1
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Le Barbu-Debus K, Pérez-Mellor A, Lepère V, Zehnacker A. How change in chirality prevents β-amyloid type interaction in a protonated cyclic dipeptide dimer. Phys Chem Chem Phys 2022; 24:19783-19791. [PMID: 35969161 DOI: 10.1039/d2cp03110h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The protonated dimers of the diketopiperazine dipeptide cyclo (LPhe-LHis) and cyclo (LPhe-DHis) are studied by laser spectroscopy combined with mass spectrometry to shed light on the influence of stereochemistry on the clustering propensity of cyclic dipeptides. The marked spectroscopic differences experimentally observed in the hydride stretch region are well accounted for by the results of DFT calculations. Both diastereomeric protonated dimers involve a strong ionic hydrogen bond from the protonated imidazole ring of one monomer to the neutral imidazole nitrogen of the other. While this strong interaction is accompanied by a single NH⋯O hydrogen bond between the amide functions of the two moieties for the protonated dimer of cyclo (LPhe-DHis), that of cyclo (LPhe-LHis) involves two NH⋯O interactions, forming the motif of an antiparallel β sheet. Therefore, a change in chirality of the residue prevents the formation of the β sheet pattern observed in the amyloid type aggregation. These results emphasize the peculiar role of the histidine residue in peptide structure and interaction.
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Affiliation(s)
- Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Valéria Lepère
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
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2
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Kumar S, Borish K, Dey S, Nagesh J, Das A. Sequence dependent folding motifs of the secondary structures of Gly-Pro and Pro-Gly containing oligopeptides. Phys Chem Chem Phys 2022; 24:18408-18418. [PMID: 35880873 DOI: 10.1039/d2cp01306a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Folding motifs of the secondary structures of peptides and proteins are primarily based on the hydrogen bonding interactions in the backbone as well as the sequence of the amino acid residues present. For instance, the β-turn structure directed by the Pro-Gly sequence is the key to the β-hairpin structure of peptides/proteins as well as a selective site for the enzymatic hydroxylation of pro-collagen. Herein, we have investigated the sequence dependent folding motifs of end-protected Gly-Pro and Pro-Gly dipeptides using a combination of gas phase laser spectroscopy, quantum chemistry calculations, solution phase IR and NMR spectroscopy and single crystal X-Ray diffraction (XRD). All three observed conformers of the Gly-Pro peptide in the gas phase have been found to have extended β-strand or polyproline-II (PP-II) structures with C5-C7 hydrogen bonding interactions, which correlates well with the structure obtained from solution phase spectroscopy and XRD. On the other hand, we have found that the Pro-Gly peptide has a C10/β-turn structure in the solution phase in contrast to the C7-C7 (i.e. 27-ribbon) structure observed in the gas phase. Although the lowest energy structure in the gas phase is not C10, we find that C7-C7 is an abundantly found structural motif of Pro-Gly containing peptides in the Cambridge Structural Database, indicating that the gas phase conformers are not sampling any unusual forms. We surmise that the role of the solvent could be crucial in dictating the preferential stabilization of the C10 structure in the solution phase. The present investigation provides a comprehensive picture of the folding motifs of the Gly-Pro and Pro-Gly peptides observed in the gas phase and condensed phase weaving a fine interplay of the intrinsic conformational properties, solvation, and crystal packing of the peptides.
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Affiliation(s)
- Satish Kumar
- 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.
| | - Jayashree Nagesh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012, 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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3
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Structural Properties of Phenylalanine-Based Dimers Revealed Using IR Action Spectroscopy. Molecules 2022; 27:molecules27072367. [PMID: 35408770 PMCID: PMC9000879 DOI: 10.3390/molecules27072367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022] Open
Abstract
Peptide segments with phenylalanine residues are commonly found in proteins that are related to neurodegenerative diseases. However, the self-assembly of phenylalanine-based peptides can be also functional. Peptides containing phenylalanine residues with different side caps, composition, and chemical alteration can form different types of nanostructures that find many applications in technology and medicine. Various studies have been performed in order to explain the remarkable stability of the resulting nanostructures. Here, we study the early stages of self-assembly of two phenylalanine derived peptides in the gas phase using IR action spectroscopy. Our focus lies on the identification of the key intra- and intermolecular interactions that govern the formation of the dimers. The far-IR region allowed us to distinguish between structural families and to assign the 2-(2-amino-2-phenylacetamido)-2-phenylacetic acid (PhgPhg) dimer to a very symmetric structure with two intermolecular hydrogen bonds and its aromatic rings folded away from the backbone. By comparison with the phenylalanine-based peptide cyclic L-phenylalanyl-L-phenylalanine (cyclo-FF), we found that the linear FF dimer likely adopts a less ordered structure. However, when one more phenylalanine residue is added (FFF), a more structurally organized dimer is formed with several intermolecular hydrogen bonds.
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4
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Yoo IT, Eun HJ, Min A, Jeon CW, Jeong J, Heo J, Kim NJ. Ultraviolet photodissociation circular dichroism spectroscopy of protonated L-phenylalanyl-L-alanine in a cryogenic ion trap. Phys Chem Chem Phys 2021; 23:24180-24186. [PMID: 34676382 DOI: 10.1039/d1cp04030h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We obtained ultraviolet photodissociation (UVPD) circular dichroism (CD) spectra of protonated L-phenylalanyl-L-alanine (L-H+PheAla) near the origin band of the S0-S1 transition using cryogenic ion spectroscopy. Infrared (IR) ion-dip, IR-UV hole burning (HB) and UV-UV HB spectra showed that L-H+PheAla existed as two different conformers in a cryogenic ion trap, and they had nearly identical peptide backbones but different conformations in the Phe side chain. The UVPD CD spectra revealed that the two conformers had opposite CD signs and significantly different CD magnitudes from each other. These results demonstrate that the CD value of L-H+PheAla near the origin band is strongly influenced by the conformation of the Phe side chain.
