[Show abstract][Hide abstract] ABSTRACT: The catalytic activity of cytochrome c (cyt c) to peroxidize cardiolipin to its oxidized form is required for the release of pro-apoptotic factors from mitochondria, and for execution of the subsequent apoptotic steps. However, the structural basis for this peroxidation reaction remains unclear. In this paper, we determined the three-dimensional NMR solution structure of yeast cyt c Y67H variant with high peroxidase activity, which is almost similar to that of its native form. The structure reveals that the hydrogen bond between Met80 and residue 67 is disrupted. This change destabilizes the sixth coordination bond between heme Fe3+ ion and Met80 sulfur atom in the Y67H variant, and further makes it more easily be broken at low pH conditions. The steady-state studies indicate that the Y67H variant has the highest peroxidase activities when pH condition is between 4.0 and 5.2. Finally, a mechanism is suggested for the peroxidation of cardiolipin catalyzed by the Y67H variant, where the residue His67 acts as a distal histidine, its protonation facilitates O-O bond cleavage of H2O2 by functioning as an acidic catalyst.
[Show abstract][Hide abstract] ABSTRACT: The differences between mouse mA beta(1-42) and human hA beta(1-42), explored using CD and fluorescence spectroscopy, transmission electron microscopy, ROS fluorescent assay, and neuronal cell viability, revealed that mA beta(1-42) as a three-site mutant (R5G, Y10F and H13R) of hA beta(1-42) altered the metal (copper and zinc) binding sites, reduced the proneness to form beta-sheet structures and aggregated fibrils, alleviated the generation of ROS, and decreased the cytotoxicity, in contrast to hA beta(1-42).
No preview · Article · May 2013 · Chemical Communications
[Show abstract][Hide abstract] ABSTRACT: The continued interest in protein engineering has led to intense efforts in developing novel stable enzymes, which could not only give boost to industrial and biomedical applications, but also enhance our understanding of the structure-function relationships of proteins. We present here the generation of three hybrid proteins of cytochrome c (cyt c) and peroxidase via structure-based rational mutagenesis of cyt c. Several residues (positions 67, 70, 71 and 80) in the distal heme region of cyt c were mutated to the highly conserved amino acids in the heme pocket of peroxidases. The multiple mutants were found to exhibit high peroxidase activity and conserve the impressive stability of cyt c. We expect that this strategy could be extended to other cases of metalloprotein engineering, and lead to the development of stable and active biocatalysts for industrial uses. Besides, this study also provides insight into the structure-function relationships of hemoproteins.
No preview · Article · Mar 2013 · Protein Engineering Design and Selection
[Show abstract][Hide abstract] ABSTRACT: Truncated acetyl-coenzyme A synthase (ACS) was successfully converted into functional nickel superoxide dismutase (Ni-SOD) by molecular design and the designed metalloproteins possess new spectroscopic, structural, and electrochemical characteristics required for catalyzing O(2)˙(-) disproportionation, and exhibit impressive Ni-SOD activity.
No preview · Article · Jan 2013 · Chemical Communications
[Show abstract][Hide abstract] ABSTRACT: Aggregation and cytotoxicity of Aβ with redox-active metals in neuronal cells have been implicated in the progression of Alzheimer disease. Human metallothionein (MT) 3 is highly expressed in the normal human brain and is downregulated in Alzheimer disease. Zn(7)MT3 can protect against the neuronal toxicity of Aβ by preventing copper-mediated Aβ aggregation, abolishing the production of reactive oxygen species (ROS) and the related cellular toxicity. In this study, we intended to decipher the roles of single-domain proteins (α/β) and the α-β domain-domain interaction of Zn(7)MT3 to determine the molecular mechanism for protection against the neuronal cytotoxicity of Aβ(1-42) with copper ions. With this in mind, the α and β single-domain proteins, heterozygous β(MT3)-α(MT1), and a linker-truncated mutant ∆31-34 were prepared and characterized. In the presence/absence of various Zn(7)MT3 proteins, the Aβ(1-42)-Cu(2+)-mediated aggregation, the production of ROS, and the cellular toxicity were investigated by transmission electron microscopy, ROS assay by means of a fluorescent probe, and SH-SY5Y cell viability, respectively. The β domain cannot abolish Aβ(1-42)-Cu(2+)-induced aggregation, and neither the β domain nor the α domain can quench the production of ROS because of the redox cycling of Aβ-Cu(2+). Similarly to wild-type Zn(7)MT3, the heterozygous β(MT3)-α(MT1) possesses the characteristic of alleviating Aβ(1-42) aggregation and oxidative stress to neuronal cells. Therefore, the two domains through the linker Lys-Lys-Ser form a cooperative unit, and each of them is indispensable in conducting its bioactivity. The α domain plays an important role in modulating the stability of the metal-thiolate cluster, and the α-β domain-domain interaction through the linker is critical for its protective role in the brain.
