Biomedical subjects

M Bolognesi

Publications and source records attributed to M Bolognesi.

At least 55 records · Page 3Linked to original sources

PubMed2000

Arterioportal fistulas in patients with liver cirrhosis: usefulness of color Doppler US for screening.

PURPOSE: To evaluate the usefulness of routine ultrasonographic (US) evaluation of the hepatic arterial resistive and pulsatility indexes and of the direction of portal venous blood flow for the diagnosis of intrahepatic arterioportal fistulas (APFs) in patients with liver cirrhosis. MATERIALS AND METHODS: In all patients with cirrhosis examined at one center over 4 years, the resistive (RI) and the pulsatility (PI) indexes in the right and left branches of the hepatic artery were evaluated with Doppler US. An APF was suspected when an RI decrease of at least 20% and a PI decrease of at least 30% were present in one hepatic lobe relative to values in the other lobe and portal blood flow in the lobe with the decreased values was reversed. The RI and PI in patients with an APF were compared with those in 75 patients with cirrhosis and without APFs at angiography. RESULTS: Seven patients with an APF were identified. APFs suspected at Doppler US were always confirmed with angiography. The percent differences +/- SD in the RI and the PI between the two intrahepatic branches of the hepatic artery in patients with versus in patients without an APF were as follows: RI, 35% +/- 6 (range, 27%-42%) versus 5% +/- 4 (range, 0%-15%) (P: <.001); PI, 50% +/- 5 (range, 41%-58%) versus 11% +/- 7 (range, 0%-26%) (P: <.001). CONCLUSION: The intrahepatic arterial resistive and pulsatility indexes and the direction of portal blood flow should be evaluated in routine screening for APFs in patients with liver cirrhosis.

Adult↗

PubMed2000

Re-evaluation of amino acid sequence and structural consensus rules for cysteine-nitric oxide reactivity.

Nitric oxide (NO), produced in different cell types through the conversion of L-arginine into L-citrulline by the enzyme NO synthase, has been proposed to exert its action in several physiological and pathological events. The great propensity for nitrosothiol formation and breakdown represents a mechanism which modulates the action of macromolecules containing NO-reactive Cys residues at their active centre and/or allosteric sites. Based on the human haemoglobin (Hb) structure and accounting for the known acid-base catalysed Cys beta93-nitrosylation and Cys beta393NO-denitrosylation processes, the putative amino acid sequence (Lys/Arg/His/Asp/Glu)Cys(Asp/Glu) (sites -1, 0, and + 1, respectively) has been proposed as the minimum consensus motif for Cys-NO reactivity. Although not found in human Hb, the presence of a polar amino acid residue (Gly/Ser/Thr/Cys/Tyr/Asn/Gln) at the -2 position has been observed in some NO-reactive protein sequences (e.g., NMDA receptors). However, the most important component of the tri- or tetra-peptide consensus motif has been recognised as the Cys(Asp/Glu) pair [Stamler et al., Neuron (1997) 18, 691-696]. Here, we analyse the three-dimensional structure of several proteins containing NO-reactive Cys residues, and show that their nitrosylation and denitrosylation processes may depend on the Cys-Sy atomic structural microenvironment rather than on the tri- or tetra-peptide sequence consensus motif.

Amino Acid Sequence↗

PubMed1999

The X-ray three-dimensional structure of avidin.

Avidin is a basic, highly stable, homotetrameric protein, isolated from bird egg-white, binding up to four molecules of D-biotin with extremely high affinity (Kd approximately 10(-15) M). The protein has been the object of different crystallographic investigations. In all the crystal structures, the four avidin subunits display almost exact 222 symmetry. Each avidin chain (128 amino acids) is arranged in a eight-stranded antiparallel beta-barrel, whose inner region defines the D-biotin binding site. The molecular bases of D-biotin affinity can be recognised in a fairly rigid binding site, which is sterically complementary to the shape and polarity of the incoming vitamin, and is readily accessible in the apoprotein structure. Avidin displays remarkable structural and functional relationships to the acidic protein sretpavidin, isolated from Streptomyces avidinii.

Amino Acid Sequence↗

PubMed1999

Binding of non-catalytic ATP to human hexokinase I highlights the structural components for enzyme-membrane association control.

