4.7 Review

Common Post-translational Modifications (PTMs) of Proteins: Analysis by Up-to-Date Analytical Techniques with an Emphasis on Barley

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Chemistry, Analytical

Labeling strategies for analysis of oligosaccharides and glycans by capillary electrophoresis

Denisa Smolkova et al.

Summary: Capillary electrophoresis is widely used for oligosaccharide and glycan analysis, but the low electrophoretic mobility and lack of chromophore or fluorophore in saccharide molecules require modification before separation and detection. This review summarizes the labeling strategies used for oligosaccharide/glycan analysis, categorized based on the labeling mechanism and saccharide molecule. In addition to the commonly used 8-aminopyrene-1,3,6-trisulfonic acid trisodium salt, less common and recently developed tags applicable in glycomics are also summarized.

TRAC-TRENDS IN ANALYTICAL CHEMISTRY (2023)

Review Biochemistry & Molecular Biology

Identification and characterization of post-translational modifications: Clinical implications

Juliane Hermann et al.

Summary: Post-translational modifications play a key role in protein function and disease progression, but their reliable detection and quantification remain a challenge in clinical diagnosis. Mass spectrometry offers a solution, but its clinical translation still faces challenges.

MOLECULAR ASPECTS OF MEDICINE (2022)

Review Biochemical Research Methods

Combinatorial peptides: A library that continuously probes low-abundance proteins

Egisto Boschetti et al.

Summary: This review focuses on the experimental applications of combinatorial peptide ligand libraries for low-abundance proteins, discussing recent technical developments and the potential future directions of the technology.

ELECTROPHORESIS (2022)

Article Biochemistry & Molecular Biology

New insights into the type A glycan modification of Clostridioides difficile flagellar protein flagellin C by phosphoproteomics analysis

Paul J. Hensbergen et al.

Summary: In this study, we demonstrate that a commonly used enrichment strategy can reliably identify peptides carrying a type A glycan modification and discovered a rare modification structure. These findings can be used to advance the understanding of biosynthesis models for this modification.

JOURNAL OF BIOLOGICAL CHEMISTRY (2022)

Article Biochemical Research Methods

Analysis of protein phosphorylation using Phos-tag gels

Lorna O'Donoghue et al.

Summary: Phosphorylation is a crucial regulatory mechanism in controlling protein and cell function. Phosphoproteomics has revealed the extent and complexity of protein phosphorylation, but the functional roles of individual phospho-sites are still not fully understood. The Phos-tag gel method, along with other tools, can provide a more comprehensive understanding of multi-site phosphorylation.

JOURNAL OF PROTEOMICS (2022)

Article Multidisciplinary Sciences

Posttranslational modification of the RHO of plants protein RACB by phosphorylation and cross-kingdom conserved ubiquitination

Lukas Weiss et al.

Summary: Small RHO-type G-proteins are crucial for signaling and polarity regulation in eukaryotic cells. The activity of these proteins is tightly controlled through nucleotide exchange and posttranslational modification (PTM). In this study, phosphorylation and ubiquitination of the barley ROP RACB were identified, suggesting their roles in regulating RACB stability and activity.

PLOS ONE (2022)

Review Biochemical Research Methods

Proteomics and glycoproteomics of beer and wine

Shulei Liu et al.

Summary: This article reviews recent studies on proteomic and glycoproteomic analyses of beer and wine. Many grape and yeast proteins are glycosylated, while barley proteins can be glycated during the beer making process. The use of high-resolution mass spectrometry allows for the identification, quantification, and characterization of the glyco/proteomes of fermented beverages, which helps in controlling the quality of the final products.

PROTEOMICS (2022)

Review Chemistry, Multidisciplinary

Covalent Chemical Tools for Profiling Post-Translational Modifications

Benjamin Emenike et al.

Summary: Nature increases the functional diversity of the proteome through posttranslational modifications (PTMs), which can be correlated to diseases. Therefore, it is important to qualitatively and quantitatively detect these transformations. One effective method is to use chemical strategies to label different PTMs, facilitating the study of their roles.

FRONTIERS IN CHEMISTRY (2022)

Article Plant Sciences

Global proteome analyses of phosphorylation and succinylation of barley root proteins in response to phosphate starvation and recovery

Juncheng Wang et al.

Summary: Phosphate (Pi) stress is a crucial environmental factor that limits plant growth and development. This study provides a comprehensive analysis of protein phosphorylation and succinylation in barley roots in response to Pi stress, revealing their underlying mechanisms and interactions.

FRONTIERS IN PLANT SCIENCE (2022)

Article Biochemistry & Molecular Biology

Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant-Pathogen Interactions

Sadegh Balotf et al.

