Effect of single-site charge-reversal mutations on the catalytic properties of yeast cytochrome c peroxidase: mutations near the high-affinity cytochrome c binding site

Enhancing the population of the encounter complex affects protein complex formation efficiency

Optimal charge distribution is considered to be important for efficient formation of protein complexes. Electrostatic interactions guide encounter complex formation that precedes the formation of an active protein complex. However, disturbing the optimized distribution by introduction of extra charged patches on cytochrome c peroxidase does not lead to a reduction in productive encounters with its partner cytochrome c. To test whether a complex with a high population of encounter complex is more easily affected by suboptimal charge distribution, the interactions of cytochrome c mutant R13A with wild‐type cytochrome c peroxidase and a variant with an additional negative patch were studied. The complex of the peroxidase and cytochrome c R13A was reported to have an encounter state population of 80%, compared to 30% for the wild‐type cytochrome c. NMR analysis confirms the dynamic nature of the interaction and demonstrates that the mutant cytochrome c samples the introduced negative patch. Kinetic experiments show that productive complex formation is fivefold to sevenfold slower at moderate and high ionic strength values for cytochrome c R13A but the association rate is not affected by the additional negative patch on cytochrome c peroxidase, showing that the total charge on the protein surface can compensate for less optimal charge distribution. At low ionic strength (44 mm), the association with the mutant cytochrome c reaches the same high rates as found for wild‐type cytochrome c, approaching the diffusion limit.

The Charge Distribution on a Protein Surface Determines Whether Productive or Futile Encounter Complexes Are Formed

Protein complex formation depends strongly on electrostatic interactions. The distribution of charges on the surface of redox proteins is often optimized by evolution to guide recognition and binding. To test the degree to which the electrostatic interactions between cytochrome c peroxidase (CcP) and cytochrome c (Cc) are optimized, we produced five CcP variants, each with a different charge distribution on the surface. Monte Carlo simulations show that the addition of negative charges attracts Cc to the new patches, and the neutralization of the charges in the regular, stereospecific binding site for Cc abolishes the electrostatic interactions in that region entirely. For CcP variants with the charges in the regular binding site intact, additional negative patches slightly enhance productive complex formation, despite disrupting the optimized charge distribution. Removal of the charges in the regular binding site results in a dramatic decrease in the complex formation rate, even in the presence of highly negative patches elsewhere on the surface. We conclude that additional charge patches can result in either productive or futile encounter complexes, depending on whether negative residues are located also in the regular binding site.

Efficient Encounter Complex Formation and Electron Transfer to Cytochrome c Peroxidase with an Additional, Distant Electrostatic Binding Site

Electrostatic interactions can strongly increase the efficiency of protein complex formation. The charge distribution in redox proteins is often optimized to steer a redox partner to the electron transfer active binding site. To test whether the optimized distribution is more important than the strength of the electrostatic interactions, an additional negative patch was introduced on the surface of cytochrome c peroxidase, away from the stereospecific binding site, and its effect on the encounter complex as well as the rate of complex formation was determined. Monte Carlo simulations and paramagnetic relaxation enhancement NMR experiments indicate that the partner, cytochrome c, interacts with the new patch. Unexpectedly, the rate of the active complex formation was not reduced, but rather slightly increased. The findings support the idea that for efficient protein complex formation the strength of the electrostatic interaction is more critical than an optimized charge distribution.

Cerebral ganglion ultrastructure and differential proteins revealed using proteomics in the aplysiid (Notarcus leachii cirrosus Stimpson) under cadmium and lead stress

Cadmium (Cd) and lead (Pb) are both highly toxic metals in environments. However the toxicological mechanism is not clear. In this study, the aplysiid, Notarcus leachii cirrosus Stimpson (NLCS) was subjected to Cd (NLCS-Cd) or Pb (NLCS-Pb). The cerebral ganglion of NLCS was investigated with a transmission electron microscope. Next the differential proteins were separated and identified using proteomic approaches. Eighteen protein spots in NLCS-Cd and seventeen protein spots in NLCS-Pb were observed to be significantly changed. These protein spots were further excised in gels and identified. A hypothetical pathway was drawn to show the correlation between the partially identified proteins. The results indicated that damage to the cerebral ganglion was follows: cell apoptosis, lysosomes proliferation, cytoskeleton disruption, and oxidative stress. These phenomena and data indicated potential biomarkers for evaluating the contamination levels of Cd and Pb. This study provided positive insights into the mechanisms of Cd and Pb toxicity.

