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Dasgupta S, Sen S, Sathe RY, Pophali S, Kadu A, Jain R, Bera S, Roy S, Misra R. Conformation Controlled Hydrogelation of Minimalistic α, γ Hybrid Peptide. Biomacromolecules 2024; 25:3715-3723. [PMID: 38723225 DOI: 10.1021/acs.biomac.4c00270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
A majority of short peptide (≤7 amino acids) hydrogels are primarily assembled via cross β-structure formation. In contrast to the natural trend, herein, we report the formation of supramolecular hydrogel from the ultrashort hybrid folded peptide composed of canonical α-amino acid and noncanonical γ-amino acid, Fmoc-γPhe-Phe-OH. The designed hybrid peptide hydrogel is composed of entangled fibers, has viscoelastic properties, exhibits proteolytic stability, and exhibits cytocompatibility with L929 fibroblast cells. Mutating the peptide sequence by altering the position of γPhe from the N-termini to C-termini transforms the self-assembly into crystalline aggregates. Combining FTIR, 2D NMR, and DFT calculations revealed that the hydrogel-forming peptide adopts a C9 H-bonded conformation, resembling the well-known γ-turn. However, the isomeric hybrid peptide adopts an extended structure. The present study highlights the importance of secondary structure in the higher order assembly of minimalist hybrid peptides and broadens the range of secondary structures to design short peptide-based hydrogels.
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Affiliation(s)
- Sneha Dasgupta
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar (Mohali) 160062, India
| | - Sourav Sen
- Institute of Nano Science and Technology (INST), Sector 81, Knowledge City, Mohali 140306, Punjab, India
| | - Rohit Y Sathe
- Department of Biological Sciences and Biotechnology, Institute of Chemical Technology, Mumbai, Maharashtra 400019, India
| | - Salil Pophali
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar (Mohali) 160062, India
| | - Archit Kadu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar (Mohali) 160062, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar (Mohali) 160062, India
| | - Santu Bera
- Department of Chemistry, Ashoka University, Sonipat, Haryana 131029, India
| | - Sangita Roy
- Institute of Nano Science and Technology (INST), Sector 81, Knowledge City, Mohali 140306, Punjab, India
| | - Rajkumar Misra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar (Mohali) 160062, India
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2
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Le Barbu-Debus K, Pérez-Mellor A, Lepère V, Zehnacker A. How change in chirality prevents β-amyloid type interaction in a protonated cyclic dipeptide dimer. Phys Chem Chem Phys 2022; 24:19783-19791. [PMID: 35969161 DOI: 10.1039/d2cp03110h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The protonated dimers of the diketopiperazine dipeptide cyclo (LPhe-LHis) and cyclo (LPhe-DHis) are studied by laser spectroscopy combined with mass spectrometry to shed light on the influence of stereochemistry on the clustering propensity of cyclic dipeptides. The marked spectroscopic differences experimentally observed in the hydride stretch region are well accounted for by the results of DFT calculations. Both diastereomeric protonated dimers involve a strong ionic hydrogen bond from the protonated imidazole ring of one monomer to the neutral imidazole nitrogen of the other. While this strong interaction is accompanied by a single NH⋯O hydrogen bond between the amide functions of the two moieties for the protonated dimer of cyclo (LPhe-DHis), that of cyclo (LPhe-LHis) involves two NH⋯O interactions, forming the motif of an antiparallel β sheet. Therefore, a change in chirality of the residue prevents the formation of the β sheet pattern observed in the amyloid type aggregation. These results emphasize the peculiar role of the histidine residue in peptide structure and interaction.
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Affiliation(s)
- Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Valéria Lepère
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
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3
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Fischer JL, Blodgett KN, Harrilal CP, Walsh PS, Davis ZS, Choi S, Choi SH, Zwier TS. Conformer-Specific Spectroscopy and IR-Induced Isomerization of a Model γ-Peptide: Ac-γ 4-Phe-NHMe. J Phys Chem A 2022; 126:1837-1847. [PMID: 35275624 DOI: 10.1021/acs.jpca.2c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single-conformation IR and UV spectroscopy of the prototypical capped γ-peptide Ac-γ4-Phe-NHMe (γ4F) was carried out under jet-cooled conditions in the gas phase in order to understand its innate conformational preferences in the absence of a solvent. We obtained conformer-specific IR and UV spectra and compared the results with calculations to make assignments and explore the differences between the γ2- and γ4-substituted molecules. We found four conformers of γ4F in our experiment. Three conformers form nine-membered hydrogen-bonded rings (C9) enclosed by an NH···O═C H-bond but differing in their phenyl ring positions (a, g+, and g-). The fourth conformer forms a strained seven-membered hydrogen-bonded ring in which the amide groups lie in a nominally anti-parallel arrangement stacked on top of one another (labeled S7). This conformer is a close analogue of the amide-stacked conformer (S) found previously in γ2F, in which the Phe side chain is substituted at the γ2 position, Ac-γ2-Phe-NHMe (J. Am. Chem. Soc. 2009, 131, 14243-14245). IR population transfer spectroscopy was used to determine the fractional abundances of the γ4F conformers in the expansion. A combination of force field and density functional theory calculations is used to map out the conformational potential energy surfaces for γ4F and compare it with its γ2F counterpart. Based on this analysis, the phenyl ring prefers to take up structures that facilitate NH···π interactions in γ4F or avoid phenyl interactions with the C═O group in γ2F. The disconnectivity graph for γ4F reveals separate basins associated with the C9 and amide-stacked conformational families, which are separated by a barrier of about 42 kJ/mol. The overall shape of the potential energy surface bears a resemblance to peptides and proteins that have a misfolding pathway that competes with the formation of the native structure.
