Protein aggregation

Amyloid-like RIP1/RIP3 RHIM Fragments' Characterization and Application as a Drug Depot

Amyloid aggregates play a major role in diseases as well as in normal physiological function. Receptor-interacting protein kinases 1 and 3 (RIP1/RIP3) aggregates complexes in cellular necroptosis is one example of protein aggregation in normal cellular function. Although recently there have been several studies on full kinase proteins aggregation, the aggregation potential of small peptide sequences of RIP1/RIP3, the physicochemical properties, and the potential in biomedical applications have not been explored. Hence, in this paper, we study the aggregation propensity of peptides consisting of four and twelve amino acid sequences in the RHIM region of RIP1/RIP3 proteins that are known to drive the beta-sheet formation and the subsequent aggregation. The aggregation kinetics, physicochemical characterization, mechanosensitive properties, cellular effects, and potential as a cancer drug depot have been investigated. The results show that the number and concentration of amino acids play a role in amyloid-like aggregates' properties. Further, the aggregates when formulated with cisplatin-induced significant lung cancer cell toxicity compared to an equal amount of cisplatin with and without ultrasound. The study would serve as a platform for further investigation on RIP1/RIP3 peptide and protein aggregates, their role in multiple cellular functions and diseases, and their potential as drug depots.

The role of altered protein acetylation in neurodegenerative disease

Acetylation is a key post-translational modification (PTM) involved in the regulation of both histone and non-histone proteins. It controls cellular processes such as DNA transcription, RNA modifications, proteostasis, aging, autophagy, regulation of cytoskeletal structures, and metabolism. Acetylation is essential to maintain neuronal plasticity and therefore essential for memory and learning. Homeostasis of acetylation is maintained through the activities of histone acetyltransferases (HAT) and histone deacetylase (HDAC) enzymes, with alterations to these tightly regulated processes reported in several neurodegenerative diseases including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS). Both hyperacetylation and hypoacetylation can impair neuronal physiological homeostasis and increase the accumulation of pathophysiological proteins such as tau, α-synuclein, and Huntingtin protein implicated in AD, PD, and HD, respectively. Additionally, dysregulation of acetylation is linked to impaired axonal transport, a key pathological mechanism in ALS. This review article will discuss the physiological roles of protein acetylation and examine the current literature that describes altered protein acetylation in neurodegenerative disorders.

Insights on Aggregation of Hen Egg-White Lysozyme from Raman Spectroscopy and MD Simulations

Protein misfolding and aggregation play a significant role in several neurodegenerative diseases. In the present work, the spontaneous aggregation of hen egg-white lysozyme (HEWL) in an alkaline pH 12.2 at an ambient temperature was studied to obtain molecular insights. The time-dependent changes in spectral peaks indicated the formation of β sheets and their effects on the backbone and amino acids during the aggregation process. Introducing iodoacetamide revealed the crucial role of intermolecular disulphide bonds amidst monomers in the aggregation process. These findings were corroborated by Molecular Dynamics (MD) simulations and protein-docking studies. MD simulations helped establish and visualize the unfolding of the proteins when exposed to an alkaline pH. Protein docking revealed a preferential dimer formation between the HEWL monomers at pH 12.2 compared with the neutral pH. The combination of Raman spectroscopy and MD simulations is a powerful tool to study protein aggregation mechanisms.

Structural Insights into the Design of Synthetic Nanobody Libraries

Single domain antibodies from camelids, or nanobodies, are a unique class of antibody fragments with several advantageous characteristics: small monomeric size, high stability and solubility and easy tailoring for multiple applications. Nanobodies are gaining increasing acceptance as diagnostic tools and promising therapeutic agents in cancer and other diseases. While most nanobodies are obtained from immunized animals of the camelid family, a few synthetic nanobody libraries constructed in recent years have shown the capability of generating high quality nanobodies in terms of affinity and stability. Since this synthetic approach has important advantages over the use of animals, the recent advances are indeed encouraging. Here we review over a dozen synthetic nanobody libraries reported so far and discuss the different approaches followed in their construction and validation, with an emphasis on framework and hypervariable loop design as critical issues defining their potential as high-class nanobody sources.

