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1.
J Am Soc Mass Spectrom ; 35(5): 1040-1054, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38626331

ABSTRACT

Mass-spectrometry-based methods have made significant progress in the characterization of post-translational modifications (PTMs) in peptides and proteins; however, room remains to improve fragmentation methods. Ideal MS/MS methods are expected to simultaneously provide extensive sequence information and localization of PTM sites and retain labile PTM groups. This collection of criteria is difficult to meet, and the various activation methods available today offer different capabilities. In order to examine the specific case of phosphorylation on peptides, we investigate electron transfer dissociation (ETD), electron-activated dissociation (EAD), and 193 nm ultraviolet photodissociation (UVPD) and compare all three methods with classical collision-induced dissociation (CID). EAD and UVPD show extensive backbone fragmentation, comparable in scope to that of CID. These methods provide diverse backbone fragmentation, producing a/x, b/y, and c/z ions with substantial sequence coverages. EAD displays a high retention efficiency of the phosphate modification, attributed to its electron-mediated fragmentation mechanisms, as observed in ETD. UVPD offers reasonable retention efficiency, also allowing localization of the PTM site. EAD experiments were also performed in an LC-MS/MS workflow by analyzing phosphopeptides spiked in human plasma, and spectra allow accurate identification of the modified sites and discrimination of isomers. Based on the overall performance, EAD and 193 nm UVPD offer alternative options to CID and ETD for phosphoproteomics.


Subject(s)
Phosphopeptides , Tandem Mass Spectrometry , Ultraviolet Rays , Phosphopeptides/chemistry , Phosphopeptides/analysis , Tandem Mass Spectrometry/methods , Phosphorylation , Electrons , Amino Acid Sequence , Humans , Protein Processing, Post-Translational , Chromatography, Liquid/methods
2.
Anal Bioanal Chem ; 415(27): 6619-6632, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37755489

ABSTRACT

The study of protein oxidation remains a challenge despite the biomedical interest in reliable biomarkers of oxidative stress. This is particularly true for carbonylations although, recently, liquid chromatography-mass spectrometry techniques (LC-MS) have been proposed to detect this non-enzymatic and poorly distributed oxidative modification of proteins using untargeted or carbonyl-reactive probe methods. These methods proved to be feasible but could not preserve the dynamic range of the protein sample, making it impossible to quantify oxidatively modified proteoforms compared with native proteoforms. Here, we propose an innovative method based on the implementation of a reactive carbonyl probe conjugated with a laser-sensitive chromophore, dabcyl-aminooxy, which confers optical specificity to the LC-MS approach. In addition, our protein carbonyl detection method allows us to localize individual carbonylation sites by observing fragments of derivatized oxidized peptides. Two model proteins, alpha-synuclein and beta-lactoglobulin, were oxidized and carbonylation sites were detected, resulting in the identification of respectively 34 and 77 different carbonylated amino acids. Thus, we demonstrated the application of a direct and sensitive method for studying protein carbonylation sites in complex protein extracts.

3.
Sci Technol Adv Mater ; 23(1): 446-456, 2022.
Article in English | MEDLINE | ID: mdl-36081837

ABSTRACT

The development of highly ultraviolet (UV) and near-infrared (NIR) absorbent transparent coatings is an important enabling technology and area of research for environmental sustainability and energy conservation. Different amounts of K4[{Nb5TaXi 12}Xa 6] cluster compounds (X = Cl, Br) dispersed into polyvinylpyrrolidone matrices were prepared by a simple, nontoxic and low-cost wet chemical method. The resulting solutions were used to fabricate visibly transparent, highly UV and NIR absorbent coatings by drop casting. The properties of the solution and films were investigated by complementary techniques (optical absorption, electrospray ionization mass spectrometry and Raman spectroscopy). The UV and NIR absorption of such samples strongly depended on the concentration, dispersion and oxidation state of the [{Nb5TaXi 12}Xa 6] nanocluster-based units. By varying and controlling these parameters, a remarkable improvement of the figures of merit TL/TE and SNIR for solar-glazing applications was achieved compared to the previous results on nanocomposite coatings based on metal atom clusters.

