2006
Journal Articles
251.
Silvio C.E. Tosatto; S. Toppo
Large-scale prediction of protein structure and function from sequence Journal Article
In: Current Pharmaceutical Design, vol. 12, no. 17, pp. 2067 – 2086, 2006, (Cited by: 15).
Abstract | Links:
@article{Tosatto20062067,
title = {Large-scale prediction of protein structure and function from sequence},
author = { Silvio C.E. Tosatto and S. Toppo},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33645817062\&doi=10.2174%2f138161206777585238\&partnerID=40\&md5=6eb6c488a85f9aa1d5ee85d496476732},
doi = {10.2174/138161206777585238},
year = {2006},
date = {2006-01-01},
journal = {Current Pharmaceutical Design},
volume = {12},
number = {17},
pages = {2067 \textendash 2086},
abstract = {The identification of novel drug targets from genomic data involves the large-scale analysis of many protein sequences. Methods for automated structure and function prediction are an essential tool for this purpose. In this review we concentrate on the recent developments in the field of protein structure prediction and how these can be used to gain hints about the function of proteins. The current state-of-the-art is highlighted through recent community-wide experiments aimed at comparing different approaches. For structure prediction this allows the identification of key improvements to increase the crucial sequence to structure alignment needed for accurate models. Function prediction is a rapidly maturing field that is still being benchmarked. Definitions for protein function are presented and available methods, mostly concentrating on functional site descriptors and structural motifs, presented. © 2006 Bentham Science Publishers Ltd.},
note = {Cited by: 15},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The identification of novel drug targets from genomic data involves the large-scale analysis of many protein sequences. Methods for automated structure and function prediction are an essential tool for this purpose. In this review we concentrate on the recent developments in the field of protein structure prediction and how these can be used to gain hints about the function of proteins. The current state-of-the-art is highlighted through recent community-wide experiments aimed at comparing different approaches. For structure prediction this allows the identification of key improvements to increase the crucial sequence to structure alignment needed for accurate models. Function prediction is a rapidly maturing field that is still being benchmarked. Definitions for protein function are presented and available methods, mostly concentrating on functional site descriptors and structural motifs, presented. © 2006 Bentham Science Publishers Ltd.
252.
Alessandro Albiero; Silvio C. E. Tosatto
Fine-grained statistical torsion angle potentials are effective in discriminating native protein structures Journal Article
In: Current Drug Discovery Technologies, vol. 3, no. 1, pp. 75 – 81, 2006, (Cited by: 3).
Abstract | Links:
@article{Albiero200675,
title = {Fine-grained statistical torsion angle potentials are effective in discriminating native protein structures},
author = { Alessandro Albiero and Silvio C. E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33645811319\&doi=10.2174%2f157016306776637591\&partnerID=40\&md5=950f1def8fd1065c3e298cfa2fd6358a},
doi = {10.2174/157016306776637591},
year = {2006},
date = {2006-01-01},
journal = {Current Drug Discovery Technologies},
volume = {3},
number = {1},
pages = {75 \textendash 81},
abstract = {Modelling of drug targets requires the reliable selection of an accurate and representative structure from large ensembles of alternate models. Statistical potentials developed to discriminate native protein structures generally represent pairwise interactions between atoms, which are less sensitive to local conformational details. The discrimination of local distortions is therefore particularly difficult. Local interaction preferences, expressed through torsion angles, are rarely used, as some controversy exists in the literature regarding their discrimination power. The present study aims to benchmark the efficiency of different implementations of torsion angle propensities for selecting the native structure from ensembles of well-constructed decoys. Several statistical potentials derived from fine-grained discretisations of torsion angle space are constructed and evaluated. Results from a comparison with nine widely used statistical scoring functions show the torsion angle potentials to be more effective in recognising native structures and to improve with the number of torsion angles considered. These data suggest local structural propensities to be important for estimating the overall quality of native-like models. © 2006 Bentham Science Publishers Ltd.},
note = {Cited by: 3},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Modelling of drug targets requires the reliable selection of an accurate and representative structure from large ensembles of alternate models. Statistical potentials developed to discriminate native protein structures generally represent pairwise interactions between atoms, which are less sensitive to local conformational details. The discrimination of local distortions is therefore particularly difficult. Local interaction preferences, expressed through torsion angles, are rarely used, as some controversy exists in the literature regarding their discrimination power. The present study aims to benchmark the efficiency of different implementations of torsion angle propensities for selecting the native structure from ensembles of well-constructed decoys. Several statistical potentials derived from fine-grained discretisations of torsion angle space are constructed and evaluated. Results from a comparison with nine widely used statistical scoring functions show the torsion angle potentials to be more effective in recognising native structures and to improve with the number of torsion angles considered. These data suggest local structural propensities to be important for estimating the overall quality of native-like models. © 2006 Bentham Science Publishers Ltd.
253.
Silvio C.E. Tosatto; Alessandro Albiero; Alessandra Mantovan; Carlo Ferrari; Eckart Bindewald; Stefano Toppo
Align: A C++ class library and web server for rapid sequence alignment prototyping Journal Article
In: Current Drug Discovery Technologies, vol. 3, no. 3, pp. 167 – 173, 2006, (Cited by: 1).
Abstract | Links:
@article{Tosatto2006167,
title = {Align: A C++ class library and web server for rapid sequence alignment prototyping},
author = { Silvio C.E. Tosatto and Alessandro Albiero and Alessandra Mantovan and Carlo Ferrari and Eckart Bindewald and Stefano Toppo},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33947324043\&doi=10.2174%2f157016306780136754\&partnerID=40\&md5=c0a4671708cf2ad9b583c627e15ce75f},
doi = {10.2174/157016306780136754},
year = {2006},
date = {2006-01-01},
journal = {Current Drug Discovery Technologies},
volume = {3},
number = {3},
pages = {167 \textendash 173},
abstract = {Sequence alignment remains a fundamental tool in most tasks related to the prediction of protein sequence and structure. A C++ class library was developed to facilitate the rapid implementation of a variety of state-of-the-art pairwise sequence alignment techniques. These range from simple sequence to sequence to the advanced profile to profile alignments with optional secondary structure information. Suboptimal alignments, frequently used to estimate regions of confidence, can also be generated. The object oriented design facilitates rapid implementation, testing and extension of existing functionality. A simple web interface, which can also be useful in bioinformatics education, is also provided. Source code, online documentation and a prototypical web interface are freely accessible to academic users from the URL: http://protein.cribi.unipd. it/align/. A sample case study in the modelling of human Cytochrome P450 is discussed. © 2006 Bentham Science Publishers Ltd.},
note = {Cited by: 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sequence alignment remains a fundamental tool in most tasks related to the prediction of protein sequence and structure. A C++ class library was developed to facilitate the rapid implementation of a variety of state-of-the-art pairwise sequence alignment techniques. These range from simple sequence to sequence to the advanced profile to profile alignments with optional secondary structure information. Suboptimal alignments, frequently used to estimate regions of confidence, can also be generated. The object oriented design facilitates rapid implementation, testing and extension of existing functionality. A simple web interface, which can also be useful in bioinformatics education, is also provided. Source code, online documentation and a prototypical web interface are freely accessible to academic users from the URL: http://protein.cribi.unipd. it/align/. A sample case study in the modelling of human Cytochrome P450 is discussed. © 2006 Bentham Science Publishers Ltd.
254.
Ingolf Sommer; Stefano Toppo; Oliver Sander; Thomas Lengauer; Silvio C.E. Tosatto
Improving the quality of protein structure models by selecting from alignment alternatives Journal Article
In: BMC Bioinformatics, vol. 7, 2006, (Cited by: 18; All Open Access, Gold Open Access).
