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A Desideri

Publications and source records attributed to A Desideri.

At least 19 recordsLinked to original sources
PubMed2006

Structural dynamics of the mitochondrial ADP/ATP carrier revealed by molecular dynamics simulation studies.

The mitochondrial adenosine diphosphate/adenosine triphosphate (ADP/ATP) carrier has been recently crystallized in complex with its specific inhibitor carboxyatractyloside (CATR). In the crystal structure, the six-transmembrane helix bundle that defines the nucleotide translocation pathway is closed on the matrix side due to sharp kinks in the odd-numbered helices. The closed conformation is further sealed by the loops protruding into the matrix that interact through an intricate network of charge-pairs. To gain insight into its structural dynamics we performed molecular dynamics (MD) simulation studies of the ADP/ATP carrier with and without its cocrystallized inhibitor. The two trajectories sampled a conformational space around two different configurations characterized by distinct salt-bridge networks with a significant shift from inter- to intrarepeat bonding on the matrix side in the absence of CATR. Analysis of the geometrical parameters defining the transmembrane helices showed that even-numbered helices can undergo a face rotation, whereas odd-numbered helices can undergo a change in the wobble angle with a conserved proline acting as molecular hinge. Our results provide new information on the dynamical properties of the ADP/ATP carrier and for the first time yield a detailed picture of a stable carrier conformation in absence of the inhibitor.

Animals↗
PubMed2006

Gene expression profile study in CFTR mutated bronchial cell lines.

Cystic fibrosis (CF) is caused by mutations in the gene encoding the cystic fibrosis conductance transmembrane regulator (CFTR). Symptoms are pancreatic insufficiency, chronic obstructive lung disease, liver disease, chronic sinusitis and infertility in male patients. The phenotypic variability may be explained only in part by the more than 1200 CFTR mutations, which are grouped into six different classes, according to their effect on the protein ranging from a severe (no synthesis or blocked processing) to mild mutation (altered conductance or reduced synthesis). However, it is now accepted that other genes (CF modifiers) influence the phenotypic spectrum of the disease. In order to identify CF modifier genes, we built a low-density home-made oligoarray containing 144 genes selected according to biochemical criteria and evaluated their expression in two CF bronchial epithelial cell lines (CuFi1 F508del/F508del; CuFi3 F508del/R553X). If we consider both cell lines, 38 genes (26.3%) show an altered expression pattern with a threshold > +/-1.5. Of these 38 genes, 12 are altered in CuFi1, and 26 in CuFi3. Some of these genes share the same expression pattern in both cell lines, while others have a different behaviour. These results were validated by a QRT-PCR assay (R2 CuFi1 = 0.81 and R2 CuFi3 = 0.91). These data could suggest that the presence of a class I allele (R553X) determines a more profound alteration of gene expression pattern than the presence of a class II allele (F508del). The identification of the genes altered by a specific CF mutation could lead to the development of a pharmacological approach specific for different CFTR genotypes.

Alleles↗
PubMed2005

Evidence of domain formation in cardiolipin-glycerophospholipid mixed monolayers. A thermodynamic and AFM study.

The interaction of the three main components of the mitochondrial membrane, namely cardiolipin, phosphatidylcholine, and phosphatidylethanolamine, has been studied investigating mixed cardiolipin-phosphatidylcholine and cardiolipin-phosphatidylethanolamine monolayers at different cardiolipin molar fractions. The thermodynamic behavior of the mixed monolayers was investigated by means of surface pressure and surface potential measurements, and atomic force microscopy was employed to characterize the morphology of the monolayers. Langmuir isotherms and surface potential curves show a regular behavior with a progressive transition toward the isotherm of the pure component. Positive deviations from ideality in the excess Gibbs energies of mixing suggest the presence of repulsive interactions in both systems. Analysis of partial molecular dipole moment indicates a discontinuity at a definite cardiolipin/phosphatidylethanolamine molar fraction, suggesting the formation of a stoichiometric complex; as a consequence, in mixed cardiolipin-phosphatidylethanolamine monolayers, a phase separation is observed at phosphatidylethanolamine excess. AFM measurements indicate the presence of two domains: one made by phosphatidylethanolamine and the other by a regular arrangement of phosphatidylethanolamine and cardiolipin at a fixed molecular ratio.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2005

Experimental and simulative dissociation of dimeric Cu,Zn superoxide dismutase doubly mutated at the intersubunit surface.

