Stabilizing non-covalent interactions of ligand aromatic moieties and proline in ligand-protein systems
Abstract
Proline, due to its conformational specificity, is known to show some unique properties and has significant functions in the tertiary structure of proteins. It was suggested that proline could have an important influence on some vital interactions in protein as well, by engaging in non-covalent stabilization interactions with some aromatic moieties. In this work, the interactions that occur between proline and some aromatic moieties in ligands were investigated by means of the density functional theory using an exchange-correlation functional capable of taking into account dispersion interactions. The obtained results showed that the stabilization energy between a properly placed proline and an aromatic moiety could be as large as 25 kJ/mol and hence be a significant factor in placing a ligand in binding site of a protein. This indicates that the error in determining the most favorable structure of ligand-protein complexes obtained by usual molecular docking experiments sometimes could... be the result of neglecting this type of interactions.
Keywords:
Ab initio calculations / Non-covalent interactions / Proteins / Molecular modeling / Density functional theorySource:
Monatshefte Fur Chemie, 2015, 146, 2, 389-397Publisher:
- Springer Wien, Wien
Funding / projects:
- Interactions of natural products, their derivatives and coordination compounds with proteins and nucleic acids (RS-MESTD-Basic Research (BR or ON)-172055)
- NATOs Public Diplomacy Division in the framework of Science for Peace project [SfP983638]
Note:
- Supplementary material: http://cherry.chem.bg.ac.rs/handle/123456789/3423
DOI: 10.1007/s00706-014-1357-8
ISSN: 0026-9247
WoS: 000348985900021
Scopus: 2-s2.0-84925463608
Collections
Institution/Community
Hemijski fakultet / Faculty of ChemistryTY - JOUR AU - Jovanović, Milena AU - Gruden-Pavlović, Maja AU - Zlatović, Mario PY - 2015 UR - https://cherry.chem.bg.ac.rs/handle/123456789/1652 AB - Proline, due to its conformational specificity, is known to show some unique properties and has significant functions in the tertiary structure of proteins. It was suggested that proline could have an important influence on some vital interactions in protein as well, by engaging in non-covalent stabilization interactions with some aromatic moieties. In this work, the interactions that occur between proline and some aromatic moieties in ligands were investigated by means of the density functional theory using an exchange-correlation functional capable of taking into account dispersion interactions. The obtained results showed that the stabilization energy between a properly placed proline and an aromatic moiety could be as large as 25 kJ/mol and hence be a significant factor in placing a ligand in binding site of a protein. This indicates that the error in determining the most favorable structure of ligand-protein complexes obtained by usual molecular docking experiments sometimes could be the result of neglecting this type of interactions. PB - Springer Wien, Wien T2 - Monatshefte Fur Chemie T1 - Stabilizing non-covalent interactions of ligand aromatic moieties and proline in ligand-protein systems VL - 146 IS - 2 SP - 389 EP - 397 DO - 10.1007/s00706-014-1357-8 ER -
@article{ author = "Jovanović, Milena and Gruden-Pavlović, Maja and Zlatović, Mario", year = "2015", abstract = "Proline, due to its conformational specificity, is known to show some unique properties and has significant functions in the tertiary structure of proteins. It was suggested that proline could have an important influence on some vital interactions in protein as well, by engaging in non-covalent stabilization interactions with some aromatic moieties. In this work, the interactions that occur between proline and some aromatic moieties in ligands were investigated by means of the density functional theory using an exchange-correlation functional capable of taking into account dispersion interactions. The obtained results showed that the stabilization energy between a properly placed proline and an aromatic moiety could be as large as 25 kJ/mol and hence be a significant factor in placing a ligand in binding site of a protein. This indicates that the error in determining the most favorable structure of ligand-protein complexes obtained by usual molecular docking experiments sometimes could be the result of neglecting this type of interactions.", publisher = "Springer Wien, Wien", journal = "Monatshefte Fur Chemie", title = "Stabilizing non-covalent interactions of ligand aromatic moieties and proline in ligand-protein systems", volume = "146", number = "2", pages = "389-397", doi = "10.1007/s00706-014-1357-8" }
Jovanović, M., Gruden-Pavlović, M.,& Zlatović, M.. (2015). Stabilizing non-covalent interactions of ligand aromatic moieties and proline in ligand-protein systems. in Monatshefte Fur Chemie Springer Wien, Wien., 146(2), 389-397. https://doi.org/10.1007/s00706-014-1357-8
Jovanović M, Gruden-Pavlović M, Zlatović M. Stabilizing non-covalent interactions of ligand aromatic moieties and proline in ligand-protein systems. in Monatshefte Fur Chemie. 2015;146(2):389-397. doi:10.1007/s00706-014-1357-8 .
Jovanović, Milena, Gruden-Pavlović, Maja, Zlatović, Mario, "Stabilizing non-covalent interactions of ligand aromatic moieties and proline in ligand-protein systems" in Monatshefte Fur Chemie, 146, no. 2 (2015):389-397, https://doi.org/10.1007/s00706-014-1357-8 . .