@article{saikia_yanez-orozco_qiu_hao_milikisiyants_ou_hamilton_weninger_smirnova_sanabria_et al._2021, title={Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25}, volume={2}, ISSN={["2666-3864"]}, DOI={10.1016/j.xcrp.2021.100616}, abstractNote={SNAP-25 (synaptosomal-associated protein of 25 kDa) is a prototypical intrinsically disordered protein (IDP) that is unstructured by itself but forms coiled-coil helices in the SNARE complex. With high conformational heterogeneity, detailed structural dynamics of unbound SNAP-25 remain elusive. Here, we report an integrative method to probe the structural dynamics of SNAP-25 by combining replica-exchange discrete molecular dynamics (rxDMD) simulations and label-based experiments at ensemble and single-molecule levels. The rxDMD simulations systematically characterize the coil-to-molten globular transition and reconstruct structural ensemble consistent with prior ensemble experiments. Label-based experiments using Förster resonance energy transfer and double electron-electron resonance further probe the conformational dynamics of SNAP-25. Agreements between simulations and experiments under both ensemble and single-molecule conditions allow us to assign specific helix-coil transitions in SNAP-25 that occur in submillisecond timescales and potentially play a vital role in forming the SNARE complex. We expect that this integrative approach may help further our understanding of IDPs.}, number={11}, journal={CELL REPORTS PHYSICAL SCIENCE}, author={Saikia, Nabanita and Yanez-Orozco, Inna S. and Qiu, Ruoyi and Hao, Pengyu and Milikisiyants, Sergey and Ou, Erkang and Hamilton, George L. and Weninger, Keith R. and Smirnova, Tatyana I and Sanabria, Hugo and et al.}, year={2021}, month={Nov} }
 @article{hellenkamp_schmid_doroshenko_opanasyuk_kuehnemuth_adariani_ambrose_aznauryan_barth_birkedal_et al._2018, title={Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study}, volume={15}, ISSN={["1548-7105"]}, DOI={10.1038/s41592-018-0085-0}, abstractNote={Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods.}, number={9}, journal={NATURE METHODS}, author={Hellenkamp, Bjoern and Schmid, Sonja and Doroshenko, Olga and Opanasyuk, Oleg and Kuehnemuth, Ralf and Adariani, Soheila Rezaei and Ambrose, Benjamin and Aznauryan, Mikayel and Barth, Anders and Birkedal, Victoria and et al.}, year={2018}, month={Sep}, pages={669-+} }
 @article{gauer_leblanc_hao_qiu_case_sakato_hingorani_erie_weninger_2016, title={Single-molecule FRET to measure conformational dynamics of DNA mismatch repair proteins}, volume={581}, journal={Single-molecule enzymology: fluorescence-based and high-throughput methods}, author={Gauer, J. W. and LeBlanc, S. and Hao, P. and Qiu, R. and Case, B. C. and Sakato, M. and Hingorani, M. M. and Erie, D. A. and Weninger, K. R.}, year={2016}, pages={285–315} }
 @article{qiu_sakato_sacho_wilkins_zhang_modrichd_hingorani_erie_weninger_2015, title={MutL traps MutS at a DNA mismatch}, volume={112}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1505655112}, abstractNote={Significance}, number={35}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Qiu, Ruoyi and Sakato, Miho and Sacho, Elizabeth J. and Wilkins, Hunter and Zhang, Xingdong and Modrichd, Paul and Hingorani, Manju M. and Erie, Dorothy A. and Weninger, Keith R.}, year={2015}, month={Sep}, pages={10914–10919} }
 @article{mooney_qiu_kim_sacho_rajagopalan_johng_shiraishi_kulkarni_weninger_2014, title={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}, volume={53}, ISSN={["0006-2960"]}, DOI={10.1021/bi500013w}, abstractNote={Prostate-associated gene 4 (PAGE4) is a cancer/testis antigen that is typically restricted to the testicular germ cells but is aberrantly expressed in cancer. Furthermore, PAGE4 is developmentally regulated with dynamic expression patterns in the developing prostate and is also a stress-response protein that is upregulated in response to cellular stress. PAGE4 interacts with c-Jun, which is activated by the stress-response kinase JNK1, and plays an important role in the development and pathology of the prostate gland. Here, we have identified homeodomain-interacting protein kinase 1 (HIPK1), also a component of the stress-response pathway, as a kinase that phosphorylates PAGE4 at T51. We show that phosphorylation of PAGE4 is critical for its transcriptional activity since mutating this T residue abolishes its ability to potentiate c-Jun transactivation. In vitro single molecule FRET indicates phosphorylation results in compaction of (still) intrinsically disordered PAGE4. Interestingly, however, while our previous observations indicated that the wild-type nonphosphorylated PAGE4 protein interacted with c-Jun [RajagopalanK. et al. (2014) Biochim, Biophys. Acta1842, 154−16324263171], here we show that phosphorylation of PAGE4 weakens its interaction with c-Jun in vitro. These data suggest that phosphorylation induces conformational changes in natively disordered PAGE4 resulting in its decreased affinity for c-Jun to promote interaction of c-Jun with another, unidentified, partner. Alternatively, phosphorylated PAGE4 may induce transcription of a novel partner, which then potentiates c-Jun transactivation. Regardless, the present results clearly implicate PAGE4 as a component of the stress-response pathway and uncover a novel link between components of this pathway and prostatic development and disease.}, number={10}, journal={BIOCHEMISTRY}, author={Mooney, Steven M. and Qiu, Ruoyi and Kim, John J. and Sacho, Elizabeth J. and Rajagopalan, Krithika and Johng, Dorhyun and Shiraishi, Takumi and Kulkarni, Prakash and Weninger, Keith R.}, year={2014}, month={Mar}, pages={1670–1679} }
