Characterization of Catalytic Activities and Heme Coordination

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Characterization of Catalytic Activities and Heme Coordination Structures of Heme-DNA Complexes Composed of Some Chemically-modified Hemes and an All Parallel-stranded Tetrameric G-quadruplex DNA Formed from d(TTAGGG) Ryosuke Shinomiya, Yuya Katahira, Haruka Araki, Tomokazu Shibata, Atsuya Momotake, Sachiko Yanagisawa, Takashi Ogura, Akihiro Suzuki, Saburo Neya, and Yasuhiko Yamamoto Biochemistry, Just Accepted Manuscript • DOI: 10.1021/acs.biochem.8b00793 • Publication Date (Web): 12 Sep 2018 Downloaded from http://pubs.acs.org on September 15, 2018

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Biochemistry

Characterization of Catalytic Activities and Heme Coordination Structures of Heme-DNA Complexes Composed of Some Chemically-modified Hemes and an All Parallel-stranded Tetrameric G-quadruplex DNA Formed from d(TTAGGG)

Ryosuke Shinomiya,1 Yuya Katahira,1 Haruka Araki,1 Tomokazu Shibata,1 Atsuya Momotake,1 Sachiko Yanagisawa,2 Takashi Ogura,2†Akihiro Suzuki,3 Saburo Neya,4 and Yasuhiko Yamamoto1,5,6,*

1

Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan, 2Graduate School of Life

Science, University of Hyogo, Hyogo 678-1297, Japan, 3Department of Materials Engineering, National Institute of Technology, Nagaoka College, Nagaoka 940-8532, Japan, 4Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan, 5

Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba

305-8571, Japan, and 6Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba 305-8577, Japan

†

Deceased on July 23, 2017.

*

Corresponding author.

Phone/Fax: +81-29-853-6521, E-mail: [email protected]

†

This work was supported by Grants-in-Aid for Scientific Research from the Ministry of Education,

Culture, Sports, Science and Technology, Japan.

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Abstract: Heme binds selectively to the 3’-terminal G-quartet (G6 G-quartet) of an all parallel-stranded tetrameric G-quadruplex DNA, (d(TTAGGG))4, to form a heme-DNA complex. Complexes between (d(TTAGGG))4 and a series of chemically-modified hemes possessing a heme Fe atom with a variety of electron densities were characterized in terms of their peroxidase activities to evaluate the effect of a change in the electron density of the heme Fe atom (Fe) on their activities.

The peroxidase activity of a

complex decreased with decreasing Fe, supporting the point that the activity of the complex is elicited through a reaction mechanism similar to that of a peroxidase.

In the ferrous heme-DNA complex, carbon

monoxide (CO) can bind to the heme Fe atom on the side of the heme opposite the G6 G-quartet, and a water molecule (H2O) is coordinated to the Fe atom as another axial ligand, trans to the CO. The stretching frequencies of Fe-bound CO (CO) and the Fe-C bond (Fe-C) of CO adducts of the heme-DNA complexes were determined to investigate the structural and electronic natures of the axial ligands coordinated to the heme Fe atom.

Comparison of the CO and Fe-C values of the heme-DNA complexes

with the corresponding ones of myoglobin (Mb) revealed that the donor strength of the axial ligation trans to the CO in a complex is considerably weaker than that of the proximal histidine in Mb, as expected from the coordination of H2O trans to the CO in the complex.


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Biochemistry

INTRDUCTION Heme in its ferric state (heme(Fe3+)) binds to G-quadruplex DNAs to form stable complexes that exhibit enhanced peroxidase activities.1-5

These complexes might be recognized as counterparts of hemoproteins

because of their versatility and accessibility in biological and chemical analyses.

