CPLC Publications

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2016

  1. 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).
  2. 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).
  3. 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).
  4. 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).
  5. 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).
  6. 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).
  7. 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).
  8. 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).
  9. 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).
  10. 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).
  11. 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).
  12. 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).
  13. 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).
  14. 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).
  15. 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).
  16. 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).
  17. 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).
  18. 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).
  19. 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).
  20. 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).
  21. 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).
  22. J. Wilson, L. Sloman, Z. He, A. Aksimentiev. “Graphene nanopores for protein sequencing.” Adv. Funct. Mater. DOI: 10.1002/adfm.201601272 (2016).
  23. 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).
  24. 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).
  25. 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).
  26. 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).
  27. 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).
  28. 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).
  29. 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).
  30. 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).
  31. 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).
  32. 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).
  33. 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).
  34. 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).
  35. 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).
  36. 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).
  37. 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).
  38. 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).
  39. 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).
  40. 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).
  41. 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).
  42. 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).
  43. 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).
  44. 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).
  45. 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).
  46. 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).
  47. 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).
  48. 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).
  49. 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).
  50. 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).
  51. 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).
  52. 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).
  53. 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).
  54. 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).
  55. 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).
  56. 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).

2015

  1. J.R Peterson, J.A. Cole, J. Fei, T. Ha, Z.A. Luthey-Schulten. “Effects of DNA replication on mRNA noise.” Proc Natl Acad Sci U S A. 112(52), 15886–15891. DOI: 10.1073/pnas.1516246112 (2015).
  2. H. Yu, W. Han, W. Ma, K. Schulten. “Transient ß-hairpin formation in a-synuclein monomer revealed by coarse-grained molecular dynamics simulation.” Nano Lett. 143(24): 243142. DOI: 10.1063/1.4936910 (2015).
  3. X. Wang, J. Sun, Q. Xu, F. Chowdhury, M. Roein-Peikar, Y. Wang, T. Ha. “Integrin molecular tension within motile focal adhesions.” Biophys J. 109(11), 2259–2267. DOI: 10.1016/j.bpj.2015.10.029 (2015).
  4. J. Zhang, J. Fei, B.J. Leslie, K.Y. Han, T.E. Kuhlman, T. Ha. “Tandem spinach array for mRNA imaging in living bacterial cells.” Sci Rep. 5:17295. DOI: 10.1038/srep17295 (2015).
  5. M. Lu, G. Hou, H. Zhang, C.L Suiter, J. Ahn, I.J. Byeon, J.R. Perilla, C.J. Langmead, I. Hung, P.L. Gor'kov, Z. Gan, W. Brey, C. Aiken, P. Zhang, K. Schulten, A.M. Gronenborn, T. Polenova. “Dynamic allostery governs cyclophilin A-HIV capsid interplay.” Proc Natl Acad Sci U S A. 112(47), 14617–14622. DOI: 10.1073/pnas.1516920112 (2015).
  6. H. Qiu, A. Sarathy, J.P. Leburton, K. Schulten. “Intrinsic stepwise translocation of stretched ssDNA in graphene nanopores.” Nano Lett. 15(12), 8322–8330. DOI: 10.1021/acs.nanolett.5b03963 (2015).
  7. C.K. Cassidy, B.A. Himes, F.J. Alvarez, J. Ma, G. Zhao, J.R. Perilla, K. Schulten, P. Zhang. “CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling.” eLife. 4:e08419. DOI: 10.7554/eLife.08419 (2015).
  8. J Yoo and A. Aksimentiev. “Molecular dynamics of membrane-spanning DNA channels: conductance mechanism, electro-osmotic transport and mechanical gating.” J Phys Chem Lett. 6(23), 4680–4687. DOI: 10.1021/acs.jpclett.5b01964 (2015).
  9. H.R. Lee, J. Mitra, S. Lee, S.J. Gao, T.K. Oh, M.H. Kim, T. Ha, J.U. Jung. “Kaposi's sarcoma-associated herpesvirus viral interferon regulatory factor 4 (vIRF4) perturbs the G1-S cell cycle progression via deregulation of the cyclin D1 gene.” J Virol. 90(2), 1139–1143. DOI: 10.1128/JVI.01897-15 (2015).
  10. S.K. Misra, G. Ghoshal, M.R. Gartia, Z. Wu, A.K. De, M. Ye, C.R. Bromfield, E.M. Williams, K. Singh, K.V. Tangella, L. Rund, K. Schulten, L.B. Schook, P.S. Ray, E.C. Burdette, D. Pan. “Trimodal therapy: combining hyperthermia with repurposed bexarotene and ultrasound for treating liver cancer.” ACS Nano. 9(11), 10695–10718. DOI: 10.1021/acsnano.5b05974 (2015).
