Metal templated design of protein interfaces

Abstract

Metal coordination is a key structural and functional component of a large fraction of proteins. Given this dual role we considered the possibility that metal coordination may have played a templating role in the early evolution of protein folds and complexes. We describe here a rational design approach, Metal Templated Interface Redesign (MeTIR), that mimics the time course of a hypothetical evolutionary pathway for the formation of stable protein assemblies through an initial metal coordination event. Using a folded monomeric protein, cytochrome cb 562 , as a building block we show that its non-self-associating surface can be made self-associating through a minimal number of mutations that enable Zn coordination. The protein interfaces in the resulting Zn-directed, D 2 -symmetrical tetramer are subsequently redesigned, yielding unique protein architectures that self-assemble in the presence or absence of metals. Aside from its evolutionary implications, MeTIR provides a route to engineer de novo protein interfaces and metal coordination environments that can be tuned through the extensive noncovalent bonding interactions in these interfaces.evolution | metal coordination | protein self-assembly | protein-protein interactions | templating

An approach to crystallizing proteins by metal‐mediated synthetic symmetrization

“…Such coordination geometries are commonly found in proteins 33,54 and have been engineered previously. [37][38][39][40][41][42] On the basis of the crystal structures of T4L and MBP in each protein, we chose three pairs of solvent-accessible residues that are located close to the ends of helices (Fig. 1).…”

“…37 The crystal structure of this complex reveals a trimer of Atx1 molecules mediated through the bound tetrathiomolybdate molecule. Tezcan and coworkers [38][39][40][41][42] have studied metaldirected protein self-assembly on the model protein, cytochrome b 562 , focusing primarily on the evolution of metal coordination in protein folds and complexes. Their work has shown that by introducing histidine mutations on the alpha helical surface of cytochrome b 562 , the protein can oligomerize to form dimers to tetramers, all of which are mediated through metal binding.…”

EDITORIAL (Hot Topic: Recognition of Functional Roles of Free Radicals)

“…Protein-folding malfunctions play key roles in numbers of disorders and the metal coordination is a key structural and functional factor in most proteins [12]. It is more probable that various stresses, for example, can produce defective structure formations of proteins that perturb homeostasis of transition metals (mainly Cu + or Fe…”

Metal ions as matchmakers for proteins

“…Despite these successes, few studies have addressed the issue of how two proteins with few interfacial interactions are able to find each other by overcoming the entropic barriers in early events of protein structural evolution. In this issue, Salgado et al (1) propose and demonstrate that metal ions could possibly fulfill such a role by being a matchmaker. In a strategy called metal templated interface redesign (MeTIR), these investigators first designed histidines into the interface of cytochrome cb 562 , a monomeric protein even at millimolar concentration, to allow Zn 2+ -histidine coordination to bring monomeric cytochrome cb 562 together.…”

“…Matchmakers bring together two people who otherwise have little chance of being associated with each other, nurture the closeness between the two parties by enhancing their commonality and smoothing out their differences, and then quietly disappear after the marriage. In this issue, Salgado et al (1) describe such a matchmaker for single-domain proteins, with significant implications for protein structural evolution and design ( Fig. 1).…”