دورية أكاديمية

Structural basis of substrate recognition and allosteric activation of the proapoptotic mitochondrial HtrA2 protease.

التفاصيل البيبلوغرافية
العنوان: Structural basis of substrate recognition and allosteric activation of the proapoptotic mitochondrial HtrA2 protease.
المؤلفون: Aspholm EE; Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden., Lidman J; Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden., Burmann BM; Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden. bjorn.marcus.burmann@gu.se.; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden. bjorn.marcus.burmann@gu.se.
المصدر: Nature communications [Nat Commun] 2024 May 30; Vol. 15 (1), pp. 4592. Date of Electronic Publication: 2024 May 30.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : Nature Pub. Group
مواضيع طبية MeSH: High-Temperature Requirement A Serine Peptidase 2*/metabolism , High-Temperature Requirement A Serine Peptidase 2*/genetics , Apoptosis* , PDZ Domains*, Humans ; Allosteric Regulation ; Substrate Specificity ; Mitochondria/metabolism ; Models, Molecular ; Magnetic Resonance Spectroscopy
مستخلص: The mitochondrial serine protease HtrA2 is a human homolog of the Escherichia coli Deg-proteins exhibiting chaperone and proteolytic roles. HtrA2 is involved in both apoptotic regulation via its ability to degrade inhibitor-of-apoptosis proteins (IAPs), as well as in cellular maintenance as part of the cellular protein quality control machinery, by preventing the possible toxic accumulation of aggregated proteins. In this study, we use advanced solution NMR spectroscopy methods combined with biophysical characterization and biochemical assays to elucidate the crucial role of the substrate recognizing PDZ domain. This domain regulates the protease activity of HtrA2 by triggering an intricate allosteric network involving the regulatory loops of the protease domain. We further show that divalent metal ions can both positively and negatively modulate the activity of HtrA2, leading to a refined model of HtrA2 regulation within the apoptotic pathway.
(© 2024. The Author(s).)
References: Hartl, F. U., Bracher, A. & Hayer-Hartl, M. Molecular chaperones in protein folding and proteostasis. Nature 475, 324–332 (2011). (PMID: 2177607810.1038/nature10317)
Burmann, B. M. & Hiller, S. Chaperones and chaperone-substrate complexes: dynamic playgrounds for NMR spectroscopists. Prog. Nucl. Magn. Reson. Spectrosc. 86–87, 41–64 (2015). (PMID: 2591919810.1016/j.pnmrs.2015.02.004)
Clausen, T., Kaiser, M., Huber, R. & Ehrmann, M. HTRA proteases: regulated proteolysis in protein quality control. Nat. Rev. Mol. Cell Biol. 12, 152–162 (2011). (PMID: 2132619910.1038/nrm3065)
Hiller, S. & Burmann, B. M. Chaperone–client complexes: a dynamic liaison. J. Magn. Reson. 289, 142–155 (2018). (PMID: 2954462610.1016/j.jmr.2017.12.008)
Merdanovic, M., Clausen, T., Kaiser, M., Huber, R. & Ehrmann, M. Protein quality control in the bacterial periplasm. Annu. Rev. Microbiol. 65, 149–168 (2011). (PMID: 2163978810.1146/annurev-micro-090110-102925)
Vande Walle, L., Lamkanfi, M. & Vandenabeele, P. The mitochondrial serine protease HtrA2/Omi: an overview. Cell. Death Differ. 15, 453–460 (2008). (PMID: 1817490110.1038/sj.cdd.4402291)
Sawa, J., Heuck, A., Ehrmann, M. & Clausen, T. Molecular transformers in the cell: lessons learned from the DegP protease-chaperone. Curr. Opin. Struct. Biol. 20, 253–258 (2010). (PMID: 2018853810.1016/j.sbi.2010.01.014)
