1
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Fischer TLL, Bödecker MADI, Zehnacker A, Mata RA, Suhm MA. Setting up the HyDRA blind challenge for the microhydration of organic molecules. Phys Chem Chem Phys 2022; 24:11442-11454. [DOI: 10.1039/d2cp01119k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The procedure leading to the first HyDRA blind challenge for the prediction of water donor stretching vibrations in monohydrates of organic molecules is described. A training set of 10 monohydrates...
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2
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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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3
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Donon J, Habka S, Mons M, Brenner V, Gloaguen E. Conformational analysis by UV spectroscopy: the decisive contribution of environment-induced electronic Stark effects. Chem Sci 2021; 12:2803-2815. [PMID: 34164044 PMCID: PMC8179363 DOI: 10.1039/d0sc06074g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022] Open
Abstract
UV chromophores are frequently used as probes of the molecular structure. In particular, they are sensitive to the electric field generated by the molecular environment, resulting in the observation of Stark effects on UV spectra. While these environment-induced electronic Stark effects (EI-ESE) are already used for conformational analysis in the condensed phase, this work explores the potential of such an approach when performed at much higher conformational resolution in the gas phase. By investigating model alkali benzylacetate and 4-phenylbutyrate ion pairs, where the electric field applied to the phenyl ring is chemically tuned by changing the nature of the alkali cation, this work demonstrates that precise conformational assignments can be proposed based on the correlation between the conformation-dependent calculated electric fields and the frequency of the electronic transitions observed in the experimental UV spectra. Remarkably, the sole analysis of Stark effects and fragmentation patterns in mass-selected UV spectra provided an accurate and complete conformational analysis, where spectral differences as small as a few cm-1 between electronic transitions were rationalized. This case study illustrates that the identification of EI-ESE together with their interpretation at the modest cost of a ground state electric field calculation qualify UV spectroscopy as a powerful tool for conformational analysis.
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Affiliation(s)
- Jeremy Donon
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay Bât 522 91191 Gif-sur-Yvette France
| | - Sana Habka
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay Bât 522 91191 Gif-sur-Yvette France
| | - Michel Mons
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay Bât 522 91191 Gif-sur-Yvette France
| | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay Bât 522 91191 Gif-sur-Yvette France
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay Bât 522 91191 Gif-sur-Yvette France
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4
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Gloaguen E, Mons M, Schwing K, Gerhards M. Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues. Chem Rev 2020; 120:12490-12562. [PMID: 33152238 DOI: 10.1021/acs.chemrev.0c00168] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.
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Affiliation(s)
- Eric Gloaguen
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Kirsten Schwing
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
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5
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Thomas DA, Chang R, Mucha E, Lettow M, Greis K, Gewinner S, Schöllkopf W, Meijer G, von Helden G. Probing the conformational landscape and thermochemistry of DNA dinucleotide anions via helium nanodroplet infrared action spectroscopy. Phys Chem Chem Phys 2020; 22:18400-18413. [PMID: 32797142 DOI: 10.1039/d0cp02482a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Isolation of biomolecules in vacuum facilitates characterization of the intramolecular interactions that determine three-dimensional structure, but experimental quantification of conformer thermochemistry remains challenging. Infrared spectroscopy of molecules trapped in helium nanodroplets is a promising methodology for the measurement of thermochemical parameters. When molecules are captured in a helium nanodroplet, the rate of cooling to an equilibrium temperature of ca. 0.4 K is generally faster than the rate of isomerization, resulting in "shock-freezing" that kinetically traps molecules in local conformational minima. This unique property enables the study of temperature-dependent conformational equilibria via infrared spectroscopy at 0.4 K, thereby avoiding the deleterious effects of spectral broadening at higher temperatures. Herein, we demonstrate the first application of this approach to ionic species by coupling electrospray ionization mass spectrometry (ESI-MS) with helium nanodroplet infrared action spectroscopy to probe the structure and thermochemistry of deprotonated DNA dinucleotides. Dinucleotide anions were generated by ESI, confined in an ion trap at temperatures between 90 and 350 K, and entrained in traversing helium nanodroplets. The infrared action spectra of the entrained ions show a strong dependence on pre-pickup ion temperature, consistent with the preservation of conformer population upon cooling to 0.4 K. Non-negative matrix factorization was utilized to identify component conformer infrared spectra and determine temperature-dependent conformer populations. Relative enthalpies and entropies of conformers were subsequently obtained from a van't Hoff analysis. IR spectra and conformer thermochemistry are compared to results from ion mobility spectrometry (IMS) and electronic structure methods. The implementation of ESI-MS as a source of dopant molecules expands the diversity of molecules accessible for thermochemical measurements, enabling the study of larger, non-volatile species.
