Giorgio Colombo

Summary

Affiliation: Istituto di Chimica del Riconoscimento Molecolare
Country: Italy

Publications

  1. ncbi request reprint The determinants of stability in the human prion protein: insights into folding and misfolding from the analysis of the change in the stabilization energy distribution in different conditions
    Stefano Colacino
    Dipartimento di Fisica, Universita di Milano, Milano, Italy
    Proteins 62:698-707. 2006
  2. doi request reprint A molecular dynamics study of the interaction of D-peptide amyloid inhibitors with their target sequence reveals a potential inhibitory pharmacophore conformation
    Alexandra Esteras-Chopo
    Computational and Structural Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden Wurttemberg, Germany
    J Mol Biol 383:266-80. 2008
  3. pmc Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer
    Giulia Morra
    Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milano, Italy
    PLoS Comput Biol 5:e1000323. 2009
  4. pmc Molecular dynamics simulations of hsp90 with an eye to inhibitor design
    Elisabetta Moroni
    Institute of Molecular Recognition Chemistry, CNR, Via Mario Bianco 9, 20131 Milano, Italy
    Pharmaceuticals (Basel) 5:944-62. 2012
  5. ncbi request reprint The Dynamics of Drug Discovery
    Elisabetta Moroni
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131, Milano, Italy
    Curr Top Med Chem . 2015
  6. ncbi request reprint The Dynamics of Drug Discovery
    Elisabetta Moroni
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131, Milano, Italy
    Curr Top Med Chem 15:2043-55. 2015
  7. pmc A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators
    Federico Fogolari
    Dipartimento di Scienze e Tecnologie Biomediche, Universita di Udine, P, le Kolbe 4, 33100 Udine, Italy
    BMC Bioinformatics 6:301. 2005
  8. ncbi request reprint Computational studies of the structure, dynamics and native content of amyloid-like fibrils of ribonuclease A
    Giorgio Colombo
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco, 9, 20131 Milano, Italy
    Proteins 70:863-72. 2008
  9. pmc Methionine sulfoxides on prion protein Helix-3 switch on the alpha-fold destabilization required for conversion
    Giorgio Colombo
    Isto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milano, Italy
    PLoS ONE 4:e4296. 2009
  10. pmc Combined in silico and experimental approach for drug design: the binding mode of peptidic and non-peptidic inhibitors to hsp90 N-terminal domain
    Simona Tomaselli
    Istituto per lo Studio delle Macromolecole, Consiglio Nazionale delle Ricerche, Milano, Italy
    Chem Biol Drug Des 76:382-91. 2010

Collaborators

Detail Information

Publications76

  1. ncbi request reprint The determinants of stability in the human prion protein: insights into folding and misfolding from the analysis of the change in the stabilization energy distribution in different conditions
    Stefano Colacino
    Dipartimento di Fisica, Universita di Milano, Milano, Italy
    Proteins 62:698-707. 2006
    ..Misfolding appears to be a rearrangement of the chain that disrupts most of the native secondary structure of the protein, producing some beta-rich conformations with an energy distribution similar to that of the native state...
  2. doi request reprint A molecular dynamics study of the interaction of D-peptide amyloid inhibitors with their target sequence reveals a potential inhibitory pharmacophore conformation
    Alexandra Esteras-Chopo
    Computational and Structural Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden Wurttemberg, Germany
    J Mol Biol 383:266-80. 2008
    ..We propose that the inhibitory determinants derived from this work be used as structural templates in the development of pharmacophore models for the identification of novel nonpeptidic inhibitors of aggregation...
  3. pmc Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer
    Giulia Morra
    Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milano, Italy
    PLoS Comput Biol 5:e1000323. 2009
    ....
  4. pmc Molecular dynamics simulations of hsp90 with an eye to inhibitor design
    Elisabetta Moroni
    Institute of Molecular Recognition Chemistry, CNR, Via Mario Bianco 9, 20131 Milano, Italy
    Pharmaceuticals (Basel) 5:944-62. 2012
    ....
  5. ncbi request reprint The Dynamics of Drug Discovery
    Elisabetta Moroni
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131, Milano, Italy
    Curr Top Med Chem . 2015
    ....
  6. ncbi request reprint The Dynamics of Drug Discovery
    Elisabetta Moroni
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131, Milano, Italy
    Curr Top Med Chem 15:2043-55. 2015
    ....
