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Maitre P, Scuderi D, Corinti D, Chiavarino B, Crestoni ME, Fornarini S. Applications of Infrared Multiple Photon Dissociation (IRMPD) to the Detection of Posttranslational Modifications. Chem Rev 2019; 120:3261-3295. [PMID: 31809038 DOI: 10.1021/acs.chemrev.9b00395] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy allows for the derivation of the vibrational fingerprint of molecular ions under tandem mass spectrometry (MS/MS) conditions. It provides insight into the nature and localization of posttranslational modifications (PTMs) affecting single amino acids and peptides. IRMPD spectroscopy, which takes advantage of the high sensitivity and resolution of MS/MS, relies on a wavelength specific fragmentation process occurring on resonance with an IR active vibrational mode of the sampled species and is well suited to reveal the presence of a PTM and its impact in the molecular environment. IRMPD spectroscopy is clearly not a proteomics tool. It is rather a valuable source of information for fixed wavelength IRMPD exploited in dissociation protocols of peptides and proteins. Indeed, from the large variety of model PTM containing amino acids and peptides which have been characterized by IRMPD spectroscopy, specific signatures of PTMs such as phosphorylation or sulfonation can be derived. High throughput workflows relying on the selective fragmentation of modified peptides within a complex mixture have thus been proposed. Sequential fragmentations can be observed upon IR activation, which do not only give rise to rich fragmentation patterns but also overcome low mass cutoff limitations in ion trap mass analyzers. Laser-based vibrational spectroscopy of mass-selected ions holding various PTMs is an increasingly expanding field both in the variety of chemical issues coped with and in the technological advancements and implementations.
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Affiliation(s)
- Philippe Maitre
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - Debora Scuderi
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
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Hanson-Heine MWD. Benchmarking DFT-D Dispersion Corrections for Anharmonic Vibrational Frequencies and Harmonic Scaling Factors. J Phys Chem A 2019; 123:9800-9808. [PMID: 31633366 DOI: 10.1021/acs.jpca.9b07886] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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Borotto NB, McClory PJ, Martin BR, Håkansson K. Targeted Annotation of S-Sulfonylated Peptides by Selective Infrared Multiphoton Dissociation Mass Spectrometry. Anal Chem 2017; 89:8304-8310. [PMID: 28708386 DOI: 10.1021/acs.analchem.7b01461] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein S-sulfinylation (R-SO2-) and S-sulfonylation (R-SO3-) are irreversible oxidative post-translational modifications of cysteine residues. Greater than 5% of cysteines are reported to occupy these higher oxidation states, which effectively inactivate the corresponding thiols and alter the electronic and physical properties of modified proteins. Such higher oxidation states are reached after excessive exposure to cellular oxidants, and accumulate across different disease states. Despite widespread and functionally relevant cysteine oxidation across the proteome, there are currently no robust methods to profile higher order cysteine oxidation. Traditional data-dependent liquid chromatography/tandem mass spectrometry (LC/MS/MS) methods generally miss low-occupancy modifications in complex analyses. Here, we present a data-independent acquisition (DIA) LC/MS-based approach, leveraging the high IR absorbance of sulfoxides at 10.6 μm, for selective dissociation and discovery of S-sulfonated peptides. Across peptide standards and protein digests, we demonstrate selective infrared multiphoton dissociation (IRMPD) of S-sulfonated peptides in the background of unmodified peptides. This selective DIA IRMPD LC/MS-based approach allows identification and annotation of S-sulfonated peptides across complex mixtures while providing sufficient sequence information to localize the modification site.