Quirós, P. M., Langer, T. & López-Otín, C. New roles for mitochondrial proteases in health, ageing and disease. Nat. Rev. Mol. Cell Biol. 16, 345–359 (2015). (PMID: 2597055810.1038/nrm3984)
Deshwal, S., Fiedler, K. U. & Langer, T. Mitochondrial proteases: multifaceted regulators of mitochondrial plasticity. Annu. Rev. Biochem. 89, 501–528 (2020). (PMID: 3207541510.1146/annurev-biochem-062917-012739)
Zurawa-Janicka, D., Skorko-Glonek, J. & Lipinska, B. HtrA proteins as targets in therapy of cancer and other diseases. Expert Opin. Ther. Targets 14, 665–679 (2010). (PMID: 2046996010.1517/14728222.2010.487867)
Faccio, L. et al. Characterization of a novel human serine protease that has extensive homology to bacterial heat shock endoprotease HtrA and is regulated by kidney ischemia. J. Biol. Chem. 275, 2581–2588 (2000). (PMID: 1064471710.1074/jbc.275.4.2581)
Gray, C. W. et al. Characterization of human HtrA2, a novel serine protease involved in the mammalian cellular stress response. Eur. J. Biochem. 267, 5699–5710 (2000). (PMID: 1097158010.1046/j.1432-1327.2000.01589.x)
Suzuki, Y. et al. A serine protease, HtrA2, is released from the mitochondria and interacts with XIAP, inducing cell death. Mol. Cell 8, 613–621 (2001). (PMID: 1158362310.1016/S1097-2765(01)00341-0)
Kennedy, M. Origin of PDZ (DHR, GLGF) domains. Trends Biochem. Sci. 20, 350 (1995). (PMID: 748270110.1016/S0968-0004(00)89074-X)
Clausen, T., Southan, C. & Ehrmann, M. The HtrA family of proteases: implications for protein composition and cell fate. Mol. Cell. 10, 443–455 (2002). (PMID: 1240881510.1016/S1097-2765(02)00658-5)
Li, W. et al. Structural insights into the pro-apoptotic function of mitochondrial serine protease HtrA2/Omi. Nat. Struct. Biol. 9, 436–441 (2002). (PMID: 1196756910.1038/nsb795)
Martins, L. M. et al. The serine protease Omi/HtrA2 regulates apoptosis by binding XIAP through a Reaper-like motif. J. Biol. Chem. 277, 439–444 (2002). (PMID: 1160261210.1074/jbc.M109784200)
Suzuki, Y., Takahashi-Niki, K., Akagi, T., Hashikawa, T. & Takahashi, R. Mitochondrial protease Omi/HtrA2 enhances caspase activation through multiple pathways. Cell Death Differ. 11, 208–216 (2004). (PMID: 1460567410.1038/sj.cdd.4401343)
Aspholm, E. E., Matečko-Burmann, I. & Burmann, B. M. Keeping α-synuclein at bay: A more active role of molecular chaperones in preventing mitochondrial interactions and transition to pathological states? Life 10, 289 (2020). (PMID: 33227899769922910.3390/life10110289)
Martins, L. M. et al. Neuroprotective role of the Reaper-related serine protease HtrA2/Omi revealed by targeted deletion in mice. Mol. Cell Biol. 24, 9848–9862 (2004). (PMID: 1550978852549010.1128/MCB.24.22.9848-9862.2004)
Jones, J. M. et al. Loss of Omi mitochondrial protease activity causes the neuromuscular disorder of mnd2 mutant mice. Nature 425, 721–727 (2003). (PMID: 1453454710.1038/nature02052)
Unal Gulsuner, H. et al. Mitochondrial serine protease HTRA2 p.G399S in a kindred with essential tremor and Parkinson disease. Proc. Natl. Acad. Sci. USA 111, 18285–18290 (2014). (PMID: 25422467428058210.1073/pnas.1419581111)
Strauss, K. M. et al. Loss of function mutations in the gene encoding Omi/HtrA2 in Parkinson’s disease. Hum. Mol. Genet. 14, 2099–2111 (2005). (PMID: 1596141310.1093/hmg/ddi215)
