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Mazo N, Navo CD, Peccati F, Andreo J, Airoldi C, Goldsztejn G, Çarçabal P, Usabiaga I, Sodupe M, Wuttke S, Busto JH, Peregrina JM, Cocinero EJ, Jiménez-Osés G. Conformationally Restricted β-Sheet Breaker Peptides Incorporating Cyclic α-Methylisoserine Sulfamidates. Chemistry 2023; 29:e202202913. [PMID: 36377879 DOI: 10.1002/chem.202202913] [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: 09/18/2022] [Revised: 10/28/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022]
Abstract
Peptides containing variations of the β-amyloid hydrophobic core and five-membered sulfamidates derived from β-amino acid α-methylisoserine have been synthesized and fully characterized in the gas phase, solid state and in aqueous solution by a combination of experimental and computational techniques. The cyclic sulfamidate group effectively locks the secondary structure at the N-terminus of such hybrid peptides imposing a conformational restriction and stabilizing non-extended structures. This conformational bias, which is maintained in the gas phase, solid state and aqueous solution, is shown to be resistant to structure templating through assays of in vitro β-amyloid aggregation, acting as β-sheet breaker peptides with moderate activity.
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Affiliation(s)
- Nuria Mazo
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006, Logroño, Spain.,3P Biopharmaceuticals, 31110, Noáin, Navarra, Spain
| | - Claudio D Navo
- Computational Chemistry Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) Bizkaia Technology Park, Building 800, 48160, Derio, Spain
| | - Francesca Peccati
- Computational Chemistry Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) Bizkaia Technology Park, Building 800, 48160, Derio, Spain
| | - Jacopo Andreo
- BCMaterials, Basque Center for Materials, UPV/EHU Science Park, Leioa, 48940, Spain
| | - Cristina Airoldi
- BioOrgNMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy
| | - Gildas Goldsztejn
- Institut des Sciences Moléculaires d'Orsay (ISMO), Université Paris Saclay, CNRS, 91405, Orsay, France
| | - Pierre Çarçabal
- Institut des Sciences Moléculaires d'Orsay (ISMO), Université Paris Saclay, CNRS, 91405, Orsay, France
| | - Imanol Usabiaga
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), 48080, Bilbao, Spain.,Instituto Biofisika (CSIC, UPV/EHU), 48080, Bilbao, Spain
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Stefan Wuttke
- BCMaterials, Basque Center for Materials, UPV/EHU Science Park, Leioa, 48940, Spain.,Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain
| | - Jesús H Busto
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006, Logroño, Spain
| | - Jesús M Peregrina
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006, Logroño, Spain
| | - Emilio J Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), 48080, Bilbao, Spain.,Instituto Biofisika (CSIC, UPV/EHU), 48080, Bilbao, Spain
| | - Gonzalo Jiménez-Osés
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006, Logroño, Spain.,Computational Chemistry Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) Bizkaia Technology Park, Building 800, 48160, Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain
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2
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Goldsztejn G, Mundlapati VR, Brenner V, Gloaguen E, Mons M. Selenium in Proteins: Conformational Changes Induced by Se Substitution on Methionine, as Studied in Isolated Model Peptides by Optical Spectroscopy and Quantum Chemistry. Molecules 2022; 27:molecules27103163. [PMID: 35630640 PMCID: PMC9144663 DOI: 10.3390/molecules27103163] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 02/01/2023] Open
Abstract
The side-chain of methionine residues is long enough to establish NH⋯S H-bonds with neighboring carbonyl groups of the backbone, giving rise to so-called intra-residue 6δ and inter-residue 7δ H-bonds. The aim of the present article is to document how the substitution of sulfur with a selenium atom affects the H-bonding of the Met system. This was investigated both experimentally and theoretically by conformation-resolved optical spectroscopy, following an isolated molecule approach. The present work emphasizes the similarities of the Met and Sem residues in terms of conformational structures, energetics, NH⋯Se/S H-bond strength and NH stretch spectral shifts, but also reveals subtle behavior differences between them. It provides evidence for the sensitivity of the H-bonding network with the folding type of the Sem/Met side-chains, where a simple flip of the terminal part of the side-chain can induce an extra 50 cm−1 spectral shift of the NH stretch engaged in a 7δ NH⋯S/Se bond.
