1
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Monti M, Scarel E, Hassanali A, Stener M, Marchesan S. Diverging conformations guide dipeptide self-assembly into crystals or hydrogels. Chem Commun (Camb) 2023; 59:10948-10951. [PMID: 37605851 DOI: 10.1039/d3cc02682e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
The prediction of dipeptide assembly into crystals or gels is challenging. This work reveals the diverging conformational landscape that guides self-organization towards different outcomes. In silico and experimental data enabled deciphering of the electronic circular dichroism (ECD) spectra of self-assembling dipeptides to reveal folded or extended conformers as key players.
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Affiliation(s)
- M Monti
- Chem. Pharm. Sc. Dept., University of Trieste, Via L. Giorgieri 1, Trieste 34127, Italy.
| | - E Scarel
- Chem. Pharm. Sc. Dept., University of Trieste, Via L. Giorgieri 1, Trieste 34127, Italy.
| | - A Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
| | - M Stener
- Chem. Pharm. Sc. Dept., University of Trieste, Via L. Giorgieri 1, Trieste 34127, Italy.
| | - S Marchesan
- Chem. Pharm. Sc. Dept., University of Trieste, Via L. Giorgieri 1, Trieste 34127, Italy.
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2
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Liu D, Bardaud JX, Imani Z, Robin S, Gloaguen E, Brenner V, Aitken DJ, Mons M. Length-Dependent Transition from Extended to Folded Shapes in Short Oligomers of an Azetidine-Based α-Amino Acid: The Critical Role of NH···N H-Bonds. Molecules 2023; 28:5048. [PMID: 37446709 DOI: 10.3390/molecules28135048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/15/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Hydrogen bonds (H-bonds) are ubiquitous in peptides and proteins and are central to the stabilization of their structures. Inter-residue H-bonds between non-adjacent backbone amide NH and C=O motifs lead to the well-known secondary structures of helices, turns and sheets, but it is recognized that other H-bonding modes may be significant, including the weak intra-residue H-bond (called a C5 H-bond) that implicates the NH and C=O motifs of the same amino acid residue. Peptide model compounds that adopt stable C5 H-bonds are not readily available and the so-called 2.05-helix, formed by successive C5 H-bonds, is an elusive secondary structure. Using a combination of theoretical chemistry and spectroscopic studies in both the gas phase and solution phase, we have demonstrated that derivatives of 3-amino-1-methylazetidine-3-carboxylic acid, Aatc(Me) can form sidechain-backbone N-H···N C6γ H-bonds that accompany-and thereby stabilize-C5 H-bonds. In the capped trimer of Aatc(Me), extended C5/C6γ motifs are sufficiently robust to challenge classical 310-helix formation in solution and the fully-extended 2.05-helix conformer has been characterized in the gas phase. Concurrent H-bonding support for successive C5 motifs is a new axiom for stabilizing the extended backbone secondary structure in short peptides.
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Affiliation(s)
- Dayi Liu
- Université Paris-Saclay, CNRS, ICMMO, 91400 Orsay, France
| | | | - Zeynab Imani
- Université Paris-Saclay, CNRS, ICMMO, 91400 Orsay, France
| | - Sylvie Robin
- Université Paris-Saclay, CNRS, ICMMO, 91400 Orsay, France
- Université Paris Cité, Faculté de Pharmacie, 75006 Paris, France
| | - Eric Gloaguen
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
| | - Valérie Brenner
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
| | - David J Aitken
- Université Paris-Saclay, CNRS, ICMMO, 91400 Orsay, France
| | - Michel Mons
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
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3
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Villard J, Kılıç M, Rothlisberger U. Surrogate Based Genetic Algorithm Method for Efficient Identification of Low-Energy Peptide Structures. J Chem Theory Comput 2023; 19:1080-1097. [PMID: 36692853 PMCID: PMC9933449 DOI: 10.1021/acs.jctc.2c01078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Identification of the most stable structure(s) of a system is a prerequisite for the calculation of any of its properties from first-principles. However, even for relatively small molecules, exhaustive explorations of the potential energy surface (PES) are severely hampered by the dimensionality bottleneck. In this work, we address the challenging task of efficiently sampling realistic low-lying peptide coordinates by resorting to a surrogate based genetic algorithm (GA)/density functional theory (DFT) approach (sGADFT) in which promising candidates provided by the GA are ultimately optimized with DFT. We provide a benchmark of several computational methods (GAFF, AMOEBApro13, PM6, PM7, DFTB3-D3(BJ)) as possible prescanning surrogates and apply sGADFT to two test case systems that are (i) two isomer families of the protonated Gly-Pro-Gly-Gly tetrapeptide (Masson, A.; J. Am. Soc. Mass Spectrom.2015, 26, 1444-1454) and (ii) the doubly protonated cyclic decapeptide gramicidin S (Nagornova, N. S.; J. Am. Chem. Soc.2010, 132, 4040-4041). We show that our GA procedure can correctly identify low-energy minima in as little as a few hours. Subsequent refinement of surrogate low-energy structures within a given energy threshold (≤10 kcal/mol (i), ≤5 kcal/mol (ii)) via DFT relaxation invariably led to the identification of the most stable structures as determined from high-resolution infrared (IR) spectroscopy at low temperature. The sGADFT method therefore constitutes a highly efficient route for the screening of realistic low-lying peptide structures in the gas phase as needed for instance for the interpretation and assignment of experimental IR spectra.
