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Milosavljević AR, Jänkälä K, Ranković ML, Canon F, Bozek J, Nicolas C, Giuliani A. Oxygen K-shell spectroscopy of isolated progressively solvated peptide. Phys Chem Chem Phys 2020; 22:12909-12917. [DOI: 10.1039/d0cp00994f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
X-ray spectroscopy of an isolated controllably hydrated peptide: core excitation of the first solvation shell enhances peptide backbone fragmentation.
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Affiliation(s)
| | - Kari Jänkälä
- Nano and Molecular Systems Research Unit
- University of Oulu
- 90014 Oulu
- Finland
| | | | - Francis Canon
- Centre des Sciences du Goût et de l’Alimentation
- CNRS
- INRAE
- Université de Bourgogne Franche-Comté
- France
| | - John Bozek
- SOLEIL, l’Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
| | | | - Alexandre Giuliani
- SOLEIL, l’Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
- INRAE
- UAR1008
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2
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Mistarz UH, Rand KD. Installation, validation, and application examples of two instrumental setups for gas-phase HDX-MS analysis of peptides and proteins. Methods 2018; 144:113-124. [PMID: 29753788 DOI: 10.1016/j.ymeth.2018.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/17/2018] [Accepted: 05/04/2018] [Indexed: 01/15/2023] Open
Abstract
Gas-phase hydrogen/deuterium exchange measured by mass spectrometry in a millisecond timeframe after ESI (gas-phase HDX-MS) is a fast and sensitive, yet unharnessed method to analyze the primary- and higher-order structure, intramolecular and intermolecular interactions, surface properties, and charge location of peptides and proteins. During a gas-phase HDX-MS experiment, heteroatom-bound non-amide hydrogens are made to exchange with deuterium during a millisecond timespan after electrospray ionization (ESI) by reaction with the highly basic reagent ND3, enabling conformational analysis of protein states that are pertinent to the native solution-phase. Here, we describe two different instrumental approaches to enable gas-phase HDX-MS for analysis of peptides and proteins on high-resolution Q-TOF mass spectrometers. We include a description of the procedure and equipment required for successful installation as well as suggested procedures for testing, validation, and troubleshooting of a gas-phase HDX-MS setup. In the two described approaches, gas-phase HDX-MS are performed either immediately after ESI in the cone exit region by leading N2-gas over a deuterated ND3/D2O solution, or by leading purified ND3-gas into different traveling wave ion guides (TWIG) of the mass spectrometer. We envision that a detailed description of the two gas-phase HDX-MS setups and their practical implementation and validation can pave the way for gas-phase HDX-MS to become a more routinely used MS technique for structural analysis of peptides and proteins.
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Affiliation(s)
- Ulrik H Mistarz
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
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3
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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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4
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Schwob L, Lalande M, Rangama J, Egorov D, Hoekstra R, Pandey R, Eden S, Schlathölter T, Vizcaino V, Poully JC. Single-photon absorption of isolated collagen mimetic peptides and triple-helix models in the VUV-X energy range. Phys Chem Chem Phys 2017; 19:18321-18329. [DOI: 10.1039/c7cp02527k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By monitoring ionization and fragmentation after single-photon absorption, we show that an isolated collagen triple helix model is stabilized by proline hydroxylation.
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Affiliation(s)
- Lucas Schwob
- CIMAP
- UMR 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - Mathieu Lalande
- CIMAP
- UMR 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - Jimmy Rangama
- CIMAP
- UMR 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - Dmitrii Egorov
- Zernike Institute for Advanced Materials
- University of Groningen
- Nijenborgh 4
- 9747AG Groningen
- The Netherlands
| | - Ronnie Hoekstra
- Zernike Institute for Advanced Materials
- University of Groningen
- Nijenborgh 4
- 9747AG Groningen
- The Netherlands
| | - Rahul Pandey
- Dept. of Physical Sciences
- The Open University
- Walton Hall
- Milton Keynes
- UK
| | - Samuel Eden
- Dept. of Physical Sciences
- The Open University
- Walton Hall
- Milton Keynes
- UK
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials
- University of Groningen
- Nijenborgh 4
- 9747AG Groningen
- The Netherlands
| | - Violaine Vizcaino
- CIMAP
- UMR 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
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5
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Castrovilli MC, Markush P, Bolognesi P, Rousseau P, Maclot S, Cartoni A, Delaunay R, Domaracka A, Kočišek J, Huber BA, Avaldi L. Fragmentation of pure and hydrated clusters of 5Br-uracil by low energy carbon ions: observation of hydrated fragments. Phys Chem Chem Phys 2017; 19:19807-19814. [DOI: 10.1039/c7cp02233f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The fragmentation of the isolated 5-bromouracil (5BrU) molecule and pure and nano-hydrated 5BrU clusters induced by low energy 12C4+ ions has been studied.
