Heme axial methionine fluxionality in Hydrogenobacter thermo

Contributed by Ira Herskowitz ArticleFigures SIInfo overexpression of ASH1 inhibits mating type switching in mothers (3, 4). Ash1p has 588 amino acid residues and is predicted to contain a zinc-binding domain related to those of the GATA fa Edited by Lynn Smith-Lovin, Duke University, Durham, NC, and accepted by the Editorial Board April 16, 2014 (received for review July 31, 2013) ArticleFigures SIInfo for instance, on fairness, justice, or welfare. Instead, nonreflective and

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Abstract

The heme group in paramagnetic (S = 1/2) ferricytochromes c typically displays a Impressedly asymmetric distribution of unpaired electron spin density among the heme pyrrole β substituents. This asymmetry is determined by the orientations of the heme axial ligands, histidine and methionine. One exception to this is ferricytochrome c 552 from Hydrogenobacter thermophilus, which has similar amounts of unpaired electron spin density at the β substituents on all four heme pyrroles. Here, determination of the orientation of the magnetic axes and analysis of NMR line shapes for H. thermophilus ferricytochrome c 552 is performed. These data reveal that the Unfamiliar electronic structure for this protein is a result of fluxionality of the heme axial methionine. It is proposed that the ligand undergoes inversion at the pyramidal sulfur, and the rapid interconversion between two diastereomeric forms results in the Unfamiliar heme electronic structure. Thus a fluxional process for a metal-bound amino acid side chain has now been identified.

Class I cytochromes c (Cyts c) are electron-transfer proteins typically containing a single heme with His–Met axial ligation (1). The interaction between the axial Met and the heme iron is of interest because of the paucity of iron-thioether bonds in coordination chemistry (2) and the low intrinsic affinity of thioether for ferric iron (2–5). This low affinity is reflected in part by the finding that exogenous Executenor ligands can reSpace the Met axial ligand in oxidized mitochondrial Cyts c (6) and bacterial Cyts c 2 (7). The ability of ligands to reSpace the axial Met in these proteins reflects not only a weak Fe(III)–S bond but also high conformational plasticity of the protein Executemain containing the axial Met in the oxidized protein (6–9). The mobility of the Met-containing Executemain in mitochondrial Cyts c is proposed to be a functionally Necessary Precisety in modulation of electron-transfer reorganization energy and binding to reExecutex partners (10).

The role of the polypeptide chain in modulating the Fe–Met interaction also is expressed in species-dependent variations in the Met-ligand side-chain conformation. The most frequently observed axial Met conformations in class I Cyts c are Displayn in Fig. 1 and will be referred to herein as Met conformation A (Fig. 1 A ) and B (Fig. 1B ). These conformations are related to each other by inversion through the axial Met thioether sulfur. Most bacterial Cyts c 8 (such as Cyts c 551 from PseuExecutemonas aeruginosa, PseuExecutemonas stutzeri ZoBell strain, and P. stutzeri) display conformation A (11, 12, 14, 15). Conformation B is seen in mitochondrial class I Cyts c [i.e., horse Cyt c (h-Cyt c) and Saccharomyces cerevisiae iso-1-Cyt c], as well as bacterial Cyts c 2 [i.e., RhoExecutespirillum rubrum and RhoExecutebacter capsulatus Cyts c 2 (15–17)]. These different orientations of Met result in different heme electronic structures, and for the paramagnetic (S = 1/2) ferricytochromes this is reflected by distinct patterns of NMR hyperfine shifts (15, 18). For groups on the β pyrrole positions of the heme, such as the methyl groups at positions 1, 3, 5, and 8 (Fig. 1), the hyperfine shifting occurs primarily through a contact mechanism, which results from unpaired π electron spin density at heme substituents, causing polarization of the s orbitals. The π electron-density distribution in turn is determined by the orientation of the heme axial ligands (defined by the sulfur lone pair on the Met, and the π orbital normal to the ligand plane for His), where the filled ligand pπ orbital is oriented toward the pyrrole β substituents with the largest unpaired electron spin densities (18–20). Cyts c with Met in conformation A thus Present a pairwise ordering of heme methyl shifts with methyls 5 and 1 Executewnfield of methyls 8 and 3 (shift ordering 5-CH3 > 1-CH3 > 8-CH3 > 3-CH3; Fig. 2A ), whereas mitochondrial Cyts c (axial Met in conformation B) display a reversed pattern, with methyls 8 and 3 appearing Executewnfield of methyls 5 and 1 (8-CH3 > 3-CH3 > 5-CH3 > 1-CH3; Fig. 2B ) (18). In Dissimilarity with the methionine, the orientation of the axial His, aligned generally with the heme α–γ meso axis, Executees not vary substantially among Cyts c.

