The importance of post-translational modifications in systems biology approaches to identify therapeutic targets in cancer metabolism

Martín-Bernabé, Alfonso; Balcells, Cristina; Tarragó-Celada, Josep; Foguet, Carles; Bourgoin-Voillard, Sandrine; Sève, Michel; Cascante, Marta

doi:10.1016/j.coisb.2017.05.011

Cited by 10 publications

(11 citation statements)

References 59 publications

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“…Direct regulation of enzymes with diverse mechanisms is typically accomplished through the dynamic utilization of PTMs. Signal transducers responsible for the mobility of PTMs are guided the same way, thus, balancing and driving the comprehensive network of intracellular signal exchange in response to internal and external stimuli [11]. Generally, identification of a specific PTM or, more commonly, their profile in a large-scale proteomic study is purposed to associate them with pathophysiological mechanisms [12].…”

Section: Introductionmentioning

confidence: 99%

“…Generally, identification of a specific PTM or, more commonly, their profile in a large-scale proteomic study is purposed to associate them with pathophysiological mechanisms [12]. Dysfunction of phosphorylation makes the most pronounced input in cancer initiation and development since kinases and phosphatases inflect proteins function to provide the capability for the regulation of signals transduction [11].…”

Section: Introductionmentioning

confidence: 99%

“…The duet of lysine acetyltransferases and deacetylases delivers an acetyl group from acetyl-CoA to ε-N-lysine of proteins, thereby providing regulation of DNA replication and transcription through modification of histones as the most well-characterized process, but it may also impact on other proteins to perform their activities [11].…”

Section: Introductionmentioning

confidence: 99%

“…Regulation of protein uptake is generally accomplished through the attachment of the short ubiquitin moiety to ε-N-lysine residues. Recent reports demonstrated that malfunctioning of ubiquitination at any stage (transferring and ligation) may play a critical role in cells' metabolic reprogramming and trigger cancer development [11].…”

Section: Introductionmentioning

confidence: 99%

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Super Secondary Structures of Proteins with Post-Translational Modifications in Colon Cancer

et al. 2020

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New advances in protein post-translational modifications (PTMs) have revealed a complex layer of regulatory mechanisms through which PTMs control cell signaling and metabolic pathways, contributing to the diverse metabolic phenotypes found in cancer. Using conformational templates and the three-dimensional (3D) environment investigation of proteins in patients with colorectal cancer, it was demonstrated that most PTMs (phosphorylation, acetylation, and ubiquitination) are localized in the supersecondary structures (helical pairs). We showed that such helical pairs are represented on the outer surface of protein molecules and characterized by a largely accessible area for the surrounding solvent. Most promising and meaningful modifications were observed on the surface of vitamin D-binding protein (VDBP), complement C4-A (CO4A), X-ray repair cross-complementing protein 6 (XRCC6), Plasma protease C1 inhibitor (IC1), and albumin (ALBU), which are related to colorectal cancer developing. Based on the presented data, we propose the impact of the observed modifications in immune response, inflammatory reaction, regulation of cell migration, and promotion of tumor growth. Here, we suggest a computational approach in which high-throughput analysis for identification and characterization of PTM signature, associated with cancer metabolic reprograming, can be improved to prognostic value and bring a new strategy to the targeted therapy.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Super Secondary Structures of Proteins with Post-Translational Modifications in Colon Cancer

et al. 2020

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“…Currently, the well-resolved PTMs in cells include acetylation of protein N-terminal and lysine (Lys) residues [ 13 ], methionine (Met) oxidation [ 14 ], and methylation of Lys and arginine (Arg) residues [ 15 ]. The PTMs and their relevant biological functions have also been extensively studied in cells [ 11 , 16 ]. Moreover, we recently reported that food protein-derived peptides can be modified by Met oxidation and asparagine (Asn)/glutamine (Gln) de-amidation during isolation and enzymatic hydrolysis with pepsin [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

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

Yao

Udenigwe

2018

R. Soc. open sci.

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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.

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The language of posttranslational modifications and deciphering it from proteomics data

Aggarwal

Gupta

Dhawan

et al. 2023

Transcription and Translation in Health and Disease

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The importance of post-translational modifications in systems biology approaches to identify therapeutic targets in cancer metabolism

Cited by 10 publications

References 59 publications

Super Secondary Structures of Proteins with Post-Translational Modifications in Colon Cancer

Super Secondary Structures of Proteins with Post-Translational Modifications in Colon Cancer

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

The language of posttranslational modifications and deciphering it from proteomics data

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