  7. pmc A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators
    Federico Fogolari
    Dipartimento di Scienze e Tecnologie Biomediche, Universita di Udine, P, le Kolbe 4, 33100 Udine, Italy
    BMC Bioinformatics 6:301. 2005
    ..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...
  8. ncbi request reprint Computational studies of the structure, dynamics and native content of amyloid-like fibrils of ribonuclease A
    Giorgio Colombo
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco, 9, 20131 Milano, Italy
    Proteins 70:863-72. 2008
    ....
  9. pmc Methionine sulfoxides on prion protein Helix-3 switch on the alpha-fold destabilization required for conversion
    Giorgio Colombo
    Isto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milano, Italy
    PLoS ONE 4:e4296. 2009
    ..To investigate whether such modification may play a role in the misfolding process we have studied the impact of methionine oxidation on the dynamics and energetics of the HuPrP(125-229) alpha-fold...
  10. pmc Combined in silico and experimental approach for drug design: the binding mode of peptidic and non-peptidic inhibitors to hsp90 N-terminal domain
    Simona Tomaselli
    Istituto per lo Studio delle Macromolecole, Consiglio Nazionale delle Ricerche, Milano, Italy
    Chem Biol Drug Des 76:382-91. 2010
    ..The first experimental structural data on these inhibitors are presented and discussed as hints for future design of improved molecules...
  11. ncbi request reprint A dynamic perspective on the molecular recognition of chitooligosaccharide ligands by hevein domains
    Giorgio Colombo
    Istituto di Chimica del Riconoscimento Molecolare, CNR via Mario Bianco, 9, 20131 Milano, Italy
    Carbohydr Res 340:1039-49. 2005
    ..This structural and dynamical view parallels the results based on NOE NMR data for the three disaccharide, trisaccharide, and pentasaccharide complexes...
  12. doi request reprint Molecular simulations of peptides: a useful tool for the development of new drugs and for the study of molecular recognition
    Massimiliano Meli
    Istituto di Chimica del Riconoscimento Molecolare ICRM C N R, Milano, Italy
    Methods Mol Biol 570:77-153. 2009
    ....
  13. pmc Direct and allosteric inhibition of the FGF2/HSPGs/FGFR1 ternary complex formation by an antiangiogenic, thrombospondin-1-mimic small molecule
    Katiuscia Pagano
    Laboratorio NMR, Istituto per lo Studio delle Macromolecole, Consiglio Nazionale delle Ricerche, Milano, Italy
    PLoS ONE 7:e36990. 2012
    ..We propose that sm27 antiangiogenic activity is based on a twofold-direct and allosteric-mechanism, inhibiting FGF2 binding to both its receptors...
  14. pmc Investigating the mechanism of peptide aggregation: insights from mixed monte carlo-molecular dynamics simulations
    Massimiliano Meli
    Istituto di Chimica del Ricoscimento Molecolare, Consiglio Nazionale delle Ricerche, 20131 Milano, Italy
    Biophys J 94:4414-26. 2008
    ..Simulation results are consistent with experimentally derived observations and provide an atomically detailed view of the putative initial stages of fibril formation...
  15. ncbi request reprint Molecular dynamics simulations of proteins and peptides: from folding to drug design
    Giulia Morra
    Istituto di Chimica del Riconoscimento Molecolare, CNR Via Mario Bianco 9, Milano, Italy
    Curr Protein Pept Sci 9:181-96. 2008
    ....
  16. pmc Understanding ligand-based modulation of the Hsp90 molecular chaperone dynamics at atomic resolution
    Giorgio Colombo
    Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy
    Proc Natl Acad Sci U S A 105:7976-81. 2008
    ..The present study agrees with the experimental structural data and provides a plausible molecular model for understanding mechanisms of modulation of molecular chaperone activities by binding partners...
  17. pmc Similar folds with different stabilization mechanisms: the cases of Prion and Doppel proteins
    Stefano Colacino
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 10131 Milano, Italy
    BMC Struct Biol 6:17. 2006
    ..Doppel is a protein that shares a similar native fold, but lacks the scrapie isoform. Understanding the molecular determinants of these different behaviours is important both for biomedical and biophysical research...
  18. pmc Non-peptidic thrombospondin-1 mimics as fibroblast growth factor-2 inhibitors: an integrated strategy for the development of new antiangiogenic compounds
    Giorgio Colombo
    Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milan 20131, Italy
    J Biol Chem 285:8733-42. 2010
    ..Altogether, this study demonstrates that new biological insights obtained by integrated multidisciplinary approaches can be used to develop small molecule mimics of endogenous proteins as therapeutic agents...