A light-inducible protein clustering system for in vivo analysis of α-synuclein aggregation in Parkinson disease

Neurodegenerative disorders refer to a group of diseases commonly associated with abnormal protein accumulation and aggregation in the central nervous system. However, the exact role of protein aggregation in the pathophysiology of these disorders remains unclear. This gap in knowledge is due to the lack of experimental models that allow for the spatiotemporal control of protein aggregation, and the investigation of early dynamic events associated with inclusion formation. Here, we report on the development of a light-inducible protein aggregation (LIPA) system that enables spatiotemporal control of α-synuclein (α-syn) aggregation into insoluble deposits called Lewy bodies (LBs), the pathological hallmark of Parkinson disease (PD) and other proteinopathies. We demonstrate that LIPA-α-syn inclusions mimic key biochemical, biophysical, and ultrastructural features of authentic LBs observed in PD-diseased brains. In vivo, LIPA-α-syn aggregates compromise nigrostriatal transmission, induce neurodegeneration and PD-like motor impairments. Collectively, our findings provide a new tool for the generation, visualization, and dissection of the role of α-syn aggregation in PD.

Patterns in Dried Droplets to Detect Unfolded BSA

The morphological analysis of patterns in dried droplets has allowed the generation of efficient techniques for the detection of molecules of medical interest. However, the effectiveness of this method to reveal the coexistence of macromolecules of the same species, but different conformational states, is still unknown. To address this problem, we present an experimental study on pattern formation in dried droplets of bovine serum albumin (BSA), in folded and unfolded conformational states, in saline solution (NaCl). Folded proteins produce a well-defined coffee ring and crystal patterns all over the dry droplet. Depending on the NaCl concentration, the crystals can be small, large, elongated, entangled, or dense. Optical microscopy reveals that the relative concentration of unfolded proteins determines the morphological characteristics of deposits. At a low relative concentration of unfolded proteins (above 2%), small amorphous aggregates emerge in the deposits, while at high concentrations (above 16%), the "eye-like pattern", a large aggregate surrounded by a uniform coating, is produced. The radial intensity profile, the mean pixel intensity, and the entropy make it possible to characterize the patterns in dried droplets. We prove that it is possible to achieve 100% accuracy in identifying 4% of unfolded BSA contained in a protein solution.

LISTERIN E3 Ubiquitin Ligase and Ribosome-Associated Quality Control (RQC) Mechanism

According to cellular demands, ribosomes synthesize and maintain the desired pool of proteins inside the cell. However, sometimes due to defects in ribosomal machinery and faulty mRNAs, these nascent polypeptides are constantly under threat to become non-functional. In such conditions, cells acquire the help of ribosome-associated quality control mechanisms (RQC) to eliminate such aberrant nascent proteins. The primary regulator of RQC is RING domain containing LISTERIN E3 ubiquitin ligase, which is associated with ribosomes and alleviates non-stop proteins-associated stress in cells. Mouse RING finger protein E3 ubiquitin ligase LISTERIN is crucial for embryonic development, and a loss in its function causes neurodegeneration. LISTERIN is overexpressed in the mouse brain and spinal cord regions, and its perturbed functions generate neurological and motor deficits, but the mechanism of the same is unclear. Overall, LISTERIN is crucial for brain health and brain development. The present article systematically describes the detailed nature, molecular functions, and cellular physiological characterization of LISTERIN E3 ubiquitin ligase. Improve comprehension of LISTERIN's neurological roles may uncover pathways linked with neurodegeneration, which in turn might elucidate a promising novel therapeutic intervention against human neurodegenerative diseases.

Protein Misfolding and Aggregation: The Relatedness between Parkinson's Disease and Hepatic Endoplasmic Reticulum Storage Disorders

Dysfunction of cellular homeostasis can lead to misfolding of proteins thus acquiring conformations prone to polymerization into pathological aggregates. This process is associated with several disorders, including neurodegenerative diseases, such as Parkinson’s disease (PD), and endoplasmic reticulum storage disorders (ERSDs), like alpha-1-antitrypsin deficiency (AATD) and hereditary hypofibrinogenemia with hepatic storage (HHHS). Given the shared pathophysiological mechanisms involved in such conditions, it is necessary to deepen our understanding of the basic principles of misfolding and aggregation akin to these diseases which, although heterogeneous in symptomatology, present similarities that could lead to potential mutual treatments. Here, we review: (i) the pathological bases leading to misfolding and aggregation of proteins involved in PD, AATD, and HHHS: alpha-synuclein, alpha-1-antitrypsin, and fibrinogen, respectively, (ii) the evidence linking each protein aggregation to the stress mechanisms occurring in the endoplasmic reticulum (ER) of each pathology, (iii) a comparison of the mechanisms related to dysfunction of proteostasis and regulation of homeostasis between the diseases (such as the unfolded protein response and/or autophagy), (iv) and clinical perspectives regarding possible common treatments focused on improving the defensive responses to protein aggregation for diseases as different as PD, and ERSDs.

