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.

Základní údaje

Originální název

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

Autoři

HOUSER, Josef (203 Česká republika, domácí), Stanislav KOZMON (703 Slovensko, domácí), Deepti MISHRA (356 Indie, domácí), Zuzana HAMMEROVÁ (203 Česká republika, domácí), Michaela WIMMEROVÁ (203 Česká republika, garant, domácí) a Jaroslav KOČA (203 Česká republika, domácí)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Švýcarsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.236

Kód RIV

RIV/00216224:14740/20:00114712

Organizační jednotka

Středoevropský technologický institut

DOI

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

UT WoS

000552350100001

Klíčová slova anglicky

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

Štítky

CF BIC, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 27. 10. 2024 15:07, Ing. Martina Blahová

Anotace

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.

Návaznosti

GA18-18964S, projekt VaV

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

Investor: Grantová agentura ČR, Lektiny a jejich úloha v interakci patogen/hostitel a buněčném rozpoznávání

LM2015085, projekt VaV

Název: CERIT Scientific Cloud (Akronym: CERIT-SC)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CERIT Scientific Cloud

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

LTC17076, projekt VaV

Název: Interdisciplinární přístup ke studiu biologických systémů na molekulární úrovni

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Interdisciplinární přístup ke studiu biologických systémů na molekulární úrovni, INTER-COST

90042, velká výzkumná infrastruktura

Název: CESNET II

90127, velká výzkumná infrastruktura

Název: CIISB II

Citovat

HOUSER, Josef, Stanislav KOZMON, Deepti MISHRA, Zuzana HAMMEROVÁ, Michaela WIMMEROVÁ a Jaroslav KOČA. The CH-pi Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification. Chemistry - A European Journal. WEINHEIM: Wiley, 2020, roč. 26, č. 47, s. 10769-10780. ISSN 0947-6539. Dostupné z: 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 a Jaroslav KOČA. The CH-pi Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification. \textit{Chemistry - A European Journal}. WEINHEIM: Wiley, 2020, roč.~26, č.~47, s.~10769-10780. ISSN~0947-6539. Dostupné z: https://dx.doi.org/10.1002/chem.202000593.

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