  19. pmc Dynamic diagnosis of familial prion diseases supports the β2-α2 loop as a universal interference target
    Massimiliano Meli
    Department of Computational Biology, Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milano, Italy
    PLoS ONE 6:e19093. 2011
    ....
  20. pmc Predicting interaction sites from the energetics of isolated proteins: a new approach to epitope mapping
    Guido Scarabelli
    Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milan, Italy
    Biophys J 98:1966-75. 2010
    ..The combination of dynamics and energetics can thus discriminate between epitopes and other substructures based only on physical properties. We discuss implications for vaccine design...
  21. ncbi request reprint Peptide self-assembly at the nanoscale: a challenging target for computational and experimental biotechnology
    Giorgio Colombo
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
    Trends Biotechnol 25:211-8. 2007
    ..The combination of experimental observations and theoretical advances will be fundamental to fully realizing the biotechnological potential of peptide self-organization...
  22. ncbi request reprint Folding and mis-folding of peptides and proteins: insights from molecular simulations
    Giacomo M S de Mori
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
    Mini Rev Med Chem 5:353-9. 2005
    ..Finally, we will give a critical outlook on the possible developments of this field in the near future...
  23. pmc Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis
    Claudio Peri
    Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR Via Mario Bianco 9, 20131, Milano Italy
    Sci Rep 6:32873. 2016
    ..The method is general and immediately applicable to other bacteria. ..
  24. pmc Investigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes
    Rubben Torella
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
    BMC Struct Biol 10:42. 2010
    ..Herein, we present a computational study of the sequence modulation of internal dynamic properties and of intraprotein networks of aminoacid interactions that determine the stability and specificity of protein-DNA complexes...
  25. ncbi request reprint Molecular dynamics simulation of the aggregation of the core-recognition motif of the islet amyloid polypeptide in explicit water
    Giorgio Colombo
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
    Proteins 59:519-27. 2005
    ..These observations may yield information on new ways to control this process for either materials development or drug design...
  26. doi request reprint Selecting sequences that fold into a defined 3D structure: A new approach for protein design based on molecular dynamics and energetics
    Giulia Morra
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
    Biophys Chem 146:76-84. 2010
    ..The results show that our approach can correctly identify 70% of the sequences known to populate the typical WW domain fold...
  27. ncbi request reprint Screening Complex Biological Samples with Peptide Microarrays: The Favorable Impact of Probe Orientation via Chemoselective Immobilization Strategies on Clickable Polymeric Coatings
    Alessandro Gori
    Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare ICRM Via Mario Bianco, 9, 20131 Milano, Italy
    Bioconjug Chem 27:2669-2677. 2016
    ..On the basis of our results, we critically discuss the immobilization parameters that need to be carefully considered for peptide ligand immobilization purposes...
  28. doi request reprint Energetic and dynamic aspects of the affinity maturation process: characterizing improved variants from the bevacizumab antibody with molecular simulations
    Dario Corrada
    Istituto di Chimica del Riconoscimento Molecolare Consiglio Nazionale delle Ricerche CNR ICRM, Via Mario Bianco 9, 20131 Milano, Italy
    J Chem Inf Model 53:2937-50. 2013
    ..Overall, our results can help in understanding the molecular determinants of antigen recognition and have implications in the rational design of new antibodies with optimized affinities. ..
  29. doi request reprint Peptides for immunological purposes: design, strategies and applications
    Alessandro Gori
    Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milan, Italy
    Amino Acids 45:257-68. 2013
    ..Case studies are described to provide illustrative examples, and cross references to more topic-focused and exhaustive reviews are proposed throughout the text. ..
  30. pmc Corresponding functional dynamics across the Hsp90 Chaperone family: insights from a multiscale analysis of MD simulations
    Giulia Morra
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
    PLoS Comput Biol 8:e1002433. 2012
    ..This latter site could represent a promising novel druggable allosteric site common to all chaperones...
  31. doi request reprint Identification of domains in protein structures from the analysis of intramolecular interactions
    Alessandro Genoni
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
    J Phys Chem B 116:3331-43. 2012
    ....
