Determination of Methylated Basic Amino Acids with the Amino Acid Analyzer

Chemical probes and methods for the study of protein arginine methylation

Protein arginine methylation is a widespread post-translational modification (PTM) in eukaryotic cells. This chemical modification in proteins functionally modulates diverse cellular processes from signal transduction, gene expression, and DNA damage repair to RNA splicing. The chemistry of arginine methylation entails the transfer of the methyl group from S-adenosyl-l-methionine (AdoMet, SAM) onto a guanidino nitrogen atom of an arginine residue of a target protein. This reaction is catalyzed by about 10 members of protein arginine methyltransferases (PRMTs). With impacts on a variety of cellular processes, aberrant expression and activity of PRMTs have been shown in many disease conditions. Particularly in oncology, PRMTs are commonly overexpressed in many cancerous tissues and positively correlated with tumor initiation, development and progression. As such, targeting PRMTs is increasingly recognized as an appealing therapeutic strategy for new drug discovery. In the past decade, a great deal of research efforts has been invested in illuminating PRMT functions in diseases and developing chemical probes for the mechanistic study of PRMTs in biological systems. In this review, we provide a brief developmental history of arginine methylation along with some key updates in arginine methylation research, with a particular emphasis on the chemical aspects of arginine methylation. We highlight the research endeavors for the development and application of chemical approaches and chemical tools for the study of functions of PRMTs and arginine methylation in regulating biology and disease.

A liquid chromatography tandem mass spectroscopy approach for quantification of protein methylation stoichiometry

Post-translational modifications are biologically important and wide-spread modulators of protein function. Although methods for detecting the presence of specific modifications are becoming established, approaches for quantifying their mol modification/mol protein stoichiometry are less well developed. Here we introduce a ratiometric, label-free, targeted liquid chromatography tandem mass spectroscopy-based method for estimating Lys and Arg methylation stoichiometry on post-translationally modified proteins. Methylated Lys and Arg were detected with limits of quantification at low fmol and with linearity extending from 20 to 5000 fmol. This level of sensitivity allowed estimation of methylation stoichiometry from microgram quantities of various proteins, including those derived from either recombinant or tissue sources. The method also disaggregated total methylation stoichiometry into its elementary mono-, di-, and tri-methylated residue components. In addition to being compatible with kinetic experiments of protein methylation, the approach will be especially useful for characterizing methylation states of proteins isolated from cells and tissues.

Quantitative assessment of arginine methylation in free versus protein-incorporated amino acids in vitro and in vivo using protein hydrolysis and high-performance liquid chromatography

Arginine methylation constitutes a posttranslational modification dependent on the action of protein arginine methyltransferases (PRMTs). Using S-adenosylmethionine as a methyl donor, PRMTs catalyze the formation of monomethylarginine (L-NMMA), asymmetric dimethylarginine (ADMA), or symmetric dimethyl arginine (SDMA). Protein arginine methylation is involved in the regulation of signal transduction, RNA export, and cell proliferation, but a quantitative view of arginine methylation of the cell and tissue proteome remains to be performed. In this study, we developed a high-performance liquid chromatography (HPLC)-based method to accurately quantify methylated arginines in free and protein-incorporated amino acid pools of cell and tissue extracts, using protein precipitation and hydrolysis, HPLC separation, and fluorescence detection for the simultaneous quantification of L-arginine (L-Arg), L-NMMA, ADMA, and SDMA. This method permits accurate assessment of the degree of protein arginine methylation in complex biological samples. Using this method, we determined dynamic changes in protein methylation in vitro in cells subjected to proteasome inhibition. We furthermore demonstrate differential methylation patterns in heart and kidney lysates in vivo. Thus, the described method will greatly facilitate our understanding of the role of arginine methylation in physiology and pathophysiology and of the effects of pharmacological interventions on arginine methylation in select cell culture models.