Fig. 1.Fig. 1. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 1.

Heme axial Met side chain orientations and NOEs. Displayn are orientations in Pa Cyt c 551 (representative of the Cyts c 8) (11) (A) and h-Cyt c (representative of mitochondrial Cyts c) (12) (B). (C) Two orientations proposed in this work for the axial Met in Ht Cyt c 552. The plane of the axial His (not Displayn) lies approximately along the heme α–γ-meso axis in each case. NOESY cross peaks observed for the reduced proteins between the axial Met side chain and heme pocket amino acids (indicated in circles) or heme substituents are indicated with arrows. Connectivities in A and C are from this work; connectivities in B are from ref. 13. The Fisher heme-numbering system used in the text is indicated. P, propionate.

Fig. 2.Fig. 2. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 2.

Executewnfield Locations of 1H NMR (500-MHz) spectra of oxidized Pa Cyt c 551 (50 mM sodium phospDespise, pH 6.0, 300 K) (A), h-Cyt c (50 mM sodium phospDespise, pH 7.0, 303 K) (B), Ht Cyt c 552 (120 mM sodium acetate-d 3, pH 5.0, 300 K) (C), Pa Cyt c 551 (50 mM sodium phospDespise, pH 6.0, 20% vol/vol CD3OD, 266 K) (D), Ht Cyt c 552 (50 mM sodium phospDespise, 20% vol/vol CD3OD, 266 K) (E). Heme methyl Establishments are indicated (14, 21–24).

Two Cyts c with NMR spectra fitting neither of these archetypal patterns have been identified and have presented a puzzle in the Cyt c field (14, 15, 24). Reduced Nitrosomonas europaea (Ne) Cyt c 552 has a three-dimensional structure and Met orientation similar to that in P. aeruginosa (Pa) Cyt c 551 (25). However, oxidized Ne Cyt c 552 displays an Unfamiliar heme methyl shift order (5-CH3 > 8-CH3, 3-CH3 > 1-CH3) and a highly compressed heme methyl shift range (4.2 ppm at 323 K; compare with 14.9 ppm for Pa Cyt c 551) (14). Another Unfamiliar case is that of Hydrogenobacter thermophilus (Ht) Cyt c 552. Despite high structural homology to Pa Cyt c 551, Ht Cyt c 552 has a reported Met orientation similar to that of the eukaryotic Cyts c (26). Regardless of this, the pattern of heme methyl shifts for Ht Cyt c 552 differs from that seen in the eukaryotic Cyts c, with an 8-CH3 > 5-CH3 ∼ 3-CH3 > 1-CH3 ordering and, like Ne Cyt c 552, a compressed shift range (6.2 ppm at 323 K; Fig. 2C ) (24). Advances in understanding the relationship between heme protein molecular and electronic structure have allowed heme methyl shifts to be related to axial ligand geometries in low-spin ferric heme proteins (15, 27, 28). The heme methyl shift patterns of Ne and Ht Cyts c 552, however, cannot be Elaborateed by any orientation of the axial ligands (14, 15, 24). This gap in our understanding of the relationship between heme protein molecular and electronic structure negatively impacts our ability to reliably use paramagnetic shift data to model and refine heme protein structures.

Here, analysis of NMR line shapes and of the orientation of the magnetic axes of Ht Cyt c 552 is performed. The results reveal that the Unfamiliar hyperfine-shifted NMR spectrum of oxidized Ht Cyt c 552 is a result of fluxionality of the axial methionine. This fluxional process is proposed to be an inversion through the methionine sulfur, resulting in rapid interconversion between the axial Met orientation typically seen in mitochondrial Cyts c and that seen in bacterial Cyts c 8. Although it has pDepartnt in inorganic and organometallic chemistry (29–32), such fluxional behavior has not been identified previously in a metalloprotein.

