OH Labeling Research Articles

Evaluating Mass Spectrometry-Based Hydroxyl Radical Protein Footprinting of a Benchtop Flash Oxidation System against a Synchrotron X-ray Beamline.

Hydroxyl radical protein footprinting (HRPF) using synchrotron X-ray radiation (XFP) and mass spectrometry is a well-validated structural biology method that provides critical insights into macromolecular structural dynamics, such as determining binding sites, measuring affinity, and mapping epitopes. Numerous alternative sources for generating the hydroxyl radicals (•OH) needed for HRPF, such as laser photolysis and plasma irradiation, complement synchrotron-based HRPF, and a recently developed commercially available instrument based on flash lamp photolysis, the FOX system, enables access to laboratory benchtop HRPF. Here, we evaluate performing HRPF experiments in-house with a benchtop FOX instrument compared to synchrotron-based X-ray footprinting at the NSLS-II XFP beamline. Using lactate oxidase (LOx) as a model system, we carried out •OH labeling experiments using both instruments, followed by nanoLC-MS/MS bottom-up peptide mass mapping. Experiments were performed under high glucose concentrations to mimic the highly scavenging conditions present in biological buffers and human clinical samples, where less •OH are available for reaction with the biomolecule(s) of interest. The performance of the FOX and XFP HRPF methods was compared, and we found that tuning the •OH dosage enabled optimal labeling coverage for both setups under physiologically relevant highly scavenging conditions. Our study demonstrates the complementarity of FOX and XFP labeling approaches, demonstrating that benchtop instruments such as the FOX photolysis system can increase both the throughput and the accessibility of the HRPF technique.

Multiplex Chemical Labeling of Amino Acids for Protein Footprinting Structure Assessment.

Protein footprinting with mass spectrometry is an established structural biology technique for mapping solvent accessibility and assessing molecular-level interactions of proteins. In hydroxyl radical protein footprinting (HRPF), hydroxyl (OH) radicals generated by water radiolysis or other methods covalently label protein side chains. Because of the wide dynamic range of OH reactivity, not all side chains are easily detected in a single experiment. Novel reagent development and the use of radical chain reactions for labeling, including trifluoromethyl radicals, is a potential approach to normalize the labeling across a diverse set of residues. HRPF in the presence of a trifluoromethylation reagent under the right conditions could provide a "one-pot" reaction for multiplex labeling of protein side chains. Toward this goal, we have systematically evaluated amino acid labeling with the recently investigated Langlois' reagent (LR) activated by X-ray-mediated water radiolysis, followed by three different mass spectrometry methods. We compared the reactivity of CF3 and OH radical labeling for all 20 protein side chains in a competition-free environment. We found that all 20 amino acids exhibited CF3 or OH labeling in LR. Our investigations provide the evidence and knowledge set to perfect hydroxyl radical-activated trifluoromethyl chemistry as "one-pot" reaction for multiplex labeling of protein side chains to achieve higher resolution in HRPF.

Hydroxyl-Radical Reaction Pathways for the Fast Photochemical Oxidation of Proteins Platform As Revealed by 18O Isotopic Labeling.

Fast photochemical oxidation of protein (FPOP) has become an important mass spectrometry-based protein footprinting approach. Although the hydroxyl radical (•OH) generated by photolysis of hydrogen peroxide (H2O2) is most commonly used, the pathways for its reaction with amino-acid side chains remain unclear. Here, we report a systematic study of •OH oxidative modification of 13 amino acid residues by using 18O isotopic labeling. The results differentiate three classes of residues on the basis of their oxygen uptake preference toward different oxygen sources. Histidine, arginine, tyrosine, and phenylalanine residues preferentially take oxygen from H2O2. Methionine residues competitively take oxygen from H2O2 and dissolved oxygen (O2), whereas the remaining residues take oxygen exclusively from O2. Results reported in this work deepen the understanding of •OH labeling pathway on a FPOP platform, opening new possibilities for tailoring FPOP conditions in addressing many biological questions in a profound way.

