Ribosome and me

Ribosome and me, Cape Cod, Summer 2007.

I was a graduate student in the TCBG. In 2008, I received my Ph.D. in Biophysics.
You can still reach me at villa@ks.uiu.edu

At present, I am a Marie Curie Postdoctoral Fellow in the Department of Wolfgang Baumeister at the Max Planck Institute of Biochemistry in Munich.


Contact:

    Max Planck Institute of Biochemistry
    Abt. Baumeister
    Am Klopferspitz 18
    82152 Martinsried
    Germany

    Phone: +49 (89) 8578 2617
    E-mail: villa@biochem.mpg.de


Research Projects

multiscale
Multiscale modeling of protein-DNA complexes Flexible Fitting of Atomic Structures into EM maps Structure and Dynamics of the Ribosome

Publications

Structural insight into nascent polypeptide chain-mediated translational stalling.
Birgit Seidelt, C. Axel Innis, Daniel N. Wilson, Marco Gartmann, Jean-Paul Armache, EV , Leonardo G. Trabuco, Thomas Becker, Thorsten Mielke, Klaus Schulten, Thomas A. Steitz, and Roland Beckmann. Science, 2009. In press.

Regulation of the protein-conducting channel by a bound ribosome.
James Gumbart, Leonardo G. Trabuco, Eduard Schreiner, EV , and Klaus Schulten. Structure , 2009. In press.

Protein-induced membrane curvature investigated through molecular dynamics flexible fitting.
Jen Hsin, James Gumbart, Leonardo G. Trabuco, EV, Pu Qian, C. Neil Hunter, and Klaus Schulten. Biophysical Journal, 97:321-329, 2009.

Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and x-ray crystallography.
Leonardo G. Trabuco*, EV*, Eduard Schreiner, Christopher B. Harrison, and Klaus Schulten. Methods, 49:174-180, 2009.

Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis.
EV*, Jayati Sengupta*, Leonardo G. Trabuco, Jamie LeBarron, William T. Baxter, Tanvir R. Shaikh, Robert A. Grassucci, Poul Nissen, Måns Ehrenberg, Klaus Schulten, and Joachim Frank. Proceedings of the National Academy of Sciences, USA, 106:1063-1068, 2009.

Structural model and excitonic properties of the dimeric RC-LH1-PufX complex from Rhodobacter sphaeroides.
Melih K. Sener, Jen Hsin, Leonardo G. Trabuco, EV, Pu Qian, C. Neil Hunter, and Klaus Schulten. Chemical Physics,, 357:188-197, 2009.

Long time and large size molecular dynamics simulations made feasible through new TeraGrid hardware and software.
Kirby Vandivort, James C. Phillips, EV, Peter L. Freddolino, James Gumbart, Leonardo G. Trabuco, Danielle E. Chandler, Jen Hsin, Christopher B. Harrison, Laxmikant Kale, and Klaus Schulten. Proceedings of the 2008 TeraGrid Conference, 2008.

Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
Leonardo G. Trabuco*, EV*, Kakoli Mitra, Joachim Frank, and Klaus Schulten. Structure, 16:673-683, 2008.

Molecular mechanisms of cellular mechanics.
Mu Gao, Marcos Sotomayor, EV, Eric Lee, and Klaus Schulten. Physical Chemistry - Chemical Physics, 8:3692-3706, 2006.

Scalable molecular dynamics with NAMD.
James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, EV, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Journal of Computational Chemistry, 26:1781-1802, 2005.

Structural dynamics of the Lac repressor-DNA complex revealed by a multiscale simulation.
EV, Alexander Balaeff, and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 102:6783-6788, 2005.

Multi-scale method for simulating protein-DNA complexes.
EV, Alexander Balaeff, L. Mahadevan, and Klaus Schulten. Multiscale Modeling and Simulation, 2:527-553, 2004.


*Equal contribution