1
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Langeland J, Lindkvist TT, Kjær C, Nielsen SB. Gas-phase Förster resonance energy transfer in mass-selected and trapped ions. MASS SPECTROMETRY REVIEWS 2024; 43:477-499. [PMID: 36514825 DOI: 10.1002/mas.21828] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/21/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Förster Resonance Energy transfer (FRET) is a nonradiative process that may occur from an electronically excited donor to an acceptor when the emission spectrum of the donor overlaps with the absorption spectrum of the acceptor. FRET experiments have been done in the gas phase based on specially designed mass-spectroscopy setups with the goal to obtain structural information on biomolecular ions labeled with a FRET pair (i.e., donor and acceptor dyes) and to shed light on the energy-transfer process itself. Ions are accumulated in a radio-frequency ion trap or a Penning trap where mass selection of those of interest takes place, followed by photoexcitation. Gas-phase FRET is identified from detection of emitted light either from the donor, the acceptor, or both, or from a fragmentation channel that is specific to the acceptor when electronically excited. The challenge associated with the first approach is the collection and detection of photons emitted from a thin ion cloud that is not easily accessible while the second approach relies both on the photophysical and chemical behavior of the acceptor. In this review, we present the different instrumentation used for gas-phase FRET, including a discussion of advantages and disadvantages, and examples on how the technique has provided important structural information that is not easily obtainable otherwise. Furthermore, we describe how the spectroscopic properties of the dyes are affected by nearby electric fields, which is readily discernable from experiments on simple model systems with alkyl or π-conjugated bridges. Such spectral changes can have a significant effect on the FRET efficiency. Ideas for new directions are presented at the end with special focus on cold-ion spectroscopy.
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Affiliation(s)
- Jeppe Langeland
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | | | - Christina Kjær
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
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2
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Saparbaev E, Zviagin A, Boyarkin OV. Identification of Isomeric Biomolecules by Infrared Spectroscopy of Solvent-Tagged Ions. Anal Chem 2022; 94:9514-9518. [PMID: 35759744 DOI: 10.1021/acs.analchem.2c01612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The difference in functionality of many isomeric biomolecules requires their analytical identification for life science studies. We present a universal approach for quantitative identification of different small- to medium-sized isomeric biomolecules that can be brought to the gas phase from solution by electrospray ionization (ESI). The method involves infrared (IR) fragment cold ion spectroscopy of analyte molecules that are incompletely desolvated by soft ESI. The use of solvent molecules as natural tags removes a need for adding to solutions any special compounds, which may interfere with liquid chromatography or mass spectrometric measurements. The tested peptides and especially monosaccharides and lipids exhibit highly isomer-specific IR fragment spectra of such noncovalent complexes, which were produced from water, methanol, acetonitrile, and 2-butanol solutions. The relative concentrations in solution mixtures of, for instance, two isomeric dipeptides can be quantified with the accuracy of 1.6% and 2.9% for the acquisition time of 25 min and, potentially, 5 s, respectively; for three isomeric phospho-octapeptides, the accuracy becomes 4.1% and 11% for 17 min and, potentially, 10 s measurements, respectively.
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Affiliation(s)
- Erik Saparbaev
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Andrei Zviagin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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3
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Pereverzev A, Roithová J. Experimental techniques and terminology in gas-phase ion spectroscopy. JOURNAL OF MASS SPECTROMETRY : JMS 2022; 57:e4826. [PMID: 35434805 PMCID: PMC9285946 DOI: 10.1002/jms.4826] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/24/2022] [Accepted: 03/31/2022] [Indexed: 06/01/2023]
Abstract
This perspective gives an overview of the action spectroscopy methods for measurements of electronic, vibrational, and rotational spectra of mass-selected ions in the gas phase. We classify and give a short overview of the existing experimental approaches in this field. There is currently a plethora of names used for, essentially, the same techniques. Hence within this overview, we scrutinized the notations and suggested terms to be generally used. The selection was either driven by making the name unique and straightforward or the term being the most broadly used one. We believe that a simplification and a unification of the notation in ion spectroscopy can make this field better accessible for experts outside the mass spectrometry community where the applications of gas-phase action ion spectroscopy can make a large impact.