The equilibrium properties of dimeric Photobacterium leiognathi Cu,Zn superoxide dismutase mutant bearing two negative charges in the amino acid clusters at the association interface has been studied, experimentally and computationally, and compared to those of the native enzyme. Pressure-dependent dissociation is observed for the mutant, as observed by the fluorescence shift of the unique tryptophan residue located at the intersubunit surface. The spectral shift occurs slowly, reaching a plateau after 15-20 min, and is fully reversible. Measurement of the degree of dissociation allows us to calculate the standard volume variation upon association and the dissociation constant at atmospheric pressure. On the other hand the native protein is undissociable at any pressure. In the simulative approach, the dissociation free energy has been calculated through the blue moon calculation method for the case of a multidimensional reaction coordinate, corrected for the rotational contribution within the semiclassical approximation for a free rigid-body rotor. The scheme permits to define a definite path for the rupture of the dimer and to calculate the effective force involved in the process. The calculated free energy difference is close to the experimental one, and the value obtained for the mutant is well below that obtained for the native protein, indicating that the theoretical reaction scheme is able to reproduce the experimental trend. Moreover, we find that, when the separation distance increases, the protein structure of the monomer is stable in line with the fast recovery of the original fluorescence properties after decompression, which excludes the presence of partly unfolded intermediates during the dimer-monomer transition.

Amino Acids↗
PubMed2005

Pre-discharge stress echocardiography and exercise ECG for risk stratification after uncomplicated acute myocardial infarction: results of the COSTAMI-II (cost of strategies after myocardial infarction) trial.

OBJECTIVE: To compare in a prospective, randomised, multicentre trial the relative merits of pre-discharge exercise ECG and early pharmacological stress echocardiography concerning risk stratification and costs of treating patients with uncomplicated acute myocardial infarction. DESIGN: 262 patients from six participating centres with a recent uncomplicated myocardial infarction were randomly assigned to early (day 3-5) pharmacological stress echocardiography (n = 132) or conventional pre-discharge (day 7-9) maximum symptom limited exercise ECG (n = 130). RESULTS: No complication occurred during either stress echocardiography or exercise ECG. At one year follow up there were 26 events (1 death, 5 non-fatal reinfarctions, 20 patients with unstable angina requiring hospitalisation) in patients randomly assigned to early stress echocardiography and 18 events (2 reinfarctions, 16 unstable angina requiring hospitalisation) in the group randomly assigned to exercise ECG (not significant). The negative predictive value was 92% for stress echocardiography and 88% for exercise ECG (not significant). Total costs of the two strategies were similar (not significant). CONCLUSION: Early pharmacological stress echocardiography and conventional pre-discharge symptom limited exercise ECG have similar clinical outcome and costs after uncomplicated infarction. Early pharmacological stress echocardiography should be considered a valid alternative even for patients with interpretable baseline ECG who can exercise.

Adult↗
PubMed2004

Role of the linker domain and the 203-214 N-terminal residues in the human topoisomerase I DNA complex dynamics.

