Publications

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See our publications in PubMedGoogle Scholar, or ResearcherID

Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cells Simulations. T.M. Earnest, R. Watanabe, J. E. Stone, J. Mahamid, W. Baumeister, E. Villa, and Z. Luther-Schulten. Klaus Schulten Memorial Issue, J. Phys. Chem. B. 121:3871–3881, 2017.

Assembly of a nucleus-like structure during viral replication in bacteria.
V. Chaikeeratisak, K. Nguyen, K. Khanna, A.F. Brilot, M.L. Erb, J.K. C. Coker,  A. Vavilina, G.L. Newton, R.Buschauer, K.Pogliano, E.Villa, D.A. Agard,  J. Pogliano. Science. 355:194-197, 2017.

Visualizing the molecular sociology at the HeLa cell nuclear periphery.
J. Mahamid, S. Pfeffer, M. Schaffer, E. Villa, R. Danev, L. Kuhn-Cuellar, F. Foerster, A. A. Hyman, J. M. Plitzko and W. Baumeister. Science. 351:969-972, 2016.

A photoactivable multi- inhibitor nanoliposome for tumour control and simultaneous inhibition of treatment escape pathways.
B. Q. Spring, R. B. Sears, L.Z. Zheng, Z. Mai, R. Watanabe, M. E. Sherwood, D. A. Schoenfeld, B. W. Pogue, S. P. Pereira, E. Villa, and T. Hasan.  Nature Nanotechnology11:378, 2016.

Architecture of the RNA polymerase II-Mediator core transcription initiation complex. C. Plaschka, L. Lariviere, L. Wenzeck, M. Hemann, D. Tegunov, E.V. Petrotchenko, C.H. Borchers, W. Baumeister, F. Herzog, E. Villa, and P. Cramer. Nature, 518, 2014.

Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography. B. D. Engel, M. Schaffer, L. K. Cuellar, E. Villa, J.M. Plitzko, W. Baumeister. eLife, 2014.

Finding the right fit: chiseling structures out of cryo-electron microscopy maps. E. Villa, K. Lasker. Curr. Opin. Struct. Biol., 25:118–25, 2014.

Opening windows into the cell: focused-ion-beam milling for cryo-electron tomography. E. Villa, M. Schaffer, J.M. Plitzko and W. Baumeister. Curr. Opin. in Struct. Biol., 23, 771–777, 2013.

Three-dimensional architecture of actin filaments in Listeria monocytogenes comet tails. M.Jasnin, S. Asano, E. Gouin, R. Hegerl, J.M. Plitzko, E. Villa, et al. PNAS, 110:20521- 20526, 2013.

Near-atomic resolution structural model of the yeast 26S proteasome. F. Beck, P. Unverdorben, S. Bohn, A. Schweitzer , G. Pfeifer, E. Sakata, S. Nickell, J.M. Plitzko, E. Villa, W. Baumeister, F. Foerster. PNAS 109:14870-14875, 2012.

Promiscuous behaviour of archaeal ribosomal proteins: Implications for eukaryotic ribosome evolution. J.P. Armache, A.M. Anger, V. Marquez, S. Frackenberg, E. Villa, M. Thomm., R. Beckmann, D.N. Wilson. NAR 41, 1284–1293, 2013.

Integrative Approaches for Cellular Cryo-electron Tomography: Correlative Imaging and Focused Ion Beam Micromachining. A. Rigort, E. Villa, F. Baeuerlein, B.D. Engel, and J.M. Plitzko. Met. Cell. Biology, 111, 259281, 2012.

The structure of human Tripeptidyl peptidase II as determined by a hybrid approach. A. Schoenegge, E. Villa, F. Foerster, R. Hegerl, J. Peters, W. Baumeister, and B. Rockel. Structure 20, 593-603, 2012.

Focused ion beam micromachining of eukaryotic cells for cryo-electron tomography. A. Rigort*, F.J.B. Baeuerlein*, E. Villa, M. Eibauer, T. Laugks, W. Baumeister and J.M. Plitzko. PNAS 109, 4449-4454, 2012.

Molecular architecture of the 26S pro- teasome holocomplex determined by an integrative approach. K. Lasker, F. Foerster, S. Bohn, T. Walzthoenid, E. Villa, P. Unverdorben, F. Beck, R. Aebersold, A. Sali, and W. Baumeister. PNAS, 109,1380-1387, 2012.

Dynein achieves processive motion using both stochastic and coordinated stepping. W. Qiu, N.D. Derr, B.S. Goodman, E. Villa, D. Wu, W. Shih and S.L. Reck-Peterson. Nat Struct Mol Biol. 19, 193-200, 2012.