Summary: This review provides an overview of the application of shotgun proteomics based on mass spectrometry (MS) in studying plant-pathogen interactions. Proteomics can reveal the mechanisms involved in plant-pathogen interactions by quantitatively measuring the dynamic changes of proteins, biological pathways, and post-translational modifications. The review summarizes the essential steps for shotgun proteomic studies of plants, pathogens, and plant-pathogen interactions, including methods for protein digestion, identification, separation, and quantification. Additionally, it discusses how protein post-translational modifications may participate in the interaction between a pathogen and its host plant.

PROTEOMES (2022)

Review Chemistry, Analytical

Enrichment and analysis of glycated proteins

Seonghyeon Cho et al.

Summary: Glycation is a post-translational modification of proteins that is closely related to the pathogenesis of various human diseases. This review focuses on the enrichment and analysis methods used to identify glycation as a disease biomarker in exploratory studies.

REVIEWS IN ANALYTICAL CHEMISTRY (2022)

Review Nutrition & Dietetics

Wheat ATIs: Characteristics and Role in Human Disease

Sabrina Geisslitz et al.

Summary: Amylase/trypsin-inhibitors (ATIs) are proteins in wheat grains that may play a role in natural defense and adverse reactions in humans. Studies have shown that ATIs can activate the innate immune system, potentially affecting conditions like coeliac disease and non-coeliac wheat sensitivity. Further research is needed to understand the mechanisms and implications of ATIs in wheat.

FRONTIERS IN NUTRITION (2021)

Article Biochemical Research Methods

Phos-tag diagonal electrophoresis precisely detects the mobility change of phosphoproteins in Phos-tag SDS-PAGE

Yuki Okawara et al.

Summary: Phos-tag diagonal electrophoresis, a technique developed to precisely identify changes in phosphoprotein electrophoretic mobility, resolves the issue of determining mobility shifts by Mn2+ Phos-tag when using separate SDS-PAGE and Phos-tag SDS-PAGE. By providing SDS-PAGE and Phos-tag SDS-PAGE patterns on a single gel, this technique is useful for identifying phosphorylation states of various proteins.

JOURNAL OF PROTEOMICS (2021)

Review Biochemical Research Methods

A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics

Nicholas M. Riley et al.

Summary: Glycosylation, a prevalent but heterogeneous modification in molecular biology, has broad implications. The choice of enrichment strategy significantly impacts experimental outcomes in glycoproteomics research, which continues to gain interest with advancements in mass spectrometry instrumentation and software.

MOLECULAR & CELLULAR PROTEOMICS (2021)

Article Chemistry, Analytical

Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry

Yao Chen et al.

Summary: The CHO-GlcNAc strategy developed in this study efficiently enriches O-GlcNAc glycopeptides and has been successfully applied to analyze O-GlcNAcylation in the nucleus of HeLa cells, identifying a large number of potential O-GlcNAcylation sites and associated proteins. This method could serve as a versatile tool for proteomic analysis of O-GlcNAcylation.

ANALYTICAL CHEMISTRY (2021)

Article Plant Sciences

Protein phosphorylation regulates maize endosperm starch synthase IIa activity and protein-protein interactions

Sahar Mehrpouyan et al.

Summary: This study focuses on the post-translational modification of SSIIa and its interactions with SSI and SBEIIb in maize amyloplast stroma, revealing that phosphorylation can promote the interaction between SSIIa and SBEIIb to enhance its activity. Protein phosphorylation plays a dual role in the stability and dissociation of heteromeric starch synthase complexes in the maize amyloplast stroma, providing new insights into the regulation of starch biosynthesis in plants.

PLANT JOURNAL (2021)

Review Plant Sciences

Cracking the Sugar Code: A Snapshot of N- and O-Glycosylation Pathways and Functions in Plants Cells

Richard Strasser et al.

Summary: Glycosylation is a crucial modification process that can alter the biological function of proteins and lipids, affecting the development and physiology of an organism. While challenges remain in understanding plant glycosylation, high throughput approaches may help to address these gaps, revolutionizing the identification and characterization of unknown plant glycosyltransferases and hydrolases.

FRONTIERS IN PLANT SCIENCE (2021)

Review Plant Sciences

Advances on Post-translational Modifications Involved in Seed Germination

Feng Yu et al.

Summary: Seed germination and seedling establishment are crucial developmental processes that undergo complex physiological changes, precisely regulated at transcriptional and translational levels. Phytohormones like ABA and GA play key roles in modulating this process, while proteins such as ABI5 and DELLA are central in seed germination. Post-translational modifications, particularly phosphorylation and ubiquitination, are shown to be decisive in regulating seed germination.