BACKGROUND: Hexokinase I sets the pace of glycolysis in the brain, catalyzing the ATP-dependent phosphorylation of glucose. The catalytic properties of hexokinase I are dependent on product inhibition as well as on the action of phosphate. In vivo, a large fraction of hexokinase I is bound to the mitochondrial outer membrane, where the enzyme adopts a tetrameric assembly. The mitochondrion-bound hexokinase I is believed to optimize the ATP/ADP exchange between glucose phosphorylation and the mitochondrial oxidative phosphorylation reactions. RESULTS: The crystal structure of human hexokinase I has been determined at 2.25 A resolution. The overall structure of the enzyme is in keeping with the closed conformation previously observed in yeast hexokinase. One molecule of the ATP analogue AMP-PNP is bound to each N-terminal domain of the dimeric enzyme in a surface cleft, showing specific interactions with the nucleotide, and localized positive electrostatic potential. The molecular symmetry brings the two bound AMP-PNP molecules, at the centre of two extended surface regions, to a common side of the dimeric hexokinase I molecule. CONCLUSIONS: The binding of AMP-PNP to a protein site separated from the catalytic centre of human hexokinase I can be related to the role played by some nucleotides in dissociating the enzyme from the mitochondrial membrane, and helps in defining the molecular regions of hexokinase I that are expected to be in contact with the mitochondrion. The structural information presented here is in keeping with monoclonal antibody mapping of the free and mitochondrion-bound forms of the enzyme, and with sequence analysis of hexokinases that differ in their mitochondria binding properties.

Adenosine Triphosphate↗

PubMed1999

Anticooperative ligand binding properties of recombinant ferric Vitreoscilla homodimeric hemoglobin: a thermodynamic, kinetic and X-ray crystallographic study.

Thermodynamics and kinetics for cyanide, azide, thiocyanate and imidazole binding to recombinant ferric Vitreoscilla sp. homodimeric hemoglobin (Vitreoscilla Hb) have been determined at pH 6.4 and 7.0, and 20.0 degrees C, in solution and in the crystalline state. Moreover, the three-dimensional structures of the diligated thiocyanate and imidazole derivatives of recombinant ferric Vitreoscilla Hb have been determined by X-ray crystallography at 1.8 A (Rfactor=19.9%) and 2.1 A (Rfactor=23.8%) resolution, respectively. Ferric Vitreoscilla Hb displays an anticooperative ligand binding behaviour in solution. This very unusual feature can only be accounted for by assuming ligand-linked conformational changes in the monoligated species, which lead to the observed 300-fold decrease in the affinity of cyanide, azide, thiocyanate and imidazole for the monoligated ferric Vitreoscilla Hb with respect to that of the fully unligated homodimer. In the crystalline state, thermodynamics for azide and imidazole binding to ferric Vitreoscilla Hb may be described as a simple process with an overall ligand affinity for the homodimer corresponding to that for diligation in solution. These data suggest that the ligand-free homodimer, observed in the crystalline state, is constrained in a low affinity conformation whose ligand binding properties closely resemble those of the monoligated species in solution. From the kinetic viewpoint, anticooperativity is reflected by the 300-fold decrease of the second-order rate constant for cyanide and imidazole binding to the monoligated ferric Vitreoscilla Hb with respect to that for ligand association to the ligand-free homodimer in solution. On the other hand, values of the first-order rate constant for cyanide and imidazole dissociation from the diligated and monoligated derivatives of ferric Vitreoscilla Hb in solution are closely similar. As a whole, ligand binding and structural properties of ferric Vitreoscilla Hb appear to be unique among all Hbs investigated to date.

Crystallography, X-Ray↗

PubMed1999

A SOD1 gene mutation in a patient with slowly progressing familial ALS.

We report a new missense mutation (Gly12Arg) [corrected] in exon 1 of the Cu/Zn superoxide dismutase (SOD1) gene in a 67-year-old patient with familial ALS (FALS). The clinical course showed an unusually slow progression. The enzymatic activity of the mutated SOD1 was 80% of normal. At the molecular level, the Gly12Arg [corrected] mutation occurs in a region outside the active site and may lead to local distortion strain in the protein structure.

