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Journal Articles
2012
71.
Walsh I; Minervini G; Corazza A; Esposito G; Tosatto S C E; Fogolari F
Bluues server: Electrostatic properties of wild-type and mutated protein structures Journal Article
In: Bioinformatics, vol. 28, no. 16, pp. 2189-2190, 2012, (Cited by: 72; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:84865101042,
title = {Bluues server: Electrostatic properties of wild-type and mutated protein structures},
author = {Ian Walsh and Giovanni Minervini and Alessandra Corazza and Gennaro Esposito and Silvio C. E. Tosatto and Federico Fogolari},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84865101042&origin=inward},
doi = {10.1093/bioinformatics/bts343},
year = {2012},
date = {2012-01-01},
journal = {Bioinformatics},
volume = {28},
number = {16},
pages = {2189-2190},
abstract = {Motivation: Electrostatic calculations are an important tool for deciphering many functional mechanisms in proteins. Generalized Born (GB) models offer a fast and convenient computational approximation over other implicit solvent-based electrostatic models. Here we present a novel GB-based web server, using the program Bluues, to calculate numerous electrostatic features including pKa-values and surface potentials. The output is organized allowing both experts and beginners to rapidly sift the data. A novel feature of the Bluues server is that it explicitly allows to find electrostatic differences between wild-type and mutant structures. © The Author (2012). Published by Oxford University Press. All rights reserved.},
note = {Cited by: 72; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Motivation: Electrostatic calculations are an important tool for deciphering many functional mechanisms in proteins. Generalized Born (GB) models offer a fast and convenient computational approximation over other implicit solvent-based electrostatic models. Here we present a novel GB-based web server, using the program Bluues, to calculate numerous electrostatic features including pKa-values and surface potentials. The output is organized allowing both experts and beginners to rapidly sift the data. A novel feature of the Bluues server is that it explicitly allows to find electrostatic differences between wild-type and mutant structures. © The Author (2012). Published by Oxford University Press. All rights reserved.
72.
Walsh I; Sirocco F G; Minervini G; Domenico T D; Ferrari C; Tosatto S C E
RAPHAEL: Recognition, periodicity and insertion assignment of solenoid protein structures Journal Article
In: Bioinformatics, vol. 28, no. 24, pp. 3257-3264, 2012, (Cited by: 27; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:84870806739,
title = {RAPHAEL: Recognition, periodicity and insertion assignment of solenoid protein structures},
author = {Ian Walsh and Francesco G. Sirocco and Giovanni Minervini and Tomás Di Domenico and Carlo Ferrari and Silvio C. E. Tosatto},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84870806739&origin=inward},
doi = {10.1093/bioinformatics/bts550},
year = {2012},
date = {2012-01-01},
journal = {Bioinformatics},
volume = {28},
number = {24},
pages = {3257-3264},
abstract = {Motivation: Repeat proteins form a distinct class of structures where folding is greatly simplified. Several classes have been defined, with solenoid repeats of periodicity between ca. 5 and 40 being the most challenging to detect. Such proteins evolve quickly and their periodicity may be rapidly hidden at sequence level. From a structural point of view, finding solenoids may be complicated by the presence of insertions or multiple domains. To the best of our knowledge, no automated methods are available to characterize solenoid repeats from structure. Results: Here we introduce RAPHAEL, a novel method for the detection of solenoids in protein structures. It reliably solves three problems of increasing difficulty: (1) recognition of solenoid domains, (2) determination of their periodicity and (3) assignment of insertions. RAPHAEL uses a geometric approach mimicking manual classification, producing several numeric parameters that are optimized for maximum performance. The resulting method is very accurate, with 89.5% of solenoid proteins and 97.2% of non-solenoid proteins correctly classified. RAPHAEL periodicities have a Spearman correlation coefficient of 0.877 against the manually established ones. A baseline algorithm for insertion detection in identified solenoids has a Q2 value of 79.8%, suggesting room for further improvement. RAPHAEL finds 1931 highly confident repeat structures not previously annotated as solenoids in the Protein Data Bank records. © 2012 The Author.},
note = {Cited by: 27; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Motivation: Repeat proteins form a distinct class of structures where folding is greatly simplified. Several classes have been defined, with solenoid repeats of periodicity between ca. 5 and 40 being the most challenging to detect. Such proteins evolve quickly and their periodicity may be rapidly hidden at sequence level. From a structural point of view, finding solenoids may be complicated by the presence of insertions or multiple domains. To the best of our knowledge, no automated methods are available to characterize solenoid repeats from structure. Results: Here we introduce RAPHAEL, a novel method for the detection of solenoids in protein structures. It reliably solves three problems of increasing difficulty: (1) recognition of solenoid domains, (2) determination of their periodicity and (3) assignment of insertions. RAPHAEL uses a geometric approach mimicking manual classification, producing several numeric parameters that are optimized for maximum performance. The resulting method is very accurate, with 89.5% of solenoid proteins and 97.2% of non-solenoid proteins correctly classified. RAPHAEL periodicities have a Spearman correlation coefficient of 0.877 against the manually established ones. A baseline algorithm for insertion detection in identified solenoids has a Q2 value of 79.8%, suggesting room for further improvement. RAPHAEL finds 1931 highly confident repeat structures not previously annotated as solenoids in the Protein Data Bank records. © 2012 The Author.
