UO BIOCHEMISTRY AND MOLECULAR BIOLOGY

This Operative Unit (OU) focus on:

  • functional genomics (transcriptomics and phenotypic analysis of genome-wide) also applied to the characterization of compounds of pharmaceutical interest and toxicology;
  • evelopment of specific functional assays based on genetic engineering and recombinant DNA technology with particular reference to the identification of xeno-estrogenic compounds (both agonists that antagonists) and the modeling of diseases amyloid nell'eucariote model Saccharomyces cerevisiae;
  • production of recombinant proteins in detoxified form, in particular, peptide immunogens engineered and equipped with auto-properties adjuvants, usable as vaccines;
  • proteomics and differential proteomics of biological samples in the presence and absence of drugs;
  • expression and purification of proteins of pharmaceutical interest;
  • Spectroscopic and functional characterization of proteins of pharmaceutical interest;
  • chemically modified hemoglobins as blood substitutes;
  • clinical chemical analyzes of blood and plasma;
  • design and validation of ligands to proteins by an integrated computational-experimental;
  • iimmobilization of enzymes in nanoporous silica gel for the development of biosensors and bioreactors;
  • cloning and expression of fluorescent protein (green fluorescent protein and variants - GFPs), and fusion constructs between proteins of biomedical interest and GFPs, for applications of high-resolution fluorescence microscopy.

resbonsable (RUO)
Prof. Simone Ottonello
Dipartimento di Biochimica e Biologia Molecolare
Viale delle Scienze 23/a - 43124 Parma
e-mail: simone.ottonello@unipr.it
CV

Competences
The skills of this OU are: i) functional genomics and its applications in the pharmaceutical / toxicological ii) the design and prototyping of recombinant peptide vaccines and their validation in preclinical animal models of amyloid pathology (disease Alzheimer's disease) and infectious diseases (human papillomavirus) of marked clinical and therapeutic interest.

(Prof. Simone Ottonello)
This group has expertise in the following areas: i) development, consultation and exploitation of application of genomic databases, ii) transcriptomic analysis applied to probiotic microorganisms and human diseases of marked clinical interest, iii) microbial genomics and exploitation for application purposes , also of type immuno-therapeutic, of microorganisms "useful", in particular gram-positive bacteria approved for human use (eg Lactococcus spp.); iv) development of optimized solutions for the production of medium-scale recombinant proteins usable as vaccines or for the production of antibodies for diagnostic use, and protein ("lectins") with antiviral properties, employable as "microbicides" for topical use.

(Prof. Andrea Mozzarelli)
This group has expertise in the following areas: characterization of mitochondrial proteome using bottom-up approaches and top-down as an analytical tool for understanding the mechanisms associated with oxidative stress; characterization of the salivary proteome neonatal early identification of markers of infection; development of hemoglobin-based blood substitutes and understanding of the mechanisms associated with adverse effects on mice as animal model system, study of the spectroscopic properties of proteins of pharmaceutical interest, in the presence of intrinsic and extrinsic fluorophores, as a tool for the evaluation of the reproducibility of lots and for the stability of formulations; development of new methods for the expression and purification of proteins of pharmaceutical interest, development of clinical chemical analysis of blood and plasma samples in a high content of heme; development of new ligands for kynurenine aminotransferase and serine racemase, dependent enzymes pyridoxal 5'-phosphate target for therapies of neuropathologies, such as Alzheimer's disease, schizophrenia and amyotrophic lateral sclerosis; development of new ligands for O-acetylserine sulfhydrylase, bacterial enzyme dependent pyridoxal 5'-phosphate synthesizing cysteine, as new agents with an antibiotic.

(Prof. Stefano Bettati)
This group has expertise in the following areas: immobilization of proteins in nanoporous silica gel, both for biophysical studies on the structural, dynamic and functional properties of proteins encapsulated, for both svipuppo of bioreactors and biosensors based on spectroscopic techniques, cloning and expression site-specific mutants of the green fluorescent protein, alone or in fusion constructs with proteins of biomedical interest, optimized for microscopy applications of high resolution fluorescence; microspectrophotometry absorption of protein samples with micrometric dimensions (single crystals or samples of immobilized proteins in three-dimensional matrices); characterization of neonatal salivary proteome for the early identification of markers of infection, development of hemoglobin-based blood substitutes and understanding of the mechanisms associated with adverse effects on mice as animal model system, study of the spectroscopic properties of proteins of pharmaceutical interest, in the presence of intrinsic and extrinsic fluorophores, as a tool for the evaluation of the reproducibility and stability of lots of formulas, dynamic and functional characterization of enzymes dependent on pyridoxal 5'-phosphate which are targets for the development of therapeutic approaches ionnovativi against neuropathologies; development of new ligands for the O-acetylserine sulfhydrylase, bacterial enzyme dependent pyridoxal 5'-phosphate synthesizing cysteine, as new agents for antibiotic activity.

