<i>De Novo</i>Design of Mercury-Binding Two- and Three-Helical Bundles

Dieckmann, Gregg R.; MoRorie, D. K.; Tierney, David L.; Utschig, Lisa M.; Singer, Christopher P.; O’Halloran, Thomas V.; Penner‐Hahn, James E.; DeGrado, William F.; Pecoraro, Vincent L.

doi:10.1021/ja964351i

Cited by 158 publications

(263 citation statements)

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“…The substantial research incorporating metal cofactors into designed peptide frameworks has been described in several recent reviews (13-15). Helical scaffolds have been the predominant structural motif used for the incorporation of many types of metal-binding sites, including hemes (16), iron-sulfur clusters (17), dinuclear metal centers (18), copper centers (19,20), and heavy metal-binding trigonal thiolate sites (7,21). ␤-Hairpins and other globular structures that bind As(III), Zn(II), and other metal cofactors have also been designed (22)(23)(24)(25).…”

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confidence: 99%

“…Previously, we have shown that the three-stranded coiled coil TRI peptides [Ac-G(L a K b A c L d E e E f K g ) 4 G-NH 2 ] designed with the heptad repeat strategy, such as TRI L16C (sequences of all peptides are in Table 1), were able to model the unusual trigonal thiolate Hg(II) coordination geometry seen in the MerR metalloregulatory protein (7). We have also examined the binding of the heavy metals Cd(II), Pb(II), and Bi(III) to the TRI peptides to better understand their modes of toxicity (8,9).…”

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Identifying important structural characteristics of arsenic resistance proteins by using designed three-stranded coiled coils

Touw

Nordman

Stuckey³

et al. 2007

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

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154

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Arsenic, a contaminant of water supplies worldwide, is one of the most toxic inorganic ions. Despite arsenic's health impact, there is relatively little structural detail known about its interactions with proteins. Bacteria such as Escherichia coli have evolved arsenic resistance using the Ars operon that is regulated by ArsR, a repressor protein that dissociates from DNA when As(III) binds. This protein undergoes a critical conformational change upon binding As(III) with three cysteine residues. Unfortunately, structures of ArsR with or without As(III) have not been reported. Alternatively, de novo designed peptides can bind As(III) in an endo configuration within a thiolate-rich environment consistent with that proposed for both ArsR and ArsD. We report the structure of the As(III) complex of Coil Ser L9C to a 1.8-Å resolution, providing x-ray characterization of As(III) in a Tris thiolate protein environment and allowing a structural basis by which to understand arsenated ArsR.arsenic-binding proteins ͉ coiled coil peptides ͉ crystallography ͉ heavy metal toxicity ͉ protein design A rsenic toxicity is a worldwide problem as a natural contaminant of water supplies. Despite the fact that it is a human toxin and carcinogen, few structural reports on its interaction with biological ligands have appeared. Escherichia coli and other bacteria have evolved a detoxification mechanism that employs the arsRDABC operon (1). Arsenic removal by these encoded proteins is initiated when As(III) binds to ArsR, resulting in the dissociation of the repressor protein from the promoter DNA. The structure of the ArsA component of the ATP-dependent extrusion pump ArsAB with antimonite bound in close proximity to the nucleotide-binding site was able to provide some insight into the active transport of As(III) out of the cell (2). Additionally, structural characterization of substrate and product complexes of the arsenate reductase ArsC, which reduces arsenate (AsO 4 3Ϫ ) to arsenite (AsO 2 Ϫ ), has helped elucidate this step of the arsenic detoxification pathway (3, 4). Recent studies of E. coli ArsD indicate that it is a metallochaperone, transporting As(III) to ArsA for extrusion (5). Extended x-ray absorption fine structure and mutagenesis studies have shown that ArsR coordinates As(III) with three cysteine thiolates at a distance of 2.25 Å, a coordination mode that ArsD is also proposed to employ (1, 5). However, no x-ray or NMR structures of ArsR, the repressor protein, or ArsD have been reported to date. Furthermore, AsS 3 structures have not been reported for any biologically relevant small-molecule thiolates, such as glutathione, and only a handful of related AsS 3 complexes with aromatic ligands or chelated alkyl dithiolate coordination are reported (6).We set out to model the putative As(III) coordination environments of ArsR and ArsD in a designed peptide system. Previously, we have shown that the three-stranded coiled coildesigned with the heptad repeat strategy, such as TRI L16C (sequences of all peptides are in Table 1...

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confidence: 99%

mentioning

confidence: 99%

Identifying important structural characteristics of arsenic resistance proteins by using designed three-stranded coiled coils

Touw

Nordman

Stuckey³

et al. 2007

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

Self Cite

154

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“…Work in our group involves the designed TRI and GRAND peptides based on the heptad repeat, L a K b A c L d E e E f K g , and derivatives thereof (12,13). These sequences (shown in Table 1) were designed to assemble in aqueous solution into ␣-helices, which aggregate to form 3-stranded coiled coils at pH values Ͼ5.5.…”

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confidence: 99%

“…Substitution of either an a or d Leu with Cys provides a preorganized homoleptic thiol site in the interior of these coiled coils. The binding of numerous heavy metals such as Hg(II), Bi(III), Pb(II), and As(III) has been explored (12)(13)(14)(15)(16)(17)(18)(19), although the most intriguing system has been Cd(II) that binds to TRIL16C as a mixture of 3-and 4-coordinate CdS 3 and CdS 3 O (O from an exogenous water molecule) forms, respectively.…”

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Using diastereopeptides to control metal ion coordination in proteins

Peacock

Hemmingsen

Pecoraro

2008

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

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Here, we report a previously undescribed approach for controlling metal ion coordination geometry in biomolecules by reorientating amino acid side chains through substitution of L-to D-amino acids. These diastereopeptides allow us to manipulate the spatial orientation of amino acid side chains to alter the sterics of metal binding pockets. We have used this approach to design the de novo metallopeptide, Cd (TRIL12L DL16C)

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“…Metal binding sites engineered in de novo proteins in early designs incorporated zinc and mercury. [104,105] Subsequently, the 'Duo Ferri' (DF) series of maquettes was developed to mimic di-iron proteins. The DF maquettes bind two iron atoms and will also bind other metals ions (Zn, Co and Mn) with the stoichiometry of two ions per protein.…”

Section: Modified Bacterioferritin As a Photoactive Reaction Centrementioning

confidence: 99%

Perspectives for Photobiology in Molecular Solar Fuels

Hingorani

Hillier

2012

Aust. J. Chem.

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This paper presents an overview of the prospects for bio-solar energy conversion. The Global Artificial Photosynthesis meeting at Lord Howe Island (14–18 August 2011) underscored the dependence that the world has placed on non-renewable energy supplies, particularly for transport fuels, and highlighted the potential of solar energy. Biology has used solar energy for free energy gain to drive chemical reactions for billions of years. The principal conduits for energy conversion on earth are photosynthetic reaction centres – but can they be harnessed, copied and emulated? In this communication, we initially discuss algal-based biofuels before investigating bio-inspired solar energy conversion in artificial and engineered systems. We show that the basic design and engineering principles for assembling photocatalytic proteins can be used to assemble nanocatalysts for solar fuel production.

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De NovoDesign of Mercury-Binding Two- and Three-Helical Bundles

Cited by 158 publications

References 21 publications

Identifying important structural characteristics of arsenic resistance proteins by using designed three-stranded coiled coils

Identifying important structural characteristics of arsenic resistance proteins by using designed three-stranded coiled coils

Using diastereopeptides to control metal ion coordination in proteins

Perspectives for Photobiology in Molecular Solar Fuels

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