Biomedical subjects

S Clarke

Publications and source records attributed to S Clarke.

At least 325 records · Page 18Linked to original sources

PubMed1987

Deamidation, isomerization, and racemization at asparaginyl and aspartyl residues in peptides. Succinimide-linked reactions that contribute to protein degradation.

Aspartyl and asparaginyl deamidation, isomerization, and racemization reactions have been studied in synthetic peptides to model these spontaneous processes that alter protein structure and function. We show here that the peptide L-Val-L-Tyr-L-Pro-L-Asn-Gly-L-Ala undergoes a rapid deamidation reaction with a half-life of only 1.4 days at 37 degrees C, pH 7.4, to give an aspartyl succinimide product. Under these conditions, the succinimide product can further react by hydrolysis (half-time, 2.3h) and by racemization (half-time, 19.5 h). The net product of the deamidation reaction is a mixture of L- and D-normal aspartyl and beta-transpeptidation (isoaspartyl) hexapeptides. Replacement of the asparagine residue by an aspartic acid residue results in a 34-fold decrease in the rate of succinimide formation. Significant racemization was found to accompany the deamidation and isomerization reactions, and most of this could be accounted for by the rapid racemization of the succinimide intermediate. Replacement of the glycyl residue in the asparagine-containing peptide with a bulky leucyl or prolyl residue results in a 33-50-fold decrease in the rate of degradation. Peptide cleavage products are observed when these Asn-Leu and Asn-Pro-containing peptides are incubated. Our studies indicate that both aspartic acid and asparagine residues may be hot spots for the nonenzymatic degradation of proteins, especially in cells such as erythrocytes and eye lens, where these macromolecules must function for periods of about 120 days and 80 years, respectively.

Amino Acid Sequence↗

PubMed1987

Enzymatic methylation of band 3 anion transporter in intact human erythrocytes.

Band 3, the anion transport protein of erythrocyte membranes, is a major methyl-accepting substrate of the intracellular erythrocyte protein carboxyl methyltransferase (S-adenosyl-L-methionine: protein-D-aspartate O-methyltransferase; EC 2.1.1.77) [Freitag, C., & Clarke, S. (1981) J. Biol. Chem. 256, 6102-6108]. The localization of methylation sites in intact cells by analysis of proteolytic fragments indicated that sites were present in the cytoplasmic N-terminal domain as well as the membranous C-terminal portion of the polypeptide. The amino acid residues that serve as carboxyl methylation sites of the erythrocyte anion transporter were also investigated. 3H-Methylated band 3 was purified from intact erythrocytes incubated with L-[methyl-3H]methionine and from trypsinized and lysed erythrocytes incubated with S-adenosyl-L-[methyl-3H]methionine. After proteolytic digestion with carboxypeptidase Y, D-aspartic acid beta-[3H]methyl ester was isolated in low yields (9% and 1%, respectively) from each preparation. The bulk of the radioactivity was recovered as [3H]methanol, and the amino acid residue(s) originally associated with these methyl groups could not be determined. No L-aspartic acid beta-[3H]methyl ester or glutamyl gamma-[3H]methyl ester was detected. The formation of D-aspartic acid beta-[3H]methyl esters in this protein in intact cells resulted from protein carboxyl methyltransferase activity since it was inhibited by adenosine and homocysteine thiolactone, which increases the intracellular concentration of the potent product inhibitor S-adenosylhomocysteine, and cycloleucine, which prevents the formation of the substrate S-adenosyl-L-[methyl-3H]methionine.

Anion Exchange Protein 1, Erythrocyte↗

PubMed1987

The stereospecificity of protein kinases.