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Affiliation(s)
- Nicholas B Borotto
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Phillip J McClory
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Brent R Martin
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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4
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Chiavarino B, Crestoni ME, Fornarini S, Scuderi D, Salpin JY. Undervalued N3 Coordination Revealed in the Cisplatin Complex with 2'-Deoxyadenosine-5'-monophosphate by a Combined IRMPD and Theoretical Study. Inorg Chem 2017; 56:8793-8801. [PMID: 28718635 DOI: 10.1021/acs.inorgchem.7b00570] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The complex obtained by the reaction of cisplatin and 2'-deoxyadenosine-5'-monophosphate (5'-dAMP) in water has been isolated and detected by electrospray ionization mass spectrometry. The so-formed cis-[PtCl(NH3)2(5'-dAMP)]+ complex has been studied in detail by infrared multiple photon dissociation (IRMPD) spectroscopy in two spectral ranges, namely, 700-1900 and 2800-3800 cm-1, backed by quantum-chemical calculations at the B3LYP/LACV3P/6-311G** level of theory. In agreement with the computational results, the vibrational spectroscopic characterization of cis-[PtCl(NH3)2(5'-dAMP)]+ shows that the sampled ionic population comprises two major isomers, differentiated in the X-H stretching region by their distinct fragmentation patterns. One of these species presents coordination of the platinum moiety at the N3 position of adenine, whereas in the second one, platinum is bound at the N1 position of adenine. IRMPD kinetics have allowed an estimation of their relative proportions. Surprisingly, the most abundant component of cis-[PtCl(NH3)2(5'-dAMP)]+ is the N3 isomer, although it is slightly less stable than the other potential isomers in the gas phase. In contrast, the lowest-energy species, namely, the one showing cisplatin binding to the N7 position of adenine, seems to be the one less represented in the sampled ionic population. These findings suggest that the reaction of cisplatin with 5'-dAMP is governed by the kinetics of the process occurring in solution rather than by the thermodynamic factors.
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Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza" , Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza" , Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza" , Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Debora Scuderi
- LCP, Université Paris Sud Orsay, CNRS, Université Paris-Saclay , F-91405 Orsay, France
| | - Jean-Yves Salpin
- LAMBE, Université d'Evry Val d'Essonne, CEA, CNRS, Université Paris-Saclay , F-91025 Evry, France.,LAMBE, Université Cergy-Pontoise, Université Paris-Seine , F-91025 Evry, France
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5
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Scuderi D, Ignasiak MT, Serfaty X, de Oliveira P, Houée Levin C. Tandem mass spectrometry and infrared spectroscopy as a tool to identify peptide oxidized residues. Phys Chem Chem Phys 2016; 17:25998-6007. [PMID: 26292724 DOI: 10.1039/c5cp03223g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The final products obtained by the oxidation of small model peptides containing the thioether function, either methionine or S-methyl cysteine, have been characterized by tandem mass spectrometry and IR Multiple Photon Dissociation (IRMPD) spectroscopy. The modified positions have been clearly identified by the CID-MS(2) fragmentation mass spectra with or without loss of sulfenic acid, as well as by the vibrational signature of the sulfoxide bond at around 1000 cm(-1). The oxidation of the thioether function did not lead to the same products in these model peptides. The sulfoxide and sulfone (to a lesser extent) have been clearly identified as final products of the oxidation of S-methyl-glutathione (GS-Me). Decarboxylation or hydrogen loss are the major oxidation pathways in GS-Me, while they have not been observed in tryptophan-methionine and methionine-tryptophan (Trp-Met and Met-Trp). Interestingly, tryptophan is oxidized in the dipeptide Met-Trp, while that is not the case in the reverse sequence (Trp-Met).
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Affiliation(s)
- D Scuderi
- Laboratoire de Chimie Physique, Université Paris Sud, 91405 Orsay Cedex, France.
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Dunbar RC, Martens J, Berden G, Oomens J. Complexes of Ni(ii) and Cu(ii) with small peptides: deciding whether to deprotonate. Phys Chem Chem Phys 2016; 18:26923-26932. [DOI: 10.1039/c6cp03974j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy differentiates two binding modes (iminol versus charge solvated) for Ni(ii) bound to model peptides.