Submillisecond Protein Folding Events Monitored by Rapid Mixing and Mass Spectrometry-Based Oxidative Labeling

Kinetic measurements can provide insights into protein folding mechanisms. However, the initial (submillisecond) stages of folding still represent a formidable analytical challenge. A number of ultrarapid triggering techniques have been available for some time, but coupling of these techniques with detection methods that are capable of providing detailed structural information has proven to be difficult. The current work addresses this issue by combining submillisecond mixing with laser-induced oxidative labeling. Apomyoglobin (aMb) serves as a model system for our measurements. Exposure of the protein to a brief pulse of hydroxyl radical (·OH) at different time points during folding introduces covalent modifications at solvent accessible side chains. The extent of labeling is monitored using mass spectrometry-based peptide mapping, providing spatially resolved measurements of changes in solvent accessibility. The submillisecond mixer used here improves the time resolution by a factor of 50 compared to earlier ·OH labeling experiments from our laboratory. Data obtained in this way indicate that early aMb folding events are driven by both local and sequence-remote docking of hydrophobic side chains. Assembly of a partially formed A(E)G(H) scaffold after 0.2 ms is followed by stepwise consolidation that ultimately yields the native state. Major conformational changes go to completion within 0.1 s. The technique introduced here is capable of providing in-depth structural information on very short time scales that have thus far been dominated by low resolution (global) spectroscopic probes. By employing submillisecond mixing in conjunction with slower mixing techniques, it is possible to observe complete folding pathways, from fractions of a millisecond all the way to minutes.

Exploring membrane protein structural features by oxidative labeling and mass spectrometry

Despite their biological importance, the structural characterization of integral membrane proteins (IMPs) by x-ray crystallography and NMR spectroscopy remains challenging. Hence, there is a need for complementary approaches that are capable of probing IMP conformational features in a robust fashion. Covalent labeling relies on the principle that solvent accessible regions can be modified by reactive species, whereas buried segments are protected. The readout of the labeling pattern is conducted by mass spectrometry. Hydroxyl radical (·OH) introduces oxidative modifications at amino acid side chains. In this article, the authors discuss the application of ·OH labeling for the structural interrogation of IMPs. Kyte-Doolittle hydropathy analyses are widely used for generating IMP topology models. The validation of these models by mutational techniques is labor intensive. ·OH labeling can readily distinguish transmembrane elements from solvent-exposed loops, thereby providing an alternative topology validation tool. For IMPs with published crystal structures, oxidative modifications can report on functionally relevant dynamic features that are invisible in the static x-ray data. The coupling of pulsed ·OH labeling with rapid mixing techniques represents a novel approach for studying IMP folding kinetics. In conclusion, ·OH labeling is a versatile tool that can provide insights into the structure and dynamics of IMPs.

Kinetic Folding Mechanism of an Integral Membrane Protein Examined by Pulsed Oxidative Labeling and Mass Spectrometry

We report the application of pulsed oxidative labeling for deciphering the folding mechanism of a membrane protein. SDS-denatured bacteriorhodopsin (BR) was refolded by mixing with bicelles in the presence of free retinal. At various time points (20 ms to 1 day), the protein was exposed to a microsecond ·OH pulse that induces oxidative modifications at solvent-accessible methionine side chains. The extent of labeling was determined by mass spectrometry. These measurements were complemented by stopped-flow spectroscopy. Major time-dependent changes in solvent accessibility were detected for M20 (helix A) and M118 (helix D). Our kinetic data indicate a sequential folding mechanism, consistent with models previously suggested by others on the basis of optical data. Yet, ·OH labeling provides additional structural insights. An initial folding intermediate I 1 gets populated within 20 ms, concomitantly with formation of helix A. Subsequent structural consolidation leads to a transient species I 2. Noncovalent retinal binding to I 2 induces folding of helix D, thereby generating an intermediate I R⁎. In the absence of retinal, the latter transition does not take place. Hence, formation of helix D depends on retinal binding, whereas this is not the case for helix A. As the cofactor settles deeper into its binding pocket, a final transient species I R⁎⁎ is generated. This intermediate converts into native BR within minutes by formation of the retinal–K216 Schiff base linkage. The combination of pulsed covalent labeling and optical spectroscopy employed here should also be suitable for exploring the folding mechanisms of other membrane proteins.

