Metal-binding properties and structural characterization of a self-assembled coiled coil: Formation of a polynuclear Cd–thiolate cluster

Zaytsev, Daniil V.; Morozov, Vasily; Fan, Jiufeng; Zhu, Xianchun; Mukherjee, Madhumita; Ni, Shuisong; Kennedy, Michael A.; Ogawa, Michael Y.

doi:10.1016/j.jinorgbio.2012.10.010

Cited by 32 publications

(33 citation statements)

References 74 publications

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“…A notable exception is the duo ferro (two-iron) series of designs, which have explored numerous aspects of structure and reactivity of enzymes such as ribonucleotide reductase and methane monooxygenase, using a minimal model of a common dinuclear center within a four-α-helix bundle [5]. Other de novo systems with multinuclear metal sites exist [6], but examples where high-resolution structures have been solved are rare. This is due to a combination of challenges including effective de novo design of host proteins, synthesis and assembly of metal clusters in proteins, and characterization of structure and activity.…”

Section: Introductionmentioning

confidence: 99%

Structural principles for computational and de novo design of 4Fe–4S metalloproteins

Nanda

Senn

Pike

et al. 2016

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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Iron-sulfur centers in metalloproteins can access multiple oxidation states over a broad range of potentials, allowing them to participate in a variety of electron transfer reactions and serving as catalysts for high-energy redox processes. The nitrogenase FeMoCO cluster converts di-nitrogen to ammonia in an eight-electron transfer step. The 2(Fe4S4) containing bacterial ferredoxin is an evolutionarily ancient metalloprotein fold and is thought to be a primordial progenitor of extant oxidoreductases. Controlling chemical transformations mediated by iron-sulfur centers such as nitrogen fixation, hydrogen production as well as electron transfer reactions involved in photosynthesis are of tremendous importance for sustainable chemistry and energy production initiatives. As such, there is significant interest in the design of iron-sulfur proteins as minimal models to gain fundamental understanding of complex natural systems and as lead-molecules for industrial and energy applications. Herein, we discuss salient structural characteristics of natural iron-sulfur proteins and how they guide principles for design. Model structures of past designs are analyzed in the context of these principles and potential directions for enhanced designs are presented, and new areas of iron-sulfur protein design are proposed.

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Section: Introductionmentioning

confidence: 99%

Structural principles for computational and de novo design of 4Fe–4S metalloproteins

Nanda

Senn

Pike

et al. 2016

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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“…51 Multi-copper clusters have been also obtained by Ogawa and co-workers, who reported the Cu(I) binding properties of a designed four-helix bundle, 52,53 with spectroscopic features similar to cysteine rich metallothioneins. More recently, the same group has reported the design of a three-helix bundle binding a tetra-Cd 2+ cluster 54 featuring a tetrahedral adamantane like cluster [Cd 4 ( μ 2 -S•Cys) 6 (O 2 C•Glu) 3 (H 2 O)] stabilized by a CXXCE motif. Of particular significance, the structure was determined by X-ray crystallography, which has not always been possible for many of the above-mentioned examples.…”

Section: Introductionmentioning

confidence: 99%

De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles

et al. 2018

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De novo design provides an attractive approach to test the mechanism by which metalloproteins define the geometry and reactivity of their metal ion cofactors. While there has been considerable progress in designing proteins that bind transition metal ions including iron-sulphur clusters, the design of tetranuclear clusters with oxygen-rich environments has not been accomplished. Here, we describe the design of tetranuclear clusters, consisting of four Zn2+ and four carboxylate oxygens situated at the vertices of a distorted cube-like structure. The tetra-Zn2+ clusters are bound at a buried site within a four-helix bundle, with each helix donating a single carboxylate (Glu or Asp) and imidazole (His) ligand, as well as second- and third-shell ligands. Overall, the designed site consists of four Zn2+ and 16 polar sidechains in a fully connected hydrogen-bonded network. The designed proteins have apolar cores at the top and bottom of the bundle, which drive the assembly of the liganding residues near the center of the bundle. The steric bulk of the apolar residues surrounding the binding site was varied to determine how subtle changes in helix-helix packing affect the binding site. The crystal structures of two of four proteins synthesized were in good agreement with the overall design; both formed a distorted cuboidal site stabilized by flanking second and third-shell interactions that stabilize the primary ligands. A third structure bound a single Zn2+ in an unanticipated geometry and the fourth bound multiple Zn2+ at multiple sites at partial occupancy. The metal-binding and conformational properties of the helical bundles in solution, probed by circular dichroism spectroscopy, analytical ultracentrifugation and NMR, were consistent with the crystal structures.

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“…[1] In particular,metal nanoclusters (NCs) have attracted special attention in recent years owing to their size-dependent electronic transitions,s trong fluorescence,p hotostability,a nd biocompatibility.T hese assemblies of af ew to several atoms,w hich are smaller than 2nmi n size, [2] have discrete electron energy levels,resulting in highly distinct properties from bulk metals or classical nanoparticles. [8,10] Thiol, amine,a nd carboxylic acid side-chain functionalities seem to promote metal binding. [4] Metal NCs need to be stabilized by different molecules, such as dendrimers, [5] small molecules, [6] DNA, [7] peptides, [8] and proteins.…”

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confidence: 99%

“…[3] Such properties make metal NCs promising in biological analysis and imaging, environmental monitoring, industrial catalysis,and electronic devices. [8,10] Thiol, amine,a nd carboxylic acid side-chain functionalities seem to promote metal binding. [9] NCs stabilized by peptides and proteins can be produced under mild conditions,a nd the obtained structures are stable under aw ide range of pH values and ionic forces, making them ideal for biological applications.N atural and designed histidine-rich and cysteine-rich peptides have been used for the synthesis and stabilization of metal NCs.…”

mentioning

confidence: 99%

A Simple Approach to Design Proteins for the Sustainable Synthesis of Metal Nanoclusters

et al. 2019

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Metal nanoclusters (NCs) are considered ideal nanomaterials for biological applications owing to their strong photoluminescence (PL), excellent photostability, and good biocompatibility. This study presents a simple and versatile strategy to design proteins, via incorporation of a di‐histidine cluster coordination site, for the sustainable synthesis and stabilization of metal NCs with different metal composition. The resulting protein‐stabilized metal NCs (Prot‐NCs) of gold, silver, and copper are highly photoluminescent and photostable, have a long shelf life, and are stable under physiological conditions. The biocompatibility of the clusters was demonstrated in cell cultures in which Prot‐NCs showed efficient cell internalization without affecting cell viability or losing luminescence. Moreover, the approach is translatable to other proteins to obtain Prot‐NCs for various biomedical applications such as cell imaging or labeling.

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Metal-binding properties and structural characterization of a self-assembled coiled coil: Formation of a polynuclear Cd–thiolate cluster

Cited by 32 publications

References 74 publications

Structural principles for computational and de novo design of 4Fe–4S metalloproteins

Structural principles for computational and de novo design of 4Fe–4S metalloproteins

De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles

A Simple Approach to Design Proteins for the Sustainable Synthesis of Metal Nanoclusters

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