bims-proned 2023-08-06 papers

bims-proned

Biomed News

on Proteostasis in neurodegeneration

Issue of 2023–08–06
ten papers selected by
Verena Kohler, University of Graz

Flanking regions, amyloid cores, and polymorphism: the potential interplay underlying structural diversity.
Probing the effects of N-terminal acetylation on α-synuclein structure, aggregation and cytotoxicity.
Human herpesvirus 8 ORF57 protein is able to reduce TDP-43 pathology: network analysis identifies interacting pathways.
Protein aggregation and neurodegenerative disease: Structural outlook for the novel therapeutics.
Non-coding RNAs in Regulation of Protein Aggregation and Clearance Pathways: Current Perspectives Towards Alzheimer's Research and Therapy.
Linking Heat Shock Protein 70 and Parkin in Parkinson's Disease.
Amplifying the Heat Shock Response Ameliorates ALS and FTD Pathology in Mouse and Human Models.
Computational and Functional Insights of Protein Misfolding in Neurodegeneration.
Raman spectroscopy and its plasmon-enhanced counterparts: A toolbox to probe protein dynamics and aggregation.
Oxymatrine-mediated prevention of amyloid β-peptide-induced apoptosis on Alzheimer's model PC12 cells: in vitro cell culture studies and in vivo cognitive assessment in rats.

J Biol Chem. 2023 Aug 01. pii: S0021-9258(23)02150-6. [Epub ahead of print] 105122

Flanking regions, amyloid cores, and polymorphism: the potential interplay underlying structural diversity.

Anukool A Bhopatkar, Rakez Kayed.

  The β-sheet rich amyloid core is the defining feature of protein aggregates associated with neurodegenerative disorders. Recent investigations have revealed that there exist multiple examples of the same protein, with the same sequence, forming a variety of amyloid cores with distinct structural characteristics. These structural variants, termed as polymorphs, are hypothesized to influence the pathological profile and the progression of different neurodegenerative diseases, giving rise to unique phenotypic differences. Thus, identifying the origin and properties of these structural variants remain a focus of studies, as a preliminary step in the development of therapeutic strategies. Here, we review the potential role of the flanking regions of amyloid cores in inducing polymorphism. These regions, adjacent to the amyloid cores, show a preponderance for being structurally disordered, imbuing them with functional promiscuity. The dynamic nature of the flanking regions can then manifest in the form of conformational polymorphism of the aggregates. We take a closer look at the sequences flanking the amyloid cores, followed by a review of the polymorphic aggregates of the well-characterized proteins Amyloid-β, α-Synuclein, Tau, and TDP-43. We also consider different factors that can potentially influence aggregate structure and how these regions can be viewed as novel targets for therapeutic strategies by utilizing their unique structural properties.

Keywords:  Neurodegeneration; TDP-43; alpha-synuclein; amyloid polymorphism; amyloid-beta; intrinsically disordered proteins; protein aggregation; protein folding; tau protein

DOI:  https://doi.org/10.1016/j.jbc.2023.105122
Methods Enzymol. 2023 ;pii: S0076-6879(22)00384-6. [Epub ahead of print]686 45-65

Probing the effects of N-terminal acetylation on α-synuclein structure, aggregation and cytotoxicity.

Rosie Bell, Michele Vendruscolo, Janet R Kumita.

  Parkinson's disease is associated with the aberrant aggregation of α-synuclein within brain cells. Although the causes of this process are still unclear, post-translational modifications of α-synuclein are likely to play a modulatory role. Since α-synuclein is constitutively N-terminally acetylated, we previously investigated how this protein modification affects the aggregation behavior of the protein using a variety of methods in vitro and in cell systems. This chapter describes the production of N-terminally acetylated (NTA) α-synuclein, the preparation of different seeds of NTA α-synuclein for aggregation assays and the experimental methods for the kinetic analysis of the aggregation process of NTA α-synuclein. We also detail our protocol to evaluate the effects of preformed protofibrils of NTA α-synuclein in cell-based assays. These methods can be applied to study other post-translational modifications of α-synuclein, or adapted for the study of N-acetylation of other aggregation-prone proteins.

Keywords:  Aggregation; Amyloid; N-terminal acetylation; Parkinson's disease; α-Synuclein

DOI:  https://doi.org/10.1016/bs.mie.2022.09.003
Hum Mol Genet. 2023 Jul 31. pii: ddad122. [Epub ahead of print]

Human herpesvirus 8 ORF57 protein is able to reduce TDP-43 pathology: network analysis identifies interacting pathways.