 @article{derocco_sass_qiu_weninger_erie_2014, title={Dynamics of MutS-Mismatched DNA Complexes Are Predictive of Their Repair Phenotypes}, volume={53}, ISSN={["0006-2960"]}, DOI={10.1021/bi401429b}, abstractNote={MutS recognizes base–base mismatches and base insertions/deletions (IDLs) in newly replicated DNA. Specific interactions between MutS and these errors trigger a cascade of protein–protein interactions that ultimately lead to their repair. The inability to explain why different DNA errors are repaired with widely varying efficiencies in vivo remains an outstanding example of our limited knowledge of this process. Here, we present single-molecule Förster resonance energy transfer measurements of the DNA bending dynamics induced by Thermus aquaticus MutS and the E41A mutant of MutS, which is known to have error specific deficiencies in signaling repair. We compared three DNA mismatches/IDLs (T-bulge, GT, and CC) with repair efficiencies ranging from high to low. We identify three dominant DNA bending states [slightly bent/unbent (U), intermediately bent (I), and significantly bent (B)] and find that the kinetics of interconverting among states varies widely for different complexes. The increased stability of MutS–mismatch/IDL complexes is associated with stabilization of U and lowering of the B to U transition barrier. Destabilization of U is always accompanied by a destabilization of B, supporting the suggestion that B is a “required” precursor to U. Comparison of MutS and MutS-E41A dynamics on GT and the T-bulge suggests that hydrogen bonding to MutS facilitates the changes in base–base hydrogen bonding that are required to achieve the U state, which has been implicated in repair signaling. Taken together with repair propensities, our data suggest that the bending kinetics of MutS–mismatched DNA complexes may control the entry into functional pathways for downstream signaling of repair.}, number={12}, journal={BIOCHEMISTRY}, author={DeRocco, Vanessa C. and Sass, Lauryn E. and Qiu, Ruoyi and Weninger, Keith R. and Erie, Dorothy A.}, year={2014}, month={Apr}, pages={2043–2052} }
 @article{rajagopalan_qiu_mooney_rao_shiraishi_sacho_huang_shapiro_keith_kulkarni_et al._2014, title={The Stress-response protein prostate-associated gene 4, interacts with c-Jun and potentiates its transactivation}, volume={1842}, ISSN={["0006-3002"]}, DOI={10.1016/j.bbadis.2013.11.014}, abstractNote={The Cancer/Testis Antigen (CTA), Prostate-associated Gene 4 (PAGE4), is a stress-response protein that is upregulated in prostate cancer (PCa) especially in precursor lesions that result from inflammatory stress. In cells under stress, translocation of PAGE4 to mitochondria increases while production of reactive oxygen species decreases. Furthermore, PAGE4 is also upregulated in human fetal prostate, underscoring its potential role in development. However, the proteins that interact with PAGE4 and the mechanisms underlying its pleiotropic functions in prostatic development and disease remain unknown. Here, we identified c-Jun as a PAGE4 interacting partner. We show that both PAGE4 and c-Jun are overexpressed in the human fetal prostate; and in cell-based assays, PAGE4 robustly potentiates c-Jun transactivation. Single-molecule Förster resonance energy transfer experiments indicate that upon binding to c-Jun, PAGE4 undergoes conformational changes. However, no interaction is observed in presence of BSA or unilamellar vesicles containing the mitochondrial inner membrane diphosphatidylglycerol lipid marker cardiolipin. Together, our data indicate that PAGE4 specifically interacts with c-Jun and that, conformational dynamics may account for its observed pleiotropic functions. To our knowledge, this is the first report demonstrating crosstalk between a CTA and a proto-oncogene. Disrupting PAGE4/c-Jun interactions using small molecules may represent a novel therapeutic strategy for PCa.}, number={2}, journal={BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE}, author={Rajagopalan, K. and Qiu, R. Y. and Mooney, S. M. and Rao, S. and Shiraishi, T. and Sacho, E. and Huang, H. Y. and Shapiro, E. and keith and Kulkarni, P. and et al.}, year={2014}, month={Feb}, pages={154–163} }
 @article{qiu_derocco_harris_sharma_hingorani_erie_weninger_2012, title={Large conformational changes in MutS during DNA scanning, mismatch recognition and repair signalling}, volume={31}, ISSN={["1460-2075"]}, DOI={10.1038/emboj.2012.95}, abstractNote={MutS protein recognizes mispaired bases in DNA and targets them for mismatch repair. Little is known about the transient conformations of MutS as it signals initiation of repair. We have used single-molecule fluorescence resonance energy transfer (FRET) measurements to report the conformational dynamics of MutS during this process. We find that the DNA-binding domains of MutS dynamically interconvert among multiple conformations when the protein is free and while it scans homoduplex DNA. Mismatch recognition restricts MutS conformation to a single state. Steady-state measurements in the presence of nucleotides suggest that both ATP and ADP must be bound to MutS during its conversion to a sliding clamp form that signals repair. The transition from mismatch recognition to the sliding clamp occurs via two sequential conformational changes. These intermediate conformations of the MutS:DNA complex persist for seconds, providing ample opportunity for interaction with downstream proteins required for repair.}, number={11}, journal={EMBO JOURNAL}, author={Qiu, Ruoyi and DeRocco, Vanessa C. and Harris, Credle and Sharma, Anushi and Hingorani, Manju M. and Erie, Dorothy A. and Weninger, Keith R.}, year={2012}, month={May}, pages={2528–2540} }