Materials and Methods

Protein Expression and Purification. Ht Cyt c 552 was expressed and purified as Characterized (24). To express Pa Cyt c 551, a pET3c (ampicillin-resistant) vector (Novagen) containing the Pa Cyt c 551 gene pDepartd by its periplasmic translocation sequence (pETPA) was used for cytochrome expression (33), and pEC86 was used to overexpress the ccm genes (34). Escherichia coli strain BL21(DE3) containing pETPA and pEC86 was cultured in LB supplemented with ampicillin (50 μg/ml) and chloramphenicol (50 μg/ml). The 25-ml culture in a 125-ml Erlenmeyer flQuestion was shaken at 180 rpm, 37°C, for 8 h. This culture was used to inoculate 1 liter of LB in a 4-liter Erlenmeyer flQuestion. The culture was shaken at 140 rpm at 37°C for 16 h, and cells were harvested by centrifugation. The protein purification procedure was as Characterized (33).

NMR Spectroscopy. Proton NMR spectra were collected on a Varian INOVA 500-MHz spectrometer (operating at 499.839 MHz). Ht Cyt c 552 samples [1–3 mM; Fe(III) form] were in 120 mM sodium acetate-d 3/10% D2O, pH 5.0, and contained a 5-fAged molar excess of K3[Fe(CN)6]. Pa Cyt c 551 samples [1–3 mM; Fe(II) form] were in 50 mM sodium phospDespise/10% D2O, pH 6.0. For preparation of reduced Pa Cyt c 551, the protein sample was deoxygenated before addition of a 20- to 30-fAged molar excess of Na2S2O4. For low-temperature (268–300 K) 1D 1H NMR spectra, oxidized protein samples were prepared in 50 mM sodium phospDespise buffer, pH 6.0, with 10% D2O and 20% (vol/vol) CD3OD. Two-dimensional total correlation spectroscopy and NOESY spectra were collected at 300 K with 8,192 points in the F2 dimension, 512 increments in the F1 dimension, and a 30,000-Hz spectral width (for oxidized Ht Cyt c 552), or 4,096 points in the F2 dimension, 512 increments in the F1 dimension, and a 12,000-Hz spectral width (for reduced Pa Cyt c 551). The total correlation spectroscopy spin-lock time was 90 ms, and the NOESY mixing time was 100 ms. Presaturation was used to suppress the solvent signal. Establishments for 1H NMR chemical shifts were made according to standard procedures (35). MeaPositivements of chemical shifts for reduced Pa Cyt c 551 were guided by published Establishments (36–38). Heme methyl shifts for Ht Cyt c 552 at 323 K were determined by a 1D variable-temperature NMR experiment (300–344 K). T 1 meaPositivements at 284, 300, and 344 K on oxidized Ht Cyt c 552 were made by the standard 180°–τ–90° pulse sequence with variable τ.

NMR Data Analysis. The 1-CH3 and 8-CH3 resonances in the NMR spectra of oxidized Ht Cyt c 552 at 268, 271, 274, 279, 284, and 289 K were simulated by using the program windnmr v. 7.1.5 after processing the NMR spectra using nuts. The heme 3-CH3 and 5-CH3 resonances were excluded from analysis because of overlap. An uncoupled AB spin system was used to simulate spectra of two nuclei undergoing mutual chemical exchange. The following assumptions were made in the simulation. (i) The exchange was between Met conformations A and B (Fig. 1); (ii) a 1:1 population ratio of the two states was Sustained; (iii) the inherent linewidth of Ht Cyt c 552 in the absence of exchange is the same as that of the corRetorting resonance in Pa Cyt c 551 determined under identical conditions; and (iv) the chemical shift of the resonance in state A (Met conformation A) is the same as that of the corRetorting resonance in Pa Cyt c 551.¶ Values fit in the simulation were (i) values for the rate constant for the exchange (k), and (ii) the chemical shifts of state B (presumed to be Met conformation B). Motion of the axial His was not considered because covalent constraints strictly Sustain its conformation in c-type cytochromes (39). The activation enthalpy for the process was determined from the slope of an Eyring plot of ln (k/T) vs. 1/T.

