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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. Spectrochim Acta A Mol Biomol Spectrosc 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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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. Spectrochim Acta A Mol Biomol Spectrosc 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Finnegan A, Salem K, Green N, Ainsworth-Moore L, Ghomi M. Evaluation of the NHS England 'Op COURAGE' High Intensity Service for military veterans with significant mental health problems. BMJ Mil Health 2023:e002385. [PMID: 37451820 DOI: 10.1136/military-2023-002385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/10/2023] [Indexed: 07/18/2023]
Abstract
INTRODUCTION In November 2020, The NHS for England launched a pilot High Intensity Service (HIS) programme for treating military veterans complex mental health problems. Seven regional grants were awarded to manage the HIS, including NHS Solent, in South East England. This paper details an evaluation of the HIS, which was conducted from February 2021 to August 2022. METHODS This mixed-methods study gained quantitative data from a specifically designed questionnaire that included a number of validated psychometric questionnaires. These were completed by either HIS staff or beneficiaries at entry and exit from the HIS, and qualitative data were gained from semi-structured interviews with the HIS staff. RESULTS Data were sourced from 45 pre-questionnaires, 25 post programme questionnaires and 11 interviews. This evaluation identified reductions in situational stressors, symptoms and reported illnesses for veterans in crisis. There were reductions in depression, anxiety and post-traumatic stress disorder following programme exit. Staff reported that there was no notable changes in stress levels which appeared to remain high at programme exit. Staff interviews highlighted the importance of simultaneously understanding the social and psychological needs of veterans in mental health crisis. The benefits of integrating veteran staff members into military veteran health services were identified, demonstrating improvements in education around military culture in civilian services. CONCLUSIONS The importance of collaboration between clinical and veteran staff members in veteran health services was noted, demonstrating the positive impact social care provision has on veteran's overall health and well-being. Veteran engagement with the service was advocated as a result of veterans accessing the service feeling understood. This first independent evaluation of the HIS provides a positive reflection, and adds to the limited empirical evidence exploring veteran engagement in health services.
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Affiliation(s)
- Alan Finnegan
- Westminster Centre for Research in Veterans, University of Chester, Chester, UK
| | - K Salem
- Westminster Centre for Research in Veterans, University of Chester, Chester, UK
| | - N Green
- Westminster Centre for Research in Veterans, University of Chester, Chester, UK
| | - L Ainsworth-Moore
- Westminster Centre for Research in Veterans, University of Chester, Chester, UK
| | - M Ghomi
- Psychological Services, Solent NHS Trust, Portsmouth, UK
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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O'Brien DP, Perez ACS, Karst J, Cannella SE, Enguéné VYN, Hessel A, Raoux-Barbot D, Voegele A, Subrini O, Davi M, Guijarro JI, Raynal B, Baron B, England P, Hernandez B, Ghomi M, Hourdel V, Malosse C, Chamot-Rooke J, Vachette P, Durand D, Brier S, Ladant D, Chenal A. Calcium-dependent disorder-to-order transitions are central to the secretion and folding of the CyaA toxin of Bordetella pertussis, the causative agent of whooping cough. Toxicon 2018; 149:37-44. [DOI: 10.1016/j.toxicon.2018.01.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/20/2017] [Accepted: 01/10/2018] [Indexed: 02/07/2023]
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Hernández B, Coïc YM, López-Tobar E, Sanchez-Cortes S, Baron B, Pflüger F, Kruglik SG, Cohen R, Ghomi M. Dynamical Behavior of Somatostatin-14 and Its Cyclic Analogues as Analyzed in Bulk and on Plasmonic Silver Nanoparticles. Adv Protein Chem Struct Biol 2018; 112:81-121. [PMID: 29680244 DOI: 10.1016/bs.apcsb.2018.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Primarily known as the inhibitor of growth hormone release, the role of somatostatin in many other inhibiting activities upon binding to its five G-protein-coupled receptors has been elucidated. Because of the short half-life of somatostatin, a number of synthetic analogues were elaborated for this peptide hormone. Herein, after recalling the main somatostatin therapeutic interests, we present the dynamical behavior of somatostatin-14 and its two currently used synthetic cyclic analogues, octreotide and pasireotide. Physical techniques, such as fluorescence, UV-visible absorption, circular dichroism, Raman spectroscopy, surface-enhanced Raman spectroscopy, and transmission electron microscopy, were jointly used in order to get information on the solution structural features, as well as on the anchoring sites of the three peptides on silver colloids. While somatostatin-14 adopts a rather unordered chain within the submillimolar concentration range, its cyclic analogues were revealed to be ordered, i.e., stabilized either in a type-II' β-turn (octreotide) or in a face-to-face γ-turn/type-I β-turn (pasireotide) structure. Nevertheless, a progressive structuring trend was observed in somatostatin-14 upon increasing concentration to the millimolar range. Because of their cationic character, the three peptides have revealed their capability to bind onto negatively charged silver nanoparticles. The high affinity of the peptides toward metallic particles seems to be extremely promising for the elaboration of somatostatin-based functionalized plasmonic nanoparticles that can be used in diagnosis, drug delivery, and therapy.
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Affiliation(s)
- Belén Hernández
- Laboratoire Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), UMR 7369, Université de Reims, Faculté des Sciences, Reims Cedex 2, France; Groupe de Biophysique Moléculaire, Sorbonne Paris Cité, Université Paris 13, UFR Santé-Médecine-Biologie Humaine, Bobigny, France
| | - Yves-Marie Coïc
- Institut Pasteur, Unité de Chimie des Biomolécules, UMR 3523, Paris Cedex 15, France
| | | | | | - Bruno Baron
- Institut Pasteur, Plate-Forme de Biophysique de Macromolécules et de leurs Interactions, Paris Cedex 15, France
| | - Fernando Pflüger
- Groupe de Biophysique Moléculaire, Sorbonne Paris Cité, Université Paris 13, UFR Santé-Médecine-Biologie Humaine, Bobigny, France
| | - Sergei G Kruglik
- Laboratoire Jean-Perrin, Sorbonne Université, UPMC Univ. Paris 06, CNRS UMR 8237, Paris, France
| | - Régis Cohen
- Service d'Endocrinologie, Centre Hospitalier de Saint-Denis, Saint-Denis, France
| | - Mahmoud Ghomi
- Laboratoire Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), UMR 7369, Université de Reims, Faculté des Sciences, Reims Cedex 2, France; Groupe de Biophysique Moléculaire, Sorbonne Paris Cité, Université Paris 13, UFR Santé-Médecine-Biologie Humaine, Bobigny, France.
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Hernández B, Houzé P, Pflüger F, Kruglik SG, Ghomi M. Raman scattering-based multiconformational analysis for probing the structural differences between acetylcholine and acetylthiocholine. J Pharm Biomed Anal 2017; 138:54-62. [PMID: 28182991 DOI: 10.1016/j.jpba.2017.01.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/20/2017] [Accepted: 01/25/2017] [Indexed: 10/20/2022]
Abstract
Acetylcholine is the first discovered neurotransmitter that has received a great attention regarding its capability of binding to several cellular targets. The chemical composition of acetylcholine, including a positively charged trimethylammonium and a carbonyl group, as well as its conformational flexibility was pointed out as the key factors in the stabilization of its interactions. Here, the possibilities offered by a Raman scattering-based multiconformatioal analysis to access the most stable conformers of acetylcholine, is discussed. To control the validity of this protocol, acetylcholine and one of its closely structured analogues, acetylthiocholine, were simultaneously analyzed. Solution Raman spectra revealed distinct and well resolved strong markers for each molecule. Density functional theory calculations were consistent with the fact that the energy order of the low energy conformers is considerably affected by the acyloxy oxygen→sulfur atom substitution. Raman spectra were calculated on the basis of the thermal average of the spectra arising from the low energy conformers. It has been evidenced that the carbonyl and trimethylammonium groups are the most favorable hydration sites in aqueous environment. Taking into account the large gap between the carbonyl bond-stretch and aliphatic bending bands, Raman spectra also allowed separation of the HOH bending vibrations arising from the bound and bulk water molecules.
