• Genomics & Informatics
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• v.15 no.4
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• pp.162-169
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• 2017

Metal binding proteins or metallo-proteins are important for the stability of the protein and also serve as co-factors in various functions like controlling metabolism, regulating signal transport, and metal homeostasis. In structural genomics, prediction of metal binding proteins help in the selection of suitable growth medium for overexpression's studies and also help in obtaining the functional protein. Computational prediction using machine learning approach has been widely used in various fields of bioinformatics based on the fact all the information contains in amino acid sequence. In this study, random forest machine learning prediction systems were deployed with simplified amino acid for prediction of individual major metal ion binding sites like copper, calcium, cobalt, iron, magnesium, manganese, nickel, and zinc.

• Journal of Microbiology and Biotechnology
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• v.25 no.4
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• pp.503-510
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• 2015

The iLOV protein belongs to a family of blue-light photoreceptor proteins containing a light-oxygen-voltage sensing domain with a noncovalently bound flavin mononucleotide (FMN) as its chromophore. Owing to advantages such as its small size, oxygen-independent nature, and pH stability, iLOV is an ideal candidate over other reporter fluorescent proteins such as GFP and DsRed. Here, for the first time, we describe the feasibility of applying LOV domain-based fluorescent iLOV as a metal sensor by measuring the fluorescence quenching of a protein with respect to the concentration of metal ions. In the present study, we demonstrated the inherent copper sensing property of the iLOV protein and identified the possible amino acids responsible for metal binding. The fluorescence quenching upon exposure to Cu²⁺ was highly sensitive and exhibited reversibility upon the addition of the metal chelator EDTA. The copper binding constant was found to be 4.72 ± 0.84 µM. In addition, Cu²⁺-bound iLOV showed high fluorescence quenching at near physiological pH. Further computational analysis yielded a better insight into understanding the possible amino acids responsible for Cu²⁺ binding with the iLOV protein.

• YAKHAK HOEJI
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• v.39 no.4
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• pp.380-384
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• 1995

The isoelelectric points of Cd-BP(l) and Cd-BP(II), cadmium-binding proteins, were 6.01 and 5.35, respectively. Both of them contained zinc. As for the amino acid composition, Cd-BP(I) contained a lot of glycine and lysine but none of such aromatic amino acids as tyrosine and phenylalanine.. On the other hand, Cd-BP(II) contained leucine, histidine, asparti cacid and alanine but no aromatic amino acids.

• Bulletin of the Korean Chemical Society
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• v.35 no.4
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• pp.1087-1090
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• 2014

A simple and general method that selectively introduces metal binding sites into a protein can greatly increase the ability to design and biosynthesize artificial metalloproteins. Here, we report the incorporation of a phenanthroline-containing amino acid (Phen-Ala) into proteins in Escherichia coli by using the $tRNA{^{Tyr}}_{CUA}$ and tyrosyl aminoacyl-tRNA synthetase pair (BpyRS) from Methanococcus jannaschii, which was originally developed for a bipyridine-containing amino acid (Bpy-Ala). The incorporation efficiency of BpyRS for Phen-Ala was comparable to that for Bpy-Ala. Because of its high metal-binding ability and characteristic spectral properties, Phen-Ala can be a useful alternative to the existing metal-chelating amino acids for the design and synthesis of artificial metalloproteins.

• Bulletin of the Korean Chemical Society
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• v.31 no.8
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• pp.2201-2206
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• 2010

To improve the separation property and stability of metal chelate Cu(II) column, three new kinds of multidentate aminocarboxy silica columns with cation-exchange properties were synthesized using glutamic acid (Glu), glutamic acidbromoacetic acid (Glu-BAA), glutamic acid-bromosuccinic acid (Glu-BSUA) as ligands and silica gel as matrix. The standard proteins were separated with prepared chromatographic columns. The stationary phases exhibited the metal chelate property after fixing copper ion (II) on the synthesized multidentate ligand silica columns. The binding capacity of immobilized metal ion was related with the dentate number of multidentate ligands. Chromatographic behavior of proteins and the leakage of immobilized metal ion on multidentate chelate Cu(II) columns were affected by the dentate number of multidentate ligands and competitive elution system directly. The results showed that quinquedentate Glu-BSUA-Cu(II) column exhibited better chromatographic property and stability as compared with tridentate Glu-Cu(II) column, tetradentate Glu-BAA-Cu(II) column and commonly used IDA-Cu(II) column.

