An intramolecular disulfide bond designed in myoglobin fine-tunes both protein structure and peroxidase activity

Functional metalloenzymes based on myoglobin and neuroglobin that exploit covalent interactions

Globins, such as myoglobin (Mb) and neuroglobin (Ngb), are ideal protein scaffolds for the design of functional metalloenzymes. To date, numerous approaches have been developed for enzyme design. This review presents a summary of the progress made in the design of functional metalloenzymes based on Mb and Ngb, with a focus on the exploitation of covalent interactions, including coordination bonds and covalent modifications. These include the construction of a metal-binding site, the incorporation of a non-native metal cofactor, the formation of Cys/Tyr-heme covalent links, and the design of disulfide bonds, as well as other Cys-covalent modifications. As exemplified by recent studies from our group and others, the designed metalloenzymes have potential applications in biocatalysis and bioconversions. Furthermore, we discuss the current trends in the design of functional metalloenzymes and highlight the importance of covalent interactions in the design of functional metalloenzymes.

Peroxidase activity of rice (Oryza sativa) hemoglobin: distinct role of tyrosines 112 and 151

Five non-symbiotic hemoglobins (nsHb) have been identified in rice (Oryza sativa). Previous studies have shown that stress conditions can induce their overexpression, but the role of those globins is still unclear. To better understand the functions of nsHb, the reactivity of rice Hb1 toward hydrogen peroxide (H2O2) has been studied in vitro. Our results show that recombinant rice Hb1 dimerizes through dityrosine cross-links in the presence of H2O2. By site-directed mutagenesis, we suggest that tyrosine 112 located in the FG loop is involved in this dimerization. Interestingly, this residue is not conserved in the sequence of the five rice non-symbiotic hemoglobins. Stopped-flow spectrophotometric experiments have been performed to measure the catalytic constants of rice Hb and its variants using the oxidation of guaiacol. We have shown that Tyrosine112 is a residue that enhances the peroxidase activity of rice Hb1, since its replacement by an alananine leads to a decrease of guaiacol oxidation. In contrast, tyrosine 151, a conserved residue which is buried inside the heme pocket, reduces the protein reactivity. Indeed, the variant Tyr151Ala exhibits a higher peroxidase activity than the wild type. Interestingly, this residue affects the heme coordination and the replacement of the tyrosine by an alanine leads to the loss of the distal ligand. Therefore, even if the amino acid at position 151 does not participate to the formation of the dimer, this residue modulates the peroxidase activity and plays a role in the hexacoordinated state of the heme.

Phenoxazinone Synthase-like Activity of Rationally Designed Heme Enzymes Based on Myoglobin

The design of functional metalloenzymes is attractive for the biosynthesis of biologically important compounds, such as phenoxazinones and phenazines catalyzed by native phenoxazinone synthase (PHS). To design functional heme enzymes, we used myoglobin (Mb) as a model protein and introduced an artificial CXXC motif into the heme distal pocket by F46C and L49C mutations, which forms a de novo disulfide bond, as confirmed by the X-ray crystal structure. We further introduced a catalytic Tyr43 into the heme distal pocket and found that the F43Y/F46C/L49C Mb triple mutant and the previously designed F43Y/F46S Mb exhibit PHS-like activity (80-98% yields in 5-15 min), with the catalytic efficiency exceeding those of natural metalloenzymes, including o-aminophenol oxidase, laccase, and dye-decolorizing peroxidase. Moreover, we showed that the oxidative coupling product of 1,6-disulfonic-2,7-diaminophenazine is a potential pH indicator, with the orange-magenta color change at pH 4-5 (pK_a = 4.40). Therefore, this study indicates that functional heme enzymes can be rationally designed by structural modifications of Mb, exhibiting the functionality of the native PHS for green biosynthesis.

Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere

Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.

Structural and functional regulations by a disulfide bond designed in myoglobin like human neuroglobin

An artificial disulfide bond (Cys46-Cys61) was designed in the heme distal site of myoglobin, which regulates the conformation of the heme distal His64 and the protein reactivity, as confirmed by X-ray crystallography, EPR, and kinetic UV-vis studies. This study shows the successful design of a disulfide bond with suitable positions in globins, conferring a structure and function like those of the native human neuroglobin.

