Elena Papaleo

Summary

Affiliation: University of Milano-Bicocca
Country: Italy

Publications

  1. ncbi request reprint Conformational diseases: structural studies of aggregation of polyglutamine proteins
    Elena Papaleo
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
    Curr Comput Aided Drug Des 7:23-43. 2011
  2. doi request reprint Conformational plasticity of the calcium-binding pocket in the Burkholderia glumae lipase: remodeling induced by mutation of calcium coordinating residues
    Elena Papaleo
    Department of Biotechnology and Biosciences, Milano Bicocca University, Piazza della Scienza 2, 20126 Milano, Italy
    Biopolymers 95:117-26. 2011
  3. ncbi request reprint Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes
    Elena Papaleo
    Department of Biotechnology and Biosciences, University of Milano Bicocca, P zza della Scienza 2, 20126, Milan, Italy
    Curr Protein Pept Sci 12:657-83. 2011
  4. pmc Intramolecular interactions stabilizing compact conformations of the intrinsically disordered kinase-inhibitor domain of Sic1: a molecular dynamics investigation
    Matteo Lambrughi
    Department of Biotechnology and Biosciences, University of Milano Bicocca Milan, Italy
    Front Physiol 3:435. 2012
  5. pmc Mechanisms of intramolecular communication in a hyperthermophilic acylaminoacyl peptidase: a molecular dynamics investigation
    Elena Papaleo
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
    PLoS ONE 7:e35686. 2012
  6. pmc Loop 7 of E2 enzymes: an ancestral conserved functional motif involved in the E2-mediated steps of the ubiquitination cascade
    Elena Papaleo
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
    PLoS ONE 7:e40786. 2012
  7. doi request reprint Coupled motions during dynamics reveal a tunnel toward the active site regulated by the N-terminal α-helix in an acylaminoacyl peptidase
    Elena Papaleo
    Department of Biotechnology and Biosciences, University of Milano Bicocca, P zza della Scienza 2, 20126 Milan, Italy
    J Mol Graph Model 38:226-34. 2012
  8. pmc Molecular dynamics of mesophilic-like mutants of a cold-adapted enzyme: insights into distal effects induced by the mutations
    Elena Papaleo
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
    PLoS ONE 6:e24214. 2011
  9. pmc An acidic loop and cognate phosphorylation sites define a molecular switch that modulates ubiquitin charging activity in Cdc34-like enzymes
    Elena Papaleo
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
    PLoS Comput Biol 7:e1002056. 2011
  10. doi request reprint Molecular dynamics investigation of cyclic natriuretic peptides: dynamic properties reflect peptide activity
    Elena Papaleo
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
    J Mol Graph Model 28:834-41. 2010

