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]


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