Chelsea J Webber, Caroline N Murphy, Alejandro N Rondón-Ortiz, Sophie J F van der Spek, Elena X Kelly, Noah M Lampl, Giulio Chiesa, Ahmad S Khalil, Andrew Emili, Benjamin Wolozin.

Aggregation of TAR DNA-binding protein 43 kDa (TDP-43) is thought to drive the pathophysiology of ALS and some Frontotemporal dementias. TDP-43 is normally a nuclear protein that in neurons translocates to the cytoplasm and can form insoluble aggregates upon activation of the integrated stress response (ISR). Viruses evolved to control the ISR. In the case of Herpesvirus 8, the protein ORF57 acts to bind protein kinase R, inhibit phosphorylation of eIF2α and reduce activation of the ISR. We hypothesized that ORF57 might also possess the ability to inhibit aggregation of TDP-43. ORF57 was expressed in the neuronal SH-SY5Y line and its effects on TDP-43 aggregation characterized. We report that ORF57 inhibits TDP-43 aggregation by 55% and elicits a 2.45-fold increase in the rate of dispersion of existing TDP-43 granules. These changes were associated with a 50% decrease in cell death. Proteomic studies were carried out to identify the protein interaction network of ORF57. We observed that ORF57 directly binds to TDP-43 as well as interacts with many components of the ISR, including elements of the proteostasis machinery known to reduce TDP-43 aggregation. We propose that viral proteins designed to inhibit a chronic ISR can be engineered to remove aggregated proteins and dampen a chronic ISR.

DOI: https://doi.org/10.1093/hmg/ddad122
Proteins. 2023 Aug 02.

Protein aggregation and neurodegenerative disease: Structural outlook for the novel therapeutics.

Sharif Arar, Md Anzarul Haque, Rakez Kayed.

  Before the controversial approval of humanized monoclonal antibody lecanemab, which binds to the soluble amyloid-β protofibrils, all the treatments available earlier, for Alzheimer's disease (AD) were symptomatic. The researchers are still struggling to find a breakthrough in AD therapeutic medicine, which is partially attributable to lack in understanding of the structural information associated with the intrinsically disordered proteins and amyloids. One of the major challenges in this area of research is to understand the structural diversity of intrinsically disordered proteins under in vitro conditions. Therefore, in this review, we have summarized the in vitro applications of biophysical methods, which are aimed to shed some light on the heterogeneity, pathogenicity, structures and mechanisms of the intrinsically disordered protein aggregates associated with proteinopathies including AD. This review will also rationalize some of the strategies in modulating disease-relevant pathogenic protein entities by small molecules using structural biology approaches and biophysical characterization. We have also highlighted tools and techniques to simulate the in vivo conditions for native and cytotoxic tau/amyloids assemblies, urge new chemical approaches to replicate tau/amyloids assemblies similar to those in vivo conditions, in addition to designing novel potential drugs.

Keywords:  Alzheimer's disease; amyloids; biophysical methods; drug development; immunotherapy

DOI:  https://doi.org/10.1002/prot.26561
Curr Gene Ther. 2023 Jul 31.

Non-coding RNAs in Regulation of Protein Aggregation and Clearance Pathways: Current Perspectives Towards Alzheimer's Research and Therapy.

Sonali Sundram, Neerupma Dhiman, Rishabha Malviya, Rajendra Awasthi.

  Alzheimer's disease (AD) is the leading cause of dementia, affecting approximately 45.0 million people worldwide and ranking as the fifth leading cause of mortality. AD is identified by neurofibrillary tangles (NFTs), which include abnormally phosphorylated tau-protein and amyloid protein (amyloid plaques). Peptide dysregulation is caused by an imbalance between the production and clearance of the amyloid-beta (Aβ) and NFT. AD begins to develop when these peptides are not cleared from the body. As a result, understanding the processes that control both normal and pathological protein recycling in neuronal cells is critical. Insufficient Aβ and NFT clearance are important factors in the development of AD. Autophagy, lysosomal dysfunction, and ubiquitin-proteasome dysfunction have potential roles in the pathogenesis of many neurodegenerative disorders, particularly in AD. Modulation of these pathways may provide a novel treatment strategy for AD. Non-coding RNAs (ncRNAs) have recently emerged as important biological regulators, with particular relevance to the emergence and development of neurodegenerative disorders such as AD. ncRNAs can be used as potential therapeutic targets and diagnostic biomarkers due to their critical regulatory functions in several biological processes involved in disease development, such as the aggregation and accumulation of Aβ and NFT. It is evident that ncRNAs play a role in the pathophysiology of AD. In this communication, we explored the link between ncRNAs and AD and their regulatory mechanisms that may help in finding new therapeutic targets and AD medications.