Collaborators

Detail Information

Publications32

  1. ncbi request reprint Conformational diseases: structural studies of aggregation of polyglutamine proteins
    Elena Papaleo
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
    Curr Comput Aided Drug Des 7:23-43. 2011
    ..These aspects are of crucial relevance for a complete understanding of the onset of polyQ conformational diseases and can also shed light on putative therapeutic targets and future development of aggregation inhibitors...
  2. doi request reprint Conformational plasticity of the calcium-binding pocket in the Burkholderia glumae lipase: remodeling induced by mutation of calcium coordinating residues
    Elena Papaleo
    Department of Biotechnology and Biosciences, Milano Bicocca University, Piazza della Scienza 2, 20126 Milano, Italy
    Biopolymers 95:117-26. 2011
    ..It turns out that additional acidic residues, which are conserved in other microbial lipases, help in overcoming effects induced by mutation of D241 Ca²+-coordinating residue, upon rearrangements induced in the calcium binding site...
  3. ncbi request reprint Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes
    Elena Papaleo
    Department of Biotechnology and Biosciences, University of Milano Bicocca, P zza della Scienza 2, 20126, Milan, Italy
    Curr Protein Pept Sci 12:657-83. 2011
    ....
  4. pmc Intramolecular interactions stabilizing compact conformations of the intrinsically disordered kinase-inhibitor domain of Sic1: a molecular dynamics investigation
    Matteo Lambrughi
    Department of Biotechnology and Biosciences, University of Milano Bicocca Milan, Italy
    Front Physiol 3:435. 2012
    ..The results identify a group of putative hub residues and networks of electrostatic interactions, which are likely to be involved in the stabilization of the globular states...
  5. pmc Mechanisms of intramolecular communication in a hyperthermophilic acylaminoacyl peptidase: a molecular dynamics investigation
    Elena Papaleo
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
    PLoS ONE 7:e35686. 2012
    ..Moreover, a subset of residues characterized by relevant interaction networks or coupled motions have been identified, which are likely to modulate the conformational properties at the interdomain interface...
  6. pmc Loop 7 of E2 enzymes: an ancestral conserved functional motif involved in the E2-mediated steps of the ubiquitination cascade
    Elena Papaleo
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
    PLoS ONE 7:e40786. 2012
    ..Its different functions are exploited thank to its conserved hydrophobic and acidic residues in a finely orchestrate mechanism...
  7. doi request reprint Coupled motions during dynamics reveal a tunnel toward the active site regulated by the N-terminal α-helix in an acylaminoacyl peptidase
    Elena Papaleo
    Department of Biotechnology and Biosciences, University of Milano Bicocca, P zza della Scienza 2, 20126 Milan, Italy
    J Mol Graph Model 38:226-34. 2012
    ..The evidence here provided can be a useful guide for a better understanding of the mechanistic aspects related to AAP activity, but also for drug design purposes...
  8. pmc Molecular dynamics of mesophilic-like mutants of a cold-adapted enzyme: insights into distal effects induced by the mutations
    Elena Papaleo
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
    PLoS ONE 6:e24214. 2011
    ....
  9. pmc An acidic loop and cognate phosphorylation sites define a molecular switch that modulates ubiquitin charging activity in Cdc34-like enzymes
    Elena Papaleo
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
    PLoS Comput Biol 7:e1002056. 2011
    ....
  10. doi request reprint Molecular dynamics investigation of cyclic natriuretic peptides: dynamic properties reflect peptide activity
    Elena Papaleo
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
    J Mol Graph Model 28:834-41. 2010
    ....
  11. doi request reprint Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: the myoglobin case
    Elena Papaleo
    Department of Biotechnology and Bioscience, University of Milano Bicocca, 20126 Milan, Italy
    J Mol Graph Model 27:889-99. 2009
    ....
  12. doi request reprint Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin-like serine-proteases
    Elena Papaleo
    Department of Biotechnology and Bioscience, University of Milano Bicocca, 20126 Milan, Italy
    FEBS Lett 582:1008-18. 2008
    ....
  13. ncbi request reprint Near native-state conformational landscape of psychrophilic and mesophilic enzymes: probing the folding funnel model
    Paolo Mereghetti
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza, 2, 20126 Milan, Italy
    J Phys Chem B 114:7609-19. 2010
    ..According to the model, a cold-adapted enzyme in its native-state consists of a large population of conformations which can easily interconvert and result in high structural flexibility...
  14. doi request reprint The conformational ensemble of the disordered and aggregation-protective 182-291 region of ataxin-3
    Gaetano Invernizzi
    Department of Biotechnology and Biosciences, University of Milano Bicocca, 20126 Milan, Italy Electronic address
    Biochim Biophys Acta 1830:5236-47. 2013
    ..The disordered region between the polyQ and the JD, AT3182-291 plays a key role in the development of the disease...
  15. pmc Reciprocal influence of protein domains in the cold-adapted acyl aminoacyl peptidase from Sporosarcina psychrophila
    Federica Parravicini
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
    PLoS ONE 8:e56254. 2013
    ..Overall, a strict interaction of the SpAAP domains seems to be mandatory for the preservation of their reciprocal structural integrity and may witness their co-evolution...
  16. ncbi request reprint Dynamic properties of a psychrophilic alpha-amylase in comparison with a mesophilic homologue
    Marco Pasi
    Department of Biotechnology and Biosciences, University of Milano Bicocca, P za della Scienza 2, 20126 Milan, Italy
    J Phys Chem B 113:13585-95. 2009
    ....
  17. ncbi request reprint Flexibility and enzymatic cold-adaptation: a comparative molecular dynamics investigation of the elastase family
    Elena Papaleo
    Department of Biotechnology and Bioscience, University of Milano Bicocca, P za della Scienza 2, 20126, Milan, Italy
    Biochim Biophys Acta 1764:1397-406. 2006
    ....
  18. doi request reprint C-type natriuretic peptide: Structural studies, fragment synthesis, and preliminary biological evaluation in human osteosarcoma cell lines
