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Keith Weninger Group

List of Publications

  1. Erie, D, Weninger K “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)

 

  1. F. Pan, P. Xu, C. Roland, C. Sagui, K. Weninger “Structural and Dynamical Properties of Nucleic Acid Hairpins Implicated in Trinucleotide Repeat Expansion Diseases” , Biomolecules, 233, 109550 (2024)

 

  1. M. 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)

 

  1. Himebaugh NE, Robertson JB, Weninger K, Gilger BC, Ekesten B, Oh A “Ex Vivo analysis of ultraviolet radiation transmission through ocular media and retina in select species” , Experimental Eye Research, 233, 109550 (2023)

 

  1. Xu P, Zhang J, Pan F, Mahn C, Roland C, Sagui C, Weninger K “Frustration between preferred states of complementary trinucleotide repeat DNA hairpins anticorrelates with expansion disease propensity” , J. of Molecular Biology, 435, 168086 (2023)

 

  1. Ghaffari A, Kashani S, Do K, Weninger KR, Riehn R. “A Nanophotonic Interferometer” , Nanotechnology, 34, 185201 (2023)

 

  1. R. Evans, S. Ramisetty, P. Kulkarni, K. Weninger “Illuminating intrinsically disordered proteins with integrative structural biology” , Biomolecules, 13, 124 (2023)

 

  1. M. 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)

 

  1. J. 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”, Chemical Science, 13, 9668-9677 (2022)

 

  1. P. 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)

 

  1. N. Saikia, I.S.Yanez-Orozco, R. Qiu, P. Hao, S. Milikisiyants, E. Ou, G. L. Hamilton, K. R. Weninger, T. I. Smirnova, H. Sanabria, F. Ding, “Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25”,Cell Reports Physical Science,2, 100616 (2021)

 

  1. H. 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. Piehler, G. Xu, K. Weninger, R. Riehn, P. L. Opresko, H. Wang, “Structure, dynamics, and regulation of TRF1-TIN2-mediated trans- and cis-interactions on telomeric DNA”,J. of Biol. Chem.,297, 101080 (2021)

 

  1. Pan, F., Zhang, Y., Xu, P., Man, V.H., 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)

 

  1. 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”,Proc. Nat. Acad. Sci. USA,117, 17775-17784 (2020)

 

  1. 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 MutSα-MutLα complexes compact mismatched DNA”,Proc. Nat. Acad. Sci. USA,117, 16302-16312 (2020)

 

  1. 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 Cent. Sci.,6, 1159-1168 (2020)

 

  1. P. Xu, F. Pan, C. Roland, C. Sagui, K. Weninger, “Dynamics of strand slippage in DNA hairpins formed by CAG repeats: roles of sequence parity and trinucleotide interrupts”,Nucleic Acids Research,48, 2232-2245 (2020)

 

  1. U.B. Choi, H. Sanabria, T. Smirnova, M.E. Bowen, K.R. Weninger, “Spontaneous Switching among Conformational Ensembles in Intrinsically Disordered Proteins”,Biomolecules,9, 114 (2019)

 

  1. X. Lin, P. Kulkarni, F. Bocci, N.P. Schafer, S. Roy, M. Tsai, Y. He, Y. Chen, K. Rajagopalan, S.M. Mooney, Y. Zeng, K. Weninger, A. Grishaev, J.N. Onuchic, H. Levine, P.G. Wolynes, R. Salgia, G. Rangarajan, V. Uversky, J. Orban, and M.K. Jolly, “Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level”,Biomolecules,9, 77 (2019)

 

  1. LeBlanc S, Gauer J, Hao P, Case B, Hingorani M, Weninger K, Erie D, “Coordinated protein and DNA conformational changes govern mismatch repair initiation by MutS”,Nucleic Acids Research,46, 10782 (2018)

 

  1. LeBlanc S, Kulkarni P, Weninger K, “Single molecule FRET: A powerful tool to study intrinsically disordered proteins”,Biomolecules,8, 140 (2018)