RNA and protein interactions modulated by protein arginine methylation

This review summarizes the current status of protein arginine N-methylation reactions. These covalent modifications of proteins are now recognized in a number of eukaryotic proteins and their functional significance is beginning to be understood. Genes that encode those methyltransferases specific for catalyzing the formation of asymmetric dimethylarginine have been identified. The enzyme modifies a number of generally nuclear or nucleolar proteins that interact with nucleic acids, particularly RNA. Postulated roles for these reactions include signal transduction, nuclear transport, or a direct modulation of nucleic acid interactions. A second methyltransferase activity that symmetrically dimethylates an arginine residue in myelin basic protein, a major component of the axon sheath, has also been characterized. However, a gene encoding this activity has not been identified to date and the cellular function for this methylation reaction has not been clearly established. From the analysis of the sequences surrounding known arginine methylation sites, we have determined consensus methyl-accepting sequences that may be useful in identifying novel substrates for these enzymes and may shed further light on their physiological role.

Structural specificity of substrate for S-adenosylmethionine:protein arginine N-methyltransferases

The enzymatic methylation of polypeptides on the guanidino group of internal arginine residues by S-adenosylmethionine:protein arginine N-methyltransferase (protein methylase I) yields NG-monomethylarginine, NG,NG-dimethylarginine and NG,NG-dimethylarginine. It has commonly been observed that these arginine residues are present in glycine-and-arginine rich motifs. To understand structural features which are essential for serving as the methyl acceptor for protein methylase I, we have investigated substrate capacities of several synthetic oligopeptides whose sequences are homologous and/or analogous to the methyl acceptor region of the naturally occurring arginine-methylated proteins. These studies have led to the following conclusions. (i) The preferred amino-acid sequence of methyl-accepting peptides was shown to be an arginine-containing peptide with glycine in both the N- and C-flanking positions. While a tetrapeptide with such a sequence (residues 106-109 of bovine myelin basic protein) exhibited almost negligible substrate activity, an overlapping hexapeptide was a moderate substrate. (ii) Substitution of the C-flanking glycine in GKGRGL (residues 104-109 of myelin basic protein) with histidine, phenylalanine, lysine or aspartic acid completely abolished the ability of these hexapeptides to serve as substrates. (iii) A heptapeptide with a repeated glycine-arginine motif (GRGRGRG) was an excellent substrate for the enzyme. (iv) A cyclic octapeptide (CGKGRGLC), which was formed by cyclization of GKGRGL by introduction of disulfide bridge to cross-link N- and C-terminus of the hexapeptide, was an even better substrate than the hexapeptide. (v) Upon HPLC amino-acid analysis, all enzymatically methyl-14C-labeled oligopeptides were found to yield predominantly NG-monomethylarginine with a minor fraction of NG,NG-dimethylarginine in certain peptide samples. However, no NG,NG-dimethylarginine formation was detectable. (vi) The recombinant hnRNP protein A1 (residues 1-320) is known to be methylated at arginine-194 by nuclear-protein/histone protein methylase I (Rajpurohit et al. (1994) J. Biol. Chem. 269, 1079-1082). However, the hexapeptide (SSSQRG) which corresponds to residues 189-194 of protein A1 containing the methylatable arginine residue was relatively inert as a substrate. Furthermore, the N-terminal fragment of protein A1 (residues 1-196) generated by controlled trypsin digestion was also completely inactive as a substrate for the enzyme. These results indicate that the remainder of the A1 protein molecule plays an important though not yet understood role in enzymatic methylation of the arginine-194.

Urinary excretion of NG-dimethylarginines in multiple sclerosis patients: preliminary observations

The concentrations of NG,N'G-dimethylarginine [Me2(sym)Arg] and NG,NG-dimethylarginine [Me2(asym)Arg] were determined in the urine samples from multiple sclerosis (MS) and control subjects, using a highly sensitive HPLC post-column o-phthaldialdehyde derivatization method. The presence of approximately equal amounts of both dimethylarginine isomers, of Arg concentration nearly half of Me2Arg, and of the undetectable amount of NG-monomethylarginine were the characteristic urinary excretion pattern in all human samples studied. The urinary excretion of Me2(asym)Arg and Me2(sym)Arg from MS (n = 9) and control (n = 7) were analyzed: the mean values from the samples were approximately 20% (for all MS) and 33% (for chronic-progressive MS) lower than those from the control for both dimethylarginine-derivatives when compared to the respective compounds. Although there were contrasting trends between controls and MS patients in the relationship of urinary NG-dimethylarginines and myelin basic protein like material (MBPLM), the correlations were not significant. Differences in the ratios of the concentrations of the two dimethyl derivatives, Me2(sym)Arg/Me2(asym)Arg, were not significantly different between MS and control groups. These findings warrant further investigation of possible links between urinary excretion of NG-dimethylarginine and MBPLM in MS. The possible significance of myelin metabolism in relation to urinary NG-dimethylarginines in MS is discussed.

