Aging of alpha-crystallins during development of the lens

Computational Analysis of the Mechanism of Nonenzymatic Peptide Bond Cleavage at the C-Terminal Side of an Asparagine Residue

The nonenzymatic peptide bond cleavage at the C-terminal side of Asn residues is a protein post-translational modification that occurs under physiological conditions. This reaction proceeds much slower than the deamidation of the Asn side chain and causes denaturation and hypofunction of proteins. The peptide bond cleavage of Asn is detected primarily in crystallins and aquaporin 0 in the eye lens. Therefore, cleavage is thought to be involved in age-related cataracts. In this study, to clarify the mechanism underlying succinimide formation for the peptide bond cleavage of the Asn residue, we performed quantum chemical calculations on the model compound Ace-Asn-Gly-Nme (Ace = acetyl and Nme = methylamino). The density functional theory with the B3LYP/6-31+G(d,p) level of theory was used to obtain optimized geometries. The results suggested that the reaction proceeds through two steps, cyclization and C-terminal fragment release, and the required proton transfers can be mediated by H₂PO₄ ^- and HCO₃ ^- ions. The conformational change of the main chain on the N-terminal side of Asn was needed for the C-terminal fragmentation step, and a separate conformational change at the C-terminal side was required for the cyclization step. Furthermore, the calculated activation barriers of the reactions catalyzed by the H₂PO₄ ^- ion (130 kJ mol^-1) and the HCO₃ ^- ion (123 kJ mol^-1) were sufficiently low for the reactions to occur under normal physiological conditions.

Mechanisms of Deamidation of Asparagine Residues and Effects of Main-Chain Conformation on Activation Energy

Deamidation of asparagine (Asn) residues is a nonenzymatic post-translational modification of proteins. Asn deamidation is associated with pathogenesis of age-related diseases and hypofunction of monoclonal antibodies. Deamidation rate is known to be affected by the residue following Asn on the carboxyl side and by secondary structure. Information about main-chain conformation of Asn residues is necessary to accurately predict deamidation rate. In this study, the effect of main-chain conformation of Asn residues on deamidation rate was computationally investigated using molecular dynamics (MD) simulations and quantum chemical calculations. The results of MD simulations for γS-crystallin suggested that frequently deamidated Asn residues have common main-chain conformations on the N-terminal side. Based on the simulated structure, initial structures for the quantum chemical calculations were constructed and optimized geometries were obtained using the B3LYP density functional method. Structures that were frequently deamidated had a lower activation energy barrier than that of the little deamidated structure. We also showed that dihydrogen phosphate and bicarbonate ions are important catalysts for deamidation of Asn residues.

Computational Studies on the Nonenzymatic Deamidation Mechanisms of Glutamine Residues

The nonenzymatic deamidation reactions of asparagine (Asn) and glutamine (Gln) residues in proteins are associated with protein turnover and age-related diseases. The reactions are also believed to provide a molecular clock for biological processes. Although Gln deamidation is assumed to occur through the glutarimide intermediate, the mechanisms for this are unclear because under normal physiological conditions, Gln deamidation occurs relatively less frequently and at a lower rate than Asn deamidation. We investigate the mechanisms underlying glutarimide formation from Gln residues, which proceeds in two steps (cyclization and deammoniation) catalyzed by phosphate and carbonate. We also compare these reactions with noncatalytic mechanisms and water-catalyzed mechanisms. The calculations were performed on the model compound Ace-Gln-Nme (Ace = acetyl, Nme = methylamino) using the density functional theory with the B3LYP/6-31+G(d,p) level of theory. Our results suggest that all the catalysts used in our study can mediate the proton relays required for glutarimide formation. We further determined that the calculated activation barriers of the reactions catalyzed by phosphate ions (115 kJ mol^-1) and carbonate ions (112 kJ mol^-1) are sufficiently low for the reactions to occur under normal physiological conditions. We also show that nucleophilic enhancement of Nme nitrogen is essential for the cyclization of Gln residues.

Structure-dependent nonenzymatic deamidation of glutaminyl and asparaginyl pentapeptides

Nonenzymatic deamidation rates for 52 glutaminyl and 52 asparaginyl pentapeptides in pH 7.4, 37.0 degrees C. 0.15 m Tris-HCl buffer have been determined by direct injection mass spectrometry. These and the previously reported 306 asparginyl rates have been combined in a self-consistent model for peptide deamidation. This model depends quantitatively upon peptide structure and involves succinimide, glutarimide and hydrolysis mechanisms. The experimental values and suitable interpolated values have been combined to provide deamidation rate values in pH 7.4, 37.0 degrees C. 0.15 m Tris-HCl buffer for the entire set of 648 single-amide permutations of ordinary amino acid residues in GlyXxxAsnYyyGly and GlyXxxGlnYyyGly. Thus, knowledge about sequence-dependent deamidation in peptides is extended to include very long deamidation half-times in the range of 2-50 years.