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Affiliation(s)
| | - Jonathan Martens
- FELIX Laboratory
- Institute for Molecules and Materials
- Radboud University
- 6525ED Nijmegen
- The Netherlands
| | - Giel Berden
- FELIX Laboratory
- Institute for Molecules and Materials
- Radboud University
- 6525ED Nijmegen
- The Netherlands
| | - Jos Oomens
- FELIX Laboratory
- Institute for Molecules and Materials
- Radboud University
- 6525ED Nijmegen
- The Netherlands
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Stover ML, Plummer CE, Miller SR, Cassady CJ, Dixon DA. Gas-Phase Acidities of Phosphorylated Amino Acids. J Phys Chem B 2015; 119:14604-21. [DOI: 10.1021/acs.jpcb.5b08616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michele L. Stover
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Chelsea E. Plummer
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Sean R. Miller
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Carolyn J. Cassady
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - David A. Dixon
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
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Masson A, Williams ER, Rizzo TR. Molecular hydrogen messengers can lead to structural infidelity: A cautionary tale of protonated glycine. J Chem Phys 2015; 143:104313. [DOI: 10.1063/1.4930196] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Antoine Masson
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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9
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Chiavarino B, Crestoni ME, Fornarini S, Scuderi D, Salpin JY. Interaction of cisplatin with 5'-dGMP: a combined IRMPD and theoretical study. Inorg Chem 2015; 54:3513-22. [PMID: 25798661 DOI: 10.1021/acs.inorgchem.5b00070] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
IR multiple photon dissociation (IRMPD) spectroscopy of cis-[Pt(NH3)2(5'-dGMP-H)](+) and cis-[PtCl(NH3)2(5'-dGMP)](+) ions (where 5'-dGMP is 2'-deoxyguanosine-5'-monophosphate), generated in the gas phase by electrospray ionization, was performed in two spectral regions, namely, 700-1900 cm(-1) and 2800-3800 cm(-1). For structural assignment, experimental IRMPD spectra were compared to IR spectra computed at the B3LYP/LACV3P/6-311G** level of theory. In agreement with computational results, the vibrational spectroscopic characterization of the cis-[Pt(NH3)2(5'-dGMP-H)](+) ion points to macrochelate species resulting from the simultaneous interaction of the metal with both the N7 atom of the guanine residue and an O atom of the phosphate group, structures that bear features in common with those characterized in solution by NMR spectroscopy. Concerning the cis-[PtCl(NH3)2(5'-dGMP)](+) ion, our study points to a monodentate complex involving exclusively the N7 position of guanine, as observed in solution. Also this species exhibits a compact form due to the formation of two hydrogen bonds involving the same ammonia ligand. For both complexes, IRMPD experiments show that a strong intramolecular hydrogen bond is established between one ammonia hydrogen and the carbonyl group of guanine. The strength of this particular interaction can be qualitatively estimated by looking at the redshift of the CO vibration with respect to an unperturbed C═O stretching mode in the fingerprint region. This point is also highlighted in the X-H (X = N, O) stretch region, by the shift of the N-H stretch frequency as a function of the number of hydrogen bonds involving the ammonia ligand.
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Affiliation(s)
- Barbara Chiavarino
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy
| | | | - Jean-Yves Salpin
- ∥Université d'Evry Val d'Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Boulevard François Mitterrand, 91025 Evry, France
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10
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Accuracy of density functionals in the description of dispersion interactions and IR spectra of phosphates and phosphorylated compounds. J Mol Model 2014; 20:2426. [DOI: 10.1007/s00894-014-2426-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022]
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Langer J, Günther A, Seidenbecher S, Berden G, Oomens J, Dopfer O. Probing protonation sites of isolated flavins using IR spectroscopy: from lumichrome to the cofactor flavin mononucleotide. Chemphyschem 2014; 15:2550-62. [PMID: 24895155 DOI: 10.1002/cphc.201402146] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Indexed: 11/06/2022]
Abstract
Infrared spectra of the isolated protonated flavin molecules lumichrome, lumiflavin, riboflavin (vitamin B2), and the biologically important cofactor flavin mononucleotide are measured in the fingerprint region (600-1850 cm(-1)) by means of IR multiple-photon dissociation (IRMPD) spectroscopy. Using density functional theory calculations, the geometries, relative energies, and linear IR absorption spectra of several low-energy isomers are calculated. Comparison of the calculated IR spectra with the measured IRMPD spectra reveals that the N10 substituent on the isoalloxazine ring influences the protonation site of the flavin. Lumichrome, with a hydrogen substituent, is only stable as the N1-protonated tautomer and protonates at N5 of the pyrazine ring. The presence of the ribityl unit in riboflavin leads to protonation at N1 of the pyrimidinedione moiety, and methyl substitution in lumiflavin stabilizes the tautomer that is protonated at O2. In contrast, flavin mononucleotide exists as both the O2- and N1-protonated tautomers. The frequencies and relative intensities of the two C=O stretch vibrations in protonated flavins serve as reliable indicators for their protonation site.
