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El Guerdaoui A, Tijar R, El Merbouh B, Bourjila M, El Bouzaidi RD, El Gridani A. A comprehensive conformational space analysis of N-formyl-l-tryptophanamide system by using a genetic algorithm for multi-modal search. J Mol Graph Model 2017; 75:137-148. [PMID: 28575796 DOI: 10.1016/j.jmgm.2017.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/28/2017] [Accepted: 05/15/2017] [Indexed: 11/16/2022]
Abstract
The conformational space of protected amino acid HCO-Tryptophane-NH2 was explored by using a new optimization procedure, in order to localize the stable minima on its potential energy surface (PES). The genetic algorithm based on the Multi-Niche Crowding (MNC) technique was used initially to generate a set of optimized structures for title compound. Resulting structures from the genetic algorithm technique will be used hereafter as input conformers at a hierarchy of increasingly more accurate electronic structure calculations (RHF/6-31G+(d) and DFT/B3LYP/6-31G+(d) geometry optimizations). The lowest energy conformer γL(g+g+) presents a folded Backbone that is stabilized by strong hydrogen bond noted C7. This links the carbonyl oxygen of the formyl group and the hydrogen of the amine group. There are further interactions from one hand between the carbonyl oxygen of the formyl group and the neighboring CH group on the pyrrole ring and from other hand between the N-terminus hydrogen and the indole ring in accordance with the experimental results. This work includes also a comparison between the theoretical calculations and the experimental results of X-ray crystallography extracted from protein data bank (PDB).
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Affiliation(s)
- Anouar El Guerdaoui
- Equipe de Chimie Théorique, Electrochimie et Environnement CT2E, Faculté des Sciences, B.P. 8106, Université Ibn Zohr, 8000, Agadir, Morocco.
| | - Rachida Tijar
- Equipe de Chimie Théorique, Electrochimie et Environnement CT2E, Faculté des Sciences, B.P. 8106, Université Ibn Zohr, 8000, Agadir, Morocco
| | - Brahim El Merbouh
- Equipe de Chimie Théorique, Electrochimie et Environnement CT2E, Faculté des Sciences, B.P. 8106, Université Ibn Zohr, 8000, Agadir, Morocco
| | - Malika Bourjila
- Equipe de Chimie Théorique, Electrochimie et Environnement CT2E, Faculté des Sciences, B.P. 8106, Université Ibn Zohr, 8000, Agadir, Morocco
| | - Rachid Drissi El Bouzaidi
- Equipe de Chimie Théorique, Electrochimie et Environnement CT2E, Faculté des Sciences, B.P. 8106, Université Ibn Zohr, 8000, Agadir, Morocco; Centre Régional des Métiers de l'Education et de la Formation (CRMEF), Souss Massa Daraa, Inezgan, Morocco
| | - Abderrahman El Gridani
- Equipe de Chimie Théorique, Electrochimie et Environnement CT2E, Faculté des Sciences, B.P. 8106, Université Ibn Zohr, 8000, Agadir, Morocco
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2
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Barone V, Biczysko M, Bloino J, Puzzarini C. Accurate structure, thermodynamic and spectroscopic parameters from CC and CC/DFT schemes: the challenge of the conformational equilibrium in glycine. Phys Chem Chem Phys 2013; 15:10094-111. [PMID: 23599122 DOI: 10.1039/c3cp50439e] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structures, relative stabilities, and infrared spectra of the six low-energy conformers of glycine have been characterized using a state-of-the-art quantum-mechanical approach allowing the bond distances, conformational enthalpies and vibrational frequencies to be determined well within the chemical accuracy. Transition state structures governing interconversion among the different energy minima have also been characterized. In detail, the gas-phase thermodynamic properties (at 15 K and 410 K) of the glycine conformers considered have been obtained with a 1 kJ mol(-1) accuracy, and it has been shown that the employment of DFT geometries usually reduces such accuracy by at most 0.1 kJ mol(-1). Regarding molecular structures, the use of two different composite schemes allowed us to further confirm the suitability of a rather cost-effective approach and provide geometrical parameters with an overall accuracy better than 0.002 Å for distances and 1 degree for angles. Thanks to a hybrid CC/DFT approach, the infrared spectra of all conformers considered and of several deuterated isotopologues have been reproduced (when experimental data were available) or predicted with an accuracy of 10 cm(-1). Finally, the joint thermodynamic and spectroscopic investigation allowed us to shed some light on the possible observation of elusive conformers. On the whole, the high accuracy of the computational results allows us to draw a fully consistent interpretation of the available experimental data and to obtain a more complete characterization of the potential energy surface of glycine.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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3
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Variation of conformational properties at a glance. True graphical visualization of the Ramachandran surface topology as a periodic potential energy surface. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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4