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Mundlapati VR, Imani Z, Goldsztejn G, Gloaguen E, Brenner V, Le Barbu-Debus K, Zehnacker-Rentien A, Baltaze JP, Robin S, Mons M, Aitken DJ. A theoretical and experimental case study of the hydrogen bonding predilection of S-methylcysteine. Amino Acids 2021; 53:621-633. [PMID: 33743071 DOI: 10.1007/s00726-021-02967-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/12/2021] [Indexed: 12/17/2022]
Abstract
S-containing amino acids can lead to two types of local NH···S interactions which bridge backbone NH sites to the side chain to form either intra- or inter-residue H-bonds. The present work reports on the conformational preferences of S-methyl-L-cysteine, Cys(Me), using a variety of investigating tools, ranging from quantum chemistry simulations, gas-phase UV and IR laser spectroscopy, and solution state IR and NMR spectroscopies, on model compounds comprising one or two Cys(Me) residues. We demonstrate that in gas phase and in low polarity solution, the C- and N-capped model compound for one Cys(Me) residue adopts a preferred C5-C6γ conformation which combines an intra-residue N-H···O=C backbone interaction (C5) and an inter-residue N-H···S interaction implicating the side-chain sulfur atom (C6γ). In contrast, the dominant conformation of the C- and N-capped model compound featuring two consecutive Cys(Me) residues is a regular type I β-turn. This structure is incompatible with concomitant C6γ interactions, which are no longer in evidence. Instead, C5γ interactions occur, that are fully consistent with the turn geometry and additionally stabilize the structure. Comparison with the thietane amino acid Attc, which exhibits a rigid cyclic side chain, pinpoints the significance of side chain flexibility for the specific conformational behavior of Cys(Me).
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Affiliation(s)
- Venkateswara Rao Mundlapati
- Laboratoire Interactions, Dynamiques Et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
- Institut de Recherche en Astrophysique Et Planétologie (IRAP), Université de Toulouse (UPS), CNRS, CNES, 9 Avenue du Colonel Roche, 31028, Toulouse, France
| | - Zeynab Imani
- Institut de Chimie Moléculaire Et Des Matériaux D'Orsay (ICMMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
| | - Gildas Goldsztejn
- Laboratoire Interactions, Dynamiques Et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
- Institut Des Sciences Moléculaires D'Orsay (ISMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
| | - Eric Gloaguen
- Laboratoire Interactions, Dynamiques Et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Valérie Brenner
- Laboratoire Interactions, Dynamiques Et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Katia Le Barbu-Debus
- Institut Des Sciences Moléculaires D'Orsay (ISMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
| | - Anne Zehnacker-Rentien
- Institut Des Sciences Moléculaires D'Orsay (ISMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
| | - Jean-Pierre Baltaze
- Institut de Chimie Moléculaire Et Des Matériaux D'Orsay (ICMMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
| | - Sylvie Robin
- Institut de Chimie Moléculaire Et Des Matériaux D'Orsay (ICMMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
- Faculté de Pharmacie, Université de Paris, 75006, Paris, France
| | - Michel Mons
- Laboratoire Interactions, Dynamiques Et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France.
| | - David J Aitken
- Institut de Chimie Moléculaire Et Des Matériaux D'Orsay (ICMMO), Université Paris-Saclay, CNRS, 91405, Orsay, France.
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Goldsztejn G, Mundlapati VR, Brenner V, Gloaguen E, Mons M, Cabezas C, León I, Alonso JL. Intrinsic folding of the cysteine residue: competition between folded and extended forms mediated by the -SH group. Phys Chem Chem Phys 2021; 22:20284-20294. [PMID: 32966425 DOI: 10.1039/d0cp03136d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A dual microwave and optical spectroscopic study of a capped cysteine amino acid isolated in a supersonic expansion, combined with quantum chemistry modelling, enabled us to characterize the conformational preferences of Cys embedded in a protein chain. IR/UV double resonance spectroscopy provided evidence for the coexistence of two conformers, assigned to folded and extended backbones (with classical C7 and C5 backbone H-bonding respectively), each of them additionally stabilized by specific main-chain/side-chain H-bonding, where the sulfur atom essentially plays the role of H-bond acceptor. The folded structure was confirmed by microwave spectroscopy, which demonstrated the validity of the DFT-D methods currently used in the field. These structural and spectroscopic results, complemented by a theoretical Natural Bond Orbital analysis, enabled us to document the capacity of the weakly polar -CH2-SH side chain of Cys to adapt itself to the intrinsic local preferences of the peptide backbone, i.e., a γ-turn or a β-sheet extended secondary structure. The corresponding local H-bonding bridges the side chain acceptor S atom to the backbone NH donor site of the same or the next residue along the chain, through a 5- or a 6-membered ring respectively.
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Affiliation(s)
- Gildas Goldsztejn
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | | | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Michel Mons
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Carlos Cabezas
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - Iker León
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - José Luis Alonso
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
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Gloaguen E, Mons M, Schwing K, Gerhards M. Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues. Chem Rev 2020; 120:12490-12562. [PMID: 33152238 DOI: 10.1021/acs.chemrev.0c00168] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.
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Affiliation(s)
- Eric Gloaguen
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Kirsten Schwing
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
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