Evolutionary change of the heme c electronic structure: ferricytochrome c-551 from Pseudomonas aeruginosa and horse heart ferricytochrome c

Brownian motion, spin diffusion and protein structure determination in solution

This paper presents my recollections on the development of protein structure determination by NMR in solution from 1968 to 1992. The key to success was to identify NMR-accessible parameters that unambiguously determine the spatial arrangement of polypeptide chains. Inspired by work with cyclopeptides, model considerations showed that enforcing short non-bonding interatomic distances imposes «ring closure conditions» on polypeptide chains. Given that distances are scalar parameters, this indicated an avenue for studies of proteins in solution, i.e., under the regime of stochastic rotational and translational motions at frequencies in the nanosecond range (Brownian motion), where sharp pictures could not be obtained by photography-related methods. Later-on, we used distance geometry calculations with sets of inter-atomic distances derived from protein crystal structures to confirm that measurements of short proton-proton distances could provide atomic-resolution structures of globular proteins. During the years 1976-1984 the following four lines of research then led to protein structure determination by NMR in solution. First, the development of NMR experiments enabling the use of the nuclear Overhauser effect (NOE) for measurements of interatomic distances between pairs of hydrogen atoms in proteins. Second, obtaining sequence-specific resonance assignment solved the "phase problem" for protein structure determination by NMR. Third, generating and programming novel distance geometry algorithms enabled the calculation of atomic-resolution protein structures from limited sets of distance constraints measured by NMR. Fourth, the introduction of two-dimensional NMR provided greatly improved spectral resolution of the complex spectra of proteins as well as efficient delineation of scalar and dipole-dipole ¹H-¹H connectivities, thus making protein structure determination in solution viable and attractive.

NMR as a "Gold Standard" Method in Drug Design and Discovery

Studying disease models at the molecular level is vital for drug development in order to improve treatment and prevent a wide range of human pathologies. Microbial infections are still a major challenge because pathogens rapidly and continually evolve developing drug resistance. Cancer cells also change genetically, and current therapeutic techniques may be (or may become) ineffective in many cases. The pathology of many neurological diseases remains an enigma, and the exact etiology and underlying mechanisms are still largely unknown. Viral infections spread and develop much more quickly than does the corresponding research needed to prevent and combat these infections; the present and most relevant outbreak of SARS-CoV-2, which originated in Wuhan, China, illustrates the critical and immediate need to improve drug design and development techniques. Modern day drug discovery is a time-consuming, expensive process. Each new drug takes in excess of 10 years to develop and costs on average more than a billion US dollars. This demonstrates the need of a complete redesign or novel strategies. Nuclear Magnetic Resonance (NMR) has played a critical role in drug discovery ever since its introduction several decades ago. In just three decades, NMR has become a "gold standard" platform technology in medical and pharmacology studies. In this review, we present the major applications of NMR spectroscopy in medical drug discovery and development. The basic concepts, theories, and applications of the most commonly used NMR techniques are presented. We also summarize the advantages and limitations of the primary NMR methods in drug development.

Mitochondrial cytochrome c reacts with nitric oxide via S-nitrosation

The present study demonstrates that mitochondrial cytochrome c reacts with the thiol-reacting agent N-ethylmaleimide (NEM) to produce a one NEM-adducted cytochrome c. Mitochondrial cytochrome c also reacts with 5,5'-dithio-bis-(2-nitrobenzoic acid) and 1-chloro-2,4-dinitrobenzene in a manner prevented with NEM or iodoacetic acid (IAA). NEM-treated cytochrome c has lower reducibility and lower function to support mitochondrial oxygen consumption. These findings suggest that mitochondrial cytochrome c contains a reactive thiol that is involved in the functions of cytochrome c for mitochondria. Nitric oxide reacts with the cytochrome c thiol to generate S-nitroso (SNO)-cytochrome c in a manner prevented with NEM or IAA. SNO-cytochrome c has lower reducibility and function to support mitochondrial oxygen consumption, similar to NEM-treated cytochrome c.

Folding, Conformational Changes, and Dynamics of Cytochromes c Probed by NMR Spectroscopy

NMR spectroscopy has become a vital tool for studies of protein conformational changes and dynamics. Oxidized Fe(III)cytochromes c are a particularly attractive target for NMR analysis because their paramagnetism (S = (1)/(2)) leads to high (1)H chemical shift dispersion, even for unfolded or otherwise disordered states. In addition, analysis of shifts induced by the hyperfine interaction reveals details of the structure of the heme and its ligands for native and nonnative protein conformational states. The use of NMR spectroscopy to investigate the folding and dynamics of paramagnetic cytochromes c is reviewed here. Studies of nonnative conformations formed by denaturation and by anomalous in vivo maturation (heme attachment) are facilitated by the paramagnetic, low-spin nature of native and nonnative forms of cytochromes c. Investigation of the dynamics of folded cytochromes c also are aided by their paramagnetism. As an example of this analysis, the expression in Escherichia coli of cytochrome c(552) from Nitrosomonas europaea is reported here, along with analysis of its unusual heme hyperfine shifts. The results are suggestive of heme axial methionine fluxion in N. europaea ferricytochrome c(552). The application of NMR spectroscopy to investigate paramagnetic cytochrome c folding and dynamics has advanced our understanding of the structure and dynamics of both native and nonnative states of heme proteins.