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Affiliation(s)
- Belén Hernández
- CNRS UMR 7369, Laboratoire Matrice Extracellulaire et Dynamique Cellulaire, Université de Reims Champagne Ardenne, UFR Sciences Exactes et Naturelles, Moulin de la Housse, 51687 Reims Cedex 2, France; Groupe de Biophysique Moléculaire, Sorbonne Paris Cité, Université Paris 13, UFR Santé-Médecine-Biologie Humaine, 74 Rue Marcel Cachin, 93017 Bobigny Cedex, France
| | - Pascal Houzé
- Laboratoire de Biochimie, Hôpital Saint Louis, 1 Avenue Claude Vellefaux, 75010 Paris, France; UTCBS, CNRS UMR8258 - U1022, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, 75006 Paris, France
| | - Fernando Pflüger
- Groupe de Biophysique Moléculaire, Sorbonne Paris Cité, Université Paris 13, UFR Santé-Médecine-Biologie Humaine, 74 Rue Marcel Cachin, 93017 Bobigny Cedex, France
| | - Sergei G Kruglik
- CNRS UMR 8237, Laboratoire Jean-Perrin, Sorbonne Universités, UPMC Univ. Paris 06, 75005 Paris, France
| | - Mahmoud Ghomi
- CNRS UMR 7369, Laboratoire Matrice Extracellulaire et Dynamique Cellulaire, Université de Reims Champagne Ardenne, UFR Sciences Exactes et Naturelles, Moulin de la Housse, 51687 Reims Cedex 2, France; Groupe de Biophysique Moléculaire, Sorbonne Paris Cité, Université Paris 13, UFR Santé-Médecine-Biologie Humaine, 74 Rue Marcel Cachin, 93017 Bobigny Cedex, France.
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O’Brien DP, Cannella SE, Durand D, Ntsogo Enguéné VY, Hernandez B, Ghomi M, Subrini O, Hessel A, Malosse C, Hourdel V, Vachette P, Chamot-Rooke J, Brier S, Ladant D, Chenal A. Calcium Tightly Regulates Disorder-To-Order Transitions Involved in the Secretion, Folding and Functions of the CyaA Toxin of Bordetella Pertussis, the Causative Agent of Whooping Cough. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Hernández B, Pflüger F, Dauchez M, Ghomi M. Privileged hydration sites in aromatic side chains: effect on conformational equilibrium. Phys Chem Chem Phys 2017; 19:28684-28695. [DOI: 10.1039/c7cp04685e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The most energetically favourable hydration sites of aromatic (Phe, Tyr, Trp and His) side chains revealed by DFT-based theoretical calculations.
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Affiliation(s)
- Belén Hernández
- Laboratoire Matrice Extracellulaire et Dynamique Cellulaire (MEDyC)
- UMR 7369
- 51687 Reims Cedex 2
- France
- Sorbonne Paris Cité
| | - Fernando Pflüger
- Sorbonne Paris Cité
- Université Paris 13
- Groupe de Biophysique Moléculaire
- UFR Santé-Médecine-Biologie Humaine
- 93017 Bobigny cedex
| | - Manuel Dauchez
- Laboratoire Matrice Extracellulaire et Dynamique Cellulaire (MEDyC)
- UMR 7369
- 51687 Reims Cedex 2
- France
| | - Mahmoud Ghomi
- Laboratoire Matrice Extracellulaire et Dynamique Cellulaire (MEDyC)
- UMR 7369
- 51687 Reims Cedex 2
- France
- Sorbonne Paris Cité
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Patrick O'Brien D, Hernandez B, Durand D, Hourdel V, SotomayorPérez AC, Vachette P, Ghomi M, Chamot-Rooke J, Ladant D, Brier S, Chenal A. Structural Models of an Intrinsically Disordered Protein Adapted for Bacterial Secretion. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Hernández B, López-Tobar E, Sanchez-Cortes S, Coïc YM, Baron B, Chenal A, Kruglik SG, Pflüger F, Cohen R, Ghomi M. From bulk to plasmonic nanoparticle surfaces: the behavior of two potent therapeutic peptides, octreotide and pasireotide. Phys Chem Chem Phys 2016; 18:24437-50. [DOI: 10.1039/c6cp04421b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural dynamics of two potent somatostatin analogues in an aqueous environment and their binding sites on plasmonic nanoparticles were described.
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Affiliation(s)
- Belén Hernández
- Sorbonne Paris Cité
- Université Paris 13
- Groupe de Biophysique Moléculaire
- UFR Santé-Médecine-Biologie Humaine
- 93017 Bobigny Cedex
| | | | | | - Yves-Marie Coïc
- Institut Pasteur
- Unité de Chimie des Biomolécules
- UMR 3523
- 75724 Paris Cedex 15
- France
| | - Bruno Baron
- Institut Pasteur
- Plate-Forme de Biophysique de Macromolécules et de leurs Interactions
- 75724 Paris Cedex 15
- France
| | - Alexandre Chenal
- Institut Pasteur
- Unité Biochimie des Interactions Macromoléculaires
- UMR CNRS 3528
- 75724 Paris Cedex 15
- France
| | - Sergei G. Kruglik
- Sorbonne Universités
- UPMC Univ. Paris 06
- UMR 8237
- Laboratoire Jean Perrin
- 75005 Paris
| | - Fernando Pflüger
- Sorbonne Paris Cité
- Université Paris 13
- Groupe de Biophysique Moléculaire
- UFR Santé-Médecine-Biologie Humaine
- 93017 Bobigny Cedex
| | - Régis Cohen
- Service d’Endocrinologie
- Centre Hospitalier de Saint-Denis
- 93200 Saint-Denis
- France
| | - Mahmoud Ghomi
- Sorbonne Paris Cité
- Université Paris 13
- Groupe de Biophysique Moléculaire
- UFR Santé-Médecine-Biologie Humaine
- 93017 Bobigny Cedex
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Hernández B, Pflüger F, Kruglik SG, Cohen R, Ghomi M. Protonation–deprotonation and structural dynamics of antidiabetic drug metformin. J Pharm Biomed Anal 2015; 114:42-8. [DOI: 10.1016/j.jpba.2015.04.041] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 04/27/2015] [Accepted: 04/30/2015] [Indexed: 10/23/2022]
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O'Brien DP, Hernandez B, Durand D, Hourdel V, Sotomayor-Pérez AC, Vachette P, Ghomi M, Chamot-Rooke J, Ladant D, Brier S, Chenal A. Structural models of intrinsically disordered and calcium-bound folded states of a protein adapted for secretion. Sci Rep 2015; 5:14223. [PMID: 26374675 PMCID: PMC4642704 DOI: 10.1038/srep14223] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 08/20/2015] [Indexed: 01/28/2023] Open
Abstract
Many Gram-negative bacteria use Type I secretion systems, T1SS, to secrete virulence factors that contain calcium-binding Repeat-in-ToXin (RTX) motifs. Here, we present structural models of an RTX protein, RD, in both its intrinsically disordered calcium-free Apo-state and its folded calcium-bound Holo-state. Apo-RD behaves as a disordered polymer chain comprising several statistical elements that exhibit local rigidity with residual secondary structure. Holo-RD is a folded multi-domain protein with an anisometric shape. RTX motifs thus appear remarkably adapted to the structural and mechanistic constraints of the secretion process. In the low calcium environment of the bacterial cytosol, Apo-RD is an elongated disordered coil appropriately sized for transport through the narrow secretion machinery. The progressive folding of Holo-RD in the extracellular calcium-rich environment as it emerges form the T1SS may then favor its unidirectional export through the secretory channel. This process is relevant for hundreds of bacterial species producing virulent RTX proteins.
