The effect of ultraviolet irradiation on collagen-fold formation

1. A study has been made of the effect of ultraviolet irradiation, in the presence of air and nitrogen, on the conformational changes taking place in cooled solutions of gelatin prepared from thermally denatured neutral-salt-soluble collagen. 2. The increase in negative rotation and viscosity at 15 degrees for irradiated and thermally denatured solutions of collagen becomes less as the irradiation time is increased. 3. The principal effect of ultraviolet irradiation is the fission of the primary collagen peptide chains, eventually yielding chain lengths incapable of stabilizing a helical structure. 4. Irradiation in both air and nitrogen results in a loss of tyrosine, histidine and phenylalanine, with more denaturation occurring in the presence of nitrogen.     

Pathways and intermediates of amyloid fibril formation

The lack of understanding of amyloid fibril formation at the molecular level is a major obstacle in devising strategies to interfere with the pathologies linked to peptide or protein aggregation. In particular, little is known on the role of intermediates and fibril elongation pathways as well as their dependence on the intrinsic tendency of a polypeptide chain to self-assembly by β-sheet formation (β-aggregation propensity). Here, coarse-grained simulations of an amphipathic polypeptide show that a decrease in the β-aggregation propensity results in a larger heterogeneity of elongation pathways, despite the essentially identical structure of the final fibril. Protofibrillar intermediates that are thinner, shorter and less structured than the final fibril accumulate along some of these pathways. Moreover, the templated formation of an additional protofilament on the lateral surface of a protofibril is sometimes observed as a collective transition. Conversely, for a polypeptide model with a high β-aggregation propensity, elongation proceeds without protofibrillar intermediates. Therefore, changes in intrinsic β-aggregation propensity modulate the relative accessibility of parallel routes of aggregation.     

Carbohydrate carbonyl mobility--the key process in the formation of alpha-dicarbonyl intermediates

Covalently cross-linked proteins are among the major modifications caused by the advanced Maillard reaction. In the present study, the formation pathway of the dideoxyosone N6-(2,3-dihydroxy-5,6-dioxohexyl)-L-lysine is shown. To elucidate the formation of this glucose-derived dideoxyosone D-lactose (O-beta-D-galp-(1-->4)-D-glcp) and D-glucose-6-phosphate were incubated with lysine in the presence of the trapping reagent o-phenylenediamine (OPD). Synthesis and unequivocal structural characterization were reported for the quinoxalines of the dideoxyosones N6-(5,6-dihydroxy-2,3-dioxohexyl)-L-lysine and N6-(2,3-dihydroxy-4,5-dioxohexyl)-L-lysine, respectively. Additionally, dicarbonyl compounds derived from D-erythrose, D-glycero-D-mannoheptose, and D-gluco-L-talooctose were synthesized and structurally characterized.     

Structural changes during the formation of early intermediates in the bacteriorhodopsin photocycle

Early intermediates of bacteriorhodopsin's photocycle were modeled by means of ab initio quantum mechanical/molecular mechanical and molecular dynamics simulations. The photoisomerization of the retinal chromophore and the formation of photoproducts corresponding to the early intermediates were simulated by molecular dynamics simulations. By means of the quantum mechanical/molecular mechanical method, the resulting structures were refined and the respective excitation energies were calculated. Two sequential intermediates were found with absorption maxima that exhibit red shifts from the resting state. The intermediates were therefore assigned to the K and KL states. In K, the conformation of the retinal chromophore is strongly deformed, and the N--H bond of the Schiff base points almost perpendicular to the membrane normal toward Asp-212. The strongly deformed conformation of the chromophore and weakened interaction of the Schiff base with the surrounding polar groups are the means by which the absorbed energy is stored. During the K-to-KL transition, the chromophore undergoes further conformational changes that result in the formation of a hydrogen bond between the N--H group of the Schiff base and Thr-89 as well as other rearrangements of the hydrogen-bond network in the vicinity of the Schiff base, which are suggested to play a key role in the proton transfer process in the later phase of the photocycle.     