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Affiliation(s)
| | - Jana Roithová
- Institute for Molecules and MaterialsRadboud UniversityNijmegenThe Netherlands
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4
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Zviagin A, Kopysov V, Nagornova NS, Boyarkin OV. Tracking local and global structural changes in a protein by cold ion spectroscopy. Phys Chem Chem Phys 2022; 24:8158-8165. [PMID: 35332911 DOI: 10.1039/d2cp00217e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Characterization of native structures of proteins in the gas phase remains challenging due to the unpredictable conformational changes the molecules undergo during desolvation and ionization. We spectroscopically studied cryogenically cooled protonated protein ubiquitin and its microhydrated complexes prepared in the gas phase in a range of charge states under different ionization conditions. The UV spectra appear vibrationally resolved for the unfolded protein, but become redshifted and smooth for the native-like structures of ubiquitin. This spectroscopic change results from the H-bonding of the hydroxyl of Tyr to the amide group of Glu-51 in the compact structures; the minimum length of this bond was estimated to be ∼1.7 Å. IR spectroscopy reflects the global structural change by observing redshifts of free NH/OH-stretch vibrational transitions. Evaporative cooling of microhydrated complexes of ubiquitin keeps the protein chilly during ionization, enabling native-like conformers with up to eight protons to survive in the gas phase.
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Affiliation(s)
- Andrei Zviagin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Natalia S Nagornova
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
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5
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Dit Fouque KJ, Scutelnic V, Hegemann JD, Rebuffat S, Maître P, Rizzo TR, Fernandez-Lima F. Structural Insights from Tandem Mass Spectrometry, Ion Mobility-Mass Spectrometry, and Infrared/Ultraviolet Spectroscopy on Sphingonodin I: Lasso vs Branched-Cyclic Topoisomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1096-1104. [PMID: 33765377 DOI: 10.1021/jasms.1c00041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lasso peptides form a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by a mechanically interlocked topology, where the C-terminal tail of the peptide is threaded and trapped within an N-terminal macrolactam ring. Sphingonodin I is a lasso peptide that has not yet been structurally characterized using the traditional structural biology tools (e.g., NMR and X-ray crystallography), and its biological function has not yet been elucidated. In the present work, we describe structural signatures characteristic of the class II lasso peptide sphingonodin I and its branched-cyclic analogue using a combination of gas-phase ion tools (e.g., tandem mass spectrometry, MS/MS, trapped ion mobility spectrometry, TIMS, and infrared, IR, and ultraviolet, UV, spectroscopies). Tandem MS/MS CID experiments on sphingonodin I yielded mechanically interlocked species with associated bi and yj fragments demonstrating the presence of a lasso topology, while tandem MS/MS ECD experiments on sphingonodin I showed a significant increase in hydrogen migration in the loop region when compared to the branched-cyclic analogue. The high-mobility resolving power of TIMS permitted the separation of both topoisomers, where sphingonodin I adopted a more compact structure than its branched-cyclic analogue. Cryogenic and room-temperature IR spectroscopy experiments evidenced a different hydrogen bond network between the two topologies, while cryogenic UV spectroscopy experiments clearly demonstrated a distinct phenylalanine environment for the lasso peptide.
