CPLC Publications

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2017

  1. D.T. Fraebel, H. Mickalide, D. Schnitkey, J. Merritt, T.E. Kuhlman, S. Kuehn. “Environment determines evolutionary trajectory in a constrained phenotypic space.” eLife 6:e24669. DOI: 10.7554/eLife.24669 (2017).
  2. V.C. Luca, B.C. Kim, C. Ge, S. Kakuda, D. Wu, M. Roein-Peikar, R.S. Haltiwanger, C. Zhu, T. Ha, K.C. Garcia. “Notch-Jagged complex structure implicates a catch bond in tuning ligand sensitivity.” Science 355(6331), 1320–1324. DOI: 10.1126/science.aaf9739 (2017).
  3. I.T.S. Li, T. Ha, Y.R. Chemla. “Mapping cell surface adhesion by rotation tracking and adhesion footprinting.” Sci. Rep. 7:44502. DOI: 10.1038/srep44502 (2017).
  4. J.A. Englaender, J.A. Jones, B.F. Cress, T.E. Kuhlman, R.J. Linhardt, M.A.G. Koffas. “Effect of genomic integration location on heterologous protein expression and metabolic engineering in E. coli.” ACS Synth. Biol. 6(4), 710–720. DOI: 10.1021/acssynbio.6b00350 (2017).

2016

  1. M.E. Kandel, K.W. Teng, P.R. Selvin, G. Popescu. “Label-free imaging of single microtubule dynamics using spatial light interference microscopy.” ACS Nano. 11(1), 647–655. DOI: 10.1021/acsnano.6b06945 (2016).
  2. I. Masuda, 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), 4081–4093. DOI: 10.1093/nar/gkw1229 (2016).
  3. A. Singharoy, 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), 293–310. DOI: 10.1021/jacs.6b10744 (2016).
  4. K.D. Whitley, M.J. Comstock, Y.R. Chemla. “Elasticity of the transition state for oligonucleotide hybridization.” Nucleic Acids Res. 45(2), 547–555. DOI: 10.1093/nar/gkw1173 (2016).
  5. C.-T. Lin and T. Ha. “Probing single helicase dynamics on long nucleic acids through fluorescence-force measurement.” Optical Tweezers – Methods and Protocols 1486, 295–316. DOI: 10.1007/978-1-4939-6421-5_11 (2016).
  6. K.D. Whitley, 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, 183–256. DOI: 10.1007/978-1-4939-6421-5_8 (2016).
  7. A. Singharoy, C. Chipot. “Methodology for the simulation of molecular motors at different scales.” J. Phys. Chem. B. 121(15), 3502–3514. DOI: 10.1021/acs.jpcb.6b09350 (2016).
  8. C. Xue and N. Goldenfeld. “Stochastic predator-prey dynamics of transposons in the human genome.” Phys. Rev. Lett. 117:208101. DOI: 10.1103/PhysRevLett.117.208101 (2016).
  9. E. Fouquerel, 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, 1092–1100. DOI: 10.1038/nsmb.3319 (2016).
  10. R. Zhang, 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), 249–257. DOI: 10.1021/acsnano.6b05356 (2016).
  11. Y. Qiu and S. Myong.“Chapter Two - Single-molecule imaging With one color fluorescence.” Methods in Enzymology. 581, 33–51. DOI: 10.1016/bs.mie.2016.08.011 (2016).
  12. S. Myong.“Single molecule probing by fluorescence and force detection.” Methods. 105, 1–2. DOI: 10.1016/j.ymeth.2016.06.026 (2016).
  13. H.R. Koh, M.A. Kidwell, J. Doudna, S. Myong. “RNA scanning of a molecular machine with a built-in ruler.” J. Am. Chem. Soc. 139(1), 262–268. DOI: 10.1021/jacs.6b10387 (2016).
  14. K.W. Teng, 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:e20378. DOI: 10.7554/eLife.20378 (2016).
  15. A. Singharoy, C. Chipot, M. Moradi, K. Schulten. “Chemomechanical coupling in hexameric protein–protein interfaces harnesses energy within V-Type ATPases.” J. Am. Chem. Soc. 139(1), 293–310. DOI: 10.1021/jacs.6b10744 (2016).
