CPLC Publications

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2010

  1. A. Aksimentiev. “Deciphering ionic current signatures of DNA transport through a nanopore.” Nanoscale 2, 468-483 (2010).
  2. A. B. Pyrkosz, J. Eargle, A. Sethi and Z. Luthey-Schulten. “Exit strategies for charged tRNA from GluRS,” J. Mol. Biol. 397(5), 1350-1371 (2010).
  3. A. Dhar, A. Samiotakis, S. Ebbinghaus, L. Nienhaus, D. Homouz, M. Gruebele and M. S. Cheung. “Structure, function and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding,” Proc. Natl. Acad. Sci. USA 107, 17586-17591 (2010).
  4. A. Dhar, S. Ebbinghaus, Z. Shen, T. Mishra and M. Gruebele. “The diffusion coefficient for PGK folding in eukaryotic cells,” Biophys. J. Lett. 99, L69-L71 2010).
  5. A. Rajan, P. L. Freddolino and K. Schulten. “Going beyond clustering in MD trajectory analysis: an application to villin headpiece folding,” PLoS One 5:e9890, 12 pp (2010).
  6. B. Luan and A. Aksimentiev. “Control and reversal of the electrophoretic force on DNA in a charged nanopore,” Journal of Physics: Condensed Matter 22:454123-5 (2010).
  7. B. Luan and A. Aksimentiev. “Electric and electrophoretic inversion of the DNA charge in multivalent electrolytes,” Soft Matter 6, 243-246 2010).
  8. B. Luan, R. Carr, M. Caffrey and A. Aksimentiev. “The effect of calciumi on the conformation of cobalamin transporter BtuB,” Proteins: Structure, Function, and Bioinformatics 78:1153-1162 (2010).
  9. C. Grashoff, B. D. Hoffman, M. D. Brenner, R. Zhou, M. Parsons, M. T. Yang, M. A. McLean, S. G. Sligar, C. S. Chen, T. Ha and M. A. Schwartz. “Measuring mechanical tension across vinculin reveals regulation of focal adhesion dynamics,” Nature 466, 263-266 (2010).
  10. C. Maffeo, R. Schopflin, H. Brutzer, R. Stehr, A. Aksimentiev, G. Wedemann and R. Seidel. “A small effective charge describes DNA-DNA interactions in tight supercoils,” Phys. Rev. Lett 105:158101 (2010).
  11. C. Zong, L. So, L. Sepulveda, S. O. Skinner and I. Golding. “Lysogen stability is determined By the frequency of activity bursts from the fate-determining gene,” Molecular Systems Biology 6:440 (2010).
  12. D.  Wells  and  A.  Aksimentiev.  “Mechanical  properties  of  a  complete  microtubule  revealed through molecular dynamics simulation,” Biophysical Journal 99:629-637 (2010).
  13. E. J. Tomko, H. Jia, J. Park, N. K. Maluf, T. Ha and T. M. Lohman. “5' Single-stranded/duplex DNA junctions are loading sites for E. coli UvrD translocase,” EMBO J 29, 3826-3839 (2010).
  14. E. R. Cruz-Chu and K. Schulten. “Computational microscopy of the role of protonable surface residues in nanoprecipitation oscillations,” ACS Nano 4:4463-4474, 2010.
  15. F. E. Müllner, S. Syed, P. R. Selvin and F. J. Sigworth. “Improved hidden Markov models for molecular motors, 1: Basic theory,” Biophysical Journal 99(11), 3684-3695 (2010).
  16. G. Lee, S. Hartung, K. P. Hopfner and T. Ha. “Reversible and controllable nano-locomotion of an RNA-processing machinery,” Nano Letters 10(12), 5123-5130 (2010).
  17. H. J. Kim, J. Hsin, Y. Liu, P. R. Selvin and K. Schulten. “Formation of salt bridges mediates internal dimerization of myosin VI medial tail domain,” Structure 18:1443-1449 (2010).
  18. I. A. Solov’yov, H. Mouritsen and K. Schulten. “Acuity of a cryptochrome and vision based magnetoreception system in birds,” Biophys. J. 99:40-49 (2010).
  19. I. A. Solov’yov, K. Schulten and W. Greiner. “How birds and other animals orient in the Earth magnetic field,” Physik Journal 9:23-28 (2010). (article in German only.)
  20. J.  Hsin, J.  Strümpfer,  M.  Sener,  P.  Qian,  C.  N.  Hunter  and  K.  Schulten.  “Energy 
    Transfer dynamics in an RC-LH1-PufX tubular photosynthetic membrane,” New J. Phys. 12:085005, 19 pp (2010).
  21. J. Lee, S. Lee, K. Ragunathan, C. Joo, T. Ha and S. Hohng. “Single-molecule four-color FRET,” Angew. Chem. Int. Ed. 49(51), 9922- 9925 (2010).
  22. J. G. Yodh, M. Schlierf and T. Ha. “Insight into helicase mechanism and function Revealed through single-molecule approaches,” Quarterly Reviews of Biophysics 43(02), 185-217 (2010).
