Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: Application to galectin-1

Biomolecular surface mapping methods offer an important alternative method for characterizing protein-protein and protein-ligand interactions in cases in which it is not possible to determine high-resolution three-dimensional (3D) structures of complexes. Hydroxyl radical footprinting offers a significant advance in footprint resolution compared with traditional chemical derivatization. Here we present results of footprinting performed with hydroxyl radicals generated on the nanosecond time scale by laser-induced photodissociation of hydrogen peroxide. We applied this emerging method to a carbohydrate-binding protein, galectin-1. Since galectin-1 occurs as a homodimer, footprinting was employed to characterize the interface of the monomeric subunits. Efficient analysis of the mass spectrometry data for the oxidized protein was achieved with the recently developed ByOnic (Palo Alto, CA) software that was altered to handle the large number of modifications arising from side-chain oxidation. Quantification of the level of oxidation has been achieved by employing spectral intensities for all of the observed oxidation states on a per-residue basis. The level of accuracy achievable from spectral intensities was determined by examination of mixtures of synthetic peptides related to those present after oxidation and tryptic digestion of galectin-1. A direct relationship between side-chain solvent accessibility and level of oxidation emerged, which enabled the prediction of the level of oxidation given the 3D structure of the protein. The precision of this relationship was enhanced through the use of average solvent accessibilities computed from 10 ns molecular dynamics simulations of the protein.     

Future directions of structural mass spectrometry using hydroxyl radical footprinting

Hydroxyl radical protein footprinting coupled to mass spectrometry has been developed over the last decade and has matured to a powerful method for analyzing protein structure and dynamics. It has been successfully applied in the analysis of protein structure, protein folding, protein dynamics, and protein–protein and protein–DNA interactions. Using synchrotron radiolysis, exposure of proteins to a ‘white’ X‐ray beam for milliseconds provides sufficient oxidative modification to surface amino acid side chains, which can be easily detected and quantified by mass spectrometry. Thus, conformational changes in proteins or protein complexes can be examined using a time‐resolved approach, which would be a valuable method for the study of macromolecular dynamics. In this review, we describe a new application of hydroxyl radical protein footprinting to probe the time evolution of the calcium‐dependent conformational changes of gelsolin on the millisecond timescale. The data suggest a cooperative transition as multiple sites in different molecular subdomains have similar rates of conformational change. These findings demonstrate that time‐resolved protein footprinting is suitable for studies of protein dynamics that occur over periods ranging from milliseconds to seconds. In this review, we also show how the structural resolution and sensitivity of the technology can be improved as well. The hydroxyl radical varies in its reactivity to different side chains by over two orders of magnitude, thus oxidation of amino acid side chains of lower reactivity are more rarely observed in such experiments. Here we demonstrate that the selected reaction monitoring (SRM)‐based method can be utilized for quantification of oxidized species, improving the signal‐to‐noise ratio. This expansion of the set of oxidized residues of lower reactivity will improve the overall structural resolution of the technique. This approach is also suggested as a basis for developing hypothesis‐driven structural mass spectrometry experiments. Copyright © 2010 John Wiley & Sons, Ltd.     

Selective oxidation of a primary hydroxyl in the presence of secondary one

RuCl₂(PPh₃)₃-benzene system has been found to be highly effective for the title selective oxidation providing 10-hydroxyundecanal in 89% yield from 1,10-undecanediol.     

Mechanism of cysteine oxidation by a hydroxyl radical: a theoretical study.

