Article Commentary: Regulation of Protein Function by Residue Oxidation

2010 ◽  
Vol 3 ◽  
pp. PRI.S3327 ◽  
Author(s):  
Xing-Hai Zhang
Keyword(s):  
Protein Function ◽  
Regulatory Mechanism ◽  
Cellular Metabolism ◽  
Life Forms ◽  
Biological Macromolecules ◽  
Oxygen Species ◽  
Cellular Processes ◽  
Methionine Residues ◽  
Living Organisms ◽  
Face Generation

A majority of extant life forms require O2 to survive and thrive. Oxidation is inevitably one of the most active cellular processes and one constant challenge that living organisms must face. Generation of oxidants including reactive oxygen species is a natural consequence of cellular metabolism of all biological systems during normal life cycle under different environments. These oxidants oxidize many biological macromolecules such as proteins and affect their functions. Oxidation of specific amino acids in proteins may cause damage to protein structure and impair function, or may also activate protein activities and promote cellular metabolism. As an example, the reversible oxidation of cysteine and methionine residues has a profound impact on protein function and cellular process. A recent study that examines the effect of Met oxidation on Ser phosphorylation in a mitochondrial enzyme, pyruvate dehydrogenase, provides another demonstration that protein oxidation is an important regulatory mechanism for organisms to deal with developmental and environmental challenges throughout life processes.

scholarly journals PGC1s and Beyond: Disentangling the Complex Regulation of Mitochondrial and Cellular Metabolism

2021 ◽  
Vol 22 (13) ◽  
pp. 6913
Author(s):  
Lara Coppi ◽  
Simona Ligorio ◽  
Nico Mitro ◽  
Donatella Caruso ◽  
Emma De Fabiani ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Metabolic Regulation ◽  
Cellular Metabolism ◽  
Building Blocks ◽  
Peroxisome Proliferator ◽  
Peroxisome Proliferator Activated Receptor ◽  
Main Site ◽  
Cellular Processes ◽  
Essential Components ◽  
Living Organisms

Metabolism is the central engine of living organisms as it provides energy and building blocks for many essential components of each cell, which are required for specific functions in different tissues. Mitochondria are the main site for energy production in living organisms and they also provide intermediate metabolites required for the synthesis of other biologically relevant molecules. Such cellular processes are finely tuned at different levels, including allosteric regulation, posttranslational modifications, and transcription of genes encoding key proteins in metabolic pathways. Peroxisome proliferator activated receptor γ coactivator 1 (PGC1) proteins are transcriptional coactivators involved in the regulation of many cellular processes, mostly ascribable to metabolic pathways. Here, we will discuss some aspects of the cellular processes regulated by PGC1s, bringing up some examples of their role in mitochondrial and cellular metabolism, and how metabolic regulation in mitochondria by members of the PGC1 family affects the immune system. We will analyze how PGC1 proteins are regulated at the transcriptional and posttranslational level and will also examine other regulators of mitochondrial metabolism and the related cellular functions, considering approaches to identify novel mitochondrial regulators and their role in physiology and disease. Finally, we will analyze possible therapeutical perspectives currently under assessment that are applicable to different disease states.

scholarly journals Oxidative Stress in Bacteria and the Central Dogma of Molecular Biology

2021 ◽  
Vol 8 ◽  
Author(s):  
Michel Fasnacht ◽  
Norbert Polacek
Keyword(s):  
Oxidative Stress ◽  
Reactive Oxygen Species ◽  
Molecular Biology ◽  
Reactive Oxygen ◽  
Cellular Metabolism ◽  
Life Forms ◽  
Oxygen Species ◽  
Central Dogma ◽  
Great Oxidation Event ◽  
Cellular Life

Ever since the “great oxidation event,” Earth’s cellular life forms had to cope with the danger of reactive oxygen species (ROS) affecting the integrity of biomolecules and hampering cellular metabolism circuits. Consequently, increasing ROS levels in the biosphere represented growing stress levels and thus shaped the evolution of species. Whether the ROS were produced endogenously or exogenously, different systems evolved to remove the ROS and repair the damage they inflicted. If ROS outweigh the cell’s capacity to remove the threat, we speak of oxidative stress. The injuries through oxidative stress in cells are diverse. This article reviews the damage oxidative stress imposes on the different steps of the central dogma of molecular biology in bacteria, focusing in particular on the RNA machines involved in transcription and translation.