Subunit Exchange of Polydisperse Proteins

The small heat shock protein, alpha-crystallin, plays a key role in maintaining lens transparency by chaperoning structurally compromised proteins. This is of particular importance in the human lens, where proteins are exposed to post-translational modifications over the life-time of an individual. Here, we examine the structural and functional consequences of one particular modification of alphaA-crystallin involving the truncation of 5 C-terminal residues (alphaA(1-168)). Using novel mass spectrometry approaches and established biophysical techniques, we show that alphaA(1-168) forms oligomeric assemblies with a lower average molecular mass than wild-type alphaA-crystallin (alphaA(WT)). Also apparent from the mass spectra of both alphaA(WT) and alphaA(1-168) assemblies is the predominance of oligomers containing even numbers of subunits; interestingly, this preference is more marked for alphaA(1-168). To examine the rate of exchange of subunits between assemblies, we mixed alphaB crystallin with either alphaA(WT) or alphaA(1-168) and monitored in a real-time mass spectrometry experiment the formation of heteroligomers. The results show that there is a significant decrease in the rate of exchange when alphaA(1-168) is involved. These reduced exchange kinetics, however, have no effect upon chaperone efficiency, which is found to be closely similar for both alphaA(WT) and alphaA(1-168). Overall, therefore, our results allow us to conclude that, in contrast to mechanisms established for analogous proteins from plants, yeast, and bacteria, the rate of subunit exchange is not the critical parameter in determining efficient chaperone behavior for mammalian alphaA-crystallin.

Alpha B-crystallin exists as an independent protein in the heart and in the lens

Alpha B-crystallin, a polypeptide of molecular mass 22 kDa, is considered to be one of two subunits (alpha A and alpha B) of the multimeric lens-specific protein, alpha-crystallin. Recent demonstrations of the extra-lenticular presence of alpha B-crystallin have suggested that outside of the lens, this polypeptide may have functions independent of alpha A. Within the lens however, as part of the protein alpha-crystallin, its function is assumed to be structural. In an effort to investigate the functional status of alpha B-crystallin in the lens, we have characterized this polypeptide in the rat heart and the human lens. Unequivocal identity of alpha B-crystallin in the rat heart and the rat lens was established by the sequence analyses of the respective cDNA clones. Size exclusion chromatography (FPLC) and immunoblotting showed that in the rat heart, alpha B-crystallin exists as an aggregate of 300-400 kDa average molecular mass, similar to that of purified alpha B-crystallin isolated from bovine lens. Interestingly, analysis of the human lens proteins by immunoblotting showed that, with age, unlike alpha A-crystallin, the alpha B subunit remains detectable in the soluble fractions derived from normal lenses as old as 82 years. Importantly, the average molecular mass of the alpha B subunit in the soluble fractions prepared from 60-80-year-old human lens nuclei was also found to be 300-400 kDa. These data lead to the conclusion that alpha B-crystallin may exist as an independent protein not only in non-lens tissues (e.g. heart) but in the lens as well.

Protein distribution patterns in concentric layers from single bovine lenses: changes with development and ageing

Protein distribution patterns were determined in concentric layers removed from 24 bovine lenses ranging in age from about 6 months before birth to 180 months post-natal. It was possible to distinguish alterations in protein synthesis patterns during development and changes due to ageing, i.e., prolonged existence of the proteins. It was found that alpha-crystallin represents a constant 50% of the proteins synthesized by the fibre cells throughout life. However, the protein becomes progressively less soluble with increasing age. Beta-crystallin synthesis increases from 30% of the total proteins during prenatal development to around 40% in post-natal fibre cells. This increase is due to increased production of the beta-crystallin. In old tissues, beta H-crystallin is converted to a high molecular weight from (HMW beta) gamma-crystallins account for 22% of the proteins synthesized in the earliest prenatal fibre cells. This level decreases rapidly through prenatal development until they represent about 4% of the total at birth. Beta S-crystallin synthesis commences around this time and in the post-natal fibre cells is essentially the only low molecular weight protein. The possible significance of some of these changes is discussed with regard to the functional requirements of the lens.

Age associated decrease of N-acetyl-beta-glucosaminidase activity in the lens epithelial cells from C57Bl/6 mice

Lens epithelial cells were isolated from samples of C57BL/6 and CD-1 mice at different ages between 1 and 5 months, and assayed for the level of N-acetyl-beta-glucosaminidase and their ability to replicate in-vitro. The lens epithelial cells from C57BL/6 mice had a reduced replicative potential compared to other normal strains. A statistically significant decrease in active enzyme levels was demonstrated to be associated with increased animal age of C57BL/6 mice.

Human alpha-crystallin: characterization of the protein isolated from the periphery of cataractous lenses

alpha-Crystallin has been isolated from the peripheral region of old cataractous lenses. It was found to be closely related to bovine alpha-crystallin and to human newly synthesized alpha-crystallin in terms of its amino acid composition, the size of its polypeptide chains and the lack of free NH2-terminal groups. However, in contrast to the simple urea gel electrophoretic polypeptide patterns obtained with the reference proteins, 11 polypeptides were detected in the preparation. Ten of the polypeptides were isolated and shown to be either A or B chains on the basis of their amino acid compositions and comparison of the peptide maps of their tryptic hydrolysates. The four B chains as well as the six A chains were closely related, with most of the tryptic peptides being common to all members of their respective group. A nomenclature based upon the urea gel electrophoretic mobilites of the polypeptides has been proposed to define each chain. It was found that this alpha-crystallin preparation is composed of at least two populations of macromolecules, one of which contains macromolecules greater than 5 X 10(6) daltons on the basis of gel filtration with Bio-Gel A-5m. The compositions of the two fractions were found to be essentially identical.

