a 2012

Exploring the Nature of Carbohydrate-Aromatic Dispersion Interactions via Sophisticated Computational Chemistry Tools

KOZMON, Stanislav, Radek MATUŠKA, Vojtěch SPIWOK and Jaroslav KOČA

Basic information

Original name

Exploring the Nature of Carbohydrate-Aromatic Dispersion Interactions via Sophisticated Computational Chemistry Tools

Authors

KOZMON, Stanislav (703 Slovakia, belonging to the institution), Radek MATUŠKA (203 Czech Republic, belonging to the institution), Vojtěch SPIWOK (203 Czech Republic) and Jaroslav KOČA (203 Czech Republic, guarantor, belonging to the institution)

Edition

4-th EUCheMS Chemistry Congress, 2012

Other information

Language

English

Type of outcome

Konferenční abstrakt

Field of Study

10600 1.6 Biological sciences

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

RIV identification code

RIV/00216224:14310/12:00058656

Organization unit

Faculty of Science

Keywords in English

Dispersion interaction carbohydrates CH-pi interaction benzene naphtalene
Změněno: 4/4/2013 17:56, Mgr. Radek Matuška

Abstract

V originále

There are several ways how saccharides interact with proteins. The role of dispersion-driven CH-pi interactions in protein-carbohydrate interactions has been underestimated for a long time. This type of interaction occurs between carbohydrate apolar faces and aromatic amino-acid residues. We introduce first systematic study of CH-pi interactions between selected carbohydrates and aromatic amino-acid models: benzene and naphtalene. 3D interaction energy (Eint) scan was performed to elucidate interaction energy maps for carbohydrate-benzene interaction. Resulting most stable complexes were reoptimized and their Eint were refined at highly-sophisticated level. To study possible degree of additivity, we used geometries of carbohydrate-benzene complexes to build-up monodentate (interaction with one CH-group) and bidentate (interaction with two CH-groups) carbohydrate-naphtalene complexes. Also these complexes underwent the optimization and energy refinement procedure as described. Results show Eint in carbohydrate-benzene complex up to -5,40 kcal/mol, which corresponds to medium-strong hydrogen bond. We localized most attractive regions where the Eint is highest – the strongest interaction is localized above and under CH-groups of carbohydrate. Additionally, benzene can recognize the specific hydrogens of carbohydrate in specific ideal distance (|(C)H-pi| distance around 2,3 A). The aromatic ring is coplanar with the carbohydrate cycle. Localization of the strongest interaction regions for carbohydrate-benzene complex lead us to idea about possible additivity of the CH-pi interaction. Therefore, Eint of bidentate carbohydrate-napthalene complexes were analyzed. The hypothesis of total additivity of the interaction was not confirmed. However, the Eint exhibits certain degree of additivity. The Eint of bidentate complex (ranging up to -8,20 kcal/mol) forms 2/3 of sum of Eint of monodentate ones and 4/5 of sum of Eint of carbohydrate-benzene complexes.

Links

CZ.1.05/1.1.00/02.0068, interní kód MU
Name: CEITEC - středoevropský technologický institut (Acronym: CEITEC)
Investor: Ministry of Education, Youth and Sports of the CR, CEITEC - Central European Institute of Technology, 1.1 European Centres of Excellence
GD301/09/H004, research and development project
Name: Molekulární a strukturní biologie vybraných cytostatik. Od mechanistických studií k chemoterapii rakoviny
Investor: Czech Science Foundation
MSM0021622413, plan (intention)
Name: Proteiny v metabolismu a při interakci organismů s prostředím
Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment
2SGA2747, interní kód MU
Name: Saccharide - protein dispersion interactions involved in the bacterial recognition processes (Acronym: SaProDI)
Investor: South-Moravian Region, Incoming grants