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Masman MF, Lovas S, Murphy RF, Enriz RD, Rodríguez AM. Conformational Preferences of N-Acetyl-l-leucine-N‘-methylamide. Gas-Phase and Solution Calculations on the Model Dipeptide. J Phys Chem A 2007; 111:10682-91. [PMID: 17887655 DOI: 10.1021/jp0716886] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A DFT study of N-acetyl-l-leucine-N'-methylamide conformers in the gas phase and in solution was carried out. The theoretical computational analysis revealed 43 different conformations at the B3LYP/6-31G(d) level of theory in the gas phase. In addition, the effects of three solvents (water, acetonitrile, and chloroform) were included in the calculations using the isodensity polarizable continuum model (IPCM) and the Poisson-Boltzmann self-consistent reaction field (PB-SCRF) method. The stability order of the different conformers in solution has been analyzed. The theoretical results were compared with some experimental data (X-ray, IR, and NMR).
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Affiliation(s)
- Marcelo F Masman
- Departamento de Química, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina
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5
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Chin W, Mons M, Dognon JP, Mirasol R, Chass G, Dimicoli I, Piuzzi F, Butz P, Tardivel B, Compagnon I, von Helden G, Meijer G. The gas-phase dipeptide analogue acetyl-phenylalanyl-amide: a model for the study of side chain/backbone interactions in proteins. J Phys Chem A 2007; 109:5281-8. [PMID: 16839051 DOI: 10.1021/jp048037j] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The issue of the influence of the side chain/backbone interaction on the local conformational preferences of a phenylalanine residue in a peptide chain is addressed. A synergetic approach is used, which combines gas-phase UV spectroscopy as well as gas-phase IR/UV double-resonance experiments with DFT and post Hartree-Fock calculations. N-Acetyl-Phe-amide was chosen as a model system for which three different conformers were observed. The most stable conformer has been identified as an extended beta(L) conformation of the peptide backbone. It is stabilized by a weak but significant NH-pi interaction bridging the aromatic ring on the residue (i) with the NH group on residue (i+1), with the aromatic side chain being in an anti conformation. This stable conformation corresponds to the common NH(i+1)-aromatic(i) interaction encountered in proteins for the three aromatic residues (phenylalanine, tyrosine, and tryptophan), which illustrates the relevance of gas-phase investigations to structural biology issues. The two other less abundant conformers have been assigned to two gamma-folded backbone conformations that differ by the orientation of the side chain. In all cases, the IR data provided spectroscopic fingerprints of these interactions. Finally, the strong conformational dependence of the fluorescence yield found for N-acetyl-Phe-amide illustrates the role of the environment on the excited-state dynamics of these species, which is often exploited by biochemists to monitor protein structural changes from tryptophan lifetime measurements.
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Affiliation(s)
- Wutharath Chin
- Laboratoire Francis Perrin (URA CNRS 2453), Service des Photons, Atomes et Molécules, Centre d'Etudes de Saclay, Bât. 522, 91191 Gif-sur-Yvette Cedex, France
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6
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Chin W, Piuzzi F, Dimicoli I, Mons M. Probing the competition between secondary structures and local preferences in gas phase isolated peptide backbones. Phys Chem Chem Phys 2005; 8:1033-48. [PMID: 16633584 DOI: 10.1039/b516245a] [Citation(s) in RCA: 192] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Combining laser desorption with a supersonic expansion together with the selectivity of IR/UV double resonance spectroscopy makes it possible to isolate and characterise the gas phase of remarkable backbone conformations of short peptide chains mimicking protein segments. A systematic bottom-up approach involving a conformer-specific IR study of peptide sequences of increasing sizes has enabled us to map the spectral signatures of the intramolecular interactions, which shape the peptide backbone, in particular H-bonds. The precise data collected are directly comparable to the most sophisticated quantum chemistry calculations of these species and therefore constitute a stringent test for the theoretical methods used. One-residue chains reveal the local conformational preference of the backbone and its dependence upon the nature of the residue. The investigation of longer chains provides evidence for a competition between simple successions of local conformational preferences along the chain and more folded structures, in which a new H-bonding network, involving distant H-bonding sites along the backbone, takes place. From three residues, the issue of helical folding can also be addressed. The present review of the gas phase literature data emphasizes the observation of remarkable secondary structures of biology, including short segments of beta-strands, gamma- and beta-turns, combinations of turns, including a 3(10) helix. It also provides evidence for the flexibility of the peptide chains, i.e., a critical influence of rather minor interactions (like side-chain/backbone interactions) on the conformational stability. Finally, the paper will discuss future promising directions of the present approach.
