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Journal Articles
2011
71.
Chiesa S; Marzano F N; Minervini G; Lucrezia D D; Baccarani G; Bordignon G; Poli I; Ravagnan G; Argese E
The invasive Manila clam Ruditapes philippinarum (Adams and Reeve, 1850) in Northern Adriatic Sea: Population genetics assessed by an integrated molecular approach Journal Article
In: Fisheries Research, vol. 110, no. 2, pp. 259-267, 2011, (Cited by: 30).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:79959201489,
title = {The invasive Manila clam Ruditapes philippinarum (Adams and Reeve, 1850) in Northern Adriatic Sea: Population genetics assessed by an integrated molecular approach},
author = {Stefania Chiesa and Francesco Nonnis Marzano and Giovanni Minervini and Davide De Lucrezia and Gianluca Baccarani and Guido Bordignon and Irene Poli and Giampietro Ravagnan and Emanuele Argese},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-79959201489&origin=inward},
doi = {10.1016/j.fishres.2011.04.013},
year = {2011},
date = {2011-01-01},
journal = {Fisheries Research},
volume = {110},
number = {2},
pages = {259-267},
abstract = {The coastal lagoons of the Northern Adriatic Sea are among the most worldwide productive locations of Manila clam Ruditapes philippinarum. Although introduced in Italy in 1983 from the Indo-Pacific, fishing and exploitation of Manila clam improved during the years as Italy became the leading country in Europe for production of this shellfish.Despite its commercial importance, genetic structure of R. philippinarum in Northern Adriatic Sea has not been previously investigated. Here we present the first genetic study on Manila clam populations inhabiting a Mediterranean area, assessed by both mitochondrial (16S rDNA) and nuclear DNA (microsatellite loci). Our study showed that this species has a limited genetic differentiation at the mitochondrial level, but a higher rate of genetic diversity can be identified by polymorphic markers as microsatellites. In particular, out of 28 alleles, 7 private ones were recorded for the Venice Lagoon populations, 2 for those of Scardovari and one for the Po River Delta populations. These molecular markers suggest the occurrence of at least two different introduction events from different recruitment stocks, representing a powerful tool not only to assess genetic diversity of an introduced species, but also helpful information to manage aquaculture and fishery stocks, and to warrant food quality, safety and for the authentication of shellfish products, and traceabilty path. © 2011 Elsevier B.V.},
note = {Cited by: 30},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The coastal lagoons of the Northern Adriatic Sea are among the most worldwide productive locations of Manila clam Ruditapes philippinarum. Although introduced in Italy in 1983 from the Indo-Pacific, fishing and exploitation of Manila clam improved during the years as Italy became the leading country in Europe for production of this shellfish.Despite its commercial importance, genetic structure of R. philippinarum in Northern Adriatic Sea has not been previously investigated. Here we present the first genetic study on Manila clam populations inhabiting a Mediterranean area, assessed by both mitochondrial (16S rDNA) and nuclear DNA (microsatellite loci). Our study showed that this species has a limited genetic differentiation at the mitochondrial level, but a higher rate of genetic diversity can be identified by polymorphic markers as microsatellites. In particular, out of 28 alleles, 7 private ones were recorded for the Venice Lagoon populations, 2 for those of Scardovari and one for the Po River Delta populations. These molecular markers suggest the occurrence of at least two different introduction events from different recruitment stocks, representing a powerful tool not only to assess genetic diversity of an introduced species, but also helpful information to manage aquaculture and fishery stocks, and to warrant food quality, safety and for the authentication of shellfish products, and traceabilty path. © 2011 Elsevier B.V.
2009
72.