Collaboration: (prof. Simone Ottonello)

  • German Cancer Research (DKFZ, Heidelberg, Germany);
  • International Agency for Research on Cancer-World Health Organization (Lyon, France);
  • Department of Structural Biology, University of Pittsburgh School of Medicine (Pittsburgh, USA);
  • Department of Biotechnology, University of Tokyo (Tokyo, Japan);
  • Health Sciences and Technologies-Interdepartmental Center for Industrial Research (HST-ICIR), Università di Bologna;
  • IRET Foundation Research Center (Ozzano Emilia, Bologna);
  • Chiesi Farmaceutici (Parma);
  • GEMIB-Lab, Medical Research and Molecular Diagnostics Center (Parma).

Patents (prof. Simone Ottonello):
-N. 5 brevetti (3 depositati, 2 in fase di valutazione) riguardanti vaccini peptidici ricombinanti e relativi anticorpi monoclonali diretto contro il peptide Abeta42 umane e la proteina capsidica minore L2 del papillomavirus umano.

Bibliografia: (prof. Simone Ottonello)

  1. Balducci C, Mehdawy B, Mare L, Giuliani A, Lorenzini L, Sivilia S, Giardino L, Calzà L, Lanzillotta A, Sarnico I, Pizzi M, Usiello A, Viscomi AR, Ottonello S, Villetti G, Imbimbo BP, Nisticò G, Forloni G, Nisticò R (2011). The γ-Secretase Modulator CHF5074 Restores Memory and Hippocampal Synaptic Plasticity in Plaque-Free Tg2576 Mice. J Alzheimers Dis. 24 799-816.
  2. Donofrio G, Taddei S, Franceschi V, Capocefalo A, Cavirani S, Martinelli N, Ottonello S, Ferrari M (2011). Swine adipose stromal cells loaded with recombinant bovine herpesvirus 4 virions expressing a foreign antigen induce potent humoral immune responses in pigs. Vaccine 29 867-72.
  3. Rubio I, Seitz H, Canali E, Sehr P, Bolchi A, Tommasino M, Ottonello S, Müller M (2011). The N-terminal region of the human papillomavirus L2 protein contains overlapping binding sites for neutralizing, cross-neutralizing and non-neutralizing antibodies. Virology 409 348-59.
  4. Martin F, Kohler A, Murat C, Balestrini R, Coutinho PM, Jaillon O, Montanini B, Morin E, Noel B, Percudani R et al. (2010). Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature 464 1033-8.
  5. Ruotolo R, Tosi F, Vernarecci S, Ballario P, Mai A, Filetici P, Ottonello S (2010). Chemogenomic profiling of the cellular effects associated with histone H3 acetylation impairment by a quinoline-derived compound. Genomics 96 272-80.
  6. Rubio I, Bolchi A, Moretto N, Canali E, Gissmann L, Tommasino M, Müller M, Ottonello S (2009). Potent anti-HPV immune responses induced by tandem repeats of the HPV16 L2 (20-38) peptide displayed on bacterial thioredoxin. Vaccine 27 1949-1956.
  7. Koharudin LM, Viscomi AR, Jee JG, Ottonello S, Gronenborn AM (2008). The evolutionarily conserved family of cyanovirin-N homologs: structures and carbohydrate specificity. Structure 16 570-84.
  8. Ruotolo R, Marchini G, Ottonello S (2008). Membrane transporters and protein traffic networks differentially affecting metal tolerance: a genomic phenotyping study in yeast. Genome Biol 9 R67.
  9. Imbimbo BP, Del Giudice E, Cenacchi V, Volta R, Villetti G, Facchinetti F, Riccardi B, Puccini P, Moretto N, Grassi F, Ottonello S, Leon A (2007). In vitro and in vivo profiling of CHF5022 and CHF5074 Two beta-amyloid(1-42) lowering agents. Pharmacol Res 55 318-328.
  10. Moretto N, Bolchi A, Rivetti C, Imbimbo BP, Villetti G, Pietrini V, Polonelli L, Del Signore S, Smith KM, Ferrante RJ, Ottonello S (2007). Conformation-sensitive Antibodies against Alzheimer Amyloid-beta by Immunization with a Thioredoxin-constrained B-cell Epitope Peptide. J Biol Chem 282 11436-11445.