Magnetic susceptibility tensor and heme contact shifts determinations in the Rhodobacter capsulatus ferricytochrome c': NMR and magnetic susceptibility studies

The 1H and 15N resonances of the carbon monoxide complex of ferrocytochrome c' of Rhodobacter capsulatus, a ferrous diamagnetic heme protein, have been extensively assigned by TOCSY-HSQC, NOESY-HSQC, and HSQC-NOESY-HSQC 3D heteronuclear experiments performed on a 7 mM sample labeled with 15N. Based on short-range and medium-range NOEs and H(N) exchange rates, the secondary structure consists of four helices: helix 1 (3-29), helix 2 (33-48), helix 3 (78-101), and helix 4 (103-125). The 15N, 1HN, and 1H(alpha) chemical shifts of the CO complex form are compared to those of the previously assigned oxidized (or ferric) state. From the chemical shift differences between these redox states, the orientation and the anisotropy of the paramagnetic susceptibility tensor have been determined using the crystallographic coordinates of the ferric state. The chi-tensor is axial, and the orientation of the z-axis is approximately perpendicular to the heme plane. The paramagnetic chemical shifts of the protons of the heme ligand have been determined and decomposed into the Fermi shift and dipolar shift contributions. Magnetic susceptibility studies in frozen solutions have been performed. Fits of the susceptibility data using the model of Maltempo (Maltempo, M. M. J. Chem. Phys. 1974, 61, 2540-2547) are consistent with a rather low contribution of the S = 3/2 spin state over the range of temperatures and confirm the value of the axial anisotropy. Values in the range 10.4-12.5 cm(-1) have been inferred for the axial zero-field splitting parameter (D). Analysis of the contact shift and the susceptibility data suggests that cytochrome c' of Rb. capsulatus exhibits a predominant high-spin character of the iron in the oxidized state at room temperature.

Protein structure refinement based on paramagnetic NMR shifts: applications to wild-type and mutant forms of cytochrome c

A new approach to NMR solution structure refinement is introduced that uses paramagnetic effects on nuclear chemical shifts as constraints in energy minimization or molecular dynamics calculations. Chemical shift differences between oxidized and reduced forms of horse cytochrome c for more than 300 protons were used as constraints to refine the structure of the wild-type protein in solution and to define the structural changes induced by a Leu 94 to Val mutation. A single round of constrained minimization, using the crystal structure as the starting point, converged to a low-energy structure with an RMS deviation between calculated and observed pseudo-contact shifts of 0.045 ppm, 7.5-fold lower than the starting structure. At the same time, the procedure provided stereospecific assignments for more than 45 pairs of methylene protons and methyl groups. Structural changes caused by the mutation were determined to a precision of better than 0.3 A. Structure determination based on dipolar paramagnetic (pseudocontact) shifts is applicable to molecules containing anisotropic paramagnetic centers with short electronic relaxation times, including numerous naturally occurring metalloproteins, as well as proteins or nucleic acids to which a paramagnetic metal ion or ligand may be attached. The long range of paramagnetic shift effects (up to 20 A from the iron in the case of cytochrome c) provides global structural constraints, which, in conjunction with conventional NMR distance and dihedral angle constraints, will enhance the precision of NMR solution structure determination.

1H and 13C NMR assignments and structural aspects of a ferrocytochrome c-551 from the purple phototrophic bacterium Ectothiorhodospira halophila

Two-dimensional nuclear magnetic resonance was used to assign the 1H and 13C resonances of ferrocytochrome c-551 from Ectothiorhodospira halophila, a halophilic phototrophic purple bacterium. This 78-residue protein belongs to a small subgroup of class I cytochromes c together with the analogous cytochromes c-551 from E. halochloris and E. abdelmalekii. A nearly complete assignment of 13C resonances was obtained at natural abundance using a gradient-enhanced 1H-detected heteronuclear single quantum coherence experiment (HSQC). This was found to be extremely useful for the unambigous assignment of side chain protons. The secondary structure of the protein was determined from analyses of short- and medium-range nuclear Overhauser enhancements (NOE), amide proton exchange and 13C alpha chemical shifts. Three helices could be identified which are well conserved among the class I cytochromes c. There is some evidence for two other regions of less well defined helical structure. From a preliminary analysis of long-range NOE it is shown that in the E. halophila cytochrome c-551 the general cytochrome c fold is well conserved, including the three conserved helices (residues 2-8, 41-50, 63-76), the regions around the heme ligands (Cys14-Ser15-Ser16-Cys17-His18, Met55) and the omega loop (residues 18-28). In addition, three variable segments of the protein are discussed in detail, one of those including a cis-proline, a feature so far unique in the cytochrome c family. Structural alignments of the E. halophila cytochrome c-551 with two other Pseudomonas cytochrome c5 homologs (Azotobacter vinelandii cytochrome c5 and Chlorobium limicola cytochrome c-555) are provided which are based on sequence similarities and secondary structure alignments.