    Nasrin Shaikh
    Department of Biotechnology and Biosciences, University of Milano Bicocca, P za della Scienza 2 20126 Milano, Italy
    Biopolymers 94:213-9. 2010
    ....
  19. doi request reprint xPyder: a PyMOL plugin to analyze coupled residues and their networks in protein structures
    Marco Pasi
    Department of Biotechnology and Biosciences, University of Milano Bicocca, P zza della Scienza 2, 20126 Milan, Italy
    J Chem Inf Model 52:1865-74. 2012
    ..The xPyder plugin for PyMOL 1.4 and 1.5 is offered as Open Source software via the GPL v2 license, and it can be found, along with the installation package, the user guide, and examples, at http://linux.btbs.unimib.it/xpyder/...
  20. pmc Compaction properties of an intrinsically disordered protein: Sic1 and its kinase-inhibitor domain
    Stefania Brocca
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
    Biophys J 100:2243-52. 2011
    ..Comparison between the fragment and the full-length protein suggests that chain length is crucial to the stabilization of compact states of this IDP. The two proteins are compared by a length-independent compaction index...
  21. doi request reprint Evidence for the formation of a Mo-H intermediate in the catalytic cycle of formate dehydrogenase
    Matteo Tiberti
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
    Inorg Chem 51:8331-9. 2012
    ..The proposed reaction pathway is reminiscent of the key step of metal-based catalysis of the water-gas shift reaction...
  22. ncbi request reprint Functional annotation of the mesophilic-like character of mutants in a cold-adapted enzyme by self-organising map analysis of their molecular dynamics
    Domenico Fraccalvieri
    Department of Environmental Sciences, University of Milano Bicocca, Milan, Italy
    Mol Biosyst 8:2680-91. 2012
    ..In conclusion, our strategy can efficiently extract specific dynamic signatures related to function from multiple comparisons of MD conformational ensembles. Therefore, it can be a promising tool for protein engineering...
  23. doi request reprint C-Terminal acidic domain of ubiquitin-conjugating enzymes: a multi-functional conserved intrinsically disordered domain in family 3 of E2 enzymes
    Alberto Arrigoni
    Department of Biotechnology and Biosciences, University of Milano Bicocca, 20126 Milan, Italy
    J Struct Biol 178:245-59. 2012
    ..In fact, according to our calculations, Ubc1 maps at the interface between the space of the natively unfolded and folded proteins, as well as it shares common features with the acidic domain of family 3 members...
  24. ncbi request reprint Three-dimensional structure of the catalytic domain of the yeast beta-(1,3)-glucan transferase Gas1: a molecular modeling investigation
    Elena Papaleo
    Dipartimento di Biotecnologie e Bioscienze, Universita di Milano Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
    J Mol Model 12:237-48. 2006
    ..In particular, the model of the catalytic domain can be useful for designing site-directed mutagenesis experiments and for developing inhibitors of Gas1p enzymatic activity...
  25. doi request reprint The role of the central flexible region on the aggregation and conformational properties of human ataxin-3
    Carlo Santambrogio
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
    FEBS J 279:451-63. 2012
    ..Partially-folded monomers and dimers accumulate to a larger extent in AT3/291. These species represent good candidates for early intermediates of the aggregation process under the experimental conditions employed in the present study...
  26. doi request reprint Dynamic properties of extremophilic subtilisin-like serine-proteases
    Matteo Tiberti
    Department of Biotechnology and Biosciences, University of Milano Bicocca, 20126 Milan, Italy
    J Struct Biol 174:69-83. 2011
    ....
  27. ncbi request reprint PyInteraph: a framework for the analysis of interaction networks in structural ensembles of proteins
    Matteo Tiberti
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
    J Chem Inf Model 54:1537-51. 2014
    ..The program is available free of charge as Open Source software via the GPL v3 license at http://linux.btbs.unimib.it/pyinteraph/...
  28. doi request reprint Dynamics fingerprint and inherent asymmetric flexibility of a cold-adapted homodimeric enzyme. A case study of the Vibrio alkaline phosphatase
    Elena Papaleo
    Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
    Biochim Biophys Acta 1830:2970-80. 2013
    ..Here, we provide the first characterization of the dynamic fingerprint of the dimeric alkaline phosphatase (AP) from the cold-adapted Vibrio strain G15-21 (VAP), which is among the APs with the highest known kcat at low temperatures...
  29. doi request reprint Protein aggregation: mechanisms and functional consequences
    Gaetano Invernizzi
    Dipartimento di Biotecnologie e Bioscienze, Universita di Milano Bicocca, Milan, Italy
    Int J Biochem Cell Biol 44:1541-54. 2012
    ..Here we address the conformational properties of these aggregates, their formation pathways, their role in human diseases, their functional properties and how bioinformatics tools might be of help to study these protein assemblies...
  30. ncbi request reprint Ion pairs and their role in modulating stability of cold- and warm-active uracil DNA glycosylase
    Magne Olufsen
    The Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N 9037 Tromsø, Norway
    Proteins 71:1219-30. 2008
    ..Our results also suggest that care should be taken when performing statistical analysis of crystal structures with respect to ion pairs, and that crystallization conditions must be carefully examined when performing such analysis...
  31. ncbi request reprint Optimization of electrostatics as a strategy for cold-adaptation: a case study of cold- and warm-active elastases
    Elena Papaleo
    The Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N9037 Tromsø, Norway
    J Mol Graph Model 26:93-103. 2007
    ..In addition, subtle differences are also found in the electrostatic potentials in the vicinity of the catalytic residues, which may explain the increased catalytic efficiency of the cold-adapted elastase...
  32. pmc Validation of protein models by a neural network approach
    Paolo Mereghetti
    Department of Chemistry, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
    BMC Bioinformatics 9:66. 2008
    ....