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Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations
dc.creator | Stanković, Ivana | |
dc.creator | Blagojević Filipović, Jelena P. | |
dc.creator | Zarić, Snežana D. | |
dc.date.accessioned | 2020-05-11T16:18:08Z | |
dc.date.available | 2021-04-05 | |
dc.date.issued | 2020 | |
dc.identifier.issn | 0141-8130 | |
dc.identifier.uri | https://cer.ihtm.bg.ac.rs/handle/123456789/3520 | |
dc.description.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. | en |
dc.publisher | Elsevier | en |
dc.relation | info:eu-repo/grantAgreement/MESTD/Basic Research (BR or ON)/172065/RS// | |
dc.relation | Qatar Foundation for Education, Science and Community Development | |
dc.rights | embargoedAccess | |
dc.source | International Journal of Biological Macromolecules | en |
dc.subject | Carbohydrates | |
dc.subject | Aromatic amino acids | |
dc.subject | Stacking interactions | |
dc.subject | CH/π interactions | |
dc.title | Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations | en |
dc.type | article | en |
dc.rights.license | ARR | en |
dcterms.abstract | Зарић, Снежана Д.; Станковић, Ивана; Благојевић Филиповић, Јелена П.; | |
dc.rights.holder | Elsevier | |
dc.citation.volume | 157 | |
dc.citation.spage | 1 | |
dc.citation.epage | 9 | |
dc.citation.rank | aM21~ | |
dc.description.other | 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] | |
dc.description.other | The published version: [http://cer.ihtm.bg.ac.rs/handle/123456789/3519] | |
dc.identifier.doi | 10.1016/j.ijbiomac.2020.03.251 | |
dc.identifier.fulltext | https://cer.ihtm.bg.ac.rs/bitstream/id/16437/j.ijbiomac.2020.03.251.pdf | |
dc.identifier.scopus | 2-s2.0-85083772036 | |
dc.identifier.wos | 000541109300001 | |
dc.type.version | acceptedVersion |