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Affiliation(s)
- Wutharath Chin
- Laboratoire Francis Perrin (URA 2453 CEA-CNRS), Service des Photons, Atomes et Molécules, Centre d'Etudes de Saclay, 91191 Gif-sur-Yvette Cedex, France
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7
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Chin W, Dognon JP, Canuel C, Piuzzi F, Dimicoli I, Mons M, Compagnon I, von Helden G, Meijer G. Secondary structures of short peptide chains in the gas phase: Double resonance spectroscopy of protected dipeptides. J Chem Phys 2005; 122:54317. [PMID: 15740332 DOI: 10.1063/1.1839862] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The conformational structure of short peptide chains in the gas phase is studied by laser spectroscopy of a series of protected dipeptides, Ac-Xxx-Phe-NH(2), Xxx=Gly, Ala, and Val. The combination of laser desorption with supersonic expansion enables us to vaporize the peptide molecules and cool them internally; IR/UV double resonance spectroscopy in comparison to density functional theory calculations on Ac-Gly-Phe-NH(2) permits us to identify and characterize the conformers populated in the supersonic expansion. Two main conformations, corresponding to secondary structures of proteins, are found to compete in the present experiments. One is composed of a doubly gamma-fold corresponding to the 2(7) ribbon structure. Topologically, this motif is very close to a beta-strand backbone conformation. The second conformation observed is the beta-turn, responsible for the chain reversal in proteins. It is characterized by a relatively weak hydrogen bond linking remote NH and CO groups of the molecule and leading to a ten-membered ring. The present gas phase experiment illustrates the intrinsic folding properties of the peptide chain and the robustness of the beta-turn structure, even in the absence of a solvent. The beta-turn population is found to vary significantly with the residues within the sequence; the Ac-Val-Phe-NH(2) peptide, with its two bulky side chains, exhibits the largest beta-turn population. This suggests that the intrinsic stabilities of the 2(7) ribbon and the beta-turn are very similar and that weakly polar interactions occurring between side chains can be a decisive factor capable of controlling the secondary structure.
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Affiliation(s)
- Wutharath Chin
- Laboratoire Francis Perrin, Service des Photons, Atomes et Molécules, Centre d'Etudes de Saclay, Bâtiment 522, 91191 Gif-sur-Yvette Cedex, France
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8
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Chin W, Dognon JP, Piuzzi F, Tardivel B, Dimicoli I, Mons M. Intrinsic Folding of Small Peptide Chains: Spectroscopic Evidence for the Formation of β-Turns in the Gas Phase. J Am Chem Soc 2005; 127:707-12. [PMID: 15643896 DOI: 10.1021/ja045251c] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Laser desorption of model peptides coupled to laser spectroscopic techniques enables the gas-phase observation of genuine secondary structures of biology. Spectroscopic evidence for the formation of beta-turns in gas-phase peptide chains containing glycine and phenylalanine residues establishes the intrinsic stability of these forms and their ability to compete with other stable structures. The precise characterization of local minima on the potential energy surface from IR spectroscopy constitutes an acute assessment for the state-of-the-art quantum mechanical calculations also presented. The observation of different types of beta-turns depending upon the residue order within the sequence is found to be consistent with the residue propensities in beta-turns of proteins, which suggests that the prevalence of glycine in type II and II' turns stems essentially from an energetic origin, already at play under isolated conditions.
