Experts and Doctors on protein interaction mapping in Italy

Summary

Locale: Italy
Topic: protein interaction mapping

Top Publications

  1. Céol A, Verhoef L, Wade M, Muller H. Genome and network visualization facilitates the analyses of the effects of drugs and mutations on protein-protein and drug-protein networks. BMC Bioinformatics. 2016;17 Suppl 4:54 pubmed publisher
    ..Such approaches can now also be integrated with genome visualization tools to enable comparative analyses of interaction contacts. ..
  2. Bartolini D, Galli F. The functional interactome of GSTP: A regulatory biomolecular network at the interface with the Nrf2 adaption response to oxidative stress. J Chromatogr B Analyt Technol Biomed Life Sci. 2016;1019:29-44 pubmed publisher
    ..These aspects and the methodological approach to explore the cellular interactome(s) are discussed in this review paper. ..
  3. Kohestani H, Giuliani A. Organization principles of biological networks: An explorative study. Biosystems. 2016;141:31-9 pubmed publisher
    ..We highlighted as well the need of developing new theoretical generative models for biological networks overcoming the limitations of present mathematical graph idealizations. ..
  4. Lavagni P, Indrigo M, Colombo G, Martegani E, Rosenblum K, Gnesutta N, et al. Identification of novel RasGRF1 interacting partners by large-scale proteomic analysis. J Mol Neurosci. 2009;37:212-24 pubmed publisher
    ..These data indicate that RasGRF1 can interact with different protein categories and exhibits a potential RNA-binding property. ..
  5. De Grandis V, Bizzarri A, Cannistraro S. Docking study and free energy simulation of the complex between p53 DNA-binding domain and azurin. J Mol Recognit. 2007;20:215-26 pubmed
  6. Agapito G, Guzzi P, Cannataro M. Visualization of protein interaction networks: problems and solutions. BMC Bioinformatics. 2013;14 Suppl 1:S1 pubmed publisher
  7. Passerini A, Andreini C, Menchetti S, Rosato A, Frasconi P. Predicting zinc binding at the proteome level. BMC Bioinformatics. 2007;8:39 pubmed
    ..In addition, the method permits the identification of unprecedented metal sites, providing important hints for the work of experimentalists. ..
  8. Degryse B, Fernandez Recio J, Citro V, Blasi F, Cubellis M. In silico docking of urokinase plasminogen activator and integrins. BMC Bioinformatics. 2008;9 Suppl 2:S8 pubmed publisher
  9. Bartoli L, Montanucci L, Fronza R, Martelli P, Fariselli P, Carota L, et al. The bologna annotation resource: a non hierarchical method for the functional and structural annotation of protein sequences relying on a comparative large-scale genome analysis. J Proteome Res. 2009;8:4362-71 pubmed publisher
    ..biocomp.unibo.it/bar/). ..

