CPLC Publications

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  1. Y. Wang, E. Cai, T. Rosenkranz, P. Ge, K.W. Teng, S.J. Lim, A.M. Smith, H.J. Chung, F. Sachs, W.N. Green, P. Gottlieb, P.R. Selvin. “Small quantum dots conjugated to nanobodies as immunofluorescence probes for nanometric microscopy.” Bioconjug Chem. 25(12), 2205–2211. DOI: 10.1021/bc5004179 (2014).
  2. B. Hua, K.Y. Han, R. Zhou, H. Kim, X. Shi, S.C. Abeysirigunawardena, A. Jain, D. Singh, V. Aggarwal, S.A. Woodson, T. Ha. “An improved surface passivation method for single-molecule studies.” Nat Methods. 11(12), 1233–1236. DOI: 10.1038/nmeth.3143 (2014).
  3. A. Jain, E. Arauz, V. Aggarwal, N. Ikon, J. Chen, T. Ha. “Stoichiometry and assembly of mTOR complexes revealed by single-molecule pulldown.” Proc Natl Acad Sci U S A. 111(50), 17833–17838. DOI: 10.1038/nmeth.3143 (2014).
  4. A. Girdhar, C. Sathe, K. Schulten, J.P. Leburton. “Gate-modulated graphene quantum point contact device for DNA sensing.” J Comput Electron. 13(4), 839–846. DOI: 10.1007/s10825-014-0596-6 (2014).
  5. C. Sathe, A. Girdhar, J.P. Leburton, K. Schulten. “Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores.” Nanotechnology. 25(44):445105. DOI: 10.1088/0957-4484/25/44/445105 (2014).
  6. S.H. Kim, K. Ragunathan, J. Park, C. Joo, D. Kim, T. Ha. “Cooperative conformational transitions keep RecA filament active during ATPase cycle.” J Am Chem Soc. 136(42), 14796–14800. DOI: 10.1021/ja506363y (2014).
  7. R. Vafabakhsh, K. Kondabagil, T. Earnest, K.S. Lee, Z. Zhang, L. Dai, K.A. Dahmen, V.B. Rao, T. Ha. “Single-molecule packaging initiation in real time by a viral DNA packaging machine from bacteriophage T4.” Proc Natl Acad Sci U S A. 111(42), 15096–15101. DOI: 10.1073/pnas.1407235111 (2014).
  8. T. Ha. “Single-molecule methods leap ahead.” Nat Methods. 11(10), 1015–1018. DOI: 10.1038/nmeth.3107 (2014).
  9. M.B. Prigozhin, G.E. Scott, S. Denos. “Mechanical modeling and computer simulation of protein folding” J Chem Educ. 91(11), 1939–1942. DOI: 10.1021/ed400719c (2014).
  10. Y. Wang, E. Cai, J. Sheung, S.H. Lee, K.W. Teng, P.R. Selvin. “Fluorescence imaging with one-nanometer accuracy (FIONA).” J Vis Exp. 91:51774. DOI: 10.3791/51774 (2014).
  11. M. Aghtar, J. Strümpfer, C. Olbrich, K. Schulten, U. Kleinekathöfer. “Different types of vibrations interacting with electronic excitations in phycoerythrin 545 and Fenna-Matthews-Olson antenna systems.” J Phys Chem Lett. 5(18), 3131–3137. DOI: 10.1021/jz501351p (2014).
  12. W. Han and K. Schulten. “Fibril elongation by Aß(17-42): kinetic network analysis of hybrid-resolution molecular dynamics simulations.” J Am Chem Soc. 136(35), 12450–12460. DOI: 10.1021/ja507002p (2014).
  13. Z. Wu and K. Schulten. “Synaptotagmin's role in neurotransmitter release likely involves Ca(2+)-induced conformational transition.” Biophys J. 107(5), 1156–1166. DOI: 10.1016/j.bpj.2014.07.041 (2014).
  14. S.H. Chao, S.S. Matthews, R. Paxman, A. Aksimentiev, M. Gruebele, J.L. Price. “Two structural scenarios for protein stabilization by PEG.” J Phys Chem B. 118(28), 8388–8895. DOI: 10.1021/jp502234s (2014).
  15. C. Maffeo, J. Yoo, J. Comer, D.B. Wells, B. Luan and A. Aksimentiev. "Close encounters with DNA." J Phys Condens Matter. 26(41): 413101. DOI:10.1088/0953-8984/26/41/413101 (2014).