G-quadruplex DNAs are

stabilized by a unique structural motif, known as the G-quartet, which is formed from four guanine bases that are cyclically associated through Hoogsteen hydrogen-bonding (Figure 1A).6 We demonstrated that Proto(Fe3+) (or Proto(Fe2+)) (Figure 1B) binds selectively to the 3’-terminal G-quartet (G6 G-quartet) of an all parallel-stranded tetrameric G-quadruplex DNA formed from a single repeat sequence of the human telomere, (d(TTAGGG))4, to form a complex (Proto(Fe3+)-DNA or Proto(Fe2+)-DNA complex).7-15

These

heme-DNA complexes exhibit various spectroscopic and functional properties remarkably similar to those of oxygen storage hemoprotein myoglobin (Mb),7-10 implying that the complexes possess the structural essentials of heme-deoxyribozymes that mimic hemoproteins in function. Thus, heme-DNA complexes could be considered as excellent models for elucidating the interaction between the heme and G-quartet in heme-deoxyribozymes.

Figure 1. Molecular structure of the G-quartet (A), structure and numbering system for Proto(Fe3+) (R2 = R7 = CH3, R3 = R8 = CHCH2), Meso(Fe3+) (R2 = R7 = CH3, R3 = R8 = CH2CH3), 3,8-DMD(Fe3+) (R2 = R3 = R7 = R8 = CH3), 7-PF(Fe3+) (R2 = CH3, R7 = CF3 R3 = R8 = CH2CH3), and 2,8DPF(Fe3+) (R2 = R8 = CF3, R3 = R7 = CH3) (B), and schematic representation of a carbon monoxide (CO) adduct of a complex between heme(Fe2+) and an all parallel-stranded tetrameric G-quadruplex DNA of d(TTAGGG) and the heme(Fe2+) coordination structure of the complex (C). In the complex, CO binds to the heme Fe atom on the side of the heme opposite the G6 G-quartet, and then a water molecule (H2O), sandwiched between the heme and G6 G-quartet planes, is coordinated to the Fe atom as another axial ligand, trans to the CO. Carbon monoxide (CO) can bind to the Proto(Fe2+)-DNA complex to form a CO adduct.10,11,14,15

In the

CO adduct of the Proto(Fe2+)-DNA complex, CO is coordinated to the heme Fe atom on the side of the heme opposite the G6 G-quartet, and a water molecule (H2O), sandwiched between the heme and G6 3 ACS Paragon Plus Environment

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G-quartet planes, is coordinated to the Fe atom as another axial ligand, trans to the CO (Figure 1C).15 Proto(Fe2+) in the CO adduct of the complex adopts a low-spin configuration with S = 0, i.e., a diamagnetic form, and hence, owing to the absence of unpaired electrons in the complex, the interaction between the heme and G6 G-quartet in the complex has been characterized in some detail using NMR.11,14,15 Vibrational spectroscopic studies of the CO adduct of the complex afford frequencies related to the Fe-C-O bonds such as the Fe-bound CO stretching (CO), Fe-C stretching (Fe-C), and Fe-C-O bending frequencies (Fe-CO), which provide detailed structural and electronic information about the heme.16-37 The CO and Fe-C values have been shown to be influenced by  back-donation of the heme Fe atom to CO (Fe→CO  back-donation), which is modulated by the nature of the axial ligand, trans to the CO, and electronic interactions of the CO with nearby polar groups, and the Fe-CO one is closely related to the Fe-C-O geometry. 21,36,37 Characterization of the effect of a change in the electron density of the heme Fe atom (Fe) on the electronic nature of the heme in a complex is indispensable for elucidating the structure-function relationship in the heme-DNA complex, because functional regulation of heme is achieved through electronic tuning of the intrinsic heme Fe reactivity38-43 and the heme environment furnished by nearby functional groups44-49.

We have constructed a unique chemically-modified heme system composed of

mesoheme (Meso(Fe3+)), 3,8-dimethyldeuteroporphyrinatoiron(III)50,51 (3,8-DMD(Fe3+)), 13,17-bis(2carboxylatoethyl)-3,8-diethyl-2,12,18-trimethyl-7-trifluoromethylporphyrinatoiron(III)52 (7-PF(Fe3+)), and 13,17-bis(2-carboxylatoethyl)-3,7-diethyl-12,18-trimethyl-2,8-ditrifluoromethylporphyrinatoiron(III)38 (2,8-DPF(Fe3+)) that causes large and stepwise alterations of the Fe value (Figure 1B). These hemes differ from each other in the numbers of CF3, CH3, and C2H5 side chains. Since 7-PF and 2,8-DPF can be considered as counterparts of Meso and 3,8-DMD, respectively, the effects of the substitution of one and two strongly electron-withdrawing CF3 groups on the heme reactivity could be determined by pairwise comparison between Meso and 7-PF, and 3,8-DMD and 2,8-DPF, respectively.