Amyotrophic Lateral Sclerosis↗

PubMed1999

Evolutionary constraints for dimer formation in prokaryotic Cu,Zn superoxide dismutase.

Prokaryotic Cu,Zn superoxide dismutases are characterized by a distinct quaternary structure, as compared to that of the homologous eukaryotic enzymes. Here we report a newly determined crystal structure of the dimeric Cu,Zn superoxide dismutase from Photobacterium leiognathi (crystallized in space group R32, refined at 2.5 A resolution, R-factor 0.19) and analyse it in comparison with that of the monomeric enzyme from Escherichia coli. The dimeric assembly, observed also in a previously studied monoclinic crystal form of P. leiognathi Cu,Zn superoxide dismutase, is based on a ring-shaped subunit contact region, defining a solvated interface cavity. Three clusters of neighbouring residues play a direct role in the stabilization of the quaternary assembly. The present analysis, extended to the amino acid sequences of the other 11 known prokaryotic Cu,Zn superoxide dismutases, shows that at least in five other prokaryotic enzymes the interface residue clusters are under strong evolutionary constraint, suggesting the attainment of a quaternary structure coincident with that of P. leiognathi Cu,Zn superoxide dismutase. Calculation of electrostatic fields for both the enzymes from E. coli and P. leiognathi shows that the monomeric/dimeric association behaviour displayed by prokaryotic Cu, Zn superoxide dismutases is related to the distribution of surface charged residues. Moreover, Brownian dynamics simulations reproduce closely the observed enzyme:substrate association rates, highlighting the role of the active site neighbouring residues in determining the dismutase catalytic properties.

Amino Acid Sequence↗

PubMed1999

Cyanide binding to Lucina pectinata hemoglobin I and to sperm whale myoglobin: an x-ray crystallographic study.

The x-ray crystal structures of the cyanide derivative of Lucina pectinata monomeric hemoglobin I (L. pectinata HbI) and sperm whale (Physeter catodon) myoglobin (Mb), generally taken as reference models for monomeric hemoproteins carrying hydrogen sulfide and oxygen, respectively, have been determined at 1.9 A (R-factor = 0. 184), and 1.8 A (R-factor = 0.181) resolution, respectively, at room temperature (lambda = 1.542 A). Moreover, the x-ray crystal structure of the L. pectinata HbI:cyanide derivative has been studied at 1.4-A resolution (R-factor = 0.118) and 100 K (on a synchrotron source lambda = 0.998 A). At room temperature, the cyanide ligand is roughly parallel to the heme plane of L. pectinata HbI, being located approximately 2.5 A from the iron atom. On the other hand, the crystal structure of the L. pectinata HbI:cyanide derivative at 100 K shows that the diatomic ligand is coordinated to the iron atom in an orientation almost perpendicular to the heme (the Fe-C distance being 1.95 A), adopting a coordination geometry strictly reminescent of that observed in sperm whale Mb, at room temperature. The unusual cyanide distal site orientation observed in L. pectinata HbI, at room temperature, may reflect reduction of the heme Fe(III) atom induced by free radical species during x-ray data collection using Cu Kalpha radiation.

Animals↗

PubMed1999

Effect of chronic treatment with nadolol plus isosorbide mononitrate on liver blood flow and liver metabolic activity in cirrhosis.

OBJECTIVE: To assess the long-term effect of the addition of long-acting nitrates to beta-blockers on liver blood flow and liver metabolic activity in patients with cirrhosis and portal hypertension. METHODS: Eleven patients with cirrhosis and portal hypertension were investigated by using hepatic vein catheterization and indocyanine green (ICG) constant infusion on baseline conditions, after 1 month of treatment with nadolol, after 3 months of treatment with nadolol plus isosorbide mononitrate, and (in seven cases) after 1 year of combined treatment. RESULTS: The hepatic venous pressure gradient decreased significantly after nadolol, and more so after addition of isosorbide mononitrate. Hepatic blood flow, and ICG intrinsic hepatic clearance did not change significantly, although few cases showed an increase or decrease in either parameter. A significant correlation was found between changes in ICG intrinsic hepatic clearance and in hepatic venous pressure gradient (r = 0.62, P = 0.04). CONCLUSIONS: Liver blood flow and liver metabolic activity are not consistently affected by addition of isosorbide mononitrate to nadolol. Substantial decreases in portal pressure may be associated with a decrease in ICG intrinsic hepatic clearance.