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Affiliation(s)
| | | | | | | | - S. Maclot
- Normandie Université
- ENSICAEN
- UNICAEN
- CEA
- CNRS
| | - A. Cartoni
- CNR-ISM
- Monterotondo Scalo
- Italy
- Dipartimento di Chimica
- Sapienza Università di Roma
| | | | | | - J. Kočišek
- Normandie Université
- ENSICAEN
- UNICAEN
- CEA
- CNRS
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6
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Markush P, Bolognesi P, Cartoni A, Rousseau P, Maclot S, Delaunay R, Domaracka A, Kocisek J, Castrovilli MC, Huber BA, Avaldi L. The role of the environment in the ion induced fragmentation of uracil. Phys Chem Chem Phys 2016; 18:16721-9. [DOI: 10.1039/c6cp01940d] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fragmentation of uracil molecules and pure and nano-hydrated uracil clusters by 12C4+ ion impact is investigated.
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Affiliation(s)
| | | | - Antonella Cartoni
- CNR-ISM
- Monterotondo Scalo
- Italy
- Dipartimento di Chimica
- Sapienza Università di Roma
| | - Patrick Rousseau
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
| | - Sylvain Maclot
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
| | - Rudy Delaunay
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
| | - Alicja Domaracka
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
| | - Jaroslav Kocisek
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
- J. Heyrovský Institute of Physical Chemistry
| | | | - Bernd A. Huber
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
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7
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Ranković ML, Canon F, Nahon L, Giuliani A, Milosavljević AR. VUV action spectroscopy of protonated leucine-enkephalin peptide in the 6-14 eV range. J Chem Phys 2015; 143:244311. [DOI: 10.1063/1.4939080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. Lj. Ranković
- Institute of Physics Belgrade, University of Belgrade, Pregrevica 118, 11080 Belgrade, Serbia
| | - F. Canon
- INRA, UMR1324 Centre des Sciences du Goût et de l’Alimentation, F-21000 Dijon, France
| | - L. Nahon
- SOLEIL, l’Orme des Merisiers, St Aubin, BP48, 91192 Gif sur Yvette Cedex, France
| | - A. Giuliani
- SOLEIL, l’Orme des Merisiers, St Aubin, BP48, 91192 Gif sur Yvette Cedex, France
- INRA, UAR1008, CEPIA, Rue de la Géraudière, BP 71627, 44316 Nantes, France
| | - A. R. Milosavljević
- Institute of Physics Belgrade, University of Belgrade, Pregrevica 118, 11080 Belgrade, Serbia
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
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9
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Canon F, Milosavljević AR, Nahon L, Giuliani A. Action spectroscopy of a protonated peptide in the ultraviolet range. Phys Chem Chem Phys 2015; 17:25725-33. [DOI: 10.1039/c4cp04762a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Action spectroscopy of substance P, a model undecapeptide, has been probed from 5.2 eV to 20 eV.
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Affiliation(s)
- Francis Canon
- Synchrotron Soleil
- l'Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
- UMR1324 Centre des Sciences du Goût et de l'Alimentation
| | | | - Laurent Nahon
- Synchrotron Soleil
- l'Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
| | - Alexandre Giuliani
- Synchrotron Soleil
- l'Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
- Uar1008
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10
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Milosavljević AR, Cerovski VZ, Canon F, Ranković ML, Škoro N, Nahon L, Giuliani A. Energy-Dependent UV Photodissociation of Gas-Phase Adenosine Monophosphate Nucleotide Ions: The Role of a Single Solvent Molecule. J Phys Chem Lett 2014; 5:1994-1999. [PMID: 26273885 DOI: 10.1021/jz500696b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The photodissociation of gaseous protonated adenosine 5'-monophosphate (AMP) and the same system hydrated with one water molecule has been investigated in the 4 to 13 eV photon energy range by coupling a linear quadrupole ion trap with a synchrotron radiation beamline. The dissociation of the bare AMP cation upon absorption of a single ultraviolet (UV) photon below the ionization energy (IE) almost exclusively produces the protonated adenine base, with a measured photodissociation yield showing spectroscopic features with dominant absorption bands located at 4.75 and 6.5 eV, found in agreement with TD-DFT calculations. Nevertheless, the addition of a single water molecule to the system modifies the dissociation energy dependence and strongly suppresses the cleavage of the glycosidic CN bond below the IE. Both the experimental and theoretical results suggest that a single solvent molecule can intrinsically influence the structure and physicochemical properties of the AMP cation, including its UV induced dissociation pattern, beyond the simple water evaporation.
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Affiliation(s)
| | - Viktor Z Cerovski
- †Institute of Physics Belgrade, University of Belgrade, Pregrevica 118, 11080 Belgrade, Serbia
| | - Francis Canon
- ‡INRA, UMR1324 Centre des Sciences du Goût et de l'Alimentation, F-21000 Dijon, France
| | - Miloš Lj Ranković
- †Institute of Physics Belgrade, University of Belgrade, Pregrevica 118, 11080 Belgrade, Serbia
| | - Nikola Škoro
- †Institute of Physics Belgrade, University of Belgrade, Pregrevica 118, 11080 Belgrade, Serbia
| | - Laurent Nahon
- §Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, 91192 Gif-sur-Yvette, France
| | - Alexandre Giuliani
- §Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, 91192 Gif-sur-Yvette, France
- ∥UAR 1008 CEPIA, INRA, 44316 Nantes, France
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