Characterization of Heme Orientational Disorder in a Myoglobin Reconstituted with a Triﬂuoromethyl-Group-Substituted Heme Cofactor Yuki Kanai,† Ayaka Harada,‡ Tomokazu Shibata,† Ryu Nishimura,† Kosuke Namiki,† Miho Watanabe,† Shunpei Nakamura,† Fumiaki Yumoto,‡ Toshiya Senda,‡ Akihiro Suzuki,§ Saburo Neya,∥ and Yasuhiko Yamamoto*,†,⊥ †
Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan § Department of Materials Engineering, National Institute of Technology, Nagaoka College, Nagaoka 940-8532, Japan ∥ Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan ⊥ Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan ‡
S Supporting Information *
ABSTRACT: The orientation of a CF3-substituted heme in sperm whale myoglobin and L29F, H64L, L29F/H64Q, and H64Q variant proteins has been investigated using 19F NMR spectroscopy to elucidate structural factors responsible for the thermodynamic stability of the heme orientational disorder, i.e., the presence of two heme orientations diﬀering by a 180° rotation about the 5−15 meso axis, with respect to the protein moiety. Crystal structure of the metaquo form of the wild-type myoglobin reconstituted with 13,17bis(2-carboxylatoethyl)-3,8-diethyl-2,12,18-trimethyl-7triﬂuoromethylporphyrinatoiron(III), determined at resolution of 1.25 Å, revealed the presence of the heme orientational disorder. Alterations of the salt bridge between the heme 13-propionate and Arg45(CD3) side chains due to the mutations resulted in equilibrium constants of the heme orientational disorder ranging between 0.42 and 1.4. Thus, the heme orientational disorder is aﬀected by the salt bridge associated with the heme 13-propionate side chain, conﬁrming the importance of the salt bridge in the heme binding to the protein. “Heme orientational disorder” has been recognized as a general structural feature of b-type hemoproteins.1−18 Reaction between heme and apoprotein of sperm whale myoglobin (Mb) initially yields a holoprotein possessing structural heterogeneity such that the heme is inserted into the apoprotein in two distinct orientations that diﬀer by 180° rotation about the 5−15 meso axis, with respect to the protein moiety (Figure 1),1 and the newly formed holoprotein initially contains an ∼1:1 mixture of the two hemes in Forms A and B (Figure 1). Form B is slowly converted to Form A through the heme reorientational reaction.19 Hence, there are two slowly interconverting protein forms in solution, and the dominant component has the same heme orientation as found in a crystal,20,21 i.e., Form A (Figure 1).22 Therefore, Forms A and B are often called normal and reversed heme orientations, respectively. The heme orientational disorder of a b-type hemoprotein has been investigated through studies of the reconstitution of wildtype and genetic variant proteins with not only native heme, but also a variety of chemically modiﬁed ones. 23−42 © XXXX American Chemical Society
NMR1−15,17−19,22−24,27−31,35,36,38−40,42 is generally used to characterize the heme orientational disorder, and circular dichroism43 and resonance Raman44,45 spectroscopies have been reported to be useful for identifying the presence of the reversed heme orientation. As functional consequences of the heme orientational disorder, pH-dependent oxygen (O2) aﬃnity, i.e., Bohr eﬀect, in monomeric insect Chironomus thummi thummi hemoglobins (CTT Hbs),46 reduction potential of bovine cytochrome b5 (cyt b5),47 cooperative O2 binding properties of human adult Hb,48 and O2 aﬃnity of rainbow trout Mb45 have been reported to be aﬀected by the heme orientation. The equilibrium constant of the heme reorientational reaction (KA/B = [Form A]/[Form B]) has been reported to depend strongly on the individual proteins such as wild-type Mb (KA/B = ∼9),3 CTT Hb III (∼0.5)2, Glycera dibranchiata hemoglobin component IV (0.10−0.15),14 and Rhodnius Received: May 13, 2017 Revised: July 28, 2017 Published: July 31, 2017 A
DOI: 10.1021/acs.biochem.7b00457 Biochemistry XXXX, XXX, XXX−XXX
Figure 1. Molecular structures of protohemin (Proto), 13,17-bis(2-carboxylatoethyl)-3,8-diethyl-2,12,18-trimethyl-7triﬂuoromethylporphyrinatoiron(III) (7-PF), and 13,17-bis(2-carboxylatoethyl)-3,8-ethyl-2,7,12,18-tetramethylporphyrinatoiron(III) (Meso), and two heme orientations diﬀering by a 180° rotation about the 5−15 meso axis with respect to His93, known as heme orientational disorder,1 i.e., Forms A and B. The rectangle indicates the orientation of the His93 imidazole plane, and ϕ is deﬁned as the angle between the projection of the His93 imidazole onto the heme plane and the x-axis of the heme, which passes through NII−Fe−NIV and NI−Fe-NIII in Forms A and B, respectively.
