CPLC Publications

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2015

  1. J.R Peterson, J.A. Cole, J. Fei, T. Ha, Z.A. Luthey-Schulten. “Effects of DNA replication on mRNA noise.” Proc Natl Acad Sci U S A. 112(52), 15886–15891. DOI: 10.1073/pnas.1516246112 (2015).
  2. H. Yu, W. Han, W. Ma, K. Schulten. “Transient ß-hairpin formation in a-synuclein monomer revealed by coarse-grained molecular dynamics simulation.” Nano Lett. 143(24): 243142. DOI: 10.1063/1.4936910 (2015).
  3. X. Wang, J. Sun, Q. Xu, F. Chowdhury, M. Roein-Peikar, Y. Wang, T. Ha. “Integrin molecular tension within motile focal adhesions.” Biophys J. 109(11), 2259–2267. DOI: 10.1016/j.bpj.2015.10.029 (2015).
  4. J. Zhang, 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. 5:17295. DOI: 10.1038/srep17295 (2015).
  5. M. Lu, G. Hou, H. Zhang, C.L Suiter, J. Ahn, I.J. Byeon, J.R. Perilla, C.J. Langmead, I. Hung, P.L. Gor'kov, Z. Gan, W. Brey, C. Aiken, P. Zhang, K. Schulten, A.M. Gronenborn, T. Polenova. “Dynamic allostery governs cyclophilin A-HIV capsid interplay.” Proc Natl Acad Sci U S A. 112(47), 14617–14622. DOI: 10.1073/pnas.1516920112 (2015).
  6. H. Qiu, A. Sarathy, J.P. Leburton, K. Schulten. “Intrinsic stepwise translocation of stretched ssDNA in graphene nanopores.” Nano Lett. 15(12), 8322–8330. DOI: 10.1021/acs.nanolett.5b03963 (2015).
  7. C.K. Cassidy, B.A. Himes, F.J. Alvarez, J. Ma, G. Zhao, J.R. Perilla, K. Schulten, P. Zhang. “CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling.” eLife. 4:e08419. DOI: 10.7554/eLife.08419 (2015).
  8. J Yoo and A. Aksimentiev. “Molecular dynamics of membrane-spanning DNA channels: conductance mechanism, electro-osmotic transport and mechanical gating.” J Phys Chem Lett. 6(23), 4680–4687. DOI: 10.1021/acs.jpclett.5b0196 (2015).
  9. H.R. Lee, J. Mitra, S. Lee, S.J. Gao, T.K. Oh, M.H. Kim, T. Ha, J.U. Jung. “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), 1139–1143. DOI: 10.1128/JVI.01897-15 (2015).
  10. S.K. Misra, G. Ghoshal, M.R. Gartia, Z. Wu, A.K. De, M. Ye, C.R. Bromfield, E.M. Williams, K. Singh, K.V. Tangella, L. Rund, K. Schulten, L.B. Schook, P.S. Ray, E.C. Burdette, D. Pan. “Trimodal therapy: combining hyperthermia with repurposed bexarotene and ultrasound for treating liver cancer.” ACS Nano. 9(11), 10695–10718. DOI: 10.1021/acsnano.5b05974 (2015).
  11. H. Tas, C.T. Nguyen, R. Patel, N.H. Kim, T.E Kuhlman. “An integrated system for precise genome modification in Escherichia coli.” PLoS ONE. 10(9): e0136963. DOI: 10.1371/journal.pone.0136963 (2015).
  12. D. Satory, A.J. Gordon, M. Wang, J.A. Halliday, I. Golding, C. Herman. “DksA involvement in transcription fidelity buffers stochastic epigenetic change.” Nucleic Acids Res. 43(21), 10190–10199. DOI: 10.1093/nar/gkv839 (2015).
  13. A. Kreig, J. Calvert, J. Sanoica, E. Cullum, R. Tipanna, S. Myong. “G-quadruplex formation in double strand DNA probed by NMM and CV fluorescence.” Nucleic Acids Res. 43(16), 7961–7970. DOI: 10.1093/nar/gkv749 (2015).