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Affiliation(s)
- Il Tae Yoo
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea.
| | - Han Jun Eun
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea.
| | - Ahreum Min
- Department of Chemistry (BK21 +) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Korea
| | - Chang Wook Jeon
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea.
| | - Jinho Jeong
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea.
| | - Jiyoung Heo
- Department of Green Chemical Engineering, Sangmyung University, Chungnam 31066, Korea
| | - Nam Joon Kim
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea.
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5
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Bakels S, Stroganova I, Rijs AM. Probing the formation of isolated cyclo-FF peptide clusters by far-infrared action spectroscopy. Phys Chem Chem Phys 2021; 23:20945-20956. [PMID: 34545387 DOI: 10.1039/d1cp03237b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Small cyclic peptides containing phenylalanine residues are prone to aggregate in the gas phase into highly hydrophobic chains. A combination of laser desorption, mass spectrometry and conformational selective IR-UV action spectroscopy allows us to obtain detailed structural insights into the formation processes of the cyclic L-phenylalanyl-L-phenylalanine dipeptide (named cyclo-FF) aggregates. The rigid properties of cyclo-FF result in highly resolved IR spectra for the smaller clusters (n ≤ 3) and corresponding conformational assignments. For the higher order clusters (n > 3) the spectra are less resolved, however the observed ratios, peak positions and trends in IR shifts are key to make predictions on their structural details. Whereas the mid-IR spectral region between 1000-1800 cm-1 turns out to be undiagnostic for these small aggregates and the 3 μm region only for specific calculated structures, the far-IR contains valuable information that allows for clear assignments.
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Affiliation(s)
- Sjors Bakels
- Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Iuliia Stroganova
- Division of BioAnalytical Chemistry, AIMMS Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV, Amsterdam, The Netherlands. .,Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Anouk M Rijs
- Division of BioAnalytical Chemistry, AIMMS Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV, Amsterdam, The Netherlands.
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6
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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: 39] [Impact Index Per Article: 9.8] [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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7
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Hernández B, Pflüger F, Kruglik SG, Ghomi M. Multiconformational analysis of tripeptides upon consideration of implicit and explicit hydration effects. J Mol Graph Model 2020; 102:107790. [PMID: 33181423 DOI: 10.1016/j.jmgm.2020.107790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/10/2020] [Accepted: 10/23/2020] [Indexed: 10/23/2022]
Abstract
During the last two decades, numerous observed data obtained by various physical techniques, also supported by molecular modeling approaches, have highlighted the structuring features of tripeptides, as well as their aggregation properties. Herein, we focus on the structural dynamics of four trimers, i.e., Gly-Gly-Gly, Gly-Ala-Gly, Ala-Ala-Ala and Ala-Phe-Ala, in an aqueous environment. Density functional theory calculations (DFT) were carried out to assess the stability of four types of secondary structures, i.e., β-strand, polyproline-II (pP-II), α-helix and γ-turn, of which the formation had been described in these tripeptides. Both implicit and explicit hydration effects were analyzed on the conformational and energetic features of trimers. It has been shown that the use of M062X functional (versus B3LYP) improve the stability of intramolecular H-bonds, especially in inverse γ-turn structures, as well as the energetic and conformational equilibrium in all tripeptides. Explicit hydration reflected by the presence of five water molecules around the backbone polar sites (NH3+, N-H, CO and NH2) considerably changes the conformational landscapes of the trimers. Characteristic intramolecular and intermolecular interactions evidenced by the calculations, were emphasized.
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Affiliation(s)
- Belén Hernández
- Laboratoire Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), UMR 7369, Université de Reims, Faculté des Sciences, Moulin de la Housse, 51687, Reims Cedex 2, France; Université Sorbonne Paris Nord, UFR Santé-Médecine-Biologie Humaine, Groupe de Biophysique Moléculaire, 74 Rue Marcel Cachin, 93017, Bobigny cedex, France
| | - Fernando Pflüger
- Université Sorbonne Paris Nord, UFR Santé-Médecine-Biologie Humaine, Groupe de Biophysique Moléculaire, 74 Rue Marcel Cachin, 93017, Bobigny cedex, France
| | - Sergei G Kruglik
- Laboratoire Jean-Perrin, Sorbonne Université, CNRS UMR 8237, 4 Place Jussieu, 75005, Paris, France
| | - Mahmoud Ghomi
- Laboratoire Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), UMR 7369, Université de Reims, Faculté des Sciences, Moulin de la Housse, 51687, Reims Cedex 2, France; Université Sorbonne Paris Nord, UFR Santé-Médecine-Biologie Humaine, Groupe de Biophysique Moléculaire, 74 Rue Marcel Cachin, 93017, Bobigny cedex, France.
