Primary structure of ferredoxin from bovine kidney mitochondria.

Kidney mitochondrial ferredoxin (renodoxin) is a component of the cytochrome P-450-dependent enzymatic system whose main function is the hydroxylation of vitamin D3 in the 1alpha- and 24-positions. The complete amino acid sequence of renodoxin was determined by protein chemistry and mass spectrometry. The mature renodoxin has 128 amino acid residues. The N- and C-terminal regions of renodoxin are subject to proteolytic modification, this being the origin of heterogeneous molecular mass (from 14,200 to 12,400 kD) of purified protein preparations. The antigenic structure of renodoxin was studied using antibodies to peptide fragments of a homologous protein, adrenodoxin.

In vivo carbamylation and acetylation of water-soluble human lens alphaB-crystallin lysine 92.

Several post-translational modifications of lysine residues of lens proteins have been implicated in cataractogenesis. In the present study, the molecular weight of an alpha-crystallin isolated from the water-soluble portion of a cataractous human eye lens indicated that it was a modified alphaB-crystallin. Further analysis by mass spectrometry of tryptic digests of this modified protein showed that Lys 92 was modified and that the sample was structurally heterogeneous. Lys 92 was acetylated in one population and carbamylated in another. Although carbamylation of lens crystallins has been predicted, this is the first documentation of in vivo carbamylation of a specific site. These results are also the first documentation of in vivo lysine acetylation of alphaB-crystallin. Both modifications alter the net charge on alphaB-crystallin, a feature that may have significance to cataractogenesis.

Identification of an artifact in the mass spectrometry of proteins derivatized with iodoacetamide.

Derivatization of cysteinyl residues is often used to prevent the formation of disulfide bonds during protein isolation and analysis. The most commonly used reagents are iodoacetic acid and iodoacetamide, which increase the molecular mass of the protein by 58 or 57 Da, respectively, for each derivatized cysteine. A possible side reaction is derivatization of methionine. In our analysis of derivatized human lens alphaA-crystallins, we found an apparent molecular mass 48 Da lower than the mass expected for alphaA-crystallin with the cysteines carboxyamidomethylated. Analysis of a tryptic digest of this protein showed that both cysteines and one methionine had been derivatized. Peaks indicating a molecular mass 48 Da less than expected for the protein with only cysteines derivatized were attributed to fragmentation of the derivatized methionine through collision-induced dissociation in the electrospray ionization source. An awareness of this artifact is important to investigators searching for proteins and their modified forms in complex mixtures.

Mass spectrometric characterization of oat phytochrome A: isoforms and posttranslational modifications.

At least four mRNAs for oat phytochrome A (phyA) are present in etiolated oat tissue. The complete amino acid sequences of two phyA isoforms (A3 and A4) and the N-terminal amino acid sequence of a third isoform (A5) were deduced from cDNA sequencing (Hershey et al., 1985). In the present study, heterogeneity of phyA on a protein level was studied by tryptic mapping using electrospray ionization mass-spectrometry (ESIMS). The total tryptic digest of iodoacetamide-modified phyA was fractionated by gel filtration chromatography followed by reversed-phase high-performance liquid chromatography. ESIMS was used to identify peptides. Amino acid sequences of the peptides were confirmed or determined by collision-induced dissociation mass spectrometry (CID MS), MS/MS, or by subdigestion of the tryptic peptides followed by ESIMS analysis. More than 97% of the phyA3 sequence (1,128 amino acid residues) was determined in the present study. Mass-spectrometric analysis of peptides unique to each form showed that phyA purified from etiolated oat seedling is represented by three isoforms A5, A3, and A4, with ratio 3.4:2.3:1.0. Possible light-induced changes in phytochrome in vivo phosphorylation site at Ser7 (Lapko VN et al., 1997, Biochemistry 36:10595-10599) as well at Ser17 and Ser598 (known as in vitro phosphorylation sites) were also analyzed. The extent of phosphorylation at Ser7 appears to be the same for phyA isolated from dark-grown and red-light illuminated seedlings. In addition to Ser7, Ser598 was identified as an in vivo phosphorylation site in oat phyA. Ser598 phosphorylation was found only in phyA from the red light-treated seedlings, suggesting that the protein phosphorylation plays a functional role in the phytochrome A-mediated light-signal transduction.