We have demonstrated the

great value and utility of the chemically-modified heme system by revealing electronic control of the oxygen affinity of Mb through the Fe value.38-43 We have shown previously that the interaction between the heme and G6 G-quartet in a heme-DNA complex is not greatly affected by heme modifications.13-15 Hence, the chemically-modified heme system can be used to investigate the effect of a change in the Fe


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Biochemistry

value on the function of a heme-DNA complex to elucidate the molecular mechanism responsible for the enhancement of the peroxidase activity of the heme through the interaction with the G-quartet. Furthermore, the chemically-modified heme system can also be utilized to alter the Fe→CO  back-donation through the Fe value, and characterization of the effects of changes in the Fe value on the CO and Fe-C values is expected to provide information useful for gaining a deeper understanding of the electronic nature of the axial H2O ligand, trans to the CO. In this study, we characterized the peroxidase activities of the Proto(Fe3+)-DNA, Meso(Fe3+)-DNA, 3,8-DMD(Fe3+)-DNA, 7-PF(Fe3+)-DNA, and 2,8-DPF(Fe3+)-DNA complexes to elucidate the relationship between the Fe value and the activity.

We found that the peroxidase activity of the heme-DNA complexes

decreased with decreasing Fe, supporting that the activities of the complexes are elicited through a reaction mechanism similar to that of a peroxidase53,54.

The CO and Fe-C values of CO adducts of the

Proto(Fe2+)-DNA, Meso(Fe2+)-DNA, 3,8-DMD(Fe2+)-DNA, 7-PF(Fe2+)-DNA, and 2,8-DPF(Fe2+)-DNA complexes have been determined using resonance Raman spectroscopy.

We found an anticorrelation

between the Fe and CO values, which can be explained in terms of modulation of the Fe→CO  back-donation through a change in the Fe value.

In addition, similarly to the cases of various heme

complexes,16-19,22,25,27,29-32 it was shown that the CO and Fe-C values of the heme-DNA complexes are anticorrelated to each other, as expected from the electronic nature of their Fe-C-O bonds. Comparison of the CO and Fe-C values of the heme-DNA complexes with the corresponding ones of Mb revealed that the donor strength of the axial ligand trans to the CO in the complex is considerably weaker than that of the proximal histidine in Mb, as expected from the coordination of axial H2O. Furthermore, the observation of marker bands for the oxidation, spin, and ligation states of the heme Fe atom, in the 1450 - 1700 cm-1 region indicated that the CO adducts of the Proto(Fe2+)-DNA and Proto(Fe3+)-DNA complexes possess 6-coordinate low-spin heme(Fe2+) and 6-coordinate high-spin heme(Fe3+), respectively.

MATERIALS AND METHODS Sample Preparation.

A DNA sequence, d(TTAGGG), purified with a C-18 Sep-Pak cartridge was

purchased from Tsukuba Oligo Service Co. The oligonucleotides were obtained by ethanol precipitation and then desalted with Microcon YM-3 (Millipore, Bedford, MA).


The concentration of each

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oligonucleotide was determined spectrophotometrically using the absorbance at 260 nm (molar extinction coefficient 260 = 6.89 × 104 cm-1M-1).

Proto(Fe3+) was purchased from Sigma-Aldrich Co.