The presumption of proteolytic enzymes related to the formation of intermediates during the terminal differentiation

The [¹⁴C]Gly-labelled keratin polypeptides extracted with 1% SDS and 10 mM DTT were made to undergo changes with an enzyme fraction (ammonium sulfate, 50–75% saturated fraction) prepared from a human epidermis in the presence of 1% Triton X-100. In particular, 69-67 kDa peptides were considerably decreased with the above enzyme fraction in the time course experiments, and the components strongly bound to the cell membrane had little effect on the above reaction. In addition, in the case of the [¹⁴C]Gly-labelled keratin filament assembly, 69 and 62 kDa peptides were decreased and 55, 52 and 50 kDa peptides were increased with the same enzyme fraction in the time course experiments. From these results, we estimated that the proteolytic enzyme(s) may exist in the human epidermis, and may be processed to keratin intermediates from prekeratin during the initial stage of terminal differentiation in the human epidermis.     

Soluble fibrin-fibrinogen complexes as intermediates in fibrin gel formation

Oligomer formation in fibrinogen solutions following addition of thrombin was studied by addition of thrombin inhibitor at various times subsequent to thrombin, followed by size-exclusion chromatography (SEC) on a high-performance SEC column capable of resolving species of molecular weights less than or equal to 10(6). Peaks corresponding to species with 1, 2, 3, and 4 or more times the molecular weight of fibrinogen were detected and quantified via nonlinear least-squares curve-fitting procedures. The evolution of each of these peaks with time is well accounted for by a kinetic model in which the predominant component of each oligomeric molecular weight species is a linear complex of fibrinogen and fibrin. The observed predominance of trimeric over dimeric oligomers even at short times suggests that the thrombin-catalyzed release of the two A fibrinopeptides from a single molecule of fibrinogen is highly cooperative.     

Glycolytic intermediates induce amorphous calcium carbonate formation in crustaceans

It has been thought that phosphorus in biominerals made of amorphous calcium carbonate (ACC) might be related to ACC formation, but no such phosphorus-containing compounds have ever been identified. Crustaceans use ACC biominerals in exoskeleton and gastroliths so that they will have easy access to calcium carbonate inside the body before and after molting. We have identified phosphoenolpyruvate and 3-phosphoglycerate, intermediates of the glycolytic pathway, in exoskeleton and gastroliths and found them important for stabilizing ACC.     

Enzymatic formation of intermediates in the biosynthests of ajmalicine: Strictosidine and cathenamine

Pre-purified enzymes isolated from Catharanthus roseus suspension cultures synthesize strictosidine and cathenamine from tryptamine and secologanin. Whereas strictosidine showed metabolic activity, cathenamine accumulates during the cell-free incubations in the absence of reduced pyridine nucleotides. In the presence of δ-d-gluconolactone (0.1 M), strictosidine accumulates in a yield of ca 50%. Optimum conditions for its accumulation in crude extracts were found to be at pH 4.1, 0.25 mM tryptamine and 1.25 mM secologinin. Strictosidine synthase is stable for more than 1.5 months at 4°. The optimum conditions for the enzymatic synthesis of cathenamine are 1.54 mM tryptamine and 7.7 mM secologanin at pH 7.5. In the presence of NH₄⁺ the formation of the latter alkaloid decreases due to the synthesis of unidentified compounds.     

Proteolytic formation of either of the two prothrombin activation intermediates results in formation of a hirugen-binding site.

Hirugen, a synthetic dodecapeptide corresponding to the carboxyl-terminal amino acids 53-64 of hirudin, binds within a deep groove in thrombin that contains a cationic region referred to as the anion-binding exosite. This region is important in many of the binary interactions of thrombin with macromolecular substrates and cofactors. Fluorescein-labeled hirugen was used to probe which steps in the prothrombin activation process generate this anion-binding exosite. Two activation cleavage sites exist in bovine prothrombin. Cleavage at Arg274-Thr275 releases the activation fragments to generate the thrombin precursor, prethrombin 2. Cleavage of prothrombin within a disulfide loop at Arg323-Ile324 leads to formation of meizothrombin with no loss of peptide material but with formation of amidolytic activity. Cleavage of the same bond in prethrombin 2 generates thrombin. Hirugen, labeled at the amino terminus with fluorescein isothiocyanate, does not bind to prothrombin but does bind to thrombin (Kd = 9.6 +/- 1.2 x 10(-8) M), prethrombin 2 (Kd = 1.3 +/- 0.1 x 10(-7) M), thrombin-fragment-2 complex (Kd = 1.1 +/- 0.2 x 10(-6) M), and meizothrombin (Kd = 1.6 +/- 0.5 x 10(-8) M). Prothrombin fragment-2 and hirugen both bind independently to thrombin. A ternary complex can form with hirugen and fragment-2 and either thrombin or prethrombin 2, suggesting that fragment-2 and hirugen bind to discrete sites. Hirugen also alters the active site conformation of thrombin as detected by modulation of synthetic substrate hydrolytic activity. These studies suggest that conformational changes, rather than alleviating steric hindrance, are responsible for the formation of the hirugen-binding site during prothrombin activation. Furthermore, this conformational change can be effected by the cleavage of either of the two bonds required for activation of prothrombin.     