Abstract | Links:
@article{Sommer2006,
title = {Improving the quality of protein structure models by selecting from alignment alternatives},
author = { Ingolf Sommer and Stefano Toppo and Oliver Sander and Thomas Lengauer and Silvio C.E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33749344929\&doi=10.1186%2f1471-2105-7-364\&partnerID=40\&md5=b27810650e9e2c4580dfa4dc5f51b362},
doi = {10.1186/1471-2105-7-364},
year = {2006},
date = {2006-01-01},
journal = {BMC Bioinformatics},
volume = {7},
abstract = {Background: In the area of protein structure prediction, recently a lot of effort has gone into the development of Model Quality Assessment Programs (MQAPs). MQAPs distinguish high quality protein structure models from inferior models. Here, we propose a new method to use an MQAP to improve the quality of models. With a given target sequence and template structure, we construct a number of different alignments and corresponding models for the sequence. The quality of these models is scored with an MQAP and used to choose the most promising model. An SVM-based selection scheme is suggested for combining MQAP partial potentials, in order to optimize for improved model selection. Results: The approach has been tested on a representative set of proteins. The ability of the method to improve models was validated by comparing the MQAP-selected structures to the native structures with the model quality evaluation program TM-score. Using the SVM-based model selection, a significant increase in model quality is obtained (as shown with a Wilcoxon signed rank test yielding p-values below 10-15). The average increase in TMscore is 0.016, the maximum observed increase in TM-score is 0.29. Conclusion: In template-based protein structure prediction alignment is known to be a bottleneck limiting the overall model quality. Here we show that a combination of systematic alignment variation and modern model scoring functions can significantly improve the quality of alignment-based models. © 2006 Sommer et al; licensee BioMed Central Ltd.},
note = {Cited by: 18; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Background: In the area of protein structure prediction, recently a lot of effort has gone into the development of Model Quality Assessment Programs (MQAPs). MQAPs distinguish high quality protein structure models from inferior models. Here, we propose a new method to use an MQAP to improve the quality of models. With a given target sequence and template structure, we construct a number of different alignments and corresponding models for the sequence. The quality of these models is scored with an MQAP and used to choose the most promising model. An SVM-based selection scheme is suggested for combining MQAP partial potentials, in order to optimize for improved model selection. Results: The approach has been tested on a representative set of proteins. The ability of the method to improve models was validated by comparing the MQAP-selected structures to the native structures with the model quality evaluation program TM-score. Using the SVM-based model selection, a significant increase in model quality is obtained (as shown with a Wilcoxon signed rank test yielding p-values below 10-15). The average increase in TMscore is 0.016, the maximum observed increase in TM-score is 0.29. Conclusion: In template-based protein structure prediction alignment is known to be a bottleneck limiting the overall model quality. Here we show that a combination of systematic alignment variation and modern model scoring functions can significantly improve the quality of alignment-based models. © 2006 Sommer et al; licensee BioMed Central Ltd.
255.
Alberto Casarin; Maddalena Martella; Roberta Polli; Emanuela Leonardi; Laura Anesi; Alessandra Murgia
Molecular characterization of large deletions in the von Hippel-Lindau (VHL) gene by quantitative real-time PCR: The hypothesis of an Alu-mediated mechanism underlying VHL gene rearrangements Journal Article
In: Molecular Diagnosis and Therapy, vol. 10, no. 4, pp. 243 – 249, 2006, (Cited by: 24).
Abstract | Links:
@article{Casarin2006243,
title = {Molecular characterization of large deletions in the von Hippel-Lindau (VHL) gene by quantitative real-time PCR: The hypothesis of an Alu-mediated mechanism underlying VHL gene rearrangements},
author = { Alberto Casarin and Maddalena Martella and Roberta Polli and Emanuela Leonardi and Laura Anesi and Alessandra Murgia},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33747123661\&doi=10.1007%2fBF03256463\&partnerID=40\&md5=5d1d93301eaa5491155caa054d7f2a86},
doi = {10.1007/BF03256463},
year = {2006},
date = {2006-01-01},
journal = {Molecular Diagnosis and Therapy},
volume = {10},
number = {4},
pages = {243 \textendash 249},
abstract = {Introduction: Mutations of the von Hippel-Lindau (VHL) gene are responsible for VHL disease. This is a familial autosomal-dominant syndrome, predisposing to the development of benign and malignant tumors, including CNS and retinal hemangioblastomas, pheochromocytomas, and clear cell renal carcinomas. At least 30% of the disease-causing mutations in the VHL gene involve large alterations. Identification of these mutations is not possible using PCR-based mutational scanning methods. Quantitative Southern blot analysis has been traditionally employed for the detection of complete or partial deletions and more complex rearrangements of the gene. Methods: An alternative quantitative method was developed using a combination of quantitative Southern blot analysis and real-time PCR. With this approach, we studied 24 large VHL gene alterations to determine the exact nature of the mutations and to possibly characterize the boundaries of the deleted regions. Results: This combined molecular approach showed that all the VHL alterations studied were due to deletions, from which the position in the gene could be more precisely mapped. One of the samples that was completely characterized was found to carry an intragenic 2.2kb deletion with both 5′ and 3′ breakpoints located within Alu-repeat sequences. Conclusion: This is the first report on the molecular analysis of large VHL alterations. The results of our study and the complete characterization of a large deletion lead to the hypothesis that an Alu-mediated mechanism may be responsible for the common occurrence of large alterations in the VHL gene. © 2006 Adis Data Information BV. All rights reserved.},
note = {Cited by: 24},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Introduction: Mutations of the von Hippel-Lindau (VHL) gene are responsible for VHL disease. This is a familial autosomal-dominant syndrome, predisposing to the development of benign and malignant tumors, including CNS and retinal hemangioblastomas, pheochromocytomas, and clear cell renal carcinomas. At least 30% of the disease-causing mutations in the VHL gene involve large alterations. Identification of these mutations is not possible using PCR-based mutational scanning methods. Quantitative Southern blot analysis has been traditionally employed for the detection of complete or partial deletions and more complex rearrangements of the gene. Methods: An alternative quantitative method was developed using a combination of quantitative Southern blot analysis and real-time PCR. With this approach, we studied 24 large VHL gene alterations to determine the exact nature of the mutations and to possibly characterize the boundaries of the deleted regions. Results: This combined molecular approach showed that all the VHL alterations studied were due to deletions, from which the position in the gene could be more precisely mapped. One of the samples that was completely characterized was found to carry an intragenic 2.2kb deletion with both 5′ and 3′ breakpoints located within Alu-repeat sequences. Conclusion: This is the first report on the molecular analysis of large VHL alterations. The results of our study and the complete characterization of a large deletion lead to the hypothesis that an Alu-mediated mechanism may be responsible for the common occurrence of large alterations in the VHL gene. © 2006 Adis Data Information BV. All rights reserved.
2005
Journal Articles
256.
Enzo Spisni; Vittorio Tomasi; Alessandro Cestaro; Silvio C.E. Tosatto
Structural insights into the function of human caveolin 1 Journal Article
In: Biochemical and Biophysical Research Communications, vol. 338, no. 3, pp. 1383 – 1390, 2005, (Cited by: 50).
Abstract | Links:
@article{Spisni20051383,
title = {Structural insights into the function of human caveolin 1},
author = { Enzo Spisni and Vittorio Tomasi and Alessandro Cestaro and Silvio C.E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-27744551994\&doi=10.1016%2fj.bbrc.2005.10.099\&partnerID=40\&md5=11809d83d421c639e6677a7ca5b7bfd7},
doi = {10.1016/j.bbrc.2005.10.099},
year = {2005},
date = {2005-01-01},
journal = {Biochemical and Biophysical Research Communications},
volume = {338},
number = {3},
pages = {1383 \textendash 1390},
abstract = {Caveolin-1 (Cav-1) is emerging as the central protein controlling caveolae formation, caveolae trafficking, and cellular signalling. In particular, it is known that Cav-1 interacts and modulates the activity of several signalling proteins through the so-called caveolin scaffolding domain. In this paper, we used a bioinformatics approach to assess the validity of some long-standing structural features of Cav-1. We could confirm the existence of a membrane spanning region of Cav-1 and highlight an interesting pattern of palmitoylated cysteine residues explaining the structural features of the Cav-1 C-terminal region. Moreover, the scaffolding domain is predicted to have a different structure than previously reported. © 2005 Elsevier Inc. All rights reserved.},
note = {Cited by: 50},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Caveolin-1 (Cav-1) is emerging as the central protein controlling caveolae formation, caveolae trafficking, and cellular signalling. In particular, it is known that Cav-1 interacts and modulates the activity of several signalling proteins through the so-called caveolin scaffolding domain. In this paper, we used a bioinformatics approach to assess the validity of some long-standing structural features of Cav-1. We could confirm the existence of a membrane spanning region of Cav-1 and highlight an interesting pattern of palmitoylated cysteine residues explaining the structural features of the Cav-1 C-terminal region. Moreover, the scaffolding domain is predicted to have a different structure than previously reported. © 2005 Elsevier Inc. All rights reserved.
