Protein Deposition Diseases Research Articles

Therapeutic Targets in Extracellular Protein Deposition Diseases

Many litres of fluids are found outside cells in the human body. These fluids are rich in dissolved proteins that each have a characteristic three dimensional shape, necessary for normal function, which has been attained by the correct folding of their polypeptide chain(s). The structure of these extracellular proteins can be damaged by a variety of environmental stresses (e.g. heat and oxidation) leading to their partial unfolding and aggregation. This in turn can produce toxic soluble aggregates and/or large insoluble protein deposits, either of which can disrupt normal body function (e.g. in Alzheimer's disease and the systemic amyloidoses). A small family of abundant human blood proteins with the ability to inhibit the aggregation and deposition of stressed (partially unfolded) proteins has been discovered. These extracellular chaperones (ECs) form stable, soluble complexes with stressed proteins. It has been proposed that once bound to stressed proteins, ECs guide them to specific cell surface receptors that direct the "cargo" into lysosomes for degradation. Thus ECs and their receptors may be critical parts of a quality control system to protect the body against the deleterious effects of inappropriately aggregating extracellular proteins. This review focuses on the role of extracellular protein aggregation and deposition in disease, what little is known about mechanisms that act to control these processes, and, lastly, potential new targets for drug development. Newly identified potential drug targets include direct inhibition of protein aggregation, and manipulation of the expression levels of ECs and their receptors.

Aggregation Propensity of the Human Proteome

Formation of amyloid-like fibrils is involved in numerous human protein deposition diseases, but is also an intrinsic property of polypeptide chains in general. Progress achieved recently now allows the aggregation propensity of proteins to be analyzed over large scales. In this work we used a previously developed predictive algorithm to analyze the propensity of the 34,180 protein sequences of the human proteome to form amyloid-like fibrils. We show that long proteins have, on average, less intense aggregation peaks than short ones. Human proteins involved in protein deposition diseases do not differ extensively from the rest of the proteome, further demonstrating the generality of protein aggregation. We were also able to reproduce some of the results obtained with other algorithms, demonstrating that they do not depend on the type of computational tool employed. For example, proteins with different subcellular localizations were found to have different aggregation propensities, in relation to the various efficiencies of quality control mechanisms. Membrane proteins, intrinsically disordered proteins, and folded proteins were confirmed to have very different aggregation propensities, as a consequence of their different structures and cellular microenvironments. In addition, gatekeeper residues at strategic positions of the sequences were found to protect human proteins from aggregation. The results of these comparative analyses highlight the existence of intimate links between the propensity of proteins to form aggregates with β-structure and their biology. In particular, they emphasize the existence of a negative selection pressure that finely modulates protein sequences in order to adapt their aggregation propensity to their biological context.

Small Heat Shock Protein Activity Is Regulated by Variable Oligomeric Substructure

The alpha-crystallins are members of the small heat shock protein family of molecular chaperones that have evolved to minimize intracellular protein aggregation; however, they are also implicated in a number of protein deposition diseases. In this study, we employed novel mass spectrometry techniques to investigate the changes in quaternary structure associated with this switch from chaperone to adjuvant of aggregation. We replicated the oligomeric rearrangements observed for post-translationally modified alpha-crystallins, without altering the protein sequence, by refolding the alpha-crystallins in vitro. This refolding resulted in a loss of dimeric substructure concomitant with an augmentation of substrate affinity. We show that packaging of small heat shock proteins into dimeric units is used to control the level of chaperone function by regulating the exposure of hydrophobic surfaces. We propose that a bias toward monomeric substructure is responsible for the aberrant chaperone behavior associated with the alpha-crystallins in protein deposition diseases.

Thermodynamic and kinetic origins of Alzheimer's and related diseases: A chemical engineer's perspective

Thermodynamic and kinetic origins of Alzheimer's and related diseases: A chemical engineer's perspective

Amyloidogenesis of Natively Unfolded Proteins

Aggregation and subsequent development of protein deposition diseases originate from conformational changes in corresponding amyloidogenic proteins. The accumulated data support the model where protein fibrillogenesis proceeds via the formation of a relatively unfolded amyloidogenic conformation, which shares many structural properties with the pre-molten globule state, a partially folded intermediate first found during the equilibrium and kinetic (un)folding studies of several globular proteins and later described as one of the structural forms of natively unfolded proteins. The flexibility of this structural form is essential for the conformational rearrangements driving the formation of the core cross-beta structure of the amyloid fibril. Obviously, molecular mechanisms describing amyloidogenesis of ordered and natively unfolded proteins are different. For ordered protein to fibrillate, its unique and rigid structure has to be destabilized and partially unfolded. On the other hand, fibrillogenesis of a natively unfolded protein involves the formation of partially folded conformation; i.e., partial folding rather than unfolding. In this review recent findings are surveyed to illustrate some unique features of the natively unfolded proteins amyloidogenesis.

