Skip to main content
Keith Weninger Group

List of Publications

  1. M. Tran, C. Johnson, K. Weninger, D. Erie, “Expanding the capabilities of capillary electrophoresis for determining protein-DNA binding affinities: physiological conditions and mPEG-silane coating for sticky proteins”, Analytical Biochemistry, 721, 116271 (2026).
  2. Erie, S. LeBlanc, K. Weninger “Resolving the dynamics of atypical DNA structures using smFRET” Current Opinion in Structural Biology, 101, 103351 (2026)
  3. Kulkarni, S. Bhattacharya, A. Mohanty, S. Ramisetty, E. Pisick, J. Orban, V. Uversky, K. Weninger, S. Huang, T. Chou, P. W. Sternberg, R. Salgia, “Shape-shifting Proteins and the Subtlety in their form and function” iScience, 29, 117386 (2026)
  4. P Kulkarni, L Porter, T Chou, S Chong, F Chiti, J W. Schafer, A Mohanty, S Ramisetty, J N. Onuchic, M Tuite, V N. Uversky, K R. Weninger, E V. Koonin, J Orban, R Salgia,” Evolving concepts of the protein universe” iScience, 28, 112012 (2025)
  5. Zhu, Y. Zhang, H. Sahay, H. Wasserman, A. Afek, J. Williams, S. Shaltz, C. Johnson, D. M. MacAlpine, K. Weninger, D. Erie, S. Jinks-Robertson, and R. Gordân “Transcription factors increase DNA mutagenesis by interfering with the repair of replication errors” Cell, 188, 5735 (2025)
  6. Pan, P. Xu, C. Roland, C. Sagui, K. Weninger, “Structural and Dynamical Properties of Nucleic Acid Hairpins Implicated in Trinucleotide Repeat Expansion Diseases”, Biomolecules, 14, 1278 (2024)
  7. A. Erie, K.R. Weninger,” Combining single-molecule and structural studies reveals protein and DNA conformations and assemblies that govern DNA mismatch repair” Current Opinion in Structural Biology, 89, 102917 (2024)
  8. Götz, A. Barth, S. Bohr, R. Börner, J. Chen, T. Cordes, D. A. Erie, C. Gebhardt, M. Hadzic, G. Hamilton, N. Hatzakis, T. Hugel, L. Kisley, D. Lamb, C. de Lannoy, C. Mahn, D. Dunukara, D. de Ridder, H. Sanabria, J. Schimpf, C. Seidel, R. Sigel, M. Sletfjerding, J. Thomsen, L. Vollmar, S. Wanninger, K. Weninger, P. Xu, and S. Schmid “Reply to: On the statistical foundation of a recent single molecule FRET benchmark” Nature Communications 15, 3626 (2024)
  9. E. Himebaugh, B. Ekesten, B. C. Gilger, K. Weninger, J. B. Robertson, A. Oh “Ex Vivo Analysis of Ultraviolet Radiation Transmission Through Ocular Media and Retina in Select Species” Experimental Eye Research 233, 109550 (2023)
  10. Xu, J. Zhang, F. Pan, C. Mahn, C. Roland, C. Sagui, K. Weninger “Frustration between preferred states of complementary trinucleotide repeat DNA hairpins anticorrelates with expansion disease propensity” Journal of Molecular Biology 435, 168086 (2023)
  11. Ghaffari, A., Kashani, S., Do, K., Weninger, K., Riehn, R. “A nanophotonic interferometer” Nanotechnology 34, 185201 (2023)
  12. Evans, S. Ramisetty, P. Kulkarni, K. Weninger “Illuminating intrinsically disordered proteins with integrative structural biology” Biomolecules 13, 124 (2023)
  13. Götz, A. Barth, S. Bohr, R. Börner, J. Chen, T. Cordes, D. A. Erie, C. Gebhardt, M. Hadzic, G. Hamilton, N. Hatzakis, T. Hugel, L. Kisley, D. Lamb, C. de Lannoy, C. Mahn, D. Dunukara, D. de Ridder, H. Sanabria, J. Schimpf, C. Seidel, R. Sigel, M. Sletfjerding, J. Thomsen, L. Vollmar, S. Wanninger, K. Weninger, P. Xu, and S. Schmid “A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories” Nature Communications 13, 5402 (2022)
  14. Li, J. Xie, A. Godec, K. R. Weninger, C. Liu, J. C. Smith, L. Hong “Non-ergodicity of a globular protein extending beyond its functional timescale” Chemial Science 13, 9668-9677 (2022).