prolixus nitrophorins 1 (∼2), 2 (∼10), and 7 (∞).18 The studies demonstrated that KA/B is determined by steric interactions of the peripheral side chains attached to pyrrole rings I and II of the heme, i.e., the side chains at positions 2, 3, 7, and 8 (Figure 1), with the surrounding amino acid residues in the heme pocket.11,14,18,29,30,36,41 In fact, KA/B has been shown to be greatly aﬀected by replacement of the amino acid residues in close proximity to these heme side chains.14,18,41 The heme orientational disorder demonstrated that the molecular recognition upon insertion of the heme into the Mb heme pocket is not as strict as that for the formation of usual enzyme−substrate complexes.49 Furthermore, broad molecular recognition of the Mb heme pocket is clearly reﬂected in its capacity to accommodate a variety of guest molecules ranging from chemically modiﬁed heme complexes25−31,35,36,50−58 and analogues50,59−69 to metal complexes with salophen ligands.70 Characterization of the molecular recognition of the Mb heme pocket is a problem of particular importance for elucidating the heme-protein interaction and thus crucial for functional control of the protein. The protein moiety of Mb consists of 153 amino acid residues, arranged in eight helices, A−H, that fold into two hydrophobic cores made of the ABGH and CDEF helices.20,21,71,72 Studies on refolding of an apoprotein revealed that the ABGH core is ﬁrst to form within ∼10 μs, with the CDEF one following later in a separate step.73,74 The ABGH core has been shown to be well-packed in the absence of heme, whereas formation of a stable tertiary structure of the CDEF core demands the heme binding.73−75 The binding of heme to the CDEF core is stabilized by the coordination bond between the heme Fe atom and the nitrogen atom of the proximal His (His93(F8), where F8 is the alphanumeric code that refers to the number of residue within the helices and loops of the protein), the hydrophobic interaction of heme with the surrounding amino acid residues in the heme pocket, and the formation of salt bridges between the heme propionate groups and nearby polar amino acid side chains.20,21,72 The pKa values of the heme propionic acid side chains of Mb have been
reported to be smaller than 5,76 and the heme 13-propionate side chain forms a salt bridge with Arg45(CD3) one (heme 13propionate salt bridge (13-PSB)) (Figure 2). Similarly, the
Figure 2. Hydrogen bond network in the proximal and distal sites of met-aquo form of sperm whale myoglobin (PDB ID: 1A6K). Amino acid residue participating in hydrogen bonds, heme, and Fe-bound H2O are shown and broken lines represent hydrogen bonds.
