EPFL School of Life Sciences - 2010 Annual Report
Selected
Publications
Wagner, S., Stenta, M., Metzger, L.C., Dal Peraro M. and Cornelis, G.R. (2010). Length control of the injectisome needle requires only one molecule of Yop secretion protein P (YscP). Proc. Natl. Acad. Sci. USA. 107(31):13860-13865.
Team Members Post doctoral Davide Aleman Marco Stenta
Ho, M.H., De Vivo, M., Dal Peraro, M. and Klein, M.L. (2010). Understanding the Effect of Magnesium Ion Concentration on the Catalytic Activity of Ribonuclease H through Computation: Does a Third Metal Binding Site Modulate Endonuclease Catalysis. J. Am. Chem. Soc. 132:1370213712.
PhD Students Christophe Bovigny Matteo Degiacomi Hassan Pezeshki Thomas Lemmin Enrico Spiga
Khurana, E., Devane, R., Dal Peraro, M. and Klein, M.L. (2010). Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus. Biochimica et Biophysica Acta (BBA) – Biomembranes. 1808:530–537.
Adnimistrative Assistant Marie-France Radigois
Alemani, D., Collu, F., Cascella, M. and Dal Peraro, M. (2010). A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements. Journal of Chemical Theory and Computation. 6(1):315-324. Simona, F., Magistrato, A., Dal Peraro, M., Cavalli, A., Vila, A.J. and Carloni, P. (2009). Common mechanistic features among metallo-β-lactamases: a computational study of Aeromonas hydrophila CphA enzyme. The Journal of biological chemistry. 284(41):28164-28171. Cascella, M. and Dal Peraro, M. (2009). Challenges and perspectives in biomolecular simulations: from atomistic picture to multiscale modeling. CHIMIA International Journal for Chemistry. 63(1-2):14-18. Ho, M.-H., De Vivo, M., Dal Peraro, M. and Klein, M.L. (2009). Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation. Journal of Chemical Theory and Computation. 6:1657-1666 Khurana, E., Dal Peraro, M., DeVane, R.,Vemparala, S., DeGrado, W.F. and Klein, M.L. (2009). Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus. Proc. Natl. Acad. Sci. USA 106(4):1069-1074.
IBI - Institute of Bioengineering
Wagner, S., Sorg, I., Degiacomi, M., Journet, L., Dal Peraro, M. and Cornelis, G.R. (2009). The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome. Mol. Microbiol. 71(3):692-701.
On the left, needle length distribution predicted for the single-ruler static model (scenario 1) and the multi-ruler dynamic model (scenarios 2 and 3), when merodiploids express simultaneously a short (yscP388) and a long (yscP686) version of YscP (shown in the box). On the right, comparison between experimental and predicted needle length distributions according to the different scenarios. The single-ruler mechanism of needle length control (schematically reported on top) is the only compatible with experiments. (Adapted from PNAS 2010).
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