  32. ncbi request reprint Modeling the alpha-helix to beta-hairpin transition mechanism and the formation of oligomeric aggregates of the fibrillogenic peptide Abeta(12-28): insights from all-atom molecular dynamics simulations
    Fabio Simona
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
    J Mol Graph Model 23:263-73. 2004
    ....
  33. ncbi request reprint Determinants of protein stability and folding: comparative analysis of beta-lactoglobulins and liver basic fatty acid binding protein
    Laura Ragona
    Laboratorio NMR, ISMAC, CNR, Milano, Italy
    Proteins 61:366-76. 2005
    ..The results fit well with experimental folding data and, especially, with the analysis of side chain-side chain interaction conservation...
  34. doi request reprint Relationship between energy distribution and fold stability: Insights from molecular dynamics simulations of native and mutant proteins
    Giulia Morra
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131, Milano, Italy
    Proteins 72:660-72. 2008
    ..We discuss the relevance of these observations to the analysis of protein designability and to the rational evolution of new sequences...
  35. ncbi request reprint Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics
    Giacomo M S de Mori
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
    Proteins 58:459-71. 2005
    ....
  36. pmc Computational study of the resistance shown by the subtype B/HIV-1 protease to currently known inhibitors
    Alessandro Genoni
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
    Biochemistry 49:4283-95. 2010
    ..Finally, we propose a dynamic and energetic explanation for HIV-1 protease drug resistance, and, through this model, we identify a possible new site that could be helpful in the design of a new family of HIV-1 PR allosteric inhibitors...
  37. doi request reprint Flexible vs Rigid Epitope Conformations for Diagnostic- and Vaccine-Oriented Applications: Novel Insights from the Burkholderia pseudomallei BPSL2765 Pal3 Epitope
    Alessandro Gori
    Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy
    ACS Infect Dis 2:221-30. 2016
    ..On these bases, we critically discuss the implications of epitope structure engineering for diagnostic- and vaccine-oriented applications. ..
  38. pmc Investigating the dynamic aspects of drug-protein recognition through a combination of MD and NMR analyses: implications for the development of protein-protein interaction inhibitors
    Massimiliano Meli
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
    PLoS ONE 9:e97153. 2014
    ..The results presented can also be used to generate new rules for the rational expansion of the chemical diversity space of FGF2 inhibitors. ..
  39. pmc Simulation of MscL gating in a bilayer under stress
    Giorgio Colombo
    Istituto di Chimica del Riconoscimento Molecolare, CNR, 20131 Milan, Italy
    Biophys J 84:2331-7. 2003
    ..Such a mechanism could explain the partial opening or staged conductance observed in patch-clamp experiments using related large conductance mechanosensitive channel complexes...
  40. ncbi request reprint Molecular recognition and drug-lead identification: what can molecular simulations tell us?
    Giulia Morra
    Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 19, Milan, Italy
    Curr Med Chem 17:25-41. 2010
    ....
  41. ncbi request reprint Small-molecule targeting of heat shock protein 90 chaperone function: rational identification of a new anticancer lead
    Massimiliano Meli
    Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milan, Italy
    J Med Chem 49:7721-30. 2006
    ..We propose that AICAR represents a viable lead for further development of anticancer drugs with wide therapeutic opportunities...
  42. ncbi request reprint Toward the understanding of the structure and dynamics of protein-carbohydrate interactions: molecular dynamics studies of the complexes between hevein and oligosaccharidic ligands
    Giorgio Colombo
    Istituto di Chimica del Riconoscimento Molecolare, CNR via Mario Bianco, 9, I 20131 Milan, Italy
    Carbohydr Res 339:985-94. 2004
    ....
  43. pmc Surface energetics and protein-protein interactions: analysis and mechanistic implications
    Claudio Peri
    Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy
    Sci Rep 6:24035. 2016
    ....
  44. doi request reprint Crystal structure of the DFNKF segment of human calcitonin unveils aromatic interactions between phenylalanines
    Pierangelo Metrangolo
    Politecnico di Milano, Chem, MAT, and chem eng, Via Mancinelli 7, 20131, Milano, Italy
    Chemistry . 2016
    ..A detailed analysis of such interactions is reported...
  45. doi request reprint Mechanisms of Differential Allosteric Modulation in Homologous Proteins: Insights from the Analysis of Internal Dynamics and Energetics of PDZ Domains
    Giulia Morra
    Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche via Mario Bianco 9, 20131 Milano, Italy
    J Chem Theory Comput 10:5677-89. 2014
    ..Finally, we propose a model with a direct link between the modulation of the structural, energetic and dynamic properties of a protein, and its allosteric response to a perturbation. ..