Dynamics of oligomer formation by denatured carbonic anhydrase II

Aggregation and subsequent development of protein deposition diseases originate from conformational changes in corresponding amyloidogenic proteins. Many proteins unrelated to amyloidoses also fibrillate at the appropriate conditions. These proteins serve as a model for studying the processes of protein misfolding, oligomerization and fibril formation. The accumulated data support the model where protein fibrillogenesis proceeds via the formation of a relatively unfolded amyloidogenic conformation. The urea-induced unfolding of bovine carbonic anhydrase II, BCA II, is characterized by a combination of high-resolution NMR, circular dichroism spectroscopy and small angle X-ray scattering. It is shown that the formation of associates of protein molecules in complex with solvent (water and urea), APS, takes place in the presence of 4–6 M urea. The subsequent increase in urea concentration to 8 M is accompanied by a disruption of APS and leads to a complete unfolding of a protein molecule. Analysis of BCA II self-association in the presence of 4.2 M urea revealed that APS are relatively large mostly β-structural blocks with the averaged molecular mass of 190–220 kDa. This work also demonstrates some novel NMR-based methodological approaches that provide useful information on protein self-association.

Calreticulin expression in the clonal plasma cells of patients with systemic light-chain (AL-) amyloidosis is associated with response to high-dose melphalan

In high doses with stem-cell transplantation, melphalan is an effective but toxic therapy for patients with systemic light-chain (AL-) amyloidosis, a protein deposition and monoclonal plasma cell disease. Melphalan can eliminate the indolent clonal plasma cells that cause the disease, an achievement called a complete response. Such a response is usually associated with extended survival, while no response (a less than 50% reduction) is not. Gene-expression studies and a stringently supervised analysis identified calreticulin as having significantly higher expression in the pretreatment plasma cells of patients with systemic AL-amyloidosis who then had a complete response to high-dose melphalan. Calreticulin is a pleiotropic calcium-binding protein found in the endoplasmic reticulum and the nucleus whose overexpression is associated with increased sensitivity to apoptotic stimuli. Real-time PCR and immunohistochemical staining also showed that expression of calreticulin was higher in the plasma cells of those with a complete response. Furthermore, wild-type murine embryonic fibroblasts were significantly more sensitive to melphalan than calreticulin knock-out murine embryonic fibroblasts. These data have important implications for understanding the activity of melphalan in plasma-cell diseases and support further investigation of calreticulin and its modulation in patients with systemic AL-amyloidosis receiving high-dose melphalan.

Potential roles of abundant extracellular chaperones in the control of amyloid formation and toxicity

The in vivo formation of fibrillar proteinaceous deposits called amyloid is associated with more than 40 serious human diseases, collectively referred to as protein deposition diseases. In many cases the amyloid deposits are extracellular and are found associated with newly identified abundant extracellular chaperones (ECs). Evidence is presented suggesting an important regulatory role for ECs in amyloid formation and disposal in the body. A model is presented which proposes that, under normal conditions, ECs stabilize extracellular misfolded proteins by binding to them, and then guide them to specific cell receptors for uptake and subsequent degradation. Thus ECs and their receptors may be critical parts of a quality control system to protect the body against dangerously hydrophobic proteins/peptides. However, it also appears possible that in the presence of a high molar excess of misfolded protein, such as might occur during disease, the limited amounts of ECs available may actually exacerbate pathology. Further advances in understanding of the mechanisms that control extracellular protein folding are likely to identify new strategies for effective disease therapies.

