@article{SCOPUS_ID:84942198879,

title = {Unfoldome variation upon plant-pathogen interactions: strawberry infection by Colletotrichum acutatum},

author = {Elena Baraldi and Emanuela Coller and Lisa Zoli and Alessandro Cestaro and Silvio C. E. Tosatto and Barbara Zambelli},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84942198879&origin=inward},

doi = {10.1007/s11103-015-0353-7},

year  = {2015},

date = {2015-01-01},

journal = {Plant Molecular Biology},

volume = {89},

number = {1-2},

pages = {49-65},

publisher = {Kluwer Academic Publishersrbk@louisiana.edu},

abstract = {© 2015, Springer Science+Business Media Dordrecht.Intrinsically disordered proteins (IDPs) are proteins that lack secondary and/or tertiary structure under physiological conditions. These proteins are very abundant in eukaryotic proteomes and play crucial roles in all molecular mechanisms underlying the response to environmental challenges. In plants, different IDPs involved in stress response have been identified and characterized. Nevertheless, a comprehensive evaluation of protein disorder in plant proteomes under abiotic or biotic stresses is not available so far. In the present work the transcriptome dataset of strawberry (Fragariaxananassa) fruits interacting with the fungal pathogen Colletotrichum acutatum was actualized onto the woodland strawberry (Fragaria vesca) genome. The obtained cDNA sequences were translated into protein sequences, which were subsequently subjected to disorder analysis. The results, providing the first estimation of disorder abundance associated to plant infection, showed that the proteome activated in the strawberry red fruit during the active fungal propagation is remarkably depleted in disorder. On the other hand, in the resistant white fruit, no significant disorder reduction is observed in the proteins expressed in response to fungal infection. Four representative proteins, FvSMP, FvPRKRIP, FvPCD-4 and FvFAM32A-like, predicted as mainly disordered and never experimentally characterized before, were isolated, and the absence of structure was validated at the secondary and tertiary level using circular dichroism and differential scanning fluorimetry. Their quaternary structure was also established using light scattering. The results are discussed considering the role of protein disorder in plant defense.},

note = {Cited by: 4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84947284654,

title = {Comparison of protein repeat classifications based on structure and sequence families},

author = {Lisanna Paladin and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84947284654&origin=inward},

doi = {10.1042/BST20150079},

year  = {2015},

date = {2015-01-01},

journal = {Biochemical Society Transactions},

volume = {43},

pages = {832-837},

publisher = {Portland Press Ltd},

abstract = {© 2015 Authors; published by Portland Press Limited.Tandem repeats (TR) in proteins are common in nature and have several unique functions. They come in various forms that are frequently difficult to recognize from a sequence. A previously proposed structural classification has been recently implemented in the RepeatsDB database. This defines five main classes, mainly based on repeat unit length, with subclasses representing specific folds. Sequence-based classifications, such as Pfam, provide an alternative classification based on evolutionarily conserved repeat families. Here, we discuss a detailed comparison between the structural classes in RepeatsDB and the corresponding Pfam repeat families and clans. Most instances are found to map one-to-one between structure and sequence. Some notable exceptions such as leucine-rich repeats (LRRs) and α-solenoids are discussed.},

note = {Cited by: 9},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84959549790,

title = {Structural in silico dissection of the collagen v interactome to identify genotype-phenotype correlations in classic Ehlers-Danlos Syndrome (EDS)},

author = {Lisanna Paladin and Silvio C. E. Tosatto and Giovanni Minervini},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84959549790&origin=inward},

doi = {10.1016/j.febslet.2015.11.022},

year  = {2015},

date = {2015-01-01},

journal = {FEBS Letters},

volume = {589},

number = {24},

pages = {3871-3878},

publisher = {Wiley Blackwellinfo@wiley.com},

abstract = {© 2015 Federation of European Biochemical Societies.Collagen V mutations are associated with Elhers-Danlos syndrome (EDS), a group of heritable collagenopathies. Collagen V structure is not available and the disease-causing mechanism is unclear. To address this issue, we manually curated missense mutations suspected to promote classic type EDS (cEDS) insurgence from the literature and performed a genotype-phenotype correlation study. Further, we generated a homology model of the collagen V triple helix to evaluate the pathogenic effects. The resulting structure was used to map known protein-protein interactions enriched with in silico predictions. An interaction network model for collagen V was created. We found that cEDS heterogeneous manifestations may be explained by the involvement in two different extracellular matrix pathways, related to cell adhesion and tissue repair or cell differentiation, growth and apoptosis.},

note = {Cited by: 12; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84902324935,

title = {Design and analysis of a Petri Net model of the Von Hippel-Lindau (VHL) tumor suppressor interaction network},

author = {Giovanni Minervini and Elisabetta Panizzoni and Manuel Giollo and Alessandro Masiero and Carlo Ferrari and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84902324935&origin=inward},

doi = {10.1371/journal.pone.0096986},

year  = {2014},

date = {2014-01-01},

journal = {PLoS ONE},

volume = {9},

number = {6},

publisher = {Public Library of Scienceplos@plos.org},

abstract = {Von Hippel-Lindau (VHL) syndrome is a hereditary condition predisposing to the development of different cancer forms, related to germline inactivation of the homonymous tumor suppressor pVHL. The best characterized function of pVHL is the ubiquitination dependent degradation of Hypoxia Inducible Factor (HIF) via the proteasome. It is also involved in several cellular pathways acting as a molecular hub and interacting with more than 200 different proteins. Molecular details of pVHL plasticity remain in large part unknown. Here, we present a novel manually curated Petri Net (PN) model of the main pVHL functional pathways. The model was built using functional information derived from the literature. It includes all major pVHL functions and is able to credibly reproduce VHL syndrome at the molecular level. The reliability of the PN model also allowed in silico knockout experiments, driven by previous model analysis. Interestingly, PN analysis suggests that the variability of different VHL manifestations is correlated with the concomitant inactivation of different metabolic pathways. © 2014 Minervini et al.},

note = {Cited by: 11; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84903728406,

title = {Mapping and annotating obesity-related genes in pig and human genomes},

author = {Pier Luigi Martelli and Luca Fontanesi and Damiano Piovesan and Piero Fariselli and Rita Casadio},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84903728406&origin=inward},

doi = {10.2174/09298665113209990053},

year  = {2014},

date = {2014-01-01},

journal = {Protein and Peptide Letters},

volume = {21},

number = {8},

pages = {840-846},

publisher = {Bentham Science PublishersP.O. Box 294Bussum1400 AG},

abstract = {Background. Obesity is a major health problem in both developed and emerging countries. Obesity is a complex disease whose etiology involves genetic factors in strong interplay with environmental determinants and lifestyle. The discovery of genetic factors and biological pathways underlying human obesity is hampered by the difficulty in controlling the genetic background of human cohorts. Animal models are then necessary to further dissect the genetics of obesity. Pig has emerged as one of the most attractive models, because of the similarity with humans in the mechanisms regulating the fat deposition. Results. We collected the genes related to obesity in humans and to fat deposition traits in pig. We localized them on both human and pig genomes, building a map useful to interpret comparative studies on obesity. We characterized the collected genes structurally and functionally with BAR+ and mapped them on KEGG pathways and on STRING protein interaction network. Conclusions. The collected set consists of 361 obesity related genes in human and pig genomes. All genes were mapped on the human genome, and 54 could not be localized on the pig genome (release 2012). Only for 3 human genes there is no counterpart in pig, confirming that this animal is a good model for human obesity studies. Obesity related genes are mostly involved in regulation and signaling processes/pathways and relevant connection emerges between obesity-related genes and diseases such as cancer and infectious diseases. © 2014 Bentham Science Publishers.},

note = {Cited by: 3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84902011183,

title = {CDKN2A Unclassified Variants in Familial Malignant Melanoma: Combining Functional and Computational Approaches for Their Assessment},

author = {Maria Chiara Scaini and Giovanni Minervini and Lisa Elefanti and Paola Ghiorzo and Lorenza Pastorino and Silvia Tognazzo and Simona Agata and Monica Quaggio and Daniela Zullato and Giovanna Bianchi-Scarrà and Marco Montagna and Emma D'Andrea and Chiara Menin and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84902011183&origin=inward},

doi = {10.1002/humu.22550},

year  = {2014},

date = {2014-01-01},

journal = {Human Mutation},

volume = {35},

number = {7},

pages = {828-840},

publisher = {John Wiley and Sons Inc.P.O.Box 18667NewarkNJ 07191-8667},

abstract = {CDKN2A codes for two oncosuppressors by alternative splicing of two first exons: p16INK4a and p14ARF. Germline mutations are found in about 40% of melanoma-prone families, and most of them are missense mutations mainly affecting p16INK4a. A growing number of p16INK4a variants of uncertain significance (VUS) are being identified but, unless their pathogenic role can be demonstrated, they cannot be used for identification of carriers at risk. Predicting the effect of these VUS by either a "standard" in silico approach, or functional tests alone, is rather difficult. Here, we report a protocol for the assessment of any p16INK4a VUS, which combines experimental and computational tools in an integrated approach. We analyzed p16INK4a VUS from melanoma patients as well as variants derived through permutation of conserved p16INK4a amino acids. Variants were expressed in a p16INK4a-null cell line (U2-OS) and tested for their ability to block proliferation. In parallel, these VUS underwent in silico prediction analysis and molecular dynamics simulations. Evaluation of in silico and functional data disclosed a high agreement for 15/16 missense mutations, suggesting that this approach could represent a pilot study for the definition of a protocol applicable to VUS in general, involved in other diseases, as well. © 2014 WILEY PERIODICALS, INC.},

