Interruption of the internal water chain of cytochrome f impairs photosynthetic function.

The structure of cytochrome f includes an internal chain of five water molecules and six hydrogen-bonding side chains, which are conserved throughout the phylogenetic range of photosynthetic organisms from higher plants, algae, and cyanobacteria. The in vivo electron transfer capability of Chlamydomonas reinhardtii cytochrome f was impaired in site-directed mutants of the conserved Asn and Gln residues that form hydrogen bonds with water molecules of the internal chain [Ponamarev, M. V., and Cramer, W. A. (1998) Biochemistry 37, 17199-17208]. The 251-residue extrinsic functional domain of C. reinhardtii cytochrome f was expressed in Escherichia coli without the 35 C-terminal residues of the intact cytochrome that contain the membrane anchor. Crystal structures were determined for the wild type and three "water chain" mutants (N168F, Q158L, and N153Q) having impaired photosynthetic and electron transfer function. The mutant cytochromes were produced, folded, and assembled heme at levels identical to that of the wild type in the E. coli expression system. N168F, which had a non-photosynthetic phenotype and was thus most affected by mutational substitution, also had the greatest structural perturbation with two water molecules (W4 and W5) displaced from the internal chain. Q158L, the photosynthetic mutant with the largest impairment of in vivo electron transfer, had a more weakly bound water at one position (W1). N153Q, a less impaired photosynthetic mutant, had an internal water chain with positions and hydrogen bonds identical to those of the wild type. The structure data imply that the waters of the internal chain, in addition to the surrounding protein, have a significant role in cytochrome f function.

Tryptophan-heme pi-electrostatic interactions in cytochrome f of oxygenic photosynthesis.

Cytochrome f of oxygenic photosynthesis has an unprecedented structure, including the N-terminus being a heme ligand. The adjacent N-terminal heme-shielding domain is enriched in aromatic amino acids. The atomic structures of the chloroplast and cyanobacterial cytochromes f were compared to explain spectral and redox differences between them. The conserved aromatic side chain in the N-terminal heme-shielding peptide at position 4, Phe and Tyr in plants and algae, respectively, and Trp in cyanobacteria, is in contact with the heme. Mutagenesis of cytochrome f from the eukaryotic green alga Chlamydomonas reinhardtii showed that a Phe4 --> Trp substitution in the N-terminal domain was unique in causing a red shift of 1 and 2 nm in the cytochrome Soret (gamma) and Q (alpha) visible absorption bands, respectively. The resulting alpha band peak at 556 nm is characteristic of the cyanobacterial cytochrome. Conversely, a Trp4 --> Phe mutation in the expressed cytochrome from the cyanobacterium Phormidium laminosum caused a blue shift to the 554 nm alpha band peak diagnostic of the chloroplast cytochrome. Residue 4 was found to be the sole determinant of this 60 cm(-)(1) spectral shift, and of approximately one-half of the 70 mV redox potential difference between cytochrome f of P. laminosum and C. reinhardtii (E(m7) = 297 and 370 mV, respectively). The proximity of Trp-4 to the heme implies that the spectral and redox potential shifts arise through differential interaction of its sigma- or pi-electrostatic potential with the heme ring and of the pi-potential with the heme Fe orbitals, respectively. The dependence of the visible spectrum and redox potential of cytochrome f on the identity of aromatic residue 4 provides an example of the use of the relatively sharp cytochrome spectrum as a "spectral fingerprint", and of the novel structural connection between the heme and a single nonliganding residue.

Comparison of the cytochrome bc1 complex with the anticipated structure of the cytochrome b6f complex: Le plus ça change le plus c'est la même chose.

