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1.  Impact of translational error-induced and error-free misfolding on the rate of protein evolution 
Theoretical calculations suggest that, in addition to translational error-induced protein misfolding, a non-negligible fraction of misfolded proteins are error free.We propose that the anticorrelation between the expression level of a protein and its rate of sequence evolution be explained by an overarching protein-misfolding-avoidance hypothesis that includes selection against both error-induced and error-free protein misfolding, and verify this model by a molecular-level evolutionary simulation.We provide strong empirical evidence for the protein-misfolding-avoidance hypothesis, including a positive correlation between protein expression level and stability, enrichment of misfolding-minimizing codons and amino acids in highly expressed genes, and stronger evolutionary conservation of residues in which nonsynonymous changes are more likely to increase protein misfolding.
The rate of protein sequence evolution has long been of central interest to molecular evolutionists. Different proteins of the same species evolve at vastly different rates, which is commonly explained by a variation in functional constraint among different proteins (Kimura and Ohta, 1974). However, it is unclear how to quantify the functional constraint of a protein from the knowledge of its function. In the past decade, various types of genomic data from model organisms have been examined to look for the determinants of the rate of protein sequence evolution. The most unexpected discovery was a very strong anticorrelation between the expression level and evolutionary rate of a protein (E–R anticorrelation) (Pal et al, 2001). The prevailing explanation of the E–R anticorrelation is the translational robustness hypothesis (Drummond et al, 2005). This hypothesis posits that mistranslation induces protein misfolding, which is toxic to cells (Figure 1). Consequently, highly expressed proteins are under stronger pressures to be translationally robust and thus are more constrained in sequence evolution. However, the impact of the other source of misfolded proteins, translational error-free proteins (Figure 1), has not been evaluated. By theoretical calculation, computer simulation, and empirical data analysis, we examined the role of selection against both error-induced and error-free protein misfolding in creating the E–R correlation.
Our theoretical calculations suggested that a non-negligible fraction of misfolded proteins are error free. We estimated that when a protein is not very stable, on average ∼20% of misfolded molecules are error free. However, when a protein is very stable, this fraction reduces to ∼5%, which is probably a result of natural selection against protein misfolding.
We conducted a molecular-level evolutionary simulation (Figure 2A) using three different schemes: error-induced misfolding only, error-free misfolding only, and both types of misfolding. As expected, results from the first simulation are similar to those from a previous study that considers only error-induced misfolding (Drummond and Wilke, 2008). Interestingly, the second and third simulations can also generate the same patterns, including a positive correlation between the protein expression level and the unfolding energy (ΔG) of the error-free protein (Figure 2B), a negative correlation between the expression level and the fraction of protein molecules that misfold after being mistranslated (Figure 2C), a negative correlation between ΔG and the evolutionary rate (Figure 2D), and a negative correlation between the expression level and the evolutionary rate (i.e., the E–R anticorrelation) (Figure 2E). Furthermore, we found that selection against protein misfolding is more effective in reducing error-free misfolding than error-induced misfolding.
Based on these results, we propose that an overarching protein-misfolding-avoidance hypothesis that includes both sources of misfolding is superior to the prevailing translational robustness hypothesis, which considers only error-induced misfolding. We tested three key predictions of the protein-misfolding-avoidance hypotheses using yeast data. First, we showed that, consistent with our prediction, a positive correlation exists between the protein expression level and stability, which is measured by the unfolding energy or melting temperature. In addition, protein expression level is negatively correlated with protein aggregation propensity. Second, we found that codons minimizing protein misfolding are used more frequently in highly expressed proteins than in lowly expressed ones. Third, we showed that, within the same protein, amino acid residues in which random nonsynonymous mutations are more likely to increase protein misfolding are evolutionarily more conserved.
Together, these results provide unambiguous evidence that avoidance of both error-induced and error-free protein misfolding is a major source of the E–R anticorrelation and that protein stability and mistranslation have important roles in protein evolution.
What determines the rate of protein evolution is a fundamental question in biology. Recent genomic studies revealed a surprisingly strong anticorrelation between the expression level of a protein and its rate of sequence evolution. This observation is currently explained by the translational robustness hypothesis in which the toxicity of translational error-induced protein misfolding selects for higher translational robustness of more abundant proteins, which constrains sequence evolution. However, the impact of error-free protein misfolding has not been evaluated. We estimate that a non-negligible fraction of misfolded proteins are error free and demonstrate by a molecular-level evolutionary simulation that selection against protein misfolding results in a greater reduction of error-free misfolding than error-induced misfolding. Thus, an overarching protein-misfolding-avoidance hypothesis that includes both sources of misfolding is superior to the translational robustness hypothesis. We show that misfolding-minimizing amino acids are preferentially used in highly abundant yeast proteins and that these residues are evolutionarily more conserved than other residues of the same proteins. These findings provide unambiguous support to the role of protein-misfolding-avoidance in determining the rate of protein sequence evolution.
doi:10.1038/msb.2010.78
PMCID: PMC2990641  PMID: 20959819
evolutionary rate; expression level; mistranslation; protein misfolding
2.  Nanomedicine and Protein Misfolding Diseases 
Misfolding and self assembly of proteins in nano-aggregates of different sizes and morphologies (nano-ensembles, primarily nanofilaments and nano-rings) is a complex phenomenon that can be facilitated, impeded, or prevented, by interactions with various intracellular metabolites, intracellular nanomachines controlling protein folding and interactions with other proteins. A fundamental understanding of molecular processes leading to misfolding and self-aggregation of proteins involved in various neurodegenerative diseases will provide critical information to help identify appropriate therapeutic routes to control these processes. An elevated propensity of misfolded protein conformation in solution to aggregate with the formation of various morphologies impedes the use of traditional physical chemical approaches for studies of misfolded conformations of proteins. In our recent alternative approach, the protein molecules were tethered to surfaces to prevent aggregation and AFM force spectroscopy was used to probe the interaction between protein molecules depending on their conformations. It was shown that formation of filamentous aggregates is facilitated at pH values corresponding to the maximum of rupture forces. In this paper, a novel surface chemistry was developed for anchoring of amyloid β (Aβ) peptides at their N-terminal moieties. The use of the site specific immobilization procedure allowed to measure the rupture of Aβ - Aβ contacts at single molecule level. The rupture of these contacts is accompanied by the extension of the peptide chain detected by a characteristic elasto-mechanical component of the force-distance curves. Potential applications of the nanomechanical studies to understanding the mechanisms of development of protein misfolding diseases are discussed.
doi:10.1016/j.nano.2005.10.005
PMCID: PMC1351038  PMID: 16467913
Nanotechnology; amyloids; neurodegenerative diseases; protein aggregation; protein folding; intermolecular forces; AFM; Alzheimer’s disease
3.  Ligand Binding and Hydration in Protein Misfolding: Insights from Studies of Prion and p53 Tumor Suppressor Proteins† 
Accounts of Chemical Research  2009;43(2):271-279.
Protein misfolding has been implicated in a large number of diseases termed protein- folding disorders (PFDs), which include Alzheimer’s disease, Parkinson’s disease, transmissible spongiform encephalopathies, familial amyloid polyneuropathy, Huntington’s disease, and type II diabetes. In these diseases, large quantities of incorrectly folded proteins undergo aggregation, destroying brain cells and other tissues.
The interplay between ligand binding and hydration is an important component of the formation of misfolded protein species. Hydration drives various biological processes, including protein folding, ligand binding, macromolecular assembly, enzyme kinetics, and signal transduction. The changes in hydration and packing, both when proteins fold correctly or when folding goes wrong, leading to PFDs, are examined through several biochemical, biophysical, and structural approaches. Although in many cases the binding of a ligand such as a nucleic acid helps to prevent misfolding and aggregation, there are several examples in which ligands induce misfolding and assembly into amyloids. This occurs simply because the formation of structured aggregates (such as protofibrillar and fibrillar amyloids) involves decreases in hydration, formation of a hydrogen-bond network in the secondary structure, and burying of nonpolar amino acid residues, processes that also occur in the normal folding landscape. In this Account, we describe the present knowledge of the folding and misfolding of different proteins, with a detailed emphasis on mammalian prion protein (PrP) and tumoral suppressor protein p53; we also explore how ligand binding and hydration together influence the fate of the proteins.