  14. X. Wang, L. Vukovic, H.R. Koh, K. Schulten, S. Myong. “Dynamic profiling of double-stranded RNA binding proteins.” Nucleic Acids Res. 43(15), 7566–7576. DOI: 10.1093/nar/gkv726 (2015).
  15. A. Khan, S. Giri, Y. Wang, A. Chakraborty, A.K. Ghosh, A. Anantharaman, V. Aggarwal, K.M. Sathyan, T. Ha, K.V. Prasanth, S.G. Prasanth. “BEND3 represses rDNA transcription by stabilizing a NoRC component via USP21 deubiquitinase.” Proc Natl Acad Sci U S A. 112(27), 8338–8343. DOI: 10.1073/pnas.1424705112 (2015).
  16. K. Girdhar, M. Gruebele, Y.R. Chemla. “The behavioral space of zebrafish locomotion and its neural network analog.” PLoS ONE. 10(7): e0128668. DOI: 10.1371/journal.pone.0128668 (2015)
  17. F. Chowdhury, I.T. Li, B.J. Leslie, S. Doganay, R. Singh, X. Wang, J. Seong, S.H. Lee, S. Park, N. Wang, T. Ha. “Single molecular force across single integrins dictates cell spreading.” Integr Biol (Camb). 7(10), 1265–1271. DOI: 10.1039/c5ib00080g (2015).
  18. B.C. Goh, J.R. Perilla, M.R. England, K.J. Heyrana, R.Craven, K. Schulten. “Atomic modeling of an immature retroviral lattice using molecular dymanics and mutagenesis.” Structure. 23(8), 1414–1425. DOI: 10.1016/j.str.2015.05.017 (2016).
  19. H. Xu, L.A. Sepúlveda, L. Figard, A.M. Sokac, I. Golding. “Combining protein and mRNA quantification to decipher transcriptional regulation.” Nat Methods. 12(8), 739–742. DOI: 10.1038/nmeth.3446 (2015).
  20. A.J. Wirth, Y. Liu, M.B. Prigozhin, K. Schulten, M. Gruebele. “Comparing fast pressure jump and temperature jump protein folding experiments and simulations.” J Am Chem Soc. 137(22), 7152–7159. DOI: 10.1021/jacs.5b02474 (2015).
  21. J.B. Budhathoki, E.J. Stafford, J.G. Yodh, H. Balci. “ATP-dependent G-quadruplex unfolding by Bloom helicase exhibits low processivity.” Nucleic Acids Res. 43(12), 5961–5970. DOI: 10.1093/nar/gkv531 (2015).
  22. M.T. Englander, J.L. Avins, R.C. Fleisher, B. Liu, P.R. Effraim, J. Wang, K. Schulten, T.S. Leyh, R.L. Gonzalez Jr, V.W. Cornish. “The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center.” Proc Natl Acad Sci U S A. 112(19), 6038–6043. DOI: 10.1073/pnas.1424712112 (2015).
  23. K.Y. Han and T. Ha. “Dual-color three-dimensional STED microscopy with a single high-repetition-rate laser.” Opt Lett. 40(11), 2653–2656. DOI: 10.1364/OL.40.002653 (2015).
  24. M. J. Comstock, K. D. Whitley, H. Jia, J. Sokoloski, T. M. Lohman, T.J. Ha, Y. R. Chemla. “Direct observation of structure-function relationship in a nucleic acid-processing enzyme.” Science. 348(6232), 352–354. DOI:10.1126/science.aaa0130 (2015).
  25. S. Arslan, R. Khafizov, C. D. Thomas, Y. R. Chemla, T.J. Ha. “Engineering of a superhelicase through conformational control.” Science. Vol. 348 no. 6232 pp. 344–347. DOI: 10.1126/science.aaa0445 (2015).
  26. J.R. Perilla, B.C. Goh, C.K. Cassidy, B. Liu, R.C. Bernardi, T. Rudack, H. Yu, Z. Wu, K. Schulten. “Molecular dynamics simulations of large macromolecular complexes.” Curr Opin Struct Biol. 31, 64–74. DOI: 10.1016/j.sbi.2015.03.007 (2015).
