scholarly journals Currents: Deducing posttranslational modifications | Ultrasensitive protein identification | Detecting proteins in microliter volumes | Generic protein-labeling method | Protein microarrays with estrogen receptors | Semicarbazide microarrays for detecting multiple infections | A warning about flash-cooling | Protein modifications database

2004 ◽  
Vol 3 (3) ◽  
pp. 339-342
Keyword(s):  
Estrogen Receptors ◽  
Posttranslational Modifications ◽  
Protein Identification ◽  
Protein Microarrays ◽  
Protein Labeling ◽  
Multiple Infections ◽  
Protein Modifications ◽  
Flash Cooling ◽  
Labeling Method

Proteomics: current techniques and potential applications to lung disease

2004 ◽  
Vol 287 (1) ◽  
pp. L1-L23 ◽  
Author(s):  
Jan Hirsch ◽  
Kirk C. Hansen ◽  
Alma L. Burlingame ◽  
Michael A. Matthay
Keyword(s):  
Posttranslational Modifications ◽  
Protein Separation ◽  
Protein Identification ◽  
Cell Types ◽  
Protein Profiling ◽  
Complex Samples ◽  
Potential Value ◽  
Potential Applications ◽  
Tissue Specimens ◽  
Different Cell Types

Proteomics aims to study the whole protein content of a biological sample in one set of experiments. Such an approach has the potential value to acquire an understanding of the complex responses of an organism to a stimulus. The large vascular and air space surface area of the lung expose it to a multitude of stimuli that can trigger a variety of responses by many different cell types. This complexity makes the lung a promising, but also challenging, target for proteomics. Important steps made in the last decade have increased the potential value of the results of proteomics studies for the clinical scientist. Advances in protein separation and staining techniques have improved protein identification to include the least abundant proteins. The evolution in mass spectrometry has led to the identification of a large part of the proteins of interest rather than just describing changes in patterns of protein spots. Protein profiling techniques allow the rapid comparison of complex samples and the direct investigation of tissue specimens. In addition, proteomics has been complemented by the analysis of posttranslational modifications and techniques for the quantitative comparison of different proteomes. These methodologies have made the application of proteomics on the study of specific diseases or biological processes under clinically relevant conditions possible. The quantity of data that is acquired with these new techniques places new challenges on data processing and analysis. This article provides a brief review of the most promising proteomics methods and some of their applications to pulmonary research.

scholarly journals Physiological Study of Lactobacillus delbrueckii subsp. bulgaricus Strains in a Novel Chemically Defined Medium

2000 ◽  
Vol 66 (12) ◽  
pp. 5306-5311 ◽  
Author(s):  
Christian Chervaux ◽  
S. Dusko Ehrlich ◽  
Emmanuelle Maguin
Keyword(s):  
Carbon Sources ◽  
Streptococcus Thermophilus ◽  
Defined Medium ◽  
Lactobacillus Delbrueckii ◽  
Protein Labeling ◽  
Chemically Defined Medium ◽  
Phosphotransferase System ◽  
Nutritional Conditions ◽  
Labeling Method

ABSTRACT We developed a chemically defined medium called milieu proche du lait (MPL), in which 22 Lactobacillus delbrueckii subsp.bulgaricus (L. bulgaricus) strains exhibited growth rates ranging from 0.55 to 1 h−1. MPL can also be used for cultivation of other lactobacilli and Streptococcus thermophilus. The growth characteristics of L. bulgaricus in MPL containing different carbon sources were determined, including an initial characterization of the phosphotransferase system transporters involved. For the 22 tested strains, growth on lactose was faster than on glucose, mannose, and fructose. Lactose concentrations below 0.4% were limiting for growth. We isolated 2-deoxyglucose-resistant mutants from strains CNRZ397 and ATCC 11842. CNRZ397-derived mutants were all deficient for glucose, fructose, and mannose utilization, indicating that these three sugars are probably transported via a unique mannose-specific-enzyme-II-like transporter. In contrast, mutants of ATCC 11842 exhibited diverse phenotypes, suggesting that multiple transporters may exist in that strain. We also developed a protein labeling method and verified that exopolysaccharide production and phage infection can occur in MPL. The MPL medium should thus be useful in conducting physiological studies ofL. bulgaricus and other lactic acid bacteria under well controlled nutritional conditions.

scholarly journals Microarrays as Model Biosensor Platforms to Investigate the Structure and Affinity of Aptamers

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Jennifer A. Martin ◽  
Yaroslav Chushak ◽  
Jorge L. Chávez ◽  
Joshua A. Hagen ◽  
Nancy Kelley-Loughnane
Keyword(s):  
Minimum Distance ◽  
Limit Of Detection ◽  
Signal To Noise Ratio ◽  
Protein Labeling ◽  
Target Interaction ◽  
Starting Conditions ◽  
Recognition Elements ◽  
Labeling Method ◽  
Biosensor Applications ◽  
Magnitude Improvement

