Intracellular protein aggregation causes proteotoxic stress, underlying highly debilitating neurodegenerative disorders in parallel with decreased proteasome activity. Nevertheless, under such stress conditions, the expression of proteasome subunits is upregulated by Nuclear Factor Erythroid 2-related factor 1 (NRF1), a transcription factor that is encoded by NFE2L1. Activating the NRF1 pathway could accordingly delay the onset of neurodegenerative and other disorders with impaired cell proteostasis. Here, we present a series of small-molecule compounds based on bis(phenylmethylen)cycloalkanones and their heterocyclic analogues, identified via targeted library screening, that can induce NRF1-dependent downstream events, such as proteasome synthesis, heat shock response, and autophagy, in both model cell lines and Caenorhabditis elegans strains. These compounds increase proteasome activity and decrease the size and number of protein aggregates without causing any cellular stress or inhibiting the ubiquitin-proteasome system (UPS). Therefore, our compounds represent a new promising therapeutic approach for various protein conformational diseases, including the most debilitating neurodegenerative diseases.

• Klíčová slova
• DDI2, NGLY1, NRF1(NFE2L1), Proteasome, Protein aggregates, Small molecules,
• MeSH
• aktivace transkripce účinky léků   MeSH
• autofagie účinky léků   MeSH
• Caenorhabditis elegans * účinky léků   metabolismus   MeSH
• faktor 1 související s NF-E2 metabolismus   genetika   MeSH
• knihovny malých molekul farmakologie   MeSH
• lidé MeSH
• patologická konformace proteinů metabolismus   farmakoterapie   MeSH
• proteasomový endopeptidasový komplex * metabolismus   MeSH
• proteinové agregáty * účinky léků   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• faktor 1 související s NF-E2 MeSH
• knihovny malých molekul MeSH
• proteasomový endopeptidasový komplex * MeSH
• proteinové agregáty * MeSH

One of the grand challenges of biophysical chemistry is to understand the principles that govern protein misfolding and aggregation, which is a highly complex process that is sensitive to initial conditions, operates on a huge range of length- and timescales, and has products that range from protein dimers to macroscopic amyloid fibrils. Aberrant aggregation is associated with more than 25 diseases, which include Alzheimer's, Parkinson's, Huntington's, and type II diabetes. Amyloid aggregation has been extensively studied in the test tube, therefore under conditions that are far from physiological relevance. Hence, there is dire need to extend these investigations to in vivo conditions where amyloid formation is affected by a myriad of biochemical interactions. As a hallmark of neurodegenerative diseases, these interactions need to be understood in detail to develop novel therapeutic interventions, as millions of people globally suffer from neurodegenerative disorders and type II diabetes. The aim of this review is to document the progress in the research on amyloid formation from a physicochemical perspective with a special focus on the physiological factors influencing the aggregation of the amyloid-β peptide, the islet amyloid polypeptide, α-synuclein, and the hungingtin protein.

• MeSH
• amyloid chemie   MeSH
• lidé MeSH
• patologická konformace proteinů * MeSH
• proteinové agregáty * MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• amyloid MeSH
• proteinové agregáty * MeSH

The presence of surfaces influences the fibril formation kinetics of peptides and proteins. We present a systematic study of the aggregation kinetics of amyloidogenic peptides caused by different surfaces using molecular simulations of model peptides and thioflavin T fluorescence experiments. Increasing the monomer-surface attraction affects the nucleation and growth of small oligomers in a nonlinear manner: Weakly attractive surfaces lead to retardation; strongly attractive surfaces lead to acceleration. Further, the same type of surface either accelerates or retards growth, depending on the bulk propensity of the peptide to form fibrils: An attractive surface retards fibril formation of peptides with a high tendency for fibril formation, while the same surface accelerates fibril formation of peptides with a low propensity for fibril formation. The surface effect is thus determined by the relative association propensity of peptides for the surface compared to bulk and by the surface area to protein concentration ratio. This rationalization is in agreement with the measured fibrillar growth of α-synuclein from Parkinson and amyloid β peptide from Alzheimer disease in the presence of surface area introduced in a controlled way in the form of nanoparticles. These findings offer molecular insight into amyloid formation kinetics in complex environments and may be used to tune fibrillation properties in diverse systems.