Characteristics of the paramagnetic 1H-NMR spectra of the ferricytochrome c-551 family

Heme proton resonances have been assigned for ferricytochromes c-551 isolated from four distinct species of bacteria. While the available structure information indicates that the four cytochromes have very similar conformations in solution, including the chirality of the methionine ligand sulfur bond, the chemical shifts of the paramagnetically shifted resonances are surprisingly different, more so than has been previously reported for a homologous series of ferricytochromes. The resonances are contrasted in terms of chemical shift and the temperature dependence of the shift, which gives rise to a very strong anti-Curie effect for some specific protons. Non-methyl heme resonances do display an approximately conserved set of chemical shifts, but the heme methyl groups demonstrate a wide range of values. The 12(1) heme methyl group is always the highest frequency heme methyl, but the relative positions of the other methyl groups may change. The 7(1) heme methyl group always displayed strong anti-Curie behavior, while the 12(1) methyl group displayed normal Curie behavior. The behavior of the other methyl groups was variable. Possible reasons for the range of observations will be discussed. In spite of their NMR differences, all the ferricytochromes c-551 demonstrated comparable electron-transfer rates to a membrane-bound cytochrome reductase system.

1H one-dimensional and two-dimensional NMR studies of the ferricytochrome c 551 from Rhodocyclus gelatinosus

1H two-dimensional NMR spectroscopy has been applied to the oxidized form of cytochrome c 551 from Rhodocyclus gelatinosus, which is paramagnetic with S = 1/2. The investigation has allowed a complete and unambiguous assignment of the heme protons and some residues around the heme. We have learned that: the conformation of the axial methionine is equal to that of horse heart cytochrome c and different from two isoenzymes of the same cytochrome c 551 from a different strain; pKa of 6.6 +/- 0.3 has been detected through the shift variations of seventh propionate protons. The detailed differences with other cytochromes c in the hyperfine shifts are discussed.

Spectroscopic characterization of a newly isolated cytochrome P450 from Rhodococcus rhodochrous

Cytochrome P450 (P450) from Rhodococcus rhodochrous have been characterized through circular dichroism and nuclear magnetic resonance (NMR) spectroscopy, both in the substrate-free and substrate-bound forms. The data are compared with those of P450cam and indicate a close similarity of the structure of the active site in the two proteins. The substrate-free species contains low-spin iron(III), while the 2-ethoxyphenol bound species contains high-spin iron(III). The substrate is in slow exchange on the NMR time scale. The binding of CN- has been investigated and the final adduct characterized through NMR spectra. Nuclear relaxation times of the isotropically shifted signals turn out to be shorter than in other heme proteins, both in the high- and in the low-spin species. This is the result of longer electron relaxation times in P450s than in peroxidases and metmyoglobin. This property, as well as the electron paramagnetic resonance (EPR) spectrum of the substrate-free form, are discussed in terms of the presence of the cysteine as the fifth ligand of the iron ion instead of a histidine as it occurs in peroxidases and myoglobin.

Two-dimensional 1H NMR spectra of ferricytochrome c551 from Pseudomonas aeruginosa

The full assignment of 1H NMR signals of heme proton resonances of ferricytochrome c551 from Pseudomonas aeruginosa has been performed by means of 2D NMR experiments. This technique allows the complete and unequivocal assignment of all heme resonances, including methylene resonances of the propionic groups, directly implicated in the pH dependence of the redox properties of cytochrome c551.

Kinetic characterization of the acid-alkaline transition in Dolabella auricularia ferric myoglobin using 1H-NMR saturation transfer experiments

The acid-alkaline transition in ferric myoglobin of the mollusc, Dolabella auricularia, exerts the changes in both the coordination and spin states of the heme iron. Slower transition rate, compared to the NMR time scale, in this myoglobin allowed the observation of separate signals arising from the two forms, and pH titration yielded a pK value of 7.8. 1H-NMR saturation transfer experiments have been successfully used not only to provide the first signal assignments for the heme methyl proton resonances of the Met-hydroxyl form of the myoglobin, but also to determine the kinetics of the transition.

Sequential 1H NMR assignments of iron(II) cytochrome c551 from Pseudomonas aeruginosa

Sequence-specific 1H NMR resonance assignments for all but the C-terminal Lys 82 are reported for iron(II) cytochrome c551 from Pseudomonas aeruginosa at 25 degrees C and pH = 6.8. Spin systems were identified by using TOCSY and DQF-COSY spectra in 2H2O and 1H2O. Sequential assignments were made by using NOESY connectivities between adjacent amide, alpha, and beta protons. Resonances from several amino acids including His 16, Gly 24, Ile 48, and Met 61 experience strong ring-current shifts due to their placement near the heme. All heme protons, including the previously unassigned propionates, have been identified. Preliminary analysis of sequential and medium-range NOEs provides evidence for substantial amounts of helix in the solution structure. Long-range NOEs indicate that the folds in solution and crystal structures are similar. For one aromatic side chain (Tyr 27) that is close to the heme group we found a transition from hindered ring rotation at low temperature to rapid rotation at high temperature.

