Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds

Roessler, Christian G.; Hall, Branwen M.; Anderson, William J.; Ingram, Wendy Marie; Roberts, S.A.; Montfort, W.R.; Cordes, Matthew

doi:10.1073/pnas.0711589105

Cited by 84 publications

(130 citation statements)

References 49 publications

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“…If a fold switch occurs in nature, sequences rapidly diverge thereafter. Lymphotactin and the Cro transcription factors seem to be 2 natural proteins that have been ''caught in the act,'' however (27,28).…”

Section: Discussionmentioning

confidence: 99%

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A minimal sequence code for switching protein structure and function

Alexander

He²,

Chen³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

231

330

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We present here a structural and mechanistic description of how a protein changes its fold and function, mutation by mutation. Our approach was to create 2 proteins that (i) are stably folded into 2 different folds, (ii) have 2 different functions, and (iii) are very similar in sequence. In this simplified sequence space we explore the mutational path from one fold to another. We show that an IgG-binding, 4␤؉␣ fold can be transformed into an albumin-binding, 3-␣ fold via a mutational pathway in which neither function nor native structure is completely lost. The stabilities of all mutants along the pathway are evaluated, key high-resolution structures are determined by NMR, and an explanation of the switching mechanism is provided. We show that the conformational switch from 4␤؉␣ to 3-␣ structure can occur via a single amino acid substitution. On one side of the switch point, the 4␤؉␣ fold is >90% populated (pH 7.2, 20°C). A single mutation switches the conformation to the 3-␣ fold, which is >90% populated (pH 7.2, 20°C). We further show that a bifunctional protein exists at the switch point with affinity for both IgG and albumin.evolution ͉ NMR ͉ protein design ͉ protein folding

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Section: Discussionmentioning

confidence: 99%

“…Each conformation has a different binding function. In addition, natural Cro transcription factors exist with 40% identity but different structures for the 25 aa at their C-termini (28).…”

Section: Discussionmentioning

confidence: 99%

A minimal sequence code for switching protein structure and function

Alexander

He²,

Chen³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

231

330

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“…The involvement of structural metamorphism in fold transitions has been reported for a small cysteine-rich domain (12). Different folds have been observed for natural proteins that are close in sequence (40% identity) (9) or artificially designed proteins that are even closer (88% identity, up to a single amino acid difference) (13,14). Here we show that fragments of ∼100-amino acid length that were truncated from a naturally occurring monomeric protein of 236 amino acids assemble into functional oligomers via the metamorphism of their monomeric subunits.…”

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confidence: 99%

“…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)(9)(10). Oligomerization may therefore serve as a means of augmenting structural metamorphism and of facilitating the emergence of new folds (11).…”

mentioning

confidence: 99%

Metamorphic proteins mediate evolutionary transitions of structure

Yadid

Kirshenbaum²,

Sharon³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

100

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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...

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“…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. In addition, sequences with two folds or functions may confer a fitness advantage under certain models of adaptive evolution.…”

Section: Introductionmentioning

confidence: 99%

A polymetamorphic protein

et al. 2013

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Arc repressor is a homodimeric protein with a ribbon-helix-helix fold. A single polar-tohydrophobic substitution (N11L) at a solvent-exposed position leads to population of an alternate dimeric fold in which 3 10 helices replace a b-sheet. Here we find that the variant Q9V/N11L/R13V (S-VLV), with two additional polar-to-hydrophobic surface mutations in the same b-sheet, forms a highly stable, reversibly folded octamer with approximately half the©a-helical content of wild-type Arc. At low protein concentration and low ionic strength, S-VLV also populates both dimeric topologies previously observed for N11L, as judged by NMR chemical shift comparisons. Thus, accumulation of simple hydrophobic mutations in Arc progressively reduces fold specificity, leading first to a sequence with two folds and then to a manifold bridge sequence with at least three different topologies. Residues 9-14 of S-VLV form a highly hydrophobic stretch that is predicted to be amyloidogenic, but we do not observe aggregates of higher order than octamer. Increases in sequence hydrophobicity can promote amyloid aggregation but also exert broader and more complex effects on fold specificity. Altered native folds, changes in fold coupled to oligomerization, toxic pre-amyloid oligomers, and amyloid fibrils may represent a near continuum of accessible alternatives in protein structure space.

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Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds

Cited by 84 publications

References 49 publications

A minimal sequence code for switching protein structure and function

A minimal sequence code for switching protein structure and function

Metamorphic proteins mediate evolutionary transitions of structure

A polymetamorphic protein

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