CPLC Publications

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2016

  1. Arauz, E., V. Aggarwal, A. Jain, T. Ha, J. Chen. “Single-molecule analysis of lipid–protein interactions in crude cell lysates." Anal. Chem. 88(8), 4269–4276DOI: 10.1021/acs.analchem.5b04127 (2016).
  2. Barragan, A.M., K. Schulten, I.A. Solov’yov. “Mechanism of the primary charge transfer reaction in the cytochrome bc1 complex." J. Phys. Chem. B. 120(44), 11369–11380DOI: 10.1021/acs.jpcb.6b07394 (2016).
  3. Bhattacharya, S., J. Yoo, A. Aksimentiev. “Water mediates recognition of DNA sequence via ionic current blockade in a biological nanopore." ACS Nano. 10(4), 4644–4651DOI: 10.1021/acsnano.6b00940 (2016).
  4. Brenner, M.D., R. Zhou, D.E. Conway, L. Lanzano, E. Gratton, M.A. Schwartz, T. Ha. “Spider silk peptide is a compact, linear nanospring ideal for intracellular tension sensing." Nano Lett. 16(3), 2096–2102DOI: 10.1021/acs.nanolett.6b00305 (2016).
  5. Budhathoki, J.B., P. Maleki, W.A. Roy, P. Janscak, J.G. Yodh, H. Balci. “A comparative study of G-Quadruplex unfolding and DNA reeling activities of human RECQ5 helicase." Biophys J. 110(12), 2585–2596DOI: 10.1016/j.bpj.2016.05.016 (2016).
  6. Chemla, Y.R., “High-resolution, hybrid optical trapping methods and their application to nucleic acid processing proteins." Biopolymers. 105(10), 704–714DOI: 10.1002/bip.22880 (2016).
  7. Chowdhury, F., I.T.S. Li, T.T.M. Ngo, B.J. Leslie, B.C. Kim, J.E. Sokoloski, E. Weiland, X.W. Y.R. Chemla, T.M. Lohman, T. Ha. “Defining single molecular forces required for notch activation using nano yoyo." Nano Lett. 16, 3892–3897DOI: 10.1021/acs.nanolett.6b01403 (2016).
  8. Deeng, J., K.Y. Chan, E.O. van der Sluis, O. Berninghausen, W. Han, J. Gumbart, K. Schulten, B. Beatrix, R. Beckmann. “Dynamic behavior of trigger factor on the ribosome." J. Mol. Biol. 428(18), 3588–3602DOI: 10.1016/j.jmb.2016.06.007 (2016).
  9. Earnest, T.M., J.A. Cole, J.R. Peterson, M.J. Hallock, T.E. Kuhlman, Z. Luthey-Schulten. “Ribosome biogenesis in replicating cells: integration of experiment and theory." Biopolymers. 105(10), 735–751DOI: 10.1002/bip.22892 (2016).
  10. Figard, L., M. Wang, L. Zheng, I. Golding, A.M. Sokac. “Membrane supply and demand regulates F-actin in a cell surface reservoir." Dev Cell. 37(3), 267–278DOI: 10.1016/j.devcel.2016.04.010 (2016).
  11. Fouquerel, E., J. Lormand, A. Bose, T. Lee, G. Kim, J, Li, R.W. Sobol, B. Freudenthal, S. Myong, P.L. Opresko.“Oxidative guanine base damage regulates telomerase activity." Nat. Struct. Mol. Biol. 12, 1092–1100DOI: 10.1038/nsmb.3319 (2016).
  12. Goh, B.C., J.A. Hadden, R.C. Bernardi, A. Singharoy, R. McGreevy, T. Rudack, C.K. Cassidy, K. Schulten. “Computational methodologies for real-space structural refinement of large macromolecular complexes." Annu Rev Biophys. 45, 253–278DOI: 10.1146/annurev-biophys-062215-011113 (2016).
