The covalent structure of the blue copper-containing nitrite reductase from Achromobacter xylosoxidans

The complete amino acid sequence of the blue copper-containing nitrite reductase enzyme (NiR) from Achromobacter xylosoxidans has been determined by chemical analysis, supported by high precision mass analysis. The polypeptide chain contains 336 residues with an overall charge of 0, including the +2 state of each of the copper ions. The two NiR enzymes for which the three-dimensional structures have been solved are green in color and have different absorption spectra than those of the blue-colored protein from A. xylosoxidans. The ligands to the two copper atoms are conserved. Therefore, the difference between the blue and the green NiR must depend on subtle changes in the geometry of the type I copper-sulfur bond. Both overall protein charge and active site charge are different in A. xylosoxidans NiR which may reflect the use of azurin as electron donor as opposed to the other enzymes that use pseudoazurin.

Purification and primary structure analysis of two cytochrome c2 isozymes from the purple phototrophic bacterium Rhodospirillum centenum

The isolation and amino acid sequences of two cytochromes c-552 from the thermotolerant bacterium Rhodospirillum (R.) centenum have been determined. They are very similar to one another with 85% identity. They are homologous to the cytochromes c2 from purple bacteria with approximately 67% identity to that from Rhodopseudomonas (Rps.) palustris compared to only 42% identity with others of the c2 subclass. In addition, they share an unusual six-residue insertion with Rps. palustris cytochrome c2 not found in any other cytochrome. The relationship with Rps. palustris is thus highly significant. The redox potentials of the R. centenum isozymes are 293 and 316 mV. Although the proteins have strongly different iso-electric points, both have three conserved lysine residues at the proposed site of electron transfer. These results suggest that they may be functionally interchangeable.

Ligand binding and covalent structure of an oxygen-binding heme protein from Rhodobacter sphaeroides, a representative of a new structural family of c-type cytochromes

The amino acid sequence of an oxygen-binding heme protein (SHP) from Rhodobacter sphaeroides has been determined. The cysteines, which bind the single heme group in the 112-residue protein, are located at positions 43 and 46. SHP is similar in size to the large membrane-bound form of the class I cytochrome c5 of Azotobacter vinelandii (116 residues) and in the location of the heme binding site at positions 48 and 51. Two extra cysteines in SHP (residues 89 and 97) are located in positions similar to those of cytochrome c5 (residues 98 and 101) and form a disulfide bridge in both proteins. In total, four regions of alpha-helix are predicted, covering 46% of the protein, which is comparable to that in other small cytochromes. SHP is thus distantly related to small class I c-type cytochromes but is representative of a distinct family by virtue of its high-spin nature, the lack of a strong sixth ligand, and its capacity to bind oxygen. Potentially, the most important characteristic of SHP is its ability to transiently bind oxygen during autoxidation, which occurs with a half-life of 3 min with a 4-fold excess of O2. SHP also binds carbon monoxide, azide, and cyanide. The kinetics of reduction by free flavins indicate that SHP is less reactive than other class I cytochromes c and that the heme is less accessible to solvent. There is localized positive charge (+3) at the site of reduction of SHP, although the overall protein charge is -2. This may account in part for the ability of SHP to bind anions.

Fiber-optic nitric oxide-selective biosensors and nanosensors

Fiber-optic biosensors that are selective for nitric oxide and do not respond to most potential interferents have been prepared with cytochromes c'. Both micro- and nanosensors have been prepared, and their response is fast (< 1 s), reversible, and linear up to 1 mM nitric oxide. The detection limit is 20 microM, making the sensor useful for some biological samples, such as the macrophages studied here. While sensors have been prepared based on the fluorescence of the cytochromes c', optodes with greatly enhanced signal-to-noise ratios have been made by labeling the cytochrome c' with a fluorescent dye. Comparisons of cytochromes c' from three species of bacteria as well as of two matrixes were performed and the optimum sensor configuration is described.

