The Experts below are selected from a list of 5703 Experts worldwide ranked by ideXlab platform
Francesco Salvatore - One of the best experts on this subject based on the ideXlab platform.
-
five human phenylalanine hydroxylase proteins identified in mild hyperphenylalaninemia patients are disease causing variants
Biochimica et Biophysica Acta, 2008Co-Authors: Aurora Daniele, Adriana Zagari, Giuseppe Cardillo, Cinzia Pennino, M T Carbone, Domenico Scognamiglio, Luciana Esposito, Antonio Correra, Giuseppe Castaldo, Francesco SalvatoreAbstract:Hyperphenylalaninemia is a group of autosomal recessive disorders caused by a wide range of phenylalanine hydroxylase (PAH) gene variants. To study the effects of mutations on PAH activity, we have reproduced five mutations (p.N223Y, p.R297L, p.F382L, p.K398N and p.Q419R) that we recently identified in a population of Southern Italy. Transient expression of mutant full-length cDNAs in human HEK293 cells yielded PAH variants whose l-phenylalanine hydroxylase activity was between 40% and 70% that of the wild-type enzyme. Moreover, Western blot analysis revealed a 50-kD monomer in all mutants thereby indicating normal synthesis of the mutant proteins. Because of the clinical mild nature of the phenotypes we performed an in vivo BH4 loading test. This was positive in all tested patients, which indicates that they are likely to respond to the coenzyme in vivo. We also analysed the environment of each mutation site in the available crystal structures of PAH by using Molecular Graphics tools. The structural alteration produced by each mutation was elucidated and correlated to the mutated properties of the mutant enzymes. All the data obtained demonstrate the disease-causing nature of the five novel variants.
-
six novel alleles identified in italian hereditary fructose intolerance patients enlarge the mutation spectrum of the aldolase b gene
Human Mutation, 2004Co-Authors: Gabriella Esposito, Luigi Vitagliano, Antonietta Viola, Luigi Ieno, L Fiori, Rita Santamaria, Adriana Zagari, Giancarlo Parenti, Lucia Zancan, Francesco SalvatoreAbstract:Hereditary fructose intolerance (HFI) is a recessively inherited disorder of carbohydrate metabolism caused by impaired functioning of human liver aldolase (B isoform; ALDOB). To-date, 29 enzyme-impairing mutations have been identified in the aldolase B gene. Here we report six novel HFI single nucleotide changes identified by sequence analysis in the aldolase B gene. Three of these are missense mutations (g.6846T>C, g.10236G>T, g.10258T>C), one is a nonsense mutation (g.8187C>T) and two affect splicing sites (g.8180G>C and g.10196A>G). We have expressed in bacterial cells the recombinant proteins corresponding to the g.6846T>C (p.I74T), g.10236G>T (p.V222F), and g.10258T>C (p.L229P) natural mutants to study their effect on aldolase B function and structure. All the new variants were insoluble; Molecular Graphics data suggest this is due to impaired folding. © 2004 Wiley-Liss, Inc.
-
structural and functional analysis of aldolase b mutants related to hereditary fructose intolerance
FEBS Letters, 2002Co-Authors: Gabriella Esposito, Luigi Vitagliano, Antonietta Viola, Rita Santamaria, Adriana Zagari, Francesco SalvatoreAbstract:Hereditary fructose intolerance (HFI) is a recessively inherited disorder of carbohydrate metabolism caused by impaired function of human liver aldolase (B isoform). 25 enzyme-impairing mutations have been identified in the aldolase B gene. We have studied the HFI-related mutant recombinant proteins W147R, A149P, A174D, L256P, N334K and Δ6ex6 in relation to aldolase B function and structure using kinetic assays and Molecular Graphics analysis. We found that these mutations affect aldolase B function by decreasing substrate affinity, maximal velocity and/or enzyme stability. Finally, the functional and structural analyses of the non-natural mutant Q354E provide insight into the catalytic role of Arg303, whose natural mutants are associated to HFI.
