Torches, Candles, Lamps, Lanterns, Flashlights, Spotlights, Night Vision Goggles… You Need Them All to See in Darkness.

Abstract:

:Articles assembled in the second part of this Special Issue describe some experimental and computational approaches for the structural and functional characterization of intrinsically disordered proteins. Since these tools represent specialized gear for the focused analysis of various aspects of dark proteome, they can be viewed as torches, candles, lamps, lanterns, flashlights, spotlights, night vision goggles, and other means needed to see in darkness.

journal_name

Proteomics

journal_title

Proteomics

authors

Uversky VN

doi

10.1002/pmic.201900085

subject

Has Abstract

pub_date

2019-03-01 00:00:00

pages

e1900085

issue

6

eissn

1615-9853

issn

1615-9861

journal_volume

19

pub_type

社论
  • Quality control for a large-scale study using protein arrays and protein beads to measure immune response in serum and plasma.

    abstract::We report on quality control performed in the context of a large-scale, multi-institutional study of the immune response in blood samples from prostate cancer patients. The measurements were performed by two commercially available techniques/services: protein arrays and an automated bead-based ELISA-like technique on ...

    journal_title:Proteomics

    pub_type: 杂志文章,多中心研究

    doi:10.1002/pmic.201200082

    authors: Ghevaria N,Visser M,Hoffmann R

    更新日期:2012-09-01 00:00:00

  • A widespread picture of the Streptococcus thermophilus proteome by cell lysate fractionation and gel-based/gel-free approaches.

    abstract::Among the group of lactic acid bacteria, Streptococcus thermophilus has found a wide application in industrial processes used for the manufacture of dairy products. Taking advantage of different proteome extraction and subfractionation protocols, bacterial cytosolic and membrane proteins were isolated and resolved by ...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200601030

    authors: Salzano AM,Arena S,Renzone G,D'Ambrosio C,Rullo R,Bruschi M,Ledda L,Maglione G,Candiano G,Ferrara L,Scaloni A

    更新日期:2007-05-01 00:00:00

  • Advances in high-resolution accurate mass spectrometry application to targeted proteomics.

    abstract::Targeted quantitative proteomic analyses aim at systematically measuring the abundance of proteins in large sets of samples, without biases or missing values. One typical implementation is the verification of biomarker candidates in bodily fluids, which measures extended lists of validated transitions using triple qua...

    journal_title:Proteomics

    pub_type: 杂志文章,评审

    doi:10.1002/pmic.201400450

    authors: Lesur A,Domon B

    更新日期:2015-03-01 00:00:00

  • Proteome of synaptosome-associated proteins in spinal cord dorsal horn after peripheral nerve injury.

    abstract::Peripheral nerve injury may lead to neuroadaptive changes of cellular signals in spinal cord that are thought to contribute to central mechanisms underlying neuropathic pain. Here we used a 2-DE-based proteomic technique to determine the global expression changes of synaptosome-associated proteins in spinal cord dorsa...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200800636

    authors: Singh OV,Yaster M,Xu JT,Guan Y,Guan X,Dharmarajan AM,Raja SN,Zeitlin PL,Tao YX

    更新日期:2009-03-01 00:00:00

  • Proteomics analyses of prostate cancer cells reveal cellular pathways associated with androgen resistance.

    abstract::While significant advances have been made in the diagnosis and treatment of prostate cancer, each year tens of thousands of men still die from prostate cancer in the United States. Thus, greater understanding of cellular pathways and molecular basis of prostate cancer progression in the development of androgen resista...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201600228

    authors: Höti N,Shah P,Hu Y,Yang S,Zhang H

    更新日期:2017-03-01 00:00:00

  • Proteomic analysis reveals a novel role for the actin cytoskeleton in vincristine resistant childhood leukemia--an in vivo study.

    abstract::Intrinsic or acquired resistance to vincristine (VCR), an antimicrotubule agent used in the treatment of childhood acute lymphoblastic leukemia (ALL), is a major clinical problem. Using a clinically relevant NOD/SCID mouse xenograft model of ALL, we established that alterations in the actin and tubulin cytoskeleton ar...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200500417

    authors: Verrills NM,Liem NL,Liaw TY,Hood BD,Lock RB,Kavallaris M

    更新日期:2006-03-01 00:00:00

  • A proteomics approach towards understanding blast fungus infection of rice grown under different levels of nitrogen fertilization.

