Application of chemical selective cleavage methods to analyze post-translational modification in proteins

Three chemical specific cleavage reactions, one for the carboxyl side of aspartyl peptide bonds, one for the carboxyl side of asparaginyl peptide bonds and another for the amino side of seryl/threonyl peptide bonds have been recently established. Additionally, these reactions simultaneously react on several post-translationally modified groups in peptides or proteins. The modified groups cover the external modifications N-formyl, N-acetyl, N-pyroglutamyi residues and C-terminal-alpha amide, as well as the internal modifications such as O-acetyl serine, phosphorylated serine/tyrosine, sulfonylated tyrosine, glycosylated serine/threonine and glycosylated asparagine. These three cleavage reactions relate to key amino acids for modifications, deamidation for asparagine, phosphorylation and acetylation for serine, and glycosylation for asparagine, serine and threonine. The chemical reactions on these modifications change the peptide mapping pattern, and information from these reactions may contribute characterization and location of post-translational modified groups in the protein.

Discharge properties of human motor units during sustained contraction at low level force

The characteristic of discharge behaviors of motor units (MUs) during low level contraction was investigated. The discharge of MUs in the m. vastus medialis was observed during the sustained contraction at 4 different levels below 10% MVC (2, 4, 8 and 10% MVC) for 15 min. The spike interval of all observed MUs gradually elongated during an initial several minutes of the contraction and the characteristic discharge patterns following the elongation were observed. i.e. continuous discharge throughout the contraction (CONT), decruitment (D-N), and re-recruitment following decruitment (D-REC). The relationship between recruitment threshold force (F(th)) and discharge pattern was not significant at 2% MVC but, at 10% MVC, there were significant differences in F(th) between D-N and CONT, and between D-REC and CONT MU populations. In pooled data, the MUs with the shorter mean spike interval at the beginning of the contraction (MSI(0), below 90 ms) tend to discharge continuously, but the MUs with longer MSI(0) showed various discharge patterns. In conclusion, during low level contraction MUs discharge characteristically, and the MU with high excitation levels tend to discharge continuously, but individual MU represents an intrinsic discharge pattern at not a high excitation level.

Restoration of immunocyte functions by thymosin alpha1 in cyclophosphamide-induced immunodeficient mice

Thymosin alpha1 (Talpha1) is an oligopeptide hormone originally isolated from the thymus gland, and has been reported to have stimulating effects on the differentiation of T cells and NK cells. These immunostimulating properties have been considered to be useful for improving immune disorders associated with various diseases including cancer, AIDS and hepatitis. Here, we characterized immunostimulating properties of Talpha1 in experimental immunodeficiency of mice that was induced by the administration of cyclophosphamide (CY). Repeated injection of 30-300 microg/kg/day of Talpha1 after CY-treatment significantly accelerated the restoration of the reduced number of CD4+CD8+ T cells in the thymus. Talpha1 administration was effective in restoring the suppressed activities of helper T cells and cytotoxic T cells in CY-treated mice. Talpha1 also had stimulating effects on reduced activity of lymphokine-activated killer cells in CY-treated mice. These results indicate that Talpha1 is stimulatory for both humoral and cellular immune responses, thus providing the immunological basis for the clinical benefit of this compound.

Purification of ferredoxins and their reaction with purified reaction center complex from the green sulfur bacterium Chlorobium tepidum

Four ferredoxin (Fd) fractions, namely, FdA-D were purified from the green sulfur bacterium Chlorobium tepidum. Their absorption spectra are typical of 2[4Fe-4S] cluster type Fds with peaks at about 385 and 280 nm and a shoulder at about 305 nm. The A(385)/A(280) ratios of the purified Fds were 0.76-0.80. Analysis of the N-terminal amino acid sequences of these Fds (15-25 residues) revealed that those of FdA and FdB completely agree with those deduced from the genes, fdx3 and fdx2, respectively, found in this bacterium (Chung and Bryant, personal communication). The N-terminal amino acid sequences of FdC and FdD (15 residues) were identical, and agree with that deduced from the gene fdx1 (Chung and Bryant, personal communication). The A(385) values of these Fds were unchanged when they were stored for a month at -80 degrees C under aerobic conditions and decreased by 10-15% when they were stored for 6 days at 4 degrees C under aerobic conditions, indicating that they are not extremely unstable. In the presence of Fd-NADP(+) reductase from spinach, and a purified reaction center (RC) preparation from C. tepidum composed of five kinds of polypeptides, these Fds supported the photoreduction of NADP(+) at room temperature with the following K(m) and V(max) (in micromol NADP(+) micromol BChl a(-1) h(-1)): FdA, 2.0 microm and 258; FdB, 0.49 microM and 304; FdC, 1.13 microM and 226; FdD, 0.5 microM and 242; spinach Fd, 0.54 microM and 183. The V(max) value of FdB was more than twice that previously reported for purified RC preparations from green sulfur bacteria.