NMR comparison of prokaryotic and eukaryotic cytochromes c

1H NMR spectroscopy has been used to examine ferrocytochrome c-551 from Pseudomonas aeruginosa (ATCC 19429) over the pH range 3.5-10.6 and the temperature range 4-60 degrees C. Resonance assignments are proposed for main-chain and side-chain protons. Comparison of results for cytochrome c-551 to recently assigned spectra for horse cytochrome c (Wand et al. (1989) Biochemistry 28, 186-194) and mutants of yeast iso-1 cytochrome (Pielak et al. (1988) Eur. J. Biochem. 177, 167-177) reveals some unique resonances with unusual chemical shifts in all cytochromes that may serve as markers for the heme region. Results for cytochrome c-551 indicate that in the smaller prokaryotic cytochrome, all benzoid side chains are rapidly flipping on the NMR time scale. In contrast, in eukaryotic cytochromes there are some rings flipping slowly on the NMR time scale. The ferrocytochrome c-551 undergoes a transition linked to pH with a pK around 7. The pH behavior of assigned resonances provides evidence that the site of protonation is the inner or buried 17-propionic acid heme substituent (IUPAC-IUB porphyrin nomenclature). Conformational heterogeneity has been observed for segments near the inner heme propionate substituent.

Redox-dependent structure change and hyperfine nuclear magnetic resonance shifts in cytochrome c

Proton nuclear magnetic resonance assignments for reduced and oxidized equine cytochrome c show that many individual protons exhibit different chemical shifts in the two protein forms, reflecting diamagnetic shift effects due to structure change, and in addition contact and pseudocontact shifts that occur only in the paramagnetic oxidized form. To evaluate the chemical shift differences (delta delta) for structure change, we removed the pseudocontact shift contribution by a calculation based on knowledge of the electron spin g tensor. The g-tensor parameters were determined from the delta delta values of a large set (64) of C alpha H protons at well-defined spatial positions in the oxidized horse protein. The g-tensor calculation, when repeated using only 12 available C alpha H proton resonances for cytochrome c from tuna, proved to be remarkably stable. The largest principal value of the g tensor (gz) falls precisely along the ligand bond between the heme iron and methionine-80 sulfur, while gx and gy closely match the natural heme axes defined by the pyrrole nitrogens. The derived g tensor was then used together with spatial coordinates for the oxidized form to calculate the pseudocontact shift contribution (delta pc) to proton resonances at 400 identifiable sites throughout the protein, so that the redox-dependent chemical shift discrepancy, delta delta-delta pc, could be evaluated. Large residual changes in chemical shift define the Fermi contact shifts, which are found as expected to be limited to the immediate covalent structure of the heme and its ligands and to be asymmetrically distributed over the heme. Smaller chemical shift discrepancies point to a concerted change, involving residues 39-43 and 50-60 (bottom of the protein), and to other changes in the immediate vicinity of the heme ligands. Also, the three internal water molecules are implicated in redox sensitivity. The residues found to change are in good but not perfect agreement with prior X-ray diffraction observations of subangstrom redox-related displacements in the tuna protein. The chemical shift discrepancies observed appear in the main to reflect structure-dependent diamagnetic shifts rather than hyperfine effects due to displacements in the pseudocontact shift field. Although 51 protons in 29 different residues exhibit significant chemical shift changes, the general impression is one of small structural adjustments to redox-dependent strain rather than sizeable structural displacements or rearrangements.

Assignments of 15N and 1H NMR resonances and a neutral pH ionization in Rhodospirillum rubrum cytochrome c2

The phi NH proton and 15N resonances of the ligand histidine of Rhodospirillum rubrum fericytochrome c2 are found at 14.7 and 184 ppm, respectively, contradicting the proposal that this proton is absent in the R. rubrum ferricytochrome. Substitution of the deuterium atom for this proton causes small upfield shifts of the phi nitrogen in both oxidation states, indicating that the phi NH-peptide carboxyl hydrogen bond is not substantially weakened by the substitution. The proton and 15N resonances of the indolic NH group of the invariant tryptophan-62 and numerous proton resonances of the heme and extraheme ligands in the spectrum of the ferricytochrome are also assigned. An ionization in the ferrocytochrome occurring at neutral pH is assigned to the single nonligand histidine. This attribution is supported by the direct measurement of the ionization by NOE difference spectroscopy and by comparative structural arguments involving closely related cytochromes and chemically modified cytochromes.