Lautenschläger, J. et al. Intramitochondrial proteostasis is directly coupled to α-synuclein and amyloid β1-42 pathologies. J. Biol. Chem. 295, 10138–10152 (2020). (PMID: 32385113738336810.1074/jbc.RA119.011650)
Toyama, Y., Harkness, R. W., Lee, T. Y. T., Maynes, J. T. & Kay, L. E. Oligomeric assembly regulating mitochondrial HtrA2 function as examined by methyl-TROSY NMR. Proc. Natl. Acad. Sci. USA 118, e2025022118 (2021). (PMID: 33692127798037710.1073/pnas.2025022118)
Šulskis, D., Thoma, J. & Burmann, B. M. Structural basis of DegP protease temperature-dependent activation. Sci. Adv. 7, eabj1816 (2021). (PMID: 34878848865428810.1126/sciadv.abj1816)
Merski, M. et al. Molecular motion regulates the activity of the mitochondrial serine protease HtrA2. Cell Death Dis. 8, e3119 (2017). (PMID: 29022916575909510.1038/cddis.2017.487)
Wagh, A. R. & Bose, K. Structural basis of inactivation of human counterpart of mouse motor neuron degeneration 2 mutant in serine protease HtrA2. Biosci. Rep. 38, 1–12 (2018). (PMID: 10.1042/BSR20181072)
Rosenzweig, R. & Kay, L. E. Bringing dynamic molecular machines into focus by methyl-TROSY NMR. Annu. Rev. Biochem. 83, 291–315 (2014). (PMID: 2490578410.1146/annurev-biochem-060713-035829)
Toyama, Y., Harkness, R. W. & Kay, L. E. Dissecting the role of interprotomer cooperativity in the activation of oligomeric high-temperature requirement A2 protein. Proc. Natl. Acad. Sci. USA 118, e2111257118 (2021). (PMID: 34446566853633810.1073/pnas.2111257118)
McConnell, H. M. Reaction rates by nuclear magnetic resonance. J. Chem. Phys. 28, 430–431 (1958). (PMID: 10.1063/1.1744152)
Walsh, N. P., Alba, B. M., Bose, B., Gross, C. A. & Sauer, R. T. OMP peptide signals initiate the envelope-stress response by activating DegS protease via relief of inhibition mediated by its PDZ domain. Cell 113, 61–71 (2003). (PMID: 1267903510.1016/S0092-8674(03)00203-4)
Palmer, A. G., Kroenke, C. D. & Loria, J. P. Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Methods Enzymol. 339, 204–238 (2001). (PMID: 1146281310.1016/S0076-6879(01)39315-1)
Lipari, G. & Szabo, A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104, 4546–4559 (1982). (PMID: 10.1021/ja00381a009)
Lipari, G. & Szabo, A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results. J. Am. Chem. Soc. 104, 4559–4570 (1982). (PMID: 10.1021/ja00381a010)
Franco, R., Gil-Caballero, S., Ayala, I., Favier, A. & Brutscher, B. Probing conformational exchange dynamics in a short-lived protein folding intermediate by real-time relaxation–dispersion NMR. J. Am. Chem. Soc. 139, 1065–1068 (2017). (PMID: 2806749610.1021/jacs.6b12089)
Korzhnev, D. M., Kloiber, K., Kanelis, V., Tugarinov, V. & Kay, L. E. Probing slow dynamics in high molecular weight proteins by methyl-TROSY NMR spectroscopy: application to a 723-residue enzyme. J. Am. Chem. Soc. 126, 3964–3973 (2004). (PMID: 1503875110.1021/ja039587i)
Morgado, L., Burmann, B. M., Sharpe, T., Mazur, A. & Hiller, S. The dynamic dimer structure of the chaperone Trigger Factor. Nat. Commun. 8, 1992 (2017). (PMID: 29222465572289510.1038/s41467-017-02196-7)
Bernegger, S. et al. A novel FRET peptide assay reveals efficient Helicobacter pylori HtrA inhibition through zinc and copper binding. Sci. Rep. 10, 10563 (2020). (PMID: 32601479732460810.1038/s41598-020-67578-2)