References: (Prof. Andrea Mozzarelli)

  • Progetto STREP della Unione Europea FP6 “Euroblood substitutes” per lo sviluppo di sostituti del sangue;
  • Progetto della Fondazione Cariparma per lo sviluppo di sostituti del sangue e lo studio dei meccanismi degli effetti avversi in modelli animali;
  • Progetto del National Institutes of Health (NIH) per lo studio della funzione e regolazione di emoglobine;
  • Progetto MIUR internazionalizzazione con la Virginia Commonwealth University, Richmond, USA e University of Oklahoma, Norman, USA, per lo sviluppo di inibitori di O-acetilserina sulfidrilasi.
  • Progetto MIUR-PRIN per lo sviluppo di inibitori di enzimi dipendenti da piridossal fosfato di interesse farmaceutico;

Collaborations: (Prof. Andrea Mozzarelli)
Institute of Structural Biology and Drug Discovery, Virginia Commonwealth University, Rickmond, Virginia, USA
University of Oklahoma, Norman, Oklahoma, USA
University of Georgia, Athens, Georgia, USA
University of California, Davis, California, USA
Russian Academy of Science, Moscow, Russia
National Institute for Medical Research, London, United Kingdom
University of California at Los Angeles, California, USA
National Institutes of Health, Bethesda, Maryland, USA
Massachusetts General Hospital, Harvard, Massachusetts, USA

Pubblicazioni recenti (Prof. Andrea Mozzarelli)

  • Conti P, Tamborini L, Pinto A, Blondel A, Minoprio P, Mozzarelli A, De Micheli C., Drug Discovery Targeting Amino Acid Racemases, Chem. Rev. 2011, 111, 6919-6946,
  • Ahmed MH, Spyrakis F, Cozzini P, Tripathi PK, Mozzarelli A, Scarsdale JN, Safo MA, Kellogg GE. Bound Water at Protein-Protein Interfaces: Partners, Roles and Hydrophobic Bubbles as a Conserved Motif. PlosOne. 2011, 6(9):e24712
  • Mozzarelli A., Bettati S. Eds. Chemistry and biochemistry of oxygen therapeutics: from transfusion to artificial blood. John Wiley and Sons Ltd, Chichester, UK , 2011.
  • Passera E, Campanini B, Rossi F, Casazza V, Rizzi M, Pellicciari R, Mozzarelli A. Human kynurenine aminotransferase II: reactivity with substrates and inhibitors. FEBS J. 2011, 278, 1882-1900
  • Bruno S, Ronda L, Faggiano S, Bettati S, Mozzarelli A. Oxygen delivery via allosteric effectors of haemoglobin and blood substitutes. Burger’s Medicinal Chemistry, Drug Discovery and Development, 7th Ed, 2010, Vol. 4, pp 609 - 659.
  • Ronda L, Pioselli B, Bruno S, Faggiano S, Mozzarelli A. Electrophoretic analysis of PEGylated hemoglobin-based blood substitutes. Anal. Biochem. 2011, 408, 118-123.
  • Salsi E, Bayden A, Spyrakis F, Amadasi A, Campanini B, Bettati S, Cozzini P, Kellogg GE, Cook PF, Dodatko T, Roderick SL, Mozzarelli A. Design of O-acetylserine sulfhydrylase inhibitors by mimicking Nature. J. Med Chem. 2010, 53, 345-356
  • Jacoby E, Mozzarelli A. Chemogenomic Strategies to Expand the Bioactive Chemical Space. Curr. Med. Chem. 2009, 16, 4374-4381
  • Abbruzzetti S, Faggiano S, Bruno S, Spyrakis F, Mozzarelli A, Dewilde S, Moens L, Viappiani C. Ligand migration through the internal hydrophobic cavities in human neuroglobin. Proc. Natl. Acad. Sci. USA, 2009 106, 18984-18989
  • Caccia D, Ronda L, Frassi R, Perrella M, Del Favero E, Bruno S, Pioselli B, Abbruzzetti S, Viappiani C, Mozzarelli A. PEGylation promotes hemoglobin tetramer dissociation. Bioconjug. Chem. 2009, 20, 1356-66.