 

  1. 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)

 

  1. M. Roushan, Z. Azad, S. Movahed, P.D. Ray, G.I. Livshits, S.F. Lim, K.R. Weninger, R. Riehn, “Motor-like DNA motion due to an ATP-hydrolyzing protein under nanoconfinement” ,Scientific Reports,8, 10036 (2018)

 

  1. R. Salgia, M.K. Jolly, T. Dorff, C. Lau, K. Weninger, J. Orban and 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)

 

  1. X. Lin, S. Roy, M.K. Jolly, F. Bocci, N. Schafer, Tsai, Y. Chen, Y. He, A.M. Grishaev, K. Weninger, J. Orban, P. Kulkarni, G. Rangarajan, H. Levine, J.N. Onuchic, “PAGE4 and conformational switching: Insights from molecular dynamics simulations and implications for prostate cancer” ,Journal of Molecular Biology,430, 2422 (2018)

 

  1. M. Jolly, P. Kulkarni, K. Weninger, J. Orban, H Levine “Phenotypic plasticity, bet-hedging, and androgen independence in prostate cancer: role of non-genetic heterogeneity”,Frontiers in Oncology,8:50 (2018)

 

  1. P. Kulkarni, M. K. Jolly, D. Jia, S. M. Mooney, A. Bhargava, Luciane T. Kagohara, Yihong Chen, Pengyu Hao, Yanan He, R. W. Veltri, A. Grishaev, K. Weninger, H. Levine & J. Orban “Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and potential role in phenotypic heterogeneity”,Proc. Nat. Acad. Sci. USA,114, E2644-E2653 (2017)

 

  1. 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)

 

  1. P. 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)

 

  1. R. Qiu, M. Sakato, E.J. Sacho, H. Wilkins, X. Zhang, P. Modrich, M.M. Hingorani, D.A. Erie, K.R. Weninger “MutL traps MutS at a DNA mismatch”,Proc. Nat. Acad. Sci. USA,112, 10914-10919 (2015)

 

  1. Y. He, Y. Chen, S.M. Mooney, K. Rajagopalan, A. Bhargava, E. Sacho, K. Weninger, P.N. Bryan, P. Kulkarni, J. Orban “Phosphorylation-Induced Conformational Ensemble switching in an Intrinsically Disordered Cancer/Testis antigen”,J. Biol. Chem.,290, 25090-25102 (2015)

 

  1. D.A. Erie, K.R. Weninger “Single Molecule Studies of DNA Mismatch Repair”,DNA Repair,20, 71-81 (2014)

 

  1. V.C. DeRocco, L.E. Sass, R. Qiu, K.R. Weninger, D.A. Erie “Dynamics of MutS-mismatched DNA complexes are predictive of their repair pheontypes”,Biochemistry,53, 2043-2052 (2014)

 

  1. S.M. Mooney, R. Qiu, J.J. Kim, E.J. Sacho, K. Rajagopalan, D. Johng, T. Shiraishi, P. Kulkarni, K.R. Weninger “The Cancer/Testis antigen PAGE4, a regulator of c-Jun transactivation, is phosphorylated by Homeo-domain interacting protein kinase 1, a component of the stress-response pathway”,Biochemistry,53, 1670-1679 (2014)

 

  1. K. 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)

 

  1. A.T. Brunger, P. Strop, M. Vrljic, M. Bowen, S. Chu, K.R. 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 (2013)

 

  1. U.B. Choi, K.R. Weninger, M.E. Bowen “Immobilization of proteins for single-molecule fluorescence resonance energy transfer measurements of conformation and dynamics”,Methods Mol Bio,896, 3-20 (2012).

 

  1. R. Qiu, V.C. DeRocco, C. Harris, A. Sharma, M.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).

 

  1. Shahzad Khalid, B. Kappus, K. Weninger, S. Putterman “Opacity and transport measurments reveal that dilute plasma models of sonoluminescence are not valid”,Physical Review Letters,108,104302 (2012).