note = {Cited by: 17},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84891766568,

title = {RepeatsDB: A database of tandem repeat protein structures},

author = {Tomás Di Domenico and Emilio Potenza and Ian Walsh and Gonzalo Parra and Manuel Giollo and Giovanni Minervini and Damiano Piovesan and Awais Ihsan and Carlo Ferrari and Andrey V. Kajava and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84891766568&origin=inward},

doi = {10.1093/nar/gkt1175},

year  = {2014},

date = {2014-01-01},

journal = {Nucleic Acids Research},

volume = {42},

number = {D1},

abstract = {RepeatsDB (http://repeatsdb.bio.unipd.it/) is a database of annotated tandem repeat protein structures. Tandem repeats pose a difficult problem for the analysis of protein structures, as the underlying sequence can be highly degenerate. Several repeat types haven been studied over the years, but their annotation was done in a case-by-case basis, thus making large-scale analysis difficult. We developed RepeatsDB to fill this gap. Using state-of-the-art repeat detection methods and manual curation, we systematically annotated the Protein Data Bank, predicting 10 745 repeat structures. In all, 2797 structures were classified according to a recently proposed classification schema, which was expanded to accommodate new findings. In addition, detailed annotations were performed in a subset of 321 proteins. These annotations feature information on start and end positions for the repeat regions and units. RepeatsDB is an ongoing effort to systematically classify and annotate structural protein repeats in a consistent way. It provides users with the possibility to access and download high-quality datasets either interactively or programmatically through web services. © 2013 The Author(s). Published by Oxford University Press.},

note = {Cited by: 56; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84904786762,

title = {PASTA 2.0: An improved server for protein aggregation prediction},

author = {Ian Walsh and Flavio Seno and Silvio C. E. Tosatto and Antonio Trovato},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84904786762&origin=inward},

doi = {10.1093/nar/gku399},

year  = {2014},

date = {2014-01-01},

journal = {Nucleic Acids Research},

volume = {42},

number = {W1},

publisher = {Oxford University Pressjnl.info@oup.co.uk},

abstract = {The formation of amyloid aggregates upon protein misfolding is related to several devastating degenerative diseases. The propensities of different protein sequences to aggregate into amyloids, how they are enhanced by pathogenic mutations, the presence of aggregation hot spots stabilizing pathological interactions, the establishing of cross-amyloid interactions between co-aggregating proteins, all rely at the molecular level on the stability of the amyloid cross-beta structure. Our redesigned server, PASTA 2.0, provides a versatile platform where all of these different features can be easily predicted on a genomic scale given input sequences. The server provides other pieces of information, such as intrinsic disorder and secondary structure predictions, that complement the aggregation data. The PASTA 2.0 energy function evaluates the stability of putative cross-beta pairings between different sequence stretches. It was re-derived on a larger dataset of globular protein domains. The resulting algorithm was benchmarked on comprehensive peptide and protein test sets, leading to improved, state-of-the-art results with more amyloid forming regions correctly detected at high specificity. The PASTA 2.0 server can be accessed at http://protein.bio.unipd.it/pasta2/. © 2014 The Author(s).},

note = {Cited by: 360; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84925286085,

title = {NeEMO: A method using residue interaction networks to improve prediction of protein stability upon mutation},

author = {Manuel Giollo and Alberto J. M. Martin and Ian Walsh and Carlo Ferrari and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84925286085&origin=inward},

doi = {10.1186/1471-2164-15-S4-S7},

year  = {2014},

date = {2014-01-01},

journal = {BMC Genomics},

volume = {15},

publisher = {BioMed Central Ltd.info@biomedcentral.com},

abstract = {© 2014 Manuel et al.Background: The rapid growth of un-annotated missense variants poses challenges requiring novel strategies for their interpretation. From the thermodynamic point of view, amino acid changes can lead to a change in the internal energy of a protein and induce structural rearrangements. This is of great relevance for the study of diseases and protein design, justifying the development of prediction methods for variant-induced stability changes. Results: Here we propose NeEMO, a tool for the evaluation of stability changes using an effective representation of proteins based on residue interaction networks (RINs). RINs are used to extract useful features describing interactions of the mutant amino acid with its structural environment. Benchmarking shows NeEMO to be very effective, allowing reliable predictions in different parts of the protein such as β-strands and buried residues. Validation on a previously published independent dataset shows that NeEMO has a Pearson correlation coefficient of 0.77 and a standard error of 1 Kcal/mol, outperforming nine recent methods. The NeEMO web server can be freely accessed from URL: http://protein.bio.unipd.it/neemo/. Conclusions: NeEMO offers an innovative and reliable tool for the annotation of amino acid changes. A key contribution are RINs, which can be used for modeling proteins and their interactions effectively. Interestingly, the approach is very general, and can motivate the development of a new family of RIN-based protein structure analyzers. NeEMO may suggest innovative strategies for bioinformatics tools beyond protein stability prediction.},

note = {Cited by: 90; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84898906108,

title = {RUBI: Rapid proteomic-scale prediction of lysine ubiquitination and factors influencing predictor performance},

author = {Ian Walsh and Tomás Di Domenico and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84898906108&origin=inward},

doi = {10.1007/s00726-013-1645-3},

year  = {2014},

date = {2014-01-01},

journal = {Amino Acids},

volume = {46},

number = {4},

pages = {853-862},

publisher = {Springer-Verlag Wienmichaela.bolli@springer.at},

abstract = {Post-translational modification of protein lysines was recently shown to be a common feature of eukaryotic organisms. The ubiquitin modification is regarded as a versatile regulatory mechanism with many important cellular roles. Large-scale datasets are becoming available for H. sapiens ubiquitination. However, using current experimental techniques the vast majority of their sites remain unidentified and in silico tools may offer an alternative. Here, we introduce Rapid UBIquitination (RUBI) a sequence-based ubiquitination predictor designed for rapid application on a genome scale. RUBI was constructed using an iterative approach. At each iteration, important factors which influenced performance and its usability were investigated. The final RUBI model has an AUC of 0.868 on a large cross-validation set and is shown to outperform other available methods on independent sets. Predicted intrinsic disorder is shown to be weakly anti-correlated to ubiquitination for the H. sapiens dataset and improves performance slightly. RUBI predicts the number of ubiquitination sites correctly within three sites for ca. 80 % of the tested proteins. The average potentially ubiquitinated proteome fraction is predicted to be at least 25 % across a variety of model organisms, including several thousand possible H. sapiens proteins awaiting experimental characterization. RUBI can accurately predict ubiquitination on unseen examples and has a signal across different eukaryotic organisms. The factors which influenced the construction of RUBI could also be tested in other post-translational modification predictors. One of the more interesting factors is the influence of intrinsic protein disorder on ubiquitinated lysines where residues with low disorder probability are preferred. © 2013 Springer-Verlag Wien.},

note = {Cited by: 29},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84908207041,

title = {Identification of Four Novel PCDH19 Mutations and Prediction of Their Functional Impact},

author = {Emanuela Leonardi and Stefano Sartori and Marilena Vecchi and Elisa Bettella and Roberta Polli and Luca De Palma and Clementina Boniver and Alessandra Murgia},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84908207041&origin=inward},

doi = {10.1111/ahg.12082},

year  = {2014},

date = {2014-01-01},

journal = {Annals of Human Genetics},

volume = {78},

number = {6},

pages = {389-398},

publisher = {Blackwell Publishing Ltdcustomerservices@oxonblackwellpublishing.com},

abstract = {© 2014 John Wiley & Sons Ltd/University College London.The PCDH19 gene encodes protocadherin-19, a transmembrane protein with six cadherin (EC) domains, containing adhesive interfaces likely to be involved in neuronal connection. Over a hundred mostly private mutations have been identified in girls with epilepsy, with or without intellectual disability (ID). Furthermore, transmitting hemizygous males are devoid of seizures or ID, making it difficult to establish the pathogenic nature of newly identified variants. Here, we describe an integrated approach to evaluate the pathogenicity of four novel PCDH19 mutations. Segregation analysis has been complemented with an in silico analysis of mutation effects at the protein level. Using sequence information, we compared different computational prediction methods. We used homology modeling to build structural models of two PCDH19 EC-domains, and compared wild-type and mutant models to identify differences in residue interactions or biochemical properties of the model surfaces. Our analysis suggests different molecular effects of the novel mutations in exerting their pathogenic role. Two of them interfere with or alter functional residues predicted to mediate ligand or protein binding, one alters the EC-domain folding stability; the frame-shift mutation produces a truncated protein lacking the intracellular domain. Interestingly, the girl carrying the putative loss of function mutation presents the most severe phenotype.},

note = {Cited by: 18; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84906097745,

title = {Evaluation of the steric impact of flavin adenine dinucleotide in Drosophila melanogaster cryptochrome function},

author = {Alessandro Masiero and Simona Aufiero and Giovanni Minervini and Stefano Moro and Rodolfo Costa and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84906097745&origin=inward},