Russell, T. M., Tang, X., Goldstein, J. M., Bagarozzi, D. & Johnson, B. J. B. The salt-sensitive structure and zinc inhibition of Borrelia burgdorferi protease BbHtrA. Mol. Microbiol. 99, 586–596 (2016). (PMID: 2648089510.1111/mmi.13251)
Miao, Q. et al. Paramagnetic chemical probes for studying biological macromolecules. Chem. Rev. 122, 9571–9642 (2022). (PMID: 35084831913693510.1021/acs.chemrev.1c00708)
Waudby, C. A., Ramos, A., Cabrita, L. D. & Christodoulou, J. Two-dimensional NMR lineshape analysis. Sci. Rep. 6, 24826 (2016). (PMID: 27109776484300810.1038/srep24826)
Gupta, S. et al. The C-terminal tail of presenilin regulates Omi/HtrA2 protease activity. J. Biol. Chem. 279, 45844–45854 (2004). (PMID: 1529490910.1074/jbc.M404940200)
Martins, L. M. et al. Binding specificity and regulation of the serine protease and PDZ domains of HtrA2/Omi. J. Biol. Chem. 278, 49417–49427 (2003). (PMID: 1451242410.1074/jbc.M308659200)
Meltzer, M. et al. Allosteric activation of HtrA protease DegP by stress signals during bacterial protein quality control. Angew. Chem. 47, 1332–1334 (2008). (PMID: 10.1002/anie.200703273)
Zhang, Y., Appleton, B. A., Wu, P., Wiesmann, C. & Sidhu, S. S. Structural and functional analysis of the ligand specificity of the HtrA2/Omi PDZ domain. Protein Sci. 16, 1738–1750 (2007). (PMID: 17656586220337910.1110/ps.072833207)
Bejugam, P. R. et al. Allosteric regulation of serine protease HtrA2 through novel non-canonical substrate binding pocket. PLoS ONE 8, e55416 (2013). (PMID: 23457469357303310.1371/journal.pone.0055416)
de Vries, S. J., van Dijk, M. & Bonvin, A. M. J. J. The HADDOCK web server for data-driven biomolecular docking. Nat. Protoc. 5, 883–897 (2010). (PMID: 2043153410.1038/nprot.2010.32)
Honorato, R. V. et al. Structural biology in the clouds: the WeNMR-EOSC ecosystem. Front. Mol. Biosci. 8, 729513 (2021). (PMID: 34395534835636410.3389/fmolb.2021.729513)
Dong, W., Wang, J., Niu, G., Zhao, S. & Liu, L. Crystal structure of the zinc-bound HhoA protease from Synechocystis sp. PCC 6803. FEBS Lett. 590, 3435–3442 (2016). (PMID: 2761629210.1002/1873-3468.12416)
Gaudreault, F., Chartier, M. & Najmanovich, R. Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding. Bioinformatics 28, 423–430 (2012). (PMID: 10.1093/bioinformatics/bts395)
Troussicot, L., Vallet, A., Molin, M., Burmann, B. M. & Schanda, P. Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. J. Am. Chem. Soc. 145, 10700–10711 (2023). (PMID: 371403451019713010.1021/jacs.3c01200)
Parra, R. G. et al. Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics. Nucleic Acids Res. 44, W356–W360 (2016). (PMID: 27131359498788910.1093/nar/gkw304)
Ravera, E., Cerofolini, L., Fragai, M., Parigi, G. & Luchinat, C. Characterization of lanthanoid-binding proteins using NMR spectroscopy. Methods Enzym. 651, 103–137 (2021). (PMID: 10.1016/bs.mie.2021.01.039)
Bertini, I., Gelis, I., Katsaros, N., Luchinat, C. & Provenzani, A. Tuning the affinity for lanthanides of calcium binding proteins. Biochemistry 42, 8011–8021 (2003). (PMID: 1283435310.1021/bi034494z)
Lu, C. H. et al. MIB2: metal ion-binding site prediction and modelling server. Bioinformatics 38, 4428–4429 (2022). (PMID: 3590454210.1093/bioinformatics/btac534)
Hunkeler, M., Jin, C. Y. & Fischer, E. S. Structures of BIRC6-client complexes provide a mechanism of SMAC-mediated release of caspases. Science 379, 1105–1111 (2023). (PMID: 3675810410.1126/science.ade5750)