To test whether cellular protein kinases exist that phosphorylate D-amino acid residues, a method was developed for separating O-phospho-D-serine from O-phospho-L-serine and O-phospho-L-tyrosine from O-phospho-D-tyrosine. This was accomplished by converting these amino acids to the L-leucyl dipeptide derivatives followed by separation of the diastereomers by anion-exchange high-performance liquid chromatography. The enantiomeric content of these D- and L-residues were measured in hydrolysates of 32P-labeled proteins produced by the protein kinases of human erythrocytes and the tyrosyl protein kinase of the Abelson leukemia virus. We found no measurable D-phosphoserine in erythrocyte membrane proteins under conditions where a 1% content of this residue relative to L-phosphoserine would have been detected. These values can be used to place an upper hypothetical limit on the fraction of erythrocyte protein kinase activity that is specific for serine residues in the D-configuration. In separate experiments, we examined the specificity of the tyrosyl protein kinases. We found that all of the phosphotyrosine that we isolated from the erythrocyte band 3 NH2-terminal fragment and from the autophosphorylation of the Abelson virus tyrosyl kinase was in the L-configuration.

Blood Proteins↗

PubMed1987

Conversion of isoaspartyl peptides to normal peptides: implications for the cellular repair of damaged proteins.

The hypothesis that cellular protein carboxyl-methylation reactions recognize altered aspartyl residues as part of a protein repair pathway has been tested in an in vitro system using tetragastrin (Trp-Met-Asp-Phe-NH2) as a model sequence. The L-isoaspartyl form of tetragastrin, where the phenylalanine residue is linked to the side-chain carboxyl group of the aspartate residue ([iso-Asp3]tetragastrin), is a substrate for the erythrocyte protein carboxyl methyltransferases, while the normal form is not. The enzymatically produced alpha-methyl ester of [iso-Asp3]tetragastrin, [iso-Asp(OMe)3]tetragastrin, is unstable at pH 7.4 and 37 degrees C and spontaneously demethylates with a half-time of 41 min to an intermediate L-succinimide form ([Asu3]tetragastrin) that, in turn, spontaneously hydrolyzes with a half time of 116 min to give a mixture of normal tetragastrin (20%) and [iso-Asp3]tetragastrin (80%). This sequence of enzymatic and nonenzymatic reactions can be coupled in a single reaction mixture; the [iso-Asp3]tetragastrin that is produced upon succinimide hydrolysis can reenter the reaction sequence by enzymatic methylation, and the net result of the process is the conversion of the isomerized peptide to the normal peptide. The efficiency of this "repair" reaction is limited by a side reaction of racemization at the alpha-carbon of the succinimide (half-time = 580 min). In a 24-hr time period, normal L-aspartyl-containing tetragastrin is obtained in about 50% yield from the coupled reaction mixture; other products include [D-iso-Asp3]tetragastrin and [D-Asp3]tetragastrin. The versatile chemistry of succinimide peptides suggests that methylated L-isoaspartyl sites (and possibly methylated D-aspartyl sites) in cellular polypeptides can eventually yield "repaired" normal L-aspartyl sites through succinimide intermediates.

Animals↗

PubMed1987

Regulation of stage II of sporulation in Bacillus subtilis.

A mutation, spo-87, in the spo0J locus of Bacillus subtilis allows appreciable transcription of spoIIA, spoIID and spoIIG and later operons, even though most of the cells are morphologically blocked at stage 0 and the incidence of heat-resistant spores is about 1 per 10(4) cells. This mutation therefore appears to disengage the genetic control of sporulation from the morphological changes to which it should be connected. spoIIA and spoIIG are transcribed independently of one another. However, the products of both operons are needed for the activation of spoIID which occurs later. This indicates a convergence of parallel pathways of operon expression. We have also shown that nonsense mutations in spoIIAC (which codes for a sigma factor of RNA polymerase) prevent transcription of spoIID; by contrast, missense mutations in the same gene allow transcription of spoIID.

Alkaline Phosphatase↗

PubMed1987

Propensity for spontaneous succinimide formation from aspartyl and asparaginyl residues in cellular proteins.