Prymula K; Piwowar M; Kochanczyk M; Flis L; Malawski M; Szepieniec T; Evangelista G; Minervini G; Polticelli F; Wiśniowski Z; Sałapa K; Matczyńska E; Roterman I
In silico structural study of random amino acid sequence proteins not present in nature Journal Article
In: Chemistry and Biodiversity, vol. 6, no. 12, pp. 2311-2336, 2009, (Cited by: 9).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:74749091402,
title = {In silico structural study of random amino acid sequence proteins not present in nature},
author = {Katarzyna Prymula and Monika Piwowar and Marek Kochanczyk and Lukasz Flis and Maciej Malawski and Tomasz Szepieniec and Giovanni Evangelista and Giuseppe Minervini and Fabio Polticelli and Zdzisław Wiśniowski and Kinga Sałapa and Ewa Matczyńska and Irena Roterman},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-74749091402&origin=inward},
doi = {10.1002/cbdv.200800338},
year = {2009},
date = {2009-01-01},
journal = {Chemistry and Biodiversity},
volume = {6},
number = {12},
pages = {2311-2336},
abstract = {The three-dimensional structures of a set of 'never born proteins' (NBP, random amino acid sequence proteins with no significant homology with known proteins) were predicted using two methods: Rosetta and the one based on the 'fuzzy-oil-drop' (FOD) model. More than 3000 different random amino acid sequences have been generated, filtered against the non redundant protein sequence data base, to remove sequences with significant homology with known proteins, and subjected to three-dimensional structure prediction. Comparison between Rosetta and FOD predictions allowed to select the ten top (highest structural similarity) and the ten bottom (the lowest structural similarity) structures from the ranking list organized according to the RMS-D value. The selected structures were taken for detailed analysis to define the scale of structural accordance and discrepancy between the two methods. The structural similarity measurements revealed discrepancies between structures generated on the basis of the two methods. Their potential biological function appeared to be quite different as well. The ten bottom structures appeared to be 'unfoldable' for the FOD model. Some aspects of the general characteristics of the NBPs are also discussed. The calculations were performed on the EUChinaGRID grid platform to test the performance of this infrastructure for massive protein structure predictions. © 2009 Verlag Helvetica Chimica Acta AG.},
note = {Cited by: 9},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The three-dimensional structures of a set of ‘never born proteins’ (NBP, random amino acid sequence proteins with no significant homology with known proteins) were predicted using two methods: Rosetta and the one based on the ‘fuzzy-oil-drop’ (FOD) model. More than 3000 different random amino acid sequences have been generated, filtered against the non redundant protein sequence data base, to remove sequences with significant homology with known proteins, and subjected to three-dimensional structure prediction. Comparison between Rosetta and FOD predictions allowed to select the ten top (highest structural similarity) and the ten bottom (the lowest structural similarity) structures from the ranking list organized according to the RMS-D value. The selected structures were taken for detailed analysis to define the scale of structural accordance and discrepancy between the two methods. The structural similarity measurements revealed discrepancies between structures generated on the basis of the two methods. Their potential biological function appeared to be quite different as well. The ten bottom structures appeared to be ‘unfoldable’ for the FOD model. Some aspects of the general characteristics of the NBPs are also discussed. The calculations were performed on the EUChinaGRID grid platform to test the performance of this infrastructure for massive protein structure predictions. © 2009 Verlag Helvetica Chimica Acta AG.
2008
73.
