CPLC Publications

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2018

  1. Alexander, E.J., Niaki, A. E., A. G., Zhang T., Sarkar J., Liu Y., Nirujogi R. S., Pandey A., Myong S., Wang J. “Ubiquilin 2 Modulates ALS/FTD-linked FUS-RNA Complex Dynamics and Stress Granule Formation”, Proc. Natl. Acad. Sci. USA, Dec 4; 115(49):E11485-E11494. " DOI: 10.1073/pnas.1811997115 (2018).
  2. Bensona, C. R., Maffeo, C., Fatilaa, E.M., Liu, Yun, Sheetz, E.G. Aksimentiev, A., Singharoy, A., Amar H. “Inchworm movement of two rings switching onto a thread by biased Brownian diffusion a three-body problem." Proc Natl Acad Sci. USA 115(38), 9391-9396DOI: 10.1073/pnas.1719539115 (2018).
  3. Bianchi, D.M., J.R. Peterson, T.M. Earnest, M.J. Hallock, and Z. Luthey-Schulten. “A hybrid CME-ODE method for efficient simulation of the galactose switch in yeast." IET Systems Biology, 12(4) 170-176DOI: 10.1049/iet-syb.2017.0070 (2018).
  4. Breuer, M., Earnest, T.M., Merryman, C. Wise, K.S., Sun, L., Lynott, M.R., Hutchison III, C.A., Smith, H.O., Lapek Jr., J.D., Gonzalez, D.J., de Crecy-Lagard, V., Haas, D., Hanson, A.D., Labhsetwar, P., Glass, J.I., Luthey-Schulten, Z. “Essential metabolism for a minimal cell." eLife 18(8), e36842DOI: 10.7554/eLife.36842 (2018).
  5. Chen, M. C., Tippana R., Demeshkina N. A., Murat P., Balasubramanian S., Myong S., Ferré-D'Amaré A. R. “Structural basis of G-quadruplex unwinding by the DEAH/RHA helicase DHX36." Nature. Jun; 558(7710), 465-469DOI: 10.1038/s41586-018-0209-9 (2018).
  6. Davis, C., L. Zanetti-Polzi, M. Gruebele, A. Amadei, R. B. Dyer and I. Daidone, “A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy." Chem. Sci. 9(48), 9002-9011DOI: 10.1039/C8SC03786H (2018).
  7. Davis, C., M. Gruebele. “Labeling for quantitative comparison of imaging measurements in vitro and in cells." Biochemistry 57, 1929-1938DOI: 10.1021/acs.biochem.8b00141 (2018).
  8. Davis, C.M., Gruebele, M. “Non-steric interactions predict the trend and steric interactions the offset of protein stability in cells." ChemPhysChem, 19(18), 2290-2294DOI: 10.1002/cphc.201800534 (2018).
  9. Davis, C. M., Gruebele, M., Sukenik, S. “How does solvation in the cell affect protein folding and binding?" Curr Op Struct Biol. 48, 23-29DOI: 10.1016/j.sbi.2017.09.003 (2018).
  10. Delgado, J.Y., Selvin, P.R. “A revised view on the role of surface AMPAR mobility in tuning synaptic transmission: limitations, tools, and alternative views." Frontiers in Neuroscience, Vol. 10, article 21 pp 1-12DOI: 10.3389/fnsyn.2018.00021 (2018).
  11. Earnest, T.M., J.A. Cole, and Z. Luthey-Schulten. “Simulating biological processes: Stochastic physics from whole cells to colonies." Rep.Prog Phys. 81(5), 052601DOI:10.1088/1361-6633/aaae2c (2018).
  12. Figiel, M., Krepl, M., Park, S., Poznanski, J., Skowronek, K., Golab, A., Ha, T., Šponer, J., Nowotny, M. “Mechanism of polypurine tract primer generation by HIV-1 reverse transcriptase." J Biol Chem. 293, 191-202DOI: 10.1074/jbc.M117.798256 (2018).
  13. Gapinske, M., Luu, A., Winter, J., Woods, W.S., Kostan, K.A., Shiva, N., Song, J.S., Perez-Pinera, P.. “CRISPR-SKIP: Programmable gene splicing with single base editors." Genome Biol. 19, 107DOI: 10.1186/s13059-018-1482-5 (2018).
  14. Golding, I. “Infection by bacteriophage lambda: An evolving paradigm for cellular individuality." Curr Opin Microbiol. 43, 9-13DOI: 10.1016/J.MIB.2017.09.014 (2018).
  15. Hemmig, E.A., Fitzgerald, C., Maffeo, C., Hecker, L., Aksimentiev, A., Tinnefeld, P., Keyser, U.F. “Optical voltage sensing using DNA origami." Nano Lett. 18, 1962–1971DOI: 10.1021/acs.nanolett.7B05354 (2018).
  16. Hua, B., Panja, S., Wang, Y., Woodson, S.A., Ha, T. “Mimicking Co-Transcriptional RNA Folding Using a Superhelicase." J Am Chem Soc. 140(32) 10067-10070DOI: 10.1021/jacs.8b03784 (2018).