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Affiliation(s)
- Darragh P O'Brien
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, 75724 PARIS cedex 15, France
| | - Belen Hernandez
- Sorbonne Paris Cité, Université Paris 13, Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine, 74 rue Marcel Cachin, 93017 Bobigny Cedex, France
| | - Dominique Durand
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Université Paris-Sud, F-91405 ORSAY Cedex, France
| | - Véronique Hourdel
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, 75724 PARIS cedex 15, France
| | | | - Patrice Vachette
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Université Paris-Sud, F-91405 ORSAY Cedex, France
| | - Mahmoud Ghomi
- Sorbonne Paris Cité, Université Paris 13, Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine, 74 rue Marcel Cachin, 93017 Bobigny Cedex, France
| | - Julia Chamot-Rooke
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, 75724 PARIS cedex 15, France
| | - Daniel Ladant
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, 75724 PARIS cedex 15, France
| | - Sébastien Brier
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, 75724 PARIS cedex 15, France
| | - Alexandre Chenal
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, 75724 PARIS cedex 15, France
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Hernández B, Coïc YM, Baron B, Kruglik SG, Pflüger F, Cohen R, Carelli C, Ghomi M. Low concentration structural dynamics of lanreotide and somatostatin-14. Biopolymers 2014; 101:1019-28. [DOI: 10.1002/bip.22491] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 03/21/2014] [Accepted: 03/26/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Belén Hernández
- Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine; Université Paris 13; Sorbonne Paris Cité, 74 rue Marcel Cachin, 93017 Bobigny cedex France
| | - Yves-Marie Coïc
- Institut Pasteur, Unité de Chimie des Biomolécules; UMR 3523, 28 rue du Docteur Roux, 75724 Paris Cedex 15 France
| | - Bruno Baron
- Institut Pasteur, Plate-Forme de Biophysique de Macromolécules et de leurs Interactions; 25, Rue du Docteur Roux, 75724 Paris Cedex 15 France
| | - Sergei G. Kruglik
- Sorbonne Universités, UPMC Université Paris 06; UMR 8237, Laboratoire Jean Perrin F-75005 Paris France
- CNRS; UMR 8237, Laboratoire Jean-Perrin F-75005 Paris France
| | - Fernando Pflüger
- Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine; Université Paris 13; Sorbonne Paris Cité, 74 rue Marcel Cachin, 93017 Bobigny cedex France
| | - Régis Cohen
- Service d'Endocrinologie; Centre Hospitalier de Saint-Denis; 2 Rue du Docteur Delafontaine 93200 Saint-Denis France
| | - Claude Carelli
- Regulaxis; Parc Scientifique Biocitech; 102 avenue Gaston Roussel 93230 Romainville France
| | - Mahmoud Ghomi
- Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine; Université Paris 13; Sorbonne Paris Cité, 74 rue Marcel Cachin, 93017 Bobigny cedex France
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Hernández B, Coïc YM, Kruglik SG, Carelli C, Cohen R, Ghomi M. Octreotide used for probing the type-II' β-turn CD and Raman markers. J Phys Chem B 2012; 116:9337-45. [PMID: 22793173 DOI: 10.1021/jp3036428] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Octreotide, a potent somatostatin (SST) analogue, is used as an antiproliferative drug in numerous endocrine tumors. Previous NMR investigations, basically performed in DMSO, had evidenced a type-II' β-turn structure for this cyclic peptide. However, apart a few incomplete studies by circular dichroism, a systematic analysis of the structural behavior of octreotide in aqueous solution as a function of concentration and ionic strength was still lacking. Here, we report the chemical synthesis and purification of octreotide for optical spectroscopic purposes accompanied by its structural analysis. Furthermore, we have used octreotide as a short size, well-defined model compound for analyzing the CD and Raman markers of a type-II' β-turn. CD data collected in the 25-250 μM range revealed the general trend of octreotide to undergo a disordered toward ordered structural transition upon increasing concentration. Especially, the β-turn CD markers could be characterized above 50 μM by a negative band at ~202 nm flanked by a shoulder at ~218 nm. On the basis of Raman spectra recorded as a function of concentration (1-20 mM), we could assign the markers at ~1678 and ~1650 cm(-1) in the amide I region, and at ~1303, ~1288, and ~1251 cm(-1) in the amide III region, to the type-II' β-turn structure. The stability of the intermolecular antiparallel β-sheet formed in octreotide could be confirmed by the rigidity of the disulfide bridge which adopts a preferential gauche-gauche-gauche rotamer along the -Cβ-S-S-Cβ- moiety of the linked cysteines. The present analysis permits a better understanding of the differences between the structural features of SST-14 and its routinely used analogue, octreotide.
