Protein-Metabolite Interactions Analysis Service

Molecular recognition between proteins and small molecule metabolites plays a crucial role in regulating protein function and controlling various cellular processes. The activities of metabolic enzymes, transcription factors, transporter proteins and membrane receptors can all be mediated by protein-metabolite interactions (PMIs), thereby linking cellular metabolism to genetic/epigenetic regulation, environmental sensing and signal transduction. In addition to binding directly to the active or orthosteric site of the native homologous protein, metabolites are known to interact with different allosteric sites, allowing for additional specialized modulation of protein and macromolecular protein assembly structure and function . Metabolic protein interaction studies (PMIs) are a method for assessing the binding of proteomes to related metabolites, revealing new allosteric and enzymatic functions, and are an excellent tool for the study of drug targets.

Protein-Metabolite Interactions Analysis in Creative Proteomics

At Creative Proteomics, we invite you to delve into the fascinating realm of Protein-Metabolite Interactions Analysis, a cutting-edge service designed to decipher the intricate conversations that occur within living cells. Our comprehensive suite of advanced methodologies empowers researchers to explore the dynamic interactions between proteins and metabolites, providing critical insights into cellular functions, metabolic pathways, and disease mechanisms.

Method Principle and Description Advantages
Surface Plasmon Resonance (SPR) Real-time, label-free quantification of binding kinetics between proteins and metabolites. Direct measurement of binding kinetics, equilibrium constants, and affinity. Label-free analysis preserves natural interaction conditions.
Mass Spectrometry Profiling and quantification of protein-metabolite interactions, providing insights into binding stoichiometry and dynamics. Enables identification of interacting partners and characterization of binding strength. Offers high-throughput analysis and versatility.
Nuclear Magnetic Resonance (NMR) High-resolution analysis of protein-metabolite complexes, revealing structural details and binding interfaces. Provides atomic-level structural insights, identifies key binding residues, and characterizes complex dynamics.
Enzymatic Assays Functional assays to explore how metabolites influence enzyme activities and catalytic efficiencies. Direct measurement of enzymatic activity changes upon metabolite binding. Enables mechanistic understanding of enzymatic regulation.
Microscale Thermophoresis (MST) Precise measurement of interactions between proteins and metabolites, offering insights into binding affinity and thermodynamics. Requires minimal sample volume, provides label-free detection, and allows determination of binding constants and thermodynamic parameters.
Fluorescence Resonance Energy Transfer (FRET) Detects energy transfer between fluorophores attached to proteins and metabolites, indicating proximity and interactions. Offers real-time monitoring of interactions in solution, sensitive to molecular distances and conformational changes.
Isothermal Titration Calorimetry (ITC) Measures heat changes during protein-metabolite interactions, enabling determination of binding constants and stoichiometry. Provides quantitative thermodynamic data, including binding affinity and enthalpy changes. Useful for characterizing weak and strong interactions.
Differential Scanning Calorimetry (DSC) Measures thermal stability changes of proteins in the presence of metabolites, revealing binding events. Provides insights into protein-metabolite interactions and their effects on protein stability.
Bio-layer Interferometry (BLI) Monitors real-time interactions between proteins and metabolites using biosensor-coated tips. Offers label-free, real-time kinetics analysis with high sensitivity and versatility.
Surface-Enhanced Raman Spectroscopy (SERS) Enhances Raman scattering signals to study protein-metabolite interactions at the molecular level. Provides vibrational information about binding events, offering insights into structural changes and conformational alterations.
Co-immunoprecipitation (Co-IP) Isolates protein-metabolite complexes using antibodies against specific proteins, followed by metabolite detection. Enables detection of endogenous interactions and provides insights into protein-metabolite associations in complex biological samples.

Application of Protein-Metabolite Interactions Assay

Metabolic Pathway Elucidation: Gain a comprehensive view of metabolic pathways by studying how proteins interact with metabolites, uncovering regulatory mechanisms and potential targets for metabolic diseases.

Enzyme Function and Regulation: Explore how metabolites modulate enzyme activities, providing insights into enzymatic regulation and potential therapeutic interventions.

Biomarker Discovery: Identify potential biomarkers for diseases by studying altered protein-metabolite interactions, aiding in early diagnosis and treatment strategies.

Drug Target Identification: Uncover novel drug targets by investigating protein-metabolite interactions, facilitating drug discovery and development processes.

Cell Signaling Insights: Understand how metabolites contribute to cell signaling cascades through interactions with proteins, offering insights into cellular communication.

Microbiome Studies: Probe interactions between host proteins and microbial metabolites, enhancing our understanding of host-microbe relationships.

Case Studies

Title: A Map of Protein-Metabolite Interactions Reveals Principles of Chemical Communication

Impact factor: 38.637

Subjects studied: Escherichia coli and yeast

Methods: Mass Spectrometry Analysis of Protein Metabolism Interactions

Protein-metabolite Interactions Analysis Service

Research Content:

Metabolite-protein interactions control a variety of cellular processes and thus play an important role in maintaining cellular homeostasis. Metabolites make up the largest fraction of molecules in cells, yet less metabolite-protein interactomes are currently understood than protein-protein or protein-DNA interactions. Here, the authors present a chemical proteomic methodology pipeline for the systematic identification of metabolite-protein interactions directly in the natural environment. This approach uncovered a network of known and novel interaction and binding sites in E. coli, demonstrating the functional relevance of some of the newly discovered interactions. These data enable the identification of novel relationships between of enzyme and substrate and metabolite-induced protein complex. The study found that the metabolite-protein interactome consists of 1,678 interactions and 7,345 putative binding sites. The data reveal the functional and structural principles of chemical communication, elucidate the prevalence and mechanisms of enzyme promiscuity, enabling the quantification of metabolite binding at the proteome scale.


  1. Piazza Ilaria,Kochanowski Karl,Cappelletti Valentina et al. A Map of Protein-Metabolite Interactions Reveals Principles of Chemical Communication.Cell, 2018, 172: 358-372.e23.
* This service is for RESEARCH USE ONLY, not intended for any clinical use.