  17. Hua, B., Y. Wang, Park, S., Han, K.Y., Singh, D., Kim, J.H., Cheng, W., Ha, T. “The single-molecule centroid localization algorithm improves the accuracy of fluorescence binding assays." Biochem., 57 (10), pp 1572–1576DOI: 10.1021/acs.biochem.7b01293 (2018).
  18. Kang, H, Kang, H., Yoo, J., Sohn, B.-K., Lee, S.-W., Lee, H.S., Ma, W., Kee, J.-M., Aksimentiev, A., Kim, H. “Sequence-dependent DNA condensation as a driving force of DNA phase separation." Nucl Acids Res, 46 (18), pp. 9401-9413DOI: 10.1093/NAR/GKY639 (2018).
  19. Karig, D., Martini, K.M., Lu, T., DeLateur, N., Goldenfeld, N., Weiss, R. “Stochastic turing patterns in a synthetic bacterial population." Proc Natl Acad Sci. USA 115, 6572-6577DOI: 10.1073/pnas.1720770115 (2018).
  20. Kisley, L., Serrano, K.A., Davis, C.M., Guin, D., Murphy, E.A., Gruebele, M., Leckband, D.E. “Soluble zwitterionic poly(sulfobetaine) destabilizes proteins." Biomacromolecules 19(9), 3894-3901DOI: 10.1021/acs.biomac.8b01120 (2018).
  21. Koh, H., Myong S. “Single-cell imaging approaches for studying small RNA induced gene regulation." Biophys J. 115(2), 203-208DOI: 10.1016/J.BPJ.2018.05.040 (2018).
  22. Langdon, E. M., Qiu, Y., Niaki, A. G., McLaughlin G. A., Weidmann C., Gerbich, T. M., Smith J. A., Crutchley J. M., Termini C. M., Weeks K. M., Myong S., and Gladfelter A. S. “mRNA structure determines specificity of a polyQ-driven phase separation." Science 360(6391), 922-927DOI: 10.1126/science.aar7432 (2018).
  23. Lee, G., Sherer, N., Kim, N., Rajic, E., Kaur, D., Urriola, N., Martini, K.M., Xue, C., Goldenfeld, N., Kuhlman, T. “Testing the retroelement invasion hypothesis for the emergence of the ancestral eukaryotic cell." Proc Natl Acad Sci. USA 115(49), 12465-12470DOI: 10.1073/pnas.1807709115 (2018).
  24. Ma, W., Whitley, K.D., Chemla, Y.R., Luthey-Schulten, Z., Schulten, K. “Free energy simulations reveal molecular mechanism for functional switch of a DNA helicase." Elife 7, e34186DOI: 10.7554/eLife.34186 (2018).
  25. Melo, M.C.R., M.C.R., Bernardi, R.C., Rudack, T., Scheurer, M., Riplinger, C., Phillips, J.C., Maia, J.D.C., Rocha, G.B., Ribeiro, J.V., Stone, J.E., Neese, F., Schulten, K., Luthey-Schulten, Z. “NAMD goes quantum: An integrative suite for hybrid simulations." Nat Methods 15, 351-354DOI: 10.1038/nmeth.4638. (2018).
  26. Merritt, J., Kuehn, S. “Frequency and amplitude dependent microbial population dynamics during cycles of feast and famine." Phys Rev Lett. 121, 098101DOI: 10.1103/PhysRevLett.121.098101 (2018).
  27. Ohmann, A., Li, C.-Y., Maffeo, C., Al Nahas, K., Baumann, K.N., Göpfrich, K., Yoo, J., Keyser, U.F., Aksimentiev, A. “A synthetic enzyme built from DNA flips 107 lipids per second in biological membranes." Nat Commun, 9(1) 2426DOI: 10.1038/s41467-018-04821-5 (2018).
  28. Qiu, Y., Koh, H.R., Myong, S. “Probing dynamic assembly and disassembly of Rad51 tuned by Srs2 using smFRET." Methods Enzymol. 600, 321-345DOI: 10.1016/BS.MIE.2018.01.001 (2018).
  29. Reid, K.A., Davis, C.M., Dyer, R.B., Kindt, J.T. “Binding, folding and insertion of a ß-hairpin peptide at a lipid bilayer surface: Influence of electrostatics and lipid tail packing" Biochim Biophys Acta Biomembr, 1860(3), pp. 792-800DOI: 10.1016/j.bbamem.2017.12.019 (2018).
  30. Sarkar, J., Myong S. “Single-molecule and ensemble methods to probe initial stages of RNP granule assembly." Methods Molec Biol. 1814, 325-338DOI: 10.1007/978-1-4939-8591-3_19 (2018).
  31. Sheung, J.Y., Ge, P., Lim, S.J., Lee, S.H., Smith, A.M., Selvin, P.R.. “Structural contributions to hydrodynamic diameter for quantum dots optimized for live-cell single-molecule tracking." J Phys Chem C, 122(30), 17406–17412DOI: 10.1021/acs.jpcc.8b02516 (2018).
