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

Abstract

Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) is a rapidly evolving technique for analyzing structural features and dynamic properties of proteins. It may stand alone or serve as a complementary method to cryo-electron-microscopy (EM) or other structural biology approaches. HDX-MS is capable of providing information on individual proteins as well as large protein complexes. Owing to recent methodological advancements and improving availability of instrumentation, HDX-MS is becoming a routine technique for some applications. When dealing with samples of low to medium complexity and sizes of less than 150 kDa, conformation and ligand interaction analyses by HDX-MS are already almost routine applications. This is also well supported by the rapid evolution of the computational (software) background that facilitates the analysis of the obtained experimental data. HDX-MS can cope at times with analytes that are difficult to tackle by any other approach. Large complexes like viral capsids as well as disordered proteins can also be analyzed by this method. HDX-MS has recently become an established tool in the drug discovery process and biopharmaceutical development, as it is now also capable of dissecting post-translational modifications and membrane proteins. This mini review provides the reader with an introduction to the technique and a brief overview of the most common applications. Furthermore, the most challenging likely applications, the analyses of glycosylated and membrane proteins, are also highlighted.

Structure–function relationship of terpenoid glycosyltransferases from plants

“…However, protein–ligand studies using e.g. micro-scale thermophoresis 151 and isothermal titration calorimetry 152 and, in recent years, hydrogen deuterium exchange mass spectrometry 153 have also been valuable tools in elucidating the interaction of UGTs with their substrates and effectors. This results in a growing need for reliable computational methods to determine the biochemical function of these proteins.…”

Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein–Protein Interactions─A Method for All Seasons

“…It monitors the rates of exchanging hydrogen by deuterium atoms at the amide backbone of proteins from solvent D 2 O in solution. , These exchanges reflect the SASA and are recorded by a mass spectrometer as a function of time. Thus, HDX-MS provides information on solvent accessibility, secondary and tertiary structures, conformational changes, protein states, and binding interfaces. , HDX-MS is able to capture protein dynamics and allosteric regulation in solution of a protein or a protein complex and, as such, is a local sensor for conformational changes at single amino acid resolution . The HDX-MS method is now also being used to address the conformational dynamics and structural transitions of IDPs and IDRs following protein–protein and protein–ligand binding, in analogy to other footprinting methods. , For example, HDX-MS has been used to investigate conformational changes of the full-length microtubule-associated protein tau when it undergoes a transition from monomers to soluble aggregatesa conformational transition that precedes fibril formation during pathogenic neurodegenerative processes .…”

Unveiling the biological interface of protein complexes by mass spectrometry-coupled methods

“…Due to the large size and complexity of the antigen-antibody complex, the epitope mapping was inaccessible by NMR or X-ray crystallography. Desirably, HDMS was readily applicable to the complex, yielding comparative epitope analyses between two different antibodies in parallel, and required less overall effort than the conventional epitope mapping strategies such as mutagenesis and peptide scanning (Gershoni et al, 2007;Ozohanics and Ambrus 2020;Ständer et al, 2021).…”