CPLC Publications

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2015

  1. Arslan, S., Khafizov, R., Thomas, C.D., Chemla, Y.R., Ha, T.J.. “Engineering of a superhelicase through conformational control." Science. 348(6232), 344–347DOI: 10.1126/science.aaa0445 (2015).
  2. Barragan, A.M., Crofts, A.R., Schulten, K., Solov'yov, I.A. “Identification of ubiquinol binding motifs at the Qo-site of the cytochrome bc1 complex." J Phys Chem B. 119(2), 433–447DOI: 10.1021/jp510022w (2015).
  3. Budhathoki, J.B., Stafford, E.J., Yodh, J.G., Balci, H. “ATP-dependent G-quadruplex unfolding by Bloom helicase exhibits low processivity." Nucl Acids Res. 43(12), 5961–5970DOI: 10.1093/nar/gkv531 (2015).
  4. Cassidy, C.K., Himes, B.A., Alvarez, F.J., Ma, J., Zhao, G., Perilla, J.R., Schulten, K., Zhang, P. “CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling." eLife. 4, e08419DOI: 10.7554/eLife.08419 (2015).
  5. Chowdhury, F., Li, L.T., Leslie, B.J., Doganay, S., Singh, R., Wang, X., Seong, J., Lee, S.H. Park, S., Wang, N., Ha, T. “Single molecular force across single integrins dictates cell spreading." Integr Biol (Camb). 7(10), 1265–1271DOI: 10.1039/c5ib00080g (2015).
  6. Cole, J.A., Kohler, L., Hedhli, J., Luthey-Schulten, Z. “Spatially-resolved metabolic cooperativity within dense bacterial colonies." BMC Syst Biol. 9(15DOI: 10.1186/s12918-015-0155-1 (2015).
  7. Comstock, M. J., Whitley, K.D., Jia, J., Sokoloski, J., Lohman, T.M., Ha, T.J., Chemla, Y.R.. “Direct observation of structure-function relationship in a nucleic acid-processing enzyme." Science. 348(6232), 352–354DOI:10.1126/science.aaa0130 (2015).
  8. Englander, M.T., Avins, J.L., Fleisher, R.C., Liu, B. Effraim, P.R., Wang, J., Schulten, K., Leyh, T.S., Gonzalez Jr, R.L., Cornish, V.W.. “The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center." Proc Natl Acad Sci U S A. 112(19), 6038–6043DOI: 10.1073/pnas.1424712112 (2015).
  9. Fei, J., Singh, D., Zhang, Q., Park, S., Balaasubramanin, D., Golding, I., Vanderpool, C.K., Ha, T. “Determination of in vivo target search kinetics of regulatory noncoding RNA." Science. 347(6228), 1371–1374DOI:10.1126/science.1258849 (2015).
  10. Fraiberg, M., Afanzar, O., Cassidy, C.K., Gabashvili, A., Schulten, K., Levin, Y., Eisenbach, M. “CheY's acetylation sites responsible for generating clockwise flagellar rotation in Escherichia coli." Mol Microbiol. 95(2), 231–244DOI: 10.1111/mmi.12858 (2015).
  11. Girdhar, A., Sathe, C., Schulten, K., Leburton, J.P.. “Tunable graphene quantum point contact transistor for DNA detection and characterization." Nanotechnology 26(13), 134005DOI: 10.1088/0957-4484/26/13/134005 (2015).
  12. Girdhar, K., Gruebele, M., Chemla, Y.R.. “The behavioral space of zebrafish locomotion and its neural network analog." PLoS ONE. 10(7), e0128668DOI: 10.1371/journal.pone.0128668 (2015).
  13. Han, K.Y., Ha, T.. “Dual-color three-dimensional STED microscopy with a single high-repetition-rate laser." Opt Lett. 40(11), 2653–2656DOI: 10.1364/OL.40.002653 (2015).
  14. Hardy, D.J., Wu, Z., Phillips, J.C., Stone, J.E., Skeel, R.D., Schulten, K. “Multilevel summation method for electrostatic force evaluation." J Chem Theory Comput. 11(2), 766–779DOI: 10.1021/ct5009075 (2015).