  32. Shih, H.Y., Mickalide, H., Fraebel, D.T., Goldenfeld, N., Kuehn, S. “Biophysical constraints determine the selection of phenotypic fluctuations during directed evolution." Phys Biol. 15(6), 065003DOI: 10.1088/1478-3975/aac4e6 (2018).
  33. Singh, C., Mallon, J., Poddar, A., Wang, Y.B., Tippana, R., Yang, O., Bailey, S., Ha, T. “Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a)." Proc Natl Acad Sci. USA. 115(21), 5444-5449DOI: 10.1073/pnas.1718686115 (2018).
  34. Singh, D., Ha, T. “Understanding the molecular mechanisms of the CRISPR toolbox using single molecule approaches." ACS Chem. Biol. 13(3) 516-526DOI: 10.1021/acschembio.7b00905 (2018).
  35. Singh, D., Wang, Y., Mallon, J., Yang, O., Poddar, A., Ceylan, D., Bailey, S., Ha, T. “Mechanisms of improved specificity of engineered Cas9s revealed by single-molecule FRET analysis." Nat Struct Mol Biol, 25, 347–354DOI: 10.1038/s41594-018-0051-7 (2018).
  36. Teng, K.W., Ren, P., Selvin, P.R. “Delivery of fluorescent probes using streptolysin O for fluorescence microscopy of living cells." Current Protocols in Protein Science, Vol. 93, e60DOI: 10.1002/cpps.60 (2018).
  37. Tjioe, M., Ryoo, H., Ishitsuka, Y., Ge, P., Bookwalter, C. Huynh, W., McKenney, R.J., Trybus, K.M., Selvin, P.R. “Magnetic cytoskeleton affinity purification of microtubule motors conjugated to quantum dots." Bioconjugate Chemistry, 29(7), 2278-2286DOI: acs.bioconjchem.8b00264 (2018).
  38. Voter, A., Qiu Y., Tippana R., Myong S., Keck J. “A guanine-flipping and sequestration mechanism for G-quadruplex unwinding by RecQ helicases." Nat Commun. 10; 9(1), 4201DOI: 10.1038/s41467-018-06751-8 (2018).
  39. Wang, X., Park, S., Zeng, L., Jain, A., Ha, T. “Toward single-cell single-molecule pull-down." Biophys J, 115 (2), pp. 283-288DOI: 10.1016/j.bpj.2018.05.013 (2018).
  40. Wang, Y., Sukenik, S., Davis, C.M, Gruebele, M. “Cell volume controls protein stability and compactness of the unfolded state." J Phys Chem B 122:49, 11762-11770DOI: 10.1021/acs.jpcb.8b08216 (2018).
  41. Whitley, K.D., Comstock, M.J., Chemla, Y.R. “Ultrashort nucleic acid duplexes exhibit long wormlike chain behavior with force-dependent edge effects." Phys Rev Lett. 120(6), 068102DOI: 10.1103/PhysRevLett.120.068102 (2018).
  42. 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 26098021 (2018).
  43. Yang, Z., Loh K.Y., Chu, Y.T., Feng, R., Satyavolu, N.S.R., Xiong, M., Huynh, S.M.N., Hwang K,, Li. L., Xing, H., Zhang, X., Chemla, Y.R., Gruebele, M., Lu, Y. “Optical control of metal ion probes in cells and zebrafish using highly selective DNAzymes conjugated to upconversion nanoparticles." J Am Chem Soc. 140(50), 17656-17665DOI: 10.1021/jacs.8b09867 (2018).
  44. Yoo, J., Aksimentiev, A. “New tricks for old dogs: Improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions." Phys Chem Chem Phys 20, 8432 – 8449DOI: 10.1039/C7CP08185E (2018).
  45. Youn, Y., Ishitsuka, Y., Jin, C., Selvin, P.R. “Thermal nanoimprint lithography for drift correction in super-resolution fluorescence microscopy." Optics Express 26(2), 1670-1680DOI: 10.1364/OE.26.001670 (2018).
  46. Zhang, T., Wu YC., Mullane, P., Ji, Y.J., Liu H., He, L., Arora, A., Hwang, H.Y., Alessi, A.F., Niaki, A.G., Periz, G., Guo, L., Wang, H., Elkayam, E., Joshua-Tor L., Myong, S., Kim, J., Shorter, J., Ong, S.E., Leung, A.K.L., Wang, J. “FUS regulates activity of microRNA-mediated gene silencing." Molecular Cell. Mar 1; 69(5), 787-801. e8DOI: 10.1016/j.molcel.2018.02.001 (2018).
  47. Zhu, W., Kim, B.C., Wang, M.Y., Huang, J., Isak, A., Bexiga, N.M., Monticone, R., Ha, T., Lakatta, E.G. An, S.S. “TGF Beta 1 reinforces arterial aging in the vascular smooth muscle cell through a long-range regulation of the cytoskeletal stiffness." Sci. Rep. 8, 2668DOI: 10.1038/s41598-018-20763-w (2018).