No preview · Article · Oct 2012 · European Journal of Biochemistry
[Show abstract][Hide abstract] ABSTRACT: Soluble guanylate cyclase (sGC) mediates NO signaling for a wide range of physiological effects in the cardiovascular system and the central nervous system. The α1β1 isoform is ubiquitously distributed in cytosolic fractions of tissues, whereas α2β1 is mainly found in the brain. The major occurrence and the unique characteristic of human sGC α2β1 indicate a special role in the mediation of neuronal communication. We have efficiently purified and characterized the recombinant heme-binding domain of the human sGC α2 subunit (hsGC α2H) and heterodimeric α2β1 (hsGC β1H–α2H) by UV–vis spectroscopy, circular dichrosim spectroscopy, EPR spectroscopy, and homology modeling. The heme dissociation and related NO/CO binding/dissociation of both hsGC α2H and hsGC β1H–α2H were investigated. The two truncated proteins interact with heme noncovalently. The CO binding affinity of hsGC α2H is threefold greater than that of human sGC α1H, whereas the dissociation constant k
1 for dissociation of NO from hsGC α2H is sevenfold larger than that for dissociation of NO from hsGC α1H, although k
2 is almost identical. The results indicate that in comparison with the α1β1 isoform, the brain α2β1 isoform exhibits a distinctly different CO/NO affinity and binding rate in favor of NO signaling, and this is consistent with its physiological role in the activation and desensitization. Molecular modeling and sequence alignments are consistent with the hypothesis that His105 contributes to the different CO/NO binding properties of different isoforms. This valuable information is helpful to understand the molecular mechanism by which human sGC α2β1 mediates NO/CO signaling.
No preview · Article · Mar 2012 · European Journal of Biochemistry
[Show abstract][Hide abstract] ABSTRACT: To convert cyt c into a peroxidase-like metalloenzyme, the P71H mutant was designed to introduce a distal histidine. Unexpectedly, its peroxidase activity was found even lower than that of the native, and that the axial ligation of heme iron was changed to His71/His18 in the oxidized state, while to Met80/His18 in the reduced state, characterized by UV-visible, circular dichroism, and resonance Raman spectroscopy. To further probe the functional importance of Pro71 in oxidation state dependent conformational changes occurred in cyt c, the solution structures of P71H mutant in both oxidation states were determined. The structures indicate that the half molecule of cyt c (aa 50-102) presents a kind of "zigzag riveting ruler" structure, residues at certain positions of this region such as Pro71, Lys73 can move a big distance by altering the tertiary structure while maintaining the secondary structures. This finding provides a molecular insight into conformational toggling in different oxidation states of cyt c that is principle significance to its biological functions in electron transfer and apoptosis. Structural analysis also reveals that Pro71 functions as a key hydrophobic patch in the folding of the polypeptide of the region (aa 50-102), to prevent heme pocket from the solvent.
