutions had been heated for 20 h at pH 2.0. Following heating of pea proteins, it was observed that all of the proteins were hydrolyzed into peptides and that 50% of these peptides were assembled into fibrils. Changes on a structural level in pea proteins were studied using circular dichroism, transmission electron microscopy, and particle size analysis. During the fibril assembly process, an increase in aggregate size was observed, which coincided with an increase in thioflavin T binding, indicating the presence of β-sheet aggregates. Fibrils made using pea proteins were more branched and curly. Gel formation of preformed fibrils was induced by slow acidification from pH 7.0 to a final pH of around pH 5.0. The ability of pea protein-based fibrillar gels to fracture during an amplitude sweep was comparable to those of soy protein and whey protein-based fibrillar gels, although gels prepared from fibrils made using pea protein and soy protein were weaker than those of whey protein. The findings show that fibrils can be prepared from pea protein, which can be incorporated into protein-based fibrillar gels.

  16. Improving decoy databases for protein folding algorithms

    KAUST Repository

    Lindsey, Aaron

    2014-01-01

    Copyright © 2014 ACM. Predicting protein structures and simulating protein folding are two of the most important problems in computational biology today. Simulation methods rely on a scoring function to distinguish the native structure (the most energetically stable) from non-native structures. Decoy databases are collections of non-native structures used to test and verify these functions. We present a method to evaluate and improve the quality of decoy databases by adding novel structures and removing redundant structures. We test our approach on 17 different decoy databases of varying size and type and show significant improvement across a variety of metrics. We also test our improved databases on a popular modern scoring function and show that they contain a greater number of native-like structures than the original databases, thereby producing a more rigorous database for testing scoring functions.

  17. Annotation and retrieval in protein interaction databases

    Science.gov (United States)

    Cannataro, Mario; Hiram Guzzi, Pietro; Veltri, Pierangelo

    2014-06-01

    Biological databases have been developed with a special focus on the efficient retrieval of single records or the efficient computation of specialized bioinformatics algorithms against the overall database, such as in sequence alignment. The continuos production of biological knowledge spread on several biological databases and ontologies, such as Gene Ontology, and the availability of efficient techniques to handle such knowledge, such as annotation and semantic similarity measures, enable the development on novel bioinformatics applications that explicitly use and integrate such knowledge. After introducing the annotation process and the main semantic similarity measures, this paper shows how annotations and semantic similarity can be exploited to improve the extraction and analysis of biologically relevant data from protein interaction databases. As case studies, the paper presents two novel software tools, OntoPIN and CytoSeVis, both based on the use of Gene Ontology annotations, for the advanced querying of protein interaction databases and for the enhanced visualization of protein interaction networks.

  18. HCVpro: Hepatitis C virus protein interaction database

    KAUST Repository

    Kwofie, Samuel K.

    2011-12-01

    It is essential to catalog characterized hepatitis C virus (HCV) protein-protein interaction (PPI) data and the associated plethora of vital functional information to augment the search for therapies, vaccines and diagnostic biomarkers. In furtherance of these goals, we have developed the hepatitis C virus protein interaction database (HCVpro) by integrating manually verified hepatitis C virus-virus and virus-human protein interactions curated from literature and databases. HCVpro is a comprehensive and integrated HCV-specific knowledgebase housing consolidated information on PPIs, functional genomics and molecular data obtained from a variety of virus databases (VirHostNet, VirusMint, HCVdb and euHCVdb), and from BIND and other relevant biology repositories. HCVpro is further populated with information on hepatocellular carcinoma (HCC) related genes that are mapped onto their encoded cellular proteins. Incorporated proteins have been mapped onto Gene Ontologies, canonical pathways, Online Mendelian Inheritance in Man (OMIM) and extensively cross-referenced to other essential annotations. The database is enriched with exhaustive reviews on structure and functions of HCV proteins, current state of drug and vaccine development and links to recommended journal articles. Users can query the database using specific protein identifiers (IDs), chromosomal locations of a gene, interaction detection methods, indexed PubMed sources as well as HCVpro, BIND and VirusMint IDs. The use of HCVpro is free and the resource can be accessed via http://apps.sanbi.ac.za/hcvpro/ or http://cbrc.kaust.edu.sa/hcvpro/. © 2011 Elsevier B.V.

  19. Stimuli responsive smart-gels realized via modular protein design

    OpenAIRE

    2010-01-01

    Smart-gels have a variety of applications including tissue engineering and controlled drug delivery. Here we present a modular, bottom-up approach that permits the creation of protein-based smart-gels with encoded morphology, functionality, and responsiveness to external stimuli. The properties of these gels are encoded by the proteins from which they are synthesized. In particular, the strength and density of the network of intermolecular cross-links are specified by the interactions of the ...

  20. Human cellular protein patterns and their link to genome DNA sequence data: usefulness of two-dimensional gel electrophoresis and microsequencing

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Leffers, H;

    1991-01-01

    Analysis of cellular protein patterns by computer-aided 2-dimensional gel electrophoresis together with recent advances in protein sequence analysis have made possible the establishment of comprehensive 2-dimensional gel protein databases that may link protein and DNA information and that offer a...

  1. Rheological properties of soybean protein isolate gels containing emulsion droplets

    NARCIS (Netherlands)

    Kim, K.H.; Renkema, J.M.S.; Vliet, van T.

    2001-01-01

    Rheological properties of soybean protein gels containing various volume fractions oil droplets have been studied at small and large deformations. Dynamic viscoelastic properties of soybean protein isolate gels were determined as a function of the volume fraction of oil droplets stabilised by the sa

  2. Proteomics: Protein Identification Using Online Databases

    Science.gov (United States)

    Eurich, Chris; Fields, Peter A.; Rice, Elizabeth

    2012-01-01

    Proteomics is an emerging area of systems biology that allows simultaneous study of thousands of proteins expressed in cells, tissues, or whole organisms. We have developed this activity to enable high school or college students to explore proteomic databases using mass spectrometry data files generated from yeast proteins in a college laboratory…

  3. Proteomics: Protein Identification Using Online Databases

    Science.gov (United States)

    Eurich, Chris; Fields, Peter A.; Rice, Elizabeth

    2012-01-01

    Proteomics is an emerging area of systems biology that allows simultaneous study of thousands of proteins expressed in cells, tissues, or whole organisms. We have developed this activity to enable high school or college students to explore proteomic databases using mass spectrometry data files generated from yeast proteins in a college laboratory…

  4. Human cellular protein patterns and their link to genome DNA sequence data: usefulness of two-dimensional gel electrophoresis and microsequencing

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Leffers, H

    1991-01-01

    Analysis of cellular protein patterns by computer-aided 2-dimensional gel electrophoresis together with recent advances in protein sequence analysis have made possible the establishment of comprehensive 2-dimensional gel protein databases that may link protein and DNA information and that offer...... a global approach to the study of the cell. Using the integrated approach offered by 2-dimensional gel protein databases it is now possible to reveal phenotype specific protein (or proteins), to microsequence them, to search for homology with previously identified proteins, to clone the cDNAs, to assign...... partial protein sequence to genes for which the full DNA sequence and the chromosome location is known, and to study the regulatory properties and function of groups of proteins that are coordinately expressed in a given biological process. Human 2-dimensional gel protein databases are becoming...

  5. Western Blot of Stained Proteins from Dried Polyacrylamide Gels

    Science.gov (United States)

    Gruber, Claudia; Stan-Lotter, Helga

    1996-01-01

    Western blotting of proteins is customarily performed following their separation on polyacrylamide gels, either prior to staining (1) or, as recently reported, following staining (2). We describe here Western blotting with stained gels, which had been dried and some of which had been stored for years. This procedure permits immunological analysis of proteins, to which antisera may have become available only later, or where the application of newly developed sensitive detection methods is desired. Once rehydration of the gels is achieved, proteins can be-transferred to blotting membranes by any appropriate protocol. Proteins stained with Coomassie Blue have to be detected with a non-chromogenic method, such as the film-based enhanced chemiluminescence (ECL)2) procedure (3). Silver stained proteins, which transfer in the colorless form, may be visualized by any detection method, although, because of the usually very low amounts of proteins, detection by ECL is preferable. Blotting of stained proteins from rehydrated gels is as rapid and as quantitative as from freshly prepared gels, in contrast to blotting from wet stained gels, which requires extensive washing and results in low transfer efficiency (2). Together with a photographic record of the gel pattern, unambiguous identification of immunoreactive proteins from complex mixtures is possible. Some further applications of this work are discussed.

  6. RPG: the Ribosomal Protein Gene database

    OpenAIRE

    Nakao, Akihiro; Yoshihama, Maki; Kenmochi, Naoya

    2004-01-01

    RPG (http://ribosome.miyazaki-med.ac.jp/) is a new database that provides detailed information about ribosomal protein (RP) genes. It contains data from humans and other organisms, including Drosophila melanogaster, Caenorhabditis elegans, Saccharo myces cerevisiae, Methanococcus jannaschii and Escherichia coli. Users can search the database by gene name and organism. Each record includes sequences (genomic, cDNA and amino acid sequences), intron/exon structures, genomic locations and informa...

  7. Sentra, a database of signal transduction proteins.

    Energy Technology Data Exchange (ETDEWEB)

    Maltsev, N.; Marland, E.; Yu, G. X.; Bhatnagar, S.; Lusk, R.; Mathematics and Computer Science

    2002-01-01

    Sentra (http://www-wit.mcs.anl.gov/sentra) is a database of signal transduction proteins with the emphasis on microbial signal transduction. The database was updated to include classes of signal transduction systems modulated by either phosphorylation or methylation reactions such as PAS proteins and serine/threonine kinases, as well as the classical two-component histidine kinases and methyl-accepting chemotaxis proteins. Currently, Sentra contains signal transduction proteins from 43 completely sequenced prokaryotic genomes as well as sequences from SWISS-PROT and TrEMBL. Signal transduction proteins are annotated with information describing conserved domains, paralogous and orthologous sequences, and conserved chromosomal gene clusters. The newly developed user interface supports flexible search capabilities and extensive visualization of the data.

  8. Gel table - RPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available hod experiment Data analysis method Proteins were extracted from organs or organelle of rice at various growing...Tissue ID ID of the 2D-PAGE image. Tissue type Type of organ column. tissue: growing

  9. Alkali cold gelation of whey proteins. Part I: sol-gel-sol(-gel) transitions.

    Science.gov (United States)

    Mercadé-Prieto, Ruben; Gunasekaran, Sundaram

    2009-05-19

    The cold gelation of preheated whey protein isolate (WPI) solutions at alkaline conditions (pH>10) has been studied to better understand the effect of NaOH in the formation and destruction of whey protein aggregates and gels. Oscillatory rheology has been used to follow the gelation process, resulting in novel and different gelation profiles with the gelation pH. At low alkaline pH, typical sol-gel transitions are observed, as in many other biopolymers. At pH>11.5, the system gels quickly, after approximately 300 s, followed by a slow degelation step that transforms the gel to a viscous solution. Finally, there is a second gelation step. This results in a surprising sol-gel-sol-gel transition in time at constant gelation conditions. At very high pH (>12.5), the degelation step is very severe, and the second gelation step is not observed, resulting in a sol-gel-sol transition. The first quick gelation step is related to the quick swelling of the WPI aggregates in alkali, as observed from light scattering, which enables the formation of new noncovalent interactions to form a gel network. These interactions are argued to be destroyed in the subsequent degelation step. Disulfide cross-linking is observed only in the second gelation step, not in the first step.

  10. Whey protein particles modulate mechanical properties of gels at high protein concentrations

    NARCIS (Netherlands)

    Saglam, D.; Venema, P.; Vries, de R.J.; Berg, van den L.; Linden, van der E.

    2014-01-01

    We have studied the influence of dense whey protein particles on the mechanical properties of whey protein isolate (WPI) gels at high protein concentrations (16–22% (w/w)). Incorporation of dense whey protein particles in the gel, while keeping the total protein concentration constant, leads to a co

  11. Gene and protein nomenclature in public databases

    Directory of Open Access Journals (Sweden)

    Zimmer Ralf

    2006-08-01

    Full Text Available Abstract Background Frequently, several alternative names are in use for biological objects such as genes and proteins. Applications like manual literature search, automated text-mining, named entity identification, gene/protein annotation, and linking of knowledge from different information sources require the knowledge of all used names referring to a given gene or protein. Various organism-specific or general public databases aim at organizing knowledge about genes and proteins. These databases can be used for deriving gene and protein name dictionaries. So far, little is known about the differences between databases in terms of size, ambiguities and overlap. Results We compiled five gene and protein name dictionaries for each of the five model organisms (yeast, fly, mouse, rat, and human from different organism-specific and general public databases. We analyzed the degree of ambiguity of gene and protein names within and between dictionaries, to a lexicon of common English words and domain-related non-gene terms, and we compared different data sources in terms of size of extracted dictionaries and overlap of synonyms between those. The study shows that the number of genes/proteins and synonyms covered in individual databases varies significantly for a given organism, and that the degree of ambiguity of synonyms varies significantly between different organisms. Furthermore, it shows that, despite considerable efforts of co-curation, the overlap of synonyms in different data sources is rather moderate and that the degree of ambiguity of gene names with common English words and domain-related non-gene terms varies depending on the considered organism. Conclusion In conclusion, these results indicate that the combination of data contained in different databases allows the generation of gene and protein name dictionaries that contain significantly more used names than dictionaries obtained from individual data sources. Furthermore, curation of

  12. Using Gel Electrophoresis To Illustrate Protein Diversity and Isoelectric Point.

    Science.gov (United States)

    Browning, Mark; Vanable, Joseph

    2002-01-01

    Demonstrates the differences in protein structures by focusing on isoelectric point with an experiment that is observable under certain pH levels in gel electrophoresis. Explains the electrophoresis procedure and reports results of the experiments. (YDS)

  13. Blotting protein complexes from native gels to electron microscopy grids.

    Science.gov (United States)

    Knispel, Roland Wilhelm; Kofler, Christine; Boicu, Marius; Baumeister, Wolfgang; Nickell, Stephan

    2012-01-08

    We report a simple and generic method for the direct transfer of protein complexes separated by native gel electrophoresis to electron microscopy grids. After transfer, sufficient material remains in the gel for identification and characterization by mass spectrometry. The method should facilitate higher-throughput single-particle analysis by substantially reducing the time needed for protein purification, as demonstrated for three complexes from Thermoplasma acidophilum.

  14. Interleukin-1beta induced changes in the protein expression of rat islets: a computerized database

    DEFF Research Database (Denmark)

    Andersen, H U; Fey, S J; Larsen, Peter Mose

    1997-01-01

    Insulin-dependent diabetes mellitus is caused by an autoimmune destruction of the beta-cells in the islets of Langerhans. The cytokine interleukin 1 inhibits insulin release and is selectively cytotoxic to beta-cells in isolated pancreatic rat islets. The antigen(s) triggering the immune response...... as well as the intracellular mechanisms of action of interleukin 1-mediated beta-cell cytotoxicity are unknown. However, previous studies have found an association of beta-cell destruction with alterations in protein synthesis. Thus, two-dimensional (2-D) gel electrophoresis of pancreatic islet proteins......% of %IOD was 45.7% in the NEPHGE gels. Addition of interleukin-1beta (IL-1beta) to the cultures resulted in statistically significant modulation or de novo synthesis of 105 proteins in the 10% gels. In conclusion, we present the first 10% and 15% acrylamide 2-D gel protein databases of neonatal rat islets...

  15. Creep and Fracture of a Protein Gel under Stress

    Science.gov (United States)

    Leocmach, Mathieu; Perge, Christophe; Divoux, Thibaut; Manneville, Sébastien

    2014-07-01

    Biomaterials such as protein or polysaccharide gels are known to behave qualitatively as soft solids and to rupture under an external load. Combining optical and ultrasonic imaging to shear rheology we show that the failure scenario of a protein gel is reminiscent of brittle solids: after a primary creep regime characterized by a power-law behavior whose exponent is fully accounted for by linear viscoelasticity, fractures nucleate and grow logarithmically perpendicularly to shear, up to the sudden rupture of the gel. A single equation accounting for those two successive processes nicely captures the full rheological response. The failure time follows a decreasing power law with the applied shear stress, similar to the Basquin law of fatigue for solids. These results are in excellent agreement with recent fiber-bundle models that include damage accumulation on elastic fibers and exemplify protein gels as model, brittlelike soft solids.

  16. Responsive Gel-Gel Phase Transitions in Artificially Engineered Protein Hydrogels

    Science.gov (United States)

    Olsen, B. D.

    2012-02-01

    Artificially engineered protein hydrogels provide an attractive platform for biomedical materials due to their similarity to components of the native extracellular matrix. Engineering responsive transitions between shear-thinning and tough gel phases in these materials could potentially enable gels that are both shear-thinning and tough to be produced as novel injectable biomaterials. To engineer a gel with such transitions, a triblock copolymer with thermoresponsive polymer endblocks and an artificially engineered protein gel midblock is designed. Temperature is used to trigger a transition from a single network protein hydrogel phase to a double network phase with both protein and block copolymer networks present at different length scales. The thermodynamics of network formation and resulting structural changes are established using small-angle scattering, birefringence, and dynamic scanning calorimetry. The formation of the second network is shown to produce a large, nonlinear increase in the elastic modulus as well as enhancements in creep compliance and toughness. Although the gels show yielding behavior in both the single and double network regimes, a qualitative change in the deformation mechanism is observed due to the structural changes.

  17. Database of osmoregulated proteins in mammalian cells.

    Science.gov (United States)

    Grady, Cameron R; Knepper, Mark A; Burg, Maurice B; Ferraris, Joan D

    2014-10-28

    Biological information, even in highly specialized fields, is increasing at a volume that no single investigator can assimilate. The existence of this vast knowledge base creates the need for specialized computer databases to store and selectively sort the information. We have developed a manually curated database of the effects of hypertonicity on target proteins. Effects include changes in mRNA abundance and protein abundance, activity, phosphorylation state, binding, and cellular compartment. The biological information used in this database was derived from three research approaches: transcriptomic, proteomic, and reductionist (hypothesis-driven). The data are presented in the form of grammatical triplets consisting of subject, verb phrase, and object. The purpose of this format is to allow the data to be read from left to right as an English sentence. It is readable either by humans or by computers using natural language processing algorithms. An example of a data entry reads "Hypertonicity increases activity of ABL1 in HEK293." This database was created to provide access to a wealth of information on the effects of hypertonicity in a format that can be selectively sorted. Published 2014. This article is a U.S. Government work and is in the public domain in the USA. Physiological Reports published by Wiley Periodicals, Inc. on behalf of The Physiological Society and the American Physiological Society.

  18. A Biophysical Analysis of the Ocr Protein Gel

    OpenAIRE

    Higham, Richard G

    2007-01-01

    Ocr is unusual among proteins in its ability to form a transparent gel at high ammonium sulphate concentrations. This transition was investigated using a combination of spectroscopic, microscopic and rheological techniques. It occurs sharply at a concentration of 3.2M ammonium sulphate and is not observed with other types of salt. Rheological measurements showed that rather than precipitating under such conditions, ocr forms a weak viscoelastic gel. Far UV circular dichroism sp...

  19. Database for protein adsorption: update on developments

    Science.gov (United States)

    Paszek, Ewa; Vasina, Elena N.; Nicolau, Dan V.

    2008-12-01

    Protein adsorption at solid-liquid interfaces is critical to many applications, including biomaterials, protein microarrays and lab-on-a-chip devices. Despite this general interest, and a large amount of research in the last half a century, protein adsorption cannot be predicted with an engineering level, design-orientated accuracy. Here we describe a Biomolecular Adsorption Database (BAD), freely available online, which archives the published protein adsorption data. Piecewise linear regression with breakpoint applied to the data in the BAD suggests that the input variables to protein adsorption, i.e., protein concentration in solution; protein descriptors derived from primary structure (number of residues, protein hydrophobicity and spread of amino acid hydrophobicity, isoelectric point); surface descriptors (contact angle); and fluid environment descriptors (pH, ionic strength), correlate well with the output variable - the protein concentration on the surface. Furthermore, neural network analysis revealed that the size of the BAD makes it sufficiently representative, with a neural network-based predictive error of 5% or less. Interestingly, a consistently better fit is obtained if the BAD is divided into two separate subsets representing protein adsorption on hydrophilic and hydrophobic surfaces. Based on these findings, selected entries from the BAD have been used to construct neural network-based estimation routines, which predict the amount of adsorbed protein, the thickness of the absorbed layer and the surface tension of the proteincovered surface. While the BAD is of general interest, the prediction of the thickness and the surface tension of the protein-covered layers are of particular relevance to the design of microfluidics devices.

  20. Heat-induced whey protein gels: protein-protein interactions and functional properties.

    Science.gov (United States)

    Havea, Palatasa; Watkinson, Philip; Kuhn-Sherlock, Barbara

    2009-02-25

    Heat-induced gelation (80 degrees C for 30 min or 85 degrees C for 60 min) of whey protein concentrate (WPC) solutions was studied using small deformation dynamic rheology, small and large deformation compression, and polyacrylamide gel electrophoresis (PAGE). The WPC solutions (15% w/w, pH 6.9) were prepared by dispersing WPC powder in water (control), 1% (w/w) sodium dodecyl sulfate (SDS) solution, and N-ethylmaleimide (NEM) solution at a protein/NEM molar ratio of 1:1 or in 10 mM dithiothreitol (DTT) solution. PAGE analyses showed that the heat treatment of control solutions contained both disulfide and non-covalent linkages between denatured protein molecules. Only disulfide linkages were formed in heated SDS-WPC solutions, whereas only non-covalent linkages were formed in DTT-WPC and NEM-WPC solutions during heating. In heated NEM-WPC solutions, the pre-existing disulfide linkages remained unaltered. Small deformation rheology measurements showed that the storage modulus (G') values, compared with those of the control WPC gels (approximately 14000 Pa), were 3 times less for the SDS-WPC gels (approximately 4000 Pa), double for the NEM-WPC gels (approximately 24000 Pa), and even higher for the DTT-WPC gels (approximately 30000 Pa). Compression tests suggested that the rubberiness (fracture strain) of the WPC gels increased as the degree of disulfide linkages within the gels increased, whereas the stiffness (modulus) of the gels increased as the degree of non-covalent associations among the denatured protein molecules increased.

  1. RPG: the Ribosomal Protein Gene database.

    Science.gov (United States)

    Nakao, Akihiro; Yoshihama, Maki; Kenmochi, Naoya

    2004-01-01

    RPG (http://ribosome.miyazaki-med.ac.jp/) is a new database that provides detailed information about ribosomal protein (RP) genes. It contains data from humans and other organisms, including Drosophila melanogaster, Caenorhabditis elegans, Saccharo myces cerevisiae, Methanococcus jannaschii and Escherichia coli. Users can search the database by gene name and organism. Each record includes sequences (genomic, cDNA and amino acid sequences), intron/exon structures, genomic locations and information about orthologs. In addition, users can view and compare the gene structures of the above organisms and make multiple amino acid sequence alignments. RPG also provides information on small nucleolar RNAs (snoRNAs) that are encoded in the introns of RP genes.

  2. Crystal growth of proteins, nucleic acids, and viruses in gels.

    Science.gov (United States)

    Lorber, Bernard; Sauter, Claude; Théobald-Dietrich, Anne; Moreno, Abel; Schellenberger, Pascale; Robert, Marie-Claire; Capelle, Bernard; Sanglier, Sarah; Potier, Noëlle; Giegé, Richard

    2009-11-01

    Medium-sized single crystals with perfect habits and no defect producing intense and well-resolved diffraction patterns are the dream of every protein crystallographer. Crystals of biological macromolecules possessing these characteristics can be prepared within a medium in which mass transport is restricted to diffusion. Chemical gels (like polysiloxane) and physical gels (such as agarose) provide such an environment and are therefore suitable for the crystallisation of biological macromolecules. Instructions for the preparation of each type of gel are given to urge crystal growers to apply diffusive media for enhancing crystallographic quality of their crystals. Examples of quality enhancement achieved with silica and agarose gels are given. Results obtained with other substances forming gel-like media (such as lipidic phases and cellulose derivatives) are presented. Finally, the use of gels in combination with capillary tubes for counter-diffusion experiments is discussed. Methods and techniques implemented with proteins can also be applied to nucleic acids and nucleoprotein assemblies such as viruses.

  3. Comparative fluorescence two-dimensional gel electrophoresis using a gel strip sandwich assembly for the simultaneous on-gel generation of a reference protein spot grid.

    Science.gov (United States)

    Ackermann, Doreen; Wang, Weiqun; Streipert, Benjamin; Geib, Birgit; Grün, Lothar; König, Simone

    2012-05-01

    The comparison of proteins separated on 2DE is difficult due to gel-to-gel variability. Here, a method named comparative fluorescence gel electrophoresis (CoFGE) is presented, which allows the generation of an artificial protein grid in parallel to the separation of an analytical sample on the same gel. Different fluorescent stains are used to distinguish sample and marker on the gel. The technology combines elements of 1DE and 2DE. Special gel combs with V-shaped wells are placed in a stacking gel above the pI strip. Proteins separated on the pI strip are electrophoresed at the same time as marker proteins (commercially available purified protein of different molecular weight) placed in V-wells. In that way, grids providing approximately 100 nodes as landmarks for the determination of protein spot coordinates are generated. Data analysis is possible with commercial 2DE software capable of warping. The method improves comparability of 2DE protein gels, because they are generated in combination with regular in-gel anchor points formed by protein standards. This was shown here for two comparative experiments with three gels each using Escherichia coli lysate. For a set of 47 well-defined samples spots, the deviation of the coordinates was improved from 7% to less than 1% applying warping using the marker grid. Conclusively, as long as the same protein markers, the same size of pI-strips and the same technology are used, gel matching is reproducibly possible. This is an important advancement for projects involving comparison of 2DE-gels produced over several years and in different laboratories. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Full Data of Yeast Interacting Proteins Database (Annotation Updated Version) - Yeast Interacting Proteins Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available st proteins and their interactions are required. Several sources including YPD (Yeast Proteome Database, Cos...ome database (WormPD): comprehensive resources for the organization and comparison of model organism protein

  5. A Brief Review of RNA-Protein Interaction Database Resources

    Directory of Open Access Journals (Sweden)

    Ying Yi

    2017-01-01

    Full Text Available RNA-protein interactions play critical roles in various biological processes. By collecting and analyzing the RNA-protein interactions and binding sites from experiments and predictions, RNA-protein interaction databases have become an essential resource for the exploration of the transcriptional and post-transcriptional regulatory network. Here, we briefly review several widely used RNA-protein interaction database resources developed in recent years to provide a guide of these databases. The content and major functions in databases are presented. The brief description of database helps users to quickly choose the database containing information they interested. In short, these RNA-protein interaction database resources are continually updated, but the current state shows the efforts to identify and analyze the large amount of RNA-protein interactions.

  6. Protein interactions with nanoporous sol-gel derived bioactive glasses.

    Science.gov (United States)

    Lin, Sen; Van den Bergh, Wouter; Baker, Simon; Jones, Julian R

    2011-10-01

    Sol-gel derived bioactive glasses are excellent candidates for bone regenerative implant materials as they bond with bone, stimulate bone growth and degrade in the body. Their interactions with proteins are critical to understanding their performance after implantation. This study focuses on the interactions between fibrinogen and sol-gel glass particles of the 70S30C (70 mol.% SiO(2), 30 mol.% CaO composition). Sol-gel silica and melt-derived Bioglass® were also used for comparison. Fibrinogen penetration into the nanoporous glasses was observed by live tracking the fluorescent-labelled fibrinogen with confocal microscopy. The effect of pore size on protein penetration was investigated. Nanoporous networks with modal pore diameters larger than 6 nm were accessible to fibrinogen. When the modal nanopore diameter was decreased to 2 nm or less, the penetration of fibrinogen was inhibited. The surface properties of the glasses, which can be modulated by media pH, glass composition and final stabilisation temperature in the sol-gel process, have effects on fibrinogen adsorption via long-range Coulombic forces before the adsorption and via short-range interactions such as hydrogen bonding after the adsorption.

  7. Influence of pre-cooking protein paste gelation conditions and post-cooking gel storage conditions on gel texture.

    Science.gov (United States)

    Paker, Ilgin; Matak, Kristen E

    2016-01-15

    Gelation conditions affect the setting of myofibrillar fish protein gels. Therefore the impact of widely applied pre-cooking gelation time/temperature strategies and post-cooking period on the texture and color of final protein gels was determined. Four pre-cooking gelation strategies (no setting time, 30 min at 25 °C, 1 h at 40 °C or 24 h at 4 °C) were applied to protein pastes (fish protein concentrate and standard functional additives). After cooking, texture and color were analyzed either directly or after 24 h at 4 °C on gels adjusted to 25 °C. No-set gels were harder, gummier and chewier (P gelation strategy. Pre-cooking gelation conditions will affect final protein gel texture and color, with gel stability benefiting from a gel-setting period. However, post-cooking storage may have a greater impact on final gels, with textural attributes becoming more consistent between all samples. © 2015 Society of Chemical Industry.

  8. Digestion of protein and protein gels in simulated gastric environment

    NARCIS (Netherlands)

    Luo, Q.; Boom, R.M.; Janssen, A.E.M.

    2015-01-01

    Despite the increasing attention to food digestion research, food scientists still need to better understand the underlying mechanisms of digestion. Most in vitro studies on protein digestion are based on experiments with protein solutions. In this study, the digestion of egg white protein and whey

  9. Separation and sequencing of familiar and novel murine proteins using preparative two-dimensional gel electrophoresis.

    Science.gov (United States)

    Merrick, B A; Patterson, R M; Witcher, L L; He, C; Selkirk, J K

    1994-05-01

    Strategies are needed for rapid protein isolation in order to identify disease-related proteins and facilitate the design of oligonucleotides for further molecular inquiry. In our laboratory, C3H10T1/2 murine fibroblasts have been found to express a variety of proteins in various subcellular fractions which are relevant to experimental transformation and carcinogenesis. Preparative two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) procedures were developed to identify major cytoplasmic proteins by electroblotting and microsequencing. Isoelectric focusing tube gels were enlarged to 6 mm ID to accommodate larger protein loads at 0.5 to 2 mg protein. Separated proteins were electrotransferred from 6 mm thick slab gels onto 0.22 mu polyvinylidene difluoride membranes. Nearly 100 prominent blotted proteins were stained with Coomassie Brilliant Blue between pI 4.5-7.0 and 18-106 kDa and, of these, 27 prominent and well-resolved proteins were selected for sequencing. Sequences of 14 to 24 amino acid residues in length were obtained from 11 proteins which were identified from computerized databases. Some of these identified proteins had structural or enzymatic functions while others had only recently been discovered, including a newly reported Hsp 70 class member and a novel calcium-binding protein, reticulocalbin. The new heat shock protein has a molecular mass of 75 kDa and has been designated as Grp75, PBP74, CSA or p66mot-1 in mice and humans with purported roles in transformation and antigen processing. Reticulocalbin is an endoplasmic reticular protein which contains six domains of the EF-hand motif associated with high-affinity calcium-binding proteins. It may be involved in protein transport and luminal protein processing. In addition, sequences of 5 to 11 residues in length were also obtained from six other unidentified proteins. Thus, we have found that preparative 2-D PAGE serves as a powerful one-step purification method for protein isolation and

  10. Protein Beverage vs. Protein Gel on Appetite Control and Subsequent Food Intake in Healthy Adults

    Directory of Open Access Journals (Sweden)

    Sha Zhang

    2015-10-01

    Full Text Available The objective of this study was to compare the effects of food form and physicochemical properties of protein snacks on appetite and subsequent food intake in healthy adults. Twelve healthy subjects received a standardized breakfast and then 2.5 h post-breakfast consumed the following snacks, in randomized order: 0 kcal water (CON or 96 kcal whey protein snacks as beverages with a pH of either 3.0 (Bev-3.0 or 7.0 (Bev-7.0 or gels as acid (Gel-Acid or heated (Gel-Heated. In-vitro study showed that Bev-3.0 was more resistant to digestion than Bev-7.0, while Gel-Acid and Gel-Heated had similar digestion pattern. Appetite questionnaires were completed every 20 min until an ad libitum lunch was provided. Post-snack hunger, desire to eat, and prospective food consumption were lower following the beverages and gels vs. CON (all, p < 0.05, and post-snack fullness was greater following the snacks (except for the Bev-3.0 vs. CON (all, p < 0.05. Gel-Heated treatment led to lower prospective food consumption vs. Bev-3.0; however, no other differences were detected. Although all snacks reduced energy intake vs. CON, no differences were observed among treatments. This study suggested that whey protein in either liquid or solid form improves appetite, but the physicochemical property of protein has a minimal effect.

  11. Viscoelastic Characterization of Gels at Metal-Protein Interfaces

    Science.gov (United States)

    Martin, Elizabeth; Shull, Kenneth

    2015-03-01

    The interfacial gelation of proteins at metallic surfaces was investigated with an electrochemical quartz crystal microbalance (QCM). When Cr electrodes were corroded in proteinaceous solutions, it was found that gels will form at the Cr surfaces if molybdate ions are also present in the solution. A similar film will form on Cr when the proteins are replaced with a poly(allylamine) polyelectrolyte, suggesting that the gelation is due to a cross-linking reaction between the protein amine groups and the molybdate ions. Further, a method was developed to characterize the viscoelastic properties of thin polymeric films in liquid media using the QCM as a high frequency rheometer. By measuring the frequency and dissipation at multiple harmonics of the resonant frequency, the viscoelastic phase angle, density --modulus product, and mass per unit area of a film can be determined. The method was applied to characterize the protein films, demonstrating that they have a phase angle near 80° and a density --modulus product of ~107 Pa-g/cm3. Data imply that the gels are comprised of a weak proteinaceous network and exhibit similar mechanical properties as solutions containing 50 wt% protein. This project was funded by NSF Grant CMMI-1200529.

  12. MIPS: a database for genomes and protein sequences.

    Science.gov (United States)

    Mewes, H W; Frishman, D; Güldener, U; Mannhaupt, G; Mayer, K; Mokrejs, M; Morgenstern, B; Münsterkötter, M; Rudd, S; Weil, B

    2002-01-01

    The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) continues to provide genome-related information in a systematic way. MIPS supports both national and European sequencing and functional analysis projects, develops and maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences, and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the databases for the comprehensive set of genomes (PEDANT genomes), the database of annotated human EST clusters (HIB), the database of complete cDNAs from the DHGP (German Human Genome Project), as well as the project specific databases for the GABI (Genome Analysis in Plants) and HNB (Helmholtz-Netzwerk Bioinformatik) networks. The Arabidospsis thaliana database (MATDB), the database of mitochondrial proteins (MITOP) and our contribution to the PIR International Protein Sequence Database have been described elsewhere [Schoof et al. (2002) Nucleic Acids Res., 30, 91-93; Scharfe et al. (2000) Nucleic Acids Res., 28, 155-158; Barker et al. (2001) Nucleic Acids Res., 29, 29-32]. All databases described, the protein analysis tools provided and the detailed descriptions of our projects can be accessed through the MIPS World Wide Web server (http://mips.gsf.de).

  13. PSSARD: protein sequence-structure analysis relational database.

    Science.gov (United States)

    Guruprasad, Kunchur; Srikanth, K; Babu, A V N

    2005-09-15

    We have implemented a relational database comprising a representative dataset of amino acid sequences and their associated secondary structure. The representative amino acid sequences were selected according to the PDB_SELECT program by choosing proteins corresponding to protein crystal structure data deposited in the protein data bank that share less than 25% overall pair-wise sequence identity. The secondary structure was extracted from the protein data bank website. The information content in the database includes the protein description, PDB code, crystal structure resolution, total number of amino acid residues in the protein chain, amino acid sequence, secondary structure conformation and its summary. The database is freely accessible from the website mentioned below and is useful to query on any of the above fields. The database is particularly useful to quickly retrieve amino acid sequences that are compatible to any super-secondary structure conformation from several proteins simultaneously.

  14. Physicochemical and structural properties of composite gels prepared with myofibrillar protein and lard diacylglycerols.

    Science.gov (United States)

    Diao, Xiaoqin; Guan, Haining; Zhao, Xinxin; Diao, Xinping; Kong, Baohua

    2016-11-01

    The objective of this study was to investigate the physicochemical and structural properties of composite gels prepared with porcine myofibrillar protein (MP) and lard, glycerolized lard (GL) or purified glycerolized lard (PGL). The gels prepared with MP and GL or PGL had significantly higher penetration force and water-holding capacity (WHC) than the gel with lard (Pgel, T21 and T22 of the gels that were prepared with GL or PGL moved in the direction of slower relaxation time, which suggests that the water mobility in the gel system was restricted. The presence of lard, GL and PGL did not affect the participating proteins in composite gels. The presence of GL and PGL altered the secondary and tertiary structures of MP in composite gels, which changed the gel properties. In general, the composite gels that were prepared with MP and GL or PGL showed improved gel quality.

  15. Structure and rheological properties of acid-induced egg white protein gels

    NARCIS (Netherlands)

    Weijers, M.; Velde, van de F.; Stijnman, A.; Pijpekamp, van de A.; Visschers, R.W.

    2006-01-01

    This study compares the rheological properties of acid-induced gels prepared of industrial spray-dried egg white proteins (EWP) with the acid-induced gels prepared of ovalbumin (OA) and whey protein isolate (WPI). Also we aimed to form transparent gels of EWP by means of the cold-gelation process. W

  16. PHProteomicDB: A Module for Two-dimensional Gel Electrophoresis Database Creation on Personal Web Sites

    Institute of Scientific and Technical Information of China (English)

    Pascal Pernet; Arnaud Bruneel; Bruno Baudin; Michel Vaubourdolle

    2006-01-01

    PHProteomicDB is a PHP-written module to help researchers in proteomics to share two-dimensional gel electrophoresis data using personal web sites. No technical or PHP knowledge is necessary except a few basics about web site management. PHProteomicDB has a user-friendly administration interface to enter and update data. It creates web pages on the fly displaying gel characteristics,gel pictures, and numbered gel spots with their related identifications pointing to their reference pages in protein databanks. The module is freely available at http://www.huvec.com/index.php3?rub=Download.

  17. Protein Beverage vs. Protein Gel on Appetite Control and Subsequent Food Intake in Healthy Adults.

    Science.gov (United States)

    Zhang, Sha; Leidy, Heather J; Vardhanabhuti, Bongkosh

    2015-10-21

    The objective of this study was to compare the effects of food form and physicochemical properties of protein snacks on appetite and subsequent food intake in healthy adults. Twelve healthy subjects received a standardized breakfast and then 2.5 h post-breakfast consumed the following snacks, in randomized order: 0 kcal water (CON) or 96 kcal whey protein snacks as beverages with a pH of either 3.0 (Bev-3.0) or 7.0 (Bev-7.0) or gels as acid (Gel-Acid) or heated (Gel-Heated). In-vitro study showed that Bev-3.0 was more resistant to digestion than Bev-7.0, while Gel-Acid and Gel-Heated had similar digestion pattern. Appetite questionnaires were completed every 20 min until an ad libitum lunch was provided. Post-snack hunger, desire to eat, and prospective food consumption were lower following the beverages and gels vs. CON (all, p intake vs. CON, no differences were observed among treatments. This study suggested that whey protein in either liquid or solid form improves appetite, but the physicochemical property of protein has a minimal effect.

  18. Salivary proteins and early childhood caries: A gel electrophoretic analysis

    Directory of Open Access Journals (Sweden)

    Sumati Bhalla

    2010-01-01

    Full Text Available Background: Early childhood caries (ECC is a common disease process that afflicts a large proportion of the child population worldwide. Extensive research in past indicates that it is the result of bacterial infection, also influenced by host and dietary factors. Current caries research seeks to identify risk factors as well as natural oral defenses that may protect against or prevent caries development. Saliva, in spite of being the strongest defense system, still has a wide array of properties and proteins whose role is yet not clearly known. Aim: To compare the resting human whole salivary characteristics in children with ECC and those who are caries free. Settings and Design: The study was conducted over a period of 9 months in 4- to 6-year-old 100 children comprising two groups - 50 with ECC and 50 caries free. Materials and Methods: The whole salivary flow rate, pH, mean protein concentration, and the electrophoretic profile of salivary proteins by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE were compared among both groups. Statistical Analysis: The SPSS (version 11.0 software package was used to conduct the chi-square, Fisher′s exact and Pearson′s chi-square tests to compare the data. Results: On gel electrophoresis, there was a significant difference among both groups with caries-free subjects having a higher number of proline-rich protein bands, substantiating the protective role of this protein. A significantly higher number of glycoprotein bands were observed in the whole saliva of subjects with ECC. A significant inverse correlation between the mean protein concentration and the whole salivary flow rate was observed in both groups.