Molecular cloning of the myelin basic proteins in the shark, Squalus acanthias, and the ray, Raja erinacia

Myelin basic proteins (MBPs) are a family of alternatively spliced isoforms present in myelin sheaths of most vertebrates. A reverse transcriptase-polymerase chain reaction (RT-PCR) approach was used to clone MBP isoforms in species representing two superorders of elasmobranchs: Squalus acanthias, representing Squalomorph sharks, and Raja erinacia, representing Batoidea rays. Two products were generated from each species. The larger product encoded a 155 amino acid protein, the same size as MBPs from two Galeomorph sharks, Heterodontus francisci and Carcharhinus obscurus, which, based upon alignment with other vertebrate MBPs, contained six of the seven MBP exons; only exon II was absent. The smaller product encoded a 141 amino acid protein that lacked exon II and exon V. There were 26 and 30 nucleotide differences between Squalus and Heterodontus, and Raja and Heterodontus, respectively. Sequences from Squalus and Raja were far more similar, having only five nucleotide differences. Both isoforms of elasmobranch MBP contain 18.5% basic (lysine plus arginine) amino acids, compared with 17.5% in mammalian MBPs comprised of the corresponding exons. Northern blot analysis of whole brain total RNA revealed a single band of 2.5 kb in Squalus, and three bands of 1.2, 1.4, and 2.3 kb in Raja. The finding that MBPs of a Squalomorph shark and a Batoidea ray are closer to one another than either is to the Galeomorph sharks suggests that MBP sequence information may prove useful in classifying modern day Chondrichthytes.

An enzyme-linked immunosorbent assay for myelin basic protein-specific protein methylase I

A sandwich enzyme-linked immunosorbent assay (ELISA) has been developed to determine myelin basic protein (MBP)-specific protein methylase I. Rabbit immunoglobulin anti-bovine MBP-specific protein methylase I, purified by Sepharose-A affinity chromatography, was utilized as the primary antibodies, while the same antibodies which had been conjugated to peroxidase were employed as the indicator antibodies. This assay method was about 280 times more sensitive than the conventional trichloracetic acid (TCA) precipitation method. Employing the ELISA, the level of MBP-specific protein methylase I during mouse brain development was examined; the peak level of the methylase was shown to be at 16th postnatal day, indicating temporal correlation with myelination. Among several species of brains examined, human showed the highest and carp the least amount of MBP-specific protein methylase I; 6.33 micrograms and 0.33 micrograms per mg of brain cytosol protein, respectively. Dysmyelinating jimpy hemizygous mouse brain showed the immunoreactive MBP-specific protein methylase only 60% that of the control at 20 days of age. The high sensitivity of the method together with the fact that MBP-specific protein methylase is present in human cerebrospinal fluid suggests a possible clinical application of this method for evaluating demyelinating disorders.

Conservation throughout vertebrate evolution of the predicted beta-strands in myelin basic protein

To identify functionally important parts of the 18.5-kDa myelin basic protein (MBP), the amino acid sequences from 10 species ranging from shark to human were aligned using the SEQHP computer program. The residues that are invariant or very conservatively substituted (Arg/Lys, Ser/Thr, Ile/Leu, Asp/Glu) among all 10 proteins were scored. Of the 72 conserved residues in the 170-residue human protein (42% conserved), 32 are found within the five beta-strands previously predicted (45 residues, 71% conserved), 23 within the small-loops region (42 residues, 55% conserved), but only 17 within the large-loops region (83 residues, 20% conserved). Of the 22 hydrophobic residues within the predicted beta-sheet of human MBP, 20 hydrophobic residues remain in the shark protein, 19 of them in the same positions. In contrast, there are 10 hydrophobic residues elsewhere in the human protein, but only 7 remain in the shark protein and only 1 of them is in the same position. The triprolyl sequence found in all mammalian MBPs and in the chicken MBP is not conserved in the shark protein. The four alternately spliced forms of mouse MBP can be accommodated by the beta-structural model, but not the 17-kDa human MBP, which lacks exon 5. These findings confirm the crucial role of the hydrophobic residues in the predicted beta-sheet for the structure and function of the protein. It seems likely that the conserved portions of the protein make an important contribution to the highly ordered lamellar structure of myelin.