Epigenetic Mechanisms of Maternal Dietary Protein and Amino Acids Affecting Growth and Development of Offspring

2019 ◽  
Vol 20 (7) ◽  
pp. 727-735 ◽  
Author(s):  
Yi Wu ◽  
Zhibin Cheng ◽  
Yueyu Bai ◽  
Xi Ma
Keyword(s):  
Amino Acids ◽  
Dna Methylation ◽  
Dietary Protein ◽  
Growth And Development ◽  
Later Life ◽  
Biological Macromolecules ◽  
Epigenetic Mechanisms ◽  
Maternal Circulation ◽  
Energy Processing ◽  
Living Organisms

Nutrients can regulate metabolic activities of living organisms through epigenetic mechanisms, including DNA methylation, histone modification, and RNA regulation. Since the nutrients required for early embryos and postpartum lactation are derived in whole or in part from maternal and lactating nutrition, the maternal nutritional level affects the growth and development of fetus and creates a profound relationship between disease development and early environmental exposure in the offspring’s later life. Protein is one of the most important biological macromolecules, involved in almost every process of life, such as information transmission, energy processing and material metabolism. Maternal protein intake levels may affect the integrity of the fetal genome and alter DNA methylation and gene expression. Most amino acids are supplied to the fetus from the maternal circulation through active transport of placenta. Some amino acids, such as methionine, as dietary methyl donor, play an important role in DNA methylation and body’s one-carbon metabolism. The purpose of this review is to describe effects of maternal dietary protein and amino acid intake on fetal and neonatal growth and development through epigenetic mechanisms, with examples in humans and animals.

scholarly journals Redox Regulation of Lipid Mobilization in Adipose Tissues

Antioxidants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1090
Author(s):  
Ursula Abou-Rjeileh ◽  
G. Andres Contreras
Keyword(s):  
Adipose Tissue ◽  
Energy Metabolism ◽  
Redox Regulation ◽  
Cellular Metabolism ◽  
Antioxidant Response ◽  
Redox Signaling ◽  
Nitrogen Species ◽  
Adipose Tissues ◽  
Lipid Mobilization ◽  
Cellular Processes

Lipid mobilization in adipose tissues, which includes lipogenesis and lipolysis, is a paramount process in regulating systemic energy metabolism. Reactive oxygen and nitrogen species (ROS and RNS) are byproducts of cellular metabolism that exert signaling functions in several cellular processes, including lipolysis and lipogenesis. During lipolysis, the adipose tissue generates ROS and RNS and thus requires a robust antioxidant response to maintain tight regulation of redox signaling. This review will discuss the production of ROS and RNS within the adipose tissue, their role in regulating lipolysis and lipogenesis, and the implications of antioxidants on lipid mobilization.

scholarly journals Upconversion-based nanosystems for fluorescence sensing of pH and H2O2

2021 ◽  
Author(s):  
Chunning Sun ◽  
Michael Gradzielski
Keyword(s):  
Reactive Oxygen Species ◽  
Hydrogen Peroxide ◽  
Excitation Energy ◽  
Reactive Oxygen ◽  
Oxygen Species ◽  
Fluorescence Sensing ◽  
Living Organisms

Hydrogen peroxide (H2O2), a key reactive oxygen species, plays an important role in living organisms, industrial and environmental fields. Here, a non-contact upconversion nanosystem based on the excitation energy attenuation...

Development of manganese dioxide-based nanoprobe for fluorescent detection and imaging of glutathione

2021 ◽  
Author(s):  
Ali Qaitoon ◽  
Jiaxi Yong ◽  
Zexi Zhang ◽  
Jie Liu ◽  
Zhi Ping Xu ◽  
...  
Keyword(s):  
Manganese Dioxide ◽  
Fluorescent Detection ◽  
Cellular Processes ◽  
Living Organisms

Tripeptide glutathione (GSH) is an abundant and ubiquitous metabolite in living organisms and plays critical roles in various cellular processes. In this work, we report the development of a new...

scholarly journals Effect of Flotation Time and Collector Dosage on Estonian Phosphorite Beneficiation

Minerals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 114
Author(s):  
Kadriann Tamm ◽  
Zeinab Arab Zadeh ◽  
Rein Kuusik ◽  
Juha Kallas ◽  
Jason Yang ◽  
...  
Keyword(s):  
Phosphate Rock ◽  
Froth Flotation ◽  
Fine Fraction ◽  
The European Union ◽  
High Recovery ◽  
Know How ◽  
Cellular Processes ◽  
Reliable Source ◽  
Living Organisms ◽  
The Relationship

Phosphorus is an essential and non-substitutable element for the cellular processes of all living organisms. The main source of phosphorus in the biosphere is phosphate rock. With more than 700 Mt phosphate rock, Estonia holds the largest sedimentary phosphate rock deposits in the European Union. Estonian phosphate rock is particularly outstanding due to its remarkably low content of hazardous heavy metals such as Cadmium (<5 ppm) and trace elements of Uranium (<50 ppm). It is also a reliable source of valuable elements such as rear earth elements (REEs). The aim of this study was to investigate the distribution of the main minerals (apatite and quartz) between slimes, tailings, and concentrates that formed at the froth flotation of Estonian phosphate rock with the up-to-date level of know-how and techniques. Subsequently, the relationship between the obtained grades and recovery levels in concentrates was determined based on the collector dosage and flotation duration. It was observed that the fine fraction of the tailings contains 17.9–33.49 wt% P2O5 that can be added to the final product. Moreover, it was found that, with the lower dosage of the collector, the extended flotation time does not influence the phosphate grade and a high amount of quartz remains in the concentrates. It was also shown that, by raising the collector dosage and setting the flotation time, an adequate grade (>32 wt% P2O5) and recovery (up to 98%) can be gained. The results showed that Estonian phosphate rock can be beneficiated to produce a high-quality concentrate at high recovery levels by modifying the main flotation parameters depending on the properties of the ore.