  19. Meta-analysis of pulsed-field gel electrophoresis fingerprints based on a constructed Salmonella database.

    Directory of Open Access Journals (Sweden)

    Wen Zou

    Full Text Available A database was constructed consisting of 45,923 Salmonella pulsed-field gel electrophoresis (PFGE patterns. The patterns, randomly selected from all submissions to CDC PulseNet during 2005 to 2010, included the 20 most frequent serotypes and 12 less frequent serotypes. Meta-analysis was applied to all of the PFGE patterns in the database. In the range of 20 to 1100 kb, serotype Enteritidis averaged the fewest bands at 12 bands and Paratyphi A the most with 19, with most serotypes in the 13-15 range among the 32 serptypes. The 10 most frequent bands for each of the 32 serotypes were sorted and distinguished, and the results were in concordance with those from distance matrix and two-way hierarchical cluster analyses of the patterns in the database. The hierarchical cluster analysis divided the 32 serotypes into three major groups according to dissimilarity measures, and revealed for the first time the similarities among the PFGE patterns of serotype Saintpaul to serotypes Typhimurium, Typhimurium var. 5-, and I 4,[5],12:i:-; of serotype Hadar to serotype Infantis; and of serotype Muenchen to serotype Newport. The results of the meta-analysis indicated that the pattern similarities/dissimilarities determined the serotype discrimination of PFGE method, and that the possible PFGE markers may have utility for serotype identification. The presence of distinct, serotype specific patterns may provide useful information to aid in the distribution of serotypes in the population and potentially reduce the need for laborious analyses, such as traditional serotyping.

  20. Water holding as determinant for the elastically stored energy in protein-based gels

    NARCIS (Netherlands)

    Pouvreau, L.A.M.; Wijlen, van Emke; Klok, Jan; Urbonaite, V.; Munialo, C.D.; Jongh, de H.H.J.

    2016-01-01

    To evaluate the importance of the water holding capacity for the elastically stored energy of protein gels, a range of gels were created from proteins from different origin (plant: pea and soy proteins, and animal: whey, blood plasma, egg white proteins, and ovalbumin) varying in network morphology

  1. Analysis of proteins in the extracellular matrix of the plant pathogenic fungus Bipolaris sorokiniana using 2-D gel electrophoresis and MS/MS.

    Science.gov (United States)

    Apoga, D; Ek, B; Tunlid, A

    2001-04-13

    A method was developed for isolating and sequencing proteins present in the extracellular matrix (ECM) of germlings and hyphae of filamentous fungi. Surface proteins of the cereal pathogen Bipolaris sorokiniana were labelled with a membrane impermeable biotinylating agent and extracted using a glycine-HCl buffer. Extracted proteins were purified by affinity binding to streptavidin-conjugated magnetic beads or by two-dimensional gel electrophoresis. Four of the biotinylated proteins from the ECM of B. sorokiniana were isolated, in gel digested with trypsin and partly sequenced by tandem mass spectrometry. No significant sequence similarities to proteins in databases were obtained.

  2. The PIR integrated protein databases and data retrieval system

    Directory of Open Access Journals (Sweden)

    H Huang

    2006-01-01

    Full Text Available The Protein Information Resource (PIR provides many databases and tools to support genomic and proteomic research. PIR is a member of UniProt—Universal Protein Resource—the central repository of protein sequence and function, which maintains UniProt Knowledgebase with extensively curated annotation, UniProt Reference databases to speed sequence searches, and UniProt Archive to reflect sequence history. PIR also provides PIRSF family classification system based on evolutionary relationships of full-length proteins, and iProClass integrated database of protein family, function, and structure. These databases are easily accessible from PIR web site using a centralized data retrieval system for information retrieval and knowledge discovery.

  3. The human keratinocyte two-dimensional protein database (update 1994): towards an integrated approach to the study of cell proliferation, differentiation and skin diseases

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Olsen, E

    1994-01-01

    The master two-dimensional (2-D) gel database of human keratinocytes currently lists 3087 cellular proteins (2168 isoelectric focusing, IEF; and 919 none-quilibrium pH gradient electrophoresis, NEPHGE), many of which correspond to posttranslational modifications, 890 polypeptides have been...... identified (protein name, organelle components, etc.) using one or a combination of procedures that include (i) comigration with known human proteins, (ii) 2-D gel immunoblotting using specific antibodies (iii) microsequencing of Coomassie Brilliant Blue stained proteins, (iv) mass spectrometry and (v...... in the database. We also report a database of proteins recovered from the medium of noncultured, unfractionated keratinocytes. This database lists 398 polypeptides (309 IEF; 89 NEPHGE) of which 76 have been identified. The aim of the comprehensive databases is to gather, through a systematic study...

  4. DBMLoc: a Database of proteins with multiple subcellular localizations

    Directory of Open Access Journals (Sweden)

    Zhou Yun

    2008-02-01

    Full Text Available Abstract Background Subcellular localization information is one of the key features to protein function research. Locating to a specific subcellular compartment is essential for a protein to function efficiently. Proteins which have multiple localizations will provide more clues. This kind of proteins may take a high proportion, even more than 35%. Description We have developed a database of proteins with multiple subcellular localizations, designated DBMLoc. The initial release contains 10470 multiple subcellular localization-annotated entries. Annotations are collected from primary protein databases, specific subcellular localization databases and literature texts. All the protein entries are cross-referenced to GO annotations and SwissProt. Protein-protein interactions are also annotated. They are classified into 12 large subcellular localization categories based on GO hierarchical architecture and original annotations. Download, search and sequence BLAST tools are also available on the website. Conclusion DBMLoc is a protein database which collects proteins with more than one subcellular localization annotation. It is freely accessed at http://www.bioinfo.tsinghua.edu.cn/DBMLoc/index.htm.

  5. Reducing the stiffness of concentrated whey protein isolate (WPI) gels by using WPI microparticles

    NARCIS (Netherlands)

    Purwanti, N.; Moerkens, A.; Goot, van der A.J.; Boom, R.M.

    2012-01-01

    Concentrated protein gels were prepared using native whey protein isolate (WPI) and WPI based microparticles. WPI microparticles were produced by making gel pieces from a concentrated WPI suspension (40% w/w), which were dried and milled. The protein within the microparticles was denatured and the

  6. How well are protein structures annotated in secondary databases?

    Science.gov (United States)

    Rother, Kristian; Michalsky, Elke; Leser, Ulf

    2005-09-01

    We investigated to what extent Protein Data Bank (PDB) entries are annotated with second-party information based on existing cross-references between PDB and 15 other databases. We report 2 interesting findings. First, there is a clear "annotation gap" for structures less than 7 years old for secondary databases that are manually curated. Second, the examined databases overlap with each other quite well, dividing the PDB into 2 well-annotated thirds and one poorly annotated third. Both observations should be taken into account in any study depending on the selection of protein structures by their annotation.

  7. 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

  8. On the quantitative Amido Black B staining of protein spots in agar gel at low local protein concentrations

    NARCIS (Netherlands)

    Jansen, M.T.

    1962-01-01

    Protein spots in agar gel of identical protein content but different in surface area are found to bind different amounts of dye upon staining with Amido Black B. The lower the protein concentration within the agar gel, the more the Amido Black B content of the spot falls short of the value expected

  9. LocSigDB: a database of protein localization signals

    OpenAIRE

    Negi, Simarjeet; Pandey, Sanjit; Srinivasan, Satish M; Mohammed, Akram; Guda, Chittibabu

    2015-01-01

    LocSigDB (http://genome.unmc.edu/LocSigDB/) is a manually curated database of experimental protein localization signals for eight distinct subcellular locations; primarily in a eukaryotic cell with brief coverage of bacterial proteins. Proteins must be localized at their appropriate subcellular compartment to perform their desired function. Mislocalization of proteins to unintended locations is a causative factor for many human diseases; therefore, collection of known sorting signals will hel...

  10. ARAMEMNON, a novel database for Arabidopsis integral membrane proteins

    DEFF Research Database (Denmark)

    Schwacke, Rainer; Schneider, Anja; van der Graaff, Eric

    2003-01-01

    A specialized database (DB) for Arabidopsis membrane proteins, ARAMEMNON, was designed that facilitates the interpretation of gene and protein sequence data by integrating features that are presently only available from individual sources. Using several publicly available prediction programs, put...... is accessible at the URL http://aramemnon.botanik.uni-koeln.de....

  11. cuticleDB: a relational database of Arthropod cuticular proteins

    Directory of Open Access Journals (Sweden)

    Willis Judith H

    2004-09-01

    Full Text Available Abstract Background The insect exoskeleton or cuticle is a bi-partite composite of proteins and chitin that provides protective, skeletal and structural functions. Little information is available about the molecular structure of this important complex that exhibits a helicoidal architecture. Scores of sequences of cuticular proteins have been obtained from direct protein sequencing, from cDNAs, and from genomic analyses. Most of these cuticular protein sequences contain motifs found only in arthropod proteins. Description cuticleDB is a relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the Drosophila melanogaster and the Anopheles gambiae genomes, that have been predicted to be cuticular proteins, based on a Pfam motif (PF00379 responsible for chitin binding in Arthropod cuticle. The total number of the database entries is 445: 370 derive from insects, 60 from Crustacea and 15 from Chelicerata. The database can be accessed from our web server at http://bioinformatics.biol.uoa.gr/cuticleDB. Conclusions CuticleDB was primarily designed to contain correct and full annotation of cuticular protein data. The database will be of help to future genome annotators. Users will be able to test hypotheses for the existence of known and also of yet unknown motifs in cuticular proteins. An analysis of motifs may contribute to understanding how proteins contribute to the physical properties of cuticle as well as to the precise nature of their interaction with chitin.

  12. A Laboratory Exercise for Visible Gel Filtration Chromatography Using Fluorescent Proteins

    Science.gov (United States)

    Zhang, Wenqiang; Cao, Yibin; Xu, Lishan; Gong, Jufang; Sun, Meihao

    2015-01-01

    Gel filtration chromatography (GFC) separates molecules according to size and is one of the most widely used methods for protein purification. Here, red fluorescent protein (RFP), green fluorescent protein (GFP), yellow fluorescent protein (YFP), cyan fluorescent protein (CFP), and/or their fusion proteins were prokaryotically expressed, purified,…

  13. A Laboratory Exercise for Visible Gel Filtration Chromatography Using Fluorescent Proteins

    Science.gov (United States)

    Zhang, Wenqiang; Cao, Yibin; Xu, Lishan; Gong, Jufang; Sun, Meihao

    2015-01-01

    Gel filtration chromatography (GFC) separates molecules according to size and is one of the most widely used methods for protein purification. Here, red fluorescent protein (RFP), green fluorescent protein (GFP), yellow fluorescent protein (YFP), cyan fluorescent protein (CFP), and/or their fusion proteins were prokaryotically expressed, purified,…

  14. Human protein reference database as a discovery resource for proteomics

    Science.gov (United States)

    Peri, Suraj; Navarro, J. Daniel; Kristiansen, Troels Z.; Amanchy, Ramars; Surendranath, Vineeth; Muthusamy, Babylakshmi; Gandhi, T. K. B.; Chandrika, K. N.; Deshpande, Nandan; Suresh, Shubha; Rashmi, B. P.; Shanker, K.; Padma, N.; Niranjan, Vidya; Harsha, H. C.; Talreja, Naveen; Vrushabendra, B. M.; Ramya, M. A.; Yatish, A. J.; Joy, Mary; Shivashankar, H. N.; Kavitha, M. P.; Menezes, Minal; Choudhury, Dipanwita Roy; Ghosh, Neelanjana; Saravana, R.; Chandran, Sreenath; Mohan, Sujatha; Jonnalagadda, Chandra Kiran; Prasad, C. K.; Kumar-Sinha, Chandan; Deshpande, Krishna S.; Pandey, Akhilesh

    2004-01-01

    The rapid pace at which genomic and proteomic data is being generated necessitates the development of tools and resources for managing data that allow integration of information from disparate sources. The Human Protein Reference Database (http://www.hprd.org) is a web-based resource based on open source technologies for protein information about several aspects of human proteins including protein–protein interactions, post-translational modifications, enzyme–substrate relationships and disease associations. This information was derived manually by a critical reading of the published literature by expert biologists and through bioinformatics analyses of the protein sequence. This database will assist in biomedical discoveries by serving as a resource of genomic and proteomic information and providing an integrated view of sequence, structure, function and protein networks in health and disease. PMID:14681466

  15. AMYPdb: A database dedicated to amyloid precursor proteins

    Directory of Open Access Journals (Sweden)

    Delamarche Christian

    2008-06-01

    Full Text Available Abstract Background Misfolding and aggregation of proteins into ordered fibrillar structures is associated with a number of severe pathologies, including Alzheimer's disease, prion diseases, and type II diabetes. The rapid accumulation of knowledge about the sequences and structures of these proteins allows using of in silico methods to investigate the molecular mechanisms of their abnormal conformational changes and assembly. However, such an approach requires the collection of accurate data, which are inconveniently dispersed among several generalist databases. Results We therefore created a free online knowledge database (AMYPdb dedicated to amyloid precursor proteins and we have performed large scale sequence analysis of the included data. Currently, AMYPdb integrates data on 31 families, including 1,705 proteins from nearly 600 organisms. It displays links to more than 2,300 bibliographic references and 1,200 3D-structures. A Wiki system is available to insert data into the database, providing a sharing and collaboration environment. We generated and analyzed 3,621 amino acid sequence patterns, reporting highly specific patterns for each amyloid family, along with patterns likely to be involved in protein misfolding and aggregation. Conclusion AMYPdb is a comprehensive online database aiming at the centralization of bioinformatic data regarding all amyloid proteins and their precursors. Our sequence pattern discovery and analysis approach unveiled protein regions of significant interest. AMYPdb is freely accessible 1.

  16. LocSigDB: a database of protein localization signals.

    Science.gov (United States)

    Negi, Simarjeet; Pandey, Sanjit; Srinivasan, Satish M; Mohammed, Akram; Guda, Chittibabu

    2015-01-01

    LocSigDB (http://genome.unmc.edu/LocSigDB/) is a manually curated database of experimental protein localization signals for eight distinct subcellular locations; primarily in a eukaryotic cell with brief coverage of bacterial proteins. Proteins must be localized at their appropriate subcellular compartment to perform their desired function. Mislocalization of proteins to unintended locations is a causative factor for many human diseases; therefore, collection of known sorting signals will help support many important areas of biomedical research. By performing an extensive literature study, we compiled a collection of 533 experimentally determined localization signals, along with the proteins that harbor such signals. Each signal in the LocSigDB is annotated with its localization, source, PubMed references and is linked to the proteins in UniProt database along with the organism information that contain the same amino acid pattern as the given signal. From LocSigDB webserver, users can download the whole database or browse/search for data using an intuitive query interface. To date, LocSigDB is the most comprehensive compendium of protein localization signals for eight distinct subcellular locations. Database URL: http://genome.unmc.edu/LocSigDB/

  17. Pepsin diffusivity in whey protein gels and its effect on gastric digestion

    NARCIS (Netherlands)

    Luo, Q.; Borst, J.W.; Westphal, A.H.; Boom, R.M.; Janssen, A.E.M.

    2017-01-01

    Protein is essential to human health, but its digestion kinetics in varied structures are not yet well understood. We previously found different kinetics of protein hydrolysis in solution and in gels, and we hypothesized that the difference stemmed from the steric hindrance of gel structure to the d

  18. Heat-Induced Gel Formation by Soy Proteins at Neutral pH

    NARCIS (Netherlands)

    Renkema, J.M.S.; Vliet, van T.

    2002-01-01

    Heat-induced gel formation by soy protein isolate at pH 7 is discussed. Different heating and cooling rates, heating times, and heating temperatures were used to elucidate the various processes that occur and to study the relative role of covalent and noncovalent protein interactions therein. Gel fo

  19. Manually Curated Database of Rice Proteins (MCDRP, a database of digitized experimental data on rice

    Directory of Open Access Journals (Sweden)

    Saurabh Raghuvanshi

    2016-11-01

    Full Text Available MCDRP or ‘Manually Curated Database of Rice Proteins’ is a database of digitized experimental datasets on rice proteins. Every aspect of the experimental data published in peer-reviewed research articles on rice biology has been digitized with the help of novel data curation models. These models use a semantic and structured arrangement of alpha-numeric notation, including several well known ontologies, to represent various aspect of the data. As a result data from more than 15,000 different experiments pertaining to about 2400 rice proteins has been digitized from over 540 published and peer-reviewed research articles. The database portal provides access to the digitized experimental data via search or browse functions. In essence, one can instantly access data from even a single data-point from a collection of thousands of the experimental datasets. On the other hand, one can easily access the digitized experimental data from multiple research articles on a rice protein. Based on the analysis and integration of the digitized experimental data, more than 800 different traits (molecular, biochemical or phenotypic have been precisely mapped onto the rice proteins along with the underlying experimental evidences. Similarly, over 4370 associations, based on experimental evidence, have been established between the rice proteins and various gene ontology terms. The database is being continuously updated and is freely available at www.genomeindia.org.in/biocuration.

  20. Yeast Interacting Proteins Database: YGL198W, YDR084C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available les; computational analysis of large-scale protein-protein interaction data suggests a possible role in vesi... GTPases, localized to late Golgi vesicles; computational analysis of large-scale protein-protein interactio

  1. Yeast Interacting Proteins Database: YDR425W, YGL161C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available icles; computational analysis of large-scale protein-protein interaction data sug...olgi vesicles; computational analysis of large-scale protein-protein interaction data suggests a possible ro

  2. Yeast Interacting Proteins Database: YPL070W, YOR155C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available utational analysis of large-scale protein-protein interaction data suggests a possible role in transcription...9 domain; computational analysis of large-scale protein-protein interaction data suggests a possible role in

  3. Yeast Interacting Proteins Database: YNL189W, YOR284W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ait as prey (0) YOR284W HUA2 Cytoplasmic protein of unknown function; computational analysis of large-scal...protein of unknown function; computational analysis of large-scale protein-protein interaction data suggests

  4. Yeast Interacting Proteins Database: YPL070W, YLR245C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available utational analysis of large-scale protein-protein interaction data suggests a possible role in transcription...Vps9 domain; computational analysis of large-scale protein-protein interaction data suggests a possible role

  5. Yeast Interacting Proteins Database: YPL070W, YPR193C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available utational analysis of large-scale protein-protein interaction data suggests a possible role in transcription...in; computational analysis of large-scale protein-protein interaction data suggests a possible role in trans

  6. Yeast Interacting Proteins Database: YGL161C, YDR084C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available les; computational analysis of large-scale protein-protein interaction data suggests a possible role in vesi...GTPases, localized to late Golgi vesicles; computational analysis of large-scale protein-protein interaction

  7. Yeast Interacting Proteins Database: YHR111W, YIL008W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YHR111W UBA4 Protein that activates Urm1p before its conjugation to proteins (urmyl...description Protein that activates Urm1p before its conjugation to proteins (urmylation); one target is the

  8. Yeast Interacting Proteins Database: YDL226C, YGL198W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available omputational analysis of large-scale protein-protein interaction data suggests a ... computational analysis of large-scale protein-protein interaction data suggests a possible role in vesicle-

  9. Rapid (ten-minute) pore-gradient electrophoresis of proteins and peptides in Micrograd gels.

    Science.gov (United States)

    Wrigley, C W; Margolis, J

    1992-01-01

    Precast gradient gels of short migration length (25 mm) have been developed to provide rapid electrophoretic separation without loss of resolution. These Micrograd gels have been prepared in gel ranges (conventional and unique) to match pore-gradient electrophoresis conditions to proteins/peptides ranging in size from several hundreds to millions. The Hylinx Micrograd gel combines an extreme gel range (6 to 48% polyacrylamide) with a novel crosslinker to provide sieving of polypeptides, and pore-limit electrophoresis of the smallest proteins (e.g. insulin monomer). All gel ranges (such as 3 to 30%) provide zone sharpening in routine analysis of conventional protein mixtures (e.g. serum) within 10 min electrophoresis at 200 to 300 volts. The gels are thin (1 mm) and thus stain quickly, but the gel cassette is of conventional overall width (83 mm), thus fitting many apparatus designs and accommodating 12 samples. The gels are finding valuable use in screening applications, requiring the electrophoretic analysis of many samples, and in cases where a rapid answer is needed, such as monitoring protein purification. The gels have proved particularly useful, in-house, for the latter application in developing Gradipore's new large-scale preparative electrophoresis system, the Gradiflow.

  10. Yeast Interacting Proteins Database: YNL189W, YJL199C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available tein; not conserved in closely related Saccharomyces species; protein detected in large-scale protein-protein interaction studies...myces species; protein detected in large-scale protein-protein interaction studies Rows with this prey as pr

  11. Yeast Interacting Proteins Database: YGR268C, YER125W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available larity to that of Type I J-proteins; computational analysis of large-scale protein-protein interaction data ...equence similarity to that of Type I J-proteins; computational analysis of large-scale protein-protein inter

  12. Injectable, thermo-reversible and complex coacervate combination gels for protein drug delivery.

    Science.gov (United States)

    Jin, Kwang-Mi; Kim, Yong-Hee

    2008-05-01

    Injectable and thermo-reversible physical combination gels were formed in aqueous solution by preparing complex coacervate with two oppositely charged biomacromolecules that composed of negatively charged chondroitin 6-sulfate and positively charged high molecular weight gelatin type A and co-formulating with a negative, thermo-sensitive polysaccharide, methylcellulose containing a salting-out salt, ammonium sulfate. The combination of complex coacervation and a thermo-reversible gel demonstrated synergistic effects on the complex coacervate formation the release rates of model proteins and in situ gel depot formation. Gels indicated sustained release patterns of the protein over 25 days with minimal initial bursts. Optimized novel in situ gel depot systems containing dual advantages of complex coacervation and temperature responsiveness demonstrated a potential for efficient protein drug delivery in terms of high protein loading, sustained protein release, ease of administration, an aqueous environment without toxic organic solvents, and a simple fabrication method.

  13. Yeast Interacting Proteins Database: YOR124C, YGR268C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available that of Type I J-proteins; computational analysis of large-scale protein-protein interaction data suggests a...tational analysis of large-scale protein-protein interaction data suggests a possible role in actin patch as

  14. Yeast Interacting Proteins Database: YLR291C, YJL199C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ved in closely related Saccharomyces species; protein detected in large-scale protein-protein interaction studies...in large-scale protein-protein interaction studies Rows with this prey as prey Rows with this prey as prey (

  15. Yeast Interacting Proteins Database: YML064C, YJL199C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available y related Saccharomyces species; protein detected in large-scale protein-protein interaction studies Rows wi...in-protein interaction studies Rows with this prey as prey (4) Rows with this prey as bait (1) 28 6 3 4 0 0 ...d in closely related Saccharomyces species; protein detected in large-scale prote

  16. Detection of seminal fluid proteins in the bed bug, Cimex lectularius, using two-dimensional gel electrophoresis and mass spectrometry.

    Science.gov (United States)

    Reinhardt, K; Wong, C H; Georgiou, A S

    2009-03-01

    The global increase of the human parasite, the common bed bug Cimex lectularius, calls for specific pest control target sites. The bed bug is also a model species for sexual conflict theory which suggests that seminal fluids may be highly diverse. The species has a highly unusual sperm biology and seminal proteins may have unique functions. One-dimensional PAGE gels showed 40-50% band sharing between C. lectularius and another cimicid species, Afrocimex constrictus. However, adult, sexually rested C. lectularius males were found to store 5-7 microg of seminal protein and with only 60 microg of protein we obtained informative 2-D PAGE gels. These showed 79% shared protein spots between 2 laboratory populations, and more than half of the shared protein spots were detected in the mated female. Further analysis using liquid chromatography electrospray ionization tandem mass spectrometry revealed that 26.5% of the proteins had matches among arthropods in databases and 14.5% matched Drosophila proteins. These included ubiquitous proteins but also those more closely associated with reproduction such as moj 29, ubiquitin, the stress-related elongation factor EF-1 alpha, a protein disulfide isomerase and an antioxidant, Peroxiredoxin 6.

  17. Yeast Interacting Proteins Database: YLR291C, YPL070W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YPL070W MUK1 Cytoplasmic protein of unknown function containing a Vps9 domain; computation...rotein of unknown function containing a Vps9 domain; computational analysis of large-scale protein-protein i

  18. Yeast Interacting Proteins Database: YPL095C, YGL198W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available d to late Golgi vesicles; computational analysis of large-scale protein-protein interaction data suggests a ...gene name YIP4 Prey description Protein that interacts with Rab GTPases, localized to late Golgi vesicles; computation

  19. Yeast Interacting Proteins Database: YML109W, YGL190C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available sential regulatory subunit B of protein phosphatase 2A, which has multiple roles ...-essential regulatory subunit B of protein phosphatase 2A, which has multiple roles in mitosis and protein b

  20. Yeast Interacting Proteins Database: YML064C, YOR284W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available th this bait as prey (0) YOR284W HUA2 Cytoplasmic protein of unknown function; computational analysis of large-scale... unknown function; computational analysis of large-scale protein-protein interact

  1. Yeast Interacting Proteins Database: YIL008W, YHR111W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ait as prey (1) YHR111W UBA4 Protein that activates Urm1p before its conjugation ...4 Prey description Protein that activates Urm1p before its conjugation to proteins (urmylation); one target

  2. Yeast Interacting Proteins Database: YJR091C, YKL076C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpre...NA-binding proteins, interacts with mRNAs encoding membrane-associated proteins; involved in localizing the

  3. Yeast Interacting Proteins Database: YJR091C, YNR048W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpre...y of RNA-binding proteins, interacts with mRNAs encoding membrane-associated proteins; involved in localizing

  4. Yeast Interacting Proteins Database: YJR091C, YML015C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpre...y of RNA-binding proteins, interacts with mRNAs encoding membrane-associated proteins; involved in localizing

  5. Yeast Interacting Proteins Database: YDL239C, YPL070W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available Vps9 domain; computational analysis of large-scale protein-protein interaction data suggests a possible role...ey description Cytoplasmic protein of unknown function containing a Vps9 domain; computational analysis of large-scale

  6. Affi-gel blue treatment simplifies the protein composition of sarcoplasmic reticulum vesicles.

    Science.gov (United States)

    Papp, S; Dux, L; Martonosi, A

    1986-04-01

    Sarcoplasmic reticulum vesicles isolated by conventional techniques usually contain, in addition to the recognized sarcoplasmic reticulum components, several other proteins (phosphorylase, myosin, glyceraldehyde-3-phosphate dehydrogenase, etc.) in variable amounts; these proteins complicate the interpretation of chemical modification data. Incubation of sarcoplasmic reticulum vesicles with Affi-Gel blue particles for 1-4 h at 2 degrees C, followed by sedimentation of the Affi-Gel in a clinical centrifuge, simplifies the protein composition by selective adsorption of the accessory proteins, and improves the consistency of the preparations. The Affi-Gel blue treatment is recommended as part of the standard procedure for the isolation of sarcoplasmic reticulum vesicles.

  7. Yeast Interacting Proteins Database: YDL226C, YJL151C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available s bait as prey (0) YJL151C SNA3 Integral membrane protein localized to vacuolar intralumenal vesicles, computation...intralumenal vesicles, computational analysis of large-scale protein-protein interaction data suggests a pos... gene name SNA3 Prey description Integral membrane protein localized to vacuolar

  8. Yeast Interacting Proteins Database: YEL043W, YOR164C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available on quantitative analysis of protein-protein interaction maps; may interact with ribosomes, based on co-purification studies...ing based on quantitative analysis of protein-protein interaction maps; may interact with ribosomes, based on co-purification studies

  9. Images of gel electrophoresis - RGP caps | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us RGP caps Images of gel... electrophoresis Data detail Data name Images of gel electrophoresis Description of da...ta contents Detailed information and images of gel electrophoresis of each marker. Data file File name: rgp_...mM KCl, and 0.001% (w/v) gelatin), and 40 mM MgCl 2 in 20.0 μL volume. Amplification was performed in GeneAm...d 72°C (2 min), and a final cycle of 72°C for 7 min. The amplified DNA products were electrophoresed on 3.0% agarose gel

  10. Separation and identification of Musa acuminate Colla (banana) leaf proteins by two-dimensional gel electrophoresis and mass spectrometry.

    Science.gov (United States)

    Lu, Y; Qi, Y X; Zhang, H; Zhang, H Q; Pu, J J; Xie, Y X

    2013-12-19

    To establish a proteomic reference map of Musa acuminate Colla (banana) leaf, we separated and identified leaf proteins using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Tryptic digests of 44 spots were subjected to peptide mass fingerprinting (PMF) by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS. Three spots that were not identified by MALDI-TOF MS analysis were identified by searching against the NCBInr, SwissProt, and expressed sequence tag (EST) databases. We identified 41 unique proteins. The majority of the identified leaf proteins were found to be involved in energy metabolism. The results indicate that 2D-PAGE is a sensitive and powerful technique for the separation and identification of Musa leaf proteins. A summary of the identified proteins and their putative functions is discussed.

  11. Yeast Interacting Proteins Database: YHL002W, YNR006W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ycling of Golgi proteins and formation of lumenal membranes Rows with this bait as bait (1) Rows with this b...required for recycling Golgi proteins, forming lumenal membranes and sorting ubiquitinated proteins destined...on, as well as for recycling of Golgi proteins and formation of lumenal membranes...ith Hse1p; required for recycling Golgi proteins, forming lumenal membranes and sorting ubiquitinated protei

  12. Yeast Interacting Proteins Database: YOR047C, YKL038W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available racts with protein kinase Snf1p, glucose sensors Snf3p and Rgt2p, and TATA-binding protein Spt15p; acts as a...Bait description Protein involved in control of glucose-regulated gene expression; interacts with protein kinase Snf1p, glucose senso...rs Snf3p and Rgt2p, and TATA-binding protein Spt15p; acts as a regulator of the tra

  13. Yeast Interacting Proteins Database: YOR284W, YOR284W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YOR284W HUA2 Cytoplasmic protein of unknown function; computational analysis of lar...it as bait (1) Rows with this bait as prey (4) YOR284W HUA2 Cytoplasmic protein of unknown function; computa...tein of unknown function; computational analysis of large-scale protein-protein i... HUA2 Prey description Cytoplasmic protein of unknown function; computational ana

  14. A comparison of protein extraction methods suitable for gel-based proteomic studies of aphid proteins.

    Science.gov (United States)

    Cilia, M; Fish, T; Yang, X; McLaughlin, M; Thannhauser, T W; Gray, S

    2009-09-01

    Protein extraction methods can vary widely in reproducibility and in representation of the total proteome, yet there are limited data comparing protein isolation methods. The methodical comparison of protein isolation methods is the first critical step for proteomic studies. To address this, we compared three methods for isolation, purification, and solubilization of insect proteins. The aphid Schizaphis graminum, an agricultural pest, was the source of insect tissue. Proteins were extracted using TCA in acetone (TCA-acetone), phenol, or multi-detergents in a chaotrope solution. Extracted proteins were solubilized in a multiple chaotrope solution and examined using 1-D and 2-D electrophoresis and compared directly using 2-D Difference Gel Electrophoresis (2-D DIGE). Mass spectrometry was used to identify proteins from each extraction type. We were unable to ascribe the differences in the proteins extracted to particular physical characteristics, cell location, or biological function. The TCA-acetone extraction yielded the greatest amount of protein from aphid tissues. Each extraction method isolated a unique subset of the aphid proteome. The TCA-acetone method was explored further for its quantitative reliability using 2-D DIGE. Principal component analysis showed that little of the variation in the data was a result of technical issues, thus demonstrating that the TCA-acetone extraction is a reliable method for preparing aphid proteins for a quantitative proteomics experiment. These data suggest that although the TCA-acetone method is a suitable method for quantitative aphid proteomics, a combination of extraction approaches is recommended for increasing proteome coverage when using gel-based separation techniques.

  15. Yeast Interacting Proteins Database: YEL017W, YEL017W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available 17W GTT3 Protein of unknown function with a possible role in glutathione metabolism, as suggested by compu...Bait description Protein of unknown function with a possible role in glutathione metabolism, as suggested by comput...ion Protein of unknown function with a possible role in glutathione metabolism, as suggested by computationa...YEL017W GTT3 Protein of unknown function with a possible role in glutathione metabolism, as suggested by com...putational analysis of large-scale protein-protein interaction data; GFP-fusion pro

  16. Yeast Interacting Proteins Database: YDL121C, YDL100C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YDL121C - Putative protein of unknown function; green fluorescent protein (GFP)-fus...ion protein localizes to the endoplasmic retiuculum; YDL121C is not an essential protein Rows with this bait... as bait (1) Rows with this bait as prey (0) YDL100C GET3 Guanine nucleotide exchange factor for Gpa1p; ampl...his prey as prey (10) Rows with this prey as bait (2) 3 5 2 2 0 0 0 0 0 - - - - - 0 0 8 - Show YDL121C Bait ORF YDL...n; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic retiuculum; YDL121C is not an

  17. Yeast Interacting Proteins Database: YKR092C, YKL023W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available W - Putative protein of unknown function, predicted by computational methods to b...ait as prey (0) Prey ORF YKL023W Prey gene name - Prey description Putative protein of unknown function, predicted by computation

  18. Yeast Interacting Proteins Database: YLR291C, YOR284W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YOR284W HUA2 Cytoplasmic protein of unknown function; computational analysis of l...prey (0) Prey ORF YOR284W Prey gene name HUA2 Prey description Cytoplasmic protein of unknown function; computation

  19. Yeast Interacting Proteins Database: YLR373C, YGL190C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ase 2A, which has multiple roles in mitosis and protein biosynthesis; involved in regulation of mitotic exit...phosphatase 2A, which has multiple roles in mitosis and protein biosynthesis; involved in regulation of mito

  20. Yeast Interacting Proteins Database: YPL204W, YHR185C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available Sporulation protein required for prospore membrane formation at selected spindle poles...n Sporulation protein required for prospore membrane formation at selected spindle poles, ensures functional

  1. Yeast Interacting Proteins Database: YJR091C, YEL013W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpression causes...ed proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpression causes increased sens

  2. Yeast Interacting Proteins Database: YPL070W, YBR176W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available utational analysis of large-scale protein-protein interaction data suggests a possible role in transcription...otein of unknown function containing a Vps9 domain; computational analysis of large-scale

  3. Yeast Interacting Proteins Database: YDR084C, YGL198W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available with Rab GTPases, localized to late Golgi vesicles; computational analysis of large-scale...omputational analysis of large-scale protein-protein interaction data suggests a possible role in vesicle-me

  4. Yeast Interacting Proteins Database: YMR077C, YML015C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available lumen; cytoplasmic protein recruited to endosomal membranes Rows with this bait as bait (3) Rows with this b...o the multivesicular body pathway to the lysosomal/vacuolar lumen; cytoplasmic protein recruited to endosomal membranes

  5. Yeast Interacting Proteins Database: YMR316W, YER125W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YMR316W DIA1 Protein of unknown function, involved in invasive and pseudohyphal gro... of unknown function, involved in invasive and pseudohyphal growth; green fluorescent protein (GFP)-fusion p

  6. Yeast Interacting Proteins Database: YPR148C, YDL237W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YPR148C - Protein of unknown function that may interact with ribosomes, based on co-purification experiments... with ribosomes, based on co-purification experiments; green fluorescent protein

  7. Yeast Interacting Proteins Database: YER081W, YOR318C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YOR318C - Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative...likely to encode a protein, based on available experimental and comparative seque

  8. Yeast Interacting Proteins Database: YBL033C, YNL105W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; p...a protein, based on available experimental and comparative sequence data; partial

  9. Yeast Interacting Proteins Database: YER081W, YPR126C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YPR126C - Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative...ubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative

  10. Yeast Interacting Proteins Database: YLR263W, YDR510W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YLR263W RED1 Protein component of the axial elements of the synaptonemal complex, i...ait gene name RED1 Bait description Protein component of the axial elements of the synaptonemal complex, inv

  11. Yeast Interacting Proteins Database: YNL152W, YMR032W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YNL152W INN1 Essential protein that associates with the contractile actomyosin ring... Bait description Essential protein that associates with the contractile actomyosin ring, required for ingre

  12. Yeast Interacting Proteins Database: YKL002W, YOR047C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available integral membrane proteins into lumenal vesicles of multivesicular bodies, and for delivery of newly synthes...ng of integral membrane proteins into lumenal vesicles of multivesicular bodies, and for delivery of newly s

  13. Yeast Interacting Proteins Database: YJR091C, YKL002W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available g of integral membrane proteins into lumenal vesicles of multivesicular bodies, and for delivery of newly sy... integral membrane proteins into lumenal vesicles of multivesicular bodies, and for delivery of newly synthe

  14. Yeast Interacting Proteins Database: YLR347C, YLR377C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ucleoporins to mediate nuclear import of NLS-containing cargo proteins via the nuclear pore complex; regulat...0p; interacts with nucleoporins to mediate nuclear import of NLS-containing cargo proteins via the nuclear p

  15. Yeast Interacting Proteins Database: YLR347C, YBR176W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ucleoporins to mediate nuclear import of NLS-containing cargo proteins via the nuclear pore complex; regulat...p; interacts with nucleoporins to mediate nuclear import of NLS-containing cargo proteins via the nuclear po

  16. Yeast Interacting Proteins Database: YML064C, YKL103C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available he peptidase family M18; often used as a marker protein in studies of autophagy a... to the peptidase family M18; often used as a marker protein in studies of autophagy and cytosol to vacuole

  17. Yeast Interacting Proteins Database: YHR114W, YDL134C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available y (0) YDL134C PPH21 Catalytic subunit of protein phosphatase 2A, functionally red...gene name PPH21 Prey description Catalytic subunit of protein phosphatase 2A, functionally redundant with Pp

  18. Yeast Interacting Proteins Database: YLR288C, YLR125W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available prey (1) YLR125W - Putative protein of unknown function; mutant has decreased Ty3... name - Prey description Putative protein of unknown function; mutant has decreased Ty3 transposition; YLR12

  19. Yeast Interacting Proteins Database: YPL002C, YJR102C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ndent sorting of proteins into the endosome; appears to be functionally related to SNF7; involved in glucose...x, which is involved in ubiquitin-dependent sorting of proteins into the endosome; appears

  20. Yeast Interacting Proteins Database: YDL089W, YML008C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available rDNA repeat stability; null mutant causes increase in unequal sister-chromatid exchange; GFP-fusion protein...peat stability; null mutant causes increase in unequal sister-chromatid exchange; GFP-fusion protein localiz

  1. Yeast Interacting Proteins Database: YPL059W, YIL105C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available oxidoreductase; mitochondrial matrix protein involved in the synthesis/assembly of iron-sulfur centers; mono...oreductase; mitochondrial matrix protein involved in the synthesis/assembly of iron-sulfur centers; monothio

  2. Yeast Interacting Proteins Database: YJR091C, YOR014W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpre...ssociated proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpression causes increas

  3. Yeast Interacting Proteins Database: YJR091C, YLR059C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpre... mRNAs encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; ove

  4. Yeast Interacting Proteins Database: YJR091C, YOR317W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpre...NAs encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; overex

  5. Yeast Interacting Proteins Database: YPL077C, YLR423C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YPL077C - Putative protein of unknown function; regulates PIS1 expression; mutant display...Bait description Putative protein of unknown function; regulates PIS1 expression; mutant display

  6. Yeast Interacting Proteins Database: YPR029C, YFR043C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available his bait as prey (1) YFR043C IRC6 Putative protein of unknown function; null mutant displays increased level...C6 Prey description Putative protein of unknown function; null mutant displays increased levels of spontaneo

  7. Yeast Interacting Proteins Database: YPR040W, YDL188C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YPR040W TIP41 Protein that interacts physically and genetically with Tap42p, which ...ait ORF YPR040W Bait gene name TIP41 Bait description Protein that interacts physically and genetically

  8. Yeast Interacting Proteins Database: YPR040W, YDL134C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YPR040W TIP41 Protein that interacts physically and genetically with Tap42p, which ...Bait ORF YPR040W Bait gene name TIP41 Bait description Protein that interacts physically and genetically

  9. Yeast Interacting Proteins Database: YGR086C, YKL142W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ption induced under cell wall stress; protein levels are reduced under anaerobic conditions; originally thou...iption induced under cell wall stress; protein levels are reduced under anaerobic conditions; originally tho

  10. Yeast Interacting Proteins Database: YPL204W, YOL149W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YPL204W HRR25 Protein kinase involved in regulating diverse events including vesicu...tion Protein kinase involved in regulating diverse events including vesicular trafficking, DNA repair, and c

  11. Yeast Interacting Proteins Database: YPL204W, YER095W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YPL204W HRR25 Protein kinase involved in regulating diverse events including vesicu... gene name HRR25 Bait description Protein kinase involved in regulating diverse events including vesicular t

  12. Yeast Interacting Proteins Database: YPR103W, YOR047C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available tein involved in control of glucose-regulated gene expression; interacts with protein kinase Snf1p, glucose sensors...gulated gene expression; interacts with protein kinase Snf1p, glucose sensors Snf

  13. Yeast Interacting Proteins Database: YCL020W, YDR510W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available R510W SMT3 Ubiquitin-like protein of the SUMO family, conjugated to lysine residu... name SMT3 Prey description Ubiquitin-like protein of the SUMO family, conjugated to lysine residues of targ

  14. Yeast Interacting Proteins Database: YGL145W, YNL258C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ripheral membrane protein required for Golgi-to-ER retrograde traffic; component ... membrane protein required for Golgi-to-ER retrograde traffic; component of the ER target site that interact

  15. Yeast Interacting Proteins Database: YNL258C, YGL145W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YNL258C DSL1 Peripheral membrane protein required for Golgi-to-ER retrograde traffi...t description Peripheral membrane protein required for Golgi-to-ER retrograde traffic; component of the ER t

  16. Yeast Interacting Proteins Database: YHR114W, YLR112W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available y (0) YLR112W - Dubious open reading frame unlikely to encode a protein, based on...e name - Prey description Dubious open reading frame unlikely to encode a protein, based on available experi

  17. Yeast Interacting Proteins Database: YNL258C, YKR022C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ity (BRITE) - Alternative path with 1 intervening protein (YPD) 0 Alternative path with 2 intervening proteins (YPD) 0 IST hit 3 IST hit in the opposite bait/prey orientation - ...