heme 17-propionate side chain forms a salt bridge with His97(FG3) side chain imidazole of which pKa value was reported to be 5.6377 (heme 17-propionate salt bridge (17PSB)), together with a hydrogen bond with Ser92 side chain hydroxyl group (Figure 2). Compared with the 17-PSB, the 13PSB has been considered to be particularly important for the process of heme binding.27,34 Crystallographic studies demonstrated that the Arg45 side chain is also hydrogen-bonded to not only the Asp60(E3) side chain, but also to the distal His (His64(E7)) one through an intervening water molecule (Figure 2), stabilizing the 13-PSB through strengthening of the hydrogen-bonding network associated with the Arg45 side chain.72 Consequently, the 13-PSB important for the heme B
DOI: 10.1021/acs.biochem.7b00457 Biochemistry XXXX, XXX, XXX−XXX
containing 2.9 M ammonium sulfate and 0.1 M Bis-Trispropane HCl buﬀer, pH 6.3. Crystal Structure Determination and Reﬁnement. Xray diﬀraction data were collected at BL-1A (Photon Factory at the High Energy Accelerator Research Organization, Tsukuba, Japan). The protein crystal was soaked in a reservoir solution containing 30% xylitol and then ﬂash-frozen in liquid nitrogen. The protein crystal was maintained at 100 K, by a cold nitrogen stream, throughout the data collection. All diﬀraction data were processed with XDS.84 The structures were determined by the molecular replacement method using the program PHASER.85 A crystal structure of Mb (PDB ID: 1A6K)72 was used as a search model. Crystallographic reﬁnement was carried out using the program Phenix.reﬁne.86 The structures were visualized and modiﬁed using the program COOT. 87 Diﬀraction and reﬁnement data statistics are summarized in Table 1.
recognition could be perturbed through replacement of His64.78,79 Replacement of His64 with Gln, i.e., the H64Q mutation, was found to result in complete breakdown of the Arg45 hydrogen bond network, and hence the 13-PSB was no longer retained in this variant protein.78 Similarly replacement of His64 with Leu, i.e., the H64L mutation, is expected to perturb the 13-PSB. In addition, replacement of Leu29(B10), adjacent to the heme and His64, with Phe, i.e., the L29F mutation, alters the His64 side chain conformation, leading to a sizable change in the 13-PSB.80 Finally, the 13-PSB is further perturbed through simultaneous replacement of Leu29 and His64 with Phe and Gln, respectively, i.e., the L29F/H64Q double mutation.79 In this study, we carried out the H64Q, H64L, L29F, and L29F/H64Q mutations of the protein in order to alter the 13PSB, and characterized the heme orientational disorder in the variant proteins reconstituted with 13,17-bis(2-carboxylatoethyl)-3,8-diethyl-2,12,18-trimethyl-7-tri ﬂuoromethylporphyrinatoiron(III)81 (7-PF (Figure 1)). The thermodynamic stabilities of Forms A and B in the wild-type Mb reconstituted with 7-PF (Mb(7-PF)) are almost comparable to each other, as reﬂected in the ΔG value of ∼2.0 kJ mol−1, yielded from the value of 0.44 determined as the KA/B of Mb(7PF). Hence, the eﬀect of changes in the heme-protein contacts, induced by the amino acid replacements, on the ΔG value between Forms A and B is sensitively reﬂected in the KA/B values of the proteins reconstituted with 7-PF. Furthermore, the use of 7-PF allowed ready and accurate determination of KA/B using 19F NMR. Thus, 7-PF is quite useful as a heme cofactor for characterizing the relationship between the heme orientational disorder and the heme-protein contacts. The KA/B values determined for the H64Q, H64L, L29F, and L29F/ H64Q variant proteins reconstituted with 7-PF (H64Q(7-PF), H64L(7-PF), L29F(7-PF), and L29F/H64Q(7-PF), respectively) ranged from 0.42 in L29F(7-PF) to 1.4 in H64Q(7-PF), conﬁrming the importance of the 13-PSB in the heme binding to the protein.
