Scientists unveiled ways to measure the molecular interactions

A Map of Protein-Metabolite Interactions.

New study unveiled ways to measure the molecular interactions
Molecular model of a protein membrane receptor bound to its small molecule ligands with structural details of the allosteric binding site (right). (Graphics: Ilaria Piazza / ETH Zurich / PDB database entry 4MQT)

ETH researchers have utilized a novel approach to discover antecedently unbeknown interactions amid proteins and tiny metabolic molecules in bacterial cells. The method can likewise be utilized to test the effect of medications.

Scientists have a new “omics” (an interactomics), which deals with the interactions amid proteins and small molecules. Antecedently studied genomics or proteomics, system biologists can now add protein-metabolite interactomics to the blend. Genomics is affined with the systematic analysis of all of an organism’s genes, while proteomics deals with the exhaustive set of proteins within a biological unit.

Subsequently, protein-metabolite interactomics, the group led by Paola Picotti, professor of Molecular Systems Biology at ETH Zurich, has now linked another level to the existing “omics”.

The researchers recently published a study in the journal Cell, in which they systematically analyzed and quantified the interactions of all proteins with metabolites (small metabolic molecules) on the level of the whole proteome for the first time, establishing the relationships amid them.

The group of examiners demonstrated the number of the proteins and enzymes present in an E. coli bacterial cell interact with metabolites. To enact this experiment they utilized an approach known as limited proteolysis (LiP), combined with mass spectrometric analysis.

The researchers extracted cellular fluid, which contains proteins, from the bacterial cells. They then added a metabolite to each sample and allowed it to interact with the proteins.

Determinately, they chop up the proteins into smaller pieces (peptides) utilizing “molecular scissors”. Altogether, the researchers tested 20 different metabolites and their interactions with proteins.

When a protein interacts with a metabolite, whether it settles in the protein’s active site or links to another site, the protein structure is altered. The “molecular scissors” then chop it at different sites from the original structure, resulting in a different set of peptides.

Utilizing the mass spectrometer, the researchers gauged all of the pieces present in the sample and enter the data obtained into a computer to reconstruct the structural differences and changes, and wherein the protein these are localized.

The information about the protein-metabolite interactome (the interactions between proteins and metabolites and the molecular (signal) networks belonging to them), was antecedently short in supply compared with what was learned about interactions amid various proteins or proteins and DNA or RNA. The study has now sharply increased this information.

Post utilizing this approach with E. coli, Picotti and her team discovered about 1,650 different protein-metabolite interactions, of which over 1,400 were antecedently unbeknown. Thousands of binding sites on proteins to which metabolites can link also came to light.

Picotti states, “Although the metabolism of E. coli and associated molecules is already very well known, we succeeded in discovered many new interactions and the corresponding binding sites.”

“The data that we produce with this technique will help to identify new regulatory mechanisms, unknown enzymes and new metabolic reactions in the cell.”

In their study, the researchers likewise demonstrated that small metabolic molecules prefer to bind to (and thus regulate) proteins whose concentration is more or less constant over time. This suggests that the binding of metabolites to proteins and changes in protein concentrations are two complementary pathways by which cells regulate protein activity.

Now proteins can be activated or inactivated relatively immediately by a structural change mediated by metabolites.

Picotti explained, “This kind of structural change can be reversed more quickly.”

Through cell’s perspective, this often makes sense, because utilizing the pathway involving a change in concentration means that the cell must dismantle or rebuild proteins, which costs it more time, energy and resources.

Picotti and her colleagues have also been able to show that numerous enzymes are less choosy than previously thought, they can apparently bind to and chemically alter several different metabolites.

Yet, it was fictitious that enzymes were mostly specific to a few very similar molecules.