One mechanism for the spontaneous degradation of polypeptides is the intramolecular attack of the peptide bond nitrogen on the side chain carbonyl carbon atom of aspartic acid and asparagine residues. This reaction results in the formation of succinimide derivatives and has been shown to be largely responsible for the racemization, isomerization, and deamidation of these residues in several peptides under physiological conditions (Geiger, T. & Clarke, S. J. Biol. Chem. 262, 785-794 (1987]. To determine if similar reactions might occur in proteins, I examined the sequence and conformation about aspartic acid and asparagine residues in a sample of stable, well-characterized proteins. There did not appear to be any large bias against dipeptide sequences that readily form succinimides in small peptides. However, it was found that aspartyl and asparaginyl residues generally exist in native proteins in conformations where the peptide bond nitrogen atom cannot approach the side chain carbonyl carbon to form a succinimide ring. These orientations also represent energy minimum states, and it appears that this factor may account for a low rate of spontaneous damage to proteins by succinimide-linked reactions. The presence of aspartic acid and asparagine residues in other conformations, such as those in partially denatured, conformationally flexible regions, may lead to more rapid succinimide formation and contribute to the degradation of the molecule. The possible role of isoimide intermediates, formed by the attack of the peptide oxygen atom on the side chain carboxyl group, in protein racemization, isomerization, and deamidation is also considered.

Asparagine↗

PubMed1986

Age-dependent accumulation of protein residues which can be hydrolyzed to D-aspartic acid in human erythrocytes.

We have measured the rate of accumulation of amino acid residues in human erythrocyte membrane and cytosolic proteins which give D-aspartic acid upon acid hydrolysis. These residues would include D-aspartic acid, D-asparagine, as well as the beta-transpeptidation product, D-isoaspartic acid. Measurements made using age (density) fractionated cells indicate that racemization at these residues occurs on membrane proteins with a t1% (the time required to convert 1% to the D configuration) of about 38.6 days. Fractionation of membrane components revealed a faster rate of racemization for intrinsic proteins than for extrinsic proteins. On the other hand, significant age-dependent racemization was not detected for cytosolic proteins, and the calculated t1% value for these proteins is at least 4 times larger. These results suggest that in the 120-day life span of an erythrocyte, significant racemization of membrane (but not cytosolic) proteins can occur. We have also determined that the rates of accumulation of these residues for erythrocyte membrane and cytosolic proteins incubated in vitro are similar to those observed in vivo. These observations are discussed in terms of the possible cellular metabolism of racemized proteins.

Asparagine↗

PubMed1986

Chemical conversion of aspartyl peptides to isoaspartyl peptides. A method for generating new methyl-accepting substrates for the erythrocyte D-aspartyl/L-isoaspartyl protein methyltransferase.

Mammalian protein carboxyl methyltransferases have recently been proposed to recognize atypical configurations of aspartic acid and may possibly function in the metabolism of covalently altered cellular proteins. Consistent with this proposal, the tetrapeptide tetragastrin, containing a single "normal" L-aspartyl residue (L-Trp-L-Met-L-Asp-L-Phe-NH2) was found here not to be an in vitro substrate for erythrocyte carboxyl methyltransferase activity. However, chemical treatment of tetragastrin by methyl esterification and then de-esterification of the aspartic acid residue yielded a mixture of peptide products, the major one of which could now be enzymatically methylated. We show here that this new peptide species is the isomeric beta-aspartyl form of tetragastrin (L-iso-tetragastrin; L-Trp-L-Met-L-Asp-L-Phe-NH2), and it appears that isomerization proceeds via an intramolecular succinimide intermediate during the de-esterification procedure. L-iso-Tetragastrin is stoichiometrically methylated (up to 90% in these experiments) with a Km for the enzyme of 5.0 microM. Similar chemical treatment of several other L-aspartyl peptides also resulted in the formation of new methyltransferase substrates. This general method for converting normal aspartyl peptides to isoaspartyl peptides may have application in the reverse process as well.

