Magnesium and manganese binding sites on proteins have the same predominant motif of secondary structure

Khrustalev, Vladislav Victorovich; Barkovsky, Eugene Victorovich; Khrustaleva, Tatyana Aleksandrovna

doi:10.1016/j.jtbi.2016.02.006

Cited by 31 publications

(16 citation statements)

References 26 publications

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“…Therefore, the Mg(II) can interfere with the detection of Pd(II). To the best of our knowledge, amino acid residues alone [25] or hydrophilic amino acids such as asparagine and glutamine at certain positions in a peptide can provide an ideal environment to coordinate Mg(II), similar to the complex reported in the previous report [26]. Therefore, the colorimetric method detecting Pd(II) is certainly applicable to the specific circumstances of wastewater produced from Pdcatalyzed organic reactions and glassware contaminated with Pd(II).…”

Section: Selectivitysupporting

confidence: 58%

Whey peptide-encapsulated silver nanoparticles as a colorimetric and spectrophotometric probe for palladium(II)

et al. 2019

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Silver nanoparticles (AgNPs) coated with whey peptides are shown to be a useful optical nanoprobe for the highly sensitive determination of Pd(II). The peptidic surface of the AgNPs works as a molecular receptor for the rapid detection of Pd(II) via a color change from dark yellow to orange/red along with a spectral red-shift with a gap about 120 nm. The effect is caused by the formation of a coordination complex between Pd(II) and the peptide ligands. This results in the aggregation of AgNPs and an absorbance spectral shift from 410 to 530 nm. The absorbance response is linear in the range 0.1 to 1.3 μM Pd(II) with a low detection limit of 115 nM. The nanoprobe responds within a few minutes and is not interfered by other metal ions except for Mg(II). The probe potentially can be applied to the determination of Pd(II) contamination in the products of Pd(II)−catalyzed organic reactions and in pharmaceutical settings.

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Section: Selectivitysupporting

confidence: 58%

Whey peptide-encapsulated silver nanoparticles as a colorimetric and spectrophotometric probe for palladium(II)

et al. 2019

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“…Thus, generally few differences exist between Mg and Mn coordination spheres responsible for the cation specificity. Khrustalev et al [27] investigated several hundred Mn and Mg metalloproteins and found that Mg and Mn are typically bound to oxygen in the carboxylate groups of Asp and Glu. Histidine (His) residues appear underrepresented in Asp and Glu rich pockets binding Mg 2+ , while His groups are overrepresented in Asp and Glu pockets binding Mn 2+ .…”

Section: Manganese In Metalloenzymesmentioning

confidence: 99%

The Biochemical Properties of Manganese in Plants

Schmidt

Husted

2019

Plants

152

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Manganese (Mn) is an essential micronutrient with many functional roles in plant metabolism. Manganese acts as an activator and co-factor of hundreds of metalloenzymes in plants. Because of its ability to readily change oxidation state in biological systems, Mn plays and important role in a broad range of enzyme-catalyzed reactions, including redox reactions, phosphorylation, decarboxylation, and hydrolysis. Manganese(II) is the prevalent oxidation state of Mn in plants and exhibits fast ligand exchange kinetics, which means that Mn can often be substituted by other metal ions, such as Mg(II), which has similar ion characteristics and requirements to the ligand environment of the metal binding sites. Knowledge of the molecular mechanisms catalyzed by Mn and regulation of Mn insertion into the active site of Mn-dependent enzymes, in the presence of other metals, is gradually evolving. This review presents an overview of the chemistry and biochemistry of Mn in plants, including an updated list of known Mn-dependent enzymes, together with enzymes where Mn has been shown to exchange with other metal ions. Furthermore, the current knowledge of the structure and functional role of the three most well characterized Mn-containing metalloenzymes in plants; the oxygen evolving complex of photosystem II, Mn superoxide dismutase, and oxalate oxidase is summarized.

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“…We chose the 197 residue‐AAV5 Rep nuclease domain in complex with Mg 2+ (PDB Code: 1UUT; hereafter referred to as AAV5 Rep197) as our model for further studies because 1) all the bioinformatics tools used predicted SIRV1 Rep metal‐binding with this complex as a model; 2) the metal‐coordinating residues are identical, and 3) the superimposed active site residues of both model and query have the minimum root mean square deviation (RMSD) of all active sites compared, and therefore represented the best match. Although the model used comprised of Mg 2+ , structural studies have indicated that both Mg 2+ and Mn 2+ use identical coordination chemistries .…”

Section: Resultsmentioning

confidence: 99%

Design and implementation of structural bioinformatics projects for biological sciences undergraduate students

Oke

Agbalajobi

Osifeso

et al. 2018

Biochem Molecular Bio Educ

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Contemporary biology is currently undergoing a revolution, driven by the availability of high‐throughput technologies and a wide variety of bioinformatics tools. However, bioinformatics education and practice is still in its infancy in most of the African continent. Consequently, concerted efforts have been made in recent years to incorporate bioinformatics modules into biological sciences curriculum of African Universities. Despite this, one aspect of bioinformatics that is yet to be incorporated is structural bioinformatics. In this article, we report on a structural bioinformatics project carried out by final year project students in a Nigerian university. The target protein was the thermoacidophilic Sulfolobus islandicus rod‐shaped virus 1 (SIRV1) Rep protein, which was further characterized using various free, user‐friendly and online sequence‐based and structure‐based bioinformatics tools. This exercise gave students the opportunity to generate new data, interpret the data, and acquire collaborative research skills. In this report, emphasis is placed on analysis of the data generated to further encourage analytical skills. By sharing this experience, it is anticipated that other similar institutions would adopt parallel strategies to expose undergraduate students to structural biology, and increase awareness of freely available bioinformatics tools for tackling pertinent biological questions. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):547–554, 2018.

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Magnesium and manganese binding sites on proteins have the same predominant motif of secondary structure

Cited by 31 publications

References 26 publications

Whey peptide-encapsulated silver nanoparticles as a colorimetric and spectrophotometric probe for palladium(II)

Whey peptide-encapsulated silver nanoparticles as a colorimetric and spectrophotometric probe for palladium(II)

The Biochemical Properties of Manganese in Plants

Design and implementation of structural bioinformatics projects for biological sciences undergraduate students

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