Protein Folding and Mechanisms of Proteostasis

International Journal of Molecular Sciences - Tập 16 Số 8 - Trang 17193-17230
José Fernando Díaz‐Villanueva1, Raúl Díaz-Molina2, Víctor García‐González3
1Facultad de Medicina, Universidad Autónoma de Baja California, Mexicali, Baja California 21000, México. [email protected].
2Facultad de Medicina, Universidad Autónoma de Baja California, Mexicali, Baja California 21000, México. [email protected].
3Facultad de Medicina, Universidad Autónoma de Baja California, Mexicali, Baja California 21000, México. [email protected].

Tóm tắt

Highly sophisticated mechanisms that modulate protein structure and function, which involve synthesis and degradation, have evolved to maintain cellular homeostasis. Perturbations in these mechanisms can lead to protein dysfunction as well as deleterious cell processes. Therefore in recent years the etiology of a great number of diseases has been attributed to failures in mechanisms that modulate protein structure. Interconnections among metabolic and cell signaling pathways are critical for homeostasis to converge on mechanisms associated with protein folding as well as for the preservation of the native structure of proteins. For instance, imbalances in secretory protein synthesis pathways lead to a condition known as endoplasmic reticulum (ER) stress which elicits the adaptive unfolded protein response (UPR). Therefore, taking this into consideration, a key part of this paper is developed around the protein folding phenomenon, and cellular mechanisms which support this pivotal condition. We provide an overview of chaperone protein function, UPR via, spatial compartmentalization of protein folding, proteasome role, autophagy, as well as the intertwining between these processes. Several diseases are known to have a molecular etiology in the malfunction of mechanisms responsible for protein folding and in the shielding of native structure, phenomena which ultimately lead to misfolded protein accumulation. This review centers on our current knowledge about pathways that modulate protein folding, and cell responses involved in protein homeostasis.

Từ khóa


Tài liệu tham khảo

Badyaev, 2005, Stress-induced variation in evolution: From behavioural plasticity to genetic assimilation, Proc. Biol. Sci., 272, 877

Nussinov, 2013, The spatial structure of cell signaling systems, Phys. Biol., 10, 045004, 10.1088/1478-3975/10/4/045004

Nussinov, 2014, A second molecular biology revolution? The energy landscapes of biomolecular function, Phys. Chem. Chem. Phys., 16, 6321, 10.1039/c4cp90027h

Rutkowski, 2010, Regulation of basal cellular physiology by the homeostatic unfolded protein response, J. Cell Biol., 189, 783, 10.1083/jcb.201003138

Dobson, 1999, Protein misfolding, evolution and disease, Trends Biochem. Sci., 24, 329, 10.1016/S0968-0004(99)01445-0

Seong, 2004, Hydrophobicity: An ancient damage-associated molecular pattern that initiates innate immune responses, Nat. Rev. Immunol., 4, 469, 10.1038/nri1372

Campioni, 2010, A causative link between the structure of aberrant protein oligomers and their toxicity, Nat. Chem. Biol., 6, 140, 10.1038/nchembio.283

Cheon, 2007, Structural reorganisation and potential toxicity of oligomeric species formed during the assembly of amyloid fibrils, PLoS Comput. Biol., 3, 1727, 10.1371/journal.pcbi.0030173

Olzscha, 2011, Amyloid-like aggregates sequester numerous metastable proteins with essential cellular functions, Cell, 144, 67, 10.1016/j.cell.2010.11.050

Narayan, 2013, Single molecule characterization of the interactions between amyloid-β peptides and the membranes of hippocampal cells, J. Am. Chem. Soc., 135, 1491, 10.1021/ja3103567

Liu, 2011, Proteostasis regulation at the endoplasmic reticulum: A new perturbation site for targeted cancer therapy, Cell Res., 21, 867, 10.1038/cr.2011.75

Princiotta, 2003, Quantitating protein synthesis, degradation, and endogenous antigen processing, Immunity, 18, 343, 10.1016/S1074-7613(03)00051-7

Zhong, 2012, Regular patterns for proteome-wide distribution of protein abundance across species, PLoS ONE, 7, e32423, 10.1371/journal.pone.0032423

Walter, 2011, The unfolded protein response: From stress pathway to homeostatic regulation, Science, 334, 1081, 10.1126/science.1209038

Chambers, 2014, Cellular mechanisms of endoplasmic reticulum stress signaling in health and disease. 2. Protein misfolding and ER stress, Am. J. Physiol. Cell Physiol., 307, C657, 10.1152/ajpcell.00183.2014

Lebeau, 2014, Cellular mechanisms of endoplasmic reticulum stress signaling in health and disease. 3. Orchestrating the unfolded protein response in oncogenesis: An update, Am. J. Physiol. Cell Physiol., 307, C901, 10.1152/ajpcell.00292.2014

Sano, 2013, ER stress-induced cell death mechanisms, Biochim. Biophys. Acta, 1833, 3460, 10.1016/j.bbamcr.2013.06.028

Hinault, 2006, Chaperones and proteases: Cellular fold-controlling factors of proteins in neurodegenerative diseases and aging, J. Mol. Neurosci., 30, 249, 10.1385/JMN:30:3:249

Huang, K. (2005). Lectures on Statistical Physics and Protein Folding, World Scientific. [1st ed.].

