CPLC Publications

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2014

  1. Aghtar, M., Strümpfer, J., Olbrich, C, Schulten, K., Kleinekathöfer, U.. “Different types of vibrations interacting with electronic excitations in Phycoerythrin 545 and Fenna-Matthews-Olson Antenna Systems." J Phys Chem Lett. 5(18), 3131–3137DOI: 10.1021/jz501351p (2014).
  2. Bednarz, M., Halliday, J.A., Herman, C. Golding, I.. “Revisiting bistability in the lysis/lysogeny circuit of bacteriophange lambda." PloS ONE. 9(6), e100876DOI: 10.1371/journal.pone.0100876 (2014).
  3. Bhattacharyya, B., George, N.P., Thurmes, T.M., Zhou, R., Jani, N., Wessel, S.R., Sandler, S.J., Ha, T., Keck, J.L. “Structural mechanisms of PriA-mediated DNA replication restart." Proc Natl Acad Sci U S A. 111(4), 1373–1378DOI: 10.1073/pnas.1318001111 (2014).
  4. Blehm, B. H., Selvin, P.R.. “Single-molecule fluorescence and in vivo optical traps: How Mmltiple dyneins and kinesins interact." Chem Rev. 114(6), 3335–3352DOI: 10.1021/cr4005555 (2014).
  5. Budhathoki, J.B., Ray, S., Urban, V., Janscak, P., Yodh, J.G., Balci, H. “RecQ-core of BLM unfolds telomeric G-quadruplex in the absence of ATP." Nucl Acids Res. 42(18), 11528–11545DOI:10.1093/nar/gku856 (2014).
  6. Cai, E., Ge, P., Lee, S.H., Jeyifous, O., Wang, Y., Liu, Y., Wilson, K.M., Lim, S.J., M.A. Baird, M.A., Stone, J.E., Lee, K.Y., Davidson, M.W., Chung H.J., Schulten, K., Smith, A.M., Green, W.N., Selvin, P.R.. “Stable small quantum dots for synaptic receptor tracking on live neurons."Angew Chem Int Ed. 53(46), 12484–12488DOI: 10.1002/anie.201405735 (2014).
  7. Cartron, M. L., Olsen, J.D., Sener, M., Jackson, P.J., Brindley, A.A., Qian, P., Dickman, M.J., Leggett, G.J., Schulten, K., Hunter, C.N.. “Integration of energy and electron transfer processes in the photosynthetic membrane of Rhodobacter sphaeroides." BBA – Bioenergetics. 1837(10), 1769–1780DOI: 10.1016/j.bbabio.2014.02.003 (2014).
  8. Chandler, D., Strumpfer, J., Sener, M., Scheuring, S., Schulten, K.. “Light harvesting by lamellar chromatophores in Rhodospirillum photometricum." Biophys J 106(11), 2503–2510DOI: 10.1016/j.bpj.2014.04.030 (2014).
  9. Chao, S.H., Matthews, S.S., Paxman, R., Aksimentiev, A., Gruebele, M., Price, J.L.. “Two structural scenarios for protein stabilization by PEG." J Phys Chem B. 118(28), 8388–8895DOI: 10.1021/jp502234s (2014).
  10. Cole, J., Hallock, M.J., Labhsetwar, P., Peterson, J.R., Stone, J.E., Luthey-Schulten, Z.. “Whole cell modeling: from single cells to colonies." Isr J Chem. 54(8-9), 1219–1229DOI:10.1002/ijch.201300147 (2014).
  11. Girdhar, A., Sathe, C., Schulten, K., Leburton, J.P. “Gate-modulated graphene quantum point contact device for DNA sensing." J Comput Electron. 13(4), 839–846DOI: 10.1007/s10825-014-0596-6 (2014).
  12. Ha, T., “Single-molecule methods leap ahead." Nat Methods 11(10), 1015–1018DOI: 10.1038/nmeth.3107 (2014).
  13. Han, W., Schulten, K.. “Fibril elongation by Aß(17-42): kinetic network analysis of hybrid-resolution molecular dynamics simulations." J Am Chem Soc 136(35), 12450–12460DOI: 10.1021/ja507002p (2014).
  14. Hayashi, S., Schulten, K. “Quantum biology of retinal." M. Mohseni, Y. Omar, G. Engel, M.B. Plenio, Eds. Quantum Effects in Biology. Cambridge University Press. 237–263DOI: 10.1017/CBO9780511863189 (2014).
  15. Hua, B., Han, K.Y., Zhou, R., Kim, H., Shi, X., Abeysirigunawardena, S.C., Jain, A., Singh, D., Aggarwal, V., Woodson, S.A., Ha, T. “An improved surface passivation method for single-molecule studies." Nat Methods 11(12), 1233–1236DOI: 10.1038/nmeth.3143 (2014).