Substrate specificity for myelin basic protein-specific protein methylase I

The substrate specificity of bovine brain myelin basic protein (MBP)-specific protein methylase I (S-adenosyl-L-methionine:protein-L-arginine N-methyltransferase, EC 2.1.1.23), which methylates arginine residues of protein, has been studied using various MBPs, several synthetic peptides and heterogeneous nuclear ribonucleoprotein complex protein (hnRNP). (1) Among MBPs from different species of brain, the carp MBP was found to be the best substrate for MBP-specific protein methylase I. This high degree of methyl acceptability is most likely due to the fact that carp MBP is not in vivo methylated at the arginine residue (Deibler, G.E. and Martenson, R.E. (1973) J. Biol. Chem. 248, 2387-2391) and that the methylatable amino acid sequence is present in this protein. (2) In order to study the minimum chain length of MBP polypeptide which functions as the methyl acceptor, several synthetic polypeptides whose sequences are identical to the region surrounding the residue 107 of bovine MBP (the in vivo methylation site) were synthesized. It was found that the hexapeptide, Gly-Lys-Gly-Arg-Gly-Leu (corresponding to residues 104-109 of bovine MBP), was the shortest methyl accepting peptide, while the tetrapeptide, Gly-Arg-Gly-Leu (corresponding to residues 106-109) was inactive as a substrate. (3) hnRNP protein is known to contain methylarginine at residue 193 (Williams, K.R., Stone, K.L., LoPresti, M.B., Merrill, B.M. and Plank, S.R. (1985) Proc. Natl. Acad. Sci. USA 82, 5666-5670) which is post-translationally modified. Thus, the RNP protein overproduced in Escherichia coli and therefore did not contain methylarginine was examined for its methyl acceptability. It was found that neither MBP-specific nor histone-specific protein methylase I could methylate this methylarginine-less RNP protein. This suggests a possible existence of a distinct protein methylase I specific for this nuclear protein.

Studies on protein methyltransferase in human cerebrospinal fluid

Protein methyltransferases, rich in most mammalian brains, were studied in human cerebrospinal fluid (CSF). Among several well-characterized groups of methyltransferases, protein methylase I (S-adenosylmethionine:protein-arginine N-methyltransferase, EC 2.1.1.23) was found in significant amounts in human CSF samples. Both myelin basic protein (MBP) -specific and histone-specific protein methylase I activities were observed, the latter being generally higher in most CSF. S-Adenosyl-L-homocysteine, a potent product inhibitor for the methyltransferase, inhibited approximately 90% of MBP-specific protein methylase I activity at a concentration of 1 mM. The optimum pH of the MBP-specific protein methylase I was found to be around 7.2. Identity of exogenously added MBP as the methylated substrate for CSF enzyme was confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. An amino acid analysis of the [methyl-3H]protein hydrolysate showed two major radioactive peaks cochromatographing with monomethyl- and dimethyl (symmetric)-arginine. Human CSF contained relatively high endogenous protein methylase I activity (activity measured without added substrate protein): The endogenous substrate can be immunoprecipitated by antibody raised against calf brain MBP. Finally, CSF from several neurological patients were analyzed for protein methylase I, and the results are presented.