Proteome analysis of mouse brain: two-dimensional electrophoresis profiles of tissue proteins during the course of aging

Mouse brain proteins were isolated from five regions (cerebellum, cerebral cortex, hippocampus, striatum, and cervical spinal cord) at five ages from the 10th week to the 24th month, and separated by two-dimensional gel electrophoresis (2-DE). 2-DE was carried out with an immobilized pH gradient bar in the first dimension, and by sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the second dimension. Over one thousand protein spots were visualized by silver staining and quantified by image processing. In the analyses, 58 protein spots were distinguishable among the above five brain regions, and 17 proteins were shown to be varied in quantity in the course of aging. Partial amino-terminal sequences and/or internal sequences for a total of 301 protein spots were analyzed. One hundred and eighty proteins appeared to have blocked N-termini and 122 proteins were identified. Twenty-seven new proteins were identified by sequence homology search. A mouse brain proteome database was constructed, which consists of the 2-DE map images and the respective spot data files with 15 related references.

Comparative analysis of brain proteins from p53-deficient mice by two-dimensional electrophoresis

p53 is a tumor suppressor protein that regulates many cellular processes including the cell cycle, DNA repair, and apoptosis. It also serves as a critical regulator of neuronal apoptosis in the central nervous system (CNS). To elucidate the role of p53 in the CNS, brain proteins of p53 knock-out mice (p53-/-) were analyzed by two-dimensional gel electrophoresis (2-DE) and compared with those from p53 wild type (p53+/+) mice. Six types of brain tissue (temporal cortex, cerebellum, hippocampus, striatum, olfactory bulb, and cervical spinal cord) and other control tissues (lung and blood) from 18-week-old non-stress-induced mice were analyzed. The morphology of brains from p53-/- mice appeared to be normal and identical to that of p53+/+ mice, although lungs showed diffuse tumors that may have been caused by p53 deficiency. Comparative 2-D gel analysis showed that, on average, 7 of 886 spots from brain tissue were p53-/- specific, whereas 12 of 1008 spots from lung tissue were p53-/- specific. N-terminal amino acid sequence was determined for p53-/- specific proteins. In all brain tissues from p53-/- mice, a newly identified mouse mitochondrial NADH-ubiquinone oxidoreductase 24 kDa subunit showed decreased expression, and apolipoprotein A1 acidic forms showed increased expression. In addition, brain-type creatine kinase B chain and tubulin beta-5 N-terminal fragment were increased in the p53-/- cerebellum, and a new protein in mouse, hydroxyacylglutathione hydrolase (glyoxalase II) was decreased in the temporal cortex of p53-/- mice. The alterations in protein expression identified in this study may imply a p53-related brain function. This is the first proteomic analysis on the p53-/- mouse brain, and further information based on this study will provide new insights into the p53 function in the CNS.

Cloning, expression of the psbU gene, and functional studies of the recombinant 12-kDa protein of photosystem II from a red alga Cyanidium caldarium

The encoding extrinsic 12-kDa protein of oxygen-evolving PS II complex from a red alga, Cyanidium caldarium, was cloned and sequenced by means of PCR and a rapid amplification of cDNA ends (RACE) procedure. The gene encodes a putative polypeptide of 154 amino acids with a calculated molecular mass of 16,714 Da. The full sequence of the protein includes two characteristic transit peptides, one for transfer across the chloroplast envelope and another for targeting into the thylakoid lumen. This indicates that the protein is encoded in the nuclear genome. The mature protein consists of 93 amino acids with a calculated molecular mass of 10,513 Da. The cloned gene was successfully expressed in Escherichia coli and the resulting protein was purified, reconstituted to CaCl2-washed PS II complex together with the other extrinsic proteins of 33 and 20 kDa and cyt c-550. The recombinant 12-kDa protein bound completely with the PSII complex, which resulted in a restoration of oxygen evolution equal to the level achieved by binding of the native 12-kDa protein.

Specific cleavage of amino side chains of serine and threonine in peptides and proteins with S-ethyltrifluorothioacetate vapor

A vapor of S-ethyltrifluorothioacetate was found to specifically cleave the amino side of serine and threonine peptide bonds. The cleavage reactions were carried out at 50 degrees C for 6 h-24 h or at 30 degrees C for 24 h. When vapors were generated in a solution containing several conventional organic solvents, the cleavage reactions were reduced or stopped, or modification took place. When the reagent vapor was made in an aqueous solution, the cleavage reaction at glycine residues was enhanced. This reagent did not oxidize any amino acid residues, such as methionine, cysteine and tryptophan. The cleavage was also effective on proteins on membranes blotted or electroblotted from polyacrylamide gels. This method therefore may be used for the peptide mass fingerprinting [Patterson, S. D. (1995) Electrophoresis 16, 1104-1114] after two-dimensional electrophoresis.

A uniformly cleaved epitaxically grown diamond crystal for synchrotron radiation

A homoepitaxic single-crystal diamond (111) film grown by microwave-assisted chemical vapour deposition (CVD) and fractured along the [110] directions to form small triangles was investigated by X-ray double-crystal topography. The X-ray topographic image showed that all parts of the cleaved CVD diamond film sections uniformly reflected X-rays at the peak position of the rocking curve, which was measured in the Bragg case. Furthermore, no bending effect was observed and the CVD diamond film appeared to be more perfect than and showed higher integrated intensity than the natural diamond substrate.