  18. Two-dimensional gel-based protein standardization verified by western blot analysis.

    Science.gov (United States)

    Haniu, Hisao; Watanabe, Daisuke; Kawashima, Yusuke; Matsumoto, Hiroyuki

    2015-01-01

    In data presentation of biochemical investigation the amount of a target protein is shown in the y-axis against the x-axis representing time, concentrations of various agents, or other parameters. Western blot is a versatile and convenient tool in such an analysis to quantify and display the amount of proteins. In western blot, so-called housekeeping gene product(s), or "housekeeping proteins," are widely used as internal standards. The rationale of using housekeeping proteins for standardization of western blot is based on the assumption that the expression of chosen housekeeping gene is always constant, which could be false under certain physiological or pathological conditions. We have devised a two-dimensional gel-based standardization method in which the protein content of each sample is determined by scanning the total protein density of two-dimensional gels and the expression of each protein is quantified as the density ratio of each protein divided by the density of the total proteins on the two-dimensional gel. The advantage of this standardization method is that it is not based on any presumed "housekeeping proteins" that are supposed to be being expressed constantly under all physiological conditions. We will show that the total density of a two-dimensional gel can render a reliable protein standardization parameter by running western blot analysis on one of the proteins analyzed by two-dimensional gels.

  19. The Protein Identifier Cross-Referencing (PICR service: reconciling protein identifiers across multiple source databases

    Directory of Open Access Journals (Sweden)

    Leinonen Rasko

    2007-10-01

    Full Text Available Abstract Background Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. Results We have created the Protein Identifier Cross-Reference (PICR service, a web application that provides interactive and programmatic (SOAP and REST access to a mapping algorithm that uses the UniProt Archive (UniParc as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV or Microsoft Excel (XLS files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. Conclusion We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR

  20. Yeast Interacting Proteins Database: YGL198W, YGL161C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YGL198W YIP4 Protein that interacts with Rab GTPases, localized to late Golgi vesicles; comput...that interacts with Rab GTPases, localized to late Golgi vesicles; computational ...eracts with Rab GTPases, localized to late Golgi vesicles; computational analysis of large-scale protein-pro...ized to late Golgi vesicles; computational analysis of large-scale protein-protein interaction data suggests

  1. Yeast Interacting Proteins Database: YGL161C, YGL198W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YGL161C YIP5 Protein that interacts with Rab GTPases, localized to late Golgi vesicles; comput...that interacts with Rab GTPases, localized to late Golgi vesicles; computational ...eracts with Rab GTPases, localized to late Golgi vesicles; computational analysis of large-scale protein-pro...ized to late Golgi vesicles; computational analysis of large-scale protein-protein interaction data suggests

  2. A technique for detecting antifungal activity of proteins separated by polyacrylamide gel electrophoresis.

    Science.gov (United States)

    De Bolle, M F; Goderis, I J; Terras, F R; Cammue, B P; Broekaert, W F

    1991-06-01

    A technique was developed for the detection of antifungal activity of proteins after discontinuous polyacrylamide gel electrophoresis under native conditions. The antifungal activity is detected as growth inhibition zones in a homogeneous fungal lawn, grown in an agar layer spread on top of the polyacrylamide gel. The position of proteins with antifungal activity can be determined on a diffusion blot prepared from the same gel. The technique is illustrated for three antifungal plant proteins, i.e. alpha-purothionin, Urtica dioica agglutinin, and tobacco chitinase.

  3. Yeast Interacting Proteins Database: YJR091C, YKL113C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpre...r of the Puf family of RNA-binding proteins, interacts with mRNAs encoding membrane-associated proteins; involved in localizing

  4. Yeast Interacting Proteins Database: YJR091C, YDR389W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpre...d proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpression causes increased sensi...scription Member of the Puf family of RNA-binding proteins, interacts with mRNAs encoding membrane-associate

  5. Yeast Interacting Proteins Database: YJR091C, YDL147W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpre...g proteins, interacts with mRNAs encoding membrane-associated proteins; involved in localizing the Arp2/3 co

  6. Yeast Interacting Proteins Database: YOR037W, YCL056C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern; null mutant displays decreased thermo...e pattern; null mutant displays decreased thermotolerance Rows with this prey as prey Rows with this prey as... of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctat

  7. Yeast Interacting Proteins Database: YGL237C, YOR047C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ene expression; interacts with protein kinase Snf1p, glucose sensors Snf3p and Rgt2p, and TATA-binding prote... expression; interacts with protein kinase Snf1p, glucose sensors Snf3p and Rgt2p, and TATA-binding protein

  8. Yeast Interacting Proteins Database: YOR358W, YOR047C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ; interacts with protein kinase Snf1p, glucose sensors Snf3p and Rgt2p, and TATA-binding protein Spt15p; act...rotein kinase Snf1p, glucose sensors Snf3p and Rgt2p, and TATA-binding protein Spt15p; acts as a regulator o

  9. Yeast Interacting Proteins Database: YGL127C, YOR047C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ith protein kinase Snf1p, glucose sensors Snf3p and Rgt2p, and TATA-binding protein Spt15p; acts as a regula...rotein involved in control of glucose-regulated gene expression; interacts with protein kinase Snf1p, glucose sensors

  10. Yeast Interacting Proteins Database: YLR295C, YDR510W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available 7) Rows with this bait as prey (0) YDR510W SMT3 Ubiquitin-like protein of the SUMO family, conjugated to lys...uitin-like protein of the SUMO family, conjugated to lysine residues of target proteins; regulates chromatid

  11. Differential saliva-induced breakdown of starch filled protein gels in relation to sensory perception

    NARCIS (Netherlands)

    Janssen, A.M.; Pijpekamp, van de A.M.; Labiausse, D.

    2009-01-01

    In this study, the differential breakdown of protein gels containing four types of high and low cross-linked starch granules were studied. Susceptibility to saliva-induced breakdown of starch granules and the consequences of these for overall breakdown of the gel matrix were captured using a multipl

  12. pH shift protein recovery with organic acids on texture and color of cooked gels.

    Science.gov (United States)

    Paker, Ilgin; Beamer, Sarah; Jaczynski, Jacek; Matak, Kristen E

    2015-01-01

    Isoelectric solubilization and precipitation (ISP) processing uses pH shifts to separate protein from fish frames, which may increase commercial interest for silver carp. Texture and color properties of gels made from silver carp protein recovered at different pH strategies and organic acid types were compared. ISP was applied to headed gutted silver carp using 10 mol L(-1) sodium hydroxide (NaOH) and either glacial acetic acid (AA) or a (1:1) formic and lactic acid combination (F&L). Protein gels were made with recovered protein and standard functional additives. Texture profile analysis and the Kramer shear test showed that protein gels made from protein solubilized at basic pH values were firmer, harder, more cohesive, gummier and chewier (P proteins solubilized under acidic conditions. Acidic solubilization led to whiter (P protein using organic acids show potential for use as a functional ingredient in restructured foods. © 2014 Society of Chemical Industry.

  13. PPT-DB: the protein property prediction and testing database.

    Science.gov (United States)

    Wishart, David S; Arndt, David; Berjanskii, Mark; Guo, An Chi; Shi, Yi; Shrivastava, Savita; Zhou, Jianjun; Zhou, You; Lin, Guohui

    2008-01-01

    The protein property prediction and testing database (PPT-DB) is a database housing nearly 30 carefully curated databases, each of which contains commonly predicted protein property information. These properties include both structural (i.e. secondary structure, contact order, disulfide pairing) and dynamic (i.e. order parameters, B-factors, folding rates) features that have been measured, derived or tabulated from a variety of sources. PPT-DB is designed to serve two purposes. First it is intended to serve as a centralized, up-to-date, freely downloadable and easily queried repository of predictable or 'derived' protein property data. In this role, PPT-DB can serve as a one-stop, fully standardized repository for developers to obtain the required training, testing and validation data needed for almost any kind of protein property prediction program they may wish to create. The second role that PPT-DB can play is as a tool for homology-based protein property prediction. Users may query PPT-DB with a sequence of interest and have a specific property predicted using a sequence similarity search against PPT-DB's extensive collection of proteins with known properties. PPT-DB exploits the well-known fact that protein structure and dynamic properties are highly conserved between homologous proteins. Predictions derived from PPT-DB's similarity searches are typically 85-95% correct (for categorical predictions, such as secondary structure) or exhibit correlations of >0.80 (for numeric predictions, such as accessible surface area). This performance is 10-20% better than what is typically obtained from standard 'ab initio' predictions. PPT-DB, its prediction utilities and all of its contents are available at http://www.pptdb.ca.

  14. Yeast Interacting Proteins Database: YER179W, YER179W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YER179W DMC1 Meiosis-specific protein required for repair of double-strand breaks and pairing... double-strand breaks and pairing between homologous chromosomes; homolog of Rad5...ific protein required for repair of double-strand breaks and pairing between homo...name DMC1 Prey description Meiosis-specific protein required for repair of double-strand breaks and pairin

  15. Yeast Interacting Proteins Database: YPL003W, YPR066W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YPL003W ULA1 Protein that acts together with Uba3p to activate Rub1p before its con... (1) Rows with this bait as prey (0) YPR066W UBA3 Protein that acts together with Ula1p to activate Rub1p before...it gene name ULA1 Bait description Protein that acts together with Uba3p to activate Rub1p before...together with Ula1p to activate Rub1p before its conjugation to proteins (neddylation), which may play a rol

  16. Yeast Interacting Proteins Database: YMR077C, YLR417W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available lumen; cytoplasmic protein recruited to endosomal membranes Rows with this bait as bait (3) Rows with this b...-dependent sorting of proteins into the endosome Rows with this prey as prey (3) Rows with this prey as bait...oplasmic protein recruited to endosomal membranes Rows with this bait as bait Row...s with this bait as bait (3) Rows with this bait as prey Rows with this bait as prey (0) Prey ORF YLR417W Pr... proteins into the endosome Rows with this prey as prey Rows with this prey as prey (3) Row

  17. Yeast Interacting Proteins Database: YNL086W, YGL172W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ion protein localizes to endosomes Rows with this bait as bait (3) Rows with this bait as prey (2) YGL172W N...clear export of ribosomes Rows with this prey as prey (3) Rows with this prey as ...n Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to endosomes Row...s with this bait as bait Rows with this bait as bait (3) Rows with this bait as prey Row...he Nsp1p-Nup57p-Nup49p-Nic96p subcomplex of the nuclear pore complex (NPC), required for nuclear export of ribosomes Row

  18. Yeast Interacting Proteins Database: YMR077C, YJR102C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available lumen; cytoplasmic protein recruited to endosomal membranes Rows with this bait as bait (3) Rows with this b...d in ubiquitin-dependent sorting of proteins into the endosome Rows with this prey as prey (3) Rows with thi...lar lumen; cytoplasmic protein recruited to endosomal membranes Rows with this bait as bait Rows with this bait as bait (3) Row...s with this bait as prey Rows with this bait as prey (0) Prey ...iquitin-dependent sorting of proteins into the endosome Rows with this prey as prey Rows with this prey as prey (3) Row

  19. Yeast Interacting Proteins Database: YKL103C, YKL103C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available he peptidase family M18; often used as a marker protein in studies of autophagy and cytosol to vacuole targe...; often used as a marker protein in studies of autophagy and cytosol to vacuole targeting (CVT) pathway Rows...e yscI; zinc metalloproteinase that belongs to the peptidase family M18; often used as a marker protein in studies...t belongs to the peptidase family M18; often used as a marker protein in studies of autophagy and cytosol to

  20. Resolving Acetylated and Phosphorylated Proteins by Neutral Urea Triton-Polyacrylamide Gel Electrophoresis, NUT-PAGE

    Science.gov (United States)

    Buehl, Christopher J.; Deng, Xiexiong; Liu, Mengyu; Hovde, Stacy; Xu, Xinjing; Kuo, Min-Hao

    2014-01-01

    Protein acetylation and phosphorylation can be key modifications that regulate both normal and pathological protein functions. Current gel systems used to analyze modified proteins require either expensive reagents or time–consuming second dimension electrophoresis. In this manuscript, we present a neutral pH gel system that allows the analysis of acetylated and phosphorylated proteins. This neutral pH urea Triton-polyacrylamide gel electrophoresis system, or NUT-PAGE, separates proteins based on their charge at pH 7 and generates discrete bands from each acetylated and phosphorylated species. In addition, the gel is composed of common and inexpensive laboratory reagents, and requires only a single dimension of electrophoresis. We are able to demonstrate the effectiveness of this system by analyzing phosphorylated species of an acidic protein, α-synuclein, and both acetylated and phosphorylated species of a basic protein, histone H3. NUT-PAGE thus provides a cost-effective alternative to resolving acetylated and phosphorylated proteins, and potentially proteins with other post-translational modifications that alter net charge. Method Summary Here we present a single-dimension neutral pH urea Triton-polyacrylamide gel electrophoresis (NUT-PAGE) system affording high-resolution separation of acetylated and phosphorylated proteins. PMID:25109292

  1. Rheological and microstructural properties of porcine myofibrillar protein-lipid emulsion composite gels.

    Science.gov (United States)

    Wu, Mangang; Xiong, Youling L; Chen, Jie; Tang, Xueyan; Zhou, Guanghong

    2009-01-01

    The objective of the study was to investigate the role of emulsified fat (lard) and oil (peanut oil) in the rheology and microstructure of porcine myofibrillar protein (MP) gels. Heat-induced composite gels were prepared from 2% MP with 0% to 15% pre-emulsified lipids at 0.6 M NaCl, pH 6.2. Dynamic rheological testing upon temperature sweeping (20 to 80 degrees C at 2 degrees C/min) showed substantial increases in G' (an elastic modulus) of MP sols/gels with the addition of emulsions. Gel hardness was markedly enhanced (P or=10% emulsions, and the composite gel with 15% lard was 33% more rigid (P gels by 28% to 44% (P gel structure filled with protein-coated fat/oil globules that interacted with the protein matrix via disulfide bonds. The results indicated that both physical and chemical forces contributed to the enhancements in the rheology, moisture retention, and lipid stabilization in the MP-emulsion composite gels.

  2. Yeast Interacting Proteins Database: YDR425W, YGL198W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available with this bait as prey (0) YGL198W YIP4 Protein that interacts with Rab GTPases, localized to late Golgi vesicles; computation...IP4 Prey description Protein that interacts with Rab GTPases, localized to late Golgi vesicles; computatio

  3. Yeast Interacting Proteins Database: YMR025W, YGR120C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available or removal of the ubiquitin-like protein Rub1p from Cdc53p (cullin); involved in adaptation to pheromone sig... (cullin); involved in adaptation to pheromone signaling Rows with this bait as bait Rows with this bait as ...signalosome, which is required for deneddylation, or removal of the ubiquitin-like protein Rub1p from Cdc53p

  4. Yeast Interacting Proteins Database: YKR100C, YDL100C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YKR100C SKG1 Transmembrane protein with a role in cell wall polymer composition; lo...position; localizes on the inner surface of the plasma membrane at the bud and in t...RF YKR100C Bait gene name SKG1 Bait description Transmembrane protein with a role in cell wall polymer com

  5. Yeast Interacting Proteins Database: YER081W, YDR194C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YDR194C MSS116 DEAD-box protein required for efficient splicing of mitochondrial Group I and II introns; non...e name MSS116 Prey description DEAD-box protein required for efficient splicing of mitochondrial Group I and

  6. Yeast Interacting Proteins Database: YMR047C, YDR229W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available R229W IVY1 Phospholipid-binding protein that interacts with both Ypt7p and Vps33p, may partially...holipid-binding protein that interacts with both Ypt7p and Vps33p, may partially counteract the action of Vp

  7. Yeast Interacting Proteins Database: YHR180W, YDL100C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available on Dubious open reading frame unlikely to encode a protein, based on available experimental and comparativ...YHR180W - Dubious open reading frame unlikely to encode a protein, based on available experimental and compa...rative sequence data Rows with this bait as bait (1) Rows with this bait as prey (0

  8. Yeast Interacting Proteins Database: YDR271C, YOR128C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available n Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative...YDR271C - Dubious open reading frame unlikely to encode a protein, based on available experimental and compa...rative sequence data; partially overlaps the verified ORF CCC2/YDR270W Rows with th

  9. Yeast Interacting Proteins Database: YOR264W, YCR086W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YOR264W DSE3 Daughter cell-specific protein, may help establish daughter fate Rows ...0 42 - Show YOR264W Bait ORF YOR264W Bait gene name DSE3 Bait description Daughter cell-specific protein, ma

  10. Yeast Interacting Proteins Database: YML064C, YBR072W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available th this bait as prey (0) YBR072W HSP26 Small heat shock protein (sHSP) with chaperone activity; forms hollow...tein (sHSP) with chaperone activity; forms hollow, sphere-shaped oligomers that suppress unfolded proteins a

  11. Yeast Interacting Proteins Database: YKR007W, YGR163W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available (1) YGR163W GTR2 Putative GTP binding protein that negatively regulates Ran/Tc4 ...163W Prey gene name GTR2 Prey description Putative GTP binding protein that negatively regulates Ran/Tc4 GTP

  12. Yeast Interacting Proteins Database: YDL167C, YBR212W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available as bait (2) Rows with this bait as prey (0) YBR212W NGR1 RNA binding protein that negatively regulates grow...ption RNA binding protein that negatively regulates growth rate; interacts with the 3' UTR of the mitochondr

  13. Yeast Interacting Proteins Database: YNL189W, YKL103C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available that belongs to the peptidase family M18; often used as a marker protein in studies of autophagy and cytoso...amily M18; often used as a marker protein in studies of autophagy and cytosol to vacuole targeting (CVT) pat

  14. Yeast Interacting Proteins Database: YDL239C, YKL103C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available that belongs to the peptidase family M18; often used as a marker protein in studies of autophagy and cytosol...ily M18; often used as a marker protein in studies of autophagy and cytosol to vacuole targeting (CVT) pathw

  15. Yeast Interacting Proteins Database: YDR311W, YKL103C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ngs to the peptidase family M18; often used as a marker protein in studies of aut...ase that belongs to the peptidase family M18; often used as a marker protein in studies of autophagy and cyt

  16. Yeast Interacting Proteins Database: YPL105C, YDR429C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available co-purification experiments; authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies...entic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies Rows with t

  17. Yeast Interacting Proteins Database: YPL002C, YLR417W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ndent sorting of proteins into the endosome; appears to be functionally related to SNF7; involved in glucose...ESCRT-II complex, which is involved in ubiquitin-dependent sorting of proteins into the endosome; appears to be functionally

  18. Yeast Interacting Proteins Database: YOR111W, YDL161W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available with this bait as prey (2) YDL161W ENT1 Epsin-like protein involved in endocytosis and actin patch assembly and functionally...-like protein involved in endocytosis and actin patch assembly and functionally redundant with Ent2p; binds

  19. Yeast Interacting Proteins Database: YHR114W, YDR422C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available substrate specificity; vacuolar protein containing KIS (Kinase-Interacting Sequence) and ASC (Association w...strate specificity; vacuolar protein containing KIS (Kinase-Interacting Sequence) and ASC (Association with ...e 4 CuraGen (0 or 1) 0 S. Fields (0 or 1) 0 Association (0 or 1,YPD) 0 Complex (0

  20. Yeast Interacting Proteins Database: YDL089W, YDR233C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available rDNA repeat stability; null mutant causes increase in unequal sister-chromatid exchange; GFP-fusion protein...DNA repeat stability; null mutant causes increase in unequal sister-chromatid exchange; GFP-fusion protein l

  1. Yeast Interacting Proteins Database: YDL089W, YPR028W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available rDNA repeat stability; null mutant causes increase in unequal sister-chromatid exchange; GFP-fusion protein...ility; null mutant causes increase in unequal sister-chromatid exchange; GFP-fusion protein localizes to the

  2. Yeast Interacting Proteins Database: YJR091C, YDL013W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpre...h mRNAs encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; ov

  3. Yeast Interacting Proteins Database: YJR091C, YHR026W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpre...s with mRNAs encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondri

  4. Yeast Interacting Proteins Database: YBR108W, YDR388W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YBR108W AIM3 Protein interacting with Rvs167p; null mutant is viable and displays e...l mutant is viable and displays elevated frequency of mitochondrial genome loss R...8 - Show YBR108W Bait ORF YBR108W Bait gene name AIM3 Bait description Protein interacting with Rvs167p; nul

  5. Yeast Interacting Proteins Database: YBR108W, YGR136W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YBR108W AIM3 Protein interacting with Rvs167p; null mutant is viable and displays e...w YBR108W Bait ORF YBR108W Bait gene name AIM3 Bait description Protein interacting with Rvs167p; null mutant is viable and display

  6. Yeast Interacting Proteins Database: YMR280C, YOR047C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available olved in control of glucose-regulated gene expression; interacts with protein kinase Snf1p, glucose sensor... glucose-regulated gene expression; interacts with protein kinase Snf1p, glucose sensors Snf3p and Rgt2p, an

  7. Yeast Interacting Proteins Database: YOR302W, YOR047C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available rol of glucose-regulated gene expression; interacts with protein kinase Snf1p, glucose sensors Snf3p and Rgt...tein kinase Snf1p, glucose sensors Snf3p and Rgt2p, and TATA-binding protein Spt1

  8. Yeast Interacting Proteins Database: YNL189W, YDR510W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ait as prey (0) YDR510W SMT3 Ubiquitin-like protein of the SUMO family, conjugated...s prey (0) Prey ORF YDR510W Prey gene name SMT3 Prey description Ubiquitin-like protein of the SUMO family, conjugated

  9. Yeast Interacting Proteins Database: YKL043W, YDR510W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available s prey (0) YDR510W SMT3 Ubiquitin-like protein of the SUMO family, conjugated to ... Prey ORF YDR510W Prey gene name SMT3 Prey description Ubiquitin-like protein of the SUMO family, conjugated

  10. Yeast Interacting Proteins Database: YLR295C, YJR083C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available 7) Rows with this bait as prey (0) YJR083C ACF4 Protein of unknown function, computational analysis of large-scale...me ACF4 Prey description Protein of unknown function, computational analysis of large-scale

  11. Yeast Interacting Proteins Database: YHR129C, YMR294W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YHR129C ARP1 Actin-related protein of the dynactin complex; required for spindle orientation...ein of the dynactin complex; required for spindle orientation and nuclear migrati...PD) 1 Alternative path with 2 intervening proteins (YPD) 2 IST hit 21 IST hit in the opposite bait/prey orientation 7 ...

  12. Yeast Interacting Proteins Database: YJR008W, YHR129C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available the dynactin complex; required for spindle orientation and nuclear migration; put...dynactin complex; required for spindle orientation and nuclear migration; putative ortholog of mammalian cen...ervening protein (YPD) 0 Alternative path with 2 intervening proteins (YPD) 0 IST hit 3 IST hit in the opposite bait/prey orientation - ...

  13. ARAMEMNON, a Novel Database for Arabidopsis Integral Membrane Proteins1

    Science.gov (United States)

    Schwacke, Rainer; Schneider, Anja; van der Graaff, Eric; Fischer, Karsten; Catoni, Elisabetta; Desimone, Marcelo; Frommer, Wolf B.; Flügge, Ulf-Ingo; Kunze, Reinhard

    2003-01-01

    A specialized database (DB) for Arabidopsis membrane proteins, ARAMEMNON, was designed that facilitates the interpretation of gene and protein sequence data by integrating features that are presently only available from individual sources. Using several publicly available prediction programs, putative integral membrane proteins were identified among the approximately 25,500 proteins in the Arabidopsis genome DBs. By averaging the predictions from seven programs, approximately 6,500 proteins were classified as transmembrane (TM) candidate proteins. Some 1,800 of these contain at least four TM spans and are possibly linked to transport functions. The ARAMEMNON DB enables direct comparison of the predictions of seven different TM span computation programs and the predictions of subcellular localization by eight signal peptide recognition programs. A special function displays the proteins related to the query and dynamically generates a protein family structure. As a first set of proteins from other organisms, all of the approximately 700 putative membrane proteins were extracted from the genome of the cyanobacterium Synechocystis sp. and incorporated in the ARAMEMNON DB. The ARAMEMNON DB is accessible at the URL http://aramemnon.botanik.uni-koeln.de. PMID:12529511

  14. Benchmarking NMR experiments: a relational database of protein pulse sequences.

    Science.gov (United States)

    Senthamarai, Russell R P; Kuprov, Ilya; Pervushin, Konstantin

    2010-03-01

    Systematic benchmarking of multi-dimensional protein NMR experiments is a critical prerequisite for optimal allocation of NMR resources for structural analysis of challenging proteins, e.g. large proteins with limited solubility or proteins prone to aggregation. We propose a set of benchmarking parameters for essential protein NMR experiments organized into a lightweight (single XML file) relational database (RDB), which includes all the necessary auxiliaries (waveforms, decoupling sequences, calibration tables, setup algorithms and an RDB management system). The database is interfaced to the Spinach library (http://spindynamics.org), which enables accurate simulation and benchmarking of NMR experiments on large spin systems. A key feature is the ability to use a single user-specified spin system to simulate the majority of deposited solution state NMR experiments, thus providing the (hitherto unavailable) unified framework for pulse sequence evaluation. This development enables predicting relative sensitivity of deposited implementations of NMR experiments, thus providing a basis for comparison, optimization and, eventually, automation of NMR analysis. The benchmarking is demonstrated with two proteins, of 170 amino acids I domain of alphaXbeta2 Integrin and 440 amino acids NS3 helicase.

  15. Protein differences between normal and oligospermic human sperm demonstrated by two-dimensional gel electrophoresis.

    Science.gov (United States)

    Morgentaler, A; Schopperle, W M; Crocker, R H; DeWolf, W C

    1990-11-01

    Protein expression by sperm obtained from men with normal semen analysis and men with oligospermia were evaluated by two-dimensional gel electrophoresis. Proteins were solubilized in a 9.5 M urea/2% Nonidet-P40 (LKB, Bromma, Sweden) lysis buffer and underwent second dimension separation on 10 to 16% polyacrylamide gradient gels. A set of 36 invariant proteins was identified in all normospermic samples, whereas 8 of 10 evaluable oligospermic samples lacked 1 or more of the invariant proteins. Proteins absent in oligospermic samples may be critical to normal sperm function and may serve as markers for infertility.

  16. Development of Deduced Protein Database Using Variable Bit Binary Encoding

    Directory of Open Access Journals (Sweden)

    B. Parvathavarthini

    2008-01-01

    Full Text Available A large amount of biological data is semi-structured and stored in any one the following file formats such as flat, XML and relational files. These databases must be integrated with the structured data available in relational or object-oriented databases. The sequence matching process is difficult in such file format, because string comparison takes more computation cost and time. To reduce the memory storage size of amino acid sequence in protein database, a novel probability-based variable bit length encoding technique has been introduced. The number of mapping of triplet CODON for every amino acid evaluates the probability value. Then, a binary tree has been constructed to assign unique bits of binary codes to each amino acid. This derived unique bit pattern of amino acid replaces the existing fixed byte representation. The proof of reduced protein database space has been discussed and it is found to be reduced between 42.86 to 87.17%. To validate our method, we have collected few amino acid sequences of major organisms like Sheep, Lambda phage and etc from NCBI and represented them using proposed method. The comparison shows that of minimum and maximum reduction in storage space are 43.30% and 72.86% respectively. In future the biological data can further be reduced by applying lossless compression on this deduced data.

  17. Increase in local protein concentration by field-inversion gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Paulus Aran

    2007-09-01

    Full Text Available Abstract Background Proteins that migrate through cross-linked polyacrylamide gels (PAGs under the influence of a constant electric field experience negative factors, such as diffusion and non-specific trapping in the gel matrix. These negative factors reduce protein concentrations within a defined gel volume with increasing migration distance and, therefore, decrease protein separation efficiency. Enhancement of protein separation efficiency was investigated by implementing pulsed field-inversion gel electrophoresis (FIGE. Results Separation of model protein species and large protein complexes was compared between FIGE and constant field electrophoresis (CFE in different percentages of PAGs. Band intensities of proteins in FIGE with appropriate ratios of forward and backward pulse times were superior to CFE despite longer running times. These results revealed an increase in band intensity per defined gel volume. A biphasic protein relative mobility shift was observed in percentages of PAGs up to 14%. However, the effect of FIGE on protein separation was stochastic at higher PAG percentage. Rat liver lysates subjected to FIGE in the second-dimension separation of two-dimensional polyarcylamide gel electrophoresis (2D PAGE showed a 20% increase in the number of discernible spots compared with CFE. Nine common spots from both FIGE and CFE were selected for peptide sequencing by mass spectrometry (MS, which revealed higher final ion scores of all nine protein spots from FIGE. Native protein complexes ranging from 800 kDa to larger than 2000 kDa became apparent using FIGE compared with CFE. Conclusion The present investigation suggests that FIGE under appropriate conditions improves protein separation efficiency during PAGE as a result of increased local protein concentration. FIGE can be implemented with minimal additional instrumentation in any laboratory setting. Despite the tradeoff of longer running times, FIGE can be a powerful protein

  18. Gel Electrophoresis of Proteins for the Identification of Crop Varieties

    Institute of Scientific and Technical Information of China (English)

    LAN Hai-yan; LI Li-hui

    2002-01-01

    With the development of the international trade and agricultural science and technology, especially after the execution of the rules on protection of new plant varieties, considerable emphasis has been placed on variety identification. Many evidences have suggested that gel electrophoresis have great influence on this area. This paper reviewed study status of various gel electrophoresis, including development of the methods, comparison of these techniques, influence factors, practical applications, achievements obtained and aspects in the future study. With the wider range on protection of new plant varieties in China, electrophoresis will play a more important role in variety identification.

  19. Multivariate data analysis of two-dimensional gel electrophoresis protein patterns from few samples

    DEFF Research Database (Denmark)

    Jensen, Kristina Nedenskov; Jessen, Flemming; Jørgensen, Bo

    2008-01-01

    One application of 2D gel electrophoresis is to reveal differences in protein pattern between two or more groups of individuals, attributable to their group membership. Multivariate data analytical methods are useful in pinpointing the spots relevant for discrimination by focusing not only...... on single spot differences, but on the covariance structure between proteins. However, their outcome is dependent on data scaling, and they may fail in producing valid multivariate models due to the much higher number of "irrelevant" spots present in the gels. The case where only few gels are available...

  20. A protein domain interaction interface database: InterPare

    Directory of Open Access Journals (Sweden)

    Lee Jungsul

    2005-08-01

    Full Text Available Abstract Background Most proteins function by interacting with other molecules. Their interaction interfaces are highly conserved throughout evolution to avoid undesirable interactions that lead to fatal disorders in cells. Rational drug discovery includes computational methods to identify the interaction sites of lead compounds to the target molecules. Identifying and classifying protein interaction interfaces on a large scale can help researchers discover drug targets more efficiently. Description We introduce a large-scale protein domain interaction interface database called InterPare http://interpare.net. It contains both inter-chain (between chains interfaces and intra-chain (within chain interfaces. InterPare uses three methods to detect interfaces: 1 the geometric distance method for checking the distance between atoms that belong to different domains, 2 Accessible Surface Area (ASA, a method for detecting the buried region of a protein that is detached from a solvent when forming multimers or complexes, and 3 the Voronoi diagram, a computational geometry method that uses a mathematical definition of interface regions. InterPare includes visualization tools to display protein interior, surface, and interaction interfaces. It also provides statistics such as the amino acid propensities of queried protein according to its interior, surface, and interface region. The atom coordinates that belong to interface, surface, and interior regions can be downloaded from the website. Conclusion InterPare is an open and public database server for protein interaction interface information. It contains the large-scale interface data for proteins whose 3D-structures are known. As of November 2004, there were 10,583 (Geometric distance, 10,431 (ASA, and 11,010 (Voronoi diagram entries in the Protein Data Bank (PDB containing interfaces, according to the above three methods. In the case of the geometric distance method, there are 31,620 inter-chain domain

  1. Yeast Interacting Proteins Database: YJR091C, YMR067C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpression causes...olved in localizing the Arp2/3 complex to mitochondria; overexpression causes increased sensitivity to benom

  2. Yeast Interacting Proteins Database: YMR154C, YLR025W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available the multivesicular body (MVB) pathway; recruited from the cytoplasm to endosomal membranes Rows with this pr...mbrane proteins into the multivesicular body (MVB) pathway; recruited from the cytoplasm to endosomal membranes

  3. Yeast Interacting Proteins Database: YER081W, YDR105C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YDR105C TMS1 Vacuolar membrane protein of unknown function that is conserved in mammals; predicted to contai...tion that is conserved in mammals; predicted to contain eleven transmembrane heli

  4. Yeast Interacting Proteins Database: YMR047C, YDL065C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available L065C PEX19 Chaperone and import receptor for newly-synthesized class I peroxisom...scription Chaperone and import receptor for newly-synthesized class I peroxisomal membrane proteins (PMPs),

  5. Yeast Interacting Proteins Database: YCL029C, YER016W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available rotubules and kinetochore, involved in sister chromatid separation; essential in polyploid cells but not in ...le-associated protein, component of the interface between microtubules and kinetochore, involved in sister chromatid separation

  6. Yeast Interacting Proteins Database: YCL032W, YLR423C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YCL032W STE50 Protein involved in mating response, invasive/filamentous growth, and...lved in mating response, invasive/filamentous growth, and osmotolerance, acts as an adaptor that links G pro

  7. Yeast Interacting Proteins Database: YPL114W, YMR133W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available iotic recombination; possibly involved in the coordination of recombination and m...tion Protein involved in early stages of meiotic recombination; possibly involved in the coordination of rec

  8. Yeast Interacting Proteins Database: YCL046W, YGL115W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available le experimental and comparative sequence data; partially overlaps the uncharacterized ORF YCL045C Rows with ...ading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially

  9. Yeast Interacting Proteins Database: YLR295C, YOL050C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available on available experimental and comparative sequence data; overlaps verified gene G...en reading frame unlikely to encode a protein, based on available experimental and comparative sequence data

  10. Yeast Interacting Proteins Database: YHR114W, YJL086C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available available experimental and comparative sequence data; partially overlaps the verified genes YJL085W/EXO70 a... reading frame unlikely to encode a protein, based on available experimental and comparative sequence data;

  11. Yeast Interacting Proteins Database: YJR091C, YDR008C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ailable experimental and comparative sequence data Rows with this prey as prey (1) Rows with this prey as ba... - Prey description Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative

  12. Yeast Interacting Proteins Database: YKL002W, YLR423C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available integral membrane proteins into lumenal vesicles of multivesicular bodies, and for delivery of newly synthes... into lumenal vesicles of multivesicular bodies, and for delivery of newly synthesized vacuolar enzymes to t

  13. Yeast Interacting Proteins Database: YFL003C, YDL154W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YFL003C MSH4 Protein involved in meiotic recombination, required for normal levels of crossing...in involved in meiotic recombination, required for normal levels of crossing over, colocalizes with Zip2p to

  14. Yeast Interacting Proteins Database: YJR091C, YOR265W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpression causes...ns; involved in localizing the Arp2/3 complex to mitochondria; overexpression causes increased sensitivity t

  15. Yeast Interacting Proteins Database: YKL166C, YIL033C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available tein kinase (PKA), a component of a signaling pathway that controls a variety of cellular processes, includi...dependent protein kinase (PKA), a component of a signaling pathway that controls a variety of cellular processes

  16. Yeast Interacting Proteins Database: YJL164C, YIL033C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available tein kinase (PKA), a component of a signaling pathway that controls a variety of cellular processes, includi...dependent protein kinase (PKA), a component of a signaling pathway that controls a variety of cellular processes

  17. Yeast Interacting Proteins Database: YBR239C, YPL133C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available cytoplasm and nucleus; null mutation affects periodicity of transcriptional and metabolic oscillation; play...ion; GFP-fusion protein localizes to the cytoplasm and nucleus; null mutation affects

  18. Yeast Interacting Proteins Database: YOR014W, YNL042W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available P3 Protein of unknown function, potential Cdc28p substrate; overproduction confers resistance to methylmercury...l Cdc28p substrate; overproduction confers resistance to methylmercury Rows with this prey as prey Rows with

  19. Yeast Interacting Proteins Database: YDR026C, YDL030W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YDR026C - Protein of unknown function that may interact with ribosomes, based on co-purification...ein of unknown function that may interact with ribosomes, based on co-purification

  20. Yeast Interacting Proteins Database: YNL311C, YKL001C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YNL311C - Protein of unknown function that may interact with ribosomes, based on co-purification...nknown function that may interact with ribosomes, based on co-purification experi

  1. Yeast Interacting Proteins Database: YLR319C, YGL015C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YLR319C BUD6 Actin- and formin-interacting protein, involved in actin cable nucleation and polarized...in actin cable nucleation and polarized cell growth; isolated as bipolar budding mutant; potential Cdc28p su

  2. Yeast Interacting Proteins Database: YHR113W, YOL082W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available cargo proteins aminopeptidase I (Lap4p) and alpha-mannosidase (Ams1p) to the phagophore assembly site for packaging...vt) pathway; delivers cargo proteins aminopeptidase I (Lap4p) and alpha-mannosidase (Ams1p) to the phagophore assembly site for packa...ging into Cvt vesicles Rows with this prey as prey (6) Rows with this prey as bait

  3. Yeast Interacting Proteins Database: YCL032W, YLR362W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YCL032W STE50 Protein involved in mating response, invasive/filamentous growth, and...STE11 Signal transducing MEK kinase involved in pheromone response and pseudohyphal/invasive...2W Bait gene name STE50 Bait description Protein involved in mating response, invasive/filamentous growth, a... STE11 Prey description Signal transducing MEK kinase involved in pheromone response and pseudohyphal/invasive

  4. Yeast Interacting Proteins Database: YLR362W, YCL032W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YLR362W STE11 Signal transducing MEK kinase involved in pheromone response and pseudohyphal/invasive...ait as prey (1) YCL032W STE50 Protein involved in mating response, invasive/filam...2W Bait gene name STE11 Bait description Signal transducing MEK kinase involved in pheromone response and pseudohyphal/invasive...F YCL032W Prey gene name STE50 Prey description Protein involved in mating response, invasive/filamentous gr

  5. Yeast Interacting Proteins Database: YGR058W, YGR136W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available main; binds Las17p, which is a homolog of human Wiskott-Aldrich Syndrome protein involved in actin... patch assembly and actin polymerization Rows with this prey as prey (4) Rows with this pre...erminal SH3 domain; binds Las17p, which is a homolog of human Wiskott-Aldrich Syndrome protein involved in actin... patch assembly and actin polymerization Rows with this prey as prey Rows with this prey as prey (4) Row

  6. Yeast Interacting Proteins Database: YHR114W, YJL180C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YHR114W BZZ1 SH3 domain protein implicated in the regulation of actin polymerization, able to recruit actin... polymerization machinery through its SH3 domains, colocalizes with cortical actin p...YHR114W Bait gene name BZZ1 Bait description SH3 domain protein implicated in the regulation of actin polyme...rization, able to recruit actin polymerization machinery through its SH3 domains, colocalizes with cortical actin

  7. Yeast Interacting Proteins Database: YMR294W, YHR129C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available complex; required for spindle orientation and nuclear migration; putative ortholo...PD) 1 Alternative path with 2 intervening proteins (YPD) 2 IST hit 7 IST hit in the opposite bait/prey orientation 21 ... ...ne name ARP1 Prey description Actin-related protein of the dynactin complex; required for spindle orientat...ion and nuclear migration; putative ortholog of mammalian centractin Rows with this

  8. Release behavior of non-network proteins and its relationship to the structure of heat-induced soy protein gels.

    Science.gov (United States)

    Wu, Chao; Hua, Yufei; Chen, Yeming; Kong, Xiangzhen; Zhang, Caimeng

    2015-04-29

    Heat-induced soy protein gels were prepared by heating protein solutions at 12%, 15% ,or 18% for 0.5, 1.0, or 2.0 h. The release of non-network proteins from gel slices was conducted in 10 mM pH 7.0 sodium phosphate buffer. SDS-PAGE and diagonal electrophoresis demonstrated that the released proteins consisted of undenatured AB subunits and denatured proteins including monomers of A polypeptides, disulfide bond linked dimers, trimers, and polymers of A polypeptides, and an unidentified 15 kDa protein. SEC-HPLC analysis of non-network proteins revealed three major protein peaks, with molecular weights of approximately 253.9, 44.8, and 9.7 kDa. The experimental data showed that the time-dependent release of the three fractions from soy protein gels fit Fick's second law. An increasing protein concentration or heating time resulted in a decrease in diffusion coefficients of non-network proteins. A power law expression was used to describe the relationship between non-network protein diffusion coefficient and molecular weight, for which the exponent (α) shifted to higher value with an increase in protein concentration or heating time, indicating that a more compact gel structure was formed.