Binding of Yeast Cytochrome c to Forty-Four Charge-Reversal Mutants of Yeast Cytochrome c Peroxidase: Isothermal Titration Calorimetry

Previously, we constructed, expressed, and purified 46 charge-reversal mutants of yeast cytochrome c peroxidase (CcP) and determined their electronic absorption spectra, their reaction with H2O2, and their steady-state catalytic properties [ Pearl , N. M. et al. (2008) Biochemistry 47 , 2766 - 2775 ]. Forty-four of the mutants involve the conversion of either an aspartate or glutamate residue to a lysine residue, while two are positive-to-negative mutations, R31E and K149D. In this paper, we report on a calorimetric study of the interaction of each charge-reversal mutant (excluding the internal mutants D76K and D235K) with recombinant yeast iso-1 ferricytochrome c(C102T) (yCc) under conditions where only one-to-one yCc/CcP complex formation is observed. Thirteen of the 44 surface-site charge-reversal mutants decrease the binding affinity for yCc by a factor of 2 or more. Eight of the 13 mutations (E32K, D33K, D34K, E35K, E118K, E201K, E290K, E291K) occur within, or on the immediate periphery, of the crystallographically defined yCc binding site [ Pelletier , H. and Kraut , J. (1992) Science 258 , 1748 - 1755 ], three of the mutations (D37K, E98K, E209K) are slightly removed from the crystallographic site, and two of the mutations (D165K, D241K) occur on the "back-side" of CcP. The current study is consistent with a model for yCc binding to CcP in which yCc binds predominantly near the region defined by crystallographic structure of the 1:1 yCc-CcP complex, whether as a stable electron-transfer active complex or as part of a dynamic encounter complex.

Binding of imidazole, 1-methylimidazole and 4-nitroimidazole to yeast cytochrome c peroxidase (CcP) and the distal histidine mutant, CcP(H52L)

Imidazole, 1-methylimidazole and 4-nitroimidazole bind to yeast cytochrome c peroxidase (yCcP) with apparent equilibrium dissociation constants (KD(app)) of 3.3±0.4, 0.85±0.11, and ~0.2M, respectively, at pH7. This is the weakest imidazole binding to a heme protein reported to date and it is about 120 times weaker than imidazole binding to metmyoglobin. Spectroscopic changes associated with imidazole and 1-methylimidazole binding to yCcP suggest partial ionization of bound imidazole to imidazolate. The pKa for ionization of bound imidazole is estimated to be 7.4±0.2, about 7 units lower than that of free imidazole and about 3 units lower than imidazole bound to metmyoglobin. Equilibrium binding of imidazole to CcP(H52L) is biphasic with low- and high-affinity phases having KD(app) values of 9.5±4.5 and 0.13±0.04M, respectively. CcP(H52L) binding of 1-methylimidazole is monophasic with an affinity similar to those of yCcP and rCcP. Binding of 1-methylimidazole to rCcP is associated with two kinetic phases, the initial binding complete within 10s, followed by a process that is consistent with 1-methylimidazole binding to a cavity created by movement of Trp-191 from the interior of the protein to the surface. Both the equilibrium binding and kinetics of 1-methylimidazole binding to yCcP are pH dependent. yCcP has a four-fold increase in 1-methylimidazole binding affinity on decreasing the pH from 7.5 to 4.0, an observation that is unique among the many studies on binding of imidazole and imidazole derivatives to heme proteins.

Kinetic and equilibrium studies of acrylonitrile binding to cytochrome c peroxidase and oxidation of acrylonitrile by cytochrome c peroxidase compound I

Ferric heme proteins bind weakly basic ligands and the binding affinity is often pH dependent due to protonation of the ligand as well as the protein. In an effort to find a small, neutral ligand without significant acid/base properties to probe ligand binding reactions in ferric heme proteins we were led to consider the organonitriles. Although organonitriles are known to bind to transition metals, we have been unable to find any prior studies of nitrile binding to heme proteins. In this communication we report on the equilibrium and kinetic properties of acrylonitrile binding to cytochrome c peroxidase (CcP) as well as the oxidation of acrylonitrile by CcP compound I. Acrylonitrile binding to CcP is independent of pH between pH 4 and 8. The association and dissociation rate constants are 0.32±0.16 M(-1) s(-1) and 0.34±0.15 s(-1), respectively, and the independently measured equilibrium dissociation constant for the complex is 1.1±0.2 M. We have demonstrated for the first time that acrylonitrile can bind to a ferric heme protein. The binding mechanism appears to be a simple, one-step association of the ligand with the heme iron. We have also demonstrated that CcP can catalyze the oxidation of acrylonitrile, most likely to 2-cyanoethylene oxide in a "peroxygenase"-type reaction, with rates that are similar to rat liver microsomal cytochrome P450-catalyzed oxidation of acrylonitrile in the monooxygenase reaction. CcP compound I oxidizes acrylonitrile with a maximum turnover number of 0.61 min(-1) at pH 6.0.