Table 1. Crystallographic Data Summary of Met-aquo form of Mb(7-PF) data collection light source T (K) space group cell dimensions a, b, c (Å) α, β, γ resolution (Å) Rmerge I/σI completeness (%) redundancy resolution (Å) no. reﬂections Rwork Rfree no. atoms protein ligand/ion water B-factors (Å2) protein ligand/ion water rms deviations bond lengths (Å) bond angles (deg) PDB ID
MATERIALS AND METHODS Materials and Protein Samples. All reagents and chemicals were obtained from commercial sources and used as received. Sperm whale Mb was purchased as a lyophilized powder from Biozyme and used without further puriﬁcation. The expression and puriﬁcation of the H64Q, H64L, L29F, and L29F/H64Q variant proteins were carried out according to the methods described by Springer et al.82 7-PF was synthesized as previously described.81 The apoproteins of the wild-type and variant proteins were prepared at 4 °C according to the procedure of Teale,83 and the reconstitution of the prepared apoproteins with 7-PF was carried out as described previously.57 The reconstituted proteins were kept at 4 °C for at least 3 days for equilibration of the heme reorientation reaction. Met-cyano forms of the proteins were prepared by adding KCN (Nacalai Chemicals Ltd.) to the reconstituted proteins. The pH of each sample was measured with a Horiba F-22 pH meter equipped with a Horiba type 6069-10c electrode. The pH of a sample was adjusted with 0.1 M NaOH or HCl. Protein Crystallization. Crystallization of met-aquo Mb(7PF) was performed at 4 °C using the hanging-drop vapordiﬀusion method.56 The protein drops were prepared by mixing 1.5 μL of the protein solution (18 mg/mL in 10 mM potassium phosphate buﬀer, pH 7.0) with 1.5 μL of the reservoir solution
PF BL-1A 100 P21 34.26, 30.85, 64.13 90.0, 105.4, 90.0 33.04−1.25 (1.27−1.25)a 0.073 (0.366)a 15.9 (5.4)a 99.8 (99.2) 6.3 (5.9)a reﬁnement 30.92−1.25 36 020 0.163 0.173 1189 92/15 136 10.20 7.65/16.36 18.92 0.006 0.958 5XL0
Numbers in parentheses indicate the highest resolution shell.
19 F NMR Spectroscopy. 19F NMR spectra of the reconstituted proteins were recorded on a Bruker AVANCE500 spectrometer operating at a 19F frequency of 471 MHz. Typical 19F NMR spectra consisted of about 20k transients with a 100 kHz spectral width and 16k data points. The signal-tonoise ratio of the spectra was improved by apodization, which introduced ∼30 Hz line broadening. The chemical shifts of 19F NMR spectra are given in ppm downﬁeld from triﬂuoroacetic acid as an external reference.
DOI: 10.1021/acs.biochem.7b00457 Biochemistry XXXX, XXX, XXX−XXX
RESULTS Crystal Structure of Met-aquo Mb(7-PF). The crystal structure of met-aquo Mb(7-PF) indicated not only that the protein structure of Mb(7-PF) is essentially identical to that of the wild-type protein, but also that 7-PF is accommodated properly as for the heme of the wild-type protein (Figure 3).
Figure 3. 2mF0 − DFc map for Forms A and B of met-aquo Mb(7PF): side-view (a) and view from His93 (b). The contour levels of the maps are 1.2σ.
Figure 4. Simulated annealing omit maps for 7-PF side chain conformations of Forms A (left) and B (right) in met-aquo Mb(7-PF). Side-views from the 5-C carbon atom (top) and views from His93 (bottom). The contour levels of the maps are 3.0σ.
