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Žerovnik E. Human stefin B: from its structure, folding, and aggregation to its function in health and disease. Front Mol Neurosci 2022; 15:1009976. [PMID: 36340691 PMCID: PMC9634419 DOI: 10.3389/fnmol.2022.1009976] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/01/2022] [Indexed: 01/11/2024] Open
Abstract
Mutations in the gene for human stefin B (cystatin B) cause progressive myoclonic epilepsy type 1 (EPM1), a neurodegenerative disorder. The most common change is dodecamer repeats in the promoter region of the gene, though missense and frameshift mutations also appear. Human stefin B primarily acts as a cysteine cathepsin inhibitor, and it also exhibits alternative functions. It plays a protective role against oxidative stress, likely via reducing mitochondrial damage and thus generating fewer mitochondrial reactive oxygen species (ROS). Accordingly, lack of stefin B results in increased inflammation and NLRP3 inflammasome activation, producing more ROS. The protein is cytosolic but also has an important role in the nucleus, where it prevents cleavage of the N terminal part of histone 3 by inhibiting cathepsins L and B and thus regulates transcription and cell cycle. Furthermore, it has been shown that stefin B is oligomeric in cells and that it has a specific role in the physiology of the synapse and in vesicular transport. On the basis of my research team's data on the structure, folding, and aggregation of stefin B, we have proposed that it might regulate proteostasis, possessing a chaperone-like function. In this review, I synthesize these observations and derive some conclusions on possible sources of EPM1 pathology. The interaction partners of stefin B and other gene mutations leading to EPM1-like pathology are discussed and common pathways are pinpointed.
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Affiliation(s)
- Eva Žerovnik
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
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2
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Perveen N, Ashraf W, Alqahtani F, Fawad Rasool M, Samad N, Imran I. Temporal Lobe Epilepsy: What do we understand about protein alterations? Chem Biol Drug Des 2021; 98:377-394. [PMID: 34132061 DOI: 10.1111/cbdd.13858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/22/2021] [Accepted: 04/18/2021] [Indexed: 01/19/2023]
Abstract
During neuronal diseases, neuronal proteins get disturbed due to changes in the connections of neurons. As a result, neuronal proteins get disturbed and cause epilepsy. At the genetic level, many mutations may take place in proteins like axon guidance proteins, leucine-rich glioma inactivated 1 protein, microtubular protein, pore-forming, chromatin remodeling, and chemokine proteins which may lead toward temporal lobe epilepsy. These proteins can be targeted in the future for the treatment purpose of epilepsy. Novel avenues can be developed for therapeutic interventions by these new insights.
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Affiliation(s)
- Nadia Perveen
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Waseem Ashraf
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Faleh Alqahtani
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Fawad Rasool
- Department of Pharmacy Practice, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Noreen Samad
- Department of Biochemistry, Faculty of Science, Bahauddin Zakariya University, Multan, Pakistan
| | - Imran Imran
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
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3
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Venko K, Novič M, Stoka V, Žerovnik E. Prediction of Transmembrane Regions, Cholesterol, and Ganglioside Binding Sites in Amyloid-Forming Proteins Indicate Potential for Amyloid Pore Formation. Front Mol Neurosci 2021; 14:619496. [PMID: 33642992 PMCID: PMC7902868 DOI: 10.3389/fnmol.2021.619496] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/12/2021] [Indexed: 12/26/2022] Open
Abstract
Besides amyloid fibrils, amyloid pores (APs) represent another mechanism of amyloid induced toxicity. Since hypothesis put forward by Arispe and collegues in 1993 that amyloid-beta makes ion-conducting channels and that Alzheimer's disease may be due to the toxic effect of these channels, many studies have confirmed that APs are formed by prefibrillar oligomers of amyloidogenic proteins and are a common source of cytotoxicity. The mechanism of pore formation is still not well-understood and the structure and imaging of APs in living cells remains an open issue. To get closer to understand AP formation we used predictive methods to assess the propensity of a set of 30 amyloid-forming proteins (AFPs) to form transmembrane channels. A range of amino-acid sequence tools were applied to predict AP domains of AFPs, and provided context on future experiments that are needed in order to contribute toward a deeper understanding of amyloid toxicity. In a set of 30 AFPs we predicted their amyloidogenic propensity, presence of transmembrane (TM) regions, and cholesterol (CBM) and ganglioside binding motifs (GBM), to which the oligomers likely bind. Noteworthy, all pathological AFPs share the presence of TM, CBM, and GBM regions, whereas the functional amyloids seem to show just one of these regions. For comparative purposes, we also analyzed a few examples of amyloid proteins that behave as biologically non-relevant AFPs. Based on the known experimental data on the β-amyloid and α-synuclein pore formation, we suggest that many AFPs have the potential for pore formation. Oligomerization and α-TM helix to β-TM strands transition on lipid rafts seem to be the common key events.