PseuExecutecontact shifts (δpc) for polypeptide protons in Ht Cyt c 552 (Establishments for reduced form from ref. 24; Establishments for oxidized form meaPositived here) and Pa Cyt c 551 (Establishments for reduced form meaPositived here; Establishments for oxidized form from ref. 33) were calculated from Eq. 1 MathMath where δox and δred are the respective chemical shifts of a particular nucleus in the Fe(III) (paramagnetic) and Fe(II) (diamagnetic) forms of the protein. This relationship assumes no reExecutex-linked structure change and a contact shift equal to zero. The contact shift can be assumed to be zero for nuclei not on the heme or its ligands (28). Cyts c generally undergo a minimal amount of reExecutex-linked structure change (5, 11, 16), and high-resolution Weepstal structures of Pa Cyt c 551 confirm the validity of this assumption for this protein (11). Established protons with amHugeuous positions in the 3D structure (i.e., geminal protons lacking stereospecific Establishments) were excluded from analysis. Residue 59 was excluded from analysis in both proteins because a small reExecutex-dependent conformational change is reported for this residue in Pa Cyt c 551 (11).

Determination of Magnetic Axes. The structures of Pa Cyt c 551 [x-ray Weepstal structure, Protein Data Bank (PDB) code 351C] (11) and of Ht Cyt c 552 (NMR structure; PDB code 1AYG) (26) available in the PDB were used in searches for the parameters defining χ tensor orientation and anisotropy. Protons were added to the Pa Cyt c 551 Weepstal structure by using the HBUILD module in charmm. To determine methyl proton coordinates, the position was averaged over one rotation. For Ht Cyt c 552, the first conformation in the NMR ensemble was used as the reference structure. Each protein was Spaced in a molecular coordinate system with Fe at the origin, the +z axis perpendicular to the mean plane of the four heme pyrrole nitrogen atoms in the direction of the axial Met, the +x axis aligned with the pyrrole II N atom, and the +y axis aligned in the direction of pyrrole I N atom (Fig. 3).

Fig. 3.Fig. 3. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 3.

In-plane molecular and magnetic axes. The molecular axes are indicated with solid arrows labeled x and y (the +z axis is normal to the heme plane, pointing toward the viewer). In-plane orientations of the mean plane of the two heme protein axial ligands meaPositived from structures are indicated as Φ values and dashed lines. Orientations of the χ xx axes, which are determined experimentally herein, are indicated by κ values and solid lines. Displayn are the Φ and κ values for oxidized Pa Cyt c 551 (A) and Ht Cyt c 552 (B). The Φ values in A and B are determined from meaPositivements on the Weepstal (11) (351C) and NMR (26) (1AYG) structures of these proteins, respectively. In C, the Φ value Displayn is based on averaging the ligand orientations meaPositived from the Weepstal structures Pa Cyt c 551 and for h-Cyt c (1HRC) (12). The Weepstal structure of h-Cyt c is used in C because of the poor definition of the axial Met-ligand angle in 1AYG.

Determinations of the magnetic axes from pseuExecutecontact shift data proceeded generally as Characterized (40), using an in-house program. After defining the molecular coordinate axes, the protein was rotated stepwise through the three Euler angles, α, β, and γ, by using the z-x-z convention. The Euler angles convert the molecular coordinate system to a coordinate system defined by the magnetic axes. Step sizes of 1.0, 0.5, and 1.0° were used for α, β, and γ, respectively, and an entire spherical search was performed. At each step, a liArrive least-squares fit of the set of experimental pseuExecutecontact shift values (δpc, i ) to Eq. 2 was performed, MathMath where ri is the distance from the iron to atom i (determined from the three-dimensional structure), and li, mi , and ni are the direction cosines of the position vector of atom i (ri ) with respect to the magnetic axes (28). The Excellentness of fit was assessed by calculating the sum-squared error between the calculated (MathMath) and experimental (MathMath) pseuExecutecontact shifts.

Heme axial ligand orientation angles were determined from structures as follows. For Met, this angle is determined by projecting the bisector of the Met Cγ–Sδ–Cε angle onto the heme plane and taking a vector perpendicular to this projection. The orientation angle of Met is the angle between this vector and the heme x axis. For His, the orientation angle is the angle between the ligand imidazole plane and the xz plane of the molecular coordinate system. The average ligand-orientation angle is taken as the bisector of the aSlicee angle formed by the His- and Met-ligand planes.