  15. Ghaffari, A., Do, K., Kashani, S., Weninger, K., Riehn, R. “A nanophotonic interferometer for small particle detection” Proc. SPIE 12223, Interferometry XXI, 122230L (2022).
  16. Kulkarni, V. B P Leite, S. Roy, S. Bhattacharyya, A. Mohanty, S. Achuthan, D. Singh, R. Appadurai, G. Rangarajan, K. Weninger, J. Orban, A. Srivastava, M. K. Jolly, J. Onuchic, V. N. Uversky, R. Salgia “Intrinsically Disordered Proteins: Ensembles at the Limits of Anfinsen’s Dogma” Biophysics Reviews 3, 011306 (2022).
  17. Saikia, N., Yanez-Orozco, I.S., Qiu, R., Hao, P., Milikisiyants, S., Ou, E., Hamilton, G.L., Weninger, K.R., Smirnova, T., Sanabria, H., Ding, F., “Integrative Structural Dynamics Probing of the Conformational Heterogeneity in Synaptosomal-Associated Protein 25”, Cell Reports Physical Science 2, 100616 (2021).
  18. Pan, P. Kaur, R. Barnes, A. C Detwiler, S. L. Sanford, M. Liu, P. Xu, C. Mahn, Q. Tang, P. Hao, D. Bhattaram, C. You, X. Gu, W. Lu, J. Pieler, G. Xu, K. Weninger, R. Riehn, P. L. Opresko, and H. Wang “Structure, dynamics, and regulation of TRF1-TIN2 mediated trans- and cis-interactions on telomeric DNA”, J. Biol. Chem. 297, 101080 (2021)
  19. Pan, F., Man, V.H., Xu, P., Zhang, Y., Roland, C., Weninger, K., Sagui, C., “Molecular conformations and dynamics of nucleotide repeats associated with neurodegenerative diseases: double helices and CAG hairpin loops” Computational and Structural Biotechnology Journal 19, 2819-2832 (2021).
  20. Hao, P., LeBlanc, S., Case, B.C., Elston, T.C., Hingorani, M.M., Erie, D.A., Weninger, K.R., “Recurrent mismatch binding by MutS mobile clamps on DNA localizes repair complexes nearby” Nat. Acad. Sci. USA 117, 17775-17784 (2020)
  21. Bradford, K.C., Wilkins, H., Hao, P., Li, Z., Wang, B., Burke, D., Wu, D., Smith, A., Spaller, L., Du, C., Gauer, J.W., Chan, E., Hsieh, P., Weninger, K., Erie, D., “Dynamic human MutSa-MutLa complexes compact mismatch DNA” Nat. Acad. Sci. USA 117, 16302-16312 (2020)
  22. J B Larsen, K R Rosholm, C Kennard, S L Pedersen, H K Munch, V Tkach, J J Sakon, T Bjørnholm, K R Weninger, P M Bendix, K J Jensen, N S Hatzakis, M J Uline, and D. Stamou “How membrane geometry regulates protein sorting independently of mean curvature” ACS Central Science 6, 1159-1168 (2020)
  23. Xu, P., Pan, F. Roland, C., Sagui, C., Weninger, K. “Dynamics of strand slippage in DNA hairpins formed by CAG repeats: roles of sequence parity and trinucleotide interrupts” Nucleic Acids Research 48, 2232 (2020)
  24. Choi, U.B., Sanabria, H., Smirnova, T., Bowen, M.E., Weninger, K.R., “Spontaneous switching among conformational ensembles in intrinsically disordered proteins” Biomolecules 9, 114 (2019)
  25. Lin, X., Kulkarni, P., Bocci, F. Schafer, N.P., Roy, S., Tsai, M., He, Y., Chen, Y., Rajagopalan, K., Mooney, S.M., Zeng, Y., Weninger, K., Grishaev, A., Onuchic, J., Levine, H., Wolynes, P., Slagia, R., Rangarajan, G., Uversky, V., Orban, J., Jolly, M.K. “Structural and Dynamical Order of a Disordered Protein: Molecular Insights into conformational switching of PAGE4 at the systems level” Biomolecules 9, 77 (2019)