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Affiliation(s)
- Belén Hernández
- Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine, Université Paris 13, Sorbonne Paris Cité, 74 rue Marcel Cachin, 93017 Bobigny Cedex, France
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Hernández B, Pflüger F, Adenier A, Nsangou M, Kruglik SG, Ghomi M. Energy maps, side chain conformational flexibility, and vibrational features of polar amino acidsL-serine andL-threonine in aqueous environment. J Chem Phys 2011; 135:055101. [DOI: 10.1063/1.3617415] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Hernández B, Pflüger F, Adenier A, Kruglik SG, Ghomi M. Side chain flexibility and protonation states of sulfur atom containing amino acids. Phys Chem Chem Phys 2011; 13:17284-94. [DOI: 10.1039/c1cp21054h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Hernández B, Pflüger F, Adenier A, Kruglik SG, Ghomi M. Vibrational Analysis of Amino Acids and Short Peptides in Hydrated Media. VIII. Amino Acids with Aromatic Side Chains: l-Phenylalanine, l-Tyrosine, and l-Tryptophan. J Phys Chem B 2010; 114:15319-30. [DOI: 10.1021/jp106786j] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Belén Hernández
- Groupe de Biophysique Moléculaire, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France; Laboratoire ITODYS, UMR 7086, Université Paris Diderot, Bâtiment Lavoisier, 15, rue Jean-Antoine de Baïf, 75205 Paris cedex 13, France; and Laboratoire Acides Nucléiques et Biophotonique (FRE 3207), Université Pierre et Marie Curie Paris 06, 75252 Paris, France
| | - Fernando Pflüger
- Groupe de Biophysique Moléculaire, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France; Laboratoire ITODYS, UMR 7086, Université Paris Diderot, Bâtiment Lavoisier, 15, rue Jean-Antoine de Baïf, 75205 Paris cedex 13, France; and Laboratoire Acides Nucléiques et Biophotonique (FRE 3207), Université Pierre et Marie Curie Paris 06, 75252 Paris, France
| | - Alain Adenier
- Groupe de Biophysique Moléculaire, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France; Laboratoire ITODYS, UMR 7086, Université Paris Diderot, Bâtiment Lavoisier, 15, rue Jean-Antoine de Baïf, 75205 Paris cedex 13, France; and Laboratoire Acides Nucléiques et Biophotonique (FRE 3207), Université Pierre et Marie Curie Paris 06, 75252 Paris, France
| | - Sergei G. Kruglik
- Groupe de Biophysique Moléculaire, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France; Laboratoire ITODYS, UMR 7086, Université Paris Diderot, Bâtiment Lavoisier, 15, rue Jean-Antoine de Baïf, 75205 Paris cedex 13, France; and Laboratoire Acides Nucléiques et Biophotonique (FRE 3207), Université Pierre et Marie Curie Paris 06, 75252 Paris, France
| | - Mahmoud Ghomi
- Groupe de Biophysique Moléculaire, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France; Laboratoire ITODYS, UMR 7086, Université Paris Diderot, Bâtiment Lavoisier, 15, rue Jean-Antoine de Baïf, 75205 Paris cedex 13, France; and Laboratoire Acides Nucléiques et Biophotonique (FRE 3207), Université Pierre et Marie Curie Paris 06, 75252 Paris, France
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Pflüger F, Hernández B, Ghomi M. Vibrational Analysis of Amino Acids and Short Peptides in Hydrated Media. VII. Energy Landscapes, Energetic and Geometrical Features of L-Histidine with Protonated and Neutral Side Chains. J Phys Chem B 2010; 114:9072-83. [DOI: 10.1021/jp103348y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Fernando Pflüger
- Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine (SMBH), Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
| | - Belén Hernández
- Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine (SMBH), Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
| | - Mahmoud Ghomi
- Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine (SMBH), Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
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Hernández B, Pflüger F, Derbel N, De Coninck J, Ghomi M. Vibrational analysis of amino acids and short peptides in hydrated media. VI. Amino acids with positively charged side chains: L-lysine and L-arginine. J Phys Chem B 2010; 114:1077-88. [PMID: 20025231 DOI: 10.1021/jp909517r] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In two recent reports of the same series (J. Phys. Chem. B 2007, 111, 1470-1477 and J. Phys. Chem. B 2009, 113, 3169-3178), we have described the geometrical and vibrational analysis of glycine and amino acids (AAs) with hydrophobic side chains through the joint use of optical spectroscopy and quantum mechanical calculations. Here, we report Raman scattering and Fourier-Transform Infrared (FT-IR) Attenuated Total Reflectance (ATR) spectra measured from the aqueous solutions (H(2)O and D(2)O) of L-lysine and L-arginine, i.e. two alpha-AAs with positively charged hydrophilic side chains. The discussion on the vibrational features of both AAs could be carried out thanks to the theoretical calculations performed by means of the Density Functional Theory (DFT) approach at the B3LYP/6-31++G* level. We have analyzed the influence of implicit (with a polarizable dielectric continuum) and explicit (by means of an H(2)O cluster interacting with H-donor and H-acceptor sites of AAs) hydration models. In addition, through the calculated geometrical parameters and vibrational wavenumbers, a discussion was performed on the effect of the Cl(-) anion interacting with the positively charged side chains of explicitly hydrated AAs.
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Affiliation(s)
- Belén Hernández
- Groupe de Biophysique Moléculaire, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
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Hernández B, Carelli C, Coïc YM, De Coninck J, Ghomi M. Vibrational analysis of amino acids and short peptides in aqueous media. V. The effect of the disulfide bridge on the structural features of the peptide hormone somatostatin-14. J Phys Chem B 2009; 113:12796-803. [PMID: 19708669 DOI: 10.1021/jp904737v] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
To emphasize the role played by the S-S bridge in the structural features of somatostatin-14 (SST-14), newly recorded CD and Raman spectra of this cyclic peptide and its open analogue obtained by Cys-->Ser substitution are presented. CD spectra of both peptides recorded in aqueous solutions in the 100-500 microM concentration range are strikingly similar. They reveal principally that random conformers constitute the major population in both peptides. Consequently, the S-S bridge has no structuring effect at submillimolar concentrations. In methanol, the CD spectrum of somatostatin-14 keeps globally the same spectral shape as that observed in water, whereas its open analogue presents a major population of helical conformers. Raman spectra recorded as a function of peptide concentration (5-20 mM) and also in the presence of 150 mM NaCl provide valuable conformational information. All Raman spectra present a mixture of random and beta-hairpin structures for both cyclic and open peptides. More importantly, the presence or the absence of the disulfide bridge does not seem to influence considerably different populations of secondary structures within this range of concentrations. CD and Raman data obtained in the submillimolar and millimolar ranges of concentrations, respectively, lead us to accept the idea that SST-14 monomers aggregate upon increasing concentration, thus stabilizing beta-hairpin conformations in solution. However, even at high concentrations, random conformers do not disappear. Raman spectra of SST-14 also reveal a concentration effect on the flexibility of the S-S linkage and consequently on that of its cyclic part. In conclusion, although the disulfide linkage does not seem to markedly influence the SST-14 conformational features in aqueous solutions, its presence seems to be necessary to ensure the flexibility of the cyclic part of this peptide and to maintain its closed structure in lower dielectric constant environments.
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Affiliation(s)
- Belén Hernández
- Groupe de Biophysique Moléculaire (GBM), UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny Cedex, France
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Hernández B, Pflüger F, Nsangou M, Ghomi M. Vibrational analysis of amino acids and short peptides in hydrated media. IV. Amino acids with hydrophobic side chains: L-alanine, L-valine, and L-isoleucine. J Phys Chem B 2009; 113:3169-78. [PMID: 19708268 DOI: 10.1021/jp809204d] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In the framework of our investigations on the analysis of vibrational spectra of amino acids (AAs) in hydrated media, Raman scattering and Fourier transform infrared (FT-IR) attenuated transmission reflectance (ATR) spectra of three alpha-amino acids with hydrophobic hydrocarbon side chains, i.e., alanine, valine, and isoleucine, were measured in H2O and D2O solutions. The present data complete those recently published by our group on glycine and leucine. This series of observed vibrational data gave us the opportunity to analyze the vibrational features of these amino acids in hydrated media by means of the density functional theory (DFT) calculations at the B3LYP/6-31++G* level. Harmonic vibrational modes calculated after geometry optimization on the clusters containing five water molecules interacting with H-donor and H-acceptor sites of amino acids are performed and allowed the observed main Raman and infrared bands to be assigned. Additional calculations on a cluster formed by leucine (L) and five water (W) molecules and the comparison of the obtained data with those recently published by our group on L+12W, allowed us to justify the number of hydration considered in the present report.