doi = {10.1016/j.bbrc.2014.07.038},

year  = {2014},

date = {2014-01-01},

journal = {Biochemical and Biophysical Research Communications},

volume = {450},

number = {4},

pages = {1606-1611},

publisher = {Academic Press Inc.apjcs@harcourt.com},

abstract = {Photoreceptors are crucial components for circadian rhythm entrainment in animals, plants, fungi and cyanobacteria. Cryptochromes (CRYs) are flavin adenine dinucleotide (FAD) containing photoreceptors, and FAD is responsible for signal transduction, in contrast to photolyases where it promotes DNA-damage repair. In this work, we investigated an alternative role for FAD in CRY. We analyzed the Drosophila melanogaster CRY crystal structure by means of molecular dynamics, elucidating how this large co-factor within the receptor could be crucial for CRY structural stability. The co-factor appears indeed to improve receptor motility, providing steric hindrance. Moreover, multiple sequence alignments revealed that conserved motifs in the C-terminal tail could be necessary for functional stability. © 2014 Elsevier Inc. All rights reserved.},

note = {Cited by: 3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84879314610,

title = {How to inherit statistically validated annotation within BAR+ protein clusters},

author = {Damiano Piovesan and Pier Luigi Martelli and Piero Fariselli and Giuseppe Profiti and Andrea Zauli and Ivan Rossi and Rita Casadio},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84879314610&origin=inward},

doi = {10.1186/1471-2105-14-S3-S4},

year  = {2013},

date = {2013-01-01},

journal = {BMC Bioinformatics},

volume = {14},

number = {SUPPL.3},

abstract = {Background: In the genomic era a key issue is protein annotation, namely how to endow protein sequences, upon translation from the corresponding genes, with structural and functional features. Routinely this operation is electronically done by deriving and integrating information from previous knowledge. The reference database for protein sequences is UniProtKB divided into two sections, UniProtKB/TrEMBL which is automatically annotated and not reviewed and UniProtKB/Swiss-Prot which is manually annotated and reviewed. The annotation process is essentially based on sequence similarity search. The question therefore arises as to which extent annotation based on transfer by inheritance is valuable and specifically if it is possible to statistically validate inherited features when little homology exists among the target sequence and its template(s).Results: In this paper we address the problem of annotating protein sequences in a statistically validated manner considering as a reference annotation resource UniProtKB. The test case is the set of 48,298 proteins recently released by the Critical Assessment of Function Annotations (CAFA) organization. We show that we can transfer after validation, Gene Ontology (GO) terms of the three main categories and Pfam domains to about 68% and 72% of the sequences, respectively. This is possible after alignment of the CAFA sequences towards BAR+, our annotation resource that allows discriminating among statistically validated and not statistically validated annotation. By comparing with a direct UniProtKB annotation, we find that besides validating annotation of some 78% of the CAFA set, we assign new and statistically validated annotation to 14.8% of the sequences and find new structural templates for about 25% of the chains, half of which share less than 30% sequence identity to the corresponding template/s.Conclusion: Inheritance of annotation by transfer generally requires a careful selection of the identity value among the target and the template in order to transfer structural and/or functional features. Here we prove that even distantly remote homologs can be safely endowed with structural templates and GO and/or Pfam terms provided that annotation is done within clusters collecting cluster-related protein sequences and where a statistical validation of the shared structural and functional features is possible. © 2013 Piovesan et al.; licensee BioMed Central Ltd.},

note = {Cited by: 7; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84881520207,

title = {The role of the N-terminal tail for the oligomerization, folding and stability of human frataxin},

author = {Santiago E. Faraj and Leandro Venturutti and Ernesto A. Roman and Cristina B. Marino-Buslje and Astor Mignone and Silvio C. E. Tosatto and José M. Delfino and Javier Santos},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84881520207&origin=inward},

doi = {10.1016/j.fob.2013.07.004},

year  = {2013},

date = {2013-01-01},

journal = {FEBS Open Bio},

volume = {3},

pages = {310-320},

abstract = {The N-terminal stretch of human frataxin (hFXN) intermediate (residues 42-80) is not conserved throughout evolution and, under defined experimental conditions, behaves as a random-coil. Overexpression of hFXN56-210 in Escherichia coli yields a multimer, whereas the mature form of hFXN (hFXN81-210) is monomeric. Thus, cumulative experimental evidence points to the N-terminal moiety as an essential element for the assembly of a high molecular weight oligomer. The secondary structure propensity of peptide 56-81, the moiety putatively responsible for promoting protein-protein interactions, was also studied. Depending on the environment (TFE or SDS), this peptide adopts α-helical or β-strand structure. In this context, we explored the conformation and stability of hFXN56-210. The biophysical characterization by fluorescence, CD and SEC-FPLC shows that subunits are well folded, sharing similar stability to hFXN90-210. However, controlled proteolysis indicates that the N-terminal stretch is labile in the context of the multimer, whereas the FXN domain (residues 81-210) remains strongly resistant. In addition, guanidine hydrochloride at low concentration disrupts intermolecular interactions, shifting the ensemble toward the monomeric form. The conformational plasticity of the N-terminal tail might impart on hFXN the ability to act as a recognition signal as well as an oligomerization trigger. Understanding the fine-tuning of these activities and their resulting balance will bear direct relevance for ultimately comprehending hFXN function. © 2013 The Authors.},

note = {Cited by: 11; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84892759581,

title = {SUS-BAR: A database of pig proteins with statistically validated structural and functional annotation},

author = {Damiano Piovesan and Giuseppe Profiti and Pier Luigi Martelli and Piero Fariselli and Luca Fontanesi and Rita Casadio},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84892759581&origin=inward},

doi = {10.1093/database/bat065},

year  = {2013},

date = {2013-01-01},

journal = {Database},

volume = {2013},

abstract = {Given the relevance of the pig proteome in different studies, including human complex maladies, a statistical validation of the annotation is required for a better understanding of the role of specific genes and proteins in the complex networks underlying biological processes in the animal. Presently, approximately 80% of the pig proteome is still poorly annotated, and the existence of protein sequences is routinely inferred automatically by sequence alignment towards preexisting sequences. In this article, we introduce SUS-BAR, a database that derives information mainly from UniProt Knowledgebase and that includes 26 206 pig protein sequences. In SUS-BAR, 16 675 of the pig protein sequences are endowed with statistically validated functional and structural annotation. Our statistical validation is determined by adopting a cluster-centric annotation procedure that allows transfer of different types of annotation, including structure and function. Each sequence in the database can be associated with a set of statistically validated Gene Ontologies (GOs) of the three main subontologies (Molecular Function, Biological Process and Cellular Component), with Pfam functional domains, and when possible, with a cluster Hidden Markov Model that allows modelling the 3D structure of the protein. A database search allows some statistics demonstrating the enrichment in both GO and Pfam annotations of the pig proteins as compared with UniProt Knowledgebase annotation. Searching in SUS-BAR allows retrieval of the pig protein annotation for further analysis. The search is also possible on the basis of specific GO terms and this allows retrieval of all the pig sequences participating into a given biological process, after annotation with our system. Alternatively, the search is possible on the basis of structural information, allowing retrieval of all the pig sequences with the same structural characteristics. © The Author(s) 2013. Published by Oxford University Press.},

note = {Cited by: 5; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84879800008,

title = {Early-onset epileptic encephalopathy in a girl carrying a truncating mutation of the ARX gene: Rethinking the ARX phenotype in females},

author = {Bettella and Di Rosa and Polli and Leonardi and Tortorella and Sartori and Murgia},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84879800008&origin=inward},

doi = {10.1111/cge.12034},

year  = {2013},

date = {2013-01-01},

journal = {Clinical Genetics},

volume = {84},

number = {1},

pages = {82-85},

abstract = {Severe early-onset epilepsy is due to a number of known causes, although a clear etiology is not identifiable in up to a third of all the cases. Pathogenic sequence variations in the ARX gene have been described almost exclusively in males, whereas heterozygous female relatives, such as mothers, sisters and even grandmothers have been largely reported as asymptomatic or mildly affected. To investigate the pathogenic role of ARX in refractory epilepsy of early onset even in females, we have screened the ARX sequence in a population of 50 female subjects affected with unexplained epileptic encephalopathy with onset in the first year of life. We report the identification of a novel truncating mutation of the coding region of the ARX gene in a girl with a structurally normal brain. Our findings confirm the role of ARX in the pathogenesis of early epilepsy and underline the importance of screening of the ARX gene in both male and female subjects with otherwise unexplained early onset epileptic encephalopathy.© 2012 John Wiley & Sons A/S.},

note = {Cited by: 13},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84879373603,

title = {Protein conformational diversity correlates with evolutionary rate},

author = {Diego Javier Zea and Alexander Miguel Monzon and Maria Silvina Fornasari and Cristina Marino-Buslje and Gustavo Parisi},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84879373603&origin=inward},