3,8-DMD(Fe3+),50,51 7-PF(Fe3+),52 and 2,8-DPF(Fe3+)38 were synthesized as previously described. Preparation of the heme(Fe3+)-DNA complex was carried out by mixing 5 - 20 µM heme(Fe3+) and 10 - 40 µM DNA as described previously.11

The carbon monoxide (CO) adduct of the heme(Fe2+)-DNA complex

was prepared by reduction of heme(Fe3+) of the complex with Na2S2O4 (Wako Pure Chemical Industries, Ltd.) and (±)-dithiothreitol (Wako Pure Chemical Industries, Ltd.) in the presence of CO gas. Measurement of UV-Vis Absorption and Amplex Red Oxidation Kinetics. UV-Vis absorption spectra were recorded at 25 ºC with a Beckman DU 640 spectrophotometer using 50 mM potassium phosphate buffer, pH 6.80, containing 300 mM KCl as the solvent.

The chromogenic substrate, Amplex Red

(10-acethyl-3,7-dihydroxyphenoxazine), was purchased from Sigma-Aldrich, and the reaction was monitored by following the appearance of the oxidized product, 7-hydroxyphenoxazin-3-one (resorufin), which absorbs light at ~570 nm.

Kinetic studies were performed on a Beckman DU640 spectrometer.

(d(TTAGGG))4 in 50 mM potassium phosphate buffer, pH 6.80, was heat-denatured at 90 °C for 5 min., followed by cooling to 25 °C. Amplex Red was dissolved in dimethylformamide to prepare a 10 mM stock solution. Heme(Fe3+) and then Amplex Red were added to 0.5 µM and 50 µM, respectively, to 20 µM DNA in 50 mM potassium phosphate buffer, pH 6.80. To initiate the oxidation reaction, hydrogen peroxide (H2O2) was added to 200 μM to the solution mixture. The initial slope (R0) of the time evolution of 570-nm absorbance was used as an index for the peroxidase activities of the complexes. Resonance Raman spectroscopy. Resonance Raman scattering was performed with excitation at 405.1 nm with a laser (LM-405-PLR-40-2, Ondax), and detected with a spectrometer (750M, SPEX) equipped with a liquid nitrogen-cooled charge coupled device detector (7375-0001, Nippon Roper).56 Laser power of 130 µW was used for the measurements.

The CO isotope, 13C18O, was purchased from SI Science Co.,

Ltd, Japan. Raman shifts were calibrated with indene as a frequency standard. The positions of the Fe-bound CO (CO) and the Fe-C (Fe-C) bands were determined through fitting with Voigt profiles that comprised convolutions of Gaussian and Lorentzian functions.32 The accuracy of the peak positions of well-defined Raman bands was ±1 cm−1.

Concentrations of heme and DNA used to prepare heme-DNA

complex were 20 M and 40 M, respectively, in 50 mM potassium phosphate buffer, pH 6.80. Heme(Fe3+)-DNA and CO adducts of heme(Fe2+)-DNA complexes were prepared as described above. 6 ACS Paragon Plus Environment

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Biochemistry

Calculation. The density function theory (DFT) calculations were carried out using the Gaussian 09 program package57. The restricted spin orbital approach involving the B3LYP method, together with electron basis sets of Pople’s 6-31G(d), was employed.

For simplification, the calculations were

performed with the 2,3,7,8,12,13,17,18-octamethylporphinatoiron(II) complex as a model for Proto(Fe2+) (see Figure S1 in the Supporting Information), in order to determine the CO and Fe-C values. Geometry optimization of the model compounds was carried out in the gas phase, with a fixed CH3 group orientation, i.e., one C-H fragment was in the porphyrin plane, and the others were pointing above and below the plane (see Figure S1 in the Supporting Information).38

In addition, the oxidation, spin, and coordination states

of the heme Fe atoms of the model compounds were assumed to be Fe(II), S = 0, and a 6-coordinated structure with H2O or imidazole as an axial ligand, trans to the CO ligand (see Figure S1 in the Supporting Information).

For calculations, the restricted spin orbital approach involving the B97D method38, together

with electron basis sets of Pople’s 6-31G(d), was employed.

RESULTS Binding Constants.

The absorption spectra of Meso(Fe3+) at pH 6.80 in the presence of various

stoichiometric ratios of (d(TTAGGG))4 showed ~160 % hyperchromism of the Soret band of Meso(Fe3+), together with isosbestic points at ~384.5 and ~424.5 nm (see Figure S2 in the Supporting Information). The spectral features of Meso(Fe3+) observed upon DNA titration were similar to those observed for the other hemes15.