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Affiliation(s)
- Joshua L Fischer
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Karl N Blodgett
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Christopher P Harrilal
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Patrick S Walsh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Zachary S Davis
- Department of Chemistry, Wofford College, Spartanburg, South Carolina 29303, United States
| | - Sunglim Choi
- Department of Chemistry, Yonsei University, Seoul 03722, South Korea
| | - Soo Hyuk Choi
- Department of Chemistry, Yonsei University, Seoul 03722, South Korea
| | - Timothy S Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States.,Gas Phase Chemical Physics, Sandia National Laboratories, Livermore, California 94550, United States
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4
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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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5
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Raghunathan S, Jaganade T, Priyakumar UD. Urea-aromatic interactions in biology. Biophys Rev 2020; 12:65-84. [PMID: 32067192 PMCID: PMC7040157 DOI: 10.1007/s12551-020-00620-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Noncovalent interactions are key determinants in both chemical and biological processes. Among such processes, the hydrophobic interactions play an eminent role in folding of proteins, nucleic acids, formation of membranes, protein-ligand recognition, etc.. Though this interaction is mediated through the aqueous solvent, the stability of the above biomolecules can be highly sensitive to any small external perturbations, such as temperature, pressure, pH, or even cosolvent additives, like, urea-a highly soluble small organic molecule utilized by various living organisms to regulate osmotic pressure. A plethora of detailed studies exist covering both experimental and theoretical regimes, to understand how urea modulates the stability of biological macromolecules. While experimentalists have been primarily focusing on the thermodynamic and kinetic aspects, theoretical modeling predominantly involves mechanistic information at the molecular level, calculating atomistic details applying the force field approach to the high level electronic details using the quantum mechanical methods. The review focuses mainly on examples with biological relevance, such as (1) urea-assisted protein unfolding, (2) urea-assisted RNA unfolding, (3) urea lesion interaction within damaged DNA, (4) urea conduction through membrane proteins, and (5) protein-ligand interactions those explicitly address the vitality of hydrophobic interactions involving exclusively the urea-aromatic moiety.
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Affiliation(s)
- Shampa Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - Tanashree Jaganade
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India.
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6
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Blodgett KN, Zhu X, Walsh PS, Sun D, Lee J, Choi SH, Zwier TS. Conformer-Specific and Diastereomer-Specific Spectroscopy of αβα Synthetic Foldamers: Ac–Ala−βACHC–Ala–NHBn. J Phys Chem A 2018; 122:3697-3710. [PMID: 29558801 DOI: 10.1021/acs.jpca.8b01273] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karl N. Blodgett
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Xiao Zhu
- Research Computing, Information Technology at Purdue (ITaP), West Lafayette, Indiana 47907-2114, United States
| | - Patrick S. Walsh
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Dewei Sun
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Jaeyeon Lee
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Soo Hyuk Choi
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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7
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BenNasr F, Pérez-Mellor A, Alata I, Lepere V, Jaïdane NE, Zehnacker A. Stereochemistry-dependent hydrogen bonds stabilise stacked conformations in jet-cooled cyclic dipeptides: (LD) vs. (LL) cyclo tyrosine-tyrosine. Faraday Discuss 2018; 212:399-419. [PMID: 30229773 DOI: 10.1039/c8fd00079d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Tyrosine-containing cyclic dipeptides based on a diketopiperazine (DKP) ring are studied under jet-cooled conditions using resonance-enhanced multi-photon ionisation (REMPI), conformer-selective IR-UV double resonance vibrational spectroscopy and quantum chemical calculations. The conformational landscape of the dipeptide containing natural L tyrosine (Tyr), namely c-LTyr-LTyr strongly differs from that of its diastereomer c-LTyr-DTyr. A similar family of conformers exists in both systems, with one aromatic ring folded on the dipeptide DKP ring and the other one extended. Weak NHπ and CHπ interactions are observed, which are slightly different in c-LTyr-LTyr and c-LTyr-DTyr. These structures are identical to those of LL and LD cyclo diphenylalanine, which only differ from c-Tyr-Tyr by the absence of hydroxyl on the benzene rings. While this is the only conformation observed for c-LTyr-DTyr, c-LTyr-LTyr exhibits an additional form stabilised by the interaction of the two hydroxyls, in which the two aromatic rings are in a stacked geometry. Stereochemical effects are still visible in the radical cation, for which one structure is observed for c-LTyr-DTyr, while the spectrum of the c-LTyr-LTyr radical cation is explained in terms of two co-existing structures.