Furthermore, the heme Fe coordination structure of Mb(7-PF) was almost identical to that of the wild-type protein (see Figure S1 in the Supporting Information). These ﬁndings supported the validity of the studies on the structure−function relationship of Mb through analysis of the proteins reconstituted with chemically modiﬁed hemes possessing CF3 groups as side chains.57,88−93 The presence of both Forms A and B has been revealed by the crystal structure of Mb(7-PF). The orientation of the porphyrin moiety of 7-PF, with respect to the protein, was not greatly aﬀected by the heme orientational disorder (Figure 3). To elucidate the structural origin of the dominance of Form B over Form A in Mb(7-PF), as reported previously,36 steric interactions of the heme side chains at positions 2, 3, 7, and 8 with the surrounding amino acid residues in the protein were examined on the basis of the crystal structure. In Form A, the CF3 group at position 7 (7-CF3) is in close contact with Leu104(G5) CδH3, and the ethyl ones at positions 3 and 8 (3and 8-C2H5, respectively) are in contact with Leu104 CδH3:Phe138(H15) CζH and Thr39(C4) CαH, respectively (see Figure S2 in the Supporting Information). Particularly, the distance between 7-CF3 ﬂuorine and Leu104 CδH3 carbon atoms of Form A in the protein was determined to be 0.29 nm. Since the van der Waals radii of carbon and ﬂuorine atoms are 0.147 and 0.170 nm, respectively,94 the steric contact between them is thought to contribute to destabilization of Form A in the protein. On the other hand, in Form B, no obvious steric contact was detected between the heme side chains at positions 2, 3, 7, and 8 with the surrounding amino acid residues (see Figure S2 in the Supporting Information). The crystal structure of met-aquo Mb(7-PF) provided the conformations of the 3- and 8-C2H5 groups in Form A are also ﬁxed with χ angles of ∼ −130° and ∼ +109° for the 3- and 8C2H5 groups, respectively, and similarly those of Form B are ﬁxed with χ angles of ∼ +111° and ∼ −98°, respectively (χ values are the dihedral angles between the planes of the (n + 1)−C−n-C−CH2 carbon atoms and the n-C−CH2−CH3 ones, where n = 3 and 8 for the 3- and 8-C2H5 groups, respectively, and positive and negative χ values indicate that the terminal CH3 groups are pointing toward and away from His93, respectively (Figure 4)).
Thus, the conformations of 3-C2H5 in Form A and 8-C2H5 in Form B (or 8-C2H5 in Form A and 3-C2H5 in Form B) could be interconverted with each other, indicating that the conformations of the C2H5 groups are primarily determined by steric contact with nearby amino acid residues. Furthermore, the conformations of the side chain propionate groups at positions 13 and 17 could be completely interconverted between Forms A and B (Figure 4). 19 F NMR Spectra of Wild-Type and Variant Proteins Reconstituted with 7-PF. We next determined KA/B values of the proteins using 19F NMR. Since the KA/B value of Mb has been shown to be essentially independent of the heme Fe oxidation, spin, and ligation states, the heme orientational disorder of the protein can be readily characterized through analysis of an NMR spectrum of its paramagnetic met-cyano form,1,3,4 as shown in Figure 5. The heme orientational disorder was clearly manifested in the observation of two signals in each of the 19F NMR spectra of the met-cyano forms of Mb(7-PF), L29F(7-PF), H64L(7-PF), L29F/H64Q(7-PF), and H64Q(7PF) at 25 °C (Figure 5). Since Form B has been shown to dominate over Form A in the carbon monoxide (CO) form of Mb(7-PF)39 (see Figure S3 in the Supporting Information), comparison of the signal intensities allowed assignment of the signals at 21.37 and 36.86 ppm to the CF3 groups of Forms A and B, respectively. Therefore, the signals at ∼21 and ∼36 ppm in the spectra of the variant proteins were similarly assigned to Forms A and B, respectively (Table 2). The observation of the two separate signals allowed the determination of KA/B through analysis of the signal intensities. The analysis yielded KA/B values of 0.42, 0.94, 1.0, and 1.4 for L29F(7-PF), H64L(7-PF), L29F/H64Q(7-PF), and H64Q(7PF), respectively. The KA/B values yielded through analysis of 1 H NMR signal intensities were essentially identical to those determined by 19F NMR (see Table S1 in the Supporting Information). These results indicated that KA/B is quite sensitive to the mutations, as expected, and that the preference of the 7-PF orientation in the protein can be controlled through structural changes of the 13-PSB induced by replacement of the nearby amino acid residues. D