  9. Microstructure and rheology of globular protein gels in the presence of gelatin

    NARCIS (Netherlands)

    Ersch, C.; Meinders, M.B.J.; Bouwman, W.G.; Nieuwland, M.; Linden, van der E.; Venema, P.; Martin, A.H.

    2016-01-01

    The microstructure and rheological response of globular protein gels (whey protein isolate (WPI) and soy protein isolate (SPI)) in the presence of gelatin (type A, type B and hydrolyzed type A) was investigated. Microstructural information was obtained using a combination of confocal laser scanning

  10. Mixing whey and soy proteins: Consequences for the gel mechanical response and water holding

    NARCIS (Netherlands)

    Jose, J.; Pouvreau, L.A.M.; Martin, Anneke

    2016-01-01

    To design food products based on mixtures of proteins from animal and plant sources, understanding of how the structural and mechanical properties of mixed protein systems can benefit from selectively mixing is essential. Heat-induced gels were prepared from mixtures of whey proteins (WP) and soy pr

  11. Concentration dependence of dynamic moduli of heat-induced soy protein gels

    NARCIS (Netherlands)

    Renkema, J.M.S.; Vliet, van T.

    2004-01-01

    The concentration dependence of dynamic moduli of soy protein gels was studied for different protein preparations (soy protein isolate), purified glycinin and a -conglycinin rich fraction) at various pHs and salt concentrations. The concentration dependence of the storage modulus of glycinin and

  12. Analysis of soybean embryonic axis proteins by two-dimensional gel electrophoresis and mass spectrometry

    Science.gov (United States)

    A proteomic approach based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) for protein separation and subsequent mass spectrometry (MS) for protein identification was applied to establish a proteomic reference map for the soybean embryonic axis. Proteins were extracted from dissecte...

  13. CREDO: a protein-ligand interaction database for drug discovery.

    Science.gov (United States)

    Schreyer, Adrian; Blundell, Tom

    2009-02-01

    Harnessing data from the growing number of protein-ligand complexes in the Protein Data Bank is an important task in drug discovery. In order to benefit from the abundance of three-dimensional structures, structural data must be integrated with sequence as well as chemical data and the protein-small molecule interactions characterized structurally at the inter-atomic level. In this study, we present CREDO, a new publicly available database of protein-ligand interactions, which represents contacts as structural interaction fingerprints, implements novel features and is completely scriptable through its application programming interface. Features of CREDO include implementation of molecular shape descriptors with ultrafast shape recognition, fragmentation of ligands in the Protein Data Bank, sequence-to-structure mapping and the identification of approved drugs. Selected analyses of these key features are presented to highlight a range of potential applications of CREDO. The CREDO dataset has been released into the public domain together with the application programming interface under a Creative Commons license at http://www-cryst.bioc.cam.ac.uk/credo. We believe that the free availability and numerous features of CREDO database will be useful not only for commercial but also for academia-driven drug discovery programmes.

  14. Exploring Protein Function Using the Saccharomyces Genome Database.

    Science.gov (United States)

    Wong, Edith D

    2017-01-01

    Elucidating the function of individual proteins will help to create a comprehensive picture of cell biology, as well as shed light on human disease mechanisms, possible treatments, and cures. Due to its compact genome, and extensive history of experimentation and annotation, the budding yeast Saccharomyces cerevisiae is an ideal model organism in which to determine protein function. This information can then be leveraged to infer functions of human homologs. Despite the large amount of research and biological data about S. cerevisiae, many proteins' functions remain unknown. Here, we explore ways to use the Saccharomyces Genome Database (SGD; http://www.yeastgenome.org ) to predict the function of proteins and gain insight into their roles in various cellular processes.

  15. The effect of polysaccharides on the ability of whey protein gels to either store or dissipate energy upon mechanical deformation

    NARCIS (Netherlands)

    Darizu Munialo, C.; Linden, E. van der; Ako, K.; Nieuwland, M.; As, H. van; Jongh, H.H.J. de

    2016-01-01

    The addition of polysaccharides to proteins during gel formation can alter the mechanical and textural properties of the resultant gels. However, the effect of addition of different polymers on mechanical properties of whey protein (WP) gels including their ability to elastically store energy, often

  16. The effect of polysaccharides on the ability of whey protein gels to either store or dissipate energy upon mechanical deformation

    NARCIS (Netherlands)

    Munialo, C.D.; Linden, van der E.; Ako, K.; Nieuwland, M.; As, van H.; Jongh, de H.H.J.

    2016-01-01

    The addition of polysaccharides to proteins during gel formation can alter the mechanical and textural properties of the resultant gels. However, the effect of addition of different polymers on mechanical properties of whey protein (WP) gels including their ability to elastically store energy, often

  17. MannDB: A microbial annotation database for protein characterization

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, C; Lam, M; Smith, J; Zemla, A; Dyer, M; Kuczmarski, T; Vitalis, E; Slezak, T

    2006-05-19

    MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins) are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. MannDB comprises a large number of genomes and comprehensive protein sequence analyses representing organisms listed as high

  18. Yeast Interacting Proteins Database: YNL056W, YNL032W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available a1p and Siw14p; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YNL056W is not an essential gene Row...s with this bait as bait (2) Rows with this bait as prey (0) YNL032W SIW14 Tyrosine phosp...hatase that plays a role in actin filament organization and endocytosis; localized to the cytoplasm Row...s with this prey as prey (2) Rows with this prey as bait (0) 6 8 4 14 1 0 0 0 0 - - - ...in (GFP)-fusion protein localizes to the cytoplasm; YNL056W is not an essential gene Rows with this bait as bait Row

  19. Rheology of reconstituted silk fibroin protein gels: the epitome of extreme mechanics.

    Science.gov (United States)

    Tabatabai, A Pasha; Kaplan, David L; Blair, Daniel L

    2015-01-28

    In nature, silk fibroin proteins assemble into hierarchical structures with dramatic mechanical properties. With the hope of creating new classes of on demand silk-based biomaterials, Bombyx mori silk is reconstituted back into stable aqueous solutions that can be reassembled into functionalized materials; one strategy for reassembly is electrogelation. Electrogels (e-gels) are particularly versatile and can be produced using electrolysis with small DC electric fields. We characterize the linear and nonlinear rheological behavior of e-gels to provide fundamental insights into these distinct protein-based materials. We observe that e-gels form robust biopolymer networks that exhibit distinctive strain hardening and are recoverable from strains as large as γ=27, i.e. 2700%. We propose a simple microscopic model that is consistent with local restructuring of single proteins within the e-gel network.

  20. Impact of protein pre-treatment conditions on the iron encapsulation efficiency of whey protein cold-set gel particles

    NARCIS (Netherlands)

    Martin, A.H.; Jong, G.A.H. de

    2012-01-01

    This paper investigates the possibility for iron fortification of food using protein gel particles in which iron is entrapped using cold-set gelation. The aim is to optimize the iron encapsulation efficiency of whey protein by giving the whey protein different heat treatment prior to gelation with i

  1. Yeast Interacting Proteins Database: YDL108W, YGL134W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available TFIIH; involved in transcription initiation at RNA polymerase II promoters Rows with this bait as bait (1) Row...ependent protein kinase to its substrate Rows with this prey as prey (2) Rows wit... transcription initiation at RNA polymerase II promoters Rows with this bait as bait Row...s with this bait as bait (1) Rows with this bait as prey Rows with this bait as prey (0) Prey ORF YGL...endent protein kinase to its substrate Rows with this prey as prey Rows with this prey as prey (2) Row

  2. Yeast Interacting Proteins Database: YBR170C, YGR048W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available the proteasome for degradation Rows with this bait as bait (2) Rows with this bait as prey (1) YGR048W UFD1...roteins from the ER to the cytosol Rows with this prey as prey (1) Rows with this prey as bait (1) 15 10 5 1...hat recognizes ubiquitinated proteins in the endoplasmic reticulum and delivers them to the proteasome for degradation Row...s with this bait as bait Rows with this bait as bait (2) Rows with this bait as prey Row...esentation to the 26S proteasome for degradation; involved in transporting proteins from the ER to the cytosol Row

  3. Yeast Interacting Proteins Database: YOR059C, YGL053W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YOR059C - Hypothetical protein Rows with this bait as bait (1) Rows with this bait ...nce, a motif involved in COPII binding; forms a complex with Prp9p in the ER; member of DUP240 gene family Row...s with this prey as prey (1) Rows with this prey as bait (0) 5 6 3 4 0 0 0 0 0 ...- - - - - 0 0 5 - Show YOR059C Bait ORF YOR059C Bait gene name - Bait description Hypothetical protein Rows ...with this bait as bait Rows with this bait as bait (1) Rows with this bait as prey Rows with this bait as pr

  4. Yeast Interacting Proteins Database: YGR048W, YBR170C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available sporting proteins from the ER to the cytosol Rows with this bait as bait (1) Rows with this bait as prey (1)... to the proteasome for degradation Rows with this prey as prey (1) Rows with this prey as bait (2) 10 15 5 1...m the ER to the cytosol Rows with this bait as bait Rows with this bait as bait (1) Row...s with this bait as prey Rows with this bait as prey (1) Prey ORF YBR170C Prey gene name NPL4 Prey des...gnizes ubiquitinated proteins in the endoplasmic reticulum and delivers them to the proteasome for degradation Row

  5. Yeast Interacting Proteins Database: YNL189W, YEL066W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available may also play a role in regulation of protein degradation Rows with this bait as bait (55) Rows with this b...is last product liberated; similar to Hpa2p, acetylates histones weakly in vitro Rows with this prey as prey (3) Row...bstrate during import; may also play a role in regulation of protein degradation Row...s with this bait as bait Rows with this bait as bait (55) Rows with this bait as prey Rows with this bait...nd and CoA is last product liberated; similar to Hpa2p, acetylates histones weakly in vitro Row

  6. Yeast Interacting Proteins Database: YNR006W, YHL002W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available has Ubiquitin Interaction Motifs which bind ubiquitin (Ubi4p) Rows with this bait as bait (1) Rows with this..., as well as for recycling of Golgi proteins and formation of lumenal membranes Rows with this prey as prey (1) Row...ined for degradation; has Ubiquitin Interaction Motifs which bind ubiquitin (Ubi4p) Row...s with this bait as bait Rows with this bait as bait (1) Rows with this bait as prey Rows with this ba...degradation, as well as for recycling of Golgi proteins and formation of lumenal membranes Row

  7. Yeast Interacting Proteins Database: YBR187W, YNR032W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available st a possible role in ribosome biogenesis Rows with this bait as bait (1) Rows with this bait as prey (0) YN...ccumulation; interacts with Tap42p, which binds to and regulates other protein phosphatases Rows with this prey as prey (2) Row... and physical interactions suggest a possible role in ribosome biogenesis Rows with this bait as bait Rows w...ith this bait as bait (1) Rows with this bait as prey Rows with this bait as prey...quired for glycogen accumulation; interacts with Tap42p, which binds to and regulates other protein phosphatases Row

  8. Yeast Interacting Proteins Database: YNL020C, YGR241C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available actin cytoskeleton; involved in control of endocytosis Rows with this bait as bait (1) Rows with this bait ... to Yap1801p, member of the AP180 protein family Rows with this prey as prey (1) Row...skeleton; involved in control of endocytosis Rows with this bait as bait Rows wit...h this bait as bait (1) Rows with this bait as prey Rows with this bait as prey (0) Prey ORF YGR241C Prey ge...ogous to Yap1801p, member of the AP180 protein family Rows with this prey as prey Row

  9. Yeast Interacting Proteins Database: YJR055W, YPL193W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YJR055W HIT1 Protein of unknown function, required for growth at high temperature Row...s with this bait as bait (1) Rows with this bait as prey (0) YPL193W RSA1 Protein involved in the assembly... of 60S ribosomal subunits; functionally interacts with Dbp6p; functions in a late nucleoplasmic step of the assembly Row...s with this prey as prey (1) Rows with this prey as bait (0) 6 5 2 2...unknown function, required for growth at high temperature Rows with this bait as bait Rows with this bait as bait (1) Row

  10. Yeast Interacting Proteins Database: YDL239C, YPL255W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YDL239C ADY3 Protein required for spore wall formation, thought to mediate assembly... of a Don1p-containing structure at the leading edge of the prospore membrane via interaction with spindle p...it as prey (1) YPL255W BBP1 Protein required for the spindle pole body (SPB) dupl...ows with this prey as bait (0) 4 8 3 4 0 0 0 0 0 - - - - - 0 0 7 - Show YDL239C Bait ORF YDL...ediate assembly of a Don1p-containing structure at the leading edge of the prospore membrane via interaction with spindl

  11. Yeast Interacting Proteins Database: YJL070C, YDR504C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ired for growth on nonfermentable carbon sources Rows with this prey as prey (1) Rows with this prey as bait...on Protein required for survival at high temperature during stationary phase; not required for growth on nonfermentable carbon source

  12. Yeast Interacting Proteins Database: YGR173W, YDR152W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ding protein Rows with this bait as bait (1) Rows with this bait as prey (0) YDR152W GIR2 Highly-acidic cyto...ws with this bait as prey Rows with this bait as prey (0) Prey ORF YDR152W Prey gene name GIR2 Prey description Highly

  13. Yeast Interacting Proteins Database: YGR196C, YBR260C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YGR196C FYV8 Protein of unknown function, required for survival upon exposure to K1...n, required for survival upon exposure to K1 killer toxin Rows with this bait as bait Rows with this bait as

  14. Yeast Interacting Proteins Database: YJR091C, YLR156W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ion with Jsn1p in a large-scale analysis Rows with this prey as prey (1) Rows with this prey as bait (0) 7 5...scription Putative protein of unknown function; exhibits a two-hybrid interaction with Jsn1p in a large-scale

  15. Yeast Interacting Proteins Database: YGR119C, YDL065C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available this bait as bait (5) Rows with this bait as prey (0) YDL065C PEX19 Chaperone and import receptor for newly-synthesized...y description Chaperone and import receptor for newly-synthesized class I peroxisomal membrane proteins (PMP

  16. Yeast Interacting Proteins Database: YGR218W, YDL065C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available PEX19 Chaperone and import receptor for newly-synthesized class I peroxisomal membrane proteins (PMPs), bin...ith this bait as prey (0) Prey ORF YDL065C Prey gene name PEX19 Prey description Chaperone and import receptor for newly-synthesized

  17. Yeast Interacting Proteins Database: YKL002W, YFL034C-B [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available eral genes involved in cell separation; Mob1p-like protein Rows with this prey as prey (2) Rows with this pr...tes the Ace2p in the daughter cell nucleus to direct daughter cell-specific transcription of several genes involved in cell separatio

  18. Yeast Interacting Proteins Database: YIR016W, YFL034C-B [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available the daughter cell nucleus to direct daughter cell-specific transcription of several genes involved in cell separation...ter cell-specific transcription of several genes involved in cell separation; Mob1p-like protein Rows with t

  19. Yeast Interacting Proteins Database: YKL103C, YOL082W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available go proteins aminopeptidase I (Lap4p) and alpha-mannosidase (Ams1p) to the phagophore assembly site for packaging...-mannosidase (Ams1p) to the phagophore assembly site for packaging into Cvt vesicles Rows with this prey as

  20. Yeast Interacting Proteins Database: YER081W, YPR136C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available mental and comparative sequence data; partially overlaps verified ORF RRP9 Rows w...tially overlaps verified ORF RRP9 Rows with this prey as...YPR136C - Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; par

  1. Yeast Interacting Proteins Database: YNL041C, YDR229W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available pholipid-binding protein that interacts with both Ypt7p and Vps33p, may partially...teracts with both Ypt7p and Vps33p, may partially counteract the action of Vps33p and vice versa, localizes

  2. Yeast Interacting Proteins Database: YEL005C, YGL079W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available endosome; identified as a transcriptional activator in a high-throughput yeast one-hybrid assay Rows with th...protein localizes to the endosome; identified as a transcriptional activator in a high-throughput yeast one-hybrid assay

  3. Yeast Interacting Proteins Database: YIL007C, YOR117W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YIL007C NAS2 Proteasome-interacting protein involved in the assembly of the base su... - - - - - 0 0 3 4 Show YIL007C Bait ORF YIL007C Bait gene name NAS2 Bait description Proteasome-interacti

  4. Yeast Interacting Proteins Database: YNL189W, YGL221C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available urified mitochondria in high-throughput studies Rows with this prey as prey (2) Rows with this prey as bait ...a factor (rpoD gene product); the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studie

  5. Yeast Interacting Proteins Database: YDL044C, YLR386W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available of mitochondrial RNA polymerase (Rpo41p) and couples RNA processing and translation to transcription Rows wi...protein that interacts with an N-terminal region of mitochondrial RNA polymerase (Rpo41p) and couples RNA pr

  6. Yeast Interacting Proteins Database: YDL167C, YBL081W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available as bait (2) Rows with this bait as prey (0) YBL081W - Non-essential protein of unknown function; null mutation results in a decrease... function; null mutation results in a decrease in plasma membrane electron transp

  7. Yeast Interacting Proteins Database: YDL089W, YCR086W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available rDNA repeat stability; null mutant causes increase in unequal sister-chromatid exchange; GFP-fusion protein...p, Lrs4p; required for rDNA repeat stability; null mutant causes increase in unequal sister-chromatid exchan

  8. Yeast Interacting Proteins Database: YLR026C, YDR189W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ait as prey (0) YDR189W SLY1 Hydrophilic protein involved in vesicle trafficking between the ER and Golgi; S...it (1) Rows with this bait as prey Rows with this bait as prey (0) Prey ORF YDR189W Prey gene name SLY1 Prey description Hydrophilic

  9. Yeast Interacting Proteins Database: YLR295C, YDL118W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available tein of unconfirmed function; mutants are defective in telomere maintenance, and ...7) Rows with this bait as prey (0) YDL118W - Non-essential protein of unconfirmed function; mutants are defective in telomere mainten...ance, and are synthetically sick or lethal with alpha-sy

  10. Yeast Interacting Proteins Database: YHR166C, YLR451W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YHR166C CDC23 Subunit of the Anaphase-Promoting Complex/Cyclosome (APC/C), which is...ait description Subunit of the Anaphase-Promoting Complex/Cyclosome (APC/C), which is a ubiquitin-protein li

  11. Yeast Interacting Proteins Database: YJR091C, YFR036W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available 0) YFR036W CDC26 Subunit of the Anaphase-Promoting Complex/Cyclosome (APC/C), whi...rey description Subunit of the Anaphase-Promoting Complex/Cyclosome (APC/C), which is a ubiquitin-protein li

  12. Yeast Interacting Proteins Database: YGR223C, YOR089C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available micronucleophagy; predicted to fold as a seven-bladed beta-propeller; displays punctate cytoplasmic localiz...tion Phosphatidylinositol 3,5-bisphosphate-binding protein, plays a role in micronucleophagy; predicted to fold as a seven-blade

  13. A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

    Science.gov (United States)

    Mobilio, Dominick; Walker, Gary; Brooijmans, Natasja; Nilakantan, Ramaswamy; Denny, R Aldrin; Dejoannis, Jason; Feyfant, Eric; Kowticwar, Rupesh K; Mankala, Jyoti; Palli, Satish; Punyamantula, Sairam; Tatipally, Maneesh; John, Reji K; Humblet, Christine

    2010-08-01

    The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.

  14. PROXiMATE: a database of mutant protein-protein complex thermodynamics and kinetics.

    Science.gov (United States)

    Jemimah, Sherlyn; Yugandhar, K; Michael Gromiha, M

    2017-09-01

    We have developed PROXiMATE, a database of thermodynamic data for more than 6000 missense mutations in 174 heterodimeric protein-protein complexes, supplemented with interaction network data from STRING database, solvent accessibility, sequence, structural and functional information, experimental conditions and literature information. Additional features include complex structure visualization, search and display options, download options and a provision for users to upload their data. The database is freely available at http://www.iitm.ac.in/bioinfo/PROXiMATE/ . The website is implemented in Python, and supports recent versions of major browsers such as IE10, Firefox, Chrome and Opera. gromiha@iitm.ac.in. Supplementary data are available at Bioinformatics online.

  15. Structure and kinetics of chemically cross-linked protein gels from small-angle X-ray scattering

    CERN Document Server

    Kaieda, Shuji; Halle, Bertil

    2014-01-01

    Glutaraldehyde (GA) reacts with amino groups in proteins, forming intermolecular cross-links that, at sufficiently high protein concentration, can transform a protein solution into a gel. Although GA has been used as a cross-linking reagent for decades, neither the cross-linking chemistry nor the microstructure of the resulting protein gel have been clearly established. Here we use small-angle X-ray scattering (SAXS) to characterise the microstructure and structural kinetics of gels formed by cross-linking of pancreatic trypsin inhibitor, myoglobin or intestinal fatty acid-binding protein. By comparing the scattering from gels and dilute solutions, we extract the structure factor and the pair correlation function of the gel. The protein gels are spatially heterogeneous, with dense clusters linked by sparse networks. Within the clusters, adjacent protein molecules are almost in contact, but the protein concentration in the cluster is much lower than in a crystal. At the $\\sim$ 1 nm SAXS resolution, the native ...

  16. Yeast Interacting Proteins Database: YGR247W, YOR327C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ferred by null mutation or by overexpression Rows with this bait as bait (1) Rows with this bait as prey (0)...f R-type v-SNARE proteins Rows with this prey as prey (2) Rows with this prey as bait (0) 7 27 3 4 0 0 0 0 0...phosphate; may have a role in tRNA splicing; no detectable phenotype is conferred by null mutation or by overexpression Row...s with this bait as bait Rows with this bait as bait (1) Rows with this bait as prey Row...h the plasma membrane; member of the synaptobrevin/VAMP family of R-type v-SNARE proteins Rows with this prey as prey Row

  17. Yeast Interacting Proteins Database: YNL189W, YGL166W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available may also play a role in regulation of protein degradation Rows with this bait as bait (55) Rows with this b...cription of the metallothionein genes CUP1-1 and CUP1-2 in response to elevated copper concentrations Rows w...ith this prey as prey (1) Rows with this prey as bait (0) 67 47 3 5 0 0 0 0 0 - - - - - 0 0 5 - Show YNL189W...ation signal of the substrate during import; may also play a role in regulation of protein degradation Rows ...with this bait as bait Rows with this bait as bait (55) Rows with this bait as prey Row

  18. Yeast Interacting Proteins Database: YHL004W, YPL255W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YHL004W MRP4 Mitochondrial ribosomal protein of the small subunit Rows with this bait as bait (3) Row...2p and SPB components Spc29p and Kar1p; required for mitotic functions of Cdc5p Row...s with this prey as prey (4) Rows with this prey as bait (0) 9 8 2 2 0 0 0 0 0 - - - - - 0 0 6 - Show YHL0...04W Bait ORF YHL004W Bait gene name MRP4 Bait description Mitochondrial ribosomal protein of the small subunit Row...s with this bait as bait Rows with this bait as bait (3) Rows with this bait as prey Row

  19. Yeast Interacting Proteins Database: YOR167C, YEL015W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ical to Rps28Bp and has similarity to rat S28 ribosomal protein Rows with this bait as bait (2) Rows with th...calizes to cytoplasmic mRNA processing bodies Rows with this prey as prey (4) Rows with this prey as bait (3...8Bp and has similarity to rat S28 ribosomal protein Rows with this bait as bait Rows with this bait as bait (2) Row...s with this bait as prey Rows with this bait as prey (0) Prey ORF YEL015W Prey gene name EDC3 Prey de...NA decapping by specifically affecting the function of the decapping enzyme Dcp1p; localizes to cytoplasmic

  20. Yeast Interacting Proteins Database: YER071C, YDR366C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available in localizes to the cytoplasm in a punctate pattern Rows with this bait as bait (2) Rows with this bait as p...rey (0) YDR366C - Putative protein of unknown function Rows with this prey as prey (1) Rows with this prey a...calizes to the cytoplasm in a punctate pattern Rows with this bait as bait Rows with this bait as bait (2) Row...s with this bait as prey Rows with this bait as prey (0) Prey ORF YDR366C Prey ...gene name - Prey description Putative protein of unknown function Rows with this prey as prey Rows with this prey as prey (1) Row

  1. Yeast Interacting Proteins Database: YEL015W, YLR264W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available mRNA processing bodies Rows with this bait as bait (3) Rows with this bait as prey (4) YLR264W RPS28B Prote...d has similarity to rat S28 ribosomal protein Rows with this prey as prey (1) Rows with this prey as bait (0... by specifically affecting the function of the decapping enzyme Dcp1p; localizes to cytoplasmic mRNA processing bodies Row...s with this bait as bait Rows with this bait as bait (3) Rows with this bait as prey Rows with...otein component of the small (40S) ribosomal subunit; nearly identical to Rps28Ap and has similarity to rat S28 ribosomal protein Row

  2. Yeast Interacting Proteins Database: YOR285W, YDR233C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available racts with exocyst subunit Sec6p and with Yip3p; also interacts with Sbh1p; null mutant has an altered (most...tion ER membrane protein that interacts with exocyst subunit Sec6p and with Yip3p; also interacts with Sbh1p; null mutant has an alte...red (mostly cisternal) ER morphology; member of the RTNL

  3. Yeast Interacting Proteins Database: YDR020C, YDR020C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available a screen for mutants with increased levels of rDNA transcription; weak similarity with uridine kinases and ...e protein of unknown function; non-essential gene identified in a screen for mutants with increased levels...n of unknown function; non-essential gene identified in a screen for mutants with increased levels of rDNA t...sential gene identified in a screen for mutants with increased levels of rDNA transcription; weak similarity

  4. Yeast Interacting Proteins Database: YDL239C, YLR423C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YDL239C ADY3 Protein required for spore wall formation, thought to mediate assembly... of a Don1p-containing structure at the leading edge of the prospore membrane via interaction with spindle p...0 0 - - - - - 0 0 34 - Show YDL239C Bait ORF YDL239C Bait gene name ADY3 Bait des...ure at the leading edge of the prospore membrane via interaction with spindle pole body components; potentia

  5. SynProt: A Database for Proteins of Detergent-Resistant Synaptic Protein Preparations

    Science.gov (United States)

    Pielot, Rainer; Smalla, Karl-Heinz; Müller, Anke; Landgraf, Peter; Lehmann, Anne-Christin; Eisenschmidt, Elke; Haus, Utz-Uwe; Weismantel, Robert; Gundelfinger, Eckart D.; Dieterich, Daniela C.

    2012-01-01

    Chemical synapses are highly specialized cell–cell contacts for communication between neurons in the CNS characterized by complex and dynamic protein networks at both synaptic membranes. The cytomatrix at the active zone (CAZ) organizes the apparatus for the regulated release of transmitters from the presynapse. At the postsynaptic side, the postsynaptic density constitutes the machinery for detection, integration, and transduction of the transmitter signal. Both pre- and postsynaptic protein networks represent the molecular substrates for synaptic plasticity. Their function can be altered both by regulating their composition and by post-translational modification of their components. For a comprehensive understanding of synaptic networks the entire ensemble of synaptic proteins has to be considered. To support this, we established a comprehensive database for synaptic junction proteins (SynProt database) primarily based on proteomics data obtained from biochemical preparations of detergent-resistant synaptic junctions. The database currently contains 2,788 non-redundant entries of rat, mouse, and some human proteins, which mainly have been manually extracted from 12 proteomic studies and annotated for synaptic subcellular localization. Each dataset is completed with manually added information including protein classifiers as well as automatically retrieved and updated information from public databases (UniProt and PubMed). We intend that the database will be used to support modeling of synaptic protein networks and rational experimental design. PMID:22737123

  6. Yeast Interacting Proteins Database: YMR047C, YBR137W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available aryopherin Kap95p; homologous to Nup100p Rows with this bait as bait (15) Rows with this bait as prey (0) YB...tion Protein A (RPA); YBR137W is not an essential gene Rows with this prey as prey (4) Rows with this prey a...pherin Kap95p; homologous to Nup100p Rows with this bait as bait Rows with this bait as bait (15) Rows with this bait as prey Row...(RPA); YBR137W is not an essential gene Rows with this prey as prey Rows with this prey as prey (4) Rows with this prey as bait Row

  7. Yeast Interacting Proteins Database: YHR169W, YKL075C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available activity stimulated by association with Esp2p Rows with this bait as bait (1) Rows with this bait as prey (0...-fusion protein localizes to the cytoplasm; proposed to be involved in resistance to streptozotocin and camptothecin Row...s with this prey as prey (1) Rows with this prey as bait (0) 6 5 2 2 0 0 0 0 0 - - - - - 0 0 3 -...rRNA and assembly of 40S small ribosomal subunit; ATPase activity stimulated by association with Esp2p Rows ...with this bait as bait Rows with this bait as bait (1) Rows with this bait as prey Row

  8. Yeast Interacting Proteins Database: YNL273W, YMR048W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available ing gap repair of damaged DNA; interacts with the MCM helicase Rows with this bait as bait (1) Rows with thi...s bait as prey (0) YMR048W CSM3 Protein required for accurate chromosome segregation during meiosis Row...s with this prey as prey (1) Rows with this prey as bait (0) 4 3 2 2 0 0 0 0 0 - - - -...rk to promote sister chromatid cohesion after DNA damage, facilitating gap repair of damaged DNA; interacts with the MCM helicase Row...s with this bait as bait Rows with this bait as bait (1) Rows with this bait as prey Row

  9. Yeast Interacting Proteins Database: YBR254C, YKR068C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available oepiphyseal dysplasia tarda (SEDL) disorder Rows with this bait as bait (2) Rows with this bait as prey (0) ...targeting and fusion of ER to Golgi transport vesicles; component of the TRAPP (transport protein particle) complex Row...s with this prey as prey (1) Rows with this prey as bait (1) 9 9 5 20 0 0 1 1 0 - - - - - 1 1 4 -... fusion; mutations in the human homolog cause the spondyloepiphyseal dysplasia tarda (SEDL) disorder Rows with this bait as bait Row...s with this bait as bait (2) Rows with this bait as prey Row

  10. Yeast Interacting Proteins Database: YBR246W, YDR520C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available a screen for mutants with increased levels of rDNA transcription; null mutants display a weak carboxypeptid...ene identified in a screen for mutants with increased levels of rDNA transcription; similar to S. kluyveri U... description Putative protein of unknown function; non-essential gene identified in a screen for mutants with increased levels...ative Zn(II)2Cys6 motif containing transcription factor; non-essential gene identified in a screen for mutants with increased levels

  11. Yeast Interacting Proteins Database: YDL239C, YDR273W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YDL239C ADY3 Protein required for spore wall formation, thought to mediate assembly... of a Don1p-containing structure at the leading edge of the prospore membrane via interaction with spindle p...it as prey (1) YDR273W DON1 Meiosis-specific component of the spindle pole body, ...0 - - - - - 0 0 5 - Show YDL239C Bait ORF YDL239C Bait gene name ADY3 Bait descri... at the leading edge of the prospore membrane via interaction with spindle pole body components; potentially

  12. Yeast Interacting Proteins Database: YDL239C, YOR324C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YDL239C ADY3 Protein required for spore wall formation, thought to mediate assembly... of a Don1p-containing structure at the leading edge of the prospore membrane via interaction with spindle p... as bait (0) 4 5 3 4 0 0 0 0 0 - - - - - 0 0 4 - Show YDL239C Bait ORF YDL239C Ba... a Don1p-containing structure at the leading edge of the prospore membrane via interaction with spindle pole

  13. Yeast Interacting Proteins Database: YDL239C, YDR148C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YDL239C ADY3 Protein required for spore wall formation, thought to mediate assembly... of a Don1p-containing structure at the leading edge of the prospore membrane via interaction with spindle p...s prey as bait (0) 4 15 2 5 0 0 0 0 0 - - - - - 0 0 3 - Show YDL239C Bait ORF YDL...mbly of a Don1p-containing structure at the leading edge of the prospore membrane via interaction with spindl

  14. Yeast Interacting Proteins Database: YDL239C, YAL028W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YDL239C ADY3 Protein required for spore wall formation, thought to mediate assembly... of a Don1p-containing structure at the leading edge of the prospore membrane via interaction with spindle p...(1) Rows with this prey as bait (0) 4 5 4 7 0 0 0 0 0 - - - - - 0 0 3 - Show YDL239C Bait ORF YDL... to mediate assembly of a Don1p-containing structure at the leading edge of the prospore membrane via interaction with spindl

  15. Yeast Interacting Proteins Database: YDL239C, YBR072W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YDL239C ADY3 Protein required for spore wall formation, thought to mediate assembly... of a Don1p-containing structure at the leading edge of the prospore membrane via interaction with spindle p... (3) Rows with this prey as bait (0) 4 52 1 1 0 0 0 0 0 - - - - - 0 0 3 - Show YDL239C Bait ORF YDL...ht to mediate assembly of a Don1p-containing structure at the leading edge of the prospore membrane via interaction with spindl

  16. Yeast Interacting Proteins Database: YDL239C, YLR072W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available YDL239C ADY3 Protein required for spore wall formation, thought to mediate assembly... of a Don1p-containing structure at the leading edge of the prospore membrane via interaction with spindle p... with this prey as prey (1) Rows with this prey as bait (0) 4 5 4 7 0 0 0 0 0 - - - - - 0 0 4 - Show YDL239C Bait ORF YDL...pore membrane via interaction with spindle pole body components; potentially phosphorylated by Cdc28p Rows w

  17. ArachnoServer: a database of protein toxins from spiders

    Directory of Open Access Journals (Sweden)

    Kaas Quentin

    2009-08-01

    Full Text Available Abstract Background Venomous animals incapacitate their prey using complex venoms that can contain hundreds of unique protein toxins. The realisation that many of these toxins may have pharmaceutical and insecticidal potential due to their remarkable potency and selectivity against target receptors has led to an explosion in the number of new toxins being discovered and characterised. From an evolutionary perspective, spiders are the most successful venomous animals and they maintain by far the largest pool of toxic peptides. However, at present, there are no databases dedicated to spider toxins and hence it is difficult to realise their full potential as drugs, insecticides, and pharmacological probes. Description We have developed ArachnoServer, a manually curated database that provides detailed information about proteinaceous toxins from spiders. Key features of ArachnoServer include a new molecular target ontology designed especially for venom toxins, the most up-to-date taxonomic information available, and a powerful advanced search interface. Toxin information can be browsed through dynamic trees, and each toxin has a dedicated page summarising all available information about its sequence, structure, and biological activity. ArachnoServer currently manages 567 protein sequences, 334 nucleic acid sequences, and 51 protein structures. Conclusion ArachnoServer provides a single source of high-quality information about proteinaceous spider toxins that will be an invaluable resource for pharmacologists, neuroscientists, toxinologists, medicinal chemists, ion channel scientists, clinicians, and structural biologists. ArachnoServer is available online at http://www.arachnoserver.org.

  18. Preparation of protein samples for gel electrophoresis by sequential extraction

    Institute of Scientific and Technical Information of China (English)

    钟伯雄; 翁宏飚; 等

    2002-01-01

    Since preparation and solubilization of protein samples are crucial factors in proteome research,the authors established a sequential extraction technique to prepare protein samples from the body wall of the 5th instar larvae of silkworm.Bombyx mori.Two kinds of protein samples were obtained from the body wall using the method.Between the two types of samples only about 15% proteins were identical;the majority were different,indicating that more species of proteins could be obtained with the sequential extraction method;which will be useful for preparation of protein samples for proteome study.

  19. Preparation of protein samples for gel electrophoresis by sequential extraction

    Institute of Scientific and Technical Information of China (English)

    钟伯雄; 翁宏飚; 方维焕

    2002-01-01

    Since preparation and solubilization of protein samples are crucial factors in proteome research, the authors established a sequential extraction technique to prepare protein samples from the body wall of the 5th instar larvae of silkworm, Bombyx mori. Two kinds of protein samples were obtained from the body wall using the method. Between the two types of samples only about 15% proteins were identical; the majority were different, indicating that more species of proteins could be obtained with the sequential extraction method; which will be useful for preparation of protein samples for proteome study.

  20. Yeast Interacting Proteins Database: YPR029C, YLR170C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available complex; binds clathrin; involved in vesicle mediated transport Rows with this bait as bait (3) Rows with t...t of the mammalian clathrin AP-1 complex Rows with this prey as prey (1) Rows with this prey as bait (1) 7 1...lathrin; involved in vesicle mediated transport Rows with this bait as bait Rows with this bait as bait (3) Row...s with this bait as prey Rows with this bait as prey (1) Prey ORF YLR170C Prey gene name APS1 Prey descri...olved in protein sorting at the trans-Golgi network; homolog of the sigma subunit of the mammalian clathrin AP-1 complex Row

  1. Influence of pH and Ionic Strength on Heat-Induced Formation and Rheological Properties of Soy Protein Gels in Relation to Denaturation and Their Protein Compositions

    NARCIS (Netherlands)

    Renkema, J.M.S.; Gruppen, H.; Vliet, van T.

    2002-01-01

    The influence of pH and ionic strength on gel formation and gel properties of soy protein isolate (SPI) in relation to denaturation and protein aggregation/precipitation was studied. Denaturation proved to be a prerequisite for gel formation under all conditions of pH and ionic strength studied.

  2. MALDI analysis of proteins after extraction from dissolvable ethylene glycol diacrylate cross-linked polyacrylamide gels.

    Science.gov (United States)

    Papasotiriou, Dimitrios G; Markoutsa, Stavroula; Gorka, Jan; Schleiff, Enrico; Karas, Michael; Meyer, Bjoern

    2013-09-01

    Although the extraction of intact proteins from polyacrylamide gels followed by mass spectrometric molecular mass determination has been shown to be efficient, there is room for alternative approaches. Our study evaluates ethylene glycol diacrylate, a cleavable cross-linking agent used for a new type of dissolvable gels. It attains an ester linkage that can be hydrolyzed in alkali conditions. The separation performance of the new gel system was tested by 1D and 2D SDS-PAGE using the outer chloroplast envelope of Pisum sativum as well as a soluble protein fraction of human lymphocytes, respectively. Gel spot staining (CBB), dissolving, and extracting were conducted using a custom-developed workflow. It includes protein extraction with an ammonia-SDS buffer followed by methanol treatment to remove acrylamide filaments. Necessary purification for MALDI-TOF analysis was implemented using methanol-chloroform precipitation and perfusion HPLC. Both cleaning procedures were applied to several standard proteins of different molecular weight as well as 'real' biological samples (8-75 kDa). The protein amounts, which had to be loaded on the gel to detect a peak in MALDI-TOF MS, were in the range of 0.1 to 5 μg, and the required amount increased with increasing mass.

  3. An effective placental cotyledons proteins extraction method for 2D gel electrophoresis.

    Science.gov (United States)

    Tan, Niu J; Daim, Leona D J; Jamil, Amilia A M; Mohtarrudin, Norhafizah; Thilakavathy, Karuppiah

    2017-03-01

    Effective protein extraction is essential especially in producing a well-resolved proteome on 2D gels. A well-resolved placental cotyledon proteome, with good reproducibility, have allowed researchers to study the proteins underlying the physiology and pathophysiology of pregnancy. The aim of this study is to determine the best protein extraction protocol for the extraction of protein from placental cotyledons tissues for a two-dimensional gel electrophoresis (2D-GE). Based on widely used protein extraction strategies, 12 different extraction methodologies were carefully selected, which included one chemical extraction, two mechanical extraction coupled protein precipitations, and nine chemical extraction coupled protein precipitations. Extracted proteins were resolved in a one-dimensional gel electrophoresis and 2D-GE; then, it was compared with set criteria: extraction efficacy, protein resolution, reproducibility, and recovery efficiency. Our results revealed that a better profile was obtained by chemical extraction in comparison to mechanical extraction. We further compared chemical extraction coupled protein precipitation methodologies, where the DNase/lithium chloride-dense sucrose homogenization coupled dichloromethane-methanol precipitation (DNase/LiCl-DSH-D/MPE) method showed good protein extraction efficiency. This, however, was carried out with the best protein resolution and proteome reproducibility on 2D-gels. DNase/LiCl-DSH-D/MPE was efficient in the extraction of proteins from placental cotyledons tissues. In addition, this methodology could hypothetically allow the protein extraction of any tissue that contains highly abundant lipid and glycogen. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Interactions of protein content and globulin subunit composition of soybean proteins in relation to tofu gel properties.