257.
Mario Albrecht; Carola Huthmacher; Silvio C.E. Tosatto; Thomas Lengauer
Decomposing protein networks into domain-domain interactions Journal Article
In: Bioinformatics, vol. 21, no. SUPPL. 2, pp. ii220–ii221, 2005, (Cited by: 19; All Open Access, Bronze Open Access).
Abstract | Links:
@article{Albrecht2005ii220,
title = {Decomposing protein networks into domain-domain interactions},
author = { Mario Albrecht and Carola Huthmacher and Silvio C.E. Tosatto and Thomas Lengauer},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-27544487034\&doi=10.1093%2fbioinformatics%2fbti1135\&partnerID=40\&md5=2fdc1846433ab76916e6ed5df2f27b30},
doi = {10.1093/bioinformatics/bti1135},
year = {2005},
date = {2005-01-01},
journal = {Bioinformatics},
volume = {21},
number = {SUPPL. 2},
pages = {ii220\textendashii221},
abstract = {Summary: The application of novel experimental techniques has generated large networks of protein-protein interactions. Frequently, important information on the structure and cellular function of protein-protein interactions can be gained from the domains of interacting proteins. We have designed a Cytoscape plugin that decomposes interacting proteins into their respective domains and computes a putative network of corresponding domain-domain interactions. To this end, the network graph of proteins has been extended by additional node and edge types for domain interactions, including different node and edge shapes and coloring schemes used for visualization. An additional plugin provides supplementary web links to Internet resources on domain function and structure. © The Author 2005. Published by Oxford University Press. All rights reserved.},
note = {Cited by: 19; All Open Access, Bronze Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Summary: The application of novel experimental techniques has generated large networks of protein-protein interactions. Frequently, important information on the structure and cellular function of protein-protein interactions can be gained from the domains of interacting proteins. We have designed a Cytoscape plugin that decomposes interacting proteins into their respective domains and computes a putative network of corresponding domain-domain interactions. To this end, the network graph of proteins has been extended by additional node and edge types for domain interactions, including different node and edge shapes and coloring schemes used for visualization. An additional plugin provides supplementary web links to Internet resources on domain function and structure. © The Author 2005. Published by Oxford University Press. All rights reserved.
258.
Silvio C.E. Tosatto
The Victor/FRST function for model quality estimation Journal Article
In: Journal of Computational Biology, vol. 12, no. 10, pp. 1316 – 1327, 2005, (Cited by: 96).
Abstract | Links:
@article{Tosatto20051316,
title = {The Victor/FRST function for model quality estimation},
author = { Silvio C.E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-28144448406\&doi=10.1089%2fcmb.2005.12.1316\&partnerID=40\&md5=f987fbb758159f92abb594d01fc50b9d},
doi = {10.1089/cmb.2005.12.1316},
year = {2005},
date = {2005-01-01},
journal = {Journal of Computational Biology},
volume = {12},
number = {10},
pages = {1316 \textendash 1327},
abstract = {Scoring functions are widely used in the final step of model selection in protein structure prediction. This is of interest both for comparative modeling targets, where it is important to select the best model among a set of many good, "correct" ones, as well as for other (fold recognition or novel fold) targets, where the set may contain many incorrect models. A novel combination of four knowledge-based potentials recognizing different features of native protein structures is introduced and tested. The pairwise, solvation, hydrogen bond, and torsion angle potentials contain largely orthogonal information. Of these, the torsion angle potential is found to show the strongest correlation with model quality. Combining these features with a linear weighting function, it was possible to construct a robust energy function capable of discriminating native-like structures on several benchmarking sets. In a recent blind test (CAFASP-4 MQAP), the scoring function ranked consistently well and was able to reliably distinguish the correct template from an ensemble of high quality decoys in 52 of 70 cases (33 of 34 for comparative modeling). An executable version of the Victor/FRST function for Linux PCs is available for download from the URL http://protein.cribi.unipd.it/frst/. © Mary Ann Liebert, Inc.},
note = {Cited by: 96},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Scoring functions are widely used in the final step of model selection in protein structure prediction. This is of interest both for comparative modeling targets, where it is important to select the best model among a set of many good, “correct” ones, as well as for other (fold recognition or novel fold) targets, where the set may contain many incorrect models. A novel combination of four knowledge-based potentials recognizing different features of native protein structures is introduced and tested. The pairwise, solvation, hydrogen bond, and torsion angle potentials contain largely orthogonal information. Of these, the torsion angle potential is found to show the strongest correlation with model quality. Combining these features with a linear weighting function, it was possible to construct a robust energy function capable of discriminating native-like structures on several benchmarking sets. In a recent blind test (CAFASP-4 MQAP), the scoring function ranked consistently well and was able to reliably distinguish the correct template from an ensemble of high quality decoys in 52 of 70 cases (33 of 34 for comparative modeling). An executable version of the Victor/FRST function for Linux PCs is available for download from the URL http://protein.cribi.unipd.it/frst/. © Mary Ann Liebert, Inc.
259.
Federico Fogolari; Silvio C. E. Tosatto
Application of MM/PBSA colony free energy to loop decoy discrimination: Toward correlation between energy and root mean square deviation Journal Article
In: Protein Science, vol. 14, no. 4, pp. 889 – 901, 2005, (Cited by: 42; All Open Access, Green Open Access).
Abstract | Links:
@article{Fogolari2005889,
title = {Application of MM/PBSA colony free energy to loop decoy discrimination: Toward correlation between energy and root mean square deviation},
author = { Federico Fogolari and Silvio C. E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-15244349255\&doi=10.1110%2fps.041004105\&partnerID=40\&md5=29fe3494158a771b68f3a05d2e187bfe},
doi = {10.1110/ps.041004105},
year = {2005},
date = {2005-01-01},
journal = {Protein Science},
volume = {14},
number = {4},
pages = {889 \textendash 901},
abstract = {Accurate free energy estimation is needed in many predictive tasks. The molecular mechanics/Poisson-Boltzmann solvent accessible surface area (MM/PBSA) approach has proven to be accurate. However, the correlation between the estimated free energy and the distance (e.g., root mean square deviation [RMSD]) from the most stable conformation is hindered by the strong free energy dependence on minor conformational variations. In this paper, a protocol for MM/PBSA free energy estimation is designed and tested on several loop decoy sets. We show that further integration of MM/PBSA free energy estimator with the colony energy approach makes the correlation between the free energy and RMSD from the native structure apparent, for the test sets on which it could be applied. Our results suggest that (1) the MM/PBSA free energy estimator is able to detect native-like structures for most decoy sets, and (2) application of the colony energy approach greatly hampers the MM/energy strong dependence on minor conformational changes. Copyright © 2005 The Protein Society.},
note = {Cited by: 42; All Open Access, Green Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Accurate free energy estimation is needed in many predictive tasks. The molecular mechanics/Poisson-Boltzmann solvent accessible surface area (MM/PBSA) approach has proven to be accurate. However, the correlation between the estimated free energy and the distance (e.g., root mean square deviation [RMSD]) from the most stable conformation is hindered by the strong free energy dependence on minor conformational variations. In this paper, a protocol for MM/PBSA free energy estimation is designed and tested on several loop decoy sets. We show that further integration of MM/PBSA free energy estimator with the colony energy approach makes the correlation between the free energy and RMSD from the native structure apparent, for the test sets on which it could be applied. Our results suggest that (1) the MM/PBSA free energy estimator is able to detect native-like structures for most decoy sets, and (2) application of the colony energy approach greatly hampers the MM/energy strong dependence on minor conformational changes. Copyright © 2005 The Protein Society.
260.