  16. Hwang, H., Opresko, P.L., Myong, S. “Single-molecule real-time detection of telomerase extension activity." Sci Rep. 4, 6391DOI: 10.1038/srep06391 (2014).
  17. Jain, A., Arauz, E., Aggarwal, V., Ikon, N., Chen, J., Ha, T. “Stoichiometry and assembly of mTOR complexes revealed by single-molecule pulldown." Proc Natl Acad Sci USA. 111(50), 17833–17838DOI: 10.1073/pnas.1419425111 (2014).
  18. Johnson-Chavarria, E.M., Agrawal, U., Tanyeri, M., Kuhlman, T.E., Schroeder, C.M. “Automated single cell microbioreactor for monitoring intracellular dynamics and cell growth in free solution." Lab Chip. 14(15), 2688–2697DOI: 10.1039/c4lc00057a (2014).
  19. Kim, H., Abeysirigunawardena, S.C., Chen, K., Mayerle, M., Ragunathan, K., Luthey-Schulten, Z., Ha, T., Woodson, S.A.. “Protein-guided RNA dynamics during early ribosome assembly." Nature. 23(13), 4449–4460DOI: 10.1038/nature13039 (2014).
  20. Kim, S.H., Ragunathan, K., Park, J., Joo, C., Kim, D., Ha, T. “Cooperative conformational transitions keep RecA filament active during ATPase cycle." J Am Chem Soc. 136(42), 14796–14800DOI: 10.1021/ja506363y (2014).
  21. Koh, H., Xing, L,. Kleiman, L., Myong, S. “Repetitive RNA unwinding by RNA helicase A facilitates RNA annealing." Nucl Acid Res. 42(13), 8556–8564DOI: 10.1093/nar/gku523 (2014).
  22. Kondabagil, K., Dai, L., Vafabakhsh, R., Ha, T., Draper, B., Rao, V.B. “Designing a nine cysteine-less DNA packaging motor from bacteriophage T4 reveals new insights into ATPase structure and function." Virology, 468, pp. 660-668DOI: 10.1016/j.virol.2014.08.033 (2014).
  23. Kosztin, I., Schulten, K. “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, 123–143DOI: 10.1017/CBO9780511863189 (2014).
  24. Lee, K. S., Marciel, A.B., Kozlov, A.G., Schroeder, C.M., Lohman, T.M., Ha, T. “Ultrafast redistribution of E. coli SSB along long single-stranded DNA via intersegment transfer." J Mol Bio. 426(13), 2413–2421DOI: 10.1016/j.jmb.2014.04.023 (2014).
  25. Lee, S. J., Syed, S. Enemark, E.J., Schuck, S., Stenlund, A., Ha, T., Joshua-Tor, L. “Dynamic look at DNA unwinding by a replicative helicase." Proc Natl Acad Sci USA. 111(9), E827–E835DOI: 10.1073/pnas.1322254111 (2014).
  26. Liu, Y., Prigozhin, M.B., Schulten, K., Gruebele, M. “Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment." J Am Chem Soc. 136(11), 4265–4272DOI: 10.1021/ja412639u (2014).
  27. Maffeo, C., Ngo, T., Ha, T., Aksimentiev, A.. “A coarse-grained model of unstretched single-stranded DNA derived from atomistic simulation and single-molecule experiment." J. Chem Theory Comput 8(10), 2891–2896DOI: 10.1021/ct500193u (2014).
  28. Maffeo, C., Yoo, J., Comer, J., Wells, D.B. Luan, B. Aksimentiev, A.. “Close encounters with DNA." J Phys Condens Matter. 26(41): 413101DOI: 10.1088/0953-8984/26/41/413101 (2014).
  29. Mears, P. J., Koirala, S., Rao, C.V., Golding, I., Chemla, Y.R.. “Escherichia coli swimming is robust against variations in flagellar number." eLife 3, e01916DOI: 10.7554/eLife.01916 (2014).
  30. Peterson, J., Labhsetwar, P., Ellermeier, J.R., Kohler, P.R.A., Jain, A., Ha, T., Metcalf, W.W., Luthey-Schulten, Z.A.. “Towards a computational model of a methane producing archaeum." Archaea. 2014:898453DOI:10.1155/2014/898453 (2014).
  31. Prigozhin, M.B., Scott, G.E., Denos, S. “Mechanical modeling and computer simulation of protein folding" J Chem Educ. 91(11), 1939–1942DOI: 10.1021/ed400719c (2014).
  32. Sathe, C., Girdhar, A., Leburton, J.P., Schulten, K.. “Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores." Nanotechnol.. 25(44), 445105DOI: 10.1088/0957-4484/25/44/445105 (2014).