Dobson, 2004, Protein chemistry: In the footsteps of alchemists, Science, 304, 1259, 10.1126/science.1093078

Anfinsen, 1973, Principles that govern folding of protein chains, Science, 181, 223, 10.1126/science.181.4096.223

Dyson, 2005, Intrinsically unstructured proteins and their functions, Nat. Rev. Mol. Cell Biol., 6, 197, 10.1038/nrm1589

Uversky, 2010, Understanding protein non-folding, Biochim. Biophys. Acta, 1804, 1231, 10.1016/j.bbapap.2010.01.017

Vuillon, 2015, From local to global changes in proteins: A network view, Curr. Opin. Struct. Biol., 31, 1, 10.1016/j.sbi.2015.02.015

Nussinov, 2013, Allostery in disease and in drug discovery, Cell, 153, 293, 10.1016/j.cell.2013.03.034

Lipinski, 2004, Navigating chemical space for biology and medicine, Nature, 432, 855, 10.1038/nature03193

Zuiderweg, 2013, Allostery in the Hsp70 chaperone proteins, Top. Curr. Chem., 328, 99, 10.1007/128_2012_323

Tompa, 2014, Multisteric regulation by structural disorder in modular signaling proteins: An extension of the concept of allostery, Chem. Rev., 114, 6715, 10.1021/cr4005082

Deshpande, 2015, Real-time dynamics of emerging actin networks in cell-mimicking compartments, PLoS ONE, 10, e011652, 10.1371/journal.pone.0116521

Manz, 2010, Spatial organization and signal transduction at intercellular junctions, Nat. Rev. Mol. Cell Biol., 11, 342, 10.1038/nrm2883

He, 2006, Why do hubs tend to be essential in protein networks?, PLoS Genet., 2, e88, 10.1371/journal.pgen.0020088

Housaindokht, 2015, Molecular crowding effects on conformation and stability of G-quadruplex DNA structure: Insights from molecular dynamics simulation, J. Theor. Biol., 364, 103, 10.1016/j.jtbi.2014.09.015

Karplus, 2002, Molecular dynamics simulations of biomolecules, Nat. Struct. Biol., 9, 646, 10.1038/nsb0902-646

Moreno, 2009, Disorder-to-order conformational transitions in protein structure and its relationship to disease, Mol. Cell. Biochem., 330, 105, 10.1007/s11010-009-0105-6

Bardwell, 2012, Conditional disorder in chaperone action, Trends Biochem. Sci., 37, 517, 10.1016/j.tibs.2012.08.006

Górecki, A., Bonarek, P., Górka, A.K., Figiel, M., Wilamowski, M., and Dziedzicka-Wasylewska, M. (2015). Intrinsic disorder of human Yin Yang 1 protein. Proteins.

2011, Amyloidogenic properties of a D/N mutated 12 amino acid fragment of the C-terminal domain of the Cholesteryl-Ester Transfer Protein (CETP), Int. J. Mol. Sci., 12, 2019, 10.3390/ijms12032019

Guharoy, 2015, SnapShot: Intrinsic structural disorder, Cell, 161, 1230, 10.1016/j.cell.2015.05.024

Mittag, 2013, From sequence and forces to structure, function, and evolution of intrinsically disordered proteins, Structure, 21, 1492, 10.1016/j.str.2013.08.001

García-González, V.G., and Mas-Oliva, J. (2012). El Concepto de Enfermedad Asociado a la Conformación de Proteínas, Universidad Nacional Autónoma de México and El Manual Moderno. [1st ed.].

Dunker, 2008, Function and structure of inherently disordered proteins, Curr. Opin. Struct. Biol., 18, 756, 10.1016/j.sbi.2008.10.002

Tompa, 2009, Close encounters of the third kind: Disordered domains and the interactions of proteins, BioEssays, 31, 328, 10.1002/bies.200800151

Sickmeier, 2007, DisProt: The database of disordered proteins, Nucleic Acids Res., 35, D786, 10.1093/nar/gkl893

Tantos, 2012, Intrinsic disorder in cell signaling and gene transcription, Mol. Cell. Endocrinol., 348, 457, 10.1016/j.mce.2011.07.015

Hilser, 2007, Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins, Proc. Natl. Acad. Sci. USA, 104, 8311, 10.1073/pnas.0700329104

Ferreon, 2013, Modulation of allostery by protein intrinsic disorder, Nature, 498, 390, 10.1038/nature12294

Tompa, 2005, Structural disorder throws new light on moonlighting, Trends Biochem. Sci., 30, 484, 10.1016/j.tibs.2005.07.008

Gould, 2010, ELM: The status of the 2010 eukaryotic linear motif resource, Nucleic Acids Res., 38, D167, 10.1093/nar/gkp1016

Stein, 2008, Contextual specificity in peptide-mediated protein interactions, PLoS ONE, 3, e2524, 10.1371/journal.pone.0002524

Ward, 2004, Prediction and functional analysis of native disorder in proteins from the three kingdoms of life, J. Mol. Biol., 337, 635, 10.1016/j.jmb.2004.02.002

Lobley, 2007, Inferring function using patterns of native disorder in proteins, PLoS Comput. Biol., 3, e162, 10.1371/journal.pcbi.0030162

Dunker, A.K., Garner, E., Guilliot, S., Romero, P., Albrecht, K., Hart, J., Obradovic, Z., Kissinger, C., and Villafranca, J.E. (1998). Protein disorder and the evolution of molecular recognition: Theory, predictions and observations. Pac. Symp. Biocomput., 473–484.

Oldfield, 2008, Flexible nets: Disorder and induced fit in the associations of p53 and 14-3-3 with their partners, BMC Genomics, 9, S1, 10.1186/1471-2164-9-S1-S1

Andresen, 2012, Transient structure and dynamics in the disordered c-Myc transactivation domain affect Bin1 binding, Nucleic Acids Res., 40, 6353, 10.1093/nar/gks263

Tompa, 2002, Intrinsically unstructured proteins, Trends Biochem. Sci., 27, 527, 10.1016/S0968-0004(02)02169-2

James, 2003, Conformational diversity and protein evolution—A 60-year-old hypothesis revisited, Trends Biochem. Sci., 28, 361, 10.1016/S0968-0004(03)00135-X

Bustos, 2006, Intrinsic disorder is a key characteristic in partners that bind 14-3-3 proteins, Proteins, 63, 35, 10.1002/prot.20888

Kriwacki, 1996, Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: Conformational disorder mediates binding diversity, Proc. Natl. Acad. Sci. USA, 93, 11504, 10.1073/pnas.93.21.11504

