ANALYTICAL

186,%%100

BIOCHEMISTRY

(1990)

Detection of Methylated Asparagine Residues in Polypeptides’ Alan V. Klotz,*,”

Beth Ann Thomas,*

Alexander

and Glutamine

N. Glazer,?

and Russell

W. Blacher$

*Department of Biochemistry, Louisiana State University, Baton Rouge, Louisiana 70803; tDivision of Biochemistry and Molecular Biology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720; and $Athena Neurosciences, Inc., 800-F Gateway Boulevard, South San Francisco, California 94080

Received

September

121989

A residue of y-N-methylasparagine (r-NMA) is found at position D-72 of many phycobiliproteins. 8-N-Methylglutamine is present in some bacterial ribosomal proteins. r-NMA was synthesized by reacting the w-methyl ester of aspartate with methylamine and b-N-methylglutamine by reaction of pyroglutamate with methylamine. These derivatives and the w-methyl esters of aspartate and glutamate were characterized by melting point, by thin-layer chromatography, by amino acid analysis, by NMR spectroscopy, and after conversion to the phenylthiohydantoin (PTH) derivative. The yNMA residues in peptides from allophycocyanin, Cphycocyanin, and B-phycoerythrin were stable under the conditions of automated sequential gas-liquid phase Edman degradation. On HPLC, PTH-r-NMA coeluted with PTH-serine and was accompanied by a minor component eluting just prior to dimethylphenylthiourea. Similar results were obtained on manual derivatization of synthetic y-NMA to prepare the PTH derivative. The PTH-6-N-methylglutamine standard eluted near the position of dimethylphenylthiourea under the usual conditions employed for the identification of PTH-amino acid derivatives in automated protein sequencing. 0 1990 Academic Press, Inc.

This study was prompted by the recent discovery that a y-N-methylasparaginyl residue occupies position p-72 (C-phycocyanin sequence numbering) in each of the major phycobiliproteins (1,2). The presence of this residue went unnoticed in numerous sequence determinations ’ This research was supported in part by the Donors of The Petroleum Research Fund, administered by the American Chemical Society, and by grants from the Department of Health and Human Services (GM 28994) and the National Science Foundation (DMB8816727).

* To whom

correspondence

should

0003.2697/90 $3.00 Copyright 0 1990 by Academic Press, All rights of reproduction in any form

be addressed.

Inc. reserved.

on phycobiliproteins (reviewed in Refs. (3,4)) until 1985 when Minami et al. (5) noted a discrepancy between the amino acid composition and the sequence of an allophycocyanin peptide. This observation indicated the presence of an unidentified aspartyl derivative in the 0 subunit of Anabaena cylindrica allophycocyanin. Our subsequent work established the structure of this derivative as the N-methyl amide form (1). Protein sequence determination is increasingly based upon the use of automated versions of Edman chemistry. Assignment of amino acid sequence then relies solely on the identification of the phenylthiohydantoin (PTH)3amino acid derivatives. We now realize that the earlier failures to detect y-N-methylasparagine residues were in large part due to the coelution of the PTH-y-N-methylasparagine and PTH-serine under the conditions of high-performance liquid chromatography generally used for separations of PTH-amino acids. Dependence on a single criterion of identification, while necessary for some samples when the available quantity is limited, inevitably results in this type of oversight when unusual residues coelute with standard derivatives. Thus far y-N-methylasparagine has been detected only in phycobiliproteins (1,2,6). Escherichia cob ribosomal protein L-3 contains a 6-N-methylglutamine (7) and to date this is the sole known target for glutamine methylation. Carboxyl methylation of selected glutamyl residues on specific membrane receptors in E. coli and Salmonella modulates processing of sensory input (8,9). Protein carboxyl methyl transferases have also been described which esterify D-EqX&yl and L-isoaspartyl resi3 Abbreviations used: AspOCH,, aspartate w-methyl ester; DMPTU, dimethylphenylthiourea; I-NMG, 6-N-methylglutamine; GluOCHB, glutamate w-methyl ester; y-NMA, y-iV-methylasparagine; MA, methylamine; Nle, norleucine; PITC, phenyl isothiocyanate; PTH, phenylthiohydantoin derivative; Hse), homoserine lactone. The Chemical Abstracts registry numbers for r-NMA and &NMG are [7175-34-O] and [3081-62-71, respectively. 95

96

KLOTZ TABLE Melting

Points Glutamate

Methyl Melting

Amino

acid

AspOCH, GluOCH3 r-NMA &NMG ’ AspOCH,

1

and Yields of Aspartate Derivatives

point

Observed (“C)

Literature” (“Cl

191-192 154 234 188-190

190 154 235-236 192

and GluOCH3

(16);

and

r-NMA

(22);

Synthetic yield (So) 72 86 38 9 &NMG

(17).

