Computational Analysis of Protein Tunnels and Channels

C 2017

Computational Analysis of Protein Tunnels and Channels

BREZOVSKÝ, Jan, Barbora KOZLÍKOVÁ and Jiří DAMBORSKÝ

Basic information

Original name

Computational Analysis of Protein Tunnels and Channels

Authors

BREZOVSKÝ, Jan (203 Czech Republic, belonging to the institution), Barbora KOZLÍKOVÁ (203 Czech Republic, belonging to the institution) and Jiří DAMBORSKÝ (203 Czech Republic, guarantor, belonging to the institution)

Edition

New York, PROTEIN ENGINEERING. METHODS AND PROTOCOLS, p. 25-42, 18 pp. 2017

Publisher

Springer

Other information

Language

English

Type of outcome

Kapitola resp. kapitoly v odborné knize

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

printed version "print"

References:

URL

RIV identification code

RIV/00216224:14310/17:00106494

Organization unit

Faculty of Science

ISBN

978-1-4939-7366-8

Keywords in English

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

Abstract

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

Links

LM2015047, research and development project

Name: Česká národní infrastruktura pro biologická data (Acronym: ELIXIR-CZ)

Investor: Ministry of Education, Youth and Sports of the CR, Czech National Infrastructure for Biological Data

LM2015051, research and development project

Name: Centrum pro výzkum toxických látek v prostředí (Acronym: RECETOX RI)

Investor: Ministry of Education, Youth and Sports of the CR

LM2015055, research and development project

Name: Centrum pro systémovou biologii (Acronym: C4SYS)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

BREZOVSKÝ, Jan, Barbora KOZLÍKOVÁ and 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, p. 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 and 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, p.~25-42. ISBN~978-1-4939-7366-8.

Detailed Information on Publication Record