Analysis of the observed changes afforded an association constant (Ka) = (4.5 ± 0.5) × 106

M-1, close to those observed for Proto(Fe3+), 3,8-DMD(Fe3+), 7-PF(Fe3+), and 2,8-DPF(Fe3+), i.e., (16 ± 2), (5.5 ± 0.5), (11 ± 0.9), and (5.5 ± 0.5) × 106 M-1, respectively.15 Amplex Red Oxidation.

The peroxidase activities of Proto(Fe3+), Meso(Fe3+), 3,8-DMD(Fe3+),

7-PF(Fe3+), and 2,8-DPF(Fe3+) in the absence and presence of (d(TTAGGG))4 were analyzed (see Figure S3 in the Supporting Information), and the initial slopes (R0) of the time evolution of 570-nm absorbance are summarized in Table 1. For all the hemes used in the study, the R0 values increased by factors of ~3 to ~14 in the presence of (d(TTAGGG))4, indicating the enhancement of their peroxidase activities through their interaction with the DNA.

Interestingly, the heme-DNA complexes could be ranked as

2,8-DPF(Fe3+)-DNA < 7-PF(Fe3+)-DNA < Proto(Fe3+)-DNA < 3,8-DMD(Fe3+)-DNA ≈ Meso(Fe3+)-DNA,


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in order of increasing R0. The determined ranking is essentially identical to that of the hemes, in order of increasing Fe (see below). Vibrational Frequencies of Fe-bound CO. We determined the CO and Fe-C values of the CO adducts of the Proto(Fe2+)-, Meso(Fe2+)-, 3,8-DMD(Fe2+)-, 7-PF(Fe2+)-, and 2,8-DPF(Fe2+)-DNA complexes (Figure 2 and see Figure S4 in the Supporting Information).

In the resonance Raman spectrum of the CO

adduct of the Proto(Fe2+)-DNA complex, the bands at 1958 and 532 cm-1 exhibited 12C16O/13C18O isotope shifts of -88 and -14 cm-1, respectively (see Figures S5 and S6 in the Supporting Information), and hence these bands were unambiguously assignable as the CO and Fe-C bands, respectively.

The determined CO

and Fe-C values were roughly within the ranges of the corresponding ones of native and mutant Mbs40-43, i.e., the CO and Fe-C bands of the proteins were observed in the ranges of ~1930 - ~1970 and ~490 - ~530 cm-1, respectively.

The CO and Fe-C values of the other complexes were similarly determined (see Figure

S4 in the Supporting Information), and are summarized in Table 2. The complexes were ranked as 2,8-DPF(Fe2+)-DNA < 7-PF(Fe2+)-DNA < Proto(Fe2+)-DNA < Meso(Fe2+)-DNA ≈ 3,8-DMD(Fe2+)-DNA, in order of increasing CO, and, in contrast, as 2,8-DPF(Fe2+)-DNA < 7-PF(Fe2+)-DNA < Meso(Fe2+)-DNA < Proto(Fe2+)-DNA < 3,8-DMD(Fe2+)-DNA in order of increasing Fe-C. These rankings correlated well with increasing Fe of the hemes, i.e., 2,8-DPF(Fe2+) < 7-PF(Fe2+) < Proto(Fe2+) < Meso(Fe2+) ≈ 3,8-DMD(Fe2+).


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Biochemistry

Figure 2. The Fe-bound CO (CO) and Fe-C (Fe-C) bands of the 3,8-DMD(Fe2+)-(d(TTAGGG))4 (DNA), Meso(Fe2+)-DNA, Proto(Fe2+)-DNA, 7-PF(Fe2+)-DNA, and 2,8-DPF(Fe2+)-DNA complexes in 50 mM potassium phosphate buffer, pH 6.80, at 25 ºC. The positions of the CO and Fe-C bands of the complexes determined through fitting with Voigt profiles32 are indicated with the spectra. The band at 518 cm-1 in the spectrum of 7-PF(Fe2+)-DNA complex is not due to Fe-C (see trace D in Figure S6 in the Supporting Information).

