Computational Analysis of Protein Tunnels and Channels

C 2018

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, NY, Protein Engineering. Methods in Molecular Biology, p. 25-42, 18 pp. 1685, 2018

Publisher

Humana Press

Other information

Language

English

Type of outcome

Kapitola resp. kapitoly v odborné knize

Field of Study

20400 2.4 Chemical engineering

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

printed version "print"

RIV identification code

RIV/00216224:14310/18:00102092

Organization unit

Faculty of Science

ISBN

978-1-4939-7364-4

DOI

http://dx.doi.org/10.1007/978-1-4939-7366-8_3

UT WoS

000684272200004

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.

Citovat

BREZOVSKÝ, Jan, Barbora KOZLÍKOVÁ and Jiří DAMBORSKÝ. Computational Analysis of Protein Tunnels and Channels. In Bornscheuer U., Höhne M. Protein Engineering. Methods in Molecular Biology. New York, NY: Humana Press, 2018, p. 25-42. 1685. ISBN 978-1-4939-7364-4. Available from: https://dx.doi.org/10.1007/978-1-4939-7366-8_3.

@inbook{1394439,
   author = {Brezovský, Jan and Kozlíková, Barbora and Damborský, Jiří},
   address = {New York, NY},
   booktitle = {Protein Engineering. Methods in Molecular Biology},
   doi = {http://dx.doi.org/10.1007/978-1-4939-7366-8_3},
   editor = {Bornscheuer U., Höhne M.},
   keywords = {Binding;Protein;Tunnel;Channel;Gate;Rational design;Software;CAVER;Transport},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {New York, NY},
   isbn = {978-1-4939-7364-4},
   pages = {25-42},
   publisher = {Humana Press},
   title = {Computational Analysis of Protein Tunnels and Channels},
   year = {2018}
}

TY  - CHAP
ID  - 1394439
AU  - Brezovský, Jan - Kozlíková, Barbora - Damborský, Jiří
PY  - 2018
TI  - Computational Analysis of Protein Tunnels and Channels
VL  - 1685
PB  - Humana Press
CY  - New York, NY
SN  - 9781493973644
KW  - Binding;Protein;Tunnel;Channel;Gate;Rational design;Software;CAVER;Transport
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 Bornscheuer U., Höhne M. \textit{Protein Engineering. Methods in Molecular Biology}. New York, NY: Humana Press, 2018, p.~25-42. 1685. ISBN~978-1-4939-7364-4. Available from: https://dx.doi.org/10.1007/978-1-4939-7366-8\_{}3.

Detailed Information on Publication Record