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Gotowe bibliografie tematyczne / Proteins – Identification / Artykuły w czasopismach

Artykuły w czasopismach na temat „Proteins – Identification”

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Autor: Grafiati

Data publikacji: 4 czerwca 2021

Data aktualizacji: 12 lutego 2022

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1

Paape, M., S. Nell, S. von Bargen i J. W. Kellmann. "Identification and characterization of host proteins interacting with NSm, the Tomato spotted wilt virus movement protein". Plant Protection Science 38, SI 1 - 6th Conf EFPP 2002 (1.01.2002): S108—S111. http://dx.doi.org/10.17221/10331-pps.

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To search for host proteins involved in systemic spreading of Tomato spotted wilt virus (TSWV), the virus-encoded NSm movement protein has been utilized as a bait in yeast two-hybrid interaction trap assays. J-domain chaperones from different host species and a protein denominated At-4/1 from Arabidopsis thaliana showing homologies to myosins and kinesins were identified as NSm-interacting partners. In this communication we illustrate that following TSWV infection, J-domain proteins accumulated in systemically infected leaves of A. thaliana, whereas At-4/1 was constitutively detected in leaves of A. thaliana and Nicotiana rustica.

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2

Shaw, G. "Rapid identification of proteins." Proceedings of the National Academy of Sciences 90, nr 11 (1.06.1993): 5138–42. http://dx.doi.org/10.1073/pnas.90.11.5138.

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Ryšlavá, H., M. Janatová, G. Čalounová, I. Selicharová, J. Barthová i T. Barth. "Separation and identification of carp pituitary proteins and glycoproteins". Czech Journal of Animal Science 50, No. 9 (11.12.2011): 430–37. http://dx.doi.org/10.17221/4232-cjas.

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Carp pituitary proteins and glycoproteins were separated by the combination of immobilized metal affinity chromatography (IMAC) and affinity chromatography on Con A-Sepharose. The protein fractions were analysed by SDS-PAGE. Luteinizing hormone (in the α<sub>1</sub>β and α<sub>2</sub>β forms), growth hormone, free α<sub>1</sub> subunit and β subunit of thyroid-stimulating hormone were identified by N-terminal amino acid sequencing. N-linked oligosaccharide chains of thyroid-stimulating hormone (β TSH) were separated after fluorescent labelling on a GlycoSep N column and treated by exoglycosidases. Among the saccharide components, complex and hybrid structures terminating SO<sub>4</sub>-GalNAc-GlcNAc-Man-, and high mannose structures, with 1 to 8 mannose units attached to the oligosaccharide core (GlcNAc)<sub>2</sub>(Man)<sub>3</sub>, were found.  

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4

Donnini, Martino, Andrea Lapucci, Laura Papucci, Ewa Witort, Alain Jacquier, Gary Brewer, Angelo Nicolin, Sergio Capaccioli i Nicola Schiavone. "Identification of TINO". Journal of Biological Chemistry 279, nr 19 (9.02.2004): 20154–66. http://dx.doi.org/10.1074/jbc.m314071200.

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Modulation of mRNA stability by regulatory cis-acting AU-rich elements (AREs) and ARE-binding proteins is an important posttranscriptional mechanism of gene expression control. We previously demonstrated that the 3′-untranslated region ofBCL-2mRNA contains an ARE that accounts for rapidBCL-2down-regulation in response to apoptotic stimuli. We also demonstrated that theBCL-2ARE core interacts with a number of ARE-binding proteins, one of which is AU-rich factor 1/heterogeneous nuclear ribonucleoprotein D, known for its interaction with mRNA elements of others genes. In an attempt to search for otherBCL-2mRNA-binding proteins, we used the yeast RNA three-hybrid system assay and identified a novel human protein that interacts withBCL-2ARE. We refer to it as TINO. The predicted protein sequence of TINO reveals two amino-terminal heterogeneous nuclear ribonucleoprotein K homology motifs for nucleic acid binding and a carboxyl-terminal RING domain, endowed with a putative E3 ubiquitin-protein ligase activity. In addition the novel protein is evolutionarily conserved; the two following orthologous proteins have been identified with protein-protein BLAST: posterior end mark-3 (PEM-3) ofCiona savignyiand muscle excess protein-3 (MEX-3) ofCaenorhabditis elegans. Upon binding, TINO destabilizes a chimeric reporter construct containing theBCL-2ARE sequence, revealing a negative regulatory action onBCL-2gene expression at the posttranscriptional level.