doi = {10.1093/molbev/mst065},

year  = {2013},

date = {2013-01-01},

journal = {Molecular Biology and Evolution},

volume = {30},

number = {7},

pages = {1500-1503},

abstract = {Native state of proteins is better represented by an ensemble of conformers in equilibrium than by only one structure. The extension of structural differences between conformers characterizes the conformational diversity of the protein. In this study, we found a negative correlation between conformational diversity and protein evolutionary rate. Conformational diversity was expressed as the maximum root mean square deviation (RMSD) between the available conformers in Conformational Diversity of Native State database. Evolutionary rate estimations were calculated using 16 different species compared with human sharing at least 700 orthologous proteins with known conformational diversity extension. The negative correlation found is independent of the protein expression level and comparable in magnitude and sign with the correlation between gene expression level and evolutionary rate. Our findings suggest that the structural constraints underlying protein dynamism, essential for protein function, could modulate protein divergence. © 2013 The Author.},

note = {Cited by: 27; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84893166471,

title = {PANADA: Protein Association Network Annotation, Determination and Analysis},

author = {Alberto J. M. Martin and Ian Walsh and Tomás Di Domenico and Ivan Mičetić and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84893166471&origin=inward},

doi = {10.1371/journal.pone.0078383},

year  = {2013},

date = {2013-01-01},

journal = {PLoS ONE},

volume = {8},

number = {11},

abstract = {Increasingly large numbers of proteins require methods for functional annotation. This is typically based on pairwise inference from the homology of either protein sequence or structure. Recently, similarity networks have been presented to leverage both the ability to visualize relationships between proteins and assess the transferability of functional inference. Here we present PANADA, a novel toolkit for the visualization and analysis of protein similarity networks in Cytoscape. Networks can be constructed based on pairwise sequence or structural alignments either on a set of proteins or, alternatively, by database search from a single sequence. The Panada web server, executable for download and examples and extensive help files are available at URL: http://protein.bio.unipd.it/panada/. © 2013 Martin et al.},

note = {Cited by: 7; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84878095702,

title = {FFPred 2.0: Improved Homology-Independent Prediction of Gene Ontology Terms for Eukaryotic Protein Sequences},

author = {Federico Minneci and Damiano Piovesan and Domenico Cozzetto and David T. Jones},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84878095702&origin=inward},

doi = {10.1371/journal.pone.0063754},

year  = {2013},

date = {2013-01-01},

journal = {PLoS ONE},

volume = {8},

number = {5},

abstract = {To understand fully cell behaviour, biologists are making progress towards cataloguing the functional elements in the human genome and characterising their roles across a variety of tissues and conditions. Yet, functional information - either experimentally validated or computationally inferred by similarity - remains completely missing for approximately 30% of human proteins. FFPred was initially developed to bridge this gap by targeting sequences with distant or no homologues of known function and by exploiting clear patterns of intrinsic disorder associated with particular molecular activities and biological processes. Here, we present an updated and improved version, which builds on larger datasets of protein sequences and annotations, and uses updated component feature predictors as well as revised training procedures. FFPred 2.0 includes support vector regression models for the prediction of 442 Gene Ontology (GO) terms, which largely expand the coverage of the ontology and of the biological process category in particular. The GO term list mainly revolves around macromolecular interactions and their role in regulatory, signalling, developmental and metabolic processes. Benchmarking experiments on newly annotated proteins show that FFPred 2.0 provides more accurate functional assignments than its predecessor and the ProtFun server do; also, its assignments can complement information obtained using BLAST-based transfer of annotations, improving especially prediction in the biological process category. Furthermore, FFPred 2.0 can be used to annotate proteins belonging to several eukaryotic organisms with a limited decrease in prediction quality. We illustrate all these points through the use of both precision-recall plots and of the COGIC scores, which we recently proposed as an alternative numerical evaluation measure of function prediction accuracy. © 2013 Minneci et al.},

note = {Cited by: 40; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84885843727,

title = {A novel SACS mutation results in non-ataxic spastic paraplegia and peripheral neuropathy},

author = {Gregianin and Vazza and Scaramel and Boaretto and Vettori and Leonardi and Tosatto and Manara and Pegoraro and Mostacciuolo},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84885843727&origin=inward},

doi = {10.1111/ene.12220},

year  = {2013},

date = {2013-01-01},

journal = {European Journal of Neurology},

volume = {20},

number = {11},

pages = {1486-1491},

publisher = {Blackwell Publishing Ltdcustomerservices@oxonblackwellpublishing.com},

abstract = {Background and purpose: Mutations in the SACS gene are commonly associated with autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS), a complex neurodegenerative disorder characterized by progressive degeneration of the cerebellum and spinal cord tracts. The aim of this study was to identify the genetic cause of the disease in an Italian family with spastic paraplegia and peripheral neuropathy. Methods: Affected subjects were subjected to a comprehensive neurological examination including electromyography and brain magnetic resonance imaging. Genetic studies included exclusion of known disease genes, genome-wide linkage analysis using high density single nucleotide polymorphism genotyping and candidate gene sequencing. Results: Molecular analyses revealed a novel missense mutation in the SACS gene (c.11,104A>G) occurring in a homozygous state in patients and absent in 700 Italian control chromosomes. The mutation led to the amino acid substitution p.Thr3702Ala in the sacsin protein, in a possible protein-protein interaction site of UBE3A binding domain. Conclusion: This study broadens the genetic spectrum of SACS mutations and expands the clinical ARSACS phenotype suggesting that the SACS gene can be considered in patients with non-canonical ARSACS clinical presentations. © 2013 EFNS.},

note = {Cited by: 25; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84874663959,

title = {A large-scale evaluation of computational protein function prediction},

author = {Predrag Radivojac and Wyatt T. Clark and Tal Ronnen Oron and Alexandra M. Schnoes and Tobias Wittkop and Artem Sokolov and Kiley Graim and Christopher Funk and Karin Verspoor and Asa Ben-Hur and Gaurav Pandey and Jeffrey M. Yunes and Ameet S. Talwalkar and Susanna Repo and Michael L. Souza and Damiano Piovesan and Rita Casadio and Zheng Wang and Jianlin Cheng and Hai Fang and Julian Gough and Patrik Koskinen and Petri Törönen and Jussi Nokso-Koivisto and Liisa Holm and Domenico Cozzetto and Daniel W. A. Buchan and Kevin Bryson and David T. Jones and Bhakti Limaye and Harshal Inamdar and Avik Datta and Sunitha K. Manjari and Rajendra Joshi and Meghana Chitale and Daisuke Kihara and Andreas M. Lisewski and Serkan Erdin and Eric Venner and Olivier Lichtarge and Robert Rentzsch and Haixuan Yang and Alfonso E. Romero and Prajwal Bhat and Alberto Paccanaro and Tobias Hamp and Rebecca Kaßner and Stefan Seemayer and Esmeralda Vicedo and Christian Schaefer and Dominik Achten and Florian Auer and Ariane Boehm and Tatjana Braun and Maximilian Hecht and Mark Heron and Peter Hönigschmid and Thomas A. Hopf and Stefanie Kaufmann and Michael Kiening and Denis Krompass and Cedric Landerer and Yannick Mahlich and Manfred Roos and Jari Björne and Tapio Salakoski and Andrew Wong and Hagit Shatkay and Fanny Gatzmann and Ingolf Sommer and Mark N. Wass and Michael J. E. Sternberg and Nives Škunca and Fran Supek and Matko Bošnjak and Panče Panov and Sašo Džeroski and Tomislav Šmuc and Yiannis A. I. Kourmpetis and Aalt D. J. Van Dijk and Cajo J. F. Ter Braak and Yuanpeng Zhou and Qingtian Gong and Xinran Dong and Weidong Tian and Marco Falda and Paolo Fontana and Enrico Lavezzo and Barbara Di Camillo and Stefano Toppo and Liang Lan and Nemanja Djuric and Yuhong Guo and Slobodan Vucetic and Amos Bairoch and Michal Linial and Patricia C. Babbitt and Steven E. Brenner and Christine Orengo and Burkhard Rost and ...},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84874663959&origin=inward},

doi = {10.1038/nmeth.2340},

year  = {2013},

date = {2013-01-01},

journal = {Nature Methods},

volume = {10},

number = {3},

pages = {221-227},

abstract = {Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools. © 2013 Nature America, Inc. All rights reserved.},

note = {Cited by: 728; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84885748326,

title = {Seasonal variation in genetic population structure of sábalo (Prochilodus lineatus) in the Lower Uruguay River},

author = {Eva Carolina Rueda and Pedro Carriquiriborde and Alexander Miguel Monzón and Gustavo M. Somoza and Guillermo Ortí},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84885748326&origin=inward},

doi = {10.1007/s10709-013-9739-0},

year  = {2013},

date = {2013-01-01},

journal = {Genetica},

volume = {141},

number = {7-9},

pages = {401-407},

abstract = {Prochilodus lineatus is a highly migratory fish species that sustains the most important commercial fishery of Paraná-Paraguay basin. Migratory patterns are poorly known and only few population genetic studies are available for this species in the Upper Paraná. To assess genetic population structure, we genotyped a sample of 93 individuals from the Lower Uruguay River close to Gualeguaychú city (Entre Ríos, Argentina) at three different times, July 2008 (Winter), September 2008 (Spring) and May 2009 (Fall). All individuals were genotyped for 12 microsatellite loci previously found to be informative to assess populations of P. lineatus. Our results show seasonal variation of the genetic sub-structuring at this locality that may be related to the presence of different migratory stocks throughout the year. The Fall sample includes an additional genetic cluster of individuals not detected in Winter and Spring, suggesting that this species should be considered a mixed stock fishery. © 2013 Springer Science+Business Media Dordrecht.},