Apolar distal pocket mutants of yeast cytochrome c peroxidase: hydrogen peroxide reactivity and cyanide binding of the TriAla, TriVal, and TriLeu variants

Three yeast cytochrome c peroxidase (CcP) variants with apolar distal heme pockets have been constructed. The CcP variants have Arg48, Trp51, and His52 mutated to either all alanines, CcP(triAla), all valines, CcP(triVal), or all leucines, CcP(triLeu). The triple mutants have detectable enzymatic activity at pH 6 but the activity is less than 0.02% that of wild-type CcP. The activity loss is primarily due to the decreased rate of reaction between the triple mutants and H(2)O(2) compared to wild-type CcP. Spectroscopic properties and cyanide binding characteristics of the triple mutants have been investigated over the pH stability region of CcP, pH 4 to 8. The absorption spectra indicate that the CcP triple mutants have hemes that are predominantly five-coordinate, high-spin at pH 5 and six-coordinate, low-spin at pH 8. Cyanide binding to the triple mutants is biphasic indicating that the triple mutants have two slowly-exchanging conformational states with different cyanide affinities. The binding affinity for cyanide is reduced at least two orders of magnitude in the triple mutants compared to wild-type CcP and the rate of cyanide binding is reduced by four to five orders of magnitude. Correlation of the reaction rates of CcP and 12 distal pocket mutants with H(2)O(2) and HCN suggests that both reactions require ionization of the reactants within the distal heme pocket allowing the anion to bind the heme iron. Distal pocket features that promote substrate ionization (basic residues involved in base-catalyzed substrate ionization or polar residues that can stabilize substrate anions) increase the overall rate of reaction with H(2)O(2) and HCN while features that inhibit substrate ionization slow the reactions.

Effect of alternative distal residues on the reactivity of cytochrome c peroxidase: properties of CcP mutants H52D, H52E, H52N, and H52Q

To test the effect of alternative bases at the distal histidine position, four CcP variants have been constructed that substitute the two basic residues, aspartate and glutamate, and their amides, asparagine and glutamine, for histidine-52, i.e., CcP(H52D), CcP(H52E), CcP(H52N), and CcP(H52Q). All four mutants catalyze oxidation of ferrocytochrome c by H(2)O(2) with steady-state activities that are between 250 and 7700 times slower than wild-type CcP at pH 6.0, 0.10M ionic strength, 25°C. The rate of Compound I formation is decreased between 3.5 and 5.4 orders of magnitude for the mutants compared to wild-type CcP, with the rate of the reaction between CcP(H52Q) and H(2)O(2) the slowest yet observed for any CcP mutant. A correlation between the rate of Compound I formation and the rate of HCN binding for CcP and various CcP distal pocket mutants provides strong evidence that the rate-limiting step in CcP Compound I formation is deprotonation of H(2)O(2) within the distal heme pocket under the experimental conditions employed in this study. While CcP(H52E) reacts stoichiometrically with H(2)O(2) to form Compound I, only ~36% of CcP(H52D), ~21% of CcP(H52Q) and ~8% of CcP(H52N) appear to be converted to Compound I during their respective reactions with H(2)O(2). This is partially due to the slow rate of Compound I formation and the rapid endogenous decay of Compound I for these mutants. The pathways for the endogenous decay of Compound I for the four mutants used in this study are distinct from that of wild-type CcP Compound I.

Shifting the equilibrium between the encounter state and the specific form of a protein complex by interfacial point mutations

Recent experimental studies have confirmed a long-held view that protein complex formation proceeds via a short-lived encounter state. The population of this transient intermediate, stabilized mainly by long-range electrostatic interactions, varies among different complexes. Here we show that the occupancy of the encounter state can be modulated across a broad range by single point mutations of interfacial residues. Using a combination of Monte Carlo simulations and paramagnetic relaxation enhancement NMR spectroscopy, we illustrate that it is possible to both enhance and diminish the binding specificity in an electron transfer complex of yeast cytochrome c (Cc) and cytochrome c peroxidase. The Cc T12A mutation decreases the population of the encounter to 10% as compared with 30% in the wild-type complex. More dramatically, the Cc R13A substitution reverses the relative occupancies of the stereospecific and the encounter forms, with the latter now being the dominant species with the population of 80%. This finding indicates that the encounter state can make a large contribution to the stability of a protein complex. Also, it appears that by adjusting the amount of the encounter through a judicious choice of point mutations, we can remodel the energy landscape of a protein complex and tune its binding specificity.