Mechanism of the interaction between myelin basic protein and the myelin membrane; the role of arginine methylation

The addition of solutions of bovine myelin basic protein to suspensions of unilamellar vesicles prepared from whole myelin suspensions results in the rapid equilibrium association of the vesicles into dimers, followed by time-dependent aggregation reactions. Other cationic proteins also induce the dimerization of the vesicles and equilibrium constants for dimer formation are obtained for bovine myelin basic protein, lysozyme, polyhistidine and myelin basic protein from carp, which differs from the bovine protein in that it contains no methylarginine residues. The bovine protein is more efficient at inducing dimer formation than the carp protein by approximately 0.93 kcal/mole; the carp protein is approximately as effective as the other cationic proteins examined. Complete methylation of the bovine MBP by AdoMet:MBP methyltransferase increases the interaction between MBP and the membrane by approximately 0.13 kcal/mole, consistent with the suggestion that a large portion of the free energy difference between the carp and bovine proteins arises from favorable interactions involving the methylarginine residues.

Determination of methylated basic, 5-hydroxylysine, elastin crosslinks, other amino acids, and the amino sugars in proteins and tissues

Analytical single-column chromatographic methods have been developed for determining all methylated basic amino acids, isodesmosine, desmosine, the amino sugars glucosamine and galactosamine, the diastereoisomers of 5-hydroxylysine, and related compounds at picomole levels in protein and tissue hydrolysates. Complete resolution of all these unique basic amino acids as discrete peaks was achieved in 5.4 on a 50 X 0.28-cm microcolumn of Dionex type DC-4A spherical resin (9.0 +/- 0.5 micron) using updated instrumentation commonly available for amino acid analysis. The column was operated at 5.65 ml/h with two 0.35 M sodium citrate buffers (pH 5.700 and 4.501), at two temperatures (31.5 and 73 degrees C). Excellent resolution of all omega-N-methylarginines and related compounds was also achieved in 3 h using a 17.5 X 0.28-cm microcolumn of Dionex DC-5A resin (sized to 6.0 +/- 0.5 microns), two citrate buffers (0.21 M Na+, pH 5.125; 0.35 M Na+, pH 5.700), a buffer flow rate of 5.75 ml/h, and a temperature of 52 degrees C. Complete separation of all other amino acids found in protein or tissue hydrolysates including S-carboxymethyl cysteine, 4-hydroxyproline, methionine S,S-dioxide, and the amino sugars was also carried out in 95 min using a 23.5 X 0.28-cm microcolumn of Dionex DC-5A resin. The use of purified microcolumn buffers gave smooth baselines without interference from artifacts or minor hydrolysate components. The major advantages of these methods are: first, their high resolving power; second, their high sensitivity which is comparable and in some aspects superior to the newer instruments; and third, their high reproducibility (100 +/- 2.5%) and low operating costs. These methods should be especially valuable for determining myosin, actin, and elastin in tissue hydrolysates from the amounts of N tau-methylhistidine, desmosine, or isodesmosine present, respectively, and for studying protein methylation, hydroxylation, cross-linking formation, and the turnover rates of contractile and connective tissue proteins in biological systems.

Time dependence of the methylation of myelin basic protein from bovine brain; evidence for protein-methylarginine demethylation

In the presence of excess S-adenosylmethionine (AdoMet), the extent of methylation of myelin basic protein (MBP) by partially purified AdoMet:MBP methyltransferase is a non-linear function of time, reaching a limiting value as available MBP is depleted and then decreasing monotonically. This decrease is not caused by proteolytic cleavage of MBP nor by effects related to substrate or product instability under the incubation conditions and is not observed in heat-inactivated samples. S-Adenosylhomocysteine is not required for the demethylation to occur, and with purified enzyme, the decrease is not observed. The data strongly suggest that the decrease in methyl content represents an enzyme-catalyzed demethylation reaction. This would represent the first report of an enzyme which catalyzes protein-methylarginine demethylation.

