Chloroperoxidase (CPO), secreted by marine fungus Caldariomyces fumago, is the most versatile catalyst among known heme enzymes. Chloroperoxidase can catalyze epoxidation reactions with high enantioselectivity and high yield, which makes CPO an attractive candidate for both industrial and medicinal chiral synthesis. Toward this end, we have constructed two CPO mutants, F103A and N74V. Chiral HPLC was used to evaluate the enantioselectivity and yield of CPO and the mutants toward the epoxidation of styrene and its derivatives. Both of the mutants show dramatically changed epoxidation profiles compared to the parent protein. This information provided fresh insight into the mechanism through which CPO achieves its enantioselectivity. Furthermore, effort was made to understand the biological function of CPO through characterization of CPO catalyzed oxidation of dimethylsulfoniopropionate (DMSP), a secondary metabolite of many marine algal species that plays a pivotal role in marine ecology and global climate.

While genetic improvement of susceptible crop species may enhance resistance to microbial pathogens and facilitate reduced pesticide load, the possibility for transmission of novel genes to wild relatives has hampered acceptance of GM crops in some markets. Chloroplast transformation presents an attractive alternative to nuclear transformation and offers the potential to ameliorate these environmental concerns. Most agronomically important species exhibit maternal inheritance of organellar genomes which eliminates the threat of transgene escape through pollen. Gene silencing is absent due to site directed, single copy insertion by homologous recombination. Foreign proteins can accumulate to high levels (up to 50% of total soluble protein) and are retained within the chloroplast envelope protecting them from degradation by host cytoplasmic proteases. A bacterial chloroperoxidase gene (cpo-p) was transformed into the tobacco chloroplast genome to test its efficacy against plant pathogens and the mycotoxin producing saprophyte Aspergillus flavus.

Mechanistically and structurally chloroperoxidase (CPO) occupies a unique niche among heme containing enzymes. Chloroperoxidase catalyzes a broad range of reactions, such as oxidation of organic substrates, dismutation of hydrogen peroxide, and mono-oxygenation of organic molecules. To expand the synthetic utility of CPO and to appreciate the important interactions that lead to CPO’s exceptional properties, a site-directed mutagenesis study was undertaken. Recombinant CPO and CPO mutants were heterologously expressed in Aspergillus niger. The overall protein structure was almost the same as that of wild type CPO, as determined by UV-vis, NMR and CD spectroscopies. Phenylalanine103, which was proposed to regulate substrate access to the active site by restricting the size of substrates and to control CPO’s enantioselectivity, was mutated to Ala. The ligand binding affinity and most importantly the catalytic activity of F103A was dramatically different from wild type CPO. The mutation essentially eliminated the chlorination and dismutation activities but enhanced, 4-10 fold, the epoxidation, peroxidation, and N-demethylation activities. As expected, the F103A mutant displayed dramatically improved epoxidation activity for larger, more branched styrene derivatives. Furthermore, F103A showed a distinctive enantioselectivity profile: losing enantioselectivity to styrene and cis-β-methylstyrene; having a different configuration preference on α-methylstyrene; showing higher enatioselectivites and conversion rates on larger, more branched substrates. Our results show that F103 acts as a switch box that controls the catalytic activity, substrate specificity, and product enantioselectivity of CPO. Given that no other mutant of CPO has displayed distinct properties, the results with F103A are dramatic. The diverse catalytic activity of CPO has long been attributed to the presence of the proximal thiolate ligand. Surprisingly, a recent report on a C29H mutant suggested otherwise. A new CPO triple mutant C29H/C79H/C87H was prepared, in which all the cysteines were replaced by histidine to eliminate the possibility of cysteine coordinating to the heme. No active form protein was isolated, although, successful transformation and transcription was confirmed. The result suggests that Cys79 and Cys87 are critical to maintaining the structural scaffold of CPO. In vitro biodegradation of nanotubes by CPO were examined by scanning electron microscope method, but little oxidation was observed.

