The endogenous calcium ions of horseradish peroxidase C are required to maintain the functional nonplanarity of the heme

Feeling the Strain: Quantifying Ligand Deformation in Photosynthesis

Structural distortion of protein-bound ligands can play a critical role in enzyme function by tuning the electronic and chemical properties of the ligand molecule. However, quantifying these effects is difficult due to the limited resolution of protein structures and the difficulty of generating accurate structural restraints for nonprotein ligands. Here, we seek to quantify these effects through a statistical analysis of ligand distortion in chlorophyll proteins (CP), where ring deformation is thought to play a role in energy and electron transfer. To assess the accuracy of ring-deformation estimates from available structural data, we take advantage of the C2 symmetry of photosystem II (PSII), comparing ring-deformation estimates for equivalent sites both within and between 113 distinct X-ray and cryogenic electron microscopy PSII structures. Significantly, we find that several deformation modes exhibit considerable variability in predictions, even for equivalent monomers, down to a 2 Å resolution, to an extent that probably prevents their utilization in optical calculations. We further find that refinement restraints play a critical role in determining deformation values to resolution as low as 2 Å. However, for those modes that are well-resolved in the structural data, ring deformation in PSII is strongly conserved across all species tested from cyanobacteria to algae. These results highlight both the opportunities and limitations inherent in structure-based analyses of the bioenergetic and optical properties of CPs and other protein-ligand complexes.

Activity of AC electrokinetically immobilized horseradish peroxidase

Dielectrophoresis (DEP) is an AC electrokinetic effect mainly used to manipulate cells. Smaller particles, like virions, antibodies, enzymes, and even dye molecules can be immobilized by DEP as well. In principle, it was shown that enzymes are active after immobilization by DEP, but no quantification of the retained activity was reported so far. In this study, the activity of the enzyme horseradish peroxidase (HRP) is quantified after immobilization by DEP. For this, HRP is immobilized on regular arrays of titanium nitride ring electrodes of 500 nm diameter and 20 nm widths. The activity of HRP on the electrode chip is measured with a limit of detection of 60 fg HRP by observing the enzymatic turnover of Amplex Red and H₂ O₂ to fluorescent resorufin by fluorescence microscopy. The initial activity of the permanently immobilized HRP equals up to 45% of the activity that can be expected for an ideal monolayer of HRP molecules on all electrodes of the array. Localization of the immobilizate on the electrodes is accomplished by staining with the fluorescent product of the enzyme reaction. The high residual activity of enzymes after AC field induced immobilization shows the method's suitability for biosensing and research applications.

Potassium-induced partial inhibition of lactoperoxidase: structure of the complex of lactoperoxidase with potassium ion at 2.20 Å resolution

Lactoperoxidase, a heme-containing glycoprotein, catalyzes the oxidation of thiocyanate by hydrogen peroxide into hypothiocyanite which acts as an antibacterial agent. The prosthetic heme moiety is attached to the protein through two ester linkages via Glu258 and Asp108. In lactoperoxidase, the substrate-binding site is formed on the distal heme side. To study the effect of physiologically important potassium ion on the structure and function of lactoperoxidase, the fresh protein samples were isolated from yak (Bos grunniens) colostrum and purified to homogeneity. The biochemical studies with potassium fluoride showed a significant reduction in the catalytic activity. Lactoperoxidase was crystallized using 200 mM ammonium nitrate and 20% PEG-3350 at pH 6.0. The crystals of LPO were soaked in the solution of potassium fluoride and used for the X-ray intensity data collection. Structure determination at 2.20 Å resolution revealed the presence of a potassium ion in the distal heme cavity. Structure determination further revealed that the propionic chain attached to pyrrole ring C of the heme moiety, was disordered into two components each having an occupancy of 0.5. One component occupied a position similar to the normally observed position of propionic chain while the second component was found in the distal heme cavity. The potassium ion in the distal heme cavity formed five coordinate bonds with two oxygen atoms of propionic moiety, N^ε2 atom of His109 and two oxygen atoms of water molecules. The presence of potassium ion in the distal heme cavity hampered the catalytic activity of lactoperoxidase.