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5

Shionyu, M., i M. Go. "Domain identification of large proteins". Seibutsu Butsuri 41, supplement (2001): S76. http://dx.doi.org/10.2142/biophys.41.s76_4.

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6

Roth, Amy F., Junmei Wan, William N. Green, John R. Yates i Nicholas G. Davis. "Proteomic identification of palmitoylated proteins". Methods 40, nr 2 (październik 2006): 135–42. http://dx.doi.org/10.1016/j.ymeth.2006.05.026.

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7

Guo, Dayong, Andrew Keightley, Jill Guthrie, Patricia A. Veno, Stephen E. Harris i Lynda F. Bonewald. "Identification of osteocyte-selective proteins". PROTEOMICS 10, nr 20 (15.09.2010): 3688–98. http://dx.doi.org/10.1002/pmic.201000306.

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8

Wan, Junmei, Amy F. Roth, Aaron O. Bailey i Nicholas G. Davis. "Palmitoylated proteins: purification and identification". Nature Protocols 2, nr 7 (21.06.2007): 1573–84. http://dx.doi.org/10.1038/nprot.2007.225.

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9

Yonezawa, K. "Identification of TOR-interacting Proteins". Molecular Interventions 3, nr 4 (1.06.2003): 189–93. http://dx.doi.org/10.1124/mi.3.4.189.

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10

Mirzaei, Hamid, i Fred Regnier. "Identification of yeast oxidized proteins". Journal of Chromatography A 1141, nr 1 (luty 2007): 22–31. http://dx.doi.org/10.1016/j.chroma.2006.11.009.

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11

Medeńska, Weronika, Alicja Dratwa-Chałupnik, Małgorzata Ożgo, Aleksandra Cichy, Ryszard Pikuła i Janusz Bobik. "Identification of mare colostrum proteins". Acta Scientiarum Polonorum Zootechnica 19, nr 4 (20.05.2021): 25–32. http://dx.doi.org/10.21005/asp.2020.19.4.03.

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Colostrum is an essential feed of foals. It is a source of nutrients and functional proteins significant for foals’ growth and development. In the presented research using two-dimensional electrophoresis coupled via spectrometry mass MALDI-TOF in the mares’ colostrum (whey proteins fraction) were identified 24 proteins representing 15 different gene products. The identified proteins were involved in supporting foals’ immature immune systems and in the transport of various compounds. Further research of mares’ colostrum will allow determining more gene products. An in-depth analysis of mares’ milk will provide information about biochemical processes occurring in the mammary gland of the mare during the lactation period.

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12

Islam, Suhail A., Jingchu Luo i Michael J. E. Sternberg. "Identification and analysis of domains in proteins". "Protein Engineering, Design and Selection" 8, nr 6 (1995): 513–26. http://dx.doi.org/10.1093/protein/8.6.513.

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13

Pop, Cristina, Cristina Mogosan i Felicia Loghin. "EVALUATION OF RAPIGEST EFFICACY FOR THE DIGESTION OF PROTEINS FROM CELL CULTURES AND HEART TISSUE". Medicine and Pharmacy Reports 87, nr 4 (12.11.2014): 258–62. http://dx.doi.org/10.15386/cjmed-367.

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Introduction: Rapigest is an acid-labile detergent used in proteomics for the improvement of protein digestion.Materials and Method: To test the efficacy of Rapigest for proteomics analysis of different sample types we used protein extracts from S9 cell line and mouse heart tissue and performed protein isolation, digestion and mass spectrometry analysis.Results: For the S9 cell line, there was no significant difference concerning the number of identifications (peptides, proteins) between Rapigest and No Rapigest samples, though slightly more peptides and proteins were identified in the Rapigest samples. For the mouse heart tissue samples, Rapigest use resulted in the identification of a higher number of proteins. Rapigest did not modify the protein profile with respect to the biological compartments covered by the identified proteins in S9 cell line samples, but produced a small increase in the representation of cytoplasm proteins and a small decrease in the representation of membrane proteins in the mouse heart tissue samples.Discussions: Results are comparable to other studies that evaluated the efficacy of Rapigest for the analysis of tissue samples, recommending Rapigest for the improvement of protein digestion and implicitly identification, without the modification of the protein profile in the samples. Conclusion: Rapigest may be successfully used for the improvement of protein identification from heart tissue samples using mass spectrometry.