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Affiliation(s)
- Katja Venko
- Theory Department, National Institute of Chemistry, Ljubljana, Slovenia
| | - Marjana Novič
- Theory Department, National Institute of Chemistry, Ljubljana, Slovenia
| | - Veronika Stoka
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Eva Žerovnik
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
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Hasanbašić S, Taler-Verčič A, Puizdar V, Stoka V, Tušek Žnidarič M, Vilfan A, Berbić S, Žerovnik E. Prolines Affect the Nucleation Phase of Amyloid Fibrillation Reaction; Mutational Analysis of Human Stefin B. ACS Chem Neurosci 2019; 10:2730-2740. [PMID: 30924329 PMCID: PMC6727212 DOI: 10.1021/acschemneuro.8b00621] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
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Proline
residues play a prominent role in protein folding and aggregation.
We investigated the influence of single prolines and their combination
on oligomerization and the amyloid fibrillation reaction of human
stefin B (stB). The proline mutants influenced the distribution of
oligomers between monomers, dimers, and tetramers as shown by the
size-exclusion chromatography. Only P74S showed higher oligomers,
reminiscent of the molten globule reported previously for the P74S
of stB-Y31 variant. The proline mutants also inhibited to various
degree the amyloid fibrillation reaction. At 30 and 37 °C, inhibition
was complete for the P74S single mutant, two double mutants (P6L P74S
and P74S P79S), and for the triple mutant P6L P11S P74S. At 30 °C
the single mutant P6L completely inhibited the reaction, while P11S
and P79S formed amyloid fibrils with a prolonged lag phase. P36D did
not show a lag phase, reminiscent of a downhill polymerization model.
At 37 °C in addition to P36D, P11S, and P79S, P6L and P11S P74S
also started to fibrillate; however, the yield of the fibrils was
much lower than that of the wild-type protein as judged by transmission
electron microscopy. Thus, Pro 74 cis/trans isomerization
proves to be the key event, acting as a switch toward an amyloid transition.
Using our previous model of nucleation and growth, we simulated the
kinetics of all the mutants that exhibited sigmoidal fibrillation
curves. To our surprise, the nucleation phase was most affected by
Pro cis/trans isomerism, rather than the fibril elongation
phase.
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Affiliation(s)
- Samra Hasanbašić
- Jožef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia
- Faculty of Pharmacy, Department of Biochemistry, University of Tuzla, Univerzitetska 1, 75000 Tuzla, Bosnia and Herzegovina
| | - Ajda Taler-Verčič
- Center of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | | | - Veronika Stoka
- Jožef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | | | - Selma Berbić
- Faculty of Pharmacy, Department of Biochemistry, University of Tuzla, Univerzitetska 1, 75000 Tuzla, Bosnia and Herzegovina
| | - Eva Žerovnik
- Jožef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia
- Center of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
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Inhibition of Protein Aggregation by Several Antioxidants. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:8613209. [PMID: 29765505 PMCID: PMC5889867 DOI: 10.1155/2018/8613209] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 12/31/2017] [Accepted: 01/09/2018] [Indexed: 01/27/2023]
Abstract
Amyloid fibril formation is a shared property of all proteins; therefore, model proteins can be used to study this process. We measured protein aggregation of the model amyloid-forming protein stefin B in the presence and absence of several antioxidants. Amyloid fibril formation by stefin B was routinely induced at pH 5 and 10% TFE, at room temperature. The effects of antioxidants NAC, vitamin C, vitamin E, and the three polyphenols resveratrol, quercetin, and curcumin on the kinetics of fibril formation were followed using ThT fluorescence. Concomitantly, the morphology and amount of the aggregates and fibrils were checked by transmission electron microscopy (TEM). The concentration of the antioxidants was varied, and it was observed that different modes of action apply at low or high concentrations relative to the binding constant. In order to obtain more insight into the possible mode of binding, docking of NAC, vitamin C, and all three polyphenols was done to the monomeric form of stefin B.
