Quantitative Evaluation of Native Protein Folds and Assemblies by Hydrogen Deuterium Exchange Mass Spectrometry (HDX-MS)

Matthew J Harris,Deepika Raghavan,Antoni J Borysik

doi:10.1007/s13361-018-2070-3

Matthew J Harris, Deepika Raghavan + Show 1 more

Open Access

https://doi.org/10.1007/s13361-018-2070-3

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Abstract

Hydrogen deuterium exchange mass spectrometry (HDX-MS) has significant potential for protein structure initiatives but its relationship with protein conformations is unclear. We report on the efficacy of HDX-MS to distinguish between native and non-native proteins using a popular approach to calculate HDX protection factors (PFs) from protein structures. The ability of HDX-MS to identify native protein conformations is quantified by binary structural classification such that merits of the approach for protein modelling can be quantified and better understood. We show that highly accurate PF calculations are not a prerequisite for HDX-MS simulations that are capable of effectively discriminating between native and non-native protein folds. The simulations can also be performed directly on unique structures facilitating high-throughput evaluation of many alternate conformations. The ability of HDX-MS to classify the conformations of homo-protein assemblies is also investigated. In contrast to protein monomers, we show a significant lack of correspondence between the simulated and experimental HDX-MS data for these systems with a subsequent decrease in the ability of HDX-MS to identify native states. However, we demonstrate surprisingly high diagnostic ability of the simulated data for assemblies in which a significant proportion of the individual chains occupy protein-protein interfaces. We relate this to the number of peptides that can sample alternate subunit orientations and discuss these observations within the larger context of applying HDX-MS to evaluate protein structures.Graphical

Highlights

Hydrogen deuterium exchange mass spectrometry (HDXMS) reports on time-dependent changes in the deuterium uptake of a protein in D2O solvent with a structural probe at virtually every amino acid along the protein backbone [1,2,3]
The ability of Hydrogen deuterium exchange mass spectrometry (HDX-molecular dynamics (MS)) to identify native protein folds was evaluated with alpha lactalbumin and barnase with the protection factors (PFs) of these proteins simulated according to Eq 1 after minor optimisation (Fig. S1, BMethods^) [5]
The aim of this work was to quantify the ability of HDX-MS to discriminate between native and non-native protein conformations based on a popular approach to estimate PFs from protein structures

Summary

Introduction

Hydrogen deuterium exchange mass spectrometry (HDXMS) reports on time-dependent changes in the deuterium uptake of a protein in D2O solvent with a structural probe at virtually every amino acid along the protein backbone [1,2,3]. The capacity to discriminate between native and non-native quaternary structures of protein complexes is high for protein assemblies in which each subunit has multiple interchain contacts. We relate this to an increase in the number of peptides that can sample alternate chain orientations in these systems. Taken together, these data add to our understanding of the use of HDX-MS for structural evaluation and provide an important foundation on which future developments in the area can be built

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