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Affiliation(s)
- Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.
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6
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Bakels S, Gaigeot MP, Rijs AM. Gas-Phase Infrared Spectroscopy of Neutral Peptides: Insights from the Far-IR and THz Domain. Chem Rev 2020; 120:3233-3260. [PMID: 32073261 PMCID: PMC7146864 DOI: 10.1021/acs.chemrev.9b00547] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Gas-phase, double
resonance IR spectroscopy has proven to be an
excellent approach to obtain structural information on peptides ranging
from single amino acids to large peptides and peptide clusters. In
this review, we discuss the state-of-the-art of infrared action spectroscopy
of peptides in the far-IR and THz regime. An introduction to the field
of far-IR spectroscopy is given, thereby highlighting the opportunities
that are provided for gas-phase research on neutral peptides. Current
experimental methods, including spectroscopic schemes, have been reviewed.
Structural information from the experimental far-IR spectra can be
obtained with the help of suitable theoretical approaches such as
dynamical DFT techniques and the recently developed Graph Theory.
The aim of this review is to underline how the synergy between far-IR
spectroscopy and theory can provide an unprecedented picture of the
structure of neutral biomolecules in the gas phase. The far-IR signatures
of the discussed studies are summarized in a far-IR map, in order
to gain insight into the origin of the far-IR localized and delocalized
motions present in peptides and where they can be found in the electromagnetic
spectrum.
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Affiliation(s)
- Sjors Bakels
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED Nijmegen, The Netherlands
| | - Marie-Pierre Gaigeot
- LAMBE CNRS UMR8587, Université d'Evry val d'Essonne, Blvd F. Mitterrand, Bât Maupertuis, 91025 Evry, France
| | - Anouk M Rijs
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED Nijmegen, The Netherlands
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7
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Kumar S, Mishra KK, Singh SK, Borish K, Dey S, Sarkar B, Das A. Observation of a weak intra-residue C5 hydrogen-bond in a dipeptide containing Gly-Pro sequence. J Chem Phys 2019; 151:104309. [DOI: 10.1063/1.5115040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Satish Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Kamal K. Mishra
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Santosh K. Singh
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Kshetrimayum Borish
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Sanjit Dey
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Biplab Sarkar
- Department of Chemistry, North Eastern Hill University, Shillong, Meghalaya 793022, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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8
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Pérez-Mellor A, Alata I, Lepère V, Zehnacker A. Conformational Study of the Jet-Cooled Diketopiperazine Peptide Cyclo Tyrosyl-Prolyl. J Phys Chem B 2019; 123:6023-6033. [PMID: 31268717 DOI: 10.1021/acs.jpcb.9b04529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The conformational landscape of the diketopiperazine (DKP) dipeptide built on tyrosine and proline, namely, cyclo Tyr-Pro, is studied by combining resonance-enhanced multiphoton ionization, double resonance infrared ultraviolet (IR-UV) spectroscopy, and quantum chemical calculations. Despite the geometrical constraints due the two aliphatic rings, DKP and proline, cyclo Tyr-Pro is a flexible molecule. For both diastereoisomers, cyclo LTyr-LPro and cyclo LTyr-DPro, two structural families coexist under supersonic jet conditions. In the most stable conformation, the aromatic tyrosine substituent is folded over the DKP ring (g+ geometry of the aromatic ring) as it is in the solid state. The other structure is completely extended (g- geometry of the aromatic ring) and resembles that proposed for the vapor phase. IR-UV results are not sufficient for unambiguous assignment of the observed spectra to either folded or extended conformations and the simulation of the vibronic pattern of the S0-S1 transition is necessary. Still, the comparison between IR-UV results and anharmonic calculations allows explanation of the minor structural differences between cyclo LTyr-LPro and cyclo LTyr-DPro in terms of different NH···π and CH···π interactions.