  13. Goh, B.C., J.R. Perilla, M.R. England, K.J. Heyrana, R. Craven, K. Schulten. “Atomic modeling of an immature retroviral lattice using molecular dynamics and mutagenesis." Structure. 23(8), 1414–1425DOI: 10.1016/j.str.2015.05.017 (2016).
  14. Golding, I., “Single-cell studies of phage Lambda: hidden treasures under Occam’s rug." Annu. Rev. Virol. 3, 7.1–7.20DOI: 10.1146/annurev-virology-110615-042127 (2016).
  15. Göpfrich, K., C.-Y. Li, I. Mames, S.P. Bhamidimarri, M. Ricci, J. Yoo, A. Mames, A. Ohmann, M. Winterhalter, E. Stulz, A. Aksimentiev, U.F. Keyser. “Ion channels made from a single membrane-spanning DNA duplex." Nano Lett. 16(7), 4665–4669DOI: 10.1021/acs.nanolett.6b02039 (2016).
  16. Göpfrich, K., C.-Y. Li, M. Ricci, S.P. Bhamidimarri, J. Yoo, B. Gyenes, A. Ohmann, M. Winterhalter, A. Aksimentiev, U.F. Keyser. “Large-conductance transmembrane porin made from DNA origami." ACS Nano. 10 (9), 8207–8214DOI: 10.1021/acsnano.6b03759 (2016).
  17. Gupta, P., B. Liu, D. Klepacki, V. Gupta, K. Schulten, A.S. Mankin, N. Vázquez-Laslop. “Nascent peptide assists the ribosome in recognizing chemically distinct small molecules." Nat Chem Biol. 12, 153–158DOI: 10.1038/nchembio.1998 (2016).
  18. Heo, P., Y. Yang, K.Y. Han, B. Kong, J.-H. Shin, Y. Jung, C. Jeong, J. Shin, Y.-K. Shin, T. Ha, D.-H. Kweon. “A chemical controller of SNARE-driven membrane fusion that primes vesicles for Ca2+-triggered millisecond exocytosis." J. Am. Chem. Soc. 138(13), 4512–452144DOI: 10.1021/jacs.5b13449 (2016).
  19. Heyrana, K., B.C. Goh, J.R. Perilla, T-L.N. Nguyen, M.R. England, M.C. Bewley, K. Schulten, R. Craven. “Contributions of charged residues in structurally dynamic capsid surface loops to Rous sarcoma virus assembly." J. Virol. 90(12), 5700–5714DOI: 10.1128/JVI.00378-16 (2016).
  20. Kandel, M.E., K.W. Teng, P.R. Selvin, G. Popescu. “Label-free imaging of single microtubule dynamics using spatial light interference microscopy." ACS Nano. 11(1), 647–655DOI: 10.1021/acsnano.6b06945 (2016).
  21. Kim, M., A. Kreig, C.-Y. Lee, H.T. Rube, J. Calvert, J.S. Song, S. Myong. “Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA." Nucleic Acids Res. 44(10), 4807–4817DOI: 10.1093/nar/gkw272 (2016).
  22. Kim, N.H., G. Lee, N.A. Sherer, K.M. Martini, N. Goldenfeld, T.E. Kuhlman. “Real-time transposable element activity in individual live cells." Proc Natl Acad Sci. USA. 113(26). 7278–7283DOI: 10.1073/pnas.1601833113 (2016).
  23. Kim, Y., S. Myong. “RNA remodeling activity of DEAD box proteins tuned by protein concentration, RNA length, and ATP." Mol Cell. 63(5), 865–876DOI: 10.1016/j.molcel.2016.07.010 (2016).
  24. Koh, H.R., M.A. Kidwell, J. Doudna, S. Myong. “RNA scanning of a molecular machine with a built-in ruler." J. Am. Chem. Soc. 139(1), 262–268DOI: 10.1021/jacs.6b10387 (2016).
  25. Koh, H.R., X. Wang, S. Myong. “Visualizing repetitive diffusion activity of double-strand RNA binding proteins by single molecule fluorescence assays." Methods 105, 109-118DOI: 10.1016/j.ymeth.2016.03.009 (2016).