-
novel six nucleotide deletion in the hepatic fructose 1 6 bisphosphate aldolase gene in a patient with hereditary fructose intolerance and enzyme structure function implications
European Journal of Human Genetics, 1999Co-Authors: Rita Santamaria, Luigi Vitagliano, Adriana Zagari, Lucia Zancan, Sonia Tamasi, Paola Izzo, Francesco SalvatoreAbstract:Hereditary fructose intolerance (HFI) is an autosomal recessive human disease that results from the deficiency of the hepatic aldolase isoenzyme. Affected individuals will succumb to the disease unless it is readily diagnosed and fructose eliminated from the diet. Simple and non-invasive diagnosis is now possible by direct DNA analysis that scans for known and unknown mutations. Using a combination of several PCR-based methods (restriction enzyme digestion, allele specific oligonucleotide hybridisation, single strand conformation analysis and direct sequencing) we identified a novel six-nucleotide deletion in exon 6 of the aldolase B gene (delta 6ex6) that leads to the elimination of two amino acid residues (Leu182 and Val183) leaving the message inframe. The three-dimensional structural alterations induced in the enzyme by delta 6ex6 have been elucidated by Molecular Graphics analysis using the crystal structure of the rabbit muscle aldolase as reference model. These studies showed that the elimination of Leu182 and Val183 perturbs the correct orientation of adjacent catalytic residues such as Lys146 and Glu187.
Adriana Zagari - One of the best experts on this subject based on the ideXlab platform.
-
five human phenylalanine hydroxylase proteins identified in mild hyperphenylalaninemia patients are disease causing variants
Biochimica et Biophysica Acta, 2008Co-Authors: Aurora Daniele, Adriana Zagari, Giuseppe Cardillo, Cinzia Pennino, M T Carbone, Domenico Scognamiglio, Luciana Esposito, Antonio Correra, Giuseppe Castaldo, Francesco SalvatoreAbstract:Hyperphenylalaninemia is a group of autosomal recessive disorders caused by a wide range of phenylalanine hydroxylase (PAH) gene variants. To study the effects of mutations on PAH activity, we have reproduced five mutations (p.N223Y, p.R297L, p.F382L, p.K398N and p.Q419R) that we recently identified in a population of Southern Italy. Transient expression of mutant full-length cDNAs in human HEK293 cells yielded PAH variants whose l-phenylalanine hydroxylase activity was between 40% and 70% that of the wild-type enzyme. Moreover, Western blot analysis revealed a 50-kD monomer in all mutants thereby indicating normal synthesis of the mutant proteins. Because of the clinical mild nature of the phenotypes we performed an in vivo BH4 loading test. This was positive in all tested patients, which indicates that they are likely to respond to the coenzyme in vivo. We also analysed the environment of each mutation site in the available crystal structures of PAH by using Molecular Graphics tools. The structural alteration produced by each mutation was elucidated and correlated to the mutated properties of the mutant enzymes. All the data obtained demonstrate the disease-causing nature of the five novel variants.
-
six novel alleles identified in italian hereditary fructose intolerance patients enlarge the mutation spectrum of the aldolase b gene
Human Mutation, 2004Co-Authors: Gabriella Esposito, Luigi Vitagliano, Antonietta Viola, Luigi Ieno, L Fiori, Rita Santamaria, Adriana Zagari, Giancarlo Parenti, Lucia Zancan, Francesco SalvatoreAbstract:Hereditary fructose intolerance (HFI) is a recessively inherited disorder of carbohydrate metabolism caused by impaired functioning of human liver aldolase (B isoform; ALDOB). To-date, 29 enzyme-impairing mutations have been identified in the aldolase B gene. Here we report six novel HFI single nucleotide changes identified by sequence analysis in the aldolase B gene. Three of these are missense mutations (g.6846T>C, g.10236G>T, g.10258T>C), one is a nonsense mutation (g.8187C>T) and two affect splicing sites (g.8180G>C and g.10196A>G). We have expressed in bacterial cells the recombinant proteins corresponding to the g.6846T>C (p.I74T), g.10236G>T (p.V222F), and g.10258T>C (p.L229P) natural mutants to study their effect on aldolase B function and structure. All the new variants were insoluble; Molecular Graphics data suggest this is due to impaired folding. © 2004 Wiley-Liss, Inc.