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Affiliation(s)
- Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud, Université Paris-Saclay , F-91405 Orsay , France
| | - Ivan Alata
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud, Université Paris-Saclay , F-91405 Orsay , France
| | - Valeria Lepère
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud, Université Paris-Saclay , F-91405 Orsay , France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud, Université Paris-Saclay , F-91405 Orsay , France
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9
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Habka S, Very T, Donon J, Vaquero-Vara V, Tardivel B, Charnay-Pouget F, Mons M, Aitken DJ, Brenner V, Gloaguen E. Identification of ion pairs in solution by IR spectroscopy: crucial contributions of gas phase data and simulations. Phys Chem Chem Phys 2019; 21:12798-12805. [PMID: 30977483 DOI: 10.1039/c9cp00700h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In a context where structure elucidation of ion pairs in solution remains a contemporary challenge, this work explores an original approach where accurate gas phase spectroscopic data are used to refine high level quantum chemistry calculations of ion pairs in solution, resulting in an unprecedented level of accuracy in vibrational frequency prediction. First, gas phase studies focus on a series of isolated contact ion pairs (M+, Ph-CH2-COO-, with M = Li, Na, K, Rb, Cs) for which conformer-selective IR spectra in the CO2- stretch region are recorded. These experiments reveal the interactions at play in isolated contact ion pairs, and provide vibrational frequencies enabling us to assess the accuracy of the theoretical approach used, i.e., mode-dependent scaled harmonic frequency calculations at the RI-B97-D3/dhf-TZVPP level. This level of calculation is then employed on large water clusters embedding either a free acetate ion or its contact or solvent-shared pairs with a sodium cation in order to simulate the individual vibrational spectra of these species in solution. This study shows that the stretching modes of carboxylate are sensitive to both solvent-shared and contact ion pair formation. FTIR spectra of solutions of increasing concentrations indeed reveal several spectral changes consistent with the presence of specific types of solvent-shared and contact ion pairs. By providing relevant guidelines for the interpretation of solution phase IR spectra, this work illustrates the potential of the approach for the elucidation of supramolecular structures in electrolyte solutions.
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Affiliation(s)
- Sana Habka
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Thibaut Very
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Jeremy Donon
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Vanesa Vaquero-Vara
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Benjamin Tardivel
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Florence Charnay-Pouget
- ICMMO, CNRS, Université Paris Sud, Université Paris Saclay, UMR 8182, Bât. 420, 15 rue Georges Clémenceau, 91405 Orsay cedex, France
| | - Michel Mons
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - David J Aitken
- ICMMO, CNRS, Université Paris Sud, Université Paris Saclay, UMR 8182, Bât. 420, 15 rue Georges Clémenceau, 91405 Orsay cedex, France
| | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
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10
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Yatsyna V, Mallat R, Gorn T, Schmitt M, Feifel R, Rijs AM, Zhaunerchyk V. Conformational Preferences of Isolated Glycylglycine (Gly-Gly) Investigated with IRMPD-VUV Action Spectroscopy and Advanced Computational Approaches. J Phys Chem A 2019; 123:862-872. [DOI: 10.1021/acs.jpca.8b10881] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Vasyl Yatsyna
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Ranim Mallat
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Tim Gorn
- Institut für Physikalische Chemie I, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | - Michael Schmitt
- Institut für Physikalische Chemie I, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | - Raimund Feifel
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Anouk M. Rijs
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Vitali Zhaunerchyk
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
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11
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Yatsyna V, Mallat R, Gorn T, Schmitt M, Feifel R, Rijs AM, Zhaunerchyk V. Competition between folded and extended structures of alanylalanine (Ala-Ala) in a molecular beam. Phys Chem Chem Phys 2019; 21:14126-14132. [DOI: 10.1039/c9cp00140a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural analysis of the neutral dipeptide Ala-Ala by action spectroscopy using IRMPD-VUV spectroscopy reveals predominance of extended structure.