[Show abstract][Hide abstract] ABSTRACT: Human soluble guanylate cyclase (sGC), a critical heme-containing enzyme in the NO-signaling pathway of eukaryotes, is an αβ heterodimeric hemoprotein. Upon the binding of NO to the heme, sGC catalyzes the conversion of GTP to cyclic GMP, playing a crucial role in many physiological processes. However, the specific contribution of the α and β subunits of sGC in the intact heme binding remained intangible. The recombinant human sGC α1 subunit has been expressed in Escherichia coli and characterized for the first time. The heme binding and related NO/CO binding properties of both the α1 subunit and the β1 subunit were investigated via heme reconstitution, UV-vis spectroscopy, EPR spectroscopy, stopped-flow kinetics, and homology modeling. These results indicated that the α1 subunit of human sGC, lacking the conserved axial ligand, is likely to interact with heme noncovalently. On the basis of the equilibrium and kinetics of CO binding to sGC, one possible CO binding model was proposed. CO binds to human sGCβ195 by simple one-step binding, whereas CO binds to human sGCα259, possibly from both axial positions through a more complex process. The kinetics of NO dissociation from human sGC indicated that the NO dissociation from sGC was complex, with at least two release phases, and human sGCα259 has a smaller k (1) but a larger k (2). Additionally, the role of the cavity of the α1 subunit of human sGC was explored, and the results indicate that the cavity likely accommodates heme. These results are beneficial for understanding the overall structure of the heme binding site of the human sGC and the NO/CO signaling mechanism.
No preview · Article · Jul 2011 · European Journal of Biochemistry
[Show abstract][Hide abstract] ABSTRACT: The β-amyloid peptide (Aβ) aggregation in the brain, known as amyloid plaques, is a hallmark of Alzheimer's disease (AD). The aberrant interaction of Cu(2+) ion with Aβ potentiates AD by inducing Aβ aggregation and generating neurotoxic reactive oxygen species (ROS). In this study, the biosynthesized recombinant Aβ(1-40) was, for the first time, used to investigate the mechanism for heme to prevent Aβ(1-40) aggregation and its cytotoxicity. Cell viability studies of SH-SY5Y cells and rat primary hippocampal neurons showed that exogenous heme can protect the cells by reducing cytotoxicity in the presence of Cu(2+) and/or Aβ(1-40). UV-vis spectroscopy, circular dichroism spectroscopy, and differential pulse voltammetry were applied to examine the interaction between heme and Aβ(1-40). It was proven that a heme-Aβ(1-40) complex is formed and can stabilize the α-helix structure of Aβ(1-40) to inhibit Aβ(1-40) aggregation. The heme-Aβ(1-40) complex possesses peroxidase activity and it may catalyze the decomposition of H(2)O(2), reduce the generation of ROS downstream, and ultimately protect the cells. These results indicated that exogenous heme is able to alleviate the cytotoxicity induced by Aβ(1-40) and Cu(2+). This information may be a foundation to develop a potential strategy to treat AD.
No preview · Article · Jun 2011 · European Journal of Biochemistry
[Show abstract][Hide abstract] ABSTRACT: The cytochrome P450 (CYP) superfamily plays a key role in the oxidative metabolism of a wide range of drugs and exogenous chemicals. CYP2C8 is the principal enzyme responsible for the metabolism of the anti-cancer drug paclitaxel in the human liver. Nearly all previous works about polymorphic variants of CYP2C8 were focused on unpurified proteins, either cells or human liver microsomes; therefore their structure-function relationships were unclear. In this study, two polymorphic enzymes of CYP2C8 (CYP2C8.4 (I264M) and CYP2C8 P404A) were expressed in E. coli and purified. Metabolic activities of paclitaxel by the two purified polymorphic enzymes were observed. The activity of CYP2C8.4 was 25% and CYP2C8 P404A was 30% of that of WT CYP2C8, respectively. Their structure-function relationships were systematically investigated for the first time. Paclitaxel binding ability of CYP2C8.4 increased about two times while CYP2C8 P404A decreased about two times than that of WT CYP2C8. The two polymorphic mutant sites of I264 and P404, located far from active site and substrate binding sites, significantly affect heme and/or substrate binding. This study indicated that two important nonsubstrate recognition site (SRS) residues of CYP2C8 are closely related to heme binding and/or substrate binding. This discovery could be valuable for explaining clinically individual differences in the metabolism of drugs and provides instructed information for individualized medication.
