Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations
Abstract
The geometries of the contacts between monosaccharides and aromatic rings of amino acids found in X-ray crystallography structures, in the Protein Data Bank (PDB), were analyzed, while the energies of the interactions were calculated using quantum chemical method. We found 1913 sugar/aromatic ring contacts, 1054 of them (55%) with CH/π interactions and 859 of them (45%) without CH/π interactions. We showed that only the carbohydrate/aromatic contacts with CH/π interactions are preferentially parallel and enable sliding in the plane parallel to aromatic ring. The calculated interaction energies in systems with CH/π interactions are in the range from −1.7 kcal/mol to −6.8 kcal/mol, while in the systems without CH/π interactions are in the range −0.2 to −3.2 kcal/mol. Hence, the binding that does not include CH/π interactions, can also be important for aromatic amino acid and carbohydrate binding processes, since some of these interactions can be as strong as the CH/π interactions. At the... same time, these interactions can be weak enough to enable releasing of small carbohydrate fragments after the enzymatic reaction. The analysis of the protein-substrate patterns showed that every second or third carbohydrate unit in long substrates stacks with protein aromatic amino acids.
Keywords:
Aromatic amino acids / Carbohydrates / CH/π interactions / Stacking interactionsSource:
International Journal of Biological Macromolecules, 2020, 157, 1-9Publisher:
- Elsevier
Note:
- Supplementary material: http://cherry.chem.bg.ac.rs/handle/123456789/3987
- Peer-reviewed manuscript: http://cherry.chem.bg.ac.rs/handle/123456789/3984
DOI: 10.1016/j.ijbiomac.2020.03.251
ISSN: 0141-8130
WoS: 000541109300001
Scopus: 2-s2.0-85083772036
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Institution/Community
Hemijski fakultet / Faculty of ChemistryTY - JOUR AU - Stanković, Ivana M. AU - Blagojević Filipović, Jelena P. AU - Zarić, Snežana D. PY - 2020 UR - https://cherry.chem.bg.ac.rs/handle/123456789/3983 AB - The geometries of the contacts between monosaccharides and aromatic rings of amino acids found in X-ray crystallography structures, in the Protein Data Bank (PDB), were analyzed, while the energies of the interactions were calculated using quantum chemical method. We found 1913 sugar/aromatic ring contacts, 1054 of them (55%) with CH/π interactions and 859 of them (45%) without CH/π interactions. We showed that only the carbohydrate/aromatic contacts with CH/π interactions are preferentially parallel and enable sliding in the plane parallel to aromatic ring. The calculated interaction energies in systems with CH/π interactions are in the range from −1.7 kcal/mol to −6.8 kcal/mol, while in the systems without CH/π interactions are in the range −0.2 to −3.2 kcal/mol. Hence, the binding that does not include CH/π interactions, can also be important for aromatic amino acid and carbohydrate binding processes, since some of these interactions can be as strong as the CH/π interactions. At the same time, these interactions can be weak enough to enable releasing of small carbohydrate fragments after the enzymatic reaction. The analysis of the protein-substrate patterns showed that every second or third carbohydrate unit in long substrates stacks with protein aromatic amino acids. PB - Elsevier T2 - International Journal of Biological Macromolecules T1 - Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations VL - 157 SP - 1 EP - 9 DO - 10.1016/j.ijbiomac.2020.03.251 ER -
@article{ author = "Stanković, Ivana M. and Blagojević Filipović, Jelena P. and Zarić, Snežana D.", year = "2020", abstract = "The geometries of the contacts between monosaccharides and aromatic rings of amino acids found in X-ray crystallography structures, in the Protein Data Bank (PDB), were analyzed, while the energies of the interactions were calculated using quantum chemical method. We found 1913 sugar/aromatic ring contacts, 1054 of them (55%) with CH/π interactions and 859 of them (45%) without CH/π interactions. We showed that only the carbohydrate/aromatic contacts with CH/π interactions are preferentially parallel and enable sliding in the plane parallel to aromatic ring. The calculated interaction energies in systems with CH/π interactions are in the range from −1.7 kcal/mol to −6.8 kcal/mol, while in the systems without CH/π interactions are in the range −0.2 to −3.2 kcal/mol. Hence, the binding that does not include CH/π interactions, can also be important for aromatic amino acid and carbohydrate binding processes, since some of these interactions can be as strong as the CH/π interactions. At the same time, these interactions can be weak enough to enable releasing of small carbohydrate fragments after the enzymatic reaction. The analysis of the protein-substrate patterns showed that every second or third carbohydrate unit in long substrates stacks with protein aromatic amino acids.", publisher = "Elsevier", journal = "International Journal of Biological Macromolecules", title = "Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations", volume = "157", pages = "1-9", doi = "10.1016/j.ijbiomac.2020.03.251" }
Stanković, I. M., Blagojević Filipović, J. P.,& Zarić, S. D.. (2020). Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations. in International Journal of Biological Macromolecules Elsevier., 157, 1-9. https://doi.org/10.1016/j.ijbiomac.2020.03.251
Stanković IM, Blagojević Filipović JP, Zarić SD. Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations. in International Journal of Biological Macromolecules. 2020;157:1-9. doi:10.1016/j.ijbiomac.2020.03.251 .
Stanković, Ivana M., Blagojević Filipović, Jelena P., Zarić, Snežana D., "Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations" in International Journal of Biological Macromolecules, 157 (2020):1-9, https://doi.org/10.1016/j.ijbiomac.2020.03.251 . .