Polticelli ; Bocedi ; Minervini ; Ascenzi
Human haptoglobin structure and function – A molecular modelling study Journal Article
In: FEBS Journal, vol. 275, no. 22, pp. 5648-5656, 2008, (Cited by: 75; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:54849423259,
title = {Human haptoglobin structure and function - A molecular modelling study},
author = {Polticelli and Bocedi and Minervini and Ascenzi},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-54849423259&origin=inward},
doi = {10.1111/j.1742-4658.2008.06690.x},
year = {2008},
date = {2008-01-01},
journal = {FEBS Journal},
volume = {275},
number = {22},
pages = {5648-5656},
abstract = {Hemoglobin is the most prominent protein in blood, transporting O 2 and facilitating reactive oxygen and nitrogen species detoxification. Hemoglobin metabolism leads to the release of extra-erythrocytic hemoglobin, with potentially severe consequences for health. Extra-erythrocytic hemoglobin is complexed to haptoglobin for clearance by tissue macrophages. The human gene for haptoglobin consists of three structural alleles: Hp1F, Hp1S and Hp2. The products of the Hp1F and Hp1S alleles differ by only one amino acid, whereas the Hp2 allele is the result of a fusion of the Hp1F and Hp1S alleles, is present only in humans and gives rise to a longer α-chain. Haptoglobin consists of a dimer of αβ-chains covalently linked by a disulphide bond between the Cys15 residue of each α-chain. However, the presence of the Hp1 and Hp2 alleles in humans gives rise to HPT1-1 dimers (covalently linked by Cys15 residues), HPT1-2 hetero-oligomers and HPT2-2 oligomers. In fact, the HPT2 variant displays two free Cys residues (Cys15 and Cys74) whose participation in intermolecular disulphide bonds gives rise to higher-order covalent multimers. Here, the complete modelling of both haptoglobin variants, together with their basic quaternary structure arrangements (i.e. HPT1 dimer and HPT2 trimer), is reported. The structural details of the models, which represent the first complete view of the molecular details of human haptoglobin variants, are discussed in relation to the known haptoglobin function(s). © 2008 The Authors.},
note = {Cited by: 75; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hemoglobin is the most prominent protein in blood, transporting O 2 and facilitating reactive oxygen and nitrogen species detoxification. Hemoglobin metabolism leads to the release of extra-erythrocytic hemoglobin, with potentially severe consequences for health. Extra-erythrocytic hemoglobin is complexed to haptoglobin for clearance by tissue macrophages. The human gene for haptoglobin consists of three structural alleles: Hp1F, Hp1S and Hp2. The products of the Hp1F and Hp1S alleles differ by only one amino acid, whereas the Hp2 allele is the result of a fusion of the Hp1F and Hp1S alleles, is present only in humans and gives rise to a longer α-chain. Haptoglobin consists of a dimer of αβ-chains covalently linked by a disulphide bond between the Cys15 residue of each α-chain. However, the presence of the Hp1 and Hp2 alleles in humans gives rise to HPT1-1 dimers (covalently linked by Cys15 residues), HPT1-2 hetero-oligomers and HPT2-2 oligomers. In fact, the HPT2 variant displays two free Cys residues (Cys15 and Cys74) whose participation in intermolecular disulphide bonds gives rise to higher-order covalent multimers. Here, the complete modelling of both haptoglobin variants, together with their basic quaternary structure arrangements (i.e. HPT1 dimer and HPT2 trimer), is reported. The structural details of the models, which represent the first complete view of the molecular details of human haptoglobin variants, are discussed in relation to the known haptoglobin function(s). © 2008 The Authors.
2005
74.
Polticelli F; Basran J; Faso C; Cona A; Minervini G; Angelini R; Federico R; Scrutton N S; Tavladoraki P
Lys300 plays a major role in the catalytic mechanism of maize polyamine oxidase Journal Article
In: Biochemistry, vol. 44, no. 49, pp. 16108-16120, 2005, (Cited by: 45; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:28944433027,
title = {Lys300 plays a major role in the catalytic mechanism of maize polyamine oxidase},
author = {Fabio Polticelli and Jaswir Basran and Carmen Faso and Alessandra Cona and Giovanni Minervini and Riccardo Angelini and Rodolfo Federico and Nigel S. Scrutton and Paraskevi Tavladoraki},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-28944433027&origin=inward},
doi = {10.1021/bi050983i},
year = {2005},
date = {2005-01-01},
journal = {Biochemistry},
volume = {44},
number = {49},
pages = {16108-16120},