note = {Cited by: 26},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84888597395,

title = {Extended and robust protein sequence annotation over conservative nonhierarchical clusters: The case study of the abc transporters},

author = {Damiano Piovesan and Giuseppe Profiti and Pier Luigi Martell and Piero Fariselli and Rita Casadio},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84888597395&origin=inward},

doi = {10.1145/2504729},

year  = {2013},

date = {2013-01-01},

journal = {ACM Journal on Emerging Technologies in Computing Systems},

volume = {9},

number = {4},

abstract = {Genome annotation is one of the most important issues in the genomic era. The exponential growth rate of newly sequenced genomes and proteomes urges the development of fast and reliable annotation methods, suited to exploit all the information available in curated databases of protein sequences and structures. To this aim we developed BAR+, the Bologna Annotation Resource.1 The basic notion is that sequences with high identity value to a counterpart can inherit the same function/s and structure, if available. As a case study we describe how the ATP-binding domain of the ABC transporters can be found and modeled in over 30,000 new sequences not annotated before. We also mapped into BAR+ all the ABC transporters listed in the Transporter Classification DataBase2 and found that within our environment annotation could be extended to another 256,866 sequences. ©c 2013 ACM 1550-4832/2013/11-ART27 15.00.},

note = {Cited by: 2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84884764376,

title = {2mit, an Intronic Gene of Drosophila melanogaster timeless2, Is Involved in Behavioral Plasticity},

author = {Francesca Baggio and Andrea Bozzato and Clara Benna and Emanuela Leonardi and Ottavia Romoli and Moira Cognolato and Silvio C. E. Tosatto and Rodolfo Costa and Federica Sandrelli},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84884764376&origin=inward},

doi = {10.1371/journal.pone.0076351},

year  = {2013},

date = {2013-01-01},

journal = {PLoS ONE},

volume = {8},

number = {9},

abstract = {Background:Intronic genes represent textasciitilde 6% of the total gene complement in Drosophila melanogaster and textasciitilde 85% of them encode for proteins. We recently characterized the D. melanogaster timeless2 (tim2) gene, showing its active involvement in chromosomal stability and light synchronization of the adult circadian clock. The protein coding gene named 2mit maps on the 11th tim2 intron in the opposite transcriptional orientation.Methodology/Principal Findings:Here we report the molecular and functional characterization of 2mit. The 2mit gene is expressed throughout Drosophila development, localizing mainly in the nervous system during embryogenesis and mostly in the mushroom bodies and ellipsoid body of the central complex in the adult brain. In silico analyses revealed that 2mit encodes a putative leucine-Rich Repeat transmembrane receptor with intrinsically disordered regions, harboring several fully conserved functional interaction motifs in the cytosolic side. Using insertional mutations, tissue-specific over-expression, and down-regulation approaches, it was found that 2mit is implicated in adult short-term memory, assessed by a courtship conditioning assay. In D. melanogaster, tim2 and 2mit do not seem to be functionally related. Bioinformatic analyses identified 2MIT orthologs in 21 Drosophilidae, 4 Lepidoptera and in Apis mellifera. In addition, the tim2-2mit host-nested gene organization was shown to be present in A. mellifera and maintained among Drosophila species. Within the Drosophilidae 2mit-hosting tim2 intron, in silico approaches detected a neuronal specific transcriptional binding site which might have contributed to preserve the specific host-nested gene association across Drosophila species. Conclusions/Significance:Taken together, these results indicate that 2mit, a gene mainly expressed in the nervous system, has a role in the behavioral plasticity of the adult Drosophila. The presence of a putative 2mit regulatory enhancer within the 2mit-hosting tim2 intron could be considered an evolutionary constraint potentially involved in maintaining the tim2-2mit host-nested chromosomal architecture during the evolution of Drosophila species. © 2013 Baggio et al.},

note = {Cited by: 7; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84897366399,

title = {CoDNaS: A database of conformational diversity in the native state of proteins},

author = {Alexander Miguel Monzon and Ezequiel Juritz and María Silvina Fornasari and Gustavo Parisi},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84897366399&origin=inward},

doi = {10.1093/bioinformatics/btt405},

year  = {2013},

date = {2013-01-01},

journal = {Bioinformatics},

volume = {29},

number = {19},

pages = {2512-2514},

publisher = {Oxford University Press},

abstract = {Motivation: Conformational diversity is a key concept in the understanding of different issues related with protein function such as the study of catalytic processes in enzymes, protein-protein recognition, protein evolution and the origins of new biological functions. Here, we present a database of proteins with different degrees of conformational diversity. Conformational Diversity of Native State (CoDNaS) is a redundant collection of three-dimensional structures for the same protein derived from protein data bank. Structures for the same protein obtained under different crystallographic conditions have been associated with snapshots of protein dynamism and consequently could characterize protein conformers. CoDNaS allows the user to explore global and local structural differences among conformers as a function of different parameters such as presence of ligand, post-translational modifications, changes in oligomeric states and differences in pH and temperature. Additionally, CoDNaS contains information about protein taxonomy and function, disorder level and structural classification offering useful information to explore the underlying mechanism of conformational diversity and its close relationship with protein function. Currently, CoDNaS has 122 122 structures integrating 12 684 entries, with an average of 9.63 conformers per protein. © The Author 2013.},

note = {Cited by: 28; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84887176187,

title = {Analysis and consensus of currently available intrinsic protein disorder annotation sources in the MobiDB database},

author = {Tomás Di Domenico and Ian Walsh and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84887176187&origin=inward},

doi = {10.1186/1471-2105-14-S7-S3},

year  = {2013},

date = {2013-01-01},

journal = {BMC Bioinformatics},

volume = {14},

number = {SUPPL7},

abstract = {Background: Intrinsic protein disorder is becoming an increasingly important topic in protein science. During the last few years, intrinsically disordered proteins (IDPs) have been shown to play a role in many important biological processes, e.g. protein signalling and regulation. This has sparked a need to better understand and characterize different types of IDPs, their functions and roles. Our recently published database, MobiDB, provides a centralized resource for accessing and analysing intrinsic protein disorder annotations.Results: Here, we present a thorough description and analysis of the data made available by MobiDB, providing descriptive statistics on the various available annotation sources. Version 1.2.1 of the database contains annotations for ca. 4,500,000 UniProt sequences, covering all eukaryotic proteomes. In addition, we describe a novel consensus annotation calculation and its related weighting scheme. The comparison between disorder information sources highlights how the MobiDB consensus captures the main features of intrinsic disorder and correlates well with manually curated datasets. Finally, we demonstrate the annotation of 13 eukaryotic model organisms through MobiDB's datasets, and of an example protein through the interactive user interface.Conclusions: MobiDB is a central resource for intrinsic disorder research, containing both experimental data and predictions. In the future it will be expanded to include additional information for all known proteins. © 2013 Di Domenico et al.; licensee BioMed Central Ltd.},

note = {Cited by: 27; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84876047815,

title = {Fly cryptochrome and the visual system},

author = {Gabriella Mazzotta and Alessandro Rossi and Emanuela Leonardi and Moyra Mason and Cristiano Bertolucci and Laura Caccin and Barbara Spolaore and Alberto J. M. Martin and Matthias Schlichting and Rudi Grebler and Charlotte Helfrich-Förster and Stefano Mammi and Rodolfo Costa and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84876047815&origin=inward},

doi = {10.1073/pnas.1212317110},

year  = {2013},

date = {2013-01-01},

journal = {Proceedings of the National Academy of Sciences of the United States of America},

volume = {110},

number = {15},

pages = {6163-6168},

abstract = {Cryptochromes are flavoproteins, structurally and evolutionary related to photolyases, that are involved in the development, magnetoreception, and temporal organization of a variety of organisms. Drosophila CRYPTOCHROME (dCRY) is involved in light synchronization of the master circadian clock, and its C terminus plays an important role in modulating light sensitivity and activity of the protein. The activation of dCRY by light requires a conformational change, but it has been suggested that activation could be mediated also by specific "regulators" that bind the C terminus of the protein. This C-terminal region harbors several protein-protein interaction motifs, likely relevant for signal transduction regulation. Here, we show that some functional linear motifs are evolutionarily conserved in the C terminus of cryptochromes and that class III PDZ-binding sites are selectively maintained in animals. A coimmunoprecipitation assay followed by mass spectrometry analysis revealed that dCRY interacts with Retinal Degeneration A (RDGA) and with Neither Inactivation Nor Afterpotential C (NINAC) proteins. Both proteins belong to a multiprotein complex (the Signalplex) that includes visualsignaling molecules. Using bioinformatic and molecular approaches, dCRY was found to interact with Neither Inactivation Nor Afterpotential C through Inactivation No Afterpotential D (INAD) in a light-dependent manner and that the CRY-Inactivation No Afterpotential D interaction is mediated by specific domains of the two proteins and involves the CRY C terminus. Moreover, an impairment of the visual behavior was observed in fly mutants for dCRY, indicative of a role, direct or indirect, for this photoreceptor in fly vision.},

note = {Cited by: 65; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84883490214,

title = {In silico investigation of PHD-3 specific HIF1-α proline 567 hydroxylation: A new player in the VHL/HIF-1α interaction pathway?},