Anfinsen’s paradigm that the structure of a protein is determined by its amino acid sequence is to some extent contradicted by the observation that there are two isoforms of the prion protein with the same sequence: the cellular and the misfolded isoform. The cellular isoform of PrP has a disordered N-terminal domain and a highly flexible, not-well-packed C-terminal domain, which might account for its significant hydration. When PrP binds to biological molecules, such as glycosaminoglycans and nucleic acids, the disordered segments appear to fold and become less hydrated. Formation of the PrP−nucleic acid complex seems to accelerate the conversion of the cellular form of the protein into the disease-causing isoform. For p53, binding to some ligands, including nucleic acids, would prevent misfolding of the protein. Recently, several groups have begun to analyze the folding−misfolding of the individual domains of p53, but several questions remain unanswered. We discuss the implications of these findings for understanding the productive and incorrect folding pathways of these proteins in normal physiological states and in human disease, such as prion disorders and cancer. These studies are shown to lay the groundwork for the development of new drugs.
doi:10.1021/ar900179t
PMCID: PMC2825094  PMID: 19817406
4.  Nanoimaging for prion related diseases 
Prion  2010;4(4):265-274.
Misfolding and aggregation of prion proteins is linked to a number of neurodegenerative disorders such as Creutzfeldt-Jacob disease (CJD) and its variants: Kuru, Gerstmann-Straussler-Scheinker syndrome and fatal familial insomnia. In prion diseases, infectious particles are proteins that propagate by transmitting a misfolded state of a protein, leading to the formation of aggregates and ultimately to neurodegeneration. Prion phenomenon is not restricted to humans. There are a number of prion-related diseases in a variety of mammals, including bovine spongiform encephalopathy (BSE, also known as “mad cow disease”) in cattle. All known prion diseases, collectively called transmissible spongiform encephalopathies (TSEs), are untreatable and fatal. Prion proteins were also found in some fungi where they are responsible for heritable traits. Prion proteins in fungi are easily accessible and provide a powerful model for understanding the general principles of prion phenomenon and molecular mechanisms of mammalian prion diseases. Presently, several fundamental questions related to prions remain unanswered. For example, it is not clear how prions cause the disease. Other unknowns include the nature and structure of infectious agent and how prions replicate. Generally, the phenomenon of misfolding of the prion protein into infectious conformations that have the ability to propagate their properties via aggregation is of significant interest. Despite the crucial importance of misfolding and aggregation, very little is currently known about the molecular mechanisms of these processes. While there is an apparent critical need to study molecular mechanisms underlying misfolding and aggregation, the detailed characterization of these single molecule processes is hindered by the limitation of conventional methods. Although some issues remain unresolved, much progress has been recently made primarily due to the application of nanoimaging tools. The use of nanoimaging methods shows great promise for understanding the molecular mechanisms of prion phenomenon, possibly leading toward early diagnosis and effective treatment of these devastating diseases. This review article summarizes recent reports which advanced our understanding of the prion phenomenon through the use of nanoimaging methods.
doi:10.4161/pri.4.4.13125
PMCID: PMC3268959  PMID: 20724837
protein misfolding; prion; atomic force microscopy; nanomedicine; force spectroscopy
5.  HLA-B27 Misfolding and Ankylosing Spondylitis 
Molecular immunology  2013;57(1):10.1016/j.molimm.2013.07.013.
Understanding how HLA-B27 contributes to the pathogenesis of spondyloarthritis continues to be an important goal. Current efforts are aimed largely on three areas of investigation; peptide presentation to CD8 T cells, abnormal forms of the HLA-B27 heavy chain and their recognition by leukocyte immunoglobulin-like receptors on immune effector cells, and HLA-B27 heavy chain misfolding and intrinsic biological effects on affected cells. In this chapter we review our current understanding of the causes and consequences of HLA-B27 misfolding, which can be defined biochemically as a propensity to oligomerize and form complexes in the endoplasmic reticulum (ER) with the chaperone BiP (HSPA5/GRP78). HLA-B27 misfolding is linked to an unusual combination of polymorphisms that identify this allele, and cause the heavy chain to fold and load peptides inefficiently. Misfolding can result in ER-associated degradation (ERAD) of heavy chains, which is mediated in part by the E3 ubiquitin ligase HRD1 (SYVN1), and the ubiquitin conjugating enzyme UBE2JL. Upregulation of HLA-B27 and accumulation of misfolded heavy chains can activate ER stress signaling pathways that orchestrate the unfolded protein response. In transgenic rats where HLA-B27 is overexpressed, UPR activation is prominent. However, it is specific for heavy chain misfolding, since overexpression of HLA-B7, an allele that does not misfold, fails to generate ER stress. UPR activation has been linked to cytokine dysregulation, promoting lL-23, IFNβ, and lL-1α production, and may activate the IL-23/IL-17 axis in these rats. IL-1α and IFNβ are pro- and anti-osteoclastogenic cytokines, respectively, that modulate osteoclast development in HLA-B27-expressing transgenic rat monocytes. Translational studies of patient derived cells expressing HLA-B27 at physiologic levels have provided evidence that ER stress and UPR activation can occur in peripheral blood, but this has not been reported to date in isolated macrophages. Inflamed gastrointestinal tissue reveals evidence for HLA-B27 misfolding, ERAD, and autophagy, without acute UPR activation. A more complete picture of conditions that impact HLA-B27 folding and misfolding, the full spectrum and time course of consequences of ER stress, and critical cell types involved is needed to understand the role of HLA-B27 misfolding in spondyloarthritis pathogenesis.
doi:10.1016/j.molimm.2013.07.013
PMCID: PMC3857088  PMID: 23993278
MHC class I; protein misfolding; endoplasmic reticulum stress; unfolded protein response; autophagy; ankylosing spondylitis; spondyloarthritis
6.  Mechanisms of Hybrid Oligomer Formation in the Pathogenesis of Combined Alzheimer's and Parkinson's Diseases 
PLoS ONE  2008;3(9):e3135.
Background
Misfolding and pathological aggregation of neuronal proteins has been proposed to play a critical role in the pathogenesis of neurodegenerative disorders. Alzheimer's disease (AD) and Parkinson's disease (PD) are frequent neurodegenerative diseases of the aging population. While progressive accumulation of amyloid β protein (Aβ) oligomers has been identified as one of the central toxic events in AD, accumulation of α-synuclein (α-syn) resulting in the formation of oligomers and protofibrils has been linked to PD and Lewy body Disease (LBD). We have recently shown that Aβ promotes α-syn aggregation and toxic conversion in vivo, suggesting that abnormal interactions between misfolded proteins might contribute to disease pathogenesis. However the molecular characteristics and consequences of these interactions are not completely clear.
Methodology/Principal Findings
In order to understand the molecular mechanisms involved in potential Aβ/α-syn interactions, immunoblot, molecular modeling, and in vitro studies with α-syn and Aβ were performed. We showed in vivo in the brains of patients with AD/PD and in transgenic mice, Aβ and α-synuclein co-immunoprecipitate and form complexes. Molecular modeling and simulations showed that Aβ binds α-syn monomers, homodimers, and trimers, forming hybrid ring-like pentamers. Interactions occurred between the N-terminus of Aβ and the N-terminus and C-terminus of α-syn. Interacting α-syn and Aβ dimers that dock on the membrane incorporated additional α-syn molecules, leading to the formation of more stable pentamers and hexamers that adopt a ring-like structure. Consistent with the simulations, under in vitro cell-free conditions, Aβ interacted with α-syn, forming hybrid pore-like oligomers. Moreover, cells expressing α-syn and treated with Aβ displayed increased current amplitudes and calcium influx consistent with the formation of cation channels.