Finally, although the Fe-C-O bending frequency, i.e., the Fe-CO value, was determined in the range of ~570 - ~580 cm-1 in the spectra of the Mbs,21,28,36,37,40-43 it was not observed in the spectra of the complexes, probably due to the orientation of the Fe-bound CO along the heme normal (see Figure S7 in the Supporting Information).


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Raman Marker Bands. Well-resolved bands in the region of 1450 - 1700 cm-1 of Raman spectra of various heme complexes and hemoproteins, recorded with Soret band excitation, have been recognized as marker bands for the oxidation, spin, and ligation states of the heme Fe atom.58-64

In the spectrum of a CO

adduct of Proto(Fe2+)-DNA complex (Figure 3A and see trace A in Figure S8 in the Supporting Information), bands at 1500, 1583, and 1632 cm-1 could be assigned to A1g modes 3 and 2, and B1g mode 10, respectively, and the one at 1557 cm-1 might be due to Eu mode 38. The observation of these bands could be considered as representing the 6-coordinate low-spin heme(Fe2+) in the complex,64 this being consistent with the coordination of H2O to the heme Fe atom, trans to the CO. On the other hand, in the spectrum of the Proto(Fe3+)-DNA complex (Figure 3B and see Figure S9 in the Supporting Information), the observation of bands at 1560, 1483, and 1516 cm-1 assignable to A1g modes 2 and 3, and Eu mode 38, respectively,61,63,64 indicated the 6-coordinate high-spin heme(Fe3+) in the complex.

Figure 3. High-frequency regions of visible resonance Raman spectra of the CO adduct of the Proto(Fe2+)-(d(TTAGGG))4 (DNA) complex (A) and Proto(Fe3+)-DNA one (B) in 50 mM potassium phosphate buffer, pH 6.80, at 25 ºC. The band assignments, together with the positions of the bands of the complexes determined through fitting with Voigt profiles32, are indicated with the spectra.

DISCUSSION Relationship between Peroxidase Activity and Fe. We have shown that the equilibrium constant, pKa, of the so-called “acid-alkaline transition” in the met-form of a protein38 and the CO value of a CO adduct of the protein40 can be used as indicators of the Fe value of the hemes incorporated into apoproteins of native Mb (see Figure S10 in the Supporting Information). A decrease in the Fe value was sharply reflected in a decrease in the pKa value due to lowering of the H+ affinity of Fe-bound OH- in the alkaline 10 ACS Paragon Plus Environment

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Biochemistry

form of the protein,38 and an increase in the CO value due to a decrease in  back-donation of the heme Fe atom to CO (Fe→CO  back-donation) in the protein40. We demonstrated that the pKa and CO values of the proteins correlate well with each other, confirming that the effects of the heme modifications on the Fe value are independent of the oxidation state of the heme Fe atom.40 Hence, the ranking of the hemes found in studies involving the reconstituted protein system, i.e., 2,8-DPF < 7-PF < Proto < 3,8-DMD ≈ Meso in order of increasing Fe, is also thought to hold for the heme-DNA complex system, as reflected in the effects on the heme chemical modifications on the CO value of the heme-DNA complex (Table 2). From the determined R0 values, as a measure of the activity (Table 1), the complexes could be ranked as 2,8-DPF(Fe3+)-DNA < 7-PF(Fe3+)-DNA < Proto(Fe3+)-DNA < 3,8-DMD(Fe3+)-DNA ≈ Meso(Fe3+)-DNA, in order of increasing peroxidase activity. The determined ranking of the heme-DNA complexes is identical to that of the hemes, in order of increasing Fe.

These results suggested that an increase in the

Fe value results in an increase in the Lewis basicity of the heme Fe atom, which in turn promotes heterolytic cleavage of the O-O bond of Fe-bound H2O2, possibly to generate a highly reactive intermediate known as compound I53-55.