    Science.gov (United States)

    James, Andrew T; Yang, Aijun

    2016-03-01

    The content and globulin subunit composition of soybean proteins are known to affect tofu quality and food-grade soybeans usually have higher levels of proteins. We studied the tofu quality of soybeans with high (44.8%) or low (39.1%) protein content and with or without the 11S globulin polypeptide, 11SA4. Both protein content and 11SA4 significantly affected tofu gel properties. Soybeans containing more protein had smaller seeds which produced significantly firmer (0.663 vs.0.557 N, pprotein subunits, which may have contributed to the improvement in tofu gel properties. These results suggest that, in combination with higher protein content, certain protein subunits or their polypeptides can also be targeted in selecting soybeans to further improve soy food quality.

  5. Flavor release and perception of flavored whey protein gels: Perception is determined by texture rather than by release

    NARCIS (Netherlands)

    Weel, K.G.C.; Boelrijk, A.E.M.; Alting, A.C.; Mil, van P.J.J.M.; Burger, J.J.; Gruppen, H.; Voragen, A.G.J.; Smit, G.

    2002-01-01

    Five whey protein gels, with different gel hardnesses and waterholding capacities, were flavored with ethylbutyrate or diacetyl and evaluated by a 10-person panel to study the relation between the gel structure and the sensory perception, as well as the nosespace flavor concentration during eating.

  6. Flavor release and perception of flavored whey protein gels: Perception is determined by texture rather than by release

    NARCIS (Netherlands)

    Weel, K.G.C.; Boelrijk, A.E.M.; Alting, A.C.; Mil, van P.J.J.M.; Burger, J.J.; Gruppen, H.; Voragen, A.G.J.; Smit, G.

    2002-01-01

    Five whey protein gels, with different gel hardnesses and waterholding capacities, were flavored with ethylbutyrate or diacetyl and evaluated by a 10-person panel to study the relation between the gel structure and the sensory perception, as well as the nosespace flavor concentration during eating.

  7. Explaining the texture properties of whey protein isolate/starch co-gels from fracture structures.

    Science.gov (United States)

    Fu, Wei; Nakamura, Takashi

    2017-04-01

    The effects of tapioca starch (TS) and potato starch (PS) on texture properties of whey protein isolate (WPI)/starch co-gels were investigated for fracture structures. We focused on two types of WPI network structures. In a fine-stranded structure at pH 6.8, the WPI/TS co-gel fractured similarly to the WPI single gel. The WPI/PS co-gel was broken at a lower strain and lower stress. In a random aggregation at pH 5.8, the WPI/TS co-gel reached a yielding point at a lower strain, whereas the WPI/PS co-gel fractured at a higher strain and higher stress. In the fracture structures, it was revealed that breaks occurred in different places in these cases, which could explain the different texture properties of samples. This study tries to explain the texture properties of WPI/starch co-gels from fracture structures and provides a reference to predict texture properties of the WPI/starch food system.

  8. Databases

    Data.gov (United States)

    National Aeronautics and Space Administration — The databases of computational and experimental data from the first Aeroelastic Prediction Workshop are located here. The databases file names tell their contents by...

  9. Characterization of immunoreactive proteins of Setaria cervi isolated by preparative polyacrylamide gel electrophoresis.

    Science.gov (United States)

    Priyadarshi, Priyanka; Dravid, Piyush; Sheikh, Inayat Hussain; Saxena, Sunita; Tandon, Ashish; Kaushal, Deep C; Ali, Shakir; Kaushal, Nuzhat A

    2017-03-01

    Filarial parasites are complex mixtures of antigenic proteins and characterization of these antigenic molecules is essential to identify the diagnostically important filaria-specific antigens. In the present study, we have fractionated the somatic extracts from adults of Setaria cervi (bovine filarial parasite) on preparative SDS-polyacrylamide gel electrophoresis and tested the immunoreactivity of the separated gel fractions with polyclonal antibodies against filarial excretory-secretory antigens as well as filarial patients sera. The SDS-PAGE analysis of gel eluted fractions revealed 1 protein band in F-1 fraction, 2 protein bands in F-2 fraction and 2-3 protein bands in all other fractions (F3- F11). Seven gel eluted fractions (F1, F2, F3, F4, F5, F6 and F11) showed high ELISA reactivity with the polyclonal antibody (against excretory-secretory antigen) and four of these fractions (F-1, F-2, F3 and F6) exhibited high ELISA reactivity with antibodies present in filarial patient sera. The reactivities of the gel fractions (F1 and F2), recognized by filarial patients sera, were also tested with the monoclonal antibody (detecting the filarial circulating antigen). The F1 and F2 gel eluted fractions were found to have the target antigen of monoclonal antibody as evident by high reactivity with the monoclonal antibody in ELISA and immunoblotting. The S. cervi gel eluted F1 fraction (containing single antigen) could detect antibodies in filarial patients sera and not in non-filarial sera thereby suggesting its usefulness for specific serodiagnosis of human filariasis.

  10. Electrophoretic analysis of proteins from Mycoplasma hominis strains detected by SDS-PAGE, two-dimensional gel electrophoresis and immunoblotting

    DEFF Research Database (Denmark)

    Andersen, H; Birkelund, Svend; Christiansen, Gunna

    1987-01-01

    The proteins of 14 strains of Mycoplasma hominis were compared by SDS-PAGE in gradient gels, by two-dimensional (2D) gel electrophoresis of extracts of 35S-labelled cells and by immunoblot analysis of cell proteins. The strains examined included the M. hominis type strain PG21 and 13 others...... isolated variously from genital tract, mouth, blood, upper urinary tract and a wound. These 14 strains shared 76-99% of proteins in SDS-gradient gel analysis and 41-72% in the 2D gels. As expected, the immunoblot analysis likewise revealed the existence of an extensive common protein pattern in M. hominis...

  11. A simple monolithic column electroelution for protein recovery from gel electrophoresis.

    Science.gov (United States)

    Li, Guo-Qing; Shao, Jing; Guo, Chen-Gang; Dong, Jing-Yu; Fan, Liu-Yin; Cao, Cheng-Xi

    2012-11-01

    Protein recovery from gel electrophoresis plays an important role in functional genomics and proteomics but faces a series of issues (e.g., complex procedure, low recovery, long experimental time). In this study, a monolithic column electroelution (MCE) was developed for protein recovery from gel electrophoresis. With the model proteins of bovine serum albumin (BSA), hemoglobin (Hb), and myoglobin (Mb), the developed device and method were compared with common electroelution procedures in agarose gel electrophoresis (AGE). The comparative experiments revealed that (i) the protein recovery achieved with the developed device was greater than 83%, much higher than the 41% to 50% achieved with the common devices; (ii) the running time to obtain 70% recovery was approximately 15 min, evidently shorter than the 240 min with the common devices; and (iii) the device and procedure were simple and less time-consuming as compared with those of the common devices. It was observed that the serum protein bands cut from polyacrylamide gel electrophoresis could be transferred into solution in 15 to 30 min with 82% yield. The device, along with its relevant procedure, has potential use in protein extraction and proteomics as well as in DNA studies. Copyright © 2012 Elsevier Inc. All rights reserved.

  12. Electrostatic protein immobilization using charged polyacrylamide gels and cationic detergent microfluidic Western blotting.

    Science.gov (United States)

    Kim, Dohyun; Karns, Kelly; Tia, Samuel Q; He, Mei; Herr, Amy E

    2012-03-06

    We report a novel protein immobilization matrix for fully integrated microfluidic Western blotting (WB). The electrostatic immobilization gel (EIG) enables immobilization of all proteins sized using cetyl trimethylammonium bromide polyacrylamide gel electrophoresis (CTAB-PAGE), for subsequent electrophoretic probing with detection affinity reagents (e.g., labeled antibodies). The "pan-analyte" capture strategy introduced here uses polyacrylamide gel grafted with concentrated point charges (zwitterionic macromolecules), in contrast to existing microfluidic WB strategies that rely on a sandwich immunoassay format for analyte immobilization and detection. Sandwich approaches limit analyte immobilization to capture of only a priori known targets. A charge interaction mechanism study supports the hypothesis that electrostatic interaction plays a major role in analyte immobilization on the EIG. We note that protein capture efficiency depends on both the concentration of copolymerized charges and ionic strength of the gel buffer. We demonstrate pan-analyte immobilization of sized CTAB-laden model proteins (protein G, ovalbumin, bovine serum albumin, β-galactosidase, lactoferrin) on the EIG with initial capture efficiencies ranging from 21 to 100%. Target proteins fixed on the EIG (protein G, lactoferrin) are detected using antibody probes with signal-to-noise ratios of 34 to 275. The approach advances protein immunoblotting performance through 200× reduction on sample consumption, 12× reduction in assay duration, and automated assay operation, compared to slab-gel WB. Using the microfluidic WB assay, assessment of lactoferrin in human tear fluid is demonstrated with a goal of advancing toward nonbiopsy-based diagnosis of Sjögren's Syndrome, an autoimmune disease.

  13. Development of human protein reference database as an initial platform for approaching systems biology in humans

    DEFF Research Database (Denmark)

    Peri, Suraj; Navarro, J Daniel; Amanchy, Ramars

    2003-01-01

    Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, di...

  14. Tris-acetate polyacrylamide gradient gel electrophoresis for the analysis of protein oligomerization.

    Science.gov (United States)

    Cubillos-Rojas, Monica; Schneider, Taiane; Sánchez-Tena, Susana; Bartrons, Ramon; Ventura, Francesc; Rosa, Jose Luis

    2016-02-01

    Here we report a new approach for studying protein oligomerization in cells using a single electrophoresis gel. We combined the use of a crosslinking reagent for sample preparation, such as glutaraldehyde, with the analysis of oligomers by Tris-acetate polyacrylamide gel electrophoresis. The use of a 3-15% Tris-acetate polyacrylamide gradient gel allows for the simultaneous analysis of proteins of masses ranging from 10 to 500 kDa. We showed the usefulness of this method for analyzing endogenous p53 oligomerization with high resolution and sensitivity in human cells. Oligomerization analysis was dependent on the crosslinker concentration used. We also showed that this method could be used to study the regulation of oligomerization. In all experiments, Tris-acetate polyacrylamide gel electrophoresis proved to be a robust, manageable, and cost- and time-efficient method that provided excellent results using a single gel. This approach can be easily extrapolated to the study of other oligomers. All of these features make this method a highly useful tool for the analysis of protein oligomerization.

  15. Aphid Gel Saliva: Sheath Structure, Protein Composition and Secretory Dependence on Stylet-Tip Milieu

    Science.gov (United States)

    Will, Torsten; Steckbauer, Kathrin; Hardt, Martin; van Bel, Aart J. E.

    2012-01-01

    In order to separate and analyze saliva types secreted during stylet propagation and feeding, aphids were fed on artificial diets. Gel saliva was deposited as chains of droplets onto Parafilm membranes covering the diets into which watery saliva was secreted. Saliva compounds collected from the diet fluid were separated by SDS-PAGE, while non-soluble gel saliva deposits were processed in a novel manner prior to protein separation by SDS-PAGE. Soluble (watery saliva) and non-soluble (gel saliva) protein fractions were significantly different. To test the effect of the stylet milieu on saliva secretion, aphids were fed on various diets. Hardening of gel saliva is strongly oxygen-dependent, probably owing to formation of sulfide bridges by oxidation of sulphydryl groups. Surface texture of gel saliva deposits is less pronounced under low-oxygen conditions and disappears in dithiothreitol containing diet. Using diets mimicking sieve-element sap and cell-wall fluid respectively showed that the soluble protein fraction was almost exclusively secreted in sieve elements while non-soluble fraction was preferentially secreted at cell wall conditions. This indicates that aphids are able to adapt salivary secretion in dependence of the stylet milieu. PMID:23056521

  16. Total protein extraction and 2-D gel electrophoresis methods for Burkholderia species.

    Science.gov (United States)

    Velapatiño, Billie; Zlosnik, James E A; Hird, Trevor J; Speert, David P

    2013-10-15

    The investigation of the intracellular protein levels of bacterial species is of importance to understanding the pathogenic mechanisms of diseases caused by these organisms. Here we describe a procedure for protein extraction from Burkholderia species based on mechanical lysis using glass beads in the presence of ethylenediamine tetraacetic acid and phenylmethylsulfonyl fluoride in phosphate buffered saline. This method can be used for different Burkholderia species, for different growth conditions, and it is likely suitable for the use in proteomic studies of other bacteria. Following protein extraction, a two-dimensional (2-D) gel electrophoresis proteomic technique is described to study global changes in the proteomes of these organisms. This method consists of the separation of proteins according to their isoelectric point by isoelectric focusing in the first dimension, followed by separation on the basis of molecular weight by acrylamide gel electrophoresis in the second dimension. Visualization of separated proteins is carried out by silver staining.

  17. Effects of oxidative modification on gel properties of isolated porcine myofibrillar protein by peroxyl radicals.

    Science.gov (United States)

    Zhou, Feibai; Zhao, Mouming; Zhao, Haifeng; Sun, Weizheng; Cui, Chun

    2014-04-01

    AAPH-derived (2,2'-azobis (2-amidinopropane) dihydrochloride) peroxyl radicals were selected as representative free radicals of lipid peroxidation to investigate the effects of oxidative modifications on isolated porcine myofibrillar protein structures as well as their rheological and gelling properties. Incubation of myofibrillar protein with increasing concentrations of AAPH resulted in a gradual increase (p3 mM) concentrations of AAPH induced aggregation of myosin and denaturation of myosin, troponin and tropomyosin, respectively. These structural changes resulted in changes on gelation of myofibrillar protein. Low level protein oxidation (AAPH≤0.5 mM) had no remarkable effect (p>0.05) on the viscoelastic pattern of myofibrillar protein gelation. Moderate oxidative modification (AAPH~1mM) enhanced the water-holding capacity (WHC) and texture properties of gels, while further oxidation (AAPH>3mM) significantly reduced the gel quality.

  18. Discovery of protein- and DNA-imperceptible nanoparticle hard coating using gel-based reaction tuning.

    Science.gov (United States)

    Welsher, Kevin; McManus, Simon A; Hsia, Chih-Hao; Yin, Shuhui; Yang, Haw

    2015-01-21

    The seemingly inevitable protein corona appears to be an insurmountable obstacle to wider application of functional nanomaterials in biotechnology. The accumulation of serum proteins can block targeting functionalities and alter the in vivo fate of these nanomaterials. Here we demonstrate a method to generate non-stick, robustly passivated functional nanoparticles (NPs) using a tailored silica coating. We apply agarose gel electrophoresis to sensitively evaluate protein binding to NPs with different surface chemistry. Using gel banding and retardation as a read-out for protein adsorption, we optimize the surface chemistry to yield a mixed charge surface which displays remarkable binding resistance to a wide range of serum proteins and nucleic acids. The hard silica shell also protects the functional NP core in harsh environments (down to pH 1) while still showing the ability to be targeted for cellular uptake with little or no non-specific binding.

  19. Choosing an Optimal Database for Protein Identification from Tandem Mass Spectrometry Data.

    Science.gov (United States)

    Kumar, Dhirendra; Yadav, Amit Kumar; Dash, Debasis

    2017-01-01

    Database searching is the preferred method for protein identification from digital spectra of mass to charge ratios (m/z) detected for protein samples through mass spectrometers. The search database is one of the major influencing factors in discovering proteins present in the sample and thus in deriving biological conclusions. In most cases the choice of search database is arbitrary. Here we describe common search databases used in proteomic studies and their impact on final list of identified proteins. We also elaborate upon factors like composition and size of the search database that can influence the protein identification process. In conclusion, we suggest that choice of the database depends on the type of inferences to be derived from proteomics data. However, making additional efforts to build a compact and concise database for a targeted question should generally be rewarding in achieving confident protein identifications.

  20. Download - Yeast Interacting Proteins Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...らダウンロード Joomla SEF URLs by Artio About This Database Database Description Download License Update History of

  1. ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites

    Directory of Open Access Journals (Sweden)

    Selbig Joachim

    2007-06-01

    Full Text Available Abstract Background In the last decade, techniques were established for the large scale genome-wide analysis of proteins, RNA, and metabolites, and database solutions have been developed to manage the generated data sets. The Golm Metabolome Database for metabolite data (GMD represents one such effort to make these data broadly available and to interconnect the different molecular levels of a biological system 1. As data interpretation in the light of already existing data becomes increasingly important, these initiatives are an essential part of current and future systems biology. Results A mass spectral library consisting of experimentally derived tryptic peptide product ion spectra was generated based on liquid chromatography coupled to ion trap mass spectrometry (LC-IT-MS. Protein samples derived from Arabidopsis thaliana, Chlamydomonas reinhardii, Medicago truncatula, and Sinorhizobium meliloti were analysed. With currently 4,557 manually validated spectra associated with 4,226 unique peptides from 1,367 proteins, the database serves as a continuously growing reference data set and can be used for protein identification and quantification in uncharacterized biological samples. For peptide identification, several algorithms were implemented based on a recently published study for peptide mass fingerprinting 2 and tested for false positive and negative rates. An algorithm which considers intensity distribution for match correlation scores was found to yield best results. For proof of concept, an LC-IT-MS analysis of a tryptic leaf protein digest was converted to mzData format and searched against the mass spectral library. The utility of the mass spectral library was also tested for the identification of phosphorylated tryptic peptides. We included in vivo phosphorylation sites of Arabidopsis thaliana proteins and the identification performance was found to be improved compared to genome-based search algorithms. Protein identification by Pro

  2. Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins

    Directory of Open Access Journals (Sweden)

    Bradley Michael E

    2006-02-01

    Full Text Available Abstract Background When accurate models for the divergent evolution of protein sequences are integrated with complementary biological information, such as folded protein structures, analyses of the combined data often lead to new hypotheses about molecular physiology. This represents an excellent example of how bioinformatics can be used to guide experimental research. However, progress in this direction has been slowed by the lack of a publicly available resource suitable for general use. Results The precomputed Magnum database offers a solution to this problem for ca. 1,800 full-length protein families with at least one crystal structure. The Magnum deliverables include 1 multiple sequence alignments, 2 mapping of alignment sites to crystal structure sites, 3 phylogenetic trees, 4 inferred ancestral sequences at internal tree nodes, and 5 amino acid replacements along tree branches. Comprehensive evaluations revealed that the automated procedures used to construct Magnum produced accurate models of how proteins divergently evolve, or genealogies, and correctly integrated these with the structural data. To demonstrate Magnum's capabilities, we asked for amino acid replacements requiring three nucleotide substitutions, located at internal protein structure sites, and occurring on short phylogenetic tree branches. In the cellular retinoid binding protein family a site that potentially modulates ligand binding affinity was discovered. Recruitment of cellular retinol binding protein to function as a lens crystallin in the diurnal gecko afforded another opportunity to showcase the predictive value of a browsable database containing branch replacement patterns integrated with protein structures. Conclusion We integrated two areas of protein science, evolution and structure, on a large scale and created a precomputed database, known as Magnum, which is the first freely available resource of its kind. Magnum provides evolutionary and structural

  3. Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins

    Science.gov (United States)

    Bradley, Michael E; Benner, Steven A

    2006-01-01

    Background When accurate models for the divergent evolution of protein sequences are integrated with complementary biological information, such as folded protein structures, analyses of the combined data often lead to new hypotheses about molecular physiology. This represents an excellent example of how bioinformatics can be used to guide experimental research. However, progress in this direction has been slowed by the lack of a publicly available resource suitable for general use. Results The precomputed Magnum database offers a solution to this problem for ca. 1,800 full-length protein families with at least one crystal structure. The Magnum deliverables include 1) multiple sequence alignments, 2) mapping of alignment sites to crystal structure sites, 3) phylogenetic trees, 4) inferred ancestral sequences at internal tree nodes, and 5) amino acid replacements along tree branches. Comprehensive evaluations revealed that the automated procedures used to construct Magnum produced accurate models of how proteins divergently evolve, or genealogies, and correctly integrated these with the structural data. To demonstrate Magnum's capabilities, we asked for amino acid replacements requiring three nucleotide substitutions, located at internal protein structure sites, and occurring on short phylogenetic tree branches. In the cellular retinoid binding protein family a site that potentially modulates ligand binding affinity was discovered. Recruitment of cellular retinol binding protein to function as a lens crystallin in the diurnal gecko afforded another opportunity to showcase the predictive value of a browsable database containing branch replacement patterns integrated with protein structures. Conclusion We integrated two areas of protein science, evolution and structure, on a large scale and created a precomputed database, known as Magnum, which is the first freely available resource of its kind. Magnum provides evolutionary and structural bioinformatics resources that

  4. License - Yeast Interacting Proteins Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available freely redistribute part or whole of the data from this database; and freely create and distribute database and other derivative wor...ks based on part or whole of the data from this database, under the Standard Licens

  5. Protein Structural Change Data - PSCDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PSCDB Protein Structural Change Data Data detail Data name Protein Structural Change Data DO...History of This Database Site Policy | Contact Us Protein Structural Change Data - PSCDB | LSDB Archive ...

  6. Formation, structure and rheological properties of soy protein gels.

    NARCIS (Netherlands)

    Renkema, J.M.S.

    2001-01-01

    Keywords: soy protein isolate, glycinin,β-conglycinin, heat denaturation, gelation, network structure, rheology, permeability measurements, microscopy, pH, ionic strength, emulsified oil dropletsThis study was performed to understand the factors determining heat-induced formation an

  7. Databases

    Directory of Open Access Journals (Sweden)

    Nick Ryan

    2004-01-01

    Full Text Available Databases are deeply embedded in archaeology, underpinning and supporting many aspects of the subject. However, as well as providing a means for storing, retrieving and modifying data, databases themselves must be a result of a detailed analysis and design process. This article looks at this process, and shows how the characteristics of data models affect the process of database design and implementation. The impact of the Internet on the development of databases is examined, and the article concludes with a discussion of a range of issues associated with the recording and management of archaeological data.

  8. Proteomic Analysis of Bovine Pregnancy-specific Serum Proteins by 2D Fluorescence Difference Gel Electrophoresis

    Directory of Open Access Journals (Sweden)

    Jae Eun Lee

    2015-06-01

    Full Text Available Two dimensional-fluorescence difference gel electrophoresis (2D DIGE is an emerging technique for comparative proteomics, which improves the reproducibility and reliability of differential protein expression analysis between samples. The purpose of this study was to investigate bovine pregnancy-specific proteins in the proteome between bovine pregnant and non-pregnant serum using DIGE technique. Serums of 2 pregnant Holstein dairy cattle at day 21 after artificial insemination and those of 2 non-pregnant were used in this study. The pre-electrophoretic labeling of pregnant and non-pregnant serum proteins were mixed with Cy3 and Cy5 fluorescent dyes, respectively, and an internal standard was labeled with Cy2. Labeled proteins with Cy2, Cy3, and Cy5 were separated together in a single gel, and then were detected by fluorescence image analyzer. The 2D DIGE method using fluorescence CyDye DIGE flour had higher sensitivity than conventional 2D gel electrophoresis, and showed reproducible results. Approximately 1,500 protein spots were detected by 2D DIGE. Several proteins showed a more than 1.5-fold up and down regulation between non-pregnant and pregnant serum proteins. The differentially expressed proteins were identified by MALDI-TOF mass spectrometer. A total 16 protein spots were detected to regulate differentially in the pregnant serum, among which 7 spots were up-regulated proteins such as conglutinin precursor, modified bovine fibrinogen and IgG1, and 6 spots were down-regulated proteins such as hemoglobin, complement component 3, bovine fibrinogen and IgG2a three spots were not identified. The identified proteins demonstrate that early pregnant bovine serum may have several pregnancy-specific proteins, and these could be a valuable information for the development of pregnancy-diagnostic markers in early pregnancy bovine serum.

  9. Proteomic Analysis of Bovine Pregnancy-specific Serum Proteins by 2D Fluorescence Difference Gel Electrophoresis

    Science.gov (United States)

    Lee, Jae Eun; Lee, Jae Young; Kim, Hong Rye; Shin, Hyun Young; Lin, Tao; Jin, Dong Il

    2015-01-01

    Two dimensional-fluorescence difference gel electrophoresis (2D DIGE) is an emerging technique for comparative proteomics, which improves the reproducibility and reliability of differential protein expression analysis between samples. The purpose of this study was to investigate bovine pregnancy-specific proteins in the proteome between bovine pregnant and non-pregnant serum using DIGE technique. Serums of 2 pregnant Holstein dairy cattle at day 21 after artificial insemination and those of 2 non-pregnant were used in this study. The pre-electrophoretic labeling of pregnant and non-pregnant serum proteins were mixed with Cy3 and Cy5 fluorescent dyes, respectively, and an internal standard was labeled with Cy2. Labeled proteins with Cy2, Cy3, and Cy5 were separated together in a single gel, and then were detected by fluorescence image analyzer. The 2D DIGE method using fluorescence CyDye DIGE flour had higher sensitivity than conventional 2D gel electrophoresis, and showed reproducible results. Approximately 1,500 protein spots were detected by 2D DIGE. Several proteins showed a more than 1.5-fold up and down regulation between non-pregnant and pregnant serum proteins. The differentially expressed proteins were identified by MALDI-TOF mass spectrometer. A total 16 protein spots were detected to regulate differentially in the pregnant serum, among which 7 spots were up-regulated proteins such as conglutinin precursor, modified bovine fibrinogen and IgG1, and 6 spots were down-regulated proteins such as hemoglobin, complement component 3, bovine fibrinogen and IgG2a three spots were not identified. The identified proteins demonstrate that early pregnant bovine serum may have several pregnancy-specific proteins, and these could be a valuable information for the development of pregnancy-diagnostic markers in early pregnancy bovine serum. PMID:25925056

  10. Affi-Gel Blue for nucleic acid removal and early enrichment of nucleotide binding proteins.

    Science.gov (United States)

    Deutscher, Murray P

    2009-01-01

    Passage of an extract or supernatant fraction through a column of Affi-Gel Blue and batchwise elution can be a rapid and effective early procedure for removal of nucleic acid, concentration of the sample and purification of nucleotide binding proteins.

  11. Relations between rheological properties and network structure of soy protein gels

    NARCIS (Netherlands)

    Renkema, J.M.S.

    2004-01-01

    This paper focuses on the relations between network structure and rheological properties of soy protein gels as a function of pH and ionic strength. Network structure has been characterized independently by permeability measurements and confocal scanning laser microscopy in terms of coarseness.

  12. Introducing Proteomics in the Undergraduate Curriculum: A Simple 2D Gel Electrophoresis Exercise with Serum Proteins

    Science.gov (United States)

    Kim, Thomas D.; Craig, Paul A.

    2010-01-01

    Two-dimensional gel electrophoresis (2DGE) remains an important tool in the study of biological systems by proteomics. While the use of 2DGE is commonplace in research publications, there are few instructional laboratories that address the use of 2DGE for analyzing complex protein samples. One reason for this lack is the fact that the preparation…

  13. Relations between rheological properties and network structure of soy protein gels

    NARCIS (Netherlands)

    Renkema, J.M.S.

    2004-01-01

    This paper focuses on the relations between network structure and rheological properties of soy protein gels as a function of pH and ionic strength. Network structure has been characterized independently by permeability measurements and confocal scanning laser microscopy in terms of coarseness. Resu

  14. Physical Properties Giving the Sensory Perception of Whey Proteins/Polysaccharide Gels

    NARCIS (Netherlands)

    Berg, van den L.; Vliet, van T.; Linden, van der E.; Boekel, van M.A.J.S.; Velde, van de F.

    2008-01-01

    Establishing relationships between physical and sensorial properties of semi-solid foods is essential to develop tailored products. Whey protein/polysaccharide mixed gels were used to model both natural and fabricated semi-solid foods. The presence of various polysaccharides modulated the microstruc

  15. Application of difference gel electrophoresis to the identification of inner medullary collecting duct proteins

    NARCIS (Netherlands)

    Hoffert, J.D.; Balkom, B.W.M. van; Chou, C.L.; Knepper, M.A.

    2004-01-01

    In this study, we present a standardized approach to purification of native inner medullary collecting duct (IMCD) cells from rat kidney for proteomic analysis and apply the approach to identification of abundant proteins utilizing two-dimensional difference gel electrophoresis (DIGE) coupled with m

  16. Introducing Proteomics in the Undergraduate Curriculum: A Simple 2D Gel Electrophoresis Exercise with Serum Proteins

    Science.gov (United States)

    Kim, Thomas D.; Craig, Paul A.

    2010-01-01

    Two-dimensional gel electrophoresis (2DGE) remains an important tool in the study of biological systems by proteomics. While the use of 2DGE is commonplace in research publications, there are few instructional laboratories that address the use of 2DGE for analyzing complex protein samples. One reason for this lack is the fact that the preparation…

  17. THE EFFECTS OF A CARBOHYDRATE-PROTEIN GEL SUPPLEMENT ON ALPINE SLALOM SKI PERFORMANCE

    Directory of Open Access Journals (Sweden)

    John G. Seifert

    2012-09-01

    Full Text Available Alpine slalom ski racing is a high intensity, complex sport in which racers execute turns every second. Acute fatigue can make the difference in not finishing a run (DNF or finishing out of contention. The quantity and quality of training often dictates racing success. It is not known if nutritional supplementation can improve performance in this high intensity, short duration activity. The objective of this study was to determine if ingesting a carbohydrate-protein energy gel (GEL improves finishing success and number of gates completed during 2 hr slalom sessions on two consecutive days of training. Twenty-four racers were matched; one group ingested the GEL, the second group received a liquid placebo (PLA. Total carbohy-drate, protein, and water ingested by the GEL group were 60g, 15g, and 450 mL, while the PLA group ingested 450 mL of PLA. The GEL group had significantly fewer DNF's (7/48 vs. 18/48; p = 0.02 on both days, completed a greater number of training gates on Day 2 (260.3 ± 20.1 vs. 246.3 ± 17.5 gates; p = 0.03, and had a lower RPE (3.9 ± 1.2 vs. 5.3 ± 1.2 on Day 2 (p = 0.004 vs. PLA. The statistical analysis of combined finishing times was not possible due to the high number of DNF's in the PLA group. High intensity slalom performance can be im-proved by the ingestion of an energy gel. The GEL allowed the athletes to improve training quantity and quality and their per-ception of effort was less than skiers who ingested a placebo

  18. Study on the rheological properties and volatile release of cold-set emulsion-filled protein gels.

    Science.gov (United States)

    Mao, Like; Roos, Yrjö H; Miao, Song

    2014-11-26

    Emulsion-filled protein gels (EFP gels) were prepared through a cold-set gelation process, and they were used to deliver volatile compounds. An increase in the whey protein isolate (WPI) content from 4 to 6% w/w did not show significant effect on the gelation time, whereas an increase in the oil content from 5 to 20% w/w resulted in an earlier onset of gelation. Gels with a higher WPI content had a higher storage modulus and water-holding capacity (WHC), and they presented a higher force and strain at breaking, indicating that a more compact gel network was formed. An increase in the oil content contributed to gels with a higher storage modulus and force at breaking; however, this increase did not affect the WHC of the gels, and gels with a higher oil content became more brittle, resulting in a decreased strain at breaking. GC headspace analysis showed that volatiles released at lower rates and had lower air-gel partition coefficients in EFP gels than those in ungelled counterparts. Gels with a higher WPI content had lower release rates and partition coefficients of the volatiles. A change in the oil content significantly modified the partition of volatiles at equilibrium, but it produced a minor effect on the release rate of the volatiles. The findings indicated that EFP gels could be potentially used to modulate volatile release by varying the rheological properties of the gel.

  19. A modular approach to the design of protein-based smart gels.

    Science.gov (United States)

    Grove, Tijana Z; Forster, Jason; Pimienta, Genaro; Dufresne, Eric; Regan, Lynne

    2012-07-01

    The modular nature of repeat proteins makes them a versatile platform for the design of smart materials with predetermined properties. Here, we present a general strategy for combining protein modules with specified stability and function into arrays for the assembly of stimuli-responsive gels. We have designed tetratricopeptide repeat (TPR) arrays which contain peptide-binding modules that specify the strength and reversibility of network crosslinking in combination with spacer modules that specify crosslinking geometry and overall stability of the array. By combining such arrays with multivalent peptide ligands, self-supporting stimuli-responsive gels are formed. Using microrheology, we characterized the kinetics of gelation as a function of concentration and stoichiometry of the components. We also show that such gels are effective in encapsulating and releasing small molecules. Moreover, TPR gels alone are fully compatible with cell growth, whereas gels loaded with an anticancer compound release the compound, resulting in cell death. Thus, we have demonstrated that this new class of tunable biomaterials is ripe for further development as tissue engineering and drug delivery platform.

  20. A Novel Strategy for Characterization of Glycosylated Proteins Separated by Gel Electrophoresis

    DEFF Research Database (Denmark)

    Larsen, Martin; Skottrup, Peter; Enghild, Jan J.;

    2005-01-01

    Protein glycosylation can be vital for changing the function or physiochemical properties of a protein. Abnormal glycosylation can lead to protein malfunction, resulting in severe diseases. Therefore, it is important to develop techniques for characterization of such modifications in proteins...... at a sensitivity level comparable with state-of-the-art proteomics. Whereas techniques exist for characterization of high abundant glycoproteins, no single method is presently capable of providing information on both site occupancy and glycan structure on a single band or spot excised from an electrophoretic gel....... We present a new technique, which allows full characterization of low amounts of glycoproteins separated by gel electrophoresis. The method takes advantage of sequential specific and non-specific enzymatic treatment, followed by selective purification and characterization of the glycopeptides using...

  1. Identification of Methanococcus Jannaschii Proteins in 2-D Gel Electrophoresis Patterns by Mass Spectrometry

    Science.gov (United States)

    Liang, X.

    1998-06-10

    The genome of Methanococcus jannaschii has been sequenced completely and has been found to contain approximately 1,770 predicted protein-coding regions. When these coding regions are expressed and how their expression is regulated, however, remain open questions. In this work, mass spectrometry was combined with two-dimensional gel electrophoresis to identify which proteins the genes produce under different growth conditions, and thus investigate the regulation of genes responsible for functions characteristic of this thermophilic representative of the methanogenic Archaea.

  2. Application of native agarose gel electrophoresis of serum proteins in veterinary diagnostics

    OpenAIRE

    Jania Bartosz; Andraszek Katarzyna

    2016-01-01

    Electrophoretic techniques, used to separate mixtures of electrically charged particles, are widely used in science. One of these techniques, native protein electrophoresis in an agarose gel, is applied in human and veterinary medicine. Changes in the proportions of individual protein fractions correspond to significant changes in the physiology of the body. Although the pattern obtained by electrophoretic separation rarely indicates a specific disease, it provides valuable information for th...

  3. Polyacrylamide gel electrophoresis-SDS as a tool to study myofibrillar proteins. A review.

    Directory of Open Access Journals (Sweden)

    Perez-Chabela, M. Lourdes

    2015-12-01

    Full Text Available Miofibrillar proteins are part of land and sea animals’ muscle. Nonetheless, even when muscle proteins are the same type of proteins, their structure, rigor mortis time, and biochemical process associated to muscle to meat conversion, are different among animal species. This review has the aim to describe the advantages of SDS-polyacrylamide gel electrophoresis (SDS-PAGE in the study of myofibrillar proteins structure, besides the influence of many parameters on this technique to obtain an electrophoretic profile. Applications of this technique as a diagnostic tool in the food science, ecology and health are described as well.

  4. Alginate and Chitosan Gel Nanoparticles for Efficient Protein Entrapment

    Science.gov (United States)

    Masalova, O.; Kulikouskaya, V.; Shutava, T.; Agabekov, V.

    Alginate and chitosan nanoparticles were synthesized by ionic gelation of the polymers in the presence of stabilizers (PEG 1500, PEG 6000, TWEEN 80). The stability of 210-240 nm Ca-alginate colloids is affected by nanoparticles ageing and by the presence of a stabilizer. The diameter of chitosan nanoparticles is in the range of 180 to 260 nm and depends on polymer concentration in the reaction mixture, its molecular weight, and stabilizer type. The nanoparticles efficiently entrap a model protein, bovine serum albumin, in the amount up to 0.24 mg per 1 mg of polysaccharide.

  5. Whey protein isolate gel for separation: A formation, characterization, and application study

    Science.gov (United States)

    Teo, Jiunn Yeong

    Novel microporous membranes made of whey protein isolate (WPI) were developed. Aggregates of WPI comprised the bulk of the membrane, the size and packing density of which were varied by changing CaCl2 concentration (0.05--0.3M) and WPI concentration (30--40wt%), respectively. Aggregate sizes of the membranes made with 0.3M, 0.1M, 0.05M CaCl2 were roughly 1.5mum, 1mum, and 0.8mum, respectively. Skin layer of thickness about 0.5mum was found on either side of the membrane, but the thickness could reach 5mum at 0.3M CaCl2. Additionally, the porosity of the skin layer was shown to be modifiable with the addition of surfactant. Membranes were stable in hexane with flux values on the order of 1--1000gal/ft 2·d depending on the morphology of the membrane. The molecular weight cutoffs (MWCOs) of the WPI membranes with skins were evaluated using two different methods: (i) dextran marker method and (ii) protein/vitamin marker method. Membranes were found to have MWCOs of 1,000 or greater with variations when the concentration of salt used to control aggregate size, or surfactant used to modify skin properties were selected. The microporous WPI gel was also used as a cation exchanger and a hydrophobic adsorbent. The WPI cation exchanger has a maximum capacity of 68mg cupric chloride per gram dry WPI gel at neutral pH and can be regenerated effectively by reducing the pH of the solution. The WPI gel has also been found to be an excellent adsorbent for total phenolic compounds from grape extract with a partition coefficient higher than 1000 in aqueous system. The mechanism for total phenolic compounds adsorption is believed to be physical sorption, particularly sorption/condensation of total phenolic compounds in the pores and on all surfaces of WPI gel. The gel has a low extractables of 1ng/ml.g gel, and has an isoelectric point of 5.5. Although WPI gel was made into a monolith for continuous bed chromatography, channeling problems have made it very hard to evaluate the

  6. Preparation of Barley Storage Protein, Hordein, for Analytical Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis

    DEFF Research Database (Denmark)

    Doll, Hans; Andersen, Bente

    1981-01-01

    The extraction, reduction, and alkylation of barley hordein for routine electrophoresis in sodium dodecyl sulfate-polyacrylamide gels were studied to set up a simple preparation procedure giving well-resolved bands in the electrophoresis gel. Hordein was extracted from single crushed seeds or flour...... by aqueous 50% propan-2-ol containing a Tris-borate buffer, pH 8.6. The presence of the buffer facilitates the consecutive complete reduction of the extracted protein in the alcohol. Reduction and alkylation in the buffer containing propan-2-ol give sharper bands in the electrophoresis than reduction...

  7. Core Data of Yeast Interacting Proteins Database (Annotation Updated Version) - Yeast Interacting Proteins Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available nteractions are required. Several sources including YPD (Yeast Proteome Database, Costanzo, M. C., Hogan, J....erse direction. *1 The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources

  8. A Database of Domain Definitions for Proteins with Complex Interdomain Geometry

    OpenAIRE

    Indraneel Majumdar; Kinch, Lisa N.; Grishin, Nick V.

    2009-01-01

    Protein structural domains are necessary for understanding evolution and protein folding, and may vary widely from functional and sequence based domains. Although, various structural domain databases exist, defining domains for some proteins is non-trivial, and definitions of their domain boundaries are not available. Here, we present a novel database of manually defined structural domains for a representative set of proteins from the SCOP "multi-domain proteins" class. (http://prodata.swmed....

  9. Scanning protein analysis of electrofocusing gels using X-ray fluorescence.

    Science.gov (United States)

    Matsuyama, Satoshi; Matsunaga, Akihiro; Sakamoto, Shinichi; Iida, Yutaka; Suzuki, Yoshinari; Ishizaka, Yukihito; Yamauchi, Kazuto; Ishikawa, Tetsuya; Shimura, Mari

    2013-05-01

    Recently, "metallomics," in addition to genomics and proteomics, has become a focus as a novel approach to identify sensitive fluctuations in homeostasis that accompany metabolic processes, such as stress responses, differentiation, and proliferation. Cellular elements and associated protein behavior provide important clues for understanding cellular and disease mechanism(s). It is important to develop a system for measuring the native status of the protein. In this study, we developed an original freeze-dried electrofocusing native gel over polyimide film (native-gel film) for scanning protein analysis using synchrotron radiation excited X-ray fluorescence (SPAX). To our knowledge, this is the first report detailing the successful mapping of metal-associated proteins of electrofocusing gels using X-ray fluorescence. SPAX can provide detection sensitivity equivalent to that of LA-ICP-MS. In addition to this increased sensitivity, SPAX has the potential to be combined with other X-ray spectroscopies. Our system is useful for further applications in proteomics investigating cellular element-associated protein behaviors and disease mechanisms.