Surface topography of phytochrome A deduced from specific chemical modification with iodoacetamide.

Phytochromes are a photoreversible photochromic light switch for photomorphogenesis in plants. The molecular structure and functional mechanism of phytochromes are not fully understood. On the basis of complete mapping of total tryptic digest of the iodoacetamide-modified oat phytochrome A (phyA), the molecular surface topography of phyA was probed by specific chemical modification of cysteine residues with [14C]iodoacetamide. Under native conditions, only two cysteines (Cys-158 and Cys-311) of eleven half-cystines of the N-terminal chromophore binding domain were modified to a significant extent. In the C-terminal domain, six cysteine residues (Cys-715, Cys-774, Cys-809, Cys-869, Cys-961, Cys-995) were readily accessible to iodoacetamide. Among the reactive cysteine residues, only cysteine-311 displayed reactivity that was dependent on the photochromic form (Pr left arrow over right arrow Pfr) of the photoreceptor. Surprisingly, the modification of Cys-311 in the vicinity of the chromophore attachment site (Cys-321) did not have any detectable effect on spectral properties of phyA. Most of the cysteines of the N-terminal domain (Cys-83, Cys-175, Cys-291, Cys-370, Cys-386, Cys-445, Cys-506) are deeply buried in the core of the chromophore binding domain, as they can be modified only after denaturation of the chromoprotein. In the C-terminal domain, modification of only one cysteine residue (Cys-939) required protein denaturation. Since all 22 half-cystines can be modified with iodoacetamide without reduction of the chromoprotein, it follows that oat phyA does not have any disulfide bonds. We found that Cys-311, Cys-774, Cys-961, and Cys-995 could be easily partially oxidized under the conditions used for phytochrome isolation. The surface topography/conformation of oat phyA and its role in protein-protein recognition in phytochrome-mediated signal transduction are discussed in terms of the relative reactivity of cysteine residues.

Posttranslational modification of oat phytochrome A: phosphorylation of a specific serine in a multiple serine cluster.

Phytochrome A (phyA) is a photoreceptor of higher plants which mediates a variety of biochemical and physiological processes in response to red/far-red light. By detailed structural analysis of the peptides of the total tryptic digest of oat phyA, we found that the photoreceptor isolated from red light irradiated seedlings contains only one site of phosphate attachment, in the N-terminal Ser-rich region. The N-terminal tryptic phosphopeptide (residues 1-12) contains eight serine residues, any of which may be phosphorylated. Direct fast atom bombardment mass spectrometry (FAB MS/MS) analysis of the phosphorylated peptide as well as of its phosphate-containing fragment (residues 1-9) was not successful due to their hydrophilic nature and instability of the phosphate bond. beta-Elimination of the phosphorylated tryptic peptide in the presence of ethanethiol converted the phosphoserine residue to S-ethylcysteine that is stable under FAB MS/MS. FAB MS/MS analysis of the modified peptide clearly showed that the phosphate group was attached to Ser7. The in vivo phosphorylation site at Ser7 in oat phyA is discussed for its possible regulatory role in phyA function.

Dynamics of the N-terminal alpha-helix unfolding in the photoreversion reaction of phytochrome A.

Time-resolved circular dichroism spectroscopy in the far-UV spectral region was used to examine the intermediates of the phytochrome photoreversion reaction (Pfr --> Pr). Three intermediates, lumi-F (tau = 320 ns), meta-Fa (tau = 265 micros) and meta-Fb (tau = 5.5 ms), have been identified in a simple sequential kinetic photoreversion mechanism by absorption spectroscopy [Linschitz, H., Kasche, V., Butler, W. L., & Siegelman, H. W. (1966) J. Biol. Chem. 241, 3395-3403; Pratt, L. H., & Butler, W. L. (1968) Photochem. Photobiol. 8, 477-485; Burke, M., Pratt, D. C., & Moscowitz, A. (1972) Biochemistry 11, 4025-4031; Spruit, C. J. P., Kendrick, R. E., & Cooke, R. J. (1975) Planta (Berlin) 127, 121-132; Eilfeld, P., & Rüdiger, W. (1985) Z. Naturforsch. 40c, 109-114; Chen, E., Lapko, V. N., Lewis, J. W., Song, P.-S., & Kliger, D. S. (1996) Biochemistry 35, 843-850]. In order to correlate the unfolding of the N-terminal alpha-helical segment with one or more of the intermediate species, time-resolved methods were coupled with the structurally sensitive probe of CD in the far-UV spectral region. Analysis of the TRCD data associates the decrease in alpha-helical content that occurs upon formation of Pr with decay of the meta-Fa intermediate. This unfolding process occurs with a time constant of 310 +/- 125 micros, which is consistent with the 265-micros lifetime for meta-Fa.