Electron self-exchange in Pseudomonas cytochromes

Electron self-exchange has been measured by an NMR technique for cytochromes c551 from Pseudomonas aeruginosa and Pseudomonas stutzeri. The rate for P. aeruginosa cyt c551 is 1.2 x 10(7) M-1 s-1 at 40 degrees C in 50 mM phosphate at pH 7. For P. stutzeri, under the same conditions, the rate is 4 x 10(7) M-1 s-1. For both cytochromes, the rate was independent of ionic strength up to 0.5 M in added NaC1, the enthalpy of activation was 20 +/- 4 kcal mol-1, and the entropy of activation was 38 +/- 10 cal mol-1 deg-1.

Proton NMR studies of horse ferricytochrome c. Completion of the assignment of the well resolved hyperfine shifted resonances

1H NMR saturation transfer and nuclear Overhauser effect (NOE) measurements have been used together with two-dimensional spectra to complete the assignment of the well resolved hyperfine shifted resonances in the spectrum of horse ferricytochrome c and obtain their shifts in the reduced protein. New assignments include the beta-CH2 protons of Met-80, both ring protons of His-18, and the alpha-CH2 of Gly-29 and delta-CH2 of Pro-30, which resonate surprisingly far upfield despite the absence of any Fermi contact contribution to the shift.

Identification of the ligand-exchange process in the alkaline transition of horse heart cytochrome c

Magnetic-circular-dichroism (m.c.d.) spectra over the wavelength range 300-2000 nm at room temperature and at 4.2K of horse heart cytochrome c are reported at a series of pH values between 7.8 and 11.0, encompassing the alkaline transition. The effect of glassing agents on the e.p.r. spectrum at various pH values is also reported. Comparison of these results with spectra obtained for the n-butylamine adduct of soybean leghaemoglobin support the hypothesis that lysine is the sixth ligand in the alkaline form of horse heart cytochrome c. The m.c.d. and e.p.r. spectra of horse heart cytochrome c in the presence of 1-methylimidazole have also been examined. These studies strongly suggest that histidine-18, the proximal ligand of the haem, is the ionizing group that triggers the alkaline transition. Low-temperature m.c.d. and e.p.r. spectra are also reported for Pseudomonas aeruginosa cytochrome c551. It is shown that no ligand exchange takes place at the haem in this species over the pH range 6.0-11.3.

Proton hyperfine resonance assignments using the nuclear Overhauser effect for ferric forms of horse and tuna cytochrome c

Proton hyperfine resonance assignments for cytochromes c from several species are currently being successfully pursued by several laboratories. These efforts focus mostly on the ferrous forms. In contrast to that work, we have pursued assignments of the proton hyperfine shifted resonances for horse and tuna ferricytochromes c. Our results indicate that assignments are nearly identical in those two proteins. Using the pre-steady state nuclear Overhauser effect, several additional assignments have been made for the tuna protein, whereas for the horse protein, the following protons have been assigned: heme 7, alpha CH2; heme 7, beta CH2; histidine 18, beta CH2 and alpha CH; and the methionine 80, beta CH2.

Comparison of the solution and crystal structures of mitochondrial cytochrome c. Analysis of paramagnetic shifts in the nuclear magnetic resonance spectrum of ferricytochrome c

The two accompanying papers describe the assignment of methyl-containing spin-systems in the 1H nuclear magnetic resonance spectra of tuna ferricytochrome c and tuna ferrocytochrome c. At present, 104 resonances from 208 C-H protons are assigned in both oxidation states. In this paper, the difference in chemical shift of a resonance between the two oxidation states is used together with a dipolar model of the unpaired electron spin of ferricytochrome c to compare the structure of cytochrome c in solution with three high-resolution structures of cytochrome c obtained by X-ray diffraction in single crystals. The overall protein fold and the positions of most of the haem-packing residues are shown to be invariant between the crystal and solution. However, three regions of the protein, at the C terminus, around the haem propionic acid groups and at the haem crevice near thioether-2, are found to undergo conformational changes on the removal of crystal packing constraints.

Use of the nuclear Overhauser effect to assign 1H NMR resonances in a low-spin paramagnetic hemin

The nuclear Overhauser effect has been used to assign the 1H resonances of the paramagnetic low-spin biscyano complex of Fe(III) protoporphyrin. When the meso protons are irradiated, changes in integrated signal intensity are seen at neighboring methyl or methylene groups and vice versa. Although the changes ar small (less than 1% negative NOEs for Fe(III)protoporphyrin(CN)2 in Me2SO-d6 at 30 degrees C and 360 MHz), they can be seen clearly. This technique has been used to assign the 6-alpha-CH2 (6.21), 7-alpha-CH2 (5.82), beta-meso (0.50) and delta-meso (0.03 ppm) resonances of this species. The nuclear Overhauser effect will allow rapid assignment of 1H NMR resonances in a wide variety of low-spin paramagnetic hemins.