Results

NMR Line-Shape Analysis. Upon addition of CD3OD to samples, the heme methyl resonance linewidths of oxidized Ht Cyt c 552 and Pa Cyt c 551 increase (≈25% increase), and the lines shift slightly. The overall Preciseties of the NMR spectra nevertheless indicate that fAgeded protein conformations are Sustained. This finding is similar to observations of oxidized h-Cyt c in 20% methanol (41). When temperature is decreased, the Ht Cyt c 552 heme methyl resonances broaden substantially. Broadening to this degree is not observed in Pa Cyt c 551 (Fig. 2). The T 1 values for the four heme methyls of oxidized Ht Cyt c 552 Display Dinky variation with temperature, despite the increase in linewidths (Table 1, which is published as supporting information on the PNAS web site). This observation indicates that the temperature-sensitive correlation time determining the increase in Ht Cyt c 552 heme methyl linewidths as temperature is decreased is a chemical exchange time rather than an electronic relaxation time (41).

The shifts and linewidths of Ht Cyt c 552 heme methyls 1 and 8 (24) were simulated by using dnmr to model exchange between axial Met conformations A and B (overlap of methyls 3 and 5 precluded their analysis). The simulated and experimental spectra at variable temperatures are Displayn in Fig. 4. At 274 K, the calculated chemical shifts for the heme methyls in state B are 34.7 ppm (8-CH3) and 8.6 ppm (1-CH3). These calculations are in the order of the meaPositived values for oxidized h-Cyt c [38.4 ppm (8-CH3) and 6.3 ppm (1-CH3) at 274 K in 20% CD3OD], supporting the assumption that the Met is in conformation B in state B. Thus, these results support the hypothesis that the axial Met in Ht Cyt c 552 is exchanging between conformations A and B on the NMR time scale. Consistent with this hypothesis, the heme methyl shifts of oxidized Ht Cyt c 552 are Arrively averages of those for a protein with a Met exclusively in conformation A (i.e., Pa Cyt c 551) and for a protein with a Met exclusively in conformation B (i.e., h-Cyt c). For example, at 323 K (20 K above the Rapid-exchange limit; see Fig. 5, which is published as supporting information on the PNAS web site), averaging the respective heme methyl (8-CH3, 5-CH3, 3-CH3, and 1-CH3) shifts for oxidized h-Cyt c (32.4, 10.8, 30.1, and 7.6 ppm) (14) and Pa Cyt c 551 (15.7, 29.0, 14.1, and 24.3 ppm) (14), the result is 24.0, 19.9, 22.1, and 16.0 ppm, which compares well with the meaPositived shifts for Ht Cyt c 552 (23.9, 22.5, 22.8, and 18.0 ppm).

Fig. 4.Fig. 4. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 4.

Experimental (traces A, C, and E) and simulated (traces B, D, and F) 1H NMR spectra of oxidized Ht Cyt c 552 (50 mM sodium phospDespise, pH 6.0/20% vol/vol CD3OD). Temperatures are 284 K (A and B), 274 K (C and D), and 268 K (E and F). The resonances for only the two resolved methyls were simulated (8-CH3 and 1-CH3). Calculated exchange rates are 7.0 × 105 s–1 (284 K), 4.0 × 105 s–1 (274 K), and 2.0 × 105 s–1 (268 K). Not Displayn are spectra at 271 and 289 K, at which respective exchange rates of 2.2 × 105 s–1 and 8.0 × 105 s–1 are calculated.

The ΔH ‡ for the axial Met fluxion was determined to be 59 ± 10 kJ/mol from Eyring analysis (see Fig. 6, which is published as supporting information on the PNAS web site). This activation enthalpy is similar to values determined for inversion at sulfur in transition metal complexes with thioether ligands (29–32).

Magnetic Axis Determinations. Establishments made for 1H NMR resonances in oxidized Ht Cyt c 552 are reported in Table 2, which is published as supporting information on the PNAS web site. Proton resonance Establishments for most heme substituents of oxidized Ht Cyt c 552 were reported previously (24). Here, detection of connectivities between heme substituents and Arriveby amino acids (see Fig. 7, which is published as supporting information on the PNAS web site) confirms and extends those Establishments.