author = {Giovanni Minervini and Alessandro Masiero and Stefano Moro and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84883490214&origin=inward},

doi = {10.1016/j.febslet.2013.07.019},

year  = {2013},

date = {2013-01-01},

journal = {FEBS Letters},

volume = {587},

number = {18},

pages = {2996-3001},

abstract = {Hypoxia inducible factor 1α (HIF-1α) regulates oxygen homeostasis in the cell through a sensing mechanism involving its hydroxylation and binding to the von Hippel-Lindau (VHL) tumor suppressor. This mechanism is mediated through hydroxylation of HIF-1α proline 564, although in vitro tests have previously shown an alternative hydroxylation at proline 567 by PHD-3. Here, molecular dynamics simulations were used to investigate the structural effect of this alternative hydroxylation. A specific hydrogen bond network rearrangement and improved electrostatic energy for hydroxylated P567 are compatible with an increase in HIF-1α binding affinity. Sequence analysis also confirms P567 to be vastly conserved during evolution, indicating a possible role for this alternative, PHD-3 driven, post translational modification in pVHL-HIF-1α complex formation.© 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.},

note = {Cited by: 11; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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: 71; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84857170967,

title = {Espritz: Accurate and fast prediction of protein disorder},

author = {Ian Walsh and Alberto J. M. Martin and Tomàs Di domenico and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84857170967&origin=inward},

doi = {10.1093/bioinformatics/btr682},

year  = {2012},

date = {2012-01-01},

journal = {Bioinformatics},

volume = {28},

number = {4},

pages = {503-509},

abstract = {Motivation: Intrinsically disordered regions are key for the function of numerous proteins, and the scant available experimental annotations suggest the existence of different disorder flavors. While efficient predictions are required to annotate entire genomes, most existing methods require sequence profiles for disorder prediction, making them cumbersome for high-throughput applications.Results: In this work, we present an ensemble of protein disorder predictors called ESpritz. These are based on bidirectional recursive neural networks and trained on three different flavors of disorder, including a novel NMR flexibility predictor. ESpritz can produce fast and accurate sequence-only predictions, annotating entire genomes in the order of hours on a single processor core. Alternatively, a slower but slightly more accurate ESpritz variant using sequence profiles can be used for applications requiring maximum performance. Two levels of prediction confidence allow either to maximize reasonable disorder detection or to limit expected false positives to 5%. ESpritz performs consistently well on the recent CASP9 data, reaching a S w measure of 54.82 and area under the receiver operator curve of 0.856. The fast predictor is four orders of magnitude faster and remains better than most publicly available CASP9 methods, making it ideal for genomic scale predictions. Conclusions: ESpritz predicts three flavors of disorder at two distinct false positive rates, either with a fast or slower and slightly more accurate approach. Given its state-of-the-art performance, it can be especially useful for high-throughput applications. © The Author 2011. Published by Oxford University Press. All rights reserved.},

note = {Cited by: 429; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84869206683,

title = {Cardiomyopathy in patients with POMT1-related congenital and limb-girdle muscular dystrophy},

author = {Luca Bello and Paola Melacini and Raffaele Pezzani and Adele D'Amico and Luisa Piva and Emanuela Leonardi and Annalaura Torella and Gianni Soraru and Arianna Palmieri and Gessica Smaniotto and Bruno F. Gavassini and Andrea Vianello and Vincenzo Nigro and Enrico Bertini and Corrado Angelini and Silvio C. E. Tosatto and Elena Pegoraro},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84869206683&origin=inward},

doi = {10.1038/ejhg.2012.71},

year  = {2012},

date = {2012-01-01},

journal = {European Journal of Human Genetics},

volume = {20},

number = {12},

pages = {1234-1239},

abstract = {Protein-o-mannosyl transferase 1 (POMT1) is a glycosyltransferase involved in α-dystroglycan (α-DG) glycosylation. Clinical phenotype in POMT1-mutated patients ranges from congenital muscular dystrophy (CMD) with structural brain abnormalities, to limb-girdle muscular dystrophy (LGMD) with microcephaly and mental retardation, to mild LGMD. No cardiac involvement has until now been reported in POMT1-mutated patients. We report three patients who harbored compound heterozygous POMT1 mutations and showed left ventricular (LV) dilation and/or decrease in myocardial contractile force: two had a LGMD phenotype with a normal or close-to-normal cognitive profile and one had CMD with mental retardation and normal brain MRI. Reduced or absent α-DG immunolabeling in muscle biopsies were identified in all three patients. Bioinformatic tools were used to study the potential effect of POMT1-detected mutations. All the detected POMT1 mutations were predicted in silico to interfere with protein folding and/or glycosyltransferase function. The report on the patients described here has widened the clinical spectrum associated with POMT1 mutations to include cardiomyopathy. The functional impact of known and novel POMT1 mutations was predicted with a bioinformatics approach, and results were compared with previous in vitro studies of protein-o-mannosylase function. © 2012 Macmillan Publishers Limited All rights reserved.},

note = {Cited by: 26; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84858145212,

title = {Studying interactions by molecular dynamics simulations at high concentration},

author = {Federico Fogolari and Alessandra Corazza and Stefano Toppo and Silvio C. E. Tosatto and Paolo Viglino and Fulvio Ursini and Gennaro Esposito},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84858145212&origin=inward},

doi = {10.1155/2012/303190},

year  = {2012},

date = {2012-01-01},

journal = {Journal of Biomedicine and Biotechnology},

volume = {2012},

abstract = {Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples. Copyright © 2012 Federico Fogolari et al.},

note = {Cited by: 17; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84865129593,

title = {MobiDB: A comprehensive database of intrinsic protein disorder annotations},

author = {Tomás Di domenico and Ian Walsh and Alberto J. M. Martin and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84865129593&origin=inward},

doi = {10.1093/bioinformatics/bts327},

year  = {2012},

date = {2012-01-01},

journal = {Bioinformatics},

volume = {28},

number = {15},

pages = {2080-2081},

abstract = {Motivation: Disordered protein regions are key to the function of numerous processes within an organism and to the determination of a protein's biological role. The most common source for protein disorder annotations, DisProt, covers only a fraction of the available sequences. Alternatively, the Protein Data Bank (PDB) has been mined for missing residues in X-ray crystallographic structures. Herein, we provide a centralized source for data on different flavours of disorder in protein structures, MobiDB, building on and expanding the content provided by already existing sources. In addition to the DisProt and PDB X-ray structures, we have added experimental information from NMR structures and five different flavours of two disorder predictors (ESpritz and IUpred). These are combined into a weighted consensus disorder used to classify disordered regions into flexible and constrained disorder. Users are encouraged to submit manual annotations through a submission form. MobiDB features experimental annotations for 17 285 proteins, covering the entire PDB and predictions for the SwissProt database, with 565 200 annotated sequences. Depending on the disorder flavour, 6-20% of the residues are predicted as disordered. © The Author 2012. Published by Oxford University Press. All rights reserved.},

note = {Cited by: 131; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:84866150728,

title = {Looking for putative phenoloxidases of compound ascidians: Haemocyanin-like proteins in Polyandrocarpa misakiensis and Botryllus schlosseri},

author = {Loriano Ballarin and Nicola Franchi and Filippo Schiavon and Silvio C. E. Tosatto and Ivan Mičetić and Kazuo Kawamura},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84866150728&origin=inward},

doi = {10.1016/j.dci.2012.05.008},

year  = {2012},

date = {2012-01-01},

journal = {Developmental and Comparative Immunology},

volume = {38},

number = {2},

pages = {232-242},

publisher = {Elsevier Ltd},

abstract = {Phenoloxidases (POs) and haemocyanins constitute a family of copper-containing proteins widely distributed among invertebrates. Both of them are able, under appropriate conditions, to convert polyphenols to quinones and induce cytotoxicity through the production of reactive oxygen species, a fundamental event in many immune responses. In ascidians, PO activity has been described and studied in both solitary and colonial species and the enzyme is involved in inflammatory and cytotoxic reactions against foreign cells or molecules, and in the formation of the cytotoxic foci which characterise the nonfusion reaction of botryllids. Expressed genes for two putative POs (CiPO1 and CiPO2) have been recently identified in C. intestinalis. In the present study, we determined the cDNA sequences of two haemocyanin-like proteins from two colonial ascidians: Botryllus schlosseri from the Mediterranean Sea and Polyandrocarpa misakiensis from Japan. Multiple sequence alignments evidenced the similarity between the above sequences and crustacean proPOs whereas the analysis of the three-dimensional structure reveals high similarity with arthropod haemocyanins which share common precursors with arthropod proPOs. Botryllus HLP grouped in the same cluster with Ciona POs, whereas Polyandrocarpa HLP clustered with arthropod haemocyanins; all of them share the full conservation of the six histidines at the two copper-binding sites as well as of other motifs, also found in arthropod haemocyanin subunits, involved in the regulation of enzyme activity. In situ hybridisation indicated that the genes are transcribed inside morula cells, a characteristic haemocyte type in ascidians where PO activity is located, at the beginning of their differentiation. These results represent a first attempt to identify candidate molecules responsible of the PO activity in compound ascidians. © 2012 Elsevier Ltd.},

note = {Cited by: 16},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@article{SCOPUS_ID:84872285924,

title = {The human "magnesome": Detecting magnesium binding sites on human proteins},