Additional possible tools for identification of proteins on one- or two-dimensional electrophoresis

Additional, essentially chemical, identification methods of proteins in polyacrylamide gel electrophoresis are described. Two cleavages of peptide bonds were used at the C-side of aspartic acid with a 0.2% pentafluoropropionic acid (PFPA) aqueous vapor at 90 degrees C for 4-16 h, and the N-side of serine/threonine with an S-ethyl trifluorothioacetate vapor at 50 degrees C for 6-24 h. The products were analyzed by mass spectrometry-peptide mass fingerprinting. A new type of C-terminal sequencing at multisites of protein was introduced. An aqueous vapor of 90% PFPA at 90 degrees C for 2-16 h provided cleavages at the C-side of aspartic acid and the N-side of serine/threonine and simultaneous successive truncation at the C-termini of the cleaved fragments. The product resulted in C-terminal sequences at multisites in proteins by mass spectrometric analysis. The following chemical deblocking methods were used. Anhydrous hydrazine vapor at -5 degrees C for 8 h deblocked the N-formyl group, and the vapor at 20 degrees C for 4 h deblocked pyrrolidone carboxylate. N-acetylserine/threonine was deblocked by aqueous vapor of 75% PFPA at 50 degrees C for 1 h, followed by reaction with p-sulfophenylisothiocyanate at pH 6.0. These methods were applied to a variety of protein spots on polyacrylamide gels. A new stepwise C-terminal sequencing of protein from polyacrylamide gels is also described.

Intramolecular cross-linking of the extrinsic 33-kDa protein leads to loss of oxygen evolution but not its ability of binding to photosystem II and stabilization of the manganese cluster

The extrinsic 33-kDa protein of photosystem II (PSII) was intramolecularly cross-linked by a zero-length cross-linker, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide. The resulting cross-linked 33-kDa protein rebound to urea/NaCl-washed PSII membranes, which stabilized the binding of manganese as effectively as the untreated 33-kDa protein. In contrast, the oxygen evolution was not restored by binding of the cross-linked protein, indicating that the binding and manganese-stabilizing capabilities of the 33-kDa protein are retained but its reactivating ability is lost by intramolecular cross-linking of the protein. From measurements of CD spectra at high temperatures, the secondary structure of the intramolecularly cross-linked 33-kDa protein was found to be stabilized against heat treatment at temperatures 20 degrees C higher than that of the untreated 33-kDa protein, suggesting that structural flexibility of the 33-kDa protein was much decreased by the intramolecular cross-linking. The rigid structure is possibly responsible for the loss of the reactivating ability of the 33-kDa protein, which implies that binding of the 33-kDa protein to PSII is accompanied by a conformational change essential for the reactivation of oxygen evolution. Peptide mapping, N-terminal sequencing, and mass spectroscopic analysis of protease-digested products of the intramolecularly cross-linked 33-kDa protein revealed that cross-linkings occurred between the amino group of Lys48 and the carboxyl group of Glu246, and between the carboxyl group of Glu10 and the amino group of Lys14. These cross-linked amino acid residues are thus closely associated with each other through electrostatic interactions.

Identification of domains on the 43 kDa chlorophyll-carrying protein (CP43) that are shielded from tryptic attack by binding of the extrinsic 33 kDa protein with photosystem II complex

The structural association of the spinach 33 kDa extrinsic protein with the 43 kDa chlorophyll-carrying protein (CP43) in oxygen-evolving photosystem II (PS II) complexes was investigated by comparing the peptide mappings and N-terminal sequences of the trypsin-digested products of NaCl-washed PS II membranes, which bind the 33 kDa protein, with those of CaCl2-washed PS II membranes, which lack the 33 kDa protein. (1) Peptide from N-terminus to Arg26 of CP43, which is exposed to stromal side, was digested in both PS II membranes, independent of binding of the 33 kDa protein. (2) Peptide bond of Arg357-Phe358 located in the large extrinsic loop E of CP43, which is exposed to lumenal side, was cleaved by trypsin in CaCl2-washed PS II membranes but not in NaCl-washed PS II membranes. This indicates that the region around Arg357-Phe358 in loop E of CP43 is shielded from tryptic attack by binding of the 33 kDa protein to PS II. (3) Trypsin treatment of CaCl2-washed PS II membranes also cleaved peptide bond between Lys457 and Gly458 in C-terminal region of CP43, while no cleavage of this region was detected by trypsin treatment of NaCl-washed PS II membranes. This implies that a conformational change of the C-terminal region of CP43 which is exposed to stromal side occurred upon removal of the 33 kDa protein, which makes the C-terminal region accessible to trypsin. (4) Release of peptide from Gln60 to C-terminus of the alpha-subunit of cytochrome b-559 was detected only in trypsin treatment of CaCl2-washed PS II membranes, indicating that the C-terminal region of this subunit is shielded from tryptic attack by binding of the 33 kDa protein. (5) The PS II membranes, in which Arg357-Phe358, Lys457-Gly458 of CP43 and the C-terminal part of the cytochrome b-559 alpha-subunit had been cleaved by trypsin, was no longer able to bind the 33 kDa protein. This strongly suggests that a domain in loop E of CP43 and/or the C-terminal region of the cytochrome b-559 alpha-subunit are necessary for binding of the extrinsic 33 kDa protein to PS II.