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Affiliation(s)
- Wutharath Chin
- Laboratoire Francis Perrin (URA CEA-CNRS 2453), Service des Photons, Atomes et Molécules, Centre d'Etudes de Saclay, Bât. 522, 91191 Gif-sur-Yvette Cedex, France
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9
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Calaza FC, Rigo MV, Rinaldoni AN, Masman MF, Koo JC, Rodrı́guez AM, Enriz RD. Comprehensive conformational analysis of N-acetyl-l-isoleucine-N-methylamide: an ab initio study. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0166-1280(03)00344-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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10
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Perczel A, Farkas O, Jákli I, Topol IA, Csizmadia IG. Peptide models. XXXIII. Extrapolation of low-level Hartree-Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory. J Comput Chem 2003; 24:1026-42. [PMID: 12759903 DOI: 10.1002/jcc.10267] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
At the dawn of the new millenium, new concepts are required for a more profound understanding of protein structures. Together with NMR and X-ray-based 3D-structure determinations in silico methods are now widely accepted. Homology-based modeling studies, molecular dynamics methods, and quantum mechanical approaches are more commonly used. Despite the steady and exponential increase in computational power, high level ab initio methods will not be in common use for studying the structure and dynamics of large peptides and proteins in the near future. We are presenting here a novel approach, in which low- and medium-level ab initio energy results are scaled, thus extrapolating to a higher level of information. This scaling is of special significance, because we observed previously on molecular properties such as energy, chemical shielding data, etc., determined at a higher theoretical level, do correlate better with experimental data, than those originating from lower theoretical treatments. The Ramachandran surface of an alanine dipeptide now determined at six different levels of theory [RHF and B3LYP 3-21G, 6-31+G(d) and 6-311++G(d,p)] serves as a suitable test. Minima, first-order critical points and partially optimized structures, determined at different levels of theory (SCF, DFT), were completed with high level energy calculations such as MP2, MP4D, and CCSD(T). For the first time three different CCSD(T) sets of energies were determined for all stable B3LYP/6-311++G(d,p) minima of an alanine dipeptide. From the simplest ab initio data (e.g., RHF/3-21G) to more complex results [CCSD(T)/6-311+G(d,p)//B3LYP/6-311++G(d,p)] all data sets were compared, analyzed in a comprehensive manner, and evaluated by means of statistics.
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Affiliation(s)
- András Perczel
- Department of Organic Chemistry, Eötvös University, PO Box 32, H-1518 Budapest 112, Hungary.
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11
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Klipfel MW, Zamora MA, Rodriguez AM, Fidanza NG, Enriz RD, Csizmadia IG. Exploration of the Full Conformational Space of N-Acetyl-l-glutamine-N-methylamide. An ab Initio and Density Functional Theory Study. J Phys Chem A 2003. [DOI: 10.1021/jp030111v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco W. Klipfel
- Departamento de Química, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina, Area de Química Física, Departamento de Química, U.N.N.E., Av. Libertad 5460, 3400 Corrientes, Argentina, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada, and Department of Medical Chemistry, University of Szeged, 8 Dom ter, H-6720 Szeged, Hungary
| | - Miguel A. Zamora
- Departamento de Química, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina, Area de Química Física, Departamento de Química, U.N.N.E., Av. Libertad 5460, 3400 Corrientes, Argentina, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada, and Department of Medical Chemistry, University of Szeged, 8 Dom ter, H-6720 Szeged, Hungary
| | - Ana M. Rodriguez
- Departamento de Química, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina, Area de Química Física, Departamento de Química, U.N.N.E., Av. Libertad 5460, 3400 Corrientes, Argentina, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada, and Department of Medical Chemistry, University of Szeged, 8 Dom ter, H-6720 Szeged, Hungary
| | - Noemí G. Fidanza
- Departamento de Química, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina, Area de Química Física, Departamento de Química, U.N.N.E., Av. Libertad 5460, 3400 Corrientes, Argentina, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada, and Department of Medical Chemistry, University of Szeged, 8 Dom ter, H-6720 Szeged, Hungary