Improved high-performance liquid chromatographic method for the determination of 6-N,N,N-trimethyllysine in plasma and urine: biomedical application of chromatographic figures of merit and amine mobile phase modifiers

An internally standardized method for the determination of 6-N,N,N-trimethyllysine in human plasma, human urine, rat plasma, rat urine and hydrolyzed rat urine is described. This methylated amino acid and the procedural internal standard 6-N,N,N-trimethyllysine were isolated from the sample matrices using short ion-exchange columns and detected following high-performance liquid chromatography using a postcolumn reaction (o-phthalic-dicarboxaldehyde-2-mercaptoethanol) and fluorometric detection. The reliable detection limit for 6-N,N,N-trimethyllysine was 0.2 nmol/ml in 200 microliters of human plasma. The chromatographic separation exploits the unique properties of a novel tertiary amine mobile phase modifier, 3-(N,N-dimethylamino)-1,2-propanediol. The capacity factor and "Chromatographic Figures of Merit" (including peak asymmetry and relative system efficiency) were calculated for the chromatographic peak representing 6-N,N,N-trimethyllysine in over 2200 injections made while evaluating 900 biological specimens.

Studies on myelin basic protein-specific protein methylase I in various dysmyelinating mutant mice

Jimpy mice are dysmyelinating mutants characterized by producing near normal levels of myelin basic protein (MBP) in the brain but failing to incorporate these proteins into the myelin sheath. In this study, the activity of MBP-specific protein-arginine N-methyltransferase (protein methylase I) was studied in the brains of normal and jimpy mice of different ages. The enzyme activity varied little with age in normal mice but in 18 and 21 days-old homozygous jimpy mice the activity was reduced by 50% and 75% respectively from the level of their normal littermates. Interestingly, however, heterozygous jimpy mice who are phenotypically normal and quaking mice (a similar dysmyelinating mutant) showed unaltered enzyme levels.

Determination of free trimethyllysine in plasma and tissue specimens by high-performance liquid chromatography

A method for the determination of 6-N-trimethyllysine in tissues and plasma is described. Trimethyllysine and the chemically analogous 6-N-triethyllysine (internal standard) were isolated from acid-soluble fractions of tissue homogenates or plasma by combined ion-exchange--ion-exclusion chromatography. Trimethyllysine and triethyllysine were separated from other sample constituents by reversed-phase ion-pair high-performance liquid chromatography, derivatized post-column by reaction with o-phthalicdicarboxaldehyde and 2-mercaptoethanol, and detected fluorometrically. Standard curves were linear over a sample concentration range of 0.5--4 nmol/ml. The detection limit corresponded with 25 pmol trimethyllysine injected into the chromatograph. The procedure was used for the determination of trimethyllysine in plasma, liver, kidney, and mixed skeletal muscle of rat.

Determination of 6-N-trimethyllysine in urine by high-performance liquid chromatography

A method for determination of 6-N-trimethyllysine in urine is described. Trimethyllysine and the chemically analogous 6-N-triethyllysine internal standard were isolated from aqueous samples by microcolumn ion-exclusion chromatography. The specimens were derivatized by reaction with 1-fluoro-2,4-dinitrobenzene and reaction byproducts extracted by organic solvents. The trimethyllysine and internal standard derivatives were separated easily from other sample constituents by reversed-phase paired-ion high-performance liquid chromatography with spectrophotometric detection at 405 nm. Standard curves were linear over a sample concentration range of 10-150 nmol/ml; the detection limit corresponded with 0.1 nmol trimethyllysine injected into the chromatograph. The procedure was used for determination of trimethyllysine in human urine.

In vivo methylation of an arginine in chicken myelin basic protein

The amino acid sequence around the sole methylarginine residue in chicken myelin basic protein was determined and was found to be similar to that previously reported for mammalian myelin basic protein. The ratio NG, N'G-dimethylarginine: NG-monomethylarginine:arginine was approximately 1.3:0.9:1.0. No NG, NG-dimethylarginine was detected in the protein. The in vivo incorporation of methyl groups from [methyl-3H]methionine into methylarginines in myelin was found to occur readily in 2-day-old chickens. Radioactively labelled NG,N'G-dimethylarginine and NG-monomethylarginine in myelin were derived solely from myelin basic protein. Radioactivity was also incorporated into NG,NG-dimethylargnine, although this was not derived from myelin basic protein. As NG-monomethylarginine was easily separated from the dimethylarginines, and as it was derived from myelin basic protein, it may be a good marker for myelin basic protein turnover in vivo. A time course study of the incorporation showed that radioactivity was incorporated into NG-monomethylarginine up to 6 h after injection, and decayed slowly, with an apparent half-life of about 40 days.