Ellagic Acid Modulates Uninduced as well as Mutation and Metal-Induced Aggregation of α-Synuclein: Implications for Parkinson's Disease

α-Synuclein (αS) is an intrinsically disordered protein whose aggregation and deposition in Lewy bodies is involved in the progression of Parkinson's disease (PD) and other related disorders. The aggregation process of αS is also triggered by mutations like A53T and E46K in the SNCA gene and disruption in metal-ion homeostasis. Currently, there is no obviating therapy available in the market that could effectively prevent the progression of the disease. In this backdrop, there exists an emerging need to consider naturally occurring polyphenols and flavonoids as potential therapeutic agents against PD. In this study, we demonstrate the modulatory effect of ellagic acid (EA) against wild-type as well as mutation and metal-induced aggregation of αS. Thioflavin T (ThT) fluorescence assay suggests that EA acts on the nucleation phase of αS fibrillization, thereby increasing the lag phase from 21.33 ± 3.01 to 48.20 ± 5.05 h and reducing the fibrils growth rate from 4.60 ± 2.06 to 0.890 ± 0.36 h^-1. 8-Anilino-1-naphthalene sulfonic acid (ANS), Congo red (CR), and intrinsic fluorescence studies indicate that the interaction of EA with αS facilitates the structural changes in the protein that lead to inhibition of fibril formation. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) images illustrate that the size of fibrils diminishes up to 100 nm in the presence of EA. Dot blot and seeding experiments put forward that EA directs the αS aggregation toward off-pathway fibrillization. Our 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay deciphers the role of EA in minimizing the αS fibril-induced toxicity, thereupon leading to an increase in cell viability. Also, EA attenuates both mutations as well as metal-induced αS fibrillization and disaggregates the preexisting fibrils. Additionally, computational studies elucidate that EA preferentially interacts with the N-terminal and NAC domain of αS. Hence, this work reveals the aggregation inhibition mechanism of EA and provides considerable therapeutic interventions against PD and related disorders.

Ataxia Telangiectasia Mutated Protein Kinase: A Potential Master Puppeteer of Oxidative Stress-Induced Metabolic Recycling

Ataxia Telangiectasia Mutated protein kinase (ATM) has recently come to the fore as a regulatory protein fulfilling many roles in the fine balancing act of metabolic homeostasis. Best known for its role as a transducer of DNA damage repair, the activity of ATM in the cytosol is enjoying increasing attention, where it plays a central role in general cellular recycling (macroautophagy) as well as the targeted clearance (selective autophagy) of damaged mitochondria and peroxisomes in response to oxidative stress, independently of the DNA damage response. The importance of ATM activation by oxidative stress has also recently been highlighted in the clearance of protein aggregates, where the expression of a functional ATM construct that cannot be activated by oxidative stress resulted in widespread accumulation of protein aggregates. This review will discuss the role of ATM in general autophagy, mitophagy, and pexophagy as well as aggrephagy and crosstalk between oxidative stress as an activator of ATM and its potential role as a master regulator of these processes.

Natural compound safranal driven inhibition and dis-aggregation of α-synuclein fibrils