In-depth research on percarbonate expediting zero-valent iron corrosion for conditioning anaerobically digested sludge

Anaerobically digested sludge (ADS) is commonly hard to dewater for the presence of extracellular polymeric substances (EPS) and the liberation of glutinous soluble microbic products during anaerobic digestion. Sodium percarbonate (SPC) expediting zero-valent iron (ZVI) corrosion (SPC/ZVI) process firstly conditioned ADS to amend its dewaterability. Results showed that SPC/ZVI conditioning decreased moisture content of dewatered cake from 90.5% (control) to 69.9% with addition of 0.10 g/g TS SPC and 0.20 g/g TS ZVI. Mechanistic research indicated that the enhanced ADS dewaterability mainly resulted from •OH and Fe(III)/iron polymers yielded in SPC/ZVI. •OH disrupted EPS, damaged cytoderm & cytomembrane, and lysed intracellular substances, unbinding the bound water. Meanwhile, the breakage and inactivation of microbe by •OH prompted the production of macro-pores in ADS. •OH adjusted the conformation of extracellular/intracellular proteins by intervening in the H-bonds and S-S bonds, availing the hydrophobicity and slight flocculation of ADS. •OH further facilitated the despiralization of α-helical to β-sheet structure in ADS pellets, benefiting cell-to-cell aggregation. Additionally, Fe(III)/iron polymers from ZVI corrosion accelerated to gather ADS and maintained its floc structure. Consequently, SPC/ZVI conditioning not only adjusted the natures of ADS and its EPS but also the features of residual pellets, which further induced the advancement of ADS dewaterability. In addition, SPC/ZVI conditioning possibly surmounts some limitations existing in ZVI/Peroxide or ZVI/Persulfate technique.

Crosslinking of human plasma C-reactive protein to human serum albumin via disulfide bond oxidation

Inter- and intra-molecular crosslinks can generate protein dysfunction, and are associated with protein aggregate accumulation in aged and diseased tissues. Crosslinks formed between multiple amino acid side chains can be reversible or irreversible. Disulfides formed either enzymatically, or as a result of oxidant-mediated reactions, are a major class of reversible crosslinks. Whilst these are commonly generated via oxidation of Cys thiol groups, they are also formed by ‘oxidant-mediated thiol-disulfide reactions’ via initial disulfide oxidation to a thiosulfinate or zwitterionic peroxide, and subsequent reaction with another thiol including those on other proteins. This generates new intermolecular protein-protein crosslinks. Here we demonstrate that photooxidation, or reaction with the biological oxidants HOCl and ONOOH, of the single disulfide present in the major human plasma inflammatory protein, C-reactive protein (CRP) can give rise to reversible disulfide bond formation with human serum albumin (HSA). This occurs in an oxidant dose-, or illumination-time-, dependent manner. These CRP-HSA crosslinks are formed both in isolated protein systems, and in fresh human plasma samples containing high, but not low, levels of CRP. The inter-protein crosslinks which involve Cys36 of CRP and Cys34 of HSA, have been detected by both immunoblotting and mass spectrometry (MS). The yield of protein-protein crosslinks depends on the nature and extent of oxidant exposure, and can be reversed by dithiothreitol and tris(2-carboxyethyl)phosphine hydrochloride. These data indicate that oxidation of disulfide bonds in proteins can be a source of novel inter-protein crosslinks, which may help rationalize the accumulation of crosslinked proteins in aged and diseased tissues.

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C-reactive protein (CRP) is a major acute phase inflammatory protein in human plasma.

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Oxidation of the single Cys36-Cys97 disulfide in CRP generates reactive intermediates.

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The oxidized disulfide reacts with Cys34 of human serum albumin to forms a new crosslink.

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The inter-protein CRP-HSA crosslink has been characterized by immunoblotting and LS-MS/MS.

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This novel crosslink may be a long-lived plasma marker of inflammation-induced damage.

Peroxide/Zero-valent iron (Fe0) pretreatment for promoting dewaterability of anaerobically digested sludge: A mechanistic study

Peroxide/Zero-valent iron (Fe⁰) was reported to promote dewaterability of anaerobically digested sludge (ADS), but the mechanism of how Peroxide/Fe⁰ facilitates ADS dewatering is unknown. This study therefore aims to uncover the details of how Peroxide/Fe° elevates ADS dewaterability. Experimental results showed that with 0.6 g Fe⁰/g TSS and 0.08 g peroxide/g TSS, capillary suction time, specific resistance to filtration, and time to filtration of ADS was 50.7 %, 41.4 %, and 54.4 % of that in the control, respectively. In this condition, water content of sludge cake decreased from 91.2 % ± 0.5 % (the control) to 68.6 % ± 1.3 %. The mechanism explorations revealed that the elevated dewaterability was mainly caused by role of OH and Fe(II)/Fe(III) species during Peroxide/Fe° pretreatment. OH decreased the polysaccharides and proteins in extracellular polymeric substance (EPS), then injured the cytoderm & cytomembrane through the releases of lactate dehydrogenase and N-acetylglucosamine, and further facilitated the decrease of intracellular substances, which disengaged the water trapped in ADS. In addition, the cell lysis caused by OH facilitated forming macro-pores. Moreover, OH converted the conformational structure of extracellular proteins, which may strengthen the ADS hydrophobicity, promoting the discharge of unbound water and ADS flocculation. Meanwhile, Fe(II)/Fe(III) benefited aggregating the denatured ADS particulates.