Cytochromes c-552 from two strains of the hydrogenotrophic bacterium Alcaligenes eutrophus are sequence homologs of the cytochromes c8 from the denitrifying pseudomonads

Soluble cytochromes c-552 were purified from two strains of the hydrogenothrophic species Alcaligenes eutrophus and their amino acid sequences determined. The two cytochromes were found to have 5 differences out of a total of 89 residues. The proteins are clearly related to the cytochromes c8 (formerly called Pseudomonas cytochromes c-551), but require a single residue insertion after the methionine sixth heme ligand relative to the Pseudomonas aeruginosa protein. The consensus residues Trp56 and Trp77, characteristic for the c8 family, are also present in the Alcaligenes proteins. Overall, the Alcaligenes cytochromes are only 43% identical to the Pseudomonas proteins which average 68% identity to one another. They are also only 45% identical to cytochrome c8 from Hydrogenobacter thermophilus, another hydrogenothrophic species, which indicates that the hydrogen utilizing bacteria are not more closely related to one another than they are to other species. The finding of cytochrome c8 in Alcaligenes eutrophus completes the recent characterization of a cytochrome cd1-nitrite reductase from this bacterial species and suggests the existence of the same denitrification pathway as in Pseudomonas where these two proteins are reaction partners.

Structure of Cytochromec' fromRhodobacter capsulatusStrain St Louis: An Unusual Molecular Association Induced by Bridging Zn Ions

Rhodobacter capsulatus strain St Louis cytochrome c' (RCCP-SL) has been crystallized and the structure solved by molecular replacement. It was refined at 2.1 A resolution to an R value of 18.4%, and compared with Rhodobacter capsulatus strain M110 cytochrome c' (RCCP-M110). Although these two proteins are very similar in sequence and structure, the intermolecular interaction is largely different. In RCCP-M110, the molecules dimerize through interaction of helix B to form an antiparallel arrangement. When crystallized in the presence of Zn ions, molecules of RCCP-SL were found to be arranged as linear polymers connected by the bridging Zn ions. The changes in conformation of the side chains induced by binding of the Zn ions, by the substitution of Glu90 for Asp90, and by the different arrangement of the molecules, are discussed in detail.

Which indexes of filling behavior should be used to characterize left ventricular diastolic function when changes in heart rate and atrioventricular delay occur?

The routine use of the peak early-to-peak atrial velocity, early velocity integral-to-atrial velocity integral, and early velocity integral-to-the total filling velocity integral ratios are limited because they are influenced by heart rate and atrioventricular delay. Hence, we sought to establish whether these ratios could be normalized to account for the differences in cycle length (RR interval) and diastolic filling period when heart rate and atrioventricular delay were altered in 18 patients with programmable dual-chamber pacemakers. We further explored whether these and other parameters of the mitral velocity profile could be used to characterize the mitral filling pattern during isoproterenol and methoxamine infusions-interventions that are likely to change both heart rate and left ventricular filling. The early velocity integral-to-atrial velocity integral and early velocity integral-to-the total filling velocity integral ratios were more sensitive to minor variations in heart rate and atrioventricular delay than the peak early-to-peak atrial velocity ratio. The early velocity integral-to-atrial velocity integral and early velocity integral-to-total filling velocity integral ratios could not be normalized to account for differences in RR interval or diastolic filling period, whereas the peak early-to-peak atrial velocity ratio became less sensitive to changes in heart rate when it was divided by the RR interval, or diastolic filling period, or square root of diastolic filling period. Because the diastolic filling period is affected by atrioventricular delay independent of changes in the RR interval, these ratios were also corrected for the functional cycle length, defined as the interval from R-wave of the electrocardiogram to the end of the diastolic filling period. When corrected for either the functional cycle length or diastolic filling period or square root of diastolic filling period, only the peak early-to-peak atrial velocity ratio became less sensitive to variations in the atrioventricular delay. The ratio of diastolic filling period expressed as a proportion of RR interval or functional cycle length changed significantly when heart rate and atrioventricular delay were altered and did not improve when diastolic filling period was divided by the square root of RR or square root of functional cycle length. However, when the square root of diastolic filling period was divided by the RR interval or functional cycle length, the effects of heart rate and atrioventricular delay were not apparent. Of all the ratios, the ratio of square root of diastolic filling period expressed as a proportion of RR interval or functional cycle length was the most useful to differentiate the confounding effects of heart rate (+/-atrioventricular delay) from the effects of isoproterenol and methoxamine on left ventricular filling. Hence, this ratio appeared to be a heart rate- and atrioventricular delay-independent index of left ventricular diastolic function.