-
structural and functional analysis of aldolase b mutants related to hereditary fructose intolerance
FEBS Letters, 2002Co-Authors: Gabriella Esposito, Luigi Vitagliano, Antonietta Viola, Rita Santamaria, Adriana Zagari, Francesco SalvatoreAbstract:Hereditary fructose intolerance (HFI) is a recessively inherited disorder of carbohydrate metabolism caused by impaired function of human liver aldolase (B isoform). 25 enzyme-impairing mutations have been identified in the aldolase B gene. We have studied the HFI-related mutant recombinant proteins W147R, A149P, A174D, L256P, N334K and Δ6ex6 in relation to aldolase B function and structure using kinetic assays and Molecular Graphics analysis. We found that these mutations affect aldolase B function by decreasing substrate affinity, maximal velocity and/or enzyme stability. Finally, the functional and structural analyses of the non-natural mutant Q354E provide insight into the catalytic role of Arg303, whose natural mutants are associated to HFI.
-
novel six nucleotide deletion in the hepatic fructose 1 6 bisphosphate aldolase gene in a patient with hereditary fructose intolerance and enzyme structure function implications
European Journal of Human Genetics, 1999Co-Authors: Rita Santamaria, Luigi Vitagliano, Adriana Zagari, Lucia Zancan, Sonia Tamasi, Paola Izzo, Francesco SalvatoreAbstract:Hereditary fructose intolerance (HFI) is an autosomal recessive human disease that results from the deficiency of the hepatic aldolase isoenzyme. Affected individuals will succumb to the disease unless it is readily diagnosed and fructose eliminated from the diet. Simple and non-invasive diagnosis is now possible by direct DNA analysis that scans for known and unknown mutations. Using a combination of several PCR-based methods (restriction enzyme digestion, allele specific oligonucleotide hybridisation, single strand conformation analysis and direct sequencing) we identified a novel six-nucleotide deletion in exon 6 of the aldolase B gene (delta 6ex6) that leads to the elimination of two amino acid residues (Leu182 and Val183) leaving the message inframe. The three-dimensional structural alterations induced in the enzyme by delta 6ex6 have been elucidated by Molecular Graphics analysis using the crystal structure of the rabbit muscle aldolase as reference model. These studies showed that the elimination of Leu182 and Val183 perturbs the correct orientation of adjacent catalytic residues such as Lys146 and Glu187.
Rita Santamaria - One of the best experts on this subject based on the ideXlab platform.
-
six novel alleles identified in italian hereditary fructose intolerance patients enlarge the mutation spectrum of the aldolase b gene
Human Mutation, 2004Co-Authors: Gabriella Esposito, Luigi Vitagliano, Antonietta Viola, Luigi Ieno, L Fiori, Rita Santamaria, Adriana Zagari, Giancarlo Parenti, Lucia Zancan, Francesco SalvatoreAbstract:Hereditary fructose intolerance (HFI) is a recessively inherited disorder of carbohydrate metabolism caused by impaired functioning of human liver aldolase (B isoform; ALDOB). To-date, 29 enzyme-impairing mutations have been identified in the aldolase B gene. Here we report six novel HFI single nucleotide changes identified by sequence analysis in the aldolase B gene. Three of these are missense mutations (g.6846T>C, g.10236G>T, g.10258T>C), one is a nonsense mutation (g.8187C>T) and two affect splicing sites (g.8180G>C and g.10196A>G). We have expressed in bacterial cells the recombinant proteins corresponding to the g.6846T>C (p.I74T), g.10236G>T (p.V222F), and g.10258T>C (p.L229P) natural mutants to study their effect on aldolase B function and structure. All the new variants were insoluble; Molecular Graphics data suggest this is due to impaired folding. © 2004 Wiley-Liss, Inc.