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14

Skvortsov, V. S., A. V. Mikurova i A. V. Rybina. "Use of de novo sequencing for proteins identification". Biomeditsinskaya Khimiya 63, nr 4 (2017): 341–50. http://dx.doi.org/10.18097/pbmc20176304341.

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Three de novo sequencing programs (Novor, PEAKS and PepNovo+) have been used for identification of 48 individual human proteins constituting the Universal Proteomics Standard Set 2 (UPS2) (“Sigma-Aldrich”, USA). Experimental data have been obtained by tandem mass spectrometry. The MS/MS was performed using pure UPS2 and UPS2 mixtures with E. coli extract and human plasma samples. Protein detection was based on identification of at least two peptides of 9 residues in length or one peptide containing at least 13 residues. Using these criteria 13 (Novor), 20 (PEAKS) and 11 (PepNovo+) proteins were detected in pure UPS2 sample. Protein identifications in mixed samples were comparable or worse. Better results (by ~20%) were obtained using prediction included high quality identified fragment (TAG) containing at least 7 residues and unidentified additional masses at N- and C-termini (PepNovo+). The latter approach confidently recognized mass-spectrometric artefacts (and probably PTM). Atypical mass changes missed in UNIMOD DB were found (PepNovo+) to be statistically significant at the C-terminus (+23.02, +26.04 and +27.03). Using peptides containing these modifications and milder detection threshold 41 of 48 UPS2 proteins were identified.

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15

Latha, Aswathi Balakrishnan, Achuthsankar Sukumaran Nair, Athmaja Sivasankaran i Pawan Kumar Dhar. "Identification of hub proteins from sequence". Bioinformation 7, nr 4 (14.10.2011): 163–68. http://dx.doi.org/10.6026/97320630007163.

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16

Crowell, Dring N., Brenda J. Biermann i Stephen K. Randall. "Identification of cDNAs encoding isoprenylated proteins". Molecular Biotechnology 5, nr 3 (czerwiec 1996): 253–58. http://dx.doi.org/10.1007/bf02900363.

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17

Chen, James K., William S. Lane i Stuart L. Schreiber. "The identification of myriocin-binding proteins". Chemistry & Biology 6, nr 4 (kwiecień 1999): 221–35. http://dx.doi.org/10.1016/s1074-5521(99)80038-6.

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18

Chen, James K., William S. Lane i Stuart L. Schreiber. "The identification of myriocin-binding proteins". Chemistry & Biology 6, nr 6 (czerwiec 1999): R186. http://dx.doi.org/10.1016/s1074-5521(99)80053-2.

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19

Conrad, Craig C., John M. Talent, Christina A. Malakowsky i Robert W. Gracy. "Post-electrophoretic identification of oxidized proteins". Biological Procedures Online 2, nr 1 (październik 1999): 39–45. http://dx.doi.org/10.1251/bpo17.

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20

Masuyama, Norihisa, Hiroshi Hanafusa, Morioh Kusakabe, Hiroshi Shibuya i Eisuke Nishida. "Identification of Two Smad4 Proteins inXenopus". Journal of Biological Chemistry 274, nr 17 (23.04.1999): 12163–70. http://dx.doi.org/10.1074/jbc.274.17.12163.

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21

Singh, Deepika, i Paul D. Lampe. "Identification of Connexin-43 Interacting Proteins". Cell Communication & Adhesion 10, nr 4-6 (styczeń 2003): 215–20. http://dx.doi.org/10.1080/cac.10.4-6.215.220.

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22

Martínez-Heredia, Juan, Josep Maria Estanyol, José Luis Ballescà i Rafael Oliva. "Proteomic identification of human sperm proteins". PROTEOMICS 6, nr 15 (sierpień 2006): 4356–69. http://dx.doi.org/10.1002/pmic.200600094.

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23

Burghoff, Sandra, Wibke Willberg i Jürgen Schrader. "Identification of extracellularly phosphorylated membrane proteins". PROTEOMICS 15, nr 19 (14.08.2015): 3310–14. http://dx.doi.org/10.1002/pmic.201400595.

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24

Maxwell, Steve A. "Identification of p53 Proteins and Targets". Methods 8, nr 3 (grudzień 1995): 182–97. http://dx.doi.org/10.1006/meth.1995.0003.

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25

Skandalis, Spyros S., Inna Kozlova, Ulla Engström, Ulf Hellman i Paraskevi Heldin. "Proteomic identification of CD44 interacting proteins". IUBMB Life 62, nr 11 (listopad 2010): 833–40. http://dx.doi.org/10.1002/iub.392.