 

  1. K. R. Weninger, “Complexin arrests a neighbor”,Nature Strucutral and Molecular Biology,18, 861 (2011).

 

  1. U.B. Choi, J.J. McCann, K. Weninger, M. Bowen, “Beyond the random coil: Stochastic conformational switching in intrinsically disordered proteins”,Structure,19, 566 (2011).

 

  1. A.T. Brunger, P. Strop, M. Vrljic, S. Chu, K. Weninger, “Three-dimensional molecular modeling with single molecule FRET”,Journal of Structural Biology,173, 497 (2011).

 

  1. V.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).

 

  1. J.J. McCann, U.B. Choi, L. Zheng, K. Weninger, M.E. Bowen, “Optimizing methods to recover absolute FRET efficiency from immobilized single molecules”,Biophysical Journal,99, 961-970 (2010).

 

  1. L.E. Sass, C. Lanyi, K. Weninger, D.A. Erie, “Single-molecule FRET TACKLE reveals highly dynamic mismatched DNA-MutS complexes”,Biochemistry,49, 3174-3190 (2010).

 

  1. U.B. Choi, P. Strop, M. Vrljic, S. Chu, A. T Brunger, K. Weninger, “Single molecule FRET derived model of the synaptotagmin 1 – SNARE fusion complex”,Nature Structural and Molecular Biology,17, 318 (2010).
  1. J. Sakon, K. Weninger, “Detecting the conformation of individual proteins in live cells”,Nature Methods,7, 203 (2010).
  1. P. Fletcher, M. Fletcher, K. Weninger, T. Anderson, B. Martin “VAMP cleavage by a new metalloprotease from the Brazilian scorpion Tityus serrulatus”,Journal of Biological Chemistry,285, 7405-7416 (2010).
  1. L. Wessels, K. Weninger, “Physical aspects of viral membrane fusion”,TheScientificWorldJOURNAL,9, 764-780 (2009).
  1. K. Weninger, “How do adhesion proteins stick?”,Structure,17, 1035 (2009).
  1. A.T. Brunger, K. Weninger, M.E. Bowen, S. Chu, “Single molecule studies of the neuronal SNARE fusion machinery”,Annual Review of Biochemistry, 78, 903 (2009).
  1. J. Sakon, G. Ribeill, J. Garguilo, J. Perkins, K. Weninger, R. Nemanich, “Fluorescence quenching effects of nanocrystalline diamond surfaces”,Diamond and Related Materials,18, 82 (2009)
  1. W. Thongthai and K. Weninger, “Photoinactivation of Sindbis virus without inhibition of membrane fusion”,Photochemistry and Photobiology,85, 801 (2009).
  1. K. Weninger, M.E.Bowen, U. Choi, S. Chu, A. Brunger, “Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex”,Structure16, 308 (2008).
  1. Y. Li, G. Augustine, K. Weninger, “Kinetics of complexin binding to the SNARE complex: correcting single molecule FRET measurements for hidden events”Biophysical Journal,93,2178 (2007).
  1. L. Wessels, M. Elting, D. Scimeca, K. Weninger, “Rapid membrane fusion of individual virus particles with supported lipid bilayers”,Biophysical Journal,93, 526 (2007).
  1. G. Wang, R. Hernandez, K. Weninger, D. Brown, “Infection of cells by Sindbis virus at low temperatures”,Virology362, 461 (2007).
  1. M.E. Bowen, K. Weninger, J. Ernst, S. Chu, A. T. Brunger, “Single Molecule Studies of Synaptotagmin and Complexin Binding to the SNARE Complex”,Biophysical Journal89, 690-702 (2005).
  1. M.E. Bowen, K. Weninger, A. T. Brunger, S. Chu, “Single Molecule Observation of Liposome Bilayer Fusion Thermally Induced by SNAREs”,Biophysical Journal87, 3569-84 (2004).