Fabio Polticelli; Jaswir Basran; Carmen Faso; Alessandra Cona; Giovanni Minervini; Riccardo Angelini; Rodolfo Federico; Nigel S. Scrutton; Paraskevi Tavladoraki
Lys300 plays a major role in the catalytic mechanism of maize polyamine oxidase Journal Article
In: Biochemistry, vol. 44, no. 49, pp. 16108 – 16120, 2005, (Cited by: 45).
Abstract | Links:
@article{Polticelli200516108,
title = {Lys300 plays a major role in the catalytic mechanism of maize polyamine oxidase},
author = { Fabio Polticelli and Jaswir Basran and Carmen Faso and Alessandra Cona and Giovanni Minervini and Riccardo Angelini and Rodolfo Federico and Nigel S. Scrutton and Paraskevi Tavladoraki},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-28944433027\&doi=10.1021%2fbi050983i\&partnerID=40\&md5=c6c6eec6c87d5b518543a5c0eb04acaf},
doi = {10.1021/bi050983i},
year = {2005},
date = {2005-01-01},
journal = {Biochemistry},
volume = {44},
number = {49},
pages = {16108 \textendash 16120},
abstract = {Maize polyamine oxidase (MPAO) is a flavin adenine dinucleotide (FAD)-dependent enzyme that catalyses the oxidation of spermine and spermidine at the secondary amino groups. The structure of MPAO indicates a 30-\^{A} long U-shaped tunnel that forms the catalytic site, with residues Glu62 and Glu170 located close to the enzyme-bound FAD and residue Tyr298 in close proximity to Lys300, which in turn is hydrogen-bonded to the flavin N5 atom via a water molecule (HOH309). To provide insight into the role of these residues in the catalytic mechanism of FAD reduction, we have performed steady-state and stopped-flow studies with wild-type, Glu62Gln, Glu170Gln, Tyr298Phe, and Lys300Met MPAO enzymes. We show that the steady-state enzyme activity is governed by an ionisable group with a macroscopic pKa of ~5.8. Kinetic analysis of the Glu62Gln, Glu170Gln, and Tyr298Phe MPAO enzymes have indicated (i) only small perturbations in catalytic activity as a result of mutation and (ii) steady-state pH profiles essentially unaltered when compared to the wild-type enzyme, suggesting that these residues do not play a critical role in the reaction mechanism. These kinetic observations are consistent with computational calculations that suggest that Glu62 and Glu170 are protonated over the pH range accessible to kinetic studies. Substitution of Lys300 with Met in MPAO resulted in a 1400-fold decrease in the rate of flavin reduction and a 160-fold decrease in the equilibrium dissociation constant for the Lys300Met- spermidine complex, consistent with a major role for this residue in the mechanism of substrate oxidation. A sizable solvent isotope effect (SIE = 5) accompanies FAD reduction in the wild-type enzyme and steady-state turnover (SIE = 2.3) of MPAO, consistent with the reductive half-reaction of MPAO making a major contribution to rate limitation in steady-state turnover. Studies using the enzyme-monitored turnover method indicate that oxidized FAD is the prominent form during steady-state turnover, consistent with the reductive half-reaction being rate-limiting. Our studies indicate the importance of Lys300 and probable importance of HOH309 to the mechanism of flavin reduction in MPAO. Possible roles for Lys300 and water in the mechanism of flavin reduction are discussed. © 2005 American Chemical Society.},
note = {Cited by: 45},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Maize polyamine oxidase (MPAO) is a flavin adenine dinucleotide (FAD)-dependent enzyme that catalyses the oxidation of spermine and spermidine at the secondary amino groups. The structure of MPAO indicates a 30-Â long U-shaped tunnel that forms the catalytic site, with residues Glu62 and Glu170 located close to the enzyme-bound FAD and residue Tyr298 in close proximity to Lys300, which in turn is hydrogen-bonded to the flavin N5 atom via a water molecule (HOH309). To provide insight into the role of these residues in the catalytic mechanism of FAD reduction, we have performed steady-state and stopped-flow studies with wild-type, Glu62Gln, Glu170Gln, Tyr298Phe, and Lys300Met MPAO enzymes. We show that the steady-state enzyme activity is governed by an ionisable group with a macroscopic pKa of ~5.8. Kinetic analysis of the Glu62Gln, Glu170Gln, and Tyr298Phe MPAO enzymes have indicated (i) only small perturbations in catalytic activity as a result of mutation and (ii) steady-state pH profiles essentially unaltered when compared to the wild-type enzyme, suggesting that these residues do not play a critical role in the reaction mechanism. These kinetic observations are consistent with computational calculations that suggest that Glu62 and Glu170 are protonated over the pH range accessible to kinetic studies. Substitution of Lys300 with Met in MPAO resulted in a 1400-fold decrease in the rate of flavin reduction and a 160-fold decrease in the equilibrium dissociation constant for the Lys300Met- spermidine complex, consistent with a major role for this residue in the mechanism of substrate oxidation. A sizable solvent isotope effect (SIE = 5) accompanies FAD reduction in the wild-type enzyme and steady-state turnover (SIE = 2.3) of MPAO, consistent with the reductive half-reaction of MPAO making a major contribution to rate limitation in steady-state turnover. Studies using the enzyme-monitored turnover method indicate that oxidized FAD is the prominent form during steady-state turnover, consistent with the reductive half-reaction being rate-limiting. Our studies indicate the importance of Lys300 and probable importance of HOH309 to the mechanism of flavin reduction in MPAO. Possible roles for Lys300 and water in the mechanism of flavin reduction are discussed. © 2005 American Chemical Society.
261.
Paolo Fontana; Eckart Bindewald; Stefano Toppo; Riccardo Velasco; Giorgio Valle; Silvio C.E. Tosatto
The SSEA server for protein secondary structure alignment Journal Article
In: Bioinformatics, vol. 21, no. 3, pp. 393 – 395, 2005, (Cited by: 36; All Open Access, Green Open Access).
Abstract | Links:
@article{Fontana2005393,
title = {The SSEA server for protein secondary structure alignment},
author = { Paolo Fontana and Eckart Bindewald and Stefano Toppo and Riccardo Velasco and Giorgio Valle and Silvio C.E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-13844292778\&doi=10.1093%2fbioinformatics%2fbti013\&partnerID=40\&md5=6acb0c2db41c9bfe809bb12995cb6299},
doi = {10.1093/bioinformatics/bti013},
year = {2005},
date = {2005-01-01},
journal = {Bioinformatics},
volume = {21},
number = {3},
pages = {393 \textendash 395},
abstract = {Summary: We present a web server that computes alignments of protein secondary structures. The server supports both performing pairwise alignments and searching a secondary structure against a library of domain folds. It can calculate global and local secondary structure element alignments. A combination of local and global alignment steps can be used to search for domains inside the query sequence or help in the discrimination of novel folds. Both the SCOP and PDB fold libraries, clustered at 95 and 40% sequence identity, are available for alignment. © Oxford University Press 2004; all rights reserved.},
note = {Cited by: 36; All Open Access, Green Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Summary: We present a web server that computes alignments of protein secondary structures. The server supports both performing pairwise alignments and searching a secondary structure against a library of domain folds. It can calculate global and local secondary structure element alignments. A combination of local and global alignment steps can be used to search for domains inside the query sequence or help in the discrimination of novel folds. Both the SCOP and PDB fold libraries, clustered at 95 and 40% sequence identity, are available for alignment. © Oxford University Press 2004; all rights reserved.
262.
Federico Fogolari; Silvio C.E. Tosatto; Giorgio Colombo
A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators Journal Article
In: BMC Bioinformatics, vol. 6, 2005, (Cited by: 15; All Open Access, Gold Open Access).