• Microbiology and Biotechnology Letters
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• v.21 no.4
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• pp.336-341
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• 1993

In metal-affinify aqueous two-phase systems, protein partitioning is affected by a variety of parameters such as pH, the number of surface-accessible histidines, and the amount and partition coefficient of metallated polythylene glyco(PEG) ligand. To enhance partitioning of proteins with surface-accessible histidines, we have synthesized and used a (Cu(II)-ininodiacetic acid)$_2$-PEG20,000($Cu(II)_2IDA_2$-PEG20,000) as well as Cu(II)IDA-PEG5,000 as an affinity ligand. The partition coefficient of $Cu(II)_2-IDA_2$-PEG20,000 in a PEG5,000/dextran two-phase system was 30.1, which corresponded to a 3.8-fold increase over that of Cu(II)IDA-PEG5,000. The partitioning experiments were performed on four proteins, horse cytochrome c, S. cerevisiae cytochrome c, horse myoglobin, and sheep myoglobin. Partitioning of proteins which convey surface-accessible histidines was enhanced dramatically by the addition of $Cu(II)_2IDA_2$-PEG20,000 ligand. These results demonstrate that enhanced partitioning of metal-binding proteins in an aqueous two -phase system can by achieved by using an appropriate metallated PEG ligand.

• Ocean Science Journal
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• v.41 no.1
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• pp.43-51
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• 2006

Concentration and distribution of Fe, Zn, Cu, Cd, Mn, Pb, Ni among subcellular fractions (cellular membrane structures and cytosol) and Zn, Cu, Cd among cytoplasmic proteins in the kidney and digestive gland of mussel Modiolus modiolus living along a polymetallic concentration gradient were studied. It was found in the kidney of M. modiolus from contaminated sites that the Fe percent increased in the "membrane" fraction, whereas Zn, Pb, Ni and Mn percent increased in the cytosol compared to the kidney of the control mussel. Note kidney cytosol of M. modiolus from clean and contaminated sites sequestered major parts of Cu and Cd. In the digestive gland of M. modiolus from contaminated sites Fe, Zn, Cd, Mn, Ni percent increased in the "membrane" fraction, whereas Cu, Pb percent increased in the cytosol compared to digestive gland of control mussel. Gel-filtration chromatography shows kidney of M. modiolus contains increased metallothionein-like protein levels irrespective of ambient dissolved metal concentrations. It was shown that the metal detoxification system in the kidney and digestive gland of M. modiolus was efficient under extremely high ambient metal levels. However, under complex environmental contamination in the kidney of M. modiolus, the metal detoxification capacity of metallothionein-like proteins was damaged.

• Journal of Microbiology and Biotechnology
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• v.14 no.3
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• pp.607-611
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• 2004

Glycinin, one of the predominant storage proteins in soybeans, was examined as to whether it could be used as a calcium-binding mediator after chemical phosphorylation and enzymatic hydrolysis. Glycinin is composed of six subunits. One of the proglycinin subunits $(A_{la}B_{lb})$ was overexpressed in E. coli to obtain nonphosphorylated proteins with homogeneity. To investigate the enhanced calcium-binding properties of the phosphopeptides, the proglycinin was purified, phosphorylated, and hydrolyzed with trypsin. The proglycinin expressed in E. coli was purified by ammonium sulfate precipitation, ion-exchange chromatography, and cryoprecipitation. Chemical phosphorylation by sodium trimetaphosphate was performed to obtain phosphorylated proglycinin. After the phosphorylation, one-dimensional isoelectric focusing gel electroanalysis confirmed the phosphorylation of the proglycinin. The phosphorylated peptides were then hydrolyzed with trypsin, followed by a binding reaction with calcium chloride. The calcium-bound phosphopeptides were finally separated using immobilized metal $(Ca^{2+})$ chromatography. Consequently, a limited tryptic hydrolysate of the isolated phosphopeptides exhibited an enhanced calcium-binding ability, suggesting the potential of glycinin phosphopeptides as a calcium-binding mediator with greater availability.

• Animal cells and systems
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• v.7 no.3
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• pp.173-186
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• 2003

The transition metal cadmium is a serious occupational and environmental toxin. To inhibit cadmium-induced damage, cells respond by increasing the expression of genes that encode stress-responsive proteins. The metal-regulatory transcription factor 1 (MTF-1) is a key regulator of heavy-metal induced transcription of metallothionein-I and II and other genes in mammals and other metazoans. Transcriptional activation of genes by MTF-1 is mediated through binding to metal-responsive elements in the target gene promoters. Phosphorylation of MTF-1 plays a critical role in the cadmium-inducible transcriptional activation of metallothionein and other responses. Studies using inhibitors indicate that multiple kinases and signal transduction cascades, including those mediated by protein kinase C, tyrosine kinase and casein kinase II, are essential for cadmium-mediated transcriptional activation. In addition, calcium signaling is also involved in regulating metal-activated transcription. In several species, cadmium induces heat shock genes. Recently much progress has been made in elucidating the cellular machinery that regulates this metal-inducible gene expression. This review summarizes these recent advances in understanding the role of some known cadmium-responsive genes and the molecular mechanisms that activate metal-responsive transcription factor, MTF-1.

• Proceedings of the Zoological Society Korea Conference
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• 1997.10b
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• pp.171.1-171
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• 1997

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