Keith R. Weninger

DNA mutagenesis driven by transcription factor competition with mismatch repair

Zhu, W., Zhang, Y., Sahay, H., Wasserman, H., Afek, A., Williams, J., … Gordân, R. (2025, July 29). Cell, Vol. 188.

Evolving concepts of the protein universe

Kulkarni, P., Porter, L., Chou, T.-F., Chong, S., Chiti, F., Schafer, J. W., … Salgia, R. (2025, February 13). IScience, Vol. 28.

Combining single-molecule and structural studies reveals protein and DNA conformations and assemblies that govern DNA mismatch repair

Erie, D. A., & Weninger, K. R. (2024, September 10). Current Opinion in Structural Biology, Vol. 89.

Reply to: On the statistical foundation of a recent single molecule FRET benchmark

Götz, M., Barth, A., Bohr, S. S.-R., Börner, R., Chen, J., Cordes, T., … Schmid, S. (2024, April 30). Nature Communications, Vol. 15.

Structural and Dynamical Properties of Nucleic Acid Hairpins Implicated in Trinucleotide Repeat Expansion Diseases

Pan, F., Xu, P., Roland, C., Sagui, C., & Weninger, K. (2024, October 10). Biomolecules, Vol. 14.

A nanophotonic interferometer

Ghaffari, A., Kashani, S., Do, K., Weninger, K., & Riehn, R. (2023, January 18). Nanotechnology, Vol. 34.

Ex vivo analysis of ultraviolet radiation transmission through ocular media and retina in select species

Experimental Eye Research, 233, 109550.

Frustration Between Preferred States of Complementary Trinucleotide Repeat DNA Hairpins Anticorrelates with Expansion Disease Propensity

Xu, P., Zhang, J., Pan, F., Mahn, C., Roland, C., Sagui, C., & Weninger, K. (2023, April 5). Journal of Molecular Biology, Vol. 435.

Illuminating Intrinsically Disordered Proteins with Integrative Structural Biology

Evans, R., Ramisetty, S., Kulkarni, P., & Weninger, K. (2023, January 7). Biomolecules, Vol. 13.

A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories

Götz, M., Barth, A., Bohr, S. S.-R., Börner, R., Chen, J., Cordes, T., … Schmid, S. (2022, September 14). Nature Communications, Vol. 9.

A nanophotonic interferometer for small particle detection

Esfehani, A. G., Do, K., Kashani, S., Weninger, K., & Riehn, R. (2022, September 30). INTERFEROMETRY XXI.

Non-ergodicity of a globular protein extending beyond its functional timescale

Li, J., Xie, J. F., Godec, A., Weninger, K. R., Liu, C., Smith, J. C., & Hong, L. (2022, January 1). Chemical Science, Vol. 8.

Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25

Saikia, N., Yanez-Orozco, I. S., Qiu, R., Hao, P., Milikisiyants, S., Ou, E., … Ding, F. (2021, October 19). Cell Reports Physical Science, Vol. 11.

Molecular conformations and dynamics of nucleotide repeats associated with neurodegenerative diseases: double helices and CAG hairpin loops

Pan, F., Zhang, Y., Xu, P., Man, V. H., Roland, C., Weninger, K., & Sagui, C. (2021, January 1). Computational and Structural Biotechnology Journal, Vol. 19, pp. 2819–2832.

Structure, dynamics, and regulation of TRF1-TIN2-mediated trans- and cis-interactions on telomeric DNA

Pan, H., Kaur, P., Barnes, R., Detwiler, A. C., Sanford, S. L., Liu, M., … Wang, H. (2021, August 14). Journal of Biological Chemistry, Vol. 9.

Dynamic human MutSα–MutLα complexes compact mismatched DNA

Bradford, K. C., Wilkins, H., Hao, P., Li, Z. M., Wang, B., Burke, D., … Erie, D. A. (2020, June 25). Proceedings of the National Academy of Sciences, Vol. 117, pp. 16302–16312.

Dynamics of strand slippage in DNA hairpins formed by CAG repeats: roles of sequence parity and trinucleotide interrupts

Xu, P., Pan, F., Roland, C., Sagui, C., & Weninger, K. (2020, January 15). Nucleic Acids Research, Vol. 1.