4.
Nanomaterials (Basel) ; 12(12)2022 Jun 15.
Article in English | MEDLINE | ID: mdl-35745391

ABSTRACT

The antagonism between global energy needs and the obligation to slow global warming is a current challenge. In order to ensure sufficient thermal comfort, the automotive, housing and agricultural building sectors are major energy consumers. Solar control materials and more particularly, selective glazing are part of the solutions proposed to reduce global energy consumption and tackle global warming. In this context, these works are focused on developing new highly ultraviolet (UV) and near-infrared (NIR) absorbent nanocomposite coatings based on K4[{Nb6-xTaxXi12}Xa6]. (X = Cl, Br, 0 ≤ x ≤ 6) transition metal cluster compounds. These compounds contain cluster-based active species that are characterized by their strong absorption of UV and NIR radiations as well as their good transparency in the visible range, which makes them particularly attractive for window applications. Their integration, by solution processes, into a silica-polyethylene glycol or polyvinylpyrrolidone matrices is discussed. Of particular interest is the control and the tuning of their optical properties during the integration and shaping processes. The properties of the solutions and films were investigated by complementary techniques (UV-Vis-NIR spectrometry, ESI-MS, SEM, HRTEM, etc.). Results of these works have led to the development of versatile solar control coatings whose optical properties are competitive with commercialized material.

5.
ACS Appl Mater Interfaces ; 14(18): 21116-21130, 2022 May 11.
Article in English | MEDLINE | ID: mdl-35500275

ABSTRACT

The high potential of [{Nb6Cli12}La6] cluster-based building blocks as near-infrared radiation blockers for energy saving applications is exposed in the present paper (i = inner edge-bridging ligand, a = apical ligand of the Nb6; L = H2O and/or Cl). To do so, a combined experimental and theoretical investigation of edge-bridged [{Nb6Cli12}Cla6-x(H2O)x]m+/0/n- cluster unit series (x = 0, 4, 6; m = 2, 3, 4; n = 2, 3, 4) has been carried out. By using the K4[{Nb6Cli12}Cla6] starting solid-state precursor, we explored the behavior of the [{Nb6Cli12}Cla6]4- cluster unit during the different steps of its integration as a building block into a polyvinylpyrrolidone (PVP) matrix to form a glass coating composite denoted {Nb6Cli12}m+@PVP (m = 2 or 3). The optical, vibrational and redox properties [{Nb6Cli12}Cla6-x(H2O)x]m+/0/n- building blocks have been interpreted with the support of electronic structure calculations and simulation of properties. The chemical modifications and oxidation properties have been identified and studied thanks to various techniques in solution. Combining Raman and ultraviolet-visible spectroscopies, electrochemistry, and quantum chemical simulations, we bring new knowledge to the understanding of the evolution of the properties of the [{Nb6Cli12}Cla6-x(H2O)x]m+/0/n- cluster units as a function of the number of valence electron per cluster (VEC) and the nature of terminal ligands (x = 0, n = 4; x = 4, charge = 0; x = 6, m = 4). The fine understanding of the physical properties and vibrational fingerprints depending on the VEC and chemical modifications in solution are mandatory to master the processing of cluster-based building blocks for the controlled design and shaping of glass coating nanocomposites. On the basis of this acquired knowledge, [{Nb6Cli12}Cla6-x(H2O)x]m+/0/n- building blocks were embedded in a PVP matrix. The resulting {Nb6Cli12}2+@PVP nanocomposite film shows excellent ultraviolet (UV, 280-380 nm) and near-infrared (NIR, 780-1080 nm) blocking ability (>90%) and a highly visible light transmittance thanks to the controlled integration of the {Nb6Cli12}2+ cluster core. The figures of merit (FOM) value of Tvis/Tsol (Tvis = visible transmittance and Tsol = solar transmittance) as well as the haze, clarity, and the NIR shielding values (SNIR) were measured. After optimization of the integration process, a {Nb6Cli12}2+@PVP nanocomposite on glass substrate has been obtained with a high FOM equal to 1.29. This high value places the transparent green olive {Nb6Cli12}2+@PVP nanocomposites at the top system in the benchmark in the field of glass coating composites for energy-saving applications.