The influence of the N-terminal residues 203-214 and the linker domain on motions in the human topoisomerase I-DNA complex has been investigated by comparing the molecular dynamics simulations of the system with (topo70) or without (topo58/6.3) these regions. Topo58/6.3 is found to fluctuate more than topo70, indicating that the presence of the N-terminal residues and the linker domain dampen the core and C-terminal fluctuations. The simulations also show that residues 203-207 and the linker domain participate in a network of correlated movements with key regions of the enzyme, involved in the human topoisomerase I catalytic cycle, providing a structural-dynamical explanation for the better DNA relaxation activity of topo70 when compared to topo58/6.3. The data have been examined in relation to a wealth of biochemical, site-directed mutagenesis and crystallographic data on human topoisomerase I. The simulations finally show the occurrence of a network of direct and water mediated hydrogen bonds in the proximity of the active site, and the presence of a water molecule in the appropriate position to accept a proton from the catalytic Tyr-723 residue, suggesting that water molecules have an important role in the stabilization and function of this enzyme.

Amino Acids↗
PubMed2004

Thermophilicity of wild type and mutant cold shock proteins by molecular dynamics simulation.

In the attempt to clarify possible mechanisms underlying thermal stability of proteins, we study through molecular dynamics thermophile Bc-Csp, mesophile Bs-CspB, and selected mutants. These proteins have been extensively characterized experimentally; researchers showed that differential thermostability among the wild type proteins is fundamentally linked to one or two mutated amino acids, and that the nature of the effect is electrostatic. They also inferred an atomistic mechanism related to removal of unfavorable interactions, rather than to the formation of salt bridges. Molecular dynamics allows us to confirm and support both hypotheses. Several other collective parameters have also been monitored in relation to thermophilicity, such as global and local rigidity, permanence and number of hydrogen bonds, or of salt links. None of these clearly correlates with the thermal stability of the presently studied proteins.

Bacillus↗
PubMed2003

Static and dynamic water molecules in Cu,Zn superoxide dismutase.

Understanding protein hydration is a crucial, and often underestimated issue, in unraveling protein function. Molecular dynamics (MD) computer simulation can provide a microscopic description of the water behavior. We have applied such a simulative approach to dimeric Photobacterium leiognathi Cu,Zn superoxide dismutase, comparing the water molecule sites determined using 1.0 ns MD simulation with those detected by X-ray crystallography. Of the water molecules detected by the two techniques, 20% fall at common sites. These are evenly distributed over the protein surface and located around crevices, which represent the preferred hydration sites. The water mean residence time, estimated by means of a survival probability function on a given protein hydration shell, is relatively short and increases for low accessibility sites constituted by polar atoms. Water molecules trapped in the dimeric protein intersubunit cavity, as identified in the crystal structure, display a trajectory mainly confined within the cavity. The simulation shows that these water molecules are characterized by relatively short residence times, because they continuously change from one site to another within the cavity, thus hinting at the absence of any relationship between spatial and temporal order for solvent molecules in proximity of protein surface.

Algorithms↗
PubMed2003

Active-site copper and zinc ions modulate the quaternary structure of prokaryotic Cu,Zn superoxide dismutase.

The influence of the constitutive metal ions on the equilibrium properties of dimeric Photobacterium leiognathi Cu,Zn superoxide dismutase has been studied for the wild-type and for two mutant protein forms bearing a negative charge in the amino acid clusters at the dimer association interface. Depletion of copper and zinc dissociates the two mutant proteins into monomers, which reassemble toward the dimeric state upon addition of stoichiometric amounts of zinc. Pressure-dependent dissociation is observed for the copper-depleted wild-type and mutated enzymes, as monitored by the fluorescence shift of a unique tryptophan residue located at the subunit association interface. The spectral shift occurs slowly, reaching a plateau after 15-20 minutes, and is fully reversible. The recovery of the original fluorescence properties, after decompression, is fast (less than four minutes), suggesting that the isolated subunit has a relatively stable structure, and excluding the presence of stable intermediates during the dimer-monomer transition. The dimer dissociation process is still incomplete at 6.5 kbar for the copper-depleted wild-type and mutated enzymes, at variance with what is generally observed for oligomeric proteins that dissociate below 3 kbar. Measurement of the degree of dissociation, at two different protein concentrations, allows us to calculate the standard volume variation upon association, Delta V, and the dissociation constant K(d0), at atmospheric pressure, (25 ml/mol and 3 x 10(-7)M, respectively). The holoprotein is fully dimeric even at 6.5 kbar, which allows us to evaluate a lower Delta G degrees limit of 11.5 kcal/mol, corresponding to a dissociation constant K(d0)<10(-9)M.