References (Prof. Stefano Bettati)

  • Progetto PRIN del MIUR (2010-2012) su “Sviluppo di proteine fluorescenti per nanoscopia ottica orientata allo studio di dinamiche cellulari” (Coordinatore UO di Parma).
  • Progetto PRIN del MIUR (2007-2009) su “Sottostati conformazionali e percorsi di folding-unfolding nella green fluorescent protein: studio sperimentale e teorico alla ricerca di stati discreti nelle proteine” (Coordinatore UO di Parma).
  • Progetto STREP della Unione Europea FP6 “Euroblood substitutes” per lo sviluppo di sostituti del sangue (membro);
  • Progetto della Fondazione Cariparma per lo sviluppo di sostituti del sangue e lo studio dei meccanismi degli effetti avversi in modelli animali (membro);
  • Progetto MIUR internazionalizzazione con la Virginia Commonwealth University, Richmond, USA e University of Oklahoma, Norman, USA, per lo sviluppo di inibitori di O-acetilserina sulfidrilasi (membro).

Collaborations: (Prof. Stefano Bettati)

  • Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
  • University of Oklahoma, Norman, Oklahoma, USA.
  • University of California at Irvine, CA, USA.

Pubblicazioni recenti: (Prof. Stefano Bettati)

  1. Mozzarelli A and Bettati S. Chemistry and biochemistry of oxygen therapeutics: from transfusion to artificial blood. John Wiley and Sons Ltd., Chichester, UK, 2011.
  2. Mozzarelli A, Bettati S, Campanini B, Salsi E, Raboni S, Singh R, Spyrakis F, Kumar V.P. and Cook P.F. The multifaceted pyridoxal 5′-phosphate-dependent O-acetylserine sulfhydrylase. Biochim. Biophys. Acta 1814, 1497–1510 (2011).
  3. Bettati S, Luque F.J. and Viappiani C. Protein dynamics: Experimental and computational approaches. Biochim. Biophys. Acta 1814, 913-915 (2011).
  4. Bettati S, Pasqualetto E, Lolli G, Campanini B and Battistutta R. Structure and single crystal spectroscopy of Green Fluorescent Proteins. Biochim. Biophys. Acta 1814, 824-833 (2011).
  5. Salsi E, Guan R, Campanini B, Bettati S, Lin J, Cook P.F. and Mozzarelli A. Exploring O-acetylserine sulfhydrylase-B isoenzyme from Salmonella typhimurium by fluorescence spectroscopy. Arch. Biochem. Biophys. 505, 178–185 (2011).
  6. Ronda L, Bruno S, Bettati S and Mozzarelli A. Protein crystal microspectrophotometry. Biochim. Biophys. Acta 1814, 734-741 (2011).
  7. Mozzarelli A, Ronda L, Faggiano S, Bettati S and Bruno S. Haemoglobin-based oxygen carriers: research and reality towards an alternative to blood transfusions. Blood Transfusion 8, Suppl. 3, s59-s68 (2010).
  8. Salsi E, Bayden AS, Spyrakis F, Amadasi A, Campanini B, Bettati S, Dodatko T, Cozzini P, Kellogg GE, Cook PF, Roderick SL and Mozzarelli, A. Design of O-acetylserine sulfhydrylase inhibitors by mimicking nature. J. Med. Chem. 53, 345-356 (2010).
  9. Quercioli V, Bosisio C, Daglio S, Rocca F, D'Alfonso L, Collini M, Baldini G, Chirico G, Bettati S, Raboni S and Campanini B. Photo-induced millisecond switching kinetics in the GFPMUT2 E222Q mutant. J. Phys. Chem. B 114, 4664-4677 (2010).
  10. Raboni S, Bettati S and Mozzarelli A. Tryptophan synthase: a mine for enzymologists. Cell. Mol. Life Sci. 66, 2391-2403 (2009).