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Affiliation(s)
- Feriel BenNasr
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France. and Laboratoire de Spectroscopie Atomique, Moléculaire et Applications (LSAMA), Université de Tunis El Manar, Tunis 1060, Tunisia
| | - Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Ivan Alata
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Valeria Lepere
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Nejm-Eddine Jaïdane
- Laboratoire de Spectroscopie Atomique, Moléculaire et Applications (LSAMA), Université de Tunis El Manar, Tunis 1060, Tunisia
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
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8
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Zhang D, Blodgett KN, Zhu X, Zwier TS. Single Conformation Spectroscopy of Suberoylanilide Hydroxamic Acid: A Molecule Bites Its Tail. J Phys Chem A 2017; 121:986-997. [PMID: 28071906 DOI: 10.1021/acs.jpca.6b12464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Suberoylanilide hydroxamic acid (SAHA) is a histone deacetylase inhibitor that causes growth arrest and differentiation of many tumor types and is an approved drug for the treatment of cancer. The chemical structure of SAHA consists of formanilide "head" and a hydroxamic acid "tail" separated by an n-hexyl chain, C6H5NH(C═O)-(CH2)6-(C═O)NHOH. The alkyl chain's preference for extended structures is in competition with tail-to-head (T-H) or head-to-tail (H-T) hydrogen bonds between the amide and hydroxamic acid groups. Laser desorption was used to bring SAHA into the gas phase and cool it in a supersonic expansion before interrogation with mass-resolved resonant two-photon ionization spectroscopy. Single conformation UV spectra in the S0-S1 region and infrared spectra in the hydride stretch and mid-IR regions were recorded using IR-UV hole-burning and resonant ion-dip infrared spectroscopy, respectively. Three conformers of SAHA were distinguished and spectroscopically characterized. Comparison of the experimental IR spectra with the predictions of density functional theory calculations (DFT, B3LYP D3BJ/6-31+G(d)) leads to assignments for the three conformers, all of which possess tightly folded alkyl chains that enable formation of a T-H (conformer A) or H-T (conformers B and C) hydrogen bonds. A modified version of the generalized Amber force field was developed to more accurately describe the hydroxamic acid OH internal rotor potential, leading to predictions for the relative energies in reasonable agreement with experiment. This force field was used to generate a disconnectivity graph for the low-energy portion of the potential energy landscape of SAHA. This disconnectivity graph contains more than one hundred minima and maps out the lowest-energy pathways between them, which could then be characterized via DFT calculations. This combination of force field and DFT calculations provides insight into the potential energy landscape and how population was funneled into the three observed conformers.
