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Hernández B, Coïc YM, Kruglik SG, Sanchez-Cortes S, Ghomi M. Relationships between conformational and vibrational features of tryptophan characteristic Raman markers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 316:124377. [PMID: 38701580 DOI: 10.1016/j.saa.2024.124377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 05/05/2024]
Abstract
Tryptophan (Trp) residue provides characteristic vibrational markers to the middle wavenumber spectral region of the Raman spectra recorded from peptides and proteins. In this report, we were particularly interested in eight Trp Raman markers, referred to as Wi (i = 1,…,8). All responsible for pronounced Raman lines, these markers originate from indole moiety, a bicyclic conjugated segment involved in the Trp structure. Numerous investigations have previously attempted to relate the variations observed in the spectral features of these markers to the environmental changes of Trp residues. To emphasize the most important points we can mention (i) the variations in the Raman profile of W4 (∼1360 cm-1) and W5 (∼1340 cm-1), frequently observed as a doublet with variable intensity ratio. These two markers were thought to result from a Fermi-resonance effect between certain planar and nonplanar modes; (ii) the changes observed in the wavenumbers and relative intensities of W4, W7 (∼880 cm-1) and W8 (∼760 cm-1) were supposed to be related to the accessibility of Trp to surrounding water molecules; and (iii) the wavenumber fluctuations of W3 (∼1550 cm-1), taken as a Trp side chain orientational marker. However, some ambiguities still exist regarding the interpretation of these markers, needing further clarification. Herein, upon a joint experimental and theoretical analysis based on a multiconformational approach, attention was paid to the relationships between structural and vibrational features of three indole-containing compounds with increasing structural complexity, i.e., skatole (3-methylindole), tryptophan, and tripeptide Gly-Trp-Gly. This study clearly shows that the existing assignments given to certain Trp Raman markers should be reconsidered, especially those based on the Fermi-resonance origin of W4-W5 (∼1360-1340 cm-1) doublet, as well as the purely environmental dependence of W7 and W8 markers.
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Affiliation(s)
- Belén Hernández
- LVTS, INSERM U1148. 74 rue Marcel Cachin. 93017 Bobigny Cédex France
| | - Yves-Marie Coïc
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Unité de Chimie des Biomolécules, F-75015 Paris, France
| | - Sergei G Kruglik
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean-Perrin, 4 Place Jussieu, 75005 Paris, France
| | | | - Mahmoud Ghomi
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 121, 28006 Madrid, Spain.
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Hernández B, Coïc YM, Kruglik SG, Sanchez-Cortes S, Ghomi M. The relationship between the tyrosine residue 850-830 cm -1 Raman doublet intensity ratio and the aromatic side chain χ 1 torsion angle. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 308:123681. [PMID: 38039641 DOI: 10.1016/j.saa.2023.123681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023]
Abstract
Tyrosine (Tyr) residue in a peptide chain is characterized by the presence of seven Raman markers, referred to as Yi (i = 1, …, 7), distributed over the middle wavenumber spectral region. Particularly, the changes observed in the relative intensity of Y5 and Y6 markers, appearing as a side by side doublet at ca. 850-830 cm-1, has received a great attention. Primarily assigned to a Fermi-resonance effect between phenol ring planar and nonplanar modes, former density functional theory calculations led us to affiliate the Y5-Y6 doublet to two distinct fundamental modes. Furthermore, despite the previous assumptions, it was evidenced that the reversal of the doublet intensity ratio cannot be solely explained by hydrogen bonding on the phenol hydroxyl group involved in Tyr. Herein, upon analyzing the observed and theoretical data collected from the cationic species of the tripeptide Gly-Tyr-Gly, the crucial effect of the aromatic side chain orientation, especially that of the χ1 torsion angle defined around the CαCβ bond, on the Tyr doublet intensity ratio has been evidenced.
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Affiliation(s)
- Belén Hernández
- LVTS, INSERM U1148, 74 rue Marcel Cachin, 93017 Bobigny Cédex, France
| | - Yves-Marie Coïc
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Unité de Chimie des Biomolécules, F-75015 Paris, France
| | - Sergei G Kruglik
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean-Perrin, 4 Place Jussieu, 75005 Paris, France
| | | | - Mahmoud Ghomi
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 121, 28006 Madrid, Spain.
