Jangra, Harish and Haindl, Michael H. and Achrainer, Florian and Hioe, Johnny and Gschwind, Ruth M. and Zipse, Hendrik (2016) Conformational Preferences in Small Peptide Models: The Relevance of cis/trans-Conformations. CHEMISTRY-A EUROPEAN JOURNAL, 22 (37). pp. 13328-13335. ISSN 0947-6539, 1521-3765
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The accurate description of cis/trans peptide structures is of fundamental relevance for the field of protein modeling and protein structure determination. A comprehensive conformational analysis of dipeptide model Ace-GlyNMe (1) has been carried out by using a combination of theoretical calculations and experimental (H-1 and C-13 NMR and NOESY) spectroscopic measurements to assess the relevance of cis-peptide conformers. NMR measurements in dimethyl sulfoxide (DMSO) solution and calculations employing a continuum solvation model both point to the extended trans,-trans conformer C5_tt as the global minimum. The cis-peptide structures C5_ct and C5_tc, with the N-or C-terminal amide group in cis-conformation, are observed separately and located 13.0 +/- 2 kJmol(-1) higher in energy. This is in close agreement with the theoretical prediction of around 12 kJmol(-1) in DMSO. The ability of common protein force fields to reproduce the energies of the cis-amide conformers C5_ct and C5_tc in 1 is limited, making these methods unsuitable for the description of cis-peptide structures in protein simulations.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | DENSITY-FUNCTIONAL THEORY; BASIS-SET CONVERGENCE; AC-GLY-NHME; AB-INITIO; FORCE-FIELD; GAS-PHASE; GLYCINE DIPEPTIDES; PROTEIN STRUCTURES; N-METHYLFORMAMIDE; CHEMICAL-EXCHANGE; conformation analysis; density functional calculations; peptides; protein folding; protein structures |
| Subjects: | 500 Science > 540 Chemistry & allied sciences |
| Divisions: | Chemistry and Pharmacy > Institut für Organische Chemie Chemistry and Pharmacy > Institut für Organische Chemie > Arbeitskreis Prof. Dr. Ruth Gschwind |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 15 Mar 2019 09:41 |
| Last Modified: | 15 Mar 2019 09:41 |
| URI: | https://pred.uni-regensburg.de/id/eprint/3302 |
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