Anatomy of Enzyme Channels

J 2014

Anatomy of Enzyme Channels

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

Basic information

Original name

Anatomy of Enzyme Channels

Authors

PRAVDA, Lukáš (203 Czech Republic, belonging to the institution), Karel BERKA (203 Czech Republic), Radka SVOBODOVÁ VAŘEKOVÁ (203 Czech Republic, belonging to the institution), David SEHNAL (203 Czech Republic, belonging to the institution), Pavel BANÁŠ (203 Czech Republic, belonging to the institution), Laskowski ROMAN A (826 United Kingdom of Great Britain and Northern Ireland), Jaroslav KOČA (203 Czech Republic, guarantor, belonging to the institution) and Michal OTYEPKA (203 Czech Republic, belonging to the institution)

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 2.576

RIV identification code

RIV/00216224:14310/14:00077325

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1186/s12859-014-0379-x

UT WoS

000345944500002

Keywords in English

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

Abstract

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.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

MUNI/A/0855/2013, interní kód MU

Name: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace III. (Acronym: FI MAV III.)

Investor: Masaryk University, Category A

Citovat

PRAVDA, Lukáš, Karel BERKA, Radka SVOBODOVÁ VAŘEKOVÁ, David SEHNAL, Pavel BANÁŠ, Laskowski ROMAN A, Jaroslav KOČA and Michal OTYEPKA. Anatomy of Enzyme Channels. BMC Bioinformatics. England: BioMed Central Ltd, 2014, vol. 15, november, p. "nestránkováno", 8 pp. ISSN 1471-2105. Available from: https://dx.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 = {http://dx.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 and Michal OTYEPKA. Anatomy of Enzyme Channels. \textit{BMC Bioinformatics}. England: BioMed Central Ltd, 2014, vol.~15, november, p.~''nestránkováno'', 8 pp. ISSN~1471-2105. Available from: https://dx.doi.org/10.1186/s12859-014-0379-x.

Detailed Information on Publication Record