• MeSH
• amyloidogenní proteiny chemie   MeSH
• kinetika MeSH
• metoda Monte Carlo MeSH
• nanočástice chemie   MeSH
• patologická konformace proteinů * MeSH
• povrchové vlastnosti MeSH
• proteinové agregáty * MeSH
• simulace molekulární dynamiky MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• amyloidogenní proteiny MeSH
• proteinové agregáty * MeSH

Recombinant proteins play pivotal roles in numerous applications including industrial biocatalysts or therapeutics. Despite the recent progress in computational protein structure prediction, protein solubility and reduced aggregation propensity remain challenging attributes to design. Identification of aggregation-prone regions is essential for understanding misfolding diseases or designing efficient protein-based technologies, and as such has a great socio-economic impact. Here, we introduce AggreProt, a user-friendly webserver that automatically exploits an ensemble of deep neural networks to predict aggregation-prone regions (APRs) in protein sequences. Trained on experimentally evaluated hexapeptides, AggreProt compares to or outperforms state-of-the-art algorithms on two independent benchmark datasets. The server provides per-residue aggregation profiles along with information on solvent accessibility and transmembrane propensity within an intuitive interface with interactive sequence and structure viewers for comprehensive analysis. We demonstrate AggreProt efficacy in predicting differential aggregation behaviours in proteins on several use cases, which emphasize its potential for guiding protein engineering strategies towards decreased aggregation propensity and improved solubility. The webserver is freely available and accessible at https://loschmidt.chemi.muni.cz/aggreprot/.

• MeSH
• algoritmy MeSH
• internet * MeSH
• konformace proteinů MeSH
• neuronové sítě MeSH
• proteinové agregáty * MeSH
• proteinové inženýrství metody   MeSH
• proteiny chemie   genetika   MeSH
• rozpustnost MeSH
• sbalování proteinů MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• proteinové agregáty * MeSH
• proteiny MeSH

BACKGROUND: Aggregation of the neuronal protein α-synuclein into amyloid fibrils is a hallmark of Parkinson's disease. The propensity of α-synuclein to aggregate increases with the protein concentration. For the development of efficient inhibitors of α-synuclein aggregation, it is important to know the critical concentration of aggregation (the concentration of monomeric protein, below which the protein does not aggregate). METHODS: We performed in vitro aggregation studies of α-synuclein at low concentrations (0.11-20 μM). Aggregation kinetics was measured by ThT fluorescence. Obtained aggregates were characterized using CD-spectroscopy, fluorescent spectroscopy, dynamic light scattering and AFM imaging. RESULTS: Monomeric α-synuclein at concentrations 0.45 μM and above was able to bind to fibril ends resulting in fibril growth. At the protein concentrations below 0.4 μM, monomers did not fibrillize, and fibrils disaggregated. In the absence of seeds, fibrils were formed only at monomer concentrations higher than 10 μM. At low micromolar concentrations, we observed formation of prefibrillar amyloid aggregates, which are able to induce fibril formation in α-synuclein solutions of high concentrations. CONCLUSIONS: The critical concentration of α-synuclein fibril growth is ~0.4 μM. Prefibrillar amyloid aggregates appear at concentrations between 0.45 and 3 μM and are an intermediate state between monomers and fibrils. Although morphologically different from fibrils, prefibrillar aggregates have similar properties to those of fibrils. GENERAL SIGNIFICANCE: We determined the critical concentration of α-synuclein fibril growth. We showed that fibrils can grow at much lower monomer concentrations than that required for de novo fibril formation. We characterized a prefibrillar intermediate species formed upon aggregation of α-synuclein at low micromolar concentration.

• Klíčová slova
• Amyloid fibrils, Critical concentration, Fibril disaggregation, Intermediates, Kd, Kinetics,
• MeSH
• alfa-synuklein chemie   metabolismus   MeSH
• amyloid chemie   metabolismus   MeSH
• cirkulární dichroismus MeSH
• fluorescenční spektrometrie MeSH
• lidé MeSH
• proteinové agregáty * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• alfa-synuklein MeSH
• amyloid MeSH
• proteinové agregáty * MeSH
• SNCA protein, human MeSH Prohlížeč

Oligomer aggregation of green-to-red photoconvertible fluorescent protein Eos (EosFP) is a natural feature of the wild‑type variant. The aim of the present study was to follow up mitochondrial nucleoid behavior under natural conditions of living cells transfected with mitochondrial single‑strand DNA‑binding protein (mtSSB) conjugated with EosFP. HEPG2 and SH‑SY5Y cells were subjected to lentiviral transfection and subsequently immunostained with anti‑DNA, anti‑transcription factor A, mitochondrial (TFAM) or anti‑translocase of the inner membrane 23 antibodies. Fluorescent microscopy, conventional confocal microscopy, superresolution biplane fluorescence photo-activation localization microscopy and direct stochastic optical reconstruction microscopy were used for imaging. In the two cell types, apparent couples of equally‑sized mtSSB‑EosFP‑visualized dots were observed. During the time course of the ongoing transfection procedure, however, a small limited number of large aggregates of mtSSB‑EosFP‑tagged protein started to form in the cells, which exhibited a great co‑localization with the noted coupled positions. Antibody staining and 3D immunocytochemistry confirmed that nucleoid components such as TFAM and DNA were co‑localized with these aggregates. Furthermore, the observed reduction of the mtDNA copy number in mtSSB‑EosFP‑transfected cells suggested a possible impairment of nucleoid function. In conclusion, the present study demonstrated that coupled nucleoids are synchronized by mtSSB‑EosFP overexpression and visualized through their equal binding capacity to mtSSB‑EosFP‑tagged protein. This observation suggested parallel replication and transcription activity of nucleoid couples native from a parental one. Preserved coupling in late stages of artificial EosFP‑mediated aggregation of tagged proteins suggested a rational manner of mitochondrial branching that may be cell-type specifically dependent on hierarchical nucleoid replication.