6.
Phys Chem Chem Phys ; 23(44): 25038-25047, 2021 Nov 17.
Article in English | MEDLINE | ID: mdl-34605499

ABSTRACT

Photo-chemistry provides a non-intuitive but very powerful way to probe kinetically limited, sometimes thermodynamically non-favored reactions and, thus, access highly specific products. However, reactivity in the excited state is difficult to characterize directly, due to short lifetimes and challenges in controlling the reaction medium. Among photo-activatable reagents, rhodamine dyes find widespread uses due to a number of favorable properties including their high absorption coefficient. Their readily adaptable synthesis allows development of tailor-made dyes for specific applications. Remarkably, few studies have directly probed the chemical reactivity of their triplet excited state. Here we present a new conceptual approach to examine the specific chemistry of the triplet excited state. We have developed a pump (488 nm) - probe (600 nm) strategy to examine the gas-phase lifetime and reactivity of the triplet cation of Rhodamine 6G (3Rh6G+) in an ion trap mass spectrometer. The confounding effects of solvent, aggregation and formation of other reactive intermediates is thus avoided allowing fundamental reactivity to be explored. In the presence, in the ion trap, of helium seeded with 1% of nitric oxide (˙NO) (∼ 60 ion/˙NO collisions per second), the triplet lifetime is shortened from 1.9 s to 0.7 s. Simultaneously, the reaction products [Rh6G-H]˙+ and [Rh6G-H + NO]+ are observed. Reaction of 3Rh6G+ with ˙NO2 yields [Rh6G-H]˙+, [Rh6G-H + NO2]+ and [Rh6G-2H]+. None of these products are observed for the singlet, 1Rh6G+. DFT calculations suggest a stepwise mechanism only allowed from 3Rh6G+, in which H atom abstraction by ˙NOx (x = 1 or 2) yields [Rh6G-H]˙+ which, then, reacts with another ˙NOx molecule. This illustrates the power of light to initiate specific chemical reactions, and the relevance of gas-phase ion-molecule reaction approaches to understand stepwise reaction mechanism from specific excited states.


Subject(s)
Nitric Oxide/chemistry , Rhodamines/chemistry , Density Functional Theory , Mass Spectrometry , Molecular Structure , Photochemical Processes
7.
Chemistry ; 27(48): 12371-12379, 2021 Aug 25.
Article in English | MEDLINE | ID: mdl-34137472

ABSTRACT

We investigated the photoionization and fragmentation of isolated metal protoporphyrin IX cations (MPPIX+ with M=Fe, Co, Zn) by means of vacuum-ultraviolet (VUV) action spectroscopy in the energy range of 8.5-35 eV. Experiments were carried out in the gas phase by interfacing an electrospray ionization tandem mass spectrometer with a synchrotron beamline. The mass spectra and partial ion yields show that photoexcitation of the precursor ions predominantly leads to . CH2 COOH radical side-chain losses of the macrocycle with additional methyl radical (. CH3 ) side-chain losses. Ionization, in contrast, leads to the formation of the intact ionized precursor and various doubly charged fragments which are mostly due to side-chain cleavages. Although statistical fragmentation dominates, we found evidence for non-statistical processes such as new fragments involving for example single and double H2 O losses, indicating that different relaxation mechanisms are at play upon photoionization compared to photoexcitation. The measured ionization energies were 9.6±0.2 eV, 9.4±0.2 eV and 9.6±0.2 eV for FePPIX+ , CoPPIX+ and ZnPPIX+ , respectively.


Subject(s)
Metalloporphyrins , Cations , Mass Spectrometry , Spectrum Analysis , Ultraviolet Rays
8.
Dalton Trans ; 50(23): 8002-8016, 2021 Jun 21.
Article in English | MEDLINE | ID: mdl-34008603