Hence, the relationship between the peroxidase activity and the Fe value

observed for a heme-DNA complexes supported the point that the peroxidase activity of the heme-DNA complex is elicited through a reaction mechanism similar to that of a peroxidase53-55.

On the other hand,

in the case of peroxidase, the cleavage of the O-O bond is further promoted by hydrogen bonding interactions of Fe-bound H2O2 with nearby amino acid residues, called the “pull effect”.53

Since, in the

case of the heme-DNA complex (see Figure 1C), H2O2 is possibly bound to the heme Fe atom on the side of the heme opposite the G6 G-quartet, there would be no functional group in the proximity of Fe-bound H2O2, facilitates the pull effect for the peroxidase activity of the complex. The CO Values of the Complexes. The CO and Fe-C values of the heme-DNA complexes provided a wealth of information for elucidating the electronic nature of the axial H2O ligand coordinated to heme Fe atom in the complex.21,36,37,65,66

The CO and Fe-C bands of the CO adducts of the heme-DNA complexes

were observed in the ranges of ~1952 - ~1967 and ~525 - ~533 cm-1, respectively (Table 2), and these values were within the ranges of the corresponding values observed for the Mb and hemoglobin system, i.e, ~1928 – ~1984 and ~479 – ~543 cm-1 for the CO and Fe-C bands,40-43,67,68 respectively.

The CO value of

hemoproteins has been shown to be affected by electronic interactions of the CO with nearby polar groups


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such as the distal histidine in native Mb29,40,69,70 (distal polar interactions), in addition to the nature of the axial ligand, trans to the axial CO one37,65,66,71. Hence the CO and Fe-C values of the heme-DNA complexes were compared with those of the H64L mutant protein of Mb41 (Table 2), where the distal histidine is replaced by non-polar leucine, and hence the distal polar interactions are substantially reduced. The comparison revealed that the CO and Fe-C values of the heme-DNA complexes were smaller and greater by ~12 and ~42 cm-1, respectively, relative to the corresponding ones of the H64L mutant proteins reconstituted with the identical hemes41 (Table 2).

The relatively large difference in the Fe-C value

between the two systems could be interpreted in terms of the donor strength of the axial ligand trans to the CO (see below).

Furthermore, as in the case of the H64L mutant protein41, the CO value of the

heme-DNA complex increased upon the introduction of CF3 group(s) into the heme peripheral side chain(s) (Table 2).

Pairwise comparison of the CO values between Meso(Fe2+)-DNA and 7-PF(Fe2+)-DNA

complexes, and 3,8-DMD(Fe2+)-DNA and 2,8-DPF(Fe2+)-DNA ones revealed increases of 5 and 10 cm-1 for the substitution of one and two CF3 groups, respectively, demonstrating the additive effect of the heme -system perturbation due to the heme chemical modifications, as reported for some Mb systems40,42,43, together with the H64L mutant protein one41 listed in Table 2. These results indicated that the effects of a change in Fe on the electronic nature of the Fe-C-O fragment is almost completely independent of the

Figure 4. Plots of the CO values against the Fe-C ones of the CO adducts of the heme(Fe2+)-(d(TTAGGG))4 (DNA) complexes in 50 mM potassium phosphate buffer, pH 6.80, at 25 ºC (3,8-DMD(Fe2+)-DNA (▲), Meso(Fe2+)-DNA (■), Proto(Fe2+)-DNA (●), 7-PF(Fe2+)-DNA (▼), and 2,8-DPF(Fe2+)-DNA (◆)). Plots of the CO values against the Fe-C ones of CO adducts of the H64L mutants of myoglobin possessing 3,8-DMD(Fe2+) (△), Meso(Fe2+) (□), Proto(Fe2+) (○), 7-PF(Fe2+) (▽), and 2,8-DPF(Fe2+) (◇)41 are shown for comparison. 12 ACS Paragon Plus Environment

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Biochemistry

heme environment.