DOI: 10.1021/acs.biochem.7b00457 Biochemistry XXXX, XXX, XXX−XXX
broken by the H64Q one, while the 17-PSB was essentially unaﬀected by the mutations. As a result, the CD-loop of the protein is slightly displaced away from the heme, as reﬂected in changes in the distance between the heme carbon atom at position 13 and the Arg45 Cα atom from 0.84 nm in the wildtype protein72 to ∼0.9 nm in the L29F,80 H64L,78 and L29F/ H64Q79 variant ones, and then up to 0.94 nm in the H64Q79 variant one. Due to the displacement of the CD-loop away from the heme, the thermodynamic energy levels of Forms A and B are almost identical to each other in L29F/H64Q(7-PF), as manifested in the KA/B of 1.0, and, on the other hand, the former is slightly more stabilized relative to the latter in H64Q(7-PF), as reﬂected by KA/B = 1.4. These results supported that the tertiary structure of the CDEF core of the protein is formed and stabilized through interaction with the heme, as reported previously.73−75 19 F NMR Shifts. The δobs value of the met-cyano Mb in Figure 5 is given by the sum of the diamagnetic (δdia) and the paramagnetic shifts (δpara), and then δpara is expressed as the sum of paramagnetic contact (δc) and pseudocontact (δpc) shifts due to Fermi contact interaction with a delocalized unpaired electron and a through-space dipolar interaction with the unpaired electron spin, respectively. Considering the shifts of signals A and B of the CO form of Mb(7-PF) at 25 °C, i.e., 30.81 and 29.03 ppm, respectively (see Figure S3 in the Supporting Information), as the δdia values for the corresponding signals of the met-cyano form of Mb(7-PF), i.e., 21.37 and 36.86 ppm, respectively (Figure 5), the δparas of signals A and B were estimated to be ∼ −9.4 and ∼ +7.8 ppm, respectively. In the case of 7-PF, delocalization of the unpaired electron from the heme Fe atom to 7-CF3 occurs through the porphyrin πsystem, and the delocalization of the unpaired electron from the π-system to the ﬂuorine atoms occurs through hyperconjugation and spin polarization mechanisms, both of which result in positive δc values. In addition, metal-centered δpc (δpc(M)) values due to an unpaired electron spin localized at the heme Fe atom are thought to be in the range of ∼ −7 to ∼ −3 ppm for signals A and B.95 Consequently, ligand-centered δpc (δpc(L)) values due to an unpaired electron spin delocalized into p orbitals of both the pyrrole carbon atom to which 7-CF3 is attached, and 7-CF3 ﬂuorine ones appeared to contribute to the relatively large extent to the δparas of signals A and B, i.e., ∼ − 9.4 and ∼ +7.8 ppm for the former and the latter, respectively. The KA/B value was found to increase with increasing δobs of signal B (Figure 5). This ﬁnding could be interpreted in terms of the eﬀect of the mutations on δc. In the met-cyano form of Mb, the energy levels for the dxz and dyz orbitals are aﬀected by the interaction with axial ligands, and a single unpaired electron resides in either the dxz or dyz orbital, whichever possesses the highest energy.95−99 Consequently, depending upon the relative energies of the dxz and dyz orbitals, π spin delocalization occurs for either pyrrole I, III or II, IV (Figure 1). The conformation of the axial His93 side chain is restricted due to the coordination bond, together with the formation of a hydrogen bond of the His93 NδH hydrogen atom with the carbonyl oxygen atom of Leu89(F4) (Figure 2), and hence, the orientation of the His93 imidazole, with respect to the heme, contributes signiﬁcantly to determination of the relative energies of the dxz and dyz orbitals. In contrast, since a cyanide ion (CN−) is coordinated to heme Fe atom with its orientation nearly normal to the heme plane,100 the eﬀect of the CN− coordination on the relative energy levels of the two orbitals is essentially negligible.101 The coordination structure of His93
Figure 5. 471 MHz 19F NMR spectra of met-cyano forms of the wildtype Mb and L29F, H64L, L29F/H64Q, and H64Q variant proteins reconstituted with 7-PF at pH 7.0 and 25 °C (Mb(7-PF), L29F(7-PF), H64L(7-PF), L29F/H64Q(7-PF), and H64Q(7-PF), respectively). Signal assignments are shown with the spectra. Circle graphs show the ratio between Forms A and B in the proteins.