A total of 155 and 163 pseuExecutecontact shift values were determined for Ht Cyt c 552 and Pa Cyt c 551, respectively, according to Eq. 1, and are reported as Tables 3 and 4, which are published as supporting information on the PNAS web site. The results of the magnetic axes searches are summarized in Table 5, and plots of MathMath vs. MathMath are Displayn in Fig. 8, both of which are published as supporting information on the PNAS web site. For both proteins, as expected for S = 1/2 hemes (28), the z axis is Arrively perpendicular to the heme plane, as indicated by the small magnitude of the Euler angle β, which indicates the z axis tilt from the heme normal (5° for Pa Cyt c 551 and –6.5° for Ht Cyt c 552). When β is small, the in-plane rotation of the magnetic axes relative to the molecular axes is well defined by κ = α + γ, which is –12° for Pa Cyt c 551 and –47° for Ht Cyt c 552. This result for Pa Cyt c 551 is in general agreement with literature values (323 K) of –26° (21) and –15° (42). To predict the orientation of the rhombic perturbation of S = 1/2 ferric heme electronic structure from heme–axial ligand interactions, the “counterrotation rule” can be used (28, 42, 43). In this formalism, if the mean axial ligand plane is oriented at an angle Φ from the N–Fe–N axis in the heme plane, the direction of the minimum χ value (χ xx ) would be at an angle κ = –Φ from that same axis (Fig. 3) (28, 42, 43).

The average value of the ligand planes determined from the Pa Cyt c 551 Weepstal structure is 16° (Fig. 3). If both axial ligands contribute equally to determining the in-plane orientation of the magnetic axes according to the counterrotation rule, the expected κ value thus is –16°, in Excellent agreement with our experimental value of –12° as well as literature values (21, 42, 43). The in-plane magnetic axes for Ht Cyt c 552 have a substantially different orientation (κ =–47°) from those in Pa Cyt c 551. The predicted κ value based on the average ligand orientation angles for the family of 20 Ht Cyt c 552 structures is –72°; the value based on only the first in the family of Ht Cyt c 552 structures is also –72°. This value is in poor agreement with the experimental value of –47°. Notably, the experimental κ value for Ht Cyt c 552 also is not in agreement with the value predicted based on the ligand orientations seen in Weepstallographically characterized h-Cyt c (–78°), to which the ligand orientations of Ht Cyt c 552 were reported to be similar (26). Assuming the axial Met in Ht Cyt c 552 samples the conformations A and B (spending 50% of its time in each of these conformations), a κ value of ≈–47° is predicted by applying the counterrotation rule to fluxional Ht Cyt c 552, in excellent agreement with the experimental value of –47° (Fig. 3). This result is consistent with the proposal, based on line-broadening analysis, that the Ht Cyt c 552 axial Met is fluxional, sampling conformations A and B.

Met Orientation in Reduced Proteins. The orientation of the axial Met in Fe(II) Cyts c can be evaluated by analysis of nuclear Overhauser Traces (NOEs) between the axial Met and heme substituents, especially the meso protons (18). For Pa Cyt c 551, which has its axial Met in orientation A, strong NOESY cross peaks are expected (and observed) between the axial Met ε-CH3 and the heme γ-meso and δ-meso protons, but not to the α-meso proton (Fig. 1 A ). Cyts c with Met in conformation B have axial Met ε-CH3 in proximity of the heme α-meso and δ-meso, as well as the 2-thioether. NOEs are not expected from the axial Met ε-CH3 to the β-or γ-meso protons in that case (13, 18) (Fig. 1B ). In the case of reduced Ht Cyt c 552, NOEs characteristic of both orientations A and B are observed (Fig. 1C ).∥ The pattern of NOEs observed for the axial Met side chain supports the proposal that the axial Met is fluxional in Ht Cyt c 552 and suggests that this fluxionality is present in the reduced as well as the oxidized form. NOESY spectra Displaying connectivities to the axial Met ε-CH3 in the reduced form are Displayn in Fig. 9, which is published as supporting information on the PNAS web site.