73.
Lucrezia D; Slanzi D; Poli I; Polticelli F; Minervini G
Do natural proteins differ from random sequences polypeptides? natural vs. random proteins classification using an evolutionary neural network Journal Article
In: PLoS ONE, vol. 7, no. 5, 2012, (Cited by: 22; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:84861209926,
title = {Do natural proteins differ from random sequences polypeptides? natural vs. random proteins classification using an evolutionary neural network},
author = {Davide Lucrezia and Debora Slanzi and Irene Poli and Fabio Polticelli and Giovanni Minervini},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84861209926&origin=inward},
doi = {10.1371/journal.pone.0036634},
year = {2012},
date = {2012-01-01},
journal = {PLoS ONE},
volume = {7},
number = {5},
abstract = {Are extant proteins the exquisite result of natural selection or are they random sequences slightly edited by evolution? This question has puzzled biochemists for long time and several groups have addressed this issue comparing natural protein sequences to completely random ones coming to contradicting conclusions. Previous works in literature focused on the analysis of primary structure in an attempt to identify possible signature of evolutionary editing. Conversely, in this work we compare a set of 762 natural proteins with an average length of 70 amino acids and an equal number of completely random ones of comparable length on the basis of their structural features. We use an ad hoc Evolutionary Neural Network Algorithm (ENNA) in order to assess whether and to what extent natural proteins are edited from random polypeptides employing 11 different structure-related variables (i.e. net charge, volume, surface area, coil, alpha helix, beta sheet, percentage of coil, percentage of alpha helix, percentage of beta sheet, percentage of secondary structure and surface hydrophobicity). The ENNA algorithm is capable to correctly distinguish natural proteins from random ones with an accuracy of 94.36%. Furthermore, we study the structural features of 32 random polypeptides misclassified as natural ones to unveil any structural similarity to natural proteins. Results show that random proteins misclassified by the ENNA algorithm exhibit a significant fold similarity to portions or subdomains of extant proteins at atomic resolution. Altogether, our results suggest that natural proteins are significantly edited from random polypeptides and evolutionary editing can be readily detected analyzing structural features. Furthermore, we also show that the ENNA, employing simple structural descriptors, can predict whether a protein chain is natural or random. © 2012 De Lucrezia et al.},
note = {Cited by: 22; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Are extant proteins the exquisite result of natural selection or are they random sequences slightly edited by evolution? This question has puzzled biochemists for long time and several groups have addressed this issue comparing natural protein sequences to completely random ones coming to contradicting conclusions. Previous works in literature focused on the analysis of primary structure in an attempt to identify possible signature of evolutionary editing. Conversely, in this work we compare a set of 762 natural proteins with an average length of 70 amino acids and an equal number of completely random ones of comparable length on the basis of their structural features. We use an ad hoc Evolutionary Neural Network Algorithm (ENNA) in order to assess whether and to what extent natural proteins are edited from random polypeptides employing 11 different structure-related variables (i.e. net charge, volume, surface area, coil, alpha helix, beta sheet, percentage of coil, percentage of alpha helix, percentage of beta sheet, percentage of secondary structure and surface hydrophobicity). The ENNA algorithm is capable to correctly distinguish natural proteins from random ones with an accuracy of 94.36%. Furthermore, we study the structural features of 32 random polypeptides misclassified as natural ones to unveil any structural similarity to natural proteins. Results show that random proteins misclassified by the ENNA algorithm exhibit a significant fold similarity to portions or subdomains of extant proteins at atomic resolution. Altogether, our results suggest that natural proteins are significantly edited from random polypeptides and evolutionary editing can be readily detected analyzing structural features. Furthermore, we also show that the ENNA, employing simple structural descriptors, can predict whether a protein chain is natural or random. © 2012 De Lucrezia et al.