Protein kinase A-catalyzed phosphorylation and its effect on conformation in phytochrome A.

Phytochromes are ubiquitous red/far-red wavelength-sensitive photoreceptors in plants. Oat phytochrome A is a phosphoprotein. Phytochrome A (phyA) possesses two spatially different sites for phosphorylation with cAMP-dependent protein kinase (PKA) [McMichael & Lagarias (1990) Biochemistry 29, 3872-3878]. To assess the modulation of protein conformation by phosphorylation/dephosphorylation and its possible implication in phytochrome-mediated signal transduction, the conformations of phytochrome have been probed by PKA catalyzed phosphorylation. The phosphorylated species were purified and analyzed, along with untreated phytochrome, by limited proteolysis, circular dichroism (CD) and fluorescence quenching measurements. No significant changes in secondary structure of the phyA molecule after its phosphorylation were observed by CD. However, a subtle topographic and/or electrostatic effect of the phytochrome phosphorylation was detected by the time-resolved fluorescence quenching of Trp residues with Cs+ ions. N-Terminal phosphorylation at Ser17 was unique to the Pr form, but both Pr and Pfr phytochromes were phosphorylated at the hinge region to some extent. Phosphorylation at the hinge region resulted in noticeable changes in the proteolytic patterns, inhibiting cleavage near the phosphorylation site and favoring tryptic digestion of the Lys536-Asn537 peptide bond. Phosphorylation at the N-terminus did not cause observable changes in the helical structure of this region, but had an inhibitory effect on proteinase V8 accessibility at a site near the chromophore attachment. The functional relevance of protein phosphorylation of phyA is also discussed.

Mechanism of native oat phytochrome photoreversion: a time-resolved absorption investigation.

The regulation of plant photomorphogenesis is mediated by the thermal reactions that follow light absorption by the phytochrome photoreceptor. Phytochromes are tetrapyrrolic chromoproteins that exist in two photochromically interconvertible forms, a red light absorbing species, Pr, and a far-red light absorbing form, Pfr. Upon irradiation with 670 nm light, the inactive, red light sensing Pr form is converted to the active Pfr form. Although the forward phototransformation has been studied extensively by several groups using various techniques, the Pfr-->Pr photoreversion reaction that occurs upon irradiation with 730 nm light is not as thoroughly characterized. In this study, time-resolved absorption (TROD) spectroscopy is used to examine the intermediate species involved in the phytochrome photoreversion mechanism at 10 degrees C. Analysis of the TROD data identifies three species with lifetimes of 320 ns, 265 microseconds, and 5.5 ms. TROD results are described in terms of the simplest parallel and sequential kinetic models. Comparison of intermediate spectra from these mechanisms with those of previously reported species from flash photoreversion and low-temperature studies indicates that Pfr photoreversion follows a sequential pathway that does not share any intermediates with the Pr phototransformation pathway.

A simple and improved method of isolation and purification for native oat phytochrome.

A simple procedure for the isolation and purification of 124 kDa phytochrome (phyA) form etiolated Avena seedlings has been developed employing ammonium sulfate back-extraction. After solubilization of the ammonium sulfate precipitate (250 g/L) an additional ammonium sulfate fractionation with 17 g per 100 mL rather than column chromatography was performed. After several steps of the "washing-out" procedure with 100 mM phosphate buffer, phytochrome was solubilized in 10 mM phosphate buffer. The resulting phytochrome had a specific absorbance ratio (SAR = A666/ A280) ranging from 0.60 to 0.85. These values are equivalent to those of phytochrome preparations after hydroxylapatite chromatography-ammonium sulfate back-extraction. The total isolation-purification time was 8 h and yield of the chromoprotein was 50% higher than the yield using conventional techniques. The phytochrome preparation, after application to a Toyopearl HW-65S gel filtration column, produced very pure 124 kDa phyA with a specific absorbance ratio greater than 1.00. The spectral characteristics are identical to those described for the best of the highly purified native chromoprotein preparations.