author = {Damiano Piovesan and Giuseppe Profiti and Pier Luigi Martelli and Rita Casadio},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-84872285924&origin=inward},

doi = {10.1186/1471-2105-13-S14-S10},

year  = {2012},

date = {2012-01-01},

journal = {BMC Bioinformatics},

volume = {13},

number = {SUPPL 1},

abstract = {Background: Magnesium research is increasing in molecular medicine due to the relevance of this ion in several important biological processes and associated molecular pathogeneses. It is still difficult to predict from the protein covalent structure whether a human chain is or not involved in magnesium binding. This is mainly due to little information on the structural characteristics of magnesium binding sites in proteins and protein complexes. Magnesium binding features, differently from those of other divalent cations such as calcium and zinc, are elusive. Here we address a question that is relevant in protein annotation: how many human proteins can bind Mg2+? Our analysis is performed taking advantage of the recently implemented Bologna Annotation Resource (BAR-PLUS), a non hierarchical clustering method that relies on the pair wise sequence comparison of about 14 millions proteins from over 300.000 species and their grouping into clusters where annotation can safely be inherited after statistical validation. Results: After cluster assignment of the latest version of the human proteome, the total number of human proteins for which we can assign putative Mg binding sites is 3,751. Among these proteins, 2,688 inherit annotation directly from human templates and 1,063 inherit annotation from templates of other organisms. Protein structures are highly conserved inside a given cluster. Transfer of structural properties is possible after alignment of a given sequence with the protein structures that characterise a given cluster as obtained with a Hidden Markov Model (HMM) based procedure. Interestingly a set of 370 human sequences inherit Mg2+ binding sites from templates sharing less than 30% sequence identity with the template. Conclusion: We describe and deliver the "human magnesome", a set of proteins of the human proteome that inherit putative binding of magnesium ions. With our BAR-hMG, 251 clusters including 1,341 magnesium binding protein structures corresponding to 387 sequences are sufficient to annotate some 13,689 residues in 3,751 human sequences as "magnesium binding". Protein structures act therefore as three dimensional seeds for structural and functional annotation of human sequences. The data base collects specifically all the human proteins that can be annotated according to our procedure as "magnesium binding", the corresponding structures and BAR+ clusters from where they derive the annotation (http://bar.biocomp.unibo.it/mg). © 2012 Piovesan et al.; licensee BioMed Central Ltd.},

note = {Cited by: 28; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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: 21; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:79959956361,

title = {CSpritz: Accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs},

author = {Ian Walsh and Alberto J. M. Martin and Toms Di Domenico and Alessandro Vullo and Gianluca Pollastri and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-79959956361&origin=inward},

doi = {10.1093/nar/gkr411},

year  = {2011},

date = {2011-01-01},

journal = {Nucleic Acids Research},

volume = {39},

number = {SUPPL. 2},

abstract = {CSpritz is a web server for the prediction of intrinsic protein disorder. It is a combination of previous Spritz with two novel orthogonal systems developed by our group (Punch and ESpritz). Punch is based on sequence and structural templates trained with support vector machines. ESpritz is an efficient single sequence method based on bidirectional recursive neural networks. Spritz was extended to filter predictions based on structural homologues. After extensive testing, predictions are combined by averaging their probabilities. The CSpritz website can elaborate single or multiple predictions for either short or long disorder. The server provides a global output page, for download and simultaneous statistics of all predictions. Links are provided to each individual protein where the amino acid sequence and disorder prediction are displayed along with statistics for the individual protein. As a novel feature, CSpritz provides information about structural homologues as well as secondary structure and short functional linear motifs in each disordered segment. Benchmarking was performed on the very recent CASP9 data, where CSpritz would have ranked consistently well with a Sw measure of 49.27 and AUC of 0.828. The server, together with help and methods pages including examples, are freely available at URL: http://protein.bio.unipd.it/cspritz/. © 2011 The Author(s).},

note = {Cited by: 76; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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: 1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:79958845071,

title = {Identification and In Silico Analysis of Novel von Hippel-Lindau (VHL) Gene Variants from a Large Population},

author = {Emanuela Leonardi and Maddalena Martella and Silvio C. E. Tosatto and Alessandra Murgia},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-79958845071&origin=inward},

doi = {10.1111/j.1469-1809.2011.00647.x},

year  = {2011},

date = {2011-01-01},

journal = {Annals of Human Genetics},

volume = {75},

number = {4},

pages = {483-496},

abstract = {Mutational inactivation of the VHL gene is the cause of von Hippel-Lindau (VHL) disease, an autosomal dominant hereditary cancer syndrome predisposing to haemangioblastomas, pheochromocytomas and clear-cell renal carcinomas. The gene product (pVHL) functions as an adapter in cellular processes including cell growth and apoptosis. VHL mutation analysis was carried out in 426 unrelated subjects with phenotypes ranging from VHL syndrome, to isolated VHL-related tumours that could represent the first manifestation of the disease. A total of 111 individuals were found to carry alterations, with large deletions representing 40% of the variants. Eighteen of the 95 detected variants were novel, seemingly disease-causing mutations; their pathogenic role has been evaluated in silico for effects on protein folding and interactions. Putative regions of interaction between pVHL and proteins involved in common pathways have been identified, assessing possible implications for the presence of mutations in these regions. All new variants predicted to truncate or cause complete pVHL loss of structure were associated with phenotypes consistent with VHL type 1. Seven of the new amino acid substitutions are disease-causing mutations, one is a neutral variant, whereas the results for two remain ambiguous. Our combined molecular and in silico approach for the evaluation of putative disease-causing mutations contributes to the interpretation of the potential pathogenicity of these novel variants. © 2011 The Authors Annals of Human Genetics © 2011 Blackwell Publishing Ltd/University College London.},

note = {Cited by: 21},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:79959918507,

title = {BAR-PLUS: The Bologna Annotation Resource Plus for functional and structural annotation of protein sequences},

author = {Damiano Piovesan and Pier Luigi Martelli and Piero Fariselli and Andrea Zauli and Ivan Rossi and Rita Casadio},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-79959918507&origin=inward},

doi = {10.1093/nar/gkr292},

year  = {2011},

date = {2011-01-01},

journal = {Nucleic Acids Research},

volume = {39},

number = {SUPPL. 2},

abstract = {We introduce BAR-PLUS (BAR+), a web server for functional and structural annotation of protein sequences. BAR+ is based on a large-scale genome cross comparison and a non-hierarchical clustering procedure characterized by a metric that ensures a reliable transfer of features within clusters. In this version, the method takes advantage of a large-scale pairwise sequence comparison of 13495736 protein chains also including 988 complete proteomes. Available sequence annotation is derived from UniProtKB, GO, Pfam and PDB. When PDB templates are present within a cluster (with or without their SCOP classification), profile Hidden Markov Models (HMMs) are computed on the basis of sequence to structure alignment and are cluster-associated (Cluster-HMM). Therefrom, a library of 10858 HMMs is made available for aligning even distantly related sequences for structural modelling. The server also provides pairwise query sequence-structural target alignments computed from the correspondent Cluster-HMM. BAR+ in its present version allows three main categories of annotation: PDB [with or without SCOP (*)] and GO and/or Pfam; PDB (*) without GO and/or Pfam; GO and/or Pfam without PDB (*) and no annotation. Each category can further comprise clusters where GO and Pfam functional annotations are or are not statistically significant. BAR+ is available at http://bar.biocomp.unibo.it/bar2.0. © 2011 The Author(s).},

note = {Cited by: 23; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@article{SCOPUS_ID:79954525041,

title = {Familial temporal lobe epilepsy with psychic auras associated with a novel LGI1 mutation},

author = {Striano and Busolin and Santulli and Leonardi and Coppola and Vitiello and Rigon and Michelucci and Tosatto and Striano and Nobile},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-79954525041&origin=inward},

doi = {10.1212/WNL.0b013e318212ab2e},

year  = {2011},

date = {2011-01-01},

journal = {Neurology},

volume = {76},

number = {13},

pages = {1173-1176},

publisher = {Lippincott Williams and Wilkins},

abstract = {Background: Autosomal dominant lateral temporal epilepsy (ADLTE) is characterized by focal seizures with auditory features or aphasia. Mutations in the LGI1 gene have been reported in up to 50% of ADLTE pedigrees. We report a family with temporal lobe epilepsy characterized by psychic symptoms associated with a novel LGI1 mutation. Methods: All participants were personally interviewed and underwent neurologic examination and video-EEG recordings. LGI1 exons were sequenced by standard methods. Mutant cDNA was transfected into human embryonic kidney 293 cells; both cell lysates and media were analyzed by Western blot. In silico modeling of the Lgi1 protein EPTP domain was carried out using the structure of WD repeat protein and manually refined. Results: Three affected family members were ascertained, 2 of whom had temporal epilepsy with psychic symptoms (déjà vu, fear) but no auditory or aphasic phenomena, while the third had complex partial seizures without any aura. In all patients, we found a novel LGI1 mutation, Arg407Cys, which did not hamper protein secretion in vitro. Mapping of the mutation on a 3-dimensional protein model showed that this mutation does not induce large structural rearrangements but could destabilize interactions of Lgi1 with target proteins. Conclusions: The Arg407Cys is the first mutation with no effect on Lgi1 protein secretion. The uncommon, isolated psychic symptoms associated with it suggests that ADLTE encompasses a wider range of auras of temporal origin than hitherto reported. © 2011 by AAN Enterprises, Inc. All rights reseved.},

