Anatomy of Enzyme Channels

J 2014

Anatomy of Enzyme Channels

PRAVDA, Lukáš; Karel BERKA; Radka SVOBODOVÁ VAŘEKOVÁ; David SEHNAL; Pavel BANÁŠ et. al.

Základní údaje

Originální název

Anatomy of Enzyme Channels

Autoři

PRAVDA, Lukáš; Karel BERKA; Radka SVOBODOVÁ VAŘEKOVÁ; David SEHNAL; Pavel BANÁŠ; Laskowski ROMAN A; Jaroslav KOČA a Michal OTYEPKA

Vydání

BMC Bioinformatics, England, BioMed Central Ltd, 2014, 1471-2105

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.576

Kód RIV

RIV/00216224:14310/14:00077325

Organizační jednotka

Přírodovědecká fakulta

DOI

https://doi.org/10.1186/s12859-014-0379-x

UT WoS

000345944500002

EID Scopus

2-s2.0-84923867540

Klíčová slova anglicky

CATALYTIC SITE ATLAS; ACTIVE-SITE; ION CHANNELS; BIOMACROMOLECULAR CHANNELS; SUBSTRATE PREFERENCES; CYTOCHROMES P450; LIGAND-BINDING; ACCESS TUNNELS; PROTEIN; RESIDUES

Štítky

AKR, kontrola MP, OA, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 28. 4. 2015 09:04, Ing. Andrea Mikešková

Anotace

V originále

Background: Enzyme active sites can be connected to the exterior environment by one or more channels passing through the protein. Despite our current knowledge of enzyme structure and function, surprisingly little is known about how often channels are present or about any structural features such channels may have in common. Results: Here, we analyze the long channels (i.e. > 15 angstrom) leading to the active sites of 4,306 enzyme structures. We find that over 64% of enzymes contain two or more long channels, their typical length being 28 angstrom. We show that amino acid compositions of the channel significantly differ both to the composition of the active site, surface and interior of the protein. Conclusions: The majority of enzymes have buried active sites accessible via a network of access channels. This indicates that enzymes tend to have buried active sites, with channels controlling access to, and egress from, them, and that suggests channels may play a key role in helping determine enzyme substrate.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

MUNI/A/0855/2013, interní kód MU

Název: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace III. (Akronym: FI MAV III.)

Investor: Masarykova univerzita, Rozsáhlé výpočetní systémy: modely, aplikace a verifikace III., DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

PRAVDA, Lukáš; Karel BERKA; Radka SVOBODOVÁ VAŘEKOVÁ; David SEHNAL; Pavel BANÁŠ; Laskowski ROMAN A; Jaroslav KOČA a Michal OTYEPKA. Anatomy of Enzyme Channels. BMC Bioinformatics. England: BioMed Central Ltd, 2014, roč. 15, november, s. "nestránkováno", 8 s. ISSN 1471-2105. Dostupné z: https://doi.org/10.1186/s12859-014-0379-x.

@article{1206148,
   author = {Pravda, Lukáš and Berka, Karel and Svobodová Vařeková, Radka and Sehnal, David and Banáš, Pavel and Roman A, Laskowski and Koča, Jaroslav and Otyepka, Michal},
   article_location = {England},
   article_number = {november},
   doi = {https://doi.org/10.1186/s12859-014-0379-x},
   keywords = {CATALYTIC SITE ATLAS; ACTIVE-SITE; ION CHANNELS; BIOMACROMOLECULAR CHANNELS; SUBSTRATE PREFERENCES; CYTOCHROMES P450; LIGAND-BINDING; ACCESS TUNNELS; PROTEIN; RESIDUES},
   language = {eng},
   issn = {1471-2105},
   journal = {BMC Bioinformatics},
   title = {Anatomy of Enzyme Channels},
   url = {http://www.biomedcentral.com/content/pdf/s12859-014-0379-x.pdf},
   volume = {15},
   year = {2014}
}

TY  - JOUR
ID  - 1206148
AU  - Pravda, Lukáš - Berka, Karel - Svobodová Vařeková, Radka - Sehnal, David - Banáš, Pavel - Roman A, Laskowski - Koča, Jaroslav - Otyepka, Michal
PY  - 2014
TI  - Anatomy of Enzyme Channels
JF  - BMC Bioinformatics
VL  - 15
IS  - november
SP  - "nestránkováno"
EP  - "nestránkováno"
PB  - BioMed Central Ltd
SN  - 14712105
KW  - CATALYTIC SITE ATLAS
KW  - ACTIVE-SITE
KW  - ION CHANNELS
KW  - BIOMACROMOLECULAR CHANNELS
KW  - SUBSTRATE PREFERENCES
KW  - CYTOCHROMES P450
KW  - LIGAND-BINDING
KW  - ACCESS TUNNELS
KW  - PROTEIN
KW  - RESIDUES
UR  - http://www.biomedcentral.com/content/pdf/s12859-014-0379-x.pdf
L2  - http://www.biomedcentral.com/content/pdf/s12859-014-0379-x.pdf
N2  - Background: Enzyme active sites can be connected to the exterior environment by one or more channels passing through the protein. Despite our current knowledge of enzyme structure and function, surprisingly little is known about how often channels are present or about any structural features such channels may have in common. Results: Here, we analyze the long channels (i.e. > 15 angstrom) leading to the active sites of 4,306 enzyme structures. We find that over 64% of enzymes contain two or more long channels, their typical length being 28 angstrom. We show that amino acid compositions of the channel significantly differ both to the composition of the active site, surface and interior of the protein. Conclusions: The majority of enzymes have buried active sites accessible via a network of access channels. This indicates that enzymes tend to have buried active sites, with channels controlling access to, and egress from, them, and that suggests channels may play a key role in helping determine enzyme substrate.
ER  -

PRAVDA, Lukáš; Karel BERKA; Radka SVOBODOVÁ VAŘEKOVÁ; David SEHNAL; Pavel BANÁŠ; Laskowski ROMAN A; Jaroslav KOČA a Michal OTYEPKA. Anatomy of Enzyme Channels. \textit{BMC Bioinformatics}. England: BioMed Central Ltd, 2014, roč.~15, november, s.~''nestránkováno'', 8 s. ISSN~1471-2105. Dostupné z: https://doi.org/10.1186/s12859-014-0379-x.

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