Self-assembly of α-synuclein (α-Syn) is linked with a variety of neurodegenerative diseases collectively called as α-synucleiopathies. Therefore, discovering suitable inhibitors for this self-association process of α-Syn is a subject of intense research. In this background, we have demonstrated here that the natural compound, Safranal, delays/inhibits α-Syn fibrillation/aggregation, and we have also characterized its mode of action. The α-Syn fibrillation/aggregation kinetics studies in combination with TEM studies demonstrated that Safranal effectively inhibits α-Syn fibrillation/aggregation. NMR studies revealed that Safranal binds with α-Syn and stabilizes the monomeric protein. ANS fluorescence and CD measurements indicated that Safranal binds to the hydrophobic residues of the protein and causes delay in the formation of β-sheet rich structures which are crucial for the fibrillation to occur. The results obtained from fluorescence quenching, NMR and ANS binding assays, when analysed taking into consideration the molecular structure of Safranal provide valuable insights into the mechanism of inhibition of α-Syn fibrillation/aggregation. We infer that inhibition of α-Syn fibrillation/aggregation is primarily driven by hydrophobic interactions between Safranal and the protein. Further, Safranal is also seen to dis-aggregates pre-formed α-Syn fibrils. These findings implicate that Safranal could become a potent therapeutic intervention in Parkinson's disease and other protein aggregation related disorders.

Serum and Urine Thioflavin-T-Enhanced Fluorescence in Severe Preeclampsia

Common features of amyloid-like proteotoxic aggregates are the ability to bind Congo red (congophilia) and to induce fluorescence of thioflavin-T (ThT). Based on the prior discovery that women with preeclampsia exhibit urine congophilia, we proposed that amyloid-like protein aggregates present in urine also circulate in the bloodstream and this feature is linked to disease severity and clinical phenotype. ThT fluorescence was investigated in 217 paired serum and urine samples from women with severe features of preeclampsia (n=101; median [interquartile range] gestational age [GA], 32 [29-35] weeks), mild features of preeclampsia (n=22; GA, 36 [36-37] weeks), chronic hypertension (n=15; GA, 38 [37-39] weeks), healthy pregnant controls (n=57; GA, 39 [38-39] weeks), and nonpregnant controls (n=22). Serum and urine fluorescence attributable to advanced glycation end products was measured in the same samples with correction for autofluorescence. There were no GA-related changes in ThT fluorescence, although near-term serum ThT fluorescence increased compared with nonpregnant state. Compared with healthy pregnant controls, serum and urine ThT fluorescence was increased in severe features of preeclampsia (P<0.001 for both) but not in mild features of preeclampsia or chronic hypertension. Except for chronic hypertension, advanced glycation end products-related fluorescence of serum or urine did not differ from controls. Urine congophilia had a stronger relationship with preeclampsia severity compared with either urine or serum ThT fluorescence. However, serum ThT fluorescence was independently associated with clinical features of hemolysis, elevated liver enzyme levels, and low platelet levels syndrome (P=0.003). We demonstrate that ThT fluorescence, a marker of amyloid-like aggregates, is increased in serum of women with preeclampsia and likely because of their cytotoxicity associated with hemolysis, elevated liver enzyme levels, and low platelet levels syndrome.

The elimination of accumulated and aggregated proteins: a role for aggrephagy in neurodegeneration

The presence of ubiquitinated protein inclusions is a hallmark of most adult onset neurodegenerative disorders. Although the toxicity of these structures remains controversial, their prolonged presence in neurons is indicative of some failure in fundamental cellular processes. It therefore may be possible that driving the elimination of inclusions can help re-establish normal cellular function. There is growing evidence that macroautophagy has two roles; first, as a non-selective degradative response to cellular stress such as starvation, and the other as a highly selective quality control mechanism whose basal levels are important to maintain cellular health. One particular form of macroautophagy, aggrephagy, may have particular relevance in neurodegeneration, as it is responsible for the selective elimination of accumulated and aggregated ubiquitinated proteins. In this review, we will discuss the molecular mechanisms and role of protein aggregation in neurodegeneration, as well as the molecular mechanism of aggrephagy and how it may impact disease. This article is part of a Special Issue entitled "Autophagy and protein degradation in neurological diseases."

Intracerebral transplantation of neural stem cells combined with trehalose ingestion alleviates pathology in a mouse model of Huntington's disease

The present investigation examined the neuroprotective benefits for combined trehalose administration with C17.2 neural stem cell transplantation in a transgenic mouse model of Huntington's disease (HD), R6/2. C17.2 neural stem cells have the potential of differentiating into a neuronal phenotype in vitro and have been shown to be effective in the treatment of a variety of lysosomal lipid storage disorders in the nervous system. In this study, we transplanted these cells into the lateral ventricle of R6/2 transgenic mice in order to examine the efficacy of using these cells for correcting the accumulated polyglutamine storage materials in HD. To improve efficacy, animals were fed with a diet rich in trehalose, which has been shown to be beneficial to retard aggregate formation. The combined treatment strategy not only decreased ubiquitin-positive aggregation in striatum, alleviated polyglutamine aggregation formation, and reduced striatal volume, but also extended life span in the R6/2 animal model. Behavioral evaluation showed that the combination treatment improved motor function. Statistical analysis revealed that the combination treatment was more effective than treatment with trehalose alone on the basis of the above biochemical and behavioral criteria. This study provides a strong a basis for further developing an effective therapeutic strategy for HD.

