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G Onori

Publications and source records attributed to G Onori.

At least 19 recordsLinked to original sources
PubMed2004

Picosecond internal dynamics of lysozyme as affected by thermal unfolding in nonaqueous environment.

A neutron-scattering investigation of the internal picosecond dynamics of lysozyme solvated in glycerol as a function of temperature in the range 200-410 K has been undertaken. The inelastic contribution to the measured intensity is characterized by the presence of a bump generally known as "boson peak", clearly distinguishable at low temperature. When the temperature is increased the quasielastic component of the spectrum becomes more and more intrusive and progressively overwhelms the vibrational bump. This happens especially for T > 345 K when the protein goes through an unfolding process, which leads to the complete denaturation. The quasielastic term is the superposition of two components whose intensities and linewidths have been studied as a function of temperature. The slower component describes motions with characteristic times of approximately 4 ps corresponding to reorientations of polypeptide side chains. Both the intensity and linewidth of this kind of relaxations show two distinct regimes with a crossover in the temperature range where the melting process occurs, thus suggesting the presence of a dynamical transition correlated to the protein unfolding. Conversely the faster component might be ascribed to the local dynamics of hydrogen atoms caged by the nearest neighbors with characteristic time of approximately 0.3 ps.

Elasticity↗
PubMed2004

Dielectric behavior of lysozyme and ferricytochrome-c in water/ethylene-glycol solutions.

This work deals with a dielectric study at radio frequencies of the influence at room temperature of two organic molecules, known as cryo-protectants, ethylene-glycol and glycerol, on conformational and dynamic properties of two model proteins, lysozyme (lys) from chicken egg-white and ferricytochrome-c (cyt-c) from horse heart. Cyt-c is a compact globular protein whereas lys is composed of two structural domains, separated by the active site cleft. Measurements were carried out at the fixed temperature of 20 degrees C varying the concentration of the cosolvent up to 90% w/w. From the analysis of the dielectric relaxation of the protein solution, the effective hydrodynamic radius and the electric dipole moment of the protein were calculated as a function of the cosolvent concentration. The data show that glycerol does not modify significantly the conformation of both proteins and cyt-c is also stable in the presence of ethylene-glycol. On the contrary ethylene-glycol strongly affects the dielectric response of lysozyme denoting a specific effect on its conformation and dynamics. The data are coherently interpreted hypothesizing that glycol molecule wedges between and separates the two domains of lys making them rotationally independent.

Animals↗
PubMed2001

Intrinsic structural differences between "tight couples" and Kaltschmidt-Wittmann ribosomes evidenced by dielectric spectroscopy and scanning microcalorimetry.

Measurements of dielectric spectroscopy (DS) and microcalorimetry (differential scanning calorimetry (DSC)) of Escherichia coli 70S, 50S and 30S were performed on particles prepared according either to the "classical" twice NH(4)Cl-washed ribosomes, also known as loose couples (LC), or to the "tight couples" preparative protocol (TC). Results show that 70S particles prepared according to the two different protocols exhibit different structural properties. Two subsequent relaxation processes occur in both samples as measured by DS. However, in LC ribosomes the first one is shifted towards a lower frequency with a higher dielectric increment. This is suggestive of a more extensive exposure of RNA to the solvent and of an overall more relaxed structure. The smaller LC subunit exhibits only one relaxation while the TC 30S shows two dielectric dispersions as well as 70S. No substantial differences were evidenced in either 50S species. Two typical melting peaks were observed by DSC both in LC and TC 70S as well as in 50S. Thermograms obtained from the TC 30S show a single well structured peak while LC particles produce a large unstructured curve. On the basis of these results we conclude that TC 70S particles are more compact than LC ribosomes and that in the former ones the rRNA is less exposed to the solvent phase. Furthermore 30S particles obtained from TC show a more stable structure with respect to LC 30S. We conclude that the 30S subunit gives a major contribution to the compact character of the whole TC 70S. These differences might be related to the intrinsic and well documented functional difference between the two ribosome species.

Calorimetry, Differential Scanning↗
PubMed2001

Structural characterization of the pH-denatured states of ferricytochrome-c by synchrotron small angle X-ray scattering.

