[{"abstract":[{"lang":"eng","text":"Coordinated conformational transitions in oligomeric enzymatic complexes modulate function in response to substrates and play a crucial role in enzyme inhibition and activation. Caseinolytic protease (ClpP) is a tetradecameric complex, which has emerged as a drug target against multiple pathogenic bacteria. Activation of different ClpPs by inhibitors has been independently reported from drug development efforts, but no rationale for inhibitor-induced activation has been hitherto proposed. Using an integrated approach that includes x-ray crystallography, solid- and solution-state nuclear magnetic resonance, molecular dynamics simulations, and isothermal titration calorimetry, we show that the proteasome inhibitor bortezomib binds to the ClpP active-site serine, mimicking a peptide substrate, and induces a concerted allosteric activation of the complex. The bortezomib-activated conformation also exhibits a higher affinity for its cognate unfoldase ClpX. We propose a universal allosteric mechanism, where substrate binding to a single subunit locks ClpP into an active conformation optimized for chaperone association and protein processive degradation."}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":" https://doi.org/10.1126/sciadv.aaw3818"}],"month":"09","intvolume":" 5","publication_identifier":{"issn":["2375-2548"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"9","volume":5,"_id":"8406","type":"journal_article","article_type":"original","status":"public","date_updated":"2021-01-12T08:19:03Z","extern":"1","publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa":1,"year":"2019","day":"04","publication":"Science Advances","doi":"10.1126/sciadv.aaw3818","date_published":"2019-09-04T00:00:00Z","date_created":"2020-09-17T10:28:36Z","article_number":"eaaw3818","citation":{"short":"J. Felix, K. Weinhäupl, C. Chipot, F. Dehez, A. Hessel, D.F. Gauto, C. Morlot, O. Abian, I. Gutsche, A. Velazquez-Campoy, P. Schanda, H. Fraga, Science Advances 5 (2019).","ieee":"J. Felix et al., “Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors,” Science Advances, vol. 5, no. 9. American Association for the Advancement of Science, 2019.","ama":"Felix J, Weinhäupl K, Chipot C, et al. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. 2019;5(9). doi:10.1126/sciadv.aaw3818","apa":"Felix, J., Weinhäupl, K., Chipot, C., Dehez, F., Hessel, A., Gauto, D. F., … Fraga, H. (2019). Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw3818","mla":"Felix, Jan, et al. “Mechanism of the Allosteric Activation of the ClpP Protease Machinery by Substrates and Active-Site Inhibitors.” Science Advances, vol. 5, no. 9, eaaw3818, American Association for the Advancement of Science, 2019, doi:10.1126/sciadv.aaw3818.","ista":"Felix J, Weinhäupl K, Chipot C, Dehez F, Hessel A, Gauto DF, Morlot C, Abian O, Gutsche I, Velazquez-Campoy A, Schanda P, Fraga H. 2019. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. 5(9), eaaw3818.","chicago":"Felix, Jan, Katharina Weinhäupl, Christophe Chipot, François Dehez, Audrey Hessel, Diego F. Gauto, Cecile Morlot, et al. “Mechanism of the Allosteric Activation of the ClpP Protease Machinery by Substrates and Active-Site Inhibitors.” Science Advances. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/sciadv.aaw3818."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jan","full_name":"Felix, Jan","last_name":"Felix"},{"first_name":"Katharina","last_name":"Weinhäupl","full_name":"Weinhäupl, Katharina"},{"first_name":"Christophe","full_name":"Chipot, Christophe","last_name":"Chipot"},{"first_name":"François","last_name":"Dehez","full_name":"Dehez, François"},{"first_name":"Audrey","full_name":"Hessel, Audrey","last_name":"Hessel"},{"last_name":"Gauto","full_name":"Gauto, Diego F.","first_name":"Diego F."},{"first_name":"Cecile","full_name":"Morlot, Cecile","last_name":"Morlot"},{"first_name":"Olga","last_name":"Abian","full_name":"Abian, Olga"},{"full_name":"Gutsche, Irina","last_name":"Gutsche","first_name":"Irina"},{"first_name":"Adrian","full_name":"Velazquez-Campoy, Adrian","last_name":"Velazquez-Campoy"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda"},{"last_name":"Fraga","full_name":"Fraga, Hugo","first_name":"Hugo"}],"article_processing_charge":"No","title":"Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors"},{"publisher":"American Chemical Society","quality_controlled":"1","doi":"10.1021/jacs.8b09258","date_published":"2019-01-08T00:00:00Z","date_created":"2020-09-17T10:29:50Z","page":"858-869","day":"08","publication":"Journal of the American Chemical Society","year":"2019","title":"Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques","author":[{"last_name":"Rovó","full_name":"Rovó, Petra","first_name":"Petra"},{"full_name":"Smith, Colin A.","last_name":"Smith","first_name":"Colin A."