Expanding the genetic code to study metalloproteins and protein posttranslational modifications

2015 ◽  
Keyword(s):  
Genetic Code ◽  
Posttranslational Modifications ◽  
Protein Posttranslational Modifications

scholarly journals E3 ligase Nedd4l promotes antiviral innate immunity by catalyzing K29-linked cysteine ubiquitination of TRAF3

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Peng Gao ◽  
Xianwei Ma ◽  
Ming Yuan ◽  
Yulan Yi ◽  
Guoke Liu ◽  
...  
Keyword(s):  
Posttranslational Modifications ◽  
Type I Interferon ◽  
Zinc Fingers ◽  
E3 Ligase ◽  
Type I ◽  
E3 Ligases ◽  
Protein Posttranslational Modifications ◽  
Antiviral Innate Immunity

AbstractUbiquitination is one of the most prevalent protein posttranslational modifications. Here, we show that E3 ligase Nedd4l positively regulates antiviral immunity by catalyzing K29-linked cysteine ubiquitination of TRAF3. Deficiency of Nedd4l significantly impairs type I interferon and proinflammatory cytokine production induced by virus infection both in vitro and in vivo. Nedd4l deficiency inhibits virus-induced ubiquitination of TRAF3, the binding between TRAF3 and TBK1, and subsequent phosphorylation of TBK1 and IRF3. Nedd4l directly interacts with TRAF3 and catalyzes K29-linked ubiquitination of Cys56 and Cys124, two cysteines that constitute zinc fingers, resulting in enhanced association between TRAF3 and E3 ligases, cIAP1/2 and HECTD3, and also increased K48/K63-linked ubiquitination of TRAF3. Mutation of Cys56 and Cys124 diminishes Nedd4l-catalyzed K29-linked ubiquitination, but enhances association between TRAF3 and the E3 ligases, supporting Nedd4l promotes type I interferon production in response to virus by catalyzing ubiquitination of the cysteines in TRAF3.

Targeted proteomics of myofilament phosphorylation and other protein posttranslational modifications

2014 ◽  
Vol 8 (7-8) ◽  
pp. 543-553 ◽  
Author(s):  
Genaro A. Ramirez-Correa ◽  
Maria Isabel Martinez-Ferrando ◽  
Pingbo Zhang ◽  
Anne M. Murphy
Keyword(s):  
Posttranslational Modifications ◽  
Targeted Proteomics ◽  
Protein Posttranslational Modifications

scholarly journals Landscapes of Protein Posttranslational Modifications of African Trypanosoma Parasites

iScience ◽  
2020 ◽  
Vol 23 (5) ◽  
pp. 101074 ◽  
Author(s):  
Naiwen Zhang ◽  
Ning Jiang ◽  
Kai Zhang ◽  
Lili Zheng ◽  
Di Zhang ◽  
...  
Keyword(s):  
Posttranslational Modifications ◽  
Protein Posttranslational Modifications

scholarly journals Genetic Code Expansion: A Powerful Tool for Understanding the Physiological Consequences of Oxidative Stress Protein Modifications

2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Joseph J. Porter ◽  
Ryan A. Mehl
Keyword(s):  
Oxidative Stress ◽  
Genetic Code ◽  
Posttranslational Modifications ◽  
Stress Protein ◽  
Physiological Effects ◽  
The Past ◽  
Arduous Task ◽  
Therapeutic Development ◽  
Genetic Code Expansion ◽  
Antibody Validation

Posttranslational modifications resulting from oxidation of proteins (Ox-PTMs) are present intracellularly under conditions of oxidative stress as well as basal conditions. In the past, these modifications were thought to be generic protein damage, but it has become increasingly clear that Ox-PTMs can have specific physiological effects. It is an arduous task to distinguish between the two cases, as multiple Ox-PTMs occur simultaneously on the same protein, convoluting analysis. Genetic code expansion (GCE) has emerged as a powerful tool to overcome this challenge as it allows for the site-specific incorporation of an Ox-PTM into translated protein. The resulting homogeneously modified protein products can then be rigorously characterized for the effects of individual Ox-PTMs. We outline the strengths and weaknesses of GCE as they relate to the field of oxidative stress and Ox-PTMs. An overview of the Ox-PTMs that have been genetically encoded and applications of GCE to the study of Ox-PTMs, including antibody validation and therapeutic development, is described.

