CPLC Publications

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  1. Abeysirigunawardena, S.C., Kim, H., Lai, J., Ragunathan, K., Rappe, M.C., Luthey-Schulten, Z., Ha, T., Woodson, S.A.. “Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes." Nature Commun, 8(1), 492DOI: 10.1038/s41467-017-00536-1 (2017).
  2. Cole, J.A., Luthey-Schulten, Z. “A careful accounting of extrinsic noise in protein expression reveals correlations among its sources." Phys Rev E, 95(6), 062418DOI: 10.1103/PhysRevE.95.062418 (2017).
  3. Doganay, S., S., Lee, M.Y., Baum, A., Peh, J., Hwang, S.Y., Yoo, J.Y., Hergenrother, P.J., Garcia-Sastre, A., Myong, S., Ha, T. “Single-cell analysis of early antiviral gene expression reveals a determinant of stochastic IFNB1 expression." Integr. Biol. 9(11), 857-567DOI: 10.1039/c7ib00146k (2017).
  4. Englaender, J.A., Jones, J.A., Cress, B.F., Kuhlman, T.E., Linhardt, R.J., Koffas, M.A.G.. “Effect of genomic integration location on heterologous protein expression and metabolic engineering in E. coli." ACS Synth. Biol. 6(4), 710–720DOI: 10.1021/acssynbio.6b00350 (2017).
  5. Fei, J., Jadaliha, M., Harmon, T.S., Li, I.T.S., Hua, B., Hao, Q., Holehouse, A. S., Reyer, M., Sun, Q., Freier, S.M., Pappu, R.V., Prasanth, K.V., Ha, T. “Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution." J. Cell Sci. 130, 4180-4192DOI: 10.1242/jcs.206854 (2017).
  6. Fraebel, D.T., H. Mickalide, D. Schnitkey, J. Merritt, T.E. Kuhlman, S. Kuehn. “Environment determines evolutionary trajectory in a constrained phenotypic space." eLife 6, e24669DOI: 10.7554/eLife.24669 (2017).
  7. Ghaemi, Z., Guzman, I., Gnutt, D., Luthey-Schulten, Z., Gruebele, M.. “Role of electrostatics in protein-RNA binding: The global vs. the local energy landscape." J Phys Chem B, 121(36), 8437-8446DOI: 10.1021/acs.jpcb.7b04318 (2017).
  8. Labhsetwar, P., Melo, M.C.R., Cole, J.A., Luthey-Schulten, Z. “Population FBA predicts metabolic phenotypes in yeast." PLoS Computational Biology, 13(9), e1005728DOI: 10.1371/journal.pcbi.1005728 (2017).
  9. Lee, H. T., H.T., Bose, A., Lee, C.Y., Opresko, P.L., Myong, S. “Molecular mechanisms by which oxidative DNA damage promotes telomerase activity." Nucl. Acids Res. 45(20), 11752-11765DOI: 10.1093/nar/gkx789 (2017).
  10. Lee, S.H., Jin, C., Cai, E., Ge, P., Ishitsuka, Y., Teng, K.W., de Thomaz, A.A., Nall, D.L., Baday,M., Jeyifous, O., Demonte, D., Dundas, C.M., Park, S., Green, W.N., Selvin, P.R.. “Super-resolution imaging of synaptic and extra-synaptic pools of AMPA receptors with different- sized fluorescent probes." eLife 6, e27744DOI: 10.7554/eLife.27744 (2017).
  11. Li, I.T.S., Ha, T., Chemla, Y.R. “Mapping cell surface adhesion by rotation tracking and adhesion footprinting." Sci. Rep. 7, 44502DOI: 10.1038/srep44502 (2017).
  12. Lin, C.-T., Tritschler, F., Lee, K.S., Gu, M.G., Rice, C.M., Ha, T. “Single-molecule imaging reveals the translocation and DNA looping dynamics of hepatitis C virus NS3 helicase." Protein Sci. 45(20), 1391-1403DOI: 10.1002/pro.3136 (2017).
  13. Luca, V.C., Kim, B.C.., Ge, C., Kakuda, S., Wu, D., Roein-Peikar, M., Haltiwanger, R.S., Zhu, C., Ha, T., Garcia, K.C.. “Notch-jagged complex structure implicates a catch bond in tuning ligand sensitivity." Science 355(6331), 1320–1324DOI: 10.1126/science.aaf9739 (2017).
  14. Maffeo, C., Aksimentiev, A. “Molecular mechanism of DNA association with single-stranded DNA binding protein." Nucl Acids Res. 45, 12125–12139DOI: 10.1093/nar/gkx917(2017).
  15. Peterson, J.R., Cole, J.A., Luthey-Schulten, Z.. “Parametric studies of metabolic cooperativity in escherichia coli colonies: Strain and geometric confinement effects." PLoS ONE, 12(8), e0182570DOI: 10.1371/journal.pone.0182570 (2017).
  16. Qiu, Y., Levendosky, R.F., Chakravarthy, S., Patel, A., Bowman, G.D., Myong, S. “The Chd1 chromatin remodelers shifts nucleosomal DNA bidirectionally as a monomer." Mol. Cell. 68(1) 76-88DOI: 10.1016/j.molcel.2017.08.018 (2017).
  17. Singh, P., Ramachandran, S.K., Zhu, J., Kim, B.C., Biswas, D., Ha, T. Iglesias, P.A., Li, R. “Sphingolipids facilitate age asymmetry of membrane proteins in dividing yeast cells." Molec. Biol. Cell. 28(20) 2712-2722DOI: 10.1091/mbc.E17-05-0335 (2017).
  18. Sivaramakrishnan, P., Sepúlveda, L.A., Halliday, J.A., Liu, J., Núñez, M.A.B., Golding, I., Rosenberg, S.M., Herman, C. “The transcription fidelity factor GreA impedes DNA break repair." Nature 550(7675) 214DOI: 10.1038/nature23907 (2017).
  19. Sun, Y., Tortarolo, G., Teng, K.W., Ishitsuka, Y., Coskun, U.C., Liao, S.J., Diaspro, A., Vicidomini, G., Selvin, P.R., Barbieri, B. “A novel pulsed STED microscopy method using FastFLIM and the phasor plots." Proc. SPIE 10069, Multiphoton Microscopy in the Biomedical Sciences XVII, 100691C-1-16DOI:10.1117/12.2267880. (2017).
  20. Zanetti-Polzi, L., Davis, C.M., Gruebele, M., Dyer, R.B., Daidone, I. Amadei, A., Daidone, I. “Parallel folding pathways of Fip35 WW domain revealed by infrared spectra and their computer simulation." FEBS Lett. 591(20), 3265-3275DOI: 10.1002/1873-3468.12836 (2017).