Dalal, 2000, Understanding the sequence determinants of conformational switching using protein design, Protein Sci., 9, 1651, 10.1110/ps.9.9.1651

Cheng, 2006, Rational drug design via intrinsically disordered protein, Trends Biotechnol., 2, 435, 10.1016/j.tibtech.2006.07.005

Chandra, 2003, A broken α-helix in folded α-synuclein, J. Biol. Chem., 278, 15313, 10.1074/jbc.M213128200

Fink, 1998, Protein aggregation: Folding aggregates, inclusion bodies and amyloid, Fold. Des., 3, R9, 10.1016/S1359-0278(98)00002-9

Eisenberg, 2012, The amyloid state of proteins in human diseases, Cell, 148, 1188, 10.1016/j.cell.2012.02.022

Meredith, 2005, Protein denaturation and aggregation: Cellular responses to denatured and aggregated proteins, Ann. N. Y. Acad. Sci., 1066, 181, 10.1196/annals.1363.030

Chiti, 2006, Protein misfolding, functional amyloid, and human disease, Annu. Rev. Biochem., 75, 333, 10.1146/annurev.biochem.75.101304.123901

Dobson, 2003, Protein folding and misfolding, Nature, 426, 884, 10.1038/nature02261

Sawaya, 2007, Atomic structures of amyloid cross-β spines reveal varied steric zippers, Nature, 447, 453, 10.1038/nature05695

Fitzpatrick, 2013, Atomic structure and hierarchical assembly of a cross-β amyloid fibril, Proc. Natl Acad. Sci. USA, 110, 5468, 10.1073/pnas.1219476110

Knowles, 2007, Role of intermolecular forces in defining material properties of protein nanofibrils, Science, 318, 1900, 10.1126/science.1150057

Chirgadze, 2015, Structure of a single-chain fv bound to the 17 N-terminal residues of huntingtin provides insights into pathogenic amyloid formation and suppression, J. Mol. Biol., 427, 2166, 10.1016/j.jmb.2015.03.021

Greenwald, 2012, On the possible amyloid origin of protein folds, J. Mol. Biol., 421, 417, 10.1016/j.jmb.2012.04.015

Carny, 2005, A model for the role of short self-assembled peptides in the very early stages of the origin of life, FASEB J., 19, 1051, 10.1096/fj.04-3256hyp

Fowler, 2007, Functional amyloid—From bacteria to humans, Trends Biochem. Sci., 32, 217, 10.1016/j.tibs.2007.03.003

Fandrich, 2002, The behaviour of polyamino acids reveals an inverse side chain effect in amyloid structure formation, EMBO J., 21, 5682, 10.1093/emboj/cdf573

Chapman, 2002, Role of Escherichia coli curli operons in directing amyloid fiber formation, Science, 295, 851, 10.1126/science.1067484

Claessen, 2003, A novel class of secreted hydrophobic proteins is involved in aerial hyphae formation in Streptomyces coelicolor by forming amyloid-like fibrils, Genes Dev., 17, 1714, 10.1101/gad.264303

Mackay, 2001, The hydrophobin EAS is largely unstructured in solution and functions by forming amyloid-like structures, Structure, 9, 83, 10.1016/S0969-2126(00)00559-1

Coustou, 1997, The protein product of the het-s heterokaryon incompatibility gene of the fungus Podospora anserina behaves as a prion analog, Proc. Natl. Acad. Sci. USA, 94, 9773, 10.1073/pnas.94.18.9773

King, 1997, Prion-inducing domain 2–114 of yeast Sup35 protein transforms in vitro into amyloid-like filaments, Proc. Natl. Acad. Sci. USA, 94, 6618, 10.1073/pnas.94.13.6618

Iconomidou, 2000, Amyloids protect the silkmoth oocyte and embryo, FEBS Lett., 479, 141, 10.1016/S0014-5793(00)01888-3

Iconomidou, 2006, Amyloid fibril formation propensity is inherent into the hexapeptide tandemly repeating sequence of the central domain of silkmoth chorion proteins of the A-family, J. Struct. Biol., 156, 480, 10.1016/j.jsb.2006.08.011

Berson, 2003, Proprotein convertase cleavage liberates a fibrillogenic fragment of a resident glycoprotein to initiate melanosome biogenesis, J. Cell Biol., 161, 521, 10.1083/jcb.200302072

Kobayashi, 1994, The Pmel 17/silver locus protein. Characterization and investigation of its melanogenic function, J. Biol. Chem., 269, 29198, 10.1016/S0021-9258(19)62030-2

Stefani, 2003, Protein aggregation and aggregate toxicity: New insights into protein folding, misfolding diseases and biological evolution, J. Mol. Med., 81, 678, 10.1007/s00109-003-0464-5

2013, Amyloid fibril formation of peptides derived from the C-terminus of CETP modulated by lipids, Biochem. Biophys. Res. Commun., 434, 54, 10.1016/j.bbrc.2013.03.067

Rousseau, 2004, Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins, Nat. Biotechnol., 22, 1302, 10.1038/nbt1012

Pawar, 2005, Prediction of “aggregation-prone” and “aggregation-susceptible” regions in proteins associated with neurodegenerative diseases, J. Mol. Biol., 350, 379, 10.1016/j.jmb.2005.04.016

Matzinger, 2007, Friendly and dangerous signals: Is the tissue in control?, Nat. Immunol., 8, 11, 10.1038/ni0107-11

Balch, 2008, Adapting proteostasis for disease intervention, Science, 319, 916, 10.1126/science.1141448

Kim, 2013, Molecular chaperone functions in protein folding and proteostasis, Annu. Rev. Biochem., 82, 323, 10.1146/annurev-biochem-060208-092442

Vendruscolo, 2011, Protein solubility and protein homeostasis: A generic view of protein misfolding disorders, Cold Spring Harb. Perspect. Biol., 3, a010454, 10.1101/cshperspect.a010454