Amino Acid Sequence↗

PubMed1986

Organization of immature intrahemispheric connections.

In the adult cat injections of retrograde fluorescent tracers near the border between areas 17 and 18 and extending to the underlying white matter label neurons in restricted parts of nine other ipsilateral visual areas. A very similar, restricted distribution of retrograde labeling is found in newborn kittens when injections near the 17/18 border are confined to the cortical gray matter. When, however, the neonatal 17/18 border injection reaches the underlying white matter, more visual areas and numerous nonvisual areas become labeled, each of them over nearly its whole tangential extent. Labeled nonvisual areas include the primary and secondary auditory areas, the auditory areas of the posterior ectosylvian gyrus, areas 7 and 5, the cingulate gyrus, and the primary and secondary somatosensory areas. The widespread labeling in kittens was not due to larger or differently placed injections, since the distribution and extent of retrograde labeling in the ipsilateral lateral geniculate nucleus were similar at all ages. The transitory projections from the auditory and somatosensory areas are not reciprocated by a projection from areas 17 or 18. In kittens injected around the end of the first postnatal month the distribution of labeled association neurons is similar to that found in the adult; i.e., many of the juvenile projections have been eliminated. Only a few of the transitory axons to areas 17 and 18 enter the gray matter; the others remain confined to the white matter. Some of these axons were anterogradely labeled with rhodamine-B-iso-thiocyanate from the auditory cortex; they show bulbous endings, some of which are probably growth cones. Retrograde double-labeling experiments showed that, in the newborn, some neurons on the lateral sulcus have at least two long collaterals, one running rostrally, the other caudally; such branching is not observed in adults. In conclusion, areas 17/18 receive at birth from a large, continuous territory including areas, or parts of areas, which will later eliminate these projections. Most of the transitory projections do not appear to enter the cortex to any great extent. The major reshaping of association projections occurs before the end of the first postnatal month. The development of association projections resembles that of callosal projections.

Animals↗

PubMed1986

Methylation of calmodulin at carboxylic acid residues in erythrocytes. A non-regulatory covalent modification?

The physiological role of protein carboxy-group methylation reactions in human erythrocytes was studied with calmodulin as an endogenous methyl-group acceptor. The steady-state degree of calmodulin carboxy-group methylation is substoichiometric both in intact cells and in a lysed-cell system (about 0.0003 mol of methyl groups/mol of polypeptide). Purified erythrocyte calmodulin is a substrate for a partially purified erythrocyte carboxy-group methyltransferase and can be methylated to the extent of about 0.0007-0.001 mol of methyl groups/mol of polypeptide. This erythrocyte protein methyltransferase displays an apparent specificity for atypical racemized and/or isomerized D-aspartate and L-isoaspartate residues [McFadden & Clarke (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 2460-2464; Murray & Clarke (1984) J. Biol. Chem. 259, 10722-10732]. Exposure of calmodulin to elevated temperatures before methylation results in racemization of aspartate and/or asparagine residues, and may result in isoaspartate formation as well. The methylatability of these samples also increases as a function of time of heating, independent of the pH (over the range pH 5-9) or Ca2+ concentration; the most significant increase occurs during the initial 60 min, when calmodulin retains a fraction of its biological activity. These results are consistent with the hypothesis that methylation of calmodulin may occur at these uncommon aspartate residues, but are not consistent with a regulatory role for the methylation reaction.

Asparagine↗

PubMed1986

Metabolism of S-adenosyl-L-methionine in intact human erythrocytes.

