Computational Analysis of Protein Tunnels and Channels

Authors

Brezovsky, J., Kozlikova, B., Damborsky, J.

Book

PROTEIN ENGINEERING. METHODS AND PROTOCOLS.: 25-42

Editor

Bornscheuer, U. T., Höhne, M. (Eds.)

Publisher

Springer, New York

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.

Full text

Citation

Brezovsky, J., Kozlikova, B., Damborsky, J., 2017: Computational Analysis of Protein Tunnels and Channels. In: Bornscheuer, U. T., Höhne, M. (Eds.), Protein Engineering. Methods and Protocols., Springer, New York, pp. 25-42.

Nikola’s Success at SOC
The Dean’s Award for Jan
Gaspar Presented at 18th IUGEN International Winter School
Event Biotechnology Innovations for the Cosmetic Industry
David Presented at ESAB Webinar
Poster Award for Andrea
Zbynek to Present at HTCD2021