Amino acid sequence, haem-iron co-ordination geometry and functional properties of mitochondrial and bacterial c-type cytochromes

Cytochromes are found in all biological oxidation Systems which involve transport of reducing equivalents through organized chains of membrane bound intermediates, regardless of the ultimate oxidant (Keilin, 1966; Bartsch, 1978; Meyer & Kamen, 1982). Thus, cytochromes are present not only in the aerobic mitochondrial and bac-terial respiratory chain, but are also found in much more diversified procariotic Systems, including all varieties of facultative anaerobes (nitrate and nitrite reducers), obligate anaerobes (sulphate reducers and phototrophic sulphur bacteria), facultative photoheterotrophes (phototrophic non-sulphur purple bacteria), and the photoautotrophic cyanobacteria (blue-green algae). Among the different types of cytochromes occurring in the cell, the soluble c-type cytochromes (‘class I’, Meyer & Kamen, 1982) are the most abundant and best characterized group of proteins (Bartsch, 1978; Meyer & Kamen, 1982; Dickerson & Timkovitch, 1975; Lemberg & Barrett, 1973; Salemme, 1977; Ferguson-Miller, Brautigan & Margoliash, 1979). The amino acid sequences of more than 80 mitochrondrial and close to 40 bacterial cytochromes c are known (Meyer & Kamen, 1982; Dickerson & Timkovitch, 1975; Schwartz & Dayhoff, 1976; Dayhoff & Barker, 1978).

Coordination of the heme iron in the low-potential cytochromes c-553 from Desulfovibrio vulgaris and Desulfovibrio desulfuricans. Different chirality of the axially bound methionine in the oxidized and reduced states

The coordination geometry at the heme iron of the cytochromes c-553 from Desulfovibrio vulgaris and Desulfovibrio desulfuricans was investigated by 1H-nuclear magnetic resonance and circular dichroism spectroscopy. Individual assignments were obtained for heme c and the axial ligands. From studies of nuclear Overhauser enhancements the axial histidine imidazole ring orientation relative to the heme group was found to coincide with other c-type cytochromes. In contrast, a new structure was observed for the axial methionine in the reduced cytochromes c-553. This includes S chirality at the iron-bound sulfur atom, but compared to cytochromes c-551 from Pseudomonads and Rhodopseudomonas gelatinosa and cytochrome c5 from Pseudomonas mendocina, which also contain S-chiral methionine, a different spatial arrangement of the gamma- and beta-methylene groups and the alpha carbon of methionine prevails. For the ferricytochromes c-553 R chirality was found for the iron-bound sulfur. This is the first observation of different methionine chirality in different oxidation states of the same c-type cytochrome.

A new spatial structure for the axial methionine observed in cytochrome c5 from Pseudomonas mendocina. Correlations with the electronic structure of heme c

Cytochrome c5 from Pseudomonas mendocina has been isolated and the coordination geometry at the heme iron was investigated by 1H nuclear magnetic resonance and circular dichroism spectroscopy. Individual assignments were obtained for heme c and the axial ligands. From studies of nuclear Overhauser enhancements the axial histidine imidazole ring orientation relative to the heme group was found to coincide with that of other c-type cytochromes. In contrast, a new structure was observed for the axial methionine. This includes S chirality at the iron-bound sulfur atom, but compared to cytochromes c-551 from Pseudomonads and Rhodopseudomonas gelatinosa, which also contain S-chiral methionine, the spatial arrangement of the gamma- and beta-methylene groups and the alpha carbon of methionine is markedly different. Analysis of the electron spin density distribution in ferricytochrome c5 in the light of this new coordination geometry provides additional support for the hypothesis that the electronic structure of heme c is primarily governed by the orientation of the sp3 lone-pair orbital of the axial sulfur atom with respect to the heme plane.

Individual 1H-NMR assignments for the heme groups and the axially bound amino acids and determination of the coordination geometry at the heme iron in a mixture of two isocytochromes c-551 from Rhodopseudomonas gelatinosa

This paper describes chemical and physicochemical studies of two small isocytochromes c-551 (approx. 9000 dalton) from Rhodopseudomonas gelatinosa. In spite of numerous amino acid substitutions in the N-terminal half of the sequence the two isoproteins could not be separated by the procedures used, presumably because they have identical size, charge and isoelectric points. Individual assignments of the 1H-NMR lines of heme c and the axial ligands to the heme iron were therefore obtained by nuclear Overhauser enhancement measurements and saturation transfer experiments in a mixed solution of the two isocytochromes c-551. The conformation of the coordination sphere was investigated by additional 1H-NMR and circular dichroism studies. For both isoproteins the electronic structure of the heme and the chirality of the methionine attachment to the iron were found to coincide with those in Pseudomonas cytochromes c-551, i.e., S chirality was observed for the axial methionine. The Rps. gelatinosa cytochromes c-551 thus differ from mammalian, yeast, Euglena gracilis and Rhodospirillum rubrum cytochromes c, which all have R chirality at the axial methionine and concomitantly a characteristically different electronic heme structure. This is the first observation of S chirality of the axially bound methionine in a species outside the Pseudomonas family. The redox potentials of the two isocytochromes c-551 of Rps. gelatinosa differ by approx. 120 mV, and there is no cross-exchange of electrons between the two species. The two isoproteins could thus function in two different, parallel electron-transfer chains or at two different locations in a single transfer sequence.