Hemoproteins are a very important class of enzymes in nature sharing the essentially same prosthetic group, heme, and are good models for exploring the relationship between protein structure and function. Three important hemoproteins, chloroperoxidase (CPO), horseradish peroxidase (HRP), and cytochrome P450cam (P450cam), have been extensively studied as archetypes for the relationship between structure and function. In this study, a series of 1D and 2D NMR experiments were successfully conducted to contribute to the structural studies of these hemoproteins. During the epoxidation of allylbenzene, CPO is converted to an inactive green species with the prosthetic heme modified by addition of the alkene plus an oxygen atom forming a five-membered chelate ring. Complete assignment of the NMR resonances of the modified porphyrin extracted and demetallated from green CPO unambiguously established the structure of this porphyrin as an NIII-alkylated product. A novel substrate binding motif of CPO was proposed from this concluded regiospecific N-alkylation structure. Soybean peroxidase (SBP) is considered as a more stable, more abundant and less expensive substitute of HRP for industrial applications. A NMR study of SBP using 1D and 2D NOE methods successfully established the active site structure of SBP and consequently fills in the blank of the SBP NMR study. All of the hyperfine shifts of the SBP-CN- complex are unambiguously assigned together with most of the prosthetic heme and all proximal His170 resonances identified. The active site structure of SBP revealed by this NMR study is in complete agreement with the recombinant SBP crystal structure and is highly similar to that of the HRP with minor differences. The NMR study of paramagnetic P450cam had been greatly restricted for a long time. A combination of 2D NMR methods was used in this study for P450cam-CN- complexes with and without camphor bound. The results lead to the first unequivocal assignments of all heme hyperfine-shifted signals, together with certain correlated diamagnetic resonances. The observed alternation of the assigned novel proximal cysteine β-CH2 resonances induced by camphor binding indicated a conformational change near the proximal side.

The widespread use of synthetic drugs and as feed additives has resulted in the release of large amounts of biologically active chemicals into the environment. Exposure to environmentally relevant concentrations of chemicals can have severe effects on human health. Therefore, effective degradation of these synthetic, biologically active compounds is of paramount importance. Diphenhydramine (DPH) has been selected as a target compound for ultrasound remediation. The results demonstrated that ultrasound-induced degradation has potential applications in managing aqueous media contaminated with DPH. Atorvastatin and roxarsone have been selected as representative substrates for chloroperoxidase (CPO) catalyzed transformation of pollutants. These studies demonstrate atorvastatin and roxarsone can be degraded efficiently by CPO. The transformation products of each compound were identified and the mechanisms of CPO catalysis postulated. This study provides a foundation for assessing the feasibility of applying CPO in the remediation of water and soil contaminated with pharmaceuticals and feed additives.

Chloroperoxidase (CPO) from Caldariomyces fumago is a versatile heme enzyme with great potential for environmental and pharmaceutical applications. It catalyzes a plethora of reactions including halogenation, dismutation, epoxidation, and oxidation. The diverse catalytic capabilities of CPO have long been attributed to the protein’s distinct active site that combines structural features of peroxidases and cytochromes P450. Particularly, the role of the axial thiolate ligand in CPO catalysis has been much debated. Furthermore, no data are available on the role of hydrogen bonding between Arg 26-Asn 37 and Ala 27-Asn 33 of the proximal helix in defining the structural and catalytic properties of CPO. In order to investigate the influence of the proximal thiolate and the proximal hydrogen bond network on the structural and biochemical properties of CPO, several mutant CPOs were constructed and characterized using various spectroscopic techniques and enzymatic assays. Cysteine 29, which coordinates to the heme, was replaced with a His (C29H) to mimic the proximal ligation of classical peroxidases. The UV-Vis spectrum of the carbon monoxide complex of ferrous C29H mutant remained essentially identical to that of wild type (WT) CPO and P450 although the ferric state of the variant enzyme showed a spectral pattern reminiscent of a classical histidine ligated heme peroxidase. Histidine ligation was further confirmed by paramagnetic NMR spectroscopy. Contrary to a previous report, the specific chlorination activity of C29H was essentially abolished (less than 1% of that of WT CPO) but the epoxidation and peroxidation activities were enhanced 10-fold and 55-fold, respectively. These findings demonstrate for the first time that the heme ligand, Cys 29 in CPO, is not a prerequisite for CPO’s unique P450-like spectroscopic signatures but is constitutive for the protein’s versatile catalytic activities. Arginine 26 and Asparagine 33 in the proximal heme pocket were replaced with Ala (R26A, N33A, and R26A/N33A) to disrupt hydrogen bonding. Tertiary structures and heme environments of R26A, N33A, and R26A/N33A differed from those of WT CPO as determined by CD spectroscopy. The specific chlorination and dismutation activities of all mutants were almost abolished but the peroxidation and epoxidation rates were increased. These results show that the proximal hydrogen bond network plays an important role in maintaining the structure and catalytic diversity of CPO.

