Conservation of metal‐coordinating residues

Kasampalidis, Ioannis; Pitas, Ioannis; Lyroudia, Kleoniki

doi:10.1002/prot.21384

Cited by 21 publications

(14 citation statements)

References 35 publications

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“…His, Cys and Met. (13) This conclusion is further supported by our analyses. Through identifying the metal-binding residues of redox metalloproteins (with Enzyme Classification of E.C.…”

Section: Introductionsupporting

confidence: 82%

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Organic cofactors participated more frequently than transition metals in redox reactions of primitive proteins

Chen

Zhang

2008

BioEssays

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Protein redox reactions are one of the most basic and important biochemical actions. As amino acids are weak redox mediators, most protein redox functions are undertaken by protein cofactors, which include organic ligands and transition metal ions. Since both kinds of redox cofactors were available in the pre-protein RNA world, it is challenging to explore which one was more involved in redox processes of primitive proteins? In this paper, using an examination of the redox cofactor usage of putative ancient proteins, we infer that organic ligands participated more frequently than transition metals in redox reactions of primitive proteins, at least as protein cofactors. This is further supported by the relative abundance of amino acids in the primordial world. Supplementary material for this article can be found on the BioEssays website.

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“…His, Cys and Met. (13) This conclusion is further supported by our analyses. Through identifying the metal-binding residues of redox metalloproteins (with Enzyme Classification of E.C.…”

Section: Introductionsupporting

confidence: 82%

“…In addition, the average Shannon's information theoretic entropies (13,15) of cofactor-binding and non-binding positions indicate that the organic cofactor-binding residues are also much more conserved than others during evolution (Fig. 1).…”

Section: Redox Cofactor Usage In Putative Ancient Proteinsmentioning

confidence: 99%

Organic cofactors participated more frequently than transition metals in redox reactions of primitive proteins

Chen

Zhang

2008

BioEssays

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“…In cells, 30–40% of the proteins depend upon at least one metal ion to carry out their biological functions [3,4]. It has been well known that regions or residues of proteins that interact with the metal ligands are very well conserved both in sequence and in structure [5,6]. …”

Section: Introductionmentioning

confidence: 99%

Computational approaches forde novodesign and redesign of metal-binding sites on proteins

Akçapınar

Sezerman

2017

Bioscience Reports

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Metal ions play pivotal roles in protein structure, function and stability. The functional and structural diversity of proteins in nature expanded with the incorporation of metal ions or clusters in proteins. Approximately one-third of these proteins in the databases contain metal ions. Many biological and chemical processes in nature involve metal ion-binding proteins, aka metalloproteins. Many cellular reactions that underpin life require metalloproteins. Most of the remarkable, complex chemical transformations are catalysed by metalloenzymes. Realization of the importance of metal-binding sites in a variety of cellular events led to the advancement of various computational methods for their prediction and characterization. Furthermore, as structural and functional knowledgebase about metalloproteins is expanding with advances in computational and experimental fields, the focus of the research is now shifting towards de novo design and redesign of metalloproteins to extend nature’s own diversity beyond its limits. In this review, we will focus on the computational toolbox for prediction of metal ion-binding sites, de novo metalloprotein design and redesign. We will also give examples of tailor-made artificial metalloproteins designed with the computational toolbox.

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“…A major obstacle to acquisition of metal cofactors by apoenzymes is that the binding sites for these cofactors frequently lack the capacity to discriminate between different divalent metal cations and cofactors (Kasampalidis et al, 2007; Waldron et al, 2009). The sulfur, oxygen, and nitrogen ligands that coordinate metals in enzymes will frequently bind non-native cofactors with affinities equal to or greater than those of the native cofactor.…”

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confidence: 99%

Special delivery: distributing iron in the cytosol of mammalian cells

Philpott

Ryu

2014

Front. Pharmacol.

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Eukaryotic cells contain hundreds of proteins that require iron cofactors for activity. These iron enzymes are located in essentially every subcellular compartment; thus, iron cofactors must travel to every compartment in the cell. Iron cofactors exist in three basic forms: Heme, iron–sulfur clusters, and simple iron ions (also called non-heme iron). Iron ions taken up by the cell initially enter a kinetically labile, exchangeable pool that is referred to as the labile iron pool. The majority of the iron in this pool is delivered to mitochondria, where it is incorporated into heme and iron–sulfur clusters, as well as non-heme iron enzymes. These cofactors must then be distributed to nascent proteins in the mitochondria, cytosol, and membrane-bound organelles. Emerging evidence suggests that specific systems exist for the distribution of iron cofactors within the cell. These systems include membrane transporters, protein chaperones, specialized carriers, and small molecules. This review focuses on the distribution of iron ions in the cytosol and will highlight differences between the iron distribution systems of simple eukaryotes and mammalian cells.

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Conservation of metal‐coordinating residues

Cited by 21 publications

References 35 publications

Organic cofactors participated more frequently than transition metals in redox reactions of primitive proteins

Organic cofactors participated more frequently than transition metals in redox reactions of primitive proteins

Computational approaches forde novodesign and redesign of metal-binding sites on proteins

Special delivery: distributing iron in the cytosol of mammalian cells

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