Structural alignment of the integral cytochrome b6-SU IV subunits with the solved structure of the mitochondrial bc1 complex shows a pronounced asymmetry. There is a much higher homology on the p-side of the membrane, suggesting a similarity in the mechanisms of intramembrane and interfacial electron and proton transfer on the p-side, but not necessarily on the n-side. Structural differences between the bc1 and b6f complexes appear to be larger the farther the domain or subunit is removed from the membrane core, with extreme differences between cytochromes c1 and f. A special role for the dimer may involve electron sharing between the two hemes b(p), which is indicated as a probable event by calculations of relative rate constants for intramonomer heme b(p) --> heme b(n), or intermonomer heme b(p) --> heme b(p) electron transfer. The long-standing observation of flash-induced oxidation of only approximately 0.5 of the chemical content of cyt f may be partly a consequence of the statistical population of ISP bound to cytfon the dimer. It is proposed that the p-side domain of cyt f is positioned with its long axis parallel to the membrane surface in order to: (i) allow its large and small domains to carry out the functions of cyt c1 and suVIII, respectively, of the bc1 complex, and (ii) provide maximum dielectric continuity with the membrane. (iii) This position would also allow the internal water chain ("proton wire") of cyt f to serve as the p-side exit port for an intramembrane H+ transfer chain that would deprotonate the semiquinol located in the myxothiazol/MOA-stilbene pocket near heme b(p). A hypothesis is presented for the identity of the amino acid residues in this chain.

Structure of the soluble domain of cytochrome f from the cyanobacterium Phormidium laminosum.

Cytochrome f from the photosynthetic cytochrome b(6)f complex is unique among c-type cytochromes in its fold and heme ligation. The 1. 9-A crystal structure of the functional, extrinsic portion of cytochrome f from the thermophilic cyanobacterium Phormidium laminosum demonstrates that an unusual buried chain of five water molecules is remarkably conserved throughout the biological range of cytochrome f from cyanobacteria to plants [Martinez et al. (1994) Structure 2, 95-105]. Structure and sequence conservation of the cytochrome f extrinsic portion is concentrated at the heme, in the buried water chain, and in the vicinity of the transmembrane helix anchor. The electrostatic surface potential is variable, so that the surface of P. laminosum cytochrome f is much more acidic than that from turnip. Cytochrome f is unrelated to cytochrome c(1), its functional analogue in the mitochondrial respiratory cytochrome bc(1) complex, although other components of the b(6)f and bc(1) complexes are homologous. Identical function of the two complexes is inferred for events taking place at sites of strong sequence conservation. Conserved sites throughout the entire cytochrome b(6)f/bc(1) family include the cluster-binding domain of the Rieske protein and the heme b and quinone-binding sites on the electrochemically positive side of the membrane within the b cytochrome, but not the putative quinone-binding site on the electrochemically negative side.

Benzo[a]pyrene and its analogues: structural studies of molecular strain.

The molecular geometry of benzo[a]pyrene, its 4-methyl-and 3,11-dimethyl derivatives, benzo[e]pyrene, and two azabenzo[a]pyrenes are described. Results of these three-dimensional crystal structure determinations, together with those from previous studies in this laboratory of 11-methylbenzo[a]pyrene, indicate the extent to which nonbonded interactions between hydrogen atoms contribute to molecular distortions, particularly in the bay-region. This strain is high if a bay-region methyl group is present. The major effect is an increase in the C-C-C angles in that area of the molecule, rather than torsion about bonds. In addition, the effect of a nitrogen atom replacing one of the C-H groups in the aromatic system is shown. Molecules stack in planes approximately 3.5 A apart. In benzo[a]pyrene, 5-azabenzo[a]pyrene and 3,11-dimethylbenzo[a]pyrene crystals the stacking is similar to that in graphite. 4-Methylbenzo[a]pyrene molecules stack with less molecular overlap. The packing in 4-aza-5-methylbenzo[a]pyrene consists of modules of four stacked molecules, packed in a 'tile-like' arrangement. Nonbonded C....H interactions between adjacent molecules lead to a herring-bone arrangement between these stacks. The types of C....H and pi-pi interactions involving PAHs in the crystalline state, described here, can also be expected to be found when the PAHs bind to hydrophobic areas of biological macromolecules such as proteins, nucleic acids and membranes.

Biological identity and diversity in photosynthesis and respiration: structure of the lumen-side domain of the chloroplast Rieske protein.