Studying significance of apoptosis in mediating tolbutamide‐induced teratogenesis in vitro

The incidence of type 2 diabetes mellitus (non-insulin-dependent diabetes mellitus) is growing worldwide and poses a serious public health problem in a current paradigm of changing life style and food habits. Tolbutamide (sulfonylurea) is among the commonly used anti-diabetic drugs worldwide for treating type 2 diabetes and is known to cause congenital malformations in animals. In this study, the effect of tolbutamide on major organogenesis period and the possible involvement of apoptosis in mediating congenital malformations have been carried out. In the present study design, post-implantation rat embryos of day 11 were cultured for 24 h with various concentrations of tolbutamide, i.e., 10, 100, and 1000 μg/mL cultures, respectively. The growth and developmental of each embryo was evaluated and compared with control ones for the presence of any malformations. The tolbutamide decreased all growth and developmental parameters in a concentration-dependent manner, when compared with control. However, exposure to tolbutamide at 10 μg/mL culture did not show any significant effect on embryonic growth and development in vitro. In parallel to this, flow cytometric analysis (cell cycle and annexin V binding) and DNA fragmentation assay were carried out followed by quantitation by 3'-OH labeling of cultured rat embryos to examine the role of apoptosis in bringing about tolbutamide-induced teratogenesis. All results were found to be dose dependent and an increase in apoptosis in embryonic tissues may be related to the increased risk of congenital malformations. The outcome of the research suggested that apoptosis might be involved in mediating teratogenesis of tolbutamide in vitro. Further research is warranted to fully understand this mechanism.

Temporal Development of Protein Structure during S100A11 Folding and Dimerization Probed by Oxidative Labeling and Mass Spectrometry

Considerable progress in deciphering the mechanisms of protein folding has been made. However, most work in this area has focused on single-chain systems, whereas the majority of proteins are oligomers. The spontaneous assembly of intact multi-subunit systems from disordered building blocks encompasses the formation of intramolecular as well as intermolecular contacts. Both types of interaction affect the solvent accessibility of individual protein segments. This work employs pulsed hydroxyl radical (·OH) labeling for tracking time-dependent accessibility changes during folding and assembly of the S100A11 homodimer. ·OH induces covalent modifications at exposed residues. Structural snapshots are obtained by combining ·OH labeling with rapid mixing and mass spectrometry. The free subunits are found to possess a partially non-native hydrophobic core that prevents subunit association during the initial stages of the reaction. Instead, the protein forms an early (10 ms) monomeric intermediate that exhibits reduced solvent accessibility in regions distant from helices I and IV, which constitute the dimerization interface. Subunit association is complete after 800 ms, although the protein retains significant disorder in helices II and III at this point. Subsequent consolidation of these elements leads to the native state. The experimental strategy used here could become a general tool for deciphering kinetic mechanisms of biomolecular self-assembly processes.

Site-Directed Mutagenesis Combined with Oxidative Methionine Labeling for Probing Structural Transitions of a Membrane Protein by Mass Spectrometry

Exposure of the membrane protein bacteriorhodopsin (BR) to SDS induces partial breakdown of the native conformation. The exact structural properties of this SDS state remain a matter of debate, despite its widespread use in BR folding experiments. The current work employs hydroxyl radical (·OH) labeling in conjunction with mass spectrometry (MS)-based peptide mapping for probing the solvent accessibility of individual BR segments in the presence of SDS. Previous work revealed methionine sulfoxide formation to be the dominant oxidative pathway. Those data suggested extensive unfolding of helices A and D in SDS. Unfortunately, the lack of Met residues in helices C and F implies that no direct information on the behavior of the latter two elements could be obtained. Here, we address this problem by employing two variants with additional Met residues, L93M (helix C) and V179M (helix F). The oxidation behavior of the resulting 11 methionines can be grouped into three categories: (1) extensively labeled both in native BR and in SDS (loop residues M32, M68, and M163); (2) protected in the native state but not in SDS (M20, M118); (3) always protected (M56, M60, M93, M145, M179, M209). These data show that a solvent-inaccessible core is retained in SDS. This core consists of partially intact helices B, C, E, F, and G. The termini of these helices are highly dynamic and/or unraveled, particularly on the cytoplasmic side. Overall, this work demonstrates how the use of engineered ·OH labeling sites can provide insights into structural properties of membrane proteins.

