Peptidomics analysis of potato protein hydrolysates: post-translational modifications and peptide hydrophobicity

2017 ◽  
Author(s):  
Shixiang Yao ◽  
Chibuike Udenigwe
Keyword(s):  
Protein Function ◽  
Structural Changes ◽  
Protein Hydrolysates ◽  
Proteolytic Processing ◽  
Methionine Oxidation ◽  
Potato Protein ◽  
Post Translational Modifications ◽  
Peptide Hydrophobicity ◽  
Proteins And Peptides

Post-translational modifications (PTMs) often <a></a><a>occur in proteins</a> and play a regulatory role in protein function. However, the role of PTMs in food-derived peptides remains largely unknown. The shotgun peptidomics strategy was employed to identify PTMs in peptides from potato protein hydrolysates. Various hydrophobicity-inducing PTMs were found to be located in different potato peptides, <i>e.g</i>. acetylation of lysine, N-terminal of proteins and peptides, C-terminal amidation, asparagine/glutamine deamidaiton, methylation and trimethylation, methionine oxidation, and N-terminal pyro-glutamate formation. Some of the PTMs are likely formed by chemical reactions that occur during isolation and proteolytic processing of potato proteins. The PTMs enhance peptide hydrophobicity, which can improve bioactivity, decrease solubility and increase the bitterness of peptides. This is the first report that food-derived peptides are widely modified by various PTMs associated with hydrophobicity-inducing structural changes. This finding will enhance understanding of the behaviour of bioactive peptides in biological matrices.

Peptidomics analysis of potato protein hydrolysates: post-translational modifications and peptide hydrophobicity

2017 ◽  
Author(s):  
Shixiang Yao ◽  
Chibuike Udenigwe
Keyword(s):  
Protein Function ◽  
Structural Changes ◽  
Protein Hydrolysates ◽  
Proteolytic Processing ◽  
Methionine Oxidation ◽  
Potato Protein ◽  
Post Translational Modifications ◽  
Peptide Hydrophobicity ◽  
Proteins And Peptides

Post-translational modifications (PTMs) often <a></a><a>occur in proteins</a> and play a regulatory role in protein function. However, the role of PTMs in food-derived peptides remains largely unknown. The shotgun peptidomics strategy was employed to identify PTMs in peptides from potato protein hydrolysates. Various hydrophobicity-inducing PTMs were found to be located in different potato peptides, <i>e.g</i>. acetylation of lysine, N-terminal of proteins and peptides, C-terminal amidation, asparagine/glutamine deamidaiton, methylation and trimethylation, methionine oxidation, and N-terminal pyro-glutamate formation. Some of the PTMs are likely formed by chemical reactions that occur during isolation and proteolytic processing of potato proteins. The PTMs enhance peptide hydrophobicity, which can improve bioactivity, decrease solubility and increase the bitterness of peptides. This is the first report that food-derived peptides are widely modified by various PTMs associated with hydrophobicity-inducing structural changes. This finding will enhance understanding of the behaviour of bioactive peptides in biological matrices.

scholarly journals Peptidomics of potato protein hydrolysates: implications of post-translational modifications in food peptide structure and behaviour

2018 ◽  
Vol 5 (7) ◽  
pp. 172425 ◽  
Author(s):  
Shixiang Yao ◽  
Chibuike C. Udenigwe
Keyword(s):  
Protein Function ◽  
Biological Activities ◽  
Chemical Properties ◽  
Peptide Structure ◽  
Aqueous Environment ◽  
Methionine Oxidation ◽  
Food Protein ◽  
Potato Protein ◽  
Post Translational Modifications ◽  
Proteins And Peptides

Post-translational modifications (PTMs) often occur in proteins and play a regulatory role in protein function. There is an increasing interest in the bioactivity of food protein-derived peptides, but the occurrence of PTMs and their influence on food peptide structure and behaviour remain largely unknown. In this study, the shotgun-based peptidomics strategy was used to identify the occurrence of PTMs in peptides generated from potato protein hydrolysis using digestive proteases. Diverse PTMs were found in the potato peptides, including acetylation of lysine, N-terminal of proteins and peptides, C-terminal amidation, de-amidation of asparagine/glutamine, methylation and trimethylation, methionine oxidation and N-terminal pyro-glutamyl residue formation. The modifications may have been formed naturally or as a result of chemical reactions during isolation and enzymatic processing of the potato proteins. Most of the PTMs were calculated to decrease the isoelectric point and increase molecular hydrophobicity of the peptides, which will influence their bioactivity while also potentially altering their solubility in an aqueous environment. This is the first study to unravel that food-derived peptides can be widely modified by PTMs associated with notable changes in peptide chemical properties. The findings have broader implications on the bioavailability, biomolecular interactions and biological activities of food peptides.