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Affiliation(s)
| | - Karl N Blodgett
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907-2084, United States
| | - Xiao Zhu
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907-2084, United States.,Rosen Center for Advanced Computing (RCAC), Purdue University , West Lafayette, Indiana 47907-2084, United States
| | - Timothy S Zwier
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907-2084, United States
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9
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Giroud M, Ivkovic J, Martignoni M, Fleuti M, Trapp N, Haap W, Kuglstatter A, Benz J, Kuhn B, Schirmeister T, Diederich F. Inhibition of the Cysteine Protease Human Cathepsin L by Triazine Nitriles: Amide⋅⋅⋅Heteroarene π-Stacking Interactions and Chalcogen Bonding in the S3 Pocket. ChemMedChem 2017; 12:257-270. [DOI: 10.1002/cmdc.201600563] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/19/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Maude Giroud
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Jakov Ivkovic
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Mara Martignoni
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Marianne Fleuti
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Wolfgang Haap
- F. Hoffmann-La Roche Ltd.; Pharma Research and Early Development (pRED); Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Andreas Kuglstatter
- F. Hoffmann-La Roche Ltd.; Pharma Research and Early Development (pRED); Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Jörg Benz
- F. Hoffmann-La Roche Ltd.; Pharma Research and Early Development (pRED); Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Bernd Kuhn
- F. Hoffmann-La Roche Ltd.; Pharma Research and Early Development (pRED); Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudinger Weg 5 55128 Mainz Germany
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
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10
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Bzymek KP, Avery KA, Ma Y, Horne DA, Williams JC. Natural and non-natural amino-acid side-chain substitutions: affinity and diffraction studies of meditope-Fab complexes. Acta Crystallogr F Struct Biol Commun 2016; 72:820-830. [PMID: 27834791 PMCID: PMC5101583 DOI: 10.1107/s2053230x16016149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/11/2016] [Indexed: 12/16/2022] Open
Abstract
Herein, multiple crystal structures of meditope peptide derivatives incorporating natural and unnatural amino acids bound to the cetuximab Fab domain are presented. The affinity of each derivative was determined by surface plasmon resonance and correlated to the atomic structure. Overall, it was observed that the hydrophobic residues in the meditope peptide, Phe3, Leu5 and Leu10, could accommodate a number of moderate substitutions, but these invariably reduced the overall affinity and half-life of the interaction. In one case, the substitution of Phe3 by histidine led to a change in the rotamer conformation, in which the imidazole ring flipped to a solvent-exposed position. Based on this observation, Phe3 was substituted by diphenylalanine and it was found that the phenyl rings in this variant mimic the superposition of the Phe3 and His3 structures, producing a moderate increase, of 1.4-fold, in the half-life of the complex. In addition, it was observed that substitution of Leu5 by tyrosine and glutamate strongly reduced the affinity, whereas the substitution of Leu5 by diphenylalanine moderately reduced the half-life (by approximately fivefold). Finally, it was observed that substitution of Arg8 and Arg9 by citrulline dramatically reduced the overall affinity, presumably owing to lost electrostatic interactions. Taken together, these studies provide insight into the meditope-cetuximab interaction at the atomic level.
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Affiliation(s)
- Krzysztof P. Bzymek
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91010, USA
| | - Kendra A. Avery
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91010, USA
| | - Yuelong Ma
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91010, USA
| | - David A. Horne
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91010, USA
| | - John C. Williams
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91010, USA
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11
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Schwing K, Gerhards M. Investigations on isolated peptides by combined IR/UV spectroscopy in a molecular beam – structure, aggregation, solvation and molecular recognition. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1229331] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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12
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Boulmene R, Boussouf K, Prakash M, Komiha N, Al-Mogren MM, Hochlaf M. Ab Initio and DFT Studies on CO2Interacting with Znq+-Imidazole (q=0, 1, 2) Complexes: Prediction of Charge Transfer through σ- or π-Type Models. Chemphyschem 2016; 17:994-1005. [DOI: 10.1002/cphc.201501185] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Reda Boulmene
- Université Paris-Est; Laboratoire Modélisation et Simulation Multi-Échelle, MSME UMR 8208 CNRS; 5 bd Descartes 77454 Marne-la-Vallée France
| | - Karim Boussouf
- Université Paris-Est; Laboratoire Modélisation et Simulation Multi-Échelle, MSME UMR 8208 CNRS; 5 bd Descartes 77454 Marne-la-Vallée France
| | - Muthuramalingam Prakash
- Université Paris-Est; Laboratoire Modélisation et Simulation Multi-Échelle, MSME UMR 8208 CNRS; 5 bd Descartes 77454 Marne-la-Vallée France
| | - Najia Komiha
- LS3 ME-Team of theoretical chemistry and modeling; Faculty of Sciences; University Mohammed V; Rabat Morocco
| | - Muneerah M. Al-Mogren
- Chemistry Department; Faculty of Science; King Saud University; P.O. Box 2455 Riyadh 11451 Kingdom of Saudi Arabia
| | - Majdi Hochlaf
- Université Paris-Est; Laboratoire Modélisation et Simulation Multi-Échelle, MSME UMR 8208 CNRS; 5 bd Descartes 77454 Marne-la-Vallée France
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13
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Prediction of molecular properties and spectroscopic profile of Riluzole with different functionals (B3LYP, M06-2X, MPWLYP): A combined theoretical and experimental study. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.10.088] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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14
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Walsh PS, Dean JC, McBurney C, Kang H, Gellman SH, Zwier TS. Conformation-specific spectroscopy of capped glutamine-containing peptides: role of a single glutamine residue on peptide backbone preferences. Phys Chem Chem Phys 2016; 18:11306-22. [PMID: 27054830 DOI: 10.1039/c6cp01062h] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The conformational preferences of a series of short, aromatic-capped, glutamine-containing peptides have been studied under jet-cooled conditions in the gas phase.