Immobilization of nucleic acid aptamer recognition elements selected free in solution onto the surface of biosensor platforms has proven challenging. This study investigated the binding of multiple aptamer/target pairs immobilized on a commercially available microarray as a model system mimicking biosensor applications. The results indicate a minimum distance (linker length) from the surface and thymine nucleobase linker provides reproducible binding across varying conditions. An indirect labeling method, where the target was labeled with a biotin followed by a brief Cy3-streptavidin incubation, provided a higher signal-to-noise ratio and over two orders of magnitude improvement in limit of detection, compared to direct Cy3-protein labeling. We also showed that the affinities of the aptamer/target interaction can change between direct and indirect labeling and conditions to optimize for the highest fluorescence intensity will increase the sensitivity of the assay but will not change the overall affinity. Additionally, some sequences which did not initially bind demonstrated binding when conditions were optimized. These results, in combination with studies demonstrating enhanced binding in nonselection buffers, provided insights into the structure and affinity of aptamers critical for biosensor applications and allowed for generalizations in starting conditions for researchers wishing to investigate aptamers on a microarray surface.

scholarly journals Protein Modifications as Manifestations of Hyperglycemic Glucotoxicity in Diabetes and Its Complications

2016 ◽  
Vol 9 ◽  
pp. BCI.S36141 ◽  
Author(s):  
Hong Zheng ◽  
Jinzi Wu ◽  
Zhen Jin ◽  
Liang-Jun Yan
Keyword(s):  
Oxidative Stress ◽  
Posttranslational Modifications ◽  
Metabolic Pathways ◽  
Polyol Pathway ◽  
Protein Modifications ◽  
Redox Imbalance ◽  
Adp Ribosylation ◽  
Carbon Stress

Diabetes and its complications are hyperglycemic toxicity diseases. Many metabolic pathways in this array of diseases become aberrant, which is accompanied with a variety of posttranslational protein modifications that in turn reflect diabetic glucotoxicity. In this review, we summarize some of the most widely studied protein modifications in diabetes and its complications. These modifications include glycation, carbonylation, nitration, cysteine S-nitrosylation, acetylation, sumoylation, ADP-ribosylation, O-GlcNAcylation, and succination. All these posttranslational modifications can be significantly attributed to oxidative stress and/or carbon stress induced by diabetic redox imbalance that is driven by activation of pathways, such as the polyol pathway and the ADP-ribosylation pathway. Exploring the nature of these modifications should facilitate our understanding of the pathological mechanisms of diabetes and its associated complications.

scholarly journals Sarcomeric protein modification during adrenergic stress enhances cross-bridge kinetics and cardiac output

2017 ◽  
Vol 122 (3) ◽  
pp. 520-530 ◽  
Author(s):  
Kenneth S. Gresham ◽  
Ranganath Mamidi ◽  
Jiayang Li ◽  
Hyerin Kwak ◽  
Julian E. Stelzer
Keyword(s):  
Cardiac Output ◽  
Posttranslational Modifications ◽  
Troponin I ◽  
Ventricular Contractility ◽  
Protein Modifications ◽  
Sarcomeric Protein ◽  
Cross Bridge ◽  
Myosin Binding Protein ◽  
Myosin Binding Protein C ◽  
Pressure Development

Molecular adaptations to chronic neurohormonal stress, including sarcomeric protein cleavage and phosphorylation, provide a mechanism to increase ventricular contractility and enhance cardiac output, yet the link between sarcomeric protein modifications and changes in myocardial function remains unclear. To examine the effects of neurohormonal stress on posttranslational modifications of sarcomeric proteins, mice were administered combined α- and β-adrenergic receptor agonists (isoproterenol and phenylephrine, IPE) for 14 days using implantable osmotic pumps. In addition to significant cardiac hypertrophy and increased maximal ventricular pressure, IPE treatment accelerated pressure development and relaxation (74% increase in dP/d tmax and 14% decrease in τ), resulting in a 52% increase in cardiac output compared with saline (SAL)-treated mice. Accelerated pressure development was maintained when accounting for changes in heart rate and preload, suggesting that myocardial adaptations contribute to enhanced ventricular contractility. Ventricular myocardium isolated from IPE-treated mice displayed a significant reduction in troponin I (TnI) and myosin-binding protein C (MyBP-C) expression and a concomitant increase in the phosphorylation levels of the remaining TnI and MyBP-C protein compared with myocardium isolated from saline-treated control mice. Skinned myocardium isolated from IPE-treated mice displayed a significant acceleration in the rate of cross-bridge (XB) detachment (46% increase) and an enhanced magnitude of XB recruitment (43% increase) at submaximal Ca2+ activation compared with SAL-treated mice but unaltered myofilament Ca2+ sensitivity of force generation. These findings demonstrate that sarcomeric protein modifications during neurohormonal stress are molecular adaptations that enhance in vivo ventricular contractility through accelerated XB kinetics to increase cardiac output. NEW & NOTEWORTHY Posttranslational modifications to sarcomeric regulatory proteins provide a mechanism to modulate cardiac function in response to stress. In this study, we demonstrate that neurohormonal stress produces modifications to myosin-binding protein C and troponin I, including a reduction in protein expression within the sarcomere and increased phosphorylation of the remaining protein, which serve to enhance cross-bridge kinetics and increase cardiac output. These findings highlight the importance of sarcomeric regulatory protein modifications in modulating ventricular function during cardiac stress.

