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A Palleschi

Publications and source records attributed to A Palleschi.

At least 37 records · Page 2Linked to original sources
PubMed1990

Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature.

The validity of a theoretical nearest-neighbor model based on conformational energy calculations, for translating the deterministic fluctuations of DNA base sequences in superstructural elements, is tested on the electrophoretic data of 450 multimeric, duplex oligonucleotides with different sequence, periodicity, and complexity, corresponding to all the experimental data so far published. An accurate semiempirical linear relation between the gel electrophoretic retardation and the dispersion of the theoretical curvature was found which allows a prediction of electrophoretic anomalies of DNA tracts, e.g., the cyclic permutation gel assays, with great confidence. Such a pattern of agreement allows the interpretation of the gel electrophoresis retardation as due to an increase of activation energy required in straightening the DNA axis.

DNA↗
PubMed1989

Periodical polydeoxynucleotides and DNA curvature.

A theoretical method to predict DNA curvature was developed, and a strikingly good correlation between the experimental retardations and theoretical curvature of all the periodical biosynthetic DNAs so far reported in the literature was found. The analysis has been extended to G- and C-rich synthetic polynucleotides, which show a behavior in agreement with the theoretical prediction. A possible application of the method to biologically significant DNA tracts is shown in the case of the regulative region of one of the genes which code for the small subunit of ribulose-1,5-bisphosphate carboxylase in Pisum sativum. While curvature measurements have not so far been reported for this system, biochemical analysis has indicated short nucleotide sequences (boxes I-III) as recognition sites for regulative proteins. On the basis of the theoretical curvature profile of the region and of the electrophoretic retardation measurements of synthetic polynucleotides, obtained by ligating monomers mimicking the boxes, we suggest that the proteins could use DNA local curvature as structural motif in the recognition process.

Base Composition↗
PubMed1989

Structure and stability of the Boc(D-Pro-L-Pro)2OCH3 Na+ complex: a model of poly(D,L-proline), an alkali ion channel across membranes.

In order to elucidate the molecular mechanisms of alkali ions conduction of poly(D,L-proline), which shows the typical behavior of an ion channel across membranes, conformations of the tetrameric derivative Boc(D-Pro-L-Pro)2OCH3 in solution, in the presence of the Na+ ion, were investigated by CD and nmr spectroscopy. Both theoretical and experimental data indicate the formation in solution of a monomeric complex between the tetramer, in the all-trans conformation, and the cation. The results allow to confirm the channel model, previously proposed on the phenomenological behavior of poly(D,L-proline) in membranes.

Hydrogen-Ion Concentration↗
PubMed1989

Stereoselective electron transfer between chiral substrates and metal chelates anchored to polypeptides.

Electron transfer from ortho-dihydroxy substrates, such as L(+)-ascorbic acid, L-adrenaline, and L-dopa, to iron(III) in [Fe(tetpy)(OH)2]+ ions anchored to sodium poly(L-glutamate) (FeTL) or poly(D-glutamate) (FeTD) was found to proceed stereoselectively when structurally ordered and partially shielded active sites prevent easy approach for redox partner. Oxidant-reductant interactions are then mediated by the polypeptide, whose conformational asymmetry ensures an efficient sterically discriminating environment. Evidence is produced that stereoselectivity chiefly arises from transition state effects, while thermodynamic discrimination is of minor importance. Theoretical models of the diastereomeric electron-transfer complexes were constructed by conformational energy calculations based on Coulombic, nonbonded, and hydrogen-bonded energy terms. The molecular parameters of the models enabled "differential" thermodynamic functions of the diastereomeric pairs and stereoselectivity to be evaluated and satisfactorily compared with those experimentally determined. The models give good insight into the observed topochemical phenomena and support the idea that stereoselectivity is coupled with a remote attack mechanism on the central metal ion where the peripheral tetpy ligand of the active sites acts as an electron-transfer agent.

Ascorbic Acid↗
PubMed1988

Preferential positioning of nucleosomes on pBR322 as evaluated via Fourier transform of data from electron microscopy.

Nucleosome positioning on pBR322 DNA has been evaluated by electron microscopy visualization, after psoralen cross-linking. The distribution function of nucleosomes on pBR322 DNA has been calculated analyzing the data of the electron microscopy via Fourier transform. This function shows definite maxima, which indicate differential interactions of the histone octamer to different DNA sequences.

Binding Sites↗
PubMed1988

A theoretical model of DNA curvature.

Distortions from the uniform idealized B-DNA structure are investigated in terms of differential interactions between adjacent nucleotide pairs on the basis of conformational energy calculations. A theoretical model of DNA curvature is proposed based on the evaluation of the curvature vector defined in the complex plane and the corresponding variance. The model appears to contain the basic physical features for translating the deterministic fluctuations of DNA sequences in superstructure elements. It allows the quantitative reproduction of all the available gel electrophoresis experiments on both periodical polynucleotides and tracts of DNAs as well as the theoretical prediction of the sequence dependent DNA writhing in good agreement with the experimental data. The general pattern of agreement between the theoretical and experimental data and the biological significance of the results obtained allow an extensive application of the model for the screening of DNA regions which are possible candidates for protein recognition.

DNA↗
PubMed1985

Poly(DL-proline), a synthetic polypeptide behaving as an ion channel across bilayer membranes.

The synthesis and characterization of poly(DL-proline) are reported in relation with its predicted property of forming ion channels across membranes. The analysis of the conductance induced in synthetic bilayer membranes doped with poly(DL-proline) shows ionic permeoselectivity and the characteristic time course of fluctuations of ion channels, according to the similarity with the active structure of gramicidin A in membranes during the ion passage. An alternative mechanism of ion transport across bilayer membranes is also advanced.

Electric Conductivity↗
PubMed1985

Channel structures in synthetic polypeptides with alternating configurations. Conformational analysis of poly(DL-proline).

Theoretical conformational analysis of L,D alternating sequences of poly alpha-amino acids is reported in connection with the ability of naturally occurring peptide and depsipeptide having alternating configurations to increase selectively the ion permeability across membranes. The most stable structures of poly(DL-proline), of which the conformational variability is practically limited to the choice between cis and trans conformations of the peptide bonds, were characterized. The all-trans conformation results in a flat helical structure possessing the main features for acting as an ion channel across membranes as actually found experimentally. Random cis-trans conformational sequences provide an alternative mechanism of ion transport intermediate between the ion channel and the ion carrier.

Journal Article↗