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Affiliation(s)
- Vasyl Yatsyna
- University of Gothenburg
- Department of Physics
- Sweden
- Radboud University
- Institute for Molecules and Materials
| | - Ranim Mallat
- University of Gothenburg
- Department of Physics
- Sweden
| | - Tim Gorn
- Heinrich-Heine-Universität
- Institut für Physikalische Chemie I
- D-40225 Düsseldorf
- Germany
| | - Michael Schmitt
- Heinrich-Heine-Universität
- Institut für Physikalische Chemie I
- D-40225 Düsseldorf
- Germany
| | | | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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12
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Molano-Arevalo JC, Gonzalez W, Jeanne Dit Fouque K, Miksovska J, Maitre P, Fernandez-Lima F. Insights from ion mobility-mass spectrometry, infrared spectroscopy, and molecular dynamics simulations on nicotinamide adenine dinucleotide structural dynamics: NAD +vs. NADH. Phys Chem Chem Phys 2018; 20:7043-7052. [PMID: 29473073 DOI: 10.1039/c7cp05602h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD) is found in all living cells where the oxidized (NAD+) and reduced (NADH) forms play important roles in many enzymatic reactions. However, little is known about NAD+ and NADH conformational changes and kinetics as a function of the cell environment. In the present work, an analytical workflow is utilized to study NAD+ and NADH dynamics as a function of the organic content in solution using fluorescence lifetime spectroscopy and in the gas-phase using trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) and infrared multiple photon dissociation (IRMPD) spectroscopy. NAD solution time decay studies showed a two-component distribution, assigned to changes from a "close" to "open" conformation with the increase of the organic content. NAD gas-phase studies using nESI-TIMS-MS displayed two ion mobility bands for NAD+ protonated and sodiated species, while four and two ion mobility bands were observed for NADH protonated and sodiated species, respectively. Changes in the mobility profiles were observed for NADH as a function of the starting solution conditions and the time after desolvation, while NAD+ profiles showed no dependence. IRMPD spectroscopy of NAD+ and NADH protonated species in the 800-1800 and 3200-3700 cm-1 spectral regions showed common and signature bands between the NAD forms. Candidate structures were proposed for NAD+ and NADH kinetically trapped intermediates of the protonated and sodiated species, based on their collision cross sections and IR profiles. Results showed that NAD+ and NADH species exist in open, stack, and closed conformations and that the driving force for conformational dynamics is hydrogen bonding of the N-H-O and O-H-O forms with ribose rings.
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13
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Sohn WY, Kim JJ, Jeon M, Aoki T, Ishiuchi SI, Fujii M, Kang H. Entropic effects make a more tightly folded conformer of a β-amino acid less stable: UV-UV hole burning and IR dip spectroscopy of l-β3-homotryptophan using a laser desorption supersonic jet technique. Phys Chem Chem Phys 2018; 20:19979-19986. [DOI: 10.1039/c8cp02106f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Gas-phase spectroscopy of homotryptophan was done to understand conformations of β-peptides.
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Affiliation(s)
- Woon Yong Sohn
- Department of Applied Chemistry
- Faculty of Science and Engineering
- Chuo University
- Tokyo 112-8551
- Japan
| | - Jeong Jin Kim
- Department of Chemistry
- Department of Energy Systems Research
- Ajou University
- Suwon 16499
- Korea
| | - Myeongwon Jeon
- Department of Chemistry
- Department of Energy Systems Research
- Ajou University
- Suwon 16499
- Korea
| | - Takuma Aoki
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Shun-ichi Ishiuchi
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Hyuk Kang
- Department of Chemistry
- Department of Energy Systems Research
- Ajou University
- Suwon 16499
- Korea
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14
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Martin-Gómez H, Tulla-Puche J. Lasso peptides: chemical approaches and structural elucidation. Org Biomol Chem 2018; 16:5065-5080. [DOI: 10.1039/c8ob01304g] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The diverse functionality and the extraordinary stability of lasso peptides make these molecules attractive scaffolds for drug discovery. The ability to generate lasso peptides chemically remains a challenging endeavor.
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Affiliation(s)
| | - Judit Tulla-Puche
- Department of Inorganic and Organic Chemistry – Organic Chemistry Section
- University of Barcelona
- Barcelona
- Spain
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15
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BenNasr F, Pérez-Mellor A, Alata I, Lepere V, Jaïdane NE, Zehnacker A. Stereochemistry-dependent hydrogen bonds stabilise stacked conformations in jet-cooled cyclic dipeptides: (LD) vs. (LL) cyclo tyrosine-tyrosine. Faraday Discuss 2018; 212:399-419. [PMID: 30229773 DOI: 10.1039/c8fd00079d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Tyrosine-containing cyclic dipeptides based on a diketopiperazine (DKP) ring are studied under jet-cooled conditions using resonance-enhanced multi-photon ionisation (REMPI), conformer-selective IR-UV double resonance vibrational spectroscopy and quantum chemical calculations. The conformational landscape of the dipeptide containing natural L tyrosine (Tyr), namely c-LTyr-LTyr strongly differs from that of its diastereomer c-LTyr-DTyr. A similar family of conformers exists in both systems, with one aromatic ring folded on the dipeptide DKP ring and the other one extended. Weak NHπ and CHπ interactions are observed, which are slightly different in c-LTyr-LTyr and c-LTyr-DTyr. These structures are identical to those of LL and LD cyclo diphenylalanine, which only differ from c-Tyr-Tyr by the absence of hydroxyl on the benzene rings. While this is the only conformation observed for c-LTyr-DTyr, c-LTyr-LTyr exhibits an additional form stabilised by the interaction of the two hydroxyls, in which the two aromatic rings are in a stacked geometry. Stereochemical effects are still visible in the radical cation, for which one structure is observed for c-LTyr-DTyr, while the spectrum of the c-LTyr-LTyr radical cation is explained in terms of two co-existing structures.
