Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) has become a key technique for monitoring structural and dynamic aspects of proteins in solution. This approach relies on the fact that exposure of a protein to D(2)O induces rapid amide H → D exchange in disordered regions that lack stable hydrogen-bonding. Tightly folded elements are much more protected from HDX, resulting in slow isotope exchange that is mediated by the structural dynamics ("breathing motions") of the protein. MS-based peptide mapping is a well established technique for measuring the mass shifts of individual protein segments. This tutorial review briefly discusses basic fundamentals of HDX/MS, before highlighting a number of recent developments and applications. Gas phase fragmentation strategies represent a promising alternative to the traditional proteolysis-based approach, but experimentalists have to be aware of scrambling phenomena that can be encountered under certain conditions. Electron-based dissociation methods provide a solution to this problem. We also discuss recent advances that facilitate the applicability of HDX/MS to membrane proteins, and to the characterization of short-lived protein folding intermediates. It is hoped that this review will provide a starting point for novices, as well as a useful reference for practitioners, who require an overview of some recent trends in HDX/MS.

Amide H/D exchange (HDX) mass spectrometry (MS) is widely used for protein structural studies. Traditionally, this technique involves protein labeling in D(2)O, followed by acid quenching, proteolytic digestion, and analysis of peptide deuteration levels by HPLC/MS. There is great interest in the development of alternative HDX approaches involving the top-down fragmentation of electrosprayed protein ions, instead of relying on enzymatic cleavage and solution-phase separations. A number of recent studies have demonstrated that electron capture dissociation (ECD) results in fragmentation of gaseous protein ions with little or no H/D scrambling. However, the successful application of this approach for in-depth protein conformational studies has not yet been demonstrated. The current work uses horse myoglobin as a model system for assessing the suitability of HDX-MS with top-down ECD for experiments of this kind. It is found that ECD can pinpoint the locations of protected amides with an average resolution of less than two residues for this 17 kDa protein. Native holo-myoglobin (hMb) shows considerable protection from exchange in all of its helices, whereas loops are extensively deuterated. Fraying is observable at some helix termini. Removal of the prosthetic heme group from hMb produces apo-myoglobin (aMb). Both hMb and aMb share virtually the same HDX protection pattern in helices A-E, whereas helix F is unfolded in aMb. In addition, destabilization is evident for some residues close to the beginning of helix G, the end of helix H, and the C-terminus of the protein. The structural changes reported herein are largely consistent with earlier NMR data for sperm whale myoglobin, although small differences between the two systems are evident. Our findings demonstrate that the level of structural information obtainable with top-down ECD for small to medium-sized proteins considerably surpasses that of traditional HDX-MS experiments, while at the same time greatly reducing undesired amide back exchange.

Complexes [{(mu-SCH2)2NCH2C6H5}{Fe(CO)2L(1)}{Fe(CO)2L(2)}] (L(1) = CO, L(2) = P(Pyr) 3, 2; L(1) = L(2) = P(Pyr)3, 3) were prepared, which have the lowest reduction potentials for the mono- and double-CO-displaced diiron complexes reported so far. Hydrogen evolution, driven by visible light, was successfully observed for a three-component system, consisting of a ruthenium polypyridine complex, the biomimetic model complex 2 or 3, and ascorbic acid as both electron and proton donor in CH3CN/H2O. The electron transfer from photogenerated Ru(bpy)3(+) to 2 or 3 was detected by laser flash photolysis. Under optimal conditions, the total turnover number for hydrogen evolution was 4.3 based on 2 and 86 based on Ru(bpy)3(2+) in a three-hour photolysis.

Mass spectrometry (MS) methods involving gas-phase fragmentation hold considerable promise for analyzing regioselective deuteration patterns of proteins following solution-phase amide hydrogen exchange (HX). However, the general viability of such an approach is questionable due to the possible occurrence of intramolecular hydrogen migration ("scrambling"), which tends to randomize or distort the spatial isotope distribution. Rand et al. (J. Am. Chem. Soc. 2008, 130, 1341-1349) have recently reported the application of electron capture dissociation (ECD) for measuring deuteration patterns of short peptides with very little scrambling by FT-MS. The current work shows that even much larger systems such as the 76-residue protein ubiquitin can be successfully analyzed by ECD following solution-phase HX. The resulting c and z. ion deuteration levels are in remarkable agreement with previous NMR data, demonstrating that the extent of scrambling and/or other gas-phase artifacts is negligible. These results open the door to future experiments on the folding, structure, and dynamics of proteins by HX/ECD-FT-MS.