[Primary structure of hepatoredoxin from bovine liver mitochondria]. / Pervichnaia struktura gepatoredoksina iz mitokhondrii pecheni byka.

The primary structure of hepatoredoxin from bovine liver mitochondria was established. It consists of 117 amino acid residues. The identity of the amino acid sequences of bovine hepatoredoxin and adrenodoxin from bovine adrenal cortex mitochondria was shown. It is assumed that the role of a ferredoxin component in mitochondrial steroid-hydroxylating systems from different organs is played by the same [2Fe-2S]-protein.

Primary structure of the cholesterol side-chain cleavage cytochrome P-450 from bovine adrenocortical mitochondria and some aspects of its functioning on a structural level.

The primary structure of the cholesterol side-chain cleavage cytochrome P-450 (P-450scc) from bovine adrenocortical mitochondria has been determined. At the initial stage an exhaustive chymotryptic digestion of carboxymethylated P-450scc was performed, and the amino acid sequence of 66 peptides was determined. At the second stage an investigation of the amino acid sequence of individual fragments I (Mr 29 800) and II (Mr 26 600) of the limited trypsinolysis of P-450scc was carried out. Fragment I was digested with trypsin, Staphylococcus aureus V8 proteinase and thermolysin; fragment II was cleaved with trypsin and S. aureus V8 proteinase. In addition, the amino acid sequence of some CNBr peptides of P-450scc has been investigated. The primary structure of cytochrome P-450scc determined with protein chemistry methods proved the multistage cholesterol transformation to pregnenolone to be catalyzed by a single species of cytochrome P-450scc which consists of 481 amino acids. The results from protein sequencing of P-450scc are in good agreement with those obtained recently from nucleotide sequencing. The localization of peptide bonds cleaved under limited proteolysis of P-450 with trypsin to fragments I and II, I and III (Mr 16 800) is presented. It is shown that the transformation of P-450scc to P-420 is accompanied by the appearance of an additional trypsin-sensitive peptide bond in the N-terminal part of P-450scc.

[Primary structure of 20S,22R-cholesterol-hydroxylating cytochrome P-450 from bovine adrenal cortex mitochondria. IV. Structure of peptides of thermolytic and limited tryptic hydrolysis of the fragment F1; peptides of cyanogen bromide hydrolysis of cytochrome P-450. Complete amino acid sequence]. / Pervichnaia struktura 20S,22R-kholesteringidroksiliruiushchego tsitokhroma P-450 iz mitokhondrii kory nadpochechnikov byka. IV. Struktura peptidov termoliticheskogo i ogranichennogo tripticheskogo gidrolizov fragmenta F1; peptidy bromtsianovogo rasshchepleniia tsitokhroma P-450. Polnaia aminokislotnaia posledovatel'nost'.

A thermolytic hydrolysis of maleinated fragment F1 has been performed, resulted in isolation of 44 peptides; their complete amino acid sequence has been determined. Non-overlapping thermolytic peptides of fragment F1 involve 178 amino acid residues, which comprises about 71% of its amino acid sequence. Also, the cleavage and structural investigation of some tryptophan-containing peptides obtained from the limited trypsinolysis of fragment F1 were carried out; reconstitution of the polypeptide chain of the fragment is completed. The cyanogen bromide cleavage of carboxymethylated cytochrome P-450 was achieved and 17 peptides, comprising almost the whole polypeptide chain of the protein molecule (91%), was isolated. To investigate structure of the cyanogen bromide peptides, we hydrolysed them at tryptophan residues with trypsin, chymotrypsin, proteinase from Staphylococcus aureus, and BNPS-skatole. The data obtained and those published earlier led to the complete primary structure of the cholesterol-hydroxylating cytochrome P-450. The proteins polypeptide chain consists of 481 amino acid residues and has the precise molecular mass 56 407.7.