Proximity Staining Using Enzymatic Protein Tagging in Diplomonads

The function of many proteins is intrinsically related to their cellular location. Novel methods for ascertainment of the ultrastructural location of proteins have been introduced in recent years, but their implementation in protists has so far not been readily realized. Here, we present an optimized proximity labeling protocol using the APEX system in the salmon pathogen Spironucleus salmonicida. This protocol was also applicable to the human pathogen Giardia intestinalis. Both organisms required extraneous addition of hemin to the growth medium to enable detectable peroxidase activity. Further, we saw no inherent limitation in labeling efficiency coupled to the cellular compartment, as evident with some other proximity labeling systems. We anticipate that the APEX proximity labeling system might offer a great resource to establish the ultrastructural localization of proteins across genetically tractable protists but might require organism-specific labeling conditions.

The diplomonads are a group of understudied eukaryotic flagellates whose most prominent member is the human pathogen Giardia intestinalis. Methods commonly used in other eukaryotic model systems often require special optimization in diplomonads due to the highly derived character of their cell biology. We have optimized a proximity labeling protocol using pea ascorbate peroxidase (APEX) as a reporter for transmission electron microscopy (TEM) to enable the study of ultrastructural cellular details in diplomonads. Currently available TEM-compatible tags require light-induced activation (1, 2) or are inactive in many cellular compartments (3), while ascorbate peroxidase has not been shown to have those limitations. Here, we have optimized the in vivo activities of two versions of pea ascorbate peroxidase (APX^W41F and APEX) using the diplomonad fish parasite Spironucleus salmonicida, a relative of G. intestinalis. We exploited the well-known peroxidase substrates, Amplex UltraRed and 3,3′-diaminobenzidine (DAB), to validate the activity of the two tags and argue that APEX is the most stable version to use in Spironucleus salmonicida. Next, we fused APEX to proteins with established localization to evaluate the activity of APEX in different cellular compartments of the diplomonad cell and used Amplex UltraRed as well as antibodies along with superresolution microscopy to confirm the protein-APEX localization. The ultrastructural details of protein-APEX fusions were determined by TEM, and we observed marker activity in all cellular compartments tested when using the DAB substrate. Finally, we show that the optimized conditions established for S. salmonicida can be used in the related diplomonad G. intestinalis.

IMPORTANCE The function of many proteins is intrinsically related to their cellular location. Novel methods for ascertainment of the ultrastructural location of proteins have been introduced in recent years, but their implementation in protists has so far not been readily realized. Here, we present an optimized proximity labeling protocol using the APEX system in the salmon pathogen Spironucleus salmonicida. This protocol was also applicable to the human pathogen Giardia intestinalis. Both organisms required extraneous addition of hemin to the growth medium to enable detectable peroxidase activity. Further, we saw no inherent limitation in labeling efficiency coupled to the cellular compartment, as evident with some other proximity labeling systems. We anticipate that the APEX proximity labeling system might offer a great resource to establish the ultrastructural localization of proteins across genetically tractable protists but might require organism-specific labeling conditions.

Expression and Characterization of Windmill Palm Tree (Trachycarpus fortunei) Peroxidase by Pichia pastoris

Currently, commercial plant peroxidases are all native and are isolated from plants such as horseradish and soybean. No recombinant plant peroxidase products have been available on the commercial market. The gene encoding peroxidase was cloned from windmill palm tree leaves. The codon-optimized gene was transformed into Pichia pastoris for expression. The recombinant windmill palm tree peroxidase (rWPTP) expressed by P. pastoris showed high stability under pH 2-10 and temperatures up to 70 °C to many metallic salts and organic solvents. The substrate specificity of WPTP was determined, and among the substrates tested, 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) was most suitable for WPTP. The Michaelis constants with the substrates H₂O₂ and ABTS were 4.6 × 10^-4 and 1.6 × 10^-4 M, respectively. The rWPTP expressed in P. pastoris may be a suitable enzyme for the biosynthesis of polymers because of its high stability and activity under acidic conditions.