scholarly journals Post-Translational Modification-Dependent Activity of Matrix Metalloproteinases

2019 ◽  
Vol 20 (12) ◽  
pp. 3077 ◽  
Author(s):  
Elizabeta Madzharova ◽  
Philipp Kastl ◽  
Fabio Sabino ◽  
Ulrich auf dem Keller
Keyword(s):  
Matrix Metalloproteinases ◽  
Transcriptional Control ◽  
Proteolytic Processing ◽  
Post Translational Modification ◽  
Proteolytic Activation ◽  
Control Of Gene Expression ◽  
Post Translational Modifications ◽  
Binding Partners ◽  
Secreted Proteases

Due to their capacity to process different proteins of the extracellular matrix (ECM), matrix metalloproteinases (MMPs) were initially described as a family of secreted proteases, functioning as main ECM regulators. However, through proteolytic processing of various biomolecules, MMPs also modulate intra- and extracellular pathways and networks. Thereby, they are functionally implicated in the regulation of multiple physiological and pathological processes. Consequently, MMP activity is tightly regulated through a combination of epigenetic, transcriptional, and post-transcriptional control of gene expression, proteolytic activation, post-translational modifications (PTMs), and extracellular inhibition. In addition, MMPs, their substrates and ECM binding partners are frequently modified by PTMs, which suggests an important role of PTMs in modulating the pleiotropic activities of these proteases. This review summarizes the recent progress towards understanding the role of PTMs (glycosylation, phosphorylation, glycosaminoglycans) on the activity of several members of the MMP family.

scholarly journals Regulation of Protein Function by Reversible Methionine Oxidation and the Role of Selenoprotein MsrB1

2015 ◽  
Vol 23 (10) ◽  
pp. 814-822 ◽  
Author(s):  
Alaattin Kaya ◽  
Byung Cheon Lee ◽  
Vadim N. Gladyshev
Keyword(s):  
Protein Function ◽  
Methionine Oxidation

Phosphoproteomic Analysis of Spiroplasma eriocheiris and Crosstalk with Acetylome Reveals the Role of Post-Translational Modifications in Metabolism

2020 ◽  
Vol 17 (5) ◽  
pp. 392-403
Author(s):  
Peng Liu ◽  
Libo Hou ◽  
Min Liu ◽  
Xuechuan Xu ◽  
Qi Gao ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Protein Function ◽  
Regulatory Mechanism ◽  
Arginine Deiminase ◽  
Phosphorylation Sites ◽  
Post Translational Modifications ◽  
Protein Protein Interaction ◽  
Fundamental Biological Process ◽  
Cell Skeleton

Background: Post-translational modifications (PTMs) such as phosphorylation are an essential regulatory mechanism of protein function and associated with a range of biological processes beyond genome and transcriptome. Spiroplasma eriocheiris, a wall-less helical bacterium, is one of the smallest known self-replicating bacteria and a novel pathogen of freshwater crustacean. Methods: To study the physiological characteristics and regulatory mechanism of S. eriocheiris, the protein phosphorylation in the bacterium were systematically investigated by iTRAQ analyzed by LC-MS/MS. Data are available via ProteomeXchange with identifier PXD015055. Results: We identified 465 phosphorylation sites in 246 proteins involved in a broad spectrum of fundamental biological process ranging from regulation of metabolic pathways to protein synthesis. Notably, most proteins in glycolysis and all proteins in the arginine deiminase system were phosphorylated. Meanwhile, the cytoskeleton proteins (Fibril, Mrebs and ET-Tu) were all phosphorylated suggest that the phosphorylation also may play a crucial role in cell skeleton formation. We have got a lot of highly conserved proteins and phosphorylation sites by analysis, and those proteins or phosphorylation sites were mainly participated in glucose metabolism and protein synthesis. Crosstalk analysis with protein-protein interaction networks in relation to phosphorylated proteins and acetylated proteins found that the two PTMs are required for playing crucial roles in many physiological processes in S. eriocheiris. By comparing the relative positions of acetylation versus phosphorylation, we found that the two modifications often found close to proximity on the same protein. Conclusions: The results imply that there is previously unreported hidden role of phosphorylation that define the functional state of Spiroplasma.