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4
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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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5
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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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6
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Goldsztejn G, Mundlapati VR, Brenner V, Gloaguen E, Mons M. Selenium in Proteins: Conformational Changes Induced by Se Substitution on Methionine, as Studied in Isolated Model Peptides by Optical Spectroscopy and Quantum Chemistry. Molecules 2022; 27:molecules27103163. [PMID: 35630640 PMCID: PMC9144663 DOI: 10.3390/molecules27103163] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 02/01/2023] Open
Abstract
The side-chain of methionine residues is long enough to establish NH⋯S H-bonds with neighboring carbonyl groups of the backbone, giving rise to so-called intra-residue 6δ and inter-residue 7δ H-bonds. The aim of the present article is to document how the substitution of sulfur with a selenium atom affects the H-bonding of the Met system. This was investigated both experimentally and theoretically by conformation-resolved optical spectroscopy, following an isolated molecule approach. The present work emphasizes the similarities of the Met and Sem residues in terms of conformational structures, energetics, NH⋯Se/S H-bond strength and NH stretch spectral shifts, but also reveals subtle behavior differences between them. It provides evidence for the sensitivity of the H-bonding network with the folding type of the Sem/Met side-chains, where a simple flip of the terminal part of the side-chain can induce an extra 50 cm−1 spectral shift of the NH stretch engaged in a 7δ NH⋯S/Se bond.
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7
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D'mello VC, Goldsztejn G, Rao Mundlapati V, Brenner V, Gloaguen E, Charnay‐Pouget F, Aitken DJ, Mons M. Characterization of Asx Turn Types and Their Connate Relationship with β‐Turns. Chemistry 2022; 28:e202104328. [DOI: 10.1002/chem.202104328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Viola C. D'mello
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
- Present address: Graphene Research Labs KIADB IT Park Near Airport Bengaluru 562149 India
| | - Gildas Goldsztejn
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
- Present address: Université Paris-Saclay, CNRS Institut des Sciences Moléculaires d'Orsay (ISMO) 91405 Orsay France
| | - Venkateswara Rao Mundlapati
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
- Present address: Institut de Recherche en Astrophysique et Planétologie (IRAP) Université de Toulouse (UPS), CNRS, CNES 9 Avenue du Colonel Roche 31028 Toulouse France
| | - Valérie Brenner
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
| | - Eric Gloaguen
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
| | - Florence Charnay‐Pouget
- Université Paris-Saclay, CNRS Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) 91405 Orsay France
- Present address: Université Clermont Auvergne, CNRS SIGMA Clermont, ICCF 63000 Clermont-Ferrand France
| | - David J. Aitken
- Université Paris-Saclay, CNRS Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) 91405 Orsay France
| | - Michel Mons
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
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8
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Lebel M, Very T, Gloaguen E, Tardivel B, Mons M, Brenner V. Excited States Computation of Models of Phenylalanine Protein Chains: TD-DFT and Composite CC2/TD-DFT Protocols. Int J Mol Sci 2022; 23:621. [PMID: 35054802 PMCID: PMC8776158 DOI: 10.3390/ijms23020621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/29/2021] [Accepted: 01/03/2022] [Indexed: 11/16/2022] Open
Abstract
The present benchmark calculations testify to the validity of time-dependent density functional theory (TD-DFT) when exploring the low-lying excited states potential energy surfaces of models of phenylalanine protein chains. Among three functionals suitable for systems exhibiting charge-transfer excited states, LC-ωPBE, CAM-B3LYP, and ωB97X-D, which were tested on a reference peptide system, we selected the ωB97X-D functional, which gave the best results compared to the approximate coupled-cluster singles and doubles (CC2) method. A quantitative agreement for both the geometrical parameters and the vibrational frequencies was obtained for the lowest singlet excited state (a ππ* state) of the series of capped peptides. In contrast, only a qualitative agreement was met for the corresponding adiabatic zero-point vibrational energy (ZPVE)-corrected excitation energies. Two composite protocols combining CC2 and DFT/TD-DFT methods were then developed to improve these calculations. Both protocols substantially reduced the error compared to CC2 and experiment, and the best of both even led to results of CC2 quality at a lower cost, thus providing a reliable alternative to this method for very large systems.