Abstract | Links:
@article{Fogolari2005,
title = {A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators},
author = { Federico Fogolari and Silvio C.E. Tosatto and Giorgio Colombo},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-29244479220\&doi=10.1186%2f1471-2105-6-301\&partnerID=40\&md5=46354122bb97838843a7126060877543},
doi = {10.1186/1471-2105-6-301},
year = {2005},
date = {2005-01-01},
journal = {BMC Bioinformatics},
volume = {6},
abstract = {Background: Estimators of free energies are routinely used to judge the quality of protein structural models. As these estimators still present inaccuracies, they are frequently evaluated by discriminating native or native-like conformations from large ensembles of so-called decoy structures. Results: A decoy set is obtained from snapshots taken from 5 long (100 ns) molecular dynamics (MD) simulations of the thermostable subdomain from chicken villin headpiece. An evaluation of the energy of the decoys is given using: i) a residue based contact potential supplemented by a term for the quality of dihedral angles; ii) a recently introduced combination of four statistical scoring functions for model quality estimation (FRST); iii) molecular mechanics with solvation energy estimated either according to the generalized Born surface area (GBSA) or iv) the Poisson-Boltzmann surface area (PBSA) method. Conclusions: The decoy set presented here has the following features which make it attractive for testing energy scoring functions: 1) it covers a broad range of RMSD values (from less than 2.0 r{A} to more than 12 r{A}); 2) it has been obtained from molecular dynamics trajectories, starting from different non-native-like conformations which have diverse behaviour, with secondary structure elements correctly or incorrectly formed, and in one case folding to a native-like structure. This allows not only for scoring of static structures, but also for studying, using free energy estimators, the kinetics of folding; 3) all structures have been obtained from accurate MD simulations in explicit solvent and after molecular mechanics (MM) energy minimization using an implicit solvent method. The quality of the covalent structure therefore does not suffer from steric or covalent problems. The statistical and physical effective energy functions tested on the set behave differently when native simulation snapshots are included or not in the set and when averaging over the trajectory is performed. © 2005 Fogolari et al., licensee BioMed Central Ltd.},
note = {Cited by: 15; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Background: Estimators of free energies are routinely used to judge the quality of protein structural models. As these estimators still present inaccuracies, they are frequently evaluated by discriminating native or native-like conformations from large ensembles of so-called decoy structures. Results: A decoy set is obtained from snapshots taken from 5 long (100 ns) molecular dynamics (MD) simulations of the thermostable subdomain from chicken villin headpiece. An evaluation of the energy of the decoys is given using: i) a residue based contact potential supplemented by a term for the quality of dihedral angles; ii) a recently introduced combination of four statistical scoring functions for model quality estimation (FRST); iii) molecular mechanics with solvation energy estimated either according to the generalized Born surface area (GBSA) or iv) the Poisson-Boltzmann surface area (PBSA) method. Conclusions: The decoy set presented here has the following features which make it attractive for testing energy scoring functions: 1) it covers a broad range of RMSD values (from less than 2.0 Å to more than 12 Å); 2) it has been obtained from molecular dynamics trajectories, starting from different non-native-like conformations which have diverse behaviour, with secondary structure elements correctly or incorrectly formed, and in one case folding to a native-like structure. This allows not only for scoring of static structures, but also for studying, using free energy estimators, the kinetics of folding; 3) all structures have been obtained from accurate MD simulations in explicit solvent and after molecular mechanics (MM) energy minimization using an implicit solvent method. The quality of the covalent structure therefore does not suffer from steric or covalent problems. The statistical and physical effective energy functions tested on the set behave differently when native simulation snapshots are included or not in the set and when averaging over the trajectory is performed. © 2005 Fogolari et al., licensee BioMed Central Ltd.
263.
Matilde Maiorino; Antonella Roveri; Louise Benazzi; Valentina Bosello; Pierluigi Mauri; Stefano Toppo; Silvio C. E. Tosatto; Fulvio Ursini
Functional interaction of phospholipid hydroperoxide glutathione peroxidase with sperm mitochondrion-associated cysteine-rich protein discloses the adjacent cysteine motif as a new substrate of the selenoperoxidase Journal Article
In: Journal of Biological Chemistry, vol. 280, no. 46, pp. 38395 – 38402, 2005, (Cited by: 79; All Open Access, Hybrid Gold Open Access).
Abstract | Links:
@article{Maiorino200538395,
title = {Functional interaction of phospholipid hydroperoxide glutathione peroxidase with sperm mitochondrion-associated cysteine-rich protein discloses the adjacent cysteine motif as a new substrate of the selenoperoxidase},
author = { Matilde Maiorino and Antonella Roveri and Louise Benazzi and Valentina Bosello and Pierluigi Mauri and Stefano Toppo and Silvio C. E. Tosatto and Fulvio Ursini},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33644670813\&doi=10.1074%2fjbc.M505983200\&partnerID=40\&md5=30bafba76cf74c0fbbb82fb35d9a9d59},
doi = {10.1074/jbc.M505983200},
year = {2005},
date = {2005-01-01},
journal = {Journal of Biological Chemistry},
volume = {280},
number = {46},
pages = {38395 \textendash 38402},
abstract = {The mitochondrial capsule is a selenium- and disulfide-rich structure enchasing the outer mitochondrial membrane of mammalian spermatozoa. Among the proteins solubilized from the sperm mitochondrial capsule, we confirmed, by using a proteomic approach, the presence of phospholipid hydroperoxide glutathione peroxidase (PHGPx) as a major component, and we also identified the sperm mitochondrion-associated cysteine-rich protein (SMCP) and fragments/aggregates of specific keratins that previously escaped detection (Ursini, F., Heim, S., Kiess, M., Maiorino, M., Roveri, A., Wissing, J., and Floh\'{e}, L. (1999) Science 285, 1393-1396). The evidence for a functional association between PHGPx, SMCP, and keratins is further supported by the identification of a sequence motif of regularly spaced Cys-Cys doublets common to SMCP and high sulfur keratin-associated proteins, involved in bundling hair shaft keratin by disulfide cross-linking. Following the oxidative polymerization of mitochondrial capsule proteins, catalyzed by PHGPx, two-dimensional redox electrophoresis analysis showed homo- and heteropolymers of SMCP and PHGPx, together with other minor components. Adjacent cysteine residues in SMCP peptides are oxidized to cystine by PHGPx. This unusual disulfide is known to drive, by reshuffling oxidative protein folding. On this basis we propose that oxidative polymerization of the mitochondrial capsule is primed by the formation of cystine on SMCP, followed by reshuffling. Occurrence of reshuffling is further supported by the calculated thermodynamic gain of the process. This study suggests a new mechanism where selenium catalysis drives the cross-linking of structural elements of the cytoskeleton via the oxidation of a keratin-associated protein. © 2005 by The American Society for Biochemistry and Molecular Biology, Inc.},
note = {Cited by: 79; All Open Access, Hybrid Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The mitochondrial capsule is a selenium- and disulfide-rich structure enchasing the outer mitochondrial membrane of mammalian spermatozoa. Among the proteins solubilized from the sperm mitochondrial capsule, we confirmed, by using a proteomic approach, the presence of phospholipid hydroperoxide glutathione peroxidase (PHGPx) as a major component, and we also identified the sperm mitochondrion-associated cysteine-rich protein (SMCP) and fragments/aggregates of specific keratins that previously escaped detection (Ursini, F., Heim, S., Kiess, M., Maiorino, M., Roveri, A., Wissing, J., and Flohé, L. (1999) Science 285, 1393-1396). The evidence for a functional association between PHGPx, SMCP, and keratins is further supported by the identification of a sequence motif of regularly spaced Cys-Cys doublets common to SMCP and high sulfur keratin-associated proteins, involved in bundling hair shaft keratin by disulfide cross-linking. Following the oxidative polymerization of mitochondrial capsule proteins, catalyzed by PHGPx, two-dimensional redox electrophoresis analysis showed homo- and heteropolymers of SMCP and PHGPx, together with other minor components. Adjacent cysteine residues in SMCP peptides are oxidized to cystine by PHGPx. This unusual disulfide is known to drive, by reshuffling oxidative protein folding. On this basis we propose that oxidative polymerization of the mitochondrial capsule is primed by the formation of cystine on SMCP, followed by reshuffling. Occurrence of reshuffling is further supported by the calculated thermodynamic gain of the process. This study suggests a new mechanism where selenium catalysis drives the cross-linking of structural elements of the cytoskeleton via the oxidation of a keratin-associated protein. © 2005 by The American Society for Biochemistry and Molecular Biology, Inc.
264.