Knowles, 2014, The amyloid state and its association with protein misfolding diseases, Nat. Rev. Mol. Cell Biol., 15, 384, 10.1038/nrm3810

Calloni, 2012, DnaK functions as a central hub in the E. coli chaperone network, Cell Rep., 1, 251, 10.1016/j.celrep.2011.12.007

Willmund, 2013, The cotranslational function of ribosome-associated Hsp70 in eukaryotic protein homeostasis, Cell, 152, 196, 10.1016/j.cell.2012.12.001

Gershenson, 2011, Protein folding in the cell: Challenges and progress, Curr. Opin. Struct. Biol., 21, 32, 10.1016/j.sbi.2010.11.001

Hartl, 2011, Molecular chaperones in protein folding and proteostasis, Nature, 475, 324, 10.1038/nature10317

Asherie, 2004, Protein crystallization and phase diagrams, Methods, 34, 266, 10.1016/j.ymeth.2004.03.028

Finka, 2013, Proteomic data from human cell cultures refine mechanisms of chaperone-mediated protein homeostasis, Cell Stress Chaperones, 18, 591, 10.1007/s12192-013-0413-3

Reichmann, 2012, Order out of disorder: Working cycle of an intrinsically unfolded chaperone, Cell, 148, 947, 10.1016/j.cell.2012.01.045

Rosenbaum, 2011, Disorder targets misorder in nuclear quality control degradation: A disordered ubiquitin ligase directly recognizes its misfolded substrates, Mol. Cell, 41, 93, 10.1016/j.molcel.2010.12.004

Mayer, 2010, Gymnastics of molecular chaperones, Mol. Cell, 39, 321, 10.1016/j.molcel.2010.07.012

Ellis, 2006, Molecular chaperones: Assisting assembly in addition to folding, Trends Biochem. Sci., 31, 395, 10.1016/j.tibs.2006.05.001

Saibil, 2008, Chaperone machines in action, Curr. Opin. Struct. Biol., 18, 35, 10.1016/j.sbi.2007.11.006

Wandinger, 2008, The Hsp90 chaperone machinery, J. Biol. Chem., 283, 18473, 10.1074/jbc.R800007200

Tokuriki, 2009, Chaperonin overexpression promotes genetic variation and enzyme evolution, Nature, 459, 668, 10.1038/nature08009

Rutherford, 1998, Hsp90 as a capacitor for morphological evolution, Nature, 396, 336, 10.1038/24550

Slepenkov, 2002, The unfolding story of the Escherichia coli Hsp70 DnaK: Is DnaK a holdase or an unfoldase?, Mol. Microbiol., 45, 1197, 10.1046/j.1365-2958.2002.03093.x

Bosl, 2006, The molecular chaperone Hsp104—A molecular machine for protein disaggregation, J. Struct. Biol., 156, 139, 10.1016/j.jsb.2006.02.004

Langer, 1992, Successive action of DnaK, DnaJ and GroEL along the pathway of chaperone-mediated protein folding, Nature, 356, 683, 10.1038/356683a0

Horwich, 2009, Chaperonin-mediated protein folding: Using a central cavity to kinetically assist polypeptide chain folding, Q. Rev. Biophys., 42, 83, 10.1017/S0033583509004764

Taldone, 2014, Protein chaperones: A composition of matter review (2008–2013), Expert Opin. Ther. Pat., 24, 501, 10.1517/13543776.2014.887681

Yan, 2011, Structural analysis of the Sil1-Bip complex reveals the mechanism for Sil1 to function as a nucleotide-exchange factor, Biochem. J., 438, 447, 10.1042/BJ20110500

Morimoto, 2011, The heat shock response: Systems biology of proteotoxic stress in aging and disease, Cold Spring Harb. Symp. Quant. Biol., 76, 91, 10.1101/sqb.2012.76.010637

Vabulas, 2010, Protein folding in the cytoplasm and the heat shock response, Cold Spring Harb. Perspect. Biol., 2, a004390, 10.1101/cshperspect.a004390

Westerheide, 2009, Stress-inducible regulation of heat shock factor 1 by the deacetylase SIRT1, Science, 323, 1063, 10.1126/science.1165946

Kovacs, 2012, Diverse functional manifestations of intrinsic structural disorder in molecular chaperones, Biochem. Soc. Trans., 40, 963, 10.1042/BST20120108

Snapp, 2012, Unfolded protein responses with or without unfolded proteins?, Cells, 1, 926, 10.3390/cells1040926

Carrara, M., Prischi, F., Nowak, P.R., Kopp, M.C., and Ali, M.M. (2015). Noncanonical binding of BiP ATPase domain to Ire1 and Perk is dissociated by unfolded protein CH1 to initiate ER stress signaling. Elife, 4.

Foit, 2013, Chaperone activation by unfolding, Proc. Natl. Acad. Sci. USA, 110, E1254, 10.1073/pnas.1222458110

Ozcan, 2012, Role of endoplasmic reticulum stress in metabolic disease and other disorders, Annu. Rev. Med., 63, 317, 10.1146/annurev-med-043010-144749

Ellgaard, 2003, Quality control in the endoplasmic reticulum, Nat. Rev. Mol. Cell Biol., 4, 181, 10.1038/nrm1052

Korennykh, 2012, Structural basis of the unfolded protein response, Annu. Rev. Cell Dev. Biol., 28, 251, 10.1146/annurev-cellbio-101011-155826

Zhou, 2006, The crystal structure of human IRE1 luminal domain reveals a conserved dimerization interface required for activation of the unfolded protein response, Proc. Natl. Acad. Sci. USA, 103, 14343, 10.1073/pnas.0606480103

Smith, 2011, Road to ruin: Targeting proteins for degradation in the endoplasmic reticulum, Science, 334, 1086, 10.1126/science.1209235