FRONTIERS IN PLANT SCIENCE (2021)

Review Chemistry, Multidisciplinary

Microfluidics for Peptidomics, Proteomics, and Cell Analysis

Rui Vitorino et al.

Summary: Microfluidics is an advanced microtechnology for manipulating fluids in small channels, offering tools for controlling chemical, biological, and physical processes. It plays a crucial role in various fields and is often combined with mass spectrometry for analysis. Recent developments include applications in proteomics, peptidomics, cell analysis, and detection methods for clinical questions.

NANOMATERIALS (2021)

Review Biochemistry & Molecular Biology

Proteomics and Post-Translational Modifications of Starch Biosynthesis-Related Proteins in Developing Seeds of Rice

Piengtawan Tappiban et al.

Summary: The study focuses on the proteomics and posttranslational modifications (PTMs) of starch biosynthesis-related proteins in rice endosperm, highlighting the differential expression of these proteins in developing seeds. Most proteins involved in starch biosynthesis increase at 6-20 days after flowering and decrease under high-temperature conditions. Various PTMs, including phosphorylation, lysine acetylation, succinylation, lysine 2-hydroxyisobutyrylation, and malonylation, target starch biosynthesis proteins in rice seeds. Further research on the role of these PTMs in starch biosynthesis is ongoing.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Review Agriculture, Multidisciplinary

Application of Mass Spectrometry-Based Proteomics to Barley Research

Mahya Bahmani et al.

Summary: This article discusses the importance of barley in the world and the application of proteomics technology in barley research, including the response of proteins to environmental conditions and their impact on food processing. Proteomics can be used to guide barley breeding programs to improve its nutritional value and application scope.

JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY (2021)

Article Plant Sciences

N-linked glycoproteome analysis reveals central glycosylated proteins involved in wheat early seedling growth

Xueqian Wang et al.

Summary: This study conducted the first N-linked glycosylation proteome analysis of wheat seedling leaves, identifying 308 glycosylated peptides corresponding to 248 unique glycoproteins. The glycoproteins play crucial roles in cell wall reconstruction, biomacromolecular metabolism, signal transduction, endoplasmic reticulum quality control, and stress response.

PLANT PHYSIOLOGY AND BIOCHEMISTRY (2021)

Article Multidisciplinary Sciences

The post-translational modification landscape of commercial beers

Edward D. Kerr et al.

Summary: Beer is a popular beverage with high molecular complexity, where research has shown a diverse range of post-translational modifications within the proteome. Proteolysis, glycation, and glycosylation were found to be prevalent, particularly in barley and yeast proteins. Brewery origin and beer styles were found to influence the glyco/proteome profile, with distinct features identified in specific beer varieties such as darker beers. The quality properties of foam formation and stability were correlated with surface-active proteins from barley and yeast.

SCIENTIFIC REPORTS (2021)

Article Plant Sciences

Global Profiling of Phosphorylation Reveals the Barley Roots Response to Phosphorus Starvation and Resupply

Zengke Ma et al.

Summary: This study reveals the phosphorylation proteins in barley roots under P starvation and resupply conditions, and their functions in various metabolic pathways. The phosphorylated proteins show significant changes under P starvation and resupply conditions, mainly participating in carbohydrate metabolism, phytohormones, signal transduction, and other metabolic processes.

FRONTIERS IN PLANT SCIENCE (2021)

Review Cell Biology

SUMOylation in Phytopathogen Interactions: Balancing Invasion and Resistance

Manisha Sharma et al.

Summary: The article discusses how post-translational modification mechanisms combat plant pathogens and the importance of SUMO in plant immunity.

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY (2021)

Review Food Science & Technology

Barley Protein Properties, Extraction and Applications, with a Focus on Brewers' Spent Grain Protein

Alice Jaeger et al.

Summary: This review discusses the importance of extracting and applying proteins from barley, particularly those from brewers' spent grain. Brewers' spent grain is a significant by-product in the brewing industry, and there is great interest in valorising and utilising its proteins.
Review Mathematical & Computational Biology

Post-translational modifications in proteins: resources, tools and prediction methods

Shahin Ramazi et al.

Summary: Posttranslational modifications (PTMs) involve modifications to amino acid side chains in proteins after biosynthesis, affecting various aspects of protein functions. Disruptions in PTMs can lead to diseases, emphasizing the need for computational methods to predict PTMs. High-throughput experimental methods for PTM discovery are laborious, prompting the exploration of computational tools and databases to advance research in this area.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2021)

Review Cell Biology

A framework for understanding the functions of biomolecular condensates across scales

Andrew S. Lyon et al.