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Affiliation(s)
| | - Jacob C. Dean
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Carl McBurney
- Department of Chemistry
- University of Wisconsin-Madison
- Madison
- USA
| | - Hyuk Kang
- Department of Chemistry
- Ajou University
- Republic of Korea
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15
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Alauddin M, Gloaguen E, Brenner V, Tardivel B, Mons M, Zehnacker‐Rentien A, Declerck V, Aitken DJ. Intrinsic Folding Proclivities in Cyclic β‐Peptide Building Blocks: Configuration and Heteroatom Effects Analyzed by Conformer‐Selective Spectroscopy and Quantum Chemistry. Chemistry 2015; 21:16479-93. [DOI: 10.1002/chem.201501794] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Mohammad Alauddin
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
- Current address: Department of Chemistry, University of Dhaka, Dhaka‐1000 (Bangladesh)
| | - Eric Gloaguen
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | - Valérie Brenner
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | - Benjamin Tardivel
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | - Michel Mons
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | | | - Valérie Declerck
- CP3A Organic Synthesis Group, ICMMO, UMR 8182, Université Paris Sud, Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex (France)
| | - David J. Aitken
- CP3A Organic Synthesis Group, ICMMO, UMR 8182, Université Paris Sud, Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex (France)
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16
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Abstract
This chapter examines the structural characterisation of isolated neutral amino-acids and peptides. After a presentation of the experimental and theoretical state-of-the-art in the field, a review of the major structures and shaping interactions is presented. Special focus is made on conformationally-resolved studies which enable one to go beyond simple structural characterisation; probing flexibility and excited-state photophysics are given as examples of promising future directions.
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17
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Chaudret R, de Courcy B, Contreras-García J, Gloaguen E, Zehnacker-Rentien A, Mons M, Piquemal JP. Unraveling non-covalent interactions within flexible biomolecules: from electron density topology to gas phase spectroscopy. Phys Chem Chem Phys 2015; 16:9876-91. [PMID: 24419903 DOI: 10.1039/c3cp52774c] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The NCI (Non-Covalent Interactions) method, a recently-developed theoretical strategy to visualize weak non-covalent interactions from the topological analysis of the electron density and of its reduced gradient, is applied in the present paper to document intra- and inter-molecular interactions in flexible molecules and systems of biological interest in combination with IR spectroscopy. We first describe the conditions of application of the NCI method to the specific case of intramolecular interactions. Then we apply it to a series of stable conformations of isolated molecules as an interpretative technique to decipher the different physical interactions at play in these systems. Examples are chosen among neutral molecular systems exhibiting a large diversity of interactions, for which an extensive spectroscopic characterization under gas-phase isolation conditions has been obtained using state-of-the-art conformer-specific experimental techniques. The interactions presently documented range from weak intra-molecular H-bonds in simple amino-alcohols, to more complex patterns, with interactions of various strengths in model peptides, as well as in chiral bimolecular systems, where invaluable hints for the understanding of chiral recognition are revealed. We also provide a detailed technical appendix, which discusses the choices of cut-offs as well as the applicability of the NCI analysis to specific constrained systems, where local effects require attention. Finally, the NCI technique provides IR spectroscopists with an elegant visualization of the interactions that potentially impact their vibrational probes, namely the OH and NH stretching motions. This contribution illustrates the power and the conditions of use of the NCI technique, with the aim of providing an easy tool for all chemists, experimentalists and theoreticians, for the visualization and characterization of the interactions shaping complex molecular systems.
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Affiliation(s)
- R Chaudret
- Sorbonne Universités, UPMC, Laboratoire de Chimie Théorique and CNRS, UMR 7616, 75252 Paris Cedex 05, Paris, France.
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18
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Wang Y, Wang J, Yao L. Computational Study of Peptide Plane Stacking with Polar and Ionizable Amino Acid Side Chains. J Phys Chem A 2015; 119:3471-8. [DOI: 10.1021/acs.jpca.5b00183] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yefei Wang
- Laboratory of Biofuels, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Laoshan District, Qingdao 266061, China
| | - Jia Wang
- Laboratory of Biofuels, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Laoshan District, Qingdao 266061, China
| | - Lishan Yao
- Laboratory of Biofuels, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Laoshan District, Qingdao 266061, China
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19
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Tamer Ö, Dege N, Avcı D, Atalay Y, Özer İlhan İ, Çadır M. Synthesis, structural and spectroscopic evaluations and nonlinear optical properties of 3,5-bis(4-methoxyphenyl)-4,5-dihydro-1H-pyrazole-1-carbothioic O-acid. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 137:1387-1396. [PMID: 25306134 DOI: 10.1016/j.saa.2014.08.111] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 08/08/2014] [Accepted: 08/24/2014] [Indexed: 06/04/2023]
Abstract
In this study, we report a combined experimental and theoretical study on 3,5-bis(4-methoxyphenyl)-4,5-dihydro-1H-pyrazole-1-carbothioic O-acid (C18H18N2O3S) molecule. The compound crystallizes in the trigonal space group R-3 with a=b=27.7151(12) Å, c=12.4866(6) Å, α=β=90.0°, γ=120.0° and Z=18. The crystal packing is stabilized by O-H⋯O and O-H⋯S intermolecular hydrogen bonds. These hydrogen bond interactions are also proved by NBO analysis. A detailed spectroscopic investigation is performed by the application of FT-IR and FT-NMR in addition to the theoretical approaches. Small energy gap between the frontier molecular orbitals is responsible for the nonlinear optical activity of the title molecule.
