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Laboratory of Computational Biochemistry and Biophysics  

Immagine lab

 

Team

Ivano Eberini, Assistant Professor 

Cristina Sensi, Research Associate

 

The Laboratory of Computational Biochemistry and Biophysics is devoted to the study of protein structure through bioinformatics and structural biochemistry-based approaches. The methods mainly consist in molecular modeling, molecular docking and molecular dynamics of proteins with transport or enzymatic activity, or involved in signal transduction. National, European and World patents for protein activity modulators have been deposited by components of the laboratory.

 

Methods

Molecular modeling

Molecular docking

Molecular dynamics

In silico mutagenesis

In silico high-throughput screening

 

Selected publications

M. Fratelli, H. Demol, M. Puype, S. Casagrande, I. Eberini, M. Salmona, V. Bonetto, M. Mengozzi, F. Duffieux, E. Miclet, A. Bachi, J. Vandekerckhove, E. Gianazza, P. Ghezzi
Identification by redox proteomics of glutathionylated proteins in oxidatively stressed human T-lymphocytes
Proceedings of the National Academy of Sciences U.S.A. 2002, 99, 3505-3510

S. Casagrande, V. Bonetto, M. Fratelli, E. Gianazza, I. Eberini, T. Massignan, M. Salmona, G. Chang, A. Holmgren, P. Ghezzi
Glutathionylation of human thioredoxin: A possible crosstalk between the glutathione and thioredoxin systems
Proceedings of the National Academy of Sciences U.S.A. 2002, 99, 9745-9749

A. Guerini Rocco, L. Mollica, E. Gianazza, L. Calabresi, G. Franceschini, C.R. Sirtori, I. Eberini
A model structure for the heterodimer apoA-IMilano-apoA-II supports its peculiar susceptibility to proteolysis
Biophysical Journal, 2006, 91, 3043-3049

A. Guerini Rocco, L. Mollica, P. Ricchiuto, A. M. Baptista, E. Gianazza, I. Eberini
Characterization of the protein unfolding process induced by urea and temperature
Biophysical Journal, 2008, 94, 2241-2251

C. Camilloni, A. Guerini Rocco, I. Eberini, E. Gianazza, R. A. Broglia, G. Tiana
Urea and guanidinium chloride denature Protein L in different ways in molecular dynamics simulations
Biophysical Journal, 2008, 94, 4654-4661

I. Eberini, A. Emerson C. Sensi, L. Ragona, P. Ricchiuto, A. Pedretti, E. Gianazza, A. Tramontano
Simulation of urea-induced protein unfolding: a lesson from bovine beta-lactoglobulin
Journal of Molecular Graphics and Modeling, 2011, 30, 24-30

I. Eberini, C. Sensi, A. Barbiroli, F. Bonomi, S. Iametti, M. Galliano, E. Gianazza
Electrostatics of folded and unfolded bovine beta-lactogobulin
Amino Acids, 2012, 42, 2019-2030

I. Eberini, S. Daniele, C. Parravicini, C. Sensi, M.L. Trincavelli, C. Martini, M.P. Abbracchio
In silico identification of new ligands for GPR17: a promising therapeutic target for neurodegenerative diseases
Journal of Computed Aided Molecular Design, 2011, 25, 743-752

I. Eberini, C. Sensi, M. Bovi, H. Molinari, M. Galliano, F. Bonomi, S. Iametti, E. Gianazza
Wards in the keyway: amino acids with anomalous pK(a)s in calycins
Amino Acids, 2012, 43, 2457-1468

S. Sciarretta, S.S. Marchitti, F. Bianchi, A. Moyes, E. Barbato, S. Di Castro, R. Stanzione, M. Cotugno, L. Castello, C. Calvieri, I. Eberini, J. Sadoshima, A.J. Hobbs, M. Volpe, S. Rubattu
The C2238 Atrial Natriuretic Peptide Molecular Variant is Associated with Endothelial Damage and Dysfunction Through Natriuretic Peptide Receptor C Signaling
Circulation Research 2013 in press

 

Patents

PCT/IB2011/054865, Gpr17-modulating compounds, diagnostic and therapeutic uses thereof

PCT/EP2012/058500, GPR17 receptor modulators

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