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.
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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
Original language English
Type of outcome Chapter(s) of a specialized book
Field of Study 20400 2.4 Chemical engineering
Country of publisher United States of America
Confidentiality degree is not subject to a state or trade secret
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
Tags International impact, Reviewed
Changed by Changed by: Mgr. Marie Šípková, DiS., učo 437722. Changed: 25/10/2021 13:30.
Abstract
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.
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