  46. doi request reprint HMGB1-carbenoxolone interactions: dynamics insights from combined nuclear magnetic resonance and molecular dynamics
    Luca Mollica
    Dulbecco Telethon Institute, Biomolecular NMR Laboratory c o Center of Genomics, Bioinformatics and Biostatistics, S Raffaele Scientific Institute, Via Olgettina 58, 20132, Milano, Italy
    Chem Asian J 6:1171-80. 2011
    ..The observations reported here may be useful for understanding the role of protein dynamics in binding at atomic resolution...
  47. doi request reprint Structural Stability and Flexibility Direct the Selection of Activating Mutations in Epidermal Growth Factor Receptor Kinase
    Antonella Paladino
    Istituto di Chimica del Riconoscimento Molecolare, CNR Via Mario Bianco 9, 20131, Milano, Italy
    J Chem Inf Model 55:1377-87. 2015
    ..Our approaches represent a promising and simple strategy toward rationalizing the effects of mutations in modulating enzymatic activities. ..
  48. doi request reprint Investigating allostery in molecular recognition: insights from a computational study of multiple antibody-antigen complexes
    Dario Corrada
    Istituto di Chimica del Riconoscimento Molecolare Consiglio Nazionale delle Ricerche CNR ICRM, Via Mario Bianco 9, 20131 Milano, Italy
    J Phys Chem B 117:535-52. 2013
    ..Our studies may have implications in practical use, such as the rational design of antibodies with specifically modulated antigen-binding affinities...
  49. pmc Interplay between hydrophobic cluster and loop propensity in beta-hairpin formation: a mechanistic study
    Giorgio Colombo
    Istituto di Chimica del Riconoscimento Molecolare, CNR, 20131 Milano, Italy
    Protein Sci 12:538-50. 2003
    ....
  50. ncbi request reprint Structure determination and dynamics of peptides overlapping the catalytic hairpin of the Ras-specific GEF Cdc25(Mm)
    Roberto Consonni
    Istituto per lo Studio delle Macromolecole, Lab NMR, CNR, v Ampere 56, I 20131 Milan, Italy
    Biochemistry 42:12154-62. 2003
    ..These results indicate that rational design and improvement of the Ras-interacting peptides should take into account conformational and flexibility features to obtain molecules with the appropriate biochemical properties...
  51. ncbi request reprint Modeling enzyme reactivity in organic solvents and water through computer simulations
    Giorgio Colombo
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco, 9, 20131, Milan, Italy
    J Biotechnol 96:23-33. 2002
    ..However, it was with the application of quantum mechanical/molecular mechanical (QM/MM) methods that quantitative models of actual reactivity patterns could be realistically formulated...
  52. pmc DNA Polymerase Conformational Dynamics and the Role of Fidelity-Conferring Residues: Insights from Computational Simulations
    Massimiliano Meli
    Computational Biochemistry Group, Istituto di Chimica del Riconoscimento Molecolare, National Research Council of Italy Milano, Italy
    Front Mol Biosci 3:20. 2016
    ..We discuss the implications of our results for the understanding of the relationships between the structure, dynamics, and function of DNA polymerase I at the atomistic level. ..
  53. pmc Molecular Dynamics Simulations Reveal the Mechanisms of Allosteric Activation of Hsp90 by Designed Ligands
    Gerolamo Vettoretti
    Istituto di Chimica del Riconoscimento Molecolare, CNR ICRM CNR, Via Mario Bianco, 9, 20131, Milan, Italy
    Sci Rep 6:23830. 2016
    ..We discuss the implications of considering the conformational dialogue between allosteric ligands and protein conformations for the design of new functional modulators. ..
  54. pmc Exploiting conformational dynamics in drug discovery: design of C-terminal inhibitors of Hsp90 with improved activities
    Elisabetta Moroni
    Istituto di Chimica del Riconoscimento Molecolare, CNR Via Mario Bianco 9, 20131 Milano, Italy
    J Chem Inf Model 54:195-208. 2014
    ..The method identified herein may be used to design chemical probes that provide additional information on structural variations of Hsp90 C-terminal binding site. ..
  55. pmc A Hamiltonian replica exchange molecular dynamics (MD) method for the study of folding, based on the analysis of the stabilization determinants of proteins
    Massimiliano Meli
    Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, Milano 20131, Italy
    Int J Mol Sci 14:12157-69. 2013
    ..We next discuss possible implications for the study of folding mechanisms via all atom simulations...
