Age-related changes in oxidized proteins

We have previously described the oxidative inactivation of several key metabolic enzymes by a variety of mixed function oxidation systems. Because many of the enzymes which are inactivated have been shown by others to accumulate as inactive or less active forms during cellular aging, we have examined the levels of oxidatively modified proteins in two model systems used for studies on aging. The results show that levels of oxidatively modified proteins increase with age in circulating erythrocytes, and this change is correlated with the loss of marker enzyme activity. Our studies also show that in cultured fibroblasts from normal donors the levels of oxidatively modified proteins increase only after the age of 60. However, the levels of oxidatively modified proteins in fibroblasts from individuals with progeria or Werner's syndrome are significantly higher than age-matched controls. Moreover, treatment of glucose-6-phosphate dehydrogenase with a mixed function oxidation system leads to oxidative modification and increased heat lability of the enzyme. Taken together these results suggest that loss of functional enzyme activity and increased heat lability of enzymes during aging may be due in part to oxidative modification by mixed function oxidation systems.     

Tracing conformational changes in proteins

Background

Many proteins undergo extensive conformational changes as part of their functionality. Tracing these changes is important for understanding the way these proteins function. Traditional biophysics-based conformational search methods require a large number of calculations and are hard to apply to large-scale conformational motions.

Results

In this work we investigate the application of a robotics-inspired method, using backbone and limited side chain representation and a coarse grained energy function to trace large-scale conformational motions. We tested the algorithm on four well known medium to large proteins and we show that even with relatively little information we are able to trace low-energy conformational pathways efficiently. The conformational pathways produced by our methods can be further filtered and refined to produce more useful information on the way proteins function under physiological conditions.

Conclusions

The proposed method effectively captures large-scale conformational changes and produces pathways that are consistent with experimental data and other computational studies. The method represents an important first step towards a larger scale modeling of more complex biological systems.

     

pH-dependent conformational changes in thrombocyte proteins

A study was made of the medium pH influence on structural states of platelets by optical methods. Within the pH range (6-8), two pH induced reversible changes of platelet state were observed. A conclusion is made that the structural rearrangements in platelets induced in the medium by changes in hydrogen ion concentration may involve some rearrangements in platelet proteins, and thus acting as a factor regulating platelet function.     

Sodium-induced conformation changes in membrane transport proteins

In the presence of KCl, tryptic digestion of vesicles derived from pigeon erythrocyte membranes inactivates sodium-dependent uptake of alanine by the vesicles, whereas digestion in the presence of NaCl does not. Extensive degradation of vesicle proteins occurs under both conditions. Similarly, the extent of inhibition by N-ethylmaleimide of the sodium-dependent influxes of both glycine and alanine into human erythrocytes is greater when the cells are exposed to the thiol reagent in the presence of KCl than when NaCl is used. These observations are interpreted as providing evidence for sodium-induced conformation changes in these transport proteins.     

Conformational changes in human lens proteins in cataract

The reactivity of protein thiol groups in human lens and the susceptibility of the proteins to tryptic digestion were investigated. Both were found to be greater in some cataractous lenses, indicating that lens proteins have unfolded during cataractogenesis. Almost all the tyrosine in the proteins of the normal human lens reacts with tetranitromethane and is therefore probably on the outside of the major lens proteins.     

Age-related changes in plasma proteins of analbuminemic rats

A mutant strain, Nagase analbuminemia rats (NAR), was established from Sprague-Dawley rats. Age-related changes in plasma proteins of NAR were investigated to obtain information of their abnormalities of protein metabolism. The total protein concentration in the serum of NAR of various ages was almost the same as that of normal rats of the same age. The albumin level of NAR was less than 0.05 mg/ml at all ages examined. The concentrations of serum alpha 1-antitrypsin, alpha-X protein, alpha 2-macroglobulin, transferrin, ceruloplasmin, IgG, IgA and IgM were higher in NAR than in normal rats except for the perinatal stage, but alpha 1-acid glycoprotein level in NAR was normal. The serum transferrin and ceruloplasmin levels were especially high in female adult NAR. The plasma fibrinogen concentration was also increased in NAR. These findings indicate that the normal total serum protein level of NAR was maintained by increase in the globulin concentration.     

Developmental changes in membrane proteins from baboon erythrocytes

1. Total membrane proteins from freshly isolated erythrocytes of fetal, newborn, and adult baboons were analyzed by electrophoresis. 2. The electrophoretic patterns of proteins from newborns and adults were similar but those from adults and fetuses were different. 3. Four proteins, P165, P155, P75, and P49, with approximate mol. wts of 165,000, 155,000, 75,000, and 49,000, respectively, were present in adult but not in fetal samples. 4. P155 and P49, were glycoproteins; P49 was a cell-surface protein. 5. The membrane protein characteristics of the adult erythrocyte differ from those of the fetal erythrocytes and at least four polypeptides are associated with development of the adult phenotype.     

Ligand-induced changes in the binding sites of proteins

Classical molecular interaction potentials, in conjunction with other theoretical techniques, are used to analyze the dependence of the binding sites of representative proteins on the bound ligand. It is found that the ligand bound introduces in general small structural perturbations at the binding site of the protein. However, such small structural changes can lead to important alterations in the recognition pattern of the protein. The impact of these findings in docking procedures is discussed.     