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Affiliation(s)
- Belén Hernández
- Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire (BioMoCeTi), UMR CNRS 7033, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
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Dhaouadi Z, Nsangou M, Hernández B, Pflüger F, Liquier J, Ghomi M. Geometrical and vibrational features of phosphate, phosphorothioate and phosphorodithioate linkages interacting with hydrated cations: a DFT study. Spectrochim Acta A Mol Biomol Spectrosc 2009; 73:805-814. [PMID: 19442575 DOI: 10.1016/j.saa.2009.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 03/19/2009] [Accepted: 04/01/2009] [Indexed: 05/27/2023]
Abstract
The effect of hexahydrated monovalent and divalent cations on the geometrical and vibrational features of dimethyl phosphate, dimethyl phosphorothioate and dimethyl phosphorodithioate anions (simple suitable model compounds representing the anionic moieties of natural and some modified nucleic acids) was studied. For this purpose, density functional theory (DFT) calculations were carried out at the B3LYP/6-31++G* level. Our results indicate that only K(+) and Mg(2+) prefer to be located in the bisector plane of the PO(2)(-) angle, whereas Li(+) and Na(+) deviate from this plane. Monovalent and divalent cations are slightly deviated from the OPS(-) bisector plane and are found closer to the free oxygen atom. Moreover, the present calculations have shown that in contrast to the general belief, the g(-)g(-) conformer (with respect to the torsion angles defined around the P-O ester bonds) is not always the energetically most favorable. For instance, the g(-)t conformer presents the lowest energy in the case of dimethyl phosphorothioate. The calculated vibrational wavenumbers obtained for dimethyl phosphate and dimethyl phosphorothioate interacting with hydrated sodium counterion, were compared with those previously recorded by Raman scattering and infrared absorption (IR) in aqueous solutions. It has been evidenced that the use of explicit solvent versus dielectric continuum, considerably improves the agreement between the theoretical and observed characteristic wavenumbers.
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Affiliation(s)
- Zoubeida Dhaouadi
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications, Faculté des Sciences de Tunis, Université Tunis El Manar, Campus Universitaire, 1060 El Manar II - Tunis, Tunisia
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Guiffo-Soh G, Hernández B, Coïc YM, Boukhalfa-Heniche FZ, Fadda G, Ghomi M. Vibrational Analysis of Amino Acids and Short Peptides in Hydrated Media. 3. Successive KL Repeats Induce Highly Stable β-Strands Capable of Forming Non-H-Bonded Aggregates. J Phys Chem B 2008; 112:1282-9. [DOI: 10.1021/jp0767967] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Guy Guiffo-Soh
- UMR CNRS 7033, BioMoCeTi, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, Université Pierre et Marie Curie, Case 138, 4 Place Jussieu, 75252 Paris cedex 05, France, and Unité de Chimie Organique, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Belén Hernández
- UMR CNRS 7033, BioMoCeTi, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, Université Pierre et Marie Curie, Case 138, 4 Place Jussieu, 75252 Paris cedex 05, France, and Unité de Chimie Organique, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Yves-Marie Coïc
- UMR CNRS 7033, BioMoCeTi, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, Université Pierre et Marie Curie, Case 138, 4 Place Jussieu, 75252 Paris cedex 05, France, and Unité de Chimie Organique, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Fatima-Zohra Boukhalfa-Heniche
- UMR CNRS 7033, BioMoCeTi, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, Université Pierre et Marie Curie, Case 138, 4 Place Jussieu, 75252 Paris cedex 05, France, and Unité de Chimie Organique, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Giulia Fadda
- UMR CNRS 7033, BioMoCeTi, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, Université Pierre et Marie Curie, Case 138, 4 Place Jussieu, 75252 Paris cedex 05, France, and Unité de Chimie Organique, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Mahmoud Ghomi
- UMR CNRS 7033, BioMoCeTi, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, Université Pierre et Marie Curie, Case 138, 4 Place Jussieu, 75252 Paris cedex 05, France, and Unité de Chimie Organique, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris cedex 15, France
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Yurenko YP, Zhurakivsky RO, Ghomi M, Samijlenko SP, Hovorun DM. Ab Initio Comprehensive Conformational Analysis of 2‘-Deoxyuridine, the Biologically Significant DNA Minor Nucleoside, and Reconstruction of Its Low-Temperature Matrix Infrared Spectrum. J Phys Chem B 2007; 112:1240-50. [DOI: 10.1021/jp074747o] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Yevgen P. Yurenko
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, vul. Zabolotnoho 150, 03143, Kyiv, Ukraine, UMR CNRS 7033, Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire (BioMoCeTi), Université Pierre et Marie Curie, GENOPOLE-Campus 1, 5 rue Henri Desbruères, 91030 Evry Cedex, France, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, and Department of Quantum Radiophysics, Faculty of
| | - Roman O. Zhurakivsky
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, vul. Zabolotnoho 150, 03143, Kyiv, Ukraine, UMR CNRS 7033, Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire (BioMoCeTi), Université Pierre et Marie Curie, GENOPOLE-Campus 1, 5 rue Henri Desbruères, 91030 Evry Cedex, France, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, and Department of Quantum Radiophysics, Faculty of
| | - Mahmoud Ghomi
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, vul. Zabolotnoho 150, 03143, Kyiv, Ukraine, UMR CNRS 7033, Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire (BioMoCeTi), Université Pierre et Marie Curie, GENOPOLE-Campus 1, 5 rue Henri Desbruères, 91030 Evry Cedex, France, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, and Department of Quantum Radiophysics, Faculty of
| | - Svitlana P. Samijlenko
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, vul. Zabolotnoho 150, 03143, Kyiv, Ukraine, UMR CNRS 7033, Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire (BioMoCeTi), Université Pierre et Marie Curie, GENOPOLE-Campus 1, 5 rue Henri Desbruères, 91030 Evry Cedex, France, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, and Department of Quantum Radiophysics, Faculty of
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, vul. Zabolotnoho 150, 03143, Kyiv, Ukraine, UMR CNRS 7033, Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire (BioMoCeTi), Université Pierre et Marie Curie, GENOPOLE-Campus 1, 5 rue Henri Desbruères, 91030 Evry Cedex, France, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, and Department of Quantum Radiophysics, Faculty of
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Guiffo-Soh G, Hernández B, Coïc YM, Boukhalfa-Heniche FZ, Ghomi M. Vibrational Analysis of Amino Acids and Short Peptides in Hydrated Media. II. Role of KLLL Repeats To Induce Helical Conformations in Minimalist LK-Peptides. J Phys Chem B 2007; 111:12563-72. [DOI: 10.1021/jp074264k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Guy Guiffo-Soh
- UMR CNRS 7033, BioMoCeTi, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, Université Pierre et Marie Curie, Case 138, 4 Place Jussieu, 75252 Paris cedex 05, France, and Unité de Chimie Organique, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Belén Hernández
- UMR CNRS 7033, BioMoCeTi, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, Université Pierre et Marie Curie, Case 138, 4 Place Jussieu, 75252 Paris cedex 05, France, and Unité de Chimie Organique, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Yves-Marie Coïc
- UMR CNRS 7033, BioMoCeTi, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, Université Pierre et Marie Curie, Case 138, 4 Place Jussieu, 75252 Paris cedex 05, France, and Unité de Chimie Organique, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Fatima-Zohra Boukhalfa-Heniche
- UMR CNRS 7033, BioMoCeTi, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, Université Pierre et Marie Curie, Case 138, 4 Place Jussieu, 75252 Paris cedex 05, France, and Unité de Chimie Organique, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Mahmoud Ghomi
- UMR CNRS 7033, BioMoCeTi, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, Université Pierre et Marie Curie, Case 138, 4 Place Jussieu, 75252 Paris cedex 05, France, and Unité de Chimie Organique, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris cedex 15, France
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Yurenko YP, Zhurakivsky RO, Samijlenko SP, Ghomi M, Hovorun DM. The whole of intramolecular H-bonding in the isolated DNA nucleoside thymidine. AIM electron density topological study. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.09.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Aamouche A, Ghomi M. Biomolecular hydrogen bonds assessed by neutron inelastic scattering. Acta Crystallogr A 2007. [DOI: 10.1107/s0108767307094986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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31
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Yurenko YP, Zhurakivsky RO, Ghomi M, Samijlenko SP, Hovorun DM. How many conformers determine the thymidine low-temperature matrix infrared spectrum? DFT and MP2 quantum chemical study. J Phys Chem B 2007; 111:9655-63. [PMID: 17655217 DOI: 10.1021/jp073203j] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A comprehensive conformational analysis of isolated 2'-beta-deoxy-thymidine (T), canonical DNA nucleoside, has been performed by means of ab initio calculations at the MP2/6-311++G(d,p)//DFT B3LYP/6-31G(d,p) level of theory. At 298.15 K, all 92 conformers of isolated dT are within a 7.49 kcal/mol Gibbs energy range. Syn orientation for the base and South (S) conformers for the sugar dominate at this temperature: syn/anti = 61.6%:38.4% and S/N = 74.5%:25.5%. However, at 420 K, the majority of conformers contain anti base and the population of North (N) sugars increases: syn/anti = 38.0%:62.0% and S/N = 59.5%:40.5%. The whole conformational parameters (P, chi, gamma, delta, beta, epsilon, nu max) were analyzed as well as the energies of the OH...O intramolecular H-bonds on the basis of nu(OH) stretching vibrations. Convolution of calculated IR spectra of all of the T conformers appears consistent with its low-temperature matrix spectrum (Ivanov et al. Low Temp. Phys. 2003, 29, 809). The maximal discrepancy in frequencies between calculated and experimental spectra is less than 1%. A conclusion was made that for reliable reconstruction of the isolated nucleoside IR spectrum the quasi whole set of conformers should be taken into consideration. In essence, this result opens up a possibility to reconstruct IR spectra of isolated nucleosides at physiological temperatures with rather satisfactory probability.