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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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Pallavi L, Tonannavar J, Tonannavar J. DFT zwitterion model for vibrational and electronic structure of unnatural 3-amino-3-(4-fluorophenyl)propionic acid, aided by IR and Raman spectroscopy. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Hernández B, Pflüger F, Ghomi M. Aspartate: An interesting model for analyzing dipole‐ion and ion pair interactions through its oppositely charged amine and acid groups. J Comput Chem 2020; 41:1402-1410. [DOI: 10.1002/jcc.26184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/10/2020] [Accepted: 02/17/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Belén Hernández
- Laboratoire Matrice Extracellulaire et Dynamique Cellulaire (MEDyC)UMR 7369, Université de Reims, Faculté des Sciences Moulin de la Housse, Reims Cedex 2 France
- Université Sorbonne Paris Nord, UFR Santé‐Médecine‐Biologie HumaineGroupe de Biophysique Moléculaire Bobigny Cedex France
| | - Fernando Pflüger
- Université Sorbonne Paris Nord, UFR Santé‐Médecine‐Biologie HumaineGroupe de Biophysique Moléculaire Bobigny Cedex France
| | - Mahmoud Ghomi
- Laboratoire Matrice Extracellulaire et Dynamique Cellulaire (MEDyC)UMR 7369, Université de Reims, Faculté des Sciences Moulin de la Housse, Reims Cedex 2 France
- Université Sorbonne Paris Nord, UFR Santé‐Médecine‐Biologie HumaineGroupe de Biophysique Moléculaire Bobigny Cedex France
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Henández B, Legrand P, Dufay S, Gahoual R, Sanchez-Cortes S, Kruglik SG, Fabreguettes JR, Wolf JP, Houzé P, Ghomi M. Disorder-to-Order Markers of a Cyclic Hexapeptide Inspired from the Binding Site of Fertilin β Involved in Fertilization Process. ACS OMEGA 2019; 4:18049-18060. [PMID: 31720508 PMCID: PMC6843708 DOI: 10.1021/acsomega.9b01885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/28/2019] [Indexed: 06/10/2023]
Abstract
Synthetic peptides mimicking the binding site of fertilin β to its receptor, integrin α6β1, were shown to inhibit sperm-egg fusion when added to in vitro media. In contrast, the synthetic cyclic hexapeptide, cyclo(Cys1-Ser2-Phe3-Glu4-Glu5-Cys6), named as cFEE, proved to stimulate gamete fusion. Owing to its biological specificity, this hexapeptide could help improve the in vitro fertilization pregnancy rate in human. In an attempt to establish the structure-activity relationship of cFEE, its structural dynamics was herein analyzed by means of ultraviolet circular dichroism (UV-CD) and Raman scattering. The low concentration CD profile in water, containing mainly a deep minimum at ∼202 nm, is consistent with a rather unordered chain. However, an ordering trend of the peptide loop has been observed in a less polar solvent such as methanol, where the UV-CD signal shape is formed by a double negative marker at ∼202/215 nm, indicating the presence of a type-II' β-turn. Raman spectra recorded in aqueous samples upon a 100-fold concentration increase, still showed an important population (∼30%) of the disordered structure. The structural flexibility of the disulfide bridge was confirmed by the Raman markers arising from the Cys1-Cys6 disulfide bond-stretch motions. Density functional theory calculations highlighted the formation of the type-II' β-turn on the four central residues of cFEE (i.e., -Ser2-Phe3-Glu4-Glu5-) either with a left- or with a right-handed disulfide. The structure with a left-handed S-S bond, however, appears to be more stable.
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Affiliation(s)
- Belén Henández
- Laboratoire
Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), UMR 7369, Université de Reims, Faculté
des Sciences, Moulin de la Housse, 51687 Reims Cedex 2, France
- Sorbonne
Paris Cité, Université Paris 13, Groupe de Biophysique
Moléculaire, UFR Santé-Médecine-Biologie Humaine, 74 Rue Marcel Cachin, 93017 Bobigny Cedex, France
| | - Pauline Legrand
- Unité
de Technologies Chimiques et Biologiques pour la Santé (UTCBS),
CNRS UMR 8258-U1022, Faculté de Pharmacie Paris Descartes, Université Paris Descartes, 75006 Paris, France
- Agence
Générale des Equipements et Produits de Santé
(AGEPS), Assistance Publique-Hôpitaux
de Paris (AP-HP), 75005 Paris, France
| | - Sophie Dufay
- Agence
Générale des Equipements et Produits de Santé
(AGEPS), Assistance Publique-Hôpitaux
de Paris (AP-HP), 75005 Paris, France
| | - Rabah Gahoual
- Unité
de Technologies Chimiques et Biologiques pour la Santé (UTCBS),
CNRS UMR 8258-U1022, Faculté de Pharmacie Paris Descartes, Université Paris Descartes, 75006 Paris, France
| | | | - Sergei G. Kruglik
- Laboratoire
Jean Perrin, Sorbonne Université,
CNRS UMR 8237, 75005 Paris, France
| | - Jean-Roch Fabreguettes
- Agence
Générale des Equipements et Produits de Santé
(AGEPS), Assistance Publique-Hôpitaux
de Paris (AP-HP), 75005 Paris, France
| | - Jean-Philippe Wolf
- Sorbonne
Paris Cité, Université Paris Descartes, Faculté
de Médecine, Assistance Publique-Hôpitaux de Paris (AP-HP),
Hôpital Universitaire Paris Centre, Centre Hospitalier Universitaire
(CHU) Cochin, Service d’Histologie-Embryologie-Biologie de
la Reproduction, 75006 Paris, France
- Département
Génomique, Epigénétique et Physiopathologie de
la Reproduction, Institut Cochin, INSERM
U1016, CNRS UMR8104, Université Paris Descartes, Sorbonne Paris
Cité, 75006 Paris, France
| | - Pascal Houzé
- Unité
de Technologies Chimiques et Biologiques pour la Santé (UTCBS),
CNRS UMR 8258-U1022, Faculté de Pharmacie Paris Descartes, Université Paris Descartes, 75006 Paris, France
- Laboratoire
de Biochimie, Hôpital Universitaire
Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris
(AP-HP), 75015 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
- Sorbonne
Paris Cité, Université Paris 13, Groupe de Biophysique
Moléculaire, UFR Santé-Médecine-Biologie Humaine, 74 Rue Marcel Cachin, 93017 Bobigny Cedex, France
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