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, AHC4-233, Miami, Florida 33199, United States
| | - Valeriu Scutelnic
- Laboratory of Molecular Physical Chemistry, Ecole Polytechnique Fedérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
| | - Julian D Hegemann
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms, National Museum of Natural History, CNRS, 57 rue Cuvier, CP-54, 75005 Paris, France
| | - Philippe Maître
- Laboratoire de Chimie Physique, Université Paris Sud, UMR 8000 CNRS, Faculté des Sciences, Bât. 349, 91405 Orsay Cedex France
| | - Thomas R Rizzo
- Laboratory of Molecular Physical Chemistry, Ecole Polytechnique Fedérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, AHC4-233, Miami, Florida 33199, United States
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6
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Saparbaev E, Aladinskaia V, Yamaletdinov R, Pereverzev AY, Boyarkin OV. Revealing Single-Bond Anomeric Selectivity in Carbohydrate-Protein Interactions. J Phys Chem Lett 2020; 11:3327-3331. [PMID: 32279507 DOI: 10.1021/acs.jpclett.0c00871] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The noncovalent binding of proteins to glycans is amazingly selective to the isoforms of carbohydrates, including α/β anomers that coexist in solution. We isolate in the gas phase and study at the atomic level the simplest model system: noncovalent complexes of monosaccharide α/β-GalNAc and protonated aromatic molecule tyramine. IR/UV cold ion spectroscopy and quantum chemistry calculations jointly solve the structures of the two complexes. Although the onsets of the measured UV absorptions of the complexes differ significantly, the networks of H bonds in both complexes appear identical and do not include the anomeric hydroxyl. The detailed analysis reveals that, through inductive polarization, the α- to β-reorientation of this group nevertheless reduces the length of one remote short intermolecular H-bond by 0.03 Å. Although small, this change substantially strengthens the bond, thus contributing to the anomeric selectivity of the binding.
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Affiliation(s)
- Erik Saparbaev
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
| | - Viktoriia Aladinskaia
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
| | - Ruslan Yamaletdinov
- Nikolaev Institute of Inorganic Chemistry, Novosibirsk, 630090, Russian Federation
| | - Aleksandr Y Pereverzev
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
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7
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Kjær C, Zhao Y, Stockett MH, Chen L, Hansen K, Nielsen SB. Gas-phase Förster resonance energy transfer in mass-selected ions with methylene or peptide linkers between two dyes: a concerted dance of charges. Phys Chem Chem Phys 2020; 22:11095-11100. [DOI: 10.1039/d0cp01287d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Emission from gaseous rhodamine 640 is redshifted when the dye is tethered to rhodamine 575 due to internal Coulomb interaction.
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Affiliation(s)
- Christina Kjær
- Department of Physics and Astronomy
- Aarhus University
- Denmark
| | - Ying Zhao
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- P. R. China
| | | | - Li Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- P. R. China
| | - Klavs Hansen
- Center for Joint Quantum Studies and Department of Physics
- Tianjin University
- 92 Weijin Road
- China
- Department of Physics
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8
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Pereverzev AY, Szabó I, Kopysov VN, Rosta E, Boyarkin OV. Gas-phase structures reflect the pain-relief potency of enkephalin peptides. Phys Chem Chem Phys 2019; 21:22700-22703. [PMID: 31579899 DOI: 10.1039/c9cp04098f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We use cold ion spectroscopy and quantum-chemical computations to solve the structures of opioid peptides enkephalins in the gas phase. The derived structural parameters clearly correlate with the known pharmacological efficiency of the studied drugs, suggesting that gas-phase methods, perhaps, can be used for predicting the relative potency of ligand drugs that target the hydrophobic pockets of receptors.
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Affiliation(s)
- Aleksandr Y Pereverzev
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland.