Identification of domains on the extrinsic 33-kDa protein possibly involved in electrostatic interaction with photosystem II complex by means of chemical modification

The extrinsic 33-kDa protein of photosystem II (PSII) was modified with various reagents, and the resulting proteins were checked for the ability to rebind to PSII and to reactivate oxygen evolution. While modification of more than eight carboxyl groups of aspartyl and glutamyl residues with glycine methyl ester did not affect the rebinding and reactivating capabilities, modification of amino groups of lysyl residues with either N-succinimidyl propionate or 2, 4,6-trinitrobenzene sulfonic acid or modification of guanidino groups of arginyl residues with 2,3-butanedione resulted in a loss of rebinding and reactivating capabilities of the 33-kDa protein. Moreover, the number of lysyl and arginyl residues susceptible to modification was significantly decreased when the protein was bound to PSII as compared with when it was free in solution, whereas the number of carboxyl groups modified was little affected. These results suggested that positive charges are important for the electrostatic interaction between the extrinsic 33-kDa protein and PSII intrinsic proteins, whereas negative charges on the protein do not contribute to such interaction. By a combination of protease digestion and mass spectroscopic analysis, the domains of lysyl residues accessible to N-succinimidyl propionate or 2,4, 6-trinitrobenzene sulfonic acid modification only when the 33-kDa protein is free in solution were determined to be Lys4, Lys20, Lys66-Lys76, Lys101, Lys105, Lys130, Lys159, Lys186, and Lys230-Lys236. These domains include those previously reported accessible to N-hydroxysuccinimidobiotin only in solution (Frankel and Bricker (1995) Biochemistry 34, 7492-7497), and may be important for the interaction of the 33-kDa protein with PSII intrinsic proteins.

Bond-specific chemical cleavages of peptides and proteins with perfluoric acid vapors: novel peptide bond cleavages of glycyl-threonine, the amino side of serine residues and the carboxyl side of aspartic acid residues

Peptide bond cleavages by vapors composed of various from aqueous solutions of perfluoric acid were studied using synthetic peptides and proteins, and specific conditions were established for peptide bond cleavages including a novel cleavage of the glycyl-threonine bond. The peptide bonds on the aminosides of serine residues were cleaved by exposure to a vapor of 75% aqueous heptafluorobutyric acid at 30 or 50 degrees C for 24 h. Glycyl-threonine peptide bonds were cleaved with vapors of various concentrations (5, 75, and 90%) of heptafluorobutyric acid at 30-40 degrees C for 24 h. The peptide bonds on the carboxylsides of aspartic acid residues were cleaved by exposure to a vapor of 0.2% heptafluorobutyric acid at 90 degrees C for 4 to 24 h. The same vapor cleaved aspartyl-proline bonds under milder conditions such as at 60 degrees C for 16 h, under which the other aspartyl bonds were uncleaved. These specific chemical cleavages were applied to several proteins including newly characterized proteins.

In vitro skin penetration and degradation of enkephalin, elcatonin and insulin

The work described in this paper was designed to evaluate the relevance of in vitro skin penetration studies of peptides across rat skin. The apparent penetration of three peptides, enkephalin, elcatonin and insulin, in the presence of enhancers was not seen in the in vitro method using Franz diffusion cells. However, when a protease inhibitor was mixed in the receptor fluid, the penetration of enkephalin and insulin was observed. Although insulin penetrated in the presence of enhancers, the penetration was extremely small in quantity and the cumulative amount did not increase with time. When the degradation of peptides in the receptor fluid of Franz cell was estimated, these peptides, especially enkephalin and insulin, were rapidly hydrolyzed and were almost completely lost within 3 h in the absence of an inhibitor, while elcatonin was slowly degraded. The addition of protease inhibitors, such as gabexate (20 mM), camostat (20 mM) or bile salt (taurocholate and deoxycholate, 10 mM), to the receptor fluid inhibited the degradation to a considerable extent, with the first-order rate constants decreased to one-tenth compared with the constants without inhibitors. From the inhibitory study using specific inhibitors, it was clarified that enkephalin and elcatonin were mainly hydrolyzed by aminopeptidases, endopeptidases and serine proteases in the viable skin. Consequently, the results obtained from the in vitro penetration studies without inhibitors did not reflect reliable penetration data. Thus, effective protease inhibitor(s) should be used to obtain the data corresponding to the in vivo transdermal experiment. This methodology will provide a means to eliminate the confounding effect of metabolism in permeation experiments.