scholarly journals A Multifeatures Fusion and Discrete Firefly Optimization Method for Prediction of Protein Tyrosine Sulfation Residues

2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Song Guo ◽  
Chunhua Liu ◽  
Peng Zhou ◽  
Yanling Li
Keyword(s):  
Feature Selection ◽  
Posttranslational Modifications ◽  
Optimization Method ◽  
Tyrosine Sulfation ◽  
Selection Scheme ◽  
Protein Tyrosine ◽  
Research Fields ◽  
Physiological Processes ◽  
Novel Method ◽  
Protein Posttranslational Modifications

Tyrosine sulfation is one of the ubiquitous protein posttranslational modifications, where some sulfate groups are added to the tyrosine residues. It plays significant roles in various physiological processes in eukaryotic cells. To explore the molecular mechanism of tyrosine sulfation, one of the prerequisites is to correctly identify possible protein tyrosine sulfation residues. In this paper, a novel method was presented to predict protein tyrosine sulfation residues from primary sequences. By means of informative feature construction and elaborate feature selection and parameter optimization scheme, the proposed predictor achieved promising results and outperformed many other state-of-the-art predictors. Using the optimal features subset, the proposed method achieved mean MCC of 94.41% on the benchmark dataset, and a MCC of 90.09% on the independent dataset. The experimental performance indicated that our new proposed method could be effective in identifying the important protein posttranslational modifications and the feature selection scheme would be powerful in protein functional residues prediction research fields.

scholarly journals Protein Posttranslational Modifications: Roles in Aging and Age-Related Disease

2017 ◽  
Vol 2017 ◽  
pp. 1-19 ◽  
Author(s):  
Ana L. Santos ◽  
Ariel B. Lindner
Keyword(s):  
Posttranslational Modifications ◽  
Molecular Mechanisms ◽  
Molecular Processes ◽  
Progressive Decline ◽  
Age Related ◽  
Evolutionarily Conserved ◽  
Protein Posttranslational Modifications ◽  
Aging Models ◽  
The Relationship

Aging is characterized by the progressive decline of biochemical and physiological function in an individual. Consequently, aging is a major risk factor for diseases like cancer, obesity, and type 2 diabetes. The cellular and molecular mechanisms of aging are not well understood, nor is the relationship between aging and the onset of diseases. One of the hallmarks of aging is a decrease in cellular proteome homeostasis, allowing abnormal proteins to accumulate. This phenomenon is observed in both eukaryotes and prokaryotes, suggesting that the underlying molecular processes are evolutionarily conserved. Similar protein aggregation occurs in the pathogenesis of diseases like Alzheimer’s and Parkinson’s. Further, protein posttranslational modifications (PTMs), either spontaneous or physiological/pathological, are emerging as important markers of aging and aging-related diseases, though clear causality has not yet been firmly established. This review presents an overview of the interplay of PTMs in aging-associated molecular processes in eukaryotic aging models. Understanding PTM roles in aging could facilitate targeted therapies or interventions for age-related diseases. In addition, the study of PTMs in prokaryotes is highlighted, revealing the potential of simple prokaryotic models to uncover complex aging-associated molecular processes in the emerging field of microbiogerontology.

Protein Posttranslational Modifications: The Chemistry of Proteome Diversifications

ChemInform ◽  
2006 ◽  
Vol 37 (7) ◽  
Author(s):  
Christopher T. Walsh ◽  
Sylvie Garneau-Tsodikova ◽  
Gregory J. Jr. Gatto
Keyword(s):  
Posttranslational Modifications ◽  
Protein Posttranslational Modifications

Quantification of protein posttranslational modifications using stable isotope and mass spectrometry. II. Performance

2012 ◽  
Vol 421 (2) ◽  
pp. 517-525 ◽  
Author(s):  
Quanzhou Luo ◽  
Jette Wypych ◽  
Xinzhao Grace Jiang ◽  
Xin Zhang ◽  
Shun Luo ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Stable Isotope ◽  
Posttranslational Modifications ◽  
Protein Posttranslational Modifications
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