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Affiliation(s)
- Ömer Tamer
- Sakarya University, Arts and Sciences Faculty, Department of Physics, 54187 Sakarya, Turkey
| | - Necmi Dege
- Ondokuz Mayıs University, Arts and Sciences Faculty, Department of Physics, 55139 Samsun, Turkey
| | - Davut Avcı
- Sakarya University, Arts and Sciences Faculty, Department of Physics, 54187 Sakarya, Turkey
| | - Yusuf Atalay
- Sakarya University, Arts and Sciences Faculty, Department of Physics, 54187 Sakarya, Turkey.
| | - İlhan Özer İlhan
- Department of Chemistry, Faculty of Science, Erciyes University, 38039 Kayseri, Turkey
| | - Mehmet Çadır
- Department of Chemistry, Faculty of Science, Erciyes University, 38039 Kayseri, Turkey
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20
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Jawaria R, Hussain M, Shafiq Z, Ahmad HB, Tahir MN, Shad HA, Naseer MM. Robustness of thioamide dimer synthon, carbon bonding and thioamide–thioamide stacking in ferrocene-based thiosemicarbazones. CrystEngComm 2015. [DOI: 10.1039/c4ce02566k] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of thioureas in crystal engineering as robust supramolecular synthons is now recognized, but their analogs, namely thiosemicarbazones/N-iminothioureas, have not received the attention they deserve.
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Affiliation(s)
- Rifat Jawaria
- Institute of Chemical Sciences
- Organic Chemistry Division
- Bahauddin Zakariya University
- Multan 60800, Pakistan
| | - Mazhar Hussain
- Institute of Chemical Sciences
- Organic Chemistry Division
- Bahauddin Zakariya University
- Multan 60800, Pakistan
| | - Zahid Shafiq
- Institute of Chemical Sciences
- Organic Chemistry Division
- Bahauddin Zakariya University
- Multan 60800, Pakistan
| | - Hafiz Badaruddin Ahmad
- Institute of Chemical Sciences
- Organic Chemistry Division
- Bahauddin Zakariya University
- Multan 60800, Pakistan
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21
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Sibert EL, Tabor DP, Kidwell NM, Dean JC, Zwier TS. Fermi Resonance Effects in the Vibrational Spectroscopy of Methyl and Methoxy Groups. J Phys Chem A 2014; 118:11272-81. [DOI: 10.1021/jp510142g] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Edwin L. Sibert
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Daniel P. Tabor
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Nathanael M. Kidwell
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Jacob C. Dean
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Timothy S. Zwier
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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22
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Loquais Y, Gloaguen E, Habka S, Vaquero-Vara V, Brenner V, Tardivel B, Mons M. Secondary Structures in Phe-Containing Isolated Dipeptide Chains: Laser Spectroscopy vs Quantum Chemistry. J Phys Chem A 2014; 119:5932-41. [DOI: 10.1021/jp509494c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yohan Loquais
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Eric Gloaguen
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Sana Habka
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Vanesa Vaquero-Vara
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Valérie Brenner
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Benjamin Tardivel
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
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23
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Kee Kang Y, Yoo IK. Influence of substituents on conformational preferences of helix foldamers of γ-dipeptides. Biopolymers 2014; 101:1077-87. [DOI: 10.1002/bip.22507] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/02/2014] [Accepted: 05/14/2014] [Indexed: 12/13/2022]
Affiliation(s)
- Young Kee Kang
- Department of Chemistry and BK21 PLUS Research Team; Chungbuk National University, Cheongju; Chungbuk 361-763 Republic of Korea
| | - In Kee Yoo
- Department of Chemistry and BK21 PLUS Research Team; Chungbuk National University, Cheongju; Chungbuk 361-763 Republic of Korea
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24
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Çırak Ç, Sert Y, Ucun F. Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of a biomolecule: 5-Hydroxymethyluracil. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 127:41-46. [PMID: 24632154 DOI: 10.1016/j.saa.2014.02.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 01/26/2014] [Accepted: 02/09/2014] [Indexed: 06/03/2023]
Abstract
In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400cm(-1)) spectrum of the molecule in the solid phase was recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data, and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational frequencies. It was observed that the NH stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular NH⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.