-
structural and functional analysis of aldolase b mutants related to hereditary fructose intolerance
FEBS Letters, 2002Co-Authors: Gabriella Esposito, Luigi Vitagliano, Antonietta Viola, Rita Santamaria, Adriana Zagari, Francesco SalvatoreAbstract:Hereditary fructose intolerance (HFI) is a recessively inherited disorder of carbohydrate metabolism caused by impaired function of human liver aldolase (B isoform). 25 enzyme-impairing mutations have been identified in the aldolase B gene. We have studied the HFI-related mutant recombinant proteins W147R, A149P, A174D, L256P, N334K and Δ6ex6 in relation to aldolase B function and structure using kinetic assays and Molecular Graphics analysis. We found that these mutations affect aldolase B function by decreasing substrate affinity, maximal velocity and/or enzyme stability. Finally, the functional and structural analyses of the non-natural mutant Q354E provide insight into the catalytic role of Arg303, whose natural mutants are associated to HFI.
-
novel six nucleotide deletion in the hepatic fructose 1 6 bisphosphate aldolase gene in a patient with hereditary fructose intolerance and enzyme structure function implications
European Journal of Human Genetics, 1999Co-Authors: Rita Santamaria, Luigi Vitagliano, Adriana Zagari, Lucia Zancan, Sonia Tamasi, Paola Izzo, Francesco SalvatoreAbstract:Hereditary fructose intolerance (HFI) is an autosomal recessive human disease that results from the deficiency of the hepatic aldolase isoenzyme. Affected individuals will succumb to the disease unless it is readily diagnosed and fructose eliminated from the diet. Simple and non-invasive diagnosis is now possible by direct DNA analysis that scans for known and unknown mutations. Using a combination of several PCR-based methods (restriction enzyme digestion, allele specific oligonucleotide hybridisation, single strand conformation analysis and direct sequencing) we identified a novel six-nucleotide deletion in exon 6 of the aldolase B gene (delta 6ex6) that leads to the elimination of two amino acid residues (Leu182 and Val183) leaving the message inframe. The three-dimensional structural alterations induced in the enzyme by delta 6ex6 have been elucidated by Molecular Graphics analysis using the crystal structure of the rabbit muscle aldolase as reference model. These studies showed that the elimination of Leu182 and Val183 perturbs the correct orientation of adjacent catalytic residues such as Lys146 and Glu187.
Paul Emsley - One of the best experts on this subject based on the ideXlab platform.
-
tools for ligand validation in coot
Acta Crystallographica Section D Structural Biology, 2017Co-Authors: Paul EmsleyAbstract:Coot is a Molecular-Graphics program primarily aimed at model building using X-ray data. Recently, tools for the manipulation and representation of ligands have been introduced. Here, these new tools for ligand validation and comparison are described. Ligands in the wwPDB have been scored by density-fit, distortion and atom-clash metrics. The distributions of these scores can be used to assess the relative merits of the particular ligand in the protein–ligand complex of interest by means of `sliders' akin to those now available for each accession code on the wwPDB websites.
-
handling ligands with coot
Acta Crystallographica Section D-biological Crystallography, 2012Co-Authors: Judit E Debreczeni, Paul EmsleyAbstract:Coot is a Molecular-Graphics application primarily aimed to assist in model building and validation of biological macromolecules. Recently, tools have been added to work with small molecules. The newly incorporated tools for the manipulation and validation of ligands include interaction with PRODRG, subgraph isomorphism-based tools, representation of ligand chemistry, ligand fitting and analysis, and are described here.
-
features and development of coot
Acta Crystallographica Section D-biological Crystallography, 2010Co-Authors: Paul Emsley, Bernhard Lohkamp, William G Scott, Kevin CowtanAbstract:Coot is a Molecular-Graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and Graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are `discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.