Determination of the coordination geometry at the heme iron in three cytochromes c from Saccharomyces cerevisiae and from Candida krusei based on individual 1H-NMR assignments for heme c and the axially coordinated amino acids

The 1H-NMR lines of heme c and the axial ligands in reduced and oxidized Iso-1 and Iso-2 cytochromes c from Saccharomyces cerevisiae and in cytochrome c from Candida krusei were individually assigned and the conformation of the coordination sphere of the heme iron was investigated with the use of proton-proton Overhauser enhancement measurements and circular dichroism spectroscopy. The coordination geometry of the axial methionine and the axial histidine and the electronic structure of the heme were found to be closely similar in these yeast cytochromes c and in mammalian cytochromes c. In particular, R chirality at the sulfur atom of the iron-bound methionine was observed in both groups of proteins. Additional nuclear Overhauser enhancement studies of the spatial arrangement relative to the heme group of amino acid side-chains in the heme crevice of yeast ferrocytochromes c showed that the conformational homologies extend beyond the immediate coordination sphere of the heme iron. These data provide a conformational basis for observations on the functional properties of cytochromes c from yeast and mammalian species, which were reported previously by other groups.

Time-resolved resonance Raman spectroscopy of cytochrome c reduced by pulse radiolysis

The first investigation of the dynamics of a redox transition of an electron-transfer enzyme by time-resolved resonance Raman spectroscopy in combination with pulse-radiolytic reduction is described by an application to cytochrome c. A long-lived transient state is observed upon reduction of the alkaline form of cytochrome c as a distinct frequency shift of one resonance Raman band. From the frequency in the stable oxidized state, 1567 cm(-1), this particular resonance Raman band shifts within less than 1 microsecond to 1533 cm(-1) in the transient reduced state, which has a lifetime longer than 20 ms but shorter than a few seconds. Finally, in the stable reduced state, this band is located at 1547 cm(-1). According to a previous normal coordinate analysis, this resonance Raman band can be assigned predominantly to a stretching mode of the outermost C-C bonds in the four pyrrole rings of porphyrin. This vibrational mode is influenced by the protein most directly through the covalent thioether linkages of two cysteines to porphyrin. We interpret the long lifetime of the transient state as due to the slow return of Met-80 as sixth ligand to the heme iron upon reduction of the alkaline form of cytochrome c.

1H-NMR studies of structural homologies between the heme environments in horse cytochrome c and in cytochrome c-552 from Euglena gracilis

With the use of proton-proton Overhauser enhancement experiment the spatial arrangement relative to the heme group of amino acid side chains in the heme crevice of horse ferrocytochrome c and ferrocytochrome c-552 from euglena gracilis was investigated. From these data and the known crystal structure for mammalian cytochromes c, individual assignments were obtained for several aromatic residues in horse ferrocytochrome c. This then provided a basis for delineating homologies between the polypeptide conformations near the heme group in horse ferrocytochrome c and ferrocytochrome c-552, for which no crystal structure has as yet been described.

N.m.r. and e.p.r. characterization of [4-carboxy-2,6-dinitrophenyl-lysine]cytochromes c

Monosubstituted [4-carboxy-2,6-dinitrophenyl-lysine]cytochromes c were investigated by n.m.r. and e.p.r. Modification of Lys-13 or Lys-72 in ferricytochrome c by 4-chloro-3,5-dinitrobenzoate yields either of two different conformers that are rapidly exchanging in the native form. The equilibrium involves small local changes in the conformation of Met-80 (the sixth ligand) and Phe-82, as a result of whether Lys-13 is the 'on' or 'off' position in the Lys-13--Glu-90 salt bridge.

1H-NMR studies of the coordination geometry at the heme iron and the electronic structure of the heme group in cytochrome c-552 from Euglena gracilis

The 1H-NMR lines of heme c in reduced and oxidized cytochrome c-552 from Euglena gracilis were individually assigned and the coordination geometry of the axial ligands was investigated. The electronic structure of the heme and the chirality of the axially bound methionine were found to be of the same type as in mammalian cytochrome c, but different from cytochrome c-551 from Pseudomonas aeruginosa. These results provide additional support for a previously proposed correlation between the chirality of attachment of the axial methionine and the electronic wave functions in oxidized cytochromes of the c type. Comparison of mammalian cytochrome c, cytochrome c-551 and cytochrome c-552 indicates that the chirality of the axially bound methionine is not linked with the evolutionary increase of the polypeptide chain length.