  16. E. Cai, P. Ge, S.H. Lee, O. Jeyifous, Y. Wang, Y. Liu, K.M. Wilson, S.J. Lim, M.A. Baird, J.E. Stone, K.Y. Lee, M.W. Davidson, H.J. Chung, K. Schulten, A.M. Smith, W.N. Green, P.R. Selvin. “Stable small quantum dots for synaptic receptor tracking on live neurons.” Angew Chem Int Ed. 53(46), 12484–12488. DOI: 10.1002/anie.201405735.
  17. B. H. Blehm and P. R. Selvin. “Single-molecule fluorescence and in-vivo optical traps: how multiple dyneins and kinesins interact.” Chem Rev. 114(6), 3335–3352. DOI: 10.1021/cr4005555 (2014).
  18. 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.” Proc Natl Acad Sci U S A. 111(4), 1373–1378. DOI: 10.1073/pnas.131800111 (2014).
  19. C. Maffeo, T. Ngo, T. Ha, A. Aksimentiev. “A coarse-grained model of unstretched single-stranded DNA derived from atomistic simulation and single-molecule experiment.” J. Chem Theory Comput. 8(10), 2891–2896. DOI:10.1021/ct500193u (2014).
  20. D. Chandler, J. Strumpfer, M. Sener, S. Scheuring, K. Schulten. “Light harvesting by lamellar chromatophores in Rhodospirillum photometricum.” Biophys J. 106(11), 2503–2510. DOI: 10.1016/j.bpj.2014.04.030 (2014).
  21. E.M. Johnson-Chavarria, U. Agrawal, M. Tanyeri, T.E. Kuhlman, C.M. Schroeder, “Automated single cell microbioreactor for monitoring intracellular dynamics and cell growth in free solution.” Lab Chip. 14(15), 2688–2697. DOI: 10.1039/c4lc00057a (2014).
  22. G.-Q. Tang, D. Nandakumar, R.P. Bandwar, K.S. Lee, R. Roy, T. Ha, and S.S. Patel, “Relaxed rotational and scrunching changes in P266L mutant of T7 RNA polymerase reduces short abortive RNAs while delaying transition into elongation.” PLoS ONE. 9(3):e91859. DOI: 10.1371/journal.pone.0091859 (2014).
  23. H. Kim, S.C. Abeysirigunawardena, K. Chen, M. Mayerle, K. Ragunathan, Z. Luthey-Schulten, T. Ha, S.A. Woodson. “Protein-guided RNA dynamics during early ribosome assembly.” Nature. 23(13), 4449–4460. DOI: 10.1038/nature13039 (2014).
  24. H. Koh, L. Xing, L. Kleiman, S. Myong, “Repetitive RNA unwinding by RNA helicase A facilitates RNA annealing.” Nucleic Acid Res. 42(13), 8556–8564. DOI: 10.1093/nar/gku523 (2014).
  25. H. Hwang, P.L. Opresko, S. Myong, “Single-molecule real-time detection of telomerase extension activity.” Sci Rep. 4:6391. DOI: 10.1038/srep06391 (2014).
  26. I. Kosztin and K. Schulten. “Structure, function, and quantum dynamics of pigment-protein complexes.” In M. Mohseni, Y. Omar, G. Engel, M.B. Plenio, Eds. Quantum Effects in Biology. Cambridge University Press. 123–143. (2014).
  27. I. Solov’yov, P.J. Hore, T. Ritz, K. Schulten. “A chemical compass for bird navigation.” In M. Mohseni, Y. Omar, G. Engel, M.B. Plenio, Eds. Quantum Effects in Biology. Cambridge University Press. 218–236. (2014).
  28. I. Solov'yov, T. Domratcheva, K. Schulten. “Separation of photo-induced radical pair in cryptochrome to a functionally critical distance.” Sci Rep. 4:3845. DOI: 10.1038/srep03845 (2014).
  29. J.B. Budhathoki, S. Ray, V. Urban, P. Janscak, J.G. Yodh, H. Balci. “RecQ-core of BLM unfolds telomeric G-quadruplex in the absence of ATP.” Nucleic Acids Res. 42(18), 11528–11545. DOI:10.1093/nar/gku856 (2014).
  30. J. Cole, M. J. Hallock, P. Labhsetwar, J. R. Peterson, J. E. Stone, Z. Luthey-Schulten. “Stochastic simulations of cellular processes: From single cells to colonies.”In A. Kriete and R. Eils, Eds. Computational Systems Biology: From Molecular Mechanisms to Disease 2nd Ed. Elsevier. (2014).
  31. J. Cole and Z. Luthey-Schulten, “Whole cell modeling: from single cells to colonies." Isr J Chem. 54:8-9, 1219–1229. DOI:10.1002/ijch.201300147 (2014).