MohamedMohaideen, N. N. et al. Structure and function of the virulence-associated high-temperature requirement A of Mycobacterium tuberculosis. Biochemistry 47, 6092–6102 (2008). (PMID: 1847914610.1021/bi701929m)
Ehrmann, J. F. et al. Structural basis for regulation of apoptosis and autophagy by the BIRC6/SMAC complex. Science 379, 1117–1123 (2023). (PMID: 3675810510.1126/science.ade8873)
Toyama, Y., Harkness, R. W. & Kay, L. E. Structural basis of protein substrate processing by human mitochondrial high-temperature requirement A2 protease. Proc. Natl. Acad. Sci. USA 119, e2203172119 (2022). (PMID: 35452308917007010.1073/pnas.2203172119)
Singh, N., D’Souza, A., Cholleti, A., Sastry, G. M. & Bose, K. Dual regulatory switch confers tighter control on HtrA2 proteolytic activity. FEBS J. 281, 2456–2470 (2014). (PMID: 2469808810.1111/febs.12799)
Bogaerts, V. et al. Genetic variability in the mitochondrial serine protease HTRA2 contributes to risk for Parkinson disease. Hum. Mutat. 29, 832–840 (2008). (PMID: 1840185610.1002/humu.20713)
Fitzgerald, J. C. et al. Phosphorylation of HtrA2 by cyclin-dependent kinase-5 is important for mitochondrial function. Cell Death Differ. 19, 257–266 (2012). (PMID: 2170149810.1038/cdd.2011.90)
Plun-Favreau, H. et al. The mitochondrial protease HtrA2 is regulated by Parkinson’s disease-associated kinase PINK1. Nat. Cell. Biol. 9, 1243–1252 (2007). (PMID: 1790661810.1038/ncb1644)
Rizzuto, R. et al. Calcium and apoptosis: facts and hypotheses. Oncogene 22, 8619–8627 (2003). (PMID: 1463462310.1038/sj.onc.1207105)
Orrenius, S., Zhivotovsky, B. & Nicotera, P. Regulation of cell death: the calcium-apoptosis link. Nat. Rev. Mol. Cell. Biol. 4, 552–565 (2003). (PMID: 1283833810.1038/nrm1150)
Yang, Q.-H., Church-Hajduk, R., Ren, J., Newton, M. L. & Du, C. Omi/HtrA2 catalytic cleavage of inhibitor of apoptosis (IAP) irreversibly inactivates IAPs and facilitates caspase activity in apoptosis. Genes Dev. 17, 1487–1496 (2003). (PMID: 1281506919607910.1101/gad.1097903)
Truong-Tran, A. Q., Carter, J., Ruffin, R. E. & Zalewski, P. D. The role of zinc in caspase activation and apoptotic cell death. BioMetals 14, 315–330 (2001). (PMID: 1183146210.1023/A:1012993017026)
Franklin, R. B. & Costello, L. C. The important role of the apoptotic effects of zinc in the development of cancers. J. Cell. Biochem. 106, 750–757 (2009). (PMID: 19160419272786710.1002/jcb.22049)
Gmeiner, W. H., Boyacioglu, O., Stuart, C. H., Jennings-Gee, J. & Balaji, K. C. The cytotoxic and pro-apoptotic activities of the novel fluoropyrimidine F10 towards prostate cancer cells are enhanced by Zn 2+ -chelation and inhibiting the serine protease Omi/HtrA2. Prostate 75, 360–369 (2015). (PMID: 2540850210.1002/pros.22922)
Geiser, M., Cèbe, R., Drewello, D. & Schmitz, R. Integration of PCR fragments at any specific site within cloning vectors without the use of restriction enzymes and DNA ligase. Biotechniques 31, 88–92 (2001). (PMID: 1146452510.2144/01311st05)
Mikolajczyk, J. et al. Small Ubiquitin-related Modifier (SUMO)-specific proteases: Profiling the specificities and activities of human SENPs. J. Biol. Chem. 282, 26217–26224 (2007). (PMID: 1759178310.1074/jbc.M702444200)
Sambrook, J. & Russell, D. Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory Press, 2000).
