CPLC Publications

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2013

  1. B. Bhattacharyya, N. P. George, T. M. Thurmes, R. Zhou, N. Jani, S. R. Wessel, S. J. Sandler, T. Ha and J. L. Keck. “Structural mechanisms of PriA-mediated DNA replication restart”, PNAS (2013).
  2. B. C. Goh, M. J. Rynkiewicz, T. R. Cafarella, M. R. White, K. L. Hartshorn, K. Allen, E.C. Crouch, O. Calin, P. H. Seeberger, K. Schulten and B. A. Seaton. “Molecular mechanisms of influenza inhibition by surfactant protein D revealed by large-scale molecular dynamics simulation”, Biochemistry 52:8527-8538 (2013).
  3. D. N. Ermolenko, P. V. Cornish, T. Ha and H. F. Noller. “Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation”, RNA 19(2), 158-166 (2013).
  4. E. Roberts, J. E. Stone and Z. Luthey-Schulten. “Lattice microbes: high-performance stochastic simulation method for the reaction-diffusion master equation”, J. Comp. Chem. 32(3), 245-255 (2013).
  5. G. Zhao, J. R. Perilla, E. L. Yufenyuy, X. Meng, B. Chen, J. Ning, J. Ahn, A. M. Gronenborn, C. Aiken, K. Schulten and P. Zhang. “Mature HIV-1 capsid sturcture by cryo-electron and all-atom molecular dynamics”, Nature 497, 643-6 (2013).
  6. H. Deberg and P. R. Selvin. “Single molecule high-resolution imaging with photobleaching (SHRImP)"Review Article. Encyclopedia of Biophysics. Springer Publishing (2013).
  7. H. Deberg, B. H. Blehm, J. Sheung, A. R. Thompson, C. S. Bookwalter, S. F. Torabi and P. R. Selvin. “Motor domain phosphorylation modulates kinesin-1 transport”, Journal of Biological Chemistry 288, 32612-32621 (2013).
  8. H. Gelman, T. Perlova and M. Gruebele. “Dodine as a protein denaturant: The best of two worlds”, J. Phys. Chem. B 117(42), 13090-7 (2013).
  9. H. J. Kim and P. R. Selvin. “Fluorescence imaging with one nano-meter accuracy (FIONA)”,  Review Article. Encyclopedia of Biophysics. Springer Publishing, 2013.
  10. H. Kim and T. Ha. “Single molecule nanometry for biological physics”, Reports on Progress in Physics 76, 016601-16 (2013).
  11. H. R. Koh, M. A. Kidwell, K. Ragunathan, J. A. Doudna and S. Myong. “ATP-independent diffusion of double-stranded RNA binding proteins”, Proc. Natl. Acad. Sci. USA 110, 151-156 (2013).
  12. I. Teo and K. Schulten. “A computational kinetic model of diffusion for molecular systems”,  Journal of Chemical Physics 139:121929 (2013). (PMC: 3795746) (DOI: 10.1063/1.4820876) (pub. 9/23/2013 online)
  13. J. A. Lamboy, H. Kim, H. Dembinski, T. Ha and E. A. Komives. “Single molecule FRET reveals the native state dynamic of the IκBα ankyrin repeat domain”, J. Mol. Biol. 425, 2578-2590 (2013).
  14. J. C. Gumbart,  I. Teo,  B. Roux  and  K. Schulten.  “Reconciling  the  roles  of  kinetic  and thermodynamic factors in membrane-protein insertion”, J. Am. Chem. Soc. 135(6), 2291-2297 (2013).
  15. R.  Peterson, M. J. Hallock, J. A. Cole and Z. Luthey-Schulten.  “A  problem  solving environment  for  stochastic  biological  simulations”,  at  the  Workshop  for  Python  for  High Performance  and  Scientific  Computing  (PyHPC  (2013)  in  Proceedings  High  Performance Computing Networking, Storage and Analysis Companion (SCC) (2013).
  16. J. Yoo and A. Aksimentiev. “In situ structure and dynamics of DNA origami determined through molecular  dynamics  simulations”,  Proceedings  of  the  National  Academy  of  Sciences  USA 110:20099-20104 (2013).
  17. J.  Zhang, R.  Zhou, J.  Inoue, T. Mikawa and T. Ha.  “Single  molecule  analysis  of  thermus thermophilus SSB protein dynamics on single-stranded DNA”, Nucleic Acids Research, 1-12 (2013).
  18. K. S. Lee, H. Balci, H. Jia, T. M. Lohman and T. Ha. “Direct imaging of single UvrD dynamics on long single-stranded DNA”, Nature Commun. 4, 1878 (2013).
  19. K.-Y. Young, B. Leslie, J. Fei, J. Zhang and T. Ha. “Understanding the photophysics of the Spinach-DFHBI RNA aptamer-fluorogen complex to improve live cell RNA imaging”, J. Am. Chem. Soc. 135(50), 19033-38 (2013).
  20. M. Assaf, E. Roberts, Z. Luthey-Schulten and N. Goldenfeld. “Extrinsic noise-driven phenotype switching in a self-regulated gene”, Phys. Rev. Lett. 111, 058102 (2013).