Prediction of the secondary structure of myelin basic protein

An investigation into the probable secondary structure of the myelin basic protein was carried out by the application of three procedures currently in use to predict the secondary structures of proteins from knowledge of their amino acid sequences. In order to increase the accuracy of the predictions, the amino acid substitutions that occur in the basic protein from different species were incorporated into the predictive algorithms. It was possible to locate regions of probable alpha-helix, beta-structure, beta-turn, and unordered conformation (coil) in the protein. One of the predictive methods introduces a bias into the algorithm to maximize or minimize the amounts of alpha-helix and/or beta-structure present; this made it possible to assess how conditions such as pH and protein concentration or the presence of anionic amphiphilic molecules could influence the protein's secondary structure. The predictions made by the three methods were in reasonably good agreement with one another. They were consistent with experimental data, provided that the stabilizing or destabilizing effects of the environment were taken into account. According to the predictions, the extent of possible alpha-helix and beta-structure formation in the protein s severely restricted by the low frequency and extensive scattering of hydrophobic residues, along with a high frequency and extensive scattering of residues that favor the formation of beta-turns and coils. Neither prolyl residues nor cationic residues per se are responsible for the low content of alpha-helix predicted in the protein. The principal ordered conformation predicted is the beta-turn. Many of the predicted beta-turns overlap extensively, involving in some cases up to 10 residues. In some of these structures it is possible for the peptide backbone to oscillate in a sinusoidal manner, generating a flat, pleated sheetlike structure. Cationic residues located in these structures would appear to be ideally oriented for interaction with lipid phosphate groups located at the cytoplasmic surface of the myelin membrane. An analysis of possible and probable conformations that the triproline sequence could assume questions the popular notion that this sequence produces a hairpin turn in the basic protein.

Recommended method for the analysis of amino acids in biological materials

Fifty-five ninhydrin-positive compounds in physiological fluids were determined with a Hitachi Model KLA-5 amino acid analyzer by a two-column chromatographic procedure. Both columns were packed with Hitachi Custom 2618 ion-exchange resin. The total analysis time was 9.5 h. In this procedure, particularly glucosamine, mannosamine and galactosamine were separated completely from normal "protein" amino acids, and NG-monomethylarginine, NG, NG-dimethylarginine and NG,NG-dimethylarginine, which were present in the myelin basic protein of several species and excreted in human urine, were separated from other basic amino acids. The method is useful for various applications with biological materials.

S-adenosylmethionine: protein-arginine methyltransferase. Purification and mechanism of the enzyme

Protein methylase I (S-adenosylmethionine: protein-arginine methyltransferase, EC 2.1.1.23) has been purified from calf brain approximately 120-fold with a 14% yield. The final preparation is completely free of any other protein-specific methyltransferases and endogenous substrate protein. The enzyme has an optimum pH of 7.2 and pI value of 5.1. The Km values for S-adenosyl-L-methionine, histone H4, and an ancephalitogenic basic protein are 7.6 X 10(-6), 2.5 X 10(-5), and 7.1 X 10(-5) M, respectively, and the Ki value for S-adenosyl-L-homocysteine is 2.62 X 10(-6) M. The enzyme is highly specific for the arginine residues of protein, and the end products after hydrolysis of the methylated protein are NG,NG-di(asymmetric), NG,N'G-di(symmetric), and NG-monomethylarginine. The ratio of [14C]methyl incorporation into these derivatives by enzyme preparation at varying stages of purification remains unchanged at 40:5:55, strongly indicating that a single enzyme is involved in the synthesis of the three arginine derivatives. The kinetic mechanism of the protein methylase I reaction was studied with the purified enzyme. Initial velocity patterns converging at a point on the extended axis of abscissas were obtained with either histone H4 or S-adenosyl-L-methionine as the varied substrate. Product inhibition by S-adenosyl-L-homocysteine with S-adenosyl-L-methionine as the varied substrate was competitive regardless of whether or not the enzyme was saturated with histone H4. On the other hand, when histone H4 is the variable substrate, noncompetitive inhibition was obtained with S-adenosyl-L-homocysteine under conditions where the enzyme is not saturated with the other substrate, S-adenosyl-L-methionine. These results suggest that the mechanism of the protein methylase I reaction is a Sequential Ordered Bi Bi mechanism with S-adenosyl-L-methionine as the first substrate, histone H4 as the second substrate, methylated histone H4 as the first product, and S-adenosyl-L-homocysteine as the second product released.

