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de Azambuja F, Loosen A, Conic D, van den Besselaar M, Harvey JN, Parac-Vogt TN. En Route to a Heterogeneous Catalytic Direct Peptide Bond Formation by Zr-Based Metal–Organic Framework Catalysts. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01782] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Alexandra Loosen
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Dragan Conic
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | | | - Jeremy N. Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
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2
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Thakkar BS, Svendsen JSM, Engh RA. Density Functional Studies on Secondary Amides: Role of Steric Factors in Cis/Trans Isomerization. Molecules 2018; 23:molecules23102455. [PMID: 30257481 PMCID: PMC6222500 DOI: 10.3390/molecules23102455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 09/21/2018] [Accepted: 09/21/2018] [Indexed: 11/16/2022] Open
Abstract
Cis/trans isomerization of amide bonds is a key step in a wide range of biological and synthetic processes. Occurring through C-N amide bond rotation, it also coincides with the activation of amides in enzymatic hydrolysis. In recently described QM studies of cis/trans isomerization in secondary amides using density functional methods, we highlighted that a peptidic prototype, such as glycylglycine methyl ester, can suitably represent the isomerization and complexities arising out of a larger molecular backbone, and can serve as the primary scaffold for model structures with different substitution patterns in order to assess and compare the steric effect of the substitution patterns. Here, we describe our theoretical assessment of such steric effects using tert-butyl as a representative bulky substitution. We analyze the geometries and relative stabilities of both trans and cis isomers, and effects on the cis/trans isomerization barrier. We also use the additivity principle to calculate absolute steric effects with a gradual increase in bulk. The study establishes that bulky substitutions significantly destabilize cis isomers and also increases the isomerization barrier, thereby synergistically hindering the cis/trans isomerization of secondary amides. These results provide a basis for the rationalization of kinetic and thermodynamic properties of peptides with potential applications in synthetic and medicinal chemistry.
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Affiliation(s)
- Balmukund S Thakkar
- Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway.
| | | | - Richard A Engh
- Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway.
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3
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Elghobashi-Meinhardt N. Exploring Peptide⁻Solvent Interactions: A Computational Study. Molecules 2018; 23:E2355. [PMID: 30223458 PMCID: PMC6225229 DOI: 10.3390/molecules23092355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 09/06/2018] [Accepted: 09/10/2018] [Indexed: 11/17/2022] Open
Abstract
The dilemma of reconciling the contradictory evidence regarding the conformation of long solvated peptide chains is the so-called "reconciliation problem". Clues regarding the stability of certain conformations likely lie in the electronic structure at the peptide⁻solvent interface, but the peptide⁻solvent interaction is not fully understood. Here, we study the influence of aqueous solvent on peptide conformations by using classical molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) energy calculations. The model systems include an 11-residue peptide, X 2 A 7 O 2 (XAO), where X, A, and O denote diaminobutyric acid, alanine, and ornithine, respectively, and a 9-mer (Arg-Pro-Pro-Gly-Phe-Ser-Ala-Phe-Lys). Spectroscopic and MD data present conflicting evidence regarding the structure of XAO in water; some results indicate that XAO adopts a polyproline II (P II ) conformation, whereas other findings suggest that XAO explores a range of conformations. To investigate this contradiction, we present here the results of MD simulations of XAO and the 9-mer in aqueous solution, combined with QM/MM energy calculations.
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Affiliation(s)
- Nadia Elghobashi-Meinhardt
- Theoretical Molecular Biophysics, Department of Physical and Theoretical Chemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstr. 36a, 14169 Berlin, Germany.
- Theoretical Molecular Biophysics, Department of Physical and Theoretical Chemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstr. 36a, 14169 Berlin, Germany.
