Structural predictions of the functions of membrane proteins from HDX-MS

Abstract

HDX-MS has emerged as a powerful tool to interrogate the structure and dynamics of proteins and their complexes. Recent advances in the methodology and instrumentation have enabled the application of HDX-MS to membrane proteins. Such targets are challenging to investigate with conventional strategies. Developing new tools are therefore pertinent for improving our fundamental knowledge of how membrane proteins function in the cell. Importantly, investigating this central class of biomolecules within their native lipid environment remains a challenge but also a key goal ahead. In this short review, we outline recent progresses in dissecting the conformational mechanisms of membrane proteins using HDX-MS. We further describe how the use of computational strategies can aid the interpretation of experimental data and enable visualisation of otherwise intractable membrane protein states. This unique integration of experiments with computations holds significant potential for future applications.

Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems

“… 689 − 691 Over the years, several tools have been developed for predicting HDX-MS properties from structures 25 , 692 to expand the information content of HDX-MS studies for structural modeling, 434 more accurate modeling of interaction surfaces, 428 , 693 or understanding allosteric networks, 694 even for complex systems such as membrane proteins. 695 , 696 From these recent trends, we expect that MD and other structural computational approaches will play a more prevalent role in both the analysis and structural interpretation of HDX-MS data. 697 …”

“…While the predominant determinants of amide exchange are well-established, there is still an incomplete understanding of all the factors that contribute to observed amide exchange kinetics. ,, Using HDX-MS in conjunction with molecular dynamics (MD) simulations has been a promising approach for acquiring more structural insight from HDX-MS. Vast ensembles of predicted structures or models can be validated by comparison to experimental HDX-MS profiles. − Over the years, several tools have been developed for predicting HDX-MS properties from structures , to expand the information content of HDX-MS studies for structural modeling, more accurate modeling of interaction surfaces, , or understanding allosteric networks, even for complex systems such as membrane proteins. , From these recent trends, we expect that MD and other structural computational approaches will play a more prevalent role in both the analysis and structural interpretation of HDX-MS data …”

Developments in Hydrogen/Deuterium Exchange Mass Spectrometry

“…Compare this value to the 21 research papers on membrane proteins that we listed in our 2015 review, and it is clear that the number of membrane protein studies by HDX MS has massively ballooned. Review topics covered included signaling proteins both in and at the membrane, peripheral membrane proteins, − integral membrane proteins, and membrane transporters, a detailed methodological discussion of how to study membrane proteins by HDX MS, HDX MS of membrane proteins when combined with molecular modeling, and a review of the use of nanodiscs for studying membrane proteins by HDX MS . One review included other types of MS for membrane proteins as well as HDX MS.…”

Mass Spectrometry Methods for Measuring Protein Stability

“…Deeper structural insights can be gained from MP by deploying LC-MS techniques in combination with chemical labeling, where the solvent-accessible sites of native MPs are labeled permanently or reversibly prior to digestion. HDX, − CXL, − and FPOP ,− have all been used to probe MP tertiary structures, as well as the interactions between MPs and both protein binding partners and solubilization agents (Figure G). Much of the mechanics of MS-based footprinting tools targeting MPs remain similar to those directed toward water-soluble protein systems and typically provide a valuable readout capable of monitoring the conformational responses of MPs upon stimulation, both temporally and spatially.…”