The ferricytochrome-c (cyt-c) shows a complex unfolding pathway characterized by a series of stable partially folded states. When titrated with HCl at low ionic strength, two transitions are detected. At pH 2, cyt-c assumes the U1 unfolded state, whereas the successive addition of Cl(-) ion from either HCl or NaCl induces the recompaction to a molten globule conformation (A1 and A2 states, respectively). A second unfolded state (U2) is also observed at pH 12. Recent data evidence different features for the local structure of the heme in the different states. To derive relationships between local and overall conformations, we analyzed the structural characteristics of the different states by synchrotron small angle X-ray scattering. The results show that in the acidic-unfolded U1 form the protein assumes a worm-like conformation, whereas in the alkaline-unfolded U2 state, the cyt-c is globular. Moreover, the molten globule states induced by adding HCl or NaCl to U1 appear structurally different: in the A1 state cyt-c is dimeric and less compact, whereas in the A2 form the protein reverts to a globular-like conformation. According to the local heme structure, a molecular model for the different forms is derived.

Animals↗
PubMed2001

pH-dependent local structure of ferricytochrome c studied by x-ray absorption spectroscopy.

We have studied, using x-ray absorption spectroscopy by synchrotron radiation, the native state of the horse heart cytochrome c (N), the HCl denatured state (U(1) at pH 2), the NaOH denatured state (U(2) at pH 12), the intermediate HCl induced state (A(1) at pH 0.5), and the intermediate NaCl induced state (A(2) at pH 2). Although many results concerning the native and denatured states of this protein have been published, a site-specific structure analysis of the denatured and intermediate solvent induced states has never been attempted before. Model systems and myoglobin in different states of coordination are compared with cytochrome c spectra to have insight into the protein site structure in our experimental conditions. New features are evidenced by our results: 1) x-ray absorption near edge structure (XANES) of the HCl intermediate state (A(1)) presents typical structures of a pentacoordinate Fe(III) system, and 2) local site structures of the two intermediate states (A(1) and A(2)) are different.

Absorptiometry, Photon↗
PubMed2001

Solvent isotope effects on the phase-transition properties of lipid bilayers.

Highly sensitive differential scanning microcalorimetry (DSC) has been used to investigate the phase transition properties of lipid vesicles prepared from 1,2-distearoyl-L-3-glyceryl-phosphatidylcholine (DSPC) in H(2)O and D(2)O. The data show that the response of pre-transition properties to D(2)O-->H(2)O substitution is stronger than the main transition properties. We find that there is a small increase in the phase transition temperature (DeltaT approximately 0.5 K) and in the co-operative unit in the main transition. The increase in enthalpy (DeltaH congruent with1 kJ(.)mol(-1)) and in transition temperature (DeltaT congruent with2 K) observed in the pre-transition is comparable with that observed in quite different processes and systems, i.e. melting of nucleic acids and proteins and gel formation. It is suggested that D(2)O-->H(2)O substitution affects the thermal transition in these systems in such a way that the contributions of enthalpy and entropy to structural reorganization of water in these processes is modified.

Journal Article↗
PubMed2001

Rotational and translational dynamics of lysozyme in water-glycerol solution.

In this paper, we report a study of the effect of solvent viscosity on both translational and rotational dynamics of a simple model protein: the egg white lysozyme. For this, we investigated the dynamical properties of lysozyme in mixtures water-glycerol by means of parallel measurements of photon correlation spectroscopy (PCS) and dielectric spectroscopy at radiofrequencies (DS). In the framework of the Debye-Stokes-Einstein theory, the translational and rotational coefficients allow an estimation of hydrodynamic radius of the protein. A decoupling between translational and rotational dynamics, observed as a different estimation of hydrodynamic radius, is reported in the literature for some systems. In order to ascertain if this effect is present also in our sample, we performed PCS and DS measurements on lysozyme-water-glycerol solutions. The content of glycerol was in the range of 0-70% w/w, with a solvent viscosity from 0.9 to about 10 cpoise, and the protein concentration was up to 20 mg ml(-1). The average sizes of lysozyme, obtained by the two methods, are remarkably different at high protein concentrations. However, the values of hydrodynamic radius extrapolated to infinite dilution are coincident and independent of glycerol. These results indicate that the diffusive behavior of lysozyme in the water-glycerol mixture is coherent with the Debye-Stokes-Einstein hydrodynamic model.

Journal Article↗
PubMed2000

Structural stability of ribosomes subjected to RNase treatment evidenced by dielectric spectroscopy and differential scanning microcalorimetry.