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Affiliation(s)
- Yevgen P Yurenko
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, vul. Zabolotnoho 150, 03143 Kyiv, Ukraine
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Yurenko YP, Zhurakivsky RO, Ghomi M, Samijlenko SP, Hovorun DM. Comprehensive Conformational Analysis of the Nucleoside Analogue 2‘-β-Deoxy-6-azacytidine by DFT and MP2 Calculations. J Phys Chem B 2007; 111:6263-71. [PMID: 17503799 DOI: 10.1021/jp066742h] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A comprehensive conformational analysis of isolated 2'-beta-deoxy-6-azacytidine (d6AC), an analogue of therapeutically active 6-azacytidine (6AC), has been performed by means of ab initio calculations at the MP2/6-311++G(2df,pd)//DFT B3LYP/6-31G(d,p) level of theory. Among the 81 conformers located within a 7.83 kcal/mol Gibbs energy range at T = 298.15 K, 38 contain syn-oriented bases with respect to 2'-deoxyribose; the other conformers include anti-oriented bases. Energetic analysis of these conformers shows that conformational equilibrium of isolated d6AC at T = 298.15 K is shifted to syn conformation with a syn/anti ratio estimated as 61.4%:38.6%. As far as the sugar conformation is concerned, 40 conformers contain north (N) (with 0.3 degrees < or = P < or = 40.1 degrees), and the rest possess south (S) (with 157.1 degrees < or = P < or = 207.0 degrees) puckers, where P is the pseudorotational angle of the furanose ring. The S/N occupancy ratio is estimated as 80.2%:19.8% (T = 298.15 K). The two most stable conformers are energetically quasidegenerate and correspond to both C2'-endo/syn conformers differing only by orientation of the O3'H hydroxyl group. They are both stabilized by means of similar intramolecular H-bonds, i.e., O5'H...O2, C2'H2...O2, and C2'H2...O5'. As examined by AIM criteria, from 1 to 3 H-bonds per conformer were identified among 13 possible interactions: O5'H...O2, O5'H...N6, O3'H...O5', O5'H...O3', C1'H...O2, C2'H2...O2, C2'H2...O5', C3'H...O2, C3'H...N6, C5'H1...O2, C5'H2...O2, C5'H1...N6, and C5'H2...N6. The biological effect of d6AC is conceived as an inhibition of replicative DNA polymerase caused by an unusual orientation of the sugar residue against the base in the only A form DNA-like conformer.
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Affiliation(s)
- Yevgen P Yurenko
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, vul. Zabolotnoho 150, 03143, Kyiv, Ukraine
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Derbel N, Hernández B, Pflüger F, Liquier J, Geinguenaud F, Jaïdane N, Lakhdar ZB, Ghomi M. Vibrational Analysis of Amino Acids and Short Peptides in Hydrated Media. I. L-glycine and L-leucine. J Phys Chem B 2007; 111:1470-7. [PMID: 17243664 DOI: 10.1021/jp0633953] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Raman scattering and Fourier-transform infrared (FT-IR) attenuated transmission reflectance (ATR) spectra of two alpha-amino acids (alpha-AAs), i.e., glycine and leucine, were measured in H2O and D2O (at neutral pH and pD). This series of observed vibrational data gave us the opportunity to analyze vibrational features of both AAs in hydrated media by density functional theory (DFT) calculations at the B3LYP/6-31++G* level. Harmonic vibrational modes calculated after geometry optimization on the clusters containing each AA and 12 surrounding water molecules, which represent primary models for hydration scheme of amino acids, allowed us to assign the main observed peaks.
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Affiliation(s)
- Najoua Derbel
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications (LASMA), Département de Physique, Faculté des Sciences de Tunis, Campus Universitaire, 2092 EL MANAR II, Tunisia
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Hernández B, Boukhalfa-Heniche FZ, Seksek O, Coïc YM, Ghomi M. Secondary conformation of short lysine- and leucine-rich peptides assessed by optical spectroscopies: effect of chain length, concentration, solvent, and time. Biopolymers 2006; 81:8-19. [PMID: 16134172 DOI: 10.1002/bip.20366] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Solution secondary structures of three synthetic cationic peptides, currently used in antisense oligonucleotide delivery into living cells, have been analyzed by means of circular dichroism (CD) and Raman scattering in different buffers as a function of concentration and time. All three peptides are of minimalist conception, i.e., formed by only two types of amino acids (leucine: L and lysine: K). Two of these peptides contain 15 aminoacids: N(ter)- KLLKLLLKLLLKLLK (L(10)K(5)), N(ter)-KLKLKLKLKLKLKLK (L(7)K(8)), and the third one has only 9 residues: N(ter)-KLKLKLKLK (L(4)K(5)). The conformational behavior of the 15-mers in pure water differs considerably one from another. Although both of them are initially disordered in the 50-350 microM range, L(10)K(5) gradually undergoes a disordered to alpha-helix transition for molecular concentrations above 100 microM. In all other solvents used, L(10)K(5) adopts a stable alpha-helical conformation. In methanol and methanol/Tris mixture, nonnative alpha-helices can be induced in both KL-alternating peptides, i.e., L(7)K(8) and L(4)K(5). However, in major cases and with a time delay depending on peptide concentration, beta-like structures can be gradually formed in both solutions. In PBS and methanol/PBS mixture, the tendency for L(7)K(8) and L(4)K(5) is to form structures belonging to beta-family. A discussion has been undertaken on the effect of counterions as well as their nature in the stabilization of ordered structures in both KL-alternating peptides.