Conclusion/Significance
These results support the contention that Aβ directly interacts with α-syn and stabilized the formation of hybrid nanopores that alter neuronal activity and might contribute to the mechanisms of neurodegeneration in AD and PD. The broader implications of such hybrid interactions might be important to the pathogenesis of other disorders of protein misfolding.
doi:10.1371/journal.pone.0003135
PMCID: PMC2519786  PMID: 18769546
7.  Misfolded Proteins in Alzheimer’s Disease and Type II Diabetes 
Chemical Society reviews  2011;41(2):608-621.
This review presents descriptions of two amyloidogenic proteins, amyloid-β (Aβ) peptides and islet amyloid polypeptide (IAPP), whose misfolding propensities are implicated in Alzheimer’s disease (AD) and type II diabetes, respectively. Protein misfolding diseases share similarities, as well as some unique protein-specific traits, that could contribute to the initiation and/or development of their associated conditions. Aβ and IAPP are representative amyloidoses and used to highlight some of the primary considerations for studying misfolded proteins associated with human diseases. Among these factors, their physiological formation, aggregation, interactions with metal ions and other protein partners, and toxicity are presented. Small molecules that target and modulate the metal-Aβ interaction and neurotoxicity are included to illustrate one of the current approaches for studying the complex nature of misfolded proteins at the molecular level.
doi:10.1039/c1cs15112f
PMCID: PMC3210870  PMID: 21818468
8.  GroEL dependency affects codon usage—support for a critical role of misfolding in gene evolution 
Integrating genome-scale sequence, expression, structural and protein interaction data from E. coli we establish an interaction between chaperone (GroEL) dependency and optimal codon usage.Highly expressed sporadic substrates of GroEL employ more optimal codons than expected, show enrichment for optimal codons at structurally sensitive sites and greater conservation of codon optimality under conditions of relaxed purifying selection.We suggest that highly expressed genes cannot routinely utilize GroEL for error control so that codon usage has evolved to provide complementary error limitation, whereas obligate GroEL substrates experience relaxed selection on codon usage.Our results support a critical role of misfolding prevention in gene evolution.
Errors during gene expression are relatively commonplace, which has prompted speculations that many features of gene and genome anatomy and organization have evolved to reduce or mitigate such errors. One type of error that can be particularly costly occurs when the polypeptide chain that emerges from the ribosome fails to fold into its native structure. Some aberrantly folded proteins, exposing hydrophobic residues that would normally be buried, may begin to promiscuously interact with other proteins, become toxic to the cell and thus pose a substantial fitness concern (Gregersen et al, 2006).
In trans, molecular chaperones have long been recognized to play crucial roles in misfolding prevention and remedy. In cis, it has recently been suggested that the use of optimal codons limits mistranslation-induced protein misfolding (Drummond and Wilke, 2008). Evidence for the latter is centred on the argument that synonymous codons differ in their propensity to cause mistranslation. Translationally optimal codons, typically represented by more abundant cognate tRNAs (Duret, 2000), are thought less likely to cause ribosomal stalling and/or incorporation of the wrong amino acid.
Here, we suggest that the role, if any, of error limitation in cis can be revealed by studying its interaction with well-established error management systems in trans (chaperones). If codon usage does indeed play a tangible role in misfolding prevention, we would expect selection on codon identity to vary with the degree to which a protein can rely on other error control mechanisms, namely chaperones. We use the E. coli chaperonin GroEL as a model system to explore whether there is any interaction between optimal codon usage and chaperone dependency.
Kerner et al (2005) had previously determined GroEL substrates on a genome-wide scale. Based on enrichment in GroEL complexes the authors assigned ∼250 proteins to three classes reflecting GroEL dependency: class-I proteins, only a small fraction of which (<1%) associates with GroEL and which spontaneously regain some activity; class-II proteins, which only exhibit spontaneous refolding at more permissive temperatures and class-III proteins, which are obligate substrates of GroEL and largely fail to refold even under more benign conditions. Notably, although on average less abundant than class-I/II proteins (‘sporadic clients'), class-III proteins (‘obligate clients') occupy ∼80% of GroEL's capacity in vivo. Consequently, a higher proportion (∼100% versus ∼20% for class-II and ∼1% for class-I) of these proteins is routinely processed by the GroEL system.
We demonstrate that sporadic but not obligate clients of GroEL exhibit enhanced codon adaptation, carefully controlling for possible confounding factors, notably expression level and protein length (Figure 1). We also point out that genes that recently entered the E. coli genome via horizontal gene transfer will distort equilibrium analyses of codon usage in bacteria and should thus be routinely eliminated from analysis.
Building on earlier work by Zhou et al (2009), we further show that sporadic substrates are conspicuously enriched for optimal codons at structurally sensitive sites, consistent with more severe fitness implications of codon choice for these proteins.
Lastly, we reveal that codon optimality in sporadic clients is more highly conserved in S. dysenteriae. S. dysenteriae is an E. coli clone that has diverged relatively recently from the E. coli K12 strain and has adopted an intracellular lifestyle (Balbi et al, 2009). Concomitant with that lifestyle, Shigella has experienced a lower effective population size and therefore reduced efficiency of purifying selection. This has generated conditions where, overall, codon optimality has started to decay. However, when we followed the fate of ancestrally optimal codons at buried sites in the S. dysenteriae and E. coli K12 genomes, we found that a lower fraction of buried sites has lost codon optimality in sporadic substrates (Figure 4), again consistent with greater structural importance of codon choice in these substrates.
Based on the these findings, we suggest the following explanation: As mentioned above, class-III substrates are defined not only by GroEL being critical for proper folding, but also by occupying most of GroEL's capacity (∼80%). With a high proportion of class-III protein passaged through the GroEL system, mistranslation errors in these proteins weigh less severely as GroEL can remedy at least some misfolding that ensues. In contrast, class-I and II genes are more highly expressed and cannot routinely rely on GroEL to rectify folding errors. Yet class-I/II proteins are clearly liable to misfold as testified by their sporadic association with GroEL. We argue that augmenting GroEL's capacity to address the misfolding propensity of these genes would be prohibitively costly to the organism and that, as an alternative strategy, these genes employ optimal codons to reduce the rate of misfolding error.
Our findings (a) reveal a cis–trans interaction between codon usage and chaperones in providing an integrated error management system, (b) provide independent evidence for a role of misfolding in shaping gene evolution and (c) suggest that the burden of deleterious mutations in long-term bottlenecking populations like that of the insect endosymbiont Buchnera not only comprises unfavourable amino-acid (Moran, 1996) but also synonymous substitutions.
It has recently been suggested that the use of optimal codons limits mistranslation-induced protein misfolding, yet evidence for this remains largely circumstantial. In contrast, molecular chaperones have long been recognized to play crucial roles in misfolding prevention and remedy. We propose that putative error limitation in cis can be elucidated by examining the interaction between codon usage and chaperoning processes. Using Escherichia coli as a model system, we find that codon optimality covaries with dependency on the chaperonin GroEL. Sporadic but not obligate substrates of GroEL exhibit higher average codon adaptation and are conspicuously enriched for optimal codons at structurally sensitive sites. Further, codon optimality of sporadic clients is more conserved in the E. coli clone Shigella dysenteriae. We suggest that highly expressed genes cannot routinely use GroEL for error control so that codon usage has evolved to provide complementary error limitation. These findings provide independent evidence for a role of misfolding in shaping gene evolution and highlight the need to co-characterize adaptations in cis and trans to unravel the workings of integrated molecular systems.
doi:10.1038/msb.2009.94
PMCID: PMC2824523  PMID: 20087338
codon bias; GroEL; misfolding
9.  Role of Protein Misfolding and Proteostasis Deficiency in Protein Misfolding Diseases and Aging 
The misfolding, aggregation, and tissue accumulation of proteins are common events in diverse chronic diseases, known as protein misfolding disorders. Many of these diseases are associated with aging, but the mechanism for this connection is unknown. Recent evidence has shown that the formation and accumulation of protein aggregates may be a process frequently occurring during normal aging, but it is unknown whether protein misfolding is a cause or a consequence of aging. To combat the formation of these misfolded aggregates cells have developed complex and complementary pathways aiming to maintain protein homeostasis. These protective pathways include the unfolded protein response, the ubiquitin proteasome system, autophagy, and the encapsulation of damaged proteins in aggresomes. In this paper we review the current knowledge on the role of protein misfolding in disease and aging as well as the implication of deficiencies in the proteostasis cellular pathways in these processes. It is likely that further understanding of the mechanisms involved in protein misfolding and the natural defense pathways may lead to novel strategies for treatment of age-dependent protein misfolding disorders and perhaps aging itself.
doi:10.1155/2013/638083
PMCID: PMC3855986  PMID: 24348562
10.  Spatial quality control bypasses cell-based limitations on proteostasis to promote prion curing 
eLife  null;3:e04288.