  26. LeBlanc, S., Gauer, J.W., Hao, P., Case, B.C., Hingorani, M.M., Weninger, K.R., Erie D.A., “Coordinated protein and DNA conformational changes govern mismatch repair initiation by MutS” Nucleic Acids Research 46, 10782 (2018)
  27. LeBlanc, S., Kulkarni, P., Weninger, K., “Single molecule FRET: A powerful tool to study intrinsically disordered proteins”, Biomolecules, 8, 140 (2018)
  28. Hellenkamp B, Schmid S, Doroshenko O, Opanasyuk O, Kühnemuth R, Rezaei Adariani S, Ambrose B, Aznauryan M, Barth A, Birkedal V, Bowen ME, Chen H, Cordes T, Eilert T, Fijen C, Gebhardt C, Götz M, Gouridis G, Gratton E, Ha T, Hao P, Hanke CA, Hartmann A, Hendrix J, Hildebrandt LL, Hirschfeld V, Hohlbein J, Hua B, Hübner CG, Kallis E, Kapanidis AN, Kim JY, Krainer G, Lamb DC, Lee NK, Lemke EA, Levesque B, Levitus M, McCann JJ, Naredi-Rainer N, Nettels D, Ngo T, Qiu R, Robb NC, Röcker C, Sanabria H, Schlierf M, Schröder T, Schuler B, Seidel H, Streit L, Thurn J, Tinnefeld P, Tyagi S, Vandenberk N, Vera AM, Weninger KR, Wünsch B, Yanez-Orozco IS, Michaelis J, Seidel CAM, Craggs TD, Hugel T “Precision and accuracy of single-molecule FRET – a worldwide benchmark study” Nature Methods 15, 669 (2018)
  29. Salgia, R., M.K. Jolly, T. Dorff, C. Lau, K. Weninger, J. Orban, P. Kulkarni, “Prostate-associated Gene 4 (PAGE4): leveraging the conformational dynamics of a dancing protein cloud as a therapeutic target”, Journal of Clinical Medicine, 7, 156 (2018)
  30. Lin, X., Roy, S., Jolly, M.K., Bocci, F., Schafer, N., Tsai, Chen, Y., He, Y., Grishaev, A., M., Weninger, K., Orban, J., Kulkarni, P., A., Rangarajan, G., Levine, H., Onuchic, J.N., “PAGE4 and conformational switching: Insights from molecular dynamics simulations and implications for prostate cancer” Mol. Biol., 430, 2422 (2018)
  31. Roushan, M.; Azad, Z.; Ray, P.; Livshits, G.; Lim, S. F.; Weninger, K.; Riehn, R. “Motor-like DNA motion due to an ATP-hydrolyzing protein under nanoconfinement”, Scientific Reports, 8, 10036 (2018)
  32. Jolly, M.K., Kulkarni, P., Weninger, K., Orban, J., Levine, H., “Phenotypic plasticity, bet-hedging, and androgen independence in prostate cancer: role of non-genetic heterogeneity”, Frontiers in Oncology, 8:50 (2018)
  33. Prakash Kulkarni, Mohit Kumar Jolly, Dongya Jia, Steven M. Mooney, Ajay Bhargava, Luciane T. Kagohara, Yihong Chen, Pengyu Hao, Yanan He, Robert W. Veltri, Alexander Grishaev, Keith Weninger, Herbert Levine & John Orban “Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and potential role in phenotypic heterogeneity”, Nat. Acad. Sci. USA, 114, 2644-2653 (2017)
  34. J.W. Gauer, S. LeBlanc, P. Hao, R. Qiu, B. Case, M. Sakato, M.M. Hingorani, D.A. Erie, K.R. Weninger “Single Molecule FRET to Measure Conformational Dynamics of DNA Mismatch Repair Proteins”,Methods in Enzymology, 581, 285-315 (2016)
  35. Kulkarni, A.K. Dunker, K. Weninger, J. Orban “Prostate-associated Gene 4 (PAGE4), an intrinsically disordered Cancer/Testis Antigen, is a novel therapeutic target for prostate cancer”,Asian Journal of Andrology, 18, 1-9 (2016)