Binding Sites↗
PubMed2003

Prokaryotic Cu,Zn superoxide dismutases.

The Cu,ZnSODs (Cu,Zn superoxide dismutases) comprise a class of ubiquitous metalloenzymes that catalyse the dismutation of the superoxide radical anion into oxygen and hydrogen peroxide. The dismutation reaction involves two successive encounters of the superoxide anion with a catalytic copper centre hosted by the enzyme at the dead end of a narrow protein channel. Cu,ZnSOD is found in all eukaryotic species as a homodimeric enzyme of approx. 2x16 kDa. Cu,ZnSODs are also widely distributed in the prokaryotic phyla, and are found in the periplasmic space of bacterial pathogens, where they are likely to play a defensive role against extracellular oxidative stress, particularly with respect to phagocytic processes. The crystallographic structures of prokaryotic Cu,ZnSODs have shown that the core structural organization of the enzyme is based on a flattened antiparallel beta-barrel, composed of eight strands arranged in a Greek-key topological order, which usually forms a dimeric structure through the interaction of residues provided by beta-strands 4f and 5e with the 2,3 and 7,8 loops. The interface residues are arranged to form a closed ring, which surrounds a central cavity filled by water molecules that are arranged differently depending on the species. The interface variability of residues and solvent structure observed in bacterial enzymes permits fine tuning of the subunit association that results in the presence of monomeric and dimeric species, and confers a particular protein flexibility that gives rise to long-range communications between different region of the enzyme.

Catalysis↗
PubMed2003

Prognostic and clinical correlates of angiographically diffuse non-obstructive coronary lesions.

OBJECTIVE: To make a prospective assessment of the clinical and prognostic correlates of angiographically diffuse non-obstructive coronary lesions. DESIGN: Angiographic vessel and extent scores were calculated in 228 clinically stable patients (mean (SD) age, 60 (11) years; 43 women, 185 men) undergoing prospective follow up for the composite end point of death and myocardial infarction. The effect on outcome of clinical variables (age, sex, previous myocardial infarction, diabetes mellitus, smoking habit, systemic hypertension, hypercholesterolaemia, ejection fraction) and angiographic variables (vessel and extent score) was evaluated by Cox's proportion hazard model. RESULTS: The vessel score was 3 in 34 patients (15%), 2 in 78 (34%), 1 in 87 (38%), and 0 in 29 (13%). Median extent score was 60 (range 6-110; first quartile 40, third quartile 70). Forty one events (nine deaths and 32 myocardial infarcts) occurred over a median follow up period of 30 months. Age and extent score were the only multivariate predictors of outcome, but the latter provided 28% additional prognostic information after adjustment for the most predictive variables (gain in chi2 = 7, p < 0.01). A vessel score of 3 was associated with worse survival, while no significant discrimination was possible among the other groups. However, assignment of patients to two groups according to an ROC curve derived cut off value for the extent score made it possible to obtain significant discrimination of survival even in cases with vessel scores of 0 to 2. Age and diabetes were clinical markers of a higher extent score. CONCLUSIONS: The angiographic extent score is a powerful marker of adverse outcome independent of severity and the number of flow limiting coronary lesions, and may reflect the link between clinical risk profile and diffusion of coronary atherosclerosis. Thus it should be of clinical value for targeting aggressive preventive measures.

Aged↗
PubMed2002

Local dynamic properties of the heme pocket in native and solvent-induced molten-globule-like states of cytochrome c.