In contrast to the CO value, comparison of the Fe-C values of the complexes yielded

differences of 1 and 8 cm-1 due to the substitution of one and two CF3 groups, respectively, and hence, as in the case of the H64L mutant protein system, an additive effect of the heme -system perturbation on the Fe-C value was not observed. A negative correlation between the CO and Fe-C values of heme complexes has been well documented.21,36,37

The correlation has been interpreted in terms of the Fe→CO  back-donation as that,

as the back-donation increases, the bond orders of the C-O and Fe-C bonds decreases and increases, respectively, leading to a decrease and an increase in the CO and Fe-C values, respectively (see Figure S10B in the Supporting Information).21,36,37

The plots of the Fe-C values against the CO ones (Fe-C-CO

plots) for the heme-DNA complexes could be represented by a straight line of Fe-C = -0.41×CO + 1333, and similarly those for the H64L mutant proteins by one of Fe-C = -0.46×CO + 1395 (Figure 4). The similarity in the slope between the Fe-C-CO plots for the heme-DNA complexes and the H64L mutant proteins suggested that the effects of a change in Fe on the Fe→CO  back-donation in these two systems are highly alike. Hence, as in the case of the H64L mutant proteins41, the effects of a change in Fe on the CO and Fe-C values in the heme-DNA complex could be interpreted in terms of a Fe-dependent shift in the resonance between the two canonical forms of the Fe-CO fragment (see Figure S10B in the Supporting Information). Spiro and Wasbotten37 demonstrated that changes in the donor strength of the axial ligand trans to the CO shift the Fe-C-CO plots to higher or lower positions.

For example, stronger trans ligand donation

leads to an increase in the Fe value, which in turn enhances the Fe→CO  back-donation, resulting in lowering of CO, but the accompanying increase in Fe-C is countered by the trans ligand, which competes with the CO  donation to the Fe dz2 orbital.37,65,66

Consequently, for a given degree of back bonding,

Fe-C is lower for a trans ligand with stronger donation. Hence, the upward shift of the Fe-C-CO plots for the heme-DNA complexes, with respect to those for the H64L mutant proteins, indicated that the donor strength of the axial H2O ligand in a heme-DNA complex is weaker than that of the proximal histidine in the protein. In fact, the theoretical calculation indicated that the replacement of the axial H2O ligand trans to the CO by imidazole leads to an increase in the CO value, together with a significant decrease in the Fe-C one (see Table S1 in the Supporting Information).

Thus, the electronic nature of the axial H2O


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ligand in a heme-DNA complex was characterized through analysis of the vibrational frequencies of Fe-bound CO, together with the effects of changes in Fe on the frequencies.

CONCLUDING REMARKS The CO and Fe-C values of CO adducts of heme(Fe2+)-DNA complexes possessing an H2O molecule coordinated to the heme Fe atom, as an axial ligand trans to the Fe-bound CO, have been determined. Analysis of the CO and Fe-C values indicated that the donor strength of the axial H2O ligand in a complex is considerably weaker than that of the proximal histidine in myoglobin.

The observation of resonance

Raman marker bands for the oxidation, spin, and ligation states of the heme Fe atom indicated that the axial H2O ligand is retained in the heme(Fe3+)-DNA complex, and hence the peroxidase activity of the complex is possibly elicited through H2O ligation.

The peroxidase activity of the complex decreased with

decreasing electron density of the heme Fe atom, most likely due to a decrease in the Lewis basicity of the heme Fe atom, which leads to a slow-down of heterolytic cleavage of the O-O bond of Fe-bound hydrogen peroxide to generate highly reactive intermediate species essential for the peroxidase activity.

These

findings provide crucial insights into the structure-function relationships in the heme-DNA complex.

ACKNOWLEDGMENT We are indebted Prof. Dipankar Sen (Simon Fraser University, Canada) for the insightful and valuable discussion. This work was financially supported by JSPS KAKENHI (No. 16KT0048 to Y.Y. and No. 16K17926 to T.S.), and the Bilateral Open Partnership Joint Research Project (No. BBD29011 to Y.Y.).

SUPPORTING INFORMATION AVAILABLE Figures S1 – S10 and Table S1.

This material is available free of charge via the internet at

http://pubs.acs.org.


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