  16. C. Xue and N. Goldenfeld. “Stochastic predator-prey dynamics of transposons in the human genome.” Phys. Rev. Lett. 117:208101. DOI: 10.1103/PhysRevLett.117.208101 (2016).
  17. A.M. Barragan, K. Schulten, I.A. Solov’yov. “Mechanism of the primary charge transfer reaction in the cytochrome bc1 complex.” J. Phys. Chem. B. 120(44), 11369–11380. DOI: 10.1021/acs.jpcb.6b07394 (2016).
  18. H. Xu, S.O. Skinner, A.M. Sokac, I. Golding. “Stochastic kinetics of nascent RNA.” Phys. Rev. Lett. 117:128101. DOI: 10.1103/PhysRevLett.117.128101 (2016).
  19. J. Yoo and A. Aksimentiev. “Refined parameterization of nonbonded interactions improves conformational sampling and kinetics of protein folding simulations.” J. Phys. Chem. Lett. 7(19), 3812–3818. DOI: 10.1021/acs.jpclett.6b01747 (2016).
  20. M. Sener, J. Strumpfer, A. Singharoy, C.N. Hunter, K. Schulten.“Overall energy conversion efficiency of a photosynthetic vesicle.” eLife. 5:e09541. DOI: 10.7554/eLife.09541 (2016).
  21. Y. Kim and S. Myong. “RNA remodeling activity of DEAD box proteins tuned by protein concentration, RNA length, and ATP.” Mol Cell. 63(5), 865–876. DOI: 10.1016/j.molcel.2016.07.010 (2016).
  22. A. Singharoy, 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), 12077–12089. DOI: 10.1021/jacs.6b01193 (2016).
  23. K. Göpfrich, 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), 8207–8214. DOI: 10.1021/acsnano.6b03759 (2016).
  24. J. Tong, 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), 90–99. DOI: 10.1016/j.bpj.2016.05.039 (2016).
  25. A. Schweitzer, 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), 7816–7821. DOI: 10.1073/pnas.1608050113 (2016).
  26. J. Merritt and S. Kuehn. “Quantitative high-throughput population dynamics in continuous-culture by automated microscopy.” Sci Rep. 6:33173. DOI: 10.1038/srep33173 (2016).
  27. R. Tippana, 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), 8448–8453. DOI: 10.1073/pnas.1603724113 (2016).
  28. I. Golding. “Single-cell studies of phage Lambda: hidden treasures under Occam’s rug.” Annu. Rev. Virol. 3:7.1–7.20. DOI: 10.1146/annurev-virology-110615-042127 (2016).
  29. Y.R. Chemla. “High-resolution, hybrid optical trapping methods and their application to nucleic acid processing proteins.” Biopolymers. 105(10), 704–714. DOI: 10.1002/bip.22880 (2016).
  30. J. Yoo, J. Wilson, A. Aksimentiev. “Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields.” Biopolymers. 105(10), 752–763. DOI: 10.1002/bip.22868 (2016).
  31. K. Göpfrich, 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), 4665–4669. DOI: 10.1021/acs.nanolett.6b02039 (2016).
  32. J.B. Budhathoki, 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), 2585–2596. DOI: 10.1016/j.bpj.2016.05.016 (2016).
  33. J. Deeng, 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), 3588–3602. DOI: 10.1016/j.jmb.2016.06.007 (2016).
  34. J. Wilson, L. Sloman, Z. He, A. Aksimentiev. “Graphene nanopores for protein sequencing.” Adv. Funct. Mater. DOI: 10.1002/adfm.201601272 (2016).
  35. T.M. Earnest, 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), 735–751. DOI: 10.1002/bip.22892 (2016).
  36. S.M. Slone, C.-Y. Li, J. Yoo, A. Aksimentiev. “Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity.” New J. Phys. 18:055012. DOI:10.1088/1367-2630/18/5/055012 (2016).
  37. J.V. Ribeiro, 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. 6:26536. DOI: 10.1038/srep26536 (2016).
  38. F. Chowdhury, 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, 3892–3897. DOI: 10.1021/acs.nanolett.6b01403 (2016).
  39. L. Figard, 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), 267–278. DOI: 10.1016/j.devcel.2016.04.010 (2016).
  40. N.H. Kim, 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). 7278–7283. DOI: 10.1073/pnas.1601833113 (2016).
  41. B.C. Goh, 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, 253–278. DOI: 10.1146/annurev-biophys-062215-011113 (2016).