Callon, M., Burmann, B. M. & Hiller, S. Structural mapping of a chaperone-substrate interaction surface. Angew. Chem. 53, 5069–5072 (2014). (PMID: 10.1002/anie.201310963)
Goto, N. K., Gardner, K. H., Mueller, G. A., Willis, R. C. & Kay, L. E. A robust and cost-effective method for the production of Val, Leu, Ile (δ1) methyl-protonated 15 N-, 13 C-, 2 H-labeled proteins. J. Biomol. NMR 13, 369–374 (1999). (PMID: 1038319810.1023/A:1008393201236)
Tzeng, S.-Ru, Pai, M.-T. & Kalodimos, C. NMR studies of large protein systems. Methods Mol. Biol. 831, 133–140 (2012). (PMID: 22167672342761710.1007/978-1-61779-480-3_8)
Gans, P. et al. Stereospecific isotopic labeling of methyl groups for NMR spectroscopic studies of high-molecular-weight proteins. Angew. Chem. 49, 1958–1962 (2010). (PMID: 10.1002/anie.200905660)
Mas, G., Crublet, E., Hamelin, O., Gans, P. & Boisbouvier, J. Specific labeling and assignment strategies of valine methyl groups for NMR studies of high molecular weight proteins. J. Biomol. NMR 57, 251–262 (2013). (PMID: 2407804110.1007/s10858-013-9785-z)
Pervushin, K., Riek, R., Wider, G. & Wüthrich, K. Relaxation by mutual cancellation of dipole–dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc. Natl. Acad. Sci. USA 94, 12366–12371 (1997). (PMID: 93564552494710.1073/pnas.94.23.12366)
Sattler, M., Schleucher, J. & Griesinger, C. Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog. Nucl. Magn. Reson. Spectrosc. 34, 93–158 (1999). (PMID: 10.1016/S0079-6565(98)00025-9)
Rossi, P., Xia, Y., Khanra, N., Veglia, G. & Kalodimos, C. G. 15 N and 13 C-SOFAST-HMQC editing enhances 3D-NOESY sensitivity in highly deuterated, selectively [ 1 H, 13 C]-labeled proteins. J. Biomol. NMR 66, 259–271 (2016). (PMID: 27878649521889410.1007/s10858-016-0074-5)
Kerfah, R. et al. Scrambling free combinatorial labeling of alanine-β, isoleucine-δ1, leucine-proS and valine-proS methyl groups for the detection of long range NOEs. J. Biomol. NMR 61, 73–82 (2015). (PMID: 2543006110.1007/s10858-014-9887-2)
Tugarinov, V., Choy, W. Y., Orekhov, V. Y. & Kay, L. E. Solution NMR-derived global fold of a monomeric 82-kDa enzyme. Proc. Natl. Acad. Sci. USA 102, 622–627 (2005). (PMID: 1563715254555010.1073/pnas.0407792102)
Jaravine, V., Ibraghimov, I. & Orekhov, V. Y. Removal of a time barrier for high-resolution multidimensional NMR spectroscopy. Nat. Methods 3, 605–607 (2006). (PMID: 1686213410.1038/nmeth900)
Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes*. J. Biomol. NMR 6, 277–293 (1995). (PMID: 852022010.1007/BF00197809)
Keller, R. L. J. The Computer Aided Resonance Assignment Tutorial (Cantina Verlag, Goldau, 2004).