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26

Fredriksen, Ãse, i Vidar Bakken. "Identification ofRenibacterium salmoninarumsurface proteins by radioiodination". FEMS Microbiology Letters 121, nr 3 (wrzesień 1994): 297–301. http://dx.doi.org/10.1111/j.1574-6968.1994.tb07116.x.

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27

Singh, Deepika, i Paul Lampe. "Identification of Connexin-43 Interacting Proteins". Cell Communication & Adhesion 10, nr 4 (lipiec 2003): 215–20. http://dx.doi.org/10.1080/714040430.

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28

Sambrook, Joseph, i David W. Russell. "Identification of Associated Proteins by Coimmunoprecipitation". Cold Spring Harbor Protocols 2006, nr 1 (czerwiec 2006): pdb.prot3898. http://dx.doi.org/10.1101/pdb.prot3898.

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29

Butterfield, Erin R., Christopher J. Howe i R. Ellen R. Nisbet. "Identification of Sequences EncodingSymbiodinium minutumMitochondrial Proteins". Genome Biology and Evolution 8, nr 2 (21.01.2016): 439–45. http://dx.doi.org/10.1093/gbe/evw002.

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30

Warner, Dennis R., Emily A. Roberts, Robert M. Greene i M. Michele Pisano. "Identification of novel Smad binding proteins". Biochemical and Biophysical Research Communications 312, nr 4 (grudzień 2003): 1185–90. http://dx.doi.org/10.1016/j.bbrc.2003.11.049.

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31

Rossi, C., O. Rey, P. Jenik i M. T. Franze-Fernández. "Immunological identification of tacaribe virus proteins". Research in Virology 147, nr 4 (styczeń 1996): 203–11. http://dx.doi.org/10.1016/0923-2516(96)89650-6.

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32

BACHS, O., L. LANINI, J. SERRATOSA, M. JOSEPCOLL, R. BASTOS, R. ALIGUE, E. RIUS i E. CARAFOLI. "Identification of nuclear calmodulin-binding proteins". Cell Biology International Reports 14 (wrzesień 1990): 191. http://dx.doi.org/10.1016/0309-1651(90)90863-t.

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33

Meister, Gunter, Markus Landthaler, Lasse Peters, Po Yu Chen, Henning Urlaub, Reinhard Lührmann i Thomas Tuschl. "Identification of Novel Argonaute-Associated Proteins". Current Biology 15, nr 23 (grudzień 2005): 2149–55. http://dx.doi.org/10.1016/j.cub.2005.10.048.

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34

Manzano, Concepción, Zamira Abraham, Gema López-Torrejón i Juan C. Del Pozo. "Identification of ubiquitinated proteins in Arabidopsis". Plant Molecular Biology 68, nr 1-2 (6.06.2008): 145–58. http://dx.doi.org/10.1007/s11103-008-9358-9.

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35

Küchler, Philipp, Gunther Zimmermann, Michael Winzker, Petra Janning, Herbert Waldmann i Slava Ziegler. "Identification of novel PDEδ interacting proteins". Bioorganic & Medicinal Chemistry 26, nr 8 (maj 2018): 1426–34. http://dx.doi.org/10.1016/j.bmc.2017.08.033.

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36

Jiang, M., S. M. Sullivan, A. K. Walker, J. R. Strahler, P. C. Andrews i J. R. Maddock. "Identification of Novel Escherichia coli Ribosome-Associated Proteins Using Isobaric Tags and Multidimensional Protein Identification Techniques". Journal of Bacteriology 189, nr 9 (2.03.2007): 3434–44. http://dx.doi.org/10.1128/jb.00090-07.

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ABSTRACT Biogenesis of the large ribosomal subunit requires the coordinate assembly of two rRNAs and 33 ribosomal proteins. In vivo, additional ribosome assembly factors, such as helicases, GTPases, pseudouridine synthetases, and methyltransferases, are also critical for ribosome assembly. To identify novel ribosome-associated proteins, we used a proteomic approach (isotope tagging for relative and absolute quantitation) that allows for semiquantitation of proteins from complex protein mixtures. Ribosomal subunits were separated by sucrose density centrifugation, and the relevant fractions were pooled and analyzed. The utility and reproducibility of the technique were validated via a double duplex labeling method. Next, we examined proteins from 30S, 50S, and translating ribosomes isolated at both 16°C and 37°C. We show that the use of isobaric tags to quantify proteins from these particles is an excellent predictor of the particles with which the proteins associate. Moreover, in addition to bona fide ribosomal proteins, additional proteins that comigrated with different ribosomal particles were detected, including both known ribosomal assembly factors and unknown proteins. The ribosome association of several of these proteins, as well as others predicted to be associated with ribosomes, was verified by immunoblotting. Curiously, deletion mutants for the majority of these ribosome-associated proteins had little effect on cell growth or on the polyribosome profiles.