Production strategies for active heme-containing peroxidases from E. coli inclusion bodies - a review

Heme-containing peroxidases are frequently used in medical applications. However, these enzymes are still extracted from their native source, which leads to inadequate yields and a mixture of isoenzymes differing in glycosylation which limits subsequent enzyme applications. Thus, recombinant production of these enzymes in Escherichia coli is a reasonable alternative. Even though production yields are high, the product is frequently found as protein aggregates called inclusion bodies (IBs). These IBs have to be solubilized and laboriously refolded to obtain active enzyme. Unfortunately, refolding yields are still very low making the recombinant production of these enzymes in E. coli not competitive. Motivated by the high importance of that enzyme class, this review aims at providing a comprehensive summary of state-of-the-art strategies to obtain active peroxidases from IBs. Additionally, various refolding techniques, which have not yet been used for this enzyme class, are discussed to show alternative and potentially more efficient ways to obtain active peroxidases from E. coli.

Ligand binding reveals a role for heme in translationally-controlled tumor protein dimerization

The translationally-controlled tumor protein (TCTP) is a highly conserved, ubiquitously expressed, abundant protein that is broadly distributed among eukaryotes. Its biological function spans numerous cellular processes ranging from regulation of the cell cycle and microtubule stabilization to cell growth, transformation, and death processes. In this work, we propose a new function for TCTP as a “buffer protein” controlling cellular homeostasis. We demonstrate that binding of hemin to TCTP is mediated by a conserved His-containing motif (His⁷⁶His⁷⁷) followed by dimerization, an event that involves ligand-mediated conformational changes and that is necessary to trigger TCTP's cytokine-like activity. Mutation in both His residues to Ala prevents hemin from binding and abrogates oligomerization, suggesting that the ligand site localizes at the interface of the oligomer. Unlike heme, binding of Ca²⁺ ligand to TCTP does not alter its monomeric state; although, Ca²⁺ is able to destabilize an existing TCTP dimer created by hemin addition. In agreement with TCTP's proposed buffer function, ligand binding occurs at high concentration, allowing the “buffer” condition to be dissociated from TCTP's role as a component of signal transduction mechanisms.

Origins of activity enhancement in enzyme cascades on scaffolds

The concept of "metabolic channeling" as a result of rapid transfer of freely diffusing intermediate substrates between two enzymes on nanoscale scaffolds is examined using simulations and mathematical models. The increase in direct substrate transfer due to the proximity of the two enzymes provides an initial but temporary boost to the throughput of the cascade and loses importance as product molecules of enzyme 1 (substrate molecules of enzyme 2) accumulate in the surrounding container. The characteristic time scale at which this boost is significant is given by the ratio of container volume to the product of substrate diffusion constant and interenzyme distance and is on the order of milliseconds to seconds in some experimental systems. However, the attachment of a large number of enzyme pairs to a scaffold provides an increased number of local "targets", extending the characteristic time. If substrate molecules for enzyme 2 are sequestered by an alternative reaction in the container, a scaffold can result in a permanent boost to cascade throughput with a magnitude given by the ratio of the above-defined time scale to the lifetime of the substrate molecule in the container. Finally, a weak attractive interaction between substrate molecules and the scaffold creates a "virtual compartment" and substantially accelerates initial throughput. If intermediate substrates can diffuse freely, placing individual enzyme pairs on scaffolds is only beneficial in large cells, unconfined extracellular spaces or in systems with sequestering reactions.

Controlled immobilisation of active enzymes on the cowpea mosaic virus capsid

Immobilisation of horseradish peroxidase (HRP) and glucose oxidase (GOX) via covalent attachment of modified enzyme carbohydrate to the exterior of the cowpea mosaic virus (CPMV) capsid gave high retention of enzymatic activity. The number of enzymes bound per virus was determined to be about eleven for HRP and 2-3 for GOX. This illustrates that relatively large biomacromolecules can be readily coupled to the virus surface using simple conjugation strategies. Virus-biomacromolecule hybrids have great potential for uses in catalysis, diagnostic assays or biosensors.