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8
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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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9
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Brenner V, Gloaguen E, Mons M. Rationalizing the diversity of amide-amide H-bonding in peptides using the natural bond orbital method. Phys Chem Chem Phys 2019; 21:24601-24619. [PMID: 31670335 DOI: 10.1039/c9cp03825f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Natural bond orbital (NBO) analysis of electron delocalization in a series of capped isolated peptides is used to diagnose amide-amide H-bonding and backbone-induced hyperconjugative interactions, and to rationalize their spectral effects. The sum of the stabilization energies corresponding to the interactions between NBOs that are involved in the H-bonding is demonstrated as an insightful indicator for the H-bond strength. It is then used to decouple the effect of the H-bond distance from that, intrinsic, of the donor/acceptor relative orientation, i.e., the geometrical approach. The diversity of the approaches given by the series of peptides studied enables us to illustrate the crucial importance of the approach when the acceptor is a carbonyl group, and emphasizes that efficient approaches can be achieved despite not matching the usual picture of a proton donor directly facing a lone pair of the proton acceptor, i.e., that encountered in intermolecular H-bonds. The study also illustrates the role of backbone flexibility, partly controlled by backbone-amide hyperconjugative interactions, in influencing the equilibrium structures, in particular by frustrating or enhancing the HB for a given geometrical approach. Finally, the presently used NBO-based HB strength indicator enables a fair prediction of the frequency of the proton donor amide NH stretching mode, but this simple picture is blurred by ubiquitous hyperconjugative effects between the backbone and amide groups, whose magnitude can be comparable to that of the weakest H-bonds.
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Affiliation(s)
- Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
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10
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Bakels S, Porskamp SBA, Rijs AM. Formation of Neutral Peptide Aggregates as Studied by Mass‐Selective IR Action Spectroscopy. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sjors Bakels
- Radboud UniversityInstitute for Molecules and MaterialsFELIX Laboratory Toernooiveld 7c 6525 ED Nijmegen The Netherlands
| | - Sebastiaan B. A. Porskamp
- Radboud UniversityInstitute for Molecules and MaterialsFELIX Laboratory Toernooiveld 7c 6525 ED Nijmegen The Netherlands
| | - Anouk M. Rijs
- Radboud UniversityInstitute for Molecules and MaterialsFELIX Laboratory Toernooiveld 7c 6525 ED Nijmegen The Netherlands
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11
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Bakels S, Porskamp SBA, Rijs AM. Formation of Neutral Peptide Aggregates as Studied by Mass-Selective IR Action Spectroscopy. Angew Chem Int Ed Engl 2019; 58:10537-10541. [PMID: 31125499 PMCID: PMC6772166 DOI: 10.1002/anie.201902644] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Indexed: 01/28/2023]
Abstract
The spontaneous aggregation of proteins and peptides is widely studied owing to its relation to neurodegenerative diseases. To understand the underlying principles of peptide aggregation, elucidation of structure and structural changes upon their formation is key. This level of detail can be obtained by studying the peptide self-assembly in the gas phase. Structural characterization of aggregates is mainly done on charged species, as adding charges is an intrinsic part of the technique to bring molecules into the gas phase. Studying neutral peptide aggregates will complement the existing picture. These studies are restricted to dimers due to experimental limitations. Herein, we present advances in laser desorption molecular beam spectroscopy to form neutral peptide aggregates consisting of up to 14 monomeric peptides in the gas phase. The combination of this technique with IR-UV spectroscopy allowed us to select each aggregate by size and subsequently characterize its structure.
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Affiliation(s)
- Sjors Bakels
- Radboud UniversityInstitute for Molecules and MaterialsFELIX LaboratoryToernooiveld 7c6525EDNijmegenThe Netherlands
| | - Sebastiaan B. A. Porskamp
- Radboud UniversityInstitute for Molecules and MaterialsFELIX LaboratoryToernooiveld 7c6525EDNijmegenThe Netherlands
| | - Anouk M. Rijs
- Radboud UniversityInstitute for Molecules and MaterialsFELIX LaboratoryToernooiveld 7c6525EDNijmegenThe Netherlands
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12
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Bakels S, Meijer E, Greuell M, Porskamp SBA, Rouwhorst G, Mahé J, Gaigeot MP, Rijs AM. Interactions of aggregating peptides probed by IR-UV action spectroscopy. Faraday Discuss 2019; 217:322-341. [DOI: 10.1039/c8fd00208h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The interplay between intramolecular and formed inter-sheet hydrogen bonds and the effect of dispersion interactions on the formation of peptide dimers is studied using IR-UV action spectroscopy.
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Affiliation(s)
- Sjors Bakels
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Eline M. Meijer
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Mart Greuell
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Sebastiaan B. A. Porskamp
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - George Rouwhorst
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Jerôme Mahé
- LAMBE CNRS UMR8587
- Université d’Evry val d’Essonne
- 91025 Evry
- France
| | | | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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13
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El Guerdaoui A, Tijar R, Bourjila M, El Merbouh B, El Bouzaidi RD, El Gridani A. Conformational Space Analysis of Protected N-Formyl-L-Phenylalanine-N-Amide Amino Acid: Effects of the Intramolecular Basis Set Superposition Error. J STRUCT CHEM+ 2019. [DOI: 10.1134/s0022476619010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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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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15
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Brand C, Stickler BA, Knobloch C, Shayeghi A, Hornberger K, Arndt M. Conformer Selection by Matter-Wave Interference. PHYSICAL REVIEW LETTERS 2018; 121:173002. [PMID: 30411911 DOI: 10.1103/physrevlett.121.173002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Indexed: 06/08/2023]
Abstract
We establish that matter-wave diffraction at near-resonant ultraviolet optical gratings can be used to spatially separate individual conformers of complex molecules. Our calculations show that the conformational purity of the prepared beam can be close to 100% and that all molecules remain in their electronic ground state. The proposed technique is independent of the dipole moment and the spin of the molecule and thus paves the way for structure-sensitive experiments with hydrocarbons and biomolecules, such as neurotransmitters and hormones, which have evaded conformer-pure isolation so far.