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Affiliation(s)
| | | | | | | | | | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (M.L.); (T.V.); (E.G.); (B.T.); (M.M.)
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9
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Mundlapati VR, Imani Z, D'mello VC, Brenner V, Gloaguen E, Baltaze JP, Robin S, Mons M, Aitken DJ. N-H⋯X interactions stabilize intra-residue C5 hydrogen bonded conformations in heterocyclic α-amino acid derivatives. Chem Sci 2021; 12:14826-14832. [PMID: 34820098 PMCID: PMC8597926 DOI: 10.1039/d1sc05014a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/21/2021] [Indexed: 12/23/2022] Open
Abstract
Nature makes extensive and elaborate use of hydrogen bonding to assemble and stabilize biomolecular structures. The shapes of peptides and proteins rely significantly on N–H⋯O
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C interactions, which are the linchpins of turns, sheets and helices. The C5 H-bond, in which a single residue provides both donor and acceptor, is generally considered too weak to force the backbone to adopt extended structures. Exploiting the synergy between gas phase (experimental and quantum chemistry) and solution spectroscopies to decipher IR spectroscopic data, this work demonstrates that the extended C5-based conformation in 4-membered ring heterocyclic α-amino acid derivatives is significantly stabilized by the formation of an N–H⋯X H-bond. In this synergic system the strength of the C5 interaction remains constant while the N–H⋯X H-bond strength, and thereby the support provided by it, varies with the heteroatom. In 4-membered ring heterocyclic α-amino acid derivatives, extended conformations based on intraresidue C5 H-bonds can be stabilized by N–H⋯X H-bonds, making the combined C5–C6γ structures prominent in both gas phase and in weakly polar solutions.![]()
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Affiliation(s)
| | - Zeynab Imani
- Université Paris-Saclay, CNRS, ICMMO 91405 Orsay France
| | - Viola C D'mello
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
| | - Valérie Brenner
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
| | - Eric Gloaguen
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
| | | | - Sylvie Robin
- Université Paris-Saclay, CNRS, ICMMO 91405 Orsay France .,Université de Paris, Faculté de Pharmacie 75006 Paris France
| | - Michel Mons
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
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10
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Goldsztejn G, Mundlapati VR, Donon J, Tardivel B, Gloaguen E, Brenner V, Mons M. An intraresidue H-bonding motif in selenocysteine and cysteine, revealed by gas phase laser spectroscopy and quantum chemistry calculations. Phys Chem Chem Phys 2021; 22:20409-20420. [PMID: 32914809 DOI: 10.1039/d0cp02825h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Models of protein chains containing a seleno-cysteine (Sec) residue have been investigated by gas phase laser spectroscopy in order to document the effect of the H-bonding properties of the SeH group in the folding of the Sec side chain, by comparison with recent data on Ser- and Cys-containing sequences. Experimental data, complemented by quantum chemistry calculations and natural bonding orbital (NBO) analyses, are interpreted in terms of the formation of a so-called 5γ intra-residue motif, which bridges the acceptor chalcogen atom of the side chain to the NH bond of the same residue. This local structure, in which the O/S/Se atom is close to the plane of the N-terminal side amide, is constrained by local backbone-side chain hyperconjugation effects involving the S and Se atoms. Theoretical investigations of the Cys/Sec side chain show that (i) this 5γ motif is an intrinsic feature of these residues, (ii) the corresponding H-bond is strongly non-linear and intrinsically weak, (iii) but enhanced by γ- and β-turn secondary structures, which promote a more favorable 5γ H-bonding approach and distance. The resulting H-bonds are slightly stronger in selenocysteine than in cysteine, but nearly inexistent in serine, whose side chain in contrast behaves as a H-bonding donor. The modest spectral shifts of the Cys/Sec NH stretches measured experimentally reflect the moderate strength of the 5γ H-bonding, in agreement with the correlation obtained with a NBO-based H-bond strength indicator. The evolution along the Ser, Cys and Sec series emphasizes the compromise between the several factors that control the H-bonding in a hyperconjugation-constrained geometry, among them the chalcogen van der Waals and covalent radii. It also illustrates the 5γ H-bond enhancements with the Sec and Cys residues favoured by the constraints imposed by the γ- and β-turn structures of the peptide chain.