The nature of the multiple forms of cytoplasmic aspartate aminotransferase from pig and sheep heart

Starch-gel electrophoresis of sheep heart aspartate aminotransferase was carried out over the range pH7.0-8.5. The enzyme separates into three subforms in the same way as the pig heart enzyme. As the pH was increased the distance migrated by each subform increased by the same amount, so that they remained the same distance apart. Titration of the enzyme over the appropriate pH range was used to calculate the difference in charge between the subforms and it was concluded that they differ by one charged group per dimer from their nearest neighbour on the electrophoretogram over the whole pH range studied. It was also shown that the pig-heart alpha and beta subforms differ by almost one charged group per dimer in the range pH5.5-5.7 and that the spacing between the subforms on starch-gel electrophoresis at pH8.0 is the same as that for the sheep enzyme. Since the charge difference between the subforms is maintained over such a wide range of pH, it is concluded that they probably differ from each other in covalent structure, because of the improbability that conformational differences can give rise to such behaviour. The relationship between the subforms and inactive binding of the coenzyme is also examined.

Acceleration of the rate of deamidation of GlyArgAsnArgGly and of human transferrin by addition of L-ascorbic acid

Experiments on the model peptide, GlyArgAsnArgGly, and the protein, human transferrin, have shown that hydrolytic deamidation of these molecules is markedly accelerated by addition of physiologically significant concentrations of l-ascorbic acid. Since hydrolytic demidation has been suggested as an important timer of biological events, the effects on hydrolytic deamidation of substances that are normally present in living organisms and are subject to nutritional control are of special relevance.

Inactive enzyme molecules in aging mice: liver aldolase

Evidence is presented that there is a considerable accumulation of inactive fructose-1,6-diphosphate aldolase (EC 4.1.2.7) in the liver of senescent mice. Liver aldolase was purified from 3-month-old mice and used to immunize rabbits. It was demonstrated with the monospecific antibody thus produced that the liver aldolase of young adult (3 month) and aged (31 month) mice are antigenically identical. With the antibody, inactive enzyme molecules (crossreacting material) in liver homogenate of old mice were detected. The liver aldolase of senescent mice had half as much active enzyme per mg of protein, as well as per antigenic unit, as did the liver aldolase of young adult mice. The accumulation of faulty enzyme molecules may be one of the causes of debilitation leading to senescence and death.

-Crystallin. Fractionation of subunits and sequence studies on an isolated polypeptide

alpha-Crystallin was carboxymethylated with radioactive iodoacetic acid in the presence of 7.6m-urea and then separated into six major fractions by chromatography on DEAE-cellulose in 7m-urea. Based on the amino acid compositions, specific radioactivities and sodium dodecyl sulphate-gel electrophoresis of the fractions, it was concluded that alpha-crystallin contains at least four different subunits: DU1A and DU1B, containing no cysteine; a third component represented by DU2B and DU3 containing one cysteine one cysteine residue per subunit; and DU4, which probably contains two residues of cysteine per subunit. Subunit DU1A was shown to be of sufficient purity for sequence studies. Cyanogen bromide cleavage yielded two peptides, CB-1 and CB-2, in approximately equal amounts as expected. The sum of the molecular weights and amino acid compositions of the peptides were both in excellent agreement with the results obtained for subunit DU1A. The amino acid sequence of the first sixteen residues of peptide CB-1 is: Ser-Leu-Thr-Lys-Asp-Phe-Asp-Glu-Val-Asn-Ile-Asp-Val-Ser-His-Phe-. The sequence of the first seventeen residues of peptide CB-2 is: Asp-Ile-Ala-Ile-Ser-His-Pro-Trp-Ile-Arg-Pro-Ser-Phe-Phe-Glu-Phe-His-. The N-terminal sequence of subunit DU1A was shown to be N-acetylmethionine followed by peptide CB-2.

Amino acid sequences around the cysteine residue of calf lens -crystallin

1. Calf lens alpha-crystallin was carboxymethylated with radioactive sodium iodoacetate to label the thiol group. 2. The protein was then digested with trypsin or alternatively fractionated in urea to obtain the acidic (A) chains, which were then digested with trypsin. Either procedure gave two radioactive peptides containing carboxymethylcysteine. 3. These two peptides were closely related: the longer form contained 28 amino acid residues, and the shorter lacked two residues at the N-terminal end of the longer form. 4. The amino acid sequence of the peptides have been determined. 5. No evidence for the presence of more than one cysteine residue/chain was found. 6. The question of the molecular weight of the chains is discussed.