Cysteine oxidation by HO(.) was studied at a high level of ab initio theory in both gas phase and aqueous solution. Potential energy surface scans in the gas phase performed for the model system methanethiol+HO(.) indicate that the reactants can form two intermediate states: a sulfur-oxygen adduct and a hydrogen bound reactant complex. However these states appear to play a minor role in the reaction mechanism as long as they are fast dissociating states. Thus the main reaction channel predicted at the QCISD(T)/6-311+G(2df,2pd) level of theory is the direct hydrogen atom abstraction. The reaction mechanism is not perturbed by solvation which was found to induce only small variations in the Gibbs free energy of different reactant configurations. The larger size reactant system cysteine+HO* was treated by the integrated molecular orbital+molecular orbital (IMOMO) hybrid method mixing the QCISD(T)/6-311+G(2df,2pd) and the UMP2/6-311+G(d,p) levels of theory. The calculated potential energy, enthalpy, and Gibbs free energy barriers are slightly different from those of methanethiol. The method gave a rate constant for cysteine oxidation in aqueous solution, k=2.4 x 10(9) mol(-1) dm(3) s(-1), which is in good agreement with the experimental rate constant. Further analysis showed that the reaction is not very sensitive to hydrogen bonding and electrical polarity of the molecular environment.     

Impact of limited oxidation on protein ion mobility and structure of importance to footprinting by radical probe mass spectrometry

The effect of hydroxyl radical induced oxidation on the collision cross-sections of hen egg lysozyme and bovine ubiquitin was investigated by travelling wave ion mobility mass spectrometry for the first time. The oxidized ions of lysozyme and ubiquitin share common collision cross-sections with their unoxidized counterparts suggesting that they share common structures that were unaffected by limited oxidation. In the case of bovine ubiquitin, two distinct conformers were detected for the protein in its unoxidized and oxidized states though no change in the levels of each was observed upon oxidation. This supports the validity of Radical Probe Mass Spectrometry (RP-MS) using an electrical discharge source for protein footprinting experiments. Travelling wave ion mobility mass spectrometry has been used for the first time to confirm that limited oxidation does not have an impact on the global structure of proteins.     

Theoretical and experimental interpretations of phenol oxidation by the hydroxyl radical

Phenol oxidation by OH radicals produced by the Fenton reaction was studied and the oxidation process was monitored by the UV–visible, ¹³C NMR and LC techniques. The results show that benzoquinone is formed. In the NMR and LC experiments, since the peaks corresponding to isomers ortho and para- benzoquinones are unresolved, DFT was used to determine the branching ratios of the isomers formation that coincides with their ΔG values (ortho > para > meta): 72% for ortho, 23% for para and 5.0% for meta. Furthermore, the energy profile of the OH attack at ortho is quite similar to that at the para position while the meta position attack is less favored by 2.0 kcal/mol.     

Heterogeneous glyoxal oxidation: a potential source of secondary organic aerosol

Laboratory studies are described that suggest reactive uptake of glyoxal on particulate containing HNO(3) could contribute to the formation of secondary organic aerosol (SOA) in the upper troposphere (UT). Using a Knudsen cell flow reactor, glyoxal is observed to react on supercooled H(2)O/HNO(3) surfaces to form condensed-phase glyoxylic acid. This product was verified by derivatization and GC-MS analysis. The reactive uptake coefficient, γ, of glyoxal varies only slightly with the pressure of nitric acid, from γ = 0.5 to 3.0 × 10(-3) for nitric acid pressures between 10(-8) and 10(-6) Torr. The data do not show any dependence on temperature (181-201 K) or pressure of glyoxal (10(-7) to 10(-5) Torr). Using the determined reactive uptake kinetics in a simple model shows that glyoxal uptake to supercooled H(2)O/HNO(3) may account for 4-53% of the total organic mass fraction of aerosol in the UT.     

Reactivity of nucleosides with a hydroxyl radical in non-aqueous medium

DNA damage: The reactivity of HO(.) with silylated 2'-deoxyribonucleosides was investigated in acetonitrile by means of a time-resolved technique. The obtained rate constants were in general slightly lower than those reported for the natural nucleosides in water. Analysis of the reaction mixture by UPLC-MS revealed that HO(.) attack occurred at the nucleobase (see scheme).     

Determination of hydroxyl radical in Fenton system

Under visible light illumination,2,3-diaminophenazine(DAPN) was generated from the oxidation of o-phenylenediamine (OPDA) in Fe~(3+)/H_2O_2 solution.Hydroxyl radical(~·OH) produced in this system was determined by directly measuring the concentration of DAPN.In comparison with the traditional methods,the determination is more accurate and simple.     