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4
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Thakkar BS, Svendsen JSM, Engh RA. Cis/Trans Isomerization in Secondary Amides: Reaction Paths, Nitrogen Inversion, and Relevance to Peptidic Systems. J Phys Chem A 2017; 121:6830-6837. [DOI: 10.1021/acs.jpca.7b05584] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Balmukund S. Thakkar
- Department of Chemistry, UiT The Arctic University of Norway, Tromsø-9037, Norway
| | | | - Richard A. Engh
- Department of Chemistry, UiT The Arctic University of Norway, Tromsø-9037, Norway
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6
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Jangra H, Haindl MH, Achrainer F, Hioe J, Gschwind RM, Zipse H. Conformational Preferences in Small Peptide Models: The Relevance ofcis/trans-Conformations. Chemistry 2016; 22:13328-35. [DOI: 10.1002/chem.201601828] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Harish Jangra
- Department of Chemistry; LMU München; Butenandstrasse 5-14 81377 München Germany
| | - Michael H. Haindl
- Institut für Organische Chemie; Universität Regensburg; 93053 Regensburg Germany
| | - Florian Achrainer
- Department of Chemistry; LMU München; Butenandstrasse 5-14 81377 München Germany
| | - Johnny Hioe
- Institut für Organische Chemie; Universität Regensburg; 93053 Regensburg Germany
| | - Ruth M. Gschwind
- Institut für Organische Chemie; Universität Regensburg; 93053 Regensburg Germany
| | - Hendrik Zipse
- Department of Chemistry; LMU München; Butenandstrasse 5-14 81377 München Germany
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7
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Thakare S, Stachelek P, Mula S, More AB, Chattopadhyay S, Ray AK, Sekar N, Ziessel R, Harriman A. Solvent-Driven Conformational Exchange for Amide-Linked Bichromophoric BODIPY Derivatives. Chemistry 2016; 22:14356-66. [DOI: 10.1002/chem.201602354] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Shrikant Thakare
- Department of Dyestuff Technology; Institute of Chemical Technology; Mumbai 400019 India
| | - Patrycja Stachelek
- Molecular Photonics Laboratory; School of Chemistry; Newcastle University; Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Soumyaditya Mula
- Bio-Organic Division; Bhabha Atomic Research Centre; Mumbai 400085 India
| | - Ankush B. More
- Department of Dyestuff Technology; Institute of Chemical Technology; Mumbai 400019 India
| | | | - Alok K. Ray
- Laser and Plasma Technology Division; Bhabha Atomic Research Centre; Mumbai 400085 India
| | - Nagaiyan Sekar
- Department of Dyestuff Technology; Institute of Chemical Technology; Mumbai 400019 India
| | - Raymond Ziessel
- Laboratoire de Chimie Organique et Spectroscopies Avancées (LCOSA); Ecole Européenne de Chimie; Polymères et Matériaux; Université de Strasbourg; 25 rue Becquerel 67087 Strasbourg Cedex 02 France
| | - Anthony Harriman
- Molecular Photonics Laboratory; School of Chemistry; Newcastle University; Bedson Building Newcastle upon Tyne NE1 7RU UK
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8
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Horta BAC, Lin Z, Huang W, Riniker S, van Gunsteren WF, Hünenberger PH. Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol. J Comput Chem 2012; 33:1907-17. [DOI: 10.1002/jcc.23021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 04/10/2012] [Accepted: 04/19/2012] [Indexed: 11/09/2022]
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9
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Ingrosso F, Monard G, Hamdi Farag M, Bastida A, Ruiz-López MF. Importance of Polarization and Charge Transfer Effects to Model the Infrared Spectra of Peptides in Solution. J Chem Theory Comput 2011; 7:1840-9. [DOI: 10.1021/ct2000588] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Francesca Ingrosso
- Equipe de Chimie et Biochimie Théoriques, UMR 7565 SRSMC, CNRS-Nancy Université, BP 70239 Vandœuvre-lès Nancy, France
| | - Gérald Monard
- Equipe de Chimie et Biochimie Théoriques, UMR 7565 SRSMC, CNRS-Nancy Université, BP 70239 Vandœuvre-lès Nancy, France
| | - Marwa Hamdi Farag
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain
| | - Adolfo Bastida
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain
| | - Manuel F. Ruiz-López
- Equipe de Chimie et Biochimie Théoriques, UMR 7565 SRSMC, CNRS-Nancy Université, BP 70239 Vandœuvre-lès Nancy, France
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10
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Yonezawa Y, Standley DM, Nakamura H. Degree of pyramidality governs the height and peak position of the free-energy-barrier for the cis–trans isomerization of N-Methylacetamide. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Te JA, Tan ML, Ichiye T. Solvation of Biomolecules by the Soft Sticky Dipole-Quadrupole-Octupole Water Model. Chem Phys Lett 2010; 486:70-73. [PMID: 21031143 DOI: 10.1016/j.cplett.2009.12.089] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The soft sticky dipole-quadrupole-octupole (SSDQO) potential energy function represents a water molecule by a single site with a van der Waals sphere and point multipoles. Previously, SSDQO was shown to give good properties for liquid water and solvation of simple ions and is faster than three point models. Here, SSDQO is assessed for solvating biologically relevant molecules having a multi-site, partial charge description. Monte Carlo simulations of ethanol, benzene, and N-methylacetamide in SSDQO with SPC/E moments showed the water structure was as good as in SPC/E. Thus, SSDQO is potentially useful for simulations of biological macromolecules in aqueous solution.