Horseradish peroxidase: modulation of properties by chemical modification of protein and heme

Horseradish peroxidase (HRP) is one of the most studied enzymes of the plant peroxidase superfamily. HRP is also widely used in different bioanalytical applications and diagnostic kits. The methods of genetic engineering and protein design are now widely used to study the catalytic mechanism and to improve properties of the enzyme. Here we review the results of another approach to HRP modification-through the chemical modification of amino acids or prosthetic group of the enzyme. Computer models of HRPs with modified hemes are in good agreement with the experimental data.

Predicting the functionally distinct residues in the heme, cation, and substrate-binding sites of peroxidase from stress-tolerant mangrove specie, Avicennia marina

Recent work was conducted to predict the structure of functionally distinct regions of Avicennia marina peroxidase (AP) by using the structural coordinates of barley grains peroxidase as the template. This enzyme is utilized by all living organisms in many biosynthetic or degradable processes and in defense against oxidative stress. The homology model showed some distinct structural changes in the heme, calcium, and substrate-binding regions. Val53 was found to be an important coordinating residue between distal calcium ion and the distal heme site while Ser176 is coordinated to the proximal histidine through Ala174 and Leu172. Different ionic and hydrogen-bonded interactions were also observed in AP. Analyses of various substrate-enzyme interactions revealed that the substrate-binding pocket is provided by the residues, His41, Phe70, Gly71, Asp138, His139, and Lys176; the later three residues are not conserved in the peroxidase family. We have also performed structural comparison of the A. marina peroxidase with that of two class III salt-sensitive species, peanut and soybean. Four loop regions were found to have largest structural deviation. The overall protein sequence was also analyzed for the presence of probable post-translational modification sites and the functional significance of these sites were outlined.

Two efficient methods for the conjugation of smooth-form lipopolysaccharides with probes bearing hydrazine or amino groups. II. LPS activation with a cyanopyridinium agent

This chapter presents a conjugation method for coupling probes bearing hydrazine or primary amino groups to a lipopolysaccharide (LPS). LPS is modified by the activation of the hydroxyl groups present in its O-antigen moiety with 1-cyano-4-dimethylaminopyridinium tetrafluoroborate (CDAP). The method yields conjugates with good labeling ratios, preserving the endotoxic activity of the lipid A moiety. Conjugation of smooth-form LPS from Salmonella enterica sv. Minnesota with dansyl hydrazine and horseradish peroxidase yields labeling ratios above 110 nmol dansyl/mg LPS, with nearly no loss of the original endotoxic activity. In the case of horseradish peroxidase, introducing a spacer, a ratio of 29 nmol HRP/mg LPS was obtained, preserving 65% of the original endotoxic activity and an enzymatic activity of 120 U/mg.

The tightly bound calcium of MauG is required for tryptophan tryptophylquinone cofactor biosynthesis

The diheme enzyme MauG catalyzes a six-electron oxidation required for posttranslational modification of a precursor of methylamine dehydrogenase (preMADH) to complete the biosynthesis of its protein-derived tryptophan tryptophylquinone (TTQ) cofactor. The crystal structure of the MauG-preMADH complex revealed the presence of a Ca(2+) in proximity to the two hemes [Jensen, L. M. R., Sanishvili, R., Davidson, V. L., and Wilmot, C. M. (2010) Science 327, 1392-1394]. This Ca(2+) did not readily dissociate; however, after extensive treatment with EGTA or EDTA MauG was no longer able to catalyze TTQ biosynthesis and exhibited altered absorption and resonance Raman spectra. The changes in spectral features are consistent with Ca(2+)-dependent changes in heme spin state and conformation. Addition of H(2)O(2) to the Ca(2+)-depleted MauG did not yield spectral changes characteristic of formation of the bis-Fe(IV) state which is stabilized in native MauG. After addition of Ca(2+) to the Ca(2+)-depleted MauG, full TTQ biosynthesis activity and reactivity toward H(2)O(2) were restored, and the spectral properties returned to those of native MauG. Kinetic and equilibrium studies of Ca(2+) binding to Ca(2+)-depleted MauG indicated a two-step mechanism. Ca(2+) initially reversibly binds to Ca(2+)-depleted MauG (K(d) = 22.4 μM) and is followed by a relatively slow (k = 1.4 × 10(-3) s(-1)) but highly favorable (K(eq) = 4.2) conformational change, yielding an equilibrium dissociation constant K(d,eq) value of 5.3 μM. The circular dichroism spectra of native and Ca(2+)-depleted MauG were essentially the same, consistent with Ca(2+)-induced conformational changes involving domain or loop movements rather than general unfolding or alteration of secondary structure. These results are discussed in the context of the structures of MauG and heme-containing peroxidases.

Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia)

Royal palm tree peroxidase (RPTP) is a very stable enzyme in regards to acidity, temperature, H(2)O(2), and organic solvents. Thus, RPTP is a promising candidate for developing H(2)O(2)-sensitive biosensors for diverse applications in industry and analytical chemistry. RPTP belongs to the family of class III secretory plant peroxidases, which include horseradish peroxidase isozyme C, soybean and peanut peroxidases. Here we report the X-ray structure of native RPTP isolated from royal palm tree (Roystonea regia) refined to a resolution of 1.85A. RPTP has the same overall folding pattern of the plant peroxidase superfamily, and it contains one heme group and two calcium-binding sites in similar locations. The three-dimensional structure of RPTP was solved for a hydroperoxide complex state, and it revealed a bound 2-(N-morpholino) ethanesulfonic acid molecule (MES) positioned at a putative substrate-binding secondary site. Nine N-glycosylation sites are clearly defined in the RPTP electron-density maps, revealing for the first time conformations of the glycan chains of this highly glycosylated enzyme. Furthermore, statistical coupling analysis (SCA) of the plant peroxidase superfamily was performed. This sequence-based method identified a set of evolutionarily conserved sites that mapped to regions surrounding the heme prosthetic group. The SCA matrix also predicted a set of energetically coupled residues that are involved in the maintenance of the structural folding of plant peroxidases. The combination of crystallographic data and SCA analysis provides information about the key structural elements that could contribute to explaining the unique stability of RPTP.

Interaction between lanthanum ion and horseradish peroxidase in vitro

The interaction between lanthanum ion (La(3+)) and horseradish peroxidase (HRP) in vitro was investigated using a combination of biophysical and biochemical methods. When the molar ratio of La(3+) and HRP is low, it was found that the interaction between La(3+) and HRP mainly depends on the electrostatic attraction, van der waals force and hydrogen bond etc. Thus, the interaction is weak and the La-HRP complex cannot be formed in vitro. As expected, the interaction can change the conformation of HRP molecule, leading to the increase in the non-planarity of the porphyrin ring in the heme group of HRP molecule, and then in the exposure degree of the active center, Fe(III) of the porphyrin ring of HRP molecule. Therefore, the catalytic activity of HRP for the H(2)O(2) reduction is improved. When the molar ratio of La(3+) and HRP is high, La(3+) can strongly coordinate with O and/or N in the amide group of the polypeptide chain of HRP molecule, forming the La-HRP complex. The formation of the La-HRP complex causes the change in the conformation of HRP molecule, leading to the decrease in the non-planarity of the porphyrin ring in the heme group of HRP molecule, and then in the exposure degree of the active center, Fe(III) of the porphyrin ring of HRP molecule. Thus, the catalytic activity of HRP for the H(2)O(2) reduction is decreased comparing with that of HRP in the absence of La(3+). The results can provide some references for understanding the interaction mechanism between trace elements ions and peroxidase in living organisms.

Adsorption behavior and activity of horseradish peroxidase onto polysaccharide-decorated particles

The adsorption behavior of horseradish peroxidase (HRP) onto hybrid particles of poly(methylmethacrylate) (PMMA) and carboxymethylcellulose (CMC) was investigated by means of spectrophotometry. Dispersions of PMMA/CMC particles were characterized by light scattering, zeta potential measurements and scanning electron microscopy before and after HRP adsorption. HRP adsorbed irreversibly onto PMMA/CMC particles; the adsorption isotherm showed an initial step and an adsorption plateau. The enzymatic activity of free HRP and immobilized HRP (plateau region) was monitored by means of spectrophotometry as a function of storing time. Upon adsorbing HRP there is little (up to 20%) or no reduction of enzymatic activity in comparison to that observed for free HRP in solution. After storing free HRP and HRP-covered PMMA/CMC particles for 18 days the level of enzymatic activity is kept. HRP-covered PMMA/CMC particles dispersions, which were dried and re-dispersed, retained 50% of their catalytic properties. These interesting findings were discussed in the light of a beneficial effect of a hydrated microenvironment for maintenance of enzyme conformation and activity.