Summary: Biomolecular condensates are membraneless molecular assemblies formed via liquid-liquid phase separation, playing important roles in controlling biochemical reactions and regulating cell organization and function throughout eukaryotic cells.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2021)

Article Biochemical Research Methods

Glycopeptide variable window SWATH for improved data independent acquisition glycoprotein analysis

Chun Zhou et al.

ANALYTICAL BIOCHEMISTRY (2020)

Review Multidisciplinary Sciences

Beyond mass spectrometry, the next step in proteomics

Winston Timp et al.

SCIENCE ADVANCES (2020)

Review Biochemical Research Methods

Use of Lectin-based Affinity Techniques in Breast Cancer Glycoproteomics: A Review

Marketa Lastovickova et al.

JOURNAL OF PROTEOME RESEARCH (2020)

Article Nutrition & Dietetics

Immunogenic Potential of Beer Types Brewed WithHordeumandTriticumspp. Malt Disclosed by Proteomics

Valentina Spada et al.

FRONTIERS IN NUTRITION (2020)

Review Biochemistry & Molecular Biology

Nucleotide Sugars in Chemistry and Biology

Satu Mikkola

MOLECULES (2020)

Article Plant Sciences

Stable Protein Sialylation in Physcomitrella

Lennard L. Bohlender et al.

FRONTIERS IN PLANT SCIENCE (2020)

Article Biochemical Research Methods

Posttranslational Modifications Drive Protein Stability to Control the Dynamic Beer Brewing Proteome

Edward D. Kerr et al.

MOLECULAR & CELLULAR PROTEOMICS (2019)

Review Biochemistry & Molecular Biology

Chemical biology approaches for studying posttranslational modifications

Aerin Yang et al.

RNA BIOLOGY (2018)

Review Biochemistry & Molecular Biology

Function of N-glycosylation in plants

Yukihiro Nagashima et al.

PLANT SCIENCE (2018)

Review Nanoscience & Nanotechnology

Paving the way to single-molecule protein sequencing

Laura Restrepo-Perez et al.

NATURE NANOTECHNOLOGY (2018)

Article Biochemical Research Methods

iTRAQ-based quantitative proteomic analysis of key barley proteins reveals changes after malting

Dana Strouhalova et al.

JOURNAL OF LIQUID CHROMATOGRAPHY & RELATED TECHNOLOGIES (2018)

Review Chemistry, Multidisciplinary

Functional protein nanostructures: a chemical toolbox

Seah Ling Kuan et al.

CHEMICAL SOCIETY REVIEWS (2018)

Article Biochemical Research Methods

Neutral Loss Is a Very Common Occurrence in Phosphotyrosine-Containing Peptides Labeled with Isobaric Tags

Robert A. Everley et al.

JOURNAL OF PROTEOME RESEARCH (2017)

Review Chemistry, Multidisciplinary

Synthesis and Applications of Boronate Affinity Materials: From Class Selectivity to Biomimetic Specificity

Zhen Liu et al.

ACCOUNTS OF CHEMICAL RESEARCH (2017)

Article Agronomy

Cereal n-glycoproteins Enrichment by Lectin Affinity Monolithic Chromatography

D. Flodrova et al.

CEREAL RESEARCH COMMUNICATIONS (2016)

Article Biochemical Research Methods

Phosphopeptide enrichment with inorganic nanofibers prepared by forcespinning technology

Jana Krenkova et al.

JOURNAL OF CHROMATOGRAPHY A (2016)

Article Biochemical Research Methods

Interactions between the Powdery Mildew Effector BEC1054 and Barley Proteins Identify Candidate Host Targets

Helen G. Pennington et al.

JOURNAL OF PROTEOME RESEARCH (2016)

Article Plant Sciences

A Role for Barley Calcium-Dependent Protein Kinase CPK2a in the Response to Drought

Agata Ciesla et al.

FRONTIERS IN PLANT SCIENCE (2016)

Review Biochemistry & Molecular Biology

Impact of Post-Translational Modifications of Crop Proteins under Abiotic Stress

Akiko Hashiguchi et al.

PROTEOMES (2016)

Review Biochemistry & Molecular Biology

Tyrosine Sulfation as a Protein Post-Translational Modification

Yuh-Shyong Yang et al.

MOLECULES (2015)

Article Agriculture, Multidisciplinary

Study of quantitative changes of cereal allergenic proteins after food processing

Dana Flodrova et al.

JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE (2015)

Review Biochemical Research Methods

Isobaric Labeling-Based Relative Quantification in Shotgun Proteomics

Navin Rauniyar et al.

