Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase

Hicks, Kevin G.; Cluntun, Ahmad A.; Schubert, Heidi; Hackett, Sean R.; Berg, Jordan A.; Leonard, Paul G.; Aleixo, Mariana A. A.; Zhou, Youjia; Bott, Alex J.; Salvatore, Sonia R.; Fei, Chang; Blevins, Aubrie; Barta, Paige; Tilley, Samantha; Leifer, Aaron; Guzman, Andrea L.; Arok, Ajak; Fogarty, Sarah; Winter, Jacob M.; Ahn, Hee‐Chul; Allen, Karen N.; Block, Samuel; Cardoso, Iara Aimê; Ding, Jianping; Dreveny, Ingrid; Gasper, William C.; Ho, Quinn; Matsuura, Atsushi; Palladino, Michael J.; Prajapati, Sabin; Sun, Pengkai; Tittmann, Kai; Tolan, Dean R.; Unterlass, J.E.; VanDemark, Andrew P.; Heiden, Matthew G. Vander; Webb, Bradley A.; Yun, Cai‐Hong; Zhao, Pengkai; Wang, Bei; Schöpfer, Francisco J.; Hill, Christopher P.; Nonato, Maria Cristina; Muller, Florian L.; Cox, James E.; Rutter, Jared

doi:10.1126/science.abm3452

Cited by 64 publications

(23 citation statements)

References 91 publications

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“…As a result, 830 protein-metabolite interactions were identified with 33 human carbohydrate metabolism, a subset of which were further validated by enzyme activity assays, differential scanning fluorimetry (DSF), and X-ray crystallography. 48,50 These results indicated that MIDAS enables the identification of physiologically relevant, low-affinity protein−ligand interactions using unmodified ligand mixtures, therefore holding the potential for comprehensive PECI mapping. 2.2.2.…”

Section: Indirect Methods By Exploiting Interaction-induced Physicoch...mentioning

confidence: 89%

“…High-throughput flow injection analysis MS was then utilized to quantify total metabolite abundance (free and bound states) in the protein chamber and the metabolite chamber under the relative equilibrium condition. As a result, 830 protein-metabolite interactions were identified with 33 purified enzymes from human carbohydrate metabolism, a subset of which were further validated by enzyme activity assays, differential scanning fluorimetry (DSF), and X-ray crystallography. , These results indicated that MIDAS enables the identification of physiologically relevant, low-affinity protein–ligand interactions using unmodified ligand mixtures, therefore holding the potential for comprehensive PECI mapping.…”

Section: Overview Of the Methods For Peci Mappingmentioning

confidence: 99%

See 1 more Smart Citation

Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions

Li,

Lyu,

Wang

et al. 2023

Chem. Res. Toxicol.

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Adverse health outcomes caused by environmental chemicals are often initiated via their interactions with proteins. Essentially, one environmental chemical may interact with a number of proteins and/or a protein may interact with a multitude of environmental chemicals, forming an intricate interaction network. Omics-wide protein-environmental chemical interaction profiling (PECI) is of prominent importance for comprehensive understanding of these interaction networks, including the toxicity mechanisms of action (MoA), and for providing systematic chemical safety assessment. However, such information remains unknown for most environmental chemicals, partly due to their vast chemical diversity. In recent years, with the continuous efforts afforded, especially in mass spectrometry (MS) based omics technologies, several ligand modification-free methods have been developed, and new attention for systematic PECI profiling was gained. In this Review, we provide a comprehensive overview on these methodologies for the identification of ligand-protein interactions, including affinity interaction-based methods of affinitydriven purification, covalent modification profiling, and activity-based protein profiling (ABPP) in a competitive mode, physicochemical property changes assessment methods of ligand-directed nuclear magnetic resonance (ligand-directed NMR), MS integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS), thermal proteome profiling (TPP), limited proteolysis-coupled mass spectrometry (LiP-MS), stability of proteins from rates of oxidation (SPROX), and several intracellular downstream response characterization methods. We expect that the applications of these ligand modification-free technologies will drive a considerable increase in the number of PECI identified, facilitate unveiling the toxicological mechanisms, and ultimately contribute to systematic health risk assessment of environmental chemicals.

show abstract

Section: Indirect Methods By Exploiting Interaction-induced Physicoch...mentioning

confidence: 89%

Section: Overview Of the Methods For Peci Mappingmentioning

confidence: 99%

Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions

Li,

Lyu,

Wang

et al. 2023

Chem. Res. Toxicol.