  15. Khan, A., S. Giri, S., Wang, Y., Chakraborty, A., Ghosh, A.K., Anantharaman, A., V. Aggarwal, V., Sathyan, K.M., Ha, T., Prasanth, K.V., Prasanth, S.G.. “BEND3 represses rDNA transcription by stabilizing a NoRC component via USP21 deubiquitinase." Proc Natl Acad Sci USA. 112(27), 8338–8343DOI: 10.1073/pnas.1424705112 (2015).
  16. Kim, S.H., Park, J., Joo, C., Kim, D., Ha, T.. “Dynamic growth and shrinkage govern the pH dependence of RecA filament stability." PLoS ONE. 10(1), e0115611DOI: 10.1371/journal.pone.0115611 (2015).
  17. Kim, T.J., Joo, C., Seong, J., Vafabakhsh, R., Botvinick, E.L., Berns, M.W., Palmer, A.E., Wang, N., Ha, T., Jakobsson, E., Sun, J., Wang, Y. “Distinct mechanisms regulating mechanical force-induced Ca2+ signals at the plasma membrane and the ER in human MSCs." eLife. 4, e04876DOI: 10.7554/eLife.04876 (2015).
  18. Kreig, A., Calvert, J., Sanoica, J., Cullum, E., Tipanna, R., Myong, S. “G-quadruplex formation in double strand DNA probed by NMM and CV fluorescence." Nucl Acids Res. 43(16), 7961–7970DOI: 10.1093/nar/gkv749 (2015).
  19. Landry, M.P., Vukovic, L. Kruss, S., Bisker, G., Landry, A.M., Islam, S., Jain, R., Schulten, K., Strano, M.S.. “Comparative dynamics and sequence dependence of DNA and RNA binding to single walled carbon nanotubes." J Phys Chem C Nanomater Interfaces. 119(18), 10048–10058DOI: 10.1021/jp511448e (2015).
  20. Lee, H.R., Mitra, J., Lee, S., Gao, S.J., Oh, T.K., Kim, M.H., Ha, T., Jung, J.E.. “Kaposi's sarcoma-associated herpesvirus viral interferon regulatory factor 4 (vIRF4) perturbs the G1-S cell cycle progression via deregulation of the cyclin D1 gene." J Virol. 90(2), 1139–1143DOI: 10.1128/JVI.01897-15 (2015).
  21. Li, C.Y., Hemmig, E.A., Kong, J., Yoo, J., Hernández-Ainsa, S., Keyser, U.F., Aksimentiev, A. “Ionic conductivity, structural deformation, and programmable anisotropy of DNA origami in electric field." ACS Nano. 9(2), 1420–1433DOI: 10.1021/nn505825z (2015).
  22. Lu, M., Hou, G., Zhang, H., Suiter, C.L.,. Ahn, J., Byeon, I.J., Perilla, J.R., Langmead, C.J., Hung, I., Gor'kov, P.L., Gan, Z., Brey, W., Aiken, C., Zhang, P., Schulten, K., Gronenborn, A.M., Polenova, T. “Dynamic allostery governs cyclophilin A-HIV capsid interplay." Proc Natl Acad Sci U S A. 112(47), 14617–14622DOI: 10.1073/pnas.1516920112 (2015).
  23. Ma, W., Schulten, K. “Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution." J Am Chem Soc. 137(8), 3031–3040DOI: 10.1021/ja512605w (2015).
  24. Misra, S.K., Ghoshal, G., Gartia, M.R., Wu, Z., De, A.K., Ye, M., Bromfield, C.R., Williams, E.M., Singh, K., Tangella, K.V., Rund, L., Schulten, K., Schook, L.B., Ray, P.S., Burdette, E.C., Pan, D. “Trimodal therapy: combining hyperthermia with repurposed bexarotene and ultrasound for treating liver cancer." ACS Nano. 9(11), 10695–10718DOI: 10.1021/acsnano.5b05974 (2015).