Chloroperoxidase (CPO) is a heme-thiolate protein with exceptional versatility and great potential as a biocatalyst. The CPO reactive species, Compound I ( Cpd I) is of particular interest, as well as the Cytochrome P450 (P450) -type monoxygenase catalytic activity, which has significant biotechnological potential. Proximal hydrogen bonding of the axial sulfur with the backbone amides (NH•••S) is a conserved feature of heme-thiolate enzymes. In CPO, the effect of NH•••S bonds is amplified by the dipole moment of the proximal helix. The role of the proximal region has been disputed as to whether it simply protects the axial sulfur, or whether it additionally influences catalysis via modulation of the push effect. The objective of the research presented herein is two-fold. First, the influence of the NH•••S bonds on Cpd I formation is determined by obtaining the reaction coordinate, starting from a peroxide bound heme, for two model systems (one with proximal residues providing NH•••S bonds and one without) and comparing the results. Secondly, the influence of the proximal region on the epoxidation of Cis-β-methylsterene is obtained. This is performed similarly to the first objective however, the reaction coordinate begins with a Cpd I-CBMS complex and the proximal contribution is extended to include the influence of the proximal helix dipole. Our findings show that the proximal region stabilizes Cpd 0 relative to all other minima and reduces the barrier for Cpd 0’s formation. The stability of protonated Compound 0 is reduced, favoring a hybrid homo-heterolytic relative to a classic heterolytic mechanism for O-O bond scission. Additionally, the proximal region significantly enhances CPO’s reactivity; the Cβ-O bond barrier is stabilized, while Cα-O-Cβ ring closure becomes barrierless. The stabilization of the reaction barrier correlates with increased electron density transfer to residues of the proximal pocket and involves a change in the electron transfer mechanism. These results can be traced to a reduction in the pKa of the heme-bound substrate and an increase in oxidation potential, a result of the proximal region reducing the “push effect”.

Chloroperoxidase (CPO) is the most versatile heme-containing enzyme that catalyzes a broad spectrum of reactions. The remarkable feature of this enzyme is the high regio- and enantio-selectivity exhibited in CPO-catalyzed oxidation reactions. The aim of this dissertation is to elucidate the structural basis for regio- and enantio-selective transformations and investigate the application of CPO in biodegradation of synthetic dyes. To unravel the mechanism of CPO-catalyzed regioselective oxidation of indole, the dissertation explored the structure of CPO-indole complex using paramagnetic relaxation and molecular modeling. The distances between the protons of indole and the heme iron revealed that the pyrrole ring of indole is oriented toward the heme with its 2-H pointing directly at the heme iron. This provides the first experimental and theoretical explanation for the "unexpected" regioselectivity of CPO-catalyzed indole oxidation. Furthermore, the residues including Leu 70, Phe 103, Ile 179, Val 182, Glu 183, and Phe 186 were found essential to the substrate binding to CPO. These results will serve as a lighthouse in guiding the design of CPO mutants with tailor-made activities for biotechnological applications. To understand the origin of the enantioselectivity of CPO-catalyzed oxidation reactions, the interactions of CPO with substrates such as 2-(methylthio)thiophene were investigated by nuclear magnetic resonance spectroscopy (NMR) and computational techniques. In particular, the enantioselectivity is partly explained by the binding orientation of substrates. In third facet of this dissertation, a green and efficient system for degradation of synthetic dyes was developed. Several commercial dyes such as orange G were tested in the CPO-H2O2-Cl- system, where degradation of these dyes was found very efficient. The presence of halide ions and acidic pH were found necessary to the decomposition of dyes. Significantly, the results revealed that this degradation of azo dyes involves a ferric hypochlorite intermediate of CPO (Fe-OCl), compound X.