    abstract::Proteins extracted from leaf blades of rice plants infected with blast fungus, Magnaporthe grisea, were separated by two-dimensional polyacrylamide gel electrophoresis. The separated proteins were electroblotted onto a polyvinylidene difluoride membrane, and 63 proteins were analyzed by a gas-phase protein sequencer. ...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/1615-9861(200109)1:9<1162::AID-PROT1162>3.

    authors: Konishi H,Ishiguro K,Komatsu S

    更新日期:2001-09-01 00:00:00

  • Lipidomic Analysis Reveals Altered Fatty Acid Metabolism in the Liver of the Symptomatic Niemann-Pick, Type C1 Mouse Model.

    abstract::Niemann-Pick disease, type C1 (NPC1) is a fatal, autosomal recessive, neurodegenerative disorder caused by mutations in the NPC1 gene. As a result of the genetic defect, there is accumulation of unesterified cholesterol and sphingolipids in the late endosomal/lysosomal system causing both visceral and neurological def...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201800285

    authors: Pergande MR,Serna-Perez F,Mohsin SB,Hanek J,Cologna SM

    更新日期:2019-09-01 00:00:00

  • Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence.

    abstract::Canonical isoforms in different databases have been defined as the most prevalent, most conserved, most expressed, longest, or the one with the clearest description of domains or posttranslational modifications. In this article, we revisit these definitions of canonical isoforms based on functional genomics and proteo...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201400170

    authors: Li HD,Menon R,Omenn GS,Guan Y

    更新日期:2014-12-01 00:00:00

  • Massspectrometrical analysis of recombinant human growth hormone Norditropin reveals amino acid exchange at M14_V14 rhGH.

    abstract::Recombinant human growth hormone (rhGH) is used for the treatment of several disorders. Structural integrity of rhGH is of critical importance for its clinical use and modifications thereof may act as markers in situations such as rhGH doping, as illegal rhGH-abuse in sports is of increasing interest. In the current s...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200500334

    authors: Hepner F,Csaszar E,Roitinger E,Pollak A,Lubec G

    更新日期:2006-02-01 00:00:00

  • Comparative proteome and transcriptome analyses of embryonic stem cells during embryoid body-based differentiation.

    abstract::Gene expression analyses of embryonic stem cells (ESCs) will help to uncover or further define signaling pathways and molecular mechanisms involved in the maintenance of self-renewal and pluripotency. We employed a 2-DE-based proteomics approach to analyze human ESC line, Royan H5, in undifferentiated cells and differ...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200900003

    authors: Fathi A,Pakzad M,Taei A,Brink TC,Pirhaji L,Ruiz G,Sharif Tabe Bordbar M,Gourabi H,Adjaye J,Baharvand H,Salekdeh GH

    更新日期:2009-11-01 00:00:00

  • Synthesizing Systems Biology Knowledge from Omics Using Genome-Scale Models.

    abstract::Omic technologies have enabled the complete readout of the molecular state of a cell at different biological scales. In principle, the combination of multiple omic data types can provide an integrated view of the entire biological system. This integration requires appropriate models in a systems biology approach. Here...

    journal_title:Proteomics

    pub_type: 杂志文章,评审

    doi:10.1002/pmic.201900282

    authors: Dahal S,Yurkovich JT,Xu H,Palsson BO,Yang L

    更新日期:2020-09-01 00:00:00

  • Identification of toxicological biomarkers of di(2-ethylhexyl) phthalate in proteins secreted by HepG2 cells using proteomic analysis.

    abstract::The effects of di(2-ethylhexyl) phthalate (DEHP) on proteins secreted by HepG2 cells were studied using a proteomic approach. HepG2 cells were exposed to various concentrations of DEHP (0, 2.5, 5, 10, 25, 50, 100, and 250 microM) for 24 or 48 h. 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) and c...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200900674

    authors: Choi S,Park SY,Jeong J,Cho E,Phark S,Lee M,Kwak D,Lim JY,Jung WW,Sul D

    更新日期:2010-05-01 00:00:00

  • 2-D DIGE analysis of the proteome of extracts from peanut variants reveals striking differences in major allergen contents.

    abstract::Over the last decade, an increasing prevalence of peanut allergies was observed worldwide. Peanuts are meanwhile categorized among the most dangerous food allergens. This is particularly relevant since peanut-derived ingredients are widely used in industrial food production. To minimize the problem of hidden food alle...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200800938

    authors: Schmidt H,Gelhaus C,Latendorf T,Nebendahl M,Petersen A,Krause S,Leippe M,Becker WM,Janssen O