View full text Add to dashboard Cite

show abstract

“…This highlights potential future directions such as the inclusion of other generalistic metabolite-protein databases 54 . Moreover, experimental protocols that allow for a systematic characterization of the direct binding of protein and metabolites 55,56 will enable curation efforts in the future, for which MetalinkDB will be a suitable starting point.…”

Section: Discussionmentioning

confidence: 99%

MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions

Farr,

Dimitrov,

Turei

et al. 2023

Preprint

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Interactions between proteins and metabolites are key for cellular function, from the catalytic breakdown of nutrients to signaling. An important case is cell-cell communication, where cellular metabolites are secreted into the microenvironment and initiate a signaling cascade by binding to an intra- or extracellular receptor of another cell. While protein-protein mediated cell-cell communication is routinely inferred from transcriptomic data, for metabolite-protein interactions this is challenging due to the limitations of high-throughput single-cell and spatial metabolomics technologies, together with the absence of comprehensive prior knowledge resources that include metabolites. Here we report MetalinksDB, a comprehensive and flexible database of intercellular metabolite-protein interactions that is a magnitude larger than existing ones. MetalinksDB can be tailored to specific biological contexts such as diseases, pathways, or tissue/cellular locations by querying subsets of interactions using the web interface (https://metalinks.omnipathdb.org/) or the knowledge graph adapters. We showcase the use of MetalinksDB by identifying deregulated processes in renal cancer patients from multi-omics data as well as inferring metabolite-mediated cell-cell communication events driving acute kidney injury from spatial transcriptomic data. We anticipate that MetalinksDB will facilitate the study of metabolite-mediated communication processes.

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“…1 A variety of techniques have been reported to study PMIs 2 , including surface plasmon resonance spectroscopy, isothermal titration calorimetry, nuclear magnetic resonance spectroscopy, and electrospray ionization mass spectrometry (ESI-MS). [3][4][5][6] Unlike other methods, mass spectrometry has valuable advantages such as high sensitivity, high-speed analysis, low sample consumption, little-to-no sample preparation, etc., which make it a routine tool for protein analysis. Methods for studying PMIs based on MS can be roughly classified into two categories: metabolitecentric and protein-centric approaches.…”

Section: Introductionmentioning

confidence: 99%

Differentiating specific and non-specific protein-metabolite interactions using gradient open port probe electrospray ionization mass spectrometry

Tian,

Hopfgartner

2024

Preprint

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Native electrospray ionization mass spectrometry (ESI-MS) using nano ESI or desorption electrospray ionization (DESI) has been widely used to study interactions between macromolecules and ligands, usually protein-metabolite interactions (PMIs). In MS spectra the charge state distributions (CSD) of proteins differ between native and non-native conditions and based on this, we report a method that can differentiate specific protein-metabolite interactions from non-specific binding. Our approach is based on a 3D-printed open port probe electrospray system (gOPP-ESI) using mobile phase gradients (aqueous to methanol) for the ionization of protein/protein-metabolite complex. Notably, we found that a true protein-metabolite complex is more resistant to the denaturing effect of methanol compared to the free protein. This is corroborated by the observation that forming high charge states of protein-metabolite complexes requires higher proportions of methanol than free protein while, for non-specific complexes, there is no obvious difference in the CSD. Therefore, by comparing the changes in the CSD of free protein and protein-metabolite complex versus the increase of methanol, we can distinguish metabolites that specifically interact with the target protein. The approach is evaluated with well-characterized protein-ligand pairs, and we confirmed that cytidine phosphates, N, N′, N″-triacetylchitotriose, and fluvastatin are specific ligands for ribonuclease A, lysozyme, and beta-lactoglobulin respectively. However, cytidine-5'-triphosphate (CTP) interacts non-specifically with lysozyme and beta-lactoglobulin. We believe that after first-round native-MS assays to identify which metabolites cause mass shifts to the free protein, the gOPP-ESI-MS could be used as a quick second-round check to exclude non-specific binding and discover metabolites truly interacting with the protein of interest, reducing the number of candidates for subsequent validation experiments.

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Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase

Cited by 64 publications

References 91 publications

Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions

Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions

MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions

Differentiating specific and non-specific protein-metabolite interactions using gradient open port probe electrospray ionization mass spectrometry

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