| | - Ricardo D. Enriz
- Departamento de Química, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina, Area de Química Física, Departamento de Química, U.N.N.E., Av. Libertad 5460, 3400 Corrientes, Argentina, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada, and Department of Medical Chemistry, University of Szeged, 8 Dom ter, H-6720 Szeged, Hungary
| | - Imre G. Csizmadia
- Departamento de Química, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina, Area de Química Física, Departamento de Química, U.N.N.E., Av. Libertad 5460, 3400 Corrientes, Argentina, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada, and Department of Medical Chemistry, University of Szeged, 8 Dom ter, H-6720 Szeged, Hungary
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12
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Koo JCP, Chass GA, Perczel A, Farkas Ö, Torday LL, Varro A, Papp JG, Csizmadia IG. Exploration of the Four-Dimensional-Conformational Potential Energy Hypersurface of N-Acetyl-l-aspartic Acid N‘-Methylamide with Its Internally Hydrogen Bonded Side-Chain Orientation. J Phys Chem A 2002. [DOI: 10.1021/jp014514b] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joseph C. P. Koo
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6, Velocet R & D, 210 Dundas Street West, Suite 810, Toronto, Ontario, Canada M5G 2E8, Department of Organic Chemistry, Eotvos University, H-1117, Budapest, Hungary, Department of Pharmacology and Pharmacotherapy, Szeged University, Dóm tér 12, H-6701, Szeged, Hungary, and Division of Cardiovascular Pharmacology, Hungarian Academy of Sciences and Szeged University, Dóm tér 12, H-6701, Szeged, Hungary
| | - Gregory A. Chass
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6, Velocet R & D, 210 Dundas Street West, Suite 810, Toronto, Ontario, Canada M5G 2E8, Department of Organic Chemistry, Eotvos University, H-1117, Budapest, Hungary, Department of Pharmacology and Pharmacotherapy, Szeged University, Dóm tér 12, H-6701, Szeged, Hungary, and Division of Cardiovascular Pharmacology, Hungarian Academy of Sciences and Szeged University, Dóm tér 12, H-6701, Szeged, Hungary
| | - Andras Perczel
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6, Velocet R & D, 210 Dundas Street West, Suite 810, Toronto, Ontario, Canada M5G 2E8, Department of Organic Chemistry, Eotvos University, H-1117, Budapest, Hungary, Department of Pharmacology and Pharmacotherapy, Szeged University, Dóm tér 12, H-6701, Szeged, Hungary, and Division of Cardiovascular Pharmacology, Hungarian Academy of Sciences and Szeged University, Dóm tér 12, H-6701, Szeged, Hungary
| | - Ödon Farkas
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6, Velocet R & D, 210 Dundas Street West, Suite 810, Toronto, Ontario, Canada M5G 2E8, Department of Organic Chemistry, Eotvos University, H-1117, Budapest, Hungary, Department of Pharmacology and Pharmacotherapy, Szeged University, Dóm tér 12, H-6701, Szeged, Hungary, and Division of Cardiovascular Pharmacology, Hungarian Academy of Sciences and Szeged University, Dóm tér 12, H-6701, Szeged, Hungary
| | - Ladislaus L. Torday
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6, Velocet R & D, 210 Dundas Street West, Suite 810, Toronto, Ontario, Canada M5G 2E8, Department of Organic Chemistry, Eotvos University, H-1117, Budapest, Hungary, Department of Pharmacology and Pharmacotherapy, Szeged University, Dóm tér 12, H-6701, Szeged, Hungary, and Division of Cardiovascular Pharmacology, Hungarian Academy of Sciences and Szeged University, Dóm tér 12, H-6701, Szeged, Hungary
| | - Andras Varro
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6, Velocet R & D, 210 Dundas Street West, Suite 810, Toronto, Ontario, Canada M5G 2E8, Department of Organic Chemistry, Eotvos University, H-1117, Budapest, Hungary, Department of Pharmacology and Pharmacotherapy, Szeged University, Dóm tér 12, H-6701, Szeged, Hungary, and Division of Cardiovascular Pharmacology, Hungarian Academy of Sciences and Szeged University, Dóm tér 12, H-6701, Szeged, Hungary
| | - Julius Gy. Papp
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6, Velocet R & D, 210 Dundas Street West, Suite 810, Toronto, Ontario, Canada M5G 2E8, Department of Organic Chemistry, Eotvos University, H-1117, Budapest, Hungary, Department of Pharmacology and Pharmacotherapy, Szeged University, Dóm tér 12, H-6701, Szeged, Hungary, and Division of Cardiovascular Pharmacology, Hungarian Academy of Sciences and Szeged University, Dóm tér 12, H-6701, Szeged, Hungary