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37

Roth, Ziv, Galit Yehezkel i Isam Khalaila. "Identification and Quantification of Protein Glycosylation". International Journal of Carbohydrate Chemistry 2012 (5.04.2012): 1–10. http://dx.doi.org/10.1155/2012/640923.

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Glycosylation is one of the most abundant posttranslation modifications of proteins, and accumulating evidence indicate that the vast majority of proteins in eukaryotes are glycosylated. Glycosylation plays a role in protein folding, interaction, stability, and mobility, as well as in signal transduction. Thus, by regulating protein activity, glycosylation is involved in the normal functioning of the cell and in the development of diseases. Indeed, in the past few decades there has been a growing realization of the importance of protein glycosylation, as aberrant glycosylation has been implicated in metabolic, neurodegenerative, and neoplastic diseases. Thus, the identification and quantification of protein-borne oligosaccharides have become increasingly important both in the basic sciences of biochemistry and glycobiology and in the applicative sciences, particularly biomedicine and biotechnology. Here, we review the state-of-the-art methodologies for the identification and quantification of oligosaccharides, specifically N- and O-glycosylated proteins.

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38

Tomar, Anil Kumar, Balwinder Singh Sooch, Isha Raj, Sarman Singh, Tej P. Singh i Savita Yadav. "Isolation and Identification of Concanavalin A Binding Glycoproteins from Human Seminal Plasma: A Step Towards Identification of Male Infertility Marker Proteins". Disease Markers 31, nr 6 (2011): 379–86. http://dx.doi.org/10.1155/2011/798072.

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Human seminal plasma contains a large array of proteins of clinical importance which are essentially needed to maintain the reproductive physiology of spermatozoa and for successful fertilization. Thus, isolation and identification of seminal plasma proteins is of paramount significance for their biophysical characterization and functional analysis in reproductive physiological processes. In this study, we have isolated Concanavalin-A binding glycoproteins from human seminal plasma and subsequently identified them by MALDI-TOF/MS analysis. The major proteins, as identified in this study, are Aminopeptidase N, lactoferrin, prostatic acid phosphatase, zinc-alpha-2-glycoprotein, prostate specific antigen, progestagen-associated endometrial protein, Izumo sperm-egg fusion protein and prolactin inducible protein. This paper also reports preliminary studies to identify altered expression of these proteins in oligospermia and azoospermia in comparison to normospermia. In oligospermia, five proteins were found to be downregulated while in azoospermia, four proteins were downregulated and two proteins were upregulated. Thus, this study is of immense biomedical interest towards identification of potential male infertility marker proteins in seminal plasma.

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Meijer, Harold J. G., Peter J. I. van de Vondervoort, Qing Yuan Yin, Chris G. de Koster, Frans M. Klis, Francine Govers i Piet W. J. de Groot. "Identification of Cell Wall-Associated Proteins from Phytophthora ramorum". Molecular Plant-Microbe Interactions® 19, nr 12 (grudzień 2006): 1348–58. http://dx.doi.org/10.1094/mpmi-19-1348.

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The oomycete genus Phytophthora comprises a large group of fungal-like plant pathogens. Two Phytophthora genomes recently have been sequenced; one of them is the genome of Phytophthora ramorum, the causal agent of sudden oak death. During plant infection, extracellular proteins, either soluble secreted proteins or proteins associated with the cell wall, play important roles in the interaction with host plants. Cell walls of P. ramorum contain 1 to 1.5% proteins, the remainder almost exclusively being accounted for by glucan polymers. Here, we present an inventory of cell-wall-associated proteins based on mass spectrometric sequence analysis of tryptic peptides obtained by proteolytic digestion of sodium dodecyl sulfate-treated mycelial cell walls. In total, 17 proteins were identified, all of which are authentic secretory proteins. Functional classification based on homology searches revealed six putative mucins or mucin-like proteins, five putative glycoside hydrolases, two transglutaminases, one annexin-like protein, the elicitin protein RAM5, one protein of unknown function, and one Kazal-type protease inhibitor. We propose that the cell wall proteins thus identified are important for pathogenicity.