  25. Ngo, T.T.M., Ha, T. “Nucleosomes undergo slow spontaneous gaping." Nucleic Acids Res. 43(8), 3964–3971DOI: 10.1093/nar/gkv276 (2015).
  26. Ngo, T.T.M., Zhang, Q., Zhou, R., Yodh, J.G., Ha, T.. “Asymmetric Unwrapping of Nucleosomes under Tension Directed by DNA Local Flexibility," Cell. 160 (6), 1135–1144DOI: 10.1016/j.cell.2015.02.001 (2015).
  27. Perilla, J.R., Goh, B.C., Cassidy, C.K., Liu, B. Bernardi, R.C., Rudack, T., Yu, H., Wu, Z., Schulten, K.. “Molecular dynamics simulations of large macromolecular complexes." Curr Opin Struct Biol. 31, 64–74DOI: 10.1016/j.sbi.2015.03.007 (2015).
  28. Peterson, J.R., Cole, J.A., Fei, J., Ha, T., Luthey-Schulten, Z.A.. “Effects of DNA replication on mRNA noise." Proc Natl Acad Sci U S A. 112(52), 15886–15891DOI: 10.1073/pnas.1516246112 (2015).
  29. Qiu, H., Sarathy, A., Leburton, J.P., Schulten, K.. “Intrinsic stepwise translocation of stretched ssDNA in graphene nanopores." Nano Lett. 15(12), 8322–8330DOI: 10.1021/acs.nanolett.5b03963 (2015).
  30. Satory, D., Gordon, A. J., Wang, M., Halliday, J.A., Golding, I., Herman, C.. “DksA involvement in transcription fidelity buffers stochastic epigenetic change." Nucl Acids Res. 43(21), 10190–10199DOI: 10.1093/nar/gkv839 (2015).
  31. Tas, H., Nguyen, C.T., Patel, R., Kim, N.H., Kuhlman, T.E.. “An integrated system for precise genome modification in Escherichia coli." PLoS ONE. 10(9), e0136963DOI: 10.1371/journal.pone.0136963 (2015).
  32. Wang, X., Sun, J., Xu, Q., Chowdhury, F., Roein-Peikar, M., Wang, Y., Ha, T.. “Integrin molecular tension within motile focal adhesions." Biophys J. 109(11), 2259–2267DOI: 10.1016/j.bpj.2015.10.029 (2015).
  33. Wang, X., Vukovic, L., Koh, H.R., Schulten, K., Myong, S.. “Dynamic profiling of double-stranded RNA binding proteins." Nucl Acids Res. 43(15), 7566–7576DOI: 10.1093/nar/gkv726 (2015).
  34. Wirth, A.J., Liu, Y., Prigozhin, M.B., Schulten, K., Gruebele, M.. “Comparing fast pressure jump and temperature jump protein folding experiments and simulations." J Am Chem Soc. 137(22), 7152–7159DOI: 10.1021/jacs.5b02474 (2015).
  35. Xu, H., Sepúlveda, L.A., Figard, L., Sokac, A.M., Golding, I. “Combining protein and mRNA quantification to decipher transcriptional regulation." Nat Methods. 12(8), 739–742DOI: 10.1038/nmeth.3446 (2015).
  36. Yoo, J., Aksimentiev, A. “Molecular dynamics of membrane-spanning DNA channels: conductance mechanism, electro-osmotic transport and mechanical gating." J Phys Chem Lett. 6(23), 4680–4687DOI: 10.1021/acs.jpclett.5b01964 (2015).
  37. Yu, H., Han, W., Ma, W., Schulten, K. “Transient ß-hairpin formation in a-synuclein monomer revealed by coarse-grained molecular dynamics simulation." Nano Lett. 143(24): 243142DOI: 10.1063/1.4936910 (2015).
  38. Zhang, J., J. Fei, B.J. Leslie, K.Y. Han, T.E. Kuhlman, T. Ha. “Tandem spinach array for mRNA imaging in living bacterial cells." Sci Rep. 5, 17295DOI: 10.1038/srep17295 (2015).