},{"first_name":"Diego","full_name":"Gauto, Diego","last_name":"Gauto"},{"last_name":"de Groot","full_name":"de Groot, Bert L.","first_name":"Bert L."},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda"},{"first_name":"Rasmus","full_name":"Linser, Rasmus","last_name":"Linser"}],"external_id":{"pmid":["30620186"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Rovó, Petra, Colin A. Smith, Diego Gauto, Bert L. de Groot, Paul Schanda, and Rasmus Linser. “Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.8b09258.","ista":"Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. 2019. Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. 141(2), 858–869.","mla":"Rovó, Petra, et al. “Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.” Journal of the American Chemical Society, vol. 141, no. 2, American Chemical Society, 2019, pp. 858–69, doi:10.1021/jacs.8b09258.","apa":"Rovó, P., Smith, C. A., Gauto, D., de Groot, B. L., Schanda, P., & Linser, R. (2019). Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.8b09258","ama":"Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. 2019;141(2):858-869. doi:10.1021/jacs.8b09258","ieee":"P. Rovó, C. A. Smith, D. Gauto, B. L. de Groot, P. Schanda, and R. Linser, “Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques,” Journal of the American Chemical Society, vol. 141, no. 2. American Chemical Society, pp. 858–869, 2019.","short":"P. Rovó, C.A. Smith, D. Gauto, B.L. de Groot, P. Schanda, R. Linser, Journal of the American Chemical Society 141 (2019) 858–869."},"month":"01","intvolume":" 141","oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"NMR relaxation dispersion methods provide a holistic way to observe microsecond time-scale protein backbone motion both in solution and in the solid state. Different nuclei (1H and 15N) and different relaxation dispersion techniques (Bloch–McConnell and near-rotary-resonance) give complementary information about the amplitudes and time scales of the conformational dynamics and provide comprehensive insights into the mechanistic details of the structural rearrangements. In this paper, we exemplify the benefits of the combination of various solution- and solid-state relaxation dispersion methods on a microcrystalline protein (α-spectrin SH3 domain), for which we are able to identify and model the functionally relevant conformational rearrangements around the ligand recognition loop occurring on multiple microsecond time scales. The observed loop motions suggest that the SH3 domain exists in a binding-competent conformation in dynamic equilibrium with a sterically impaired ground-state conformation both in solution and in crystalline form. This inherent plasticity between the interconverting macrostates is compatible with a conformational-preselection model and provides new insights into the recognition mechanisms of SH3 domains."}],"issue":"2","volume":141,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0002-7863","1520-5126"]},"publication_status":"published","status":"public","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"article_type":"original","type":"journal_article","_id":"8413","extern":"1","date_updated":"2021-01-12T08:19:07Z"},{"date_updated":"2021-01-12T08:19:06Z","extern":"1","type":"journal_article","article_type":"original","status":"public","keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"_id":"8412","volume":20,"issue":"2","publication_identifier":{"issn":["1439-4235"]},"publication_status":"published","language":[{"iso":"eng"}],"month":"01","intvolume":" 20","abstract":[{"text":"Microsecond to millisecond timescale backbone dynamics of the amyloid core residues in Y145Stop human prion protein (PrP) fibrils were investigated by using 15N rotating frame (R1ρ) relaxation dispersion solid‐state nuclear magnetic resonance spectroscopy over a wide range of spin‐lock fields. Numerical simulations enabled the experimental relaxation dispersion profiles for most of the fibril core residues to be modelled by using a two‐state exchange process with a common exchange rate of 1000 s−1, corresponding to protein backbone motion on the timescale of 1 ms, and an excited‐state population of 2 %. We also found that the relaxation dispersion profiles for several amino acids positioned near the edges of the most structured regions of the amyloid core were better modelled by assuming somewhat higher excited‐state populations (∼5–15 %) and faster exchange rate constants, corresponding to protein backbone motions on the timescale of ∼100–300 μs. The slow backbone dynamics of the core residues were evaluated in the context of the structural model of human Y145Stop PrP amyloid.