Natural enzymes evolved for catalysis in an aqueous environment under mild conditions often do not meet requirements of practical applications. Changes in catalytic activity, specificity, and enantioselectivity of enzymes are typically achieved by targeting the active sites. We have recently proposed that the enzyme engineering strategies should focus both on the active sites and on the access pathways connecting buried active sites with the surrounding solvent. We have demonstrated, using the model enzymes haloalkane dehalogenases, that the concept of engineering access tunnels may lead to proteins with improved activities, stabilities, enantioselectivities and specificities. Engineering a <i>de novo</i> tunnel in the region of the dehalogenase protein without any opening has also been demonstrated. The software tools Caver and CaverDock (http://www.caver.cz/) can be used for analysis of protein tunnels and their exploration by different ligands, HotSpot Wizard (http://loschmidt.chemi.muni.cz/hotspotwizard/) atomatically identifies mutagenesis hot spots and Cavetta (http://www.caver.cz/) enables a rational redesign of tunnels using Rosetta. Several case studies illustrating the applicability of computational design targeting the protein tunnels will be discussed in this presentation.

Design and evolution of gated protein tunnels

254th National Meeting (2017)

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