-
Coot: Model-building tools for Molecular Graphics
Acta Crystallographica Section D: Biological Crystallography, 2004Co-Authors: Paul Emsley, Kevin CowtanAbstract:CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality Graphics. The map-fitting tools are available as a stand-alone package, distributed as 'Coot'.
Luigi Vitagliano - One of the best experts on this subject based on the ideXlab platform.
-
six novel alleles identified in italian hereditary fructose intolerance patients enlarge the mutation spectrum of the aldolase b gene
Human Mutation, 2004Co-Authors: Gabriella Esposito, Luigi Vitagliano, Antonietta Viola, Luigi Ieno, L Fiori, Rita Santamaria, Adriana Zagari, Giancarlo Parenti, Lucia Zancan, Francesco SalvatoreAbstract:Hereditary fructose intolerance (HFI) is a recessively inherited disorder of carbohydrate metabolism caused by impaired functioning of human liver aldolase (B isoform; ALDOB). To-date, 29 enzyme-impairing mutations have been identified in the aldolase B gene. Here we report six novel HFI single nucleotide changes identified by sequence analysis in the aldolase B gene. Three of these are missense mutations (g.6846T>C, g.10236G>T, g.10258T>C), one is a nonsense mutation (g.8187C>T) and two affect splicing sites (g.8180G>C and g.10196A>G). We have expressed in bacterial cells the recombinant proteins corresponding to the g.6846T>C (p.I74T), g.10236G>T (p.V222F), and g.10258T>C (p.L229P) natural mutants to study their effect on aldolase B function and structure. All the new variants were insoluble; Molecular Graphics data suggest this is due to impaired folding. © 2004 Wiley-Liss, Inc.
-
structural and functional analysis of aldolase b mutants related to hereditary fructose intolerance
FEBS Letters, 2002Co-Authors: Gabriella Esposito, Luigi Vitagliano, Antonietta Viola, Rita Santamaria, Adriana Zagari, Francesco SalvatoreAbstract:Hereditary fructose intolerance (HFI) is a recessively inherited disorder of carbohydrate metabolism caused by impaired function of human liver aldolase (B isoform). 25 enzyme-impairing mutations have been identified in the aldolase B gene. We have studied the HFI-related mutant recombinant proteins W147R, A149P, A174D, L256P, N334K and Δ6ex6 in relation to aldolase B function and structure using kinetic assays and Molecular Graphics analysis. We found that these mutations affect aldolase B function by decreasing substrate affinity, maximal velocity and/or enzyme stability. Finally, the functional and structural analyses of the non-natural mutant Q354E provide insight into the catalytic role of Arg303, whose natural mutants are associated to HFI.
-
novel six nucleotide deletion in the hepatic fructose 1 6 bisphosphate aldolase gene in a patient with hereditary fructose intolerance and enzyme structure function implications
European Journal of Human Genetics, 1999Co-Authors: Rita Santamaria, Luigi Vitagliano, Adriana Zagari, Lucia Zancan, Sonia Tamasi, Paola Izzo, Francesco SalvatoreAbstract:Hereditary fructose intolerance (HFI) is an autosomal recessive human disease that results from the deficiency of the hepatic aldolase isoenzyme. Affected individuals will succumb to the disease unless it is readily diagnosed and fructose eliminated from the diet. Simple and non-invasive diagnosis is now possible by direct DNA analysis that scans for known and unknown mutations. Using a combination of several PCR-based methods (restriction enzyme digestion, allele specific oligonucleotide hybridisation, single strand conformation analysis and direct sequencing) we identified a novel six-nucleotide deletion in exon 6 of the aldolase B gene (delta 6ex6) that leads to the elimination of two amino acid residues (Leu182 and Val183) leaving the message inframe. The three-dimensional structural alterations induced in the enzyme by delta 6ex6 have been elucidated by Molecular Graphics analysis using the crystal structure of the rabbit muscle aldolase as reference model. These studies showed that the elimination of Leu182 and Val183 perturbs the correct orientation of adjacent catalytic residues such as Lys146 and Glu187.