Molecular and cellular aspects of protein misfolding and disease

Proteins are essential elements for life. They are building blocks of all organisms and the operators of cellular functions. Humans produce a repertoire of at least 30,000 different proteins, each with a different role. Each protein has its own unique sequence and shape (native conformation) to fulfill its specific function. The appearance of incorrectly shaped (misfolded) proteins occurs on exposure to environmental changes. Protein misfolding and the subsequent aggregation is associated with various, often highly debilitating, diseases for which no sufficient cure is available yet. In the first part of this review we summarize the structural composition of proteins and the current knowledge of underlying forces that lead proteins to lose their native structure. In the second and third parts we describe the molecular and cellular mechanisms that are associated with protein misfolding in disease. Finally, in the last part we portray recent efforts to develop treatments for protein misfolding diseases.

Activation of Human Platelets by Misfolded Proteins

OBJECTIVE

Protein misfolding diseases result from the deposition of insoluble protein aggregates that often contain fibrils called amyloid. Amyloids are found in Alzheimer disease, atherosclerosis, diabetes mellitus, and systemic amyloidosis, which are diseases where platelet activation might be implicated.

METHODS AND RESULTS

We induced amyloid properties in 6 unrelated proteins and found that all induced platelet aggregation in contrast to fresh controls. Amyloid-induced platelet aggregation was independent of thromboxane A2 formation and ADP secretion but enhanced by feedback stimulation through these pathways. Treatments that raised cAMP (iloprost), sequestered Ca2+ (BAPTA-AM) or prevented amyloid-platelet interaction (sRAGE, tissue-type plasminogen activator [tPA]) induced almost complete inhibition. Modulation of the function of CD36 (CD36-/- mice), p38(MAPK) (SB203580), COX-1 (indomethacin), and glycoprotein Ib alpha (Nk-protease, 6D1 antibody) induced approximately 50% inhibition. Interference with fibrinogen binding (RGDS) revealed a major contribution of alphaIIb beta3-independent aggregation (agglutination).

CONCLUSIONS

Protein misfolding resulting in the appearance of amyloid induces platelet aggregation. Amyloid activates platelets through 2 pathways: one is through CD36, p38(MAPK), thromboxane A2-mediated induction of aggregation; the other is through glycoprotein Ib alpha-mediated aggregation and agglutination. The platelet stimulating properties of amyloid might explain the enhanced platelet activation observed in many diseases accompanied by the appearance of misfolded proteins with amyloid.

Thermosensitive lichen amyloidosis

BACKGROUND

A 26-year-old male presented with a 3-year history of lichen amyloidosis. On examination, there was a pigmented papular eruption with a ripple pattern affecting the limbs and trunk but sparing the axillae, antecubital and popliteal fossae, central chest, neck and face. There was also prominent sparing of the skin overlying the superficial veins of the limbs. The sparing of the superficial veins of the limbs by lichen amyloidosis raised the possible role of cutaneous temperature in governing the distribution of amyloid deposits in our patient.

OBSERVATIONS

Total body infrared thermography demonstrated consistent sparing of the amyloid deposits in areas with higher cutaneous temperatures such as the neck and axillae as well as the course of the superficial veins. The cooler areas such as the extensor surfaces of the arms and legs corresponded to areas of amyloid deposition. Narrow band ultraviolet B (NBUVB) phototherapy over a 5-month period resulted in a marked improvement of pruritus and clearing of the amyloid deposits.

CONCLUSIONS

Our patient clearly demonstrated lichen amyloidosis in a thermosensitive distribution. This may be a gross manifestation of previous reports of in vitro thermosensitivity of amyloid fibril formation and may have potential implications in treatment at least in a subset of patients demonstrating this clinical feature.