Chloroperoxidase (CPO) is a potential biocatalyst for use in asymmetric synthesis. The mechanisms of CPO catalysis are therefore of interest. The halogenation reaction, one of several chemical reactions that CPO catalyzes, is not fully understood and is the subject of this dissertation. The mechanism by which CPO catalyzes halogenation is disputed. It has been postulated that halogenation of substrates occurs at the active site. Alternatively, it has been proposed that hypochlorous acid, produced at the active site via oxidation of chloride, is released prior to reaction, so that halogenation occurs in solution. The free-solution mechanism is supported by the observation that halogenation of most substrates often occurs non-stereospecifically. On the other hand, the enzyme-bound mechanism is supported by the observation that some large substrates undergo halogenation stereospecifically. The major purpose of this research is to compare chlorination of the substrate beta-cyclopentanedione in the two environments. One study was of the reaction with limited hydration because such a level of hydration is typical of the active site. For this work, a purely quantum mechanical approach was used. To model the aqueous environment, the limited hydration environment approach is not appropriate. Instead, reaction precursor conformations were obtained from a solvated molecular dynamics simulation, and reaction of potentially reactive molecular encounters was modeled with a hybrid quantum mechanical/molecular mechanical approach. Extensive work developing parameters for small molecules was pre-requisite for the molecular dynamics simulation. It is observed that a limited and optimized (active-site-like) hydration environment leads to a lower energetic barrier than the fully solvated model representative of the aqueous environment at room temperature, suggesting that the stable water network near the active site is likely to facilitate the chlorination mechanism. The influence of the solvent environment on the reaction barrier is critical. It is observed that stabilization of the catalytic water by other solvent molecules lowers the barrier for keto-enol tautomerization. Placement of water molecules is more important than the number of water molecules in such studies. The fully-solvated model demonstrates that reaction proceeds when the instantaneous dynamical water environment is close to optimal for stabilizing the transition state.

Chloroperoxidase (CPO) is a heme-containing glycoprotein secreted by the marine fungus Caldariomyces fumago. Chloroperoxidase contains one ferriprotoporphyrin IX prosthetic group per molecule and catalyzes a variety of reactions, such as halogenation, peroxidation and epoxidation. The versatile catalytic activities of CPO coupled with the increasing demands for chiral synthesis have attracted an escalating interest in understanding the mechanistic and structural properties of this enzyme. In order to better understand the mechanisms of CPO-catalyzed enantioselective reactions and to fine-tune the catalytic properties of chloroperoxidase, asparagine 74 (N74) located in the narrow substrate access channel of CPO was replaced by a bulky, nonpolar valine and a polar glutamine using site-directed mutagenesis. The CPO N74 mutants displayed significantly enhanced activity toward nonpolar substrates compared to wild-type CPO as a result of changes in space and polarity of the heme distal environment. More interestingly, N74 mutants showed dramatically decreased chlorination and catalase activity but significantly enhanced epoxidation activity as a consequence of improved kinetic perfection introduced by the mutation as reflected by the favorable changes in kcat and kcat/KM of these reactions. It is also noted that the N74V mutant is capable of decomposing cyanide, the most notorious poison for many hemoproteins, as judged by the unique binding behavior of N74V with potassium cyanide. Histidine 105 (H105) was replaced by a nonpolar amino acid alanine using site-directed mutagenesis. The CPO H105 mutant (H105A) displayed dramatically decreased chlorination and catalase activity possibly because of the decreased polarity in the heme distal environment and loss of the hydrogen bonds between histidine 105 and glutamic acid 183. However, significantly increased enantioselectivity was observed for the epoxidation of bulky styrene derivatives. Furthermore, my study provides strong evidence for the proposed histidine/cysteine ligand switch in chloroperoxidase, providing experimental support for the structure of the 420-nm absorption maximum for a number of carbon monoxide complexes of heme-thiolate proteins. For the NMR study, [dCPO(heme)] was produced using 90% deuterated growth medium with excess heme precursors and [dCPO(Phe)] was grown in the same highly deuterated medium that had been supplemented with excess natural phenylalanine. To make complete heme proton assignments, NMR spectroscopy has been performed for high-resolution structural characterization of [dCPO(heme)] and [dCPO(Phe)] to achieve unambiguous and complete heme proton assignments, which also allows important amino acids close to the heme active center to be determined.