dues present in a small subpopulation of polypeptide chains in mammalian cells (10). The fact that S-adenosylmethionine serves as the methyl donor for aspartyl and glutamyl ester formation in proteins has been exploited to introduce radioactively labeled methyl groups defining the positions of the methylated residues in the amino acid sequence (e.g. (11)). However, in situations where such an approach has not been used, methyl esters of glutamyl and aspartyl residues may well remain undetected. In this report we present results of sequence studies on y-N-methylasparagine-containing peptides and examine the behavior of y-N-methylasparagine, 6-Nmethylglutamine, and the o-methyl esters of glutamate and aspartate under the conditions employed for sequence analysis in a gas-liquid phase sequencer. MATERIALS

AND

METHODS

Chemicals. Aspartate, asparagine, glutamate, glutamine, pyroglutamate, serine, and threonine were obtained from Sigma Chemical Co. Deuterium oxide, HCl gas, methylamine (free base and hydrochloride salt), and norleucine were purchased from Aldrich Chemical Co. Sequencing reagents including phenyl isothiocyanate, benzene, triethylamine, trifluoroacetic acid, and pyridine were sequanal-grade obtained from Pierce Chemical Co. Anhydrous methanol was freshly distilled. Sequencer reagents were purchased from Applied Biosystems, Inc.; other solvents were HPLC-grade. Sequencing of peptides containing y-N-methylasparagine. A. variabilis allophycocyanin decapeptide P(64-73) (l), Synechococcus PCC6301 C-phycocyanin octapeptide fl(67-74) (2), and Porphyridium cruentum B-phycoerythrin nonapeptide p(66-74) (12) were prepared as described previously. The A. variabilis and Synechococcus peptides were sequenced using an Applied Biosystems Model 477A sequencer and the standard program where the couphng and cleavage cycles are performed at 48°C. Briefly, in the standard program the

ET AL.

sample on the filter is exposed to 5% PITC in n-heptane for 2 s, dried with argon for 40 s, and then treated with trimethylamine vapor (present in equilibrium with a solution of 12.5% trimethylamine in water) for 400 s; this procedure is repeated three times. Conversion of the anilinothiazolinone to the phenylthiohydantoin is achieved by treatment with 25% aqueous trifluoroacetic acid for 20 min at 64°C (complete details may be found in Ref. (13)). PTH-amino acid derivatives were quantitated from filtered data sets (13,14). The P. cruentum peptide was sequenced on an Applied Biosystems Model 470A sequencer using a similar program (15). PTH-rNMA was quantitated assuming the response factor for PTH-Asn. Preparation of 0- and N-methyl amino acid derivatives. The w-methyl esters of aspartate and glutamate were prepared by suspending 1 g of free amino acid in 20 ml anhydrous methanol. HCl gas was bubbled into the solution to achieve a concentration of l-3 M for the aspartyl methyl ester preparation and 1.5 eq HCl gaswas added for the glutamyl methyl ester preparation (16). After dissolution was complete the reaction was allowed to proceed for approximately 1 h at room temperature. The crude products were then qualitatively analyzed by thin-layer chromatography using cellulose plates (EM Laboratories), a solvent system (v/v) of ethanol:acetic acidwater, 8:1:1, and visualization with ninhydrin spray. The crude reaction mixture was evaporated to dryness under reduced pressure and the methyl esters were recrystallized from ethanol by the dropwise addition of diethyl ether to approximately 20% (v/v). y-N-Methylasparagine was synthesized by reaction of the aspartate methyl ester in 10 ml anhydrous methanol with 3 M equivalents of methylamine-HCl and 10 M equivalents of anhydrous triethylamine at 65°C for 48 h TABLE 2 Chromatographic

Separation

of Amino

Acids

Amino Asp Thr -y-NMA Ser b-NMG Gln Asn AspOCH, Glu GluOCH,

acid

Ion exchange” T, (min)

9.6 11.4 12.3 12.4 12.8 13.2 13.6 14.3 15.5 28.0

TLCb Rf 0.34 0.41 0.52 0.30 0.22 0.53 0.47 0.67

’ Amino acid separation by ion exchange was performed as described under Materials and Methods. ‘Thin-layer chromatography was performed on cellulose plates in ethanohacetic acidzwater, 8:1:1, by volume as described under Materials and Methods.

PROTEIN

SEQUENCE

TABLE ‘H NMR

Assignment

Multiplicity

y-NMA W-H 8-H 8’-H -AH, IS-NMG n-H 8-C% y-CH, d-CH3

q, dd, dd, s,

were

shift

Coupling

constant, (Hz)

4.4 4.8, 16 8.0, 16

r-NMA Asp MA 6-NMG Glu MA Response factors’ r-NMA/Asp &NMG/Glu AspOCH,/Asp GluOCHJGlu MA/Nle

97

RESIDUES 5

3.74 2.12 2.40 2.73

6.0 7.2

as described

under

J

Materi-

4

Quantitation

*

1.00 0.95 f 0.11 (4) 1.00 0.74 2 0.06 (2) 0.95 1.02 0.72 1.00 0.95

k + f f Ik

0.06 0.06 0.06 0.11 0.04

’ Amino acid analysis was performed as described under and Methods. b Molar yield t standard deviation. Values in parentheses the number of determinations. ’ See text.