2011
74.
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.
75.
Zanconato S; Minervini G; Poli I; Lucrezia D D
Selection dynamic of Escherichia coli host in M13 combinatorial peptide phage display libraries Journal Article
In: Bioscience, Biotechnology and Biochemistry, vol. 75, no. 4, pp. 812-815, 2011, (Cited by: 9; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:79955824084,
title = {Selection dynamic of Escherichia coli host in M13 combinatorial peptide phage display libraries},
author = {Stefano Zanconato and Giovanni Minervini and Irene Poli and Davide De Lucrezia},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-79955824084&origin=inward},
doi = {10.1271/bbb.110099},
year = {2011},
date = {2011-01-01},
journal = {Bioscience, Biotechnology and Biochemistry},
volume = {75},
number = {4},
pages = {812-815},
abstract = {Phage display relies on an iterative cycle of selection and amplification of random combinatorial libraries to enrich the initial population of those peptides that satisfy a priori chosen criteria. The effectiveness of any phage display protocol depends directly on library amino acid sequence diversity and the strength of the selection procedure. In this study we monitored the dynamics of the selective pressure exerted by the host organism on a random peptide library in the absence of any additional selection pressure. The results indicate that sequence censorship exerted by Escherichia coli dramatically reduces library diversity and can significantly impair phage display effectiveness.},
note = {Cited by: 9; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Phage display relies on an iterative cycle of selection and amplification of random combinatorial libraries to enrich the initial population of those peptides that satisfy a priori chosen criteria. The effectiveness of any phage display protocol depends directly on library amino acid sequence diversity and the strength of the selection procedure. In this study we monitored the dynamics of the selective pressure exerted by the host organism on a random peptide library in the absence of any additional selection pressure. The results indicate that sequence censorship exerted by Escherichia coli dramatically reduces library diversity and can significantly impair phage display effectiveness.
76.
Tavladoraki P; Cervelli M; Antonangeli F; Minervini G; Stano P; Federico R; Mariottini P; Polticelli F
Probing mammalian spermine oxidase enzyme-substrate complex through molecular modeling, site-directed mutagenesis and biochemical characterization Journal Article
In: Amino Acids, vol. 40, no. 4, pp. 1115-1126, 2011, (Cited by: 35).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:79954436519,
title = {Probing mammalian spermine oxidase enzyme-substrate complex through molecular modeling, site-directed mutagenesis and biochemical characterization},
author = {Paraskevi Tavladoraki and Manuela Cervelli and Fabrizio Antonangeli and Giovanni Minervini and Pasquale Stano and Rodolfo Federico and Paolo Mariottini and Fabio Polticelli},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-79954436519&origin=inward},
doi = {10.1007/s00726-010-0735-8},
year = {2011},
date = {2011-01-01},
journal = {Amino Acids},
volume = {40},
number = {4},
pages = {1115-1126},
abstract = {Spermine oxidase (SMO) and acetylpolyamine oxidase (APAO) are FAD-dependent enzymes that are involved in the highly regulated pathways of polyamine biosynthesis and degradation. Polyamine content is strictly related to cell growth, and dysfunctions in polyamine metabolism have been linked with cancer. Specific inhibitors of SMO and APAO would allow analyzing the precise role of these enzymes in polyamine metabolism and related pathologies. However, none of the available polyamine oxidase inhibitors displays the desired characteristics of selective affinity and specificity. In addition, repeated efforts to obtain structural details at the atomic level on these two enzymes have all failed. In the present study, in an effort to better understand structure-function relationships, SMO enzyme-substrate complex has been probed through a combination of molecular modeling, site-directed mutagenesis and biochemical studies. Results obtained indicate that SMO binds spermine in a similar conformation as that observed in the yeast polyamine oxidase FMS1-spermine complex and demonstrate a major role for residues His82 and Lys367 in substrate binding and catalysis. In addition, the SMO enzyme-substrate complex highlights the presence of an active site pocket with highly polar characteristics, which may explain the different substrate specificity of SMO with respect to APAO and provide the basis for the design of specific inhibitors for SMO and APAO. © 2010 Springer-Verlag.},
note = {Cited by: 35},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Spermine oxidase (SMO) and acetylpolyamine oxidase (APAO) are FAD-dependent enzymes that are involved in the highly regulated pathways of polyamine biosynthesis and degradation. Polyamine content is strictly related to cell growth, and dysfunctions in polyamine metabolism have been linked with cancer. Specific inhibitors of SMO and APAO would allow analyzing the precise role of these enzymes in polyamine metabolism and related pathologies. However, none of the available polyamine oxidase inhibitors displays the desired characteristics of selective affinity and specificity. In addition, repeated efforts to obtain structural details at the atomic level on these two enzymes have all failed. In the present study, in an effort to better understand structure-function relationships, SMO enzyme-substrate complex has been probed through a combination of molecular modeling, site-directed mutagenesis and biochemical studies. Results obtained indicate that SMO binds spermine in a similar conformation as that observed in the yeast polyamine oxidase FMS1-spermine complex and demonstrate a major role for residues His82 and Lys367 in substrate binding and catalysis. In addition, the SMO enzyme-substrate complex highlights the presence of an active site pocket with highly polar characteristics, which may explain the different substrate specificity of SMO with respect to APAO and provide the basis for the design of specific inhibitors for SMO and APAO. © 2010 Springer-Verlag.