How Membrane Geometry Regulates Protein Sorting Independently of Mean Curvature

Larsen, J. B., Rosholm, K. R., Kennard, C., Pedersen, S. L., Munch, H. K., Tkach, V., … Stamou, D. (2020, June 23). ACS Central Science, Vol. 6, pp. 1159–1168.

Recurrent mismatch binding by MutS mobile clamps on DNA localizes repair complexes nearby

Hao, P., LeBlanc, S. J., Case, B. C., Elston, T. C., Hingorani, M. M., Erie, D. A., & Weninger, K. R. (2020, July 15). Proceedings of the National Academy of Sciences, Vol. 117, pp. 17775–17784.

Investigating the Function of Mutl Conformational Changes in Mismatch Repair using smFRET

Biophysical Journal, 116(3), 49a–50a.

Spontaneous Switching among Conformational Ensembles in Intrinsically Disordered Proteins

Choi, U., Sanabria, H., Smirnova, T., Bowen, M., & Weninger, K. (2019, March 22). Biomolecules, Vol. 9.

Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level

Biomolecules, 9(2), 77.

TIN2 is an Architectural Protein Stabilizing TRF1 at Telomere

Biophysical Journal, 116(3), 211a–212a.

Toward Single Molecule FRET Studies of DNA Mismatch Repair in Live Bacteria

Biophysical Journal, 116(3), 139a.

Untangling DNA Mismatch Repair Complexes with smFRET and Tethered Particle Motion Analysis

Biophysical Journal, 116(3), 77a.

Coordinated protein and DNA conformational changes govern mismatch repair initiation by MutS

LeBlanc, S. J., Gauer, J. W., Hao, P., Case, B. C., Hingorani, M. M., Weninger, K. R., & Erie, D. A. (2018, September 27). Nucleic Acids Research, Vol. 46, pp. 10782–10795.

Motor-like DNA motion due to an ATP-hydrolyzing protein under nanoconfinement

Scientific Reports, 8(1).

PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer

Journal of Molecular Biology, 430(16), 2422–2438.

Phenotypic Plasticity, Bet-Hedging, and Androgen Independence in Prostate Cancer: Role of Non-Genetic Heterogeneity

Jolly, M. K., Kulkarni, P., Weninger, K., Orban, J., & Levine, H. (2018, March 6). Frontiers in Oncology, Vol. 8.

Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study

Hellenkamp, B., Schmid, S., Doroshenko, O., Opanasyuk, O., Kühnemuth, R., Adariani, S. R., … Hugel, T. (2018, August 24). Nature Methods, Vol. 15, p. 669-.

Prostate-Associated Gene 4 (PAGE4): Leveraging the Conformational Dynamics of a Dancing Protein Cloud as a Therapeutic Target

Salgia, R., Jolly, M., Dorff, T., Lau, C., Weninger, K., Orban, J., & Kulkarni, P. (2018, June 17). Journal of Clinical Medicine, Vol. 7.

Publisher Correction: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study

Nature Methods, 15(11), 984–984.

Single Molecule Experiments Reveal Molecular Level Details of MutS-MutL Interactions in DNA Mismatch Activated Sliding Clamp

Biophysical Journal, 114(3), 85a.

Single Molecule FRET Observations of Folding for DNA Hairpins Containing Trinucleotide Repeats

Biophysical Journal, 114(3), 599a.

Single Molecule FRET: A Powerful Tool to Study Intrinsically Disordered Proteins

LeBlanc, S., Kulkarni, P., & Weninger, K. (2018, November 8). Biomolecules, Vol. 8, p. 140.

Dynamic Studies of MutS-MutL-DNA Complexes in Mismatch Repair

Biophysical Journal, 112(3), 516a–517a.

Mismatch Repair on the Go: Extending the Mechanical Model of DNA Mismatch Repair through Single Molecule Study

Biophysical Journal, 112(3), 514a–515a.

Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and potential role in phenotypic heterogeneity

Kulkarni, P., Jolly, M. K., Jia, D., Mooney, S. M., Bhargava, A., Kagohara, L. T., … Orban, J. (2017, March 13). Proceedings of the National Academy of Sciences, Vol. 114, pp. E2644–2653.

Single Molecule Fluorescence and Atomic Force Microscopy Studies of DNA Repair

Biophysical Journal, 112(3), 7a.