  21. M. Belkin, C. Maffeo, D. B. Wells and A. Aksimentiev. “Stretching and controlled motion ofsingle-stranded DNA in locally-heated solid-state nanopores”, ACS Nano 7, 6816-6824 (2013).
  22. M. B. Prigozhin, Y. Liu, A. J. Wirth, S. Kapoor, R. Winter, K. Schulten and M. Gruebele. “Misplaced helix slows down ultrafast pressure-jump protein folding”, Proc. Natl. Acad. Sci. USA 110, 8087-92 (2013).
  23. M. J. Hallock, J. E. Stone, E. Roberts, C. Fry and Z. Luthey-Sculten. “Simulation of reaction diffusion processes over biologically-relevant time scales using multi-GPU workstations”, (in revision 2013).
  24. M. L. Gibiansky, W. Hu, K.A. Dahmen, W. Shi and G.C.L. Wong. “Earthquake-like dynamics in Myxococcus xanthus social motility”, Proc. Natl. Acad. Sci. USA 2013; published ahead of print January 22 (2013).
  25. M. P. Landry, X. Zou, L. Wang, W.M. Huang, K. Schulten and Y.R. Chemla. “DNA targetsequence  identification  mechanism  for  dimer-active  protein  complexes”,  Nucleic  Acids  Res. 41(4), 2416-27 (2013).
  26. N. F. Lue, R. Zhou, L. Chico, N. Mao, O. Steinberg-Neifach and T. Ha. “The telomere capping complex CST has an unusual stoichiometry, makes multipartite interaction with G-tails and unfolds higher-order G-tail structures”, PLoS Genetics 9, 14 pp (2013).
  27. P. Labhsetwar, J. Cole, E. Roberts, N. Price and Z. Luthey-Schulten. “Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population”, Proc. Natl. Acad. Sci. USA 110, 14006 (2013).
  28. S. H. Kim, C. Joo, T. Ha and D. Kim. “Molecular mechanism of sequence-dependent stability of RecA filament”, Nucleic Acids Research 41(16), 7738-44 (2013).
  29. S. H. Yang, R. Zhou, J. Campbell, J. Chen, T. Ha and T. T. Paull. “The SOSS1 singlestranded DNA binding complex promotes DNA end resection in concert with Exo1”, EMBO J. 32, 126-139 (2013).
  30. S.  K.  Yang, X.  Shi, S.  Park, T.  Ha and S. C. Zimmerman.  “A dendritic single-molecule fluorescent probe that is monovalent, photostable and minimally blinking”, Nature Chem. 5, 692-697 (2013).
  31. S. O. Skinner, L. A. Sepúlveda, H. Xu and I. Golding. “Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization”, Nature Protocols 8, 1100-1113 (2013).
  32. S. R. Wessel, A. H. Marceau, S. C. Massoni, R. Zhou, T. Ha, S. J. Sandler and J. L. Keck. “PriC- mediated  DNA replication restart  requires  PriC complex  formation  with  the single-stranded DNA-binding protein”, J. Biol. Chem., Volume 288, Issue 24, Pages 17569-17578 (2013).
  33. S. Subramanyam, W. T. Jones, M. Spies and M. A. Spies. “Contributions of the RAD51 N- terminal domain to BRCA2-RAD51 interaction”, Nuc. Acids. Res. 41(19), 9020-32 (2013).
  34. T. E. Kuhlman and E. C. Cox “DNA-binding protein inhomogeneity in E. coli modeled as biphasic facilitated diffusion”, Phys. Rev. E 88, 022701 (2013).
  35. T. Earnest, E. Roberts, M. Assaf, K. A. Dahmen and Z. Luthey-Schulten. “DNA looping increases the range of bistability in a stochastic model of the lac genetic switch”, Phys. Biol. 10, 026002 (2013).
  36. T. Ha. “Single molecule approaches embrace molecular cohorts”, Cell 154(4), 723-6 (2013).  W. Li, G. C. Atkinson, N. S. Thakor, Ü. Allas, C.-C. Lu, K.-Y. Chan, T. Tenson, K. Schulten, K. S.  Wilson, V.  Hauryliuk and J.  Frank.  “Mechanism of  tetracycline  resistance  by ribosomal protection protein Tet(O)”, Nature Commun. 4:1477 (2013).
  37. X. Wang and T. Ha. “Defining single molecule forces required for activating integrin and notch signaling”, Science 340, 991-994 (2013).
  38. X. Wang, F. Xu, J. Liu, B. Gao, Y. Liu, Y. Zhai, J. Ma, K. Zhang, T. S. Baker, K. Schulten, D. Zheng, H. Pang and F. Sun. “Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography”, PLoS Pathogens 9:e1003132 (2013).
  39. Y. Qiu, E. Antony, S. Doganay, H. Koh, T. M. Lohman and S. Myong. “Srs2 prevents Rad51 filament formation by repetitive motion on DNA”. Nature Commun. 4:2281 (2013).
  40. Y. Wang, Gilbert Fruhwirth, En Cai, Tony Ng and Paul R. Selvin. “3D super-resolution Imaging with blinking quantum dots”, Nano Letters, October 2013. doi:10.1021/nl4026665