Immobilized horseradish peroxidase as a reusable catalyst for emulsion polymerization

The study on the adsorption of horseradish peroxidase (HRP) onto silicon wafers was carried out by means of in situ ellipsometry, atomic force microscopy (AFM) and contact angle measurements. A smooth HRP layer adsorbed onto Si wafers. The enzymatic activity of free or adsorbed HRP was determined by the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and by the emulsion polymerization of ethylene glycol dimethacrylate (EGDMA). Upon adsorbing, HRP molecules might have undergone some conformational changes, which caused a small reduction of enzymatic activity in comparison to that observed for HRP solution. However, it was possible to reuse the same HRP-covered Si wafer as catalyst in the polymerization of EGDMA three times.

Structural stabilization and functional improvement of horseradish peroxidase upon modification of accessible lysines: experiments and simulation

Horseradish peroxidase (HRP) is an important heme enzyme with enormous medical diagnostic, biosensing, and biotechnological applications. Thus, any improvement in the applicability and stability of the enzyme is potentially interesting. We previously reported that covalent attachment of an electron relay (anthraquinone 2-carboxylic acid) to the surface-exposed Lys residues successfully improves electron transfer properties of HRP. Here we investigated structural and functional consequences of this modification, which alters three accessible charged lysines (Lys-174, Lys-232, and Lys-241) to the hydrophobic anthraquinolysine residues. Thermal denaturation and thermoinactivation studies demonstrated that this kind of modification enhances the conformational and operational stability of HRP. The melting temperature increased 3 degrees C and the catalytic efficiency enhanced by 80%. Fluorescence and circular dichroism investigations suggest that the modified HRP benefits from enhanced aromatic packing and more buried hydrophobic patches as compared to the native one. Molecular dynamics simulations showed that modification improves the accessibility of His-42 and the heme prosthetic group to the peroxide and aromatic substrates, respectively. Additionally, the hydrophobic patch, which functions as a binding site or trap for reducing aromatic substrates, is more extended in the modified enzyme. In summary, this modification produces a new derivative of HRP with enhanced electron transfer properties, catalytic efficiency, and stability for biotechnological applications.

Conformational changes and activity alterations induced by nickel ion in horseradish peroxidase

Conformational changes induced by the binding of nickel to horseradish peroxidase C (HRPC) were studied by electronic absorption spectroscopy, fluorescence spectroscopy and circular dichroism spectroscopy. Incubation of HRPC with various concentrations of Ni(2+) for 5 minutes resulted in changes in the enzyme absorption spectrum, including variations in the intensities of the Soret, beta and charge transfer (CT1) bands absorption, shift in the Soret, beta and CT1 bands maxima and absorption increase at 275 nm. Increases in the enzyme's intrinsic fluorescence as determined by fluorescence spectroscopy, as well as changes in the alpha-helical content, as determined by circular dichroism spectroscopy, were also found. Correlatively, alterations of the enzymatic activity by Ni(2+) were studied by following the H(2)O(2)-mediated oxidation of o-dianisidine and 2,2'-azinobis(3-ethylbenzothiazolinesulfonic acid) (ABTS) by HRPC. With both reducing substrates, it was found that in the presence of sufficient amount of enzyme, 1-10 mM nickel would enhance the enzymatic activity, while higher Ni(2+) concentrations (20-50 mM) would inhibit it. The enzyme was completely inhibited after 5 minutes incubation in 50 mM Ni(2+). Prolonged incubation would induce complete inhibition at lower Ni(2+) concentrations. Spectrophotometry investigations also showed that inhibitory concentrations of Ni(2+) altered compounds I and II formation, compound II being the first affected. Based on spectrophotometry, fluorescence and circular dichroism spectroscopy, and data on compounds I and II formation, a scheme is suggested for HRPC conformational changes in different Ni(2+) concentrations. HRPC was found to have four potential attachment sites for Ni(2+) which were sequentially occupied in a dose- and time-dependent manner by the metallic ion.