[Show abstract][Hide abstract] ABSTRACT: Novel hybrid proteins based on cytochrome c (Cyt c) and cytochrome P450 (CYP450) were constructed. They retain the good stability of Cyt c and acquire the catalytic activity of CYP450. More strikingly, the peroxidase activity of one particular hybrid protein is more than 40 times greater than that of Cyt c.
[Show abstract][Hide abstract] ABSTRACT: The Wood-Ljungdahl pathway is responsible for acetyl-CoA biosynthesis and used as a major mean of generating energy for growth in some anaerobic microbes. Series of genes, from the anaerobic human pathogen Clostridium difficile, have been identified that show striking similarity to the genes involved in this pathway including methyltetrahydrofolate- and corrinoid-dependent methyltransferase. This methyltransferase plays a central role in this pathway that transfers the methyl group from methyltetrahydrofolate to a cob(I)amide center in the corrinoid iron-sulfur protein. In this study, we developed two efficient expression and purification methods for methyltransferase from C. difficile for the first time with two expression vectors MBPHT-mCherry2 and pETDuet-1, respectively. Using the latter vector, more than 50mg MeTr was produced per liter Luria-Bertani broth media. The recombinant methyltransferase was well characterized by SDS-PAGE, gel filtration chromatography, enzyme assay and far-UV circular dichroism (CD). Furthermore, a highly effective approach was established for determining the methyl transfer activity of the methyltetrahydrofolate- and cobalamin-dependent methyltransferase using exogenous cobalamin as a substrate by stopped-flow method. These results will provide a solid basis for further study of the methyltransferase and the Wood-Ljungdahl pathway.
No preview · Article · Feb 2011 · Protein Expression and Purification
[Show abstract][Hide abstract] ABSTRACT: The A-cluster of acetyl-coenzyme A synthase consists of an [Fe(4)S(4)] cubane bridged to a [Ni(p)Ni(d)] centre via C509 cysteinate. The bridging cysteinate, which could be substituted by histidine imidazole, mediates "communication" between the [Fe(4)S(4)] cubane and the [Ni(p)Ni(d)] centre during the synthesis of acetyl-coenzyme A.
Full-text · Article · Jan 2011 · Chemical Communications
[Show abstract][Hide abstract] ABSTRACT: Glu44, Glu48, Ghi56 and Asp60 are the negatively charged residues located at the molecular surface of cytochrome b5. Two mutants of cytochrome b5 were prepared, in which two or all of these four residues were mutated to alanines. The mutations give rise to slightly positive shifts of the redox potentials of cytochrome b5 and obvious decrease of the cytochrome b5-cytochrome c binding constants and electron transfer rates. The crystal structures of the two mutants were determined at 0.18 nm resolution, showing no alteration in overall structures and exhibiting slight changes in the local conformations around the mutation sites as compared with the wild-type protein. Based on the crystal structure of the quadruple-site mutant, a model for the binding of this mutant with cytochrome c is proposed, which involves the salt bridges from Glu37, Glu38 and heme propionate of cytochrome b5 to three lysines of cytochrome c and can well account for the properties and behaviors of this mutant.
No preview · Article · Nov 2010 · Chinese Journal of Chemistry
[Show abstract][Hide abstract] ABSTRACT: In order to illustrate the roles played by Pro40 in the structure, properties and functions of Cytochrome b5, three mutated genes, P40V, P40Y, P40G were constructed in this work. Only the P40V gene was successfully expressed into holoprotein in E. coli JM83. According to the results of X-ray crystallographic analysis and various kinds of spectroscopy studies, it is evident that substituting valine for Pro40 does not result in significant alterations in the protein′s overall structure; however, local conformational perturbations in the proximity of the heme do occur. The redox potential of the P40V mutant is 40 mV lower than that of the wild type protein. Its stability towards heat, urea, acid and ethanol were significantly decreased. The mutation leads to a decrease in the hydrophobicity of the heme pocket, which is probably the major factor contributing to the above changes. Binding constants and electron transfer rates between cytochrome bs and cytochrome c were determined using UV-visible spectroscopy and stopped-flow techniques for both the wild type and the mutant. The results showed that the substitution of Pro40 by valine does not influence the binding constant of cytochrome b5 to cytochrome c; however, the electron transfer rate between them decreased significantly. This indicates that proline-40 is essential to maintaining cytochrome bss stability and its electron transfer with cytochrome c. These studies also provided a good example that property and functional changes of a protein do not necessarily require large overall structural alterations; in most cases, only perturbations on the local conformations are sufficient to induce significant changes in protein′s properties and functions.