  26. Lee, M.K., J. Park, X. Wang, M. Roein-Peikar, E. Ko, E. Qin, J. Lee, T. Ha, H. Kong. “Rupture force of cell adhesion ligand tethers modulates biological activities of a cell-laden hydrogel." Chem Commun. 52, 4757–4760DOI: 10.1039/c6cc00036c (2016).
  27. Lin, C.-T., T. Ha. “Probing single helicase dynamics on long nucleic acids through fluorescence-force measurement." Optical Tweezers – Methods and Protocols 1486, 295–316DOI: 10.1007/978-1-4939-6421-5_11 (2016).
  28. Liu, C., J.R. Perilla, J. Ning, M. Lu, G. Hou, R. Ramalho, B.A. Himes, G. Zhao, G.J. Bedwell, I.J. Byeon, J. Ahn, A.M. Gronenborn, P.E. Prevelige, I. Rousso, C. Aiken, T. Polenova, K. Schulten, P. Zhang. “Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site." Nat Commun. 7, 10714DOI: 10.1038/ncomms10714 (2016).
  29. Ma, L., C. Tu, P. Le, S. Chitoor, S.J. Lim, M.U. Zahid, K.W. Teng, P. Ge, P.R. Selvin, A.M. Smith. “Multidentate polymer coatings for compact and homogeneous quantum dots with efficient bioconjugation." J. Am. Chem. Soc.138, 3382–3394DOI: 10.1021/jacs.5b12378 (2016).
  30. Maffeo, C., J. Yoo, A. Aksimentiev. “De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation." Nucleic Acids Res. 44(7), 3013–3019DOI: 10.1093/nar/gkw155 (2016).
  31. Masuda, I., T. Igarashi, R. Sakaguchi, R.G. Nitharwal, R. Takase, K.Y. Han, B.J. Leslie, C. Liu, H. Gamper, T. Ha, S. Sanyal, Y.-M. Hou. “A genetically encoded fluorescent tRNA is active in live-cell protein synthesis." Nucleic Acids Res. 45(7), 4081–4093DOI: 10.1093/nar/gkw1229 (2016).
  32. Merritt, J., S. Kuehn. “Quantitative high-throughput population dynamics in continuous-culture by automated microscopy." Sci Rep. 6, 33173DOI: 10.1038/srep33173 (2016).
  33. Myong, S., “Single molecule probing by fluorescence and force detection." Methods. 105, 1–2DOI: 10.1016/j.ymeth.2016.06.026 (2016).
  34. Ngo, T., J. Yoo, Q. Dai, Q. Zhang, C. He, A. Aksimentiev, T. Ha. “Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability." Nat Commun. 7, 10813DOI: 10.1038/ncomms10813 (2016).
  35. Perilla, J.R., J.A. Hadden, B.C. Goh, C.G. Mayne, K. Schulten. “All-atom molecular dynamics of virus capsids as drug targets." J. Phys. Chem. Lett. 7(10), 1836–1844DOI: 10.1021/acs.jpclett.6b00517 (2016).
  36. Qiu, H., A. Girdhar, K. Schulten, J-P. Leburton. “Electrically tunable quenching of DNA fluctuations in biased solid-state nanopores." ACS Nano. 10(4), 4482–4488DOI: 10.1021/acsnano.6b00226 (2016).
  37. Qiu, Y., S. Myong. “Single-molecule imaging With one color fluorescence." Methods in Enzymology. 581, 33–51DOI: 10.1016/bs.mie.2016.08.011 (2016).
  38. Ribeiro, J.V., R.C. Bernardi, T. Rudack, J.E. Stone, J.C. Phillips, P.L. Freddolino, K. Schulten. “QwikMD – Integrative molecular dynamics toolkit for novices and experts." Sci Rep. 6:26536DOI: 10.1038/srep26536 (2016).
  39. Roein-Peikar, M., Q. Xu, X. Wang, T. Ha. “Ultrasensitivity of cell adhesion to the presence of mechanically strong ligands." Phys. Rev. X. 6(1DOI: 10.1103/PhysRevX.6.011001 (2016).