The proteostasis network has evolved to support protein folding under normal conditions and to expand this capacity in response to proteotoxic stresses. Nevertheless, many pathogenic states are associated with protein misfolding, revealing in vivo limitations on quality control mechanisms. One contributor to these limitations is the physical characteristics of misfolded proteins, as exemplified by amyloids, which are largely resistant to clearance. However, other limitations imposed by the cellular environment are poorly understood. To identify cell-based restrictions on proteostasis capacity, we determined the mechanism by which thermal stress cures the [PSI+]/Sup35 prion. Remarkably, Sup35 amyloid is disassembled at elevated temperatures by the molecular chaperone Hsp104. This process requires Hsp104 engagement with heat-induced non-prion aggregates in late cell-cycle stage cells, which promotes its asymmetric retention and thereby effective activity. Thus, cell division imposes a potent limitation on proteostasis capacity that can be bypassed by the spatial engagement of a quality control factor.
DOI: http://dx.doi.org/10.7554/eLife.04288.001
eLife digest
Proteins must fold into specific shapes to work inside cells, and the misfolding of proteins is associated with a growing number of diseases. For example, prions are misfolded proteins that form insoluble aggregates called amyloids. These aggregates are not easily destroyed and can cause other nearby proteins to misfold and join the amyloid. This process of amyloid assembly leads to progressive diseases such as mad cow disease, Huntington's disease, Alzheimer's disease, and Parkinson's disease, which are collectively known as amyloidoses.
A series of biological pathways called the proteostasis network control protein integrity in a cell. Under normal conditions or even mildly stressful conditions—such as at slightly increased temperatures—the proteostasis network is able to prevent proteins from misfolding. However, if a cell is placed under lots of stress this network may become overwhelmed and misfolded proteins can accumulate. To date, the proteostasis network has not been linked to the clearance of amyloids.
A protein called Sup35, which is found in budding yeast, can exist as two different prion forms. Previous studies have shown that briefly heating the yeast cells can ‘cure’ the so-called ‘weak’ form of the prion. The ‘strong’ prion form, however, was thought to be unaffected by elevated temperature. These previous studies had only tested yeast cells that had been dividing for a few generations; it was unknown if cells that had been dividing for longer might respond differently.
Klaips et al. found that a protein called Hsp104—which helps to fold proteins properly—can break down the amyloid aggregates. This protein is normally only present in small amounts, but heating causes the levels of Hsp104 to rise. Klaips et al. found that the extra Hsp104 protein associated with the aggregates and led to their disassembly. When Hsp104 was prevented from associating with the prions, the aggregates were not cured even if high levels of Hsp104 were present in the cell.
When budding yeast form new cells, a daughter cell ‘buds’ off from the mother cell. Klaips et al. found that mother cells exposed to heat retain most of the Hsp104 when the cell divides, and this retention allowed Hsp104 to accumulate to a level required for the breakdown of amyloid aggregates. Therefore, under normal conditions, amyloids persist because cell division keeps the amount of Hsp104 below this threshold.
Previously it had been thought that the physical characteristics of amyloids accounted for their resilience in the face of the cell mechanisms designed to counteract protein misfolding. However, Klaips et al. show that the balance of the different mechanisms involved in proteostasis can be manipulated to create environments where amyloids are either created and maintained or destroyed. Targeting these mechanisms could therefore present new treatment options for amyloidosis.
DOI: http://dx.doi.org/10.7554/eLife.04288.002
doi:10.7554/eLife.04288
PMCID: PMC4270096  PMID: 25490068
chaperone; protein misfolding; amyloid; prion; S. cerevisiae
11.  An ALS-Linked Mutant SOD1 Produces a Locomotor Defect Associated with Aggregation and Synaptic Dysfunction When Expressed in Neurons of Caenorhabditis elegans 
PLoS Genetics  2009;5(1):e1000350.
The nature of toxic effects exerted on neurons by misfolded proteins, occurring in a number of neurodegenerative diseases, is poorly understood. One approach to this problem is to measure effects when such proteins are expressed in heterologous neurons. We report on effects of an ALS-associated, misfolding-prone mutant human SOD1, G85R, when expressed in the neurons of Caenorhabditis elegans. Stable mutant transgenic animals, but not wild-type human SOD1 transgenics, exhibited a strong locomotor defect associated with the presence, specifically in mutant animals, of both soluble oligomers and insoluble aggregates of G85R protein. A whole-genome RNAi screen identified chaperones and other components whose deficiency increased aggregation and further diminished locomotion. The nature of the locomotor defect was investigated. Mutant animals were resistant to paralysis by the cholinesterase inhibitor aldicarb, while exhibiting normal sensitivity to the cholinergic agonist levamisole and normal muscle morphology. When fluorescently labeled presynaptic components were examined in the dorsal nerve cord, decreased numbers of puncta corresponding to neuromuscular junctions were observed in mutant animals and brightness was also diminished. At the EM level, mutant animals exhibited a reduced number of synaptic vesicles. Neurotoxicity in this system thus appears to be mediated by misfolded SOD1 and is exerted on synaptic vesicle biogenesis and/or trafficking.
Author Summary
A new animal model of the human neurodegenerative disease amyotrophic lateral sclerosis (ALS; Lou Gehrig's Disease) is presented. Two percent of ALS cases result from heritable mutations affecting the abundant enzyme superoxide dismutase (SOD1). Such mutations have been indicated to impair the folding and stability of the enzyme, leading it to misfold and aggregate in motor neurons, associated with the paralyzing disease. Here, when a mutant form of human SOD1 was produced in neurons of C. elegans worms, it led to a severe locomotor defect—the worms were essentially paralyzed. The protein formed aggregates in the neurons, including an intermediate form of aggregate, soluble oligomers, that has been linked to toxicity to cells. By contrast, worms expressing the normal version of human SOD1 protein exhibited normal movement and no aggregation. The movement defect was further analyzed using chemical inhibitors and found to result from defective function of synapses, the connections made between neurons, and between neurons and muscle. Finally, in a screen using RNA interference, we observed that the worms' aggregation and locomotor condition was worsened when a class of molecules called molecular chaperones, which assist protein folding in the cell, were impaired in function. This is consistent with the idea that misfolded SOD1 is directly involved with causing the neuronal dysfunction.
doi:10.1371/journal.pgen.1000350
PMCID: PMC2621352  PMID: 19165329
12.  Inhibition of Protein Misfolding/Aggregation Using Polyglutamine Binding Peptide QBP1 as a Therapy for the Polyglutamine Diseases 
Neurotherapeutics  2013;10(3):440-446.