  56. doi request reprint Rational epitope design for protein targeting
    Claudio Peri
    Isituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
    ACS Chem Biol 8:397-404. 2013
    ..We discuss implications for diagnosis and vaccine development purposes...
  57. ncbi request reprint Synthesis, structure and conformation of partially-modified retro- and retro-inverso psi[NHCH(CF3)]Gly peptides
    Alessandro Volonterio
    C N R Dipartimento di Chimica, Materiali ed Ingegneria Chimica G Natta, Politecnico di Milano, Via Mancinelli 7, 20131 Milan, Italy
    Chemistry 9:4510-22. 2003
    ....
  58. pmc Understanding the determinants of stability and folding of small globular proteins from their energetics
    Guido Tiana
    Department of Physics, University of Milano, 20133 Milano, Italy
    Protein Sci 13:113-24. 2004
    ..The comparison of the results of the model with the findings of mutagenesis experiments performed for four small proteins show that the eigenvalue decomposition method is able to identify between 60% and 80% of these (hot) sites...
  59. ncbi request reprint Probing the hirudin-thrombin interaction by incorporation of noncoded amino acids and molecular dynamics simulation
    Vincenzo De Filippis
    Department of Pharmaceutical Sciences and CRIBI Biotechnology Center, University of Padua, Italy
    Biochemistry 41:13556-69. 2002
    ..Taken together, our results can have important implications for the design of novel thrombin inhibitors, of practical utility in the treatment of coagulative disorders...
  60. ncbi request reprint Structure-activity relationships of linear and cyclic peptides containing the NGR tumor-homing motif
    Giorgio Colombo
    Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare CNR ICRM, 20131 Milan, Italy
    J Biol Chem 277:47891-7. 2002
    ..The disulfide bridge constraint is critical for stabilizing the bent conformation and for increasing the tumor targeting efficiency...
  61. pmc Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: a molecular dynamics study
    Danilo Roccatano
    Dipartimento di Chimica, Ingegneria Chimica e Materiali Università Degli Studi, Via Vetoio, 67010 L Aquila, Italy
    Proc Natl Acad Sci U S A 99:12179-84. 2002
    ..Because TFE interacts only weakly with nonpolar residues, hydrophobic interactions within the peptides are not disrupted. As a consequence, TFE promotes stability rather than inducing denaturation...
  62. ncbi request reprint Folding and stability of the three-stranded beta-sheet peptide Betanova: insights from molecular dynamics simulations
    Giorgio Colombo
    Groningen Biomolecular Sciences and Biotechnology Institute, Department of Biophysical Chemistry, University of Groningen, Nijenborgh, The Netherlands
    Proteins 46:380-92. 2002
    ..A set of different structures is shown to satisfy NMR-derived distance restraints and a possible mechanism for the folding of the peptide into the NMR-determined structure is proposed...
  63. ncbi request reprint Beta-hairpin conformation of fibrillogenic peptides: structure and alpha-beta transition mechanism revealed by molecular dynamics simulations
    Isabella Daidone
    Department of Chemistry, University of Rome La Sapienza, Rome, Italy
    Proteins 57:198-204. 2004
    ..The results of MD simulation in 2,2,2-trifluoroethanol (TFE)/water mixture provide further evidence that the peptide coating effect of TFE molecules is responsible for the stabilization of the soluble helical conformation...
  64. ncbi request reprint Characterization of the conformational space of a triple-stranded beta-sheet forming peptide with molecular dynamics simulations
    Patricia Soto
    Groningen Biomolecular Sciences and Biotechnology Institute GBB, Department of Biophysical Chemistry, University of Groningen, Groningen, The Netherlands
    Proteins 57:734-46. 2004
    ..This suggests that no significant free energy barrier separates the different conformations available...
  65. doi request reprint Structural determinants of the unusual helix stability of a de novo engineered vascular endothelial growth factor (VEGF) mimicking peptide
    Donatella Diana
    Dipartimento di Scienze Ambientali, Seconda Università di Napoli via Vivaldi 43, 81100 Caserta, Italy
    Chemistry 14:4164-6. 2008
  66. doi request reprint Molecular simulation of multistate peptide dynamics: a comparison between microsecond timescale sampling and multiple shorter trajectories
    Luca Monticelli
    Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
    J Comput Chem 29:1740-52. 2008
    ....
