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Tenure Track Assistant Professor SV IBI-SV UPDALPE Tenure Track Assistant Professor SV SV-SSV SSV-ENS

Matteo Dal Peraro Prof. Dal Peraro Group Head of the Laboratory for Biomolecular Modeling nationality: Italian web site: http://lbm.epfl.ch office(s): AAB017 phone(s): [+41 21 69] 31861,30982 fax: [+41 21 69] 39665 BIOGRAPHY Matteo Dal Peraro graduated in Physics at the University of Padua in 2000. He obtained his Ph.D. in Biophysics at the International School for Advanced Studies (SISSA, Trieste) in 2004. He then received postdoctoral training at the University of Pennsylvania (Philadelphia) under the guidance of Prof. M. L. Klein. He was nominated Tenure Track Assistant Professor at the EPFL School of Life Sciences in late 2007. His research at the Laboratory for Biomolecular Modeling (LBM), within the Interfaculty Institute of Bioengineering (IBI), focuses on the multiscale modeling of large macromolecular systems. Education B.S. and M.S., Physics, University of Padua, 2000 Ph.D., Biophysics, International School for Advanced Studies (SISSA), 2004 MAIN PUBLICATIONS Journal Papers 2011 Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis B. Blasco, M. Stenta, L. Alonso-Sarduy, G. Dietler, M. Dal Peraro, S.T. Cole and F. Pojer Molecular Microbiology, no-no (2011) [ detailed record ] [ full text ] Dual Chaperone Role of the C-Terminal Propeptide in Folding and Oligomerization of the Pore-Forming Toxin Aerolysin I. Iacovache, M.T. Degiacomi, L. Pernot, S. Ho, M. Schiltz, M. Dal Peraro, V.D. Goot and F. Gisou PLoS Pathogens, 7(7), e1002135 (2011) [ detailed record ] [ full text ] An introduction to quantum chemical methods applied to drug design M. Stenta and M. Dal Peraro Frontiers in Bioscience, E3(1), 1061-1078 (2011) [ detailed record ] [ full text ] 2010 Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus E. Khurana, R.H. Devane, M.D. Peraro and M.L. Klein Biochimica et Biophysica Acta (BBA) - Biomembranes (2010) [ detailed record ] [ full text ] Length control of the injectisome needle requires only one molecule of Yop secretion protein P (YscP) S. Wagner, M. Stenta, L.C. Metzger, M. Dal Peraro and G.R. Cornelis PNAS, 107(31), 13860-13865 (2010) [ detailed record ] [ full text ] A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements D. Alemani, F. Collu, M. Cascella and M. Dal Peraro Journal of Chemical Theory and Computation, 6(1), 315-324 (2010) [ detailed record ] [ full text ] 2009 Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus E. Khurana, M. Dal Peraro, R. Devane, S. Vemparala, W.F. Degrado and M.L. Klein Proceedings of the National Academy of Sciences, 106(4), 1069-1074 (2009) [ detailed record ] [ full text ] Challenges and perspectives in biomolecular simulations: from atomistic picture to multiscale modeling M. Cascella and M. Dal Peraro CHIMIA International Journal for Chemistry, 63(1-2), 14-18 (2009) [ detailed record ] [ full text ] Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation M.-H. Ho, M. De Vivo, M. Dal Peraro and M.L. Klein Journal of Chemical Theory and Computation, (6), 1657-1666 (2009) [ detailed record ] [ full text ] Common mechanistic features among metallo-²-lactamases: a computational study of Aeromonas hydrophila CphA enzyme F. Simona, A. Magistrato, M. Dal Peraro, A. Cavalli, A.J. Vila and P. Carloni The Journal of biological chemistry, 284(41), 28164-28171 (2009) [ detailed record ] [ full text ] The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome S. Wagner, I. Sorg, M. Degiacomi, L. Journet, M. Dal Peraro and G.R. Cornelis Molecular Microbiology, 71(3), 692-701 (2009) [ detailed record ] [ full text ] 2008 Phosphodiester Cleavage in