Previous studies from our laboratory demonstrated the existence of at least two levels of structural complexity in E. coli 70S ribosomes. Ribosomal RNA seems to be principally involved in the overall stability of these structures. In this paper we present an investigation of ribosomes subjected to treatment with RNase. The study is based on both differential scanning microcalorimetry and dielectric spectroscopy. In the thermograms obtained on treated ribosomes only the low temperature peak of the two typical denaturation events observed in native ribosomes, is promptly eliminated by the enzyme treatment. Dielectric spectroscopy measurements carried out on the same samples indicate an alteration of the dielectric behavior previously shown to consist of two subsequent relaxation processes. In fact, only the low frequency relaxation is affected by the treatment. The second one, observed at higher frequency, remains unaltered. The same effect on the dielectric parameters is observed if the ribosome particles are heated and then cooled prior to measurement. These results are consistent with the idea that two different structures are present within the ribosome. One is very stable and withstands both temperature and RNase treatment while the second is promptly abolished by both treatments. Data presented here strongly suggest that the RNA domains exposed to the solvent play a fundamental role in the stability of the 3-D structure of the ribosome particle.

Calorimetry, Differential Scanning↗
PubMed2000

Differential scanning calorimetry of chromatin at different levels of condensation.

The thermal denaturation of calf thymus total chromatin and of fractions enriched in heterochromatin or euchromatin, has been investigated by differential scanning calorimetry and compared to that of calf thymus DNA and DNA-histone complexes. In our experimental conditions, chromatin melts in three thermal transitions: the main one, assigned to separation of the DNA double helix, occurs at 83 degrees C, while the other two occur at 63 degrees C and 74 degrees C. The data show that: (a) the transition enthalpy for denaturation of DNA in the total chromatin and in DNA-histone complexes is nearly the same as that of DNA in solution; (b) the transition at 63 degrees C is present in the thermogram of the heterocromatin enriched fraction, while it is completely absent in that of the euchromatin enriched one. The results suggest that this transition can be attributed to the higher order structures of heterochromatin.

Animals↗
PubMed1998

Differential stability of E. coli ribosomal particles and free RNA towards thermal degradation studied by microcalorimetry.

We investigated the thermal degradation of E. coli ribosomes by differential scanning microcalorimetry. The 70S particles show two distinctive and irreversible peaks upon thermal degradation. Free rRNA in solution produces, on the contrary, an unstructured denaturation profile. The thermal analysis of 50S particles shows a profile substantially identical to that observed in 70S, while 30S particles produce an unstructured denaturation pattern. Therefore the thermal behavior of the 70S particle is essentially attributable to the denaturation of the 50S subunit. Our data validate previous observations that the 50S has a more rigid structure as compared to 30S, which behaves as a 'floppy' particle. In addition our data suggest that protein/RNA interactions play a significant role to stabilize three-dimensional structures of the ribosome.

Calorimetry, Differential Scanning↗
PubMed1987

A spectrophotometric study of the binding of Cu(II) ions to ATP.

The interaction of copper(II) with adenosine triphosphate (ATP) has been studied as a function of pH in the range pH 3-12. Our approach is the study of the effect of binding both on the ATP ultraviolet absorption spectrum and on the optical d-d transition of copper ions. The results show that Cu(II)-ATP complexes exist in a variety of forms in equilibrium, the percentage of each species varying according to the state of ionization of the intrinsic adenine, phosphate and ribose groups. These results also show a close correlation between the rate of dephosphorylation of ATP in the presence of Cu(II) ions and Cu(II) bonding to the adenine of ATP, thus supporting the hypothesis that the metal-ion/nucleic-base interactions are crucial for the observation of a metal-ion promoted dephosphorylation of ATP (D.H. Buisson and H. Sigel, Biochim. Biophys. Acta 343 (1974) 45).

Adenosine Triphosphate↗
PubMed1986

Effect of ethanol on the thermal stability of tRNA molecules.

The thermal denaturation of E. coli unfractionated tRNA in ethanol/water mixtures has been studied as a function of alcohol concentration in the water-rich region (mole fraction of co-solvent chi 2 less than 0.2). The results show that with increasing alcohol concentration the melting temperature of tRNA first reaches a minimum at an intermediate composition chi *2 approximately equal to 0.055 and then increases with increasing chi 2. The value of chi *2 is close to that at which structural changes in the mixture occur as inferred from compressibility and optical absorption measurements. The present experimental data support the assumptions that the dominant mechanism by which ethanol affects the thermal stability of tRNA molecules is through its effect on the structure of water.

Drug Stability↗
PubMed1985

Electron paramagnetic resonance and optical spectroscopic study of the Cu2+-tRNA system.

The interaction of copper ions with tRNA has been studied by optical and EPR spectroscopies. The interaction results in two different paramagnetic complexes characterized by a tetragonal symmetry of the ligand electric field sensed by the ions. The complete set of the spin Hamiltonian parameters has been extracted by computer simulation with the Monte Carlo method. Hypotheses concerning the putative ligands are put forward.

Binding Sites↗