BACKGROUND: The cytochrome b6f complex functions in oxygenic photosynthesis as an integral membrane protein complex that mediates coupled electron transfer and proton translocation. The Rieske [2Fe-2S] protein subunit of the complex functions at the electropositive (p) membrane interface as the electron acceptor for plastoquinol and donor for the cytochrome f subunit, and may have a dynamic role in catalyzing electron and proton transfer at the membrane interface. There are significant structure/function similarities to the cytochrome bc1 complex of the respiratory chain. RESULTS: The 1.83 A crystal structure of a 139-residue C-terminal fragment of the Rieske [2Fe-2S] protein, derived from the cytochrome b6f complex of spinach chloroplasts, has been solved by multiwavelength anomalous diffraction. The structure of the fragment comprises two domains: a small 'cluster-binding' subdomain and a large subdomain. The [2Fe-2S] cluster-binding subdomains of the chloroplast and mitochondrial Rieske proteins are virtually identical, whereas the large subdomains are strikingly different despite a common folding topology. A structure-based sequence alignment of the b6f and bc1 groups of Rieske soluble domains is presented. CONCLUSIONS: The segregation of structural conservation and divergence in the cluster-binding and large subdomains of the Rieske protein correlates with the overall relatedness of the cytochrome b6f and bc1 complexes, in which redox domains in the aqueous p phase are dissimilar and those within the membrane are similar. Distinct sequences and surface charge distributions among Rieske large subdomains may provide a signature for interaction with the p-side oxidant protein and for the pH of the intraorganelle compartment.

Characterization and crystallization of the lumen side domain of the chloroplast Rieske iron-sulfur protein.

A soluble, 139-residue COOH-terminal polypeptide fragment of the Rieske iron-sulfur protein of the cytochrome b6f complex from spinach chloroplasts was obtained by limited proteolysis of the complex and a two-step chromatography purification protocol. The purified Rieske iron-sulfur protein fragment was characterized by: (i) a single NH2-terminal sequence, NH2-Phe-Val-Pro-Pro-Gly-Gly, starting with residue 41 of the intact Rieske protein; (ii) a single molecular weight species determined by mass spectrometry with a molecular weight of 14,620 +/- 2 without the [2Fe-2S] cluster; (iii) an optical absorbance spectrum with redox- and pH-dependent maxima and minima; and (iv) a reduced-oxidized optical difference spectrum characterized by DeltaepsilonmM = 3.8 mM-1 cm-1 for DeltaA at 394 versus 409 nm, which was used to determine the midpoint oxidation-reduction potential, which is +359 +/- 7 mV at 25 degrees C from pH 5.5-6.5, and +319 +/- 2 mV at pH 7, with an apparent pKox = 6.5 +/- 0.2 for the oxidized protein. The EPR spectrum measured at 17 K was characterized by the g values, gz = 2.03 and gy = 1.90, and a broad band centered at gx approximately 1.74, very similar or identical to those of the Rieske cluster in the b6f complex, implying that the environment of the [2Fe-2S] cluster is similar to that in the complex. Midpoint potential determination by low temperature EPR yielded a redox midpoint potential (Em) of +365-375 mV of the soluble Rieske fragment at pH 6 and 7 and an Em of +295-300 mV of the Rieske cluster in the cytochrome b6f complex at pH 6 and 7. The Em difference implies that the environment of the cluster in the soluble Rieske fragment is slightly more polar than that of the cluster in the intact complex. Single crystals of the Rieske polypeptide were obtained that are capable of x-ray diffraction to atomic resolution (<2.5 A), contain one molecule per asymmetric unit, a solvent content of approximately 30%, and belong to the triclinic space group P1 with cell dimensions, a = 29.1 A, b = 31.9 A, c = 35.8 A, alpha = 95.6 degrees, beta = 107.1 degrees, gamma = 117.3 degrees.

Bay-region distortions in a methanol adduct of a bay-region diol epoxide of the carcinogen 5-methylchrysene.

The three-dimensional structure of the product of the reaction of a diol epoxide of the carcinogen 5-methylchrysene with methanol has been determined by an X-ray diffraction analysis. The diol epoxide used to obtain this compound contains a stereochemically hindered bay region because of the location of the 5-methyl group, and this might be expected to affect the type of chemical reaction that occurs. The crystal structure analysis of this adduct of a polycyclic aromatic hydrocarbon (PAH) showed that a methoxy group has been added at the carbon atom of the epoxy group that is nearest to the aromatic system. The bond that is formed is axial to the ring system so that the carbon and hydrogen atoms of the methoxy group are considerably displaced from the PAH ring plane. The bay-region methyl group at position 5 is displaced out of the ring plane in the opposite direction. The major steric distortion in this methanol adduct is shown, by a comparison with crystal structures of related non-methylated compounds, to be in the area of the 5-methyl group and not in the tetrol-bearing ring. The steric effects that caused the axial conformation of the newly formed bond would also be expected to pertain in the DNA adduct of a PAH with a bay-region methyl group. Since the presence of the bay-region methyl group in 5-methylchrysene has been shown to enhance the carcinogenicity of this PAH over the parent compound or compounds with methyl groups in other positions of the molecule, it might be anticipated that this axial bond is found in carcinogenic lesions in DNA, and that any factor that ensures this axial conformation may accentuate the carcinogenic potential of a PAH of the appropriate size.