Autocatalysis in oxidation reactions of verdazyl radicals with hydroperoxides

The reaction of 2,4,6-triphenyl- and 2,3,4,6-tetraphenylverdazyl with tert-butyl hydroperoxide in acetonitrile solution and acetonitrile-water mixture was studied. This reaction was shown to be autocatalytic owing to verdazylium hydroxide formation in the course of the reaction. The main kinetic parameters were determined for the catalytic and non-catalytic reactions.     

A ‘waterproof’ catalyst for the oxidation of secondary amines to nitrones with alkyl hydroperoxides

Catalytic oxidation of secondary amines to nitrones using alkyl hydroperoxides as primary oxidant has been demonstrated for the first time. The titanium alkoxide catalyst is protected from co-product water by the combined use of a tightly binding trialkanolamine ligand and molecular sieves. Nitrones can be obtained in high yield (up to 98%) under homogeneous, anhydrous conditions and even in the absence of solvent. The reactions are fast (2-7 h) and good selectivity can be achieved with as little as 1% catalyst.     

Formation of cross-linked adducts between guanine and thymine mediated by hydroxyl radical and one-electron oxidation: a theoretical study

The role of local geometric and stereo-electronic effects in tuning the preference for different cross-linked adducts between thymine and purinic bases has been analyzed by a computational approach rooted in density functional theory. Our study points out that G--T and T--G tandem lesions are produced according to the same mechanism as A--T and T--A intrastrand adducts, and in both cases purine--T adducts are preferred rather than the opposite sequences. Moreover, use of conceptual DFT tools allows the rationalization of the preferential occurrence of G--T and T--G tandem lesions in place of their A--T and T--A counterparts.     

Regioselective sulfonation of a secondary hydroxyl group of cyclodextrins

A new and convenient procedure has been developed for the regioselective tosylation of a C-2 hydroxyl group of cyclodextrins via cyclic tin intermediate.     

Application of peptidyl radicals into a new radical cascade leading to unsaturated gamma-lactams

Radical cyclization of dipeptides 1a-h proceeds smoothly to give five- and seven-membered rings in good to moderate total yields using Stork's catalytic tin hydride method. A radical is generated on a protecting group and translocated to the peptide moiety. Following a cyclization reaction, the vinyl radical can abstract hydrogen from a benzyl group on an amine, which results in elimination of the protected amine group. Encouraging results have notably been obtained with amino acids other than glycine.     

Selective sulfonation of a secondary hydroxyl group of β-cyclodextrin

Tosylation of the secondary side of β-cyclodextrin, which has previously been incorrectly reported, can be achieved by tosyl transfer from 3-nitrophenyl toluenesulfonate to the C-2 hydroxyl of the cyclodextrin.     

Catalysis of radical reactions in mixed micelles of surfactants with hydroperoxides

The peculiarities of the catalytic action of cationic surfactants (CSurf) in combination with hydroperoxides on the generation of radicals and the influence of various factors on this process (transition metal compounds, oxygen, and external magnetic field) were considered. In the oxidized hydrocarbons (RH), hydroperoxides (ROOH), which are the primary amphiphilic products of oxidation, form mixed micelles {mROOH…nCSurf} with CSurf, in which fast decomposition of ROOH into radicals occurs and other polar components (metal compounds, inhibitors, etc.) can concentrate, which significantly affects the rate and mechanism of oxidation. The cationic surfactants immobilized on a solid support retain the ability to catalyze the decomposition of hydroperoxides, forming radicals, and to initiate radical oxidation and polymerization. It was found that acetylcholine, which is the most important neurotransmitter that plays an important role in the neuromuscular and cognitive activity of living beings, like cationic surfactants, catalyzes the radical decomposition of hydroperoxides in organic media, and the yield of radicals in this process decreases in a magnetic field and in the presence of oxygen.