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","author":[{"first_name":"Matthew D.","full_name":"Shannon, Matthew D.","last_name":"Shannon"},{"full_name":"Theint, Theint","last_name":"Theint","first_name":"Theint"},{"last_name":"Mukhopadhyay","full_name":"Mukhopadhyay, Dwaipayan","first_name":"Dwaipayan"},{"first_name":"Krystyna","last_name":"Surewicz","full_name":"Surewicz, Krystyna"},{"last_name":"Surewicz","full_name":"Surewicz, Witold K.","first_name":"Witold K."},{"first_name":"Dominique","full_name":"Marion, Dominique","last_name":"Marion"},{"last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"},{"first_name":"Christopher P.","last_name":"Jaroniec","full_name":"Jaroniec, Christopher P."}],"external_id":{"pmid":["30276945"]},"article_processing_charge":"No","title":"Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR","citation":{"ama":"Shannon MD, Theint T, Mukhopadhyay D, et al. Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. 2019;20(2):311-317. doi:10.1002/cphc.201800779","apa":"Shannon, M. D., Theint, T., Mukhopadhyay, D., Surewicz, K., Surewicz, W. K., Marion, D., … Jaroniec, C. P. (2019). Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201800779","short":"M.D. Shannon, T. Theint, D. Mukhopadhyay, K. Surewicz, W.K. Surewicz, D. Marion, P. Schanda, C.P. Jaroniec, ChemPhysChem 20 (2019) 311–317.","ieee":"M. D. Shannon et al., “Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR,” ChemPhysChem, vol. 20, no. 2. Wiley, pp. 311–317, 2019.","mla":"Shannon, Matthew D., et al. “Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” ChemPhysChem, vol. 20, no. 2, Wiley, 2019, pp. 311–17, doi:10.1002/cphc.201800779.","ista":"Shannon MD, Theint T, Mukhopadhyay D, Surewicz K, Surewicz WK, Marion D, Schanda P, Jaroniec CP. 2019. Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. 20(2), 311–317.","chicago":"Shannon, Matthew D., Theint Theint, Dwaipayan Mukhopadhyay, Krystyna Surewicz, Witold K. Surewicz, Dominique Marion, Paul Schanda, and Christopher P. Jaroniec. “Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201800779."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"311-317","doi":"10.1002/cphc.201800779","date_published":"2019-01-21T00:00:00Z","date_created":"2020-09-17T10:29:43Z","year":"2019","day":"21","publication":"ChemPhysChem","publisher":"Wiley","quality_controlled":"1"},{"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Studying protein dynamics on microsecond‐to‐millisecond (μs‐ms) time scales can provide important insight into protein function. In magic‐angle‐spinning (MAS) NMR, μs dynamics can be visualized by R1p rotating‐frame relaxation dispersion experiments in different regimes of radio‐frequency field strengths: at low RF field strength, isotropic‐chemical‐shift fluctuation leads to “Bloch‐McConnell‐type” relaxation dispersion, while when the RF field approaches rotary resonance conditions bond angle fluctuations manifest as increased R1p rate constants (“Near‐Rotary‐Resonance Relaxation Dispersion”, NERRD). Here we explore the joint analysis of both regimes to gain comprehensive insight into motion in terms of geometric amplitudes, chemical‐shift changes, populations and exchange kinetics. We use a numerical simulation procedure to illustrate these effects and the potential of extracting exchange parameters, and apply the methodology to the study of a previously described conformational exchange process in microcrystalline ubiquitin.","lang":"eng"}],"intvolume":" 20","month":"01","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1439-4235"]},"issue":"2","volume":20,"_id":"8411","keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"status":"public","type":"journal_article","article_type":"original","extern":"1","date_updated":"2021-01-12T08:19:06Z","publisher":"Wiley","quality_controlled":"1","publication":"ChemPhysChem","day":"21","year":"2019","date_created":"2020-09-17T10:29:36Z","date_published":"2019-01-21T00:00:00Z","doi":"10.1002/cphc.201800935","page":"276-284","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Marion, Dominique, et al. “Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” ChemPhysChem, vol. 20, no. 2, Wiley, 2019, pp. 276–84, doi:10.1002/cphc.201800935.","short":"D. Marion, D.F. Gauto, I. Ayala, K. Giandoreggio-Barranco, P. Schanda, ChemPhysChem 20 (2019) 276–284.","ieee":"D. Marion, D. F. Gauto, I. Ayala, K. Giandoreggio-Barranco, and P. Schanda, “Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR,” ChemPhysChem, vol. 20, no. 2. Wiley, pp. 276–284, 2019.","ama":"Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. 