Time-Dependent Changes in Side-Chain Solvent Accessibility during Cytochrome c Folding Probed by Pulsed Oxidative Labeling and Mass Spectrometry

The current work employs a novel approach for characterizing structural changes during the refolding of acid-denatured cytochrome c (cyt c). At various time points (ranging from 10 ms to 5 min) after a pH jump from 2 to 7, the protein is exposed to a microsecond hydroxyl radical (.OH) pulse that induces oxidative labeling of solvent-exposed side chains. Most of the covalent modifications appear as +16-Da adducts that are readily detectable by mass spectrometry. The overall extent of labeling decreases as folding proceeds, reflecting dramatic changes in the accessibility of numerous residues. Peptide mapping and tandem mass spectrometry reveal that the side chains of C14, C17, H33, F46, Y48, W59, M65, Y67, Y74, M80, I81, and Y97 are among the dominant sites of oxidation. Temporal changes in the accessibility of these residues are consistent with docking of the N- and C-terminal helices as early as 10 ms. However, structural reorganization at the helix interface takes place up to at least 1 s. Initial misligation of the heme iron by H33 leads to distal crowding, giving rise to low solvent accessibility of the displaced (native) M80 ligand and the adjacent I81. W59 retains a surprisingly high level of accessibility long into the folding process, indicating the presence of packing defects in the hydrophobically collapsed core. Overall, the results of this work are consistent with previous hydrogen/deuterium exchange studies that proposed a foldon-mediated mechanism. The structural data obtained by .OH labeling monitor the packing and burial of side chains, whereas hydrogen/deuterium exchange primarily monitors the formation of secondary structure elements. Hence, the two approaches yield complementary information. Considering the very short time scale of pulsed oxidative labeling, an extension of the approach used here to sub-millisecond folding studies should be feasible.

Involvement of apoptosis in mediating mitomycin C-induced teratogenesis in vitro

Mitomycin C (MMC) is among the most commonly used drugs worldwide and is known to cause congenital malformations and fetal death in animals. In this study, the effect of MMC on major organogenesis period and the role of apoptosis in mediating congenital malformations have been carried out. In the present study, post-implantation rat embryos of day 11 were cultured for 24 h with various concentrations of MMC, i.e. 1, 10, and 100 µg/ml cultures. The growth and developmental of each embryo was evaluated and compared with control ones for the presence of any malformations. The MMC decreased all growth and developmental parameters in a concentration-dependent manner, when compared with control. However, exposure to MMC at 1 µg/ml culture did not show any significant effect on embryonic growth and development. Parallel to this, flow cytometric analysis (cell cycle and annexin V binding) and DNA fragmentation assay were carried out followed by quantitation by 3′-OH labeling of cultured rat embryos to evaluate the role of apoptosis in bringing about MMC-induced teratogenesis. All results were found to be dose-dependent and an increase in apoptosis in embryonic tissues may be related to the increased risk of congenital malformations. The data suggested that apoptosis might be involved in mediating teratogenesis of MMC in vitro.

Role of Apoptosis in Mediating Salicylic Acid-Induced Teratogenesis In Vitro

Salicylic acid (SAL) is among the most commonly used drugs worldwide and is known to cause congenital malformations and fetal death in animals. In this study, the effect of SAL on major organogenesis period and the role of apoptosis in mediating congenital malformations have been carried out. In the present study, post-implantation rat embryos of day 11 were cultured for 24 h with various concentrations of SAL, i.e. 10, 100, and 1000 μg/ml cultures, respectively. The growth and developmental of each embryo was evaluated and compared with control ones for the presence of any malformations. The SAL decreased all growth and developmental parameters in a concentration-dependent manner, when compared with control. However, exposure to SAL at 10 μg/ml culture did not show any significant effect on embryonic growth and development. Parallel to this, flow cytometric analysis (cell cycle and annexin V binding) and DNA fragmentation assay were carried out followed by quantitation by 3′-OH labeling of cultured rat embryos to evaluate the role of apoptosis in bringing about SAL-induced teratogenesis. All results were found to be dose-dependent and an increase in apoptosis in embryonic tissues may be related to the increased risk of congenital malformations. The data suggested that apoptosis might be involved in mediating teratogenesis of SAL in vitro.