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Affiliation(s)
- Christian Brand
- University of Vienna, Faculty of Physics, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Benjamin A Stickler
- Faculty of Physics, University of Duisburg-Essen, Lotharstraße 1, 47048 Duisburg, Germany
| | - Christian Knobloch
- University of Vienna, Faculty of Physics, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Armin Shayeghi
- University of Vienna, Faculty of Physics, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Klaus Hornberger
- Faculty of Physics, University of Duisburg-Essen, Lotharstraße 1, 47048 Duisburg, Germany
| | - Markus Arndt
- University of Vienna, Faculty of Physics, Boltzmanngasse 5, A-1090 Vienna, Austria
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16
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Chandramouli B, Del Galdo S, Mancini G, Tasinato N, Barone V. Tailor-made computational protocols for precise characterization of small biological building blocks using QM and MM approaches. Biopolymers 2018. [DOI: 10.1002/bip.23109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Balasubramanian Chandramouli
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Compunet, Istituto Italiano di Tecnologia, via Morego 30; Genova Italy
| | - Sara Del Galdo
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
| | - Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
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17
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Hewett DM, Tabor DP, Fischer JL, Sibert EL, Zwier TS. Infrared-Enhanced Fluorescence-Gain Spectroscopy: Conformation-Specific Excited-State Infrared Spectra of Alkylbenzenes. J Phys Chem Lett 2017; 8:5296-5300. [PMID: 28994601 DOI: 10.1021/acs.jpclett.7b02276] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
An ultraviolet-infrared (UV-IR) double-resonance method for recording conformation-specific excited-state infrared spectra is described. The method takes advantage of an increase in fluorescence signal in phenylalkanes produced by infrared excitation of the S1 origin levels of different conformational isomers. The shorter lifetimes of these IR-excited molecules, combined with their red-shifted emission, provides a way to discriminate the fluorescence due to the infrared-excited molecules from the S1 origin fluorescence, resulting in spectra with high signal-to-noise ratios. Spectra for a series of phenylalkanes and a capped phenylalanine derivative (Ac-Phe-NHMe) demonstrate the potential of the method. The excited-state spectrum in the alkyl CH stretch region of ethylbenzene is well-fit by an anharmonic model developed for the ground electronic state, which explicitly takes into account stretch-bend Fermi resonance.
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Affiliation(s)
- Daniel M Hewett
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Daniel P Tabor
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Joshua L Fischer
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Edwin L Sibert
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Timothy S Zwier
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
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18
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Stamm A, Maué D, Schaly A, Schlicher S, Bartl J, Kubik S, Gerhards M. Structural analyses of isolated cyclic tetrapeptides with varying amino acid residues. Phys Chem Chem Phys 2017; 19:10718-10726. [DOI: 10.1039/c6cp08696a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Structural analyses of isolated cyclic tetrapeptides with varying amino acid residues were performed by applying combined IR/UV spectroscopy in the molecular beam and DFT calculations. The intrinsic structural properties especially with regard to the influence of different amino acid residues are fundamental for optimizing their binding ability.
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Affiliation(s)
- A. Stamm
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- Physikalische Chemie
- D-67663 Kaiserslautern
- Germany
| | - D. Maué
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- Physikalische Chemie
- D-67663 Kaiserslautern
- Germany
| | - A. Schaly
- TU Kaiserslautern
- Fachbereich Chemie
- Organische Chemie
- D-67663 Kaiserslautern
- Germany
| | - S. Schlicher
- TU Kaiserslautern
- Fachbereich Chemie
- Organische Chemie
- D-67663 Kaiserslautern
- Germany
| | - J. Bartl
- TU Kaiserslautern
- Fachbereich Chemie
- Organische Chemie
- D-67663 Kaiserslautern
- Germany
| | - S. Kubik
- TU Kaiserslautern
- Fachbereich Chemie
- Organische Chemie
- D-67663 Kaiserslautern
- Germany
| | - M. Gerhards
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- Physikalische Chemie
- D-67663 Kaiserslautern
- Germany
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19
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Forsting T, Gottschalk HC, Hartwig B, Mons M, Suhm MA. Correcting the record: the dimers and trimers of trans-N-methylacetamide. Phys Chem Chem Phys 2017; 19:10727-10737. [DOI: 10.1039/c6cp07989j] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Raman jet spectroscopy reveals three N-methylacetamide molecules organizing into a ring structure, previously overlooked in computations.
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Affiliation(s)
- Thomas Forsting
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | | | - Beppo Hartwig
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Michel Mons
- LIDYL; CEA
- CNRS
- Université Paris-Saclay
- 91191 Gif-sur-Yvette
- France
| | - Martin A. Suhm
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
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20
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León I, Alonso ER, Mata S, Cabezas C, Rodríguez MA, Grabow JU, Alonso JL. The role of amino acid side chains in stabilizing dipeptides: the laser ablation Fourier transform microwave spectrum of Ac-Val-NH2. Phys Chem Chem Phys 2017; 19:24985-24990. [DOI: 10.1039/c7cp03924g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The steric effects imposed by the isopropyl group of valine in the conformational stabilization of the capped dipeptide N-acetyl-l-valinamide (Ac-Val-NH2) have been studied by laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) spectroscopy.