More Information

Publications45

  1. Ihekwaba A, Nguyen P, Priami C. Elucidation of functional consequences of signalling pathway interactions. BMC Bioinformatics. 2009;10:370 pubmed publisher
    ..Source code is available upon request. ..
  2. Tinti M, Kiemer L, Costa S, Miller M, Sacco F, Olsen J, et al. The SH2 domain interaction landscape. Cell Rep. 2013;3:1293-305 pubmed publisher
    ..A predicted dynamic interaction between the SH2 domains of the tyrosine phosphatase SHP2 and the phosphorylated tyrosine in the extracellular signal-regulated kinase activation loop was validated by experiments in living cells. ..
  3. Sbisà E, Catalano D, Grillo G, Licciulli F, Turi A, Liuni S, et al. p53FamTaG: a database resource of human p53, p63 and p73 direct target genes combining in silico prediction and microarray data. BMC Bioinformatics. 2007;8 Suppl 1:S20 pubmed
  4. Malini E, Maurizio E, Bembich S, Sgarra R, Edomi P, Manfioletti G. HMGA Interactome: new insights from phage display technology. Biochemistry. 2011;50:3462-8 pubmed publisher
    ..The identification of these new partners suggests that HMGA can also influence general aspects of transcription and once more underlines their involvement in chromatin remodelling and dynamics. ..
  5. Piccinni E, Chelstowska A, Hanus J, Widlak P, Loreti S, Tata A, et al. Direct interaction of Gas41 and Myc encoded by amplified genes in nervous system tumours. Acta Biochim Pol. 2011;58:529-34 pubmed
    ..In fact we found that Gas41 C-terminal portion is required for Myc protein interaction in human. ..
  6. Rusolo F, Pucci B, Colonna G, Capone F, Guerriero E, Milone M, et al. Evaluation of selenite effects on selenoproteins and cytokinome in human hepatoma cell lines. Molecules. 2013;18:2549-62 pubmed publisher
    ..Finally, interactomic studies show that GPX1 and SELK, and the four pro-inflammatory cytokines are functionally correlated evidencing a putative anti-inflammatory role for the selenite. ..
  7. Boccalatte F, Voena C, Riganti C, Bosia A, D Amico L, Riera L, et al. The enzymatic activity of 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase is enhanced by NPM-ALK: new insights in ALK-mediated pathogenesis and the treatment of ALCL. Blood. 2009;113:2776-90 pubmed publisher
    ..Prediction of tumor responses to methotrexate may justify specific molecular-based chemotherapy. ..
  8. Danussi C, Del Bel Belluz L, Pivetta E, Modica T, Muro A, Wassermann B, et al. EMILIN1/?9?1 integrin interaction is crucial in lymphatic valve formation and maintenance. Mol Cell Biol. 2013;33:4381-94 pubmed publisher
  9. Margaglione M, Vecchione G, Santacroce R, D Angelo F, Casetta B, Papa M, et al. A frameshift mutation in the human fibrinogen Aalpha-chain gene (Aalpha(499)Ala frameshift stop) leading to dysfibrinogen San Giovanni Rotondo. Thromb Haemost. 2001;86:1483-8 pubmed
    ..contained substantial amounts of albumin. Present findings confirm that truncated Aalpha-chain lacking part of the terminal domain may be incorporated into mature fibrinogen molecules and normally secreted in the bloodstream. ..
  10. Costantini S, Woodbine L, Andreoli L, Jeggo P, Vindigni A. Interaction of the Ku heterodimer with the DNA ligase IV/Xrcc4 complex and its regulation by DNA-PK. DNA Repair (Amst). 2007;6:712-22 pubmed
    ..Here, we show that DNA-PK kinase activity also results in disassembly of the Ku/DNA ligase IV/Xrcc4 complex. Collectively, our findings provide novel information on the protein-protein interactions that regulate NHEJ in cells. ..
  11. Gardoni F, Picconi B, Ghiglieri V, Polli F, Bagetta V, Bernardi G, et al. A critical interaction between NR2B and MAGUK in L-DOPA induced dyskinesia. J Neurosci. 2006;26:2914-22 pubmed
    ..These data indicate abnormal NR2B redistribution between synaptic and extrasynaptic membranes as an important molecular disturbance of the glutamatergic synapse involved in L-DOPA-induced dyskinesia. ..
  12. Krenn V, Wehenkel A, Li X, Santaguida S, Musacchio A. Structural analysis reveals features of the spindle checkpoint kinase Bub1-kinetochore subunit Knl1 interaction. J Cell Biol. 2012;196:451-67 pubmed publisher