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9
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Soorkia S, Jouvet C, Grégoire G. UV Photoinduced Dynamics of Conformer-Resolved Aromatic Peptides. Chem Rev 2019; 120:3296-3327. [DOI: 10.1021/acs.chemrev.9b00316] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Satchin Soorkia
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Christophe Jouvet
- CNRS, Aix Marseille Université, PIIM UMR 7345, 13397, Marseille, France
| | - Gilles Grégoire
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
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10
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Saparbaev E, Kopysov V, Yamaletdinov R, Pereverzev AY, Boyarkin OV. Interplay of H‐Bonds with Aromatics in Isolated Complexes Identifies Isomeric Carbohydrates. Angew Chem Int Ed Engl 2019; 58:7346-7350. [DOI: 10.1002/anie.201902377] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/20/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Erik Saparbaev
- Laboratoire de Chimie Physique MoléculaireÉcole Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique MoléculaireÉcole Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
| | - Ruslan Yamaletdinov
- Nikolaev Institute of Inorganic Chemistry Novosibirsk 630090 Russian Federation
| | - Aleksandr Y. Pereverzev
- Laboratoire de Chimie Physique MoléculaireÉcole Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique MoléculaireÉcole Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
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11
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Saparbaev E, Kopysov V, Yamaletdinov R, Pereverzev AY, Boyarkin OV. Interplay of H‐Bonds with Aromatics in Isolated Complexes Identifies Isomeric Carbohydrates. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Erik Saparbaev
- Laboratoire de Chimie Physique MoléculaireÉcole Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique MoléculaireÉcole Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
| | - Ruslan Yamaletdinov
- Nikolaev Institute of Inorganic Chemistry Novosibirsk 630090 Russian Federation
| | - Aleksandr Y. Pereverzev
- Laboratoire de Chimie Physique MoléculaireÉcole Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique MoléculaireÉcole Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
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12
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Affiliation(s)
- Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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13
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Roy TK, Kopysov V, Pereverzev A, Šebek J, Gerber RB, Boyarkin OV. Intrinsic structure of pentapeptide Leu-enkephalin: geometry optimization and validation by comparison of VSCF-PT2 calculations with cold ion spectroscopy. Phys Chem Chem Phys 2018; 20:24894-24901. [PMID: 30234204 DOI: 10.1039/c8cp03989e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The intrinsic structure of an opioid peptide [Ala2, Leu5]-leucine enkephalin (ALE) has been investigated using first-principles based vibrational self-consistent field (VSCF) theory and cold ion spectroscopy. IR-UV double resonance spectroscopy revealed the presence of only one highly abundant conformer of the singly protonated ALE, isolated and cryogenically cooled in the gas phase. High-level quantum mechanical calculations of electronic structures in conjunction with a systematic conformational search allowed for finding a few low-energy candidate structures. In order to identify the observed structure, we computed vibrational spectra of the candidate structures and employed the theory at the semi-empirically scaled harmonic level and at the first-principles based anharmonic VSCF levels. The best match between the calculated "anharmonic" and the measured spectra appeared, indeed, for the most stable candidate. An average of two spectra calculated with different quantum mechanical potentials is proposed for the best match with experiment. The match thus validates the calculated intrinsic structure of ALE and demonstrates the predictive power of first-principles theory for solving structures of such large molecules.
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Affiliation(s)
- Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu 181143, India
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14
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Scutelnic V, Prlj A, Zabuga A, Corminboeuf C, Rizzo TR. Infrared Spectroscopy as a Probe of Electronic Energy Transfer. J Phys Chem Lett 2018; 9:3217-3223. [PMID: 29847947 DOI: 10.1021/acs.jpclett.8b01216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We have combined electronic and vibrational spectroscopy in a cryogenic ion trap to produce highly resolved, conformer-selective spectra for the ground and excited states of a peptide containing two chromophores. These spectra permit us to determine the precise three-dimensional structure of the peptide and give insight into the migration of the electronic excitation from phenylalanine to tyrosine because changes in the excited-state infrared spectra are sensitive to localization of the electronic energy in each chromophore. The well-controlled experimental conditions make this result a stringent test for theoretical methods dealing with electronic energy transfer.
