Ph.D. Program in Cellular, Molecular and Industrial Biology
(Project n. 2: Functional Biology of Cellular and Molecular Systems)
Structure and functions of metal ions in biomolecules
The main interest of the research activity is the elucidation of the
role of metals found in biomolecules. The final goal is the identification
of the molecular structure of the active site of metallo-enzymes, and
the elucidation of structure-function relationships. The objective is
to determine how the chemistry of the metal ion is modulated by the protein
matrix, and thus to determine the mode of interaction with the substrate
or with other proteins.
Proteins from bacteria living in waters and soils are purified, and their
biochemical characterization is performed. Then, by applying sophisticated
physical methods such as mass spectrometry, mono- and multidimensional
NMR spectroscopy, EPR, Mössbauer, circular dichroism, magnetic susceptibility,
bioelectrochemistry, X-ray spectroscopy (EXAFS), Raman and crystallography
the structure of the active site is elucidated at the molecular level.
Subsequently, mechanistic studies of the protein-substrate or protein-protein
interactions are carried out. Molecular mechanics and dynamics are used
to model protein-substrate and protein-protein interactions.
In particular, on-going research projects involve the study of the structural
biochemistry of metallo-enzymes involved in the nitrogen cycle in the
environment, and in particular the biochemistry of urease, a nickel-containig
enzyme that catalyzes the hydrolysis of urea in the last step of nitrogen
metabolism. The determination of the structure-function relationships
in urease, and in particular the role of the metal ions in the active
site, will lead to the development of a structure-based molecular design
of drugs that will enable the control of these processes in the case of
negative side effects to humans (diseases of the gastrointestinal and
urinary apparatus) and to the environment (damages to plants during soil
fertilization with urea).
Selected Publications
- S. Benini; W.R. Rypniewski; K.S. Wilson; S. Ciurli; S. Mangani "The complex of Bacillus pasteurii urease with b-mercaptoethanol from X-ray data at 1.65 Å resolution" J. Biol. Inorg. Chem. 1998, 3, 268-273
- S. Benini; W. R. Rypniewski; K. S. Wilson; S. Miletti; S. Ciurli; S. Mangani "A new proposal for urease mechanism based on the crystal structures of the native and inhibited enzyme from Bacillus pasteurii: why urea hydrolysis costs two nickels" Structure 1999, 7, 205-216
- S. Ciurli; S. Benini, W. R. Rypniewski; K.S. Wilson; S. Miletti; S. Mangani "Structural properties of the nickel ions in urease: novel insights into the catalytic and inhibition mechanisms" Coord. Chem. Rev. 1999, 190-192, 331-355
- S. Benini; W. R. Rypniewski; K. S. Wilson; S. Miletti; S. Ciurli; S. Mangani "The complex of Bacillus pasteurii urease with acetohydroxamic acid from X-ray data at 1.55 Å resolution" J. Biol. Inorg. Chem. 2000, 5, 110-118
- F. Musiani; E; Arnofi; R. Casadio; S. Ciurli "Structure-based computational study of the catalytic and inhibition mechanisms of urease" J. Biol. Inorg. Chem. 2001, 3, 300-314
- S. Ciurli; S. Mangani "Nickel-containing enzymes"
Handbook of Metalloproteins (I. Bertini, A. Sigel, and H. Sigel, Eds.);
Marcel Dekker, New York, USA, 2001, pp. 669-708
- S. Benini; W. R. Rypniewski; K. S. Wilson; S. Ciurli; S. Mangani
"Structure-based rationalization of urease inhibition by
phosphate: novel insights into the enzyme mechanism"
J. Biol. Inorg. Chem. 2001, 6, 778-790
- H. Remaut, N. Safarov; S. Ciurli; J. J. Van Beeumen Structural basis for Ni transport and assembly of the urease active site by the metallo-chaperone UreE from Bacillus pasteurii J. Biol. Chem. 2001, 276, 49365-49370
- S. Ciurli;* N. Safarov; S. Miletti; A. Dikiy; S.K. Christensen; K. Kornetzky; D.A. Bryant; I. Vandenberghe; B. Devreese; B. Samyn; H. Remaut; J. Van Beeumen “Molecular characterization of Bacillus pasteurii UreE, a metal-binding chaperone for the assembly of the urease active site” J. Biol. Inorg. Chem. 2002, 7, 623-631
- S. Ciurli "Nickel Enzymes/Models (Biological and Biomimetic)" Encyclopedia of Catalysis (I. T. Horvàth, E. Iglesia, M. T. Klein, J. A. Lercher, A. J. Russell, and E. I. Stiefel, Eds); John Wiley & Sons, Inc.; New York, USA, 2003, Vol. 5, pp. 582-589
- F. Musiani; B. Zambelli; M. Stola; S. Ciurli "Nickel trafficking: Insights into the fold and function of UreE, a urease metallochaperone" J. Inorg. Biochem. 2004, 98, 803-813
- S. Benini; W. R. Rypniewsky; K. S. Wilson, S. Mangani, S. Ciurli “Molecular details of urease inhibition by boric acid: insights into the catalytic mechanism” J. Am. Chem. Soc. 2004, 126, 3714-3715
-S. Ciurli "Urease" Biological Inorganic Chemistry: Structure and Reactivity, Chapter III: "Metal-ion containing biological systems", section B: "Hydrolytic and water chemistry"; (I. Bertini, H. B. Gray, and J. S. Valentine, Eds.); University Science Books, California, USA 2004 In press
Research Group
Stefano Ciurli (Group leader)
e-mail: stefano.ciurli@unibo.it
Francesco Musiani (post doctorate fellowship)
Massimiliano Stola (post-doctorate fellowship)
Barbara Zambelli (Ph.D. studentship)
Cristina Baia (post-laurea fellowship)
Location
Bioinorganic chemistry laboratory
Department of Agro-Environmental Science e Technology
Viale Giuseppe Fanin 40, 40127 - Bologna
Tel. Lab: 051 2096225
FAX: +39 051 2096203
