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:
Carbohydrates / Aromatic amino acids / Stacking interactions / CH/π interactionsSource:
International Journal of Biological Macromolecules, 2020, 157, 1-9Publisher:
- Elsevier BV
Projects:
- Noncovalent interactions of pi-systems and their role in molecular recognition (RS-172065)
- Qatar Foundation for Education, Science and Community Development
Note:
- This is the peer-reviewed version of the article: I.M. Stanković, J.P. Blagojević Filipović and S.D. Zarić, Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations, International Journal of Biological Macromolecules (2020), https://doi.org/10.1016/j.ijbiomac.2020.03.251
- The published version: http://cer.ihtm.bg.ac.rs/handle/123456789/3519
DOI: 10.1016/j.ijbiomac.2020.03.251
ISSN: 0141-8130