    ..These results shed light on the determinants of kinetochore recruitment of Bub1. ..
  13. Sipione S, Cattaneo E. Modeling Huntington's disease in cells, flies, and mice. Mol Neurobiol. 2001;23:21-51 pubmed
  14. Wollscheid H, Biancospino M, He F, Magistrati E, Molteni E, Lupia M, et al. Diverse functions of myosin VI elucidated by an isoform-specific α-helix domain. Nat Struct Mol Biol. 2016;23:300-308 pubmed publisher
    ..Thus, the α2-linker acts like a molecular switch that assigns myosin VI to distinct endocytic (myosin VI(long)) or migratory (myosin VI(short)) functional roles. ..
  15. Berruti G, Martegani E. The deubiquitinating enzyme mUBPy interacts with the sperm-specific molecular chaperone MSJ-1: the relation with the proteasome, acrosome, and centrosome in mouse male germ cells. Biol Reprod. 2005;72:14-21 pubmed
  16. Scorziello A, Savoia C, Sisalli M, Adornetto A, Secondo A, Boscia F, et al. NCX3 regulates mitochondrial Ca(2+) handling through the AKAP121-anchored signaling complex and prevents hypoxia-induced neuronal death. J Cell Sci. 2013;126:5566-77 pubmed publisher
    ..Collectively, these results suggest that, in neurons, NCX3 regulates mitochondrial Ca(2+) handling from the OMM through an AKAP121-anchored signaling complex, thus promoting cell survival during hypoxia. ..
  17. Tomai V, Ganti K, Pim D, Bauer C, Blattner C, Banks L. Interaction of HPV E6 oncoproteins with specific proteasomal subunits. Virology. 2013;446:389-96 pubmed publisher
    ..These results suggest a complex interplay between E6 and the proteasome, only some aspects of which are dependent upon the E6AP ubiquitin ligase...
  18. Imbriano C, Gurtner A, Cocchiarella F, Di Agostino S, Basile V, Gostissa M, et al. Direct p53 transcriptional repression: in vivo analysis of CCAAT-containing G2/M promoters. Mol Cell Biol. 2005;25:3737-51 pubmed
  19. Bonsegna S, Slocombe S, De Bellis L, Baker A. AtLACS7 interacts with the TPR domains of the PTS1 receptor PEX5. Arch Biochem Biophys. 2005;443:74-81 pubmed
  20. Lindner M, Simonini S, Kooiker M, Gagliardini V, Somssich M, Hohenstatt M, et al. TAF13 interacts with PRC2 members and is essential for Arabidopsis seed development. Dev Biol. 2013;379:28-37 pubmed publisher
    ..Our data suggest that TAF13 functions together with PRC2 in transcriptional regulation during seed development. ..
  21. Orioli D, Colaluca I, Stefanini M, Riva S, Dotti C, Peverali F. Rac3-induced neuritogenesis requires binding to Neurabin I. Mol Biol Cell. 2006;17:2391-400 pubmed
    ..These results show that Neurabin I mediates Rac3-induced neuritogenesis, possibly by anchoring Rac3 to growth cone F-actin. ..
  22. Lavagno L, Ferrero E, Ortolan E, Malavasi F, Funaro A. CD157 is part of a supramolecular complex with CD11b/CD18 on the human neutrophil cell surface. J Biol Regul Homeost Agents. 2007;21:5-11 pubmed
    ..These results confirm that CD157 physically interacts with CD11b/CD18 complex in human neutrophils. ..
  23. Miranda C, Roccato E, Raho G, Pagliardini S, Pierotti M, Greco A. The TFG protein, involved in oncogenic rearrangements, interacts with TANK and NEMO, two proteins involved in the NF-kappaB pathway. J Cell Physiol. 2006;208:154-60 pubmed
    ..TFG enhances the effect of TNF-alpha, TANK, TNF receptor-associated factor (TRAF)2, and TRAF6 in inducing NF-kappaB activity. We suggest that TFG is a novel member of the NF-kappaB pathway. ..
  24. Taramino S, Teske B, Oliaro Bosso S, Bard M, Balliano G. Divergent interactions involving the oxidosqualene cyclase and the steroid-3-ketoreductase in the sterol biosynthetic pathway of mammals and yeasts. Biochim Biophys Acta. 2010;1801:1232-7 pubmed publisher
    ..Results demonstrate that in mammals, unlike in yeast, OSC and steroid-3-ketoreductase are non-interacting proteins. ..
  25. D Angiolella V, Palazzo L, Santarpia C, Costanzo V, Grieco D. Role for non-proteolytic control of M-phase-promoting factor activity at M-phase exit. PLoS ONE. 2007;2:e247 pubmed
