Zinc-finger hydrolase: Computational selection of a linker and a sequence towards metal activation with a synthetic alpha beta beta protein

Abstract

The zinc-finger protein is targeted for computational redesign as a hydrolase enzyme. Successful in having zinc activated for hydrolase function, the study validates the stepwise approach to having the protein tuned in main-chain structure stereochemically and over side chains chemically. A leucine homopolypeptide, harboring histidines to tri coordinate zinc and D-amino-acid-nucleated alpha-helix and beta-hairpin building blocks of an alpha beta beta protein, is taken up for modeling, first with CYANA, in a mixed-chirality linker between the building blocks, and then with IDeAS, in a sequence over side chains. The designed mixed-chirality polypeptide structure is proven to order as an intended alpha beta beta fold and capture zinc to activate its role as a hydrolase catalyst. The design approach to have protein folds defined stereochemically and receptor and catalysis functions defined chemically is presented, and illustrates L-and D-alpha-amino-acid structures as the alphabet integrating chemical-and stereochemical-structure variables as its letters.