Use of liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) for routine identification of enzymatically digested proteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

Automated liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) analysis of >100 tryptic digests carried out on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) separated, Coomassie Blue-stained proteins that were prepared by >50 different laboratories demonstrates that a commercial electrospray/quadrupole ion trap mass spectrometer and the tandem mass correlation algorithm developed by Eng et al. (Am. Soc. Mass Spectrom. 1994, 5, 976-989) provide an extremely robust and facile approach to routine protein identification. By requiring a minimum of two significant matches to peptides that would be predicted to be produced by the protease that was used, low pmol levels of proteins can be identified with high confidence while minimizing the probability of identifying the protease itself and/or the ubiquitous contaminant, keratin. Hence, in only 7% of the digests analyzed was keratin identified and in only 5% of the digests analyzed was the protease itself identified. In contrast, 58% of the analyzed samples were identified and, in many instances, multiple proteins were identified in the same sample. Although the median amount of digest analyzed was 6.1 pmol, the limit of sensitivity (as the instrument is configured with a flow rate of 4 microL/min) appears to be at the 500 fmol level. Since one of the primary reasons for not identifying a sample is that its sequence is not yet in the database searched, the utility of an LC MS/MS approach to protein identification will certainly increase in the future as the sequences of more genomes are completed.

Identification of N(G)-methylarginine residues in human heterogeneous RNP protein A1: Phe/Gly-Gly-Gly-Arg-Gly-Gly-Gly/Phe is a preferred recognition motif.

Three sites of N(G),N(G)-arginine methylation have been located at residues 205, 217, and 224 in the glycine-rich, COOH-terminal one-third of the HeLa A1 heterogeneous ribonucleoprotein. Together with the previously determined dimethylated arginine at position 193 [Williams et al., (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 5666-5670], it is evident that all four sites fall within a span of sequence between residues 190 and 233 that contains multiple Arg-Gly-(Gly) sequences interspersed with phenylalanine residues. These RGG boxes have been postulated to represent an RNA binding motif [Kiledjian and Dreyfuss (1992) EMBO J. 11, 2655-2664]. Dimethylation of HeLa A1 appears to be quantitative at each of the four positions. Arginines 205 and 224 have been methylated in vitro by a nuclear protein arginine methyltransferase using recombinant (unmethylated) A1 as substrate. This suggests A1 may be an in vivo substrate for this enzyme. Examination of sequences surrounding the sites of methylation in A1 along with a compilation from the literature of sites that have been identified in other nuclear RNA binding proteins suggests a methylase-preferred recognition sequence of Phe/Gly-Gly-Gly-Arg-Gly-Gly-Gly/Phe, with the COOH-terminal flanking glycine being obligatory. Taken together with data in the literature, identification of the sites of A1 arginine methylation strongly suggests a role for this modification in modulating the interaction of A1 with nucleic acids.

Inactivation of inosine 5'-monophosphate dehydrogenase by the antiviral agent 5-ethynyl-1-beta-D-ribofuranosylimidazole-4-carboxamide 5'-monophosphate.

