@article{SCOPUS_ID:33644670813,

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/record/display.uri?eid=2-s2.0-33644670813&origin=inward},

doi = {10.1074/jbc.M505983200},

year  = {2005},

date = {2005-01-01},

journal = {Journal of Biological Chemistry},

volume = {280},

number = {46},

pages = {38395-38402},

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 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.},

note = {Cited by: 80; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:29244479220,

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/record/display.uri?eid=2-s2.0-29244479220&origin=inward},

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 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.},

note = {Cited by: 15; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:13844292778,

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/record/display.uri?eid=2-s2.0-13844292778&origin=inward},

doi = {10.1093/bioinformatics/bti013},

year  = {2005},

date = {2005-01-01},

journal = {Bioinformatics},

volume = {21},

number = {3},

pages = {393-395},

publisher = {Oxford University Press},

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; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:15244349255,

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/record/display.uri?eid=2-s2.0-15244349255&origin=inward},

doi = {10.1110/ps.041004105},

year  = {2005},

date = {2005-01-01},

journal = {Protein Science},

volume = {14},

number = {4},

pages = {889-901},

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; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:27544487034,

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/record/display.uri?eid=2-s2.0-27544487034&origin=inward},

doi = {10.1093/bioinformatics/bti1135},

year  = {2005},

date = {2005-01-01},

journal = {Bioinformatics},

volume = {21},

number = {SUPPL. 2},

publisher = {Oxford University Press},

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; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:27744551994,

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/record/display.uri?eid=2-s2.0-27744551994&origin=inward},

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 = {1383-1390},

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; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:0345600222,

title = {MANIFOLD: Protein fold recognition based on secondary structure, sequence similarity and enzyme classification},

author = {Eckart Bindewald and Alessandro Cestaro and Jürgen Hesser and Matthias Heiler and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-0345600222&origin=inward},

doi = {10.1093/protein/gzg106},

year  = {2003},

date = {2003-01-01},

journal = {Protein Engineering},

volume = {16},

number = {11},

pages = {785-789},

publisher = {Oxford University Press},

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}

}

@article{SCOPUS_ID:0042379959,

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/record/display.uri?eid=2-s2.0-0042379959&origin=inward},

doi = {10.1093/protein/gzg063},

year  = {2003},

date = {2003-01-01},

journal = {Protein Engineering},

volume = {16},

number = {7},

pages = {459-462},

publisher = {Oxford University Press},

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: 67; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:0036096608,

title = {A divide and conquer approach to fast loop modeling},

author = {Silvio C. E. Tosatto and Eckart Bindewald and Jürgen Hesser and Reinhard Männer},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-0036096608&origin=inward},

doi = {10.1093/protein/15.4.279},

year  = {2002},

date = {2002-01-01},

journal = {Protein Engineering},

volume = {15},

number = {4},

pages = {279-286},

publisher = {Oxford University Press},

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 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.},

note = {Cited by: 63; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}