2019;20(2):276-284. doi:10.1002/cphc.201800935","apa":"Marion, D., Gauto, D. F., Ayala, I., Giandoreggio-Barranco, K., & Schanda, P. (2019). Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201800935","chicago":"Marion, Dominique, Diego F. Gauto, Isabel Ayala, Karine Giandoreggio-Barranco, and Paul Schanda. “Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201800935.","ista":"Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. 2019. Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. 20(2), 276–284."},"title":"Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR","article_processing_charge":"No","external_id":{"pmid":["30444575"]},"author":[{"last_name":"Marion","full_name":"Marion, Dominique","first_name":"Dominique"},{"first_name":"Diego F.","full_name":"Gauto, Diego F.","last_name":"Gauto"},{"first_name":"Isabel","full_name":"Ayala, Isabel","last_name":"Ayala"},{"full_name":"Giandoreggio-Barranco, Karine","last_name":"Giandoreggio-Barranco","first_name":"Karine"},{"last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"}]},{"main_file_link":[{"url":"https://arxiv.org/abs/1809.08947","open_access":"1"}],"intvolume":" 374","month":"05","abstract":[{"text":"We consider billiards obtained by removing three strictly convex obstacles satisfying the non-eclipse condition on the plane. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift on three symbols that provides a natural labeling of all periodic orbits. We study the following inverse problem: does the Marked Length Spectrum (i.e., the set of lengths of periodic orbits together with their labeling), determine the geometry of the billiard table? We show that from the Marked Length Spectrum it is possible to recover the curvature at periodic points of period two, as well as the Lyapunov exponent of each periodic orbit.","lang":"eng"}],"oa_version":"Preprint","issue":"3","volume":374,"publication_status":"published","publication_identifier":{"issn":["0010-3616","1432-0916"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"status":"public","_id":"8415","date_updated":"2021-01-12T08:19:08Z","extern":"1","oa":1,"quality_controlled":"1","publisher":"Springer Nature","page":"1531-1575","date_created":"2020-09-17T10:41:27Z","date_published":"2019-05-09T00:00:00Z","doi":"10.1007/s00220-019-03448-x","year":"2019","publication":"Communications in Mathematical Physics","day":"09","article_processing_charge":"No","external_id":{"arxiv":["1809.08947"]},"author":[{"full_name":"Bálint, Péter","last_name":"Bálint","first_name":"Péter"},{"first_name":"Jacopo","last_name":"De Simoi","full_name":"De Simoi, Jacopo"},{"first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim"},{"last_name":"Leguil","full_name":"Leguil, Martin","first_name":"Martin"}],"title":"Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards","citation":{"chicago":"Bálint, Péter, Jacopo De Simoi, Vadim Kaloshin, and Martin Leguil. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” Communications in Mathematical Physics. Springer Nature, 2019. https://doi.org/10.1007/s00220-019-03448-x.","ista":"Bálint P, De Simoi J, Kaloshin V, Leguil M. 2019. Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. 374(3), 1531–1575.","mla":"Bálint, Péter, et al. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” Communications in Mathematical Physics, vol. 374, no. 3, Springer Nature, 2019, pp. 1531–75, doi:10.1007/s00220-019-03448-x.","short":"P. Bálint, J. De Simoi, V. Kaloshin, M. Leguil, Communications in Mathematical Physics 374 (2019) 1531–1575.","ieee":"P. Bálint, J. De Simoi, V. Kaloshin, and M. Leguil, “Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards,” Communications in Mathematical Physics, vol. 374, no. 3. Springer Nature, pp. 1531–1575, 2019.","ama":"Bálint P, De Simoi J, Kaloshin V, Leguil M. Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. 2019;374(3):1531-1575. doi:10.1007/s00220-019-03448-x","apa":"Bálint, P., De Simoi, J., Kaloshin, V., & Leguil, M. (2019). Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03448-x"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]