  10. iPPI-DB: an online database of modulators of protein-protein interactions.

    Science.gov (United States)

    Labbé, Céline M; Kuenemann, Mélaine A; Zarzycka, Barbara; Vriend, Gert; Nicolaes, Gerry A F; Lagorce, David; Miteva, Maria A; Villoutreix, Bruno O; Sperandio, Olivier

    2016-01-01

    In order to boost the identification of low-molecular-weight drugs on protein-protein interactions (PPI), it is essential to properly collect and annotate experimental data about successful examples. This provides the scientific community with the necessary information to derive trends about privileged physicochemical properties and chemotypes that maximize the likelihood of promoting a given chemical probe to the most advanced stages of development. To this end we have developed iPPI-DB (freely accessible at http://www.ippidb.cdithem.fr), a database that contains the structure, some physicochemical characteristics, the pharmacological data and the profile of the PPI targets of several hundreds modulators of protein-protein interactions. iPPI-DB is accessible through a web application and can be queried according to two general approaches: using physicochemical/pharmacological criteria; or by chemical similarity to a user-defined structure input. In both cases the results are displayed as a sortable and exportable datasheet with links to external databases such as Uniprot, PubMed. Furthermore each compound in the table has a link to an individual ID card that contains its physicochemical and pharmacological profile derived from iPPI-DB data. This includes information about its binding data, ligand and lipophilic efficiencies, location in the PPI chemical space, and importantly similarity with known drugs, and links to external databases like PubChem, and ChEMBL.

  11. Physical and chemical gels of lipid nanoparticles for controlled delivery of lipophilic drugs and proteins

    Science.gov (United States)

    Couffin, Anne-Claude; Delmas, Thomas; Thomann, Jean-Sébastien; Cheibani, Ismail; Bayma, Eric; Heinrich, Emilie; Escudé, Marie; Courant, Thomas; Hoang, Antoine; Auzély, Rachel; Texier, Isabelle

    2013-05-01

    The controlled delivery of drugs and biologicals (proteins, antibodies, DNA and derivatives) is a growing need to take the full benefit of new therapeutic strategies. However these new molecules or biomolecules display solubility issues, or high degradation rates once injected. Therefore, both suitable delivery materials for their encapsulation and protection from the surrounding environment, and smart delivery devices (such as micro-needles or implanted pumps) are necessary to achieve controlled delivery of these precious therapeutic agents. We have developed bio-inspired gel materials, based on lipid nanoparticles which act as reservoirs for lipophilic drugs. The lipid nanoparticles, termed lipidots™, are biocompatible, colloidally stable, non-immunogenic, and obtained from a cheap and simple solvent-free process. The particles can be assembled to form physical or chemical gels, with tunable rheological properties. Physico-chemical studies have been carried out to determine the limits of the stability domains for colloidal and gel formulations (choice of surfactants for nanoparticle surface, and composition ratios of lipids, surfactants and co-surfactants). In particular, it is demonstrated that lipid nanoparticles keep their integrity in the gels. Gels of lipidots™ could therefore constitute biocompatible materials for the efficient encapsulation and tuned delivery of lipophilic drugs and biomolecules.

  12. Whey protein isolate modified by transglutaminase aggregation and emulsion gel properties

    Science.gov (United States)

    Qi, Weiwei; Chen, Chong; Liu, Mujun; Yu, Guoping; Cai, Xinghang; Guo, Peipei; Yao, Yuxiu; Mei, Sijie

    2015-07-01

    Whey protein isolate and commercial soybean salad oil were used to produce the WPI emulsion dispersions. The properties of TG-catalyzed emulsion gelation produced from WPI emulsion dispersions were investigated by the amount of TG, temperature, pH and reaction time. Specifically, the texture properties (hardness and springiness), water-holding capacity and rheological properties (G' and G") were assessed. The result of Orthogonal tests showed WPI emulsion can form better hardness and springiness gel when the ratio of TG and WPI was 20U/g, pH 7.5, treatment temperature and time were 50°C and 3 h, respectively. The microstructure of TG emulsion gels was more compact, gel pore is smaller, distribution more uniform, the oil droplets size smaller compared with untreated emulsion gels. Compared to the control of rheological properties, G' and G" were significantly increased and G' > G", results showed that the gel was solid state, and TG speeded up the process of gelation.

  13. Protein expression of sensory and motor nerves: Two-dimensional gel electrophoresis and mass spectrometry.

    Science.gov (United States)

    Ren, Zhiwu; Wang, Yu; Peng, Jiang; Zhang, Li; Xu, Wenjing; Liang, Xiangdang; Zhao, Qing; Lu, Shibi

    2012-02-15

    The present study utilized samples from bilateral motor branches of the femoral nerve, as well as saphenous nerves, ventral roots, and dorsal roots of the spinal cord, to detect differential protein expression using two-dimensional gel electrophoresis and nano ultra-high performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry techniques. A mass spectrum was identified using the Mascot search. Results revealed differential expression of 11 proteins, including transgelin, Ig kappa chain precursor, plasma glutathione peroxidase precursor, an unnamed protein product (gi|55628), glyceraldehyde-3-phosphate dehydrogenase-like protein, lactoylglutathione lyase, adenylate kinase isozyme 1, two unnamed proteins products (gi|55628 and gi|1334163), and poly(rC)-binding protein 1 in motor and sensory nerves. Results suggested that these proteins played roles in specific nerve regeneration following peripheral nerve injury and served as specific markers for motor and sensory nerves.

  14. Protein expression of sensory and motor nerves Two-dimensional gel electrophoresis and mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    Zhiwu Ren; Yu Wang; Jiang Peng; Li Zhang; Wenjing Xu; Xiangdang Liang; Qing Zhao; Shibi Lu

    2012-01-01

    The present study utilized samples from bilateral motor branches of the femoral nerve, as well as saphenous nerves, ventral roots, and dorsal roots of the spinal cord, to detect differential protein expression using two-dimensional gel electrophoresis and nano ultra-high performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry techniques. A mass spectrum was identified using the Mascot search. Results revealed differential expression of 11 proteins, including transgelin, Ig kappa chain precursor, plasma glutathione peroxidase precursor, an unnamed protein product (gi|55628), glyceraldehyde-3-phosphate dehydrogenase-like protein, lactoylglutathione lyase, adenylate kinase isozyme 1, two unnamed proteins products (gi|55628 and gi|1334163), and poly(rC)-binding protein 1 in motor and sensory nerves. Results suggested that these proteins played roles in specific nerve regeneration following peripheral nerve injury and served as specific markers for motor and sensory nerves.

  15. Chemical properties of ω-3 fortified gels made of protein isolate recovered with isoelectric solubilisation/precipitation from whole fish.

    Science.gov (United States)

    Tahergorabi, Reza; Beamer, Sarah K; Matak, Kristen E; Jaczynski, Jacek

    2013-08-15

    Protein isolate was recovered from whole gutted fish using isoelectric solubilisation/precipitation (ISP). The objective was to determine chemical properties of heat-set gels made of the ISP protein isolate fortified with ω-3 polyunsaturated fatty acids (PUFAs)-rich oils (flaxseed, fish, algae, krill, and blend). The extent of the PUFAs increase, ω-6/ω-3 FAs and unsaturated/saturated FAs ratios, and the indices of thrombogenicity and atherogenicity depended on specific ω-3 PUFAs-rich oil used to fortify protein isolate gels. Lipid oxidation in ω-3 PUFAs fortified gels was minimal, although greater (Pgels (without ω-3 PUFAs fortification). However, all gels were in the slightly rancid, but acceptable range. The commonly used thiobarbituric-acid-reactive-substances (TBARS) assay to determine lipid oxidation in seafood may be inaccurate for samples containing krill oil due to its red pigment, astaxanthin. Protein degradation (total-volatile-basic-nitrogen) was greater (Pgels than control gels. However, all gels were considerably below the acceptability threshold for protein degradation. The shear stress of ω-3 PUFAs fortified gels was generally greater than the control gels and the shear strain was generally unchanged. This study demonstrates that ω-3 PUFAs fortification of protein isolates recovered with ISP from fish processing by-products or whole fish has potential application in the development of functional foods.

  16. Comparison of Different Protein Extraction Methods for Gel-Based Proteomic Analysis of Ganoderma spp.

    Science.gov (United States)

    Al-Obaidi, Jameel R; Saidi, Noor Baity; Usuldin, Siti Rokhiyah Ahmad; Hussin, Siti Nahdatul Isnaini Said; Yusoff, Noornabeela Md; Idris, Abu Seman

    2016-04-01

    Ganoderma species are a group of fungi that have the ability to degrade lignin polymers and cause severe diseases such as stem and root rot and can infect economically important plants and perennial crops such as oil palm, especially in tropical countries such as Malaysia. Unfortunately, very little is known about the complex interplay between oil palm and Ganoderma in the pathogenesis of the diseases. Proteomic technologies are simple yet powerful tools in comparing protein profile and have been widely used to study plant-fungus interaction. A critical step to perform a good proteome research is to establish a method that gives the best quality and a wide coverage of total proteins. Despite the availability of various protein extraction protocols from pathogenic fungi in the literature, no single extraction method was found suitable for all types of pathogenic fungi. To develop an optimized protein extraction protocol for 2-DE gel analysis of Ganoderma spp., three previously reported protein extraction protocols were compared: trichloroacetic acid, sucrose and phenol/ammonium acetate in methanol. The third method was found to give the most reproducible gels and highest protein concentration. Using the later method, a total of 10 protein spots (5 from each species) were successfully identified. Hence, the results from this study propose phenol/ammonium acetate in methanol as the most effective protein extraction method for 2-DE proteomic studies of Ganoderma spp.

  17. Acrylamide concentration determines the direction and magnitude of helical membrane protein gel shifts

    Science.gov (United States)

    Rath, Arianna; Cunningham, Fiona; Deber, Charles M.

    2013-01-01

    SDS/PAGE is universally used in biochemistry, cell biology, and immunology to resolve minute protein amounts readily from tissue and cell extracts. Although molecular weights of water-soluble proteins are reliably determined from their SDS/PAGE mobility, most helical membrane proteins, which comprise 20–30% of the human genome and the majority of drug targets, migrate to positions that have for decades been unpredictably slower or faster than their actual formula weight, often confounding their identification. Using de novo designed transmembrane-mimetic polypeptides that match the composition of helical membrane-spanning sequences, we quantitate anomalous SDS/PAGE fractionation of helical membrane proteins by comparing the relative mobilities of these polypeptides with typical water-soluble reference proteins on Laemmli gels. We find that both the net charge and effective molecular size of the migrating particles of transmembrane-mimetic species exceed those of the corresponding reference proteins and that gel acrylamide concentration dictates the impact of these two factors on the direction and magnitude of anomalous migration. Algorithms we derived from these data compensate for this differential effect of acrylamide concentration on the SDS/PAGE mobility of a variety of natural membrane proteins. Our results provide a unique means to predict anomalous migration of membrane proteins, thereby facilitating straightforward determination of their molecular weights via SDS/PAGE. PMID:24019476

  18. Gel-aided sample preparation (GASP)--a simplified method for gel-assisted proteomic sample generation from protein extracts and intact cells.

    Science.gov (United States)

    Fischer, Roman; Kessler, Benedikt M

    2015-04-01

    We describe a "gel-assisted" proteomic sample preparation method for MS analysis. Solubilized protein extracts or intact cells are copolymerized with acrylamide, facilitating denaturation, reduction, quantitative cysteine alkylation, and matrix formation. Gel-aided sample preparation has been optimized to be highly flexible, scalable, and to allow reproducible sample generation from 50 cells to milligrams of protein extracts. This methodology is fast, sensitive, easy-to-use on a wide range of sample types, and accessible to nonspecialists. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Non-decoloured In-gel Digestion of Coomassie Blue-stained Proteins

    Institute of Scientific and Technical Information of China (English)

    ZHANG Guo-an; BAO Hui-min; FAN Hui-zhi; YANG Peng-yuan

    2003-01-01

    A simplified method is presented for tryptic digestion of Coomassie brilliant blue(CBB)-stained proteins in polyacrylamide gels. Compared with conventional methods, the proposed method does not require a removal of the dye before digestion, and is thus faster and saves a lot of labor. The resulted digest can be analyzed by either RPLC/ESIMS or MALDI MS for identification of the protein in a conventional way. Model studies with bovine serum albumin(BSA) showed that 50 ng of the protein could be routinely identified. The simplified procedure displays a tendency to produce more incompletely cleaved peptides, which is favorable for improving the sequence coverage.

  20. Scanning electron microscopy study of protein immobilized on SIO2 Sol-gel surfaces

    Directory of Open Access Journals (Sweden)

    O.B.G. Assis

    2003-09-01

    Full Text Available Uniform attachment of enzymes to solid surfaces is essential in the development of bio and optical sensor devices. Immobilization by adsorption according to hydrophilic or hydrophobic nature is dependent on the charges and defects of the support surfaces. Sol-gel SiO2 densified glass surfaces, frequently used as supports for protein immobilization, are evaluated via scanning electron microscopy. The model protein is globular enzyme lysozyme, deposited by adsorption on functionalized surfaces. Formation of a protein layer is confirmed by FTIR spectroscopy, and the SEM images suggest discontinuous adsorption in areas where cracks predominate on the glass surface.

  1. A simple immunoblotting method after separation of proteins in agarose gel

    DEFF Research Database (Denmark)

    Koch, C; Skjødt, K; Laursen, I

    1985-01-01

    A simple and sensitive method for immunoblotting of proteins after separation in agarose gels is described. It involves transfer of proteins onto nitrocellulose paper simply by diffusion through pressure, a transfer which only takes about 10 min. By this method we have demonstrated the existence...... of multiple molecular forms of the complement factors C3 and factor B in serum from 2 species, man and chicken, after electrophoretic separation in agarose. We have also demonstrated the usefulness of the method for determining the isoelectric point of proteins after isoelectric focusing in agarose....

  2. SWISS-PROT: connecting biomolecular knowledge via a protein database

    OpenAIRE

    Gasteiger, Elisabeth; Jung, Eva; Bairoch, Amos Marc

    2001-01-01

    With the explosive growth of biological data, the development of new means of data storage was needed. More and more often biological information is no longer published in the conventional way via a publication in a scientific journal, but only deposited into a database. In the last two decades these databases have become essential tools for researchers in biological sciences. Biological databases can be classified according to the type of information they contain. There are basically three t...

  3. Characterization of immunogenic Clonorchis sinensis protein fractions by gel fitration chromatography

    Directory of Open Access Journals (Sweden)

    Duan Pham Ngoc

    2015-04-01

    Full Text Available Objective: To characterize immunogenic protein fraction of Clonorchis sinensis (C. sinensis by partial purification. Methods: A total of 30 hamsters were infected with 50 C. sinensis metacercariae, and then C. sinensis protein was purified by gel filtration chromatography. Indirect ELISA and immunoblot were used to detect the antibody in sera of hamsters infected with C. sinensis. Results: The gel filtration showed 2 peaks at high (fraction No. 10 to 14 and low (fraction No. 21 to 26 molecular weight proteins. Indirect ELISA showed that both antibodies of clonorchiasis and opisthorchiasis reacted strongly with early fractions (6 to 14 and the reaction was gradually reduced at middle and late fractions (15 to 50. Both antibodies showed different individual fraction of C. sinensis by immunoblot. It showed several protein bands that the 34 and 37 kDa were major proteins. The 53 kDa protein which was only found in the clonorchiasis reacted with fraction 20. Conclusions: The purified antigen of C. sinensis reacted similarly with both antibodies of clonorchiasis and opisthorchiasis where strong reaction was seen with early fractions. The C. sinensis protein fraction No. 20 may be useful for immunodiagnosis of clonorchiasis.

  4. A comparative in vitro study of the digestibility of heat- and high pressure-induced gels prepared from industrial milk whey proteins

    Science.gov (United States)

    He, Jin-Song; Mu, Tai-Hua; Wang, Juan

    2013-06-01

    We undertook this study to compare the digestibility of heat- and high pressure-induced gels produced from whey protein isolate (WPI). To simulate in vivo gastrointestinal digestion of WPI gels, a pepsin-trypsin digestion system was used. The in vitro protein digestibility of WPI gels induced by high pressure (400 MPa and 30 min; P-gel) and those induced by heat (80°C and 30 min; H-gel) was compared using a protein concentration of 0.14 g mL-1. The in vitro protein digestibility of P-gels was significantly greater than that of H-gels (p<0.05). The size-exclusion chromatography profiles of the hydrolysates showed that the P-gel generated more and smaller peptides than natural WPI and H-gels. Furthermore, Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis showed some soluble disulfide-mediated aggregation in the P-gel, while there was more insoluble aggregation in the H-gel than the P-gel. The P-gel was more sensitive to proteinase than the H-gel, which was related to the content of S-S bonds, and this in turn could be attributed to the differences in the gelation mechanism between the H-gel and P-gel.

  5. MODBASE: a database of annotated comparative protein structure models and associated resources

    OpenAIRE

    Pieper, Ursula; Eswar, Narayanan; Davis, Fred P.; Braberg, Hannes; Madhusudhan, M. S.; Rossi, Andrea; Marti-Renom, Marc; Karchin, Rachel; Webb, Ben M.; Eramian, David; Shen, Min-Yi; Kelly, Libusha; Melo, Francisco; Sali, Andrej

    2005-01-01

    MODBASE () is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on MODELLER for fold assignment, sequence–structure alignment, model building and model assessment (). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, and improvements in the software for calculat...

  6. Proteome analysis of barley seeds: Identification of major proteins from two-dimensional gels (pl 4-7)

    DEFF Research Database (Denmark)

    Østergaard, O.; Finnie, Christine; Laugesen, S.;

    2004-01-01

    -soluble proteins in extracts of mature barley (Hordeum vulgare) seeds and to follow their fate during germination. About 1200 and 600 spots of p/ 4-7 were detected on 2-D gels by silver staining and colloidal Coomassie Brilliant Blue staining, respectively. About 300 spots were selected for in-gel digestion...

  7. NMR relaxation and water self-diffusion studies in whey protein solutions and gels.

    Science.gov (United States)

    Colsenet, Roxane; Mariette, François; Cambert, Mireille

    2005-08-24

    The changes in water proton transverse relaxation behavior induced by aggregation of whey proteins are explained in terms of the simple molecular processes of diffusion and chemical exchange. The water self-diffusion coefficient was measured in whey protein solutions and gels by the pulsed field gradient NMR method. As expected, water self-diffusion was reduced with increased protein concentrations. Whatever the concentration, the water molecules were free to diffuse over distances varying from 15 to 47 mum. Water diffusion was constant over these distances, demonstrating that no restrictions were found to explain the water hindrance. The modification in protein structure by gelation induced a decrease in water diffusion. The effects of protein concentration on water diffusion are discussed and modeled. Two approaches were compared, the obstruction effect induced by a spherical particle and the cell model, which considered two water compartments with specific self-diffusion coefficients.

  8. Chromatofocusing fractionation and two-dimensional difference gel electrophoresis for low abundance serum proteins.

    Science.gov (United States)

    Qin, Shuzhen; Ferdinand, Angeline S; Richie, Jerome P; O'Leary, Michael P; Mok, Samuel C; Liu, Brian C-S

    2005-08-01

    The technical challenge to analysis of the serum proteome is that the serum proteins are present at unequal concentrations. A few are so dominant, such as serum albumin and immunoglobulins, that they mask detection of other proteins. Because of these high abundance proteins, current technologies, while theoretically capable of analyzing protein amounts spanning four orders of magnitude, are only able to analyze proteins ranging over two orders of magnitude and cannot analyze the lower abundance proteins that may be the next biomarkers and drug targets. To facilitate the identification of low abundance proteins, we fractionated serum samples from patients with prostate cancer and patients with benign prostate hyperplasia using anion displacement liquid chromatofocusing chromatography, which separates proteins by a pH gradient and a positively charged column. Differential expression of proteins from fractions was then determined and identified by IEF gels and 2-D DIGE. Results demonstrate improved resolution of proteins within the chosen pH gradient when compared to the unfractionated samples. Several proteins that were differentially expressed in serum from patients with prostate cancer were identified in the fractionated serum. Three of these proteins, squamous cell carcinoma antigen 1 (SCCA1), calgranulin B, and haptoglobin-related protein, are present in the serum at levels below the classical protein level of mg/mL. SCCA1 is normally expressed in serum at ng/mL levels, and calgranulin B is an intracellular protein. Our results demonstrate that the use of anion displacement liquid chromatofocusing chromatography may reduce the complexity of the serum proteome by separating proteins into distinct pH ranges, and facilitate the identification of low abundance proteins.

  9. Remote access to ACNUC nucleotide and protein sequence databases at PBIL.

    Science.gov (United States)

    Gouy, Manolo; Delmotte, Stéphane

    2008-04-01

    The ACNUC biological sequence database system provides powerful and fast query and extraction capabilities to a variety of nucleotide and protein sequence databases. The collection of ACNUC databases served by the Pôle Bio-Informatique Lyonnais includes the EMBL, GenBank, RefSeq and UniProt nucleotide and protein sequence databases and a series of other sequence databases that support comparative genomics analyses: HOVERGEN and HOGENOM containing families of homologous protein-coding genes from vertebrate and prokaryotic genomes, respectively; Ensembl and Genome Reviews for analyses of prokaryotic and of selected eukaryotic genomes. This report describes the main features of the ACNUC system and the access to ACNUC databases from any internet-connected computer. Such access was made possible by the definition of a remote ACNUC access protocol and the implementation of Application Programming Interfaces between the C, Python and R languages and this communication protocol. Two retrieval programs for ACNUC databases, Query_win, with a graphical user interface and raa_query, with a command line interface, are also described. Altogether, these bioinformatics tools provide users with either ready-to-use means of querying remote sequence databases through a variety of selection criteria, or a simple way to endow application programs with an extensive access to these databases. Remote access to ACNUC databases is open to all and fully documented (http://pbil.univ-lyon1.fr/databases/acnuc/acnuc.html).

  10. PACSY, a relational database management system for protein structure and chemical shift analysis.

    Science.gov (United States)

    Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

    2012-10-01

    PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

  11. Flavor release and perception of flavored whey protein gels: perception is determined by texture rather than by release.

    Science.gov (United States)

    Weel, Koen G C; Boelrijk, Alexandra E M; Alting, Arno C; Van Mil, Peter J J M; Burger, Jack J; Gruppen, Harry; Voragen, Alphons G J; Smit, Gerrit

    2002-08-28

    Five whey protein gels, with different gel hardnesses and waterholding capacities, were flavored with ethylbutyrate or diacetyl and evaluated by a 10-person panel to study the relation between the gel structure and the sensory perception, as well as the nosespace flavor concentration during eating. The sensory perception of the flavor compounds was measured by the time-intensity method, while simultaneously the nosespace flavor concentration was monitored by the MS-Nose. The nosespace flavor concentration was found to be independent of the gel hardness or waterholding capacity. However, significant changes in flavor intensity between the gels were perceived by the majority of the panelists, despite the fact that the panelists were instructed to focus only on flavor perception and to not take texture into account. From these observations it is concluded that the texture of gels determines perception of flavor intensity rather than the in-nose flavor concentration.

  12. Amino acid composition, molecular weight distribution and gel electrophoresis of walnut (Juglans regia L.) proteins and protein fractionations.

    Science.gov (United States)

    Mao, Xiaoying; Hua, Yufei; Chen, Guogang

    2014-01-01

    As a by-product of oil production, walnut proteins are considered as an additional source of plant protein for human food. To make full use of the protein resource, a comprehensive understanding of composition and characteristics of walnut proteins are required. Walnut proteins have been fractionated and characterized in this study. Amino acid composition, molecular weight distribution and gel electrophoresis of walnut proteins and protein fractionations were analyzed. The proteins were sequentially separated into four fractions according to their solubility. Glutelin was the main component of the protein extract. The content of glutelin, albumin, globulin and prolamin was about 72.06%, 7.54%, 15.67% and 4.73% respectively. Glutelin, albumin and globulin have a balanced content of essential amino acids, except for methionine, with respect to the FAO pattern recommended for adults. SDS-PAGE patterns of albumin, globulin and glutelin showed several polypeptides with molecular weights 14.4 to 66.2 kDa. The pattern of walnut proteins in two-dimension electrophoresis (2-DE) showed that the isoelectric point was mainly in the range of 4.8-6.8. The results of size exclusion chromatogram indicated molecular weight of the major components of walnut proteins were between 3.54 and 81.76 kDa.

  13. Amino Acid Composition, Molecular Weight Distribution and Gel Electrophoresis of Walnut (Juglans regia L. Proteins and Protein Fractionations

    Directory of Open Access Journals (Sweden)

    Xiaoying Mao

    2014-01-01

    Full Text Available As a by-product of oil production, walnut proteins are considered as an additional source of plant protein for human food. To make full use of the protein resource, a comprehensive understanding of composition and characteristics of walnut proteins are required. Walnut proteins have been fractionated and characterized in this study. Amino acid composition, molecular weight distribution and gel electrophoresis of walnut proteins and protein fractionations were analyzed. The proteins were sequentially separated into four fractions according to their solubility. Glutelin was the main component of the protein extract. The content of glutelin, albumin, globulin and prolamin was about 72.06%, 7.54%, 15.67% and 4.73% respectively. Glutelin, albumin and globulin have a balanced content of essential amino acids, except for methionine, with respect to the FAO pattern recommended for adults. SDS-PAGE patterns of albumin, globulin and glutelin showed several polypeptides with molecular weights 14.4 to 66.2 kDa. The pattern of walnut proteins in two-dimension electrophoresis (2-DE showed that the isoelectric point was mainly in the range of 4.8–6.8. The results of size exclusion chromatogram indicated molecular weight of the major components of walnut proteins were between 3.54 and 81.76 kDa.

  14. Development of gel-filter method for high enrichment of low-molecular weight proteins from serum.

    Directory of Open Access Journals (Sweden)

    Lingsheng Chen

    Full Text Available The human serum proteome has been extensively screened for biomarkers. However, the large dynamic range of protein concentrations in serum and the presence of highly abundant and large molecular weight proteins, make identification and detection changes in the amount of low-molecular weight proteins (LMW, molecular weight ≤ 30kDa difficult. Here, we developed a gel-filter method including four layers of different concentration of tricine SDS-PAGE-based gels to block high-molecular weight proteins and enrich LMW proteins. By utilizing this method, we identified 1,576 proteins (n = 2 from 10 μL serum. Among them, 559 (n = 2 proteins belonged to LMW proteins. Furthermore, this gel-filter method could identify 67.4% and 39.8% more LMW proteins than that in representative methods of glycine SDS-PAGE and optimized-DS, respectively. By utilizing SILAC-AQUA approach with labeled recombinant protein as internal standard, the recovery rate for GST spiked in serum during the treatment of gel-filter, optimized-DS, and ProteoMiner was 33.1 ± 0.01%, 18.7 ± 0.01% and 9.6 ± 0.03%, respectively. These results demonstrate that the gel-filter method offers a rapid, highly reproducible and efficient approach for screening biomarkers from serum through proteomic analyses.

  15. Resemblance of actin-binding protein/actin gels to covalently crosslinked networks

    Science.gov (United States)

    Janmey, Paul A.; Hvidt, Søren; Lamb, Jennifer; Stossel, Thomas P.

    1990-05-01

    THE maintainance of the shape of cells is often due to their surface elasticity, which arises mainly from an actin-rich cytoplasmic cortex1,2. On locomotion, phagocytosis or fission, however, these cells become partially fluid-like. The finding of proteins that can bind to actin and control the assembly of, or crosslink, actin filaments, and of intracellular messages that regulate the activities of some of these actin-binding proteins, indicates that such 'gel sol' transformations result from the rearrangement of cortical actin-rich networks3. Alternatively, on the basis of a study of the mechanical properties of mixtures of actin filaments and an Acanthamoeba actin-binding protein, α-actinin, it has been proposed that these transformations can be accounted for by rapid exchange of crosslinks between actin filaments4: the cortical network would be solid when the deformation rate is greater than the rate of crosslink exchange, but would deform or 'creep' when deformation is slow enough to permit crosslinker molecules to rearrange. Here we report, however, that mixtures of actin filaments and actin-binding protein (ABP), an actin crosslinking protein of many higher eukaryotes, form gels Theologically equivalent to covalently crosslinked networks. These gels do not creep in response to applied stress on a time scale compatible with most cell-surface movements. These findings support a more complex and controlled mechanism underlying the dynamic mechanical properties of cortical cytoplasm, and can explain why cells do not collapse under the constant shear forces that often exist in tissues.

  16. The effects of sucrose on the mechanical properties of acid milk proteins-kappa-carrageenan gels

    Directory of Open Access Journals (Sweden)

    E. Sabadini

    2006-03-01

    Full Text Available Mechanical properties have been widely correlated with textural characteristics to determine the interactions during the process formation of dairy gel. These interactions are strongly affected by process conditions and system composition. In the present study, the rheological of acid-induced protein dairy gels with (2(7-3 and without (2(6-2 sucrose and subjected to small and large deformations were studied using an experimental design. The independent variables were the sodium caseinate, whey protein concentrate (WPC, carrageenan and sucrose concentrations as well as stirring speed and heat treatment time and temperature. Mechanical deformation tests were performed at 0.1, 1, 5, and 9 mm/s up to 80% of initial height. A heavy dependence of rupture stress on increasing crosshead speed and the formation of harder gels with the addition of sucrose were observed. Moreover the elastic and viscous moduli, obtained by fitting the Maxwell model to stress relaxation data, increased with increasing addition of sucrose. These results can be explained by preferential hydration of the casein with sucrose, causing an induction of casein-polysaccharide and casein-casein interactions.

  17. Milk protein-gum tragacanth mixed gels: effect of heat-treatment sequence.

    Science.gov (United States)

    Hatami, Masoud; Nejatian, Mohammad; Mohammadifar, Mohammad Amin; Pourmand, Hanieh

    2014-01-30

    The aim of this study was to investigate the role of the heat-treatment sequence of biopolymer mixtures as a formulation parameter on the acid-induced gelation of tri-polymeric systems composed of sodium caseinate (Na-caseinate), whey protein concentrate (WPC), and gum tragacanth (GT). This was studied by applying four sequences of heat treatment: (A) co-heating all three biopolymers; (B) heating the milk-protein dispersion and the GT dispersion separately; (C) heating the dispersion containing Na-caseinate and GT together and heating whey protein alone; and (D) co-heating whey protein with GT and heating Na-caseinate alone. According to small-deformation rheological measurements, the strength of the mixed-gel network decreased in the order: C>B>D>A samples. SEM micrographs show that the network of sample C is much more homogenous, coarse and dense than sample A, while the networks of samples B and D are of intermediate density. The heat-treatment sequence of the biopolymer mixtures as a formulation parameter thus offers an opportunity to control the microstructure and rheological properties of mixed gels.

  18. Characterization and identification of early proteins in Chlamydia trachomatis serovar L2 by two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Lundemose, AG; Birkelund, Svend; Larsen, PM

    1990-01-01

    The synthesis of early proteins from Chlamydia trachomatis serovar L2 was analyzed by two-dimensional gel electrophoresis. By pulse-label experiments, the synthesis of seven proteins was observed at 2 to 8 h postinfection before the major outer membrane protein was detected at 8 to 10 h after...

  19. Differential analysis of two-dimensional gel electrophoresis profiles of spermatozoa protein in human normal motility sperm and idiopathic asthenospermia

    Institute of Scientific and Technical Information of China (English)

    SHEN Shu-lin; HE Da-lin; LUO Yong; NING Liang

    2006-01-01

    Objective: To evaluate the application of two-dimensional electrophoresis in the research of differentially expressed proteins in the human asthenospermia. Methods: Two-dimensional gel electrophoresis was performed on 4 normal sperm samples from healthy men and 4 sperm samples from 4 asthenospermia patients. After silver staining, the differential expression proteins were analyzed by PDQuest 2D analysis software. Results: Six differential protein spots were identified. Four spots showed increased expression in the control gels compared with the patient gels. Conclusion: The protein profiles of differential expression between the normal spermatozoa and idiopathic asthenospermia were established and some differential proteins were found. The data of this study would establish the better fundament for further isolation and identification of differentially expressed proteins in human asthenospermia sperm.

  20. In-gel microwave-assisted acid hydrolysis of proteins combined with liquid chromatography tandem mass spectrometry for mapping protein sequences.

    Science.gov (United States)

    Sun, Difei; Wang, Nan; Li, Liang

    2014-01-07

    We report an enabling method for mapping the protein sequence with high sequence coverage. This method combines the high separation power of gel electrophoresis for protein separation with the high sequence coverage capability of microwave-assisted acid hydrolysis (MAAH) mass spectrometry (MS). In-gel MAAH using 25% trifluoroacetic acid was developed and optimized for degrading the gel-separated protein into small peptides suitable for tandem MS sequencing. For bovine serum albumin (BSA) (∼67 kDa), with 4 μg of protein loading onto a gel for separation, followed by excising the protein gel band for in-gel MAAH and then injecting ∼2 μg of the resultant peptides into a liquid chromatography quadrupole time-of-flight mass spectrometer for analysis, 689 ± 54 (n = 3) unique peptides were identified with a protein sequence coverage of 99 ± 1%. Both the number of peptides detected and sequence coverage decreased as the sample amount decreased, mainly due to background interference: 316 ± 59 peptides and 94 ± 3% coverage for 2 μg loading, 136 ± 19 and 76 ± 5% for 1 μg loading, and 30 ± 2 and 32 ± 2% for 0.5 μg loading. To demonstrate the general applicability of the method, 10 gel bands from gel electrophoresis of an albumin-depleted human plasma sample were excised for in-gel MAAH LC-MS analysis. In total, 19 relatively high abundance proteins with molecular weights ranging from ∼8 to ∼160 kD could be mapped with coverage of 100% for six proteins (MW 8759 to 68 425 Da), 96-98% for five proteins (MW 11 458 to 36 431 Da), 92% for three proteins (MW 15 971 to 36 431 Da), 80-87% for four proteins (MW 42 287 to 162 134 Da), and 56% for one protein (MW 51 358 Da). Finally, to demonstrate the applicability of the method for more detailed analysis of complex protein mixtures, two-dimensional (2D) gel electrophoresis was combined with in-gel MAAH, affinity purification, and LC-MS/MS to characterize six bovine alpha-S1-casein phosphoprotein

  1. DCCP and DICP: Construction and Analyses of Databases for Copper- and Iron-Chelating Proteins

    Institute of Scientific and Technical Information of China (English)

    Hao Wu; Yan Yang; Sheng-Juan Jiang; Ling-Ling Chen; Hai-Xia Gao; Qing-Shan Fu; Feng Li; Bin-Guang Ma; Hong-Yu Zhang

    2005-01-01

    Copper and iron play important roles in a variety of biological processes, especially when being chelated with proteins. The proteins involved in the metal binding,transporting and metabolism have aroused much interest. To facilitate the study on this topic, we constructed two databases (DCCP and DICP) containing the known copper- and iron-chelating proteins, which are freely available from the website http:∥sdbi.sdut.edu.cn/en. Users can conveniently search and browse all of the entries in the databases. Based on the two databases, bioinformatic analyses were performed, which provided some novel insights into metalloproteins.

  2. Protein - TP Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available otein information on other websites. Data file File name: tp_atlas_protein.zip Fi...le URL: ftp://ftp.biosciencedbc.jp/archive/tp_atlas/LATEST/tp_atlas_protein.zip File size: 49.8 KB Simple se...arch URL http://togodb.biosciencedbc.jp/togodb/view/tp_atlas_protein#en Data acquisition method - Data analy

  3. Protein - AT Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available eins Research Program (TPRP). Data file File name: at_atlas_protein.zip File URL:... ftp://ftp.biosciencedbc.jp/archive/at_atlas/LATEST/at_atlas_protein.zip File size: 1.13 KB Simple search UR...L http://togodb.biosciencedbc.jp/togodb/view/at_atlas_protein#en Data acquisition method - Data analysis met

  4. Human immunodeficiency virus type 1, human protein interaction database at NCBI.

    Science.gov (United States)

    Fu, William; Sanders-Beer, Brigitte E; Katz, Kenneth S; Maglott, Donna R; Pruitt, Kim D; Ptak, Roger G

    2009-01-01

    The 'Human Immunodeficiency Virus Type 1 (HIV-1), Human Protein Interaction Database', available through the National Library of Medicine at www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions, was created to catalog all interactions between HIV-1 and human proteins published in the peer-reviewed literature. The database serves the scientific community exploring the discovery of novel HIV vaccine candidates and therapeutic targets. To facilitate this discovery approach, the following information for each HIV-1 human protein interaction is provided and can be retrieved without restriction by web-based downloads and ftp protocols: Reference Sequence (RefSeq) protein accession numbers, Entrez Gene identification numbers, brief descriptions of the interactions, searchable keywords for interactions and PubMed identification numbers (PMIDs) of journal articles describing the interactions. Currently, 2589 unique HIV-1 to human protein interactions and 5135 brief descriptions of the interactions, with a total of 14,312 PMID references to the original articles reporting the interactions, are stored in this growing database. In addition, all protein-protein interactions documented in the database are integrated into Entrez Gene records and listed in the 'HIV-1 protein interactions' section of Entrez Gene reports. The database is also tightly linked to other databases through Entrez Gene, enabling users to search for an abundance of information related to HIV pathogenesis and replication.

  5. Gel characteristics and microstructure of fish myofibrillar protein/cassava starch composites.

    Science.gov (United States)

    Fan, Mingcong; Hu, Ting; Zhao, Siming; Xiong, Shanbai; Xie, Jing; Huang, Qilin

    2017-03-01

    The changes in fish myofibrillar protein/cassava starch composites in the starch fraction range from 0 to 1, with their total content maintained at 60mg/mL, were investigated in terms of textural properties, rheological behaviours, morphology, spatial distribution and protein molecular structure. The results revealed that the starch fraction of 0.5 was a critical point for the conversion of the protein matrix to starch matrix and conversion of the gel from elastic to weak. Moreover, the protein-starch synergistic effect on the storage modulus was strongest at fractions of 0.5 and 0.6, due to the formation of a semi-interpenetrating network, with more amylose from the melted starch granules interpenetrated with the protein molecules, and the absorption of water by the starch granules to concentrate the protein matrix. Additionally, no covalent interaction between the protein and starch occurred with increasing starch fraction, thus having no significant influence on the protein secondary structure.

  6. Gel-free proteomic analysis of soybean root proteins affected by calcium under flooding stress

    Directory of Open Access Journals (Sweden)

    MyeongWon eOh

    2014-10-01

    Full Text Available Soybean is sensitive to flooding stress and exhibits reduced growth under flooding conditions. To better understand the flooding-responsive mechanisms of soybean, the effect of exogenous calcium on flooding-stressed soybeans was analyzed using proteomic technique. An increase in exogenous calcium levels enhanced soybean root elongation and suppressed the cell death of root tip under flooding stress. Proteins were extracted from the roots of 4-day-old soybean seedlings exposed to flooding stress without or with calcium for 2 days and analyzed using gel-free proteomic technique. Proteins involved in protein degradation/synthesis/posttranslational modification, hormone/cell wall metabolisms, and DNA synthesis were decreased by flooding stress; however, their reductions were recovered by calcium treatment. Development, lipid metabolism, and signaling-related proteins were increased in soybean roots when calcium was supplied under flooding stress. Fermentation and glycolysis-related proteins were increased in response to flooding; however, these proteins were not affected by calcium supplementation. Furthermore, urease and copper chaperone proteins exhibited similar profiles in 4-day-old untreated soybeans and 4-day-old soybeans exposed to flooding for 2 days in the presence of calcium. These results suggest that calcium might affect the cell wall/hormone metabolisms, protein degradation/synthesis, and DNA synthesis in soybean roots under flooding stress.