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Surguchov A, Surgucheva I, Sharma M, Sharma R, Singh V. Pore-Forming Proteins as Mediators of Novel Epigenetic Mechanism of Epilepsy. Front Neurol 2017; 8:3. [PMID: 28149289 PMCID: PMC5241277 DOI: 10.3389/fneur.2017.00003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 01/04/2017] [Indexed: 01/07/2023] Open
Abstract
Epilepsy is a disorder of the brain characterized by an enduring predisposition to generate epileptic seizures. In the last two decades, numerous gene defects underlying different forms of epilepsy have been identified with most of these genes encoding ion channel proteins. Despite these developments, the etiology of majority of non-familial epilepsies has no known associated genetic mutations and cannot be explained by defects in identified ion channels alone. We hypothesize that de novo formation of ion channels by naturally unfolded proteins (NUPs) increases neuronal excitability. Altered ionic homeostasis may initiate/contribute to cellular cascades related to epileptogenesis in susceptible individuals. Here, we consider two small proteins, namely, α-synuclein and stefin B, as prototypical candidates to illustrate the underlying mechanism(s). Previous work points to an association between epilepsy and α-synuclein or stefin B, but the mechanism(s) underlying such association remains elusive. We review the evidence to link the structure-function of these proteins with disease processes. Epigenetic mechanisms unrelated to altered DNA sequence(s) that may affect epileptogenesis include transcriptional or posttranscriptional regulation. Such epigenetic mechanisms or their combination(s) enhance the levels of these proteins and as a result the ability to form annular structures, which upon incorporation into membrane form novel ion channels and disturb intracellular ion homeostasis. Alternative epigenetic mechanisms may change amyloidogenic proteins by posttranslational modifications, thereby increasing their propensity to form channels. Further research elucidating the details about the formation of ion channels through these mechanisms and their role in epileptogenesis may define new molecular targets and guide the development of new drug targets.
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Affiliation(s)
- Andrei Surguchov
- Department of Neurology, Kansas University Medical Center, Kansas City, KS, USA
| | - Irina Surgucheva
- Department of Neurology, Kansas University Medical Center, Kansas City, KS, USA
| | - Mukut Sharma
- Kansas City Veterans Administration Medical Center, Kansas City, MO, USA
- Midwest Biomedical Research Foundation, Kansas City, MO, USA
| | - Ram Sharma
- Kansas City Veterans Administration Medical Center, Kansas City, MO, USA
| | - Vikas Singh
- Department of Neurology, Kansas University Medical Center, Kansas City, KS, USA
- Kansas City Veterans Administration Medical Center, Kansas City, MO, USA
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Žerovnik E. Putative alternative functions of human stefin B (cystatin B): binding to amyloid-beta, membranes, and copper. J Mol Recognit 2016; 30. [PMID: 27577977 DOI: 10.1002/jmr.2562] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/25/2016] [Accepted: 07/26/2016] [Indexed: 12/17/2022]
Abstract
We describe studies performed thus far on stefin B from the family of cystatins as a model protein for folding and amyloid fibril formation studies. We also briefly mention our studies on aggregation of some of the missense EPM1 mutants of stefin B in cells, which mimic additional pathological traits (gain in toxic function) in selected patients with EPM1 disease. We collected data on the reported interactors of stefin B and discuss several hypotheses of possible cytosolic alternative functions.