    更新日期:2009-07-01 00:00:00

  • Preparation of C60-functionalized magnetic silica microspheres for the enrichment of low-concentration peptides and proteins for MALDI-TOF MS analysis.

    abstract::In this work, for the first time, a novel C60-functionalized magnetic silica microsphere (designated C60-f-MS) was synthesized by radical polymerization of C60 molecules on the surface of magnetic silica microspheres. The resulting C60-f-MS microsphere has magnetite core and thin C60 modified silica shell, which endow...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200800335

    authors: Chen H,Qi D,Deng C,Yang P,Zhang X

    更新日期:2009-01-01 00:00:00

  • Proteome-wide analysis of the amino terminal status of Escherichia coli proteins at the steady-state and upon deformylation inhibition.

    abstract::A proteome wide analysis was performed in Escherichia coli to identify the impact on protein N-termini of actinonin, an antibiotic specifically inhibiting peptide deformylase (PDF). A strategy and tool suite (SILProNaQ) was employed to provide large-scale quantitation of N-terminal modifications. In control conditions...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201500027

    authors: Bienvenut WV,Giglione C,Meinnel T

    更新日期:2015-07-01 00:00:00

  • Prediction of subcellular locations of proteins: where to proceed?

    abstract::Since the proposal of the signal hypothesis on protein subcellular sorting, a number of computational analyses have been performed in this field. A typical example is the development of prediction algorithms for the subcellular localization sites of input protein sequences. In this review, we mainly focus on the biolo...

    journal_title:Proteomics

    pub_type: 杂志文章,评审

    doi:10.1002/pmic.201000274

    authors: Imai K,Nakai K

    更新日期:2010-11-01 00:00:00

  • Metabolic enzyme diversity in different human thyroid cell lines and their sensitivity to gravitational forces.

    abstract::Many cancer cells show unique protein expression patterns. We used proteome technology including MS, free flow isoelectric focusing and Western blotting to determine current concentrations of metabolic enzymes in healthy and malignant human thyroid cells. Three different types of human thyroid cells were investigated ...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201200070

    authors: Pietsch J,Sickmann A,Weber G,Bauer J,Egli M,Wildgruber R,Infanger M,Grimm D

    更新日期:2012-08-01 00:00:00

  • Native immunoblotting of blue native gels to identify conformation-specific antibodies.

    abstract::A large repertoire of immunological methods permits monitoring the interaction of antibodies with their specific antigen. However, recognition of a protein by a conformation-specific antibody represents a challenge because native conditions must be kept throughout the assay. Native immunoblotting of blue native gels c...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200900468

    authors: Zickermann V,Wumaier Z,Wrzesniewska B,Hunte C,Schägger H

    更新日期:2010-01-01 00:00:00

  • Citrulline enhances myofibrillar constituents expression of skeletal muscle and induces a switch in muscle energy metabolism in malnourished aged rats.

    abstract::Citrulline (Cit) actions on muscle metabolism remain unclear. Those latter were investigated using a proteomic approach on Tibialis muscles from male Sprague-Dawley rats. At 23 months of age, rats were either fed ad libitum (AL group) or subjected to dietary restriction for 12 weeks. At the end of the restriction peri...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201200262

    authors: Faure C,Morio B,Chafey P,Le Plénier S,Noirez P,Randrianarison-Huetz V,Cynober L,Aussel C,Moinard C

    更新日期:2013-07-01 00:00:00

  • Proteome and phosphoproteome analysis of chromatin associated proteins in rice (Oryza sativa).

    abstract::The eukaryotic chromatin/chromosome stores genomic information, controls genetic material distribution, and plays an essential role in the establishment and maintenance of spatial and temporal gene expression profile. Despite over a century of research, the protein composition and higher level structure of chromatin s...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200700580

    authors: Tan F,Li G,Chitteti BR,Peng Z

    更新日期:2007-12-01 00:00:00

  • A QconCAT informatics pipeline for the analysis, visualization and sharing of absolute quantitative proteomics data.

    abstract::Absolute protein concentration determination is becoming increasingly important in a number of fields including diagnostics, biomarker discovery and systems biology modeling. The recently introduced quantification concatamer methodology provides a novel approach to performing such determinations, and it has been appli...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201000454

    authors: Swainston N,Jameson D,Carroll K

    更新日期:2011-01-01 00:00:00

  • Does Intrinsic Disorder in Proteins Favor Their Interaction with Lipids?