Table 2. Equilibrium Constants of the Heme Reorientational Reactions (KA/B) in Mb and Variant Proteins, and 19F NMR Shifts of Signals A and B of Met-cyano Forms of the Proteins 19
F NMR shift (ppm)b
Mb(7-PF) L29F(7-PF) H64L(7-PF) L29F/H64Q(7-PF) H64Q(7-PF) Wild-type Mb
0.44 0.42 0.94 1.0 1.4 9.0c
21.37 21.75 21.83 21.61 21.43 N/Ad
36.86 36.37 35.74 35.60 35.41 N/Ad
The experimental errors for the KA/B were ±10%. bAt pH 7.0 and 25 °C. cObtained irom ref 3. dNot applicable.
The shift diﬀerence of Forms A and B (signals A and B, respectively) of Mb(7-PF) in Figure 5 is 15.60 ppm, which is due to a diﬀerence in paramagnetic shift (δpara) between them, because the diﬀerence in the shift between the signals of the diamagnetic CO adduct of Mb(7-PF) is rather small, i.e., 1.78 ppm at 25 °C (see Figure S3 in the Supporting Information). In addition, the observed shifts (δobs) of signals A and B varied over ranges of 0.46 and 1.45 ppm among the proteins, respectively (Table 2), and it is notable that δobs of signal B correlated with KA/B in such a manner that δobs decreases with increasing KA/B.
DISCUSSION Eﬀects of the Mutations on KA/B. The KA/B value ranging from 0.42 to 1.4 in Table 2 demonstrated that the preference of the 7-PF orientation in the protein is aﬀected by structural changes in the 13-PSB induced by the mutations. Among the side chains attached to pyrrole rings I and II of 7-PF, CF3 has the largest van der Waals volume,94 and hence exerts the largest steric hindrance with the nearby amino acid residues. According to the crystal structures reported for the wild-type and variant proteins,72,78−80 the 13-PSB is somewhat weakened by the L29F, H64L, and L29F/H64Q mutations, and is completely E
DOI: 10.1021/acs.biochem.7b00457 Biochemistry XXXX, XXX, XXX−XXX
Biochemistry imidazole, with respect to the heme, is described by the angle, ϕ, between the projection of the imidazole onto the heme plane and the x-axis of the heme, which passes through NII− Fe−NIV and NI−Fe−NIII in Forms A and B, respectively (Figure 1). With ϕ = ∼0°, as indicated by the crystal structure of met-aquo Mb(7-PF), the energy of the dyz orbital is higher than that of the dxz one, and hence, due to direct delocalization of an unpaired electron from the dyz orbital into the π system of pyrrole II, the δc of signal B is larger than that of signal A. Consequently, a slight change in the orientation of the heme, with respect to the protein moiety, leads to a small increase in ϕ, which in turn slightly increases and decreases the δc values of signals A and B, respectively. Therefore, the relationship between KA/B and δobs of signal B suggested that the steric contact between the heme and the CDEF core of the protein is a determinant of KA/B. In contrast to that of signal B, the δobs of signal A did not correlate with KA/B, possibly because the δc of signal A is not suﬃciently large enough to sharply reﬂect its ϕdependence. Eﬀects of the Heme Chemical Modiﬁcations on KA/B. The predominance of Form B in met-cyano form of Mb(7-PF) (KA/B = 0.44 at pH 7.0) is in contrast to the predominance of Form A in met-cyano form of Mb reconstituted with 13,17bis(2-carboxylatoethyl)-3,8-diethyl-2,7,12,18tetramethylporphyrinatoiron(III) (Meso (Figure 1)) (Mb(Meso), KA/B = 10 at pH 8.3).102 Because these two porphyrin derivatives diﬀer only by the CF3/CH3 replacement at position 7, the substitution is responsible for the change in KA/B values, through interactions with nearby amino acid residues. In Form A, the 2-, 3-, 7-, and 8-side chains are in close proximity to Val68(E11);Tyr103(G6);Phe138(H15), Ile99(FG5);Ile107(G8); Tyr103(G4);Leu104(G5), and Phe43(CD1);Thr39(C4); Ile99(FG5), respectively (see Figure S1 in the Supporting Information).72 Since the van der Waals volumes of CH3, C2H5, and CF3 are 0.022, 0.039, and 0.043 nm3, respectively,94 the predominance of Form B over Form A in Mb(7-PF) is possibly caused by destabilization of Form A through steric hindrance between 7-CF3 and the nearby amino acid residues.