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Affiliation(s)
- Eva Žerovnik
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia.,CipKeBip-Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia
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8
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Žganec M, Žerovnik E. Amyloid fibrils compared to peptide nanotubes. Biochim Biophys Acta Gen Subj 2014; 1840:2944-52. [DOI: 10.1016/j.bbagen.2014.05.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/22/2014] [Accepted: 05/29/2014] [Indexed: 12/30/2022]
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9
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Polajnar M, Zavašnik-Bergant T, Škerget K, Vizovišek M, Vidmar R, Fonović M, Kopitar-Jerala N, Petrovič U, Navarro S, Ventura S, Žerovnik E. Human stefin B role in cell's response to misfolded proteins and autophagy. PLoS One 2014; 9:e102500. [PMID: 25047918 PMCID: PMC4105463 DOI: 10.1371/journal.pone.0102500] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 06/18/2014] [Indexed: 11/30/2022] Open
Abstract
Alternative functions, apart from cathepsins inhibition, are being discovered for stefin B. Here, we investigate its role in vesicular trafficking and autophagy. Astrocytes isolated from stefin B knock-out (KO) mice exhibited an increased level of protein aggregates scattered throughout the cytoplasm. Addition of stefin B monomers or small oligomers to the cell medium reverted this phenotype, as imaged by confocal microscopy. To monitor the identity of proteins embedded within aggregates in wild type (wt) and KO cells, the insoluble cell lysate fractions were isolated and analyzed by mass spectrometry. Chaperones, tubulins, dyneins, and proteosomal components were detected in the insoluble fraction of wt cells but not in KO aggregates. In contrast, the insoluble fraction of KO cells exhibited increased levels of apolipoprotein E, fibronectin, clusterin, major prion protein, and serpins H1 and I2 and some proteins of lysosomal origin, such as cathepsin D and CD63, relative to wt astrocytes. Analysis of autophagy activity demonstrated that this pathway was less functional in KO astrocytes. In addition, synthetic dosage lethality (SDL) gene interactions analysis in Saccharomyces cerevisiae expressing human stefin B suggests a role in transport of vesicles and vacuoles These activities would contribute, directly or indirectly to completion of autophagy in wt astrocytes and would account for the accumulation of protein aggregates in KO cells, since autophagy is a key pathway for the clearance of intracellular protein aggregates.
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Affiliation(s)
- Mira Polajnar
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Tina Zavašnik-Bergant
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Katja Škerget
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
- Department of Molecular and Biomedical Science, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Matej Vizovišek
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Robert Vidmar
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Marko Fonović
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Nataša Kopitar-Jerala
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Uroš Petrovič
- Department of Molecular and Biomedical Science, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Susanna Navarro
- Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Spain
| | - Salvador Ventura
- Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Spain
| | - Eva Žerovnik
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
- CipKeBip - Center of Excellence for integrated approaches in chemistry and biology of proteins, Ljubljana, Slovenia
- * E-mail:
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The role of initial oligomers in amyloid fibril formation by human stefin B. Int J Mol Sci 2013; 14:18362-84. [PMID: 24013380 PMCID: PMC3794784 DOI: 10.3390/ijms140918362] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 08/21/2013] [Accepted: 08/22/2013] [Indexed: 02/03/2023] Open
Abstract
Oligomers are commonly observed intermediates at the initial stages of amyloid fibril formation. They are toxic to neurons and cause decrease in neural transmission and long-term potentiation. We describe an in vitro study of the initial steps in amyloid fibril formation by human stefin B, which proved to be a good model system. Due to relative stability of the initial oligomers of stefin B, electrospray ionization mass spectrometry (ESI MS) could be applied in addition to size exclusion chromatography (SEC). These two techniques enabled us to separate and detect distinguished oligomers from the monomers: dimers, trimers, tetramers, up to decamers. The amyloid fibril formation process was followed at different pH and temperatures, including such conditions where the process was slow enough to detect the initial oligomeric species at the very beginning of the lag phase and those at the end of the lag phase. Taking into account the results of the lower-order oligomers transformations early in the process, we were able to propose an improved model for the stefin B fibril formation.
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