Amino acid sequence of peptidyl-prolyl isomerase a of Fusarium sporotrichioides

Peptidyl-prolyl-cis-trans isomerase catalyzes the interconversion of the cis and trans isomers of the proline-containing polypeptides and the folding process of proteins. This protein was known to be cyclophilin which has high binding affinity for cyclosporin A, a cyclic undecapeptide of fungal origin with potent immunosuppressive property agent. The two cytosolic peptidyl-prolyl-isomerases were found from Fusarium sporotrichioides. The amino acid sequence of the major peptidyl-prolyl isomerase a was determined by conventional sequencing methods; the protein with a calculated molecular mass of 19.7 kDa consisting of 179 amino acids. The comparison of the amino acid sequence of peptidyl-prolyl-isomerase from Fusarium with that of Nucerospora crassa revealed a significant degree of amino acid sequence homology (82.2%).

Two-dimensional electrophoresis of plant proteins and standardization of gel patterns

Proteins of two plants, Arabidopsis thaliana and rice (Oryza sativa) were subjected to two-dimensional electrophoresis analysis with two modifications: (i) comigration of external standard marker proteins with resultant horizontal and vertical stripes in the gel, and (ii) deblocking with a vapor of aqueous heptafluorobutyric acid for N-acetylserine. Approximately 5000 protein spots were separated from both the five tissues of Arabidopsis and the nine tissues of rice. Over one hundred spots were electroblotted for N-terminal sequencing. Among the newly sequenced proteins, 62 were from Arabidopsis and 51 from rice.

Amino Acid Sequence of Trichoanguina, a Ribosomal-Inactivating Protein from Trichosanthes anguinea Seeds

In this study, we sequenced a new type I ribosome-inactivating protein, trichoanguina, from the seeds of Trichosanthes anguina (snake gourd). Trichoanguina is a basic glycoprotein having an apparent molecular mass of 35.0 kD and possessing strong ribosome-inactivating activity. Trichoanguina was cleaved with cyanogen bromide and partially digested with thermolysin, chymotrypsin, trypsin and Staphylococcus aureus V8 protease. The subsequent peptide fragments were separated by SDS-polyacrylamide gel electrophoresis, followed by electroblotting to polyvinylidene difluoride membranes and then sequencing. The sequencing of trichoanguina was completed, consisting of 245 amino acid residues. The sequencing of trichoanguina revealed a considerable homology to trichosanthin and alpha-trichosanthin, which are known as abortifacient, ribosome-inactivating and antihuman immunodeficiency virus proteins, with 46.7% and 55.6% amino acid identities, respectively. The sequence conserves two active sites: Glu-158 and Arg-161. Copyright 1996 S. Karger AG, Basel

Isolation and characterization of a Photosystem II complex from the red alga Cyanidium caldarium: association of cytochrome c-550 and a 12 kDa protein with the complex

A Photosystem II (PS II) complex was purified from an acidophilic as well as a thermophilic red alga, Cyanidium caldarium. The purified PS II complex was essentially devoid of phycobiliproteins and other contaminating components, and showed a high oxygen-evolving activity of 2375 mumol O2/mg Chl per h using phenyl-p-benzoquinone as the electron acceptor. The expression of this high activity did not require addition of exogenous Ca2+, although EDTA reduced the activity by 40%. This effect of EDTA can be reversed not only by Ca2+ but also by Mg2+; a similar Mg2+ effect has been observed in purified cyanobacterial PS II but not in higher plant PS II. Immunoblotting analysis indicated the presence of major intrinsic polypeptides commonly found in PS II from cyanobacteria and higher plants as well as the extrinsic 33 kDa protein. Antibodies against the extrinsic 23 and 17 kDa proteins of higher plant PS II, however, did not crossreact with any polypeptides in the purified PS II, indicating the absence of these proteins in the red alga. In contrast, two other extrinsic proteins of 17 and 12 kDa were present in the red algal PS II; they were released by 1 M Tris or Urea/NaCl treatment but not by 1 M NaCl. The 17 kDa polypeptide was identified to be cytochrome c-550 from heme-staining, immunoblot analysis and N-terminal amino acid sequencing, and the 12 kDa protein was found to be homologous to the 12 kDa extrinsic protein of cyanobacterial PS II from its N-terminal sequence. These results indicate that PS II from the red alga is closely related to PS II from cyanobacteria rather than to that from higher plants, and that the replacement of PS II extrinsic cytochrome c-550 and the 12 kDa protein by the extrinsic 23 and 17 kDa proteins occurred during evolution from red algae to green algae and higher plants.