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Affiliation(s)
- Feriel BenNasr
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France. and Laboratoire de Spectroscopie Atomique, Moléculaire et Applications (LSAMA), Université de Tunis El Manar, Tunis 1060, Tunisia
| | - Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Ivan Alata
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Valeria Lepere
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Nejm-Eddine Jaïdane
- Laboratoire de Spectroscopie Atomique, Moléculaire et Applications (LSAMA), Université de Tunis El Manar, Tunis 1060, Tunisia
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
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16
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Sohn WY, Habka S, Gloaguen E, Mons M. Unifying the microscopic picture of His-containing turns: from gas phase model peptides to crystallized proteins. Phys Chem Chem Phys 2017. [DOI: 10.1039/c7cp03058d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The presence in crystallized proteins of a local anchoring between the side chain of a His residue, located in the central position of a γ- or β-turn, and its local main chain environment, is assessed by the comparison of protein structures with relevant isolated model peptides.
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Affiliation(s)
- Woon Yong Sohn
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- 91191 Gif-sur-Yvette Cedex
| | - Sana Habka
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- 91191 Gif-sur-Yvette Cedex
| | - Eric Gloaguen
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- 91191 Gif-sur-Yvette Cedex
| | - Michel Mons
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- 91191 Gif-sur-Yvette Cedex
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17
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Piekarski DG, Díaz-Tendero S. Structure and stability of clusters of β-alanine in the gas phase: importance of the nature of intermolecular interactions. Phys Chem Chem Phys 2017; 19:5465-5476. [DOI: 10.1039/c6cp07792g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a theoretical study of neutral clusters of β-alanine molecules in the gas phase, (β-ala)nn ≤ 5.
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Affiliation(s)
| | - Sergio Díaz-Tendero
- Departamento de Química
- Módulo 13
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
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18
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Asselin P, Madebène B, Soulard P, Georges R, Goubet M, Huet TR, Pirali O, Zehnacker-Rentien A. Competition between inter- and intra-molecular hydrogen bonding: An infrared spectroscopic study of jet-cooled amino-ethanol and its dimer. J Chem Phys 2016; 145:224313. [DOI: 10.1063/1.4972016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Pierre Asselin
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8233, MONARIS, F-75005 Paris, France
- CNRS, UMR 8233, MONARIS, F-75005 Paris, France
| | - Bruno Madebène
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8233, MONARIS, F-75005 Paris, France
- CNRS, UMR 8233, MONARIS, F-75005 Paris, France
| | - Pascale Soulard
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8233, MONARIS, F-75005 Paris, France
- CNRS, UMR 8233, MONARIS, F-75005 Paris, France
| | - Robert Georges
- Institut de Physique de Rennes, Campus de Beaulieu, Bat 11C, UMR 6251, Université de Rennes 1-CNRS, 35042 Rennes Cedex, France
| | - Manuel Goubet
- Université Lille, CNRS, UMR 8523—PhLAM–Physique des Lasers, Atomes et Molécules, F-59000 Lille, France
| | - Thérèse R. Huet
- Université Lille, CNRS, UMR 8523—PhLAM–Physique des Lasers, Atomes et Molécules, F-59000 Lille, France
| | - Olivier Pirali
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, University of Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
- Ligne AILES — Synchrotron SOLEIL, L’Orme des Merisiers, F-91192 Gif-sur-Yvette Cedex, France
| | - Anne Zehnacker-Rentien
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, University of Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
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19
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Schwing K, Gerhards M. Investigations on isolated peptides by combined IR/UV spectroscopy in a molecular beam – structure, aggregation, solvation and molecular recognition. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1229331] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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20
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Jeanne Dit Fouque K, Lavanant H, Zirah S, Steinmetz V, Rebuffat S, Maître P, Afonso C. IRMPD Spectroscopy: Evidence of Hydrogen Bonding in the Gas Phase Conformations of Lasso Peptides and their Branched-Cyclic Topoisomers. J Phys Chem A 2016; 120:3810-6. [DOI: 10.1021/acs.jpca.6b04496] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin Jeanne Dit Fouque
- Normandie Univ, COBRA, UMR 6014, FR 3038; Univ Rouen; INSA Rouen; CNRS, 1 Rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Hélène Lavanant