Inosine 5'-monophosphate dehydrogenase (IMPDH) is the rate-limiting enzyme in de novo guanine nucleotide biosynthesis. IMPDH converts inosine 5'-monophosphate (IMP) to xanthosine 5'-monophosphate (XMP) with concomitant conversion of NAD+ to NADH. The antiviral agent 5-ethynyl-1-beta-D-ribofuranosylimidazole-4-carboxamide (EICAR) is believed to inhibit IMPDH by forming an active metabolite, the 5'-monophosphate EICARMP. The experiments reported here demonstrate that EICARMP irreversibly inactivates both human type II and Escherichia coli IMPDH. IMPDH is protected from EICARMP inactivation by IMP, but not by NAD+. Further, denaturation/renaturation of the EICARMP-inactivated enzyme did not restore enzyme activity, which indicates that EICARMP forms a covalent adduct with IMPDH. EICARMP was successfully used to titrate the active sites of IMPDH; these experiments demonstrate that four active sites are present in an IMPDH tetramer. Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry of native E. coli IMPDH established that protein translation initiates at the third ATG of the DNA sequence. Thus, the E. coli IMPDH monomer is only 488 amino acids long and contains five instead of six cysteines. In addition, MALDI-TOF mass spectrometry showed that EICARMP is covalently bound to Cys-305 (Cys-331 in human type II IMPDH numbering), suggesting that Cys-305 functions as a nucleophile in the IMPDH reaction. The inactivation of the E. coli enzyme is a single-step reaction with kon = 1.94 x 10(4) M-1 s-1. In contrast, the inactivation of human type II IMPDH involves a two-step mechanism where Ki = 16 microM, k2 = 2.7 x 10(-2) s-1 and kon = 1.7 x 10(3) M-1 s-1. These results demonstrate that significant differences exist between bacterial and human IMPDH and suggest that this enzyme may be a target for antibiotic drugs.

Hydroxyarginine-containing polyphenolic proteins in the adhesive plaques of the marine mussel Mytilus edulis.

An unusual polymorphic protein family of nine or more variants has been isolated from the byssal adhesive plaques and foot of the marine mussel Mytilus edulis. In accordance with established terminology, the family is referred to as M. edulis foot protein 3 or simply Mefp-3. Variants of Mefp-3 have molecular masses of about 6 kDa, isoelectric points greater than 10.5, and an amino acid composition dominated by six amino acids: glycine, asparagine, 3,4-dihydroxyphenylalanine (Dopa), tryptophan, arginine, and an unknown basic amino acid. The latter has been isolated and identified as 4-hydroxyarginine using fast atom bombardment mass spectrometry and appropriate standards. The primary structure of variant Mefp-3F has been determined by peptide mapping using automated Edman sequencing in combination with fast atom bombardment and matrix-assisted laser desorption ionization mass spectrometry: ADYYGPNYGPPRRYGGGNYNRYNRYGRRYGGYKGWNNGWNRGRRGKYW where Y represents Dopa, and R represents hydroxyarginine. Notably, the 4 occurrences of RY are marked by a resistance to trypsin digestion. Although the conversion of tyrosines to Dopa is essentially complete, hydroxylation of arginines varies between 40 and 80%. In contrast to other mussel adhesive proteins such as Mefp-1 and -2 which have large numbers of highly conserved, tandemly repeated peptide motifs, Mefp-3 has only short sporadic repeats. The specific function of Mefp-3 in byssal adhesion is unknown.

The primary structure and properties of thioltransferase (glutaredoxin) from human red blood cells.

Thioltransferase (glutaredoxin) was purified from human red blood cells essentially as described previously (Mieyal JJ et al., 1991a, Biochemistry 30:6088-6097). The primary sequence of the HPLC-pure enzyme was determined by tandem mass spectrometry and found to represent a 105-amino acid protein of molecular weight 11,688 Da. The physicochemical and catalytic properties of this enzyme are common to the group of proteins called glutaredoxins among the family of thiol:disulfide oxidoreductases that also includes thioredoxin and protein disulfide isomerase. Although this human red blood cell glutaredoxin (hRBC Grx) is highly homologous to the 3 other mammalian Grx proteins whose sequences are known (calf thymus, rabbit bone marrow, and pig liver), there are a number of significant differences. Most notably an additional cysteine residue (Cys-7) occurs near the N-terminus of the human enzyme in place of a serine residue in the other proteins. In addition, residue 51 of hRBC Grx displayed a mixture of Asp and Asn. This result is consistent with isoelectric focusing analysis, which revealed 2 distinct bands for either the oxidized or reduced forms of the protein. Because the enzyme was prepared from blood combined from a number of individual donors, it is not clear whether this Asp/Asn ambiguity represents inter-individual variation, gene duplication, or a deamidation artifact of purification.