Relocation of the distal histidine in cytochrome c peroxidase: properties of CcP(W51H), CcP(W51H/H52W), and CcP(W51H/H52L)

Many heme proteins have distal histidine residues that play important roles in determining heme protein reactivity. These distal histidines are in significantly different orientations,and distances from the heme iron in different heme proteins and the position of the distal histidine relative to the heme iron can influence reactivity at the heme center. To explore the effect of distal histidine position on the properties of cytochrome c peroxidase (CcP), three CcP mutants in which tryptophan 51 was replaced with a histidine residue were constructed. All three mutants, CcP(W51H), CcP(W51H/H52W), and CcP(W51H/H52L), have altered electronic absorption spectra, indicating that the heme group in the mutants is six-coordinate rather than five-coordinate as it is in wild-type CcP. The hydrogen peroxide reaction rate is 56-6200-fold slower for the mutants than for wild-type CcP. All three mutants form a CcP Compound I-like intermediate, in which the Fe(IV) site decays between 500 and 3000 times more rapidly than the Fe(IV) site in wild-type CcP Compound I. The W51H mutations have a weaker effect on cyanide binding, with the cyanide affinity only 2-8 times weaker than for CcP. The cyanide association rate constants are between 5 and 85 times slower for the W51H mutants, while the cyanide dissociation rate constants range from 3 times slower to 6 times faster than those of wild-type CcP.

Binding hot spot in the weak protein complex of physiological redox partners yeast cytochrome C and cytochrome C peroxidase

Transient protein interactions mediate many vital cellular processes such as signal transduction or intermolecular electron transfer. However, due to difficulties associated with their structural characterization, little is known about the principles governing recognition and binding in weak transient protein complexes. In particular, it has not been well established whether binding hot spots, which are frequently found in strong static complexes, also govern transient protein interactions. To address this issue, we have investigated an electron transfer complex of physiological partners from yeast: yeast iso-1-cytochrome c (Cc) and yeast cytochrome c peroxidase (CcP). Using isothermal titration calorimetry and NMR spectroscopy, we show that Cc R13 is a hot-spot residue, as R13A mutation has a strong destabilizing effect on binding. Furthermore, we employ a double-mutant cycle to illustrate that Cc R13 interacts with CcP Y39. The present results, in combination with those of earlier mutational studies, have enabled us to outline the extent of the energetically important Cc-CcP binding region. Based on our analysis, we propose that binding energy hot spots, which are prevalent in static protein complexes, could also govern transient protein interactions.

Submolecular unfolding units of Pseudomonas aeruginosa cytochrome c-551

Hydrogen exchange rates for backbone amide protons of oxidized Pseudomonas aeruginosa cytochrome c-551 (P. aeruginosa cytochrome c) have been measured in the presence of low concentrations of the denaturant guanidine hydrochloride. Analysis of the data has allowed identification of submolecular unfolding units known as foldons. The highest-energy foldon bears similarity to the proposed folding intermediate for P. aeruginosa cytochrome c. Parallels are seen to the foldons of the structurally homologous horse cytochrome c, although the heme axial methionine-bearing loop has greater local stability in P. aeruginosa cytochrome c, in accord with previous folding studies. Regions of low local stability are observed to correspond with regions that interact with redox partners, providing a link between foldon properties and function.

Effect of single-site charge-reversal mutations on the catalytic properties of yeast cytochrome c peroxidase: evidence for a single, catalytically active, cytochrome c binding domain

Forty-six charge-reversal mutants of yeast cytochrome c peroxidase (CcP) have been constructed in order to determine the effect of localized charge on the catalytic properties of the enzyme. The mutants include the conversion of all 20 glutamate residues and 24 of the 25 aspartate residues in CcP, one at a time, to lysine residues. In addition, two positive-to-negative charge-reversal mutants, R31E and K149D, are included in the study. The mutants have been characterized by absorption spectroscopy and hydrogen peroxide reactivity at pH 6.0 and 7.5 and by steady-state kinetic studies using recombinant yeast iso-1 ferrocytochrome c (C102T) as substrate at pH 7.5. Many of the charge-reversal mutations cause detectable changes in the absorption spectrum of the enzyme reflecting increased amounts of hexacoordinate heme compared to wild-type CcP. The increase in hexacoordinate heme in the mutant enzymes correlates with an increase in H 2O 2-inactive enzyme. The maximum velocity of the mutants decreases with increasing hexacoordination of the heme group. Steady-state velocity studies indicate that 5 of the 46 mutations (R31E, D34K, D37K, E118K, and E290K) cause large increases in the Michaelis constant indicating a reduced affinity for cytochrome c. Four of the mutations occur within the cytochrome c binding site identified in the crystal structure of the 1:1 complex of yeast cytochrome c and CcP [Pelletier, H., and Kraut, J. (1992) Science 258, 1748-1755] while the fifth mutation site lies outside, but near, the crystallographic site. These data support the hypothesis that the CcP has a single, catalytically active cytochrome c binding domain, that observed in the crystal structures of the cytochrome c/CcP complex.