- Normandie Univ, COBRA, UMR 6014, FR 3038; Univ Rouen; INSA Rouen; CNRS, 1 Rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Séverine Zirah
- Muséum national d’Histoire naturelle, Sorbonne Universités, Centre national de la Recherche scientifique, Laboratoire Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique, Université Paris Sud, UMR 8000 CNRS, Faculté des Sciences, Bât. 349, 91405 Orsay Cedex, France
| | - Sylvie Rebuffat
- Muséum national d’Histoire naturelle, Sorbonne Universités, Centre national de la Recherche scientifique, Laboratoire Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Philippe Maître
- Laboratoire de Chimie Physique, Université Paris Sud, UMR 8000 CNRS, Faculté des Sciences, Bât. 349, 91405 Orsay Cedex, France
| | - Carlos Afonso
- Normandie Univ, COBRA, UMR 6014, FR 3038; Univ Rouen; INSA Rouen; CNRS, 1 Rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
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21
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Burke NL, DeBlase AF, Redwine JG, Hopkins JR, McLuckey SA, Zwier TS. Gas-Phase Folding of a Prototypical Protonated Pentapeptide: Spectroscopic Evidence for Formation of a Charge-Stabilized β-Hairpin. J Am Chem Soc 2016; 138:2849-57. [PMID: 26853832 DOI: 10.1021/jacs.6b00093] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicole L. Burke
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Andrew F. DeBlase
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - James G. Redwine
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - John R. Hopkins
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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22
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Ishiuchi SI, Yamada K, Oba H, Wako H, Fujii M. Gas phase ultraviolet and infrared spectroscopy on a partial peptide of β2-adrenoceptor SIVSF-NH2 by a laser desorption supersonic jet technique. Phys Chem Chem Phys 2016; 18:23277-84. [DOI: 10.1039/c6cp04196e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Laser desorption supersonic jet laser spectroscopy has been applied to a penta-peptide, Ser-Ile-Val-Ser-Phe-NH2 (SIVSF-NH2), which is a partial sequence of a binding site in a β2-adrenaline receptor protein.
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Affiliation(s)
- Shun-ichi Ishiuchi
- Laboratory for Chemistry and Life Science
- Institute for Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Kohei Yamada
- Laboratory for Chemistry and Life Science
- Institute for Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Hikari Oba
- Laboratory for Chemistry and Life Science
- Institute for Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Hiromichi Wako
- Laboratory for Chemistry and Life Science
- Institute for Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science
- Institute for Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
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23
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Gloaguen E, Tardivel B, Mons M. Gas phase double-resonance IR/UV spectroscopy of an alanine dipeptide analogue using a non-covalently bound UV-tag: observation of a folded peptide conformation in the Ac-Ala-NH2–toluene complex. Struct Chem 2015. [DOI: 10.1007/s11224-015-0690-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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24
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Alauddin M, Gloaguen E, Brenner V, Tardivel B, Mons M, Zehnacker‐Rentien A, Declerck V, Aitken DJ. Intrinsic Folding Proclivities in Cyclic β‐Peptide Building Blocks: Configuration and Heteroatom Effects Analyzed by Conformer‐Selective Spectroscopy and Quantum Chemistry. Chemistry 2015; 21:16479-93. [DOI: 10.1002/chem.201501794] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Mohammad Alauddin
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
- Current address: Department of Chemistry, University of Dhaka, Dhaka‐1000 (Bangladesh)
| | - Eric Gloaguen
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | - Valérie Brenner
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | - Benjamin Tardivel
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | - Michel Mons
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | | | - Valérie Declerck
- CP3A Organic Synthesis Group, ICMMO, UMR 8182, Université Paris Sud, Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex (France)
| | - David J. Aitken
- CP3A Organic Synthesis Group, ICMMO, UMR 8182, Université Paris Sud, Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex (France)
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25
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Abstract
This chapter examines the structural characterisation of isolated neutral amino-acids and peptides. After a presentation of the experimental and theoretical state-of-the-art in the field, a review of the major structures and shaping interactions is presented. Special focus is made on conformationally-resolved studies which enable one to go beyond simple structural characterisation; probing flexibility and excited-state photophysics are given as examples of promising future directions.