  11. H. Tas, C.T. Nguyen, R. Patel, N.H. Kim, T.E Kuhlman. “An integrated system for precise genome modification in Escherichia coli.” PLoS ONE. 10(9): e0136963. DOI: 10.1371/journal.pone.0136963 (2015).
  12. D. Satory, A.J. Gordon, M. Wang, J.A. Halliday, I. Golding, C. Herman. “DksA involvement in transcription fidelity buffers stochastic epigenetic change.” Nucleic Acids Res. 43(21), 10190–10199. DOI: 10.1093/nar/gkv839 (2015).
  13. A. Kreig, J. Calvert, J. Sanoica, E. Cullum, R. Tipanna, S. Myong. “G-quadruplex formation in double strand DNA probed by NMM and CV fluorescence.” Nucleic Acids Res. 43(16), 7961–7970. DOI: 10.1093/nar/gkv749 (2015).
  14. X. Wang, L. Vukovic, H.R. Koh, K. Schulten, S. Myong. “Dynamic profiling of double-stranded RNA binding proteins.” Nucleic Acids Res. 43(15), 7566–7576. DOI: 10.1093/nar/gkv726 (2015).
  15. A. Khan, S. Giri, Y. Wang, A. Chakraborty, A.K. Ghosh, A. Anantharaman, V. Aggarwal, K.M. Sathyan, T. Ha, K.V. Prasanth, S.G. Prasanth. “BEND3 represses rDNA transcription by stabilizing a NoRC component via USP21 deubiquitinase.” Proc Natl Acad Sci U S A. 112(27), 8338–8343. DOI: 10.1073/pnas.1424705112 (2015).
  16. K. Girdhar, M. Gruebele, Y.R. Chemla. “The behavioral space of zebrafish locomotion and its neural network analog.” PLoS ONE. 10(7): e0128668. DOI: 10.1371/journal.pone.0128668 (2015)
  17. F. Chowdhury, I.T. Li, B.J. Leslie, S. Doganay, R. Singh, X. Wang, J. Seong, S.H. Lee, S. Park, N. Wang, T. Ha. “Single molecular force across single integrins dictates cell spreading.” Integr Biol (Camb). 7(10), 1265–1271. DOI: 10.1039/c5ib00080g (2015).
  18. B.C. Goh, J.R. Perilla, M.R. England, K.J. Heyrana, R.Craven, K. Schulten. “Atomic modeling of an immature retroviral lattice using molecular dymanics and mutagenesis.” Structure. 23(8), 1414–1425. DOI: 10.1016/j.str.2015.05.017 (2016).
  19. H. Xu, L.A. Sepúlveda, L. Figard, A.M. Sokac, I. Golding. “Combining protein and mRNA quantification to decipher transcriptional regulation.” Nat Methods. 12(8), 739–742. DOI: 10.1038/nmeth.3446 (2015).
  20. A.J. Wirth, Y. Liu, M.B. Prigozhin, K. Schulten, M. Gruebele. “Comparing fast pressure jump and temperature jump protein folding experiments and simulations.” J Am Chem Soc. 137(22), 7152–7159. DOI: 10.1021/jacs.5b02474 (2015).
  21. J.B. Budhathoki, E.J. Stafford, J.G. Yodh, H. Balci. “ATP-dependent G-quadruplex unfolding by Bloom helicase exhibits low processivity.” Nucleic Acids Res. 43(12), 5961–5970. DOI: 10.1093/nar/gkv531 (2015).
  22. M.T. Englander, J.L. Avins, R.C. Fleisher, B. Liu, P.R. Effraim, J. Wang, K. Schulten, T.S. Leyh, R.L. Gonzalez Jr, V.W. Cornish. “The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center.” Proc Natl Acad Sci U S A. 112(19), 6038–6043. DOI: 10.1073/pnas.1424712112 (2015).
  23. K.Y. Han and T. Ha. “Dual-color three-dimensional STED microscopy with a single high-repetition-rate laser.” Opt Lett. 40(11), 2653–2656. DOI: 10.1364/OL.40.002653 (2015).
  24. M. J. Comstock, K. D. Whitley, H. Jia, J. Sokoloski, T. M. Lohman, T.J. Ha, Y. R. Chemla. “Direct observation of structure-function relationship in a nucleic acid-processing enzyme.” Science. 348(6232), 352–354. DOI:10.1126/science.aaa0130 (2015).
