Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics

Lento, Cristina; Zhu, Shaolong; Brown, Kerene A.; Knox, Ruth; Liuni, Peter; Wilson, Derek J.

doi:10.3791/55464-v

Cited by 3 publications

(2 citation statements)

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“…Proteins undergo the H/D exchange during the electrophoresis while migrating in the capillary in the deuterated background electrolyte solution, and this is followed by top-down MS analysis and gas-phase fragmentations to assess the deuterium uptake levels at both the global and fragment levels. Lastly, there are also two other methods in this collection that highlight different methods of H/D exchange, namely exchange for lyophilized power 8 and exchange after electrospray ionization 9 .…”

Section: Ms-based Protein Footprinting Approaches Assess Thementioning

confidence: 99%

Mass Spectrometry-Based Approaches for the Analysis of Protein Higher Order Structure

Liu

Huang

2023

JoVE

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Section: Ms-based Protein Footprinting Approaches Assess Thementioning

confidence: 99%

Mass Spectrometry-Based Approaches for the Analysis of Protein Higher Order Structure

Liu

Huang

2023

JoVE

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“…In higher-order conformations, more structured and solvent inaccessible regions are protected from exchange compared to disordered and solvent accessible regions of the molecule [5]. The m/z shifts arising from isotopic exchange within the latter regions are currently exploited by HDX-MS to study structures of challenging systems [18][19][20][21][22][23][24][25][26] folding dynamics [27][28][29][30][31], protein-protein and protein-oligonucleotide interactions [32][33][34][35][36][37][38][39][40], as well as protein-ligand interactions and any associated conformational changes [41][42][43][44][45][46][47][48][49].…”

Section: Introductionmentioning

confidence: 99%

Examining DNA Structures with In-droplet Hydrogen/Deuterium Exchange Mass Spectrometry

Attanayake,

Mahmud,

Banerjee

et al. 2024

Preprint

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Capillary vibrating sharp-edge spray ionization (cVSSI) combined with hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has been utilized to characterize different solution-phase DNA conformers including DNA G-quadruplex topologies as well as triplex DNA and duplex DNA. In general, G-quadruplex DNA shows a wide range of protection of hydrogens extending from ~12% to ~21% deuterium incorporation. Additionally, the DNA sequences selected to represent parallel, antiparallel, and hybrid G-quadruplex topologies exhibit slight differences in deuterium uptake levels which appear to loosely relate to overall conformer stability. Notably, the exchange level for one of the hybrid sequence sub topologies of G-quadruplex DNA (24 TTG) is significantly different (compared with the others studied here) despite the DNA sequences being highly comparable. For the quadruplex-forming sequences, correlation analysis suggests protection of base hydrogens involved in tetrad hydrogen bonding. For duplex DNA ~19% deuterium incorporation is observed while only ~16% is observed for triplex DNA. This increased protection of hydrogens may be due to the added backbone scaffolding and Hoogsteen base pairing of the latter species. These experiments lay the groundwork for future studies aimed at determining the structural source of this protection as well as the applicability of the approach for ascertaining different oligonucleotide folds, co-existing conformations, and/or overall conformer flexibility.

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HDX-MS: An Analytical Tool to Capture Protein Motion in Action

2020

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Virtually all protein functions in the cell, including pathogenic processes, require coordinated motion of atoms or domains, i.e., conformational dynamics. Understanding protein dynamics is therefore critical both for drug development and to learn about the underlying molecular causes of many diseases. Hydrogen–Deuterium Exchange Mass Spectrometry (HDX-MS) provides valuable information about protein dynamics, which is highly complementary to the static picture provided by conventional high-resolution structural tools (i.e., X-ray crystallography and structural NMR). The amount of protein required to carry out HDX-MS experiments is a fraction of the amount required by alternative biophysical techniques, which are also usually lower resolution. Use of HDX-MS is growing quickly both in industry and academia, and it has been successfully used in numerous drug and vaccine development efforts, with important roles in understanding allosteric effects and mapping binding sites.

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Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics

Cited by 3 publications

References 0 publications

Mass Spectrometry-Based Approaches for the Analysis of Protein Higher Order Structure

Mass Spectrometry-Based Approaches for the Analysis of Protein Higher Order Structure

Examining DNA Structures with In-droplet Hydrogen/Deuterium Exchange Mass Spectrometry

HDX-MS: An Analytical Tool to Capture Protein Motion in Action

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