  27. T.T.M. Ngo and T. Ha. “Nucleosomes undergo slow spontaneous gaping.” Nucleic Acids Res. 43(8), 3964–3971. DOI: 10.1093/nar/gkv276 (2015).
  28. J. Fei, D. Singh, Q. Zhang,S. Park, D. Balaasubramanin, I. Golding, C.K. Vanderpool, T. Ha. “Determination of in vivo target search kinetics of regulatory noncoding RNA.” Science. 347(6228), 1371–1374. DOI:10.1126/science.1258849 (2015).
  29. J.A. Cole, L. Kohler, J. Hedhli, Z. Luthey-Schulten. “Spatially-resolved metabolic cooperativity within dense bacterial colonies.” BMC Syst Biol. 9:15. DOI: 10.1186/s12918-015-0155-1 (2015).
  30. A. Girdhar, C. Sathe, K. Schulten, J.P. Leburton. “Tunable graphene quantum point contact transistor for DNA detection and characterization.” Nanotechnology. 26(13):134005. DOI: 10.1088/0957-4484/26/13/134005 (2015).
  31. T.T.M. Ngo, Q. Zhang, R. Zhou, J.G. Yodh, T. Ha. “Asymmetric Unwrapping of Nucleosomes under Tension Directed by DNA Local Flexibility,” Cell. 160 (6), 1135–1144. DOI: 10.1016/j.cell.2015.02.001 (2015).
  32. M.P. Landry, L. Vukovic, S. Kruss, G. Bisker, A.M. Landry, S. Islam, R. Jain, K. Schulten, M.S. Strano. “Comparative dynamics and sequence dependence of DNA and RNA binding to single walled carbon nanotubes.” J Phys Chem C Nanomater Interfaces. 119(18), 10048–10058. DOI: 10.1021/jp511448e (2015).
  33. T.J. Kim, C. Joo, J. Seong, R. Vafabakhsh, E.L. Botvinick, M.W. Berns, A.E. Palmer, N. Wang, T. Ha, E. Jakobsson, J. Sun, Y. Wang. “Distinct mechanisms regulating mechanical force-induced Ca2+ signals at the plasma membrane and the ER in human MSCs.” eLife. 4:e04876. DOI: 10.7554/eLife.04876 (2015).
  34. W. Ma and K. Schulten. “Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution.” J Am Chem Soc. 137(8), 3031–3040. DOI: 10.1021/ja512605w (2015).
  35. C.Y. Li, E.A. Hemmig, J. Kong, J. Yoo, S. Hernández-Ainsa, U.F. Keyser, A. Aksimentiev. “Ionic conductivity, structural deformation, and programmable anisotropy of DNA origami in electric field.” ACS Nano. 9(2), 1420–1433. DOI: 10.1021/nn505825z (2015).
  36. S.H. Kim, J. Park, C. Joo, D. Kim, T. Ha. “Dynamic growth and shrinkage govern the pH dependence of RecA filament stability.” PLoS ONE. 10(1): e0115611. DOI: 10.1371/journal.pone.0115611 (2015).
  37. D.J. Hardy, Z. Wu, J.C. Phillips, J.E. Stone, R.D. Skeel, K. Schulten. “Multilevel summation method for electrostatic force evaluation.” J Chem Theory Comput. 11(2), 766–779. DOI: 10.1021/ct5009075 (2015).
  38. M. Fraiberg, O. Afanzar, C.K. Cassidy, A. Gabashvili, K. Schulten, Y. Levin, M. Eisenbach. “CheY's acetylation sites responsible for generating clockwise flagellar rotation in Escherichia coli.” Mol Microbiol. 95(2), 231–244. DOI: 10.1111/mmi.12858 (2015).
  39. A.M. Barragan, A.R. Crofts, K. Schulten, I.A. Solov'yov. “Identification of ubiquinol binding motifs at the Qo-site of the cytochrome bc1 complex.” J Phys Chem B. 119(2), 433–447. DOI: 10.1021/jp510022w (2015).