Amino acid sequence of spinach ferredoxin:thioredoxin reductase catalytic subunit and identification of thiol groups constituting a redox-active disulfide and a [4Fe-4S] cluster

Ferredoxin:thioredoxin reductase is a [4Fe-4S] protein involved in the light regulation of carbon metabolism in oxygenic photosynthesis. This enzyme catalyses the reduction of thioredoxins with light-generated electrons. Ferredoxin:thioredoxin reductase is composed of two dissimilar subunits, a catalytic subunit, and a variable subunit. The catalytic subunit of spinach ferredoxin:thioredoxin reductase, which contains the redox-active disulfide bridge, was sequenced by conventional protein sequencing techniques and the functional roles of all eight cysteine residues were examined by chemical modifications. The polypeptide chain with a calculated molecular mass of 12,959 Da consists of 113 amino acids and has a calculated isoelectric point of 5.30. Six of the eight cysteine residues are clustered as Cys-Pro-Cys and Cys-His-Cys groups. Cys19 and Cys27 are free cysteines with no catalytic function, Cys54 and Cys84 constitute the redox-active disulfide bridge of the active site, and the remaining four, Cys52, Cys71, Cys73, and Cys82 bind the Fe-S cluster.

Carboxy-terminal degradation of peptides using perfluoroacyl anhydrides. A C-terminal sequencing method

An accurate carboxy-terminal sequencing method has long been sought to complement the Edman degradation procedure for amino-terminal amino acid sequence analysis. The method presented here is a unique and simple method to partly fulfill the needs. Exposure of a polypeptide to perfluoroacyl anhydride vapor at -20 degrees C for 0.5-1 h causes sequential chemical degradation of the molecule from the C-terminus. Fast-atom-bombardment mass spectrometric analysis of the resultant mixture of C-terminally truncated molecules permits the determination of the C-terminal sequence by simple calculation of the mass differences in molecular ions. Experiments suggested that this C-terminal degradation proceeds by active intermediates such as oxazolone at the C-terminal carboxyl residues.

Separation and characterization of Arabidopsis thaliana proteins by two-dimensional gel electrophoresis

Arabidopsis (Arabidopsis thaliana) proteins were isolated from five tissues (leaf, stem, root, seed and callus), and separated by two-dimensional gel electrophoresis (2-DE). 2-DE was carried out by immobilized pH gradient (IPG) in the first dimension, and by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension. With the aid of comigrated five-marker proteins, the patterns of 2-DE gels for each tissue were graphically combined by a computer into a single synthetic image for the integrated Arabidopsis protein spots. The protein spot images, altogether 4763, were characterized by both molecular mass and isoelectric point. Partial amino(N)-terminal sequences of 101 protein spots were analyzed by Edman degradation. Fifty seven proteins were partially sequenced and 46 proteins appeared to have blocked N-termini. Deblocking by hydrazine vapor was carried out on 14 proteins and two of them were found to be pyroglutamyl-blocked N-termini. Forty seven new proteins were found by the present investigation.

Amino acid sequence of spinach ferredoxin:thioredoxin reductase variable subunit

Ferredoxin:thioredoxin reductase (FTR) is an iron-sulfur protein, which, in the presence of ferredoxin and thioredoxin, catalyses the light-dependent activation of several photosynthetic enzymes. Spinach FTR consists of two dissimilar polypeptide chains, A and B, present in equal amounts. Whereas subunit B seems to be responsible for the catalytic activity, subunit A has no known catalytic function. We found earlier that the N-terminus of subunit A, also called the variable subunit, shows terminal redundancy and that 2-3 of its serine residues are phosphorylated [Tsugita, A. Yano, K., Gardet-Salvi, L. & Schürmann, P. (1991) Protein Sequence Data Anal. 4, 9-13]. We now report the complete amino acid sequence of subunit A, determined by conventional protein sequencing methods. The polypeptide chain with a calculated molecular mass of 12,669 Da consists of 112 amino acids and has a calculated isoelectric point of 5.4. The analysis of the sequence supports the idea that this subunit has no catalytic function. The comparison with a known cyanobacterial FTR reveals about 58% similarity and the striking presence of a N-terminal extension in the spinach protein. This extension may be responsible for the reported size variability of this subunit.

Separation and characterization of rice proteins

Rice proteins from nine tissues and one organelle (leaf, chloroplast, stem, root, germ, dark germinated seedling, seed, bran, chaff and callus) were isolated and then separated by two-dimensional gel electrophoresis (2-DE). The protein spots were characterized according to molecular weight, isoelectric point and partial amino-terminal sequence. Electrophoresis was carried out by isoelectric focusing (IEF), nonequilibrium pH gradient electrophoresis (NEPHGE) and immobilized pH gradient (IPG) in the first dimension, and by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension. With the aid of nine marker proteins, the patterns of IEF, NEPHGE and IPG 2-DE gels were graphically combined by computer into a single synthetic image for each tissue, respectively, and these images for the nine tissues and one organelle were again combined into a single 2-DE image for the integrated rice protein spots. The rice 2-DE gel image resolved 4892 proteins. About 3% of the spots are characterized by amino-terminal sequencing.

Specific chemical cleavage of asparaginyl and glycyl-glycine bonds in peptides and proteins by anhydrous hydrazine vapor

Hydrazinolysis of peptide or protein has been used for C-terminal amino acid determination by Akabori et al. (1952). In this study, proteins were reacted with anhydrous hydrazine vapor at 20 degrees C for 16 h. Asparaginyl linkages were cleaved. Asparagine and glutamine were converted to their hydrazides, beta-hydrazidyl aspartic acid and gamma-hydrazidyl glutamic acid, respectively, even under milder conditions. The former hydrazide cyclizes to a 6-membered ring, asparaginyl bond at the carboxyl side. Other cleavages, including the glycyl-glycine bond, were also observed.