Preparation and properties of a 3,4-dihydroxycinnamic acid chromophore variant of the photoactive yellow protein

Native photoactive yellow protein (PYP) is reversibly bleached by laser excitation at the 446-nm wavelength maximum, during which the trans-4-hydroxycinnamic acid chromophore (covalently bound via a thioester to Cys 69) is isomerized, causing the protein to undergo a conformational change. We have reconstituted the holoprotein from recombinant apoprotein plus thiophenol thioester-activated chromophore and have also successfully attached a synthetic 3,4-dihydroxycinnamic acid chromophore and purified the resultant variant. The reconstituted recombinant protein has the same spectral and photochemical properties as the native protein. However, the absorption maximum of the protein with the dihydroxy chromophore variant is red-shifted to 458 nm, with an additional shoulder at about 342 nm. Following a laser flash, the rate constants for the first phase of bleaching in both the native and the variant proteins are too large to measure with the present apparatus. The second bleaching phase is only marginally accessible in the variant and has a rate constant (k approximately 2.3 x 10(4) s-1) at least an order of magnitude larger than that of the native PYP. In contrast, the rate constant for recovery of absorbance in the variant (k approximately 0.15 s-1) is about 40-fold smaller than for native PYP and is insensitive to pH (the native protein has a biphasic 16-fold variation in rate constant with pH). We previously observed similar changes in kinetic rate constants for protein denatured by urea or alcohols, which suggests that the dihydroxy protein is less stable than the native PYP. This was confirmed by measurement of protein unfolding in guanidine hydrochloride. We conclude from these results that the binding site is too small to accommodate the dihydroxybenzene ring of the variant chromophore without introducing strain into the protein, which is then reflected in the kinetic properties of the photocycle.

Effects of preload, afterload and inotropy on dynamics of ischemic segmental wall motion

OBJECTIVES

This study sought to explore the separate and combined effects of changes in preload, afterload and contractility on the dynamics of systolic bulging.

BACKGROUND

The extent of ischemic systolic bulging has been shown to be mechanically disadvantageous to left ventricular pump performance. The factors that determine ischemic segmental wall motion have not been systematically studied.

METHODS

Fourteen beagles were instrumented with sonomicrometers, micromanometer pressure gauges and a balloon in the inferior vena cava. Regional function was evaluated before and after 90 s of proximal left circumflex coronary artery occlusion. Occlusions were repeated after increasing systolic pressure by 5 to 10 (afterload I) and 15 to 20 mm Hg (afterload II) with graded aortic occlusion during inotropic stimulation with dobutamine (2.5 and 5 micrograms/kg body weight per min intravenously), with simultaneous 5 micrograms/kg per min dobutamine infusion and afterload II and during 2.5% halothane (negative inotrope) concentration. A 20-min recovery period was allowed between each stage of the experiment so that regional function returned to its preocclusion level. Ischemic wall motion was characterized by percent systolic bulging and its peak positive systolic lengthening rate (+dL/dt).

RESULTS

Because bulging is markedly influenced by regional preload, systolic bulging was characterized over a wide range of end-diastolic lengths of the ischemic segment during caval balloon occlusion. During each intervention, a decrease in regional preload increased the extent of percent systolic bulging. This preload dependency was more pronounced with dobutamine infusions. An increase in afterload was not associated with increased percent systolic bulging at any given preload. At a predetermined preload, bulging was not appreciably altered when an increase in left ventricular systolic pressure was not associated with a change in peak positive first derivative of left ventricular pressure (+dP/dt) but was significantly worse when peak +dP/dt increased. Dobutamine caused a dose-dependent increase in percent systolic bulging and peak +dL/dt that was positively correlated with peak +dP/dt.

CONCLUSIONS

By using different loading and inotropic interventions and analyzing the regional wall motion behavior over a range of regional preloads, we can conclude that preload and rate of pressure (tension) development are the principal determinants of systolic bulging. Increases in left ventricular pressure alone had a minimal effect on systolic bulging.

Active site mutants implicate key residues for control of color and light cycle kinetics of photoactive yellow protein