ABSTRACT

Edge-bridged halide tantalum clusters based on the {Ta6Br12}4+ core have been the topic of many physicostructural investigations both in solution and in the solid-state. Despite a large number of studies, the fundamental correlations between compositions, local symmetry, electronic structures of [{Ta6Bri12}La6]m+/n- cluster units (L = Br or H2O, in solution and in the solid-state), redox states, and vibrational and absorption properties are still not well established. Using K4[{Ta6Bri12}Bra6] as a starting precursor (i: inner and a: apical), we have investigated the behavior of the [{Ta6Bri12}Bra6]4- cluster unit in terms of oxidation properties and chemical modifications both in solution (water and organic solvent) and after recrystallization. A wide range of experimental techniques in combination with quantum chemical simulations afford new data that allow the puzzling behavior of the cluster units in response to changes in their environment to be revealed. Apical ligands undergo changes like modifications of interatomic distances to complete substitutions in solution that modify noticeably the cluster physical properties. Changes in the oxidation state of the cluster units also occur, which modify significantly their physical properties, including optical properties, which can thus be used as fingerprints. A subtle balance exists between the number of substituted apical ligands and the cluster oxidation state. This study provides new information about the exact nature of the species formed during the transition from the solid-state to solutions and vice versa. This shows new perspectives on optimization protocols for the design of Ta6 cluster-based materials.

9.
Rapid Commun Mass Spectrom ; 33 Suppl 1: 28-34, 2019 May.
Article in English | MEDLINE | ID: mdl-29885203

ABSTRACT

RATIONALE: Among the sources of structural diversity in biomolecular ions, the co-existence of protomers is particularly difficult to take into account, which in turn complicates structural interpretation of gas-phase data. METHODS: We investigated the sensitivity of gas-phase photo-fragmentation measurements and ion mobility spectrometry (IMS) to the protonation state of a model peptide derivatized with chromophores. Accessible interconversion pathways between the different identified conformers were probed by tandem ion mobility measurement. Furthermore, the excitation coupling between the chromophores has been probed through photo-fragmentation measurements on mobility-selected ions. All results were interpreted based on molecular dynamics simulations. RESULTS: We show that protonation can significantly affect the photo-fragmentation yields. Especially, conformers with very close collision cross sections (CCSs) may display dramatically different photo-fragmentation yields in relation with different protonation patterns. CONCLUSIONS: We show that, even if precise structure assignment based on molecular modeling is in principle difficult for large biomolecular assemblies, the combination of photo-fragmentation and IMS can help to identify the signature of protomer co-existence for a population of biomolecular ions in the gas phase. Such spectroscopic data are particularly suitable to follow conformational changes.


Subject(s)
Ion Mobility Spectrometry/methods , Photolysis , Protein Subunits , Molecular Dynamics Simulation , Peptides/analysis , Peptides/chemistry , Protein Subunits/analysis , Protein Subunits/chemistry , Tandem Mass Spectrometry/methods
10.
J Phys Chem B ; 122(35): 8317-8329, 2018 09 06.
Article in English | MEDLINE | ID: mdl-30068075

ABSTRACT

Unfolding of proteins gives detailed information about their structure and energetics and can be probed as a response to a change of experimental conditions. Ion mobility coupled to native mass spectrometry is a gas-phase technique that can observe such unfolding in the gas phase by monitoring the collision cross section (CCS) after applying an activation, for example, by collisions (collision-induced unfolding, CIU). The structural assignments needed to interpret the experiments can profit from dedicated modeling strategies. While predictions of ion-mobility data for well-defined and structurally characterized systems is straightforward, systematic free-energy calculations or biased molecular dynamics simulations that employ IMS data are still limited. The methods with which CCS values are calculated so far do not allow for analytical gradients needed in biased molecular dynamics (MD), and further, explicit CCS calculations still can pose computational bottleneck-when integrated into MD-bioinformatics workflows. These limitations motivate one to revisit known correlations of the CCS with the aim to find computationally cheap and versatile but still at least semiquantitative descriptions of the CCS by pure structural descriptors. We have therefore investigated the correlation of CCS with the key structural parameter often used in computational unfolding studies-the gyration radius-for several small monomeric and dimeric proteins. We work out the challenges and caveats of the combinations of the configurational sampling method and the CCS-calculation algorithm. The correlations were found to be sensitive to the generation conditions and additionally to the system topology. To reduce the amount of fitting to be undertaken, we devise a simple structural model for the CCS that shares some commonalities with the hard-sphere model and the projection algorithm but is designed to take unfolding into account. With this model, we suggest a two-point interpolating function rather than fitting a large data set, at only little deterioration of the predictive power. We further proceed to a model with composition and structure dependence that builds only upon the gyration radius and the chemical formula to apply the found CCS scaling behavior-the scaled macroscopic sphere (sMS) predictor. We demonstrate its applicability to describe unfolding and also its transferability for a larger set of structures from the RSCPDB. As we have found for the dimeric systems, that shape correlations with one global descriptor qualitatively break down, we finally suggest a recipe to switch between global and fragment-based CCS prediction, that takes up the ideas of coarse-graining protein complexes. The presented models and approaches might provide a basis to boost the integration of structural modeling with multistage IMS experiments, especially in the field of large-scale bioinformatics or "on-the-fly" biasing of MD, where computational efficiency is critical.

