Computational study of protein secondary structure elements: Ramachandran plots revisited
Abstract
Potential energy surface (PES) were built for nineteen amino acids using density functional theory (PW91 and DFT M062X/6-311**). Examining the energy as a function of the phi/psi dihedral angles in the allowed regions of the Ramachandran plot, amino acid groups that share common patterns on their PES plots and global minima were identified. These patterns show partial correlation with their structural and pharmacophoric features. Differences between these computational results and the experimentally noted permitted conformations of each amino acid are rationalized on the basis of attractive intra- and intermolecular non-covalent interactions. The present data are focused on the intrinsic properties of an amino acid - an element which to our knowledge is typically ignored, as larger models are always used for the sake of similarity to real biological polypeptides. (C) 2014 Elsevier Inc. All rights reserved.
Keywords:
Ramachandran / Secondary structure / Amino acid / DFT / Potential energy surfaceSource:
Journal of Molecular Graphics and Modelling, 2014, 50, 125-133Publisher:
- Elsevier Science Inc, New York
Funding / projects:
- Romanian Ministry of Education and Research [PN II 312/2008]
DOI: 10.1016/j.jmgm.2014.04.001
ISSN: 1093-3263
PubMed: 24793053
WoS: 000336875600013
Scopus: 2-s2.0-84899798171
Collections
Institution/Community
Hemijski fakultet / Faculty of ChemistryTY - JOUR AU - Carrascoza, Francisco AU - Zarić, Snežana D. AU - Silaghi-Dumitrescu, Radu PY - 2014 UR - https://cherry.chem.bg.ac.rs/handle/123456789/1785 AB - Potential energy surface (PES) were built for nineteen amino acids using density functional theory (PW91 and DFT M062X/6-311**). Examining the energy as a function of the phi/psi dihedral angles in the allowed regions of the Ramachandran plot, amino acid groups that share common patterns on their PES plots and global minima were identified. These patterns show partial correlation with their structural and pharmacophoric features. Differences between these computational results and the experimentally noted permitted conformations of each amino acid are rationalized on the basis of attractive intra- and intermolecular non-covalent interactions. The present data are focused on the intrinsic properties of an amino acid - an element which to our knowledge is typically ignored, as larger models are always used for the sake of similarity to real biological polypeptides. (C) 2014 Elsevier Inc. All rights reserved. PB - Elsevier Science Inc, New York T2 - Journal of Molecular Graphics and Modelling T1 - Computational study of protein secondary structure elements: Ramachandran plots revisited VL - 50 SP - 125 EP - 133 DO - 10.1016/j.jmgm.2014.04.001 ER -
@article{ author = "Carrascoza, Francisco and Zarić, Snežana D. and Silaghi-Dumitrescu, Radu", year = "2014", abstract = "Potential energy surface (PES) were built for nineteen amino acids using density functional theory (PW91 and DFT M062X/6-311**). Examining the energy as a function of the phi/psi dihedral angles in the allowed regions of the Ramachandran plot, amino acid groups that share common patterns on their PES plots and global minima were identified. These patterns show partial correlation with their structural and pharmacophoric features. Differences between these computational results and the experimentally noted permitted conformations of each amino acid are rationalized on the basis of attractive intra- and intermolecular non-covalent interactions. The present data are focused on the intrinsic properties of an amino acid - an element which to our knowledge is typically ignored, as larger models are always used for the sake of similarity to real biological polypeptides. (C) 2014 Elsevier Inc. All rights reserved.", publisher = "Elsevier Science Inc, New York", journal = "Journal of Molecular Graphics and Modelling", title = "Computational study of protein secondary structure elements: Ramachandran plots revisited", volume = "50", pages = "125-133", doi = "10.1016/j.jmgm.2014.04.001" }
Carrascoza, F., Zarić, S. D.,& Silaghi-Dumitrescu, R.. (2014). Computational study of protein secondary structure elements: Ramachandran plots revisited. in Journal of Molecular Graphics and Modelling Elsevier Science Inc, New York., 50, 125-133. https://doi.org/10.1016/j.jmgm.2014.04.001
Carrascoza F, Zarić SD, Silaghi-Dumitrescu R. Computational study of protein secondary structure elements: Ramachandran plots revisited. in Journal of Molecular Graphics and Modelling. 2014;50:125-133. doi:10.1016/j.jmgm.2014.04.001 .
Carrascoza, Francisco, Zarić, Snežana D., Silaghi-Dumitrescu, Radu, "Computational study of protein secondary structure elements: Ramachandran plots revisited" in Journal of Molecular Graphics and Modelling, 50 (2014):125-133, https://doi.org/10.1016/j.jmgm.2014.04.001 . .