To understand how the protein and chromophore components of a light-sensing protein interact to create a light cycle, we performed time-resolved spectroscopy on site-directed mutants of photoactive yellow protein (PYP). Recently determined crystallographic structures of PYP in the ground and colorless I2 states allowed us to design mutants and to study their photosensing properties at the atomic level. We developed a system for rapid mutagenesis and heterologous bacterial expression for PYP apoprotein and generated holoprotein through formation of a covalent thioester linkage with the p-hydroxycinnamic acid chromophore as found in the native protein. Glu46, replaced by Gln, is buried in the active site and hydrogen bonds to the chromophore's phenolate oxygen in the ground state. The Glu46Gln mutation shifted the ground state absorption maximum from 446 to 462 nm, indicating that the color of PYP can be fine-tuned by the alteration of hydrogen bonds. Arg52, which separates the active site from solvent in the ground state, was substituted by Ala. The smaller red shift (to 452 nm) of the Arg52Ala mutant suggests that electrostatic interactions with Arg52 are not important for charge stabilization on the chromophore. Both mutations cause interesting changes in light cycle kinetics. The most dramatic effect is a 700-fold increase in the rate of recovery to the ground state of Glu46Gln PYP in response to a change in pH from pH 5 to 10 (pKa = 8). Prompted by this large effect, we conducted a careful reexamination of pH effects on the wild-type PYP light cycle. The rate of color loss decreased about 3-fold with increasing pH from pH 5 to 10. The rate of recovery to the colored ground state showed a bell-shaped pH dependence, controlled by two pKa values (6.4 and 9.4). The maximum recovery rate at pH 7.9 is about 16 times faster than at pH 5. The effect of pH on Arg52Ala is like that on wild type except for faster loss of color and slower recovery. These kinetic effects of the mutations and the changes with pH demonstrate that both phases in PYP's light cycle are actively controlled by the protein component.

The substitution of proline 35 by alanine in Rhodobacter capsulatus cytochrome c2 affects the overall protein stability but not the alkaline transition

It was shown by Koshy et al. [1990, Proc. Natl Acad. Sci USA, 87, 8697-8701; 1994, Biochem. J., 299, 347-350] that the substitution of proline 30 by alanine (P30A) of Drosophila melanogaster and rat cytochromes c exhibited decreased stabilities in both the heme iron-methionine sulfur (Fe-S) bond and overall protein conformation. Now we have found that the stability properties of the equivalent mutant of Rhodobacter capsulatus cytochrome c2 (P35A) are somewhat different. Based on optical and NMR spectroscopies, the Rb.capsulatus P35A alkaline transition (pKalk) was found to be unchanged with respect to the wild type, suggesting that the mutation in Rb.capsulatus cytochrome c2 has little effect on the stability of the Fe-S bond. However, Rb.capsulatus conformational stability was found to be decreased by 1.6 kcal/mol in the oxidized state. The difference in the stability properties of the equivalent proline to alanine substitutions in various species underscores the importance of studying mutations in more than one species before drawing generalizations about the role of conserved residues in protein structure and function.

Ectothiorhodospira halophila ferrocytochrome c551: solution structure and comparison with bacterial cytochromes c

The solution structure of the Ectothiorhodospira halophila ferrocytochrome c551 has been determined. This molecule belongs to a separate class of small bacterial cytochromes c for which no 3D structure has been reported so far. It is characterized by a very low redox potential (58 mV) and is isolated from the periplasm of halophilic purple phototrophic bacteria. For the 78 residue protein, 1445 NOE derived distance constraints were used in a combined simulated annealing/restrained molecular dynamics calculation. The final ensemble of 37 structures presents a backbone r.m.s.d. of less than 0.5 A compared to the mean structure. The physical viability of these structures was investigated by subjecting eight of them to a constraint free molecular dynamics simulation. No systematic conformational change was observed and the average backbone r.m.s.d. compared to the initial structures was less than 1.5 A. The structure of the E. halophila cytochrome c551 shows a striking resemblance to Azotobacter vinelandii cytochrome c5. Significant differences in backbone conformations occur in three small regions which are implicated in solvent protection of the heme propionates and thiomethyl-8(1). Comparison with Pseudomonas aeruginosa cytochrome c551 reveals that only the common cytochrome c core, i.e. three helices, is conserved. The folding of the protein chain around the heme propionates is very different and results in more efficient solvent protection in Ps. aeruginosa. The electrostatic surface of E. halophila cytochrome c551 was found to be significantly different from mitochondrial cytochromes c and bacterial cytochromes c2 but similar to that of Ps. aeruginosa cytochrome c551.