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Affiliation(s)
- Çağrı Çırak
- Department of Physics, Faculty of Art & Sciences, Erzincan University, Erzincan, Turkey.
| | - Yusuf Sert
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat, Turkey; Sorgun Vocational School, Bozok University, Yozgat 66100, Turkey
| | - Fatih Ucun
- Department of Physics, Faculty of Art & Sciences, Süleyman Demirel University, Isparta, Turkey
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25
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Gord JR, Walsh PS, Fisher BF, Gellman SH, Zwier TS. Mimicking the First Turn of an α-Helix with an Unnatural Backbone: Conformation-Specific IR and UV Spectroscopy of Cyclically Constrained β/γ-Peptides. J Phys Chem B 2014; 118:8246-56. [PMID: 24694352 DOI: 10.1021/jp5015884] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Joseph R. Gord
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Patrick S. Walsh
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Brian F. Fisher
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Timothy S. Zwier
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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26
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Gabapentin hybrid peptides and bioconjugates. Bioorg Med Chem 2014; 22:1479-86. [DOI: 10.1016/j.bmc.2013.12.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 11/27/2013] [Accepted: 12/06/2013] [Indexed: 11/17/2022]
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27
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Walsh PS, Kusaka R, Buchanan EG, James WH, Fisher BF, Gellman SH, Zwier TS. Cyclic constraints on conformational flexibility in γ-peptides: conformation specific IR and UV spectroscopy. J Phys Chem A 2013; 117:12350-62. [PMID: 24147873 DOI: 10.1021/jp408736t] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Single-conformation spectroscopy has been used to study two cyclically constrained and capped γ-peptides: Ac-γACHC-NHBn (hereafter γACHC, Figure 1a), and Ac-γACHC-γACHC-NHBn (γγACHC, Figure 1b), under jet-cooled conditions in the gas phase. The γ-peptide backbone in both molecules contains a cyclohexane ring incorporated across each Cβ-Cγ bond and an ethyl group at each Cα. This substitution pattern was designed to stabilize a (g+, g+) torsion angle sequence across the Cα-Cβ-Cγ segment of each γ-amino acid residue. Resonant two-photon ionization (R2PI), infrared-ultraviolet hole-burning (IR-UV HB), and resonant ion-dip infrared (RIDIR) spectroscopy have been used to probe the single-conformation spectroscopy of these molecules. In both γACHC and γγACHC, all population is funneled into a single conformation. With RIDIR spectra in the NH stretch (3200-3500 cm(-1)) and amide I/II regions (1400-1800 cm(-1)), in conjunction with theoretical predictions, assignments have been made for the conformations observed in the molecular beam. γACHC forms a single nearest-neighbor C9 hydrogen-bonded ring whereas γγACHC takes up a next-nearest-neighbor C14 hydrogen-bonded structure. The gas-phase C14 conformation represents the beginning of a 2.614-helix, suggesting that the constraints imposed on the γ-peptide backbone by the ACHC and ethyl groups already impose this preference in the gas-phase di-γ-peptide, in which only a single C14 H-bond is possible, constituting one full turn of the helix. A similar conformational preference was previously documented in crystal structures and NMR analysis of longer γ-peptide oligomers containing the γACHC subunit [Guo, L., et al. Angew. Chem. Int. Ed. 2011, 50, 5843-5846]. In the gas phase, the γACHC-H2O complex was also observed and spectroscopically interrogated in the molecular beam. Here, the monosolvated γACHC retains the C9 hydrogen bond observed in the bare molecule, with the water acting as a bridge between the C-terminal carbonyl and the π-cloud of the UV chromophore. This is in contrast to the unconstrained γ-peptide-H2O complex, which incorporates H2O into both C9 and amide-stacked conformations.