  25. S. Arslan, R. Khafizov, C. D. Thomas, Y. R. Chemla, T.J. Ha. “Engineering of a superhelicase through conformational control.” Science. Vol. 348 no. 6232 pp. 344–347. DOI: 10.1126/science.aaa0445 (2015).
  26. J.R. Perilla, B.C. Goh, C.K. Cassidy, B. Liu, R.C. Bernardi, T. Rudack, H. Yu, Z. Wu, K. Schulten. “Molecular dynamics simulations of large macromolecular complexes.” Curr Opin Struct Biol. 31, 64–74. DOI: 10.1016/j.sbi.2015.03.007 (2015).
  27. T.T.M. Ngo and T. Ha. “Nucleosomes undergo slow spontaneous gaping.” Nucleic Acids Res. 43(8), 3964–3971. DOI: 10.1093/nar/gkv276 (2015).
  28. J. Fei, D. Singh, Q. Zhang,S. Park, D. Balaasubramanin, I. Golding, C.K. Vanderpool, T. Ha. “Determination of in vivo target search kinetics of regulatory noncoding RNA.” Science. 347(6228), 1371–1374. DOI:10.1126/science.1258849 (2015).
  29. J.A. Cole, L. Kohler, J. Hedhli, Z. Luthey-Schulten. “Spatially-resolved metabolic cooperativity within dense bacterial colonies.” BMC Syst Biol. 9:15. DOI: 10.1186/s12918-015-0155-1 (2015).
  30. A. Girdhar, C. Sathe, K. Schulten, J.P. Leburton. “Tunable graphene quantum point contact transistor for DNA detection and characterization.” Nanotechnology. 26(13):134005. DOI: 10.1088/0957-4484/26/13/134005 (2015).
  31. T.T.M. Ngo, Q. Zhang, R. Zhou, J.G. Yodh, T. Ha. “Asymmetric Unwrapping of Nucleosomes under Tension Directed by DNA Local Flexibility,” Cell. 160 (6), 1135–1144. DOI: 10.1016/j.cell.2015.02.001 (2015).
  32. M.P. Landry, L. Vukovic, S. Kruss, G. Bisker, A.M. Landry, S. Islam, R. Jain, K. Schulten, M.S. Strano. “Comparative dynamics and sequence dependence of DNA and RNA binding to single walled carbon nanotubes.” J Phys Chem C Nanomater Interfaces. 119(18), 10048–10058. DOI: 10.1021/jp511448e (2015).
  33. T.J. Kim, C. Joo, J. Seong, R. Vafabakhsh, E.L. Botvinick, M.W. Berns, A.E. Palmer, N. Wang, T. Ha, E. Jakobsson, J. Sun, Y. Wang. “Distinct mechanisms regulating mechanical force-induced Ca2+ signals at the plasma membrane and the ER in human MSCs.” eLife. 4:e04876. DOI: 10.7554/eLife.04876 (2015).
  34. W. Ma and K. Schulten. “Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution.” J Am Chem Soc. 137(8), 3031–3040. DOI: 10.1021/ja512605w (2015).
  35. C.Y. Li, E.A. Hemmig, J. Kong, J. Yoo, S. Hernández-Ainsa, U.F. Keyser, A. Aksimentiev. “Ionic conductivity, structural deformation, and programmable anisotropy of DNA origami in electric field.” ACS Nano. 9(2), 1420–1433. DOI: 10.1021/nn505825z (2015).
  36. S.H. Kim, J. Park, C. Joo, D. Kim, T. Ha. “Dynamic growth and shrinkage govern the pH dependence of RecA filament stability.” PLoS ONE. 10(1): e0115611. DOI: 10.1371/journal.pone.0115611 (2015).
  37. D.J. Hardy, Z. Wu, J.C. Phillips, J.E. Stone, R.D. Skeel, K. Schulten. “Multilevel summation method for electrostatic force evaluation.” J Chem Theory Comput. 11(2), 766–779. DOI: 10.1021/ct5009075 (2015).
  38. M. Fraiberg, O. Afanzar, C.K. Cassidy, A. Gabashvili, K. Schulten, Y. Levin, M. Eisenbach. “CheY's acetylation sites responsible for generating clockwise flagellar rotation in Escherichia coli.” Mol Microbiol. 95(2), 231–244. DOI: 10.1111/mmi.12858 (2015).
  39. A.M. Barragan, A.R. Crofts, K. Schulten, I.A. Solov'yov. “Identification of ubiquinol binding motifs at the Qo-site of the cytochrome bc1 complex.” J Phys Chem B. 119(2), 433–447. DOI: 10.1021/jp510022w (2015).