Surface-Confined Winding Assembly of Mesoporous Nanorods

Bending and folding are important stereoscopic geometry parameters of one-dimensional (1D) nanomaterials, yet the precise control of them has remained a great challenge. Herein, a surface-confined winding assembly strategy is demonstrated to regulate the stereoscopic architecture of uniform 1D mesoporous SiO2 (mSiO2) nanorods. Based on this brand-new strategy, the 1D mSiO2 nanorods can wind on the surface of 3D premade nanoparticles (sphere, cube, hexagon disk, spindle, rod, etc.) and inherit their surface topological structures. Therefore, the mSiO2 nanorods with a diameter of ∼50 nm and a variable length can be bent into arc shapes with variable radii and radians, as well as folded into 60, 90, 120, and 180° angular convex corners with controllable folding times. Additionally, in contrast to conventional core@shell structures, this winding structure induces partial exposure and accessibility of the premade nanoparticles. The functional nanoparticles can exhibit large accessible surface and efficient energy exchanges with the surroundings. As a proof of concept, winding-structured CuS&mSiO2 nanocomposites are fabricated, which are made up of a 100 nm CuS nanosphere and the 1D mSiO2 nanorods with a diameter of ∼50 nm winding the nanosphere in the perimeter. The winding structured nanocomposites are demonstrated to have fourfold photoacoustic imaging intensity compared with the conventional core@shell nanostructure with an inaccessible core because of the greatly enhanced photothermal conversion efficiency (increased by ∼30%). Overall, our work paves the way to the design and synthesis of 1D nanomaterials with controllable bending and folding, as well as the formation of high-performance complex nanocomposites.

New insight into modification of extracellular polymeric substances extracted from waste activated sludge by homogeneous Fe(II)/persulfate process

Fe(II)/persulfate process has been proven to be a promising technique for disintegrating sludge, while during the Fe(II)/persulfate treatment the direct information about the variation of extracellular polymeric substances (EPS) properties, which is a key factor affecting sludge dewatering, is still lacked. In this work, different dosages of Fe(II)/persulfate were employed to treat EPS fractions extracted from waste activated sludge. The experiment results showed that EPS fractions were modified by Fe(II)/persulfate process. An oxidation/flocculation process was raised to unveil how Fe(II)/persulfate modified EPS fractions: Firstly, SO₄^- and OH were formed by chemical reactions of Fe(II) activating persulfate and radical interconversion, respectively. Then these species nonselectively fragmented EPS fractions through decomposing their components, which facilitated decrement of the hydrophilic components and high/mid molecular weight of organics in EPS fractions. Furthermore, these radicals transformed the secondary structure of EPS proteins by affecting the hydrogen bonds at specific positions and inducing the cleavage of the S-S bonds in cysteine residues of proteins, which led to loose layout of protein molecules and thus increased exposure of the hydrophobic groups hidden in EPS protein molecules. Secondly, Fe(III), i.e., the oxidation product of Fe(II), assembled the ruptured colloids particles through lessening electronegativity. Consequently, Fe(II)/persulfate process elevated the flocculability and hydrophobicity of EPS fractions, which would improve physicochemical and rheological properties of sludge to facilitate its dewaterability.

Fe(II) catalyzing sodium percarbonate facilitates the dewaterability of waste activated sludge: Performance, mechanism, and implication