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Affiliation(s)
- Belén Hernández
- UMR CNRS 7033, BioMoCeTi, Université Pierre et Marie Curie, Paris, France
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35
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Grajcar L, El Amri C, Ghomi M, Fermandjian S, Huteau V, Mandel R, Lecomte S, Baron MH. Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopy. Biopolymers 2006; 82:6-28. [PMID: 16425174 DOI: 10.1002/bip.20455] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We rank the reactivity of the adenyl residues (A) of model DNA and RNA molecules with electropositive subnano size [Ag]n+ sites as a function of nucleic acid primary sequences and secondary structures and in the presence of biological amounts of Cl- and Na+ or Mg2+ ions. In these conditions A is markedly more reactive than any other nucleic acid bases. A reactivity is higher in ribo (r) than in deoxyribo (d) species [pA>pdA and (pA)n>>(pdA)n]. Base pairing decreases A reactivity in corresponding duplexes but much less in r than in d. In linear single and paired dCAG or dGAC loci, base stacking inhibits A reactivity even if A is bulged or mispaired (A.A). dA tracts are highly reactive only when dilution prevents self-association and duplex structures. In d hairpins the solvent-exposed A residues are reactive in CAG and GAC triloops and even more in ATC loops. Among the eight rG1N2R3A4 loops, those bearing a single A (A4) are the least reactive. The solvent-exposed A2 is reactive, but synergistic structural transitions make the initially stacked A residues of any rGNAA loop much more reactive. Mg2+ cross-bridging single strands via phosphates may screen A reactivity. In contrast d duplexes cross-bridging enables "A flipping" much more in rA.U pairs than in dA.T. Mg2+ promotes A reactivity in unpaired strands. For hairpins Mg2+ binding stabilizes the stems, but according to A position in the loops, A reactivity may be abolished, reduced, or enhanced. It is emphasized that not only accessibility but also local flexibility, concerted docking, and cation and anion binding control A reactivity.
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Affiliation(s)
- Lydie Grajcar
- Laboratoire de Dynamique Interactions et Réactivité, UMR 7075, Université Paris 6 CNRS, 2 rue Henri Dunant, 94320, Thiais, France
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Hernández B, Baumruk V, Gouyette C, Ghomi M. Thermal stability, structural features, and B-to-Z transition in DNA tetraloop hairpins as determined by optical spectroscopy in d(CG)(3)T(4)(CG)(3) and d(CG)(3)A(4)(CG)(3) oligodeoxynucleotides. Biopolymers 2005; 78:21-34. [PMID: 15690428 DOI: 10.1002/bip.20246] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
NMR and CD data have previously shown the formation of the T(4) tetraloop hairpin in aqueous solutions, as well as the possibility of the B-to-Z transition in its stem in high salt concentration conditions. It has been shown that the stem B-to-Z transition in T(4) hairpins leads to S (south)- to N (north)-type conformational changes in the loop sugars, as well as anti to syn orientations in the loop bases. In this article, we have compared by means of UV absorption, CD, Raman, and Fourier transform infrared (FTIR), the thermodynamic and structural properties of the T(4) and A(4) tetraloop hairpins formed in 5'-d(CGCGCG-TTTT-CGCGCG)-3' and 5'-d(CGCGCG-AAAA-CGCGCG)-3', respectively. In presence of 5M NaClO(4), a complete B-to-Z transition of the stems is first proved by CD spectra. UV melting profiles are consistent with a higher thermal stability of the T(4) hairpin compared to the A(4) hairpin. Order-to-disorder transition of both hairpins has also been analyzed by means of Raman spectra recorded as a function of temperature. A clear Z-to-B transition of the stem has been confirmed in the T(4) hairpin, and not in the A(4) hairpin. With a right-handed stem, Raman and FTIR spectra have confirmed the C2'-endo/anti conformation for all the T(4) loop nucleosides. With a left-handed stem, a part of the T(4) loop sugars adopt a N-type (C3'-endo) conformation, and the C3'-endo/syn conformation seems to be the preferred one for the dA residues involved in the A(4) tetraloop.
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Affiliation(s)
- Belén Hernández
- UMR CNRS 7033, BioMoCeTi, Université Pierre et Marie Curie, 75252 Paris cedex 05, France
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Cherrak I, Mauffret O, Santamaria F, Hocquet A, Ghomi M, Rayner B, Fermandjian S. L-nucleotides and 8-methylguanine of d(C1m8G2C3G4C5LG6LC7G8C9G10)2 act cooperatively to promote a left-handed helix under physiological salt conditions. Nucleic Acids Res 2004; 31:6986-95. [PMID: 14627831 PMCID: PMC290261 DOI: 10.1093/nar/gkg893] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The structure and thermal stability of a hetero chiral decaoligodeoxyribonucleotide duplex d(C1m8 G2C3G4C5LG6LC7G8C9G10)d(C11m8G12C13G14C15LG16LC17G18C19G20) (O1) with two contiguous pairs of enantiomeric 2'-deoxy-L-ribonucleotides (C5LG6L/C15LG16L) at its centre and an 8-methylguanine at position 2/12 was analysed by circular dichroism, NMR and molecular modelling. O1 resolves in a left-handed helical structure already at low salt concentration (0.1 M NaCl). The central L2-sugar portion assumes a B* left-handed conformation (mirror-image of right-handed B-DNA) while its flanking D4-sugar portions adopt the known Z left-handed conformation. The resulting Z4-B2*-Z4 structure (left-handed helix) is the reverse of that of B4-Z2*-B4 (right-handed helix) displayed by the nearly related decaoligodeoxyribonucleotide d(mC1G2mC3G4C5L G6LmC7G8mC9G10)2, at the same low salt concentration (0.1 M NaCl). In the same experimental conditions, d(C1m8G2C3G4C5G6C7G8C9G10)2 (O2), the stereoregular version of O1, resolves into a right-handed B-DNA helix. Thus, both the 8-methylguanine and the enantiomeric step CLpGL at the centre of the molecule are needed to induce left-handed helicity. Remarkably, in the various heterochiral decaoligodeoxyribonucleotides so far analysed by us, when the central CLpGL adopts the B* (respectively Z*) conformation, then the adjacent steps automatically resolves in the Z (respectively B) conformation. This allows a good optimisation of the base-base stackings and base-sugar van der Waals interactions at the ZB*/B*Z (respectively BZ*/Z*B) junctions so that the Z4-B2*-Z4 (respectively B4-Z2*-B4) helix displays a Tm (approximately 65 degrees C) that is only 5 degrees C lower than the one of its homochiral counterpart. Here we anticipate that a large variety of DNA helices can be generated at low salt concentration by manipulating internal factors such as sugar configuration, duplex length, nucleotide composition and base methylation. These helices can constitute powerful tools for structural and biological investigations, especially as they can be used in physiological conditions.