  1. K. 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. USA100, 14800-05 (2003).
  1. G. Vazquez, C. Camara, S. J. Putterman and K. Weninger, “Black-Body Spectra for Sonoluminescing Hydrogen Bubbles”,Phys. Rev. Lett.88, 197402-1 (2002).
  1. G. Vazquez, C. Camara, S. J. Putterman and K. Weninger, “Sonoluminescence:Nature’s Smallest Black-Body”,Optics Letters 26, 575 (2001).
  1. K. 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).
  1. C. Camara, S. J. Putterman, G. Vazquez and K. Weninger, Nature’s tiniest Black-body” Optics and Photonics News,112, (12) 45 (2001).
  1. S. J. Putterman, P.G. Evans, G. Vazquez, and K. R. Weninger”Is there a Simple Theory of Sonoluminescence?”Nature 409, 782 (2001).
  1. K. R. Weninger, C. Camara, and S. J. Putterman,”Observation of Bubble Dynamics within Luminescent Cavitation Clouds:Sonoluminescence at the Nano-Scale” Phys. Rev. E 63, 016310 (2001).
  1. S. J. Putterman and K. R. Weninger, “Sonoluminescence:How Bubbles Turn Sound into LightAnnual Review of Fluid Mechanics 32, 45 (2000).
  1. K. 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).
  1. K. R. Weninger, C. Camara, and S. J. Putterman,”Physical Acoustics of Ultrasound Assisted Liposuction”Clinics in Plastic Surgery 26, 463 (1999).
  1. K. R. Weninger, C. Camara, and S. J. Putterman,”Energy Focusing in a Converging Fluid Flow:Implications for Sonoluminescence” Phys. Rev. Lett. 83, 2081 (1999).
  1. S. J. Putterman and K. R. Weninger, “Commentary on Topaz et al.Aesthetic Surgery Journal19, 205 (1999)” Aesthetic Surgery Journal 19, 214 (1999).
  1. R. A. Hiller, S. J. Putterman, and K. R. Weninger, “Time Resolved Spectra of Sonoluminescence”Phys. Rev. Lett.80, 1090 (1998).
  1. R. Budakian, K. Weninger, R. A. Hiller and S. J. Putterman, “Picosecond Discharges and Stick-Slip Friction at the Moving Meniscus of Mercury”Nature391 266 (1998).
  1. K. 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 (1997).
  1. B.P. Barber, R. Hiller, R. Lofstedt, S. Putterman, and K. Weninger, “Defining the Unknowns of Sonoluminescence”PhysicsReports 281, 65 (1997).
  1. B.P. Barber, K. Weninger, and S. Putterman, “Sonoluminescence”Phil. Trans. R. Soc. Lond. A355, 641 (1997).
  1. K. R. Weninger, B.P. Barber and S. Putterman, “Pulsed Mie Scattering Measurements of the Collapse of a Sonoluminescing Bubble”Phys. Rev. Lett.78, 1799 (1997).
  1. K. Weninger, S. Putterman, and B.P. Barber, “Angular Correlations in Sonoluminescence:Diagnostic for the Sphericity of a Collapsing Bubble”Phys. Rev. E. 54, R2205 (1996).
  1. K. 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 (1995).
  1. B.P. Barber, K. Weninger, R. Lofstedt, and S. Putterman, “Observation of a New Phase of Sonoluminescence at Low Partial Pressures”Phys. Rev. Lett.74, 5276 (1995).
  1. R. Lofstedt,K. Weninger, S. Putterman, and B.P. Barber, “Sonoluminescing Bubbles and Mass Diffusion”Phys. Rev. E. 51, 4400 (1995).
  1. R. Hiller, K. Weninger, S. Putterman, and B.P. Barber, “Effect of Noble Gas Doping in Single-Bubble Sonoluminescence”Science265, 248 (1994).