Protein misfolding and aggregation in the brain have been recognized to be crucial in the pathogenesis of various neurodegenerative diseases, including Alzheimer’s, Parkinson’s, and the polyglutamine (polyQ) diseases, which are collectively called the “protein misfolding diseases”. In the polyQ diseases, an abnormally expanded polyQ stretch in the responsible proteins causes the proteins to misfold and aggregate, eventually resulting in neurodegeneration. Hypothesizing that polyQ protein misfolding and aggregation could be inhibited by molecules specifically binding to the expanded polyQ stretch, we identified polyQ binding peptide 1 (QBP1). We show that QBP1 does, indeed, inhibit misfolding and aggregation of the expanded polyQ protein in vitro. Furthermore overexpression of QBP1 by the crossing of transgenic animals inhibits neurodegeneration in Drosophila models of the polyQ diseases. We also introduce our attempts to deliver QBP1 into the brain by administration using viral vectors and protein transduction domains. Interestingly, recent data suggest that QBP1 can also inhibit the misfolding/aggregation of proteins responsible for other protein misfolding diseases, highlighting the potential of QBP1 as a general therapeutic molecule for a wide range of neurodegenerative diseases. We hope that in the near future, aggregation inhibitor-based drugs will be developed and bring relief to patients suffering from these currently intractable protein misfolding diseases.
Electronic supplementary material
The online version of this article (doi:10.1007/s13311-013-0184-7) contains supplementary material, which is available to authorized users.
doi:10.1007/s13311-013-0184-7
PMCID: PMC3701761  PMID: 23504628
Polyglutamine disease; Neurodegeneration; QBP1; Protein aggregation; Inhibitor peptide; Therapy
13.  Nanotools for Megaproblems: Probing Protein Misfolding Diseases Using Nanomedicine Modus Operandi 
Journal of proteome research  2006;5(10):2505-2522.
Misfolding and self-assembly of proteins in nanoaggregates of different sizes and morphologies (nanoensembles, primary nanofilaments, nanorings, filaments, protofibrils, fibrils, etc.) is a common theme unifying a number of human pathologies termed protein misfolding diseases. Recent studies highlight increasing recognition of the public health importance of protein misfolding diseases, including various neurodegenerative disorders and amyloidoses. It is understood now that the first essential elements in the vast majority of neurodegenerative processes are misfolded and aggregated proteins. Altogether, the accumulation of abnormal protein nanoensembles exerts toxicity by disrupting intracellular transport, overwhelming protein degradation pathways, and/or disturbing vital cell functions. In addition, the formation of inclusion bodies is known to represent a major problem in the production of recombinant therapeutic proteins. Formulation of these therapeutic proteins into delivery systems and their in vivo delivery are often complicated by protein association. Thus, protein folding abnormalities and subsequent events underlie a multitude of human pathologies and difficulties with protein therapeutic applications. The field of medicine therefore can be greatly advanced by establishing a fundamental understanding of key factors leading to misfolding and self-assembly responsible for various protein folding pathologies. This article overviews protein misfolding diseases and outlines some novel and advanced nanotechnologies, including nanoimaging techniques, nanotoolboxes and nanocontainers, complemented by appropriate ensemble techniques, all focused on the ultimate goal to establish etiology and to diagnose, prevent, and cure these devastating disorders.
doi:10.1021/pr0603349
PMCID: PMC1880889  PMID: 17022621
misfolding; protein aggregation; conformational disease; partially folded intermediate; nanomedicine
14.  Head-to-tail interactions of the coiled-coil domains regulate ClpB activity and cooperation with Hsp70 in protein disaggregation 
eLife  2014;3:e02481.
The hexameric AAA+ chaperone ClpB reactivates aggregated proteins in cooperation with the Hsp70 system. Essential for disaggregation, the ClpB middle domain (MD) is a coiled-coil propeller that binds Hsp70. Although the ClpB subunit structure is known, positioning of the MD in the hexamer and its mechanism of action are unclear. We obtained electron microscopy (EM) structures of the BAP variant of ClpB that binds the protease ClpP, clearly revealing MD density on the surface of the ClpB ring. Mutant analysis and asymmetric reconstructions show that MDs adopt diverse positions in a single ClpB hexamer. Adjacent, horizontally oriented MDs form head-to-tail contacts and repress ClpB activity by preventing Hsp70 interaction. Tilting of the MD breaks this contact, allowing Hsp70 binding, and releasing the contact in adjacent subunits. Our data suggest a wavelike activation of ClpB subunits around the ring.
DOI: http://dx.doi.org/10.7554/eLife.02481.001
eLife digest
Proteins are long chain-like molecules that twist and fold into complex three-dimensional shapes in order to carry out their functions. High temperatures or other types of stress can cause proteins to fold incorrectly, and misfolded proteins can form clumps (or aggregates) that are harmful to cells. Additional proteins called chaperones are therefore used by cells to help proteins to fold correctly, or to refold poorly folded proteins.
ClpB proteins (and related proteins) are chaperones found in bacteria, fungi and plants; these proteins co-operate with other chaperones to rescue misfolded proteins that have aggregated—an activity that helps cells to survive heat shock and other stresses. Six ClpB proteins work together to form a ring-shaped complex, and the misfolded protein is unfolded by threading it through the centre of this ring. Each ClpB protein also has a middle domain that acts to switch the complex on and off as needed.
The middle domains are known to form coiled-coils, with protein helices coiled together like the strands of a rope. However, previous efforts to work out the structure of the ClpB complex did not clearly establish where these coiled-coils were positioned relative to the rest of the ring.
Now Carroni et al. have used image processing to overcome these problems and reveal that the middle domains are wrapped around the outer edge of the ring complex. Analysis of ClpB mutants that lock the complex in either an off or on state revealed that the middle domains are linked head-to tail to encircle the ring when the complex is off. However, when the complex switches on, the middle domains let go of each other and tilt, allowing the ring to change shape. Carroni et al. suggest that the exposed ends of the middle domains are free to bind to other chaperones (those that work to refold the unfolded proteins), thereby activating the complex.
Although Carroni et al. have revealed how the ClpB ring complex is activated, further work is needed to understand exactly how the unlocked ring works to rescue misfolded proteins from aggregates within cells.
DOI: http://dx.doi.org/10.7554/eLife.02481.002
doi:10.7554/eLife.02481
PMCID: PMC4023160  PMID: 24843029
single particle EM; ClpB/Hsp104; protein unfolding; E. coli; S. cerevisiae
15.  Modulation of Heat Shock Transcription Factor 1 as a Therapeutic Target for Small Molecule Intervention in Neurodegenerative Disease 
PLoS Biology  2010;8(1):e1000291.
A yeast-based small molecule screen identifies a novel activator of human HSF1 and protein chaperone expression and which appears to alleviate the toxicity of protein misfolding diseases.
Neurodegenerative diseases such as Huntington disease are devastating disorders with no therapeutic approaches to ameliorate the underlying protein misfolding defect inherent to poly-glutamine (polyQ) proteins. Given the mounting evidence that elevated levels of protein chaperones suppress polyQ protein misfolding, the master regulator of protein chaperone gene transcription, HSF1, is an attractive target for small molecule intervention. We describe a humanized yeast-based high-throughput screen to identify small molecule activators of human HSF1. This screen is insensitive to previously characterized activators of the heat shock response that have undesirable proteotoxic activity or that inhibit Hsp90, the central chaperone for cellular signaling and proliferation. A molecule identified in this screen, HSF1A, is structurally distinct from other characterized small molecule human HSF1 activators, activates HSF1 in mammalian and fly cells, elevates protein chaperone expression, ameliorates protein misfolding and cell death in polyQ-expressing neuronal precursor cells and protects against cytotoxicity in a fly model of polyQ-mediated neurodegeneration. In addition, we show that HSF1A interacts with components of the TRiC/CCT complex, suggesting a potentially novel regulatory role for this complex in modulating HSF1 activity. These studies describe a novel approach for the identification of new classes of pharmacological interventions for protein misfolding that underlies devastating neurodegenerative disease.
