ZiCo:  A Peptide Designed to Switch Folded State upon Binding Zinc

Cerasoli, Eleonora; Sharpe, B.K.; Woolfson, Derek N.

doi:10.1021/ja0543604

Cited by 101 publications

(87 citation statements)

References 32 publications

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“…In the prion protein example, the driving force for the conformational switch from monomer to aggregate is extensive interaction of the edges of outer ␤-strands in the aggregated state. Metal binding has also been demonstrated to mediate major changes in secondary, tertiary, and quaternary structure in computationally designed proteins (30)(31)(32). Although our results show a switch from one monomeric fold into another, the energetic situation is similar in some ways to conformation switching driven by ligand binding.…”

Section: Discussionmentioning

confidence: 50%

A minimal sequence code for switching protein structure and function

Alexander

He²,

Chen³

et al. 2009

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

234

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: 50%

A minimal sequence code for switching protein structure and function

Alexander

He²,

Chen³

et al. 2009

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

234

330

View full text Add to dashboard Cite

show abstract

“…Furthermore, monomeric proteins sometimes can assume alternative conformations in a multimeric form. This is observed in prion proteins and with monomeric and dimeric forms of the chemokine lymphotactin (30) and also with proteins designed to switch conformation and quaternary structure in the presence of a transition metal (31,32). It has also been shown that five mutations to the core of G B result in a conformational change to a stable, intertwined tetrameric state (33).…”

Section: Discussionmentioning

confidence: 96%

The design and characterization of two proteins with 88% sequence identity but different structure and function

Alexander

Chen

et al. 2007

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

181

192

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To identify a simplified code for conformational switching, we have redesigned two natural proteins to have 88% sequence identity but different tertiary structures: a 3-␣ helix fold and an ␣/␤ fold. We describe the design of these homologous heteromorphic proteins, their structural properties as determined by NMR, their conformational stabilities, and their affinities for their respective ligands: IgG and serum albumin. Each of these proteins is completely folded at 25°C, is monomeric, and retains the native binding activity. The complete binding epitope for both ligands is encoded within each of the proteins. The IgG-binding epitope is functional only in the ␣/␤ fold, and the albumin-binding epitope is functional only in the 3-␣ fold. These results demonstrate that two monomeric folds and two different functions can be encoded with only 12% of the amino acids in a protein (7 of 56). The fact that 49 aa in these proteins are compatible with both folds shows that the essential information determining a fold can be highly concentrated in a few amino acids and that a very limited subset of interactions in the protein can tip the balance from one monomer fold to another. This delicate balance helps explain why protein structure prediction is so challenging. Furthermore, because a few mutations can result in both new conformation and new function, the evolution of new folds driven by natural selection for alternative functions may be much more probable than previously recognized.evolution ͉ folding ͉ NMR ͉ protein design ͉ protein structure

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“…The CD spectrum of RG13 changes only slightly in the presence of zinc, suggesting that zinc-binding induces more subtle changes in structure than those observed in designed zinc-dependent conformational switches (Cerasoli et al 2005; Ambroggio and Kuhlman 2006). RG13's K i and K d for Zn 2+ match, suggesting the Zn 2+ -binding sites being observed by the two methods are the same.…”

Section: Allosteric Signaling In Rg13mentioning

confidence: 96%

Ligand binding and allostery can emerge simultaneously

et al. 2007

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A heterotropic allosteric effect involves an effector molecule that is distinct from the substrate or ligand of the protein. How heterotropic allostery originates is an unanswered question. We have previously created several heterotropic allosteric enzymes by recombining the genes for TEM1 b-lactamase (BLA) and maltose binding protein (MBP) to create BLAs that are positively or negatively regulated by maltose. We show here that one of these engineered enzymes has ;10 6 M À1 affinity for Zn 2+, a property that neither of the parental proteins possesses. Furthermore, Zn 2+ is a negative effector that noncompetitively switches off b-lactam hydrolysis activity. Mutagenesis experiments indicate that the Zn 2+ -binding site does not involve a histidine or a cysteine, which is atypical of natural Zn 2+ -binding sites. These studies also implicate helices 1 and 12 of the BLA domain in allosteric signal propagation. These results support a model for the evolution of heterotropic allostery in which effector affinity and allosteric signaling emerge simultaneously.

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ZiCo: A Peptide Designed to Switch Folded State upon Binding Zinc

Cited by 101 publications

References 32 publications

A minimal sequence code for switching protein structure and function

A minimal sequence code for switching protein structure and function

The design and characterization of two proteins with 88% sequence identity but different structure and function

Ligand binding and allostery can emerge simultaneously

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