[An experimental and clinical study of chorioretinal photocoagulation using a frequency-doubled Nd: YAG laser]

We developed a new frequency-doubled Nd: YAG laser system which works on 100 volts AC and emits continuous wave green laser light of 532 nm. Histological observation of rabbit eyes revealed no difference in chorioretinal lesions produced with the frequency-doubled Nd: YAG laser or with an argon green laser. This device was then clinically applied to 69 eyes of 59 patients with several disorders such as diabetic retinopathy, retinal vein occlusion, Eales' disease, Coats' disease, age-related macular degeneration, lattice degeneration in the peripheral retina, macular hole, and retinal tear. The ophthalmoscopic findings showed no visible differences in the lesions made with this device or with the argon laser. No complications were observed in these patients except for one case of central retinal vein occlusion, which developed vitreous hemorrhage after the treatment. This solid-state laser system has some mechanical advantages over the gas laser, i.e. reduced cooling requirements, easy maintenance, and long life, and it is considered to be usable clinically.

Removal of N-terminal formyl groups and deblocking of pyrrolidone carboxylic acid of proteins with anhydrous hydrazine vapor

Many proteins have a blocked alpha-amino group which renders them inaccessible to sequence analysis by the classical Edman degradation procedure. Blockage typically occurs when the alpha-amino groups are acylated with acetyl or formyl groups or when the N-terminal residue is pyrrolidone carboxylic acid formed by cyclization of glutamine. We have found that N-formyl groups of proteins and peptides can be removed by exposure to hydrazine vapor at -5 degrees C for 8 h. Under these conditions, peptide-bond cleavage or modification of the constituent amino-acid residues does not occur. Deblocking of N-terminal pyrrolidone carboxylate residues by conversion to gamma-hydrazidyl glutamic acid can be achieved by exposure to hydrazine vapor at 20 degrees C for 4 h. These conditions cause partial modification of asparagine and glutamine residues to their corresponding hydrazides, and conversion of arginine residues to ornithine.

C-terminal sequencing of protein. A novel partial acid hydrolysis and analysis by mass spectrometry

Peptides or proteins were hydrolyzed by vapors of 90% pentafluoropropionic acid or heptafluorobutyric acid at 90 degrees C for various time periods. The hydrolyzate mixtures analyzed by both fast-atom-bombardment and electrospray ionization mass spectrometry showed a series of C-terminal successive degradation molecular ions. The degradation reaction may be due to the selective formation of an oxazolone ring at the C-terminal amino acid, followed by hydrolytic removal of the C-terminal amino acid. The major side reactions were cleavages of the peptide bonds at the C side of the internal aspartic acid residue and the N side of serine residue.

Key factors to improve survival of elderly patients on CAPD

The adequacy of dialysis is a primary concern when caring for patients undergoing CAPD. It is also important to analyze the key factors, which will reflect on the prognosis of elderly patients on CAPD. In this study, 60 CAPD patients were examined. The peritoneal and residual renal clearance of these patients were calculated every six months. These patients were divided into three groups (G-1 = poor, G-2 = fairly good, G-3 = good) according to their clinical parameter scores using a s-albumin,Ht,LBW, and s-cholesterol level. This study showed that the values of (KT/V) urea and Curea showed no statistical differences. These results therefore indicate that the major reason for the poor outcome in elderly patients is due to low dietary protein intake.

N-terminal amino acid sequence analysis of small subunits of photosystem I reaction center complex from a thermophilic cyanobacterium, Synechococcus elongatus Nägeli

Four small subunits (14, 13, 10, and 8 kDa) of the photosystem I reaction center complex were isolated from a thermophilic cyanobacterium Synechococcus elongatus and their N-terminal amino acid sequences determined. Sequence analysis of the 10-kDa subunit revealed that the distribution of cysteine residues, Cys-X-X-Cys-X-X-Cys-X-X-X-Cys-Pro, is characteristic of bacterial-type ferredoxins, and that its partial sequence is highly homologous to that deduced from the chloroplast gene frx A of liverwort. This indicates that the 10-kDa polypeptide is an apoprotein carrying two iron-sulfur centers, FA and FB, assigned as [4Fe-4S] clusters, which mediated the light-activated transfer of electrons from P700 in photosystem I reaction center complex to soluble ferredoxin. The amino acid sequence of the 14-kDa polypeptide also showed similarity to that of the 20-kDa polypeptide from spinach chloroplast that can be chemically crosslinked with soluble ferredoxin. Thus, the 14-kDa polypeptide appears to be the ferredoxin 'docking' protein.