In this work, Fe(II) catalyzing sodium percarbonate (Fe(II)/SPC) was managed to facilitate waste activated sludge (WAS) dewatering for the first time. The results showed that after WAS was treated by 20 mg/g total suspended solids (TSS) Fe(II) and 50 mg/g TSS SPC, the water content of sludge cake (WC_SC) by press filtration and capillary suction time (CST) dropped from 90.8% ± 1.6% and 96.1 ± 4.0 s (the control) to 55.6% ± 1.4% and 30.1 ± 2.5 s, respectively. The mechanism investigations indicated that four intermediates or products (i.e., •OH, H₂O₂, Fe(II), and Fe(III)) generated in the Fe(II)/SPC process were responsible for the improved WAS dewaterability, and •OH and Fe(III) were the two major contributors. It was found that •OH collapsed and fragmented extracellular polymeric substances, damaged cell wall and permeabilized cytoplasmic membrane, and transformed conformation of the extracellular proteins secondary structure via both affecting the hydrogen bond maintaining α-helix and cracking disulfide bond in cysteine residues while Fe(III), the oxidization product of Fe(II), decreased the surface electronegativity and water-affinity surface areas of WAS flocs. As a result, the bound water release, flocculability, surface hydrophobicity, drain capability, and flowability of WAS flocs were strengthened whereas the compact surface structure, colloidal forces, network strength, gel-like structure, and apparent viscosity of WAS flocs were weakened. In addition, Fe(II)/SPC process also reduced the recalcitrant organics and fecal coliforms in sludge, which facilitated land application of dewatered sludge. The findings acquired in this work not only deepens our understanding of Fe(II)/SPC-involved WAS treatment process but also may guide engineers to develop both effective and promising strategies to better condition WAS for dewatering in the future.

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

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.

Enhancement of protein stability by an additional disulfide bond designed in human neuroglobin

Human neuroglobin (Ngb) forms an intramolecular disulfide bond between Cys46 and Cys55, with a third Cys120 near the protein surface, which is a promising protein model for heme protein design. In order to protect the free Cys120 and to enhance the protein stability, we herein developed a strategy by designing an additional disulfide bond between Cys120 and Cys15 via A15C mutation. The design was supported by molecular modeling, and the formation of Cys15–Cys120 disulfide bond was confirmed experimentally by ESI-MS analysis. Molecular modeling, UV-Vis and CD spectroscopy showed that the additional disulfide bond caused minimal structural alterations of Ngb. Meanwhile, the disulfide bond of Cys15–Cys120 was found to enhance both Gdn·HCl-induced unfolding stability (increased by ∼0.64 M) and pH-induced unfolding stability (decreased by ∼0.69 pH unit), as compared to those of WT Ngb with a single native disulfide bond of Cys46–Cys55. Moreover, the half denaturation temperature (T_m) of A15C Ngb was determined to be higher than 100 °C. In addition, the disulfide bond of Cys15–Cys120 has slight effects on protein function, such as an increase in the rate of O₂ release by ∼1.4-fold. This study not only suggests a crucial role of the artificial disulfide in protein stabilization, but also lays the groundwork for further investigation of the structure and function of Ngb, as well as for the design of other functional heme proteins, based on the scaffold of A15C Ngb with an enhanced stability.

A disulfide bond of Cys120 and Cys15 was rationally designed in human neuroglobin (Ngb) by A15C mutation, which caused minimal structural alterations, whereas enhanced both chemical and pH stability, with a thermal stability higher than 100 °C.

Regulation of both the structure and function by a de novo designed disulfide bond: a case study of heme proteins in myoglobin

The V21C/V66C/F46S myoglobin mutant, with a de novo designed intramolecular disulfide bond resembling that in cytoglobin without structural evidence, exhibits a dehalogenation activity exceeding that of a native dehaloperoxidase.

Distinct roles of a tyrosine-associated hydrogen-bond network in fine-tuning the structure and function of heme proteins: two cases designed for myoglobin

A hydrogen-bond (H-bond) network, specifically a Tyr-associated H-bond network, plays key roles in regulating the structure and function of proteins, as exemplified by abundant heme proteins in nature. To explore an approach for fine-tuning the structure and function of artificial heme proteins, we herein used myoglobin (Mb) as a model protein and introduced a Tyr residue in the secondary sphere of the heme active site at two different positions (107 and 138). We performed X-ray crystallography, UV-Vis spectroscopy, stopped-flow kinetics, and electron paramagnetic resonance (EPR) studies for the two single mutants, I107Y Mb and F138Y Mb, and compared to that of wild-type Mb under the same conditions. The results showed that both Tyr107 and Tyr138 form a distinct H-bond network involving water molecules and neighboring residues, which fine-tunes ligand binding to the heme iron and enhances the protein stability, respectively. Moreover, the Tyr107-associated H-bond network was shown to fine-tune both H2O2 binding and activation. With two cases demonstrated for Mb, this study suggests that the Tyr-associated H-bond network has distinct roles in regulating the protein structure, properties and functions, depending on its location in the protein scaffold. Therefore, it is possible to design a Tyr-associated H-bond network in general to create other artificial heme proteins with improved properties and functions.