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40

Onogi, Yasuhiro, Ahmed Elagamy Mohamed Mahmoud Khalil i Siegfried Ussar. "Identification and characterization of adipose surface epitopes". Biochemical Journal 477, nr 13 (10.07.2020): 2509–41. http://dx.doi.org/10.1042/bcj20190462.

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Adipose tissue is a central regulator of metabolism and an important pharmacological target to treat the metabolic consequences of obesity, such as insulin resistance and dyslipidemia. Among the various cellular compartments, the adipocyte cell surface is especially appealing as a drug target as it contains various proteins that when activated or inhibited promote adipocyte health, change its endocrine function and eventually maintain or restore whole-body insulin sensitivity. In addition, cell surface proteins are readily accessible by various drug classes. However, targeting individual cell surface proteins in adipocytes has been difficult due to important functions of these proteins outside adipose tissue, raising various safety concerns. Thus, one of the biggest challenges is the lack of adipose selective surface proteins and/or targeting reagents. Here, we discuss several receptor families with an important function in adipogenesis and mature adipocytes to highlight the complexity at the cell surface and illustrate the problems with identifying adipose selective proteins. We then discuss that, while no unique adipocyte surface protein might exist, how splicing, posttranslational modifications as well as protein/protein interactions can create enormous diversity at the cell surface that vastly expands the space of potentially unique epitopes and how these selective epitopes can be identified and targeted.

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41

Xu, Yuanke, Yaping Wen i Guosheng Han. "Antioxidant Proteins’ Identification Based on Support Vector Machine". Combinatorial Chemistry & High Throughput Screening 23, nr 4 (19.05.2020): 319–25. http://dx.doi.org/10.2174/1386207323666200306125538.

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Background: Evidence have increasingly indicated that for human disease, cell metabolism are deeply associated with proteins. Structural mutations and dysregulations of these proteins contribute to the development of the complex disease. Free radicals are unstable molecules that seek for electrons from the surrounding atoms for stability. Once a free radical binds to an atom in the body, a chain reaction occurs, which causes damage to cells and DNA. An antioxidant protein is a substance that protects cells from free radical damage. Accurate identification of antioxidant proteins is important for understanding their role in delaying aging and preventing and treating related diseases. Therefore, computational methods to identify antioxidant proteins have become an effective prior-pinpointing approach to experimental verification. Methods: In this study, support vector machines was used to identify antioxidant proteins, using amino acid compositions and 9-gap dipeptide compositions as feature extraction, and feature reduction by Principal Component Analysis. Results: The prediction accuracy Acc of this experiment reached 98.38%, the recall rate Sn of the positive sample was found to be 99.27%, the recall rate Sp of the negative sample reached 97.54%, and the MCC value was 0.9678. To evaluate our proposed method, the predictive performance of 20 antioxidant proteins from the National Center for Biotechnology Information(NCBI) was studied. As a result, 20 antioxidant proteins were correctly predicted by our method. Experimental results demonstrate that the performance of our method is better than the state-of-the-art methods for identification of antioxidant proteins. Conclusion: We collected experimental protein data from Uniport, including 253 antioxidant proteins and 1552 non-antioxidant proteins. The optimal feature extraction used in this paper is composed of amino acid composition and 9-gap dipeptide. The protein is identified by support vector machine, and the model evaluation index is obtained based on 5-fold cross-validation. Compared with the existing classification model, it is further explained that the SVM recognition model constructed in this paper is helpful for the recognition of antioxidized proteins.

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42

Eurich, Chris, Peter A. Fields i Elizabeth Rice. "Proteomics: Protein Identification Using Online Databases". American Biology Teacher 74, nr 4 (1.04.2012): 250–55. http://dx.doi.org/10.1525/abt.2012.74.4.8.

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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 course. Students upload files of “unknown” proteins from our public website, enter them into a proteomics search engine (Mascot), identify the proteins, and use additional proteomics websites to learn about their functions and three-dimensional structures. This activity is suitable for use in units exploring protein structure and function, metabolism, or bioinformatics.

