Conformational Dynamics of the Rpt6 ATPase in Proteasome Assembly and Rpn14 Binding

Structure - Tập 21 - Trang 753-765 - 2013
Aaron Ehlinger1, Soyeon Park2, Amr Fahmy3, Jeffrey W. Lary4, James L. Cole4, Daniel Finley2, Kylie J. Walters5
1Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
2Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115 USA
3Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115 USA
4Biotechnology-Bioservices Center, University of Connecticut, Storrs, CT 06269, USA
5Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA

Tài liệu tham khảo

Barrault, 2012, Dual functions of the Hsm3 protein in chaperoning and scaffolding regulatory particle subunits during the proteasome assembly, Proc. Natl. Acad. Sci. USA, 109, E1001, 10.1073/pnas.1116538109 Beck, 2012, Near-atomic resolution structural model of the yeast 26S proteasome, Proc. Natl. Acad. Sci. USA, 109, 14870, 10.1073/pnas.1213333109 Bochtler, 2000, The structures of HsIU and the ATP-dependent protease HsIU-HsIV, Nature, 403, 800, 10.1038/35001629 Bohn, 2010, Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution, Proc. Natl. Acad. Sci. USA, 107, 20992, 10.1073/pnas.1015530107 d’Auvergne, 2008, Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces, J. Biomol. NMR, 40, 107, 10.1007/s10858-007-9214-2 d’Auvergne, 2008, Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor, J. Biomol. NMR, 40, 121, 10.1007/s10858-007-9213-3 da Fonseca, 2012, Molecular model of the human 26S proteasome, Mol. Cell., 46, 54, 10.1016/j.molcel.2012.03.026 de la Torre, 2007, Improved calculation of rotational diffusion and intrinsic viscosity of bead models for macromolecules and nanoparticles, J. Phys. Chem. B, 111, 955, 10.1021/jp0647941 Deveraux, 1994, A 26 S protease subunit that binds ubiquitin conjugates, J. Biol. Chem., 269, 7059, 10.1016/S0021-9258(17)37244-7 Djuranovic, 2009, Structure and activity of the N-terminal substrate recognition domains in proteasomal ATPases, Mol. Cell, 34, 580, 10.1016/j.molcel.2009.04.030 Fahmy, 2002, TreeDock: a tool for protein docking based on minimizing van der Waals energies, J. Am. Chem. Soc., 124, 1241, 10.1021/ja011240x Fahmy, 2011, Optimization of van der Waals energy for protein side-chain placement and design, Biophys. J., 101, 1690, 10.1016/j.bpj.2011.07.052 Finley, 2009, Recognition and processing of ubiquitin-protein conjugates by the proteasome, Annu. Rev. Biochem., 78, 477, 10.1146/annurev.biochem.78.081507.101607 Förster, 2005, The 1.9 A structure of a proteasome-11S activator complex and implications for proteasome-PAN/PA700 interactions, Mol. Cell, 18, 589, 10.1016/j.molcel.2005.04.016 Funakoshi, 2009, Multiple assembly chaperones govern biogenesis of the proteasome regulatory particle base, Cell, 137, 887, 10.1016/j.cell.2009.04.061 Garcia de la Torre, 1994, HYDRO: a computer program for the prediction of hydrodynamic properties of macromolecules, Biophys. J., 67, 530, 10.1016/S0006-3495(94)80512-0 Glickman, 1998, The regulatory particle of the Saccharomyces cerevisiae proteasome, Mol. Cell. Biol., 18, 3149, 10.1128/MCB.18.6.3149 Hershko, 1998, The ubiquitin system, Annu. Rev. Biochem., 67, 425, 10.1146/annurev.biochem.67.1.425 Horwitz, 2007, ATP-induced structural transitions in PAN, the proteasome-regulatory ATPase complex in Archaea, J. Biol. Chem., 282, 22921, 10.1074/jbc.M702846200 Husnjak, 2008, Proteasome subunit Rpn13 is a novel ubiquitin receptor, Nature, 453, 481, 10.1038/nature06926 Kaneko, 2009, Assembly pathway of the mammalian proteasome base subcomplex is mediated by multiple specific chaperones, Cell, 137, 914, 10.1016/j.cell.2009.05.008 Kim, 2010, Crystal structure of yeast rpn14, a chaperone of the 19 S regulatory particle of the proteasome, J. Biol. Chem., 285, 15159, 10.1074/jbc.M110.104042 Kisselev, 2012, Proteasome inhibitors: an expanding army attacking a unique target, Chem. Biol., 19, 99, 10.1016/j.chembiol.2012.01.003 Lam, 1997, Editing of ubiquitin conjugates by an isopeptidase in the 26S proteasome, Nature, 385, 737, 10.1038/385737a0 Lander, 2012, Complete subunit architecture of the proteasome regulatory particle, Nature, 482, 186, 10.1038/nature10774 Lasker, 2012, Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach, Proc. Natl. Acad. Sci. USA, 109, 1380, 10.1073/pnas.1120559109 Le Tallec, 2009, Hsm3/S5b participates in the assembly pathway of the 19S regulatory particle of the proteasome, Mol. Cell, 33, 389, 10.1016/j.molcel.2009.01.010 Lee, 2011, Loss of Rpt5 protein interactions with the core particle and Nas2 protein causes the formation of faulty proteasomes that are inhibited by Ecm29 protein, J. Biol. Chem., 286, 36641, 10.1074/jbc.M111.280875 Leggett, 2002, Multiple associated proteins regulate proteasome structure and