Physical training enhances sympathetic and parasympathetic control of heart rate and peripheral vessels in chronic heart failure

1. Physical training has been proposed to increase vagal control of heart rate in chronic heart failure. We studied the effects of physical training on cardiovascular control in 6 moderate to severe heart failure (NYHA II-III) patients and 6 age matched normal controls in a randomized controlled cross over trial (Training vs Detraining). 2. Five weeks training (20 min/day, 5 days/week bicycle exercise) increased peak VO2 in both C (from 31.2 +/- 1.4 to 37.7 +/- 2.4 ml/kg/min p < 0.01) and CHF patients (from 12.16 +/- 2.2 to 14.13 +/- 2 ml/kg/min p < 0.05). The sympathovagal control of heart rate and sympathetic control of the resistance vessels was assessed by the power of the oscillations (LF:0.03-0.15 Hz index of sympathetic activity, HF: 0.18-0.35 Hz index of vagal activity) in RR interval, blood pressure (systolic and diastolic by Finapres) and respiration by autoregressive spectral analysis, during free and controlled breathing (15b/min), in order to increase vagal activity. 3. T increased heart rate vagal control both in C (LF/HF ratio fb to cb: (D) 1.73 +/- 0.35 to 1.19 +/- 0.43 p = NS: (T) 2.9 +/- 1.2 to 1.13 +/- 0.3 p < 0.05) and in CHF patients (LF/HF ratio fb to cb: (D) 2.05 +/- 0.56 to 1.24 +/- 0.21 p = NS; (T) 2.6 +/- 0.89 to 0.87 +/- 0.15 p < 0.05; and in cb HF%: 36.2 +/- 2.7 (D) to 46.2 +/- 4.8 (T) p < 0.05). Before T, the sympathetic modulation of peripheral vessels (% LF compared to total variability) was depressed in CHF vs C (SBP: 9 +/- 2 vs 42 +/- 12% p < 0.05; DBP: 29 +/- 7 vs 55 +/- 31%, p < 0.05), and increased significantly after T in CHF (SBP from 9 +/- 2 (D) to 19 +/- 5% (T) p < 0.05; DBP from 29 +/- 7 to 41 +/- 11% (T) p < 0.05). This suggests an overall increase of autonomic control, both vagal on the heart and sympathetic on the peripheral vessels, in CHF by physical training.

Effects of preload on regional nonischemic end-systolic performance

BACKGROUND

Nonischemic segmental performance, assessed by end-systolic measures of shortening and thickening, decreases during ischemia. These changes in performance are likely to be dependent on the size, and, possibly, the site of the ischemic zone. This study was designed to examine the effect of preload, independently from ischemic zone size, on nonischemic end-systolic performance.

METHODS

Twelve beagles were instrumented with sonomicrometers and micromanometer pressure gauges. End-systolic pressure length and thickness relationship data were obtained during vena caval balloon inflation. Control data were obtained both in left anterior descending and in left circumflex regions at left ventricular end-diastolic pressures of 5, 10 and 15 mmHg. The left circumflex artery was occluded for 90 s and nonischemic end-systolic pressure length and thickness data were obtained at each diastolic pressure. A 20 min recovery period was allowed between coronary occlusions.

RESULTS

The isovolumic bulge in the ischemic area was more pronounced at an end-diastolic pressure of 5 mmHg than it was at an end-diastolic pressure of 15 mmHg. The slope of the nonischemic end-systolic pressure length and thickness relationships decreased at an end-diastolic pressure of 5 mmHg, whereas at 10 and 15 mmHg the slope of these relationships did not change significantly. The shift in the nonischemic end-systolic pressure-length relationship to the right was more pronounced at a low end-diastolic pressure (5 mmHg) than it was at a high end-diastolic pressure (15 mmHg). Similarly, the extent of the shift in the end-systolic pressure-thickness relationship to the left was more marked at a low end-diastolic pressure than it was at the higher end-diastolic pressure.

CONCLUSION

Regional ischemia decreases the end-systolic performance of the nonischemic region. The extent of the shift and the degree to which the slopes of the nonischemic end-systolic relations decrease are influenced by loading conditions.

Molecular structure of a high potential cytochrome c2 isolated from Rhodopila globiformis

Unlike their mitochondrial counterparts, the c-type cytochromes typically isolated from photosynthetic nonsulfur purple bacteria display a wide range of oxidation-reduction potentials. Here we describe the X-ray crystallographic analysis of the cytochrome c2 isolated from Rhodopila globiformis. This particular c-type cytochrome was selected for study because of its anomalously high redox potential of +450 mV. Crystals employed in the investigation belonged to the space group I4(1) with unit cell dimensions of a = b = 79.2 A, c = 75.2 A, and two molecules in the asymmetric unit. The structure was solved by the techniques of multiple isomorphous replacement with two heavy-atom derivatives and electron density modification procedures. Least-squares refinement of the model reduced the R-factor to 18.7% for all measured X-ray data from 30.0 to 2.2 A. The overall structural motif of the protein is composed of five alpha-helices, one type I turn, and six type II turns. As in other cytochromes c, there are two conserved water molecules located in the heme-binding pocket. Overall, the three-dimensional structure of the R. globiformis molecule is more similar to the eukaryotic c-type cytochromes than to other bacterial proteins.