Voeltz, 2002, Structural organization of the endoplasmic reticulum, EMBO Rep., 3, 944, 10.1093/embo-reports/kvf202

Schindler, 2009, In vitro reconstitution of ER-stress induced ATF6 transport in COPII vesicles, Proc. Natl. Acad. Sci. USA, 106, 17775, 10.1073/pnas.0910342106

Haze, 1999, Mammalian transcription factor ATF6 is synthesized as a transmembrane protein and activated by proteolysis in response to endoplasmic reticulum stress, Mol. Biol. Cell, 10, 3787, 10.1091/mbc.10.11.3787

Ye, 2000, ER stress induces cleavage of membrane-bound ATF6 by the same proteases that process SREBPs, Mol. Cell, 6, 1355, 10.1016/S1097-2765(00)00133-7

Marciniak, 2004, CHOP induces death by promoting protein synthesis and oxidation in the stressed endoplasmic reticulum, Genes Dev., 18, 3066, 10.1101/gad.1250704

Tsaytler, 2011, Selective inhibition of a regulatory subunit of protein phosphatase 1 restores proteostasis, Science, 332, 91, 10.1126/science.1201396

Calfon, 2002, IRE1 couples endoplasmic reticulum load to secretory capacity by processing the XBP-1 mRNA, Nature, 415, 92, 10.1038/415092a

Yoshida, 2001, XBP1 mRNA is induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor, Cell, 107, 881, 10.1016/S0092-8674(01)00611-0

Shen, 2001, Complementary signaling pathways regulate the unfolded protein response and are required for C. elegans development, Cell, 107, 893, 10.1016/S0092-8674(01)00612-2

Lee, 2002, IRE1-mediated unconventional mRNA splicing and S2P-mediated ATF6 cleavage merge to regulate XBP1 in signaling the unfolded protein response, Genes Dev., 16, 452, 10.1101/gad.964702

Yoshida, 2003, A time-dependent phase shift in the mammalian unfolded protein response, Dev. Cell, 4, 265, 10.1016/S1534-5807(03)00022-4

Reimold, 2001, Plasma cell differentiation requires the transcription factor XBP-1, Nature, 412, 300, 10.1038/35085509

Korennykh, 2011, Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1, BMC Biol., 9, 48, 10.1186/1741-7007-9-48

Brewer, 2014, Regulatory crosstalk within the mammalian unfolded protein response, Cell Mol. Life Sci., 71, 1067, 10.1007/s00018-013-1490-2

Hetz, 2012, The unfolded protein response: Controlling cell fate decisions under ER stress and beyond, Nat. Rev. Mol. Cell Biol., 13, 89, 10.1038/nrm3270

Lin, 2007, IRE1 signaling affects cell fate during the unfolded protein response, Science, 318, 944, 10.1126/science.1146361

Li, 2010, Mammalian endoplasmic reticulum stress sensor IRE1 signals by dynamic clustering, Proc. Natl. Acad. Sci. USA, 107, 16113, 10.1073/pnas.1010580107

Vonk, 2013, Spatial sequestration of misfolded proteins by a dynamic chaperone pathway enhances cellular fitness during stress, Nat. Cell Biol., 15, 1231, 10.1038/ncb2838

Duttler, 2013, Principles of cotranslational ubiquitination and quality control at the ribosome, Mol. Cell, 50, 379, 10.1016/j.molcel.2013.03.010

Wang, 2013, A cotranslational ubiquitination pathway for quality control of misfolded proteins, Mol. Cell, 50, 368, 10.1016/j.molcel.2013.03.009

Pechmann, 2014, Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo, Nat. Struct. Mol. Biol., 21, 1100, 10.1038/nsmb.2919

Wolff, 2014, Differential scales of protein quality control, Cell, 157, 52, 10.1016/j.cell.2014.03.007

Douglas, 2009, Molecular chaperones antagonize proteotoxicity by differentially modulating protein aggregation pathways, Prion, 3, 51, 10.4161/pri.3.2.8587

Cohen, 2006, Opposing activities protect against age-onset proteotoxicity, Science, 313, 1604, 10.1126/science.1124646

Arrasate, 2004, Inclusion body formation reduces levels of mutant huntingtin and the risk of neuronal death, Nature, 431, 805, 10.1038/nature02998

Kaganovich, 2008, Misfolded proteins partition between two distinct quality control compartments, Nature, 454, 1088, 10.1038/nature07195

Ogrodnik, 2014, Dynamic JUNQ inclusion bodies are asymmetrically inherited in mammalian cell lines through the asymmetric partitioning of vimentin, Proc. Natl. Acad. Sci. USA, 11, 8049, 10.1073/pnas.1324035111

Polling, 2014, Misfolded polyglutamine, polyalanine, and superoxide dismutase 1 aggregate via distinct pathways in the cell, J. Biol. Chem., 289, 6669, 10.1074/jbc.M113.520189

Weisberg, 2012, Compartmentalization of superoxide dismutase 1 (SOD1G93A) aggregates determines their toxicity, Proc. Natl. Acad. Sci. USA, 109, 15811, 10.1073/pnas.1205829109

Cohen, 2015, A molecular chaperone breaks the catalytic cycle that generates toxic Aβ oligomers, Nat. Struct. Mol. Biol., 22, 207, 10.1038/nsmb.2971

Wrighton, 2013, Protein folding: Misfolded proteins join the Q, Nat. Rev. Mol. Cell Biol., 14, 608, 10.1038/nrm3668

Labbadia, J., and Morimoto, R.I. (2015). The biology of proteostasis in aging and disease. Annu. Rev. Biochem.