PROTEIN DYNAMICS IN PHOSPHORYLATION-MEDIATED ALLOSTERY PROBED BY AMIDE EXCHANGE MASS SPECTROMETRY

COSMOS ◽  
2013 ◽  
Vol 09 (01) ◽  
pp. 19-27
Author(s):  
MADHUBRATA GHOSH ◽  
GANESH S. ANAND
Keyword(s):  
Mass Spectrometry ◽  
Protein Dynamics ◽  
Protein Function ◽  
Post Translational Modifications ◽  
Exchange Mass Spectrometry ◽  
Amide Exchange ◽  
Hydrogen Deuterium ◽  
Deuterium Exchange Mass Spectrometry ◽  
And Function

A major goal of molecular biology is to correlate molecular structure with function. Since most enzymes and biological catalysts are proteins, the focus for correlating 'form' with 'function' has been entirely on protein macromolecular structure. It is obvious that any understanding of protein function must come through an understanding protein dynamics. Furthermore, all of the regulatory reactions are through changes in dynamics brought about by post-translational modifications, the most important of which is phosphorylation. This review highlights the important role of covalent phosphorylation and noncovalent phosphates in regulating allosteric effects and function through a study of protein dynamics. Mass spectrometry is a relatively new and increasingly important tool for describing protein dynamics. All examples described in this review have been studied by amide hydrogen/deuterium exchange mass spectrometry.

scholarly journals AML1/ETO and its function as a regulator of gene transcription via epigenetic mechanisms

Oncogene ◽  
2021 ◽  
Author(s):  
Kai Rejeski ◽  
Jesús Duque-Afonso ◽  
Michael Lübbert
Keyword(s):  
Gene Transcription ◽  
Protein Function ◽  
Structural Changes ◽  
Target Genes ◽  
Chromosomal Translocation ◽  
Global Changes ◽  
Cellular Processes ◽  
Genetic Landscape ◽  
Specific Impact

AbstractThe chromosomal translocation t(8;21) and the resulting oncofusion gene AML1/ETO have long served as a prototypical genetic lesion to model and understand leukemogenesis. In this review, we describe the wide-ranging role of AML1/ETO in AML leukemogenesis, with a particular focus on the aberrant epigenetic regulation of gene transcription driven by this AML-defining mutation. We begin by analyzing how structural changes secondary to distinct genomic breakpoints and splice changes, as well as posttranscriptional modifications, influence AML1/ETO protein function. Next, we characterize how AML1/ETO recruits chromatin-modifying enzymes to target genes and how the oncofusion protein alters chromatin marks, transcription factor binding, and gene expression. We explore the specific impact of these global changes in the epigenetic network facilitated by the AML1/ETO oncofusion on cellular processes and leukemic growth. Furthermore, we define the genetic landscape of AML1/ETO-positive AML, presenting the current literature concerning the incidence of cooperating mutations in genes such as KIT, FLT3, and NRAS. Finally, we outline how alterations in transcriptional regulation patterns create potential vulnerabilities that may be exploited by epigenetically active agents and other therapeutics.

scholarly journals Unstructured Conformations Are a Substrate Requirement for the Sir2 Family of NAD-dependent Protein Deacetylases

2005 ◽  
Vol 280 (43) ◽  
pp. 36073-36078 ◽  
Author(s):  
Ahlia N. Khan ◽  
Peter N. Lewis
Keyword(s):  
Protein Function ◽  
Cellular Localization ◽  
Substrate Recognition ◽  
Histone Deacetylation ◽  
Sequence Specificity ◽  
Post Translational Modifications ◽  
Protein Substrates ◽  
Dependent Protein

The regulation of protein function is often achieved through post-translational modifications including phosphorylation, methylation, ubiquitination, and acetylation. The role of acetylation has been most extensively studied in the context of histones, but it is becoming increasingly evident that this modification now includes other proteins. The Sir2 family of NAD-dependent deacetylases was initially recognized as mediating gene silencing through histone deacetylation, but several family members display non-nuclear sub-cellular localization and deacetylate non-histone protein substrates. Although many structural and enzymatic studies of Sir2 proteins have been reported, how substrate recognition is achieved by this family of enzymes is unknown. Here we use in vitro deacetylase assays and a variety of potential substrates to examine the substrate specificity of yeast homologue Hst2. We show that Hst2 is specific for acetyl-lysine within proteins; it does not deacetylate small polycations such as acetyl-spermine or acetylated amino ter-mini of proteins. Furthermore we have found that Hst2 displays conformational rather than sequence specificity, preferentially deacetylating acetyl-lysine within unstructured regions of proteins. Our results suggest that this conformational requirement may be a general feature for substrate recognition in the Sir2 family.

