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Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations

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2020
Authors
Stanković, Ivana M.
Blagojević Filipović, Jelena P.
Zarić, Snežana D.
Article (Published version)
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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 interactions
Source:
International Journal of Biological Macromolecules, 2020, 157, 1-9
Publisher:
  • 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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http://cherry.chem.bg.ac.rs/handle/123456789/3983
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