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Affiliation(s)
- Gildas Goldsztejn
- Laboratoire Interactions Dynamiques et Lasers (LIDYL), Université Paris-Saclay, Paris, France.
| | | | - Jérémy Donon
- Laboratoire Interactions Dynamiques et Lasers (LIDYL), Université Paris-Saclay, Paris, France.
| | - Benjamin Tardivel
- Laboratoire Interactions Dynamiques et Lasers (LIDYL), Université Paris-Saclay, Paris, France.
| | - Eric Gloaguen
- Laboratoire Interactions Dynamiques et Lasers (LIDYL), Université Paris-Saclay, Paris, France.
| | - Valérie Brenner
- Laboratoire Interactions Dynamiques et Lasers (LIDYL), Université Paris-Saclay, Paris, France.
| | - Michel Mons
- Laboratoire Interactions Dynamiques et Lasers (LIDYL), Université Paris-Saclay, Paris, France.
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11
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Goldsztejn G, Mundlapati VR, Brenner V, Gloaguen E, Mons M, Cabezas C, León I, Alonso JL. Intrinsic folding of the cysteine residue: competition between folded and extended forms mediated by the -SH group. Phys Chem Chem Phys 2021; 22:20284-20294. [PMID: 32966425 DOI: 10.1039/d0cp03136d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A dual microwave and optical spectroscopic study of a capped cysteine amino acid isolated in a supersonic expansion, combined with quantum chemistry modelling, enabled us to characterize the conformational preferences of Cys embedded in a protein chain. IR/UV double resonance spectroscopy provided evidence for the coexistence of two conformers, assigned to folded and extended backbones (with classical C7 and C5 backbone H-bonding respectively), each of them additionally stabilized by specific main-chain/side-chain H-bonding, where the sulfur atom essentially plays the role of H-bond acceptor. The folded structure was confirmed by microwave spectroscopy, which demonstrated the validity of the DFT-D methods currently used in the field. These structural and spectroscopic results, complemented by a theoretical Natural Bond Orbital analysis, enabled us to document the capacity of the weakly polar -CH2-SH side chain of Cys to adapt itself to the intrinsic local preferences of the peptide backbone, i.e., a γ-turn or a β-sheet extended secondary structure. The corresponding local H-bonding bridges the side chain acceptor S atom to the backbone NH donor site of the same or the next residue along the chain, through a 5- or a 6-membered ring respectively.
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Affiliation(s)
- Gildas Goldsztejn
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | | | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Michel Mons
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Carlos Cabezas
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - Iker León
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - José Luis Alonso
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
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12
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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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13
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Dupuy MS, Gloaguen E, Tardivel B, Mons M, Brenner V. CC2 Benchmark for Models of Phenylalanine Protein Chains: 0–0 Transition Energies and IR Signatures of the ππ* Excited State. J Chem Theory Comput 2019; 16:601-611. [DOI: 10.1021/acs.jctc.9b00923] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mi-Song Dupuy
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Benjamin Tardivel
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
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14
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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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15
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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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16
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Blodgett KN, Fischer JL, Lee J, Choi SH, Zwier TS. Conformation-Specific Spectroscopy of Asparagine-Containing Peptides: Influence of Single and Adjacent Asn Residues on Inherent Conformational Preferences. J Phys Chem A 2018; 122:8762-8775. [PMID: 30343572 DOI: 10.1021/acs.jpca.8b08418] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Karl N. Blodgett
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Joshua L. Fischer
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Jaeyeon Lee
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Soo Hyuk Choi
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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17
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Bernhard D, Dietrich F, Fatima M, Pérez C, Gottschalk HC, Wuttke A, Mata RA, Suhm MA, Schnell M, Gerhards M. The phenyl vinyl ether-methanol complex: a model system for quantum chemistry benchmarking. Beilstein J Org Chem 2018; 14:1642-1654. [PMID: 30013690 PMCID: PMC6036964 DOI: 10.3762/bjoc.14.140] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/02/2018] [Indexed: 11/23/2022] Open
Abstract
The structure of the isolated aggregate of phenyl vinyl ether and methanol is studied by combining a multi-spectroscopic approach and quantum-chemical calculations in order to investigate the delicate interplay of noncovalent interactions. The complementary results of vibrational and rotational spectroscopy applied in molecular beam experiments reveal the preference of a hydrogen bond of the methanol towards the ether oxygen (OH∙∙∙O) over the π-docking motifs via the phenyl and vinyl moieties, with an additional less populated OH∙∙∙P(phenyl)-bound isomer detected only by microwave spectroscopy. The correct prediction of the energetic order of the isomers using quantum-chemical calculations turns out to be challenging and succeeds with a sophisticated local coupled cluster method. The latter also yields a quantification as well as a visualization of London dispersion, which prove to be valuable tools for understanding the role of dispersion on the docking preferences. Beyond the structural analysis of the electronic ground state (S0), the electronically excited (S1) state is analyzed, in which a destabilization of the OH∙∙∙O structure compared to the S0 state is observed experimentally and theoretically.