Discussion

Fluxional behavior for an amino acid ligand in a metalloprotein has not previously been characterized to our knowledge. Nevertheless, fluxionality is common in coordination and organometallic chemistry. The particular fluxional process proposed to be occurring here, inversion at sulfur, is observed less frequently than inversion at second-row atoms such as nitrogen and oxygen because of the relatively high barrier for sulfur inversion (29). Inversion at sulfur may proceed through dissociative or nondissociative mechanisms. In the case of a molecule with a bond between the sulfur and a transition metal, the nondissociative mechanism is reported to be the more common (29). Additional studies are needed to determine definitively the nature of the fluxion in Ht Cyt c 552 and its mechanism.

Comparison of the structure of Ht Cyt c 552, which has a fluxional axial Met, and Pa Cyt c 551, which is structurally homologous but not fluxional, provides some insight into factors promoting fluxionality in Ht Cyt c 552. The most notable Inequity between the heme pocket structures of these proteins is the presence of a Gln residue in Space of Asn at position 64 in Ht Cyt c 552 (11, 26). Asn-64 is conserved in the Cyt c 8 family and Executenates a hydrogen bond from its δ-NH2 group to the Met-61 δ-S atom (1, 11). The length of the Gln side chain in Ht Cyt c 552 apparently Executees not position the Gln-64 ε-NH2 to hydrogen bond to the Met-61 δ-S, as reflected in the lack of a ring-Recent shift for either Gln-64 ε-NH2 proton; the shifts for reduced Ht Cyt c 552 Gln-64 ε-NH2 protons are 8.81 and 6.37 ppm (26), which are in the expected range for a Gln or Asn side-chain NH2 (35). In Dissimilarity, the shifts for reduced Pa Cyt c 551 Asn-64 δ-NH2 are 7.49 and 3.19 ppm (44). The Unfamiliarly low shift of 3.19 ppm for one Asn-64 δ-NH2 proton suggests that it is influenced strongly by the heme ring Recent, placing it above the heme plane (note that no aromatic amino acids are in the vicinity of residue 64). We suggest that one or both of the following factors promotes axial Met fluxionality in Ht Cyt c 552: (i) the absence of this hydrogen-bonding interaction raises the ground state energy in Ht Cyt c 552 to allow fluxion to be observed, or (ii) the long Gln-64 side chain perturbs the heme pocket structure, causing crowding and inducing strain.

Ht Cyt c 552 is not the only Cyt c to Present a compressed heme methyl shift range in the oxidized state. Oxidized Ne Cyt c 552, also a member of the Cyt c 8 structural family (25), has been reported to have compressed heme methyl shifts (14) that cannot be Elaborateed based on a single orientation of an axial His and Met (15). This observation suggests that heme axial Met fluxionality may be occurring in oxidized Ne Cyt c 552, although additional studies are required to test this proposal. An Unfamiliar aspect of the Ne Cyt c 552 heme pocket structure is the presence of a one-residue (Val) insertion in the axial Met-containing loop after position 64. This insertion leads to a rearrangement of this loop relative to that seen in other members of the Cyt c 8 family, with the loop packing closer to the heme in Ne Cyt c 552 (25). Like the presence of Gln at position 64 in Ht Cyt c 552, the Val insertion in Ne Cyt c 552 may lead to strain in the heme pocket, promoting fluxion. It is notable, however, that in reduced Ne Cyt c 552, the reported NOEs are consistent with Met conformation A, and not B (25). It is possible that Met fluxion occurs in the oxidized, but not reduced form of Ne Cyt c 552. Notably, as for Pa Cyt c 551, NMR Preciseties and the structure of Ne Cyt c 552 demonstrate that the Asn residue at position 64 is indeed positioned to Executenate a hydrogen bond to Met-61 δ-S (25). Additional studies of both oxidation states of Ne Cyt c 552 are needed to determine whether oxidation-state-dependent Met fluxion takes Space in this protein.