Prostate-associated gene 4 (PAGE4), an intrinsically disordered cancer/testis antigen, is a novel therapeutic target for prostate cancer

Kulkarni, P., Orban, J., Dunker, A. K., & Weninger, K. (2016, January 1). Asian Journal of Andrology, Vol. 18, pp. 695–703.

Single-molecule FRET to measure conformational dynamics of DNA mismatch repair proteins

Single-Molecule Enzymology: Fluorescence-Based and High-Throughput Methods, 581, 285–315.

Venoms from Centruroides sp. Scorpions Cleave SNARE Proteins

Toxicon, 117, 109.

smFRET and DEER Distance Measurements as Applied to Disordered and Structured Proteins

Biophysical Journal, 110(3), 559a.

tN-Ras, Synaptotagmin1 C2Ab, Annexinb12 and Amphiphysin NBAR can Discriminate Spherical from Cylindrical Membrane Curvature

Biophysical Journal, 110(3), 357a.

“Metalloproteases in new world scorpion venoms cleave intracellular membrane fusion SNARE proteins VAMP2 and VAMP8”

“Metalloproteases in new world scorpion venoms cleave intracellular membrane fusion SNARE proteins VAMP2 and VAMP8.” Toxicon, 117, 104.

MutL traps MutS at a DNA mismatch

Qiu, R., Sakato, M., Sacho, E. J., Wilkins, H., Zhang, X., Modrich, P., … Weninger, K. R. (2015, August 17). Proceedings of the National Academy of Sciences, Vol. 112, pp. 10914–10919.

Phosphorylation-induced Conformational Ensemble Switching in an Intrinsically Disordered Cancer/Testis Antigen

He, Y. N., Chen, Y. H., Mooney, S. M., Rajagopalan, K., Bhargava, A., Sacho, E., … al. (2015, August 5). Journal of Biological Chemistry, Vol. 290, pp. 25090–25102.

Toward Adding Complexity in Single Molecule FRET Studies of DNA Mismatch Repair

Biophysical Journal, 108(2), 69a–70a.

Cancer/Testis Antigen PAGE4, a Regulator of c-Jun Transactivation, Is Phosphorylated by Homeodomain-Interacting Protein Kinase 1, a Component of the Stress-Response Pathway

Mooney, S. M., Qiu, R., Kim, J. J., Sacho, E. J., Rajagopalan, K., Johng, D., … Weninger, K. R. (2014, February 23). Biochemistry, Vol. 53, pp. 1670–1679.

Dynamics of MutS–Mismatched DNA Complexes Are Predictive of Their Repair Phenotypes

DeRocco, V. C., Sass, L. E., Qiu, R., Weninger, K. R., & Erie, D. A. (2014, March 4). Biochemistry, Vol. 53, pp. 2043–2052.

Investigation of Calcein for Reporting Content Mixing During Viral Membrane Fusion Experiments

Biophysical Journal, 106(2), 707a.

Single molecule studies of DNA mismatch repair

Erie, D. A., & Weninger, K. R. (2014, April 18). DNA Repair, Vol. 20, pp. 71–81.

Dynamics of DNA Mismatch Repair Initiation Complex Revealed by Single Molecule Fluorescence

Biophysical Journal, 104(2), 368a.

The Stress-response protein prostate-associated gene 4, interacts with c-Jun and potentiates its transactivation

Rajagopalan, K., Qiu, R. Y., Mooney, S. M., Rao, S., Shiraishi, T., Sacho, E., … al. (2013, November 21). Biochimica Et Biophysica Acta (BBA) - Molecular Basis of Disease, Vol. 1842, pp. 154–163.

Conformational Changes in MutS during Mismtach Repair Signaling Determined with Single Molecule FRET

Biophysical Journal, 102(3), 283a.

Cooperative All-Or-None Recruitment of Synaptotagmin C2AB on Single Vesicles Explains Why Ca2+ Regulates the Amplitude of SNARE Mediated Vesicle Fusion

Biophysical Journal, 102(3), 318a–319a.

Dynamics of DNA Mismatch Repair Revealed by Single Molecule FRET

Biophysical Journal, 102(3), 235a.