INTRACAVERNOUS TRIGEMINAL GANGLION AMYLOIDOMA

Isolated amyloidomas rarely manifest in nervous system tissues. To the authors' knowledge, there have been 52 documented cases of primary amyloid tumors of the central nervous system and closely associated structures. The authors present a case of a woman with a history of presumptive trigeminal neuralgia who was found to have an amyloidoma of the trigeminal ganglion. A 32-year-old Caucasian patient presented with a chief complaint of severe numbness and pain throughout the right side of her face. Her symptoms had been progressive over the previous 3 years. Medical management of her presumptive diseases with Zoloft (Pfizer Inc., New York, NY) and Neurontin (Pfizer Inc.) failed to improve or halt her right facial numbness and pain. Brain magnetic resonance imaging was acquired, demonstrating abnormal contrast enhancement and enlargement of the right trigeminal ganglion. The lesion abutted and indented the right internal carotid artery and extended from Meckel's cave into the inferior cavernous sinus and distally to the foramen ovale. The patient underwent a right frontotemporal craniotomy for resection of the gasserian ganglion lesion. A delicate incision was made in the wall of the cavernous sinus, allowing confirmatory biopsy of the lesion. With the site of the tumor within the cavernous sinus verified by pathology, the remainder of the tumor was removed. A final pathological review of the resected tumor confirmed a diagnosis of amyloidoma of the trigeminal ganglion. We present the case of a patient with a rare trigeminal ganglion amyloidoma that closely mimicked idiopathic trigeminal neuralgia. Even in the absence of systemic signs of amyloidosis, this benign protein deposition disease should be considered in the differential for atypical dysesthesias of the trigeminal dermatomes. Furthermore, central and peripheral nervous system amyloidomas respond well to surgical resection and rarely recur.

PH-Dependent Self-Assembly of Polyalanine Peptides

Polyalanine expansions in the nuclear RNA-binding protein PABP2 induce misfolding and aggregation of the protein into insoluble inclusions in muscle tissues and cell nuclei, leading to the disease oculopharyngeal muscular dystrophy (OPMD). We have explored the effect of solvent conditions and alanine repeat number on the propensity of fibril formation in this protein deposition disease. Three peptides mimicking the N-terminal polyalanine segment of PABP2, having the generic sequence Ac-Lys-Met-(Ala) n-Gly-Tyr with n = 7, 11, and 17 (referred to as 7-ala, 11-ala, and 17-ala, respectively), were synthesized and their conformational properties studied as a function of pH. In strongly alkaline medium (pH >10), the two longer peptides (11-ala and 17-ala, but not 7-ala) showed remarkable enhancement of β-sheet content and formed fibrils after incubation for 1–2 weeks at room temperature. Fluorescence studies suggested that tyrosyl radicals produced at high pH cross-linked to form dityrosine, which provided added stabilization for fibril growth. The kinetic progress curves for fibril formation, obtained by ThT fluorescence assay, showed exponential increase with time after an initial quiescent period (lag time) and an eventual saturation phase, all of which are indicative of a nucleation-controlled polymerization mechanism for fibrillation. Hierarchical self-assembly of the peptides led to the formation of striking fractal-shaped growth patterns on substrates, raising the possibility of designing novel materials using these peptides.

Cellular events associated with the initial phase of AA amyloidogenesis: insights from a human monocyte model

Reactive amyloidosis is a systemic protein deposition disease that develops in association with chronic inflammation. The deposits are composed of extracellular, fibrillar masses of amyloid A (AA) protein, an N-terminal fragment of the acute-phase serum protein serum amyloid A (SAA). The pathogenic conversion of SAA into amyloid has been studied in two human cell culture models, peritoneal cells and peripheral blood monocytes. Human monocyte cultures proved more robust than either mouse or human peritoneal cells at initiating amyloid formation in the absence of a preformed nidus such as amyloid-enhancing factor and particularly well suited for examination of individual cells undergoing amyloid formation. Amyloid-producing monocyte cultures were stained with Congo red and Alcian blue for detection of amyloid and glycosaminglycans, respectively; immunocytochemistry was performed to identify SAA/AA, CD68, CD14, lysosomal protein Lamp-1, and early endosomal protein EEA1. SAA interaction with monocytes was also visualized directly via fluorescence confocal microscopy. Amyloid was initially detected only in intracellular vesicles, but with time was seen extracellularly. Morphologic changes in lysosomes were noted during the early phase of amyloid formation, suggesting that exocytosis of fibrils may occur via lysosome-derived vesicles. Cultures engaged in amyloid formation remained metabolically active; no cytotoxic effects were observed. Mimicking in vivo phenomena, amyloid formation was accompanied by increased glycosaminoglycan content and C-terminal processing of SAA. The ability of human monocytes to endocytose and intracellularly transform SAA into amyloid via a mechanism that requires and maintains, rather than compromises, metabolic activity distinguishes them as a useful model for probing earliest events in the disease process.

