Detection and structural features of the betaB2-B3-crystallin heterodimer by radical probe mass spectrometry (RP-MS)

Protein Footprinting with Radical Probe Mass Spectrometry- Two Decades of Achievement

BACKGROUND

Radical Probe Mass Spectrometry (RP-MS) describes a pioneering methodology in structural biology that enables the study of protein structures, their interactions, and dynamics on fast timescales (down to sub-milliseconds). Hydroxyl radicals (•OH) generated directly from water within aqueous solutions induce the oxidation of reactive, solvent accessible amino acid side chains that are then analyzed by mass spectrometry. Introduced in 1998 at the American Society for Mass Spectrometry annual conference, RP-MS was first published on in 1999.

OBJECTIVE

This review article describes developments and applications of the RP-MS methodology over the past two decades.

METHODS

The RP-MS method has been variously referred to as synchrotron X-ray radiolysis footprinting, Hydroxyl Radical Protein Footprinting (HRPF), X-ray Footprinting with Mass Spectrometry (XF-MS), Fast Photochemical Oxidation of Proteins (FPOP), oxidative labelling, covalent oxidative labelling, and even the Stability of Proteins from Rates of Oxidation (SPROX).

RESULTS

The article describes the utility of hydroxyl radicals as a protein structural probe, the advantages of RP-MS in comparison to other MS-based approaches, its proof of concept using ion mobility mass spectrometry, its application to protein structure, folding, complex and aggregation studies, its extension to study the onset of protein damage, its implementation using a high throughput sample loading approach, and the development of protein docking algorithms to aid with data analysis and visualization.

CONCLUSION

RP-MS represents a powerful new structural approach that can aid in our understanding of the structure and functions of proteins, and the impact of sustained oxidation on proteins in disease pathogenesis.

Stability of the βB2B3 crystallin heterodimer to increased oxidation by radical probe and ion mobility mass spectrometry

Ion mobility mass spectrometry was employed to study the structure of the βB2B3-crystallin heterodimer following oxidation through its increased exposure to hydroxyl radicals. The results demonstrate that the heterodimer can withstand limited oxidation through the incorporation of up to some 10 oxygen atoms per subunit protein without any appreciable change to its average collision cross section and thus conformation. These results are in accord with the oxidation levels and timescales applicable to radical probe mass spectrometry (RP-MS) based protein footprinting experiments. Following prolonged exposure, the heterodimer is increasingly degraded through cleavage of the backbone of the subunit crystallins rather than denaturation such that heterodimeric structures with altered conformations and ion mobilities were not detected. However, evidence from measurements of oxidation levels within peptide segments, suggest the presence of some aggregated structure involving C-terminal domain segments of βB3 crystallin across residues 115-126 and 152-166. The results demonstrate, for the first time, the ability of ion mobility in conjunction with RP-MS to investigate the stability of protein complexes to, and the onset of, free radical based oxidative damage that has important implications in cataractogenesis.

Advances in radical probe mass spectrometry for protein footprinting in chemical biology applications

Radical Probe Mass Spectrometry (RP-MS), first introduced in 1999, utilizes hydroxyl radicals generated directly within aqueous solutions using synchrotron radiolysis, electrical discharge, and photochemical laser sources to probe protein structures and their interactions. It achieves this on millisecond and submillisecond timescales that can be used to capture protein dynamics and folding events. Hydroxyl radicals are ideal probes of solvent accessibility as their size approximates a water molecule. Their high reactivity results in oxidation at a multitude of amino acid side chains providing greater structural information than a chemical cross-linker that reacts with only one or few residues. The oxidation of amino acid side chains occurs at rates in accord with the solvent accessibility of the residue so that the extent of oxidation can be quantified to reveal a three-dimensional map or footprint of the protein's surface. Mass spectrometry is central to this analysis of chemical oxidative labelling. This tutorial review, some 15 years on from the first reports, highlights the development and significant growth of the application of RP-MS including its validation and utility with ion-mobility mass spectrometry (IM-MS), the use of RP-MS data to help model protein complexes, studies of the onset of oxidative damage, and more recent advances that enable high throughput applications through simultaneous protein oxidation and on-plate deposition. The accessibility of the RP-MS technology, by means of a modified electrospray ionization source, enables the approach to be implemented in many laboratories to address a wide range of applications in chemical biology.

Homology-modelled structure of the βB2B3-crystallin heterodimer studied by ion mobility and radical probe MS

Ion mobility MS was employed to study the structure of the βB2B3-crystallin heterodimer following its detection by ESI-TOF MS. The results demonstrate that the heterodimer has a similar cross-section (3 165 Å(2)) and structure to the βB2B2-crystallin homodimer. Several homology-modelled structures for the βB2B3 heterodimer were constructed and assessed in terms of their calculated collision cross-sections and whether the solvent accessibilities of reactive amino acid side chains throughout the βB3 subunit are in accord with measured oxidation levels in radical probe MS protein footprinting experiments. The βB2B3 heterodimer AD model provides the best representation of the heterodimer's structure overall following a consideration of both the ion mobility and radical probe MS data.

Ability of N-acetylcarnosine to protect lens crystallins from oxidation and oxidative damage by radical probe mass spectrometry (RP-MS)

The application of Radical Probe Mass Spectrometry based on protein footprinting studies is described to investigate the effectiveness of the antioxidant N-acetylcarnosine (NAC) in preventing oxidative damage to lens crystallins present in the eye of mammals. Despite separate clinical trials which have reported the benefit of administering NAC to the eye as a 1% topical solution for the treatment of human cataract, no evidence was found to suggest that the antioxidant had any significant direct effect on reducing the levels of oxidation within the most abundant lens crystallins, α and β-crystallin, at the molecular level at increasing concentrations of NAC. The results of this laboratory study suggest that the therapeutic benefit demonstrated in clinical trials is associated with the nature or formulation of the topical solution and/or that the mode of action of NAC as an antioxidant is not a direct one.