  32. J. Peterson, P. Labhsetwar, J. R. Ellermeier, P. R.A. Kohler, A. Jain, T. Ha, W. W. Metcalf, Z. A. Luthey-Schulten. “Towards a computational model of a methane producing archaeum.” Archaea. 2014:898453. DOI:10.1155/2014/898453 (2014).
  33. J. Zhang, R. Zhou, J. Inoue, T. Mikawa, T. Ha, “Single molecule analysis of Thermus thermophilus SSB protein dynamics on single-stranded DNA.” Nucleic Acids Res. 42(6), 3821–3832. (2014).
  34. K. S. Lee, A. B. Marciel, A. G. Kozlov, C. M. Schroeder, T. M. Lohman, T. Ha, “Ultrafast redistribution of E. coli SSB along long single-stranded DNA via intersegment transfer.” J Mol Bio. 426(13), 2413–2421. DOI: 10.1016/j.jmb.2014.04.023 (2014).
  35. L. Vukovic, H. R. Koh, S. Myong, K. Schulten. “Substrate recognition and specificity of double-stranded RNA binding proteins.” Biochemistry. 53(21), 3457–3466. DOI: 10.1021/bi500352s (2014).
  36. M. Bednarz, J.A. Halliday, C. Herman, I. Golding. “Revisiting Bistability in the Lysis/Lysogeny Circuit of Bacteriophange Lambda.” PloS ONE. 9(6), e100876. DOI: 10.1371/journal.pone.0100876 (2014).
  37. M. L. Cartron, J. D. Olsen, M. Sener, P. J. Jackson, A. A. Brindley, P. Qian, M. J. Dickman, G. J. Leggett, K. Schulten, C. N. Hunter. “Integration of energy and electron transfer processes in the photosynthetic membrane of Rhodobacter sphaeroides.” BBA – Bioenergetics. 1837(10), 1769–1780. DOI: 10.1016/j.bbabio.2014.02.003 (2014).
  38. P. J. Mears, S. Koirala, C. V. Rao, I. Golding, Y. R. Chemla. Escherichia coli swimming is robust against variations in flagellar number.” eLife. 3:e01916. DOI: 10.7554/eLife.01916 (2014).
  39. R. Tippana, W. Xiao, S. Myong, “G-quadruplex conformation and dynamics are determined by loop length and sequence.” Nucleic Acid Res. (2014) 42(12), 8106–8114. DOI: 10.1093/nar/gku464
  40. R. Zhou, J. Zhang, M.L. Bochman, V.A. Zakian, and TJ Ha. “Periodic DNA patrolling underlies diverse functions of Pif1 on R-loops and G-rich DNA.” eLife. 3:e02190. DOI: 10.7554/eLife.02190 (2014)
  41. S. Hayashi and K. Schulten. “Quantum biology of retinal.” In M. Mohseni, Y. Omar, G. Engel, M.B. Plenio, Eds. Quantum Effects in Biology. Cambridge University Press. 237–263. (2014).
  42. S. J. Lee, S. Syed, E. J. Enemark, S. Schuck, A. Stenlund, T. Ha, L. Joshua-Tor. “Dynamic look at DNA unwinding by a replicative helicase.” Proc Natl Acad Sci U S A. 111(9), E827–E835. DOI: 10.1073/pnas.1322254111 (2014).
  43. S. Syed, M. Pandey, S. S. Patel, T. Ha, “Single-molecule fluorescence reveals the unwinding stepping mechanism of replicative helicase.” Cell Rep. 6(6), 1037–1045. DOI: 10.1016/j.celrep.2014.02.022 (2014).
  44. Y. Liu, M. B. Prigozhin, K. Schulten, M. Gruebele, “Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment.” J Am Chem Soc. 136(11), 4265–4272. DOI: 10.1021/ja412639u (2014).
  45. Y. Wang, H. DeBerg, Y. Liu, T. Nomura, M. Tonks-Hoffman, P. Rohde, K. Schulten, B. Martinac and P. R. Selvin. “Single molecule FRET reveals the pore size and opening mechanism for mechanosensitive channel of large conductance,” eLife. 3:e01834. DOI: 10.7554/eLife.01834 (2014).
  46. Y. Tan, A. Tajik, J. Chen, Q. Jia, F. Chowdhury, L. Wang, J. Chen, S. Zhang, Y. Hong, H. Yi, D. Wu, Y. Zhang, F Wei, Y.-C. Poh, R. Singh, J. Seong, L.-J. Lin, S. Doğanay, Y. Li, H. Jia, T. Ha, Y. Wang, B. Huang and N. Wang, “Matrix softness regulates plasticity of tumor-repopulating cells via H3K9 demethylation and Sox2 expression.” Nat Commun. 5:4619. DOI:10.1038/ncomms5619 (2014).