Protein-Ligand Interactions

Protein interactions determine their function

Protein interactions with small molecules, which are termed protein-ligand interactions, are involved in numerous biological functions, from protein transcription to translation and signal transduction. Knowing which conformational changes are induced upon small molecule binding, and which molecules can bind target proteins better than their own natural ligands, are key goals of biotherapeutic design.

Thermo Scientific Orbitrap MS solutions deliver highly specific and sensitive workflows that help identify protein-ligand interactions, pinpoint their locations, and determine any conformational changes associated with those interactions.

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MS techniques used for protein-ligand interactions

Native mass spectrometry
Native mass spectrometry

Information on protein-ligand complex interactions, such as stoichiometry and dissociation constant, is often obtained using MS. Protein-ligand complexes are analyzed in the mass spectrometer in their native biological states. Mass measurement of the complexes can confirm the presence of protein-ligand interactions, while stoichiometry is determined by taking mass measurement with and without protein-ligand interactions.

Hydrogen deuterium exchange mass spectrometry
Hydrogen deuterium exchange mass spectrometry

Hydrogen deuterium exchange mass spectrometry (HDX-MS) aids in localization of protein-ligand interaction sites. Protein-ligand complexes are dissolved in a solution of D2O, which enables the labile amide protons of the protein to exchange with deuterium. Typically, areas of protein-ligand interaction exchange at a much slower rate than open regions exposed to D2O. MS is then used to determine proton exchange rates, helping to localize interaction sites and elucidate their structural information.

Crosslinking mass spectrometry
Crosslinking mass spectrometry

Crosslinking mass spectrometry (XL-MS) is used to determine protein-ligand binding sites. This process is initiated by using photoaffinity labels to photo-crosslink proteins with ligands. Samples are then enriched, digested, and analyzed by MS for ligand modifications on the protein.