Repurposing proteins for new bioinorganic functions

Churchfield, L.A.; George, Athira; Tezcan, F.A.

doi:10.1042/ebc20160068

Cited by 12 publications

(14 citation statements)

References 70 publications

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“… 1 − 12 In addition to their potential for application in synthesis, they are also valuable tools for the investigation of the role of the second coordination sphere in enzyme catalysis. 3 , 13 − 18 Furthermore, designed metalloproteins may allow for the stabilization of highly reactive compounds, giving rise to increased lifetimes of these species. Some metal semiquinone intermediates have been identified in natural enzymes and synthetic mimic complexes.…”

Section: Introductionmentioning

confidence: 99%

Artificial Metalloproteins for Binding and Stabilization of a Semiquinone Radical

et al. 2017

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The interaction of a number of first-row transition-metal ions with a 2,2′-bipyridyl alanine (bpyA) unit incorporated into the lactococcal multidrug resistance regulator (LmrR) scaffold is reported. The composition of the active site is shown to influence binding affinities. In the case of Fe(II), we demonstrate the need of additional ligating residues, in particular those containing carboxylate groups, in the vicinity of the binding site. Moreover, stabilization of di-tert-butylsemiquinone radical (DTB-SQ) in water was achieved by binding to the designed metalloproteins, which resulted in the radical being shielded from the aqueous environment. This allowed the first characterization of the radical semiquinone in water by resonance Raman spectroscopy.

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Section: Introductionmentioning

confidence: 99%

Artificial Metalloproteins for Binding and Stabilization of a Semiquinone Radical

et al. 2017

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“…Recycled motifs are frequently found in nature, as estimations place the number of distinct tertiary structures just over a thousand 99 . This strategy aims to graft a newly defined active site in an existing stable structure.…”

Section: Designing a Protein Scaffoldmentioning

confidence: 99%

Step‐by‐step design of proteins for small molecule interaction: A review on recent milestones

2021

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Protein design is the field of synthetic biology that aims at developing de novo custom-made proteins and peptides for specific applications. Despite exploring an ambitious goal, recent computational advances in both hardware and software technologies have paved the way to high-throughput screening and detailed design of novel folds and improved functionalities. Modern advances in the field of protein design for small molecule targeting are described in this review, organized in a step-by-step fashion: from the conception of a new or upgraded active binding site, to scaffold design, sequence optimization, and experimental expression of the custom protein. In each step, contemporary examples are described, and state-of-the-art software is briefly explored.

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“…Over the last three decades, great progress has been made in the design of metalloproteins, whereby the targets have evolved from small metal-binding peptides with stable secondary structures to novel membrane-spanning proteins and artificial enzymes with well-defined active sites. − Notwithstanding these advances, the design of an amino acid sequence to fold into a target 3D structure with the desired metal-based function still remains a daunting task. This issue is exacerbated by the fact that the proper functioning of any metalloprotein depends not only on its 3D architecture but also on other factors (e.g., local and global dynamics, solvation, and local dielectrics) that are often difficult to discern, let alone design.…”

Section: Introductionmentioning

confidence: 99%

Design and Construction of Functional Supramolecular Metalloprotein Assemblies

Churchfield

Tezcan

2019

Acc. Chem. Res.

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CONSPECTUS: Nature puts to use only a small fraction of metal ions in the periodic table. Yet, when incorporated into protein scaffolds, this limited set of metal ions carry out innumerable cellular functions and execute essential biochemical transformations such as photochemical H 2 O oxidation, O 2 or CO 2 reduction, and N 2 fixation, highlighting the outsized importance of metalloproteins in biology. Not surprisingly, elucidating the intricate interplay between metal ions and protein structures has been the focus of extensive structural and mechanistic scrutiny over the last several decades. As a result of such top-down efforts, we have gained a reasonably detailed understanding of how metal ions shape protein structures and how protein structures in turn influence metal reactivity. It is fair to say that we now have some idea−and in some cases, a good idea−about how most known metalloproteins function and we possess enough insight to quickly assess the modus operandi of newly discovered ones. However, translating this knowledge into an ability to construct functional metalloproteins from scratch represents a challenge at a whole different level: it is one thing to know how an automobile works; it is another to build one. In our quest to build new metalloproteins, we have taken an original approach in which folded, monomeric proteins are used as ligands or synthons for building supramolecular complexes through metal-mediated self-assembly (MDPSA, Metal-Directed Protein Self-Assembly). The interfaces in the resulting protein superstructures are subsequently tailored with covalent, noncovalent, or additional metal-coordination interactions for stabilization and incorporation of new functionalities (MeTIR, Metal Templated Interface Redesign). In an earlier Account, we had described the proof-of-principle studies for MDPSA and MeTIR, using a four-helix bundle, heme protein cytochrome cb 562 (cyt cb 562 ), as a model building block. By the end of those studies, we were able to demonstrate that a tetrameric, Zn-directed cyt cb 562 complex (Zn 4 :M1 4 ) could be stabilized through computationally prescribed noncovalent interactions inserted into the nascent protein−protein interfaces. In this Account, we first describe the rationale and motivation for our particular metalloprotein engineering strategy and a brief summary of our earlier work. We then describe the next steps in the "evolution" of bioinorganic complexity on the Zn 4 :M1 4 scaffold, namely, (a) the generation of a self-standing protein assembly that can stably and selectively bind metal ions, (b) the creation of reactive metal centers within the protein assembly, and (c) the coupling of metal coordination and reactivity to external stimuli through allosteric effects.

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Repurposing proteins for new bioinorganic functions

Cited by 12 publications

References 70 publications

Artificial Metalloproteins for Binding and Stabilization of a Semiquinone Radical

Artificial Metalloproteins for Binding and Stabilization of a Semiquinone Radical

Step‐by‐step design of proteins for small molecule interaction: A review on recent milestones

Design and Construction of Functional Supramolecular Metalloprotein Assemblies

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