Author Summary
The misfolding of proteins into a toxic state contributes to a variety of neurodegenerative diseases such as Huntington, Alzheimer, and Parkinson disease. Although no known cure exists for these afflictions, many studies have shown that increasing the levels of protein chaperones, proteins that assist in the correct folding of other proteins, can suppress the neurotoxicity of the misfolded proteins. As such, increasing the cellular concentration of protein chaperones might serve as a powerful therapeutic approach in treating protein misfolding diseases. Because the levels of protein chaperones in the cell are primarily controlled by the heat shock transcription factor 1 [HSF1], we have designed and implemented a pharmacological screen to identify small molecules that can promote human HSF1 activation and increase the expression of protein chaperones. Through these studies, we have identified HSF1A, a molecule capable of activating human HSF1, increasing the levels of protein chaperones and alleviating the toxicity of misfolded proteins in both cell culture as well as fruit fly models of neurodegenerative disease.
doi:10.1371/journal.pbio.1000291
PMCID: PMC2808216  PMID: 20098725
16.  Pathogenic Protein Seeding in Alzheimer’s Disease and Other Neurodegenerative Disorders 
Annals of neurology  2011;70(4):532-540.
The misfolding and aggregation of specific proteins is a seminal occurrence in a remarkable variety of neurodegenerative disorders. In Alzheimer’s disease (the most prevalent cerebral proteopathy), the two principal aggregating proteins are β-amyloid (Aβ) and tau. The abnormal assemblies formed by conformational variants of these proteins range in size from small oligomers to the characteristic lesions that are visible by optical microscopy, such as senile plaques and neurofibrillary tangles. Pathologic similarities with prion disease suggest that the formation and spread of these proteinaceous lesions might involve a common molecular mechanism – corruptive protein templating. Experimentally, cerebral β-amyloidosis can be exogenously induced by exposure to dilute brain extracts containing aggregated Aβ seeds. The amyloid-inducing agent probably is Aβ itself, in a conformation generated most effectively in the living brain. Once initiated, Aβ lesions proliferate within and among brain regions. The induction process is governed by the structural and biochemical nature of the Aβ seed, as well as the attributes of the host, reminiscent of pathogenically variant prion strains. The concept of prion-like induction and spreading of pathogenic proteins recently has been expanded to include aggregates of tau, α-synuclein, huntingtin, superoxide dismutase-1, and TDP-43, which characterize such human neurodegenerative disorders as frontotemporal lobar degeneration, Parkinson’s/Lewy body disease, Huntington’s disease, and amyotrophic lateral sclerosis. Our recent finding that the most effective Aβ seeds are small and soluble intensifies the search in bodily fluids for misfolded protein seeds that are upstream in the proteopathic cascade, and thus could serve as predictive diagnostics and the targets of early, mechanism-based interventions. Establishing the clinical implications of corruptive protein templating will require further mechanistic and epidemiologic investigations. However, the theory that many chronic neurodegenerative diseases can originate and progress via the seeded corruption of misfolded proteins has the potential to unify experimental and translational approaches to these increasingly prevalent disorders.
doi:10.1002/ana.22615
PMCID: PMC3203752  PMID: 22028219
Alzheimer’s disease; amyloid; amyotrophic lateral sclerosis; frontotemporal lobar degeneration; Huntington’s disease; inclusions; neurofibrillary tangles; Parkinson’s disease; prion; proteopathy; senile plaques; tauopathy
17.  Single molecule AFM force spectroscopy study of Aβ-40 interactions 
Biochemistry  2011;50(23):5154-5162.
Misfolding and aggregation of amyloid beta (Aβ)-40 peptide play key roles in the development of Alzheimer's disease (AD). However, very little is known about the molecular mechanisms underlying these molecular processes. We developed a novel experimental approach that can directly probe aggregation-prone states of proteins and their interactions. In this approach, the proteins are anchored to the surface of the AFM substrate (mica) and the probe, and the interaction between anchored molecules is measured in the approach-retraction cycles. We used dynamic force spectroscopy (DFS) to measure the stability of transiently formed dimers. One of the major findings from DFS analysis of α-synuclein (α-Syn) is that dimeric complexes formed by misfolded α-Syn protein are very stable and dissociate over a range of seconds. This differs markedly from the dynamics of monomers, which occurs on a microsecond-nanosecond time scale. Here we applied the same approach to quantitatively characterize interactions of Aβ-40 peptides in a broad range of pH values. These studies showed that misfolded dimers are characterized by the lifetimes in the range of seconds. This value depends on pH and varies between 2.7 s for pH 2.7 and 0.1 s for pH 7, indicating that the aggregation properties of Aβ-40 are modulated by the environmental conditions. The analysis of the contour lengths revealed the existence of various pathways for dimer dissociation, suggesting that dimers with different conformations are formed. These structural variations result in different aggregation pathways, leading to different types of oligomers and higher order aggregates, including fibrils.
doi:10.1021/bi200147a
PMCID: PMC3113552  PMID: 21553928
18.  Chaperone-mediated hierarchical control in targeting misfolded proteins to aggresomes 
Molecular Biology of the Cell  2011;22(18):3277-3288.
Not only do molecular chaperones assist protein folding, they also facilitate the degradation of misfolded polypeptides. In coordinating with cochaperones CHIP and BAG3, Hsp70 can also target misfolded proteins to aggresomes, thereby protecting cells from proteotoxic stress.
Protein misfolding is a common event in living cells. Molecular chaperones not only assist protein folding; they also facilitate the degradation of misfolded polypeptides. When the intracellular degradative capacity is exceeded, juxtanuclear aggresomes are formed to sequester misfolded proteins. Despite the well-established role of chaperones in both protein folding and degradation, how chaperones regulate the aggregation process remains controversial. Here we investigate the molecular mechanisms underlying aggresome formation in mammalian cells. Analysis of the chaperone requirements for the fate of misfolded proteins reveals an unexpected role of heat shock protein 70 (Hsp70) in promoting aggresome formation. This proaggregation function of Hsp70 relies on the interaction with the cochaperone ubiquitin ligase carboxyl terminal of Hsp70/Hsp90 interacting protein (CHIP). Disrupting Hsp70–CHIP interaction prevents the aggresome formation, whereas a dominant-negative CHIP mutant sensitizes the aggregation of misfolded protein. This accelerated aggresome formation also relies on the stress-induced cochaperone Bcl2-associated athanogene 3. Our results indicate that a hierarchy of cochaperone interaction controls different aspects of the intracellular protein triage decision, extending the function of Hsp70 from folding and degradation to aggregation.
doi:10.1091/mbc.E11-05-0388
PMCID: PMC3172255  PMID: 21775628
19.  Polyglutamine Induced Misfolding of Huntingtin Exon1 is Modulated by the Flanking Sequences 
PLoS Computational Biology  2010;6(4):e1000772.
Polyglutamine (polyQ) expansion in exon1 (XN1) of the huntingtin protein is linked to Huntington's disease. When the number of glutamines exceeds a threshold of approximately 36–40 repeats, XN1 can readily form amyloid aggregates similar to those associated with disease. Many experiments suggest that misfolding of monomeric XN1 plays an important role in the length-dependent aggregation. Elucidating the misfolding of a XN1 monomer can help determine the molecular mechanism of XN1 aggregation and potentially help develop strategies to inhibit XN1 aggregation. The flanking sequences surrounding the polyQ region can play a critical role in determining the structural rearrangement and aggregation mechanism of XN1. Few experiments have studied XN1 in its entirety, with all flanking regions. To obtain structural insights into the misfolding of XN1 toward amyloid aggregation, we perform molecular dynamics simulations on monomeric XN1 with full flanking regions, a variant missing the polyproline regions, which are hypothesized to prevent aggregation, and an isolated polyQ peptide (Qn). For each of these three constructs, we study glutamine repeat lengths of 23, 36, 40 and 47. We find that polyQ peptides have a positive correlation between their probability to form a β-rich misfolded state and their expansion length. We also find that the flanking regions of XN1 affect its probability to^x_page_count=28 form a β-rich state compared to the isolated polyQ. Particularly, the polyproline regions form polyproline type II helices and decrease the probability of the polyQ region to form a β-rich state. Additionally, by lengthening polyQ, the first N-terminal 17 residues are more likely to adopt a β-sheet conformation rather than an α-helix conformation. Therefore, our molecular dynamics study provides a structural insight of XN1 misfolding and elucidates the possible role of the flanking sequences in XN1 aggregation.