Stabilization of a Native Protein Mediated by Ligand Binding Inhibits Amyloid Formation Independently of the Aggregation Pathway

The acylphosphatases from Sulfolobus solfataricus and Drosophila melanogaster (Sso AcP and AcPDro2) were previously shown to form amyloid-like aggregates without the need to unfold initially. Inorganic phosphate (Pi), a competitive inhibitor binding specifically to the active site of these proteins, was found to stabilize, upon binding, the native state of AcPDro2 and to inhibit its conversion into amyloid-like fibrils. The inhibitory effect of Pi is suppressed only in a variant in which the Arg residue responsible for Pi binding is mutated. The study on Sso AcP shows that Pi retards both the formation of the initial nativelike oligomers and their subsequent conversion into protofibrils. Thus, stabilization of the native structure mediated by specific binding with small molecules can be an effective therapeutic strategy against protein deposition diseases that originate from initially folded proteins, independently of the structure of the protein, its aggregation pathway, and the particular aggregated species responsible for pathogenesis.

Sulfates Dramatically Stabilize a Salt-Dependent Type of Glucagon Fibrils

Recent work suggests that protein fibrillation mechanisms and the structure of the resulting protein fibrils are very sensitive to environmental conditions such as temperature and ionic strength. Here we report the effect of several inorganic salts on the fibrillation of glucagon. At acidic pH, fibrillation is much less influenced by cations than anions, for which the effects follow the electroselectivity series; e.g., the effect of sulfate is ∼65-fold higher than that of chloride per mole. Increased salt concentrations generally accelerate fibrillation, but result in formation of an alternate type of fibrils. Stability of these fibrils is highly affected by changes in anion concentration; the apparent melting temperature is increased by ∼22°C for any 10-fold concentration increase, indicating that the fibrils cannot exist without anions. In contrast, fibrillation under alkaline conditions is more affected by cations than anions. We conclude that ions interact directly as structural ligands with glucagon fibrils where they coordinate charges and assist in formation of new fibrils. As ex vivo amyloid plaques often contain large amounts of highly sulfated organic molecules, the specific effects of sulfate ions on glucagon may have general relevance in the study of amyloidosis and other protein deposition diseases.

Deposition Diseases and 3D Domain Swapping

Protein aggregation is a feature of both normal cellular assemblies and pathological protein depositions. Although the limited order of aggregates has often impeded their structural characterization, 3D domain swapping has been implicated in the formation of several protein aggregates. Here, we review known structures displaying 3D domain swapping in the context of amyloid and related fibrils, prion proteins, and macroscopic aggregates, and we discuss the possible involvement of domain swapping in protein deposition diseases.

Amyloid Formation of a Protein in the Absence of Initial Unfolding and Destabilization of the Native State

In 5% (v/v) trifluoroethanol, pH 5.5, 25°C one of the acylphosphatases from Drosophila melanogaster (AcPDro2) forms fibrillar aggregates that bind thioflavin T and Congo red and have an extensive β-sheet structure, as revealed by circular dichroism. Atomic force microscopy indicates that the fibrils and their constituent protofilaments have diameters compatible with those of natural amyloid fibrils. Spectroscopic and biochemical investigation, carried out using near- and far-UV circular dichroism, intrinsic and 1-anilino-8-naphthalenesulfonic acid-derived fluorescence, dynamic light scattering, and enzymatic activity assays, shows that AcPDro2 has, before aggregation, a secondary structure content packing around aromatic and hydrophobic residues, hydrodynamic diameter, and catalytic activity indistinguishable from those of the native protein. The native protein was found to have the same conformational stability under native and aggregating conditions, as determined from urea-induced unfolding. The kinetic analysis supports models in which AcPDro2 aggregates initially without need to unfold and subsequently undergoes a conformational change into amyloid-like structures. Although fully or partially unfolded states have a higher propensity to aggregate, the residual aggregation potential that proteins maintain upon complete folding can be physiologically relevant and be directly involved in the pathogenesis of some protein deposition diseases.

A GLYmmer of Insight into Fibril Formation

Identifying factors contributing to protein aggregation and amyloid fibril formation is essential for understanding protein deposition diseases. In this issue of Structure , Chiti and colleagues (Parrini et al., 2005) use acylphosphatase as a model to describe a new, protective role for glycine.

