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; Stanislav KOZMON; Deepti MISHRA; Zuzana HAMMEROVÁ; Michaela WIMMEROVÁ a Jaroslav KOČA

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

https://doi.org/10.1002/chem.202000593

UT WoS

000552350100001

EID Scopus

2-s2.0-85088650259

Klíčová slova anglicky

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

Štítky

14313050, 143160, 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://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 = {https://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://doi.org/10.1002/chem.202000593.

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