Protein Structure

Determining protein structure with MS

Mass spectrometry (MS) is commonly used to determine both the primary and higher-order structures of proteins. New advances in MS technologies, combined with chemical modification and proteolysis strategies, allow the study of both single proteins and protein complexes as well as further exploration of protein structure and even structural dynamics.

Thermo Scientific Orbitrap MS solutions enable highly specific and sensitive workflows that allow you to analyze samples with increasing analytical depth, delivering information to accelerate the path from structure to function.

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MS techniques used for protein structure

Peptide sequencing by LC-MS/MS
Peptide sequencing by LC-MS/MS

Peptide sequencing via mass spectrometry, when performed using a bottom-up approach, is a useful and easy tool for obtaining information about primary protein structure. Such information helps elucidate the identity of that protein, or even the identities of several proteins involved in larger protein complexes.

Hydrogen deuterium exchange mass spectrometry
Hydrogen deuterium exchange mass spectrometry

Hydrogen deuterium exchange mass spectrometry (HDX-MS) measures the conformational changes of proteins or protein-protein interactions in protein complexes. Amide protons found within close inter- or intra-molecular contact areas often form hydrogen bonds and have different exchange rates relative to more accessible regions of the complex. By monitoring such exchanges, a protein's noncovalent structure (alone or in complex) is better understood.

Crosslinking mass spectrometry
Crosslinking mass spectrometry

Protein structure data can be obtained independently or simultaneously as part of protein interaction studies using crosslinking mass spectrometry (XL-MS). In such analysis, XL-MS is often combined with high-resolution techniques (e.g., cryo-electron microscopy (cryo-EM ), X-ray crystallography). Such technologies help determine protein region distance constraints via 3-D structure information or topology. XL-MS can also be used to identify protein complexes.

Limited Proteolysis
Limited proteolysis

A limited proteolysis approach on single proteins, coupled to MS, can yield answers about the higher-order structure of proteins and their folded states. This approach can also be used to probe the quaternary structure of protein complexes. The formation of an interface between a protein and another macromolecule will protect otherwise accessible sites from protease cleavage, providing information about the residues that form that interface.