77.
Mazzucco N; Zanconato S; Lucrezia D D; Argese E; Poli I; Minervini G
Design and dynamic simulation of minimal metallo-proteins Journal Article
In: Journal of Molecular Modeling, vol. 17, no. 11, pp. 2919-2925, 2011, (Cited by: 2).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:80255127343,
title = {Design and dynamic simulation of minimal metallo-proteins},
author = {Nicolò Mazzucco and Stefano Zanconato and Davide De Lucrezia and Emanuele Argese and Irene Poli and Giovanni Minervini},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-80255127343&origin=inward},
doi = {10.1007/s00894-011-0993-8},
year = {2011},
date = {2011-01-01},
journal = {Journal of Molecular Modeling},
volume = {17},
number = {11},
pages = {2919-2925},
abstract = {Ab initio in silico design of proteins and enzymes has emerged as a powerful tool to design application-tailored proteins and catalysts for a wide range of applications. Several enzymes exploit the unique features of metal cofactors to achieve catalytic activity otherwise unattainable through the use of only natural amino acid residues. One of the major bottlenecks in ab initio design of novel proteins relies on long-range and epistatic effects that severely limit the possibility of a rational design. Within this framework there is an ongoing effort to reduce protein length and complexity to unlock the full potential of in silico protein design. In this work we specifically address this problem designing and investigating the dynamic features of 10 in silico designed minimal metallo-proteins. In particular, in this paper we investigate whether and to what extent it is possible to design a minimal metallo-enzyme made of only residues involved in metal binding. In this research we address these questions by investigating the ability of 10 different "mini-proteins" with a length shorter than 15 residues. Molecular dynamics studies clearly show that it is possible to design a minimal protein able to bind a metal atom with the correct geometry. It is noteworthy that designed mini-proteins cannot achieve the formation of a canonical hydrophobic core, rather the metal ion provides a "metal core" around which the entire protein is organized. This opens the possibility of designing synthetic enzymes composed of only functional residues organized around a "metal core" which acts as both structural and functional determinat. © 2011 Springer-Verlag.},
note = {Cited by: 2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ab initio in silico design of proteins and enzymes has emerged as a powerful tool to design application-tailored proteins and catalysts for a wide range of applications. Several enzymes exploit the unique features of metal cofactors to achieve catalytic activity otherwise unattainable through the use of only natural amino acid residues. One of the major bottlenecks in ab initio design of novel proteins relies on long-range and epistatic effects that severely limit the possibility of a rational design. Within this framework there is an ongoing effort to reduce protein length and complexity to unlock the full potential of in silico protein design. In this work we specifically address this problem designing and investigating the dynamic features of 10 in silico designed minimal metallo-proteins. In particular, in this paper we investigate whether and to what extent it is possible to design a minimal metallo-enzyme made of only residues involved in metal binding. In this research we address these questions by investigating the ability of 10 different “mini-proteins” with a length shorter than 15 residues. Molecular dynamics studies clearly show that it is possible to design a minimal protein able to bind a metal atom with the correct geometry. It is noteworthy that designed mini-proteins cannot achieve the formation of a canonical hydrophobic core, rather the metal ion provides a “metal core” around which the entire protein is organized. This opens the possibility of designing synthetic enzymes composed of only functional residues organized around a “metal core” which acts as both structural and functional determinat. © 2011 Springer-Verlag.
2009
78.
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: 10; Open Access).
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: 10; Open Access},
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
79.
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: 76; 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: 76; 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
80.
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: 46; 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: 46; 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.