The Italian journal of biochemistry最新文献

Amino acid sequence alignment is an extremely useful tool in protein family analysis. Most family characteristics, such as the localization of functional residues, structural constraints and evolutionary relationships may be retrieved through the observation of the conservation pattern highlighted by the alignments. A quantitative score for the conservation in the alignment allows different stages of an alignment to be compared and consequently the alignment information to be efficiently exploited. Many scoring methods have been proposed during the last three decades. Claude Shannon's theory of communication (1948) paved the way for a consistent scoring of protein alignments by considering the residue (or symbol) frequency. A number of modifications have been proposed since that time, but the core statistical approach is still considered one of the best. By combining many database managing tools for treatment of protein sequences, a ClustalW software integration, a flexible symbols treatment and gap normalization functions, Entropy Calculator software has been developed. This new tool provides a global and optimal approach to multiple sequence alignment scoring by offering an easy graphic interface and a series of modification options that help in interpreting alignments and allow conservation pattern inferences to be performed.

Literary evidence for a link between mutations in genes encoding respiratory chain components and human disorders is reviewed with particular emphasis on defects in respiratory complexes III and IV and their assembly factors. To date, mutations in genes encoding cytochrome band QP-C structural subunits of cytochrome bc1 complex; the BCS1L assembly factor for the bc1 complex; structural subunits I-III of cytochrome c oxidase; as well as the SURF-1, COX10, SCO1, and SCO2 assembly factors for cytochrome c oxidase, have been reported. These mutations are responsible for different neuromuscular and non-neuromuscular human diseases.

Monosodium glutamate (MSG) was administrated subcutaneously for 60 days to Wistar rats and 24h rhythms of thiobarbituric acid reactive substances (TBARS) and antioxidants such as reduced glutathione, superoxide dismutase and catalase were studied. MSG treatment was found to advance TBARS and to delay the acrophases of GSH and catalase. Amplitude and mesor values of these rhythms were found to be altered during MSG treatment. As glutamate levels in brain were found to be significantly increased (in MSG), we hypothesize that increased glutamate levels in brain could alter these biochemical rhythms probaly by modulating the transmission in several areas/nuclei in brain.

The catalysis of class III plant peroxidases is described based on the reaction scheme of horseradish peroxidase. The mechanism consists in four distinct steps: (a) binding of peroxide to the heme-Fe(III) to form a very unstable peroxide complex, Compound 0; (b) oxidation of the iron to generate Compound I, a ferryl species with a pi-cation radical in the porphyrin ring; (c) reduction of Compound I by one substrate molecule to produce a substrate radical and another ferryl species, Compound II; (d) reduction of Compound II by a second substrate molecute to release a second substrate radical and regenerate the native enzyme. Under unfavourable conditions some inactive enzyme species can be formed, known as dead-end species. Two calcium ions are normally found in plant peroxidases and appear to be important for the catalytic efficiency.

Atomic packing in proteins is not optimized, most structures containing internal cavities, which have been identified by molecular modelling and characterized experimentally. Cavities seem to play a role in assisting conformational changes between domains or subunit interfaces. Comparison between homologous proteins from thermophiles and mesophiles indicates that optimizing packing enhances stabilization at the expense of flexibility. For proteins which interact with small ligands or substrates, cavities seem to play a role in controlling binding and catalysis, rather than being mere "packing defects". We believe that a more complete analysis on the localization, conservation and role of cavities in protein structures (by modelling and site-directed mutagenesis), will reveal that rather than being randomly distributed, they are located in key positions to allow structural dynamics and thereby functional control.

Alcohol related disabilities are one of the world's major public health concerns. The effects of alcohol intake include alteration of redox state, acetaldehyde and free radical production, which lead to membrane damage. The damage caused by alcohol is enhanced by polyunsaturated fatty acid ingestion. When alcohol is taken along with thermally oxidized sunflower oil, the toxicity is still more pronounced due to toxic metabolites produced during heating. In our study, we have analysed the effects of a thiol supplier N-acetyl cysteine on alcohol, thermally oxidized sunflower oil and alcohol + thermally oxidized sunflower oil induced toxic effects in male Wistar rats. The activities of liver marker enzymes (alkaline phosphatase and gamma-glutamyl transferase), triglycerides in plasma and lipid peroxidative indices (thiobarbituric acid reactive substances and hydroperoxides) were increased in these groups when compared to normal, which were brought down in N-acetyl cysteine treated groups. The antioxidant status (Superoxide dismutase, catalase, reduced glutathione, glutathione peroxidase) was decreased in tissues of these groups, which were found to be improved in N-acetyl cysteine treated groups. Thus our results show that N-acetyl cysteine regresses the oxidative damage induced by Alcohol, thermally oxidized sunflower oil and alcohol + thermally oxidized sunflower oil.