Allophycocyanin p (64-73)”

Positiond

Recovery of Aspartic Acid, Glutamic Acid, and Methylamine on Acid Hydrolysis of r-NMA and &NMG” acid

ACID

Automated Sequential Edman Degradations of y-NMA-Containing Peptides

3.96 2.87 2.74 2.74

obtained

TABLE

AMINO

TABLE

in a sealed container. b-N-Methylglutamine was synthesized by reaction of 2 g pyroglutamate with 8.4 ml methylamine (free base) at 65°C for 96 h in a sealed container (17). The crude products in each case were evaporated under reduced pressure to a small volume and chromatographed on a lo-ml column of Dowex 5OW-X4 (18). The column was developed as follows: 10 ml of 10 mM HCl; 20 ml of H,O; 20 ml of 1 M ammonium acetate; 10 ml of 1 M ammonium hydroxide; and 10 ml of 0.1 N sodium hydroxide. The chromatographic fractions were then analyzed by thin-layer chromatography and ion-exchange chromatography (amino acid analysis) for the presence of the N-methylated derivatives which characteristically eluted in the first ammonium acetate

Amino

METHYLATED

3

Chemical bpm)

1H 1H 1H 3H

spectra

OF

Analysis”

t, 1H q, 2H m, 2H s, 3H

’ 400-MHz NMR als and Methods.

DETECTION

(6) (5) (3) (4) (4) Materials represent

64 65 66 67 68 69 70 71 72 73 74

Amino acid Ser Asp Ile Thr Av Pro QY GUY r-NMA Hse>

Yield bmol) 74 78 130 25 42 76 72 78 32 -

C-Phycocyanin (67-74) Amino acid

Ile Ala Pro Gly GUY r-NMA Ala Tyr

/3 * Yield (pmol)

104 110 74 91 73 50 80 29

B-Phycoerythrin (66-74)’ Amino acid

Leu Ile Ser Pro GUY QY r-NMA CYS Tyr

0

Yield (nmol)

2.08 3.44 0.33 2.64 1.28 1.28 1.04 0.92 1.20

’ 200 pmol of the Anabaena uariabilk peptide was applied to the disk in a Model 477A sequencer as described under Materials and Methods. The carboxyl terminal residue, homoserine plus homoserine lactone, was not identified. * 200 pmol of the Synechococcus PCC6301 peptide was applied to the disk in a Model 477A sequencer as described under Materials and Methods. ’ 4 nmol of the Porphyridium cruentum peptide was applied to the disk in a Model 470A sequencer as described under Materials and Methods. Cysteine was identified as the carboxymethyl derivative. ’ The homologous position using the C-phycocyanin sequence numbering system.

fraction off the Dowex column. The N-methyl derivatives were recrystallized from 80% aqueous ethanol (aspartate derivative) or 90% aqueous ethanol (glutamate derivative) by the dropwise addition of water. Six nanomoles of each methylated Acid hydrolysis. amino acid along with an equal amount of norleucine (used as an internal standard) were dissolved in 0.5 ml 6 N HCl, sealed in uacuo, and hydrolyzed for 22-24 h at llO-115°C. The samples were evaporated to dryness under reduced pressure and subjected to amino acid analysis by the procedure described below. Amino acid analysis. Amino acid analysis by ion-exchange chromatography employed a 3 X 250-mm, lo-pm cation-exchange column (Pickering Laboratories) operated at 45 or 65°C. An eluant system of sodium buffers was applied in steps of pH 3.28, 4.25, and 7.4 at a flow rate of 0.25 ml/min. The amino acids were reacted with o-phthalaldehyde prior to observation by an Isco FL-2 fluorescence detector equipped with a 305- to 395-nm colored glass excitation filter and a 430- to 470-nm wideband interference emission filter. Preparation of PTH derivatives. Manual preparation of PTH derivatives was performed by reacting 20

98

KLOTZ TABLE

6

PTH Derivatization and HPLC Analysis of Selected Amino Acids”

Reactant Asp Asn T-NMA Gln &NMG Glu AspOCH, GluOCH, Leu

Derivatized amino acid PTH-Asp PTH-Asn PTH-Asp PTH-y-NMA PTH-Asp PTH-Gln PTH-Glu PTH-&NMG PTH-Glu PTH-Glu PTH-AspOCH, PTH-Asp PTH-GluOCH, PTH-Glu PTH-Leu

LIPTH derivatives were prepared Materials and Methods. * Molar yield f standard deviation. the number of determinations. c Not detectable under conditions tion was estimated as approximately

T* (min)

Yield*

2.70 3.00 2.63 3.52 2.70 3.87 5.30 4.94 5.40 5.39 7.81 2.67 9.42 5.49 16.89 and analyzed Values

0.90 f 0.04 0.91 (1) 0.08 (1) 0.81 + 0.084