  7. ARCPHdb: A comprehensive protein database for SF1 and SF2 helicase from archaea.

    Science.gov (United States)

    Moukhtar, Mirna; Chaar, Wafi; Abdel-Razzak, Ziad; Khalil, Mohamad; Taha, Samir; Chamieh, Hala

    2017-01-01

    Superfamily 1 and Superfamily 2 helicases, two of the largest helicase protein families, play vital roles in many biological processes including replication, transcription and translation. Study of helicase proteins in the model microorganisms of archaea have largely contributed to the understanding of their function, architecture and assembly. Based on a large phylogenomics approach, we have identified and classified all SF1 and SF2 protein families in ninety five sequenced archaea genomes. Here we developed an online webserver linked to a specialized protein database named ARCPHdb to provide access for SF1 and SF2 helicase families from archaea. ARCPHdb was implemented using MySQL relational database. Web interfaces were developed using Netbeans. Data were stored according to UniProt accession numbers, NCBI Ref Seq ID, PDB IDs and Entrez Databases. A user-friendly interactive web interface has been developed to browse, search and download archaeal helicase protein sequences, their available 3D structure models, and related documentation available in the literature provided by ARCPHdb. The database provides direct links to matching external databases. The ARCPHdb is the first online database to compile all protein information on SF1 and SF2 helicase from archaea in one platform. This database provides essential resource information for all researchers interested in the field. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Role of disulphide linkages between protein-coated lipid droplets and the protein matrix in the rheological properties of porcine myofibrillar protein-peanut oil emulsion composite gels.

    Science.gov (United States)

    Wu, Mangang; Xiong, Youling L; Chen, Jie

    2011-07-01

    The objective of the study was to establish disulphide interaction between protein-coated oil droplets and the surrounding protein matrix in myofibrillar protein (MP)-emulsion composite gels. An MP-stabilized peanut oil emulsion was treated with 0, 1, 3, 5 and 10 mM N-ethylmaleimide (NEM, a sulphydryl-blocking agent) and subsequently incorporated into a bulk MP sol to produce 5%-lipid, 2%-protein composites at pH 6.2. About 69% of sulphydryls in the emulsion (1% protein) were blocked by 1 mM NEM, and almost all were bound at ≥3 mM NEM. The loss of free sulphydryls resulted in a significant drop in the storage modulus (G') and rupture force of the composite gels. Microstructural examination revealed pores and oil leakage from emulsion droplets by NEM treatments, corresponding to declining rheological properties of the MP-emulsion composites. The results supported the hypothesis that disulphide cross-linking between MP-coated oil droplets and protein matrix contributed to the stabilization and reinforcement of protein-emulsion composite gels formed in comminuted muscle foods.

  9. Tear film proteins deposited on high water content contact lenses identified with two-dimensional gel electrophoresis and mass spectrometry.

    Science.gov (United States)

    Nielsen, Kim; Vorum, Henrik; Ehlers, Niels; Aagaard, Nicolaj; Hjortdal, Jesper; Honoré, Bent

    2015-11-01

    Tear film proteins adhere to the surface of contact lenses (CLs). While the proteins in the tears have been extensively studied with various proteomic techniques, adhered proteins to CLs are less studied. In this pilot study, we have separated proteins with 2D gel electrophoresis prior to the conventional mass spectrometry (MS) in order to analyse the deposited proteins on hydrogel CLs from myopic patients. pHEMA and PVA hydrogel CLs worn by 3 patients for different time lengths were analysed. After wear, the CLs were frozen at -20°C. Proteins were extracted in lysis buffer, separated on 12% polyacrylamide gels and silver-stained. Protein spots were excised and identified with liquid chromatography - tandem MS. Deposited proteins were extracted with a yield of 26-66 μg and separated by 2D gel electrophoresis. The silver-stained gels showed similar protein patterns independent of the patient, hydrogel type and wear time. Seventy-two spots were analysed with MS, representing at least 12 different tear film proteins or protein fragments. Deposited tear film proteins from a single set of CLs worn for 1 day can successfully be analysed first with 2D gel electrophoresis and subsequently with MS, thus making examination of individual patients possible. The protein composition appeared homogeneous between the test persons which is a necessity for additional comparison analysis. The molecular masses of the identified proteins indicate that protein degradation occurs only as a minor event. Myopic patients were investigated in this pilot study, but the combined techniques can easily be applied to other eye diseases. © 2015 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

  10. Charge heterogeneity study of a Fc-fusion protein, abatacept, using two-dimensional gel electrophoresis.

    Science.gov (United States)

    Nebija, D; Noe, C R; Lachmann, B

    2015-08-01

    Medicinal products obtained by recombinant DNA technology are complex molecules and demonstrate a high degree of molecular heterogeneity. Charge heterogeneity and isoform pattern of this class of medicines, are parameters important for their quality, safety, and efficacy. In this study we report the application of two-dimensional gel electrophoresis (2-D electrophoresis) for the quality assessment, identification, charge heterogeneity and isoform pattern study of recombinant protein, CTLA4-Ig (abatacept), which has been selected as an example of the drug class, known as Fc-fusion proteins. In order to achieve an efficient separation of this complex analyte,2-D electrophoresis was optimized employing different experimental conditions regarding the selection of an immobilized pH gradient (IPG), sample pretreatment, presentation and detection procedure. Experimental datadocumented that 2-D electrophoresis is a suitable method for the assessment of identity, purity, structural integrity, isoform pattern and to monitor charge heterogeneity and post-translational glycosylation of the Fc-fusion protein, abatacept.

  11. Functional Evaluation of Proteins in Watery and Gel Saliva of Aphids.

    Science.gov (United States)

    van Bel, Aart J E; Will, Torsten

    2016-01-01

    Gel and watery saliva are regarded as key players in aphid-pIant interactions. The salivary composition seems to be influenced by the variable environment encountered by the stylet tip. Milieu sensing has been postulated to provide information needed for proper stylet navigation and for the required switches between gel and watery saliva secretion during stylet progress. Both the chemical and physical factors involved in sensing of the stylet's environment are discussed. To investigate the salivary proteome, proteins were collected from dissected gland extracts or artificial diets in a range of studies. We discuss the advantages and disadvantages of either collection method. Several proteins were identified by functional assays or by use of proteomic tools, while most of their functions still remain unknown. These studies disclosed the presence of at least two proteins carrying numerous sulfhydryl groups that may act as the structural backbone of the salivary sheath. Furthermore, cell-wall degrading proteins such a pectinases, pectin methylesterases, polygalacturonases, and cellulases as well as diverse Ca(2+)-binding proteins (e.g., regucalcin, ARMET proteins) were detected. Suppression of the plant defense may be a common goal of salivary proteins. Salivary proteases are likely involved in the breakdown of sieve-element proteins to invalidate plant defense or to increase the availability of organic N compounds. Salivary polyphenoloxidases, peroxidases and oxidoreductases were suggested to detoxify, e.g., plant phenols. During the last years, an increasing number of salivary proteins have been categorized under the term 'effector'. Effectors may act in the suppression (C002 or MIF cytokine) or the induction (e.g., Mp10 or Mp 42) of plant defense, respectively. A remarkable component of watery saliva seems the protein GroEL that originates from Buchnera aphidicola, the obligate symbiont of aphids and probably reflects an excretory product that induces plant defense

  12. Functional evaluation of proteins in watery and gel saliva of aphids

    Directory of Open Access Journals (Sweden)

    Aart Jan Eeuwe Van Bel

    2016-12-01

    Full Text Available AbstractGel and watery saliva are regarded as key players in aphid-pIant interactions. The salivary composition seems to be influenced by the variable environment encountered by the stylet tip. Milieu sensing has been postulated to provide information needed for proper stylet navigation and for the required switches between gel and watery saliva secretion during stylet progress. Both the chemical and physical factors involved in sensing of the stylet’s environment are discussed. To investigate the salivary proteome, proteins were collected from dissected gland extracts or artificial diets in a range of studies. We discuss the advantages and disadvantages of either collection method. Several proteins were identified by functional assays or by use of proteomic tools, while most of their functions still remain unknown. These studies disclosed the presence of at least two proteins carrying numerous sulfhydryl groups that may act as the sheath backbone. Furthermore, cell-wall degrading proteins such a pectinases, pectin methylesterases, polygalacturonases, and cellulases as well as diverse Ca2+-binding proteins (e.g. regucalcin, ARMET proteins were detected. Suppression of the plant defence may be a common goal of salivary proteins. Salivary proteases are likely involved in the breakdown of sieve-element proteins to invalidate plant defence or to increase the availability of organic N compounds. Salivary polyphenoloxidases, peroxidases and oxidoreductases were suggested to detoxify e.g. plant phenols. During the last years, an increasing number of salivary proteins have been categorized under the term ‘effector’. Effectors may act in the suppression (C002 or MIF cytokine or the induction (e.g. Mp10 or Mp 42 of plant defence, respectively. A remarkable component of watery saliva seems the protein GroEL that originates from Buchnera aphidicola, the obligate symbiont of aphids and probably reflects an excretory product that induces plant defence

  13. The influence of protein free calf blood extract eye gel on dry eye after pterygium surgery

    Directory of Open Access Journals (Sweden)

    Cai-Ni Ji

    2013-07-01

    Full Text Available AIM: To investigate the influence of protein free calf blood extract eye gel on dry eye after pterygium surgery. METHODS: Thirty six patients(40 eyeswith primary nasal pterygium were enrolled in this study, which were divided into study group and control group randomly, with 20 eyes in each group. All patients received pterygium excision and limbal stem cell autograft surgery and tobramicin dexamethasone eye drops after surgery. Patients of the study group received protein free calf blood extract eye gel while those of the control group received 0.1% sodium hyaluronate eye drops furthermore. Ocular surface disease index(OSDIquestionnaire, tear film break-up time(BUTand Schirmer's Ⅰ test Ⅰ(SⅠtwere carried before and 3 months after surgery to evaluate the dry eye degree of the patients. RESULTS: There was no statistical difference between the age, gender and size of the pterygium of the study and control groups preoperatively. There was no statistical difference between the OSDI(2.33±1.02 vs 2.32±0.93, BUT(8.80±2.48 vs 8.35±2.28seconds and SⅠt(4.30±2.30 vs 4.40±2.44of the two groups preoperatively. There was statistical difference between the OSDI(1.45±0.47 vs 1.81±0.60, BUT(11.20±2.07 vs 9.50±2.40seconds and SⅠt(8.35±3.13 vs 6.35±2.18of the two groups 3 months postoperatively, which was also different from that of the preoperative data correspondingly. CONCLUSION: Protein free calf blood extract eye gel could reduce the dry eye after pterygium surgery.

  14. Protein 3D Structure Image - PSCDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PSCDB Protein 3D Structure Image Data detail Data name Protein 3D Structure Image DOI 10.189...tory of This Database Site Policy | Contact Us Protein 3D Structure Image - PSCDB | LSDB Archive ...

  15. Detection and analysis of protein-protein interactions in organellar and prokaryotic proteomes by native gel electrophoresis: (Membrane) protein complexes and supercomplexes.

    Science.gov (United States)

    Krause, Frank

    2006-07-01

    It is an essential and challenging task to unravel protein-protein interactions in their actual in vivo context. Native gel systems provide a separation platform allowing the analysis of protein complexes on a rather proteome-wide scale in a single experiment. This review focus on blue-native (BN)-PAGE as the most versatile and successful gel-based approach to separate soluble and membrane protein complexes of intricate protein mixtures derived from all biological sources. BN-PAGE is a charge-shift method with a running pH of 7.5 relying on the gentle binding of anionic CBB dye to all membrane and many soluble protein complexes, leading to separation of protein species essentially according to their size and superior resolution than other fractionation techniques can offer. The closely related colorless-native (CN)-PAGE, whose applicability is restricted to protein species with intrinsic negative net charge, proved to provide an especially mild separation capable of preserving weak protein-protein interactions better than BN-PAGE. The essential conditions determining the success of detecting protein-protein interactions are the sample preparations, e.g. the efficiency/mildness of the detergent solubilization of membrane protein complexes. A broad overview about the achievements of BN- and CN-PAGE studies to elucidate protein-protein interactions in organelles and prokaryotes is presented, e.g. the mitochondrial protein import machinery and oxidative phosphorylation supercomplexes. In many cases, solubilization with digitonin was demonstrated to facilitate an efficient and particularly gentle extraction of membrane protein complexes prone to dissociation by treatment with other detergents. In general, analyses of protein interactomes should be carried out by both BN- and CN-PAGE.

  16. O-GLYCOBASE version 4.0: a revised database of O-glycosylated proteins

    DEFF Research Database (Denmark)

    Gupta, Ramneek; Birch, Hanne; Rapacki, Krzysztof;

    1999-01-01

    O-GLYCBASE is a database of glycoproteins with O-linked glycosylation sites. Entries with at least one experimentally verified O-glycosylation site have been complied from protein sequence databases and literature. Each entry contains information about the glycan involved, the species, sequence, ...

  17. Application of native agarose gel electrophoresis of serum proteins in veterinary diagnostics

    Directory of Open Access Journals (Sweden)

    Jania Bartosz

    2016-12-01

    Full Text Available Electrophoretic techniques, used to separate mixtures of electrically charged particles, are widely used in science. One of these techniques, native protein electrophoresis in an agarose gel, is applied in human and veterinary medicine. Changes in the proportions of individual protein fractions correspond to significant changes in the physiology of the body. Although the pattern obtained by electrophoretic separation rarely indicates a specific disease, it provides valuable information for the differential diagnosis. Decades of research on the types of patterns obtained in the case of particular diseases have led to the accumulation of substantial knowledge. The paper presents the available information on this topic. Serum protein electrophoresis is recommended in cases of increased levels of total protein in order to reveal the nature of the process. The basic information which can be obtained from electrophoretic separation includes the immune status of the organism. Both increased antigenic stimulation and immunodeficiency are clearly visible in electropherograms. Moreover, the level of heterogeneity of the corresponding protein fractions can help to distinguish between infectious diseases and cancer - multiple myeloma - the latter producing a homogeneous immunoglobulin fraction. Analysis of other protein fractions helps to detect or confirm an ongoing inflammatory process and provides information regarding liver function. Even when the concentration of total protein is within the reference range, this analysis can be recommended as a basic laboratory test.

  18. UNcleProt (Universal Nuclear Protein database of barley): The first nuclear protein database that distinguishes proteins from different phases of the cell cycle.

    Science.gov (United States)

    Blavet, Nicolas; Uřinovská, Jana; Jeřábková, Hana; Chamrád, Ivo; Vrána, Jan; Lenobel, René; Beinhauer, Jana; Šebela, Marek; Doležel, Jaroslav; Petrovská, Beáta

    2017-01-02

    Proteins are the most abundant component of the cell nucleus, where they perform a plethora of functions, including the assembly of long DNA molecules into condensed chromatin, DNA replication and repair, regulation of gene expression, synthesis of RNA molecules and their modification. Proteins are important components of nuclear bodies and are involved in the maintenance of the nuclear architecture, transport across the nuclear envelope and cell division. Given their importance, the current poor knowledge of plant nuclear proteins and their dynamics during the cell's life and division is striking. Several factors hamper the analysis of the plant nuclear proteome, but the most critical seems to be the contamination of nuclei by cytosolic material during their isolation. With the availability of an efficient protocol for the purification of plant nuclei, based on flow cytometric sorting, contamination by cytoplasmic remnants can be minimized. Moreover, flow cytometry allows the separation of nuclei in different stages of the cell cycle (G1, S, and G2). This strategy has led to the identification of large number of nuclear proteins from barley (Hordeum vulgare), thus triggering the creation of a dedicated database called UNcleProt, http://barley.gambrinus.ueb.cas.cz/ .

  19. Integrated Controlling System and Unified Database for High Throughput Protein Crystallography Experiments

    Science.gov (United States)

    Gaponov, Yu. A.; Igarashi, N.; Hiraki, M.; Sasajima, K.; Matsugaki, N.; Suzuki, M.; Kosuge, T.; Wakatsuki, S.

    2004-05-01

    An integrated controlling system and a unified database for high throughput protein crystallography experiments have been developed. Main features of protein crystallography experiments (purification, crystallization, crystal harvesting, data collection, data processing) were integrated into the software under development. All information necessary to perform protein crystallography experiments is stored (except raw X-ray data that are stored in a central data server) in a MySQL relational database. The database contains four mutually linked hierarchical trees describing protein crystals, data collection of protein crystal and experimental data processing. A database editor was designed and developed. The editor supports basic database functions to view, create, modify and delete user records in the database. Two search engines were realized: direct search of necessary information in the database and object oriented search. The system is based on TCP/IP secure UNIX sockets with four predefined sending and receiving behaviors, which support communications between all connected servers and clients with remote control functions (creating and modifying data for experimental conditions, data acquisition, viewing experimental data, and performing data processing). Two secure login schemes were designed and developed: a direct method (using the developed Linux clients with secure connection) and an indirect method (using the secure SSL connection using secure X11 support from any operating system with X-terminal and SSH support). A part of the system has been implemented on a new MAD beam line, NW12, at the Photon Factory Advanced Ring for general user experiments.

  20. Development of human protein reference database as an initial platform for approaching systems biology in humans.

    Science.gov (United States)

    Peri, Suraj; Navarro, J Daniel; Amanchy, Ramars; Kristiansen, Troels Z; Jonnalagadda, Chandra Kiran; Surendranath, Vineeth; Niranjan, Vidya; Muthusamy, Babylakshmi; Gandhi, T K B; Gronborg, Mads; Ibarrola, Nieves; Deshpande, Nandan; Shanker, K; Shivashankar, H N; Rashmi, B P; Ramya, M A; Zhao, Zhixing; Chandrika, K N; Padma, N; Harsha, H C; Yatish, A J; Kavitha, M P; Menezes, Minal; Choudhury, Dipanwita Roy; Suresh, Shubha; Ghosh, Neelanjana; Saravana, R; Chandran, Sreenath; Krishna, Subhalakshmi; Joy, Mary; Anand, Sanjeev K; Madavan, V; Joseph, Ansamma; Wong, Guang W; Schiemann, William P; Constantinescu, Stefan N; Huang, Lily; Khosravi-Far, Roya; Steen, Hanno; Tewari, Muneesh; Ghaffari, Saghi; Blobe, Gerard C; Dang, Chi V; Garcia, Joe G N; Pevsner, Jonathan; Jensen, Ole N; Roepstorff, Peter; Deshpande, Krishna S; Chinnaiyan, Arul M; Hamosh, Ada; Chakravarti, Aravinda; Pandey, Akhilesh

    2003-10-01

    Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization were extracted from the literature for a nonredundant set of 2750 human proteins. Almost all the information was obtained manually by biologists who read and interpreted >300,000 published articles during the annotation process. This database, which has an intuitive query interface allowing easy access to all the features of proteins, was built by using open source technologies and will be freely available at http://www.hprd.org to the academic community. This unified bioinformatics platform will be useful in cataloging and mining the large number of proteomic interactions and alterations that will be discovered in the postgenomic era.

  1. A Comparison of Protein Extraction Methods Suitable for Gel-Based Proteomics Studies of Aphid Proteins

    Science.gov (United States)

    Few attempts have been made to methodically compare protein isolation methods from insect tissues for proteomic studies. To address this, we compared qualitative and quantitative differences among three methods for isolation, purification and solubilization of insect proteins. Schizaphis graminum,...

  2. InterEvol database: exploring the structure and evolution of protein complex interfaces

    OpenAIRE

    Faure, Guilhem; Andreani, Jessica; Guerois, Raphaël

    2011-01-01

    Capturing how the structures of interacting partners evolved at their binding interfaces is a fundamental issue for understanding interactomes evolution. In that scope, the InterEvol database was designed for exploring 3D structures of homologous interfaces of protein complexes. For every chain forming a complex in the protein data bank (PDB), close and remote structural interologs were identified providing essential snapshots for studying interfaces evolution. The database provides tools to ...

  3. A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels

    Directory of Open Access Journals (Sweden)

    Wu Steven H

    2012-06-01

    Full Text Available Abstract Background Two-dimensional polyacrylamide gel electrophoresis (2D PAGE is commonly used to identify differentially expressed proteins under two or more experimental or observational conditions. Wu et al (2009 developed a univariate probabilistic model which was used to identify differential expression between Case and Control groups, by applying a Likelihood Ratio Test (LRT to each protein on a 2D PAGE. In contrast to commonly used statistical approaches, this model takes into account the two possible causes of missing values in 2D PAGE: either (1 the non-expression of a protein; or (2 a level of expression that falls below the limit of detection. Results We develop a global Bayesian model which extends the previously described model. Unlike the univariate approach, the model reported here is able treat all differentially expressed proteins simultaneously. Whereas each protein is modelled by the univariate likelihood function previously described, several global distributions are used to model the underlying relationship between the parameters associated with individual proteins. These global distributions are able to combine information from each protein to give more accurate estimates of the true parameters. In our implementation of the procedure, all parameters are recovered by Markov chain Monte Carlo (MCMC integration. The 95% highest posterior density (HPD intervals for the marginal posterior distributions are used to determine whether differences in protein expression are due to differences in mean expression intensities, and/or differences in the probabilities of expression. Conclusions Simulation analyses showed that the global model is able to accurately recover the underlying global distributions, and identify more differentially expressed proteins than the simple application of a LRT. Additionally, simulations also indicate that the probability of incorrectly identifying a protein as differentially expressed (i.e., the False

  4. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE of urinary protein in acute kidney injury

    Directory of Open Access Journals (Sweden)

    Sufi M Suhail

    2011-01-01

    Full Text Available Recent experimental and clinical studies have shown the importance of urinary proteomics in acute kidney injury (AKI. We analyzed the protein in urine of patients with clinical AKI using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE for its diagnostic value, and followed them up for 40 months to evaluate prognosis. Urine from 31 consecutive cases of AKI was analyzed with SDS-PAGE to determine the low, middle and high molecular weight proteins. Fractional excretion of sodium (FENa was estimated from serum and urine creatinine and sodium (Na. The cases were followed-up for 40 months from the end of the recruitment of study cases. Glomerular protein was higher in the hematuria group when compared with the non-hematuria group (P <0.04 and in the AKI group than in the acute on chronic renal failure (AKI-on-CRF group (P <0.002. Tubular protein was higher in the AKI-on-CRF group (P <0.003 than in the AKI group. Tubular protein correlated with FENa in groups with diabetes mellitus (DM, AKI-on-CRF, and without hematuria (P <0.03, P <0.02 and P <0.004, respectively. Pattern of protein did not differ between groups with and without DM and clinical acute tubular necrosis (ATN. At the end of 40 months follow-up, category with predominantly glomerular protein progressed to chronic renal failure (CRF or end-stage renal failure in higher proportion (P <0.05. In clinical AKI, we observed that glomerular protein dominated in cases with glomerular insult, as indicated by hematuria. Tubular protein was common in the study cases with CRF, DM and cases without hematuria. This indicates tubulo-interstitial injury for AKI in these cases. Patients with predominantly glomerular protein had an adverse outcome.

  5. Identification of protein complexes of microsomes in rat adipocytes by native gel coupled with LC-ESI-QTOF.

    Science.gov (United States)

    Ke, Ming; Zhang, Yongqian; Xiong, Yan; Saeed, Yasmeen; Deng, Yulin

    2016-04-01

    The study of the composition of microsome proteins/complexes/interactions in adipocytes provides useful information for researchers related to energy metabolism disorders. The native gel coupled with LC-ESI-QTOF approach was employed here for separating protein complexes. We found a series of proteins functionally clustered in biological processes of protein metabolism, cellular carbohydrate catabolism, response to stimulus and wounding, macromolecular complex subunit organization, positive regulation of molecular function, regulation of programmed cell death and biomolecule transport. According to clustering of proteins' electrophoresis profiles across native gel fractions and bioinformatics data retrieval, protein complexes/interactions involved in protein metabolism, cellular carbohydrate catabolism, macromolecular complex subunit organization and biomolecule transport were identified. Besides, the results also revealed some functional linkages, which may provide useful information for discovering previously unknown interactions. The interaction between SSAO and ALDH2 was verified by co-immunoprecipitation. The native gel combining mass spectrometry approach appeared to be a useful tool for investigating microsome proteins and complexes to complement the traditional electrophoresis approaches. The native gel strategy together with our findings should facilitate future studies of the composition of rat adipocyte microsome protein complexes under different conditions.

  6. Gel-free proteomic methodologies to study reversible cysteine oxidation and irreversible protein carbonyl formation.

    Science.gov (United States)

    Boronat, S; García-Santamarina, S; Hidalgo, E

    2015-05-01

    Oxidative modifications in proteins have been traditionally considered as hallmarks of damage by oxidative stress and aging. However, oxidants can generate a huge variety of reversible and irreversible modifications in amino acid side chains as well as in the protein backbones, and these post-translational modifications can contribute to the activation of signal transduction pathways, and also mediate the toxicity of oxidants. Among the reversible modifications, the most relevant ones are those arising from cysteine oxidation. Thus, formation of sulfenic acid or disulfide bonds is known to occur in many enzymes as part of their catalytic cycles, and it also participates in the activation of signaling cascades. Furthermore, these reversible modifications have been usually attributed with a protective role, since they may prevent the formation of irreversible damage by scavenging reactive oxygen species. Among irreversible modifications, protein carbonyl formation has been linked to damage and death, since it cannot be repaired and can lead to protein loss-of-function and to the formation of protein aggregates. This review is aimed at researchers interested on the biological consequences of oxidative stress, both at the level of signaling and toxicity. Here we are providing a concise overview on current mass-spectrometry-based methodologies to detect reversible cysteine oxidation and irreversible protein carbonyl formation in proteomes. We do not pretend to impose any of the different methodologies, but rather to provide an objective catwalk on published gel-free approaches to detect those two types of modifications, from a biologist's point of view.

  7. PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system

    Science.gov (United States)

    Droit, Arnaud; Hunter, Joanna M; Rouleau, Michèle; Ethier, Chantal; Picard-Cloutier, Aude; Bourgais, David; Poirier, Guy G

    2007-01-01

    Background In the "post-genome" era, mass spectrometry (MS) has become an important method for the analysis of proteins and the rapid advancement of this technique, in combination with other proteomics methods, results in an increasing amount of proteome data. This data must be archived and analysed using specialized bioinformatics tools. Description We herein describe "PARPs database," a data analysis and management pipeline for liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics. PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management, as well as data-mining of the peptides and proteins identified. Conclusion Using this pipeline, we have successfully identified several interactions of biological significance between PARP-1 and other proteins, namely RFC-1, 2, 3, 4 and 5. PMID:18093328

  8. PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system

    Directory of Open Access Journals (Sweden)

    Picard-Cloutier Aude

    2007-12-01

    Full Text Available Abstract Background In the "post-genome" era, mass spectrometry (MS has become an important method for the analysis of proteins and the rapid advancement of this technique, in combination with other proteomics methods, results in an increasing amount of proteome data. This data must be archived and analysed using specialized bioinformatics tools. Description We herein describe "PARPs database," a data analysis and management pipeline for liquid chromatography tandem mass spectrometry (LC-MS/MS proteomics. PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management, as well as data-mining of the peptides and proteins identified. Conclusion Using this pipeline, we have successfully identified several interactions of biological significance between PARP-1 and other proteins, namely RFC-1, 2, 3, 4 and 5.

  9. Changes in chemical interactions and protein conformation during heat-induced wheat gluten gel formation.

    Science.gov (United States)

    Wang, Kai-Qiang; Luo, Shui-Zhong; Zhong, Xi-Yang; Cai, Jing; Jiang, Shao-Tong; Zheng, Zhi

    2017-01-01

    In order to elucidate the heat-induced wheat gluten gel formation mechanism, changes in chemical interactions and protein conformation were investigated during gelation. The contribution of ionic and hydrogen bonds were found to decrease from 0.746 and 4.133g/L to 0.397 and 2.733g/L, respectively, as the temperature increased from 25 to 90°C. Moreover, the free SH content remarkably decreased from 37.91 to 19.79μmol/g during gelation. Ultraviolet absorption spectra and intrinsic fluorescence spectra suggested that wheat gluten unfolded during the heating process. In addition, wheat gluten gels treated at 80 and 90°C exhibited a "steric hindrance" effect, which can be attributed to the formation of aggregates. Fourier transform infrared spectra suggested that the random coil content increased at low temperatures (40 and 50°C), whereas the content of intermolecular β-sheets due to protein aggregation increased from 38.10% to 44.28% when the gelation temperature was 90°C.

  10. Dual Role (Anti- and Pro-oxidant) of Gallic Acid in Mediating Myofibrillar Protein Gelation and Gel in Vitro Digestion.

    Science.gov (United States)

    Cao, Yungang; True, Alma D; Chen, Jie; Xiong, Youling L

    2016-04-20

    The dose-dependent effects of gallic acid (GA; at 0, 6, 30, and 150 μmol/g protein) on chemical changes and gelling properties of oxidatively stressed porcine myofibrillar protein (MP) and in vitro digestibility of the gels were investigated. The incorporation of GA suppressed lipid oxidation and protein carbonyl formation but promoted the loss of thiol and amine groups, destabilization of the tertiary structure, aggregation, and cross-linking. The gelling potential (storage modulus) of MP was increased by nearly 50% with 6 and 30 μmol/g of GA, corresponding to enhanced protein unfolding and aggregation and formation of disulfide-dominant covalent bonds. However, GA at 150 μmol/g induced macroscopic aggregations and insolubility of MP, resulting in poorly structured gels. Despite the oxidative changes, MP gels did not show reduced susceptibility to digestive enzymes in vitro.

  11. Kinetic model for whey protein hydrolysis by alcalase multipoint-immobilized on agarose gel particles

    Directory of Open Access Journals (Sweden)

    Sousa Jr R.

    2004-01-01

    Full Text Available Partial hydrolysis of whey proteins by enzymes immobilized on an inert support can either change or evidence functional properties of the produced peptides, thereby increasing their applications. The hydrolysis of sweet cheese whey proteins by alcalase, which is multipoint-immobilized on agarose gel, is studied here. A Michaelis-Menten model that takes into account competitive inhibition by the product was fitted to experimental data. The influence of pH on the kinetic parameters in the range 6.0 to 11.0 was assessed, at 50ºC. Initial reaction-rate assays in a pHstat at different concentrations of substrate were used to estimate kinetic and Michaelis-Menten parameters, k and K M. Experimental data from long-term batch assays were used to quantify the inhibition parameter, K I. The fitting of the model to the experimental data was accurate in the entire pH range.

  12. The Histone Database: an integrated resource for histones and histone fold-containing proteins.

    Science.gov (United States)

    Mariño-Ramírez, Leonardo; Levine, Kevin M; Morales, Mario; Zhang, Suiyuan; Moreland, R Travis; Baxevanis, Andreas D; Landsman, David

    2011-01-01

    Eukaryotic chromatin is composed of DNA and protein components-core histones-that act to compactly pack the DNA into nucleosomes, the fundamental building blocks of chromatin. These nucleosomes are connected to adjacent nucleosomes by linker histones. Nucleosomes are highly dynamic and, through various core histone post-translational modifications and incorporation of diverse histone variants, can serve as epigenetic marks to control processes such as gene expression and recombination. The Histone Sequence Database is a curated collection of sequences and structures of histones and non-histone proteins containing histone folds, assembled from major public databases. Here, we report a substantial increase in the number of sequences and taxonomic coverage for histone and histone fold-containing proteins available in the database. Additionally, the database now contains an expanded dataset that includes archaeal histone sequences. The database also provides comprehensive multiple sequence alignments for each of the four core histones (H2A, H2B, H3 and H4), the linker histones (H1/H5) and the archaeal histones. The database also includes current information on solved histone fold-containing structures. The Histone Sequence Database is an inclusive resource for the analysis of chromatin structure and function focused on histones and histone fold-containing proteins.

  13. The Pfam protein families database: towards a more sustainable future.

    Science.gov (United States)

    Finn, Robert D; Coggill, Penelope; Eberhardt, Ruth Y; Eddy, Sean R; Mistry, Jaina; Mitchell, Alex L; Potter, Simon C; Punta, Marco; Qureshi, Matloob; Sangrador-Vegas, Amaia; Salazar, Gustavo A; Tate, John; Bateman, Alex

    2016-01-01

    In the last two years the Pfam database (http://pfam.xfam.org) has undergone a substantial reorganisation to reduce the effort involved in making a release, thereby permitting more frequent releases. Arguably the most significant of these changes is that Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website restricted to this smaller set. Building families on reference proteomes sequences brings greater stability, which decreases the amount of manual curation required to maintain them. It also reduces the number of sequences displayed on the website, whilst still providing access to many important model organisms. Matches to the full UniProtKB database are, however, still available and Pfam annotations for individual UniProtKB sequences can still be retrieved. Some Pfam entries (1.6%) which have no matches to reference proteomes remain; we are working with UniProt to see if sequences from them can be incorporated into reference proteomes. Pfam-B, the automatically-generated supplement to Pfam, has been removed. The current release (Pfam 29.0) includes 16 295 entries and 559 clans. The facility to view the relationship between families within a clan has been improved by the introduction of a new tool.

  14. SynProt: A Comprehensive Database for Proteins of the Detergent-Resistant Synaptic Junctions Fraction

    Directory of Open Access Journals (Sweden)

    Rainer ePielot

    2012-06-01

    Full Text Available Chemical synapses are highly specialized cell-cell contacts for communication between neurons in the CNS characterized by complex and dynamic protein networks at both synaptic membranes. The cytomatrix at the active zone (CAZ organizes the apparatus for the regulated release of transmitters from the presynapse. At the postsynaptic side, the postsynaptic density constitutes the machinery for detection, integration and transduction of the transmitter signal. Both pre- and postsynaptic protein networks represent the molecular substrates for synaptic plasticity. Their function can be altered both by regulating their composition and by post-translational modification of their components. For a comprehensive understanding of synaptic networks the entire ensemble of synaptic proteins has to be considered. To support this, we established a comprehensive database for synaptic junction proteins (SynProt database primarily based on proteomics data obtained from biochemical preparations of detergent-resistant synaptic junctions. The database currently contains 2,788 non-redundant entries of rat, mouse and some human proteins, which mainly have been manually extracted from twelve proteomic studies and annotated for synaptic subcellular localization. Each dataset is completed with manually added information including protein classifiers as well as automatically retrieved and updated information from public databases (UniProt and PubMed. We intend that the database will be used to support modeling of synaptic protein networks and rational experimental design.

  15. Protein composition of wheat gluten polymer fractions determined by quantitative two-dimensional gel electrophoresis and tandem mass spectrometry

    Science.gov (United States)

    Flour proteins from the US bread wheat Butte 86 were extracted in 0.5% SDS using a two-step procedure with and without sonication and further separated by size exclusion chromatography into monomeric and polymeric fractions. Proteins in each fraction were analyzed by quantitative two-dimensional gel...

  16. Breakdown properties and sensory perception of whey proteins/polysaccharide mixed gels as a function of microstructure.

    NARCIS (Netherlands)

    Berg, van den L.; Vliet, van T.; Linden, van der E.; Boekel, van M.A.J.S.; Velde, van de F.

    2007-01-01

    Whey protein isolate (WPI)/polysaccharide mixed gels used in the current study formed homogeneous and phase separated microstructures as visualized by confocal laser scanning microscopy (CLSM). The latter can be further classified into protein continuous, bicontinuous and coarse stranded microstruct

  17. The ability to store energy in pea protein gels is set by network dimensions smaller than 50 nm

    NARCIS (Netherlands)

    Munialo, C.D.; Linden, van der E.; Jongh, de H.H.J.

    2014-01-01

    The objective of this study was to identify which length scales set the ability to elastically store energy in pea protein network structures. Various network structures were obtained frompea proteins by varying the pH and salt conditions during gel formation. The coarseness of the network structure

  18. COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps.

    Science.gov (United States)

    Chang, Yi-Chien; Hu, Zhenjun; Rachlin, John; Anton, Brian P; Kasif, Simon; Roberts, Richard J; Steffen, Martin

    2016-01-01

    The COMBREX database (COMBREX-DB; combrex.bu.edu) is an online repository of information related to (i) experimentally determined protein function, (ii) predicted protein function, (iii) relationships among proteins of unknown function and various types of experimental data, including molecular function, protein structure, and associated phenotypes. The database was created as part of the novel COMBREX (COMputational BRidges to EXperiments) effort aimed at accelerating the rate of gene function validation. It currently holds information on ∼ 3.3 million known and predicted proteins from over 1000 completely sequenced bacterial and archaeal genomes. The database also contains a prototype recommendation system for helping users identify those proteins whose experimental determination of function would be most informative for predicting function for other proteins within protein families. The emphasis on documenting experimental evidence for function predictions, and the prioritization of uncharacterized proteins for experimental testing distinguish COMBREX from other publicly available microbial genomics resources. This article describes updates to COMBREX-DB since an initial description in the 2011 NAR Database Issue.

  19. Extracting protein alignment models from the sequence database.

    Science.gov (United States)

    Neuwald, A F; Liu, J S; Lipman, D J; Lawrence, C E

    1997-05-01

    Biologists often gain structural and functional insights into a protein sequence by constructing a multiple alignment model of the family. Here a program called Probe fully automates this process of model construction starting from a single sequence. Central to this program is a powerful new method to locate and align only those, often subtly, conserved patterns essential to the family as a whole. When applied to randomly chosen proteins, Probe found on average about four times as many relationships as a pairwise search and yielded many new discoveries. These include: an obscure subfamily of globins in the roundworm Caenorhabditis elegans ; two new superfamilies of metallohydrolases; a lipoyl/biotin swinging arm domain in bacterial membrane fusion proteins; and a DH domain in the yeast Bud3 and Fus2 proteins. By identifying distant relationships and merging families into superfamilies in this way, this analysis further confirms the notion that proteins evolved from relatively few ancient sequences. Moreover, this method automatically generates models of these ancient conserved regions for rapid and sensitive screening of sequences.

  20. Enzymatic cross-linking of soy proteins within non-fat set yogurt gel.

    Science.gov (United States)

    Soleymanpuori, Rana; Madadlou, Ashkan; Zeynali, Fariba; Khosrowshahi, Asghar

    2014-08-01

    Soy proteins as the health-promoting ingredients and candidate fat substitutes in dairy products are good substrates for the cross-linking action of the enzyme transglutaminase. Non-fat set yogurt samples were prepared from the milks enriched with soy protein isolate (SPI) and/or treated with the enzyme transglutaminase. The highest titrable acidity was recorded for the yogurt enriched with SPI and treated with the enzyme throughout the cold storage for 21 d. SPI-enrichment of yogurt milk increased the water holding capacity. Although enrichment with SPI did not influence the count of Streptococcus themophilus, increased that of Lactobacillus bulgaricus ∼3 log cycles. The enzymatic treatment of SPI-enriched milk however, suppressed the bacteria growth-promoting influence of SPI due probably to making the soy proteins inaccessible for Lactobacillus. SPI-enrichment and enzymatic treatment of milk decreased the various organic acids content in yoghurt samples; influence of the former was more significant. The cross-linking of milk proteins to soy proteins was confirmed with the gel electrophoresis results.

  1. Difference gel electrophoresis (DiGE) identifies differentially expressed proteins in endoscopically-collected pancreatic fluid

    Science.gov (United States)

    Paulo, Joao A.; Lee, Linda S.; Banks, Peter A.; Steen, Hanno; Conwell, Darwin L.

    2012-01-01

    Alterations in the pancreatic fluid proteome of individuals with chronic pancreatitis may offer insights into the development and progression of the disease. The endoscopic pancreas function test (ePFT) can safely collect large volumes of pancreatic fluid that are potentially amenable to proteomic analyses using difference gel electrophoresis (DiGE) coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Pancreatic fluid was collected endoscopically using the ePFT method following secretin stimulation from three individuals with severe chronic pancreatitis and three chronic abdominal pain controls. The fluid was processed to minimize protein degradation and the protein profiles of each cohort, as determined by DiGE and LC-MS/MS, were compared. This DiGE-LC-MS/MS analysis reveals proteins that are differentially expressed in chronic pancreatitis compared to chronic abdominal pain controls. Proteins with higher abundance in pancreatic fluid from chronic pancreatitis individuals include: actin, desmoplankin, alpha-1-antitrypsin, SNC73, and serotransferrin. Those of relatively lower abundance include carboxypeptidase B, lipase, alpha-1-antichymotrypsin, alpha-2-macroglobulin, Arp2/3 subunit 4, glyceraldehyde-3-phosphate dehydrogenase, and protein disulfide isomerase. Endoscopic collection (ePFT) in tandem with DiGE-LC-MS/MS is a suitable approach for pancreatic fluid proteome analysis, however, further optimization of our protocol, as outlined herein, may improve proteome coverage in future analyses. PMID:21792986

  2. Adsorption and protonation of peptides and proteins in pH responsive gels

    Science.gov (United States)

    Longo, Gabriel S.; Szleifer, Igal

    2016-08-01

    To describe the non-trivial features of the equilibrium protonation and physical adsorption of peptides/proteins in pH-responsive hydrogels, we summarize our recent theoretical work on the subject. In these systems, molecular confinement in nanometer-sized environments modifies the balance between chemical state, physical interactions and molecular organization, which results in a behavior that is qualitatively different from what is expected from assuming the bulk solution protonation. To enhance adsorption, the pH-dependent deprotonation curves of all amino acids of adsorbed proteins are adequately shifted and deformed, which depends, in a complex fashion, on the specific amino acid. This possibility of modifying different acid-base equilibriums gives the adsorbed protein degrees of freedom to regulate charge and enhance electrostatic attractions under a wide range of experimental conditions. Protein adsorption modifies the microenvironment inside the hydrogel, particularly the gel pH. As a result, the state of protonation of the network is different before and after adsorption. The physicochemical considerations described in this review can be useful in the design of functional materials involving protein adsorption.