No preview · Article · Nov 2010 · Chinese Journal of Chemistry
[Show abstract][Hide abstract] ABSTRACT: Soluble guanylate cyclase (sGC), as a nitric oxide (NO) sensor, is a critical heme-containing enzyme in NO-signaling pathway of eukaryotes. Human sGC is a heterodimeric hemoprotein, composed of a alpha-subunit (690 AA) and a heme-binding beta-subunit (619 AA). Upon NO binding, sGC catalyzes the conversion of guanosine 5'-triphosphate (GTP) to 3',5'-cyclic guanosine monophosphate (cGMP). cGMP is a second messenger and initiates the nitric oxide signaling, triggering vasodilatation, smooth muscle relaxation, platelet aggregation, and neuronal transmission etc. The breakthrough of the bottle neck problem for sGC-mediated NO singling was made in this study. The recombinant human sGC beta1 subunit (HsGC beta 619) and its truncated N-terminal fragments (HsGC beta 195 and HsGC beta 384) were efficiently expressed in Escherichia coli and purified successfully in quantities. The three proteins in different forms (ferric, ferrous, NO-bound, CO-bound) were characterized by UV-vis and EPR spectroscopy. The homology structure model of the human sGC heme domain was constructed, and the mechanism for NO binding to sGC was proposed. The EPR spectra showed a characteristic of five-coordinated heme-nitrosyl species with triplet hyperfine splitting of NO. The interaction between NO and sGC was investigated and the schematic mechanism was proposed. This study provides new insights into the structure and NO-binding of human sGC. Furthermore, the efficient expression system of E. coli will be beneficial to the further studies on structure and activation mechanism of human sGC.
[Show abstract][Hide abstract] ABSTRACT: Neuronal growth-inhibitory factor (GIF), also named metallothionein-3, inhibits the outgrowth of neuronal cells. Recent studies on the structure of human GIF, carried out using NMR and molecular dynamics simulation techniques, have been summarized. By studying a series of protein-engineered mutants of GIF, we showed that the bioactivity of GIF is modulated by multiple factors, including the unique TCPCP motif-induced characteristic conformation, the solvent accessibility and dynamics of the metal-thiolate cluster, and the domain-domain interactions.
[Show abstract][Hide abstract] ABSTRACT: Neuronal growth inhibitory factor (GIF), also known as metallothionein (metallothionein-3), impairs the survival and neurite formation of cultured neurons. It is known that the alpha-beta domain-domain interaction of hGIF is crucial to the neuron growth inhibitory bioactivity although the exact mechanism is not clear. Herein, the beta(MT3)-beta(MT3) mutant and the hGIF-truncated Delta33-35 mutant were constructed, and their biochemical properties were characterized by pH titration, EDTA, and DTNB reactions. Their inhibitory activity toward neuron survival and neurite extension was also examined. We found that the Delta33-35 mutant alpha-domain containing beta-domain-like M(3)S(9) cluster exhibits the function of alpha-domain with M(4)S(11) cluster in hGIF. These results showed that the stability and solvent accessibility of the metal-thiolate cluster in beta-domain is very significant to the neuronal growth inhibitory activity of hGIF and also indicated that the particular primary structure of alpha-domain is pivotal to domain-domain interaction in hGIF.
Full-text · Article · May 2010 · Bioinorganic Chemistry and Applications
[Show abstract][Hide abstract] ABSTRACT: We demonstrate for the first time that cytochrome c undergoes a distinct pathway in the alkaline conformational transition from its pro-apoptotic conformational transition, which may have important functional consequences in vivo.
No preview · Article · Apr 2010 · Chemical Communications