Author Summary
Huntington's Disease is a neurodegenerative disorder associated with protein aggregation in neurons. The aggregates formed are thought to lead to neurotoxicity and cell death. Understanding the molecular structure of these aggregates may lead to strategies to inhibit aggregation. Exon 1 (XN1) of the huntingtin protein is critical for aggregate formation. This polypeptide has a naturally occurring polyglutamine sequence (polyQ), which is elongated in patients afflicted with the disease. The polyQ region in XN1 has several flanking sequences with distinct physicochemical properties, including the N-terminal 17 residues, two polyproline regions, and C-terminal sequences, that may affect its overall structure and aggregation. What is the overall structure of XN1, and what structural effects do the neighboring sequences have on each other and polyQ? We address these questions by studying computational models of various polypeptides, including XN1 and three mutant forms associated with Huntington's Disease. Certain neighboring sequences are found to inhibit aggregation, while others may be recruited by polyQ to form aggregates. Our results suggest the role that the flanking sequences may play in XN1 aggregation and may subsequently guide future structural models of XN1 aggregation.
doi:10.1371/journal.pcbi.1000772
PMCID: PMC2861695  PMID: 20442863
20.  Quantifying Chaperone-Mediated Transitions in the Proteostasis Network of E. coli 
PLoS Computational Biology  2013;9(11):e1003324.
For cells to function, the concentrations of all proteins in the cell must be maintained at the proper levels (proteostasis). This task – complicated by cellular stresses, protein misfolding, aggregation, and degradation – is performed by a collection of chaperones that alter the configurational landscape of a given client protein through the formation of protein-chaperone complexes. The set of all such complexes and the transitions between them form the proteostasis network. Recently, a computational model was introduced (FoldEco) that synthesizes experimental data into a system-wide description of the proteostasis network of E. coli. This model describes the concentrations over time of all the species in the system, which include different conformations of the client protein, as well as protein-chaperone complexes. We apply to this model a recently developed analysis tool to calculate mediation probabilities in complex networks. This allows us to determine the probability that a given chaperone system is used to mediate transitions between client protein conformations, such as folding, or the correction of misfolded conformations. We determine how these probabilities change both across different proteins, as well as with system parameters, such as the synthesis rate, and in each case reveal in detail which factors control the usage of one chaperone system over another. We find that the different chaperone systems do not operate orthogonally and can compensate for each other when one system is disabled or overworked, and that this can complicate the analysis of “knockout” experiments, where the concentration of native protein is compared both with and without the presence of a given chaperone system. This study also gives a general recipe for conducting a transition-path–based analysis on a network of coupled chemical reactions, which can be useful in other types of networks as well.
Author Summary
To maintain proper amounts of folded, functional proteins, cells use systems of chaperones to correct misfolded proteins, disassemble aggregates, and provide sheltered environments in which proteins fold to their native structure. Typically, an individual system is studied in isolation, and its effects on a given protein are studied using “knockouts”, where the amount of native protein is compared with and without the active chaperone system. However, when multiple chaperone systems are operating simultaneously, knockouts can fail to reveal chaperone activity, as different chaperone systems can compensate for one another. We use a previously introduced computational model of chaperone systems in Escherichia coli, in combination with our transition-path analysis methods for networks, to analyze paths of individual proteins through the set of possible chaperone-bound and -unbound states. Our analysis allows us to answer questions that are inaccessible to knockout experiments, such as: How often will a given chaperone system be used to rescue a protein from a misfolded state? This approach provides a clear view of how the different systems of chaperones cooperate and compete under varying conditions.
doi:10.1371/journal.pcbi.1003324
PMCID: PMC3828153  PMID: 24244134
21.  Rapid and Sensitive RT-QuIC Detection of Human Creutzfeldt-Jakob Disease Using Cerebrospinal Fluid 
mBio  2015;6(1):e02451-14.
ABSTRACT 
Fast, definitive diagnosis of Creutzfeldt-Jakob disease (CJD) is important in assessing patient care options and transmission risks. Real-time quaking-induced conversion (RT-QuIC) assays of cerebrospinal fluid (CSF) and nasal-brushing specimens are valuable in distinguishing CJD from non-CJD conditions but have required 2.5 to 5 days. Here, an improved RT-QuIC assay is described which identified positive CSF samples within 4 to 14 h with better analytical sensitivity. Moreover, analysis of 11 CJD patients demonstrated that while 7 were RT-QuIC positive using the previous conditions, 10 were positive using the new assay. In these and further analyses, a total of 46 of 48 CSF samples from sporadic CJD patients were positive, while all 39 non-CJD patients were negative, giving 95.8% diagnostic sensitivity and 100% specificity. This second-generation RT-QuIC assay markedly improved the speed and sensitivity of detecting prion seeds in CSF specimens from CJD patients. This should enhance prospects for rapid and accurate ante mortem CJD diagnosis.
Importance  A long-standing problem in dealing with various neurodegenerative protein misfolding diseases is early and accurate diagnosis. This issue is particularly important with human prion diseases, such as CJD, because prions are deadly, transmissible, and unusually resistant to decontamination. The recently developed RT-QuIC test allows for highly sensitive and specific detection of CJD in human cerebrospinal fluid and is being broadly implemented as a key diagnostic tool. However, as currently applied, RT-QuIC takes 2.5 to 5 days and misses 11 to 23% of CJD cases. Now, we have markedly improved RT-QuIC analysis of human CSF such that CJD and non-CJD patients can be discriminated in a matter of hours rather than days with enhanced sensitivity. These improvements should allow for much faster, more accurate, and practical testing for CJD. In broader terms, our study provides a prototype for tests for misfolded protein aggregates that cause many important amyloid diseases, such as Alzheimer’s, Parkinson’s, and tauopathies.
Importance 
A long-standing problem in dealing with various neurodegenerative protein misfolding diseases is early and accurate diagnosis. This issue is particularly important with human prion diseases, such as CJD, because prions are deadly, transmissible, and unusually resistant to decontamination. The recently developed RT-QuIC test allows for highly sensitive and specific detection of CJD in human cerebrospinal fluid and is being broadly implemented as a key diagnostic tool. However, as currently applied, RT-QuIC takes 2.5 to 5 days and misses 11 to 23% of CJD cases. Now, we have markedly improved RT-QuIC analysis of human CSF such that CJD and non-CJD patients can be discriminated in a matter of hours rather than days with enhanced sensitivity. These improvements should allow for much faster, more accurate, and practical testing for CJD. In broader terms, our study provides a prototype for tests for misfolded protein aggregates that cause many important amyloid diseases, such as Alzheimer’s, Parkinson’s, and tauopathies.
doi:10.1128/mBio.02451-14
PMCID: PMC4313917  PMID: 25604790
22.  Lifespan Extension Conferred by Endoplasmic Reticulum Secretory Pathway Deficiency Requires Induction of the Unfolded Protein Response 
PLoS Genetics  2014;10(1):e1004019.
Cells respond to accumulation of misfolded proteins in the endoplasmic reticulum (ER) by activating the unfolded protein response (UPR) signaling pathway. The UPR restores ER homeostasis by degrading misfolded proteins, inhibiting translation, and increasing expression of chaperones that enhance ER protein folding capacity. Although ER stress and protein aggregation have been implicated in aging, the role of UPR signaling in regulating lifespan remains unknown. Here we show that deletion of several UPR target genes significantly increases replicative lifespan in yeast. This extended lifespan depends on a functional ER stress sensor protein, Ire1p, and is associated with constitutive activation of upstream UPR signaling. We applied ribosome profiling coupled with next generation sequencing to quantitatively examine translational changes associated with increased UPR activity and identified a set of stress response factors up-regulated in the long-lived mutants. Besides known UPR targets, we uncovered up-regulation of components of the cell wall and genes involved in cell wall biogenesis that confer resistance to multiple stresses. These findings demonstrate that the UPR is an important determinant of lifespan that governs ER stress and identify a signaling network that couples stress resistance to longevity.