  23. J. M. Grimme, M. Honda, R. Y. Wright, Y. Okuno, E. Rothenberg, A. V. Mazin, T. Ha and M. Spies. “Human Rad52 binds and wraps single-stranded DNA and mediates annealing via two hRad52-ssDNA complexes,” Nucleic Acids Research 38(9), 2917-2930 (2010).
  24. J. Park, S. Myong, A. Niedziela-Majka, K.-S. Liu, J. Yu, T. M. Lohman and T. Ha. “PcrA Helicase dismantles RecA filaments by reeling in DNA in uniform steps,” Cell 142, 544-555 (2010).
  25. K.  Chen,  J.  Eargle,  K.  Sarkar,  M.  Gruebele  and  Z.  Luthey-Schulten.  “Functional  role  of ribosomal signatures,” Biophys. J. 99(12), 3930-3940 (2010).
  26. K. Sarkar, D. A. Nguyen and M. Gruebele. “Loop and stem dynamics during RNA hairpin folding and unfolding,” RNA 16, 2427-2434 (2010).
  27. L. G. Trabuco, C. B. Harrison, E. Schreiner and K. Schulten. “Recognition of the regulatory nascent chain TnaC by the ribosome,” Structure 18:627-637 (2010).
  28. L. G. Trabuco, E. Schreiner, J. Eargle, P. Cornish, T. Ha, Z. Luthey-Schulten and K. Schulten. “The role of L1 stalk: tRNA interaction in the ribosome elongation cycle,” J. of Mol. Biol. 402(4), 741-760 (2010).
  29. L. Miao and K. Schulten. “Probing a structural model of the nuclear pore complex channel    through molecular dynamics,” Biophys. J. 98:1658-1667 (2010).
  30. M.  D.  Brenner,  M.  S.  Scanlan,  M.  K.  Nahas,  T.  Ha  and  S.  K.  Silverman.  “Multi-vector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine,” Biochemistry 49(8), 1596-1605. Erratum in: Biochemistry 16, 49(10), 2306 (2010).
  31. M. Sener, J. Strumpfer, J. A. Timney, A. Freiberg, C. N. Hunter and K. Schulten. “Photosynthetic vesicle architecture and constraints on efficient energy harvesting,” Biophys. J. 99:67-75 (2010).
  32. P. D. Simonson, H. A. Deberg, P. Ge, J. K. Alexander, O. Jeyifous, W. N. Green and P. R. Selvin. “Counting bungarotoxin binding sites of nicotinic acetylcholine receptors in mammalian cells with high signal/noise ratios,” Biophysical Journal 99(10):L81-3 (2010).
  33. P.  L.  Freddolino,  C.  B.  Harrison,  Y.  Liu  and  K.  Schulten.  “Challenges  in  protein  folding simulations,” Nature Phys. 6:751-758 (2010).
  34. R. W. Alexander, J. Eargle and Z. Luthey-Schulten. “Experimental and computational analysis Of tRNA dynamics,” FEBS Lett. 584(2), 376-386 (2010).
  35. S.  Ebbinghaus,  A.  Dhar,  J.  D.  McDonald  and  M.  Gruebele.  “Protein  folding  stability   And dynamics imaged in a living cell,” Nature Methods 7, 319-323 (2010).
  36. S. Saini, S. Koirala, E. Floess, P.J. Mears, Y.R. Chemla, I. Golding, C. Aldridge, P.D. Aldridge and  C.V.  Rao.  “FliZ  induces  a  kinetic  switch  in  flagellar  gene  expression,”  Journal  of Bacteriology 192: 6477-6481 (2010).
  37. S. Syed, F. E. Müllner, P. R. Selvin and F. J. Sigworth. “Improved hidden Markov models for molecular  motors,  2:  Extensions  and  application to experimental  data,”  Biophysical Journal 99(11), 3696-3703 (2010).
  38. W. H. Roos, M. M. Gibbons, A. Arkhipov, C. Uetrecht, N. Watts, P. Wingfield, A. C. Steven, A. W.  Timp,  U.  M.  Mirsaidov,  D.  Wang,  J.  Comer,  A.  Aksimentiev  and  G.  Timp.  “Nanopore sequencing: Electrical measurements of the code of life,” IEEE Transactions on Nanotechnology 9:281-294 (2010).
  39. J.  R.  Heck,  K.  Schulten,  W.  S.  Klug  and  G.J.L.  Wuite.  “Squeezing  protein  shells:  How continuum elastic  models,  molecular  dynamics  simulations  and  experiments  coalesce  at  the nanoscale,” Biophys. J. 99:1175-1181 (2010).
  40. Y. Liu, J. Park, K. A. Dahmen, Y. R. Chemla and T. Ha. “A comparative study of multivariate And univariate hidden Markov modelings in time-binned single-molecule FRET data analysis,” J. Phys Chem. B. 114(16), 5386-5403 (2010).