Reconstitution of collagen-fold structure with stretching of gelatin film

The gelatin film is stretched more 100% over 75% relative humidity, while the dried gelatin extended only several percent. In this experiment the gelatin film was stretched in a solution of water and ethanol. The sample was extended to 650% of its initial length when ethanol/water was 1.5(w/w) at 30°C. The wide-angle X-ray diffraction photographs of drawn samples showed the three important layer lines with approximate spacing of 10 Å, 4 Å, and 3 Å, which verify the reconstitution of collagen triple helical structure. The sharp spots appeared near 10 Å on the equatirial axis, indicating the high orientation of peptide chains. These patterns become sharp and clear on increasing the extension ratio. The content of the triple helix was investigated by wide-angle X-ray diffraction and differential scanning calorimetry. The maximum renaturation percentage is 25% at the draw ratio of 7.5. Since the formation of a collagen triple helix requires three chains, in which each chain has only three repeatin amino acids, (Gly-Pro-X)_n, and glycoprotein and other impurities interrupt helix formation, the more advanced renaturation will not be expected.     

The demonstration of ferrihemochrome intermediates in heinz body formation following the reduction of oxyhemoglobin A by acetylphenylhydrazone.

Interaction of acetylphenylhydrazine with oxyhemoglobin A in a hemolysate or in intact red cells resulted in the formation of ferrihemochromes as shown by a characteristic optical spectrum. The same optical spectrum was observed in a suspension of red cell ghosts containing numerous Heinz bodies. Electron paramagnetic resonance of actylphenylhydrazine-incubated red cells disclosed the presence of previously identified reversible ferrihemochromes, which can be reduced to functional hemoglobin, and irreversible ferrihemochromes, which cannot be reduced to functional hemoglobin. (Ferrihemochromes are defined as low spin forms of ferric hemoglobin having heme ligands endogenous to the protein structure). In contrast, only irreversible ferrihemochromes could be observed in ghosts containing Heinz bodies. In addition both optical and magnetic features of sulfhemoglobin were observed in an acetylphenylhydrazine-treated red cell hemolysate. Similar optical features are produced by the interaction of aromatic nitrogen-containg reductants with purified oxyhemoglobin in the presence of (NH4)2S. This reaction is not effected by the presence of catalase, suggesting that H2O2 is not an intermediate of the reaction. It is concluded that the mechanism of action of acetylphenylhydrazine with oxyhemoglobin is two-fold, ultimate reduction to high spin ferric hemoglobin followed by ferrihemochrome formation. Thus it appears that the pathway of denaturation of hemolytic anemias and thalassemia or induced by chemical reagents, entails a common route involving the formation of ferric hemoglobin by a reductive mechanism, followed by reversible ferrihemochromes, irreversible ferrihemochromes, and ultimately, precipitation.     

Bromine derivatives of amino acids as intermediates in the peroxidase-catalyzed formation of singlet oxygen

Recently, J. R. Kanofsky et al. (1988, J. Biol. Chem. 263, 9692-9696) reported that human eosinophils generated modest amounts of singlet oxygen. In the mechanism proposed, hypobromous acid (made from the peroxidase-catalyzed oxidation of bromide ion) reacted with hydrogen peroxide to form singlet oxygen. In contrast, human neutrophils, which generate both hypochlorous acid and hydrogen peroxide, do not make singlet oxygen. The failure of human neutrophils to generate singlet oxygen is due in part to the trapping of hypochlorous acid by endogenous amines. In this paper, I show that amino acids are much more effective traps for hypochlorous acid than for hypobromous acid. Glycine totally inhibits singlet oxygen generation from a model enzyme system composed of chloroperoxidase, hydrogen peroxide, and chloride ion, but causes only a 35% reduction in singlet oxygen generation from an analogous enzyme system containing bromide ion instead of chloride ion. The products of the reaction of hypobromous and glycine (presumably an equilibrium mixture of N-bromoglycine, N,N-dibromoglycine, and hypobromous acid) retain the ability to react with hydrogen peroxide to form singlet oxygen. In contrast, the products of the reaction of hypochlorous acid and glycine do not react with hydrogen peroxide to produce singlet oxygen. Similar results were obtained for L-alanine, L-arginine, L-asparagine, L-aspartic acid, L-cystine, L-glutamic acid, L-glutamine, L-histidine, L-lysine, L-phenylalanine, L-proline, L-serine, and L-tyrosine. Thus, bromine derivatives of amino acids may act as intermediates in the peroxidase-catalyzed generation of singlet oxygen.     