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26
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Yan B, Jaeqx S, van der Zande WJ, Rijs AM. A conformation-selective IR-UV study of the dipeptides Ac-Phe-Ser-NH2 and Ac-Phe-Cys-NH2: probing the SH···O and OH···O hydrogen bond interactions. Phys Chem Chem Phys 2015; 16:10770-8. [PMID: 24756311 DOI: 10.1039/c4cp00810c] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The conformational preferences of peptides are mainly controlled by the stabilizing effect of intramolecular interactions. In peptides with polar side chains, not only the backbone but also the side chain interactions determine the resulting conformations. In this paper, the conformational preferences of the capped dipeptides Ac-Phe-Ser-NH2 (FS) and Ac-Phe-Cys-NH2 (FC) are resolved under laser-desorbed jet cooling conditions using IR-UV ion dip spectroscopy and density functional theory (DFT) quantum chemistry calculations. As serine (Ser) and cysteine (Cys) only differ in an OH (Ser) or SH (Cys) moiety; this subtle alteration allows us to study the effect of the difference in hydrogen bonding for an OH and SH group in detail, and its effect on the secondary structure. IR absorption spectra are recorded in the NH stretching region (3200-3600 cm(-1)). In combination with quantum chemical calculations the spectra provide a direct view of intramolecular interactions. Here, we show that both FS as FC share a singly γ-folded backbone conformation as the most stable conformer. The hydrogen bond strength of OH···O (FS) is stronger than that of SH···O (FC), resulting in a more compact gamma turn structure. A second conformer is found for FC, showing a β turn interaction.
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Affiliation(s)
- Bin Yan
- Radboud University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
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27
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Mahé J, Jaeqx S, Rijs AM, Gaigeot MP. Can far-IR action spectroscopy combined with BOMD simulations be conformation selective? Phys Chem Chem Phys 2015; 17:25905-14. [DOI: 10.1039/c5cp01518a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The combination of conformation selective far-IR/UV double resonance spectroscopy with Born–Oppenheimer molecular dynamics (BOMD) simulations is presented here for the structural characterization of the Ac-Phe-Pro-NH2 peptide in the far-infrared spectral domain, i.e. for radiation below 800 cm−1.
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Affiliation(s)
- Jérôme Mahé
- LAMBE CNRS UMR8587
- Université d'Evry val d'Essonne
- 91025 Evry
- France
| | - Sander Jaeqx
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Marie-Pierre Gaigeot
- LAMBE CNRS UMR8587
- Université d'Evry val d'Essonne
- 91025 Evry
- France
- Institut Universitaire de France
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28
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Lanza G, Chiacchio MA. Interfacial water at the trialanine hydrophilic surface: a DFT electronic structure and bottom-up investigation. Phys Chem Chem Phys 2015; 17:17101-11. [DOI: 10.1039/c5cp00270b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A model describing a network of hydrogen bonded water-trialanine has been developed to estimate hydration effects on various conformers of the peptide.
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Affiliation(s)
- Giuseppe Lanza
- Dipartimento di Scienze del Farmaco
- Università di Catania
- 95125 Catania
- Italy
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29
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Schubert F, Rossi M, Baldauf C, Pagel K, Warnke S, von Helden G, Filsinger F, Kupser P, Meijer G, Salwiczek M, Koksch B, Scheffler M, Blum V. Exploring the conformational preferences of 20-residue peptides in isolation: Ac-Ala19-Lys + H+vs. Ac-Lys-Ala19 + H+ and the current reach of DFT. Phys Chem Chem Phys 2015; 17:7373-85. [DOI: 10.1039/c4cp05541a] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using a high-level density functional and an exhaustive search of conformation space, the predicted conformation of a 20-amino acid peptide explains two seemingly contradictory experiments.