Freshly isolated human erythrocytes contain S-adenosyl-L-methionine (AdoMet) at a concentration of about 3.5 mumol/l cells. When such cells are incubated in a medium containing 30 microM L-methionine, 18 mM D-glucose and 118 mM sodium phosphate (pH 7.4), intracellular AdoMet levels continuously decrease to a value of about 0.1 microM after 24 h. This occurs in spite of the fact that the cellular concentrations of the substrates for the AdoMet synthetase reaction, ATP and L-methionine, remain relatively constant. In a search for incubation conditions that lead to stable levels of AdoMet in incubated cells, we have developed a sodium-Hepes-buffered medium which includes 1 mM adenine and a stoichiometric excess of MgCl2 over its ligand, phosphate. The inclusion of magnesium ion (and a reduction in phosphate) appears to increase intracellular free Mg2+, which is required for full activity of the erythrocyte AdoMet synthetase. Even in the presence of MgCl2, however, the AdoMet pool level can drop 4-6-fold within the first 2 h of incubation. We present evidence that suggests that this initial fall in the cellular AdoMet level may be due to the activation of AdoMet-dependent protein carboxyl methyltransferase, an enzyme which accounts for a large fraction of the total cellular AdoMet utilization. Adenine, or related compounds in the medium may prevent this activation, although the mechanism of this action is not clear at present.

Adenine↗

PubMed1986

Carboxyl methylation of human erythrocyte band 3 in intact cells. Relation to anion transport activity.

The anion transport protein of the human erythrocyte membrane, band 3, is reversibly methylated by an endogenous protein carboxyl methyltransferase. The physiological consequence of this modification was studied by measuring the rate of phosphate transport by intact erythrocytes incubated under conditions where protein methylation reactions are inhibited. No change in phosphate transport was detected when cells were treated with either methionine-free media or cycloleucine, whereas cells incubated with adenosine and homocysteine thiolactone displayed a marginally slower rate of transport, which was not reversed by subsequent remethylation of the membrane proteins. These results suggest that erythrocyte protein carboxyl methylation does not directly regulate this activity of band 3.

Adenosine↗

PubMed1986

Metabolism of a synthetic L-isoaspartyl-containing hexapeptide in erythrocyte extracts. Enzymatic methyl esterification is followed by nonenzymatic succinimide formation.

The synthetic peptide, L-Val-L-Tyr-L-Pro-L-isoAsp-Gly-L-Ala, is a substrate for the erythrocyte and brain protein carboxyl methyltransferases. These enzymes catalyze the methyl esterification of the free alpha-carboxyl group of the isoaspartyl residue, to which the glycyl residue is linked through the side chain beta-carboxyl group. In this work, we show that the alpha-methyl ester of this peptide was rapidly demethylated (t1/2 = 4 min at 37 degrees C, pH 7.4) in erythrocyte cytosolic extracts and that the product of this reaction appears to be the succinimide ring derivative of the peptide. The rate of demethylation, measured at either pH 6.0 or 7.4, was the same in buffer and erythrocyte extracts, suggesting that succinimide formation was a nonenzymatic reaction. The L-succinimide is more stable than the ester, but can be hydrolyzed in buffer at pH 7.4 (t1/2 = 180 min at 37 degrees C) to give a mixture of about 75% isoaspartyl peptide and 25% normal aspartyl peptide. The metabolism of the succinimide hexapeptide in erythrocyte extracts appears to be more complex, however. The implications of this work for the methylation and demethylation of cellular proteins containing structurally altered aspartyl residues are discussed.

Chemical Phenomena↗

PubMed1986

Protein carboxyl methyltransferase and methyl acceptor proteins in aging and cataractous tissue of the human eye lens.

We have studied the enzymatic modification of proteins in human eye lens tissue where these molecules can be long-lived and can be exposed to non-enzymatic degradation processes for periods of time up to the age of the individual. We have detected a protein carboxyl methyltransferase that is similar to enzymes from other mammalian tissues which appear to catalyze the methyl esterification of altered aspartyl residues, including D-aspartyl and beta-isomerized L-aspartyl residues, but which have no activity on normal L-aspartyl sites. Upon gel filtration of human lens extracts, we find protein substrates for the lens methyltransferase in each of the major soluble classes of protein. In comparing individual lenses of various ages, protein carboxyl methyltransferase activity was present in tissue from all normal and yellow cataractous lenses tested, but was present only at very low apparent levels in brunescent lens tissue. We find that the methyltransferase is much more highly saturated by endogenous methyl acceptor substrates in lens extracts from older individuals, suggesting that the prolonged in vivo aging of lens protein leads to the accumulation and perhaps metabolism of altered aspartyl residues.

