V O L. 5 3, N. 1 M A R C H 2004

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FORUM
Genesis and evolution of the first biochemistry (formato Acrobat)
F. Ranaldi, R. Ottaviani, D. Vanni, E. Guerin, E. Giachetti, P. Vanni

SIB news (formato Acrobat)

Alcohol and thermally oxidized pufa induced oxidative stress: role of n - acetyl cysteine
P. S. Varma, K. Aruna, R. Rukkumani, V. P. Menon
The Italian Journal of Biochemistry: 2004; 53(1): 10-15

Abstract. 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 g-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.

Entropy Calculator: getting the best from your multiple protein alignments
M. Ramazzotti, D. Degl'Innocenti, G. Manao, G. Ramponi
The Italian Journal of Biochemistry: 2004; 53(1): 16-22

Abstract. 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. Availability. The Perl source code of Entropy Calculator is available upon request to matteo.ramazzotti@unifi.it. A standalone compiled Win32 version of Entropy Calculator is available at www.unifi.it/unifi/scibio/bioinfo/zip_bin/EC331Setup.exe, together with the user manual. For more information see www.unifi.it/unifi/scibio/bioinfo/ent_man.html.

Influence of monosodium glutamate on circadian rhythms of lipid peroxidation products and antioxidants in rats
T. Manivasagam, P. Subramanian

The Italian Journal of Biochemistry: 2004; 53(1): 23-27

Abstract. 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.

4-hydroxy-2,3 trans-nonenal nuclear concentration inversely correlates with the growth rate of T leukemia cells
N. Calonghi, C. Cappadone, E. Pagnotta, C. Boga, C. Bertucci, J. Fiori, P. Traldi, L. Masotti1

The Italian Journal of Biochemistry: 2004; 53(1): 28-33

Abstract. 4-hydroxy-2,3 trans-nonenal is the major diffusible product generated by linoleic and arachidonic acids peroxidation. Its endogenous content is inversely related to the rate of cell proliferation and directly related to the level of cell differentiation. As previously reported, the nuclear localization of the aldehyde has been observed by means of a fluorescent antibody and confocal microscopy, and its concentration measured by electrospray/mass spectrometry, a sensitive and selective method for 4-hydroxy-2,3 trans-nonenal determination, on nuclear extracts of leukemic cells. With the aim to establish a possible correlation between the peroxidation product nuclear concentration and cell growth rate, Jurkat 6 leukemic cells have been used and the aldehyde measured by electrospray/mass spectrometry. The cells arrested in G1 show a content of 4-hydroxy-2,3 trans-nonenal significantly increased with respect to control ones.

Mutations in respiratory chain complexes and human diseases
V. B. Borisov
The Italian Journal of Biochemistry: 2004; 53(1): 34-40

Abstract. 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 b and 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.

The reaction mechanism of plant peroxidases
S. Longu, R. Medda, A. Padiglia, J. Z. Pedersen, G. Floris

The Italian Journal of Biochemistry: 2004; 53(1): 41-45

Abstract. 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-FeIII to form a very unstable peroxide complex, Compound 0; (b) oxidation of the iron to generate Compound I, a ferryl species with a p-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 molecule 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.

Roles for holes: are cavities in proteins mere packing defects?
B. Vallone, M. Brunori
The Italian Journal of Biochemistry: 2004; 53(1): 46-52

Abstract. 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.