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Affiliation(s)
- Jerez A Te
- Department of Chemistry, Georgetown University, Washington, DC, 20057
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12
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Candelaresi M, Pagliai M, Lima M, Righini R. Chemical Equilibrium Probed by Two-Dimensional IR Spectroscopy: Hydrogen Bond Dynamics of Methyl Acetate in Water. J Phys Chem A 2009; 113:12783-90. [DOI: 10.1021/jp906072w] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Marco Candelaresi
- European Laboratory for Nonlinear Spectroscopy (LENS), Via Nello Carrara 1, and Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Fi), Italy
| | - Marco Pagliai
- European Laboratory for Nonlinear Spectroscopy (LENS), Via Nello Carrara 1, and Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Fi), Italy
| | - Manuela Lima
- European Laboratory for Nonlinear Spectroscopy (LENS), Via Nello Carrara 1, and Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Fi), Italy
| | - Roberto Righini
- European Laboratory for Nonlinear Spectroscopy (LENS), Via Nello Carrara 1, and Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Fi), Italy
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13
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Mantz YA, Branduardi D, Bussi G, Parrinello M. Ensemble of Transition State Structures for the Cis−Trans Isomerization of N-Methylacetamide. J Phys Chem B 2009; 113:12521-9. [DOI: 10.1021/jp8106556] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yves A. Mantz
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Davide Branduardi
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Giovanni Bussi
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Michele Parrinello
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
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Tulip PR, Bates SP. Peptide aggregation and solvent electrostriction in a simple zwitterionic dipeptide via molecular dynamics simulations. J Chem Phys 2009; 131:015103. [DOI: 10.1063/1.3160682] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- P. R. Tulip
- Scottish Universities Physics Alliance (SUPA), School of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
| | - S. P. Bates
- Scottish Universities Physics Alliance (SUPA), School of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
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15
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Agnihotri N, Mishra PC. Mutagenic Product Formation Due to Reaction of Guanine Radical Cation with Nitrogen Dioxide. J Phys Chem B 2009; 113:3129-38. [DOI: 10.1021/jp805942y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Neha Agnihotri
- Department of Physics, Banaras Hindu University, Varanasi - 221 005, India
| | - P. C. Mishra
- Department of Physics, Banaras Hindu University, Varanasi - 221 005, India
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16
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Mathieu S, Poteau R, Trinquier G. Estimating the "steric clash" at cis peptide bonds. J Phys Chem B 2008; 112:7894-902. [PMID: 18543981 DOI: 10.1021/jp711082d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
To account for the scarcity of cis peptide bonds in proteins, especially in nonproline (or secondary amide) cases, a steric-clash argument is often put forward, in a scheme where the R lateral chains are facing parallel one another, and the backbone is kept in an "all- trans"-like arrangement. Although such a steric conflict can be partly relieved through proper adjustment of the backbone dihedral angles, one can try to estimate its associated energy cost. To this end, quantum-chemistry approaches using a differential-torsion protocol and bond-separation-energy analyses are applied to N-ethyl propionamide CH3-CH2-CO-NH-CH2-CH3, regarded as a model capable of exhibiting C beta...C beta interaction as in alanine succession. The calculations provide an increment of 9 kcal/mol, quite close to that obtained in the nearly isostere (gsg) rotamer of n-hexane (10 kcal/mol), suggesting the local effects induced by methyl-methyl contact are similar in both cases. Analogous treatments on larger radicals as encountered in leucine or phenylalanine dimers do not change this increment much, which therefore defines the basic reference per-plaque quota to be overcome along all- cis chains. Explicit modeling indicated it can be reduced by up to a factor of 4.
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Affiliation(s)
- Simon Mathieu
- Laboratoire de Chimie et Physique Quantique, IRSAMC, Université Paul-Sabatier, Toulouse Cedex 9, France
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