scholarly journals Quantitative Proteomics and Phosphoproteomics Supports a Role for Mut9-Like Kinases in Multiple Metabolic and Signaling Pathways in Arabidopsis

2020 ◽  
Author(s):  
Margaret E. Wilson ◽  
Shin-Cheng Tzeng ◽  
Megan M. Augustin ◽  
Matthew Meyer ◽  
Xiaoyue Jiang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Protein Function ◽  
Response Factors ◽  
Post Translational Modifications ◽  
Dna Damaging Agents ◽  
Metabolism Enzymes ◽  
Damage Response ◽  
Increased Sensitivity ◽  
Work Supports

Summary/AbstractProtein phosphorylation is one of the most prevalent post-translational modifications found in eukaryotic systems. It serves as a key molecular mechanism that regulates protein function in response to environmental stimuli. The Mut9-Like Kinases (MLKs) are a plant-specific family of Ser/Thr kinases linked to light, circadian, and abiotic stress signaling. Here we use quantitative phosphoproteomics in conjunction with global proteomic analysis to explore the role of the MLKs in daily protein dynamics. Proteins involved in light, circadian, and hormone signaling, as well as several chromatin-modifying enzymes and DNA damage response factors, were found to have altered phosphorylation profiles in the absence of MLK family kinases. In addition to altered phosphorylation levels, mlk mutant seedlings have an increase in glucosinolate metabolism enzymes. Subsequently, we show that a functional consequence of the changes to the proteome and phosphoproteome in mlk mutant plants is elevated glucosinolate accumulation, and increased sensitivity to DNA damaging agents. Combined with previous reports, this work supports the involvement of MLKs in a diverse set of stress responses and developmental processes, suggesting that the MLKs serve as key regulators linking environmental inputs to developmental outputs.

Reading the phosphorylation code: binding of the 14-3-3 protein to multivalent client phosphoproteins

2020 ◽  
Vol 477 (7) ◽  
pp. 1219-1225 ◽  
Author(s):  
Nikolai N. Sluchanko
Keyword(s):  
Protein Function ◽  
Intrinsically Disordered Protein ◽  
Structural Basis ◽  
Major Protein ◽  
Post Translational Modifications ◽  
Protein Protein Interaction ◽  
Intrinsically Disordered ◽  
Biochemical Journal ◽  
Multiple Binding ◽  
And Control

Many major protein–protein interaction networks are maintained by ‘hub’ proteins with multiple binding partners, where interactions are often facilitated by intrinsically disordered protein regions that undergo post-translational modifications, such as phosphorylation. Phosphorylation can directly affect protein function and control recognition by proteins that ‘read’ the phosphorylation code, re-wiring the interactome. The eukaryotic 14-3-3 proteins recognizing multiple phosphoproteins nicely exemplify these concepts. Although recent studies established the biochemical and structural basis for the interaction of the 14-3-3 dimers with several phosphorylated clients, understanding their assembly with partners phosphorylated at multiple sites represents a challenge. Suboptimal sequence context around the phosphorylated residue may reduce binding affinity, resulting in quantitative differences for distinct phosphorylation sites, making hierarchy and priority in their binding rather uncertain. Recently, Stevers et al. [Biochemical Journal (2017) 474: 1273–1287] undertook a remarkable attempt to untangle the mechanism of 14-3-3 dimer binding to leucine-rich repeat kinase 2 (LRRK2) that contains multiple candidate 14-3-3-binding sites and is mutated in Parkinson's disease. By using the protein-peptide binding approach, the authors systematically analyzed affinities for a set of LRRK2 phosphopeptides, alone or in combination, to a 14-3-3 protein and determined crystal structures for 14-3-3 complexes with selected phosphopeptides. This study addresses a long-standing question in the 14-3-3 biology, unearthing a range of important details that are relevant for understanding binding mechanisms of other polyvalent proteins.

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