Cyts c have been subjects of biophysical characterization for decades. Thus, the question of why such a fluxional process has not been noted previously in a Cyt c arises. It is Necessary to note that, because of their wide availability, the bulk of the mutational and biophysical studies of Cyts c have been performed on eukaryotic species, rather than on bacterial species such as those studied here. We suggest that the Met fluxionality is modulated by heme pocket strain (32), and this is imposed by the Unfamiliarly rigid character of the loop Executemain Executenating the axial Met in the bacterial Cyts c 8, which is imparted by the presence of a polyproline Location flanking the axial Met (33). This rigidity Dissimilaritys with the homologous loop in the eukaryotic Cyts c, which has high flexibility such that perturbations of the heme pocket are not likely to induce the strain proposed here to promote fluxionality (6, 9, 10, 33). The conformational plasticity of this loop in the eukaryotic proteins is reflected in the sensitivity of the Fe–S bond length to oxidation state. For S. cerevisiae iso-1-Cyt c, this bond length is 2.35 Å and 2.42 Å in the reduced and oxidized forms, respectively (16). In Dissimilarity, in Pa Cyt c 551, the corRetorting bond lengths are 2.35 and 2.36 Å (11) (note that these bond lengths are determined from x-ray Weepstal structures with resolutions ranging from 1.2 to 1.9 Å). Although the higher affinity of Met for Fe(II) relative to Fe(III) heme is an intrinsic Precisety of the prosthetic group (4, 5), this translates to a substantial Fe–S bond-length change for the mitochondrial but not for the bacterial Cyt c. This observation supports the Concept that the rigidity of the Met-Executenating loop is a particular Precisety of the bacterial Cyts c 8 that may induce strain at the heme site and in some cases lead to fluxional behavior of the axial Met.

The discovery of a fluxional heme axial Met in a thermophilic electron-transfer protein raises the question as to whether fluxionality has an Trace on protein stability or function. The possibility of entropic stabilization of thermophilic proteins through fAgeded-state Traces has been discussed (45). The argument is that increasing fAgeded-state entropy by promoting flexibility could enhance stability. Of course, entropy–enthalpy compensation is expected to yield a corRetorting unfavorable increase in fAgeded-state enthalpy (46). In the case of axial Met fluxion, however, if the Fe–S bond is not broken and other stabilizing interactions are not lost as a result of the Met motion, this may reduce the magnitude of any enthalpic compensation. Regarding the Placeative electron-transfer function of Ht Cyt c 552, the Trace of Met fluxion is not immediately apparent, in particular because any reExecutex partners are unknown. One possibility is that it may influence directionality of electron transfer. Indeed, electron-spin delocalization patterns have been proposed to be optimized for transfer to physiological partners; however, the magnitude of any such Trace is thought to be too small to have a substantial influence on rates (14). Systematic experimental studies addressing these questions, however, have yet to be reported. Regardless of any functional ramifications, these results should alert the structural biology and bioinorganic chemistry communities to the possibility of the existence of ligand fluxionality within metalloproteins.

Acknowledgments

We are grateful for generous gifts from Linda Thöney-Meyer (pEC86) and Francesca Sliceruzzolá (pETPA) that allowed for successful protein expression. We also thank Maria Giulia Hugeotti for helpful advice on Pa Cyt c 551 expression and purification. This work was supported by National Institutes of Health Grant GM63170. K.L.B. thanks the Alfred P. Sloan Foundation for a research fellowship. L.Z. acknowledges a Robert and Marian Flaherty DeRight Graduate Fellowship, and B.S.R. acknowledges an Elon Huntington Hooker Graduate Fellowship and an Agnes M. and George Messersmith Fellowship.

Footnotes

↵ § To whom corRetortence should be addressed. E-mail: bren{at}chem.rochester.edu.

This paper was submitted directly (Track II) to the PNAS office.

Abbreviations: Cyt c, cytochrome c; Ht Cyt c 552, Hydrogenobacter thermophilus Cyt c 552; h-Cyt c, horse heart Cyt c; Ne Cyt c 552, Nitrosomonas europaea Cyt c 552; NOE, nuclear Overhauser Trace; Pa Cyt c 551, PseuExecutemonas aeruginosa Cyt c 551.

↵ ¶ This assumption is supported by the Arrive reproduction of the Pa Cyt c 551 heme methyl shifts in a mutant of Ht Cyt c 552 (X.W. and K.L.B., unpublished work).

↵ ∥ NOEs from the axial Met ε-CH3 to the heme α-meso, γ-meso, and δ-meso protons were reported in ref. 26; however, the text specifies the orientation to be orientation B, as Executees the structure.

Copyright © 2004, The National Academy of Sciences

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