11.
J Am Soc Mass Spectrom ; 29(9): 1826-1834, 2018 09.
Article in English | MEDLINE | ID: mdl-29949057

ABSTRACT

The nonapeptide oxytocin (OT) is used as a model sulfur-containing peptide to study the damage induced by vacuum UV (VUV) radiations. In particular, the effect of the presence (or absence in reduced OT) of oxytocin's internal disulfide bridge is evaluated in terms of photo-fragmentation yield and nature of the photo-fragments. Intact, as well as reduced, OT is studied as dianions and radical anions. Radical anions are prepared and photo-fragmented in two-color experiments (UV + VUV) in a linear ion trap. VUV photo-fragmentation patterns are analyzed and compared, and radical-induced mechanisms are proposed. The effect of VUV is principally to ionize but secondary fragmentation is also observed. This secondary fragmentation seems to be considerably enabled by the initial position of the radical on the molecule. In particular, the possibility to form a radical on free cysteines seems to increase the susceptibility to VUV fragmentation. Interestingly, disulfide bridges, which are fundamental for protein structure, could also be responsible for an increased resistance to ionizing radiations. Graphical Abstract.


Subject(s)
Anions/chemistry , Disulfides/chemistry , Oxytocin/chemistry , Mass Spectrometry , Oxidation-Reduction , Photolysis , Ultraviolet Rays , Vacuum
12.
Phys Chem Chem Phys ; 20(17): 12223-12228, 2018 May 07.
Article in English | MEDLINE | ID: mdl-29687123

ABSTRACT

Ruthenium complexes involving sulfoxide ligands can undergo linkage isomerization upon light absorption, accompanied by dramatic changes in their optical properties. These remarkable photochromic properties are sensitive to the nature of the ligand as well as to that of the solvent. We used tandem ion mobility spectrometry coupled to mass spectrometry to gain direct experimental insight into the isomerization pathways connecting the different linkage isomers of an isolated ruthenium complex with two dimethyl-sulfoxide ligands. We find that the isomerization behavior of the solvent-free complex differs from that previously reported in the solution-phase, which is in line with recent theoretical predictions.

13.
J Am Soc Mass Spectrom ; 29(2): 270-283, 2018 02.
Article in English | MEDLINE | ID: mdl-28980177

ABSTRACT

Mass spectrometry-based methods have made significant progress in characterizing post-translational modifications in peptides and proteins; however, certain aspects regarding fragmentation methods must still be improved. A good technique is expected to provide excellent sequence information, locate PTM sites, and retain the labile PTM groups. To address these issues, we investigate 10.6 µm IRMPD, 213 nm UVPD, and combined UV and IR photodissociation, known as HiLoPD (high-low photodissociation), for phospho-, sulfo-, and glyco-peptide cations. IRMPD shows excellent backbone fragmentation and produces equal numbers of N- and C-terminal ions. The results reveal that 213 nm UVPD and HiLoPD methods can provide diverse backbone fragmentation producing a/x, b/y, and c/z ions with excellent sequence coverage, locate PTM sites, and offer reasonable retention efficiency for phospho- and glyco-peptides. Excellent sequence coverage is achieved for sulfo-peptides and the position of the SO3 group can be pinpointed; however, widespread SO3 losses are detected irrespective of the methods used herein. Based on the overall performance achieved, we believe that 213 nm UVPD and HiLoPD can serve as alternative options to collision activation and electron transfer dissociations for phospho- and glyco-proteomics. Graphical Abstract ᅟ.


