Publications
| Single molecule FRET | Membrane Fusion |
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2024
Erie, DA and Weninger KR, “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) link or pubmed
Pan, F, Xu, P, Roland, C, Sage, C, and Weninger KR, “Structural and dynamical properties of nucleic acid hairpins implicated in trinucleotide repeat expansion diseases” , Biomolecules, 14, 1278 (2024) link or pubmed
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) link or pubmed
2023
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) link or pubmed
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) link or pubmed
Ghaffari A, Kashani S, Do K, Weninger KR, Riehn R. “A Nanophotonic Interferometer” , Nanotechnology, 34, 185201 (2023) link or pubmed
R. Evans, S. Ramisetty, P. Kulkarni, K. Weninger “Illuminating intrinsically disordered proteins with integrative structural biology” , Biomolecules, 13, 124 (2023) link or pubmed
2022
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) link or pubmed
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) link or pubmed
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) link or pubmed
2021
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) link or pubmed
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) link or pubmed
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) link or pubmed
2020
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) link or pubmed and a PNAS commentary
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) link or pubmed
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) link or pubmed
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) link or pubmed
2019
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) link or pubmed
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) link or pubmed
2018
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) link or pubmed
LeBlanc S, Kulkarni P, Weninger K, “Single molecule FRET: A powerful tool to study intrinsically disordered proteins”, Biomolecules, 8, 140 (2018) link or pubmed
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) link or pubmed
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) link or pubmed
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) link or pubmed
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) link or pubmed
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) link or pubmed
2017
P. Kulkarni, M. Jolly, D. Jia, S. M. Mooney, A. Bhargava, L. T. Kagohara, Y. Chen, P. Hao, Y. 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) link or pubmed
2016
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) link or pubmed
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) link or pubmed
2015
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) link or pubmed
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) link or pubmed
2014
D.A. Erie, K.R. Weninger “Single molecule studies of DNA mismatch repair”, DNA Repair,20, 71-81 (2014) link or pubmed
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) link or pubmed
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) link or pubmed or reprint
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) link or pubmed
2013
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) ( DOI 10.1007/978-94-007-4923-8 1) link or pdf
2012
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) link or try Pubmed
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) link
S. Khalid, B. Kappus, K. Weninger, S. Putterman “Opacity and transport measurements reveal that dilute plasma models of sonoluminescence are not valid”, Physical Review Letters, 108, 104302 (2012) link or see also Physics Today
2011
K. R. Weninger, “Complexin arrests a neighbor”, Nature Structural and Molecular Biology, 18, 861 (2011) link
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) link
A.T. Brunger, P. Strop, M. Vrljic, S. Chu, K. Weninger, “Three-dimensional molecular modeling with single molecule FRET”, J. Struct. Biol., 173,497-505 (2011) link
2010
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 (2010) link or pubmed
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 (2010) link
L.E. Sass, C. Lanyi, K. Weninger, D.A. Erie, “Single-molecule FRET TACKLE reveals highly dynamic mismatched DNA-MutS complexes”, Biochemistry, 49, 3174 (2010) link
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) link and a commentary
J. Sakon, K. Weninger, “Detecting the conformation of individual proteins in live cells”, Nature Methods, 7, 203 (2010) link
P. Fletcher, M. Fletcher, K. Weninger, T. Anderson, B. Martin “VAMP cleavage by a new metalloprotease from the Brazilian scorpion Tityus serrulatus”, J. Biol Chem., 285, 7405 (2010) link
2009
K. Weninger, “How do adhesion proteins stick?”, Structure, 17, 1035 (2009) link
L.Wessels, K. Weninger, “Physical aspects of viral membrane fusion”, TheScientificWorldJOURNAL, 9, 764 (2009) link or pubmed
A. Brunger, K. Weninger, M. Bowen, S. Chu “Single-molecule studies of the neuronal SNARE fusion machinery”, Annual Review of Biochemistry, 78, 903 (2009) link
W. Thongthai, K. Weninger, “Photoinactivation of Sindbis virus infectivity without inhibition of membrane fusion”, Photochemistry and Photobiology, 85, 801 (2009) link
J.J. Sakon, G.J. Ribeill, J.M. Garguilo, J. Perkins, K.R. Weninger, R.J. Nemanich, “Fluorescence quenching effects of nanocrystalline diamond surfaces”, Diamond and Related Materials, 18, 82 (2009) link
2008
K. Weninger, M. Bowen, U.B. Choi, A. Brunger, S. Chu, “Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex”, Structure, 16, 308 (2008) link or pdf
2007
L. Wessels, M.W. Elting, D. Scimeca, K. Weninger, “Rapid membrane fusion of individual virus particles w/supported lipid bilayers”, Biophysical Journal, 93, 526 (2007) link or pdf
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) link or pdf
G. Wang, R. Hernandez, K. Weninger, D.T. Brown “Infection of cells by Sindbis virus at low temperature”, Virology, 362, 461 (2007) link or pdf
2005
M. Bowen, K. Weninger, J. Ernst, S. Chu, A. Brunger, “Single-molecule studies of synaptotagmin and complexin binding to the SNARE complex”, Biophysical Journal, 89, 690 (2005) link or pdf
2004
M. Bowen, K. Weninger, A. Brunger, S. Chu, “Single molecule observation of liposome – bilayer fusion thermally induced by SNAREs”, Biophysical Journal, 87, 3569 (2004) link or pdf
2003
K. Weninger, M. Bowen, S. Chu, A. Brunger, “Single-molecule studies of SNARE complex assembly reveals parallel and antiparallel configurations”, Proc. Nat. Acad. Sci. USA, 100, 14800 (2003) link or pdf
A publication from my older work
S. Putterman, K. Weninger, “Sonoluminescence: How bubbles turn sound into light”, Annual Review of Fluid Mechanics, 32, 45 (2000) link or pdf