Protein structure and dynamics studied by mass spectrometry: H/D exchange, hydroxyl radical labeling, and related approaches

Mass spectrometry (MS) plays a central role in studies on protein structure and dynamics. This review highlights some of the recent developments in this area, with focus on applications involving the use of electrospray ionization (ESI) MS. Although this technique involves the transformation of analytes into highly nonphysiological species (desolvated gas-phase ions in the vacuum), ESI-MS can provide detailed insights into the solution-phase behavior of proteins. Notably, the ionization process itself occurs in a structurally sensitive manner. An increased degree of solution-phase unfolding is correlated with a higher level of protonation. Also, ESI allows the transfer of intact noncovalent complexes into the gas phase, thereby yielding information on binding partners, stoichiometries, and even affinities. A particular focus of this article is the use of hydrogen/deuterium exchange (HDX) methods and hydroxyl radical (.OH) labeling for monitoring dynamic and structural aspect of solution-phase proteins. Conceptual similarities and differences between the two methods are discussed. We describe a simple method for the computational simulation of protein HDX patterns, a tool that can be helpful for the interpretation of isotope exchange data recorded under mixed EX1/EX2 conditions. Important aspects of .OH labeling include a striking dependence on protein concentration, and the tendency of commonly used solvent additives to act as highly effective radical scavengers. If not properly controlled, both of these factors may lead to experimental artifacts.

γ-Ray-Mediated Oxidative Labeling for Detecting Protein Conformational Changes by Electrospray Mass Spectrometry

Exposure of proteins to hydroxyl radicals induces the incorporation of oxygen atoms into solvent-exposed side chains. Earlier studies have employed this approach for mapping protein-protein interactions in mass spectrometry-based footprinting experiments. This work explores whether the overall level of gamma-ray mediated oxidative labeling can be used for monitoring large-scale conformational changes. According to a recently developed kinetic model (Tong, X.; Wren, J. C.; Konermann, L. Anal. Chem. 2007, 79, 6376-6382), the apparent first-order rate constant for oxidative labeling can be approximated as k(app) = k(RAD)/([P](tot) + C/k(u)), where k(RAD) is the primary rate of *OH formation, [P](tot) is the protein concentration, C reflects the presence of competing radical deactivation channels, and ku is the rate constant at which hydroxyl radicals react with the protein. The current study introduces conformational effects into this model by proposing that k(u) = [see text for formula] , where N is the number of amino acids, alphai is a measure for the solvent exposure of residue i, and k(ch)(i) is the oxidation rate constant that would apply for a completely solvent-exposed side chain. Using myoglobin and cytochrome c as model systems, it is demonstrated that unfolding by addition of H(3)PO(4) increases k(app) by up to 30% and 70%, respectively. Unfolding by other commonly used denaturants such as organic acids or urea results in dramatically lower oxidation levels than for the native state, a behavior that is due to the radical scavenging activity of these substances (corresponding to an increased value of C). Control experiments on model peptides are suitable for identifying such "secondary" effects, i.e., factors that modify oxidation levels without being related to conformational changes. In conclusion, the overall *OH labeling level represents a viable probe of large-scale protein conformational changes only under conditions where secondary effects are known to be minimal and where [P](tot) is constant.

Effects of Protein Concentration on the Extent of γ-Ray-Mediated Oxidative Labeling Studied by Electrospray Mass Spectrometry

Exposure of aqueous protein solutions to gamma-rays results in the formation of *OH radicals that readily react with solvent-exposed amino acid side chains. The incorporation of oxygen leads to peak progressions with a spacing of 16 Da in the mass distribution of the polypeptide chain. Unlike some other oxidative labeling strategies, these radiolysis experiments do not require solution additives that could interfere with the analysis or that might cause secondary oxidation processes. Using myoglobin as a model system, we demonstrate that the level of oxidative labeling depends critically on the protein concentration. If ignored, this effect may lead to ambiguities in the interpretation of experiments employing *OH labeling for monitoring solvent-accessible surface areas, protein folding, and protein-protein interactions. We present a simple analysis that allows oxidation to be interpreted as a process with exponential kinetics, characterized by an apparent rate constant of the form kapp=kRAD/([P]tot+B), where kRAD is the primary rate of hydroxyl radical production, B is a constant, and [P]tot is the total protein concentration. While oxidative labeling may trigger some changes in protein conformation, it is found that the magnitude of this effect is surprisingly small, a result that is consistent with observations previously made by others.