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Affiliation(s)
- Valeriu Scutelnic
- Laboratory of Molecular Physical Chemistry , Ecole Polytechnique Fédérale de Lausanne , Station 6 , CH-1015 Lausanne , Switzerland
| | - Antonio Prlj
- Laboratory for Computational Molecular Design , Ecole Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
| | - Aleksandra Zabuga
- Laboratory of Molecular Physical Chemistry , Ecole Polytechnique Fédérale de Lausanne , Station 6 , CH-1015 Lausanne , Switzerland
| | - Clémence Corminboeuf
- Laboratory for Computational Molecular Design , Ecole Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
| | - Thomas R Rizzo
- Laboratory of Molecular Physical Chemistry , Ecole Polytechnique Fédérale de Lausanne , Station 6 , CH-1015 Lausanne , Switzerland
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15
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Sekiguchi T, Tamura M, Oba H, Çarçarbal P, Lozada-Garcia RR, Zehnacker-Rentien A, Grégoire G, Ishiuchi SI, Fujii M. Molecular Recognition by a Short Partial Peptide of the Adrenergic Receptor: A Bottom-Up Approach. Angew Chem Int Ed Engl 2018; 57:5626-5629. [DOI: 10.1002/anie.201712976] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/13/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Tsubasa Sekiguchi
- Laboratory for Chemistry and Life Science; Institute of Innovative Research; Tokyo Institute of Technology; 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
- School of Life Science and Technology; Tokyo Institute of Technology; 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
| | - Masato Tamura
- Laboratory for Chemistry and Life Science; Institute of Innovative Research; Tokyo Institute of Technology; 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
- School of Life Science and Technology; Tokyo Institute of Technology; 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
| | - Hikari Oba
- Laboratory for Chemistry and Life Science; Institute of Innovative Research; Tokyo Institute of Technology; 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
| | - Pierre Çarçarbal
- Institut des Sciences Moléculaires d'Orsay (ISMO); CNRS, Univ. Paris-Sud, Université Paris-Saclay; F-91405 Orsay France
| | - Rolando Rafael Lozada-Garcia
- Institut des Sciences Moléculaires d'Orsay (ISMO); CNRS, Univ. Paris-Sud, Université Paris-Saclay; F-91405 Orsay France
| | - Anne Zehnacker-Rentien
- Institut des Sciences Moléculaires d'Orsay (ISMO); CNRS, Univ. Paris-Sud, Université Paris-Saclay; F-91405 Orsay France
- Centre Laser de l'Université Paris-Sud (CLUPS/LUMAT); Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay; F-91405 Orsay France
| | - Gilles Grégoire
- Institut des Sciences Moléculaires d'Orsay (ISMO); CNRS, Univ. Paris-Sud, Université Paris-Saclay; F-91405 Orsay France
- Centre Laser de l'Université Paris-Sud (CLUPS/LUMAT); Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay; F-91405 Orsay France
| | - Shun-ichi Ishiuchi
- Laboratory for Chemistry and Life Science; Institute of Innovative Research; Tokyo Institute of Technology; 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science; Institute of Innovative Research; Tokyo Institute of Technology; 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
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16
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Sekiguchi T, Tamura M, Oba H, Çarçarbal P, Lozada-Garcia RR, Zehnacker-Rentien A, Grégoire G, Ishiuchi SI, Fujii M. Molecular Recognition by a Short Partial Peptide of the Adrenergic Receptor: A Bottom-Up Approach. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712976] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Tsubasa Sekiguchi
- Laboratory for Chemistry and Life Science; Institute of Innovative Research; Tokyo Institute of Technology; 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
- School of Life Science and Technology; Tokyo Institute of Technology; 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
| | - Masato Tamura
- Laboratory for Chemistry and Life Science; Institute of Innovative Research; Tokyo Institute of Technology; 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
- School of Life Science and Technology; Tokyo Institute of Technology; 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
| | - Hikari Oba
- Laboratory for Chemistry and Life Science; Institute of Innovative Research; Tokyo Institute of Technology; 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
| | - Pierre Çarçarbal
- Institut des Sciences Moléculaires d'Orsay (ISMO); CNRS, Univ. Paris-Sud, Université Paris-Saclay; F-91405 Orsay France