| | - Imre G. Csizmadia
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6, Velocet R & D, 210 Dundas Street West, Suite 810, Toronto, Ontario, Canada M5G 2E8, Department of Organic Chemistry, Eotvos University, H-1117, Budapest, Hungary, Department of Pharmacology and Pharmacotherapy, Szeged University, Dóm tér 12, H-6701, Szeged, Hungary, and Division of Cardiovascular Pharmacology, Hungarian Academy of Sciences and Szeged University, Dóm tér 12, H-6701, Szeged, Hungary
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13
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Conformational effects of one glycine residue on the other glycine residues in the Ac-Gly-Gly-Gly-NHMe tripeptide motif: an ab initio exploratory study. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0166-1280(02)00172-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Zamora MA, Baldoni HA, Rodriguez AM, Enriz RD, Sosa CP, Perczel A, Kucsman A, Farkas O, Deretey E, Vank JC, Csizmadia IG. Peptide model XXVIII: An exploratory ab initio and density functional study on the side-chain-backbone interaction in N-acetyl-L-cysteine- N-methylamide and N-formyl-L-cysteinamide in their γL-backbone conformations. CAN J CHEM 2002. [DOI: 10.1139/v02-076] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A conformational and electronic study on the energetically preferred conformations (γL) of N- and C-protected L-cysteine (P-CONH-CH(CH2SH)-CONH-Q, where P and Q may be H or Me) was carried out. After restraining the backbone (BB) conformation to its global minimum (γL or C7eq), all nine possible side-chain (SC) conformations were subjected to geometry optimization at the HF/321G and the B3LYP/631G(d,p) levels of theory. Seven of the nine side-chain conformers were located on the potential-energy surface. All conformers were subjected to an AIM (atoms in molecules) analysis. This study indicates that three of the seven optimized conformers exhibited either or both SC [Formula: see text] BB- or BB [Formula: see text] SC-type intramolecular hydrogen bonding. Five conformers, however, had distances between a proton and a heteroatom that suggested hydrogen bonding.Key words: L-cysteine diamides, side-chain potential-energy surface, ab initio and DFT geometry optimization, AIM analysis, intramolecular hydrogen bonding.
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15
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Barroso M, Cerutti E, Rodrı́guez A, Jáuregui E, Farkas O, Perczel A, Enriz R. Side-chain conformations for selected backbone conformations of N-acetyl-l-isoleucine-N-methylamide and N-acetyl-l-nor-isoleucine-N-methylamide. An exploratory ab initio study. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0166-1280(01)00355-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Tarditi A, Klipfel M, Rodriguez A, Suvire F, Chasse G, Farkas O, Perczel A, Enriz R. An ab initio exploratory study of side chain conformations for selected backbone conformations of N -acetyl- l -glutamine- N -methylamide. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0166-1280(01)00352-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Masman M, Amaya M, Rodrı́guez A, Suvire F, Chasse G, Farkas O, Perczel A, Enriz R. An exploratory study of side-chain–backbone interaction in selected conformations of N -acetyl- l -glutamate- N -methylamide. An ab initio study. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0166-1280(01)00353-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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18
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Zamora M, Baldoni H, Bombasaro J, Mak M, Perczel A, Farkas O, Enriz R. An exploratory ab initio study of the full conformational space of N -acetyl- l -cysteine- N -methylamide. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0166-1280(01)00350-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Perczel A, Hudáky P, Csizmadia I. Deciphering factors which determine the Ramachandran surface of peptides. The application of isodesmic surfaces, Δ E ID ( ϕ , ψ ), to analyze the contribution of rotating moieties to the shape of potential energy surfaces. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0166-1280(00)00431-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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21