Fibroblast Growth Factor‐2 inhibits Bleomycin‐induced DNA Damage in Murine Lung Endothelial Cells.

Fibroblast Growth Factor-2 (FGF2) protects mice from radiation- and LPS-induced lung injury. Here we investigated the effect of FGF2 on DNA damage caused by bleomycin (BLM) in mouse lung endothelial cells (MLEC). MLEC were treated with 0.1-10 ng FGF2/ml for 1 to 4h, and then with 100 or 500 ug BLM/ml for 15-45 min. Cells were either fixed with formaldehyde and permeabilized in 70% ethanol, or fixed with 95% ethanol/1% acetic acid and stored in PBS. In formaldehyde-fixed cells, DNA strand breaks containing 3′OH were labeled with fluorescein-12-dUTP by nick translation with DNA polymerase. Ethanol/acetic acid-fixed cells were immunostained with antibody to the phosphorylated histone (H) 2A variant, H2Ax (phospho-H2Ax), which accumulates at sites of double strand breakage, and a Cy3-secondary antibody. Cells were finally stained with H33342 to mark DNA. Fluorescence microscopic image intensities of fluorescein for 3′OH labeling, or Cy3 for phospho-H2Ax, were analyzed. FGF2 inhibited both measures of strand breakage. The results suggest that FGF2 can protect lung EC from BLM-induced single and/or double strand DNA breakage. Support: NIH HL68054.

Detecting Role of Apoptosis in Mediating Cyclophosphamide Induced Teratogenesis In Vitro

Programmed cell death (apoptosis) refers to a specific type of cell death under stringent genetic control. Even a slight alteration in this process leads to malformations characterized by birth defects. Based on the above hypothesis we deduced that apoptosis plays an important role in mediating the teratogenicity of cyclophosphamide in vitro. The present study was undertaken to see whether this phenomenon holds true or not. In this study, 11-day-old rat embryos were cultured for 24 hours with various concentrations of CP (i.e. 0, 5, 10 and 100 μg/ml culture). After culturing for 24 hours, embryos exposed to 10 and 100 μg/mL culture of CP were found having both malformations and growth retardation. Exposure to CP at 5 μg/mL culture did not show significant effect on embryonic development. Parallel to this, flow cytometric analysis (cell cycle and annexin V binding) and DNA fragmentation assay were also carried out followed by quantitation by 3′-OH labeling of cultured embryos to evaluate CP-induced apoptosis. All the results were found to be dose-dependant, and the data suggested that apoptosis is involved in mediating the teratogenicity of CP in vitro.

Expression of cell cycle proteins (cyclin D1 and cdk4) after controlled cortical impact in rat brain.

We measured the expression of Cyclin D1 and its kinase cdk4, 48 h after induction of cortical contusion in the rat. Brain from rats (n = 6) subjected to controlled cortical impact injury and sham-operated (n = 3) and normal (n = 2) rats were processed for dual label immunohistochemical study to identify cellular expression of these cell cycle proteins. Antibodies against neurofilaments 68 and 200 and glial fibrillary acidic protein were employed to identify neurons and astrocytes, respectively, whereas microglia were identified using histochemical detection of IB4-isolectin. Double staining for DNA fragmentation detection, using terminal deoxynucleotdyl transferase mediated biotinylated deoxyuridine triphosphate nick end 3 'OH labeling (TUNEL) and antibodies for expression of Cyclin D1 and cdk4 was also performed. Cyclin D1 and cdk4 were selectively expressed in morphologically intact or injured neurons throughout the rat brain. Apoptotic cells were not immunoreactive to Cyclin D1 and cdk4. The selective expression of cell cycle proteins observed in nonapoptotic postmitotic neurons suggests a role for these proteins in the survival of cells after cortical contusion.