Adrenergic beta-Antagonists↗

PubMed1999

Crystallization and preliminary crystallographic investigations of rhodanese from Azotobacter vinelandii.

The rhdA gene identified in Azotobacter vinelandii codes for a protein, RhdA, which displays rhodanese (thiosulfate-cyanide sulfurtransferase) activity. RhdA was overexpressed and purified to homogeneity. The protein crystallized in the orthorhombic space group P2(1)2(1)2 with unit-cell parameters a = 44.4, b = 150.8, c = 53.8 A; on a synchrotron source the diffraction patterns could be collected to a resolution limit of 1.8 A. Evaluation of the crystal density indicates that the crystal lattice accommodates one molecule per asymmetric unit and that the solvent content is 59% of the total volume.

Amino Acid Sequence↗

PubMed1999

The crystal structure of alpha-thrombin-hirunorm IV complex reveals a novel specificity site recognition mode.

The X-ray crystal structure of the human alpha-thrombin-hirunorm IV complex has been determined at 2.5 A resolution, and refined to an R-factor of 0.173. The structure reveals an inhibitor binding mode distinctive of a true hirudin mimetic, which justifies the high inhibitory potency and the selectivity of hirunorm IV. This novel inhibitor, composed of 26 amino acids, interacts through the N-terminal end with the alpha-thrombin active site in a nonsubstrate mode, and binds specifically to the fibrinogen recognition exosite through the C-terminal end. The backbone of the N-terminal tripeptide Chg1"-Arg2"-2Na13" (Chg, cyclohexyl-glycine; 2Na1, beta-(2-naphthyl)-alanine) forms a parallel beta-strand to the thrombin main-chain segment Ser214-Gly216. The Chg1" side chain occupies the S2 site, Arg2" penetrates into the S1 specificity site, while the 2Na13" side chain occupies the aryl binding site. The Arg2" side chain enters the S1 specificity pocket from a position quite apart from the canonical P1 site. This notwithstanding, the Arg2" side chain establishes the typical ion pair with the carboxylate group of Asp189.

Amino Acid Sequence↗

PubMed1999

Structural determinants of trypsin affinity and specificity for cationic inhibitors.

The binding free energies of four inhibitors to bovine beta-trypsin are calculated. The inhibitors use either ornithine, lysine, or arginine to bind to the S1 specificity site. The electrostatic contribution to binding free energy is calculated by solving the finite difference Poisson-Boltzmann equation, the contribution of nonpolar interactions is calculated using a free energy-surface area relationship and the loss of conformational entropy is estimated both for trypsin and ligand side chains. Binding free energy values are of a reasonable magnitude and the relative affinity of the four inhibitors for trypsin is correctly predicted. Electrostatic interactions are found to oppose binding in all cases. However, in the case of ornithine- and lysine-based inhibitors, the salt bridge formed between their charged group and the partially buried carboxylate of Asp189 is found to stabilize the complex. Our analysis reveals how the molecular architecture of the trypsin binding site results in highly specific recognition of substrates and inhibitors. Specifically, partially burying Asp189 in the inhibitor-free enzyme decreases the penalty for desolvation of this group upon complexation. Water molecules trapped in the binding interface further stabilize the buried ion pair, resulting in a favorable electrostatic contribution of the ion pair formed with ornithine and lysine side chains. Moreover, all side chains that form the trypsin specificity site are partially buried, and hence, relatively immobile in the inhibitor-free state, thus reducing the entropic cost of complexation. The implications of the results for the general problem of recognition and binding are considered. A novel finding in this regard is that like charged molecules can have electrostatic contributions to binding that are more favorable than oppositely charged molecules due to enhanced interactions with the solvent in the highly charged complex that is formed.

Animals↗

PubMed1999

The T-knot motif revisited.