  3. Protein profile analysis of Malaysian snake venoms by two-dimensional gel electrophoresis

    Directory of Open Access Journals (Sweden)

    J Vejayan

    2010-01-01

    Full Text Available Snake venoms comprise a highly complex mixture of proteins, which requires for their characterization the use of versatile two-dimensional electrophoresis techniques. In the present study, venoms obtained from eight snakes (Ophiophagus hannah, Naja kaouthia, Naja sumatrana, Bungarus fasciatus, Trimeresurus sumatranus, Tropidolaemus wagleri, Enhydrina schistosa and Calloselasma rhodostoma commonly found in Malaysia were separated based on two independent properties, isoelectric point (pI and molecular weight (MW. Many differences in snake venoms at the inter-family, inter-subfamily, inter-genus and inter-species levels were revealed. Notably, proteins from individuals of the Viperidae family - Trimeresurus sumatranus, Tropidolaemus wagleri and Calloselasma rhodostoma - were found to be numerous and scattered by the two-dimensional gel electrophoresis (2DE specifically in regions between 37 and 100 kDa compared to the Elapidae venom proteins. The latter were clustered at the basic and lower molecular mass region (less than 20 kDa. Trains of spots were commonly observed, indicating that these proteins may be derived from post-translational modifications. Ophiophagus hannah (Elapidae revealed a great amount of protein spots in the higher molecular mass range when compared to Enhydrina schistosa, Naja kaouthia, Naja sumatrana and Bungarus fasciatus. Overall 2DE showed large differences in the venom profile of each species, which might be employed as an ancillary tool to the identification of venomous snake species.

  4. AraPPISite: a database of fine-grained protein-protein interaction site annotations for Arabidopsis thaliana.

    Science.gov (United States)

    Li, Hong; Yang, Shiping; Wang, Chuan; Zhou, Yuan; Zhang, Ziding

    2016-09-01

    Knowledge about protein interaction sites provides detailed information of protein-protein interactions (PPIs). To date, nearly 20,000 of PPIs from Arabidopsis thaliana have been identified. Nevertheless, the interaction site information has been largely missed by previously published PPI databases. Here, AraPPISite, a database that presents fine-grained interaction details for A. thaliana PPIs is established. First, the experimentally determined 3D structures of 27 A. thaliana PPIs are collected from the Protein Data Bank database and the predicted 3D structures of 3023 A. thaliana PPIs are modeled by using two well-established template-based docking methods. For each experimental/predicted complex structure, AraPPISite not only provides an interactive user interface for browsing interaction sites, but also lists detailed evolutionary and physicochemical properties of these sites. Second, AraPPISite assigns domain-domain interactions or domain-motif interactions to 4286 PPIs whose 3D structures cannot be modeled. In this case, users can easily query protein interaction regions at the sequence level. AraPPISite is a free and user-friendly database, which does not require user registration or any configuration on local machines. We anticipate AraPPISite can serve as a helpful database resource for the users with less experience in structural biology or protein bioinformatics to probe the details of PPIs, and thus accelerate the studies of plant genetics and functional genomics. AraPPISite is available at http://systbio.cau.edu.cn/arappisite/index.html .

  5. MoonProt: a database for proteins that are known to moonlight

    Science.gov (United States)

    Mani, Mathew; Chen, Chang; Amblee, Vaishak; Liu, Haipeng; Mathur, Tanu; Zwicke, Grant; Zabad, Shadi; Patel, Bansi; Thakkar, Jagravi; Jeffery, Constance J.

    2015-01-01

    Moonlighting proteins comprise a class of multifunctional proteins in which a single polypeptide chain performs multiple biochemical functions that are not due to gene fusions, multiple RNA splice variants or pleiotropic effects. The known moonlighting proteins perform a variety of diverse functions in many different cell types and species, and information about their structures and functions is scattered in many publications. We have constructed the manually curated, searchable, internet-based MoonProt Database (http://www.moonlightingproteins.org) with information about the over 200 proteins that have been experimentally verified to be moonlighting proteins. The availability of this organized information provides a more complete picture of what is currently known about moonlighting proteins. The database will also aid researchers in other fields, including determining the functions of genes identified in genome sequencing projects, interpreting data from proteomics projects and annotating protein sequence and structural databases. In addition, information about the structures and functions of moonlighting proteins can be helpful in understanding how novel protein functional sites evolved on an ancient protein scaffold, which can also help in the design of proteins with novel functions. PMID:25324305

  6. ATtRACT-a database of RNA-binding proteins and associated motifs.

    Science.gov (United States)

    Giudice, Girolamo; Sánchez-Cabo, Fátima; Torroja, Carlos; Lara-Pezzi, Enrique

    2016-01-01

    RNA-binding proteins (RBPs) play a crucial role in key cellular processes, including RNA transport, splicing, polyadenylation and stability. Understanding the interaction between RBPs and RNA is key to improve our knowledge of RNA processing, localization and regulation in a global manner. Despite advances in recent years, a unified non-redundant resource that includes information on experimentally validated motifs, RBPs and integrated tools to exploit this information is lacking. Here, we developed a database named ATtRACT (available athttp://attract.cnic.es) that compiles information on 370 RBPs and 1583 RBP consensus binding motifs, 192 of which are not present in any other database. To populate ATtRACT we (i) extracted and hand-curated experimentally validated data from CISBP-RNA, SpliceAid-F, RBPDB databases, (ii) integrated and updated the unavailable ASD database and (iii) extracted information from Protein-RNA complexes present in Protein Data Bank database through computational analyses. ATtRACT provides also efficient algorithms to search a specific motif and scan one or more RNA sequences at a time. It also allows discoveringde novomotifs enriched in a set of related sequences and compare them with the motifs included in the database.Database URL:http:// attract. cnic. es.

  7. Protein (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD... The IDs of clusters that the amino acid sequences belong to in each taxon are indicated. Data file File name: pgd...bj_ortholog_db_cyanobacteria_protein.zip File URL: ftp://ftp.biosciencedbc.jp/archive/pgdbj-ortholog-db/LATEST/pgd...ch URL http://togodb.biosciencedbc.jp/togodb/view/pgdbj_ortholog_db_cyanobacteria_protein#en Data acquisitio...ase Database Description Download License Update History of This Database Site Policy | Contact Us Protein (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive ...

  8. Modulating protein interaction on a molecular and Microstructural level for texture control in protein based gels

    NARCIS (Netherlands)

    Martin, A.H.; Baigts Allende, D.; Munialo, C.D.; Urbonaite, V.; Pouvreau, L.A.M.; Jongh, de H.H.J.

    2014-01-01

    The exploration of microstructures and textures of protein based systems is essential to understand (oral) breakdown properties and thereby textural aspects, or macroscopic functionalities such as water holding. Upon structure breakdown, the applied energy (W) is primarily directed towards fracture

  9. Measuring binding of protein to gel-bound ligands using magnetic levitation.

    Science.gov (United States)

    Shapiro, Nathan D; Mirica, Katherine A; Soh, Siowling; Phillips, Scott T; Taran, Olga; Mace, Charles R; Shevkoplyas, Sergey S; Whitesides, George M

    2012-03-28

    This paper describes the use of magnetic levitation (MagLev) to measure the association of proteins and ligands. The method starts with diamagnetic gel beads that are functionalized covalently with small molecules (putative ligands). Binding of protein to the ligands within the bead causes a change in the density of the bead. When these beads are suspended in a paramagnetic aqueous buffer and placed between the poles of two NbFeB magnets with like poles facing, the changes in the density of the bead on binding of protein result in changes in the levitation height of the bead that can be used to quantify the amount of protein bound. This paper uses a reaction-diffusion model to examine the physical principles that determine the values of rate and equilibrium constants measured by this system, using the well-defined model system of carbonic anhydrase and aryl sulfonamides. By tuning the experimental protocol, the method is capable of quantifying either the concentration of protein in a solution, or the binding affinities of a protein to several resin-bound small molecules simultaneously. Since this method requires no electricity and only a single piece of inexpensive equipment, it may find use in situations where portability and low cost are important, such as in bioanalysis in resource-limited settings, point-of-care diagnosis, veterinary medicine, and plant pathology. It still has several practical disadvantages. Most notably, the method requires relatively long assay times and cannot be applied to large proteins (>70 kDa), including antibodies. The design and synthesis of beads with improved characteristics (e.g., larger pore size) has the potential to resolve these problems.

  10. dbPPT: a comprehensive database of protein phosphorylation in plants.

    Science.gov (United States)

    Cheng, Han; Deng, Wankun; Wang, Yongbo; Ren, Jian; Liu, Zexian; Xue, Yu

    2014-01-01

    As one of the most important protein post-translational modifications, the reversible phosphorylation is critical for plants in regulating a variety of biological processes such as cellular metabolism, signal transduction and responses to environmental stress. Numerous efforts especially large-scale phosphoproteome profiling studies have been contributed to dissect the phosphorylation signaling in various plants, while a large number of phosphorylation events were identified. To provide an integrated data resource for further investigations, here we present a comprehensive database of dbPPT (database of Phosphorylation site in PlanTs, at http://dbppt.biocuckoo.org), which contains experimentally identified phosphorylation sites in proteins from plants. The phosphorylation sites in dbPPT were manually curated from the literatures, whereas datasets in other public databases were also integrated. In total, there were 82,175 phosphorylation sites in 31,012 proteins from 20 plant organisms in dbPPT, presenting a larger quantity of phosphorylation sites and a higher coverage of plant species in comparison with other databases. The proportions of residue types including serine, threonine and tyrosine were 77.99, 17.81 and 4.20%, respectively. All the phosphoproteins and phosphorylation sites in the database were critically annotated. Since the phosphorylation signaling in plants attracted great attention recently, such a comprehensive resource of plant protein phosphorylation can be useful for the research community. Database URL: http://dbppt.biocuckoo.or

  11. MSV3d: database of human MisSense Variants mapped to 3D protein structure.

    Science.gov (United States)

    Luu, Tien-Dao; Rusu, Alin-Mihai; Walter, Vincent; Ripp, Raymond; Moulinier, Luc; Muller, Jean; Toursel, Thierry; Thompson, Julie D; Poch, Olivier; Nguyen, Hoan

    2012-01-01

    The elucidation of the complex relationships linking genotypic and phenotypic variations to protein structure is a major challenge in the post-genomic era. We present MSV3d (Database of human MisSense Variants mapped to 3D protein structure), a new database that contains detailed annotation of missense variants of all human proteins (20 199 proteins). The multi-level characterization includes details of the physico-chemical changes induced by amino acid modification, as well as information related to the conservation of the mutated residue and its position relative to functional features in the available or predicted 3D model. Major releases of the database are automatically generated and updated regularly in line with the dbSNP (database of Single Nucleotide Polymorphism) and SwissVar releases, by exploiting the extensive Décrypthon computational grid resources. The database (http://decrypthon.igbmc.fr/msv3d) is easily accessible through a simple web interface coupled to a powerful query engine and a standard web service. The content is completely or partially downloadable in XML or flat file formats. Database URL: http://decrypthon.igbmc.fr/msv3d.

  12. Literature curation of protein interactions: measuring agreement across major public databases

    Science.gov (United States)

    Turinsky, Andrei L.; Razick, Sabry; Turner, Brian; Wodak, Shoshana J.

    2010-01-01

    Literature curation of protein interaction data faces a number of challenges. Although curators increasingly adhere to standard data representations, the data that various databases actually record from the same published information may differ significantly. Some of the reasons underlying these differences are well known, but their global impact on the interactions collectively curated by major public databases has not been evaluated. Here we quantify the agreement between curated interactions from 15 471 publications shared across nine major public databases. Results show that on average, two databases fully agree on 42% of the interactions and 62% of the proteins curated from the same publication. Furthermore, a sizable fraction of the measured differences can be attributed to divergent assignments of organism or splice isoforms, different organism focus and alternative representations of multi-protein complexes. Our findings highlight the impact of divergent curation policies across databases, and should be relevant to both curators and data consumers interested in analyzing protein-interaction data generated by the scientific community. Database URL: http://wodaklab.org/iRefWeb PMID:21183497

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-10-02

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

  14. A multichannel gel electrophoresis and continuous fraction collection apparatus for high-throughput protein separation and characterization.

    Science.gov (United States)

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

    2010-01-01

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

  15. Using homology relations within a database markedly boosts protein sequence similarity search.

    Science.gov (United States)

    Tong, Jing; Sadreyev, Ruslan I; Pei, Jimin; Kinch, Lisa N; Grishin, Nick V

    2015-06-02

    Inference of homology from protein sequences provides an essential tool for analyzing protein structure, function, and evolution. Current sequence-based homology search methods are still unable to detect many similarities evident from protein spatial structures. In computer science a search engine can be improved by considering networks of known relationships within the search database. Here, we apply this idea to protein-sequence-based homology search and show that it dramatically enhances the search accuracy. Our new method, COMPADRE (COmparison of Multiple Protein sequence Alignments using Database RElationships) assesses the relationship between the query sequence and a hit in the database by considering the similarity between the query and hit's known homologs. This approach increases detection quality, boosting the precision rate from 18% to 83% at half-coverage of all database homologs. The increased precision rate allows detection of a large fraction of protein structural relationships, thus providing structure and function predictions for previously uncharacterized proteins. Our results suggest that this general approach is applicable to a wide variety of methods for detection of biological similarities. The web server is available at prodata.swmed.edu/compadre.

  16. dbSAP: single amino-acid polymorphism database for protein variation detection

    Science.gov (United States)

    Cao, Ruifang; Shi, Yan; Chen, Shuangguan; Ma, Yimin; Chen, Jiajun; Yang, Juan; Chen, Geng; Shi, Tieliu

    2017-01-01

    Millions of human single nucleotide polymorphisms (SNPs) or mutations have been identified so far, and these variants could be strongly correlated with phenotypic variations of traits/diseases. Among these variants, non-synonymous ones can result in amino-acid changes that are called single amino-acid polymorphisms (SAPs). Although some studies have tried to investigate the SAPs, only a small fraction of SAPs have been identified due to inadequately inferred protein variation database and the low coverage of mass spectrometry (MS) experiments. Here, we present the dbSAP database for conveniently accessing the comprehensive information and relationships of spectra, peptides and proteins of SAPs, as well as related genes, pathways, diseases and drug targets. In order to fully explore human SAPs, we built a customized protein database that contained comprehensive variant proteins by integrating and annotating the human SNPs and mutations from eight distinct databases (UniProt, Protein Mutation Database, HPMD, MSIPI, MS-CanProVar, dbSNP, Ensembl and COSMIC). After a series of quality controls, a total of 16 854 SAP peptides involving in 439 537 spectra were identified with large scale MS datasets from various human tissues and cell lines. dbSAP is freely available at http://www.megabionet.org/dbSAP/index.html. PMID:27903894

  17. BriX: a database of protein building blocks for structural analysis, modeling and design.

    Science.gov (United States)

    Vanhee, Peter; Verschueren, Erik; Baeten, Lies; Stricher, Francois; Serrano, Luis; Rousseau, Frederic; Schymkowitz, Joost

    2011-01-01

    High-resolution structures of proteins remain the most valuable source for understanding their function in the cell and provide leads for drug design. Since the availability of sufficient protein structures to tackle complex problems such as modeling backbone moves or docking remains a problem, alternative approaches using small, recurrent protein fragments have been employed. Here we present two databases that provide a vast resource for implementing such fragment-based strategies. The BriX database contains fragments from over 7000 non-homologous proteins from the Astral collection, segmented in lengths from 4 to 14 residues and clustered according to structural similarity, summing up to a content of 2 million fragments per length. To overcome the lack of loops classified in BriX, we constructed the Loop BriX database of non-regular structure elements, clustered according to end-to-end distance between the regular residues flanking the loop. Both databases are available online (http://brix.crg.es) and can be accessed through a user-friendly web-interface. For high-throughput queries a web-based API is provided, as well as full database downloads. In addition, two exciting applications are provided as online services: (i) user-submitted structures can be covered on the fly with BriX classes, representing putative structural variation throughout the protein and (ii) gaps or low-confidence regions in these structures can be bridged with matching fragments.

  18. Correlation of acidic and basic carrier ampholyte and immobilized pH gradient two-dimensional gel electrophoresis patterns based on mass spectrometric protein identification

    DEFF Research Database (Denmark)

    Nawrocki, A; Larsen, Martin Røssel; Podtelejnikov, A V

    1998-01-01

    Separation of proteins on either carrier ampholyte-based or immobilized pH gradient-based two-dimensional (2-D) gels gives rise to electrophoretic patterns that are difficult to compare visually. In this paper we have used matrix-assisted laser desorption/ionization mass spectrometry (MALDI......-references demonstrated that there is no obvious pattern by which the mobility of a protein in one gel system can be used to predict its mobility in the other. Thus, as laboratories adopt the immobilized pH gradient-based 2-D gel systems, the only reliable means of translating the data gained with the carrier ampholyte......-MS) to determine the identities of 335 protein spots in these two 2-D gel systems, including a substantial number of basic proteins which had never been identified before. Proteins that were identified in both gel systems allowed us to cross-reference the gel patterns. Vector analysis of these cross...

  19. The latest advancements in proteomic two-dimensional gel electrophoresis analysis applied to biological samples.

    Science.gov (United States)

    Santucci, Laura; Bruschi, Maurizio; Ghiggeri, Gian Marco; Candiano, Giovanni

    2015-01-01

    Two-dimensional gel electrophoresis (2DE) is one of the fundamental approaches in proteomics for the separation and visualization of complex protein mixtures. Proteins can be analyzed by 2DE using isoelectric focusing (IEF) in the first dimension, combined to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension, gel staining (silver and Coomassie), image analysis, and 2DE gel database. High-resolution 2DE can resolve up to 5,000 different proteins simultaneously (∼2,000 proteins routinely), and detect and quantify <1 ng of protein per spot. Here, we describe the latest developments for a more complete analysis of biological fluids.

  20. Determining degradation and synthesis rates of arabidopsis proteins using the kinetics of progressive 15N labeling of two-dimensional gel-separated protein spots.

    Science.gov (United States)

    Li, Lei; Nelson, Clark J; Solheim, Cory; Whelan, James; Millar, A Harvey

    2012-06-01

    The growth and development of plant tissues is associated with an ordered succession of cellular processes that are reflected in the appearance and disappearance of proteins. The control of the kinetics of protein turnover is central to how plants can rapidly and specifically alter protein abundance and thus molecular function in response to environmental or developmental cues. However, the processes of turnover are largely hidden during periods of apparent steady-state protein abundance, and even when proteins accumulate it is unclear whether enhanced synthesis or decreased degradation is responsible. We have used a (15)N labeling strategy with inorganic nitrogen sources coupled to a two-dimensional fluorescence difference gel electrophoresis and mass spectrometry analysis of two-dimensional IEF/SDS-PAGE gel spots to define the rate of protein synthesis (K(S)) and degradation (K(D)) of Arabidopsis cell culture proteins. Through analysis of MALDI-TOF/TOF mass spectra from 120 protein spots, we were able to quantify K(S) and K(D) for 84 proteins across six functional groups and observe over 65-fold variation in protein degradation rates. K(S) and K(D) correlate with functional roles of the proteins in the cell and the time in the cell culture cycle. This approach is based on progressive (15)N labeling that is innocuous for the plant cells and, because it can be used to target analysis of proteins through the use of specific gel spots, it has broad applicability.

  1. Titanium Dioxide Photocatalytic Polymerization of Acrylamide for Gel Electrophoresis (TIPPAGE) of Proteins and Structural Identification by Mass Spectrometry.

    Science.gov (United States)

    Zhang, Wenyang; Yuan, Zhiwei; Huang, Lulu; Kang, Jie; Jiang, Ruowei; Zhong, Hongying

    2016-02-11

    Polyacrylamide gel electrophoresis (PAGE) coupled with mass spectrometry has been well established for separating, identifying and quantifying protein mixtures from cell lines, tissues or other biological samples. The copolymerization process of acrylamide and bis-acrylamide is the key to mastering this powerful technique. In general, this is a vinyl addition reaction initiated by free radical-generating reagents such as ammonium persulfate (APS) and tetramethylethylenediamine (TEMED) under basic pH and degassing experimental condition. We report herein a photocatalytic polymerization approach that is based on photo-generated hydroxyl radicals with nanoparticles of titanium dioxide. It was shown that the polymerization process is greatly accelerated in acidic condition when ultraviolet light shots on the gel solution containing TiO2 nanoparticles without degassing. This feature makes it very useful in preparing Triton X-100 acid urea (TAU) gel that has been developed for separating basic proteins such as histones and variants in acidic experimental condition. Additionally, the presence of titanium dioxide in the gel not only improves mechanistic property of gels but also changes the migration pattern of different proteins that have different affinities to titanium dioxide.

  2. Titanium Dioxide Photocatalytic Polymerization of Acrylamide for Gel Electrophoresis (TIPPAGE) of Proteins and Structural Identification by Mass Spectrometry

    Science.gov (United States)

    Zhang, Wenyang; Yuan, Zhiwei; Huang, Lulu; Kang, Jie; Jiang, Ruowei; Zhong, Hongying

    2016-01-01

    Polyacrylamide gel electrophoresis (PAGE) coupled with mass spectrometry has been well established for separating, identifying and quantifying protein mixtures from cell lines, tissues or other biological samples. The copolymerization process of acrylamide and bis-acrylamide is the key to mastering this powerful technique. In general, this is a vinyl addition reaction initiated by free radical-generating reagents such as ammonium persulfate (APS) and tetramethylethylenediamine (TEMED) under basic pH and degassing experimental condition. We report herein a photocatalytic polymerization approach that is based on photo-generated hydroxyl radicals with nanoparticles of titanium dioxide. It was shown that the polymerization process is greatly accelerated in acidic condition when ultraviolet light shots on the gel solution containing TiO2 nanoparticles without degassing. This feature makes it very useful in preparing Triton X-100 acid urea (TAU) gel that has been developed for separating basic proteins such as histones and variants in acidic experimental condition. Additionally, the presence of titanium dioxide in the gel not only improves mechanistic property of gels but also changes the migration pattern of different proteins that have different affinities to titanium dioxide. PMID:26865351

  3. Titanium Dioxide Photocatalytic Polymerization of Acrylamide for Gel Electrophoresis (TIPPAGE) of Proteins and Structural Identification by Mass Spectrometry

    Science.gov (United States)

    Zhang, Wenyang; Yuan, Zhiwei; Huang, Lulu; Kang, Jie; Jiang, Ruowei; Zhong, Hongying

    2016-02-01

    Polyacrylamide gel electrophoresis (PAGE) coupled with mass spectrometry has been well established for separating, identifying and quantifying protein mixtures from cell lines, tissues or other biological samples. The copolymerization process of acrylamide and bis-acrylamide is the key to mastering this powerful technique. In general, this is a vinyl addition reaction initiated by free radical-generating reagents such as ammonium persulfate (APS) and tetramethylethylenediamine (TEMED) under basic pH and degassing experimental condition. We report herein a photocatalytic polymerization approach that is based on photo-generated hydroxyl radicals with nanoparticles of titanium dioxide. It was shown that the polymerization process is greatly accelerated in acidic condition when ultraviolet light shots on the gel solution containing TiO2 nanoparticles without degassing. This feature makes it very useful in preparing Triton X-100 acid urea (TAU) gel that has been developed for separating basic proteins such as histones and variants in acidic experimental condition. Additionally, the presence of titanium dioxide in the gel not only improves mechanistic property of gels but also changes the migration pattern of different proteins that have different affinities to titanium dioxide.

  4. VaProS: a database-integration approach for protein/genome information retrieval

    KAUST Repository

    Gojobori, Takashi

    2016-12-24

    Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein–protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts’ knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/.

  5. Chlorogenic acid-mediated gel formation of oxidatively stressed myofibrillar protein.

    Science.gov (United States)

    Cao, Yungang; Xiong, Youling L

    2015-08-01

    The effect of chlorogenic acid (CA) at different concentration levels (0, 6, 30, and 150 μmol/g protein) on porcine myofibrillar protein (MP) gelling potential in relation to chemical and structural changes was investigated. The results showed that CA generally inhibited protein carbonyl formation but did not prevent sulphydryl and amine losses caused by oxidation. The presence of CA intensified oxidation-initiated loss of α-helix conformation as well as tertiary structure of MP. CA at 150 μmol/g produced the greatest increase in MP surface hydrophobicity and insolubility. The physicochemical changes with 6 and 30 μmol/g CA led to a remarkably enhanced gelling capacity of MP and augmented the positive effect of oxidation in building an elastic gel network. However, CA at 150 μmol/g was detrimental to the MP gelation. The result can explain why processed meats with phenolic-rich spices and herbs often exhibit variable texture-forming properties.

  6. Medicago PhosphoProtein Database: a repository for Medicago truncatula phosphoprotein data

    Directory of Open Access Journals (Sweden)

    Christopher M. Rose

    2012-06-01

    Full Text Available The ability of legume crops to fix atmospheric nitrogen via a symbiotic association with soil rhizobia makes them an essential component of many agricultural systems. Initiation of this symbiosis requires protein phosphorylation-mediated signaling in response to rhizobial signals named Nod factors. Medicago truncatula (Medicago is the model system for studying legume biology, making the study of its phosphoproteome essential. Here, we describe the Medicago Phosphoprotein Database (http://phospho.medicago.wisc.edu, a repository built to house phosphoprotein, phosphopeptide, and phosphosite data specific to Medicago. Currently, the Medicago Phosphoprotein Database holds 3,457 unique phosphopeptides that contain 3,404 non-redundant sites of phosphorylation on 829 proteins. Through the web-based interface, users are allowed to browse identified proteins or search for proteins of interest. Furthermore, we allow users to conduct BLAST searches of the database using both peptide sequences and phosphorylation motifs as queries. The data contained within the database are available for download to be investigated at the user’s discretion. The Medicago Phosphoprotein Database will be updated continually with novel phosphoprotein and phosphopeptide identifications, with the intent of constructing an unparalleled compendium of large-scale Medicago phosphorylation data.

  7. Analysis of metal-binding proteins separated by non-denaturating gel electrophoresis using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS).

    Science.gov (United States)

    Becker, J Susanne; Mounicou, Sandra; Zoriy, Miroslav V; Becker, J Sabine; Lobinski, Ryszard

    2008-09-15

    Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) have become established as very efficient and sensitive biopolymer and elemental mass spectrometric techniques for studying metal-binding proteins (metalloproteins) in life sciences. Protein complexes present in rat tissues (liver and kidney) were separated in their native state in the first dimension by blue native gel electrophoresis (BN-PAGE). Essential and toxic metals, such as zinc, copper, iron, nickel, chromium, cadmium and lead, were detected by scanning the gel bands using quadrupole LA-ICP-MS with and without collision cell as a microanalytical technique. Several proteins were identified by using MALDI-TOF-MS together with a database search. For example, on one protein band cut from the BN-PAGE gel and digested with the enzyme trypsin, two different proteins - protein FAM44B and cathepsin B precursor - were identified. By combining biomolecular and elemental mass spectrometry, it was possible to characterize and identify selected metal-binding rat liver and kidney tissue proteins.

  8. A biofriendly silica gel for in situ protein entrapment: biopolymer-assisted formation and its kinetic mechanism.

    Science.gov (United States)

    Wang, Guan-Hai; Zhang, Li-Ming

    2009-03-05

    In an attempt to develop a biofriendly sol-gel route for the rapid formation of biofunctional silica gels, a biopolymer with good biocompatibility was used to assist the gelation of glycol-modified tetraethoxysilane (GMT) in aqueous system without the addition of any organic solvents. It was found that the biopolymer used could act as an effective accelerator for the sol-gel transition of GMT and an increase of its amount could shorten greatly the gelation time. For such a gelation reaction, its apparent activation energy was determined to be 64.9 kJ/mol according to the Arrhenius equation. In particular, the kinetic mechanism for the formation of the silica gel was investigated by using dynamic theological data and a scaling fractal model. It was revealed that the biopolymer used could change the sol-gel transition mechanism from reaction-limited kinetics to diffusion-limited kinetics. Circular dichroism analyses confirmed the suitability of using the resultant silica gel for the in situ protein encapsulation.

  9. The TissueNet v.2 database: A quantitative view of protein-protein interactions across human tissues

    Science.gov (United States)

    Basha, Omer; Barshir, Ruth; Sharon, Moran; Lerman, Eugene; Kirson, Binyamin F.; Hekselman, Idan; Yeger-Lotem, Esti

    2017-01-01

    Knowledge of the molecular interactions of human proteins within tissues is important for identifying their tissue-specific roles and for shedding light on tissue phenotypes. However, many protein–protein interactions (PPIs) have no tissue-contexts. The TissueNet database bridges this gap by associating experimentally-identified PPIs with human tissues that were shown to express both pair-mates. Users can select a protein and a tissue, and obtain a network view of the query protein and its tissue-associated PPIs. TissueNet v.2 is an updated version of the TissueNet database previously featured in NAR. It includes over 40 human tissues profiled via RNA-sequencing or protein-based assays. Users can select their preferred expression data source and interactively set the expression threshold for determining tissue-association. The output of TissueNet v.2 emphasizes qualitative and quantitative features of query proteins and their PPIs. The tissue-specificity view highlights tissue-specific and globally-expressed proteins, and the quantitative view highlights proteins that were differentially expressed in the selected tissue relative to all other tissues. Together, these views allow users to quickly assess the unique versus global functionality of query proteins. Thus, TissueNet v.2 offers an extensive, quantitative and user-friendly interface to study the roles of human proteins across tissues. TissueNet v.2 is available at http://netbio.bgu.ac.il/tissuenet. PMID:27899616

  10. Triton X-114 cloud point extraction to subfractionate blood plasma proteins for two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Jessen, Flemming; Wulff, Tune

    2015-01-01

    A simple and reproducible procedure for enrichment of a plasma protein subfraction suitable for two-dimensional polyacrylamide gel electrophoresis (2DE) was developed, using a Triton X-114-based cloud point extraction (CPE). Appropriate conditions for such a CPE procedure were found by SDS...

  11. Avoiding acidic region streaking in two-dimensional gel electrophoresis: Case study with two bacterial whole cell protein extracts

    Indian Academy of Sciences (India)

    Arnab Roy; Umesh Varshney; Debnath Pal

    2014-09-01

    Acidic region streaking (ARS) is one of the lacunae in two-dimensional gel electrophoresis (2DE) of bacterial proteome. This streaking is primarily caused by nucleic acid (NuA) contamination and poses major problem in the downstream processes like image analysis and protein identification. Although cleanup and nuclease digestion are practiced as remedial options, these strategies may incur loss in protein recovery and perform incomplete removal of NuA. As a result, ARS has remained a common observation across publications, including the recent ones. In this work, we demonstrate how ultrasound wave can be used to shear NuA in plain ice-cooled water, facilitating the elimination of ARS in the 2DE gels without the need for any additional sample cleanup tasks. In combination with a suitable buffer recipe, IEF program and frequent paper-wick changing approach, we are able to reproducibly demonstrate the production of clean 2DE gels with improved protein recovery and negligible or no ARS. We illustrate our procedure using whole cell protein extracts from two diverse organisms, Escherichia coli and Mycobacterium smegmatis. Our designed protocols are straightforward and expected to provide good 2DE gels without ARS, with comparable times and significantly lower cost.

  12. Motifs with potential physiological activity in food proteins – BIOPEP database

    Directory of Open Access Journals (Sweden)

    Bartłomiej Dziuba

    2009-09-01

    Full Text Available Proteins are the multifunctional food components affecting the living organisms. One of the proteins function is the impact on the body due to the presence of motifs that show specific physiological and biological activities. Due to the worldwide growth of demand for the food containing bioactive components, increasing attention has been paid recently to the use of bioactive peptides as physiologically active food ingredients. They are important elements of the prevention and treatment of various lifestyle diseases. In addition to its primary function and according to current knowledge, each protein may be a reserve source of peptides controlling the life processes of organisms. For this reason, in this work, application of a new, additional criterion for evaluating proteins as a potential source of biologically active peptides, contributes to a more comprehensive and objective definition of their biological value. A complementary part of such research is the strategy for evaluation of the food proteins as precursors of biologically active peptides which involves the database of proteins and bioactive peptides – BIOPEP (available online at: http://www.uwm.edu.pl/biochemia. The database contains information on 2123 peptides representing 48 types of bioactivities, their EC50 values and source of origin. Proteins (706 sequences are considered as bioactive peptide precursors based on newly introduced criteria: the profile of potential biological activity, the frequency of bioactive fragments occurrence and potential biological protein activity. This original and unprecedented so far approach, started to be successfully and more widely applied by other authors. BIOPEP can be interfaced with global databases such as e.g. TrEMBL, SWISS-PROT, EROP and PepBank. Recently the BIOPEP database was enlarged with the data about allergenic proteins, including information about structure of their epitopes and molecular markers.  

  13. HIP2: An online database of human plasma proteins from healthy individuals

    Directory of Open Access Journals (Sweden)

    Shen Changyu

    2008-04-01

    Full Text Available Abstract Background With the introduction of increasingly powerful mass spectrometry (MS techniques for clinical research, several recent large-scale MS proteomics studies have sought to characterize the entire human plasma proteome with a general objective for identifying thousands of proteins leaked from tissues in the circulating blood. Understanding the basic constituents, diversity, and variability of the human plasma proteome is essential to the development of sensitive molecular diagnosis and treatment monitoring solutions for future biomedical applications. Biomedical researchers today, however, do not have an integrated online resource in which they can search for plasma proteins collected from different mass spectrometry platforms, experimental protocols, and search software for healthy individuals. The lack of such a resource for comparisons has made it difficult to interpret proteomics profile changes in patients' plasma and to design protein biomarker discovery experiments. Description To aid future protein biomarker studies of disease and health from human plasma, we developed an online database, HIP2 (Healthy Human Individual's Integrated Plasma Proteome. The current version contains 12,787 protein entries linked to 86,831 peptide entries identified using different MS platforms. Conclusion This web-based database will be useful to biomedical researchers involved in biomarker discovery research. This database has been developed to be the comprehensive collection of healthy human plasma proteins, and has protein data captured in a relational database schema built to contain mappings of supporting peptide evidence from several high-quality and high-throughput mass-spectrometry (MS experimental data sets. Users can search for plasma protein/peptide annotations, peptide/protein alignments, and experimental/sample conditions with options for filter-based retrieval to achieve greater analytical power for discovery and validation.

  14. On-bead expression of recombinant proteins in an agarose gel matrix coated on a glass slide.

    Science.gov (United States)

    Lee, Kyung-Ho; Lee, Ka-Young; Byun, Ju-Young; Kim, Byung-Gee; Kim, Dong-Myung

    2012-05-07

    A system for expression and in situ display of recombinant proteins on a microbead surface is described. Biotinylated PCR products were immobilized on microbead surfaces, which were then embedded in a gel matrix and supplied with translation machinery and substrates. Upon the incubation of the gel matrix, target proteins encoded on the bead-immobilized DNA were expressed and captured on the same bead, thus allowing bead-mediated linkage of DNA and encoded proteins. The new method combines the simplicity and convenience of solid-phase separation of genetic information with the benefits of cell-free protein synthesis, such as instant translation of genetic information, unrestricted substrate accessibility and flexible assay configuration design.

  15. ProDis-ContSHC: Learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval

    KAUST Repository

    Wang, Jim Jing-Yan

    2012-05-08

    Background: The need to retrieve or classify protein molecules using structure or sequence-based similarity measures underlies a wide range of biomedical applications. Traditional protein search methods rely on a pairwise dissimilarity/similarity measure for comparing a pair of proteins. This kind of pairwise measures suffer from the limitation of neglecting the distribution of other proteins and thus cannot satisfy the need for high accuracy of the retrieval systems. Recent work in the machine learning community has shown that exploiting the global structure of the database and learning the contextual dissimilarity/similarity measures can improve the retrieval performance significantly. However, most existing contextual dissimilarity/similarity learning algorithms work in an unsupervised manner, which does not utilize the information of the known class labels of proteins in the database.Results: In this paper, we propose a novel protein-protein dissimilarity learning algorithm, ProDis-ContSHC. ProDis-ContSHC regularizes an existing dissimilarity measure dij by considering the contextual information of the proteins. The context of a protein is defined by its neighboring proteins. The basic idea is, for a pair of proteins (i, j), if their context N (i) and N (j) is similar to each other, the two proteins should also have a high similarity. We implement this idea by regularizing dij by a factor learned from the context N (i) and N (j). Moreover, we divide the context to hierarchial sub-context and get the contextual dissimilarity vector for each protein pair. Using the class label information of the proteins, we select the relevant (a pair of proteins that has the same class labels) and irrelevant (with different labels) protein pairs, and train an SVM model to distinguish between their contextual dissimilarity vectors. The SVM model is further used to learn a supervised regularizing factor. Finally, with the new Supervised learned Dissimilarity measure, we update

  16. Method for the typing of Clostridium difficile based on polyacrylamide gel electrophoresis of (/sup 35/S)methionine-labeled proteins

    Energy Technology Data Exchange (ETDEWEB)

    Tabaqchali, S.; O' Farrell, S.; Holland, D.; Silman, R.

    1986-01-01

    A typing method for Clostridium difficile based on the incorporation of (/sup 35/S)methionine into cellular proteins, their separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and their visualization by autoradiography is described. On analysis of the radiolabeled-protein profiles, nine distinct groups were observed (A to E and W to Z). The method, which is simple, reproducible, and readily expandable, has been applied in epidemiological studies to demonstrate cross-infection and hospital acquisition of C. difficile.

  17. STITCH 2: an interaction network database for small molecules and proteins

    DEFF Research Database (Denmark)

    Kuhn, Michael; Szklarczyk, Damian; Franceschini, Andrea

    2010-01-01

    Over the last years, the publicly available knowledge on interactions between small molecules and proteins has been steadily increasing. To create a network of interactions, STITCH aims to integrate the data dispersed over the literature and various databases of biological pathways, drug-target r......Over the last years, the publicly available knowledge on interactions between small molecules and proteins has been steadily increasing. To create a network of interactions, STITCH aims to integrate the data dispersed over the literature and various databases of biological pathways, drug......-target relationships and binding affinities. In STITCH 2, the number of relevant interactions is increased by incorporation of BindingDB, PharmGKB and the Comparative Toxicogenomics Database. The resulting network can be explored interactively or used as the basis for large-scale analyses. To facilitate links to other...

  18. Improved method for identification of low abundance proteins using 2D-gel electrophoresis, MALDI-TOF and TOF/TOF

    Science.gov (United States)

    Introduction: Differential protein expression studies have been routinely performed in our laboratory to determine the health effects of environmentally-important chemicals. In this abstract, improvements in the in-gel protein digestion, MALDI plate spotting and data acquisition...

  19. Improved method for identification of low abundance proteins using 2D-gel electrophoresis, MALDI-TOF and TOF/TOF

    Science.gov (United States)

    Introduction: Differential protein expression studies have been routinely performed in our laboratory to determine the health effects of environmentally-important chemicals. In this abstract, improvements in the in-gel protein digestion, MALDI plate spotting and data acquisition...

  20. Analysis of Sperm Membrane Protein Relevant to Antisperm Antibody by Two-Dimensional Gel Electrophoresis and Western Blotting

    Institute of Scientific and Technical Information of China (English)

    Hao-fei WANG; Zhu-qiong XIANG; Yi-xing WANG

    2003-01-01

    Objective To identify the sperm membrane proteins that are associated with antisperm antibodyMethods Using antisperm antibody positive serum through unidimensional polyacrylamide gel electrophoresis and 2-dimensional gel electrophoresis followed by Western blot analysis to determine the molecular weights (MW) and isoelectric points (pI) of sperm membrane proteins that are associated with antisperm antibody.Results Eight kinds of MW with more than ten sperm membrane proteins can be recognized by antisperm antibody positive serum, of which the MWs and pI were 23 kD, 31 kD, 32 kD, 34 kD, 41 kD, 51 kD, 60 kD, 78 kD and 5.3, 5.5,5.7, 5.0, 5.3, 5.8, 6.0, 5.5~6.2, 4.6,5.1,5.5~5.8 respectively. The identification ratios of the sperm membrane proteins on 78 kD (60.7%), 60 kD (71.4%), 51 kD (14.9%) and 23 kD (14.29%) were higher.Conclusion The sperm membrane proteins with MW of 78 kD, 60 kD, 51 kD and 23 kD were associated with antisperm antibody and immunological infertility. Two-dimensional gel electrophoresis and Western blotting can precisely identify the sperm membrane proteins that are associated with antisperm antibody.