Investigating metabolite–protein interactions: An overview of available techniques

Studies of metabolite–protein interactions: A review

“…The characterization of metabolite-protein interactions can provide a better understanding in clinical diagnostics of the cellular activity and the biochemical pathways that are present in various medical conditions [1–3,9]. There are many methods that can be used to examine the binding of metabolites with proteins.…”

“…There are many methods that can be used to examine the binding of metabolites with proteins. These methods may involve the direct examination of binding that occurs between proteins and low mass drugs, hormones and their metabolites, or may involve an examination of the free concentrations of these molecules [9–12]. The approaches that are used for this purpose can be divided into three categories: in vitro , in vivo and in silico techniques [9,11–46].…”

“…This approach involves the use of standard, well-controlled conditions and reagents that are used in the laboratory to mimic conditions seen in biological systems. To examine metabolite-protein interactions, in vitro methods may use a binding assay (e.g., one based on ultrafiltration or equilibrium dialysis) to examine an interaction or to identify the chemicals that are involved in this process [9]. This approach can provide information such as the strength of the interaction, as well as the thermodynamics and kinetics of binding and possible conformational changes that occur as a result of the interaction [13–15].…”

“…Information on these interactions can be combined with the structural data to provide a better understanding of the regulatory networks and connections in biological pathways. Such information, in turn, could provide a better understanding of how healthy and disease states differ at the molecular level and could provide vital data that can be used for pharmaceutical development [7,9]. …”

Editorial for “Advances in Protein–Protein Interactions”

“…The next contribution provides an extensive review of yeast two-hybrid-based technologies for identification of both PPIs and protein-drug interactions [6], followed by a paper describing the use of mass spectrometry to monitor protein-drug interactions [7]. Following these protein-drug assays, three contributions describe the use of the yeast one-hybrid assay to identify protein-DNA interactions [8], protein microarray technology to characterize PPIs among proteins that are secreted in human cells [9], as well as in vitro, in silico, and in vivo assays for mapping protein-metabolite interactions [10]. The next two articles, on Fluorescence Resonance Energy Transfer (FRET) and Nuclear Magnetic Resonance (NMR) spectroscopy illustrate how these two methods can be effective tools for unraveling PPIs between G-Protein Coupled Receptors [11] and GTPases [12].…”