Voisine, 2010, Chaperone networks: Tipping the balance in protein folding diseases, Neurobiol. Dis., 40, 12, 10.1016/j.nbd.2010.05.007

Fredrickson, 2012, Selective destruction of abnormal proteins by ubiquitin-mediated protein quality control degradation, Semin. Cell Dev. Biol., 23, 530, 10.1016/j.semcdb.2011.12.006

He, 2009, Regulation mechanisms and signaling pathways of autophagy, Annu. Rev. Genet., 43, 67, 10.1146/annurev-genet-102808-114910

Schmidt, 2014, Regulation of proteasome activity in health and disease, Biochim. Biophys. Acta, 1843, 13, 10.1016/j.bbamcr.2013.08.012

Murata, 2009, Molecular mechanisms of proteasome assembly, Nat. Rev. Mol. Cell Biol., 10, 104, 10.1038/nrm2630

Kusmierczyk, 2008, A multimeric assembly factor controls the formation of alternative 20S proteasomes, Nat. Struct. Mol. Biol., 15, 237, 10.1038/nsmb.1389

Konstantinova, 2008, Role of proteasomes in cellular regulation, International Review of Cell and Molecular Biology, 267, 59, 10.1016/S1937-6448(08)00602-3

He, 2012, Molecular model of the human 26S proteasome, Mol. Cell, 46, 54, 10.1016/j.molcel.2012.03.026

Rosenzweig, 2008, The central unit within the 19S regulatory particle of the proteasome, Nat. Struct. Mol. Biol., 15, 573, 10.1038/nsmb.1427

Kikuchi, 2010, Co- and post-translational modifications of the 26S proteasome in yeast, Proteomics, 10, 2769, 10.1002/pmic.200900283

Tanaka, 2009, The proteasome: Overview of structure and functions, Proc. Jpn. Acad. Ser. B, 85, 12, 10.2183/pjab.85.12

Li, 2009, Variably modulated gating of the 26S proteasome by ATP and polyubiquitin, Biochem. J., 421, 397, 10.1042/BJ20090528

Baumeister, 2013, Allosteric effects in the regulation of 26S proteasome activities, Mol. Biol., 425, 1415, 10.1016/j.jmb.2013.01.036

Price, 1991, The distribution of tangles, plaques and related immunohistochemical markers in healthy aging and Alzheimer’s disease, Neurobiol. Aging, 12, 295, 10.1016/0197-4580(91)90006-6

Masters, 198, Amyloid plaque core protein in Alzheimer disease and Down syndrome, Proc. Natl. Acad. Sci. USA, 82, 4245, 10.1073/pnas.82.12.4245

Gregori, 1997, Binding of amyloid β protein to the 20 S proteasome, J. Biol. Chem., 272, 58, 10.1074/jbc.272.1.58

Gregori, 1995, Amyloid β-protein inhibits ubiquitin-dependent protein degradation in vitro, J. Biol. Chem., 270, 19702, 10.1074/jbc.270.34.19702

Pasquini, 2003, Relationship between β-amyloid degradation and the 26S proteasome in neural cells, Exp. Neurol., 180, 131, 10.1016/S0014-4886(02)00060-2

Oh, 2005, Amyloid peptide attenuates the proteasome activity in neuronal cells, Mech. Ageing Dev., 126, 1292, 10.1016/j.mad.2005.07.006

Choi, 2013, Autophagy in human health and disease, N. Engl. J. Med., 368, 651, 10.1056/NEJMra1205406

Wang, 2015, Protein quality control and metabolism: Bidirectional control in the heart, Cell Metab., 21, 215, 10.1016/j.cmet.2015.01.016

Reggiori, 2013, Autophagic processes in yeast: Mechanism, machinery and regulation, Genetics, 194, 341, 10.1534/genetics.112.149013

Noda, N.N., and Inagaki, F. (2015). Mechanisms of autophagy. Annu. Rev. Biophys.

Cuervo, 2014, Chaperone-mediated autophagy: Roles in disease and aging, Cell Res., 24, 92, 10.1038/cr.2013.153

Yang, 2010, Mammalian autophagy: Core molecular machinery and signaling regulation, Curr. Opin. Cell Biol., 22, 124, 10.1016/j.ceb.2009.11.014

Kroemer, 2010, Autophagy and the integrated stress response, Mol. Cell, 40, 280, 10.1016/j.molcel.2010.09.023

Levine, 2008, Autophagy in the pathogenesis of disease, Cell, 132, 27, 10.1016/j.cell.2007.12.018

Yu, 2005, Macroautophagy a novel β-amyloid peptide-generating pathway activated in Alzheimer’s disease, J. Cell Biol., 171, 87, 10.1083/jcb.200505082

Rubinsztein, 2007, Potential therapeutic applications of autophagy, Nat. Rev. Drug Discov., 6, 304, 10.1038/nrd2272

Ferraro, 2007, Autophagic and apoptotic response to stress signals in mammalian cells, Arch. Biochem. Biophys., 462, 210, 10.1016/j.abb.2007.02.006

Gavrin, 2012, Small molecules that target protein misfolding, J. Med. Chem., 55, 10823, 10.1021/jm301182j

Ciryam, 2013, Widespread aggregation and neurodegenerative diseases are associated with supersaturated proteins, Cell Rep., 5, 781, 10.1016/j.celrep.2013.09.043

Brocchieri, 2005, Protein length in eukaryotic and prokaryotic proteomes, Nucleic Acids Res., 33, 3390, 10.1093/nar/gki615

Ogle, 2005, Structural insights into translational fidelity, Annu. Rev. Biochem., 74, 129, 10.1146/annurev.biochem.74.061903.155440

Pechmann, 2013, The ribosome as a hub for protein quality control, Mol. Cell, 49, 411, 10.1016/j.molcel.2013.01.020

Huang, 2007, High expression rates of human islet amyloid polypeptide induce endoplasmic reticulum stress mediated β-cell apoptosis, a characteristic of humans with type 2 but not type 1 diabetes, Diabetes, 56, 2016, 10.2337/db07-0197

Han, 2013, ER-stress-induced transcriptional regulation increases protein synthesis leading to cell death, Nat. Cell Biol., 15, 481, 10.1038/ncb2738