The formation and characteristics of China's existing system

Conclusion To sum up, the character of China's existing system is basically all-embracing totalitarianism formed by the combination of the old tradition of feudal-despotism and the new tradition of Stalinism. This system is the basic source of all the social evils in China.The ultimate aim of the democratic movement is to transform the old, allembracing totalitarian system and to establish a democratic, free, humane, and rational new system. The present ruling group is the beneficiary and defender of the existing system. The contradictions and conflicts between reformers who want to transform the old system and the hardliners who want to protect the old system formed the crux of the struggle of the 1989 democratic movement. Because the democratic movement lacked preparation in theory, organization, tactics and strategy, and because the ruling group controls the means of dictatorship — especially the army —military force was used to suppress the democratic movement with brutal bloodshed. In order to promote the democratic movement, we should sum up some lessons and experiences. First, we should study in depth the existing system and oppose feudaldespotism and Stalinism through effective propaganda and education. Second, we should arouse the democratic consciousness of the broad masses of the people, uniting with them and the healthy elements inside the Party, government, and army to struggle for the smashing of the old system and the establishment of a new system.Su Shaozhi is former Director of the Institute for the Study of Marxism-Leninism and Mao Zedong Thought, Chinese Academy of Social Sciences, Beijing, and currently Visiting Professor at the Bradley Institute for Democracy and Public Values, Marquette University, Milwaukee, Wisconsin     

The role of amino acid catabolism in the formation of the tricarboxylic acid cycle intermediates and ammonia in anoxic rat heart

Amino acid catabolism, the tricarboxylic acid cycle intermediates and ammonia formation were studied in isolated perfused rat heart under anoxia. The total net anaplerosis due to amino acid degradation in anoxia was equal to that in oxygenation (6.29 and 6.09 mumol/g dry weight per h, respectively) as a result of the increased transamination of glutamic and aspartic acids. During anoxic perfusion, the rate of catabolism of glutamic and aspartic acids was 1.5-times higher than in normoxia, while depletion of branched-chain amino acids, lysine, proline, arginine and methionine, was inhibited. Alanine was the product of excessive degradation of glutamic and aspartic acids. Under anaerobic conditions, in spite of inhibition of amino acid deamination, ammonia formation was increased 2.7-fold as compared to oxygenation. The principal amount of ammonia (96%) was produced at degradation of adenine nucleotides. A 2.5-fold increase in the pool of the tricarboxylic acid cycle intermediates under anoxia was associated mainly with accumulation of succinate. The data suggest that the coupling of alanine- and aspartate amino transferases is a mechanism controlling the tricarboxylic acid cycle pool size in anoxic heart.     

The effect of amino acid-modifying reagents on chloroplast protein import and the formation of early import intermediates

In order to identify functionally important amino acid residues in the chloroplast protein import machinery, chloroplasts were preincubated with amino-acid-modifying reagents and then allowed to import or form early import intermediates with precursor proteins. Incubation of chloroplasts with N-ethyl maleimide, diethyl pyrocarbonate, phenylglyoxal, 4,4'-di-isothiocyanatostilbene 2,2'-disulphonic acid (DIDS), dicyclohexylcarbodiimide (DCCD), and 1-ethyl- 3-dimethylaminopropylcarbodiimide (EDC) inhibited both import and formation of early import intermediates with precursor proteins by chloroplasts. This suggests that one or more of the binding components of the chloroplast protein import machinery contains functionally important solvent-exposed cysteine, histidine, arginine, and aspartate/glutamate residues, as well as functionally important lysine and aspartate/ glutamate residues in a hydrophobic environment.