    ..Thus, timely M-phase exit requires a tight coupling of proteolysis-dependent and proteolysis-independent mechanisms of MPF inactivation. ..
  26. Ragona L, Tomaselli S, Quemener C, Zetta L, Bikfalvi A. New insights into the molecular interaction of the C-terminal sequence of CXCL4 with fibroblast growth factor-2. Biochem Biophys Res Commun. 2009;382:26-9 pubmed publisher
    ..The proposed recognition mode constitutes a rationale for the observed effects of CXCL4 (47-70) on FGF-2 biological activity and lays the basis for developing novel inhibitors of angiogenesis. ..
  27. Sgarra R, Furlan C, Zammitti S, Lo Sardo A, Maurizio E, Di Bernardo J, et al. Interaction proteomics of the HMGA chromatin architectural factors. Proteomics. 2008;8:4721-32 pubmed publisher
    ..This approach allowed us to enlarge the HMGA molecular network confirming their involvement also in non-transcriptional-related processes such as RNA processing and DNA repair. ..
  28. Doliana R, Veljkovic V, Prljic J, Veljkovic N, De Lorenzo E, Mongiat M, et al. EMILINs interact with anthrax protective antigen and inhibit toxin action in vitro. Matrix Biol. 2008;27:96-106 pubmed
  29. Maggi S, Massidda O, Luzi G, Fadda D, Paolozzi L, Ghelardini P. Division protein interaction web: identification of a phylogenetically conserved common interactome between Streptococcus pneumoniae and Escherichia coli. Microbiology. 2008;154:3042-52 pubmed publisher
    ..pneumoniae proteins and the corresponding E. coli orthologues were observed. Taken together, these results suggest a phylogenetically conserved minimal common interactome of the division proteins. ..
  30. Bosio Y, Berto G, Camera P, Bianchi F, Ambrogio C, Claus P, et al. PPP4R2 regulates neuronal cell differentiation and survival, functionally cooperating with SMN. Eur J Cell Biol. 2012;91:662-74 pubmed publisher
    ..Our data indicate that PPP4R2 is a SMN partner that may modulate the differentiation and survival of neuronal cells. ..
  31. Perino A, Ghigo A, Ferrero E, Morello F, Santulli G, Baillie G, et al. Integrating cardiac PIP3 and cAMP signaling through a PKA anchoring function of p110γ. Mol Cell. 2011;42:84-95 pubmed publisher
    ..Pharmacological inhibition of p110γ normalizes β-adrenergic receptor density and improves contractility in failing hearts. ..
  32. Tomaic V, Pim D, Thomas M, Massimi P, Myers M, Banks L. Regulation of the human papillomavirus type 18 E6/E6AP ubiquitin ligase complex by the HECT domain-containing protein EDD. J Virol. 2011;85:3120-7 pubmed publisher
  33. Marcello E, Saraceno C, Musardo S, Vara H, de la Fuente A, Pelucchi S, et al. Endocytosis of synaptic ADAM10 in neuronal plasticity and Alzheimer's disease. J Clin Invest. 2013;123:2523-38 pubmed publisher
    ..These data identify and characterize a mechanism controlling ADAM10 localization and activity at excitatory synapses that is relevant to AD pathogenesis. ..
  34. Candela M, Biagi E, Centanni M, Turroni S, Vici M, Musiani F, et al. Bifidobacterial enolase, a cell surface receptor for human plasminogen involved in the interaction with the host. Microbiology. 2009;155:3294-303 pubmed publisher
    ..lactis BI07 enolase are crucial for plasminogen binding. Acting as a human plasminogen receptor, the bifidobacterial surface enolase is suggested to play an important role in the interaction process with the host. ..
  35. Madsen C, Ferraris G, Andolfo A, Cunningham O, Sidenius N. uPAR-induced cell adhesion and migration: vitronectin provides the key. J Cell Biol. 2007;177:927-39 pubmed
  36. Fichera M, Lo Giudice M, Falco M, Sturnio M, Amata S, Calabrese O, et al. Evidence of kinesin heavy chain (KIF5A) involvement in pure hereditary spastic paraplegia. Neurology. 2004;63:1108-10 pubmed
    ..Subsequent to a denaturing high performance liquid chromatography (dHPLC) mutation screening we found a new missense mutation 838C>T (R280C) at an invariant arginine residue in a region involved in the microtubule binding activity...