Covalent structure of the flavoprotein subunit of the flavocytochrome c: sulfide dehydrogenase from the purple phototrophic bacterium Chromatium vinosum

The amino acid sequence of the flavoprotein subunit of Chromatium vinosum flavocytochrome c-sulfide dehydrogenase (FCSD) was determined by automated Edman degradation and mass spectrometry in conjunction with the three-dimensional structure determination (Chen Z et al., 1994, Science 266:430-432). The sequence of the diheme cytochrome c subunit was determined previously. The flavoprotein contains 401 residues and has a calculated protein mass, including FAD, of 43,568 Da, compared with a mass of 43,652 +/- 44 Da measured by LDMS. There are six cysteine residues, among which Cys 42 provides the site of covalent attachment of the FAD. Cys 161 and Cys 337 form a disulfide bond adjacent to the FAD. The flavoprotein subunit of FCSD is most closely related to glutathione reductase (GR) in three-dimensional structure and, like that protein, contains three domains. However, approximately 20 insertions and deletions are necessary for alignment and the overall identity in sequence is not significantly greater than for random comparisons. The first domain binds FAD in both proteins. Domain 2 of GR is the site of NADP binding, but has an unknown role in FCSD. We postulate that it is the binding site for a cofactor involved in oxidation of reduced sulfur compounds. Domains 1 and 2 of FCSD, as of GR, are homologous to one another and represent an ancient gene doubling. The third domain provides the dimerization interface for GR, but is the site of binding of the cytochrome subunit in FCSD. The four functional entities, predicted to be near the FAD from earlier studies of the kinetics of sulfite adduct formation and decay, have now been identified from the three-dimensional structure and the sequence as Cys 161/Cys 337 disulfide, Trp 391, Glu 167, and the positive end of a helix dipole.

Kinetics of photo-induced electron transfer from high-potential iron-sulfur protein to the photosynthetic reaction center of the purple phototroph Rhodoferax fermentans

The kinetics of photo-induced electrontransfer from high-potential iron-sulfur protein (HiPIP) to the photosynthetic reaction center (RC) of the purple phototroph Rhodoferarfermentans were studied. The rapid photooxidation of heme c-556 belonging to RC is followed, in the presence of HiPIP, by a slower reduction having a second-order rate constant of 4.8 x 10(7) M(-1) x s(-1). The limiting value of kobs at high HiPIP concentration is 95 s(-1). The amplitude of this slow process decreases with increasing HiPIP concentration. The amplitude of a faster phase, observed at 556 and 425 nm and involving heme c-556 reduction, increases proportionately. The rate constant of this fast phase, determined at 425 and 556 nm, is approximately 3 x 10(5) s(-1). This value is not dependent on HiPIP concentration, indicating that it is related to a first-order process. These observations are interpreted as evidence for the formation of a HiPIP-RC complex prior to the excitation flash, having a dissociation constant of -2.5 microM. The fast phase is absent at high ionic strength, indicating that the complex involves mainly electrostatic interactions. The ionic strength dependence of kobs for the slow phase yields a second-order rate constant at infinite ionic strength of 5.4 x 10(6) M(-1) x s(-1) and an electrostatic interaction energy of -2.1 kcal/mol (1 cal = 4.184 J). We conclude that Rhodoferar fermentans HiPIP is a very effective electron donor to the photosynthetic RC.

High-resolution crystal structures of two polymorphs of cytochrome c' from the purple phototrophic bacterium rhodobacter capsulatus

