Bridging protein structure, dynamics, and function using hydrogen/deuterium‐exchange mass spectrometry

Abstract

Much of our understanding of protein structure and mechanistic function has been derived from static high‐resolution structures. As structural biology has continued to evolve it has become clear that high‐resolution structures alone are unable to fully capture the mechanistic basis for protein structure and function in solution. Recently Hydrogen/Deuterium‐exchange Mass Spectrometry (HDX‐MS) has developed into a powerful and versatile tool for structural biologists that provides novel insights into protein structure and function. HDX‐MS enables direct monitoring of a protein's structural fluctuations and conformational changes under native conditions in solution even as it is carrying out its functions. In this review, we focus on the use of HDX‐MS to monitor these dynamic changes in proteins. We examine how HDX‐MS has been applied to study protein structure and function in systems ranging from large, complex assemblies to intrinsically disordered proteins, and we discuss its use in probing conformational changes during protein folding and catalytic function. Statement for a Broad Audience The biophysical and structural characterization of proteins provides novel insight into their functionalities. Protein motions, ranging from small scale local fluctuations to larger concerted structural rearrangements, often determine protein function. Hydrogen/Deuterium‐exchange Mass Spectrometry (HDX‐MS) has proven a powerful biophysical tool capable of probing changes in protein structure and dynamic protein motions that are often invisible to most other techniques.

Hydrogen-Deuterium Exchange Mass Spectrometry: A Novel Structural Biology Approach to Structure, Dynamics and Interactions of Proteins and Their Complexes

“…There is a plethora of examples for the application of HDX-MS in protein interaction studies [ 21 , 106 ]. More challenging are those applications, where the protein is part of a large protein complex, such as a nuclear pore complex [ 34 , 35 ], embedded in a membrane [ 15 , 107 ], or disordered [ 108 , 109 ]. Selected protein modifications, like glycosylation and disulfide bonding, hinder proteolysis and/or mass analysis [ 26 ].…”

New Biophysical Approaches Reveal the Dynamics and Mechanics of Type I Viral Fusion Machinery and Their Interplay with Membranes

“…HDX-MS is a solution state biophysical and structural technique that monitors the accessibility of amide hydrogens along the protein backbone. HDX-MS directly monitors dynamic structural changes and motion throughout a protein that are otherwise invisible to other structural approaches [45,50,82,83]. At low pH conditions approaching fusion activation, dynamic changes across the HA were observed where the HA1-HA1 trimeric interface became bolstered and the HA2 fusion peptide proximal subdomain became more dynamic.…”

Glycan-induced protein dynamics in human norovirus P dimers depend on virus strain and deamidation status

“…These bimodal peak distributions can have many causes, e.g. two distinct protein conformations, conformational rearrangements that lead to EX1 exchange kinetics, insufficient ligand saturation or peptide carry over from the analytical or protease column [50,51].…”