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Vank JC, Sosa CP, Perczel A, Csizmadia IG. Peptide models XXVII. An exploratory ab initio study on the 21 st amino acid side-chain conformations of N-formyl-L-selenocysteinamide (For-L-Sec-NH 2) and N-acetyl-L-selenocysteine- N-methylamide (Ac-L-Sec-NHMe) in their γ L backbone conformation. CAN J CHEM 2000. [DOI: 10.1139/v00-029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Selenocysteine is expected to have 9 × 9 = 81 conformations [3 × 3 = 9 backbone: ψ (g+,a,g-) × ϕ (g+,a,g-) and 3 × 3 = 9 side-chain: χ1 (g+,a,g-) × χ2 (g+,a,g-)]. In the present study, all the torsional modes of the side-chain (χ1: rotation about the Cα-Cβ and χ2: rotation about the Cβ-Se bonds) were investigated in the relaxed γL backbone [(ϕ,ψ); (g-,g+)] conformation. Seven out of the nine expected minima were found at the RHF/3-21G level of theory for N-formyl-L-selenocysteinamide (For-L-Sec-NH2) and N-acetyl-L-selenocysteine-N-methylamide (Ac-L-Sec-NHMe). The stabilization energy exerted by the -CH2-SeH side-chain has been compared with that of -CH2-SH and -CH2-OH. Relative energies of the various conformers were also obtained via single point calculations at the B3LYP/6-31G(d,p) level of theory. Topological analysis of the electron density has been performed by Bader's Atoms in Molecule (AIM) approach using the results. The structures were also optimized at the B3LYP/6-31+G(d,p) level of theory.Key words: selenocysteine side-chain conformations, ab initio MO study, Multidimensional Conformational Analysis (MDCA), Atoms in Molecules (AIM), Bader's electron density analysis.
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Santagata L, Suvire F, Enriz R, Torday L, Csizmadia I. A geometrical algorithm to search the conformational space (GASCOS) of flexible molecules. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0166-1280(98)00498-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Császár AG, Perczel A. Ab initio characterization of building units in peptides and proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1999; 71:243-309. [PMID: 10097616 DOI: 10.1016/s0079-6107(98)00031-5] [Citation(s) in RCA: 144] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- A G Császár
- Department of Theoretical Chemistry, Eötvös University, Budapest, Hungary
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Rodrı́guez AM, Baldoni HA, Suvire F, Vázquez RN, Zamarbide G, Enriz RD, Farkas Ö, Perczel A, McAllister MA, Torday LL, Papp JG, Csizmadia IG. Characteristics of Ramachandran maps of L-alanine diamides as computed by various molecular mechanics, semiempirical and ab initio MO methods. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0166-1280(98)00221-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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Perczel A, Farkas Ö, Jákli I, Csizmadia IG. Peptide models XXI. Side-chain/backbone conformational interconversions in HCO-l-Ser-NH2. Tracing relaxation paths by ab initio modeling. An exploratory study. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0166-1280(98)00227-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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26
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Jákli I, Perczel A, Farkas Ö, Hollósi M, Csizmadia IG. Peptide models XXII. A conformational model for aromatic amino acid residues in proteins. A comprehensive analysis of all the RHF/6–31+G* conformers of For-L-Phe–NH2. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0166-1280(98)00222-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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Perczel A, Farkas Ö, Csizmadia IG. Peptide Models. 18. Hydroxymethyl Side-Chain Induced Backbone Conformational Shifts of l-Serine Amide. All ab Initio Conformers of For-l-Ser-NH2. J Am Chem Soc 1996. [DOI: 10.1021/ja960464q] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- András Perczel
- Contribution from the Institute of Organic Chemistry, Eötvös University, 112 Budapest P.O.B. 32, H-1117, Hungary, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, Department of Chemistry, Wayne State University, Detroit, Michigan 48202, and Department of Chemistry, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Ödön Farkas
- Contribution from the Institute of Organic Chemistry, Eötvös University, 112 Budapest P.O.B. 32, H-1117, Hungary, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, Department of Chemistry, Wayne State University, Detroit, Michigan 48202, and Department of Chemistry, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Imre G. Csizmadia
- Contribution from the Institute of Organic Chemistry, Eötvös University, 112 Budapest P.O.B. 32, H-1117, Hungary, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, Department of Chemistry, Wayne State University, Detroit, Michigan 48202, and Department of Chemistry, University of Toronto, Toronto, Ontario M5S 1A1, Canada
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