Subject(s)
Glycopeptides/chemistry , Peptides/chemistry , Phosphopeptides/chemistry , Protein Processing, Post-Translational , Sulfur/analysis , Amino Acid Sequence , Infrared Rays , Mass Spectrometry/methods , Photolysis , Ultraviolet Rays
14.
J Am Soc Mass Spectrom ; 29(1): 133-139, 2018 01.
Article in English | MEDLINE | ID: mdl-29038996

ABSTRACT

In the context of native mass spectrometry, the development of gas-phase structural probes sensitive to the different levels of structuration of biomolecular assemblies is necessary to push forward conformational studies. In this paper, we provide the first example of the combination of ion mobility (IM) and Förster resonance energy transfer (FRET) measurements within the same experimental setup. The possibility to obtain mass- and mobility-resolved FRET measurements is demonstrated on a model peptide and applied to monitor the collision-induced unfolding of ubiquitin. Graphical Abstract ᅟ.

15.
J Am Soc Mass Spectrom ; 28(10): 2181-2188, 2017 10.
Article in English | MEDLINE | ID: mdl-28755260

ABSTRACT

The visible photodissociation mechanisms of QSY7-tagged peptides of increasing size have been investigated by coupling a mass spectrometer and an optical parametric oscillator laser beam. The experiments herein consist of energy resolved collision- and laser-induced dissociation measurements on the chromophore-tagged peptides. The results show that fragmentation occurs by similar channels in both activation methods, but that the branching ratios are vastly different. Observation of a size-dependent minimum laser pulse energy required to induce fragmentation, and collisional cooling rates in time resolved experiments show that laser-induced dissociation occurs through the absorption of multiple photons by the chromophore and the subsequent heating through vibrational energy redistribution. The differences in branching ratio between collision- and laser-induced dissociation can then be understood by the highly anisotropic energy distribution following absorption of a photon. Graphical Abstract ᅟ.


Subject(s)
Mass Spectrometry/methods , Peptides/chemistry , Ions/chemistry , Molecular Probes/chemistry , Peptide Fragments/chemistry , Photochemical Processes , Photons , Rhodamines/chemistry
16.
Anal Chem ; 89(18): 9664-9670, 2017 09 19.
Article in English | MEDLINE | ID: mdl-28727418

ABSTRACT

Using label-free ToF-SIMS imaging mass spectrometry, we generated a map of small molecules differentially expressed in the Drosophila wing imaginal disc. The distributions of these moieties were in line with gene expression patterns observed during wing imaginal disc development. Combining ToF-SIMS imaging and coherent anti-Stokes Raman spectroscopy (CARS) microspectroscopy allowed us to locally identify acylglycerols as the main constituents of the pattern differentiating the future body wall tissue from the wing blade tissue. The findings presented herein clearly demonstrate that lipid localization patterns are strongly correlated with a developmental gene expression. From this correlation, we hypothesize that lipids play a so far unrecognized role in organ development.


Subject(s)
Drosophila melanogaster/growth & development , Drosophila melanogaster/genetics , Gene Expression Profiling , Glycerides/analysis , Imaginal Discs/growth & development , Spectrometry, Mass, Secondary Ion , Wings, Animal/growth & development , Animals , Drosophila melanogaster/anatomy & histology , Glycerides/genetics , Imaginal Discs/anatomy & histology , Spectrum Analysis, Raman , Time Factors , Wings, Animal/anatomy & histology
17.
Anal Chem ; 89(7): 4230-4237, 2017 04 04.
Article in English | MEDLINE | ID: mdl-28263061

ABSTRACT

The shape of the spectral features in arrival time distributions (ATDs) recorded by ion mobility spectrometry (IMS) can often be interpreted in terms of the coexistence of different isomeric species. Interconversion between such species is also acknowledged to influence the shape of the ATD, even if no general quantitative description of this effect is available. We present an analytical model that allows simulating ATDs resulting from interconverting species. This model is used to reproduce experimental data obtained on a bistable system and to interpret discrepancies between measurements on different types of instruments. We show that the proposed model can be further exploited to extract kinetic and thermodynamic data from tandem-IMS measurements.

