CPLC Publications

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2009

  1. A. Arkhipov and K. Schulten. “Limits for reduction of effective focal volume in multiple-beam light microscopy,” Opt. Express 17:2861-2870 (2009).
  2. A. Arkhipov, Y. Yin and K. Schulten. “Membrane-bending mechanism of amphiphysin NBAR domains,” Biophys. J. 97:2727-2735 (2009).
  3. A. Sethi, J. Eargle, A. Black and Z. Luthey-Schulten. “Dynamical networks in tRNA:protein complexes,” Proc. Natl. Acad. Sci. 106(16), 6620-6625 (2009).
  4. B. Dorvel, G. Sigalov, Q. Zhao, J. Comer, V. Dimitrov, U. Mirsaidov, A. Aksimentiev and G. Timp.  “Analyzing  the  forces  binding  restriction  endonucleases  to  DNA  using  a  synthetic nanopore,” Nucleic Acid Research 37, 4170-4179 (2009).
  5. B. Okumus, S. Arslan, S. M. Fengler, S. Myong and T. Ha. “Single molecule nanocontainer made porous using a bacterial toxin,” J. Am. Chem. Soc. 131(41), 14844-14849 (2009).
  6. 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).
  7. C. Maffeo and A. Aksimentiev. “Structure, dynamics, and ion conductance of a phospholamban pentamer,” Biophysical Journal 96, 4853-4865 (2009).
  8. E. R. Cruz-Chu, A. Aksimentiev and K. Schulten. “Ionic current rectification through Silica nanopores,” J. Phys. Chem. C 113:1850-1862 (2009).
  9. E. Roberts, J. E. Stone, L. Sepulveda, W. W. Hwu and Z. Luthey-Schulten. “Long time-scale simulations  of  in  vivo  diffusion  using  GPU  hardware,”  In  Proceedings  of  2009  IEEE International Symposium on Parallel & Distributed Processing (2009).
  10. E.  Toprak,  A.  Yildiz,  M. Hoffman,  S.  S.  Rosenfeld  and  P.  R.  Selvin.  “Why  kinesin  is  so processive,” Proc. Natl. Acad. Sci. USA 106:12717-12722 (2009).
  11. E. Villa, J. Sengupta, L. G. Trabuco, J. LeBarron, W. T. Baxter, T. R. Shaikh, R. A. Grassucci, P. Nissen, M. Ehrenberg, K. Schulten and J. Frank. “Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis,” Proc. Natl. Acad. Sci. USA 106:1063-1068 (2009).
  12. I. A.  Solov’yov  and  K.  Schulten.  “Magnetoreception  through  cryptochrome  may  involve superoxide,” Biophys. J. 96:4804-4813 (2009).
  13. J. Comer, V. Dimitrov, G. Timp and A. Aksimentiev. “Microscopic mechanics of hairpin DNA translocation through synthetic nanopores,” Biophysical Journal 96, 593-608 (2009).
  14. J. G. Yodh, B. C. Stevens, K. Radhakrishnan, P. Janscak and T. Ha. “BLM helicase measures DNA unwound before switching strands and hRPA promotes unwinding reinitiation,” EMBO J 28(4), 405-416 (2009).
  15. 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).
  16. K.  Sarkar,  K.  Meister,  A.  Sethi  and  M.  Gruebele.  “Base  stacking  and  hydrogen  bonding rearrangements during fast folding of an RNA hairpin,” Biophys. J. 97, 1418-1427 (2009).
  17. L. G. Trabuco, E. Villa, 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).
  18. L. Miao and K. Schulten. “Transport-related structures and processes of the nuclear pore complex studied through molecular dynamics,” Structure 17:449-459 (2009).
  19. M.  Honda,  J.  Park,  R.  A.  Pugh,  T.  Ha  and  M.  Spies.  “Single-molecule  analysis reveals differential effect of ssDNA-binding proteins on DNA translocation by XPD helicase,” Molecular Cell 35(5), 694-703 (2009).
  20. M. Pandey, S. Syed, I. Donmez, G. Patel, T. Ha and S. S. Patel. “Coordinating DNA replication by means of priming loop and differential synthesis rate,” Nature 462, 940-943 (2009).
  21. M. Sorokina, H. R. Koh, S. S. Patel and T. Ha. “Fluorescent lifetime trajectories of a single fluorophore Reveal reaction intermediates during transcription initiation,” J. Am. Chem. Soc. 131, 9630-9631 (2009).
  22. N. Chia, I. Golding and N. Goldenfeld. “Lambda-prophage induction modeled as a cooperative failure mode of lytic repression,” Phys. Rev. E. Rapid Communications 80, 030901 (R):1-4 (2009).
  23. P. L. Freddolino and K. Schulten. “Common structural transitions in explicit-solvent simulations of villin headpiece folding,” Biophys. J. 97:2338-2347 (2009).
  24. P.  L.  Freddolino,  S.  Park,  B.  Roux  and  K.  Schulten.  “Force  field  bias  in  protein  folding simulations,” Biophys. J. 96:3772-3780 (2009).
  25. P. V. Cornish., D. N. Ermolenko, D. W. Staple, L. Hoang, R. P. Hickerson, H. F. Noller and T. Ha. “Following movement of the L1 stalk between three functional states in single ribosomes,” Proc. Natl. Acad. Sci. USA 106(8), 2571-2576 (2009).
  26. R. Roy, A. Kozlov, T. M. Lohman and T. Ha. “SSB protein diffusion on single stranded DNAstimulates RecA filament formation,” Nature 461(7267), 1092-1097 (2009).
  27. S. Myong, S. Cui, P. V. Cornish, A. Kirchhofer, M. U. Gack, J. U. Jung, K. P. Hopfner and T. Ha. “Cytosolic viral sensor RIG-I is a 5'-triphosphate-dependent translocase on double-stranded RNA,” Science 323, 1070-1074 (2009).
  28. T. Becker, S. Bhushan, A. Jarasch, J.-P. Armache, S. Funes, F. Jossinet, J. Gumbart, T. Mielke, O. Berninghausen, K. Schulten, E. Westhof, R. Gilmore, E. C. Mandon and R..Beckman “Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome,” Science 326:1369-1373 (2009).
  29. T. L. Min, P. J. Mears, L. M. Chubiz, C. V. Rao, I. Golding and Y. R. Chemla. “High-resolution, long-term  characterization  of  bacterial  motility  using  optical  tweezers,”  Nature  Methods. 6(11):831-835 (2009).