JOURNAL OF PROTEOME RESEARCH (2014)

Article Biochemical Research Methods

Unusual Fragmentation Pathways in Collagen Glycopeptides

Irina Perdivara et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2013)

Review Biochemistry & Molecular Biology

Enrichment techniques employed in phosphoproteomics

Jan Fila et al.

AMINO ACIDS (2012)

Review Chemistry, Analytical

Glycopeptide enrichment and separation for protein glycosylation analysis

Sara Ongay et al.

JOURNAL OF SEPARATION SCIENCE (2012)

Review Chemistry, Analytical

Derivatization or Not: A Choice in Quantitative Proteonnics

Xudong Yao

ANALYTICAL CHEMISTRY (2011)

Review Biochemical Research Methods

Catch me if you can: Mass spectrometry-based phosphoproteomics and quantification strategies

Beate Eyrich et al.

PROTEOMICS (2011)

Article Food Science & Technology

Monitoring of malting process by characterization of glycation of barley protein Z

Janette Bobalova et al.

EUROPEAN FOOD RESEARCH AND TECHNOLOGY (2010)

Article Biochemical Research Methods

2D-HPLC and MALDI-TOF/TOF analysis of barley proteins glycated during brewing

Inga Petry-Podgorska et al.

JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES (2010)

Review Food Science & Technology

A Review: The Role of Barley Seed Pathogenesis-Related Proteins (PRs) in Beer Production

Gorjanovic Stanislava

JOURNAL OF THE INSTITUTE OF BREWING (2010)

Article Biochemical Research Methods

Divergent flow isoelectric focusing: fast and efficient method for protein sample preparation for mass spectrometry

Karel Mazanec et al.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2009)

Article Physics, Atomic, Molecular & Chemical

The combination of simple MALDI matrices for the improvement of intact glycoproteins and glycans analysis

Marketa Lastovickova et al.

INTERNATIONAL JOURNAL OF MASS SPECTROMETRY (2009)

Article Biochemical Research Methods

Multiple-Reaction Monitoring Liquid Chromatography Mass Spectrometry for Monosaccharide Compositional Analysis of Glycoproteins

Loubna A. Hammad et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2009)

Review Chemistry, Analytical

Proteolytic enzyme-immobilization techniques for MS-based protein analysis

Alex Monzo et al.

TRAC-TRENDS IN ANALYTICAL CHEMISTRY (2009)

Review Biochemistry & Molecular Biology

Chemical and Functional Aspects of Posttranslational Modification of Proteins

D. G. Knorre et al.

ACTA NATURAE (2009)

Article Biochemical Research Methods

Shotgun protein sequencing - Assembly of peptide tandem mass spectra from mixtures of modified proteins

Nuno Bandeira et al.

MOLECULAR & CELLULAR PROTEOMICS (2007)

Review Biochemical Research Methods

Modificomics: Posttranslational modifications beyond protein phosphorylation and glycosylation

Joerg Reinders et al.

BIOMOLECULAR ENGINEERING (2007)

Review Biochemistry & Molecular Biology

The road to advanced glycation end products: A mechanistic perspective

S.-J. Cho et al.

CURRENT MEDICINAL CHEMISTRY (2007)

Article Agriculture, Multidisciplinary

Stability of barley and malt lipid transfer protein 1 (LTP1) toward heating and reducing agents: Relationships with the brewing process

L Perrocheau et al.

JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY (2006)

Article Plant Sciences

Proteomics studies of post-translational modifications in plants

SJ Kwon et al.

JOURNAL OF EXPERIMENTAL BOTANY (2006)

Article Biochemical Research Methods

Multiple neutral loss monitoring (MNM): A multiplexed method for post-translational modification screening

MD Hoffman et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2006)

Article Chemistry, Analytical

Metal affinity capture tandem mass spectrometry for the selective detection of phosphopeptides

Grady R. Blacken et al.

ANALYTICAL CHEMISTRY (2006)

Review Biochemical Research Methods

Analysis of posttranslational modifications of proteins by tandem mass spectrometry

Martin R. Larsen et al.

BIOTECHNIQUES (2006)

Article Biochemical Research Methods

Ion-selective enrichment of tyro sine-sulfated peptides from complex protein digests

Y Amano et al.

ANALYTICAL BIOCHEMISTRY (2005)

Article Agriculture, Multidisciplinary

Evidence of the glycation and denaturation of LTP1 during the malting and brewing process

S Jégou et al.

JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY (2001)

Article Allergy

Isolation and characterization of barley lipid transfer protein and protein Z as beer allergens

G García-Casado et al.

JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY (2001)