  40. Schweitzer, A., A. Aufderheide, T. Rudack, F. Beck, G. Pfeifer, J.M. Plitzko, E. Sakata, K. Schulten, F. Förster, W. Baumeister. “Structure of the human 26S proteasome at a resolution of 3.9 Å." Proc Natl Acad Sci. USA 113(28), 7816–7821DOI: 10.1073/pnas.1608050113 (2016).
  41. Sener, M., J. Strumpfer, A. Singharoy, C.N. Hunter, K. Schulten. “Overall energy conversion efficiency of a photosynthetic vesicle." eLife. 5, e09541DOI: 10.7554/eLife.09541 (2016).
  42. Sepúlveda, L.A., H. Xu, J. Zhang, M. Wang, I. Golding. “Measurement of gene regulation in individual cells reveals rapid switching between promoter states." Science 351(6278), 1218–1222DOI: 10.1126/science.aad0635 (2016).
  43. Singh, D., S.H. Sternberg, J. Fei, T. Ha, J.A. Doudna. “Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9." Nat Commun. 7, 12778DOI: 10.1038/ncomms12778 (2016).
  44. Singharoy, A., A.M. Barragan, S. Thangapandian, E. Tajkhorshid, K. Schulten. “Binding site recognition and docking dynamics of a single electron transport protein: Cytochrome c2." J. Am. Chem. Soc 138(37), 12077–12089DOI: 10.1021/jacs.6b01193 (2016).
  45. Singharoy, A., C. Chipot. “Methodology for the simulation of molecular motors at different scales." J. Phys. Chem. B. 121(15), 3502–3514DOI: 10.1021/acs.jpcb.6b09350 (2016).
  46. Singharoy, A., C. Chipot, M. Moradi, K. Schulten. “Chemomechanical coupling in hexameric protein-protein interfaces harness energy within V- type ATPases." J. Am. Chem. Soc. 139(1), 293–310DOI: 10.1021/jacs.6b10744 (2016).
  47. Skinner, S.O., H. Xu, S. Nagarkar-Jaiswal, P.R. Freire, T.P. Zwaka, I. Golding. “Single-cell analysis of transcription kinetics across the cell cycle." eLife. 5, e12175DOI: 10.7554/eLife.12175 (2016).
  48. Slone, S.M., C.-Y. Li, J. Yoo, A. Aksimentiev. “Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity." New J. Phys. 18, 055012DOI:10.1088/1367-2630/18/5/055012 (2016).
  49. Stone, J.E., M. Sener, K.L. Vandivort, A. Barragan, A. Singharoy, I. Teo, J.V. Ribeiro, B. Isralewitz, B. Liu, B.C. Goh, J.C. Phillips, C. MacGregor-Chatwin, M.P. Johnson, L.F. Kourkoutis, C.N. Hunter, K. Schulten. “Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing." Parallel Comput. 55, 17–27DOI: 10.1016/j.parco.2015.10.015 (2016).
  50. Teng, K.W., Y. Ishitsuka, P. Ren, Y. Youn, X. Deng, P. Ge, S.H. Lee, A.S. Belmont, P.R. Selvin. “Labeling proteins inside living cells using external fluorophores for microscopy." eLife. 5, e20378DOI: 10.7554/eLife.20378 (2016).
  51. Tippana, R., H. Hwang, V.A. Bohr, P.L. Opresko, S. Myong. “Single molecule imaging reveals a common mechanism shared by G-quadruplex resolving helicases." Proc Natl Acad Sci. USA. 113(30), 8448–8453DOI: 10.1073/pnas.1603724113 (2016).
  52. Tong, J., Z. Wu, M.M. Briggs, K. Schulten, T.J. McIntosh. “The water permeability and pore entrance structure of Aquaporin-4 depend on lipid bilayer thickness." Biophys J. 111(1), 90–99DOI: 10.1016/j.bpj.2016.05.039 (2016).