18.
Anal Chem ; 89(8): 4604-4610, 2017 04 18.
Article in English | MEDLINE | ID: mdl-28351129

ABSTRACT

To obtain a more detailed understanding of how structure influences the function and interaction of biomolecules, it is important to develop structure sensitive techniques to probe these relationships. Alongside in vivo and in vitro techniques, it is instructive to consider in vacuo methodologies: for example native mass spectrometry, ion mobility mass spectrometry, and FRET. Here, we propose a novel technique for probing biomolecular structure based on the changes in photophysics of a chromophore upon dimer formation. Comparison of solution and gas phase measurements on a doubly tagged tripeptide shows that dimer-induced fluorescence quenching is accompanied by an increase in photofragmentation yield. The 12-28 fragment of amyloid beta was used to show that as the charge state was increased-previously shown to cause a conformational change from compact random coil to extended helical structure-the disappearance of a band at 495 nm could be correlated with the level of self-quenching. The presence of features in the action spectrum of the +3 charge state of both quenched and unquenched chromophores allowed inference of multiple conformations. Single wavelength measurements on doubly tagged ubiquitin cations were performed to show that the technique is feasible on a small protein. These results demonstrate that self-quenching is a sensitive and fast gas-phase probe of biomolecular structure that can be directly linked to solution phase measurements. Further, it is capable of probing very small changes in conformation, making it complementary to FRET based techniques, which are insensitive at very short chromophore separations.


Subject(s)
Amyloid beta-Peptides/chemistry , Fluorescence Resonance Energy Transfer , Amyloid beta-Peptides/metabolism , Dimerization , Fluorescent Dyes/chemistry , Gases/chemistry , Ion Mobility Spectrometry , Oligopeptides/chemistry , Oligopeptides/metabolism , Protein Structure, Secondary
19.
J Am Soc Mass Spectrom ; 28(1): 38-49, 2017 01.
Article in English | MEDLINE | ID: mdl-27506208

ABSTRACT

Mass spectrometry is an extremely powerful technique for analysis of biological molecules, in particular proteins. One aspect that has been contentious is how much native solution-phase structure is preserved upon transposition to the gas phase by soft ionization methods such as electrospray ionization. To address this question-and thus further develop mass spectrometry as a tool for structural biology-structure-sensitive techniques must be developed to probe the gas-phase conformations of proteins. Here, we report Förster resonance energy transfer (FRET) measurements on a ubiquitin mutant using specific photofragmentation as a reporter of the FRET efficiency. The FRET data is interpreted in the context of circular dichroism, molecular dynamics simulation, and ion mobility data. Both the dependence of the FRET efficiency on the charge state-where a systematic decrease is observed-and on methanol concentration are considered. In the latter case, a decrease in FRET efficiency with methanol concentration is taken as evidence that the conformational ensemble of gaseous protein cations retains a memory of the solution phase conformational ensemble upon electrospray ionization. Graphical Abstract ᅟ.


Subject(s)
Fluorescence Resonance Energy Transfer/methods , Ubiquitin/chemistry , Amino Acid Sequence , Animals , Cations/chemistry , Cattle , Circular Dichroism , Gases/chemistry , Molecular Dynamics Simulation , Mutation , Protein Conformation , Spectrometry, Mass, Electrospray Ionization , Static Electricity , Ubiquitin/genetics
20.
Chemphyschem ; 17(19): 3129-3138, 2016 Oct 05.
Article in English | MEDLINE | ID: mdl-27428813

ABSTRACT

Action spectroscopy has emerged as an analytical tool to probe excited states in the gas phase. Although comparison of gas-phase absorption properties with quantum-chemical calculations is, in principle, straightforward, popular methods often fail to describe many molecules of interest-such as xanthene analogues. We, therefore, face their nano- and picosecond laser-induced photofragmentation with excited-state computations by using the CC2 method and time-dependent density functional theory (TDDFT). Whereas the extracted absorption maxima agree with CC2 predictions, the TDDFT excitation energies are blueshifted. Lowering the amount of Hartree-Fock exchange in the DFT functional can reduce this shift but at the cost of changing the nature of the excited state. Additional bandwidth observed in the photofragmentation spectra is rationalized in terms of multiphoton processes. Observed fragmentation from higher-lying excited states conforms to intense excited-to-excited state transitions calculated with CC2. The CC2 method is thus suitable for the comparison with photofragmentation in xanthene analogues.

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