note = {Cited by: 44},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:79960149420,

title = {RING: networking interacting residues, evolutionary information and energetics in protein structures},

author = {Alberto J. M. Martin and Michele Vidotto and Filippo Boscariol and Tomàs Di Domenico and Ian Walsh and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-79960149420&origin=inward},

doi = {10.1093/bioinformatics/btr191},

year  = {2011},

date = {2011-01-01},

journal = {Bioinformatics},

volume = {27},

number = {14},

pages = {2003-2005},

abstract = {Motivation: Residue interaction networks (RINs) have been used in the literature to describe the protein 3D structure as a graph where nodes represent residues and edges physico-chemical interactions, e.g. hydrogen bonds or van-der-Waals contacts. Topological network parameters can be calculated over RINs and have been correlated with various aspects of protein structure and function. Here we present a novel web server, RING, to construct physico-chemically valid RINs interactively from PDB files for subsequent visualization in the Cytoscape platform. The additional structure-based parameters secondary structure, solvent accessibility and experimental uncertainty can be combined with information regarding residue conservation, mutual information and residue-based energy scoring functions. Different visualization styles are provided to facilitate visualization and standard plugins can be used to calculate topological parameters in Cytoscape. A sample use case analyzing the active site of glutathione peroxidase is presented. © The Author 2011. Published by Oxford University Press. All rights reserved.},

note = {Cited by: 114; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:79953202854,

title = {A computational model of the LGI1 protein suggests a common binding site for ADAM proteins},

author = {Emanuela Leonardi and Simonetta Andreazza and Stefano Vanin and Giorgia Busolin and Carlo Nobile and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-79953202854&origin=inward},

doi = {10.1371/journal.pone.0018142},

year  = {2011},

date = {2011-01-01},

journal = {PLoS ONE},

volume = {6},

number = {3},

abstract = {Mutations of human leucine-rich glioma inactivated (LGI1) gene encoding the epitempin protein cause autosomal dominant temporal lateral epilepsy (ADTLE), a rare familial partial epileptic syndrome. The LGI1 gene seems to have a role on the transmission of neuronal messages but the exact molecular mechanism remains unclear. In contrast to other genes involved in epileptic disorders, epitempin shows no homology with known ion channel genes but contains two domains, composed of repeated structural units, known to mediate protein-protein interactions. A three dimensional in silico model of the two epitempin domains was built to predict the structure-function relationship and propose a functional model integrating previous experimental findings. Conserved and electrostatic charged regions of the model surface suggest a possible arrangement between the two domains and identifies a possible ADAM protein binding site in the β-propeller domain and another protein binding site in the leucine-rich repeat domain. The functional model indicates that epitempin could mediate the interaction between proteins localized to different synaptic sides in a static way, by forming a dimer, or in a dynamic way, by binding proteins at different times. The model was also used to predict effects of known disease-causing missense mutations. Most of the variants are predicted to alter protein folding while several other map to functional surface regions. In agreement with experimental evidence, this suggests that non-secreted LGI1 mutants could be retained within the cell by quality control mechanisms or by altering interactions required for the secretion process. © 2011 Leonardi et al.},

note = {Cited by: 35; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:79955536128,

title = {Immune roles of a rhamnose-binding lectin in the colonial ascidian Botryllus schlosseri},

author = {Nicola Franchi and Filippo Schiavon and Matteo Carletto and Fabio Gasparini and Giulio Bertoloni and Silvio C. E. Tosatto and Loriano Ballarin},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-79955536128&origin=inward},

doi = {10.1016/j.imbio.2010.10.011},

year  = {2011},

date = {2011-01-01},

journal = {Immunobiology},

volume = {216},

number = {6},

pages = {725-736},

abstract = {The present paper describes the immune role played by a recently identified (Gasparini et al. 2008) member of the rhamnose-binding lectin (RBL) family from the colonial ascidian Botryllus schlosseri.B. schlosseri RBL (BsRBL) can activate phagocytes through: (i) induction of their directional movement towards the source of the molecule; (ii) modification of cytoskeleton, required for shape changes; (iii) stimulation of the respiratory burst, and consequent production of reactive oxygen species (ROS) with microbicidal activity, including superoxide anions and peroxides; and (iv) increase in the ability to phagocytose foreign particles. RBL also induces the synthesis and release, by cytotoxic morula cells (MCs), of cytokines recognised by anti-IL1α and anti-TNFα antibodies. At high concentrations, BsRBL induces degranulation of MCs and the consequent release of the cytotoxic enzyme phenoloxidase into the medium. Results are consistent with the existence of cross-talk between B. schlosseri immunocytes (phagocytes and MCs). In addition, a three-dimensional model for BsRBL is presented. © 2010 Elsevier GmbH.},

note = {Cited by: 39},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:77950937930,

title = {A novel WT1 gene mutation in a three-generation family with progressive isolated focal segmental glomerulosclerosis},

author = {Elisa Benetti and Gianluca Caridi and Cristina Malaventura and Monica Dagnino and Emanuela Leonardi and Lina Artifoni and Gian Marco Ghiggeri and Silvio C. E. Tosatto and Luisa Murer},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-77950937930&origin=inward},

doi = {10.2215/CJN.05670809},

year  = {2010},

date = {2010-01-01},

journal = {Clinical Journal of the American Society of Nephrology},

volume = {5},

number = {4},

pages = {698-702},

abstract = {Background and objectives: Wilms tumor-suppressor gene-1 (WT1) plays a key role in kidney development and function. WT1 mutations usually occur in exons 8 and 9 and are associated with Denys-Drash, or in intron 9 and are associated with Frasier syndrome. However, overlapping clinical and molecular features have been reported. Few familial cases have been described, with intrafamilial variability. Sporadic cases of WT1 mutations in isolated diffuse mesangial sclerosis or focal segmental glomerulosclerosis have also been reported. Design, setting, participants, & measurements: Molecular analysis of WT1 exons 8 and 9 was carried out in five members on three generations of a family with late-onset isolated proteinuria. The effect of the detected amino acid substitution on WT1 protein's structure was studied by bioinformatics tools. Results: Three family members reached end-stage renal disease in full adulthood. None had genital abnormalities or Wilms tumor. Histologic analysis in two subjects revealed focal segmental glomerulosclerosis. The novel sequence variant c. 1208G > A in WT1 exon 9 was identified in all of the affected members of the family. Conclusions: The lack of Wilms tumor or other related phenotypes suggests the expansion of WT1 gene analysis in patients with focal segmental glomerulosclerosis, regardless of age or presence of typical Denys-Drash or Frasier syndrome clinical features. Structural analysis of the mutated protein revealed that the mutation hampers zinc finger-DNA interactions, impairing target gene transcription. This finding opens up new issues about WT1 function in the maintenance of the complex gene network that regulates normal podocyte function. copyright © 2010 by the American Society of Nephrology.},

note = {Cited by: 31; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:77954780222,

title = {Spectrum and frequency of SLC26A4 mutations among czech patients with early hearing loss with and without enlarged vestibular aqueduct (EVA)},

author = {Radka Pourová and Petr Janoušek and Michal Jurovčík and Marcela Dvořáková and Marcela Malíková and Dagmar Rašková and Olga Bendová and Emanuela Leonardi and Alessandra Murgia and Zdenek Kabelka and Jaromír Astl and Pavel Seeman},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-77954780222&origin=inward},

doi = {10.1111/j.1469-1809.2010.00581.x},

year  = {2010},

date = {2010-01-01},

journal = {Annals of Human Genetics},

volume = {74},

number = {4},

pages = {299-307},

abstract = {Summary: Mutations in SLC26A4 cause Pendred syndrome (PS) - hearing loss with goitre - or DFNB4 - non-syndromic hearing loss (NSHL) with inner ear abnormalities such as Enlarged Vestibular Aqueduct (EVA) or Mondini Dysplasia (MD). We tested 303 unrelated Czech patients with early hearing loss (298 with NSHL and 5 with PS), all GJB2-negative, for SLC26A4 mutations and evaluated their clinical and radiological phenotype. Among 115 available HRCT/MRI scans we detected three MD (2.6%), three Mondini-like affections (2.6%), 16 EVA (13 bilateral - 19.2% and 15.6% respectively) and 61 EVA/MD-negative scans (73.4%). We found mutation(s) in 26 patients (8.6%) and biallelic mutations in eight patients (2.7%) out of 303 tested. In 18 of 26 (69%) patients, no second mutation could be detected even using MLPA. The spectrum of SLC26A4 mutations in Czech patients is broad without any prevalent mutation. We detected 21 different mutations (four novel). The most frequent mutations were p.Val138Phe and p.Leu445Trp (18% and 8.9% of pathogenic alleles respectively). Among 13 patients with bilateral EVA, six patients (50%) carry biallelic mutations. In EVA -negative patients no biallelic mutations were found but 4.9% had monoallelic mutations. SLC26A4 mutations are present mostly in patients with EVA/MD and/or progressive HL and those with affected siblings. © 2010 The Authors Journal compilation.},

note = {Cited by: 34},

keywords = {},

pubstate = {published},

tppubtype = {article}

}