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Affiliation(s)
- Ilham Cherrak
- Département de Biologie et Pharmacologie Structurales, UMR 8113 CNRS, IGR, 39 rue Camille-Desmoulins, 94805 Villejuif Cedex, France
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Boukhalfa-Heniche FZ, Hernández B, Gaillard S, Coïc YM, Huynh-Dinh T, Lecouvey M, Seksek O, Ghomi M. Complex formation and vectorization of a phosphorothioate oligonucleotide with an amphipathic leucine- and lysine-rich peptide: study at molecular and cellular levels. Biopolymers 2004; 73:727-34. [PMID: 15048776 DOI: 10.1002/bip.20018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Optical spectroscopic techniques such as CD, Raman scattering, and fluorescence imaging allowed us to analyze the complex formation and vectorization of a single-stranded 20-mer phosphorothioate oligodeoxynucleotide with a 15-mer amphipathic peptide at molecular and cellular levels. Different solvent mixtures (methanol and water) and molecular ratios of peptide/oligodeoxynucleotide complexes were tested in order to overcome the problems related to solubility. Optimal conditions for both spectroscopic and cellular experiments were obtained with the molecular ratio peptide/oligodeoxynucleotide equal to 21:4, corresponding to a 7:5 ratio for their respective +/- charge ratio. At the molecular level, CD and Raman spectra were consistent with a alpha-helix conformation of the peptide in water or in a methanol-water mixture. The presence of methanol increased considerably the solubility of the peptide without altering its alpha-helix conformation, as evidenced by CD and Raman spectroscopies. UV absorption melting profile of the oligodeoxynucleotide gave rise to a flat melting profile, corresponding to its random structure in solution. Raman spectra of oligodeoxynucleotide/peptide complexes could only be studied in methanol/water mixture solutions. Drastic changes observed in Raman spectra have undoubtedly shown: (a) the perturbation occurred in the peptide secondary structure, and (b) possible interaction between the lysine residues of the peptide and the oligodeoxynucleotide. At the cellular level, the complex was prepared in a mixture of 10% methanol and 90% cell medium. Cellular uptake in optimal conditions for the oligodeoxynucleotide delivery with low cytotoxicity was controlled by fluorescence imaging allowing to specifically locate the compacted oligonucleotide labeled with fluorescein at its 5'-terminus with the peptide into human glioma cells after 1 h of incubation at 37 degrees C.
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Affiliation(s)
- Fatima-Zohra Boukhalfa-Heniche
- UMR CNRS 7033, Laboratoire de Physicochimie Biomoléculaire et Cellulaire, Université Pierre et Marie Curie, Case 138, 4 Place Jussieu, 75252 Paris 05, France
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Vallée P, Lafait J, Ghomi M, Jouanne M, Morhange J. Raman scattering of water and photoluminescence of pollutants arising from solid–water interaction. J Mol Struct 2003. [DOI: 10.1016/s0022-2860(02)00653-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Hernández B, Baumruk V, Leulliot N, Gouyette C, Huynh-Dinh T, Ghomi M. Thermodynamic and structural features of ultrastable DNA and RNA hairpins. J Mol Struct 2003. [DOI: 10.1016/s0022-2860(02)00627-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Louit G, Hocquet A, Ghomi M, Meyer M, Sühnel J. Guanine tetrads interacting with metal ions. An AIM topological analysis of the electronic densityElectronic Supplementary Information (ESI) available: Geometric data, topologic data at the BCP and integrated properties of the hydrogen atom of every H1⋯O6 and H2⋯N7 hydrogen bond. See http://www.rsc.org/suppdata/qu/b2/b210911e/. ACTA ACUST UNITED AC 2003. [DOI: 10.1039/b210911e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Louit G, Hocquet A, Ghomi M. Intramolecular hydrogen bonding in ribonucleosides: an AIM topological study of the electronic densityElectronic supplementary information (ESI) available: Integrated properties of atomic basins, radii characterizing hydrogen bond interactions, and properties at bond critical points of hydrogen bonds (Tables 3–5). See http://www.rsc.org/suppdata/cp/b2/b201339h/. Phys Chem Chem Phys 2002. [DOI: 10.1039/b201339h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Louit G, Hocquet A, Ghomi M, Meyer M, Sühnel J. Are guanine tetrads stabilised by bifurcated hydrogen bonds? An AIM topological analysis of the electronic density. ACTA ACUST UNITED AC 2002. [DOI: 10.1039/b204736e] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Baumruk V, Gouyette C, Huynh-Dinh T, Sun JS, Ghomi M. Comparison between CUUG and UUCG tetraloops: thermodynamic stability and structural features analyzed by UV absorption and vibrational spectroscopy. Nucleic Acids Res 2001; 29:4089-96. [PMID: 11574692 PMCID: PMC60239 DOI: 10.1093/nar/29.19.4089] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2001] [Revised: 08/07/2001] [Accepted: 08/07/2001] [Indexed: 11/14/2022] Open
Abstract
CUUG loop is one of the most frequently occurring tetraloops in bacterial 16S rRNA. This tetraloop has a high thermodynamic stability as proved by previous UV absorption and NMR experiments. Here, we present our results concerning the thermodynamic and structural features of the 10mer 5'-r(GCG-CUUG-CGC)-3', forming a highly stable CUUG tetraloop hairpin in aqueous solution, by means of several optical techniques (UV and FT-IR absorption, Raman scattering). UV melting profile of this decamer provides a high melting temperature (60.7 degrees C). A set of Raman spectra recorded at different temperatures allowed us to analyze the order-to-disorder (hairpin-to-random coil) transition. Assignment of vibrational markers led us to confirm the particular nucleoside conformation, and to get information on the base stacking and base pairing in the hairpin structure. Moreover, comparison of the data obtained from two highly stable CUUG and UUCG tetraloops containing the same nucleotides but in a different order permitted an overall discussion of their structural features on the basis of Raman marker evidences.
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Affiliation(s)
- V Baumruk
- Institute of Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
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Gaigeot MP, Ghomi M. Geometrical and Vibrational Properties of Nucleic Acid Constituents Interacting with Explicit Water Molecules as Analyzed by Density Functional Theory Calculations. 1. Uracil + nwH2O (nw = 1,...,7). J Phys Chem B 2001. [DOI: 10.1021/jp0040401] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marie-Pierre Gaigeot
- Laboratoire de Physicochimie Biomoléculaire et Cellulaire, UPRESA CNRS 7033, Case courrier 138, Université Pierre et Marie Curie, 4 Place Jussieu, F-75252 Paris Cedex 05, France
| | - Mahmoud Ghomi
- Laboratoire de Physicochimie Biomoléculaire et Cellulaire, UPRESA CNRS 7033, Case courrier 138, Université Pierre et Marie Curie, 4 Place Jussieu, F-75252 Paris Cedex 05, France
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Gaigeot MP, Leulliot N, Ghomi M, Jobic H, Coulombeau C, Bouloussa O. Analysis of the structural and vibrational properties of RNA building blocks by means of neutron inelastic scattering and density functional theory calculations. Chem Phys 2000. [DOI: 10.1016/s0301-0104(00)00224-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Hocquet A, Leulliot N, Ghomi M. Ground-State Properties of Nucleic Acid Constituents Studied by Density Functional Calculations. 3. Role of Sugar Puckering and Base Orientation on the Energetics and Geometry of 2‘-Deoxyribonucleosides and Ribonucleosides. J Phys Chem B 2000. [DOI: 10.1021/jp994077p] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexandre Hocquet
- Laboratoire de Physicochimie Biomoléculaire et Cellulaire, UPRESA CNRS 7033, Case courrier 138, Université Pierre et Marie Curie, 4 Place Jussieu, F-75252 Paris Cedex 05, France
| | - Nicolas Leulliot
- Laboratoire de Physicochimie Biomoléculaire et Cellulaire, UPRESA CNRS 7033, Case courrier 138, Université Pierre et Marie Curie, 4 Place Jussieu, F-75252 Paris Cedex 05, France
| | - Mahmoud Ghomi
- Laboratoire de Physicochimie Biomoléculaire et Cellulaire, UPRESA CNRS 7033, Case courrier 138, Université Pierre et Marie Curie, 4 Place Jussieu, F-75252 Paris Cedex 05, France
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Hocquet A, Ghomi M. The peculiar role of cytosine in nucleoside conformational behaviour: Hydrogen bond donor capacity of nucleic bases. Phys Chem Chem Phys 2000. [DOI: 10.1039/b007246j] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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