  36. He, Y. Chen, S.M. Mooney, K. Rajagopalan, A. Bhargava, E. Sacho, K. Weninger, P. Kulkarni, J. Orban, “Phosphorylation-induced conformational ensemble switching in an intrinsically disordered Cancer/Testis antigen” J. Biol. Chem., 290, 25090-25102 (2015)
  37. Qiu, M. Sakato, E.J. Sacho, H. Wilkins, X. Zhang, P. Modrich, M. Hingorani, D.A. Erie, K.R. Weninger, “MutL traps MutS at a DNA mismatch” Proc. Nat. Acad. Sci. USA, 112, 10914-10919 (2015)
  38. Erie and K. Weninger, “Single molecule studies of DNA mismatch repair”, DNA repair, 20, 71-81 (2014)
  39. C. DeRocco, L.E. Sass, R. Qiu, K.R. Weninger, D.A. Erie, “Dynamics of MutS-mismatched DNA complexes are predictive of their repair phenotype”, Biochemistry, 53, 2043-2052 (2014)
  40. M. Mooney, R. Qiu, J.J. Kim, E. Sacho, K. Rajagopalan, D. Johng, T. Shiraishi, P. Kulkarni, K.R. Weninger, “The cancer/testes antigen PAGE4, a regulator of c-Jun transactivation, is phosphorylated by homeodomain-interacting protein kinase 1, a component of the stress-response pathway”, Biochemistry, 53, 1670-1679 (2014)
  41. Rajagopalan, R. Qiu, S.M. Mooney, S. Rao, T. Shiraishi, E. Sacho, H. Huang, E. Shapiro, K.R. Weninger, P. Kulkarni, “The stress-response protein prostate-associated gene 4, interacts with c-Jun and potentiates its transactivation”, Biochim Biophys Acta., 1842, 154 (2014)
  42. T. Brunger, P. Strop, M. Vrljic, M. Bowen, S. Chu, K. Weninger “Macromolecular models by single molecule FRET”, J.D. Puglisi and M.V. Margaris (eds.), Biophysics and Structure to Counter Threats and Challenges, NATO Science for Peace and Security Series B: Physics and Biophysics, 1-19 (2012)
  43. Qiu, V.C. DeRocco, C. Harris, A. Sharma, M. Hingorani, D.A. Erie, K.R. Weninger, “Large conformational changes in MutS during DNA scanning, mismatch recognition and repair signalling”, The EMBO Journal 31, 2528-2540 (2012)
  44. B. Choi, J. McCann, K.R. Weninger, M.E. Bowen, “Immobilization of proteins for single molecule FRET measurements of conformation and dynamics” Methods Mol Biol 896, 3-20 (2012)
  45. Khalid, B. Kappus, K. Weninger, S. Putterman, “Opacity and transport measurements reveal that dilute plasma models of sonoluminescence are not valid” Phys. Rev. Lett. 108, 104302:1-5 (2012)
  46. B. Choi, J.J. McCann, K.R. Weninger, M.E. Bowen, “Beyond the random coil: Stochastic conformational switching in intrinsically disordered proteins”, Structure 19, 566-576 (2011)
  47. T. Brunger, P. Strop, M. Vrljic, S. Chu, K. Weninger “Three-dimensional molecular modeling with single molecule FRET” J. Structural Biology 173, 497-505 (2011)
  48. R. Weninger “Complexin arrests a neighbor” Nature Structural & Molecular Biology 18, 861-863 (2011)
  49. J. McCann, U. B. Choi, L. Zheng, K. Weninger, and M.E. Bowen “Optimizing methods to recover absolute FRET efficiency from immobilized single molecules”, Biophysical Journal. 99, 961-970 (2010)
  50. C. DeRocco, T. Anderson, J. Piehler, D.A.Erie, K. Weninger, “Four-color single-molecule fluorescence with noncovalent dye labeling to monitor dynamic multimolecular complexes”, BioTechniques 49, 807-816 (2010)