F.J. Del Castillo; M. Rodríguez-Ballesteros; A. Álvarez; T. Hutchin; E. Leonardi; C.A. De Oliveira; H. Azaiez; Z. Brownstein; M.R. Avenarius; S. Marlin; A. Pandya; H. Shahin; Siemering; D. Weil; W. Wuyts; L.A. Aguirre; Y. Marlín; M.A. Moreno-Pelayo; M. Villamar; K.B. Avraham; H.-H.M. Dahl; M. Kanaan; W.E. Nance; C. Petit; R.J.H. Smith; G. Van Camp; E.L. Sartorato; A. Murgia; F. Moreno; Ignacio Del Castillo
A novel deletion involving the connexin-30 gene, del(GJB6-d13s1854), found in trans with mutations in the GJB2 gene (connexin-26) in subjects with DFNB1 non-syndromic hearing impairment Journal Article
In: Journal of Medical Genetics, vol. 42, no. 7, pp. 588 – 594, 2005, (Cited by: 270; All Open Access, Bronze Open Access, Green Open Access).
Abstract | Links:
@article{DelCastillo2005588,
title = {A novel deletion involving the connexin-30 gene, del(GJB6-d13s1854), found in trans with mutations in the GJB2 gene (connexin-26) in subjects with DFNB1 non-syndromic hearing impairment},
author = { F.J. Del Castillo and M. Rodr\'{i}guez-Ballesteros and A. \'{A}lvarez and T. Hutchin and E. Leonardi and C.A. De Oliveira and H. Azaiez and Z. Brownstein and M.R. Avenarius and S. Marlin and A. Pandya and H. Shahin and Siemering and D. Weil and W. Wuyts and L.A. Aguirre and Y. Marl\'{i}n and M.A. Moreno-Pelayo and M. Villamar and K.B. Avraham and H.-H.M. Dahl and M. Kanaan and W.E. Nance and C. Petit and R.J.H. Smith and G. Van Camp and E.L. Sartorato and A. Murgia and F. Moreno and Ignacio Del Castillo},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-22244489070\&doi=10.1136%2fjmg.2004.028324\&partnerID=40\&md5=c0d27bd228af054d535e39417139d339},
doi = {10.1136/jmg.2004.028324},
year = {2005},
date = {2005-01-01},
journal = {Journal of Medical Genetics},
volume = {42},
number = {7},
pages = {588 \textendash 594},
abstract = {DFNB1 deafness, caused by mutations in the gene encoding connexin-26 (GJB2), is the most frequent subtype of autosomal recessive non-syndromic hearing impairment. Molecular testing for GJB2 mutations has become a standard diagnostic approach for subjects with this disorder. However, 10-50% of affected subjects with GJB2 mutations carry only one mutant allele. A 309 kb deletion truncating the GJB6 gene (encoding connexin-30) was shown to be the accompanying mutation in up to 50% of deaf GJB2 heterozygotes in different populations. We report the molecular characterisation of the breakpoint junction of a novel 232 kb deletion in the DFNB1 locus, del(GJB6-D13S1854), which was also found in trans with pathogenic GJB2 mutations in affected subjects. The deletion arose by unequal homologous recombination, involving an AluY sequence inside GJB6 intron 2, a mechanism which might generate other deletions at DFNB1. We developed a novel diagnostic test for the combined detection of del(GJB6-D13S1830) and this new del(GJB6-D13S1854) in a single PCR assay. The del(GJB6-D13S1854) mutation accounts for 25.5% of the affected GJB2 heterozygotes which remained unresolved after screening for del(GJB6-D13S1830) in Spain, 22.2% in the UK, 6.3% in Brazil and 1.9% in northern Italy. It was not found in affected GJB2 heterozygotes from France, Belgium, Israel, the Palestinian Authority, USA, or Australia. Haplotype analysis revealed a common founder for the mutation in Spain, Italy, and the UK. Our data further support the complexity the genetic epidemiology of non-syndromic hearing impairment.},
note = {Cited by: 270; All Open Access, Bronze Open Access, Green Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
DFNB1 deafness, caused by mutations in the gene encoding connexin-26 (GJB2), is the most frequent subtype of autosomal recessive non-syndromic hearing impairment. Molecular testing for GJB2 mutations has become a standard diagnostic approach for subjects with this disorder. However, 10-50% of affected subjects with GJB2 mutations carry only one mutant allele. A 309 kb deletion truncating the GJB6 gene (encoding connexin-30) was shown to be the accompanying mutation in up to 50% of deaf GJB2 heterozygotes in different populations. We report the molecular characterisation of the breakpoint junction of a novel 232 kb deletion in the DFNB1 locus, del(GJB6-D13S1854), which was also found in trans with pathogenic GJB2 mutations in affected subjects. The deletion arose by unequal homologous recombination, involving an AluY sequence inside GJB6 intron 2, a mechanism which might generate other deletions at DFNB1. We developed a novel diagnostic test for the combined detection of del(GJB6-D13S1830) and this new del(GJB6-D13S1854) in a single PCR assay. The del(GJB6-D13S1854) mutation accounts for 25.5% of the affected GJB2 heterozygotes which remained unresolved after screening for del(GJB6-D13S1830) in Spain, 22.2% in the UK, 6.3% in Brazil and 1.9% in northern Italy. It was not found in affected GJB2 heterozygotes from France, Belgium, Israel, the Palestinian Authority, USA, or Australia. Haplotype analysis revealed a common founder for the mutation in Spain, Italy, and the UK. Our data further support the complexity the genetic epidemiology of non-syndromic hearing impairment.
2004
Journal Articles
265.
K. Cryns; E. Orzan; A. Murgia; P.L.M. Huygen; F. Moreno; I. Del Castillo; G. Parker Chamberlin; H. Azaiez; S. Prasad; R.A. Cucci; E. Leonardi; R.L. Snoeckx; P.J. Govaerts; P.H. Van De Heyning; C.M. Van De Heyning; R.J.H. Smith; G. Van Camp
A genotype-phenotype correlation for GJB2 (connexin 26) deafness Journal Article
In: Journal of Medical Genetics, vol. 41, no. 3, pp. 147 – 154, 2004, (Cited by: 190; All Open Access, Bronze Open Access, Green Open Access).
Abstract | Links:
@article{Cryns2004147,
title = {A genotype-phenotype correlation for GJB2 (connexin 26) deafness},
author = { K. Cryns and E. Orzan and A. Murgia and P.L.M. Huygen and F. Moreno and I. Del Castillo and G. Parker Chamberlin and H. Azaiez and S. Prasad and R.A. Cucci and E. Leonardi and R.L. Snoeckx and P.J. Govaerts and P.H. Van De Heyning and C.M. Van De Heyning and R.J.H. Smith and G. Van Camp},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-12144287717\&doi=10.1136%2fjmg.2003.013896\&partnerID=40\&md5=584fbdd538d85bad039fdd8b714841e8},
doi = {10.1136/jmg.2003.013896},
year = {2004},
date = {2004-01-01},
journal = {Journal of Medical Genetics},
volume = {41},
number = {3},
pages = {147 \textendash 154},
abstract = {Introduction: Mutations in GJB2 are the most common cause of non-syndromic autosomal recessive hearing impairment, ranging from mild to profound. Mutation analysis of this gene is widely available as a genetic diagnostic test. Objective: To assess a possible genotype-phenotype correlation for GJB2. Design: Retrospective analysis of audiometric data from people with hearing impairment, segregating two GJB2 mutations. Subjects: Two hundred and seventy seven unrelated patients with hearing impairment who were seen at the ENT departments of local and university hospitals from Italy, Belgium, Spain, and the United States, and who harboured bi-allelic GJB2 mutations. Results: We found that 35delG homozygotes have significantly more hearing impairment, compared with 35delG/non-35delG compound heterozygotes. People with two non-35delG mutations have even less hearing impairment. We observed a similar gradient of hearing impairment when we categorised mutations as inactivating (that is, stop mutations or frame shifts) or non-inactivating (that is, missense mutations). We demonstrated that certain mutation combinations (including the combination of 35delG with the missense mutations L90P, V37I, or the splice-site mutation IVS1+1G\>A, and the V37I/V37I genotype) are associated with significantly less hearing impairment compared with 35delG homozygous genotypes. Conclusions: This study is the first large systematic analysis indicating that the GJB2 genotype has a major impact on the degree of hearing impairment, and identifying mild genotypes. Furthermore, this study shows that it will be possible to refine this correlation and extend it to additional genotypes. These data will be useful in evaluating habilitation options for people with GJB2 related deafness.},
note = {Cited by: 190; All Open Access, Bronze Open Access, Green Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Introduction: Mutations in GJB2 are the most common cause of non-syndromic autosomal recessive hearing impairment, ranging from mild to profound. Mutation analysis of this gene is widely available as a genetic diagnostic test. Objective: To assess a possible genotype-phenotype correlation for GJB2. Design: Retrospective analysis of audiometric data from people with hearing impairment, segregating two GJB2 mutations. Subjects: Two hundred and seventy seven unrelated patients with hearing impairment who were seen at the ENT departments of local and university hospitals from Italy, Belgium, Spain, and the United States, and who harboured bi-allelic GJB2 mutations. Results: We found that 35delG homozygotes have significantly more hearing impairment, compared with 35delG/non-35delG compound heterozygotes. People with two non-35delG mutations have even less hearing impairment. We observed a similar gradient of hearing impairment when we categorised mutations as inactivating (that is, stop mutations or frame shifts) or non-inactivating (that is, missense mutations). We demonstrated that certain mutation combinations (including the combination of 35delG with the missense mutations L90P, V37I, or the splice-site mutation IVS1+1G>A, and the V37I/V37I genotype) are associated with significantly less hearing impairment compared with 35delG homozygous genotypes. Conclusions: This study is the first large systematic analysis indicating that the GJB2 genotype has a major impact on the degree of hearing impairment, and identifying mild genotypes. Furthermore, this study shows that it will be possible to refine this correlation and extend it to additional genotypes. These data will be useful in evaluating habilitation options for people with GJB2 related deafness.