scholarly journals The signalling role of ROS in the regulation of seed germination and dormancy

2019 ◽  
Vol 476 (20) ◽  
pp. 3019-3032 ◽  
Author(s):  
Christophe Bailly
Keyword(s):  
Seed Germination ◽  
Oxygen Species ◽  
Direct Oxidation ◽  
Cellular Events ◽  
Seed Physiology ◽  
Spatiotemporal Regulation ◽  
Wide Range ◽  
Living Organisms ◽  
Hormone Signalling

Abstract Reactive oxygen species (ROS) are versatile compounds which can have toxic or signalling effects in a wide range living organisms, including seeds. They have been reported to play a pivotal role in the regulation of seed germination and dormancy but their mechanisms of action are still far from being fully understood. In this review, we sum-up the major findings that have been carried out this last decade in this field of research and which altogether shed a new light on the signalling roles of ROS in seed physiology. ROS participate in dormancy release during seed dry storage through the direct oxidation of a subset of biomolecules. During seed imbibition, the controlled generation of ROS is involved in the perception and transduction of environmental conditions that control germination. When these conditions are permissive for germination, ROS levels are maintained at a level which triggers cellular events associated with germination, such as hormone signalling. Here we propose that the spatiotemporal regulation of ROS production acts in concert with hormone signalling to regulate the cellular events involved in cell expansion associated with germination.

scholarly journals Analysis of site and structure specific core fucosylation in liver disease progression using exoglycosidase-assisted data-independent LC-MS/MS

2020 ◽  
Author(s):  
Miloslav Sanda ◽  
Jaeil Ahn ◽  
Petr Kozlik ◽  
Radoslav Goldman
Keyword(s):  
Liver Disease ◽  
Disease Progression ◽  
Serum Proteins ◽  
Receptor Activation ◽  
Biological Macromolecules ◽  
The Core ◽  
Liver Disease Progression ◽  
Living Organisms ◽  
Protein Attachment ◽  
Core Fucosylation

ABSTRACTCarbohydrates form one of the major groups of biological macromolecules in living organisms. Many biological processes including protein folding, stability, immune response, and receptor activation are regulated by glycosylation. Fucosylation of proteins regulates such processes and is associated with various diseases including autoimmunity and cancer. Mass spectrometry efficiently identifies structures of fucosylated glycans or sites of core fucosylated N-glycopeptides but quantification of the glycopeptides remains less explored. We performed experiments that facilitate quantitative analysis of the core fucosylation of proteins with partial structural resolution of the glycans and we present results of the mass spectrometric SWATH-type DIA analysis of relative abundances of the core fucosylated glycoforms of 45 glycopeptides derived from 18 serum proteins in liver disease of different etiologies. Our results show that a combination of soft fragmentation with exoglycosidases is efficient at the assignment and quantification of the core fucosylated N-glycoforms at specific sites of protein attachment. In addition, our results show that disease-associated changes in core fucosylation are peptide-dependent and further differ by branching of the core fucosylated glycans. Further studies are needed to verify whether tri- and tetra-antennary core fucosylated glycopeptides could be used as markers of liver disease progression.

scholarly journals Breaking the next Cryo-EM resolution barrier – Atomic resolution determination of proteins!

2020 ◽  
Author(s):  
Ka Man Yip ◽  
Niels Fischer ◽  
Elham Paknia ◽  
Ashwin Chari ◽  
Holger Stark
Keyword(s):  
Protein Function ◽  
Model Building ◽  
Technological Development ◽  
Drug Binding ◽  
Single Atom ◽  
Biological Macromolecules ◽  
Direct Visualization ◽  
Hydrogen Atoms ◽  
Structure Based Drug Design ◽  
Electron Microscopes

SummarySingle particle cryo-EM is a powerful method to solve the three-dimensional structures of biological macromolecules. The technological development of electron microscopes, detectors, automated procedures in combination with user friendly image processing software and ever-increasing computational power have made cryo-EM a successful and largely expanding technology over the last decade. At resolutions better than 4 Å, atomic model building starts becoming possible but the direct visualization of true atomic positions in protein structure determination requires significantly higher (< 1.5 Å) resolution, which so far could not be attained by cryo-EM. The direct visualization of atom positions is essential for understanding protein-catalyzed chemical reaction mechanisms and to study drug-binding and -interference with protein function. Here we report a 1.25 Å resolution structure of apoferritin obtained by cryo-EM with a newly developed electron microscope providing unprecedented structural details. Our apoferritin structure has almost twice the 3D information content of the current world record reconstruction (at 1.54 Å resolution 1). For the first time in cryo-EM we can visualize individual atoms in a protein, see density for hydrogen atoms and single atom chemical modifications. Beyond the nominal improvement in resolution we can also show a significant improvement in quality of the cryo-EM density map which is highly relevant for using cryo-EM in structure-based drug design.

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