Tyedmers, 2010, Cellular strategies for controlling protein aggregation, Nat. Rev. Mol. Cell Biol., 11, 777, 10.1038/nrm2993

Bence, 2001, Impairment of the ubiquitin-proteasome system by protein aggregation, Science, 292, 1552, 10.1126/science.292.5521.1552

Ross, 2004, Protein aggregation and neurodegenerative disease, Nat. Med., 10, S10, 10.1038/nm1066

Glickman, 2002, The ubiquitin-proteasome proteolytic pathway: Destruction for the sake of construction, Physiol. Rev., 82, 373, 10.1152/physrev.00027.2001

Rubinsztein, 2006, The roles of intracellular protein-degradation pathways in neurodegeneration, Nature, 443, 780, 10.1038/nature05291

Mizushima, 2008, Autophagy fights disease through cellular self-digestion, Nature, 451, 1069, 10.1038/nature06639

Knowles, 2007, Kinetics and thermodynamics of amyloid formation from direct measurements of fluctuations in fibril mass, Proc. Natl. Acad. Sci. USA, 104, 10016, 10.1073/pnas.0610659104

Xu, 2013, Influence of specific Hsp70 domains on fibril formation of the yeast prion protein Ure2, Philos. Trans. R. Soc. B, 368, 20110410, 10.1098/rstb.2011.0410

Lee, 2014, Unfolded protein response signaling and metabolic diseases, J. Biol. Chem., 289, 1203, 10.1074/jbc.R113.534743

Huang, 2009, Finding order within disorder: Elucidating the structure of proteins associated with neurodegenerative disease, Future Med. Chem., 1, 467, 10.4155/fmc.09.40

Cnop, 2008, An update on lipotoxic endoplasmic reticulum stress in pancreatic β-cells, Biochem. Soc. Trans., 36, 909, 10.1042/BST0360909

Hetz, 2014, Disturbance of endoplasmic reticulum proteostasis in neurodegenerative diseases, Nat. Rev. Neurosci., 15, 233, 10.1038/nrn3689

Steiner, 2000, Intramembrane proteolysis by presenilins, Nat. Rev. Mol. Cell Biol., 1, 217, 10.1038/35043065

Arnold, 2011, Bioenergetics of neurons inhibit the translocation response of Parkin following rapid mitochondrial depolarization, Hum. Mol. Genet., 20, 927, 10.1093/hmg/ddq531

Cao, 2012, Targeting endoplasmic reticulum stress in metabolic disease, Expert Opin. Ther. Targets, 17, 437, 10.1517/14728222.2013.756471

Hotamisligil, 2010, Endoplasmic reticulum stress and the inflammatory basis of metabolic disease, Cell, 140, 900, 10.1016/j.cell.2010.02.034

Cao, 2013, Aggregation of islet amyloid polypeptide: From physical chemistry to cell biology, Curr. Opin. Struct. Biol., 23, 82, 10.1016/j.sbi.2012.11.003

2014, Human IAPP amyloidogenic properties and pancreatic β-cell death, Cell Calcium, 56, 416, 10.1016/j.ceca.2014.08.011

Casas, 2007, Impairment of the ubiquitin-proteasome pathway is a downstream endoplasmic reticulum stress response induced by extracellular human islet amyloid polypeptide and contributes to pancreatic β-cell apoptosis, Diabetes, 56, 2284, 10.2337/db07-0178

Costes, 2011, β-cell dysfunctional ERAD/ubiquitin/proteasome system in type 2 diabetes mediated by islet amyloid polypeptide-induced UCH-L1 deficiency, Diabetes, 60, 227, 10.2337/db10-0522

Ozcan, 2004, Endoplasmic reticulum stress links obesity, insulin action, and type 2 diabetes, Science, 306, 457, 10.1126/science.1103160

Welters, 2004, Mono-unsaturated fatty acids protect against β-cell apoptosis induced by saturated fatty acids, serum withdrawal or cytokine exposure, FEBS Lett., 560, 103, 10.1016/S0014-5793(04)00079-1

Díaz-Villanueva, J.F., and García-González, V. (2015). Key interactions in the binding of free fatty acids on amylin-structure transitions, manuscript in preparation.

Tabas, 2010, The role of endoplasmic reticulum stress in the progression of atherosclerosis, Circ. Res., 107, 839, 10.1161/CIRCRESAHA.110.224766

Kaufman, 2002, Orchestrating the unfolded protein response in health and disease, J. Clin. Investig., 110, 1389, 10.1172/JCI0216886

Han, 2009, IRE1α kinase activation modes control alternate endoribonuclease outputs to determine divergent cell fates, Cell, 138, 562, 10.1016/j.cell.2009.07.017

Blais, 2010, Small molecule inhibitor of endoplasmic reticulum oxidation 1 (ERO1) with selectively reversible thiol reactivity, J. Biol. Chem., 285, 20993, 10.1074/jbc.M110.126599

Ma, 2004, The role of the unfolded protein response in tumour development: Friend or foe?, Nat. Rev. Cancer, 4, 966, 10.1038/nrc1505

Moenner, 2007, Integrated endoplasmic reticulum stress responses in cancer, Cancer Res., 67, 10631, 10.1158/0008-5472.CAN-07-1705

Rouschop, 2010, The unfolded protein response protects human tumor cells during hypoxia through regulation of the autophagy genes MAP1LC3B and ATG5, J. Clin. Investig., 120, 127, 10.1172/JCI40027

Blais, 2006, Perk-dependent translational regulation promotes tumor cell adaptation and angiogenesis in response to hypoxic stress, Mol. Cell. Biol., 26, 9517, 10.1128/MCB.01145-06

Spiotto, 2010, Imaging the unfolded protein response in primary tumors reveals microenvironments with metabolic variations that predict tumor growth, Cancer Res., 70, 78, 10.1158/0008-5472.CAN-09-2747

Lee, 2007, GRP78 induction in cancer: Therapeutic and prognostic implications, Cancer Res., 67, 3496, 10.1158/0008-5472.CAN-07-0325

