Leonardo Trabuco
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I'm Leonardo Giantini Trabuco, graduate student at the Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign and working at the Theoretical and Computational Biophysics Group. Telephone: (217) 244-8946 Email: ltrabuco@ks.uiuc.edu Mailing address |
Education
B.Sc. in Molecular Sciences, University of Sao Paulo, Brazil (2005).
Research Interests
Understand the molecular mechanisms of protein synthesis by the ribosome by means of large-scale computer simulations.
Develop flexible fitting methods to combine high-resolution structures with low-resolution cryo-EM data.
Develop software for molecular modeling within VMD.
Accelerate molecular modeling applications using GPU computing.
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| Molecular Dynamics Flexible Fitting | GPU computing | Ribosome structure and function |
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Publications
Since joining TCBG:
Structural insight into nascent polypeptide chain-mediated translational stalling. Birgit Seidelt, C. Axel Innis, Daniel N. Wilson, Marco Gartmann, Jean-Paul Armache, Elizabeth Villa, Leonardo G. Trabuco, Thomas Becker, Thorsten Mielke, Klaus Schulten, Thomas A. Steitz, and Roland Beckmann. Science, 2009. Published online October 29 2009; 10.1126/science.1177662.
Regulation of the protein-conducting channel by a bound ribosome. James Gumbart, Leonardo G. Trabuco, Eduard Schreiner, Elizabeth Villa, and Klaus Schulten. Structure, 17:1453-1464, 2009.
Molecular Dynamics Flexible Fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography. Leonardo G. Trabuco, Elizabeth Villa, Eduard Schreiner, Christopher B. Harrison, and Klaus Schulten. Methods, 49:174-180, 2009.
Protein-induced membrane curvature investigated through molecular dynamics flexible fitting. Jen Hsin, James Gumbart, Leonardo G. Trabuco, Elizabeth Villa, Pu Qian, C. Neil Hunter, and Klaus Schulten. Biophysical Journal, 97:321-329, 2009.
Structural model and excitonic properties of the dimeric RC-LH1-PufX complex from Rhodobacter sphaeroides. Melih K. Sener, Jen Hsin, Leonardo G. Trabuco, Elizabeth Villa, Pu Qian, C. Neil Hunter, and Klaus Schulten. Chemical Physics, 357:188-197, 2009.
Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Elizabeth Villa, 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.
Long time and large size molecular dynamics simulations made feasible through new TeraGrid hardware and software. Kirby Vandivort, James C. Phillips, Elizabeth Villa, 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, Elizabeth Villa, Kakoli Mitra, Joachim Frank, and Klaus Schulten. Structure, 16:673-683, 2008.
Dynamics of recognition between tRNA and elongation factor Tu. John Eargle, Alexis A. Black, Anurag Sethi, Leonardo G. Trabuco, and Zaida Luthey-Schulten. Journal of Molecular Biology, 377:1382-1405, 2008.
Accelerating molecular modeling applications with graphics processors. John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, and Klaus Schulten. Journal of Computational Chemistry, 28:2618-2640, 2007.
Before joining TCBG:
ATP-Sensitive K+ Channels in Renal Mitochondria. Douglas V. Cancherini, Leonardo G. Trabuco, Nancy A. Reboucas, and Alicia J. Kowaltowski. American Journal of Physiology Renal Physiology 285:F1291-F1296, 2003.
Software
VMD plugins:
Salt Bridges
Dowser
Molfile plugins (DX, Situs, X-PLOR)
SSRestraints
RNAView
MDFF
Volutil
Oral presentations
Investigating the mechanisms of protein synthesis using multi-resolution structural data.
Centre for Genomic Regulation, October 28, 2009. Barcelona, Spain
Technical University of Munich, October 26, 2009. Munich, Germany
European Molecular Biology Laboratory, October 22, 2009. Heidelberg, Germany
University of Barcelona, September 21, 2009. Barcelona, Spain
Single-molecule studies of the ribosome in vitro and in silico.
Post-doc and Graduate Student Symposium, Center for the Physics of Living Cells, February 7, 2009. Urbana, IL
Merging data from cryo-EM and X-ray crystallography to reveal
biomolecular function.
Cell and Molecular Biology & Molecular
Biophysicst Symposium, November 14, 2008. Urbana, IL
Ribosome-induced changes in EF-Tu conformation control GTP
hydrolysis.
Beckman Institute Graduate Student Seminar Series, October
15, 2008. Urbana, IL
Poster presentations
Since joining TCBG:
Computational studies of regulatory nascent chain recognition by the ribosome. L.G. Trabuco, C.B. Harrisson, E. Schreiner, and K. Schulten. Cell and Molecular Biology & Molecular Biophysics Symposium, 2009. Urbana, IL, USA. Outstanding poster presentation award.
Computational studies of regulatory nascent chain recognition by the ribosome. L.G. Trabuco, C.B. Harrisson, E. Schreiner, and K. Schulten. EMBO Conference Series on Protein Synthesis and Translational Control, 2009. Heidelberg, Germany.
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. L.G. Trabuco, E. Villa, K. Mitra, J. Sengupta, J. Frank, and K. Schulten. 3DEM Gordon Conference, 2008. Il Ciocco (Barga), Italy.
Flexibly docking the ribosome into EM density data. E. Villa, L.G. Trabuco, J. Frank, and K. Schulten. Ribosomes 2007, 2007. Cape Cod, MA.
Modeling and simulation of a bacterial ribosome. L.G. Trabuco, E. Villa, E. Falck, K. Mitra, J. Frank, and K. Schulten. Ribosomes 2007, 2007. Cape Cod, MA.
Modeling and simulation of a bacterial ribosome. L.G. Trabuco, E. Falck, E. Villa, and K. Schulten. Biophysical Society Meeting, 2007. Baltimore, MD.
Before joining the TCBG: click here
Teaching
Teaching assistant for the Computational Biophysics Workshop - Champaign, IL - August 10-14, 2009
Teaching assistant for the Center for the Physics of Living Cells Summer School - Urbana, IL - July 26 - August 1, 2009
Teaching assistant for the Computational Biophysics Workshop - Champaign, IL - July 6-10, 2009
Teaching assistant for MCB 250 (Molecular Genetics) - Spring 2009
Author of the DNA case study (with Elizabeth Villa)