We report the Soret absorption band, down to cryogenic temperature, of native and molten-globule-like state of horse heart cytochrome c. The band profile is analyzed in terms of vibronic coupling of the heme normal modes to the electronic transition in the framework of the Franck-Condon approximation. From the temperature dependence of the Gaussian broadening and of the peak position, we obtain information on the 'bath' of low frequency harmonic motions of the heme group within the heme pocket. The reported data indicate that, compared to the native state, the less rigid tertiary structure of the molten globule is reflected in a higher flexibility of the heme pocket and in greater conformational disorder, allowing the transduction of large-amplitude motion of the protein to the dynamics of the heme pocket.

Binding Sites↗
PubMed2002

Flexibility in monomeric Cu,Zn superoxide dismutase detected by limited proteolysis and molecular dynamics simulation.

Limited proteolysis by trypsin of monomeric Cu,Zn superoxide dismutase from Escherichia coli induces a specific cleavage of the polypeptide chain at the level of Lys60 located in the S-S subloop of loop 6,5 where, when compared to the eukaryotic enzyme, a seven-residues insertion, completely exposed to the solvent, is observed. This result suggests that this subloop is disordered and flexible, thus enabling binding and adaptation to the active site of the proteolytic enzyme. Indeed, molecular dynamics simulation indicates that the S-S subloop undergoes high fluctuations and that its high flexibility coupled to an high solvent accessibility can explain the specific bond selection of the protease. As a matter of fact, of the possible 14 solvent accessible proteolytic sites only the Lys60 flexible site is cleaved. High flexibility and solvent exposure are confirmed by the short water residence time for the residues corresponding to the cleavage site evaluated by molecular dynamics simulation. These experiments demonstrate that molecular dynamics simulation and limited proteolysis are complementary and unambiguous tools to identify flexible sites in proteins.

Amino Acid Sequence↗
PubMed2001

Clinical and angiographic correlates of dobutamine-induced wall motion patterns after myocardial infarction.

The ability of different dobutamine-induced wall motion patterns to define the anatomic status of the infarct-related artery (IRA) was evaluated in 159 patients who underwent dobutamine stress echocardiography (DSE) and coronary angiography 10 +/- 2 and 18 +/- 3 days, respectively, after hospital admission. The DSE result was classified as: (1) biphasic: improvement with a low dose followed by deterioration with a high dose; (2) worsening: direct deterioration at low or high doses; (3) sustained improvement: improvement with a low dose that was maintained at high dose; and (4) no change: no change during the entire protocol. A diameter narrowing >70% (50% for the left main stem) of major coronary arteries indicated a severe lesion. Angiograms were classified according to the jeopardy score and collateral circulation graded according to Rentrop's classification. DSE was positive in 92 patients (22 had biphasic results and 70 had worsening results) and negative in 67 patients (14 had sustained improvement and 53 had no changes). Biphasic response was associated with more frequent anterior infarction (p <0.05) and higher resting (p <0.001) and peak (p <0.01) wall motion score indexes. The IRA was totally occluded in 4 of the 92 patients (4%) with positive (worsening pattern) and 12 of the 67 patients (18%) with negative (no change pattern) tests. The biphasic pattern was associated with the highest jeopardy score and was significantly (p <0.05) more specific (100%) compared with worsening (78%) in identifying a severe stenosis of the IRA. The combination of ischemic patterns provided a significantly superior sensitivity (p <0.0001). Logistic regression analysis identified the biphasic pattern as the only significant predictor. Conversely, the prediction of total occlusion of the IRA was poor. Sustained improvement was the most specific (100%) predictor of absence of severe stenosis of the IRA, whereas the combination with no change pattern provided a significantly superior sensitivity (p <0.0001). Thus, DSE effectively predicts the residual stenosis of the IRA. In particular, the biphasic response has an excellent specificity and positive predictive value and is the only significant predictor among clinical and echocardiographic variables.

Adrenergic beta-Agonists↗
PubMed2001

Dynamic features of the subunit interface of Cu,Zn superoxide dismutase as probed by tryptophan phosphorescence.