2-bromoacetoxybenzoic acid, a brominated aspirin analog.

The crystal structure of 2-bromoacetoxybenzoic acid, C9H7BrO4, shows it to be a close structural analog of aspirin. The carboxylic acid moiety is twisted by 7.7 (4) degrees out of the plane of the aromatic ring. The acetyl group, like that of aspirin, shows bond-angle distortions from ideal values while remaining essentially planar. The Br atom is rotationally disordered and has been modeled as occupying two sites related by a 13 (1) degree rotation about the C8--C9 bond.

1-(4-iodobenzoyl)-5-methoxy-2-methyl-3-indoleacetic acid, an iodinated indomethacin analog.

The crystal structure of 1-(4-iodobenzoyl)-5-methoxy-2-methyl-3-indoleacetic acid, C19H16INO4, an analog of indomethacin, is reported. Bond distances and angles in the title compound closely resemble those reported for indomethacin and reflect the presence of steric strain at the site of the linkage between the 4-iodobenzoyl group and the indole moiety. The orientation of the 4-iodobenzoyl group with respect to the indole ring is not the same in the title compound as it is in indomethacin; the two structures are related by a rotation of 186 degrees about the C2--N1--C10--C11 torsion angle.

Bay- and fjord-region distortions in dibenz[a,j]anthracene and tetrabenzo[de,hi,mn,qr]naphthacene.

The crystal structure of 7,14-dimethyldibenz[a,j]anthracene (DMDBA) has been determined, and the crystal structure of tetrabenzo[de,hi,mn,qr]naphthacene (TBNC) has been redetermined at higher precision than previously reported. These molecules are polycyclic aromatic hydrocarbons (PAHs) that have, respectively, two hindered bay regions and two fjord regions; the former PAH is a known carcinogen. The extensive out-of-plane bending as a result of steric overcrowding in the bay and fjord regions in these PAHs is shown by these studies. For DMDBA, the angle between the 14-methyl group and the outer rings is 32.6 degrees. For TBNC, the angle between the outer rings of the molecule is 31.9 degrees. These structures are compared with those of related structures of 7,12-dimethylbenz[a]anthracene and dibenzo[g,p]chrysene. It appears that steric overcrowding in such PAHs can cause distortions of up to 33 degrees C. Such steric overcrowding will affect the conformations of bay- and fjord-region diolepoxides, which are the presumed activated metabolites in the carcinogenic process.

The stereochemistry of the recognition of nitrogen-containing heterocycles by hydrogen bonding and by metal ions.

An analysis of the stereochemistry of hydrogen bonding and metal binding to some nitrogen-containing heterocycles found in crystal structure determinations has shown that the interacting atom will generally lie in the plane of the heterocyclic ring system in a direction that approximately bisects the C-N-C angle of the heterocycle. The Cambridge Structural Database (CSD) of crystal structures of small molecules was used for this analysis because stereochemical data are available at high resolution and are amendable to comparative analysis. It was found that, for hydrogen bonding, a slight out-of-plane deviation of the binding atom is marginally more likely than an in-plane deviation. Metal ions appear to bind in a manner that is similar to that of hydrogen bonding to a protonated heterocycle, no matter what the chemical identity of the metal. The binding is more rigid, with less in-plane or out-of-plane deviation of the metal ion compared to the interaction with a hydrogen-bonding group. Some ab initio molecular orbital energy calculations give a measure of the energies involved when metal ions or hydrogen-bonding groups deviate from the plane of the ring system or from the line bisecting the C-N-C angle of the heterocycle. These results are compared with reported structural data (at lower resolution) for some acridine-oligonucleotide complexes and the surroundings of histidine rings in some protein crystal structures.