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