Biochemical reactions in metabolite-protein interaction

Wang, Wen; Tekcham, Dinesh Singh; Yan, Min; Wang, Zhichao; Qi, Huan; Liu, Xiaolong; Piao, Hulin

doi:10.1016/j.cclet.2017.10.002

Cited by 10 publications

(4 citation statements)

References 14 publications

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“…The immobilization of small molecules can affect both the affinity and specificity of the interaction, so AC/AP is limited to studying only a handful of stable interactions. Most of the weak noncovalent interactions are destroyed during affinity purification [ 59 ]. Another problem with this approach is a relatively high rate of false positive results.…”

Section: Strategies For Pmi Studiesmentioning

confidence: 99%

The Knowns and Unknowns in Protein–Metabolite Interactions

Kurbatov

Dolgalev

Arzumanian

et al. 2023

IJMS

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Increasing attention has been focused on the study of protein–metabolite interactions (PMI), which play a key role in regulating protein functions and directing an orchestra of cellular processes. The investigation of PMIs is complicated by the fact that many such interactions are extremely short-lived, which requires very high resolution in order to detect them. As in the case of protein–protein interactions, protein–metabolite interactions are still not clearly defined. Existing assays for detecting protein–metabolite interactions have an additional limitation in the form of a limited capacity to identify interacting metabolites. Thus, although recent advances in mass spectrometry allow the routine identification and quantification of thousands of proteins and metabolites today, they still need to be improved to provide a complete inventory of biological molecules, as well as all interactions between them. Multiomic studies aimed at deciphering the implementation of genetic information often end with the analysis of changes in metabolic pathways, as they constitute one of the most informative phenotypic layers. In this approach, the quantity and quality of knowledge about PMIs become vital to establishing the full scope of crosstalk between the proteome and the metabolome in a biological object of interest. In this review, we analyze the current state of investigation into the detection and annotation of protein–metabolite interactions, describe the recent progress in developing associated research methods, and attempt to deconstruct the very term “interaction” to advance the field of interactomics further.

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Section: Strategies For Pmi Studiesmentioning

confidence: 99%

The Knowns and Unknowns in Protein–Metabolite Interactions

Kurbatov

Dolgalev

Arzumanian

et al. 2023

IJMS

View full text Add to dashboard Cite

show abstract

“…[ 2 , 3 ] Meanwhile, the metabolic alterations can also promote cancer development and progression through certain forms of metabolite and protein interactions (MPIs). [ 4 , 5 ] Furthermore, the metabolic reprogramming is highly‐adaptive, alternative MPIs or pathways will be activated in the absence of a certain nutrient or regulator. [ 6 , 7 ] Consequently, the metabolic landscape, composing of both metabolites, proteins and interactions between them, is highly‐variable in different cancer types, subtypes, or even the same cancer type under different conditions.…”

Section: Introductionmentioning

confidence: 99%

Identification and Characterization of Robust Hepatocellular Carcinoma Prognostic Subtypes Based on an Integrative Metabolite‐Protein Interaction Network

et al. 2021

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Metabolite-protein interactions (MPIs) play key roles in cancer metabolism. However, our current knowledge about MPIs in cancers remains limited due to the complexity of cancer cells. Herein, the authors construct an integrative MPI network and propose a MPI network based hepatocellular carcinoma (HCC) subtyping and mechanism exploration workflow. Based on the expressions of hub proteins on the MPI network, two prognosis-distinctive HCC subtypes are identified. Meanwhile, multiple interdependent features of the poor prognostic subtype are observed, including hypoxia, DNA hypermethylation of metabolic pathways, fatty acid accumulation, immune pathway up-regulation, and exhausted T-cell infiltration. Notably, the immune pathway up-regulation is probably induced by accumulated unsaturated fatty acids which are predicted to interact with multiple immune regulators like SRC and TGFB1. Moreover, based on tumor microenvironment compositions, the poor prognostic subtype is further divided into two sub-populations showing remarkable differences in metabolism. The subtyping shows a strong consistency across multiple HCC cohorts including early-stage HCC. Overall, the authors redefine robust HCC prognosis subtypes and identify potential MPIs linking metabolism to immune regulations, thus promoting understanding and clinical applications about HCC metabolism heterogeneity.

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“…17,18 As one of the important post-translational modifications, phosphorylation plays a significant role in cell transportation and metabolism. 19−22 Abnormally phosphorylated proteins are usually related to numerous diseases, such as cancer 23,24 and Alzheimer's disease. 25,26 Mass spectrometry (MS) technology is a significant means for phosphoprotein detection.…”

Section: ■ Introductionmentioning

confidence: 99%

“…As one of the important post-translational modifications, phosphorylation plays a significant role in cell transportation and metabolism. − Abnormally phosphorylated proteins are usually related to numerous diseases, such as cancer , and Alzheimer’s disease. , Mass spectrometry (MS) technology is a significant means for phosphoprotein detection. − However, the abundance of phosphoproteins in organisms is low, and there is a large amount of interference from nonphosphoproteins. Therefore, it is necessary to design effective strategies to enrich phosphoproteins before performing MS detection.…”

Section: Introductionmentioning

confidence: 99%

Design of a Spiropyran-Based Smart Adsorbent with Dual Response: Focusing on Highly Efficient Enrichment of Phosphopeptides

Zhao

et al. 2021

ACS Appl. Mater. Interfaces

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Smart responsive materials have attractive application prospects due to their tunable behaviors. In this work, we design novel spiropyran (SP)-based magnetic nanoparticles (MNP-SP) with dual response to ultraviolet light and pH and apply them to the enrichment of phosphopeptides. SP is modified on the surface of magnetic nanoparticles through a simple esterification reaction, based on which an MNP-SP-MS phosphopeptide identification platform is established. The capture and release of phosphopeptides are facilely adjusted by changing external light and the pH of the solution. The smart responsive MNP-SP has fast magnetic response performance, high sensitivity (detection limit of 0.4 fmol), and good reusability (6 cycles). In addition, MNP-SP is used for the enrichment of phosphopeptides in skimmed milk, human saliva, and human serum samples, indicating that it is an ideal adsorbent for enriching low-abundance phosphopeptides in complex biological environments.

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Biochemical reactions in metabolite-protein interaction

Cited by 10 publications

References 14 publications

The Knowns and Unknowns in Protein–Metabolite Interactions

The Knowns and Unknowns in Protein–Metabolite Interactions

Identification and Characterization of Robust Hepatocellular Carcinoma Prognostic Subtypes Based on an Integrative Metabolite‐Protein Interaction Network

Design of a Spiropyran-Based Smart Adsorbent with Dual Response: Focusing on Highly Efficient Enrichment of Phosphopeptides

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