The CH-pi Interaction in Protein-Carbohydrate Binding:
Bioinformatics and In Vitro Quantification

J 2020

The CH-pi Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification

HOUSER, Josef, Stanislav KOZMON, Deepti MISHRA, Zuzana HAMMEROVÁ, Michaela WIMMEROVÁ et. al.

Basic information

Original name

The CH-pi Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification

Authors

HOUSER, Josef (203 Czech Republic, belonging to the institution), Stanislav KOZMON (703 Slovakia, belonging to the institution), Deepti MISHRA (356 India, belonging to the institution), Zuzana HAMMEROVÁ (203 Czech Republic, belonging to the institution), Michaela WIMMEROVÁ (203 Czech Republic, guarantor, belonging to the institution) and Jaroslav KOČA (203 Czech Republic, belonging to the institution)

Edition

Chemistry - A European Journal, WEINHEIM, Wiley, 2020, 0947-6539

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

Switzerland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 5.236

RIV identification code

RIV/00216224:14740/20:00114712

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1002/chem.202000593

UT WoS

000552350100001

Keywords in English

carbohydrates; density functional calculations; glycosylation; ligand binding; stacking interaction

Abstract

V originále

The molecular recognition of carbohydrates by proteins plays a key role in many biological processes including immune response, pathogen entry into a cell, and cell-cell adhesion (e.g., in cancer metastasis). Carbohydrates interact with proteins mainly through hydrogen bonding, metal-ion-mediated interaction, and non-polar dispersion interactions. The role of dispersion-driven CH-pi interactions (stacking) in protein-carbohydrate recognition has been underestimated for a long time considering the polar interactions to be the main forces for saccharide interactions. However, over the last few years it turns out that non-polar interactions are equally important. In this study, we analyzed the CH-pi interactions employing bioinformatics (data mining, structural analysis), several experimental (isothermal titration calorimetry (ITC), X-ray crystallography), and computational techniques. The Protein Data Bank (PDB) has been used as a source of structural data. The PDB contains over 12 000 protein complexes with carbohydrates. Stacking interactions are very frequently present in such complexes (about 39 % of identified structures). The calculations and the ITC measurement results suggest that the CH-pi stacking contribution to the overall binding energy ranges from 4 up to 8 kcal mol(-1). All the results show that the stacking CH-pi interactions in protein-carbohydrate complexes can be considered to be a driving force of the binding in such complexes.

Links

GA18-18964S, research and development project

Name: Lektiny a jejich úloha v interakci patogen/hostitel a buněčném rozpoznávání

Investor: Czech Science Foundation

LM2015085, research and development project

Name: CERIT Scientific Cloud (Acronym: CERIT-SC)

Investor: Ministry of Education, Youth and Sports of the CR, CERIT Scientific Cloud

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

LTC17076, research and development project

Name: Interdisciplinární přístup ke studiu biologických systémů na molekulární úrovni

Investor: Ministry of Education, Youth and Sports of the CR, Interdisciplinary approach to study biological systems at the molecular level, INTER-COST

90042, large research infrastructures

Name: CESNET II

90127, large research infrastructures

Name: CIISB II

Citovat

HOUSER, Josef, Stanislav KOZMON, Deepti MISHRA, Zuzana HAMMEROVÁ, Michaela WIMMEROVÁ and Jaroslav KOČA. The CH-pi Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification. Chemistry - A European Journal. WEINHEIM: Wiley, 2020, vol. 26, No 47, p. 10769-10780. ISSN 0947-6539. Available from: https://dx.doi.org/10.1002/chem.202000593.

@article{1731621,
   author = {Houser, Josef and Kozmon, Stanislav and Mishra, Deepti and Hammerová, Zuzana and Wimmerová, Michaela and Koča, Jaroslav},
   article_location = {WEINHEIM},
   article_number = {47},
   doi = {http://dx.doi.org/10.1002/chem.202000593},
   keywords = {carbohydrates; density functional calculations; glycosylation; ligand binding; stacking interaction},
   language = {eng},
   issn = {0947-6539},
   journal = {Chemistry - A European Journal},
   title = {The CH-pi Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification},
   url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/chem.202000593},
   volume = {26},
   year = {2020}
}

TY  - JOUR
ID  - 1731621
AU  - Houser, Josef - Kozmon, Stanislav - Mishra, Deepti - Hammerová, Zuzana - Wimmerová, Michaela - Koča, Jaroslav
PY  - 2020
TI  - The CH-pi Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification
JF  - Chemistry - A European Journal
VL  - 26
IS  - 47
SP  - 10769-10780
EP  - 10769-10780
PB  - Wiley
SN  - 09476539
KW  - carbohydrates
KW  - density functional calculations
KW  - glycosylation
KW  - ligand binding
KW  - stacking interaction
UR  - https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/chem.202000593
L2  - https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/chem.202000593
N2  - The molecular recognition of carbohydrates by proteins plays a key role in many biological processes including immune response, pathogen entry into a cell, and cell-cell adhesion (e.g., in cancer metastasis). Carbohydrates interact with proteins mainly through hydrogen bonding, metal-ion-mediated interaction, and non-polar dispersion interactions. The role of dispersion-driven CH-pi interactions (stacking) in protein-carbohydrate recognition has been underestimated for a long time considering the polar interactions to be the main forces for saccharide interactions. However, over the last few years it turns out that non-polar interactions are equally important. In this study, we analyzed the CH-pi interactions employing bioinformatics (data mining, structural analysis), several experimental (isothermal titration calorimetry (ITC), X-ray crystallography), and computational techniques. The Protein Data Bank (PDB) has been used as a source of structural data. The PDB contains over 12 000 protein complexes with carbohydrates. Stacking interactions are very frequently present in such complexes (about 39 % of identified structures). The calculations and the ITC measurement results suggest that the CH-pi stacking contribution to the overall binding energy ranges from 4 up to 8 kcal mol(-1). All the results show that the stacking CH-pi interactions in protein-carbohydrate complexes can be considered to be a driving force of the binding in such complexes.
ER  -

HOUSER, Josef, Stanislav KOZMON, Deepti MISHRA, Zuzana HAMMEROVÁ, Michaela WIMMEROVÁ and Jaroslav KOČA. The CH-pi Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification. \textit{Chemistry - A European Journal}. WEINHEIM: Wiley, 2020, vol.~26, No~47, p.~10769-10780. ISSN~0947-6539. Available from: https://dx.doi.org/10.1002/chem.202000593.

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