University of Illinois at Urbana-Champaign
Illinois Physics
Center for the Physics of the Living Cell

Publications

2019

  1. Schlierf, M., Wang, G., Chen, X.S., Ha, T. “Hexameric helicase G40P unwinds DNA in single base pair steps." eLife, 8, e42001DOI: 10.7554/ELIFE.42001 (2019).
  2. Tortarolo, G., Sun, Y., Teng, K., Ishitsuka, Y., Lanzanó, L., Selvin, P.R., Barbieri, B., Diaspro, A., Vicidomini, G. “Photon-separation to enhance the spatial resolution in pulsed STED microscopy." Nanoscale, 11, 1754-1761DOI: 10.1039/C8NR07485B (2019).
  3. Winogradoff, D., Aksimentiev, A. “Molecular Mechanism of Spontaneous Nucleosome Unraveling." 30468737 J. Mol. Biol. 431(2) 323-5DOI: 10.1016/j.jmb.2018.11.013 (2019).
  4. Zhou R., Yang O., Déclais A.-C., Jin, H., Gwon, G.H., Freeman, A.D.J., Cho, Y., Lilley, D.M.J., Ha, T. “Junction resolving enzymes use multivalency to keep the Holliday junction dynamic." Nat. Chem. Biol. 15 3 269- 275DOI: 10.1038/s41589-018-0209-y (2019).
  5. Feng, R., M. Gruebele and C. Davis Nature Comm(in press 2019).
  6. Mitra J, Makurath MA,Ngo TTM, Troitskaia A,Chemla YR, Ha T. Extreme Mechanical Diversity of Human Telomeric DNA Revealed by Fluorescence-Force Spectroscopy PNAS (in press 2019).
  7. Perlova T, Gruebele M, Chemla Y.R. Blue light is a universal signal for Escherichia coli chemoreceptors. J Bacteriol. Mar 11. pii: JB.00762-18. doi: 10.1128/JB.00762-18 (2019).

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).

2017

  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).