| | - Rolando Rafael Lozada-Garcia
- Institut des Sciences Moléculaires d'Orsay (ISMO); CNRS, Univ. Paris-Sud, Université Paris-Saclay; F-91405 Orsay France
| | - Anne Zehnacker-Rentien
- Institut des Sciences Moléculaires d'Orsay (ISMO); CNRS, Univ. Paris-Sud, Université Paris-Saclay; F-91405 Orsay France
- Centre Laser de l'Université Paris-Sud (CLUPS/LUMAT); Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay; F-91405 Orsay France
| | - Gilles Grégoire
- Institut des Sciences Moléculaires d'Orsay (ISMO); CNRS, Univ. Paris-Sud, Université Paris-Saclay; F-91405 Orsay France
- Centre Laser de l'Université Paris-Sud (CLUPS/LUMAT); Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay; F-91405 Orsay France
| | - Shun-ichi Ishiuchi
- Laboratory for Chemistry and Life Science; Institute of Innovative Research; Tokyo Institute of Technology; 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science; Institute of Innovative Research; Tokyo Institute of Technology; 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
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17
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Pereverzev AY, Boyarkin OV. Exploring the relevance of gas-phase structures to biology: cold ion spectroscopy of the decapeptide neurokinin A. Phys Chem Chem Phys 2018; 19:3468-3472. [PMID: 28106178 DOI: 10.1039/c6cp07953a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Linking the intrinsic tertiary structures of biomolecules to their native geometries is a central prerequisite for making gas-phase studies directly relevant to biology. The isolation of molecules in the gas phase eliminates hydrophilic interactions with solvents, to some extent mimicking a hydrophobic environment. Intrinsic structures therefore may resemble native ones for peptides that in vivo reside in a hydrophobic environment (e.g., binding pockets of receptors). In this study, we investigate doubly protonated neurokinin A (NKA) using IR-UV double resonance cold ion spectroscopy and find only five conformers of this decapeptide in the gas phase. In contrast, NMR data show that in aqueous solutions, NKA exhibits high conformational heterogeneity, which reduces to a few well-defined structures in hydrophobic micelles. Do the gas-phase structures of NKA resemble these native structures? The IR spectra reported here allow the validation of future structural calculations that may answer this question.
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Affiliation(s)
- A Y Pereverzev
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Federale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| | - O V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Federale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
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18
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Ujma J, Kopysov V, Nagornova NS, Migas LG, Lizio MG, Blanch EW, MacPhee C, Boyarkin OV, Barran PE. Initial Steps of Amyloidogenic Peptide Assembly Revealed by Cold-Ion Spectroscopy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201710188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jakub Ujma
- Michael Barber Centre for Collaborative Mass Spectrometry; Manchester Institute for Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Natalia S. Nagornova
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Lukasz G. Migas
- Michael Barber Centre for Collaborative Mass Spectrometry; Manchester Institute for Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Maria Giovanna Lizio
- Michael Barber Centre for Collaborative Mass Spectrometry; Manchester Institute for Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Ewan W. Blanch
- School of Science; RMIT University; 124a La Trobe Street Melbourne VIC 3001 Australia
| | - Cait MacPhee
- The School of Physics and Astronomy; James Maxwell Clark Building; The University of Edinburgh; Edinburgh EH9 3FD UK
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Perdita E. Barran
- Michael Barber Centre for Collaborative Mass Spectrometry; Manchester Institute for Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
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19
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Kopysov V, Gorshkov MV, Boyarkin OV. Identification of isoforms of aspartic acid residues in peptides by 2D UV-MS fingerprinting of cold ions. Analyst 2018; 143:833-836. [DOI: 10.1039/c7an02044a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We use 2D UV-MS cold-ion spectroscopy for the identification of l-Asp, d-Asp, l-isoAsp and d-isoAsp residues in a fragment peptide derived from the hormone protein amylin.