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Affiliation(s)
- I. León
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - E. R. Alonso
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - S. Mata
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - C. Cabezas
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - M. A. Rodríguez
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - J.-U. Grabow
- Institut für Physikalische Chemie und Elektrochemie
- Lehrgebiet A
- Gottfried-Wilhelm-Leibniz-Universität
- D-30167 Hannover
- Germany
| | - J. L. Alonso
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
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21
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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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22
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Sohn WY, Brenner V, Gloaguen E, Mons M. Local NH–π interactions involving aromatic residues of proteins: influence of backbone conformation and ππ* excitation on the π H-bond strength, as revealed from studies of isolated model peptides. Phys Chem Chem Phys 2016; 18:29969-29978. [DOI: 10.1039/c6cp04109d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Gas phase conformer-selective IR spectroscopy combined and relevant quantum chemistry methods document the NH–π interactions in Phe residues.
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Affiliation(s)
| | | | - Eric Gloaguen
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- 91191 Gif-sur-Yvette
| | - Michel Mons
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- 91191 Gif-sur-Yvette
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23
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Stamm A, Bernhard D, Gerhards M. Structural investigations on a linear isolated depsipeptide: the importance of dispersion interactions. Phys Chem Chem Phys 2016; 18:15327-36. [DOI: 10.1039/c6cp01675h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first molecular beam investigations of an isolated linear depsipeptide are presented. By applying IR/UV spectroscopic methods and DFT calculations three structural arrangements are identified with the most stable structure being only stable by including dispersion interactions.
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Affiliation(s)
- A. Stamm
- TU Kaiserslautern, Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - D. Bernhard
- TU Kaiserslautern, Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - M. Gerhards
- TU Kaiserslautern, Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
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24
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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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25
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Chaudret R, de Courcy B, Contreras-García J, Gloaguen E, Zehnacker-Rentien A, Mons M, Piquemal JP. Unraveling non-covalent interactions within flexible biomolecules: from electron density topology to gas phase spectroscopy. Phys Chem Chem Phys 2015; 16:9876-91. [PMID: 24419903 DOI: 10.1039/c3cp52774c] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The NCI (Non-Covalent Interactions) method, a recently-developed theoretical strategy to visualize weak non-covalent interactions from the topological analysis of the electron density and of its reduced gradient, is applied in the present paper to document intra- and inter-molecular interactions in flexible molecules and systems of biological interest in combination with IR spectroscopy. We first describe the conditions of application of the NCI method to the specific case of intramolecular interactions. Then we apply it to a series of stable conformations of isolated molecules as an interpretative technique to decipher the different physical interactions at play in these systems. Examples are chosen among neutral molecular systems exhibiting a large diversity of interactions, for which an extensive spectroscopic characterization under gas-phase isolation conditions has been obtained using state-of-the-art conformer-specific experimental techniques. The interactions presently documented range from weak intra-molecular H-bonds in simple amino-alcohols, to more complex patterns, with interactions of various strengths in model peptides, as well as in chiral bimolecular systems, where invaluable hints for the understanding of chiral recognition are revealed. We also provide a detailed technical appendix, which discusses the choices of cut-offs as well as the applicability of the NCI analysis to specific constrained systems, where local effects require attention. Finally, the NCI technique provides IR spectroscopists with an elegant visualization of the interactions that potentially impact their vibrational probes, namely the OH and NH stretching motions. This contribution illustrates the power and the conditions of use of the NCI technique, with the aim of providing an easy tool for all chemists, experimentalists and theoreticians, for the visualization and characterization of the interactions shaping complex molecular systems.
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Affiliation(s)
- R Chaudret
- Sorbonne Universités, UPMC, Laboratoire de Chimie Théorique and CNRS, UMR 7616, 75252 Paris Cedex 05, Paris, France.
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26
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Loquais Y, Gloaguen E, Habka S, Vaquero-Vara V, Brenner V, Tardivel B, Mons M. Secondary Structures in Phe-Containing Isolated Dipeptide Chains: Laser Spectroscopy vs Quantum Chemistry. J Phys Chem A 2014; 119:5932-41. [DOI: 10.1021/jp509494c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yohan Loquais
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Eric Gloaguen
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Sana Habka
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Vanesa Vaquero-Vara
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Valérie Brenner
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Benjamin Tardivel
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
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27
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Lorenz UJ, Rizzo TR. Structural melting of an amino acid dimer upon intersystem crossing. J Am Chem Soc 2014; 136:14974-80. [PMID: 25250642 DOI: 10.1021/ja507981p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We present a spectroscopic investigation of the excited-state dynamics of the phenylalanine (Phe)/serine (Ser) protonated dimer in the gas phase. Using an ultraviolet (UV) laser pulse, we promote individual isomers to the S1 state and probe their fate with an infrared (IR) pulse. We find that the S1 state has a lifetime of ~70 ns and undergoes intersystem crossing (ISC) to the T1 state. Time-resolved IR spectra allow us to follow the structural evolution of the dimer. In the S1 state, the different isomers retain the hydrogen-bonding pattern of the ground state. Intersystem crossing triggers a sudden increase of the vibrational energy, so that the dimers can overcome isomerization barriers and explore large parts of the potential energy surface (PES). Their broad IR spectra largely resemble one another and indicate that the dimers adopt a molten structure.
