Molecular Dynamics Flexible Fitting

Publications

Methodological articles and reviews

  1. Parallel generalized Born implicit solvent calculations with NAMD.
    David E. Tanner, Kwok-Yan Chan, James Phillips, and Klaus Schulten. J. of Chem. Theory Comput., 7, 3635-3642, 2011.

  2. Symmetry-restrained flexible fitting for symmetric EM maps.
    Kwok-Yan Chan, James Gumbart, Ryan McGreevy, Jean M. Watermeyer, B. Trevor Sewell, and Klaus Schulten. Structure, 19, 1211-1218, 2011.

  3. Stereochemical errors and their implications for molecular dynamics simulations.
    Eduard Schreiner, Leonardo G. Trabuco, Peter L. Freddolino, and Klaus Schulten. BMC Bioinformatics, 12, 190, 2011.

  4. Applications of the molecular dynamics flexible fitting method.
    Leonardo G. Trabuco, Eduard Schreiner, James Gumbart, Jen Hsin, Elizabeth Villa, and Klaus Schulten. J. Struct. Biol., 173, 420-427, 2011.

  5. 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.

  6. 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.

MDFF applications by the TCBG group

  1. Structural characterization of mRNA-tRNA translocation intermediates.
    Xabier Agirrezabala, Hstau Liao, Eduard Schreiner, Jie Fu, Rodrigo Ortiz-Meoz, Klaus Schulten, Rachel Green, and Joachim Frank. Proc. Natl. Acad. Sci. USA, 109, 6094-6099, 2012.

  2. Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.
    Jens Frauenfeld, James Gumbart, Eli O. van der Sluis, Soledad Funes, Marco Gartmann, Birgitta Beatrix, Thorsten Mielke, Otto Berninghausen, Thomas Becker, Klaus Schulten, and Roland Beckmann. Nat. Struct. Mol. Biol., 18, 614-621, 2011.

  3. Structural insights into cognate vs. near-cognate discrimination during decoding.
    Xabier Agirrezabala, Eduard Scheiner, Leonardo G. Trabuco, Jianlin Lei, Rodrigo F. Ortiz-Meoz, Klaus Schulten, Rachel Green, and Joachim Frank. EMBO J., 30, 1497-1507, 2011.

  4. Molecular dynamics of EF-G during translocation.
    Wen Li, Leonardo G. Trabuco, Klaus Schulten, and Joachim Frank. Proteins, 79, 1478-1486, 2011.

  5. Formation of salt bridges mediates internal dimerization of myosin VI medial tail domain.
    HyeongJun Kim*, Jen Hsin*, Yanxin Liu*, Paul R. Selvin, and Klaus Schulten. Structure, 18, 1443-1449, 2010.

  6. The role of L1 stalk-tRNA interaction in the ribosome elongation cycle.
    Leonardo G. Trabuco, Eduard Schreiner, John Eargle, Peter Cornish, Taekjip Ha, Zaida Luthey-Schulten, and Klaus Schulten. J. Mol. Biol., 402, 741-760, 2010.

  7. Recognition of the regulatory nascent chain TnaC by the ribosome.
    Leonardo G. Trabuco, Christopher B Harrison, Eduard Schreiner, and Klaus Schulten. Structure, 18, 627-637, 2010.

  8. Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome.
    Thomas Becker, Elisabet Mandon, Shashi Bhushan, Alexander Jarasch, Jean-Paul Armache, Soledad Funes, Fabrice Jossinet, James Gumbart, Thorsten Mielke, Otto Berninghausen, Klaus Schulten, Eric Westhof, Reid Gilmore, and Roland Beckmann. Science, 326, 1369-1373, 2009.

  9. 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, 326, 1412-1415, 2009.

  10. 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.

  11. 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. Biophys. J., 97, 321-329, 2009.

  12. 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. Chem. Phys., 357, 188-197, 2009.

  13. 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. Proc. Natl. Acad. Sci. USA, 106, 1063-1068, 2009.

Third-party publications employing MDFF

  1. Simulations of the p97 complex suggest novel conformational states of hydrolysis intermediates.
    Jeff Wereszczynski and J. Andrew McCammon. Protein Science, 21, 475-486.

  2. Structural basis of highly conserved ribosome recycling in eukaryotes and archaea.
    Thomas Becker, Sibylle Franckenberg, Stephan Wickles, Christopher J. Shoemaker, Andreas M. Anger, Jean-Paul Armache, Heidemarie Sieber, Charlotte Ungewickell, Otto Berninghausen, Ingo Daberkow, Annette Karcher, Michael Thomm, Karl-Peter Hopfner, Rachel Green, and Roland Beckmann. Nature, 482, 501-506.

  3. Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach.
    Keren Lasker, Friedrich Förster, Stefan Bohn, Thomas Walzthoeni, Elizabeth Villa, Pia Unverdorbenc, Florian Beck, Ruedi Aebersold, Andrej Sali, and Wolfgang Baumeister. PNAS, 109, 1380-1387.

  4. Ribosome Assembly Factors Prevent Premature Translation Initiation by 40S Assembly Intermediates.
    Bethany S. Strunk, Cherisse R. Loucks, Min Su, Harish Vashisth, Shanshan Cheng, Justin Schilling, Charles L. Brooks III, Katrin Karbstein, and Georgios Skinioti. Science, 333, 1449-1453.