Probing the Structure of the Infectious Amyloid Form of the Prion-forming Domain of HET-s Using High Resolution Hydrogen/Deuterium Exchange Monitored by Mass Spectrometry

The HET-s prion protein of Podospora anserina represents a valuable model system to study the structural basis of prion propagation. In this system, prion infectivity can be generated in vitro from a recombinant protein. We have previously identified the region of the HET-s protein involved in amyloid formation and prion propagation. Herein, we show that a recombinant peptide corresponding to the C-terminal prion-forming domain of HET-s (residues 218-289) displays infectivity. We used high resolution hydrogen/deuterium exchange analyzed by mass spectrometry to gain insight into the structural organization of this infectious amyloid form of the HET-s-(218-289) protein. Deuterium incorporation was analyzed by ion trap mass spectrometry for 76 peptides generated by pepsin proteolysis of HET-s-(218-289). By taking into account sequence overlaps in these peptides, a resolution ranging from 4-amino acids stretches to a single residue could be achieved. This approach allowed us to define highly protected regions alternating with more accessible segments along the HET-s-(218-289) sequence. The HET-s-(218-289) fibrils are thus likely to be organized as a succession of beta-sheet segments interrupted by short turns or short loops.

Sedimentation velocity studies of the high-molecular weight aggregates of the HIV gp41 ectodomain.

Accumulation of the HIV envelope protein gp41 is observed in the brain tissues of patients suffering from HIV-associated dementia. Previously, we have shown by electron microscopy that the extracellular domain of SIV gp41, which is analogous to that of HIV, forms high-molecular weight aggregates in vitro, and we have postulated that such high-molecular weight aggregates are responsible for neurological damage in a manner similar to protein deposition diseases such as Alzheimer's and the prion diseases. In this manuscript, we have characterized the self-association of the HIV gp41 ectodomain by sedimentation velocity. We show that discreet species of the gp41 high-molecular weight aggregates are present. The maximum population occurs at 20 S, which corresponds to ~5 trimers of gp41, suggesting that five trimers are required for nucleation of the high-molecular weight aggregates. The concentration dependence of the gp41 self-association indicates that it occurs by mass action. The temperature dependence of gp41 self-association suggests that it is driven by entropy, indicating that intermolecular hydrophobic interactions between trimers of gp41 are driving the association.

Prefibrillar Amyloid Protein Aggregates Share Common Features of Cytotoxicity

The intracellular free Ca(2+) concentration and redox status of murine fibroblasts exposed to prefibrillar aggregates of the HypF N-terminal domain have been investigated in vitro and in vivo using a range of fluorescent probes. Aggregate entrance into the cytoplasm is followed by an early rise of reactive oxygen species and free Ca(2+) levels and eventually by cell death. Such changes correlate directly with the viability of the cells and are not observed when cell are cultured in the presence of reducing agents or in Ca(2+)-free media. In addition, moderate cell stress following exposure to the aggregates was found to be fully reversible. The results show that the cytotoxicity of prefibrillar aggregates of HypF-N, a protein not associated with clinical disease, has the same fundamental origin as that produced by similar types of aggregates of proteins linked with specific amyloidoses. These findings suggest that misfolded proteinaceous aggregates stimulate generic cellular responses as a result of the exposure of regions of the structure (such as hydrophobic residues and the polypeptide main chain) that are buried in the normally folded proteins. They also support the idea that a higher number of degenerative pathologies than previously known might be considered as protein deposition diseases.

Dopamine and L-dopa disaggregate amyloid fibrils: implications for Parkinson's and Alzheimer's disease.

Protein deposition diseases involve the aggregation of normally soluble proteins, leading to both fibrillar and amorphous deposits. The aggregation of alpha-synuclein is associated with Parkinson's disease, and the aggregation of the Abeta peptide is associated with Alzheimer's disease. Here we show that L-dopa, dopamine, and other catecholamines dissolve fibrils of alpha-synuclein and Abeta peptide generated in vitro. The catecholamines also inhibited the fibrillation of these proteins. In addition, intraneuronal alpha-synuclein deposits formed in a mouse model were dissolved by incubation of tissue slices with L-dopa. These catecholamines are susceptible to oxidative breakdown, and we show that oxidation products are more effective than the parent compounds in inhibition. The ability to dissolve fibrils provides a new approach for studying mechanisms and consequences (e.g., the relationship between fibril formation and neurodegeneration) of protein aggregation. It is also likely to help in the development of strategies for the prevention and treatment of protein deposition diseases.