[Primary structure of 20S,22R-cholesterol-hydroxylating cytochrome P-450 from bovine adrenal cortex mitochondria. III. Primary structure of peptides produced by hydrolysis of the fragment F2 with proteinase from Staphylococcus aureus]. / Pervichnaia struktura 20S,22R-kholesteringidroksiliruiushchego tsitokhroma P-450 iz mitokhondrii kory nadpochechnikov byka. III. Issledovanie struktury peptidov, poluchennykh pri gidrolize fragmenta F2 proteinazoi iz Staphylococcus aureus.

Primary structure of F2 fragment resulting from limited trypsinolysis of the native cytochrome P-450 has been investigated. Hydrolysis of F2 fragment with proteinase from Staphylococcus aureus afforded 18 homogeneous peptides covering the whole polypeptide chain of the fragment. Complete amino acid sequences were established for 16 peptides, two peptides being elucidated partially. The above data in combination with structural study of chymotryptic peptides of cytochrome P-450 and tryptic peptides of F2 fragment led to reconstitution of six peptide blocks of F2 fragment comprising 203 amino acid residues.

[Primary structure of 20S,22R-cholesterol-hydroxylating cytochrome P-450 from bovine adrenal cortex mitochondria. Study of the structure of peptides obtained by hydrolysis of fragment F1 with proteinase from Staphylococcus aureus]. / Pervichnaia struktura 20S,22R-kholesteringidroksiliruiushchego tsitokhroma P-450 iz mitokhondrii nadpochechnikov byka. II. Issledovanie struktury peptidov, poluchennykh pri gidrolize fragmenta F1 proteinazoi iz Staphylococcus aureus.

The fragment F1 resulting from the limited tryptic hydrolysis of the native molecule of cytochrome P-450 has been digested with Staphylococcus aureus protease. 24 peptides, covering the whole polypeptide chain of fragment F1, are isolated from the hydrolysate. Analysis of their amino acid sequence in combination with the earlier data on the structure of cytochrome P-450 chymotryptic peptides and fragment F1 tryptic peptides permitted to carry out a reconstruction of large peptide blocks of fragment F1 that comprise 252 amino acid residues.

The domain structure of the cholesterol side-chain cleavage cytochrome P-450 from bovine adrenocortical mitochondria. Localization of haem group and domains in the polypeptide chain.

Cytochrome P-450scc consists of two domains linked with a short loop of the polypeptide chain; under hydrolysis by trypsin the domains retain their associated state due to rigid noncovalent interactions. A partial separation of the domains by gel-chromatography on Sephadex G-200 with retention of a haem group in domain I has been achieved after incubation of the trypsin-modified cytochrome P-450scc in 50 mM phosphate buffer (pH 7.2)/1 M NaCl/0.3% sodium cholate/0.3% Tween 80. The separation of domains I and II to individual fragments of the haemoprotein polypeptide chain has been achieved by chromatography under denaturation conditions on the activated thiopropyl-Sepharose via a selective covalent immobilization of domain II. Dissociation of a complex of domains I and II has been effectuated in the presence of 7 M guanidine. Structural characteristics of individual domains have been investigated. It is established that domain I containing a haem group is the N-terminal moiety, and domain II, the C-terminal moiety of the polypeptide chain of cytochrome P-450scc. The pathways of limited trypsinolysis of the native cytochrome P-450scc have been determined. The peptides containing cysteine residues localized on the surface of domain II and responsible for the interaction of haemoprotein with activated thiopropyl-Sepharose have been isolated in a homogeneous form and their amino-acid sequences have been assessed.

[Structural organization of adrenodoxin using limited proteolysis]. / Issledovanie strukturnoi organizatsii adrenodoksina metodom organichennogo proteoliza.

The microheterogeneity of adrenodoxin preparation was established by endogenous proteolysis. The controlled limited trypsinolysis and endogenous proteolysis result in modification of the COOH-terminus of the polypeptide chain with a formation of a protein with Mr = 10 000. The interaction of this protein and of the native protein with cholesterol-specific cytochrome P-450 and adrenodoxin reductase occurs in a similar way.

Isolation, structural organization and mechanism of action of mitochondrial steroid hydroxylating systems.

A scheme for the isolation of individual proteins of the 20S,22R-cholesterol hydroxylating system is presented. Physico-chemical and structural parameters of cytochrome P-450 are furnished. Self-reconstitution of indivudal proteins of the system into an enzyme unit is shown. Furthermore a regulation process of electron transport in the 20S,22R-cholesterol system is considered.