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Affiliation(s)
- Ulrich J Lorenz
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland
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28
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Wałęsa R, Ptak T, Siodłak D, Kupka T, Broda MA. Experimental and theoretical NMR studies of interaction between phenylalanine derivative and egg yolk lecithin. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2014; 52:298-305. [PMID: 24639342 DOI: 10.1002/mrc.4064] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/18/2014] [Accepted: 02/28/2014] [Indexed: 06/03/2023]
Abstract
The interaction of phenylalanine diamide (Ac-Phe-NHMe) with egg yolk lecithin (EYL) in chloroform was studied by (1)H and (13)C NMR. Six complexes EYL-Ac-Phe-NHMe, stabilized by N-H···O or/and C-H···O hydrogen bonds, were optimized at M06-2X/6-31G(d,p) level. The assignment of EYL and Ac-Phe-NHMe NMR signals was supported using GIAO (gauge including atomic orbital) NMR calculations at VSXC and B3LYP level of theory combined with STO-3Gmag basis set. Results of our study indicate that the interaction of peptides with lecithin occurs mainly in the polar 'head' of the lecithin. Additionally, the most probable lecithin site of H-bond interaction with Ac-Phe-NHMe is the negatively charged oxygen in phosphate group that acts as proton acceptor.
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Affiliation(s)
- Roksana Wałęsa
- Faculty of Chemistry, University of Opole, Oleska 48 Str., 45-052, Opole, Poland
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29
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Mališ M, Loquais Y, Gloaguen E, Jouvet C, Brenner V, Mons M, Ljubić I, Došlić N. Non-radiative relaxation of UV photoexcited phenylalanine residues: probing the role of conical intersections by chemical substitution. Phys Chem Chem Phys 2014; 16:2285-8. [DOI: 10.1039/c3cp53953a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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30
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Loquais Y, Gloaguen E, Alauddin M, Brenner V, Tardivel B, Mons M. On the near UV photophysics of a phenylalanine residue: conformation-dependent ππ* state deactivation revealed by laser spectroscopy of isolated neutral dipeptides. Phys Chem Chem Phys 2014; 16:22192-200. [DOI: 10.1039/c4cp03401e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The primary step of the near UV photophysics is investigated in pump–probe R2PI ns experiments carried out on specific conformers of model peptide chains.
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Affiliation(s)
- Yohan Loquais
- CEA
- IRAMIS
- Laboratoire Interactions
- Dynamique et Lasers
- 91191 Gif-sur-Yvette, France
| | - Eric Gloaguen
- CNRS
- INP
- Laboratoire Francis Perrin
- URA 2453
- 91191 Gif-sur-Yvette, France
| | - Mohammad Alauddin
- CEA
- IRAMIS
- Laboratoire Interactions
- Dynamique et Lasers
- 91191 Gif-sur-Yvette, France
| | - Valérie Brenner
- CEA
- IRAMIS
- Laboratoire Interactions
- Dynamique et Lasers
- 91191 Gif-sur-Yvette, France
| | - Benjamin Tardivel
- CEA
- IRAMIS
- Laboratoire Interactions
- Dynamique et Lasers
- 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA
- IRAMIS
- Laboratoire Interactions
- Dynamique et Lasers
- 91191 Gif-sur-Yvette, France
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31
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Abstract
Although carbohydrates represent one of the most important families of biomolecules, they remain under-studied in comparison to the other biomolecular families (peptides, nucleobases). Beyond their best-known function of energy source in living systems, they act as mediator of molecular recognition processes, carrying molecular information in the so-called "sugar code," just to name one of their countless functions. Owing to their high conformational flexibility, they encode extremely rich information conveyed via the non-covalent hydrogen bonds within the carbohydrate and with other biomolecular assemblies, such as peptide subunits of proteins. Over the last decade there has been tremendous progress in the study of the conformational preferences of neutral oligosaccharides, and of the interactions between carbohydrates and various molecular partners (water, aromatic models, and peptide models), using vibrational spectroscopy as a sensitive probe. In parallel, other spectroscopic techniques have recently become available to the study of carbohydrates in the gas phase (microwave spectroscopy, IRMPD on charged species).