abstract = {Maize polyamine oxidase (MPAO) is a flavin adenine dinucleotide (FAD)-dependent enzyme that catalyses the oxidation of spermine and spermidine at the secondary amino groups. The structure of MPAO indicates a 30-Â long U-shaped tunnel that forms the catalytic site, with residues Glu62 and Glu170 located close to the enzyme-bound FAD and residue Tyr298 in close proximity to Lys300, which in turn is hydrogen-bonded to the flavin N5 atom via a water molecule (HOH309). To provide insight into the role of these residues in the catalytic mechanism of FAD reduction, we have performed steady-state and stopped-flow studies with wild-type, Glu62Gln, Glu170Gln, Tyr298Phe, and Lys300Met MPAO enzymes. We show that the steady-state enzyme activity is governed by an ionisable group with a macroscopic pKa of textasciitilde 5.8. Kinetic analysis of the Glu62Gln, Glu170Gln, and Tyr298Phe MPAO enzymes have indicated (i) only small perturbations in catalytic activity as a result of mutation and (ii) steady-state pH profiles essentially unaltered when compared to the wild-type enzyme, suggesting that these residues do not play a critical role in the reaction mechanism. These kinetic observations are consistent with computational calculations that suggest that Glu62 and Glu170 are protonated over the pH range accessible to kinetic studies. Substitution of Lys300 with Met in MPAO resulted in a 1400-fold decrease in the rate of flavin reduction and a 160-fold decrease in the equilibrium dissociation constant for the Lys300Met- spermidine complex, consistent with a major role for this residue in the mechanism of substrate oxidation. A sizable solvent isotope effect (SIE = 5) accompanies FAD reduction in the wild-type enzyme and steady-state turnover (SIE = 2.3) of MPAO, consistent with the reductive half-reaction of MPAO making a major contribution to rate limitation in steady-state turnover. Studies using the enzyme-monitored turnover method indicate that oxidized FAD is the prominent form during steady-state turnover, consistent with the reductive half-reaction being rate-limiting. Our studies indicate the importance of Lys300 and probable importance of HOH309 to the mechanism of flavin reduction in MPAO. Possible roles for Lys300 and water in the mechanism of flavin reduction are discussed. © 2005 American Chemical Society.},
note = {Cited by: 45; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Maize polyamine oxidase (MPAO) is a flavin adenine dinucleotide (FAD)-dependent enzyme that catalyses the oxidation of spermine and spermidine at the secondary amino groups. The structure of MPAO indicates a 30-Â long U-shaped tunnel that forms the catalytic site, with residues Glu62 and Glu170 located close to the enzyme-bound FAD and residue Tyr298 in close proximity to Lys300, which in turn is hydrogen-bonded to the flavin N5 atom via a water molecule (HOH309). To provide insight into the role of these residues in the catalytic mechanism of FAD reduction, we have performed steady-state and stopped-flow studies with wild-type, Glu62Gln, Glu170Gln, Tyr298Phe, and Lys300Met MPAO enzymes. We show that the steady-state enzyme activity is governed by an ionisable group with a macroscopic pKa of textasciitilde 5.8. Kinetic analysis of the Glu62Gln, Glu170Gln, and Tyr298Phe MPAO enzymes have indicated (i) only small perturbations in catalytic activity as a result of mutation and (ii) steady-state pH profiles essentially unaltered when compared to the wild-type enzyme, suggesting that these residues do not play a critical role in the reaction mechanism. These kinetic observations are consistent with computational calculations that suggest that Glu62 and Glu170 are protonated over the pH range accessible to kinetic studies. Substitution of Lys300 with Met in MPAO resulted in a 1400-fold decrease in the rate of flavin reduction and a 160-fold decrease in the equilibrium dissociation constant for the Lys300Met- spermidine complex, consistent with a major role for this residue in the mechanism of substrate oxidation. A sizable solvent isotope effect (SIE = 5) accompanies FAD reduction in the wild-type enzyme and steady-state turnover (SIE = 2.3) of MPAO, consistent with the reductive half-reaction of MPAO making a major contribution to rate limitation in steady-state turnover. Studies using the enzyme-monitored turnover method indicate that oxidized FAD is the prominent form during steady-state turnover, consistent with the reductive half-reaction being rate-limiting. Our studies indicate the importance of Lys300 and probable importance of HOH309 to the mechanism of flavin reduction in MPAO. Possible roles for Lys300 and water in the mechanism of flavin reduction are discussed. © 2005 American Chemical Society.