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Affiliation(s)
- Judith Langer
- Technische Universität Berlin, Institut für Optik und Atomare Physik, Hardenbergstraße 36, D-10623 Berlin (Germany); Current address: Parque Tecnologico de San Sebastian, Paseo Miramon 182, Edif C, 20009 San Sebastian (Spain)
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12
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Lanucara F, Fornarini S, Eyers CE, Crestoni ME. Probing the exposure of the phosphate group in modified amino acids and peptides by ion-molecule reactions with triethoxyborane in Fourier transform ion cyclotron resonance mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:1107-1116. [PMID: 24711274 DOI: 10.1002/rcm.6884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 02/27/2014] [Accepted: 02/27/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE Intramolecular hydrogen bonds between a phosphate group and charged residues play a crucial role in the chemistry of phosphorylated peptides, driving the species to specific conformations and affecting the exposure of the phosphate moiety. The nature and extent of these interactions can be investigated by measuring the reactivity of phosphate groups toward selected substrates in the gas phase. METHODS We used Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometry (MS) to perform a systematic study on the gas-phase ionic reactivity of phosphorylated amino acids and peptides with triethoxyborane (TEB). Ions of interest were generated by electrospray ionization (ESI), isolated in the cell of the FT-ICR mass spectrometer, and allowed to react with a stationary pressure of TEB. The temporal evolution of the reaction was monitored and thermal rate constants were derived. The structure of the ionic products was confirmed by Collision-Induced Dissociation (CID) tandem mass spectrometry (MS/MS). RESULTS TEB was found to react with the phosphate of protonated phosphorylated amino acids and peptides by an addition-elimination pathway. The kinetic efficiency of the reaction showed a positive correlation with the charge state of the reagent ion, suggesting the existence of charge-state-dependent exposure of the phosphate groups towards the incoming neutral during the reaction. Isomeric phosphorylated peptides, only differing for the position of the modified serine residue, showed markedly different kinetic efficiencies. CONCLUSIONS The ability of a phosphorylated species to react with TEB depends on the ease of access to the phosphate moiety in the corresponding gaseous ion. Measuring the kinetic efficiency of such reactions can represent a valuable tool to explore the accessibility of phosphate groups in biomolecules.
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Affiliation(s)
- Francesco Lanucara
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, M1 7DN, UK; Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
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Lanucara F, Chiavarino B, Scuderi D, Maitre P, Fornarini S, Crestoni ME. Kinetic control in the CID-induced elimination of H3PO4 from phosphorylated serine probed using IRMPD spectroscopy. Chem Commun (Camb) 2014; 50:3845-8. [PMID: 24589658 DOI: 10.1039/c4cc00877d] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
InfraRed Multiple Photon Dissociation (IRMPD) spectroscopy was used to assay the structural features of the fragment ions resulting from the elimination of H3PO4 in the Collision-Induced Dissociation (CID) of protonated serine. The results are interpreted with the aid of density functional theory calculations. Experiment and theory point to an aziridine-ring structure, implying participation of the vicinal amino group in the formation of this species. This finding constitutes a benchmark for investigating the same process in the CID of phosphorylated peptides.
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Affiliation(s)
- Francesco Lanucara
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, M17DN Manchester, UK.
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14
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Dunbar RC. Spectroscopy of Metal-Ion Complexes with Peptide-Related Ligands. Top Curr Chem (Cham) 2014; 364:183-223. [DOI: 10.1007/128_2014_578] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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15
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Stedwell CN, Galindo JF, Roitberg AE, Polfer NC. Structures of biomolecular ions in the gas phase probed by infrared light sources. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2013; 6:267-285. [PMID: 23560933 DOI: 10.1146/annurev-anchem-062012-092700] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Infrared (IR) spectroscopy of biomolecular ions combines mass spectrometry's high sensitivity and ability to analyze complex mixtures with the enhanced structural information available from vibrational spectroscopy. IR spectroscopy is in principle well placed to distinguish isomers and allow chemical classification of unknown molecules. This review gives an outline of current instrumentation, spectroscopic approaches, and potential bottlenecks. We discuss the most promising applications in bioanalytical mass spectrometry in view of recent experimental results, as well as future applications based on bioinformatics.
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Affiliation(s)
- Corey N Stedwell
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, USA.