Pyrko, 2007, The unfolded protein response regulator GRP78/BiP as a novel target for increasing chemosensitivity in malignant gliomas, Cancer Res., 67, 9809, 10.1158/0008-5472.CAN-07-0625

Chen, 2011, GRP78/BiP modulation of GRP78/BiP in altering sensitivity to chemotherapy, Methods Enzymol., 491, 25, 10.1016/B978-0-12-385928-0.00002-X

Li, 2011, Unfolded protein response in cancer: The physician’s perspective, J. Hematol. Oncol., 4, 8, 10.1186/1756-8722-4-8

Park, 2004, Effect on tumor cells of blocking survival response to glucose deprivation, J. Natl. Cancer Inst., 96, 1300, 10.1093/jnci/djh243

Saito, 2009, Chemical genomics identifies the unfolded protein response as a target for selective cancer cell killing during glucose deprivation, Cancer Res., 69, 4225, 10.1158/0008-5472.CAN-08-2689

Backer, 2009, Chaperone-targeting cytotoxin and endoplasmic reticulum stress-inducing drug synergize to kill cancer cells, Neoplasia, 11, 1165, 10.1593/neo.09878

Brown, 2009, Awakening guardian angels: Drugging the p53 pathway, Nat. Rev. Cancer, 12, 862, 10.1038/nrc2763

Olivier, 2010, TP53 mutations in human cancers: Origins, consequences, and clinical use, Cold Spring Harb. Perspect. Biol., 1, a001008

Cho, 1994, Crystal structure of a p53 tumor suppressor-DNA complex: Understanding tumorigenic mutations, Science, 265, 346, 10.1126/science.8023157

Segalat, 2007, Loss-of-function genetic diseases and the concept of pharmaceutical targets, Orphanet. J. Rare Dis., 2, 30, 10.1186/1750-1172-2-30

Rippin, 2002, Characterization of the p53-rescue drug CP-31398 in vitro and in living cells, Oncogene, 21, 2119, 10.1038/sj.onc.1205362

Friedler, 2002, A peptide that binds and stabilizes p53 core domain: Chaperone strategy for rescue of oncogenic mutants, Proc. Natl. Acad. Sci. USA, 99, 937, 10.1073/pnas.241629998

Ellis, 2001, Macromolecular crowding: An important but neglected aspect of the intracellular environment, Curr. Opin. Struct. Biol., 11, 114, 10.1016/S0959-440X(00)00172-X

Gribbin, J.R. (2004). Deep Simplicity: Bringing Order to Chaos and Complexity, Random House Inc.. [1st ed.].

Baigent, 2005, Efficacy and safety of cholesterol lowering treatment: Prospective meta-analysis of data from 90,056 participants in 14 randomised trials of statins, Lancet, 366, 1267, 10.1016/S0140-6736(05)67394-1

Perutz, 2002, Aggregation of proteins with expanded glutamine and alanine repeats of the glutamine-rich and asparagine rich domains of Sup35 and of the amyloid β-peptide of amyloid plaques, Proc. Natl. Acad. Sci. USA, 99, 5596, 10.1073/pnas.042681599

Guijarro, 1998, Amyloid fibril formation by an SH3 domain, Proc. Natl. Acad. Sci. USA, 95, 4224, 10.1073/pnas.95.8.4224

Wasmer, 2009, The molecular organization of the fungal prion HET-s in its amyloid form, J. Mol. Biol., 394, 119, 10.1016/j.jmb.2009.09.015

Johnson, 2005, Native state kinetic stabilization as a strategy to ameliorate protein misfolding diseases: A focus on the transthyretin amyloidoses, Acc. Chem. Res., 38, 911, 10.1021/ar020073i

Lansbury, 1999, Evolution of amyloid: What normal protein folding may tell us about fibrillogenesis and disease?, Proc. Natl. Acad. Sci. USA, 96, 3342, 10.1073/pnas.96.7.3342

Hetz, 2013, Targeting the unfolded protein response in disease, Nat. Rev. Drug Discov., 12, 703, 10.1038/nrd3976

Kraskiewicz, 2012, InterfERing with endoplasmic reticulum stress, Trends Pharmacol. Sci., 33, 53, 10.1016/j.tips.2011.10.002

Lindquist, 2011, Chemical and biological approaches for adapting proteostasis to ameliorate protein misfolding and aggregation diseases: Progress and prognosis, Cold Spring Harb. Perspect. Biol., 3, a004507, 10.1101/cshperspect.a004507

Ozcan, 2006, Chemical chaperones reduce ER stress and restore glucose homeostasis in a mouse model of type 2 diabetes, Science, 313, 1137, 10.1126/science.1128294

Ozcan, 2009, Endoplasmic reticulum stress plays a central role in development of leptin resistance, Cell Metab., 9, 35, 10.1016/j.cmet.2008.12.004

Xiao, 2011, Sodium phenylbutyrate, a drug with known capacity to reduce endoplasmic reticulum stress, partially alleviates lipid-induced insulin resistance and β-cell dysfunction in humans, Diabetes, 60, 918, 10.2337/db10-1433

Kars, 2010, Tauroursodeoxycholic Acid may improve liver and muscle but not adipose tissue insulin sensitivity in obese men and women, Diabetes, 59, 1899, 10.2337/db10-0308

Promlek, 2011, Membrane aberrancy and unfolded proteins activate the endoplasmic reticulum stress sensor Ire1 in different ways, Mol. Biol. Cell, 22, 3520, 10.1091/mbc.e11-04-0295

Wiseman, 2010, Flavonol activation defines an unanticipated ligand-binding site in the kinase-RNase domain of IRE1, Mol. Cell, 38, 291, 10.1016/j.molcel.2010.04.001

Foster, 1999, Pharmacological rescue of mutant p53 conformation and function, Science, 286, 2507, 10.1126/science.286.5449.2507