1H-NMR studies of ferric soybean leghemoglobin: assignment of hyperfine shifted resonances of complexes with cyanide, nicotinate, pyridine and azide

The 1H-NMR spectra of complexes of soybean ferric leghemoglobin a with cyanide, nicotinate, pyridine and azide have been recorded. Assignments of many of the hyperfine shifted resonances to specific groups on the periphery of the heme have been made on the basis of their intensities and chemical shifts, pH dependence, nuclear Overhauser effects, spin decoupling and the use of Gd3+ as a relaxation probe. The resonances of the protons at positions 3 and 5 of pyridine and nicotinate ligands have also been assigned. The iron(III) atom in the cyanide, nicotinate and azide complexes is almost completely low spin. In the pyridine complex, which is predominantly low spin, a high-spin state is thermally populated at room temperature. Information on the conformation of the heme propionate and vinyl side-chains is obtained. The average rotational position of one of the heme vinyl groups appears to differ between the nicotinate and cyanide complexes. In both of these complexes conformational rearrangement of a heme propionic acid side-chain occurs upon deprotonation of its carboxylic acid group (pK approx. 5.0). A further change in the conformation of this group occurs in leghemoglobin nicotinate upon deprotonation of the distal histidine. The pK of the heme propionic acid side-chain in leghemoglobin pyridine is 5.6. Its conformation and environment appears to differ from that in the nicotinate and cyanide complexes. In leghemoglobin cyanide, evidence for an interaction between the protonated distal histidine and the cyanide ligand is obtained. In each of the complexes studied the unpaired electron spin distribution over the porphyrin ring is highly anisotropic. Considerable differences exist between the unpaired spin distribution in the cyanide complexes of leghemoglobin and myoglobin. The axial ligand field is stronger in leghemoglobin and this may be of significance in the reaction with oxygen.

Proton nuclear-magnetic-resonance and resonance Raman studies of thermophilic cytochrome c-552 from Thermus thermophilus HB8

The pH and temperature dependences of the 270-MHz proton nuclear magnetic resonance and resonance Raman spectra of Thermus thermophilus cytochrome c-552 were studied. Observation of the NMR methyl signal of the iron-bound methionine indicates that a methionine residue is the sixth ligand of heme iron in both ferric and ferrous states, although the environment of this methionine is not similar to that in mitochondrial cytochrome c. The NMR methyl signal of the coordinated methionine in the ferrous state was observed even at 87 degrees C, indicating the retention of the methionine ligand at the sixth coordination position. None of resonance Raman lines in ferrous cytochrome c-552 at higher temperatures showed a prominant temperature-dependent frequency shift, which implies that the heme iron was still bound with strong ligands and retained the low-spin state. In either redox state overall thermal denaturation did not occur even at 87 degrees C, although the ferric form existed in thermal spin mixture of the low-spin and high-spin species at higher temperatures. The hyperfine-shifted NMR resonances of the ferric form indicated rapid exchange of the sixth ligand at alkaline pH in the process of a single-step alkaline isomerization.

pH dependence of the redox potential of Pseudomonas aeruginosa cytochrome c-551

The redox potential of Ps. aeruginosa cytochrome c-551 varies with pH between pH 5 and 8. The pH dependence can be analysed in terms of a pKa of 6.2 in the oxidised form and a pKa of 7.3 in the reduced form. The same pKa values are also observed in NMR spectra of the two oxidation states and the pKa of 7.3 is observed in titration of the visible absorption spectrum of the ferrocytochrome. From the NMR studies these pKa values have been assigned to the ionisation of one of the haem propionic acid groups. pH dependence of redox potential is of variable occurrence among cytochromes and the possible significance and basis of this variation is discussed.

Structural study of the heme crevice in cytochrome b5 based on individual assignments of the 1H-NMR lines of the heme group and selected amino acid residues

Measurements of saturation transfer, spin-decoupling and truncated-driven nuclear Overhauser effect difference spectra were applied to indidually assign the 1H-NMR lines of the heme group and nearby amino acid residues in reduced and oxidized cytochrome b5. These data imply that the orientation of the heme group in the major cytochrome b5 conformation in solution differs from that reported for the X-ray crystal structure by a 180 degree rotation about an axis through the meso-carbon atoms alpha and gamma. Otherwise comparison of the experimental chemical shifts with those obtained from ring current calculations using the refined X-ray atomic coordinates provide no evidence that the polypeptide conformation near the heme is different in the crystals and in solution. It seems quite likely that the previously described second solution conformation of cytochrome b5 is related to the major species through a different orientation of the heme.

Individual assignments of the heme resonances in the 360 MHz 1H NMR spectra of cytochrome c-557 from Crithidia oncopelti

With the use of nuclear Overhauser effects, spin decoupling and saturation transfer experiments individual assignments for numerous resonances of the heme group in the 360 MHz 1H NMR spectra of reduced and oxidized cytochrome c-557 from Crithidia oncopelti were obtained. These data provide direct evidence that the heme substituent in position 2 is a vinyl group. They further show that in spite of the different covalent structures of the heme groups the heme crevice and the electronic heme structure in the oxidized state are nearly identical in cytochrome c-557 and in mammalian cytochromes c.