  51. E. Sass, C.M. Lanyi, K. Weninger, D.A. Erie, “Single-molecule FRET TACKLE reveals highly dynamic mismatched DNA-MutS complexes”, Biochemistry 49, 3174-3190 (2010)
  52. J. Sakon, K.R.Weninger, “Detecting the conformation of individual proteins in live cells”, Nature Methods 7, 203-205 (2010)
  53. B. Choi, P. Strop, M. Vrljic, S. Chu, A.T. Brunger, K. R. Weninger, “Single molecule FRET derived model of the synaptotagmin 1-SNARE fusion complex”, Nature Structural & Molecular Biology 17, 318-324 (2010)
  54. L Fletcher, M.D. Fletcher, K. Weninger, T.E. Anderson, B.M. Martin, “VAMP cleavage by a new metalloprotease from the Brazilian scorpion Tityus serrulatus”, J. Biol. Chem. 285, 7405-7416 (2010)
  55. Brunger, K. Weninger, M. Bowen, S. Chu, “Single-molecule studies of the neuronal SNARE fusion machinery”, Annual Review of Biochemistry, 78¸ 903-928 (2009)
  56. Wessels, K. Weninger, “Physical aspects of viral membrane fusion”, TheScientificWorldJOURNAL, 9, 764-780 (2009)
  57. Weninger, “How do adhesion proteins stick?”, Structure, 17, 1035-1036 (2009)
  58. Thongthai, K. Weninger, “Photoinactivation of Sindbis virus infectivity without inhibition of membrane fusion”, Photochemistry and Photobiology, 85, 801-806 (2009)
  59. J. Sakon, G.J. Ribeill, J.M. Garguilo, J. Perkins, K.R. Weninger and R.J. Nemanich, “Fluorescence quenching effects of nanocrystalline diamond surfaces”, Diamond and Related Materials, 18, 82-87 (2009)
  60. Weninger, M.E. Bowen, U. Choi, S. Chu and A.T. Brunger, “Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex”, Structure 16, 308-320 (2008)
  61. Li, G.A. Augustine, K. Weninger, “Kinetics of complexin binding to the SNARE complex: correcting single molecule FRET measurements for hidden events”, Biophysical Journal 93, 2178-2187 (2007)
  62. Wessels, M.W. Elting, D. Scimeca, K. Weninger, “Rapid Membrane Fusion of Individual Virus Particles with Supported Lipid Bilayers”, Biophysical Journal 93, 526-538 (2007)
  63. Wang, R. Hernandez, K. Weninger, D.T. Brown, “Infection of Cells by Sindbis Virus at Low Temperature”, Virology 362, 461-467 (2007)
  64. E. Bowen, K. Weninger, J. Ernst, S. Chu, A.T. Brunger, “Single-Molecule Studies of Synaptotagmin and Complexin Binding to the SNARE Complex”, Biophysical Journal 89(1), 690-702 (2005)
  65. E. Bowen, K. Weninger, A.T. Brunger, S. Chu, “Single-Molecule Observation of Liposome-Bilayer Fusion Thermally Induced by SNAREs”, Biophysical Journal 87(5), 3569-3584 (2004)
  66. Weninger, M.E. Bowen, S. Chu, A.T. Brunger, “Single-Molecule Studies of SNARE Complex Assembly Reveal Parallel and Antiparallel Configurations”, Proc. Nat. Acad. Sci. USA 100, 14800-14805 (2003)
  67. Vazquez, C. Camera, S. J. Putterman and K. Weninger, “Black-Body Spectra for Sonoluminescing Hydrogen Bubbles”, Phys. Rev. Lett. 88, 197402 (2002)
  68. Camera, S. Putterman, G. Vazquez, and K. Weninger, “Sonoluminescence: Nature’s Tiniest Blackbody”, Optics & Photonics News 112, (12) 45 (2001)
  69. Vazquez, C. Camera, S. J. Putterman and K. Weninger, “Sonoluminescence: Nature’s Smallest Blackbody”, Optics Letters 26, 575-577 (2001)