Conformational changes and molecular mobility in plasticized proteins

Most biopolymers exist in a plasticized state, whether it is naturally with water or unnaturally with glycerol or other suitable polyol, to make a flexible material. We have found that the extent to which a biopolymer can be plasticized is dependent on its molecular and higher order structures outside of simply molecular weight. Lactalbumin, ovalbumin, corn zein, wheat gluten, and feather keratin were plasticized with glycerol from very low to very high amounts. The conformation of the proteins was monitored with Fourier transform-infrared (FT-IR) spectroscopy and X-ray powder diffraction (XRD) and correlated with the tensile modulus. Protein conformational changes were pronounced for polar proteins with a low amount of cysteine. FT-IR showed that the conformational changes resulted in ordering of the protein at low to moderate plasticization levels. For proteins with little resistance to conformational changes, additional small-scale ordering occurred around the glass transition, as observed in XRD. Accurate comparison of plasticized proteins was dependent on knowing whether or not the protein was glassy or rubbery at room temperature as no differences arose in the glassy state. The transition from glassy to rubbery behavior with plasticization level can be found from modulus, FT-IR, and XRD data.     

Developmental changes in cuticular proteins of Ascaris suum

1. Cuticles were isolated from developmental stages of the swine nematode Ascaris suum by a combination of mechanical disruption and detergent treatment of larvae or by surgical removal of cuticle from adults. Proteins from the isolated cuticles were solubilized with 2-mercaptoethanol (2ME) and analyzed by SDS-PAGE. 2. 2ME soluble, cuticular proteins from adults consisted of 5 to 6 bands with 80% of proteins in 2 bands with mol. wts of 106,000 and 93,000. Cuticular proteins from the third and fourth larval stages (L3 and L4) were comparable to adult, but differences in the number of bands were observed. The soluble proteins from the adult, L3 and L4 were readily degraded by a bacterial collagenase suggesting that these proteins are collagen-like structural elements of the cuticle. 3. The soluble proteins from the second stage (L2) differed from the adult and other larval stages in both the number and mol. wt of protein bands and their lack of degradation by bacterial collagenase. Amino acid composition of soluble cuticular proteins were similar for adult and L4, but glycine and proline were present in lower amounts in the L2. 4. These results support a hypothesis that there are stage specific differences in cuticular proteins from A. suum and that the greatest differences appear to exist between L2 and other stages.     

Insulin-induced changes in metabolism-related proteins during maize germination

Insulin regulates a wide range of metabolic processes in mammals, such as homeostasis and the breakdown of glucose. Recently, the existence of an insulin-related growth factor in maize (ZmIGF) and a possible receptor for this growth factor has been reported. This peptide exerts effects on plant growth and promotes germination by activating the target of rapamycin (TOR) signaling pathways, which is similar to the insulin response in mammals. In this study, we analyzed the insulin response in maize embryos using a proteomic approach. Our results indicated that insulin modulates the expression of proteins involved in processes, such as storage protein degradation, protein processing, redox and desiccation stress, and glucose metabolism. The involvement of TOR signaling pathways was analyzed using the TOR inhibitor, rapamycin. The results showed that the modulation of these proteins by insulin is independent of the TOR pathway. These results indicated that insulin promotes changes in metabolism-related proteins to ensure successful germination in maize.     

An NMR method for characterizing conformation changes in proteins

An NMR method for detecting and estimating the magnitude of conformation changes in proteins is described. By measuring both ¹⁹F and ¹H chemical shifts in a -CH₂F probe ring current shifts can be determined separately from shifts due to van der Waals interactions and electric fields. The method has been applied to lysozyme and a conformation change in a complex of the enzyme with β-methyl monofluoro-N-acetylglucosamine has been detected. The effect is due to the ionization of Asp 52, one of the catalytic groups, and the magnitude of the change is estimated to be about 1 Å. A mechanism for this conformation change is proposed.     

Disaggregation-induced changes of developmentally regulated proteins in Dictyostelium discoideum

By means of two-dimensional gel electrophoresis, we analyzed proteins present in a slug-shaped tissue mass of D. discoideum and examined the changes in their amounts after disaggregation of the slugs. Of approximately one hundred polypeptides, six were found to decrease in amount after disaggregation. The decreases of four polypeptides were inhibited by the presence of 1 mM cAMP or 250 micrograms/ml cycloheximide. The decreases of the two other proteins were not suppressed by cAMP or cycloheximide. The patterns of proteins present in vegetative and aggregative cells were also examined. None of the six proteins which showed a decrease after slug disaggregation was found in vegetative or preaggregative cells. These results indicate that both synthesis and degradation of these proteins are controlled by cell-cell contact.     

Time-dependent ultraviolet absorption changes in proteins at high pH

The effect of alkali on the ultraviolet absorption of several proteins was examined by difference spectrophotometry. In addition to the well known generation of phenolate ions from tyrosine, time-dependent changes occurred. These were relatively slow in water, but arose more quickly and to a greater degree in 6 M guanidine hydrochloride. These time-dependent changes were attributed to modification of the sulfur-containing amino acids, cystine and cysteine. The magnitude of the changes depended on the number and accessibility to solvent of the cystine, cysteine or derivatized species present. The increase in absorption at 295 nm typically reached a maximum value for disulfide containing proteins after ca. 1 h exposure to pH greater than 12 in 6 M guanidine hydrochloride; thereafter the changes were at least partially reversible. Taken in conjunction with amino acid analysis data, the results lend support to the beta-elimination mode of action of alkali on proteins. However the reaction mechanism appears to be complex and more than one chromophore, arising from more than one reaction pathway, seems to be involved in the alkaline degradation of the sulfur-containing amino acids. Particularly for proteins containing large amounts of cystine or cysteine, caution must be exercised when performing tyrosine titration experiments in order to recognize and minimize potential interference from other non-tyrosine related chromophores.