Metal Binding Proteins

Permyakov, Eugene A.

doi:10.3390/encyclopedia1010024

Cited by 67 publications

(41 citation statements)

References 112 publications

(154 reference statements)

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“…The MAP from Salmonella typhimurium is stimulated only by Co 2+ , not by Mg 2+ , Mn 2+ , or Zn 2+ and is inhibited by metal ion chelator EDTA. E. coli MAP is a monomeric protein of 29 kDa consisting of 263 residues that possess two Co 2+ ions in its active site (Permyakov, 2021 ).…”

Section: Cobalt Coenzymes and Proteinsmentioning

confidence: 99%

Cobalt: An Essential Micronutrient for Plant Growth?

et al. 2021

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Cobalt is a transition metal located in the fourth row of the periodic table and is a neighbor of iron and nickel. It has been considered an essential element for prokaryotes, human beings, and other mammals, but its essentiality for plants remains obscure. In this article, we proposed that cobalt (Co) is a potentially essential micronutrient of plants. Co is essential for the growth of many lower plants, such as marine algal species including diatoms, chrysophytes, and dinoflagellates, as well as for higher plants in the family Fabaceae or Leguminosae. The essentiality to leguminous plants is attributed to its role in nitrogen (N) fixation by symbiotic microbes, primarily rhizobia. Co is an integral component of cobalamin or vitamin B12, which is required by several enzymes involved in N2 fixation. In addition to symbiosis, a group of N2 fixing bacteria known as diazotrophs is able to situate in plant tissue as endophytes or closely associated with roots of plants including economically important crops, such as barley, corn, rice, sugarcane, and wheat. Their action in N2 fixation provides crops with the macronutrient of N. Co is a component of several enzymes and proteins, participating in plant metabolism. Plants may exhibit Co deficiency if there is a severe limitation in Co supply. Conversely, Co is toxic to plants at higher concentrations. High levels of Co result in pale-colored leaves, discolored veins, and the loss of leaves and can also cause iron deficiency in plants. It is anticipated that with the advance of omics, Co as a constitute of enzymes and proteins and its specific role in plant metabolism will be exclusively revealed. The confirmation of Co as an essential micronutrient will enrich our understanding of plant mineral nutrition and improve our practice in crop production.

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Section: Cobalt Coenzymes and Proteinsmentioning

confidence: 99%

Cobalt: An Essential Micronutrient for Plant Growth?

et al. 2021

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“…Unique metal-binding sites locate both on the external surface of the dodecamer and within the hollow cavity in the middle of the Dps dodecamer. These metal-binding sites of ferritin-like proteins, as a rule, are rich in Asp, His and Glu amino acids [ 13 , 14 , 24 , 29 , 30 , 31 ]; however, the sites are not highly conserved and the amino acids within them can be replaced by Lys, Ala and others.…”

Section: Resultsmentioning

confidence: 99%

Structural Rearrangement of Dps-DNA Complex Caused by Divalent Mg and Fe Cations

Dadinova

Kamyshinsky

Chesnokov

et al. 2021

IJMS

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Two independent, complementary methods of structural analysis were used to elucidate the effect of divalent magnesium and iron cations on the structure of the protective Dps-DNA complex. Small-angle X-ray scattering (SAXS) and cryo-electron microscopy (cryo-EM) demonstrate that Mg2+ ions block the N-terminals of the Dps protein preventing its interaction with DNA. Non-interacting macromolecules of Dps and DNA remain in the solution in this case. The subsequent addition of the chelating agent (EDTA) leads to a complete restoration of the structure of the complex. Different effect was observed when Fe cations were added to the Dps-DNA complex; the presence of Fe2+ in solution leads to the total complex destruction and aggregation without possibility of the complex restoration with the chelating agent. Here, we discuss these different responses of the Dps-DNA complex on the presence of additional free metal cations, investigating the structure of the Dps protein with and without cations using SAXS and cryo-EM. Additionally, the single particle analysis of Dps with accumulated iron performed by cryo-EM shows localization of iron nanoparticles inside the Dps cavity next to the acidic (hydrophobic) pore, near three glutamate residues.

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“…Figure 4 illustrates the structure of a calmodulin (PDB: 4HEX) that is secreted by Escherichia coli in Mus musculus [ 146 ]. Calmodulin is one of the most prevalent EF-hand calcium sensor proteins in eukaryotic cells [ 147 ]. It is a highly conserved and soluble protein, which activates enzymes and regulates many cellular functions.…”

Section: Methods Development Of Metal-binding Predictionmentioning

confidence: 99%

“…Two Zn 2+ -binding sites are surrounded by a shell of hydrophilic groups that are embedded into a larger shell of hydrophobic groups. The amino acid side chains providing ligands to Zn 2+ in these structures often form hydrogen bonds with other residues [ 147 ].…”

Section: Methods Development Of Metal-binding Predictionmentioning

confidence: 99%

A Comprehensive Review of Computation-Based Metal-Binding Prediction Approaches at the Residue Level

Zhou

Liang

et al. 2022

BioMed Research International

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Clear evidence has shown that metal ions strongly connect and delicately tune the dynamic homeostasis in living bodies. They have been proved to be associated with protein structure, stability, regulation, and function. Even small changes in the concentration of metal ions can shift their effects from natural beneficial functions to harmful. This leads to degenerative diseases, malignant tumors, and cancers. Accurate characterizations and predictions of metalloproteins at the residue level promise informative clues to the investigation of intrinsic mechanisms of protein-metal ion interactions. Compared to biophysical or biochemical wet-lab technologies, computational methods provide open web interfaces of high-resolution databases and high-throughput predictors for efficient investigation of metal-binding residues. This review surveys and details 18 public databases of metal-protein binding. We collect a comprehensive set of 44 computation-based methods and classify them into four categories, namely, learning-, docking-, template-, and meta-based methods. We analyze the benchmark datasets, assessment criteria, feature construction, and algorithms. We also compare several methods on two benchmark testing datasets and include a discussion about currently publicly available predictive tools. Finally, we summarize the challenges and underlying limitations of the current studies and propose several prospective directions concerning the future development of the related databases and methods.

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Metal Binding Proteins

Cited by 67 publications

References 112 publications

Cobalt: An Essential Micronutrient for Plant Growth?

Cobalt: An Essential Micronutrient for Plant Growth?

Structural Rearrangement of Dps-DNA Complex Caused by Divalent Mg and Fe Cations

A Comprehensive Review of Computation-Based Metal-Binding Prediction Approaches at the Residue Level

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