Metamorphic proteins mediate evolutionary transitions of structure

Abstract

The primary sequence of proteins usually dictates a single tertiary and quaternary structure. However, certain proteins undergo reversible backbone rearrangements. Such metamorphic proteins provide a means of facilitating the evolution of new folds and architectures. However, because natural folds emerged at the early stages of evolution, the potential role of metamorphic intermediates in mediating evolutionary transitions of structure remains largely unexplored. We evolved a set of new proteins based on ∼100 amino acid fragments derived from tachylectin-2-a monomeric, 236 amino acids, five-bladed β-propeller. Their structures reveal a unique pentameric assembly and novel β-propeller structures. Although identical in sequence, the oligomeric subunits adopt two, or even three, different structures that together enable the pentameric assembly of two propellers connected via a small linker. Most of the subunits adopt a wild-type-like structure within individual five-bladed propellers. However, the bridging subunits exhibit domain swaps and asymmetric strand exchanges that allow them to complete the two propellers and connect them. Thus, the modular and metamorphic nature of these subunits enabled dramatic changes in tertiary and quaternary structure, while maintaining the lectin function. These oligomers therefore comprise putative intermediates via which β-propellers can evolve from smaller elements. Our data also suggest that the ability of one sequence to equilibrate between different structures can be evolutionary optimized, thus facilitating the emergence of new structures.beta-propellers | conformational diversity | lectins | oligomerization | protein evolution M aynard-Smith's conjecture of protein evolution dictates that transitions of function and structure occur gradually (by single mutational steps), and smoothly, namely via intermediates that are all functional (1). This restriction imposes a major challenge, because mutational steps may create large structural perturbations that need to be tolerated while retaining function (2). In single domain proteins, significant "cut and paste" structural changes perturb a well-packed hydrophobic core (3, 4). Evolutionary transitions from one folded and functional domain structure into a new one should therefore (or must, by default, if one follows Maynard-Smith's conjecture) involve intermediates able to adopt more than one structure (5, 6). It has been also speculated that evolutionary intermediates of many existing folds, and folds that show internal symmetry in particular, were oligomeric assemblies of smaller subunits. Interestingly, most of the reported "metamorphic" proteins-proteins adopting more than one fold (7), are oliogomers in at least one of the two folds they adopt (8-10). Oligomerization may therefore serve as a means of augmenting structural metamorphism and of facilitating the emergence of new folds (11). However, metamorphic proteins are very rarely identified, and their evolutionary relevance is yet to be established. The involvement of struct...

A polymetamorphic protein

“…In a related but distinct example, Yadid et al 14 recently described a sequence with three subunit folding topologies within a single folded oligomeric structure. 14 Proteins that exhibit radical structural polymorphism, involving simultaneous or successive population of more than two specific folded backbone topologies in a single sequence or a series of variants, might reasonably be called 'polymetamorphic proteins'. Dill 35 referred to sequences with multiple native structures as 'gemisch' sequences, but this usage was clearly intended to encompass the detailed specificity of the native structure as well as large shifts in folding topology; thus, a protein with an intrinsically disordered or 'molten' native state might also be a gemisch sequence.…”

“…[6][7][8][9][10] Design and selection experiments have encoded two protein folds in a single amino-acid sequence or in nearly identical sequences. [11][12][13][14] Yadid et al recently evolved fragments of tachylectin-2, a monomer, into pentamers that contain three different backbone topologies. 14 Limited mutagenesis of small natural proteins populates alternate folds in certain cases, [15][16][17] and accumulation of simple mutations can lead to evolution of new folds.…”

“…[11][12][13][14] Yadid et al recently evolved fragments of tachylectin-2, a monomer, into pentamers that contain three different backbone topologies. 14 Limited mutagenesis of small natural proteins populates alternate folds in certain cases, [15][16][17] and accumulation of simple mutations can lead to evolution of new folds. [17][18][19] Some modeling studies have found numerous close approaches or paths between different structures in sequence space [20][21][22][23] and even sequence ''supernetworks'' 24,25 that span many protein folds.…”

Computational design of a self-assembling symmetrical β-propeller protein

“…In the case of β-trefoil proteins, a design procedure based on Rosetta proved much more efficient than directed evolution methods at producing a symmetrical structure (15). Structural plasticity and domain swapping (16,17) allow such extended proteins to adopt novel tertiary and quaternary structures (18), but to date there is no report of a perfectly symmetrical β-propeller protein.…”

“…Yadid and Tawfik (3,22) screened genetic libraries encoding about 100 amino acid residues from a 236-residue five-bladed propeller (tachylectin-2) in attempts to create a fivefold symmetrical propeller. The initial proteins produced were poorly stable, but subsequent directed evolution to improve expression and folding led to domain-swapped structures through strand exchange (18). An artificial WD40-based repeat protein was designed by Nikkhah et al using computational methods, but this protein failed to fold and adopted a molten globule state (23).…”