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16
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Lanucara F, Crestoni ME, Chiavarino B, Fornarini S, Hernandez O, Scuderi D, Maitre P. Infrared spectroscopy of nucleotides in the gas phase 2. The protonated cyclic 3′,5′-adenosine monophosphate. RSC Adv 2013. [DOI: 10.1039/c3ra41117f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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17
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Kawasaki T, Fujioka J, Imai T, Tsukiyama K. Effect of mid-infrared free-electron laser irradiation on refolding of amyloid-like fibrils of lysozyme into native form. Protein J 2012; 31:710-6. [PMID: 23054332 PMCID: PMC3483483 DOI: 10.1007/s10930-012-9452-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Aggregation of lysozyme in an acidic solution generates inactive amyloid-like fibrils, with a broad infrared peak appearing at 1,610-1,630 cm(-1), characteristic of a β-sheet rich structure. We report here that spontaneous refolding of these fibrils in water could be promoted by mid-infrared free-electron laser (mid-IR FEL) irradiation targeting the amide bands. The Fourier transform infrared spectrum of the fibrils reflected a β-sheet content that was as low as that of the native structure, following FEL irradiation at 1,620 cm(-1) (amide I band); both transmission-electron microscopy imaging and Congo Red assay results also demonstrated a reduced fibril structure, and the enzymatic activity of lysozyme fibrils recovered to 70-90 % of the native form. Both irradiations at 1,535 cm(-1)(amide II band) and 1,240 cm(-1) (amide III band) were also more effective for the refolding of the fibrils than mere heating in the absence of FEL. On the contrary, either irradiation at 1,100 or 2,000 cm(-1) afforded only about 60 % recovery of lysozyme activity. These results indicate that the specific FEL irradiation tuned to amide bands is efficient in refolding of lysozyme fibrils into native form.
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Affiliation(s)
- Takayasu Kawasaki
- IR Free Electron Laser Research Center, Research Institute for Science and Technology (RIST), Tokyo University of Science, Yamazaki, Noda, Chiba, Japan.
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Moss CL, Chamot-Rooke J, Nicol E, Brown J, Campuzano I, Richardson K, Williams JP, Bush MF, Bythell B, Paizs B, Turecek F. Assigning Structures to Gas-Phase Peptide Cations and Cation-Radicals. An Infrared Multiphoton Dissociation, Ion Mobility, Electron Transfer, and Computational Study of a Histidine Peptide Ion. J Phys Chem B 2012; 116:3445-56. [DOI: 10.1021/jp3000784] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher L. Moss
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700,
Seattle, Washington 981915-1700, United States
| | - Julia Chamot-Rooke
- Laboratoire des Mécanismes
Réactionnels, CNRS, École Polytechnique, Palaiseau, France
| | - Edith Nicol
- Laboratoire des Mécanismes
Réactionnels, CNRS, École Polytechnique, Palaiseau, France
| | - Jeffery Brown
- Waters Corporation, Floats Road, Wythenshawe, Manchester,
M23 9LZ, United Kingdom
| | - Iain Campuzano
- Waters Corporation, Floats Road, Wythenshawe, Manchester,
M23 9LZ, United Kingdom
| | - Keith Richardson
- Waters Corporation, Floats Road, Wythenshawe, Manchester,
M23 9LZ, United Kingdom
| | - Jonathan P. Williams
- Waters Corporation, Floats Road, Wythenshawe, Manchester,
M23 9LZ, United Kingdom
| | - Matthew F. Bush
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700,
Seattle, Washington 981915-1700, United States
| | | | - Bela Paizs
- German Cancer Research Center, Heidelberg,
Germany
| | - Frantisek Turecek
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700,
Seattle, Washington 981915-1700, United States
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Wu R, Marta RA, Martens JK, Eldridge KR, McMahon TB. Experimental and theoretical investigation of the proton-bound dimer of lysine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1651-9. [PMID: 21953268 DOI: 10.1007/s13361-011-0178-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Revised: 05/21/2011] [Accepted: 05/21/2011] [Indexed: 05/23/2023]
Abstract
The structure of the proton-bound lysine dimer has been investigated by infrared multiple photon dissociation (IRMPD) spectroscopy and electronic structure calculations. The structures of different possible isomers of the proton-bound lysine dimer have been optimized at the B3LYP/6-31 + G(d) level of theory and IR spectra calculated using the same computational method. Based on relative Gibbs free energies (298 K) calculated at the MP2/aug-cc-pVTZ//B3LYP/6-31 + G(d) level of theory, LL-CS01, and followed closely (1.1 kJ mol(-1)) by LL-CS02 are the most stable non-zwitterionic isomers. At the MP2/aug-cc-pVTZ//6-31 + G(d) and MP2/aug-cc-pVTZ//6-31 + (d,p) levels of theory, isomer LL-CS02 is favored by 3.0 and 2.3 kJ mol(-1), respectively. The relative Gibbs free energies calculated by the aforementioned levels of theory for LL-CS01 and LL-CS02 are very close and strongly suggest that diagnostic vibrational signatures found in the IRMPD spectrum of the proton-bound dimer of lysine can be attributed to the existence of both isomers. LL-ZW01 is the most stable zwitterionic isomer, in which the zwitterionic structure of the neutral lysine is well stabilized by the protonated lysine moiety via a very strong intermolecular hydrogen bond. At the MP2/aug-cc-pVTZ//B3LYP/6-31 + G(d), MP2/aug-cc-pVTZ//6-31 + G(d) and MP2/aug-cc-pVTZ//6-31 + G(d,p) levels of theory, the most stable zwitterionic isomer (LL-ZW01) is less favored than LL-CS01 by 7.3, 4.1 and 2.3 kJ mol(-1), respectively. The experimental IRMPD spectrum also confirms that the proton-bound dimer of lysine largely exists as charge-solvated isomers. Investigation of zwitterionic and charge-solvated species of amino acids in the gas phase will aid in a further understanding of structure, property, and function of biological molecules.