  53. Vukovic, L., C. Chipot, D.L. Makino, E. Conti, K. Schulten. “Molecular mechanism of processive 3' to 5' RNA translocation in the active subunit of the RNA exosome complex." J Am Chem Soc. 138(12), 4069–4078DOI: 10.1021/jacs.5b12065 (2016).
  54. Wang, S., R. Vafabakhsh, W.F. Borschel, T. Ha, C.G. Nichols. “Structural dynamics of potassium-channel gating revealed by single-molecule FRET." Nat Struct Mol Biol. 23, 31–36DOI: 10.1038/nsmb.3138 (2016).
  55. Wang, X., Z. Rahil, I.T. Li, F. Chowdhury, D.E. Leckband, Y.R. Chemla, T. Ha. “Constructing modular and universal single molecule tension sensor using protein G to study mechano-sensitive receptors." Sci Rep. 6, 21584DOI: 10.1038/srep21584 (2016).
  56. Whitley, K.D., M.J. Comstock, Y.R. Chemla. “Elasticity of the transition state for oligonucleotide hybridization." Nucleic Acids Res. 45(2), 547–555DOI: 10.1093/nar/gkw1173 (2016).
  57. Whitley, K.D., M.J. Comstock, Y.R. Chemla. “High-resolution 'fleezers': Dual-trap optical tweezers combined with single-molecule fluorescence detection." Optical Tweezers – Methods and Protocols 1486, 183–256DOI: 10.1007/978-1-4939-6421-5_8 (2016).
  58. Wilson, J., L. Sloman, Z. He, A. Aksimentiev. “Graphene nanopores for protein sequencing." Adv. Funct. Mater. 26, 4830-4838DOI: 10.1002/adfm.201601272 (2016).
  59. Xu, H., S.O. Skinner, A.M. Sokac, I. Golding. “Stochastic kinetics of nascent RNA." Phys. Rev. Lett. 117, 128101DOI: 10.1103/PhysRevLett.117.128101 (2016).
  60. Xue, C., N. Goldenfeld. “Stochastic predator-prey dynamics of transposons in the human genome." Phys. Rev. Lett. 117:208101DOI: 10.1103/PhysRevLett.117.208101 (2016).
  61. Yoo, J., A. Aksimentiev. “The structure and intermolecular forces of DNA condensates." Nucleic Acids Res. 44(5), 2036–2046DOI: 10.1093/nar/gkw081 (2016).
  62. Yoo, J., A. Aksimentiev. “Refined parameterization of nonbonded interactions improves conformational sampling and kinetics of protein folding simulations." J. Phys. Chem. Lett. 7(19), 3812–3818DOI: 10.1021/acs.jpclett.6b01747 (2016).
  63. Yoo, J., A. Aksimentiev. “Improved parameterization of amine–carboxylate and amine–phosphate interactions for molecular dynamics simulations using the CHARMM and AMBER force field." J Chem Theory Comput 12(1), 430–443DOI: 10.1021/acs.jctc.5b00967 (2016).
  64. Yoo, J., H. Kim, A. Aksimentiev, T. Ha. “Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation." Nat Commun. 7, 11045DOI: 10.1038/ncomms11045 (2016).
  65. Yoo, J., J. Wilson, A. Aksimentiev. “Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields." Biopolymers. 105(10), 752–763DOI: 10.1002/bip.22868 (2016).
  66. Zhang, R., G.O. Fruhwirth, O. Coban, J.E. Barrett, T. Burgoyne, S.H. Lee, P.D. Simonson, M. Baday, B.N. Kholodenko, C.E. Futter, T. Ng, P.R. Selvin. “Probing the heterogeneity of protein kinase activation in cells by super-resolution microscopy." ACS Nano. 11(1), 249–257DOI: 10.1021/acsnano.6b05356 (2016).
  67. Zhang, Y., L.L. Vukovic, T. Rudack, W. Han, K. Schulten. “Recognition of poly-ubiquitins by the proteasome through protein refolding guided by electrostatic and hydrophobic interactions." J Phys Chem B. 120(33), 8137–8146DOI: 10.1021/acs.jpcb.6b01327 (2016).