As part of the more general inquiry on the molecular basis of specific recognition between macromolecules, the subunit-subunit interface structure of dimeric superoxide dismutase from Photobacterium leiognathi has been probed selectively by the phosphorescence emission of Trp-73, located at the subunit contact region. Copper at the catalytic site was found to quench completely the delayed emission and therefore all studies were conducted with the copper-free or Cd(2+)-substituted protein. The spectrum at 140 K is diagnostic for an indole ring located in a hydrophobic environment whereas a degree of spectral broadening indicates that the local structure is not unique. Environmental heterogeneity is confirmed by the nonuniform phosphorescence decay in buffer, at 274 K, with lifetime components of 44 and 20 ms of practically equal amplitude. Information on the flexibility of the interface region was gathered from both the intrinsic lifetime and the accessibility of acrylamide to the site of the chromophore. The magnitude of the intrinsic lifetime, its temperature dependence, and the accessibility to solutes like acrylamide describe a tight dimeric structure in which hydrophobic interactions seem to play an important role. In particular the acrylamide bimolecular rate constant is 1.4 x 10(4) M(-1) s(-1) and indicates highly hindered diffusion of the solute through the interface region. Cd(2+) complexation to the apoprotein caused no detectable changes in protein conformation although the metal was able to influence the flexibility of the Trp-73 environment, indicating the occurrence of a long-range communication between the intersubunit surface and the active site, which is more than 16 A away.

Copper↗
PubMed2001

A novel heme protein, the Cu,Zn-superoxide dismutase from Haemophilus ducreyi.

Haemophilus ducreyi, the causative agent of the genital ulcerative disease known as chancroid, is unable to synthesize heme, which it acquires from humans, its only known host. Here we provide evidence that the periplasmic Cu,Zn-superoxide dismutase from this organism is a heme-binding protein, unlike all the other known Cu,Zn-superoxide dismutases from bacterial and eukaryotic species. When the H. ducreyi enzyme was expressed in Escherichia coli cells grown in standard LB medium, it contained only limited amounts of heme covalently bound to the polypeptide but was able efficiently to bind exogenously added hemin. Resonance Raman and electronic spectra at neutral pH indicate that H. ducreyi Cu,Zn-superoxide dismutase contains a 6-coordinated low spin heme, with two histidines as the most likely axial ligands. By site-directed mutagenesis and analysis of a structural model of the enzyme, we identified as a putative axial ligand a histidine residue (His-64) that is present only in the H. ducreyi enzyme and that was located at the bottom of the dimer interface. The introduction of a histidine residue in the corresponding position of the Cu,Zn-superoxide dismutase from Haemophilus parainfluenzae was not sufficient to confer the ability to bind heme, indicating that other residues neighboring His-64 are involved in the formation of the heme-binding pocket. Our results suggest that periplasmic Cu,Zn-superoxide dismutase plays a role in heme metabolism of H. ducreyi and provide further evidence for the structural flexibility of bacterial enzymes of this class.

Amino Acid Sequence↗
PubMed2001

Single mutations at the subunit interface modulate copper reactivity in Photobacterium leiognathi Cu,Zn superoxide dismutase.

The functional properties and X-ray structures of five mutant forms of Photobacterium leiognathi Cu,Zn superoxide dismutase carrying single mutations at residues located at the dimer association interface have been investigated. When compared to the wild-type enzyme, the three-dimensional structures of the mutants show structural perturbations limited to the proximity of the mutation sites and substantial identity of active site geometry. Nonetheless, the catalytic rates of all mutants, measured at neutral pH and low ionic strength by pulse radiolysis, are higher than that of the wild-type protein. Such enzymatic activity increase is paralleled by enhanced active site accessibility to external chelating agents, which, in the mutated enzyme, remove more readily the active site copper ion. It is concluded that mutations at the prokaryotic Cu,Zn superoxide dismutase subunit interface can transduce dynamical perturbation to the active site region, promoting substrate active site accessibility. Such long-range intramolecular communication effects have not been extensively described before within the Cu,Zn superoxide dismutase homology family.

Amino Acid Substitution↗