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Affiliation(s)
- Ronghu Wu
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada, N2L 3G1
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Wellers C, Borodin A, Vasilyev S, Offenberg D, Schiller S. Resonant IR multi-photon dissociation spectroscopy of a trapped and sympathetically cooled biomolecular ion species. Phys Chem Chem Phys 2011; 13:18799-809. [DOI: 10.1039/c1cp22428j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Coletti C, Re N, Scuderi D, Maître P, Chiavarino B, Fornarini S, Lanucara F, Sinha RK, Crestoni ME. IRMPD spectroscopy of protonated S-nitrosocaptopril, a biologically active, synthetic amino acid. Phys Chem Chem Phys 2010; 12:13455-67. [DOI: 10.1039/c0cp00671h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Marta RA, Wu R, Eldridge KR, Martens JK, McMahon TB. Infrared vibrational spectra as a structural probe of gaseous ions formed by caffeine and theophylline. Phys Chem Chem Phys 2010; 12:3431-42. [DOI: 10.1039/b921102k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Cimas A, Maitre P, Ohanessian G, Gaigeot MP. Molecular Dynamics and Room Temperature Vibrational Properties of Deprotonated Phosphorylated Serine. J Chem Theory Comput 2009; 5:2388-400. [DOI: 10.1021/ct900179d] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- A. Cimas
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Laboratoire de Chimie Physique, Université Paris Sud 11, UMR8000 CNRS, Faculté des sciences, bâtiment 350, 91405 Orsay Cedex, France, and Laboratoire des Mécanismes réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - P. Maitre
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Laboratoire de Chimie Physique, Université Paris Sud 11, UMR8000 CNRS, Faculté des sciences, bâtiment 350, 91405 Orsay Cedex, France, and Laboratoire des Mécanismes réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - G. Ohanessian
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Laboratoire de Chimie Physique, Université Paris Sud 11, UMR8000 CNRS, Faculté des sciences, bâtiment 350, 91405 Orsay Cedex, France, and Laboratoire des Mécanismes réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - M.-P. Gaigeot
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Laboratoire de Chimie Physique, Université Paris Sud 11, UMR8000 CNRS, Faculté des sciences, bâtiment 350, 91405 Orsay Cedex, France, and Laboratoire des Mécanismes réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
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Scuderi D, Correia CF, Balaj OP, Ohanessian G, Lemaire J, Maitre P. Structural Characterization by IRMPD Spectroscopy and DFT Calculations of Deprotonated Phosphorylated Amino Acids in the Gas Phase. Chemphyschem 2009; 10:1630-41. [DOI: 10.1002/cphc.200800856] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Bouteiller Y, Poully JC, Desfrançois C, Grégoire G. Evaluation of MP2, DFT, and DFT-D Methods for the Prediction of Infrared Spectra of Peptides. J Phys Chem A 2009; 113:6301-7. [DOI: 10.1021/jp901570r] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Yves Bouteiller
- Laboratoire de Physique des Lasers, CNRS, UMR 7538, Institut Galilée, Université Paris 13, 93430, Villetaneuse, France
| | - Jean Christophe Poully
- Laboratoire de Physique des Lasers, CNRS, UMR 7538, Institut Galilée, Université Paris 13, 93430, Villetaneuse, France
| | - Charles Desfrançois
- Laboratoire de Physique des Lasers, CNRS, UMR 7538, Institut Galilée, Université Paris 13, 93430, Villetaneuse, France
| | - Gilles Grégoire
- Laboratoire de Physique des Lasers, CNRS, UMR 7538, Institut Galilée, Université Paris 13, 93430, Villetaneuse, France
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