Structure determina- tion of macromolecular complexes by cryo-electron microscopy in vitro and in situ.. F. Foerster, E. Villa, D. Thomas, A. Korinek, and W. Baumeister. Chapter in Comprehensive Biophysics 1, Biophysical Techniques for Structural Characterization of Macromolecules, ed. E. Egelman, and H.J. Dyson. Elsevier B. V. Academic Press, Oxford, pp. 245-276, 2012.

Structure of the no-go mRNA decay complex Dom34- Hbs1 bound to a stalled 80S ribosome. T.Becker, J.P. Armache, A.M. Anger, E. Villa, H. Sieber, B.A. Motaal, T. Mielke, O. Berninghausen, and R. Beckmann. Nat Struct Mol Biol. 18, 715-20, 2011.

Applications of the molecular dynamics flexible fitting method. L.G. Trabuco, E. Schreiner, J. Gumbart, J. Hsin, E. Villa, and K. Schulten. Journal of Structural Biology, 173, 420-427, 2011.

Integration of cryo-EM with atomic and protein-protein interaction data. F. Foerster, E. Villa. Meth. Enzymol., 483:47-72, 2010.

Localization of eukaryote-specific ribosomal proteins in a 5.5-A ̊ cryo-EM map of the 80S eukaryotic ribosome. J.P. Armache*, A. Jarasch*, A.M. Anger*, E. Villa, T. Becker, S. Bhushan, F. Jossinet, M. Habeck, G. Dindar, S. Franckenberg, V. Marquez, T. Mielke, M. Thomm, O. Berninghausen, B. Beatrix, J. Soeding, E. Westhof, D.N. Wilson, and R. Beckmann. PNAS, 107: 19754-19759, 2010.

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A ̊ resolution. J.P. Armache*, A. Jarasch*, A.M. Anger*, E. Villa, T. Becker, S. Bhushan, F. Jossinet, M. Habeck, G. Dindar, S. Franckenberg, V. Marquez, T. Mielke, M. Thomm, O. Berninghausen, B. Beatrix, J. Soeding, E. Westhof, D.N. Wilson, and R. Beckmann. PNAS, 107: 19748-19753, 2010.

Visualizing cellular pro- cesses at the molecular level by cryo-electron tomography. K. Ben-Harush, T. Maimon, I. Patla, E. Villa, and O. Medalia.  J. Cell Science, 123:7?12, 2010.

J.Gumbart, L.G.Trabuco, E.Schreiner, E. Villa, and K. Schulten. Regulation of the protein–conducting channel by a bound ribosome. Structure, 17:1453-1464, 2009.

B. Seidelt, C.A. Innis, D.N. Wilson, M. Gartmann, J.P. Armache, E. Villa, L.G. Trabuco, T. Becker, T. Mielke, K. Schulten, T.A. Steitz, and R. Beckmann. Structural insight into nascent polypeptide chain-mediated translational stalling. Science, 326:1412-1415, 2009.

J. Hsin, J. Gumbart, L.G. Trabuco, E. Villa, P. Qian, C.N. Hunter, and K. Schulten. Protein–induced membrane curvature investigated through molecular dynamics flex- ible fitting. Biophysical Journal, 97:321:329, 2009.

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

EV*, J. Sengupta*, L. Trabuco, J. LeBarron, W.T. Baxter, T. Shaikh, R.A. Grassucci, M. Ehrenberg, K. Schulten, and J. Frank. Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. PNAS 106:1063:1068, 2009.

M.K. Sener, J. Hsin, L.G. Trabuco, E. Villa, P. Qian, P.A. Bullough, C.N. Hunter, and K. Schulten. Structural model and excitonic properties of the dimeric LH1-RC-PufX complex from Rhodobacter sphaeroides. Chemical Physics, 357:188-197, 2009.

L. G. Trabuco*, EV*, K. Mitra, J. Frank, and K. Schulten. Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics. Structure, 16:673-683, 2008.

M. Gao, M. Sotomayor, E. Villa, E. Lee, and K. Schulten. Molecular mechanisms of cellular mechanics. Phys. Chem. Chem. Phys., 8:3692?3706, 2006.

J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, and K. Schulten. Scalable molecular dynamics with NAMD. J. Comp. Chem., 26:1781-1802, 2005.

E. Villa, A. Balaeff, and K. Schulten. Structural dynamics of the Lac repressor-DNA complex revealed by a multiscale simulation. PNAS, 102:6783-6788, 2005.

E. Villa, A. Balaeff, L. Mahadevan, and K. Schulten. Multi-scale method for simulating protein-DNA complexes. Multiscale Modeling and Simulation, 2:527-553, 2004.

*Equal contribution