The structures of two polymorphs of cytochrome c' from Rhodobacter capsulatus (RCCP) strain M110 have been determined by the molecular replacement method. Iron anomalous scattering data were used to confirm the molecular replacement solution. The structures were refined at 1.72 angstrom and 2.0 angstrom resolution to R-values of 15.0% and 16.3%, respectively. The RCCP molecule is a dimer and each of the identical 129 residue subunits folds as a four-helical bundle with a covalently bound heme group in the center. This structural motif resembles that of cytochromes c' reported from Rhodospirillum molischianum (RMCP), Rhodospirillum rubrum (RRCP), Chromatium vinosum (CVCP), Achromobacter xyloseoxidans (AXCP) and Alcaligenes denitrificans (ADCP). However, the architecture of the RCCP dimer, that is, the mode of association of subunits, differs substantially from that of the other cytochromes c'. In the RCCP dimer, the subunits are roughly parallel with each other and only helix B of each subunit participates in formation of the dimer interface. Measurement of the solvent-accessible surface area indicates that the dimer interface is smaller in RCCP than in the other cytochromes c'. In RMCP, CVCP, RRCP, AXCP and ADCP the subunits cross each other to form an X shape, and two helices, A and B, of each subunit interact across the dimer interface. These results are consistent with hydrodynamic measurements, which show that there is an equilibrium between monomers and dimer in RCCP, whereas the dimer is the predominant form in the other cytochromes c' for which structures have been determined. Structural comparison of the six cytochromes c' reveal that they can be divided into two groups. In group 1 cytochromes c', CVCP and RCCP, the amino acid sequences and the folding of subunits are arranged in such a way as to allow the formation of a deep channel between helices B and C with direct solvent accessibility to the heme sixth ligand position. There is no such channel in group 2 cytochromes c', RMCP, RRCP, AXCP and ADCP. This may account, in part, for the differences in carbon monoxide binding.

Concerted movement of side chains in the haem vicinity observed on ligand binding in cytochrome c' from rhodobacter capsulatus

We have determined the structure of n-butylisocyanide-bound Rhodobacter capsulatus cytochrome c'. This is the first example of a ligand-bound structure of a class IIa cytochrome c. Compared with the structure of native cytochrome c', there are significant conformational changes of amino acid residues in the haem vicinity, accompanied by a rearrangement of the hydrogen bonding pattern. The results suggest that rearrangements resulting from ligand binding could drive dimer dissociation in some species and also that the haem propionate may participate in proton transfer.

A high-potential soluble cytochrome c-551 from the purple phototrophic bacterium Chromatium vinosum is homologous to cytochrome c8 from denitrifying pseudomonads

A minor cytochrome c-551 component of Chromatium vinosum was previously found to efficiently couple electron transfer between the cytochrome bc1 complex and the photosynthetic reaction center. We have now determined the amino acid sequence of this cytochrome c-551 and find that it is homologous to cytochrome c8 (formerly called Pseudomonas cytochrome c-551). It is most similar to Methylophilus methylotrophus, Rhodocyclus tenuis, and Azotobacter vinelandii cytochromes c8 (respectively, 57%, 52% and 51%). The C. vinosum cytochrome c8 has a single residue insertion relative to Pseudomonas and Azotobacter cytochromes c8. It has fewer charged residues than its homologs and is essentially neutral, which may explain why it is less soluble than the others. The cytochromes c8 are only very distantly related to the cytochromes c2 found in other species of purple bacteria which are much larger in size and which usually mediate electron transfer between the cytochrome bc1 complex and the reaction center. The photosynthetic pathway in Chromatium thus appears to be radically different from that in purple non-sulfur bacteria.

Sequence evidence for strong conservation of the photoactive yellow proteins from the halophilic phototrophic bacteria Chromatium salexigens and Rhodospirillum salexigens

The photoactive yellow proteins (PYP) have been found to date only in three species of halophilic purple phototrophic bacteria. They have photochemical activity remarkably similar to that of the bacteria rhodopsins. In contrast to rhodopsins, however, the PYPs are small water-soluble proteins. We now report the complete amino acid sequences of Rhodospirillum salexigens and Chromatium salexigens PYP which allow comparison with the known sequence and three-dimensional structure of the prototypic protein from Ectothiorhodospira halophila. Although isolated from three different families of bacteria, the PYP sequences are 70-76% identical. All three contain 125 amino acid residues, and no insertions or deletions are necessary for alignment. This is a remarkable result when it is considered that electron transfer proteins from these purple bacterial species are only 25-40% identical and that insertions and deletions are needed for their proper alignment. It thus appears that PYP has the same important function in each of the purple bacteria and that most of the amino acid residues are necessary to maintain structure and function. By most standards, PYP would be called a "slowly evolving protein". R. salexigens PYP is uniquely degraded by proteolysis at low ionic strength, probably as a consequence of unfolding due to electrostatic repulsion of the excess negative charge. Therefore it may also be classified as a "halophilic protein".