Novel post-digest isotope coded protein labeling method for phospho- and glycoproteome analysis

2010 ◽  
Vol 73 (10) ◽  
pp. 1986-2005 ◽  
Author(s):  
M. Fleron ◽  
Y. Greffe ◽  
D. Musmeci ◽  
A.C. Massart ◽  
V. Hennequiere ◽  
...  
Keyword(s):  
Protein Labeling ◽  
Labeling Method

scholarly journals The Plant PTM Viewer, a central resource exploring plant protein modifications. From site-seeing to protein function

2018 ◽  
Author(s):  
Patrick Willems ◽  
Alison Horne ◽  
Sofie Goormachtig ◽  
Ive De Smet ◽  
Alexander Botzki ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Posttranslational Modifications ◽  
Protein Function ◽  
Protein Sequences ◽  
Specific Protein ◽  
Specific Information ◽  
Active Site Residues ◽  
Functional Protein ◽  
Protein Modifications ◽  
Modern Mass

SUMMARYPosttranslational modifications (PTMs) of proteins are central in any kind of cellular signaling. Modern mass spectrometry technologies enable comprehensive identification and quantification of various PTMs. Given the increased number and types of mapped protein modifications, a database is necessary that simultaneouly integrates and compares site-specific information for different PTMs, especially in plants for which the available PTM data are poorly catalogued. Here, we present the Plant PTM Viewer (http://www.psb.ugent.be/PlantPTMViewer), an integrative PTM resource that comprises approximately 200,000 PTM sites for 17 types of protein modifications in plant proteins from five different species. The Plant PTM Viewer provides the user with a protein sequence overview in which the experimentally evidenced PTMs are highlighted together with functional protein domains or active site residues. The PTM sequence search tool can query PTM combinations in specific protein sequences, whereas the PTM BLAST tool searches for modified protein sequences to detect conserved PTMs in homologous sequences. Taken together, these tools facilitate to assume the role and potential interplay of PTMs in specific proteins or within a broader systems biology context. The Plant PTM Viewer is an open repository that allows submission of mass spectrometry-based PTM data to remain at pace with future PTM plant studies.

scholarly journals Pyntheon: A Functional Analysis Framework for Protein Modifications and Mutations of 83 Model Organisms

2019 ◽  
Author(s):  
Ahmed Arslan
Keyword(s):  
Posttranslational Modifications ◽  
Protein Modification ◽  
Model Organisms ◽  
Analysis Framework ◽  
Proteomics Data ◽  
Functional Protein ◽  
Protein Modifications ◽  
Community Of Researchers ◽  
Protein Mutations ◽  
The Impact

AbstractMotivationPosttranslational modifications (PTMs) modulate proteins activity depending on the dynamics of cellular conditions, in the highly regulated processes that control the reversible nature of these modifications and a cellular state. Due to the unique importance of PTMs, a number of resources are available to analyze the protein modification data for different organisms. These databases are quite informative on a limited number of popular organisms, mostly human and yeast. However there has not been a single database to date that makes it possible to analyze the modified protein residue data for up to 83 model organisms. Moreover, there are limited resources that rely on both protein mutations and modifications in evaluating a phenotype.ResultsI am presenting a comprehensive python tool Pyntheon that enables users to analyze protein modifications and mutations data. This resource can be used in different ways to know: (i) if the proteins of interest have modifications and (ii) if the modified residues overlap with mutated sites. Additional functions include, analyzing if a PTM-site is present in a functional protein region, like domain and structural regions. In summary, Pyntheon makes it possible for a larger community of researchers to evaluate their curated proteomics data and interpret the impact of mutations on phenotypes.ConclusionPyntheon has multifold functions that can help analyzing the protein mutations impact on the modified residues for a large number of popular model organisms.Code-Availabilityhttps://github.com/AhmedArslan/[email protected]

scholarly journals Ligand-directed dibromophenyl benzoate chemistry for rapid and selective acylation of intracellular natural proteins

2015 ◽  
Vol 6 (5) ◽  
pp. 3217-3224 ◽  
Author(s):  
Yousuke Takaoka ◽  
Yuki Nishikawa ◽  
Yuki Hashimoto ◽  
Kenta Sasaki ◽  
Itaru Hamachi
Keyword(s):  
Living Cells ◽  
Protein Labeling ◽  
Natural Protein ◽  
Protein Imaging ◽  
Selective Acylation ◽  
Labeling Method

A rapid and selective protein labeling method, LDBB chemistry is a useful tool for natural protein imaging in living cells.

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