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Affiliation(s)
| | - Mariana Rossi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
- Physical and Theoretical Chemistry Laboratory
- University of Oxford
| | - Carsten Baldauf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
- Institut für Chemie und Biochemie - Organische Chemie
- Freie Universität Berlin
| | - Stephan Warnke
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
| | - Frank Filsinger
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
| | - Peter Kupser
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
- Radboud University Nijmegen
- 65000 HC Nijmegen
| | - Mario Salwiczek
- Institut für Chemie und Biochemie - Organische Chemie
- Freie Universität Berlin
- D-14195 Berlin
- Germany
| | - Beate Koksch
- Institut für Chemie und Biochemie - Organische Chemie
- Freie Universität Berlin
- D-14195 Berlin
- Germany
| | | | - Volker Blum
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
- Department Mechanical Engineering and Material Science and Center for Materials Genomics
- Duke University
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30
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Leavitt CM, Moore KB, Raston PL, Agarwal J, Moody GH, Shirley CC, Schaefer HF, Douberly GE. Liquid Hot NAGMA Cooled to 0.4 K: Benchmark Thermochemistry of a Gas-Phase Peptide. J Phys Chem A 2014; 118:9692-700. [DOI: 10.1021/jp5092653] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Paul L. Raston
- Department
of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
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31
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Jaeqx S, Oomens J, Cimas A, Gaigeot MP, Rijs AM. Gas-Phase Peptide Structures Unraveled by Far-IR Spectroscopy: Combining IR-UV Ion-Dip Experiments with Born-Oppenheimer Molecular Dynamics Simulations. Angew Chem Int Ed Engl 2014; 53:3663-6. [DOI: 10.1002/anie.201311189] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Indexed: 11/11/2022]
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32
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Jaeqx S, Oomens J, Cimas A, Gaigeot MP, Rijs AM. Gas-Phase Peptide Structures Unraveled by Far-IR Spectroscopy: Combining IR-UV Ion-Dip Experiments with Born-Oppenheimer Molecular Dynamics Simulations. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201311189] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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33
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Lanza G, Chiacchio MA. Comprehensive and Accurate Ab Initio Energy Surface of Simple Alanine Peptides. Chemphyschem 2013; 14:3284-93. [DOI: 10.1002/cphc.201300445] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Giuseppe Lanza
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale A. Doria 6, 95125 Catania (Italy)
| | - Maria A. Chiacchio
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale A. Doria 6, 95125 Catania (Italy)
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34
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Baldauf C, Pagel K, Warnke S, von Helden G, Koksch B, Blum V, Scheffler M. How Cations Change Peptide Structure. Chemistry 2013; 19:11224-34. [DOI: 10.1002/chem.201204554] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Indexed: 12/12/2022]
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35
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Rossi M, Scheffler M, Blum V. Impact of Vibrational Entropy on the Stability of Unsolvated Peptide Helices with Increasing Length. J Phys Chem B 2013; 117:5574-84. [DOI: 10.1021/jp402087e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Mariana Rossi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Matthias Scheffler
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Volker Blum
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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36
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Gloaguen E, Loquais Y, Thomas JA, Pratt DW, Mons M. Spontaneous Formation of Hydrophobic Domains in Isolated Peptides. J Phys Chem B 2013; 117:4945-55. [DOI: 10.1021/jp401499x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eric Gloaguen
- Laboratoire Francis Perrin, CNRS, INP & INC, URA 2453, F-91191 Gif-sur-Yvette, France
- Laboratoire Francis
Perrin, CEA, IRAMIS, URA 2453, F-91191
Gif-sur-Yvette, France
| | - Yohan Loquais
- Laboratoire Francis Perrin, CNRS, INP & INC, URA 2453, F-91191 Gif-sur-Yvette, France
- Laboratoire Francis
Perrin, CEA, IRAMIS, URA 2453, F-91191
Gif-sur-Yvette, France
| | - Jessica A. Thomas
- Department
of Biology and Chemistry, Purdue University North Central, Westville, Indiana
46391, United States
| | - David W. Pratt
- Department
of Chemistry, University of Vermont, Burlington,
Vermont 05405, United
States
| | - Michel Mons
- Laboratoire Francis Perrin, CNRS, INP & INC, URA 2453, F-91191 Gif-sur-Yvette, France
- Laboratoire Francis
Perrin, CEA, IRAMIS, URA 2453, F-91191
Gif-sur-Yvette, France
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Dean JC, Buchanan EG, Zwier TS. Mixed 14/16 Helices in the Gas Phase: Conformation-Specific Spectroscopy of Z-(Gly)n, n = 1, 3, 5. J Am Chem Soc 2012; 134:17186-201. [PMID: 23039317 DOI: 10.1021/ja306652c] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jacob C. Dean
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084,
United States
| | - Evan G. Buchanan
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084,
United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084,
United States
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