  42. J.R. Perilla, 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), 1836–1844. DOI: 10.1021/acs.jpclett.6b00517 (2016).
  43. M. Kim, 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), 4807–4817. DOI: 10.1093/nar/gkw272 (2016) (#co-corresponding authors).
  44. D. Singh, 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. 7:12778. DOI: 10.1038/ncomms12778 (2016).
  45. S. Bhattacharya, J. Yoo, A. Aksimentiev. “Water mediates recognition of DNA sequence via ionic current blockade in a biological nanopore.” ACS Nano. 10(4), 4644–4651. DOI: 10.1021/acsnano.6b00940 (2016).
  46. K. Heyrana, 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), 5700–5714. DOI: 10.1128/JVI.00378-16 (2016).
  47. Y. Zhang, 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), 8137–8146. DOI: 10.1021/acs.jpcb.6b01327 (2016).
  48. E. Arauz, V. Aggarwal, A. Jain, T. Ha, J. Chen. “Single-molecule analysis of lipid–protein interactions in crude cell lysates.” Anal. Chem. 88(8), 4269–4276. DOI: 10.1021/acs.analchem.5b04127 (2016).
  49. J. Yoo, H. Kim, A. Aksimentiev, T. Ha. “Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation.” Nat Commun. 7:11045. DOI: 10.1038/ncomms11045 (2016).
  50. H.R. Koh, X. Wang, S. Myong. “Visualizing repetitive diffusion activity of double-strand RNA binding proteins by single molecule fluorescence assays.” Methods. DOI: 10.1016/j.ymeth.2016.03.009 (2016).
  51. H. Qiu, A. Girdhar, K. Schulten, J-P. Leburton. “Electrically tunable quenching of DNA fluctuations in biased solid-state nanopores.” ACS Nano. 10(4), 4482–4488. DOI: 10.1021/acsnano.6b00226 (2016).
  52. P. Heo, 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), 4512–452144, DOI: 10.1021/jacs.5b13449 (2016).
  53. C. Maffeo, J. Yoo, A. Aksimentiev. “De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation.” Nucleic Acids Res. 44(7), 3013–3019. DOI: 10.1093/nar/gkw155 (2016).
  54. L.A. Sepúlveda, H. Xu, J. Zhang, M. Wang, I. Golding. “Measurement of gene regulation in individual cells reveals rapid switching between promoter states.” Science 351(6278), 1218–1222. DOI: 10.1126/science.aad0635 (2016).
  55. C. Liu, 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. 7:10714. DOI: 10.1038/ncomms10714 (2016).
  56. L. Vukovic, 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), 4069–4078. DOI: 10.1021/jacs.5b12065 (2016).
  57. T. Ngo, 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. 7:10813. DOI: 10.1038/ncomms10813 (2016).
  58. J. Yoo and A. Aksimentiev. “The structure and intermolecular forces of DNA condensates.” Nucl Acids Res. 44(5), 2036–2046. DOI: 10.1093/nar/gkw081 (2016).
  59. M.K. Lee, 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, 4757–4760. DOI: 10.1039/c6cc00036c (2016).
  60. X. Wang, 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. 6:21584. DOI: 10.1038/srep21584 (2016).
  61. L. Ma, 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, 3382–3394. DOI: 10.1021/jacs.5b12378 (2016).
  62. M.D. Brenner, 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), 2096–2102. DOI: 10.1021/acs.nanolett.6b00305 (2016).
  63. S.O. Skinner, 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:e12175. DOI: 10.7554/eLife.12175 (2016).
  64. M. Roein-Peikar, Q. Xu, X. Wang, T. Ha. “Ultrasensitivity of cell adhesion to the presence of mechanically strong ligands.” Phys. Rev. X. 6(1). DOI: 10.1103/PhysRevX.6.011001 (2016).
  65. P. Gupta, 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, 153–158. DOI: 10.1038/nchembio.1998 (2016).
  66. J.E. Stone, 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, 17–27. DOI: 10.1016/j.parco.2015.10.015 (2016).
  67. S. Wang, 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, 31–36. DOI: 10.1038/nsmb.3138 (2016).
  68. J. Yoo and 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), 430–443. DOI: 10.1021/acs.jctc.5b00967 (2016).