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Affiliation(s)
- Patrick S Walsh
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907 United States
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28
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Kusaka R, Zhang D, Walsh PS, Gord JR, Fisher BF, Gellman SH, Zwier TS. Role of Ring-Constrained γ-Amino Acid Residues in α/γ-Peptide Folding: Single-Conformation UV and IR Spectroscopy. J Phys Chem A 2013; 117:10847-62. [PMID: 24070234 DOI: 10.1021/jp408258w] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ryoji Kusaka
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
- Department
of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Di Zhang
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Patrick S. Walsh
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Joseph R. Gord
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Brian F. Fisher
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Timothy S. Zwier
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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29
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Sert Y, Çırak Ç, Ucun F. Vibrational analysis of 4-chloro-3-nitrobenzonitrile by quantum chemical calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 107:248-255. [PMID: 23434551 DOI: 10.1016/j.saa.2013.01.046] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/11/2013] [Accepted: 01/17/2013] [Indexed: 06/01/2023]
Abstract
In the present study, the experimental and theoretical harmonic and anharmonic vibrational frequencies of 4-chloro-3-nitrobenzonitrile were investigated. The experimental FT-IR (400-4000 cm(-1)) and μ-Raman spectra (100-4000 cm(-1)) of the molecule in the solid phase were recorded. Theoretical vibrational frequencies and geometric parameters (bond lengths and bond angles) were calculated using ab initio Hartree Fock (HF), density functional B3LYP and M06-2X methods with 6-311++G(d,p) basis set by Gaussian 09 W program, for the first time. The assignments of the vibrational frequencies were performed by potential energy distribution (PED) analysis by using VEDA 4 program. The theoretical optimized geometric parameters and vibrational frequencies were compared with the corresponding experimental data, and they were seen to be in a good agreement with each other. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies were found.
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Affiliation(s)
- Yusuf Sert
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat, Turkey.
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30
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Buchanan EG, Dean JC, Zwier TS, Sibert EL. Towards a first-principles model of Fermi resonance in the alkyl CH stretch region: Application to 1,2-diphenylethane and 2,2,2-paracyclophane. J Chem Phys 2013; 138:064308. [DOI: 10.1063/1.4790163] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Harder M, Kuhn B, Diederich F. Efficient stacking on protein amide fragments. ChemMedChem 2013; 8:397-404. [PMID: 23355480 DOI: 10.1002/cmdc.201200512] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 01/07/2013] [Indexed: 11/07/2022]
Abstract
The less polar π-surface of protein amide groups is exposed in many receptor binding sites, either as part of the backbone or in Gln/Asn side chains. Using quantum chemical calculations and Protein Data Bank (PDB) searches on model systems, we investigate the energetics and geometric preferences for the stacking on amide groups of a large number of heteroarenes that are relevant to medicinal chemistry. From this study, we discern that the stacking energy of an aromatic ligand substituent can be improved by: 1) orienting the fragment dipole vector such that it is aligned in an antiparallel fashion with the dipole of the interacting protein amide group, 2) increasing its dipole moment, and 3) decreasing its π-electron density. These guidelines should be helpful to more rationally exploit this interaction type in future structure-based drug design.
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Affiliation(s)
- Michael Harder
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland
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32
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Adhikari U, Scheiner S. Preferred Configurations of Peptide–Peptide Interactions. J Phys Chem A 2013; 117:489-96. [DOI: 10.1021/jp310942u] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Upendra Adhikari
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United
States
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United
States
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33
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Dean JC, Buchanan EG, Zwier TS. Mixed 14/16 Helices in the Gas Phase: Conformation-Specific Spectroscopy of Z-(Gly)n, n = 1, 3, 5. J Am Chem Soc 2012; 134:17186-201. [PMID: 23039317 DOI: 10.1021/ja306652c] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jacob C. Dean
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084,
United States
| | - Evan G. Buchanan
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084,
United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084,
United States
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Buchanan EG, James WH, Choi SH, Guo L, Gellman SH, Müller CW, Zwier TS. Single-conformation infrared spectra of model peptides in the amide I and amide II regions: Experiment-based determination of local mode frequencies and inter-mode coupling. J Chem Phys 2012; 137:094301. [DOI: 10.1063/1.4747507] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Gu Q, Knee JL. Communication: Spectroscopic measurement of the binding energy of a carboxylic acid-water dimer. J Chem Phys 2012; 136:171101. [DOI: 10.1063/1.4711862] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Quanli Gu
- Chemistry Department, University of Virginia, Charlottesville, Virginia 22904, USA
- Chemistry Department, Wesleyan University, Middletown, Connecticut 06459, USA
| | - J. L. Knee
- Chemistry Department, Wesleyan University, Middletown, Connecticut 06459, USA
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Thétiot-Laurent S, Bouillère F, Baltaze JP, Brisset F, Feytens D, Kouklovsky C, Miclet E, Alezra V. Original β,γ-diamino acid as an inducer of a γ-turn mimic in short peptides. Org Biomol Chem 2012; 10:9660-3. [DOI: 10.1039/c2ob26828k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Fedorov DG, Nagata T, Kitaura K. Exploring chemistry with the fragment molecular orbital method. Phys Chem Chem Phys 2012; 14:7562-77. [DOI: 10.1039/c2cp23784a] [Citation(s) in RCA: 290] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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