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Lamy, Julie, Perrine Nogues, Lucie Combes-Soia, Guillaume Tsikis, Valérie Labas, Pascal Mermillod, Xavier Druart i Marie Saint-Dizier. "Identification by proteomics of oviductal sperm-interacting proteins". Reproduction 155, nr 5 (maj 2018): 457–66. http://dx.doi.org/10.1530/rep-17-0712.

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The interactions between oviductal fluid (OF) proteins and spermatozoa play major roles in sperm selection, storage and capacitation before fertilization. However, only a few sperm-interacting proteins in the OF has been identified and very little is known about the regulation of sperm-oviduct interactions across the estrous cycle. Samples of bovine frozen-thawed sperm from three bulls were incubated with OF at pre-, post-ovulatory stages (Pre-/Post-ov) or luteal phase (LP) of the estrous cycle (7 mg/mL proteins, treated groups) or with a protein-free media (control). The proteomes of sperm cells were assessed by nanoLC–MS/MS and quantified by label-free methods. A total of 27 sperm-interacting proteins originating in the OF were identified. Among those, 14 were detected at all stages, eight at Post-ov and LP and five only at LP. The sperm-interacting proteins detected at all stages or at LP and Post-ov were on average more abundant at LP than at other stages (P < 0.05). At Pre-ov, OVGP1 was the most abundant sperm-interacting protein while at Post-ov, ACTB, HSP27, MYH9, MYH14 and OVGP1 were predominant. Different patterns of abundance of sperm-interacting proteins related to the stage were evidenced, which greatly differed from those previously reported in the bovine OF. In conclusion, this study highlights the important regulations of sperm-oviduct interactions across the estrous cycle and provides new protein candidates that may modulate sperm functions.

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Rothé, Françoise, Cyril Gueydan, Eric Bellefroid, Georges Huez i Véronique Kruys. "Identification of FUSE-binding proteins as interacting partners of TIA proteins". Biochemical and Biophysical Research Communications 343, nr 1 (kwiecień 2006): 57–68. http://dx.doi.org/10.1016/j.bbrc.2006.02.112.

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Horisberger, Michel A., i Marie C. Gunst. "Interferon-induced proteins: Identification of Mx proteins in various mammalian species". Virology 180, nr 1 (styczeń 1991): 185–90. http://dx.doi.org/10.1016/0042-6822(91)90022-4.

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Khan, Shagufta A., Amol R. Suryawanshi, Sandeep A. Ranpura, Sudhir V. Jadhav i Vrinda V. Khole. "Identification of novel immunodominant epididymal sperm proteins using combinatorial approach". REPRODUCTION 138, nr 1 (lipiec 2009): 81–93. http://dx.doi.org/10.1530/rep-09-0052.

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Functionally immature spermatozoa leave the testis mature during epididymal transit. This process of maturation involves either addition of new proteins or modification of existing proteins onto the sperm domains that are responsible for domain-specific functions. Epididymal proteins are preferred targets for immunocontraception. In an attempt to identify epididymis-specific sperm proteins, we used a novel combinatorial approach comprising subtractive immunization (SI) followed by proteomics. Following SI, sera of mice were used for immunoproteomics, which led to the identification of 30 proteins, of which four proteins namely sperm head protein 1, sperm flagella protein 2 (SFP2), SFP3, and SFP4 are being reported for the first time on sperm. Another group of four proteins namely collagen α-2 (I) chain precursor, homeodomain-interacting protein kinase 1, GTP-binding protein Rab1, and ubiquinol cytochrome c reductase core protein II although reported earlier in testis are being reported for the first time in epididymal sperm. Furthermore, seven out of these eight novel proteins could be validated using peptide ELISA. These data are a useful repository, which could be exploited to develop targets for post-testicular immunocontraception or biomarkers for infertility diagnosis and management.

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Wickramasekara, Samanthi, Julie Neilson, Naren Patel, Linda Breci, Amy Hilderbrand, Raina M. Maier i Vicki Wysocki. "Proteomics Analyses of the Opportunistic PathogenBurkholderia vietnamiensisUsing Protein Fractionations and Mass Spectrometry". Journal of Biomedicine and Biotechnology 2011 (2011): 1–10. http://dx.doi.org/10.1155/2011/701928.

