Protein-Metabolite Interactions Analysis Service

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.

Our Protein-metabolite Interactions Analysis Service

Creative Proteomics has many years of experience analyzing protein related interactions. We provide a high-throughput platform for rapid quantification of protein-metabolite interactions in biological samples.

Technical Advantages

Simple and efficient discovery of small molecule metabolite - protein interactions with high sensitivity.

Does not require any chemical modification of ligands and is not biased towards compounds with specific properties.

Direct study of complex biological samples without protein purification or concentration.


Protein-metabolite Interactions Analysis Service

Sample Requirements

Animal and clinical tissue samples: 500 mg/sample

Serum, plasma: 1ml/sample

Cells, microorganisms: 1×109 cells/sample

Plant: 2g/sample


Protein-metabolite Interactions Analysis Service


Research on small molecule metabolite-interacting proteins;

Drug target prediction;

Research on the mechanism of action of small molecule metabolites: study the effects of small molecule metabolites on biochemical processes, signaling pathways, etc.;

PMI network map construction: Combined with other functional omics data such as PPIs network, protein post-translational modification (PTM) or metabolic flux, it brings new directions for the crosstalk between different cellular regulatory.

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

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.[J] .Cell, 2018, 172: 358-372.e23.
  2. Li Shanshan,Shui Wenqing,Systematic mapping of protein-metabolite interactions with mass spectrometry-based techniques.[J] .Curr. Opin. Biotechnol., 2020, 64: 24-31.
  3. Guo Hongbo,Peng Hui,Emili Andrew,Mass spectrometry methods to study protein-metabolite interactions.[J] .Expert Opin Drug Discov, 2017, 12: 1271-1280.
* This service is for RESEARCH USE ONLY, not intended for any clinical use.