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Affiliation(s)
- Emilio J Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV - EHU), Apartado 644, 48940, Bilbao, Spain,
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32
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Kusaka R, Zhang D, Walsh PS, Gord JR, Fisher BF, Gellman SH, Zwier TS. Role of Ring-Constrained γ-Amino Acid Residues in α/γ-Peptide Folding: Single-Conformation UV and IR Spectroscopy. J Phys Chem A 2013; 117:10847-62. [PMID: 24070234 DOI: 10.1021/jp408258w] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ryoji Kusaka
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
- Department
of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Di Zhang
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Patrick S. Walsh
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Joseph R. Gord
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Brian F. Fisher
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Timothy S. Zwier
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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33
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Stanca-Kaposta EC, Carçabal P, Cocinero EJ, Hurtado P, Simons JP. Carbohydrate-aromatic interactions: vibrational spectroscopy and structural assignment of isolated monosaccharide complexes with p-hydroxy toluene and N-acetyl l-tyrosine methylamide. J Phys Chem B 2013; 117:8135-42. [PMID: 23773008 DOI: 10.1021/jp404527s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The nature of carbohydrate binding first to p-hydroxy toluene and then the capped amino acid, N-acetyl l-tyrosine methyl amide (AcTyrNHMe), has been investigated in a solvent-free environment under molecular beam conditions. A combination of double resonance IR-UV spectroscopy and quantum chemical calculations has established the structures of complexes with the α and β anomers of methyl d-gluco- and d-galacto- and l-fucopyranosides (α/βMeGlc, MeGal, MeFuc). The new results, when combined with dispersion-corrected DFT calculations, reveal gas phase structures which are dominated by hydrogen bonding but also with evidence of CH-π bonded interactions in complexes with α/βMeGal. These adopt stacked intermolecular structures in marked contrast to those with α/βMeGlc; p-OH → O bonds linking AcTyrNHMe, or p-hydroxy toluene, to the carbohydrate provide an anchor that facilitates further binding, both through OH → O and NH → O hydrogen bonds to the peptide backbone and through CH-π dispersion interactions with the aromatic side group. "Stacked" structures associated with dispersion interactions with the aromatic ring are not detected in the corresponding complexes of capped phenylalanine, despite their common occurrence in bound carbohydrate-protein structures.
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Affiliation(s)
- E Cristina Stanca-Kaposta
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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34
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35
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Lee JJ, Albrecht M, Rice CA, Suhm MA, Stamm A, Zimmer M, Gerhards M. Adaptive Aggregation of Peptide Model Systems. J Phys Chem A 2013; 117:7050-63. [DOI: 10.1021/jp400056n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juhyon J. Lee
- Institut
für Physikalische Chemie, Universität Göttingen, Tammannstraße
6, 37077 Göttingen, Germany
| | - Merwe Albrecht
- Institut
für Physikalische Chemie, Universität Göttingen, Tammannstraße
6, 37077 Göttingen, Germany
| | - Corey A. Rice
- Institut
für Physikalische Chemie, Universität Göttingen, Tammannstraße
6, 37077 Göttingen, Germany
| | - Martin A. Suhm
- Institut
für Physikalische Chemie, Universität Göttingen, Tammannstraße
6, 37077 Göttingen, Germany
| | - Anke Stamm
- Fachbereich
Chemie and Research Center OPTIMAS, Physikalische
und Theoretische Chemie, TU Kaiserslautern, Erwin-Schrödinger-Straße 52, 67663 Kaiserslautern,
Germany
| | - Manuel Zimmer
- Fachbereich
Chemie and Research Center OPTIMAS, Physikalische
und Theoretische Chemie, TU Kaiserslautern, Erwin-Schrödinger-Straße 52, 67663 Kaiserslautern,
Germany
| | - Markus Gerhards
- Fachbereich
Chemie and Research Center OPTIMAS, Physikalische
und Theoretische Chemie, TU Kaiserslautern, Erwin-Schrödinger-Straße 52, 67663 Kaiserslautern,
Germany
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36
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Cabezas C, Varela M, Cortijo V, Jiménez AI, Peña I, Daly AM, López JC, Cativiela C, Alonso JL. The alanine model dipeptide Ac-Ala-NH2 exists as a mixture of Ceq7 and C5 conformers. Phys Chem Chem Phys 2013; 15:2580-5. [DOI: 10.1039/c2cp43924g] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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37
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Suhm MA, Kollipost F. Femtisecond single-mole infrared spectroscopy of molecular clusters. Phys Chem Chem Phys 2013; 15:10702-21. [DOI: 10.1039/c3cp51515j] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kumar S, Mukherjee A, Das A. Structure of Indole···Imidazole Heterodimer in a Supersonic Jet: A Gas Phase Study on the Interaction between the Aromatic Side Chains of Tryptophan and Histidine Residues in Proteins. J Phys Chem A 2012; 116:11573-80. [DOI: 10.1021/jp309167a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900 NCL Innovation
Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra,
India
| | - Ankita Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900 NCL Innovation
Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra,
India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900 NCL Innovation
Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra,
India
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39
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Buchanan EG, James WH, Choi SH, Guo L, Gellman SH, Müller CW, Zwier TS. Single-conformation infrared spectra of model peptides in the amide I and amide II regions: Experiment-based determination of local mode frequencies and inter-mode coupling. J Chem Phys 2012; 137:094301. [DOI: 10.1063/1.4747507] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Schwing K, Fricke H, Bartl K, Polkowska J, Schrader T, Gerhards M. Isolated β-Turn Model Systems Investigated by Combined IR/UV Spectroscopy. Chemphyschem 2012; 13:1576-82. [DOI: 10.1002/cphc.201100805] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 02/24/2012] [Indexed: 11/08/2022]
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Schwing K, Reyheller C, Schaly A, Kubik S, Gerhards M. Structural Analysis of an Isolated Cyclic Tetrapeptide and its Monohydrate by Combined IR/UV Spectroscopy. Chemphyschem 2011; 12:1981-8. [DOI: 10.1002/cphc.201001055] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 04/07/2011] [Indexed: 11/10/2022]
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42
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Shemesh D, Domcke W. Effect of the Chirality of Residues and γ-Turns on the Electronic Excitation Spectra, Excited-State Reaction Paths and Conical Intersections of Capped Phenylalanine-Alanine Dipeptides. Chemphyschem 2011; 12:1833-40. [DOI: 10.1002/cphc.201100039] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Indexed: 11/05/2022]