  70. R. Weninger, P.G. Evans, and S. J. Putterman, “Comment on Mie Scattering from a Sonoluminescing Bubble with High Spatial and Temporal Resolution” Phys. Rev. E 64, 0383011 (2001)
  71. J. Putterman, P.G. Evans, G. Vazquez, and K. R. Weninger “Is there a Simple Theory of Sonoluminescence?” Nature 409, 782-783 (2001)
  72. R. Weninger, C. Camera, and S. J. Putterman, “Observation of Bubble Dynamics within Luminescent Cavitation Clouds: Sonoluminescence at the Nano-Scale” Phys. Rev. E 63, 016310 (2001)
  73. J. Putterman and K. R. Weninger, “Sonoluminescence: How Bubbles Turn Sound into Light” Annu. Rev. Fluid Mech. 32, 445-476 (2000)
  74. R. Weninger, P.G. Evans, and S. J. Putterman, “Time correlated Single Photon Mie Scattering from a Sonoluminescing Bubble” Phys. Rev. E . 61 1020 (2000)
  75. R. Weninger, C. Camera, and S. J. Putterman, “Physical Acoustics of Ultrasound Assisted Liposuction” Clinics in Plastic Surgery 26, 463-479 (1999)
  76. R. Weninger, C. Camera, and S. J. Putterman, “Energy Focusing in a Converging Fluid Flow: Implications for Sonoluminescence” Phys. Rev. Lett.  83, 2081-2084 (1999)
  77. J. Putterman and K. R. Weninger, “Comment on Topaz et al. Aesthetic Surgery Journal 19, 205 (1999)” Aesthetic Surgery Journal 19, 214 (1999)
  78. A. Hiller, S. J. Putterman, and K. R. Weninger, “Time Resolved Spectra of Sonoluminescence” Phys. Rev. Lett. 80, 1090-1093 (1998)
  79. Budakian, K. Weninger, R. A. Hiller and S. J. Putterman, “Picosecond Discharges and Stick-Slip Friction at the Moving Meniscus of Mercury” Nature 391 266-268 (1998)
  80. Weninger, H. Cho, R. Hiller, S. J. Putterman, and G. Williams, “Sonoluminescence from an Isolated Bubble on a Solid Surface” Phys. Rev. E 56 6745-6749 (1997)
  81. P. Barber, R. Hiller, R. Löfstedt, S. Putterman, and K. Weninger, “Defining the Unknowns of Sonoluminescence” Physics Reports 281, 65-143 (1997)
  82. P. Barber, K. Weninger, and S. Putterman, “Sonoluminescence” Phil. Trans. R. Soc. Lond. A 355, 641-648 (1997)
  83. R. Weninger, B.P. Barber and S. Putterman, “Pulsed Mie Scattering Measurements of the Collapse of a Sonoluminescing Bubble” Phys. Rev. Lett. 78, 1799-1802 (1997)
  84. Weninger, S. Putterman, and B.P. Barber, “Angular Correlations in Sonoluminescence: Diagnostic for the Sphericity of a Collapsing Bubble” Phys. Rev. E. 54, R2205-R2208 (1996)
  85. Weninger, R. Hiller, B.P. Barber, D. Lacoste, and S. Putterman, “Sonoluminescence from Single Bubbles in Nonaqueous Liquids: New Parameter Space for Sonochemistry” J. Phys. Chem. 99, 14195-14197 (1995)
  86. P. Barber, K. Weninger, R. Löfstedt, and S. Putterman, “Observation of a New Phase of Sonoluminescence at Low Partial Pressures” Phys. Rev. Lett. 74, 5276-5279 (1995)
  87. Löfstedt, K. Weninger, S. Putterman, and B.P. Barber, “Sonoluminescing Bubbles and Mass Diffusion” Phys. Rev. E. 51, 4400-4410 (1995)
  88. Hiller, K. Weninger, S. Putterman, and B.P. Barber, “Effect of Noble Gas Doping in Single-Bubble Sonoluminescence” Science 265, 248-250 (1994)