  5. Characterization of the structure and function of Escherichia coli DegQ as a representative of the DegQ-like proteases of bacterial HtrA family proteins.
    Xiao-chen Bai, Xi-jiang Pan, Xiao-jing Wang, Yun-ying Ye, Lei-fu Chang, Dong Leng, Jianlin Lei, Sen-Fang Sui. Structure, 19, 1328-1337, 2011

  6. Structural basis for the function of a small GTPase RsgA on the 30S ribosomal subunit maturation revealed by cryoelectron microscopy.
    Qiang Guo, Yi Yuan, Yanji Xu, Boya Feng, Liang Liu, Kai Chen, Ming Sun, Zhixiu Yang, Jianlin Lei, and Ning Gao. Proc. Natl. Acad. Sci. USA, 108, 13100-13105, 2011

  7. The structure of Barmah Forest virus as revealed by cryo-electron microscopy at a 6-Angstrom resolution has detailed transmembrane protein architecture and interactions.
    Victor A. Kostyuchenko, Joanita Jakana, Xiangan Liu, Andrew D. Haddow, Myint Aung, Scott C. Weaver, Wah Chiu, and Shee-Mei Lok. J. Virol., 85, 9327-9333, 2011

  8. Structure and mechanism of the Swi2/Snf2 remodeller Mot1 in complex with its substrate TBP.
    Petra Wollmann, Sheng Cui, Ramya Viswanathan, Otto Berninghausen, Melissa N. Wells, Manuela Moldt, Gregor Witte, Agata Butryn, Petra Wendler, Roland Beckmann, David T. Auble, and Karl-Peter Hopfner. Nature, 475, 403-407, 2011.

  9. Computational exploration of structural hypotheses for an additional sequence in a mammalian mitochondrial protein.
    Aymen S. Yassin, Rajendra K. Agrawal, and Nilesh K. Banavali. PLoS One, 6, e21771, 2011.

  10. Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome.
    Thomas Becker, Jean-Paul Armache, Alexander Jarasch, Andreas M Anger, Elizabeth Villa, Heidemarie Sieber, Basma Abdel Motaal, Thorsten Mielke, Otto Berninghausen, and Roland Beckmann. Nat. Struct. Mol. Biol., 18, 715-720, 2011.

  11. Regulation by interdomain communication of a headful packaging nuclease from bacteriophage T4.
    Manjira Ghosh-Kumar, Tanfis I. Alam, Bonnie Draper, John D. Stack, and Venigalla B. Rao. Nucleic Acids Res., 39, 2742-2755, 2011.

  12. Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-Å resolution.
    Jean-Paul Armache, Alexander Jarasch, Andreas M. Anger, Elizabeth Villa, Thomas Becker, Shashi Bhushan, Fabrice Jossinet, Michael Habeck, Gülcin Dindar, Sibylle Franckenberg, Viter Marquez, Thorsten Mielke, Michael Thomm, Otto Berninghausen, Birgitta Beatrix, Johannes Söding, Eric Westhof, Daniel N. Wilson, and Roland Beckmann. Proc. Natl. Acad. Sci. USA, 107, 19748-19753, 2011.

  13. Localization of eukaryote-specific ribosomal proteins in a 5.5Å cryo-EM map of the 80S eukaryotic ribosome.
    Jean-Paul Armache, Alexander Jarasch, Andreas M. Anger, Elizabeth Villa, Thomas Becker, Shashi Bhushan, Fabrice Jossinet, Michael Habeck, Gülcin Dindar, Sibylle Franckenberg, Viter Marquez, Thorsten Mielke, Michael Thomm, Otto Berninghausen, Birgitta Beatrix, Johannes Södina, Eric Westhof, Daniel N. Wilson, and Roland Beckmann. Proc. Natl. Acad. Sci. USA, 107, 19754-19759, 2011.

  14. tmRNA-SmpB: a journey to the centre of the bacterial ribosome.
    Félix Weis, Patrick Bron, Emmanuel Giudice, Jean-Paul Rolland, Daniel Thomas, Brice Felden, and Reynald Gillet. EMBO J., 29, 3810-3818, 2010.

  15. Visualizing the transfer-messenger RNA as the ribosome resumes translation.
    Jie Fu, Yaser Hashem, Iwona Wower, Jianlin Lei, Hstau Y Liao, Christian Zwieb, Jacek Wower, and Joachim Frank. EMBO J., 29, 3819-3825, 2010.

  16. Structural basis for translational stalling by human cytomegalovirus and fungal arginine attenuator peptide.
    Shashi Bhushan, Helge Meyer, Agata L. Starosta, Thomas Becker, Thorsten Mielke, Otto Berninghausen, Michael Sattler, Daniel N. Wilson, and Roland Beckmann. Mol. Cell, 40, 138-146, 2010.

  17. The actin-myosin interface.
    Michael Lorenz and Kenneth C. Holmes. Proc. Natl. Acad. Sci. USA, 107, 12529-12534, 2010.

  18. α-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel.
    Shashi Bhushan, Marco Gartmann, Mario Halic, Jean-Paul Armache, Alexander Jarasch, Thorsten Mielke, Otto Berninghausen, Daniel N Wilson, and Roland Beckmann. Nat. Struct. Mol. Biol., 17, 313-317, 2010.


* Equal contribution.

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