Computational Analysis of Protein Tunnels and Channels
Authors
Brezovský J., Kozlíková B., Damborský J.
Source
Protein Engineering: Methods and Protocols, Methods in Molecular Biology, Uwe T. Bornscheuer and Matthias Hohne (eds.), vol. 1685
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 computa-
tional 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.
Source
Brezovský J., Kozlíková B., Damborský J.:
Computational Analysis of Protein Tunnels and Channels,
Protein Engineering: Methods and Protocols, Methods in Molecular Biology, Uwe T. Bornscheuer and Matthias Hohne (eds.),, vol. 1685, pp 25-42, 2018,
978-1-4939-7364-4. [PDF]