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The main objectives of this work were to obtain a more extensive coverage of theBurkholderia vietnamiensisproteome than previously reported and to identify virulence factors using tandem mass spectrometry. The proteome ofB. vietnamiensiswas precipitated into four fractions to as extracellular, intracellular, cell surface and cell wall proteins. Two different approaches were used to analyze the proteins. The first was a gel-based method where 1D SDS-PAGE was used for separation of the proteins prior to reverse phase liquid chromatography tandem mass spectrometry (LC-MS/MS). The second method used MudPIT analysis (Multi dimensional Protein Identification Technique), where proteins are digested and separated using cation exchange and reversed phase separations before the MS/MS analysis (LC/LC-MS/MS). Overall, gel-based LC-MS/MS analysis resulted in more protein identifications than the MudPIT analysis. Combination of the results lead to identification of more than 1200 proteins, approximately 16% of the proteins coded from the annotated genome ofBurkholderiaspecies. Several virulence factors were detected including flagellin, porin, peroxiredoxin and zinc proteases.

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Millett, Kenneth C., Eric J. Rawdon, Andrzej Stasiak i Joanna I. Sułkowska. "Identifying knots in proteins". Biochemical Society Transactions 41, nr 2 (21.03.2013): 533–37. http://dx.doi.org/10.1042/bst20120339.

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Polypeptide chains form open knots in many proteins. How these knotted proteins fold and finding the evolutionary advantage provided by these knots are among some of the key questions currently being studied in the protein folding field. The detection and identification of protein knots are substantial challenges. Different methods and many variations of them have been employed, but they can give different results for the same protein. In the present article, we review the various knot identification algorithms and compare their relative strengths when applied to the study of knots in proteins. We show that the statistical approach based on the uniform closure method is advantageous in comparison with other methods used to characterize protein knots.

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Lång, Emma, Kristine Haugen, Burkhard Fleckenstein, Håvard Homberset, Stephan A. Frye, Ole Herman Ambur i Tone Tønjum. "Identification of neisserial DNA binding components". Microbiology 155, nr 3 (1.03.2009): 852–62. http://dx.doi.org/10.1099/mic.0.022640-0.

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Neisseria meningitidis, a causative agent of meningitis and septicaemia, expresses type IV pili, a feature correlating with the uptake of exogenous DNA from the environment by natural transformation. The outer membrane complex PilQ, through which pili are extruded and retracted, has previously been shown to bind DNA in its pore region. In order to further elucidate how DNA is transported across the membranes, we searched for DNA binding proteins within the meningococcal inner membrane. Inner membrane fractions from a panel of neisserial strains were subjected to a solid-phase overlay assay with DNA substrates, and MS was subsequently employed to identify proteins that bind DNA. A number of DNA binding components were detected, including the pilus biogenesis component PilG, the competence protein ComL, and the cell division ATP-binding protein FtsE, as well as two hypothetical proteins. The DNA binding activity of these components was not dependent on the presence of the neisserial DNA uptake sequence. Null mutants, corresponding to each of the proteins identified, were constructed to assess their phenotypes. Only mutants defective in pilus biogenesis were non-competent and non-piliated. The DNA binding activity of the pilus biogenesis components PilQ and PilG and the phenotypes of their respective null mutants suggest that these proteins are directly involved as players in natural transformation, and not only indirectly, through pilus biogenesis.

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Rosander, Anna, Lars Frykberg, Nora Ausmees i Peter Müller. "Identification of Extracytoplasmic Proteins in Bradyrhizobium japonicum Using Phage Display". Molecular Plant-Microbe Interactions® 16, nr 8 (sierpień 2003): 727–37. http://dx.doi.org/10.1094/mpmi.2003.16.8.727.

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A novel gene bank of Bradyrhizobium japonicum USDA110spc4 was constructed using pG3DSS, a phagemid vector designed for detecting genes encoding secreted proteins. In this phagemid, the phage protein III lacks its indigenous signal peptide required for protein secretion, thus recombinant fusion proteins are displayed on the phage surface only if a functional signal peptide is provided by an inserted DNA fragment. In addition, the N-terminal half of protein III has been replaced by a short linker region (the E-tag) that is recognized by a monoclonal antibody, which enables isolation of phages displaying a fusion protein. The expression library described here, therefore, provides a powerful means to affinity select for B. japonicum genes encoding extracytoplasmic proteins. In total, 182 DNA sequences were analyzed, among which 132 different putative extracytoplasmic proteins could be identified. The function of most proteins could be predicted and support an extracytoplasmic localization. In addition, genes encoding novel extracytoplasmic proteins were found. In particular, a novel family of small proteins has been identified that is characterized by a conserved pattern of four cysteine residues.

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