2003
Journal Articles
266.
Caryn R. Rothrock; Alessandra Murgia; Edi L. Sartorato; Emanuela Leonardi; Sainan Wei; Sarah L. Lebeis; Laura E. Yu; Jill L. Elfenbein; Rachel A. Fisher; Karen H. Friderici
Connexin 26 35delG does not represent a mutational hotspot Journal Article
In: Human Genetics, vol. 113, no. 1, pp. 18 – 23, 2003, (Cited by: 48).
Abstract | Links:
@article{Rothrock200318,
title = {Connexin 26 35delG does not represent a mutational hotspot},
author = { Caryn R. Rothrock and Alessandra Murgia and Edi L. Sartorato and Emanuela Leonardi and Sainan Wei and Sarah L. Lebeis and Laura E. Yu and Jill L. Elfenbein and Rachel A. Fisher and Karen H. Friderici},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0038270170\&doi=10.1007%2fs00439-003-0944-2\&partnerID=40\&md5=d6225151947a822dedf8584a9d45240a},
doi = {10.1007/s00439-003-0944-2},
year = {2003},
date = {2003-01-01},
journal = {Human Genetics},
volume = {113},
number = {1},
pages = {18 \textendash 23},
abstract = {Non-syndromic hearing impairment (NSHI) is the most common form of deafness and presents with no other symptoms or sensory defects. Mutations in the gap junction gene GJB2 account for a high proportion of recessive NSHI. The GJB2 gene encodes connexin 26, which forms plasma membrane channels between cochlear cells. In Caucasian populations a single mutation, 35delG, accounts for most cases of NSHI. This mutation appears to be most prevalent in individuals of Mediterranean European descent, with carrier frequencies estimated as being as high as one in thirty. The 35delG region may be a mutational hotspot. The mutation arises from the deletion of a guanine from a six-guanine stretch and nearby microsatellite markers show little evidence for linkage disequilibrium. We believe that 35delG is an old mutation in a chromosomal region of high recombination. The genetic context of the 35delG mutation was examined to distinguish between an old or a recurring mutation. We identified two single-nucleotide polymorphisms (SNPs) immediately upstream of the first exon of GJB2. Polymerase chain reaction/restriction fragment length polymorphism analysis determined the SNP genotype of 35delG containing chromosomes from various populations, including Italy, Brazil, and North America. We found the same, relatively rare, polymorphism associated with the 35delG mutation in all populations studied. We have also examined microsatellite markers D13S175, which is 80kb telomeric to GJB2, and D13S1316, which is 80kb centromeric to GJB2. D13S175 appears to be in weak linkage disequilibrium with 35delG, while D13S1316 is less so. SNPs located between the 35delG mutation and the microsatellite markers show strong evidence of linkage disequilibrium. Taken together, these results indicate there has been substantial recombination near the 35delG mutation; however, we present evidence that the 35delG mutation arose in European and Middle Eastern populations from a single mutational event on a founder chromosome. © Springer-Verlag 2003.},
note = {Cited by: 48},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Non-syndromic hearing impairment (NSHI) is the most common form of deafness and presents with no other symptoms or sensory defects. Mutations in the gap junction gene GJB2 account for a high proportion of recessive NSHI. The GJB2 gene encodes connexin 26, which forms plasma membrane channels between cochlear cells. In Caucasian populations a single mutation, 35delG, accounts for most cases of NSHI. This mutation appears to be most prevalent in individuals of Mediterranean European descent, with carrier frequencies estimated as being as high as one in thirty. The 35delG region may be a mutational hotspot. The mutation arises from the deletion of a guanine from a six-guanine stretch and nearby microsatellite markers show little evidence for linkage disequilibrium. We believe that 35delG is an old mutation in a chromosomal region of high recombination. The genetic context of the 35delG mutation was examined to distinguish between an old or a recurring mutation. We identified two single-nucleotide polymorphisms (SNPs) immediately upstream of the first exon of GJB2. Polymerase chain reaction/restriction fragment length polymorphism analysis determined the SNP genotype of 35delG containing chromosomes from various populations, including Italy, Brazil, and North America. We found the same, relatively rare, polymorphism associated with the 35delG mutation in all populations studied. We have also examined microsatellite markers D13S175, which is 80kb telomeric to GJB2, and D13S1316, which is 80kb centromeric to GJB2. D13S175 appears to be in weak linkage disequilibrium with 35delG, while D13S1316 is less so. SNPs located between the 35delG mutation and the microsatellite markers show strong evidence of linkage disequilibrium. Taken together, these results indicate there has been substantial recombination near the 35delG mutation; however, we present evidence that the 35delG mutation arose in European and Middle Eastern populations from a single mutational event on a founder chromosome. © Springer-Verlag 2003.
267.
Mario Albrecht; Silvio C.E. Tosatto; Thomas Lengauer; Giorgio Valle
Simple consensus procedures are effective and sufficient in secondary structure prediction Journal Article
In: Protein Engineering, vol. 16, no. 7, pp. 459 – 462, 2003, (Cited by: 66; All Open Access, Bronze Open Access).
Abstract | Links:
@article{Albrecht2003459,
title = {Simple consensus procedures are effective and sufficient in secondary structure prediction},
author = { Mario Albrecht and Silvio C.E. Tosatto and Thomas Lengauer and Giorgio Valle},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0042379959\&doi=10.1093%2fprotein%2fgzg063\&partnerID=40\&md5=09b0719ed632b1413e2db5920b0d9432},
doi = {10.1093/protein/gzg063},
year = {2003},
date = {2003-01-01},
journal = {Protein Engineering},
volume = {16},
number = {7},
pages = {459 \textendash 462},
abstract = {We have analyzed the performance of majority voting on minimal combination sets of three state-of-the-art secondary structure prediction methods in order to obtain a consensus prediction. Using three large benchmark sets from the EVA server, our results show a significant improvement in the average Q3 prediction accuracy of up to 1.5 percentage points by consensus formation. The application of an additional trivial filtering procedure for predicted secondary structure elements that are too short, does not significantly affect the prediction accuracy. Our analysis also provides valuable insight into the similarity of the results of the prediction methods that we combine as well as the higher confidence in consistently predicted secondary structure.},
note = {Cited by: 66; All Open Access, Bronze Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We have analyzed the performance of majority voting on minimal combination sets of three state-of-the-art secondary structure prediction methods in order to obtain a consensus prediction. Using three large benchmark sets from the EVA server, our results show a significant improvement in the average Q3 prediction accuracy of up to 1.5 percentage points by consensus formation. The application of an additional trivial filtering procedure for predicted secondary structure elements that are too short, does not significantly affect the prediction accuracy. Our analysis also provides valuable insight into the similarity of the results of the prediction methods that we combine as well as the higher confidence in consistently predicted secondary structure.