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43
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Abo-Riziq A, Grace L, Crews B, Callahan MP, van Mourik T, Vries MSD. Conformational Structure of Tyrosine, Tyrosyl-glycine, and Tyrosyl-glycyl-glycine by Double Resonance Spectroscopy. J Phys Chem A 2011; 115:6077-87. [DOI: 10.1021/jp110601w] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ali Abo-Riziq
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Louis Grace
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Bridgit Crews
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Michael P. Callahan
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St. Andrews North Haugh, St. Andrews, Fife KY16 9ST, Scotland, U.K
| | - Mattanjah S. de Vries
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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44
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Cocinero EJ, Çarçabal P, Vaden TD, Davis BG, Simons JP. Exploring Carbohydrate−Peptide Interactions in the Gas Phase: Structure and Selectivity in Complexes of Pyranosides with N-Acetylphenylalanine Methylamide. J Am Chem Soc 2011; 133:4548-57. [DOI: 10.1021/ja109664k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emilio J. Cocinero
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Pierre Çarçabal
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Timothy D. Vaden
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Benjamin G. Davis
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - John P. Simons
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
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45
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Biswal HS, Loquais Y, Tardivel B, Gloaguen E, Mons M. Isolated monohydrates of a model peptide chain: effect of a first water molecule on the secondary structure of a capped phenylalanine. J Am Chem Soc 2011; 133:3931-42. [PMID: 21361380 DOI: 10.1021/ja108643p] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation of monohydrates of capped phenylalanine model peptides, CH(3)-CO-Phe-NH(2) and CH(3)-CO-Phe-NH-CH(3), in a supersonic expansion has been investigated using laser spectroscopy and quantum chemistry methods. Conformational distributions of the monohydrates have been revealed by IR/UV double-resonance spectroscopy and their structures assigned by comparison with DFT-D calculations. A careful analysis of the final hydrate distribution together with a detailed theoretical investigation of the potential energy surface of the monohydrates demonstrates that solvation occurs from the conformational distribution of the isolated peptide monomers. The distribution of the monohydrates appears to be strongly dependent on both the initial monomer conformation (extended or folded backbone) and the solvation site initially occupied by the water molecule. The solvation processes taking place during the cooling can be categorized as follows: (a) solvation without significant structural changes of the peptide, (b) solvation inducing significant distortions of the backbone but retaining the secondary structure, and (c) solvation triggering backbone isomerizations, leading to a modification of the peptide secondary structure. It is observed that solvation by a single water molecule can fold a β-strand into a γ-turn structure (type c) or induce a significant opening of a γ-turn characterized by an elongated C(7) hydrogen bond (type b). These structural changes can be considered as a first step toward the polyproline II condensed-phase structure, illustrating the role played by the very first water molecule in the solvation process.
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Affiliation(s)
- Himansu S Biswal
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM-CNRS URA 2453, CEA/Saclay, 91191 Gif-sur-Yvette, France
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46
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Sensing the anomeric effect in a solvent-free environment. Nature 2011; 469:76-9. [DOI: 10.1038/nature09693] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 11/23/2010] [Indexed: 11/08/2022]
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47
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Mayorkas N, Malka I, Bar I. Ionization-loss stimulated Raman spectroscopy for conformational probing of flexible molecules. Phys Chem Chem Phys 2011; 13:6808-15. [DOI: 10.1039/c0cp02334e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Fricke H, Schwing K, Gerlach A, Unterberg C, Gerhards M. Investigations of the water clusters of the protected amino acid Ac-Phe-OMe by applying IR/UV double resonance spectroscopy: microsolvation of the backbone. Phys Chem Chem Phys 2010; 12:3511-21. [PMID: 20336250 DOI: 10.1039/c000424c] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In order to investigate the influence of hydration on the backbone of a peptide or protected amino acid, the successive aggregation of water to Ac-Phe-OMe is analysed by means of IR/UV double resonance spectroscopy. To achieve meaningful results the spectra have been recorded in the region of the amide A and OH stretching vibrations as well as the amide I/II modes. Comparison with ab initio and DFT calculations leads to size-selective structural assignments. Two isomers of the mono- and dihydrated clusters and one isomer of the trihydrated cluster are observed in the molecular beam leading to a formation of the first solvation shell of the backbone. In case of the trihydrated cluster the backbone geometry is remarkably changed compared to the structure of the monomer since a network of water molecules can be formed.
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Affiliation(s)
- Holger Fricke
- TU Kaiserslautern, Fachbereich Chemie and research center OPTIMAS, Erwin-Schrödinger-Strasse 52, 67663 Kaiserslautern, Germany
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49
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Nagornova NS, Rizzo TR, Boyarkin OV. Highly Resolved Spectra of Gas-Phase Gramicidin S: A Benchmark for Peptide Structure Calculations. J Am Chem Soc 2010; 132:4040-1. [DOI: 10.1021/ja910118j] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Natalia S. Nagornova
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- 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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50
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Kupser P, Pagel K, Oomens J, Polfer N, Koksch B, Meijer G, von Helden G. Amide-I and -II Vibrations of the Cyclic β-Sheet Model Peptide Gramicidin S in the Gas Phase. J Am Chem Soc 2010; 132:2085-93. [DOI: 10.1021/ja909842j] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Kupser
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Jos Oomens
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Nick Polfer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Beate Koksch
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
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