Nielsen, J. T. & Mulder, F. A. A. POTENCI: prediction of temperature, neighbor and pH-corrected chemical shifts for intrinsically disordered proteins. J. Biomol. NMR 70, 141–165 (2018). (PMID: 2939972510.1007/s10858-018-0166-5)
Burmann, B. M., Wang, C. & Hiller, S. Conformation and dynamics of the periplasmic membrane-protein-chaperone complexes OmpX-Skp and tOmpA-Skp. Nat. Struct. Mol. Biol. 20, 1265–1272 (2013). (PMID: 2407722510.1038/nsmb.2677)
Wider, G. & Dreier, L. Measuring protein concentrations by NMR spectroscopy. J. Am. Chem. Soc. 128, 2571–2576 (2006). (PMID: 1649204010.1021/ja055336t)
Siemons, L., Mackenzie, H. W., Shukla, V. K. & Hansen, D. F. Intra-residue methyl–methyl correlations for valine and leucine residues in large proteins from a 3D-HMBC-HMQC experiment. J. Biomol. NMR 73, 749–757 (2019). (PMID: 31720925687554510.1007/s10858-019-00287-9)
Takeuchi, K., Tokunaga, Y., Imai, M., Takahashi, H. & Shimada, I. Dynamic multidrug recognition by multidrug transcriptional repressor LmrR. Sci. Rep. 4, 6922 (2015). (PMID: 10.1038/srep06922)
Lidman, J., Sallova, Y., Matečko-Burmann, I. & Burmann, B. M. Structure and dynamics of the mitochondrial DNA-compaction factor Abf2 from S. cerevisiae. J. Struct. Biol. 215, 108008 (2023). (PMID: 3754330110.1016/j.jsb.2023.108008)
Butterfoss, G. L. et al. Conformational dependence of 13 C shielding and coupling constants for methionine methyl groups. J. Biomol. Nmr. 48, 31–47 (2010). (PMID: 20734113559876310.1007/s10858-010-9436-6)
Hansen, D. F., Neudecker, P. & Kay, L. E. Determination of isoleucine side-chain conformations in ground and excited states of proteins from chemical shifts. J. Am. Chem. Soc. 132, 7589–7591 (2010). (PMID: 2046525310.1021/ja102090z)
Hansen, D. F., Neudecker, P., Vallurupalli, P., Mulder, F. A. A. & Kay, L. E. Determination of Leu side-chain conformations in excited protein states by NMR relaxation dispersion. J. Am. Chem. Soc. 132, 42–43 (2010). (PMID: 2000060510.1021/ja909294n)
London, R. E., Wingad, B. D. & Mueller, G. A. Dependence of amino acid side chain 13 C shifts on dihedral angle: Application to conformational analysis. J. Am. Chem. Soc. 130, 11097–11105 (2008). (PMID: 18652454271283410.1021/ja802729t)
Lakomek, N.-A., Ying, J. & Bax, A. Measurement of 15 N relaxation rates in perdeuterated proteins by TROSY-based methods. J. Biomol. NMR 53, 209–221 (2012). (PMID: 22689066341268810.1007/s10858-012-9626-5)
Lee, D., Hilty, C., Wider, G. & Wüthrich, K. Effective rotational correlation times of proteins from NMR relaxation interference. J. Magn. Res. 178, 72–76 (2006). (PMID: 10.1016/j.jmr.2005.08.014)
Niklasson, M. et al. Comprehensive analysis of NMR data using advanced line shape fitting. J. Biomol. NMR 69, 93–99 (2017). (PMID: 29043470566266110.1007/s10858-017-0141-6)
Kawale, A. A. & Burmann, B. M. Inherent backbone dynamics fine-tune the functional plasticity of Tudor domains. Structure 29, 1253–1265 (2021). (PMID: 3419773610.1016/j.str.2021.06.007)
Walton, T. A., Sandoval, C. M., Fowler, C. A., Pardi, A. & Sousa, M. C. The cavity-chaperone Skp protects its substrate from aggregation but allows independent folding of substrate domains. Proc. Natl. Acad. Sci. USA 106, 1772–1777 (2009). (PMID: 19181847264411310.1073/pnas.0809275106)