  67. ncbi request reprint The molecular dynamics of assembly of the ubiquitous aortic medial amyloidal medin fragment
    Ehud Gazit
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    J Mol Graph Model 25:903-11. 2007
    ..Taken together, the results are consistent with recent high-resolution structures of amyloid assemblies and provide unique insights into the dynamics of these structures...
  68. ncbi request reprint Misfolding of the amyloid beta-protein: a molecular dynamics study
    Dagmar Flöck
    Department of Chemistry, University of Rome La Sapienza, P le Aldo Moro 5, Rome, Italy
    Proteins 62:183-92. 2006
    ..Moreover, a hydrophobic cluster is observed involving Val18, Phe19, Ala21, and Gly25. The results are carefully compared with recent NMR and spectroscopic data, and are in global agreement with the experimental findings...
  69. pmc Effect of hexafluoroisopropanol alcohol on the structure of melittin: a molecular dynamics simulation study
    Danilo Roccatano
    School of Engineering and Science, International University of Bremen, Campus Ring 1, D 28725 Bremen, Germany
    Protein Sci 14:2582-9. 2005
    ..Finally, a stabilizing effect promoted by the presence of counter-ions was also observed in the simulations...
  70. ncbi request reprint Rational design of shepherdin, a novel anticancer agent
    Janet Plescia
    Department of Cancer Biology and the Cancer Center, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Cancer Cell 7:457-68. 2005
    ..Systemic administration of shepherdin in vivo is well tolerated, and inhibits human tumor growth in mice without toxicity. Shepherdin could provide a potent and selective anticancer agent in humans...
  71. ncbi request reprint Sequence dependence of amyloid fibril formation: insights from molecular dynamics simulations
    Manuela Lopez de la Paz
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    J Mol Biol 349:583-96. 2005
    ..Studies similar to the one presented here can guide site-directed mutations or the design of drugs that specifically disrupt the key stabilizing interactions of beta-sheet aggregates...
  72. ncbi request reprint Immunogenic and structural properties of the Asn-Gly-Arg (NGR) tumor neovasculature-homing motif
    Paola Di Matteo
    Department of Biological and Technological Research, San Raffaele H Scientific Institute, 20132 Milan, Italy
    Mol Immunol 43:1509-18. 2006
    ..These results suggest that NGR peptides could mimic from an immunological point of view a "self" structure, likely the GNGRG loop of fibronectin, with important implications for the use of these targeting peptides in patients...
  73. ncbi request reprint Mechanism of helix nucleation and propagation: microscopic view from microsecond time scale MD simulations
    Luca Monticelli
    Centre for Biomolecular Interdisciplinary Studies and Industrial Applications, University of Milan, 20131 Milan, Italy
    J Phys Chem B 109:20064-7. 2005
    ..Helix propagation in RN24 appears to occur preferentially from the N-terminus to the C-terminus, and helix unfolding preferentially in the opposite direction...
  74. ncbi request reprint Combining computational and biochemical studies for a rationale on the anti-aromatase activity of natural polyphenols
    Marco A C Neves
    Centro de Estudos Farmaceuticos, Lab Química Farmacêutica, Faculdade de Farmacia, Universidade de Coimbra, Rua do Norte, 3000 295 Coimbra, Portugal
    ChemMedChem 2:1750-62. 2007
    ..Moreover, the information generated in this approach should be further exploited for the design of new aromatase inhibitors...
  75. pmc Two amino acid substitutions within the first external loop of CCR5 induce human immunodeficiency virus-blocking antibodies in mice and chickens
    Claudia Pastori
    Infectious Diseases Clinic, San Raffaele Scientific Institute, Milan, Italy
    J Virol 82:4125-34. 2008
    ..These findings may be relevant to the induction of strong and efficient HIV-blocking antibodies...
  76. doi request reprint Biochemical and computational insights into the anti-aromatase activity of natural catechol estrogens
    Marco A C Neves
    Centro de Estudos Farmaceuticos, Lab Química Farmacêutica, Faculdade de Farmacia, Universidade de Coimbra, 3000 295 Coimbra, Portugal
    J Steroid Biochem Mol Biol 110:10-7. 2008
    ..A strong relationship between activity and electrostatic properties was found for catechol estrogens. Moreover, our results suggest that natural catechol estrogens may be involved in the control mechanisms of estrogen production...