The T-knot scaffold, a disulphide-reinforced structural motif shared by several proteins with very different biological functions, has been defined as 'a stretch of the protein chain which comprises two strands of a beta-sheet and three loops, knotted by two disulphides into the shape of the letter T'. In this communication we show that the presence of a central beta-sheet is not a required structural feature for proteins sharing the T-knot topology. Moreover, superposition of the three-dimensional structures of representative members of the T-knot family highlights a common and structurally well-defined core, formed by the two knotted disulphides, substituting for a larger residue-based hydrophobic core. These results suggest that folding and stability of the T-knot scaffold mainly depend on the geometry of the two knotted disulphides and on the loop length, and that the secondary structure elements are not a prerequisite for motif formation. Accordingly, a redefinition of the T-knot motif is proposed.

Amino Acid Sequence↗

PubMed1999

Portal hypertension: state of the art.

In the last decade, the knowledge of the pathogenesis of portal hypertension has increased dramatically. Indeed, apart from the well-known pathogenetic importance of structural factors, the role of vasoactive factors, which enhance the increase in intrahepatic resistance, has been highlighted. The two pathogenetic factors of portal hypertension are: the increase in portal outflow resistance and an increase in splanchnic blood flow, which worsens and maintains the increased pressure in the portal vein. The increase in portal inflow is part of the hyperdynamic circulatory syndrome, which is a haemodynamic characteristic of cirrhotic patients. In portal hypertensive patients, almost all the known vasoactive systems/substances are activated or increased and the most recent studies have stressed the importance of the endothelial factors, such as endothelins, nitric oxide and prostaglandins. Knowledge of the haemodynamic mechanisms allows a pathogenetic approach to the treatment of portal hypertension, particularly as far as medical therapy is concerned. The main categories of drugs used are: the vasoconstrictors (i.e., vasopressin, glypressin, somatostatin, non-selective beta-blockers), which act by decreasing portal inflow, and the vasodilators (i.e., nitroderivatives), which act mainly by decreasing intrahepatic portal resistance. Moreover, technological developments have introduced new tools for diagnosis, such as echo-colour-Doppler, and therapy, like variceal banding and transjugular intrahepatic porto-systemic shunt.

Hemodynamics↗

PubMed1998

GDP-4-keto-6-deoxy-D-mannose epimerase/reductase from Escherichia coli, a key enzyme in the biosynthesis of GDP-L-fucose, displays the structural characteristics of the RED protein homology superfamily.

BACKGROUND: The process of guanosine 5'-diphosphate L-fucose (GDP-L-fucose) biosynthesis is conserved throughout evolution from prokaryotes to man. In animals, GDP-L-fucose is the substrate of fucosyltransferases that participate in the biosynthesis and remodeling of glycoconjugates, including ABH blood group and Lewis-system antigens. The 'de novo' pathway of GDP-L-fucose biosynthesis from GDP-D-mannose involves a GDP-D-mannose 4,6 dehydratase (GMD) and a GDP-4-keto-6-deoxy-D-mannose epimerase/reductase (GMER). Neither of the catalytic mechanisms nor the three-dimensional structures of the two enzymes has been elucidated yet. The severe leukocyte adhesion deficiency (LAD) type II genetic syndrome is known to result from deficiencies in this de novo pathway. RESULTS: The crystal structures of apo- and holo-GMER have been determined at 2.1 A and 2.2 A resolution, respectively. Each subunit of the homodimeric (2 x 34 kDa) enzyme is composed of two domains. The N-terminal domain, a six-stranded Rossmann fold, binds NADP+; the C-terminal domain (about 100 residues) displays an alpha/beta topology. NADP+ interacts with residues Arg12 and Arg36 at the adenylic ribose phosphate; moreover, a protein loop based on the Gly-X-X-Gly-X-X-Gly motif (where X is any amino acid) stabilizes binding of the coenzyme diphosphate bridge. The nicotinamide and the connected ribose ring are located close to residues Ser107, Tyr136 and Lys140, the putative GMER active-site center. CONCLUSIONS: The GMER fold is reminiscent of that observed for UDP-galactose epimerase (UGE) from Escherichia coli. Consideration of the enzyme fold and of its main structural features allows assignment of GMER to the reductase-epimerase-dehydrogenase (RED) enzyme homology superfamily, to which short-chain dehydrogenase/reductases (SDRs) also belong. The location of the NADP+ nicotinamide ring at an interdomain cleft is compatible with substrate binding in the C-terminal domain.