Maciejewski, M. W. et al. NMRbox: a resource for biomolecular NMR computation. Biophys. J. 112, 1529–1534 (2017). (PMID: 28445744540637110.1016/j.bpj.2017.03.011)
Dosset, P., Hus, J. C., Blackledge, M. & Marion, D. Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. J. Biomol. NMR 16, 23–28 (2000). (PMID: 1071860910.1023/A:1008305808620)
Tugarinov, V. & Kay, L. E. An isotope labeling strategy for methyl TROSY spectroscopy. J. Biomol. NMR 28, 165–172 (2004). (PMID: 1475516010.1023/B:JNMR.0000013824.93994.1f)
Sun, H., Kay, L. E. & Tugarinov, V. An optimized relaxation-based coherence transfer NMR experiment for the measurement of side-chain order in methyl-protonated, highly deuterated proteins. J. Phys. Chem. B 115, 14878–14884 (2011). (PMID: 2204003510.1021/jp209049k)
Weinhäupl, K. et al. Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space. Cell 175, 1365–1379 (2018). (PMID: 30445040624269610.1016/j.cell.2018.10.039)
Mizukoshi, Y. et al. Improvement of ligand affinity and thermodynamic properties by NMR-based evaluation of local dynamics and surface complementarity in the receptor-bound state. Angew. Chem. 55, 14606–14609 (2016). (PMID: 10.1002/anie.201607474)
Schwieters, C. D., Kuszewski, J. J., Tjandra, N. & Marius Clore, G. The Xplor-NIH NMR molecular structure determination package. J. Magn. Reson. 160, 65–73 (2003). (PMID: 1256505110.1016/S1090-7807(02)00014-9)
Schumann, F. H. et al. Combined chemical shift changes and amino acid specific chemical shift mapping of protein–protein interactions. J. Biomol. NMR 39, 275–289 (2007). (PMID: 1795518310.1007/s10858-007-9197-z)
Burmann, B. M., Scheckenhofer, U., Schweimer, K. & Rösch, P. Domain interactions of the transcription–translation coupling factor Escherichia coli NusG are intermolecular and transient. Biochem. J. 435, 783–789 (2011). (PMID: 2134517110.1042/BJ20101679)
Benfield, C. T. O. et al. Mapping the IκB kinase β (IKKβ)-binding interface of the B14 protein, a vaccinia virus inhibitor of IKKβ-mediated activation of nuclear factor κB. J. Biol. Chem. 286, 20727–20735 (2011). (PMID: 21474453312152810.1074/jbc.M111.231381)
Squier, T. C., Bigelow, D. J., Fernandez-Belda, F. J., deMeis, L. & Inesi, G. Calcium and lanthanide binding in the sarcoplasmic reticulum ATPase. J. Biol. Chem. 265, 13713–13720 (1990). (PMID: 214318910.1016/S0021-9258(18)77408-5)
Pinto, M. F. et al. InterferENZY: a web-based tool for enzymatic assay validation and standardized kinetic analysis. J. Mol. Biol. 433, 166613 (2021). (PMID: 3276845210.1016/j.jmb.2020.07.025)
معلومات مُعتمدة: 2019-0415 Cancerfonden (Swedish Cancer Society); 2022-2490 Cancerfonden (Swedish Cancer Society); 2016.0163 Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation); 2020.0300 Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation); 2020-00466 Vetenskapsrådet (Swedish Research Council)
المشرفين على المادة: EC 3.4.21.108 (High-Temperature Requirement A Serine Peptidase 2)
EC 3.4.21.108 (HTRA2 protein, human)
تواريخ الأحداث: Date Created: 20240530 Date Completed: 20240530 Latest Revision: 20240530
رمز التحديث: 20240531
DOI: 10.1038/s41467-024-48997-5
PMID: 38816423
قاعدة البيانات: MEDLINE
الوصف
تدمد:2041-1723
DOI:10.1038/s41467-024-48997-5