Keywords:  Alzheimer's disease; Non-coding RNAs; dementia; neurodegenerative disorder; tau protein

DOI:  https://doi.org/10.2174/1566523223666230731093030
Mol Neurobiol. 2023 Aug 01.

Linking Heat Shock Protein 70 and Parkin in Parkinson's Disease.

Zhongting Zhao, Zheng Li, Fangning Du, Yixin Wang, Yue Wu, Kah-Leong Lim, Lin Li, Naidi Yang, Changmin Yu, Chengwu Zhang.

  Parkinson's disease (PD) is a neurodegenerative disease that affects millions of elderly people worldwide and is characterized by the progressive loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc). The precise mechanisms underlying the pathogenesis of PD are still not fully understood, but it is well accepted that the misfolding, aggregation, and abnormal degradation of proteins are the key causative factors of PD. Heat shock protein 70 (Hsp70) is a molecular chaperone that participates in the degradation of misfolded and aggregated proteins in living cells and organisms. Parkin, an E3 ubiquitin ligase, participates in the degradation of proteins via the proteasome pathway. Recent studies have indicated that both Hsp70 and Parkin play pivotal roles in PD pathogenesis. In this review, we focus on discussing how dysregulation of Hsp70 and Parkin leads to PD pathogenesis, the interaction between Hsp70 and Parkin in the context of PD and their therapeutic applications in PD.

Keywords:  Heat shock protein 70; Parkin; Parkinson’s disease; Protein aggregation

DOI:  https://doi.org/10.1007/s12035-023-03481-x
Mol Neurobiol. 2023 Jul 29.

Amplifying the Heat Shock Response Ameliorates ALS and FTD Pathology in Mouse and Human Models.

Mhoriam Ahmed, Charlotte Spicer, Jasmine Harley, J Paul Taylor, Michael Hanna, Rickie Patani, Linda Greensmith.

  Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are now known as parts of a disease spectrum with common pathological features and genetic causes. However, as both conditions are clinically heterogeneous, patient groups may be phenotypically similar but pathogenically and genetically variable. Despite numerous clinical trials, there remains no effective therapy for these conditions, which, in part, may be due to challenges of therapy development in a heterogeneous patient population. Disruption to protein homeostasis is a key feature of different forms of ALS and FTD. Targeting the endogenous protein chaperone system, the heat shock response (HSR) may, therefore, be a potential therapeutic approach. We conducted a preclinical study of a known pharmacological amplifier of the HSR, called arimoclomol, in mice with a mutation in valosin-containing protein (VCP) which causes both ALS and FTD in patients. We demonstrate that amplification of the HSR ameliorates the ALS/FTD-like phenotype in the spinal cord and brain of mutant VCP mice and prevents neuronal loss, replicating our earlier findings in the SOD1 mouse model of ALS. Moreover, in human cell models, we demonstrate improvements in pathology upon arimoclomol treatment in mutant VCP patient fibroblasts and iPSC-derived motor neurons. Our findings suggest that targeting of the HSR may have therapeutic potential, not only in non-SOD1 ALS, but also for the treatment of FTD.

Keywords:  ALS; Dementia; FTD; Heat shock response; Motor neuron; Proteostasis; Therapy; Treatment; VCP

DOI:  https://doi.org/10.1007/s12035-023-03509-2
Adv Exp Med Biol. 2023 ;1423 201-206

Computational and Functional Insights of Protein Misfolding in Neurodegeneration.

Marios G Krokidis, Themis P Exarchos, Antigoni Avramouli, Aristidis G Vrahatis, Panagiotis Vlamos.