Amino Acid Sequence↗

PubMed1998

A novel deamido-NAD+-binding site revealed by the trapped NAD-adenylate intermediate in the NAD+ synthetase structure.

BACKGROUND: Nicotinamide adenine dinucleotide (NAD+) has a central role in life processes. The ubiquitous enzyme NAD+ synthetase catalyzes a key step in NAD+ biosynthesis, transforming deamido-NAD+ into NAD+ by a two-step reaction. NAD+ synthetase belongs to the amidotransferase family and has been recognized as a member of the family of N-type ATP pyrophosphatases. In order to investigate the mechanism of the reaction carried out by NAD+ synthetase we have determined a high-resolution three-dimensional structure of the Bacillus subtilis homodimeric NAD+ synthetase in complex with the trapped reaction intermediate NAD-adenylate. RESULTS: Two NAD-adenylate molecules and two pyrophosphate (PPi) molecules are observed in the 1.3 A resolution structure of the NAD+ synthetase-NAD-adenylate complex. Structural studies on the NAD+ synthetase-NAD-adenylate adduct and on the cation-binding sites reveal a new deamido-NAD+-binding site located at the subunit interface, locate a binuclear magnesium cluster at the ATP-binding site and, identify two monovalent cation sites, one of which may represent an ammonium-binding site. CONCLUSIONS: Our results suggest that two different catalytic strategies have been adopted by NAD+ synthetase in the two different steps of the reaction. During the adenylation step, no protein residues seem to be located properly to directly participate in catalysis, which is likely to be carried out with the fundamental assistance of an electron-withdrawing trimetallic constellation present in the active site. A different behavior is observed for the second step, in which an ammonium ion is the binding species. In this step, Asp173 is a key residue in both deprotonation of the primarily bound ammonium ion, and stabilization of the tetrahedral transition-state intermediate. Moreover, the structural data suggest that product release can take place only after all substrates are bound to the enzyme, and product release is ultimately controlled by the conformation adopted by two mobile loops.

Adenosine Diphosphate Ribose↗

PubMed1998

Biochemical characterization and crystal structure of a recombinant hen avidin and its acidic mutant expressed in Escherichia coli.

The mature hen avidin encoded by a synthetic cDNA was expressed in Escherichia coli in an insoluble form. After resolubilization, renaturation and purification, a recovery of about 20 mg/l cell culture was obtained. ELISA assays indicated no apparent differences in biotin binding between the natural and recombinant avidins. In addition, an acidic avidin mutant, bearing the substitutions Lys3-->Glu, Lys9--> Glu, Arg26-->Asp and Arg124-->Leu of four exposed basic residues, was produced. The protein, expressed and renatured as wild-type avidin, showed unaltered biotin-binding activity. The acidic pI (approximately 5.5) and lack of aggregation of the mutant allowed easy electrophoretic analysis under non-denaturing conditions of the protein alone and of its complexes with biotin, biotinylated transferrin or peroxidase. Analysis of the sera from sensitized subjects revealed that the avidin mutant has altered antigenicity. Both recombinant avidins were crystallized and the three-dimensional structures solved by molecular replacement and refined to 0.22 nm resolution. The three-dimensional structures of the two recombinant molecules, in the absence of biotin and of glycosylation, are fully comparable with those of the natural hen avidin previously reported.

Animals↗

PubMed1998

On the coordination and oxidation states of the active-site copper ion in prokaryotic Cu,Zn superoxide dismutases.

The active-site copper ion of the prokaryotic Cu,Zn superoxide dismutase from P. leiognathi is found to undergo reversible reduction upon irradiation of the protein solution with a high-intensity X-ray beam from a third-generation synchrotron source. The same phenomenon is observed for the enzyme crystals, whose diffraction pattern has been obtained from synchrotron sources. In this case the active-site copper-ligand coordination bond lengths and in particular the Cu-NE2(His61) distance are consistent with a copper ion in the reduced state. These results are in line with previous studies on the eukaryotic Cu,Zn superoxide dismutases and suggest the conservation of an identical catalytic mechanism in both the prokaryotic and eukaryotic enzymes.

Animals↗