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Affiliation(s)
- Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- CH-1015 Lausanne
- Switzerland
| | - Mikhail V. Gorshkov
- V. L. Talroze
- Institute of Energy Problems of Chemical Physics
- Russian Academy of Sciences
- Moscow
- Russia
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- CH-1015 Lausanne
- Switzerland
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20
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Ujma J, Kopysov V, Nagornova NS, Migas LG, Lizio MG, Blanch EW, MacPhee C, Boyarkin OV, Barran PE. Initial Steps of Amyloidogenic Peptide Assembly Revealed by Cold-Ion Spectroscopy. Angew Chem Int Ed Engl 2017; 57:213-217. [DOI: 10.1002/anie.201710188] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/20/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Jakub Ujma
- Michael Barber Centre for Collaborative Mass Spectrometry; Manchester Institute for Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Natalia S. Nagornova
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Lukasz G. Migas
- Michael Barber Centre for Collaborative Mass Spectrometry; Manchester Institute for Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Maria Giovanna Lizio
- Michael Barber Centre for Collaborative Mass Spectrometry; Manchester Institute for Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Ewan W. Blanch
- School of Science; RMIT University; 124a La Trobe Street Melbourne VIC 3001 Australia
| | - Cait MacPhee
- The School of Physics and Astronomy; James Maxwell Clark Building; The University of Edinburgh; Edinburgh EH9 3FD UK
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Perdita E. Barran
- Michael Barber Centre for Collaborative Mass Spectrometry; Manchester Institute for Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
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21
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Roy TK, Nagornova NS, Boyarkin OV, Gerber RB. A Decapeptide Hydrated by Two Waters: Conformers Determined by Theory and Validated by Cold Ion Spectroscopy. J Phys Chem A 2017; 121:9401-9408. [PMID: 29091429 DOI: 10.1021/acs.jpca.7b10357] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The intrinsic structures of biomolecules in the gas phase may not reflect their native solution geometries. Microsolvation of the molecules bridges the two environments, enabling a tracking of molecular structural changes upon hydration at the atomistic level. We employ density functional calculations to compute a large pool of structures and vibrational spectra for a gas-phase complex, in which a doubly protonated decapeptide, gramicidin S, is solvated by two water molecules. Though most vibrations of this large complex are treated in a harmonic approximation, the water molecules and the vibrations of the host ion coupled to them are locally described by a quantum mechanical vibrational self-consistent field theory with second-order perturbation correction (VSCF-PT2). Guided and validated by the available cold ion spectroscopy data, the computational analysis identifies structures of the three experimentally observed conformers of the complex. They, mainly, differ by the hydration sites, of which the one at the Orn side chain is the most important for reshaping the peptide toward its native structure. The study demonstrates the ability of a quantum chemistry approach that intelligently combines the semiempirical and ab initio computations to disentangle a complex interplay of intra- and intermolecular hydrogen bonds in large molecular systems.
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Affiliation(s)
- Tapta Kanchan Roy
- Department of Chemistry & Chemical Sciences, Central University of Jammu , Jammu, 180011 India
| | - Natalia S Nagornova
- Laboratoire de Chimie Physique Molèculaire, École Polytechnique Fèdèrale de Lausanne , 1015 Lausanne, Switzerland
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Molèculaire, École Polytechnique Fèdèrale de Lausanne , 1015 Lausanne, Switzerland
| | - R Benny Gerber
- Institute of Chemistry, The Hebrew University , Jerusalem 91904, Israel.,Department of Chemistry, University of California , Irvine, California 92697, United States.,Department of Chemistry, University of Helsinki , P.O. Box 55, 00014 Helsinki, Finland
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22
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Kulesza A, Daly S, Dugourd P. Dimerization and conformation-related free energy landscapes of dye-tagged amyloid-β12–28linked to FRET experiments. Phys Chem Chem Phys 2017; 19:9470-9477. [DOI: 10.1039/c7cp00611j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The free energy landscapes of Aβ-peptide dimer models under different prototype conditions support the hypothesis that the gas-phase action-FRET measurement after electrospray ionization operates under non-equilibrium conditions, with a memory of the solution conditions – even for the dimer of this relatively short peptide.