Ribonuclease H Occurs via an Associative Two-Metal-Aided Catalytic Mechanism M. De Vivo, M. Dal Peraro and M.L. Klein Journal of the American Chemical Society, 130(33), 10955–10962 (2008) [ detailed record ] [ full text ] Topologically based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins M. Cascella, M.A. Neri, P. Carloni and M. Dal Peraro Journal of Chemical Theory Computation, 4(8), 1378–1385 (2008) [ detailed record ] [ full text ] Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement J.R. Calhoun, W. Liu, K. Spiegel, M. Dal Peraro, M.L. Klein, K.G. Valentine, A.J. Wand and W.F. DeGrado Structure, 16(2), 210-5 (2008) [ detailed record ] [ full text ] 2007 The metallo-beta-lactamase GOB is a mono-Zn(II) enzyme with a novel active site J. Moran-Barrio, J.M. Gonzalez, M.N. Lisa, A.L. Costello, M. Dal Peraro, P. Carloni, B. Bennett, D.L. Tierney, A.S. Limansky, A.M. Viale and A.J. Vila J Biol Chem, 282(25), 18286-93 (2007) [ detailed record ] [ full text ] Proton shuttles and phosphatase activity in soluble epoxide hydrolase M. De Vivo, B. Ensing, M. Dal Peraro, G.A. Gomez, D.W. Christianson and M.L. Klein J Am Chem Soc, 129(2), 387-94 (2007) [ detailed record ] [ full text ] Role of zinc content on the catalytic efficiency of B1 metallo beta-lactamases M. Dal Peraro, A.J. Vila, P. Carloni and M.L. Klein J Am Chem Soc, 129(10), 2808-16 (2007) [ detailed record ] [ full text ] Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations M. Dal Peraro, K. Spiegel, G. Lamoureux, M.D. Vivo, W.F. DeGrado and M.L. Klein J Struct Biol, 157(3), 444-53 (2007) [ detailed record ] [ full text ] Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations M. Dal Peraro, P. Ruggerone, S. Raugei, F.L. Gervasio and P. Carloni Curr Opin Struc Biol, 17(2), 149-56 (2007) [ detailed record ] [ full text ] 2006 Polarization effects and charge transfer in the KcsA potassium channel D. Bucher, S. Raugei, L. Guidoni, M. Dal Peraro, U. Rothlisberger, P. Carloni and M.L. Klein Biophysical Chemistry, 124(3), 292-301 (2006) [ detailed record ] [ full text ] 2005 Solute-solvent charge transfer in aqueous solution M. Dal Peraro, S. Raugei, P. Carloni and M.L. Klein Chemphyschem, 6(9), 1715-8 (2005) [ detailed record ] [ full text ] 2004 Substrate binding to mononuclear metallo-beta-lactamase from Bacillus cereus M. Dal Peraro, A.J. Vila and P. Carloni Proteins, 54(3), 412-23 (2004) [ detailed record ] [ full text ] Water-Assisted Reaction Mechanism of Monozinc b-Lactamases M. Dal Peraro, L.I. Llarrull, U. Rothlisberger, A.J. Vila and P. Carloni Journal of the American Chemical Society, 126(39), 12661-12668 (2004) [ detailed record ] [ full text ] 2003 Protonation state of Asp120 in the binuclear active site of the metallo-beta-lactamase from Bacteroides fragilis M. Dal Peraro, A.J. Vila and P. Carloni Inorg Chem, 42(14), 4245-7 (2003) [ detailed record ] [ full text ] 2002 Structural determinants and hydrogen-bond network of the mononuclear zinc(II)-beta-lactamase active site M. Dal Peraro, A.J. Vila and P. Carloni J Biol Inorg Chem, 7(7-8), 704-12 (2002) [ detailed record ] [ full text ] 2001 Ser133 phosphate-KIX interactions in the CREB-CBP complex: an ab initio molecular dynamics study M. Dal Peraro, F. Alber and P. Carloni Eur Biophys J, 30(1), 75-81 (2001) [ detailed record ] [ full text ]

Skills Computational biophysics Modeling of biological systems Teaching Life Sciences and Technologies Biomolecular structure and mechanics [en] (SMA SSV SCGC) Biothermodynamics [en] (SSV) Phd programs Biotechnology and Bioengineering Chemistry and Chemical Engineering (edoc) Physics (edoc) Phd Students Bovigny Christophe Degiacomi Matteo Thomas Lemmin Thomas Pezeshgi Modarres Hasan Spiga Enrico