268.
Eckart Bindewald; Alessandro Cestaro; Jürgen Hesser; Matthias Heiler; Silvio C.E. Tosatto
MANIFOLD: Protein fold recognition based on secondary structure, sequence similarity and enzyme classification Journal Article
In: Protein Engineering, vol. 16, no. 11, pp. 785 – 789, 2003, (Cited by: 35).
Abstract | Links:
@article{Bindewald2003785,
title = {MANIFOLD: Protein fold recognition based on secondary structure, sequence similarity and enzyme classification},
author = { Eckart Bindewald and Alessandro Cestaro and J\"{u}rgen Hesser and Matthias Heiler and Silvio C.E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0345600222\&doi=10.1093%2fprotein%2fgzg106\&partnerID=40\&md5=93c9966cba93bc4be9b8771411829c23},
doi = {10.1093/protein/gzg106},
year = {2003},
date = {2003-01-01},
journal = {Protein Engineering},
volume = {16},
number = {11},
pages = {785 \textendash 789},
abstract = {We present a protein fold recognition method, MANIFOLD, which uses the similarity between target and template proteins in predicted secondary structure, sequence and enzyme code to predict the fold of the target protein. We developed a non-linear ranking scheme in order to combine the scores of the three different similarity measures used. For a difficult test set of proteins with very little sequence similarity, the program predicts the fold class correctly in 34% of cases. This is an over twofold increase in accuracy compared with sequence-based methods such as PSI-BLAST or GenTHREADER, which score 13-14% correct first hits for the same test set. The functional similarity term increases the prediction accuracy by up to 3% compared with using the combination of secondary structure similarity and PSI-BLAST alone. We argue that using functional and secondary structure information can increase the fold recognition beyond sequence similarity.},
note = {Cited by: 35},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We present a protein fold recognition method, MANIFOLD, which uses the similarity between target and template proteins in predicted secondary structure, sequence and enzyme code to predict the fold of the target protein. We developed a non-linear ranking scheme in order to combine the scores of the three different similarity measures used. For a difficult test set of proteins with very little sequence similarity, the program predicts the fold class correctly in 34% of cases. This is an over twofold increase in accuracy compared with sequence-based methods such as PSI-BLAST or GenTHREADER, which score 13-14% correct first hits for the same test set. The functional similarity term increases the prediction accuracy by up to 3% compared with using the combination of secondary structure similarity and PSI-BLAST alone. We argue that using functional and secondary structure information can increase the fold recognition beyond sequence similarity.
2002
Journal Articles
269.
Silvio C.E. Tosatto; Eckart Bindewald; Jürgen Hesser; Reinhard Männer
A divide and conquer approach to fast loop modeling Journal Article
In: Protein Engineering, vol. 15, no. 4, pp. 279 – 286, 2002, (Cited by: 63; All Open Access, Bronze Open Access).
Abstract | Links:
@article{Tosatto2002279,
title = {A divide and conquer approach to fast loop modeling},
author = { Silvio C.E. Tosatto and Eckart Bindewald and J\"{u}rgen Hesser and Reinhard M\"{a}nner},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0036096608\&doi=10.1093%2fprotein%2f15.4.279\&partnerID=40\&md5=aecab2bd43683aca94f171e4f077abfd},
doi = {10.1093/protein/15.4.279},
year = {2002},
date = {2002-01-01},
journal = {Protein Engineering},
volume = {15},
number = {4},
pages = {279 \textendash 286},
abstract = {We describe a fast ab initio method for modeling local segments in protein structures. The algorithm is based on a divide and conquer approach and uses a database of precalculated look-up tables, which represent a large set of possible conformations for loop segments of variable length. The target loop is recursively decomposed until the resulting conformations are small enough to be compiled analytically. The algorithm, which is not restricted to any specific loop length, generates a ranked set of loop conformations in 20-180 s on a desktop PC. The prediction quality is evaluated in terms of global RMSD. Depending on loop length the top prediction varies between 1.06 r{A} RMSD for three-residue loops and 3.72 r{A} RMSD for eight-residue loops. Due to its speed the method may also be useful to generate alternative starting conformations for complex simulations.},
note = {Cited by: 63; All Open Access, Bronze Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We describe a fast ab initio method for modeling local segments in protein structures. The algorithm is based on a divide and conquer approach and uses a database of precalculated look-up tables, which represent a large set of possible conformations for loop segments of variable length. The target loop is recursively decomposed until the resulting conformations are small enough to be compiled analytically. The algorithm, which is not restricted to any specific loop length, generates a ranked set of loop conformations in 20-180 s on a desktop PC. The prediction quality is evaluated in terms of global RMSD. Depending on loop length the top prediction varies between 1.06 Å RMSD for three-residue loops and 3.72 Å RMSD for eight-residue loops. Due to its speed the method may also be useful to generate alternative starting conformations for complex simulations.
1999
Journal Articles
270.
A. Murgia; E. Orzan; R. Polli; M. Martella; G. Vinanzi; E. Leonardi; E. Arslan; F. Zacchello
Cx26 deafness: Mutation analysis and clinical variability Journal Article
In: Journal of Medical Genetics, vol. 36, no. 11, pp. 829 – 832, 1999, (Cited by: 127).
Abstract | Links:
@article{Murgia1999829,
title = {Cx26 deafness: Mutation analysis and clinical variability},
author = { A. Murgia and E. Orzan and R. Polli and M. Martella and G. Vinanzi and E. Leonardi and E. Arslan and F. Zacchello},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032727332\&partnerID=40\&md5=75a468b32bb154bd5b918c387163db2d},
year = {1999},
date = {1999-01-01},
journal = {Journal of Medical Genetics},
volume = {36},
number = {11},
pages = {829 \textendash 832},
abstract = {Mutations in the gap junction protein connexin 26 (Cx26) gene (GJB2) seem to account for many cases of congenital sensorineural hearing impairment, the reported prevalence being 34-50% in autosomal recessive cases and 10-37% in sporadic cases. The hearing impairment in these patients has been described as severe or profound. We have studied 53 unrelated subjects with congenital non-syndromic sensorineural hearing impairment in order to evaluate the prevalence and type of Cx26 mutations and establish better genotype-phenotype correlation. Mutations in the Cx26 gene were found in 53% of the subjects tested, 35.3% of the autosomal recessive and 60% of the sporadic cases in our series. Three new mutations were identified. The hearing deficit varied from mild to profound even in 35delG homozygotes within the same family. No evidence of progression of the impairment was found. Alterations of the Cx26 gene account for a large proportion of cases of congenital non-syndromic sensorineural deafness, so it seems appropriate to extend the molecular analysis even to subjects with mild or moderate prelingual hearing impairment of unknown cause.},
note = {Cited by: 127},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mutations in the gap junction protein connexin 26 (Cx26) gene (GJB2) seem to account for many cases of congenital sensorineural hearing impairment, the reported prevalence being 34-50% in autosomal recessive cases and 10-37% in sporadic cases. The hearing impairment in these patients has been described as severe or profound. We have studied 53 unrelated subjects with congenital non-syndromic sensorineural hearing impairment in order to evaluate the prevalence and type of Cx26 mutations and establish better genotype-phenotype correlation. Mutations in the Cx26 gene were found in 53% of the subjects tested, 35.3% of the autosomal recessive and 60% of the sporadic cases in our series. Three new mutations were identified. The hearing deficit varied from mild to profound even in 35delG homozygotes within the same family. No evidence of progression of the impairment was found. Alterations of the Cx26 gene account for a large proportion of cases of congenital non-syndromic sensorineural deafness, so it seems appropriate to extend the molecular analysis even to subjects with mild or moderate prelingual hearing impairment of unknown cause.