  33. Solov'yov, I., Domratcheva, T., Schulten, K. “Separation of photo-induced radical pair in cryptochrome to a functionally critical distance." Sci Rep. 4:3845DOI: 10.1038/srep03845 (2014).
  34. Solov’yov, I., Hore, P.J., Ritz, T., Schulten, K.. “A chemical compass for bird navigation." M. Mohseni, Y. Omar, G. Engel, M.B. Plenio, Eds. Quantum Effects in Biology. Cambridge University Press. 218–236DOI:10.1017/CBO9780511863189 (2014).
  35. Syed, S., M. Pandey, M., Patel, S.S., Ha, T. “Single-molecule fluorescence reveals the unwinding stepping mechanism of replicative helicase." Cell Rep. 6(6), 1037–1045DOI: 10.1016/j.celrep.2014.02.022 (2014).
  36. Tan, Y., A. Tajik, A., Chen, J., Jia, Q., Chowdhury, F., Wang, L., Chen, J., Zhang, S., Hong, Y., Yi, H., Wu, D., Zhang, Y.,Wei, F., Poh, Y.-C., Singh, R., Seong, J., Lin, L.-J., Doganay, S., Li, Y., Jia, H., Ha, T., Wang, Y., Huang, B., Wang, N. “Matrix softness regulates plasticity of tumor-repopulating cells via H3K9 demethylation and Sox2 expression." Nat Commun. 5, 4619DOI: 10.1038/ncomms5619 (2014).
  37. Tang, G.-Q., Nandakumar, D., Bandwar, R.P., Lee, K.S., Roy, R., Ha, T., Patel, S.S. “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), e91859DOI: 10.1371/journal.pone.0091859 (2014).
  38. Thibodeaux, C.J., Ha, T., Van Der Donk, W.A. “A price to pay for relaxed substrate specificity: A comparative kinetic analysis of the class II lanthipeptide synthetases ProcM and HalM2." J Am Chem Soc, 136(50) 17513-17529DOI: 10.1021/ja5089452 (2014).
  39. Tippana, R., Xiao, W., Myong, S. “G-quadruplex conformation and dynamics are determined by loop length and sequence." Nucl Acid Res. 42(12), 8106–8114DOI: 10.1093/nar/gku464 (2014).
  40. Vafabakhsh, R., Kondabagil, K., Earnest, T., Lee, K.S., Zhang, Z., Dai, L., Dahmen, K.A., Rao, V.B., Ha, T. “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), 15096–15101DOI: 10.1073/pnas.1407235111 (2014).
  41. Vukovic, L., Koh, H.R., Myong, S., Schulten, K.. “Substrate recognition and specificity of double-stranded RNA binding proteins." Biochemistry. 53(21), 3457–3466DOI: 10.1021/bi500352s (2014).
  42. Wang, Y., Cai, E., Rosenkranz, T., Ge, P., Teng, K.W., Lim, S.J., Smith, A.M., Chung, H.J., Sachs, F., Green, W.N., Gottlieb, P., Selvin, P.R.. “Small quantum dots conjugated to nanobodies as immunofluorescence probes for nanometric microscopy." Bioconjug Chem. 25(12), 2205–2211DOI: 10.1021/bc5004179 (2014).
  43. Wang, Y., Cai, E., Sheung, J., Lee, S.H., Teng, K.W., Selvin, P.R.. “Fluorescence imaging with one-nanometer accuracy (FIONA)." J Vis Exp. 91, 51774DOI: 10.3791/51774 (2014).
  44. Wang, Y., DeBerg, H., Liu, Y., Nomura, T., Tonks-Hoffman, M., Rohde, P., Schulten, K., Martinac, B. Selvin, P.R.. “Single molecule FRET reveals the pore size and opening mechanism for mechanosensitive channel of large conductance," eLife. 3, e01834DOI: 10.7554/eLife.01834 (2014).
  45. Wu, Z., Schulten, K.. “Synaptotagmin's role in neurotransmitter release likely involves Ca(2+)-induced conformational transition." Biophys J. 107(5), 1156–1166DOI: 10.1016/j.bpj.2014.07.041 (2014).
  46. Zhang, J., Zhou, R., Inoue, J., Mikawa, T., Ha, T. “Single molecule analysis of Thermus thermophilus SSB protein dynamics on single-stranded DNA." Nucl Acids Res. 42(6), 3821–3832DOI: 10.1093/nar/gkt1316 (2014).
  47. Zhou, R., Zhang, J., Bochman, M.L., Zakian, V.A., Ha, T. “Periodic DNA patrolling underlies diverse functions of Pif1 on R-loops and G-rich DNA." eLife. 3, e02190DOI: 10.7554/eLife.02190 (2014).