Recent advances in the studies on protein aggregation have led to a reappraisal of the concepts underlying this process. The data reported in the last few years showing that protein aggregation into assemblies of amyloid type can be considered a generic property of the polypeptide chains suggest that protein aggregation in cells can be a more common phenomenon than previously believed. Furthermore, the findings that aggregates of disease-unrelated proteins display the same cytotoxicity as those formed by proteins and peptides associated with disease suggest that toxicity is a consequence of the common structure of aggregates and that, at least in most cases, it proceeds by impairing common cellular parameters such as free Ca2+ and ROS levels. The new view that aggregation of polypeptide chains and aggregate toxicity are not linked to specific amino acid sequences rises dramatically the number of sequences one can investigate to assess the molecular features underlying protein aggregation and the molecular basis of aggregate toxicity. In addition, it rises intriguing considerations on protein and cell evolution as well as on amyloid disease pathogenesis.

1H and 13C NMR spectroscopy was used to evaluate the degree of unsaturation and the cholesterol/cholesteryl ester ratio on the total lipid fractions obtained from human renal and cerebral tissues. The unsaturated/saturated fatty acid ratio was determined in the 13C NMR spectra from the ratio of the integrated areas of the resonances at 14.13 and 14.17 ppm assigned to the terminal methyl groups of saturated and unsaturated FA, respectively, and is validated by the traditional but time consuming gas-chromatographic analysis. Cholesteryl esters are easily discriminated in the total lipid fraction extracted from human tissues by means of the well-resolved component at 0.99 ppm (1H NMR spectra) of the resonance at about 1.00 ppm generally assigned to free cholesterol. The role of NMR spectroscopy in the study of lipidic biochemistry of human tissues is confirmed.

Oxidative stress has been implicated in mechanisms leading to neuronal cell injury in various pathological states of the brain. Alzheimer's disease (AD) is a progressive disorder with cognitive and memory decline, speech loss, personality changes and synapse loss. Many approaches have been undertaken to understand AD, but the heterogeneity of the etiologic factors makes it difficult to define the clinically most important factor determining the onset and progression of the disease. However, increasing evidence indicates that factors such as oxidative stress and disturbed protein metabolism and their interaction in a vicious cycle are central to AD pathogenesis. Brains of AD patients undergo many changes, such as disruption of protein synthesis and degradation, classically associated with the heat shock response, which is one form of stress response. Heat-shock proteins are proteins serving as molecular chaperones involved in the protection of cells from various forms of stress. Recently, the involvement of the heme oxygenase (HO) pathway in anti-degenerative mechanisms operating in AD has received considerable attention, as it has been demonstrated that the expression of HO is closely related to that of amyloid precursor protein (APP). HO induction, which occurs together with the induction of other HSPs during various physiopathological conditions, by generating the vasoactive molecule carbon monoxide and the potent antioxidant bilirubin, represents a protective system potentially active against brain oxidative injury. Given the broad cytoprotective properties of the heat shock response there is now strong interest in discovering and developing pharmacological agents capable of inducing the heat shock response. Recently, increasing interest has been focused on identifying dietary compounds that can inhibit, retard or reverse the multi-stage pathophysiological events underlying AD pathology. Alzheimer's disease, in fact, involves a chronic inflammatory response associated with both brain injury and beta-amyloid associated pathology. Spice and herbs contain phenolic substances with potent antioxidative and chemopreventive properties, and it is generally assumed that the phenol moiety is responsible for the antioxidant activity. In particular, curcumin, a powerful antioxidant derived from the curry spice turmeric, has emerged as a strong inducer of the heat shock response. In light of this finding, curcumin supplementation has been recently considered as an alternative, nutritional approach to reduce oxidative damage and amyloid pathology associated with AD. Here we review the importance of the heme oxygenase pathway in brain stress tolerance and its significance as antidegenerative mechanism operating in AD pathogenesis. We also discuss the role that exogenous antioxidant supplementation, conceivably, could play in AD in combating oxidative damage and compensating for the decreased level of endogenous antioxidants. Conceivably, dietary supple