function, Mol. Cell, 10, 495, 10.1016/S1097-2765(02)00638-X Leggett, 2005, Purification of proteasomes, proteasome subcomplexes, and proteasome-associated proteins from budding yeast, Methods Mol. Biol., 301, 57 Lipari, 1982, 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, 10.1021/ja00381a009 Maytal-Kivity, 2002, MPN+, a putative catalytic motif found in a subset of MPN domain proteins from eukaryotes and prokaryotes, is critical for Rpn11 function, BMC Biochem., 3, 28, 10.1186/1471-2091-3-28 Montelione, 1989, 2D Chemical exchange NMR spectroscopy by proton-detected heteronuclear correlation, J. Am. Chem. Soc., 111, 3096, 10.1021/ja00190a072 Nakamura, 2007, Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasome, Biochem. Biophys. Res. Commun., 359, 503, 10.1016/j.bbrc.2007.05.138 Pace, 1998, A helix propensity scale based on experimental studies of peptides and proteins, Biophys. J., 75, 422, 10.1016/S0006-3495(98)77529-0 Park, 2009, Hexameric assembly of the proteasomal ATPases is templated through their C termini, Nature, 459, 866, 10.1038/nature08065 Park, 2011, Structural defects in the regulatory particle-core particle interface of the proteasome induce a novel proteasome stress response, J. Biol. Chem., 286, 36652, 10.1074/jbc.M111.285924 Rabl, 2008, Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases, Mol. Cell, 30, 360, 10.1016/j.molcel.2008.03.004 Roelofs, 2009, Chaperone-mediated pathway of proteasome regulatory particle assembly, Nature, 459, 861, 10.1038/nature08063 Rohl, 2004, Protein structure prediction using Rosetta, Methods Enzymol., 383, 66, 10.1016/S0076-6879(04)83004-0 Ruschak, 2012, Proteasome allostery as a population shift between interchanging conformers, Proc. Natl. Acad. Sci. USA, 109, E3454, 10.1073/pnas.1213640109 Saeki, 2009, Multiple proteasome-interacting proteins assist the assembly of the yeast 19S regulatory particle, Cell, 137, 900, 10.1016/j.cell.2009.05.005 Schreiner, 2008, Ubiquitin docking at the proteasome through a novel pleckstrin-homology domain interaction, Nature, 453, 548, 10.1038/nature06924 Schuck, 2000, Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling, Biophys. J., 78, 1606, 10.1016/S0006-3495(00)76713-0 Schwartz, 2009, Targeting proteins for destruction by the ubiquitin system: implications for human pathobiology, Annu. Rev. Pharmacol. Toxicol., 49, 73, 10.1146/annurev.pharmtox.051208.165340 Shen, 2008, Consistent blind protein structure generation from NMR chemical shift data, Proc. Natl. Acad. Sci. USA, 105, 4685, 10.1073/pnas.0800256105 Smith, 2007, Docking of the proteasomal ATPases’ carboxyl termini in the 20S proteasome’s alpha ring opens the gate for substrate entry, Mol. Cell, 27, 731, 10.1016/j.molcel.2007.06.033 Stafford, 2004, Analysis of heterologous interacting systems by sedimentation velocity: curve fitting algorithms for estimation of sedimentation coefficients, equilibrium and kinetic constants, Biophys. Chem., 108, 231, 10.1016/j.bpc.2003.10.028 Takagi, 2012, Structural basis for specific recognition of Rpt1p, an ATPase subunit of 26 S proteasome, by proteasome-dedicated chaperone Hsm3p, J. Biol. Chem., 287, 12172, 10.1074/jbc.M112.345876 Thompson, 2009, Subcomplexes of PA700, the 19 S regulator of the 26 S proteasome, reveal relative roles of AAA subunits in 26 S proteasome assembly and activation and ATPase activity, J. Biol. Chem., 284, 24891, 10.1074/jbc.M109.023218 Tian, 2011, An asymmetric interface between the regulatory and core particles of the proteasome, Nat. Struct. Mol. Biol., 18, 1259, 10.1038/nsmb.2147 Tomko, 2010, Heterohexameric ring arrangement of the eukaryotic proteasomal ATPases: implications for proteasome structure and assembly, Mol. Cell, 38, 393, 10.1016/j.molcel.2010.02.035 Verma, 2002, Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome, Science, 298, 611, 10.1126/science.1075898 Whitby, 2000, Structural basis for the activation of 20S proteasomes by 11S regulators, Nature, 408, 115, 10.1038/35040607 Wishart, 1994, The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data, J. Biomol. NMR, 4, 171, 10.1007/BF00175245 Yao, 2002, A cryptic protease couples deubiquitination and degradation by the proteasome, Nature, 419, 403, 10.1038/nature01071 Yu, 2010, Interactions of PAN’s C-termini with archaeal 20S proteasome and implications for the eukaryotic proteasome-ATPase interactions, EMBO J., 29, 692, 10.1038/emboj.2009.382 Zhang, 2009, Structural insights into the regulatory particle of the proteasome from Methanocaldococcus jannaschii, Mol. Cell, 34, 473, 10.1016/j.molcel.2009.04.021 Zhang, 2009, Mechanism of substrate unfolding and translocation by the regulatory particle of the proteasome from Methanocaldococcus jannaschii, Mol. Cell, 34, 485, 10.1016/j.molcel.2009.04.022