Large conformational changes in MutS during DNA scanning, mismatch recognition and repair signalling

Qiu, R., DeRocco, V. C., Harris, C., Sharma, A., Hingorani, M. M., Erie, D. A., & Weninger, K. R. (2012, April 13). The EMBO Journal, Vol. 31, pp. 2528–2540.

Macromolecular Models by Single Molecule FRET

In NATO Science for Peace and Security Series B: Physics and Biophysics (pp. 1–19).

Opacity and Transport Measurements Reveal That Dilute Plasma Models of Sonoluminescence Are Not Valid

Khalid, S., Kappus, B., Weninger, K., & Putterman, S. (2012, March 6). Physical Review Letters, Vol. 108.

Single Molecule FRET Studies of the DNA Mismatch Repair Protein MutSα using Specific Labeling with Unnatural Amino Acids

Biophysical Journal, 102(3), 282a.

Beyond the Random Coil: Stochastic Conformational Switching in Intrinsically Disordered Proteins

Choi, U. B., McCann, J. J., Weninger, K. R., & Bowen, M. E. (2011, April 1). Structure, Vol. 19, pp. 566–576.

Complexin arrests a neighbor

Weninger, K. R. (2011, August 1). Nature Structural & Molecular Biology, Vol. 18, pp. 861–863.

Single Molecule FRET Study of Nucleotide Binding Effects on Muts Proteins

Biophysical Journal, 100(3), 223a.

Detecting the conformation of individual proteins in live cells

Sakon, J. J., & Weninger, K. R. (2010, January 31). Nature Methods, Vol. 7, pp. 203–256.

Four-Color Single-Molecule Fluorescence with Noncovalent Dye Labeling to Monitor Dynamic Multimolecular Complexes

DeRocco, V. C., Anderson, T., Piehler, J., Erie, D. A., & Weninger, K. (2010, October 1). BioTechniques, Vol. 49, p. 807-.

Optimizing Methods to Recover Absolute FRET Efficiency from Immobilized Single Molecules

McCann, J. J., Choi, U. B., Zheng, L., Weninger, K., & Bowen, M. E. (2010, August 1). Biophysical Journal, Vol. 99, pp. 961–970.

Recovering Absolute Fret Efficiency from Single Molecules: Comparing Methods of Gamma Correction

Biophysical Journal, 98(3), 186a–187a.

Single-Molecule FRET TACKLE Reveals Highly Dynamic Mismatched DNA−MutS Complexes

Sass, L. E., Lanyi, C., Weninger, K., & Erie, D. A. (2010, February 24). Biochemistry, Vol. 49, pp. 3174–3190.

Single-molecule FRET–derived model of the synaptotagmin 1–SNARE fusion complex

Choi, U. B., Strop, P., Vrljic, M., Chu, S., Brunger, A. T., & Weninger, K. R. (2010, February 21). Nature Structural & Molecular Biology, Vol. 17, pp. 318–384.

Three-dimensional molecular modeling with single molecule FRET

Brunger, A. T., Strop, P., Vrljic, M., Chu, S., & Weninger, K. R. (2010, September 16). Journal of Structural Biology, Vol. 173, pp. 497–505.

How Do Adhesion Proteins Stick?

Weninger, K. (2009, August 1). Structure, Vol. 17, pp. 1035–1036.

Physical Aspects of Viral Membrane Fusion

Wessels, L., & Weninger, K. (2009, January 1). The Scientific World JOURNAL, Vol. 9, pp. 764–780.

Single-Molecule Studies of the Neuronal SNARE Fusion Machinery

Brunger, A. T., Weninger, K., Bowen, M., & Chu, S. (2009, June 1). Annual Review of Biochemistry, Vol. 78, pp. 903–928.

Vesicle-associated Membrane Protein (VAMP) Cleavage by a New Metalloprotease from the Brazilian Scorpion Tityus serrulatus

Fletcher, P. L., Fletcher, M. D., Weninger, K., Anderson, T. E., & Martin, B. M. (2009, December 22). Journal of Biological Chemistry, Vol. 285, pp. 7405–7416.

Accessory Proteins Stabilize the Acceptor Complex for Synaptobrevin, the 1:1 Syntaxin/SNAP-25 Complex

Weninger, K., Bowen, M. E., Choi, U. B., Chu, S., & Brunger, A. T. (2008, February 1). Structure, Vol. 16, pp. 308–320.