Computational Analysis of Protein Tunnels and Channels

C 2017

Computational Analysis of Protein Tunnels and Channels

BREZOVSKÝ, Jan, Barbora KOZLÍKOVÁ a Jiří DAMBORSKÝ

Základní údaje

Originální název

Computational Analysis of Protein Tunnels and Channels

Autoři

BREZOVSKÝ, Jan (203 Česká republika, domácí), Barbora KOZLÍKOVÁ (203 Česká republika, domácí) a Jiří DAMBORSKÝ (203 Česká republika, garant, domácí)

Vydání

New York, PROTEIN ENGINEERING. METHODS AND PROTOCOLS, od s. 25-42, 18 s. 2017

Nakladatel

Springer

Další údaje

Jazyk

angličtina

Typ výsledku

Kapitola resp. kapitoly v odborné knize

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

tištěná verze "print"

Odkazy

URL

Kód RIV

RIV/00216224:14310/17:00106494

Organizační jednotka

Přírodovědecká fakulta

ISBN

978-1-4939-7366-8

Klíčová slova anglicky

Binding; Protein; Tunnel; Channel; Gate; Rational design; Software; CAVER; Transport

Štítky

topvydavatel

Změněno: 5. 3. 2019 11:21, prof. Mgr. Jiří Damborský, Dr.

Anotace

V originále

Protein tunnels connecting the functional buried cavities with bulk solvent and protein channels, enabling the transport through biological membranes, represent the structural features that govern the exchange rates of ligands, ions, and water solvent. Tunnels and channels are present in a vast number of known proteins and provide control over their function. Modification of these structural features by protein engineering frequently provides proteins with improved properties. Here we present a detailed computational protocol employing the CAVER software that is applicable for: (1) the analysis of tunnels and channels in protein structures, and (2) the selection of hot-spot residues in tunnels or channels that can be mutagenized for improved activity, specificity, enantioselectivity, or stability

Návaznosti

LM2015047, projekt VaV

Název: Česká národní infrastruktura pro biologická data (Akronym: ELIXIR-CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Česká národní infrastruktura pro biologická data

LM2015051, projekt VaV

Název: Centrum pro výzkum toxických látek v prostředí (Akronym: RECETOX RI)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Výzkumná infrastruktura RECETOX

LM2015055, projekt VaV

Název: Centrum pro systémovou biologii (Akronym: C4SYS)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, The national infrastructure C4SYS - Centre for Systems Biology

Citovat

BREZOVSKÝ, Jan, Barbora KOZLÍKOVÁ a Jiří DAMBORSKÝ. Computational Analysis of Protein Tunnels and Channels. In Editors: Bornscheuer, Uwe T., Höhne, Matthias. PROTEIN ENGINEERING. METHODS AND PROTOCOLS. New York: Springer, 2017, s. 25-42. ISBN 978-1-4939-7366-8.

@inbook{1503433,
   author = {Brezovský, Jan and Kozlíková, Barbora and Damborský, Jiří},
   address = {New York},
   booktitle = {PROTEIN ENGINEERING. METHODS AND PROTOCOLS},
   editor = {Editors: Bornscheuer, Uwe T., Höhne, Matthias},
   keywords = {Binding; Protein; Tunnel; Channel; Gate; Rational design; Software; CAVER; Transport},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {New York},
   isbn = {978-1-4939-7366-8},
   pages = {25-42},
   publisher = {Springer},
   title = {Computational Analysis of Protein Tunnels and Channels},
   url = {https://loschmidt.chemi.muni.cz/peg/wp-content/uploads/2017/11/book17_brezovsky.pdf},
   year = {2017}
}

TY  - CHAP
ID  - 1503433
AU  - Brezovský, Jan - Kozlíková, Barbora - Damborský, Jiří
PY  - 2017
TI  - Computational Analysis of Protein Tunnels and Channels
VL  - neuveden pro RIV
PB  - Springer
CY  - New York
SN  - 9781493973668
KW  - Binding
KW  - Protein
KW  - Tunnel
KW  - Channel
KW  - Gate
KW  - Rational design
KW  - Software
KW  - CAVER
KW  - Transport
UR  - https://loschmidt.chemi.muni.cz/peg/wp-content/uploads/2017/11/book17_brezovsky.pdf
N2  - Protein tunnels connecting the functional buried cavities with bulk solvent and protein channels, enabling the transport through biological membranes, represent the structural features that govern the exchange rates of ligands, ions, and water solvent. Tunnels and channels are present in a vast number of known proteins and provide control over their function. Modification of these structural features by protein engineering frequently provides proteins with improved properties. Here we present a detailed computational protocol employing the CAVER software that is applicable for: (1) the analysis of tunnels and channels in protein structures, and (2) the selection of hot-spot residues in tunnels or channels that can be mutagenized for improved activity, specificity, enantioselectivity, or stability
ER  -

BREZOVSKÝ, Jan, Barbora KOZLÍKOVÁ a Jiří DAMBORSKÝ. Computational Analysis of Protein Tunnels and Channels. In Editors: Bornscheuer, Uwe T., Höhne, Matthias. \textit{PROTEIN ENGINEERING. METHODS AND PROTOCOLS}. New York: Springer, 2017, s.~25-42. ISBN~978-1-4939-7366-8.

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