Generation of a different type of beta-kallikrein from porcine pancreatic alpha-kallikrein by the action of chymotrypsin--observation of proteolytic processing occurring around "kallikrein autolysis loop" region

The generation of a different type of beta-kallikrein, designated C beta-kallikrein, from alpha-kallikrein by chymotryptic action was ascertained by the following observations: 1) When alpha-kallikrein was incubated with chymotrypsin, an increase of esterolytic activity of kallikrein was observed. 2) In sodium dodecyl sulfate polyacrylamide gel electrophoresis, C beta-kallikrein was found to be different from the beta-kallikrein obtained from alpha-kallikrein by tryptic digestion, and was designated T beta-kallikrein. 3) N-Terminal amino acid sequence analyses of internal light and heavy chains of C beta-kallikrein indicated that N-termini of the light and the heavy chains were isoleucine and lysine, respectively, and that the heavy chain had most of the "kallikrein autolysis loop" sequence in its N-terminal end. In the case of T beta-kallikrein, N-termini of the light and the heavy chains were isoleucine and alanine, respectively, and the light chain retained the "kallikrein autolysis loop" region in its C-terminal end. These observations demonstrated that C beta-kallikrein was different from the beta-kallikrein prepared from autolyzed pancreas, A beta-kallikrein, which had lost the "kallikrein autolysis loop" sequence. Structural differences of the above four kallikreins (alpha-, T beta-, C beta-, and A beta-) result in somewhat different enzyme properties. The kinetic constants for the hydrolysis of synthetic substrates (N alpha-benzoyl-L-arginine ethyl ester and N alpha-tosyl-L-arginine methyl ester) of these kallikreins differed from each other, and inhibitory profiles against alpha 1-antitrypsin were also different.(ABSTRACT TRUNCATED AT 250 WORDS)

Hemerythrin from Lingula unguis consists of two different subunits, alpha and beta

Hemerythrin, a non-heme Fe-protein, of Lingula unguis has an octamer structure. We demonstrated that the protein is composed of two distinct subunits (alpha and beta), in equal amounts by investigation of their composition and partial terminal sequence. The cross-linking reaction of the native protein with dithiobis-(succinimidyl propionate) provided evidence for the presence of a dimer composed of alpha and beta subunits.

Amino acid sequence of ferredoxin isolated from Cyanidium caldarium strain RK-1

Ferredoxin was isolated from ther eukaryotic alga Cyanidium caldarium strain RK-1 and its amino acid sequence was determined. The ferredoxin is composed of 97 amino acid residues, and its molecular weight is 10,599 excluding the iron-sulfur cluster. The amino acid sequence differs from that of C. caldarium strain 1355/1, by 24 amino acid substitutions plus one deletion at the amino terminus.

The amino acid sequence of plastocyanin from rice (Oryza sativa, subspecies japonica)

The amino acid sequence of plastocyanin from rice (subspecies japonica) was determined. It consists of a single polypeptide chain of 97 residues and has a molecular mass of 10,225 Da. The sequence shows 94.8% identity with barley plastocyanin.

Sensitization of Edman amino acid derivatives using the fluorescent reagent, 4-aminofluorescein

The ability to analyze amino acid derivatives at the femtomole level is one of the most interesting challenges in the field of protein microsequencing. 2-Anilino-5-thiazolinone amino acids, obtained by Edman degradation, were quantitatively derivatized with fluorescent primary amines. The most fluorescent reagent tested was 4-aminofluorescein. The amino acid derivatives sensitized with this reagent were separated using reversed-phase high-performance liquid chromatography and identified at the 100 attomole level. Incorporation of this method into the operation of a conventional automated sequencer is also described.

Amino acid sequences of ferredoxins from rice cultivars, japonica and indica

Ferredoxins were isolated from the leaves of two rice cultivars, japonica and indica. The purified protein preparations each contained two components, the major (I) and the minor (II) ferredoxin. Ferredoxin I from each cultivars was sequenced. The amino acid sequences of the ferredoxin I from the two strains were found to be identical to each other. The sequence similarity with wheat ferredoxin is about 90%. Most of the amino acid alterations are located at the ends of the protein, with the sequences surrounding the iron-sulfur coordinating cysteine residues being well conserved.

Primary structure of spinach-chloroplast thioredoxin f. Protein sequencing and analysis of complete cDNA clones for spinach-chloroplast thioredoxin f

The primary structure of thioredoxin f from spinach chloroplasts was determined by standard amino acid sequencing and furthermore by sequencing the corresponding nuclear genome region. The protein, with a calculated molecular mass of 12,564 Da and a molar absorption coefficient at 280 nm of 17,700 M-1 cm-1, consists of 113 residues and exhibits 24% residue identities with spinach chloroplast thioredoxin mb or Escherichia coli thioredoxin. A monospecific antibody elicited against thioredoxin f has been used to select recombinant phage from spinach cDNA libraries in lambda gt11. The inserts of positive clones were sequenced. They code for a polypeptide of 190 amino acids, composed of the thioredoxin f sequence (113 residues) and an upstream element (77 residues) which most probably constitutes the N-terminal transit peptide that directs the polypeptide into chloroplasts. In vitro transcription and translation of this construct generates a polypeptide of approximately 21 kDa, which is imported by isolated spinach chloroplasts and processed to the mature 12.5-kDa protein.