  Protein folding is the process by which a polypeptide chain self-assembles into the correct three-dimensional structure, so that it ends up in the biologically active, native state. Under conditions of proteotoxic stress, mutations, or cellular aging, proteins can begin to aggregate into non-native structures such as ordered amyloid fibrils and plaques. Many neurodegenerative diseases involve the misfolding and aggregation of specific proteins into abnormal, toxic species. Experimental approaches including crystallography and AFM (atomic force microscopy)-based force spectroscopy are used to exploit the folding and structural characterization of protein molecules. At the same time, computational techniques through molecular dynamics, fold recognition, and structure prediction are widely applied in this direction. Benchmarking analysis for combining and comparing computational methodologies with functional studies can decisively unravel robust interactions between the side groups of the amino acid sequence and monitor alterations in intrinsic protein dynamics with high precision as well as adequately determine potent conformations of the folded patterns formed in the polypeptide structure.

Keywords:  AFM-based force spectroscopy; Fold recognition; Molecular dynamics; Neurodegenerative diseases; Protein misfolding

DOI:  https://doi.org/10.1007/978-3-031-31978-5_18
Wiley Interdiscip Rev Nanomed Nanobiotechnol. 2023 Jul 30. e1917

Raman spectroscopy and its plasmon-enhanced counterparts: A toolbox to probe protein dynamics and aggregation.

Ashish Kumar Dhillon, Arti Sharma, Vikas Yadav, Ruchi Singh, Tripti Ahuja, Sanmitra Barman, Soumik Siddhanta.

  Protein unfolding and aggregation are often correlated with numerous diseases such as Alzheimer's, Parkinson's, Huntington's, and other debilitating neurological disorders. Such adverse events consist of a plethora of competing mechanisms, particularly interactions that control the stability and cooperativity of the process. However, it remains challenging to probe the molecular mechanism of protein dynamics such as aggregation, and monitor them in real-time under physiological conditions. Recently, Raman spectroscopy and its plasmon-enhanced counterparts, such as surface-enhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS), have emerged as sensitive analytical tools that have the potential to perform molecular studies of functional groups and are showing significant promise in probing events related to protein aggregation. We summarize the fundamental working principles of Raman, SERS, and TERS as nondestructive, easy-to-perform, and fast tools for probing protein dynamics and aggregation. Finally, we highlight the utility of these techniques for the analysis of vibrational spectra of aggregation of proteins from various sources such as tissues, pathogens, food, biopharmaceuticals, and lastly, biological fouling to retrieve precise chemical information, which can be potentially translated to practical applications and point-of-care (PoC) devices. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Diagnostic Tools > Diagnostic Nanodevices Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

Keywords:  machine learning; neurodegenerative diseases; protein aggregation; surface-enhanced Raman spectroscopy; tip-enhanced Raman spectroscopy

DOI:  https://doi.org/10.1002/wnan.1917
Inflammopharmacology. 2023 Jul 29.

Oxymatrine-mediated prevention of amyloid β-peptide-induced apoptosis on Alzheimer's model PC12 cells: in vitro cell culture studies and in vivo cognitive assessment in rats.

Yue Zhu, Zhuo Wang, Chao Gao, Lei Zhang, Rubo Sui.

  Alzheimer's disease (AD) is a major neurological disease affecting elderly individuals worldwide. Existing drugs only reduce the symptoms of the disease without addressing the underlying causes. Commonly, Aβ25-35 peptide aggregation is the main reason for AD development. Recently, the discovery of multiple protein-targeting molecules has provided a new strategy for treating AD. This study demonstrates the neuroprotective potential of oxymatrine against multiple mechanisms, such as acetylcholinesterase, mitochondrial damage, and β-amyloid-induced cell toxicity. The in vitro cell culture studies showed that oxymatrine possesses significant potential to inhibit acetylcholine esterase and promotes antioxidant, antiapoptotic effects while preventing Aβ25-35 peptide aggregation in PC12 cells. Furthermore, oxymatrine protects PC12 cells against Aβ25-35-induced cytotoxicity and down-regulates the reactive oxygen species generation. The in vivo acute toxicological studies confirm the safety of oxymatrine without causing organ damage or death in animals. Overall, this study provided evidence that oxymatrine is an efficient neuroprotective agent, with a potential to be a multifunctional drug for Alzheimer's disease treatment. These findings present a reliable and synergistic approach for treating AD.

Keywords:  Alzheimer’s disease (AD); Anti-aggregation; Biocompatibility; Cytotoxicity; Neurodegenerative; Oxymatrine

DOI:  https://doi.org/10.1007/s10787-023-01291-0