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Affiliation(s)
- Dominic Bernhard
- Fachbereich Chemie & Research Center Optimas, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany
| | - Fabian Dietrich
- Fachbereich Chemie & Research Center Optimas, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany
| | - Mariyam Fatima
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany.,Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
| | - Cristóbal Pérez
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany.,Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
| | - Hannes C Gottschalk
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
| | - Axel Wuttke
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
| | - Ricardo A Mata
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
| | - Martin A Suhm
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
| | - Melanie Schnell
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany.,Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany.,Institute of Physical Chemistry, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Strasse 1, D-24118 Kiel, Germany
| | - Markus Gerhards
- Fachbereich Chemie & Research Center Optimas, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany
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18
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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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19
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Yang B, Liu S, Lin Z. Computational study on single molecular spectroscopy of tyrosin-glycine, tryptophane-glycine and glycine-tryptophane. Sci Rep 2017; 7:15869. [PMID: 29158576 PMCID: PMC5696477 DOI: 10.1038/s41598-017-16234-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/09/2017] [Indexed: 12/29/2022] Open
Abstract
Quantum chemistry calculations play a fundamental role in revealing the molecular structures observed in gas-phase spectroscopic measurements. The supersonic jet cooling widely used in single molecular spectroscopy experiment is a non-equilibrium process and often causes confusion on the theoretical and experimental comparison. A computational approach is proposed here to account for the effect of the non-equilibrium cooling on the experimental spectra and applied to the cases of tyrosin-glycine (YG), tryptophane-glycine (WG) and glycine-tryptophane (GW). The low energy conformers of YG, WG and GW are obtained through thorough conformational searches. The structural features and equilibrium distributions of conformations and the energy barriers for conformer conversions are then determined. Three classes of transition energy barriers, high, medium and low, are found for the conversions among conformers with distinctly different, similar and the same structural types, respectively. The final conformation populations are determined by assuming an initial temperature of about 450 K and allowing for only the conformation conversion with a low energy barrier to occur during the rapid cooling process. The results provide a natural explanation for the numbers of YG, WG and GW conformations observed experimentally. The theoretical conformation assignments are also in good agreement with the experimental IR data.
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Affiliation(s)
- Bing Yang
- Hefei National Laboratory for Physical Sciences at Microscale & CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Department of Physics, University of Science and Technology of China, Hefei, 230026, China
| | - Shixue Liu
- Department of Nanotechnology for Sustainable Energy, Kwansei Gakuin University, Gakuen 2-1, Sanda, Hyogo, 669-1337, Japan
| | - Zijing Lin
- Hefei National Laboratory for Physical Sciences at Microscale & CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Department of Physics, University of Science and Technology of China, Hefei, 230026, China.
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20
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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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21
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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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22
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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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23
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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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24
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Walsh PS, Dean JC, McBurney C, Kang H, Gellman SH, Zwier TS. Conformation-specific spectroscopy of capped glutamine-containing peptides: role of a single glutamine residue on peptide backbone preferences. Phys Chem Chem Phys 2016; 18:11306-22. [PMID: 27054830 DOI: 10.1039/c6cp01062h] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The conformational preferences of a series of short, aromatic-capped, glutamine-containing peptides have been studied under jet-cooled conditions in the gas phase.
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Affiliation(s)
| | - Jacob C. Dean
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Carl McBurney
- Department of Chemistry
- University of Wisconsin-Madison
- Madison
- USA
| | - Hyuk Kang
- Department of Chemistry
- Ajou University
- Republic of Korea
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25
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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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26
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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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27
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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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