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Affiliation(s)
- Alexander Kulesza
- Univ Lyon
- Université Claude Bernard Lyon 1
- CNRS
- Institut Lumière Matière
- Lyon
| | - Steven Daly
- Univ Lyon
- Université Claude Bernard Lyon 1
- CNRS
- Institut Lumière Matière
- Lyon
| | - Philippe Dugourd
- Univ Lyon
- Université Claude Bernard Lyon 1
- CNRS
- Institut Lumière Matière
- Lyon
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23
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Kopysov V, Makarov A, Boyarkin OV. Identification of Isomeric Ephedrines by Cold Ion UV Spectroscopy: Toward Practical Implementation. Anal Chem 2016; 89:544-547. [PMID: 27992166 DOI: 10.1021/acs.analchem.6b04182] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ephedrine and pseudoephedrine are stimulant drugs whose use is prohibited in athletic competition by the World Anti-Doping Agency (WADA) at very different threshold doping violation concentrations. We use a recently developed universal approach that integrates UV photofragmentation spectroscopy of cold ions with Orbitrap mass spectrometry (MS) for highly selective and highly sensitive identification of these diastereomers. Both species can be selectively detected at a solution concentration of a few tens of ng/mL, which is almost 3 orders of magnitude lower than the threshold concentration required by WADA. Relative concentrations of the isomers in solutions have been determined with the standard deviation of 3.1%, when the ions were cooled in an ion trap maintained at T = 6 K. Considering practical implementation of the method, we evaluated its performance for a simplified instrumentation. At an affordable elevated temperature of ∼70 K and with a low-maintenance midbandwidth optical parametric oscillator, a few second measurement should yield nearly the same selectivity and only ten times lower sensitivity than with the current research grade instrument.
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Affiliation(s)
- Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland
| | - Alexander Makarov
- Thermo Fisher Scientific , Hanna-Kunath Str. 11, 28199 Bremen, Germany
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland
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24
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Schennach M, Schneeberger EM, Breuker K. Unfolding and Folding of the Three-Helix Bundle Protein KIX in the Absence of Solvent. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1079-88. [PMID: 26936183 PMCID: PMC4863917 DOI: 10.1007/s13361-016-1363-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 05/11/2023]
Abstract
Electron capture dissociation was used to probe the structure, unfolding, and folding of KIX ions in the gas phase. At energies for vibrational activation that were sufficiently high to cause loss of small molecules such as NH3 and H2O by breaking of covalent bonds in about 5% of the KIX (M + nH)(n+) ions with n = 7-9, only partial unfolding was observed, consistent with our previous hypothesis that salt bridges play an important role in stabilizing the native solution fold after transfer into the gas phase. Folding of the partially unfolded ions on a timescale of up to 10 s was observed only for (M + nH)(n+) ions with n = 9, but not n = 7 and n = 8, which we attribute to differences in the distribution of charges within the (M + nH)(n+) ions. Graphical Abstract ᅟ.
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Affiliation(s)
- Moritz Schennach
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Eva-Maria Schneeberger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
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25
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Kopysov V, Makarov A, Boyarkin OV. Nonstatistical UV Fragmentation of Gas-Phase Peptides Reveals Conformers and Their Structural Features. J Phys Chem Lett 2016; 7:1067-1071. [PMID: 26950179 DOI: 10.1021/acs.jpclett.6b00292] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Solving the 3D structure of a biomolecule requires recognition of its conformers and measurements of their individual structural identities, which can be compared with calculations. We employ the phenomenon of nonstatistical photofragmentation, detected by a combination of UV cold ion spectroscopy and high-resolution mass spectrometry, to identify the main conformers of gas-phase peptides and to recover individual UV absorption and mass spectra of all of these conformers in a single laser scan. We first validate this approach with a benchmark dipeptide, Tyr-Ala, and then apply it to a decapeptide, gramicidin S. The revealed characteristic structural difference between the conformers of the latter identifies some of the previously calculated structures of gramicidin S as the most likely geometries of its remaining unsolved conformer.
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Affiliation(s)
- Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne , Station-6, 1015 Lausanne, Switzerland
| | - Alexander Makarov
- Thermo Fisher Scientific , Hanna-Kunath Str. 11, 28199 Bremen, Germany
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne , Station-6, 1015 Lausanne, Switzerland
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