    abstract::Intrinsically disordered proteins (IDPs) are implicated in a range of human diseases, some of which are associated with the ability to bind to lipids. Although the presence of solvent-exposed hydrophobic regions in IDPs should favor their interactions with low-molecular-weight hydrophobic/amphiphilic compounds, this h...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201800098

    authors: Deryusheva E,Nemashkalova E,Galloux M,Richard CA,Eléouët JF,Kovacs D,Van Belle K,Tompa P,Uversky V,Permyakov S

    更新日期:2019-03-01 00:00:00

  • Proteome analysis of Escherichia coli W3110 expressing an heterologous sigma factor.

    abstract::The recombinant plasmid pASK18 carries a Streptomyces DNA fragment which includes an open reading frame, designated psfS (putative sigma factor, Streptomyces), as its putative product showed a high degree of similarity with RNA polymerase sigma factors. Previous results showed that PsfS causes transcription initiation...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200300403

    authors: Baglioni P,Bini L,Liberatori S,Pallini V,Marri L

    更新日期:2003-06-01 00:00:00

  • Identification of human nasal mucous proteins using proteomics.

    abstract::The determination of possible biomarkers in nasal secretion of healthy subjects can have a role in early diagnosis of diseases such as rhinosinusitis. For this purpose, nasal lavage fluids (NLFs) from ten volunteers, collected before and after they had been submitted to nasal provocations, were investigated. Separatio...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200401172

    authors: Casado B,Pannell LK,Iadarola P,Baraniuk JN

    更新日期:2005-07-01 00:00:00

  • Serum biomarker discovery in renal cancer using 2-DE and prefractionation by immunodepletion and isoelectric focusing; increasing coverage or more of the same?

    abstract::As an initial screen for novel markers of renal cancer and to minimise background heterogeneity, we have compared the within-patient profiles of serum samples from seven patients pre- and post-nephrectomy. Samples were depleted of six of the most abundant proteins using Agilent's multiple affinity removal system (MARS...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200800497

    authors: Vasudev NS,Ferguson RE,Cairns DA,Stanley AJ,Selby PJ,Banks RE

    更新日期:2008-12-01 00:00:00

  • Key regulators of galectin-glycan interactions.

    abstract::Protein-ligand interactions serve as fundamental regulators of numerous biological processes. Among protein-ligand pairs, glycan binding proteins (GBPs) and the glycans they recognize represent unique and highly complex interactions implicated in a broad range of regulatory activities. With few exceptions, cell surfac...

    journal_title:Proteomics

    pub_type: 杂志文章,评审

    doi:10.1002/pmic.201600116

    authors: Kamili NA,Arthur CM,Gerner-Smidt C,Tafesse E,Blenda A,Dias-Baruffi M,Stowell SR

    更新日期:2016-12-01 00:00:00

  • Increased expression of lysosome membrane protein 2 in glomeruli of patients with idiopathic membranous nephropathy.

    abstract::Urinary microvesicles constitute a rich source of membrane-bound and intracellular proteins that may provide important clues of pathophysiological mechanisms in renal disease. In the current study, we analyzed and compared the proteome of urinary microvesicles from patients with idiopathic membranous nephropathy (iMN)...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201500127

    authors: Rood IM,Merchant ML,Wilkey DW,Zhang T,Zabrouskov V,van der Vlag J,Dijkman HB,Willemsen BK,Wetzels JF,Klein JB,Deegens JK

    更新日期:2015-11-01 00:00:00

  • Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry.

    abstract::Two-dimensional difference gel electrophoresis (2-D DIGE) coupled with mass spectrometry (MS) was used to investigate tumor-specific changes in the proteome of human colorectal cancers and adjacent normal mucosa. For each of six patients with different stages of colon cancer, Cy5-labeled proteins isolated from tumor t...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200300635

    authors: Friedman DB,Hill S,Keller JW,Merchant NB,Levy SE,Coffey RJ,Caprioli RM

    更新日期:2004-03-01 00:00:00

  • Chemoenzymatic method for glycomics: Isolation, identification, and quantitation.

    abstract::Over the past decade, considerable progress has been made with respect to the analytical methods for analysis of glycans from biological sources. Regardless of the specific methods that are used, glycan analysis includes isolation, identification, and quantitation. Derivatization is indispensable to increase their ide...

    journal_title:Proteomics

    pub_type: 杂志文章,评审

    doi:10.1002/pmic.201500266

    authors: Yang S,Rubin A,Eshghi ST,Zhang H

    更新日期:2016-01-01 00:00:00