Normal mode analysis of the horseradish peroxidase collective motions: Correlation with spectroscopically observed heme distortions

Horseradish peroxidase C is a class III peroxidase whose structure is stabilized by the presence of two endogenous calcium atoms. Calcium removal has been shown to decrease the enzymatic activity of the enzyme and significantly affect the spectroscopically detectable properties of the heme, such as the spin state of the iron, heme normal modes, and distortions from planarity. In this work, we report on normal mode analysis (NMA) performed on models subjected to 2 ns of molecular dynamics simulations to describe the effect of calcium removal on protein collective motions and to investigate the correlation between active site (heme) and protein matrix fluctuations. We show that in the native peroxidase model, heme fluctuations are correlated to matrix fluctuations while they are not in the calcium-depleted model.

Formation of a misfolded conformation during refolding of HRPA1 in the presence of calcium

Horseradish peroxidase A1 can refold to a native-like structure without binding calcium, originating a Ca2+-depleted native state as previously demonstrated. Thermal unfolding studies of horseradish peroxidase anionic 1 (HRPA1) have shown that calcium ions present during refolding lead to the appearance of a misfolded conformational state, which cannot incorporate the heme group. This calcium-induced conformational state, ICa2+, is less stable than the native state and has distinct secondary and tertiary structures as probed by far-UV and visible circular dichroism and tryptophan fluorescence. The fraction of ICa2+ increases exponentially with increasing calcium concentration. The ICa2+ state is formed during refolding after calcium binding to the unfolded state, as reconstitution of HRPA1 from its apoprotein reveals that the affinity of the apoprotein to protoporphyrin IX is higher in the presence of calcium. If calcium is added after refolding only, the majority of HRPA1 molecules retain their native conformation, thus confirming the binding of calcium to the unfolded state.

Stepwise binding of nickel to horseradish peroxidase and inhibition of the enzymatic activity

The incubation of horseradish peroxidase C (HRPC) with millimolar concentrations of nickel, at room temperature and at pH 4.0, induced the progressive formation of a metal-enzyme complex characterized by alterations of the enzyme Soret absorption band that were time- as well as nickel concentration- dependent. For any given incubation period between 1 and 60 min, 2 values for the apparent dissociation constant (K(d)) were found, suggesting the presence of binding sites with different affinities for nickel. The value of each K(d) dropped as the incubation time increased, indicating a progressive stabilization of the metal-enzyme complex. Hill plots suggested a cooperative binding of up to four Ni2+ ions per molecule of HRPC. The inhibition of the enzymatic activity by nickel was studied by following the H2O2-mediated oxidation of o-dianisidine by HRPC under steady-state kinetic conditions. Ni2+ was found to be either a noncompetitive or a mixed inhibitor of HRPC depending both on the duration of preincubation with the enzyme and on Ni2+ concentration. The enzyme remained active only over a limited metal concentration range and data indicated that binding of one Ni2+ affected the substrate binding site, binding of a second Ni2+ affected both substrate and peroxide binding sites, and binding of more than 2 Ni2+ per HRPC molecule led to complete loss of enzymatic activity. Results pointed to the damaging effects of prolonged exposure to heavy metals and also to the existence of a critical metal concentration beyond which immediate abolishing of enzymatic activity was observed.