Synthesis and degradation of methylated proteins of mouse organs: correlation with protein synthesis and degradation

L-(Methyl-14C)-methionine was administered i.p. to mice, and the incorporation of radioactive methionine into proteins and methyllysine and methylarginine residues formed by the transfer of the methyl-14C group of methionine were measured. Tissue protein was actively methylated in organs having a high activity of protein synthesis, and the in vivo methylating activity in organs was not correlated with theprotein methylating activity of the organs determined in vitro. Puromycin inhibited both protein synthesis and protein methylation in mouse organs to a similar degree. Neither the formation of S-adenosyl-(methyl-14C)-methionine nor protein methylase was inhibited by puromycin. The data suggests that proteins are methylated immediately after protein synthesis, that is, newly synthesized proteins are the substrates of protein methylation. Radioactive methionine and the [C14] methyl groups of methyllysine and methylarginine residues of tissue proteins are degraded in parallel over a period of 3 wk, suggesting that protein methylation is an irreversible type of protein modification.

Sites of biological methylation of proteins in cultured chick muscle cells

The methylation of myosin and other proteins has been studied using primary cultures of 12-day-old embryonic chick leg muscle. The methyl group of [Me-3H] methionine is incorporated into basic amino acid residues with the formation of Nepsilon-monomethyllysine, Nepsilon-dimethyllysine, Nepsilon-trimethyllysine, 3-methylhistidine, NG-monomethylarginine, and NG-dimethylarginine which are isolated from acid hydrolysates of purified myosin, and of proteins from polysomes and from the cytosol of the cultured muscle cells. In the presence of 0.1 mM cycloheximide, incorporation of [Me-3H] methionine into the polysome-bound proteins was decreased to 16.3% of control levels with no change in the pattern of incorporation into the basic amino acid residues, although protein synthesis was inhibited 97.5%. When protein synthesis was allowed to resume in such cultures by the removal of cycloheximide, polypeptides containing labeled N-methylated residues were released from polysomes into the soluble fraction. Polypeptides containing N-methylated amino acids were also released from polysomes following treatment with 2 mM puromycin. Peptidyl-tRNA, isolated from ribosomes after exposure of cultures to [Me-3H] methionine, contained labeled N-methylated amino acids. When [Me-3H] methionine was incorporated in the presence of cycloheximide, the isolated peptidyl-tRNA still contained N-methylated amino acids although the amount of methylation was 22.4% of control levels. These experiments demonstrate that N-methylation of basic amino acid residues in proteins may occur while the polypeptide is still being synthesized on the ribosome. In addition, N-methylation can occur on the nascent polypeptides in the absence of protein synthesis.

Large peptides of bovine and guinea pig myelin basic proteins produced by limited peptic hydrolysis

Bovine and guinea pig myelin basic proteins were cleaved with pepsin at pH 3.0 or pH 6.0 (enzyme/substrate, 1:500, w/w), and the peptides were isolated and identified. At pH 3.0 cleavage of the bovine protein occurred principally at three sites: Phe-Phe (88-89), Phe-Phe (42-43), and Leu-Asp (36-37). Minor cleavages occurred at Leu-Ser (110-111), Phe-Ser (113-114), and Ile-Phe (152-153). A study of the time course of the hydrolysis showed that the reaction was biphasic; nearly all of the protein was cleaved at Phe-Phe (88-89) before significant cleavages at other sites occurred. At pH 6.0 cleavage of the bovine protein occurred almost exclusively at a single site, the Phe-Phe bond at position 88-89, resulting in bisection of the protein. Treatment of the guinea pig protein with pepsin under the same conditions resulted in the production of peptides which were identical with those of the bovine protein in chromatographic and electrophoretic properties and in N-terminal and C-terminal residues but which differed slightly in amino acid composition.