*Phone/Fax: +81-29-853-6521. E-mail: [email protected]
Yasuhiko Yamamoto: 0000-0003-4951-3184 Funding
This work was supported by a Grant-in-Aid for Scientiﬁc Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan. Notes
The authors declare no competing ﬁnancial interest.
ACKNOWLEDGMENTS This work was in part performed as a project for Supporting Drug Discovery and Life Science Research (Platform for Drug Discovery, Informatics, and Structural Life Science) of the Japan Agency for Medical Research and Development (AMED). The 1H and 19F NMR spectra were recorded on a Bruker AVANCE-600 spectrometer at the Chemical Analysis Center, University of Tsukuba.
ABBREVIATIONS Mb, myoglobin; CTT Hb, Chironomus thummi thummi hemoglobin; cyt b5, bovine cytochrome b5; 13-PSB, heme 13propionate salt bridge; 17-PSB, heme 17-propionate salt bridge; 7-PF, 13,17-bis(2-carboxylatoethyl)-3,8-diethyl-2,12,18-trimethyl-7- triﬂuoromethylporphyrinatoiron(III); CO, carbon monoxide; Mb(7-PF), wild-type Mb reconstituted with 7-PF; L29F(7-PF), the L29F variant protein reconstituted with 7-PF; H64L(7-PF), the H64L variant protein reconstituted with 7PF; L29F/H64Q(7-PF), the L29F/H64Q variant protein reconstituted with 7-PF; H64Q(7-PF), the H64Q variant protein reconstituted with 7-PF; Meso, 13,17-bis(2-carboxylato-ethyl)-3,8-diethyl-2,7,12,18- tetramethylporphyrinatoiron(III); Mb(Meso), the wild-type Mb reconstituted with Meso
CONCLUDING REMARKS The crystal structure of met-aquo Mb(7-PF) revealed not only that 7-PF is accommodated properly as for the heme of the wild-type protein, but also that 7-PF is incorporated into the heme pocket with the two orientations that diﬀer by 180° rotation about the 5−15 meso axis, with respect to the protein moiety. The protein structure of Mb(7-PF) was essentially independent of the heme orientation, and the orientations of the core porphyrin moieties of 7-PFs in Forms A and B, with respect to the protein, were almost identical to each other, supporting that KA/B is determined through steric interactions of the peripheral side chains of the heme with the surrounding amino acid residues in the heme pocket. This ﬁnding provides valuable information for elucidating the long-standing issue of the energetics of the heme orientational disorder in b-type hemoproteins.
Views of met-aquo native Mb; superposition of heme, His93 and Fe-bound H2O in native Mb and those of Forms A and B of Mb(7-PF); Orientations of some amino acid residues near heme in Forms A and B of metaquo Mb(7-PF); 471 MHz 19F NMR spectrum of the carbonmonoxy form of Mb(7-PF); equilibrium constants of the heme reorientational reactions in Mb and variant proteins (PDF)
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DOI: 10.1021/acs.biochem.7b00457 Biochemistry XXXX, XXX, XXX−XXX
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DOI: 10.1021/acs.biochem.7b00457 Biochemistry XXXX, XXX, XXX−XXX