Coupling of electron and proton transfer in oxidative water cleavage in photosynthesis

This minireview addresses questions on the mechanism of oxidative water cleavage with special emphasis on the coupling of electron (ET) and proton transfer (PT) of each individual redox step of the reaction sequence and on the mode of O-O bond formation. The following topics are discussed: (1) the multiphasic kinetics of Y(Z)(ox) formation by P680(+*) originate from three different types of rate limitations: (i) nonadiabatic electron transfer for the "fast" ns reaction, (ii) local "dielectric" relaxation for the "slow" ns reaction, and (iii) "large-scale" proton shift for the micros kinetics; (2) the ET/PT-coupling mode of the individual redox transitions within the water oxidizing complex (WOC) driven by Y(Z)(ox) is assumed to depend on the redox state S(i): the oxidation steps of S(0) and S(1) comprise separate ET and PT pathways while those of S(2) and S(3) take place via proton-coupled electron transfer (PCET) analogous to Jerry Babcock's hydrogen atom abstractor model [Biochim. Biophys. Acta, 1458 (2000) 199]; (3) S(3) is postulated to be a multistate redox level of the WOC with fast dynamic equilibria of both redox isomerism and proton tautomerism. The primary event in the essential O-O bond formation is the population of a state S(3)(P) characterized by an electronic configuration and nuclear geometry that corresponds with a complexed hydrogen peroxide; (4) the peroxidic type S(3)(P) is the entatic state for formation of complexed molecular oxygen through S(3) oxidation by Y(Z)(ox); and (5) the protein matrix itself is proposed to exert catalytic activity by functioning as "PCET director". The WOC is envisaged as a supermolecule that is especially tailored for oxidative water cleavage and acts as a molecular machine.

The charge transfer band in horseradish peroxidase correlates with heme in-plane distortions induced by calcium removal

Horseradish peroxidase C (HRPC) is a class III peroxidase whose structure is stabilized by the presence of two endogenous calcium atoms. Calcium removal has been shown to decrease the enzymatic activity of the enzyme. The spin state of the iron, a mixture of high spin (HS) and mixed quantum spin state (QS) consisting of intermediate spin (IS) 3/2 + (HS) 5/2, is also significantly affected by calcium removal, going from a predominant QS component to a predominant HS component upon removal of one calcium. Removal of both calcium ions, however, results in the appearance of a significant LS contribution, easily monitored in the charge transfer (CT) band region by low-T absorption. Normal structural decomposition (NSD) calculations of the in-plane (ip) modes of the heme extracted from HRPC native and Ca(2+)-depleted models show that removal of the proximal calcium is associated with perturbed E(u) and increased A(1g) ip distortions of the heme. The effect of complete or distal calcium removal on the heme also results in increased A(1g) ip distortions, but in significantly decreased E(u) distortions. The overall effect is to decrease the nonplanarity of the heme: the total ip distortion of the native HRPC heme is 0.200 and 0.134 A for the Ca(2+)-depleted species. Our NSD results corroborate the role proposed for the protein matrix, namely to fine-tune the active site by inducing subtle changes in heme planarity and spin state of the iron.

Conformational states of HRPA1 induced by thermal unfolding: Effect of low molecular weight solutes

Fluorescence, CD, and activity measurements were used to characterize the different conformational states of horseradish peroxidase A1 induced by thermal unfolding. Picosecond time-resolved fluorescence studies showed a three-exponential decay dominated by a picosecond lifetime component resulting from energy transfer from tryptophan to heme. Upon thermal unfolding a decrease in the preexponential factor of the picosecond lifetime and an increase in the quantum yield were observed approaching the characteristics observed for apoHRPA1. The fraction of heme-quenched fluorophore decreased to 0.4 after unfolding as shown by acrylamide quenching. A new unfolding pathway for HRPA1 was proposed and the effect of the low molecular weight solutes trehalose, sorbitol, and melezitose on this pathway was analyzed. Native HRPA1 unfolds with an intermediate between the native and the unfolded conformation. The unfolded conformation can refold to the native state or to a native-like conformation with no calcium ions upon cooling or can give an irreversible denatured state. The refolded conformation with no calcium ions was clearly identified in a second thermal scan in the presence of EDTA and shows secondary and tertiary structures, heme reincorporation in the cavity, and at least 59% of activity. Melezitose stabilized the refolded Ca2+-depleted protein and induced a more complex mechanism for heme disruption. The effect of sorbitol and trehalose were mainly characterized by an increase in the temperature of unfolding.