Author Summary
Impaired protein function caused by protein misfolding and aggregation has been implicated in the development of age-related diseases and regulation of lifespan. Accumulation of misfolded proteins in the endoplasmic reticulum, a cellular organelle responsible for protein folding and trafficking, activates protective signaling pathways that restore protein homeostasis. One such conserved signalling pathway is mediated by the protein misfolding sensor Ire1p and the transcription factor Hac1p, which up-regulate endoplasmic reticulum chaperones, oxidative folding components and factors that facilitate degradation of misfolded proteins to alleviate increased protein folding demand. Here, we describe the role of the Ire1p pathway and its downstream targets in regulation of lifespan in yeast. While the loss of Ire1p itself had little effect on lifespan, we found that selective inactivation of the individual protein folding and maturation factors led to increased longevity. We also provide evidence that this increased longevity depends on functional Ire1p and induction of multiple cytoprotective pathways that confer resistance to stress.
doi:10.1371/journal.pgen.1004019
PMCID: PMC3879150  PMID: 24391512
23.  Virus-Induced Chaperone-Enriched (VICE) Domains Function as Nuclear Protein Quality Control Centers during HSV-1 Infection 
PLoS Pathogens  2009;5(10):e1000619.
Virus-Induced Chaperone-Enriched (VICE) domains form adjacent to nuclear viral replication compartments (RC) during the early stages of HSV-1 infection. Between 2 and 3 hours post infection at a MOI of 10, host protein quality control machinery such as molecular chaperones (e.g. Hsc70), the 20S proteasome and ubiquitin are reorganized from a diffuse nuclear distribution pattern to sequestration in VICE domains. The observation that VICE domains contain putative misfolded proteins suggests that they may be similar to nuclear inclusion bodies that form under conditions in which the protein quality control machinery is overwhelmed by the presence of misfolded proteins. The detection of Hsc70 in VICE domains, but not in nuclear inclusion bodies, indicates that Hsc70 is specifically reorganized by HSV-1 infection. We hypothesize that HSV-1 infection induces the formation of nuclear protein quality control centers to remodel or degrade aberrant nuclear proteins that would otherwise interfere with productive infection. Detection of proteolytic activity in VICE domains suggests that substrates may be degraded by the 20S proteasome in VICE domains. FRAP analysis reveals that GFP-Hsc70 is dynamically associated with VICE domains, suggesting a role for Hsc70 in scanning the infected nucleus for misfolded proteins. During 42°C heat shock, Hsc70 is redistributed from VICE domains into RC perhaps to remodel viral replication and regulatory proteins that have become insoluble in these compartments. The experiments presented in this paper suggest that VICE domains are nuclear protein quality control centers that are modified by HSV-1 to promote productive infection.
Author Summary
Protein quality control is a protective cellular mechanism by which damaged proteins are refolded or degraded so that they cannot interfere with essential cellular processes. In the event that protein quality control machinery cannot refold or degrade damaged proteins, sequestration of misfolded protein is an alternative protective mechanism for reducing the toxic effects of misfolded protein. Several neurological diseases result from the accumulation of toxic misfolded proteins that cannot be efficiently refolded or degraded. In neurons from patients afflicted with Huntington's disease, misfolded huntingtin protein is sequestered in large aggregates in the nucleus called inclusion bodies. Inclusion bodies also contain protein quality control machinery including molecular chaperones, the proteasome and ubiquitin. Here we report that analogous structures called Virus-Induced Chaperone-Enriched (VICE) domains form in the nucleus of cells infected with Herpes Simplex Virus type 1 (HSV-1). VICE domains contain misfolded protein, chaperones and protein degradation activity. VICE domain formation is efficient in infected cells taxed with high levels of viral protein production. We hypothesize that misfolded proteins that arise in HSV-1-infected cells are sequestered in VICE domains to promote remodeling of misfolded proteins.
doi:10.1371/journal.ppat.1000619
PMCID: PMC2752995  PMID: 19816571
24.  Localization of Protein Aggregation in Escherichia coli Is Governed by Diffusion and Nucleoid Macromolecular Crowding Effect 
PLoS Computational Biology  2013;9(4):e1003038.
Aggregates of misfolded proteins are a hallmark of many age-related diseases. Recently, they have been linked to aging of Escherichia coli (E. coli) where protein aggregates accumulate at the old pole region of the aging bacterium. Because of the potential of E. coli as a model organism, elucidating aging and protein aggregation in this bacterium may pave the way to significant advances in our global understanding of aging. A first obstacle along this path is to decipher the mechanisms by which protein aggregates are targeted to specific intercellular locations. Here, using an integrated approach based on individual-based modeling, time-lapse fluorescence microscopy and automated image analysis, we show that the movement of aging-related protein aggregates in E. coli is purely diffusive (Brownian). Using single-particle tracking of protein aggregates in live E. coli cells, we estimated the average size and diffusion constant of the aggregates. Our results provide evidence that the aggregates passively diffuse within the cell, with diffusion constants that depend on their size in agreement with the Stokes-Einstein law. However, the aggregate displacements along the cell long axis are confined to a region that roughly corresponds to the nucleoid-free space in the cell pole, thus confirming the importance of increased macromolecular crowding in the nucleoids. We thus used 3D individual-based modeling to show that these three ingredients (diffusion, aggregation and diffusion hindrance in the nucleoids) are sufficient and necessary to reproduce the available experimental data on aggregate localization in the cells. Taken together, our results strongly support the hypothesis that the localization of aging-related protein aggregates in the poles of E. coli results from the coupling of passive diffusion-aggregation with spatially non-homogeneous macromolecular crowding. They further support the importance of “soft” intracellular structuring (based on macromolecular crowding) in diffusion-based protein localization in E. coli.
Author Summary
Localization of proteins to specific positions inside bacteria is crucial to several physiological processes, including chromosome organization, chemotaxis or cell division. Since bacterial cells do not possess internal sub-compartments (e.g., cell organelles) nor vesicle-based sorting systems, protein localization in bacteria must rely on alternative mechanisms. In many instances, the nature of these mechanisms remains to be elucidated. In Escherichia coli, the localization of aggregates of misfolded proteins at the poles or the center of the cell has recently been linked to aging. However, the molecular mechanisms governing this localization of the protein aggregates remain controversial. To identify these mechanisms, we have devised an integrated strategy combining innovative experimental and modeling approaches. Our results show the importance of the increased macromolecular crowding in the nucleoids, the regions within the cell where the bacterial chromosome preferentially condensates. They indicate that a purely diffusive pattern of aggregates mobility combined with nucleoid occlusion underlies their accumulation in polar and mid-cell positions.
doi:10.1371/journal.pcbi.1003038
PMCID: PMC3636022  PMID: 23633942
25.  In Vivo Disassembly and Reassembly of Protein Aggregates in Escherichia coli 
Journal of Bacteriology  2014;196(13):2325-2332.
Protein misfolding and aggregation are inevitable but detrimental cellular processes. Cells therefore possess protein quality control mechanisms based on chaperones and proteases that (re)fold or hydrolyze unfolded, misfolded, and aggregated proteins. Besides these conserved quality control mechanisms, the spatial organization of protein aggregates (PAs) inside the cell has been proposed as an important additional strategy to deal with their cytotoxicity. In the bacterium Escherichia coli, however, it remained unclear how this spatial organization is established and how this process of assembling PAs in the cell poles affects cellular physiology. In this report, high hydrostatic pressure was used to transiently reverse protein aggregation in living E. coli cells, allowing the subsequent (re)assembly of PAs to be studied in detail. This approach revealed PA assembly to be dependent on intracellular energy and metabolic activity, with the resulting PA structure being confined to the cell pole by nucleoid occlusion. Moreover, a correlation could be observed between the time needed for PA reassembly and the individual lag time of the cells, which might prevent symmetric segregation of cytotoxic PAs among siblings to occur and ensure rapid spatial clearance of molecular damage throughout the emerging population.
doi:10.1128/JB.01549-14
PMCID: PMC4054163  PMID: 24633872

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