Adult↗

PubMed1986

An analysis of possible prognostic features of long term and short term survivors of metastatic breast cancer.

Factors influencing the extremes of survival in disseminated breast cancer were analysed. From a pool of 1066 patients with distant metastatic breast cancer, the 41 patients who had survived 5 yr or more from first distant recurrence were matched with the 41 patients with the shortest survival times. Both groups were compared with the pool and, where relevant, with each other. There were no differences with respect to presentation clinical stage, histological subtype, adjuvant therapy or the likelihood of menopause during the disease-free interval. There were significant differences in age, menopausal status, primary treatment, grade, pathological node involvement, time to recurrence, situation and number of sites of metastatic involvement, and response to treatment. The interpretation of these relationships as causal or casual is uncertain; however, given the magnitude of the survival differences, we expected the associated differences to be much greater than we found.

Adult↗

PubMed1986

Cognitive impairment in the elderly--a community survey.

Previous studies have suggested that up to a fifth of people over the age of 80 years may suffer severe dementia-like illnesses. This total population survey of over a thousand people over the age of 75 suggests that the prevalence of marked cognitive impairment is much less than expected. However, differences in the age structure, representativeness, response rates and size of the samples surveyed, together with differences in methods of measurement, make comparison between studies difficult.

Age Factors↗

PubMed1986

Rheumatoid arthritis: treatment which controls the C-reactive protein and erythrocyte sedimentation rate reduces radiological progression.

One hundred and fifty consecutive patients with active, rheumatoid arthritis were assessed and treated with gold, D-penicillamine, chloroquine or dapsone. Four groups were selected from these patients. Group I consisted of 60 patients who did not complete 12 months' therapy. Group II consisted of patients in whom ESR and C-reactive protein (CRP) fell to less than 30 mm/h and less than 20 mg/l, respectively, and remained at these levels between 6 and 12 months. In group IV the ESR and CRP fell but remained greater than 30 and greater than 20, respectively, during the same period. Group III patients had variable ESRs and CRPs between 6 and 12 months. In groups II, III and IV there was a significant deterioration (p less than 0.01) in the hand and foot radiographs from 0 to 6 months. Between 6 and 12 months the radiographs in groups III and IV continued to show significant radiological progression (p less than 0.01), but those of group II did not alter. These results suggest radiological deterioration continues during the first 6 months regardless of clinical response but thereafter, further deterioration is less likely to occur when the ESR and CRP are consistently controlled.

Arthritis, Rheumatoid↗

PubMed1986

Use of lacZ gene fusions to determine the dependence pattern of the sporulation gene spoIID in spo mutants of Bacillus subtilis.

The spoIID gene, which is involved in Bacillus subtilis sporulation, was fused to the beta-galactosidase gene, lacZ, of Escherichia coli so that the expression of beta-galactosidase would be under the control of the spoIID locus. When the fused product was inserted into the B. subtilis chromosome, production of beta-galactosidase indicated that the spoIID gene was expressed 1.5 h after the start of sporulation. When the spoIID::lacZ fusion was inserted into the chromosome of sporulation mutants, all strains carrying spo0 lesions and those with mutations in spoIIA, spoIIE and spoIIG loci failed to make beta-galactosidase. The proposed provisional order of expression of operons governing stage II is spoIIA----[spoIIG, spoIIE]----[spoIID, spoIIB, spoIIF].

Bacillus subtilis↗