Rational design of heme enzymes for biodegradation of pollutants toward a green future

Lin, Ying‐Wu

doi:10.1002/bab.1788

Cited by 35 publications

(26 citation statements)

References 100 publications

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“…For more information on the design and properties of these cyclic model peptides, the readers are referred to an excellent recent review by Garai and Delangle [36]. Heme proteins are a large class of metalloproteins that contain one or multiple heme groups and exhibit diverse functions [13][14][15][16][17][18][37][38][39]. In addition to the heme prosthetic group, other metal ions may also bind to the protein if there are potential metal-binding sites.…”

Section: Binding To Potential Metal-binding Sitesmentioning

confidence: 99%

Uranyl Binding to Proteins and Structural-Functional Impacts

Lin

2020

Biomolecules

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The widespread use of uranium for civilian purposes causes a worldwide concern of its threat to human health due to the long-lived radioactivity of uranium and the high toxicity of uranyl ion (UO 2 2+ ). Although uranyl-protein/DNA interactions have been known for decades, fewer advances are made in understanding their structural-functional impacts. Instead of focusing only on the structural information, this article aims to review the recent advances in understanding the binding of uranyl to proteins in either potential, native, or artificial metal-binding sites, and the structural-functional impacts of uranyl-protein interactions, such as inducing conformational changes and disrupting protein-protein/DNA/ligand interactions. Photo-induced protein/DNA cleavages, as well as other impacts, are also highlighted. These advances shed light on the structure-function relationship of proteins, especially for metalloproteins, as impacted by uranyl-protein interactions. It is desired to seek approaches for biological remediation of uranyl ions, and ultimately make a full use of the double-edged sword of uranium.Proteins, especially for metalloproteins, play vital roles in supporting life, including electron-transfer, O 2 -binding and delivery, and catalysis, etc [11][12][13][14][15][16][17][18]. To date, a plenitude of proteins have been shown to interact with UO 2 2+ , such as proteins in blood (human serum albumin, HSA; transferrin, Tf;hemoglobin, Hb), proteins involved in bone growth (osteopontin, OPN; fetuin-A), and the intracellar proteins (metallothionein, MT; cytochromes b 5 /c; Cyt b 5 /c; calmodulin, CaM), etc [19]. Although the structural features of some uranyl-protein complexes are well-documented [7-9], fewer advances are made in understanding the functional impacts of uranyl-protein interactions, with much less for other actinides-proteins interactions, as reviewed by Creff et al. very recently [20]. Instead of focusing only on the structural information, this review highlights the recent advances in understanding the binding of uranyl to proteins, as illustrated in Scheme 1, in either potential, native or artificial metal-binding sites, or the corresponding structural-functional impacts, such as inducing conformational changes and disrupting protein-protein/DNA/ligand interactions. Future directions for studying uranyl-protein interactions are also prospected.

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Section: Binding To Potential Metal-binding Sitesmentioning

confidence: 99%

Uranyl Binding to Proteins and Structural-Functional Impacts

Lin

2020

Biomolecules

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“…Process control and quality assessment of reclaimed water may be further improved by developing efficient multi-purpose devices [ 4 , 28 ]. In particular, different oxidants, other than hydrogen peroxide, such as chlorite and chlorine dioxide [ 70 ], may be revealed through the methodology developed here, and their consumption rate may be eventually coupled to the presence of several aromatic and organophosphate pollutants [ 71 , 72 , 73 ].…”

Section: Discussionmentioning

confidence: 99%

Use of an Artificial Miniaturized Enzyme in Hydrogen Peroxide Detection by Chemiluminescence

Zambrano

Nastri

Pavone

et al. 2020

Sensors

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Advanced oxidation processes represent a viable alternative in water reclamation for potable reuse. Sensing methods of hydrogen peroxide are, therefore, needed to test both process progress and final quality of the produced water. Several bio-based assays have been developed so far, mainly relying on peroxidase enzymes, which have the advantage of being fast, efficient, reusable, and environmentally safe. However, their production/purification and, most of all, batch-to-batch consistency may inherently prevent their standardization. Here, we provide evidence that a synthetic de novo miniaturized designed heme-enzyme, namely Mimochrome VI*a, can be proficiently used in hydrogen peroxide assays. Furthermore, a fast and automated assay has been developed by using a lab-bench microplate reader. Under the best working conditions, the assay showed a linear response in the 10.0–120 μM range, together with a second linearity range between 120 and 500 μM for higher hydrogen peroxide concentrations. The detection limit was 4.6 μM and quantitation limits for the two datasets were 15.5 and 186 μM, respectively. In perspective, Mimochrome VI*a could be used as an active biological sensing unit in different sensor configurations.

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“…Protein design is able to not only reveal the structure-function relationship of native proteins, but also create artificial proteins with advanced functions [1][2][3][4][5][6][7][8][9][10][11][12]. This is especially the case for heme protein design, which has received much attention in the last few decades, and various approaches have been established for rational design, such as the introduction of non-heme metal ions and unnatural amino acids, and the use of heme mimics to act as an active site [1][2][3][4][5][6][7][8][9][10][11][12]. Importantly, computer modeling and molecular dynamics (MD) simulation play key roles in guiding the protein design [13][14][15][16][17][18].…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Simulation and Kinetic Study of Fluoride Binding to V21C/V66C Myoglobin with a Cytoglobin-like Disulfide Bond

Yin

Wang

et al. 2020

IJMS

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Protein design is able to create artificial proteins with advanced functions, and computer simulation plays a key role in guiding the rational design. In the absence of structural evidence for cytoglobin (Cgb) with an intramolecular disulfide bond, we recently designed a de novo disulfide bond in myoglobin (Mb) based on structural alignment (i.e., V21C/V66C Mb double mutant). To provide deep insight into the regulation role of the Cys21-Cys66 disulfide bond, we herein perform molecular dynamics (MD) simulation of the fluoride–protein complex by using a fluoride ion as a probe, which reveals detailed interactions of the fluoride ion in the heme distal pocket, involving both the distal His64 and water molecules. Moreover, we determined the kinetic parameters of fluoride binding to the double mutant. The results agree with the MD simulation and show that the formation of the Cys21-Cys66 disulfide bond facilitates both fluoride binding to and dissociating from the heme iron. Therefore, the combination of theoretical and experimental studies provides valuable information for understanding the structure and function of heme proteins, as regulated by a disulfide bond. This study is thus able to guide the rational design of artificial proteins with tunable functions in the future.

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Rational design of heme enzymes for biodegradation of pollutants toward a green future

Cited by 35 publications

References 100 publications

Uranyl Binding to Proteins and Structural-Functional Impacts

Uranyl Binding to Proteins and Structural-Functional Impacts

Use of an Artificial Miniaturized Enzyme in Hydrogen Peroxide Detection by Chemiluminescence

Molecular Dynamics Simulation and Kinetic Study of Fluoride Binding to V21C/V66C Myoglobin with a Cytoglobin-like Disulfide Bond

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