Aiming for better understanding of the large complexity of excited-state processes in carotenoids, we have studied the excitation wavelength dependence of the relaxation dynamics in the carotenoid zeaxanthin. Excitation into the lowest vibrational band of the S2 state at 485 nm, into the 0-3 vibrational band of the S2 state at 400 nm, and into the 2B(u)+ state at 266 nm resulted in different relaxation patterns. While excitation at 485 nm produces the known four-state scheme (S2 --> hot S1 --> S1 --> S0), excess energy excitation led to additional dynamics occurring with a time constant of 2.8 ps (400 nm excitation) and 4.9 ps (266 nm excitation), respectively. This process is ascribed to a conformational relaxation of conformers generated by the excess energy excitation. The zeaxanthin S state was observed regardless of the excitation wavelength, but its population increased after 400 and 266 nm excitation, suggesting that conformers generated by the excess energy excitation are important for directing the population toward the S state. The S2-S1 internal conversion time was shortened from 135 to 70 fs when going from 485 to 400 nm excitation, as a result of competition between the S2-S1 internal conversion from the vibrationally hot S2 state and S2 vibrational relaxation. The S1 lifetime of zeaxanthin was within experimental error the same for all excitation wavelengths, yielding approximately 9 ps. No long-lived species have been observed after excitation by femtosecond pulses regardless of the excitation wavelength, but excitation by nanosecond pulses at 266 nm generated both zeaxanthin triplet state and cation radical.

A noncovalent assembly of a pyridyl-functionalized hydrogenase active-site model complex and zinc tetraphenylporphyrin has been obtained and characterized. Upon light irradiation, fluorescence quenching by electron transfer was observed from the singlet excited state of the porphyrin to the diiron center, and the mechanism was verified by fluorescence lifetime and transient absorption spectroscopic measurements. In contrast to molecular dyads linked by covalent bonds, the assembled system was designed to avoid charge recombination via complex dissociation after photo-induced electron transfer. Visible light-driven hydrogen generation was observed from this self-assembled system. The assembling strategy employed in this study has the potential to be used for any other hydrogenase models in the future.

It remains an open question as to whether experiments involving collision-induced dissociation (CID) can provide a viable approach for monitoring spatially resolved deuteration levels in electrosprayed polypeptide ions. A number of laboratories reported the successful application of CID following solution-phase H/D exchange (HDX), whereas others found that H/D scrambling precluded site-specific measurements. The aim of the current work is to help clarify the general feasibility of HDX-CID methods, using a 22-residue zinc-bound protein domain (Zn-ZBD) as model system. Metal binding in Zn-ZBD should confer structural rigidity, and the presence of several basic residues should sequester mobile charge carriers in the gas phase. Both of these factors were expected to suppress the extent of scrambling. HDX was carried out by employing rapid on-line mixing, thereby mimicking conditions typically encountered in kinetic pulse-labeling studies. Quadrupole time-of-flight MS/MS of pulse-labeled Zn-ZBD provides high sequence coverage. However, the measured fragment deuteration levels do not correlate with the known H-bonding pattern of Zn-ZBD, suggesting the occurrence of extensive scrambling. Instead of showing a uniform distribution, the fragment ions reveal a distinct nonrandom pattern of deuteration levels. In the absence of prior information, these data could erroneously be ascribed to the presence of protected sites. However, the observed patterns clearly originate from other factors; possibly they are caused by modulations of the amide CID efficiency by kinetic isotope effects. It is concluded that scrambling does not represent the only conceptual problem in HDX-CID studies and that control experiments on uniformly labeled samples are essential for ruling out interpretation artifacts.

Aβ peptides can assemble into amyloid fibrils, which represent one of the hallmarks of Alzheimer's disease. Recent studies, however, have focused on the behavior of small soluble Aβ oligomers that possess a much greater neurotoxicity than mature fibrils. The structural characterization of these oligomers remains difficult because of their highly dynamic and polymorphic nature. This work explores the behavior of Aβ(1-40) in a slightly basic solution (pH 9.3) at a low salt concentration (10 mM ammonium acetate). These conditions lead to the formation of small oligomers, without any signs of fibrillation for several hours. The structure and dynamics of these oligomers were characterized by circular dichroism spectroscopy, size exclusion chromatography, and millisecond time-resolved hydrogen exchange mass spectrometry (MS). Our results reveal rapid interconversion between Aβ(1-40) oligomers and monomers. The mole fraction of monomeric molecules is on the order of 40%. Oligomers consist of ~4 Aβ(1-40) molecules on average, and the resulting assemblies have a predominantly β-sheet secondary structure. Hydrogen exchange proceeds in the EX1 regime. This feature allows the application of conformer-specific top-down MS. Electron capture dissociation is used for interrogating the deuteration behavior of the Aβ(1-40) oligomers. This approach provides a spatial resolution of ~2 residues. The backbone amide deuteration pattern uncovered in this way is consistent with a β-turn-β motif for L17-M35. The N-terminus is involved in hydrogen bonding, as well, whereas protection gradually tapers off for C-terminal residues 35-40. Our data are consistent with earlier proposals, according to which Aβ(1-40) oligomers adopt a β-barrel structure. In general terms, this study demonstrates how top-down MS with precursor ion selection can be employed for structural studies of specific protein conformers within a heterogeneous mix.