• MeSH
• DNA vazebné proteiny chemie   metabolismus   MeSH
• genetická transkripce MeSH
• genová dávka MeSH
• imunohistochemie MeSH
• konfokální mikroskopie MeSH
• lidé MeSH
• mitochondriální DNA metabolismus   MeSH
• mitochondriální proteiny metabolismus   MeSH
• mitochondrie metabolismus   MeSH
• multimerizace proteinu * MeSH
• nádorové buněčné linie MeSH
• rekombinantní fúzní proteiny chemie   metabolismus   MeSH
• transkripční faktory metabolismus   MeSH
• transport proteinů MeSH
• vazba proteinů MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA vazebné proteiny MeSH
• mitochondriální DNA MeSH
• mitochondriální proteiny MeSH
• rekombinantní fúzní proteiny MeSH
• TFAM protein, human MeSH Prohlížeč
• transkripční faktory MeSH

We use a meso-scale dissipative particle dynamics method to simulate the flow and aggregation of rod-like protein solutions through pores grafted with a solvent-sensitive polymer brush. The coated pores can control protein permeability and aggregation by a stretch-to-collapse conformational transition of the brush polymers in response to changes in the solvent quality. The protein solutions mimic aqueous glycoprotein solutions and proteins are represented as rod-like objects formed by coarse-grain beads. The model further employs two types of beads to represent the existence of cystein-like terminal groups in real glycoproteins and mimic the aggregation of real glycoproteins in aqueous solutions. We vary the solvent quality with respect to the brush chains and study the flow and aggregation of rod-like proteins in the slit and cylindrical pores as the brush polymers undergo the stretch-to-collapse transition. The results show that stretched brush chains close the pore, hamper proteins' flow and promote proteins' aggregation. The collapsed brush chains open the pores for proteins' flow and suppress their aggregation. Therefore, we observe more than a ten-fold reduction in the permeation rate of proteins in both pore geometries. Finally, due to pore confinement, larger proteins' aggregates are formed in the slit pore than in the cylindrical pore, while more pronounced orientation of proteins in the flow direction is seen in the cylindrical pore than in the slit pore.

• MeSH
• konformace proteinů MeSH
• molekulární modely * MeSH
• polymery chemie   MeSH
• poréznost MeSH
• povrchové vlastnosti MeSH
• proteinové agregáty * MeSH
• proteiny chemie   MeSH
• rozpouštědla chemie   MeSH
• voda chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• polymery MeSH
• proteinové agregáty * MeSH
• proteiny MeSH
• rozpouštědla MeSH
• voda MeSH

Platelet aggregation and acute inflammation are key processes in vertebrate defense to a skin injury. Recent studies uncovered the mediation of 2 serine proteases, cathepsin G and chymase, in both mechanisms. Working with a mouse model of acute inflammation, we revealed that an exogenous salivary protein of Ixodes ricinus, the vector of Lyme disease pathogens in Europe, extensively inhibits edema formation and influx of neutrophils in the inflamed tissue. We named this tick salivary gland secreted effector as I ricinus serpin-2 (IRS-2), and we show that it primarily inhibits cathepsin G and chymase, while in higher molar excess, it affects thrombin activity as well. The inhibitory specificity was explained using the crystal structure, determined at a resolution of 1.8 Å. Moreover, we disclosed the ability of IRS-2 to inhibit cathepsin G-induced and thrombin-induced platelet aggregation. For the first time, an ectoparasite protein is shown to exhibit such pharmacological effects and target specificity. The stringent specificity and biological activities of IRS-2 combined with the knowledge of its structure can be the basis for the development of future pharmaceutical applications.

• MeSH
• agregace trombocytů genetika   imunologie   MeSH
• chymasy imunologie   metabolismus   MeSH
• exprese genu MeSH
• hmyzí proteiny genetika   imunologie   metabolismus   MeSH
• kathepsin G imunologie   metabolismus   MeSH
• klíště genetika   imunologie   metabolismus   MeSH
• krystalizace MeSH
• kvarterní struktura proteinů MeSH
• lidé MeSH
• modely nemocí na zvířatech MeSH
• molekulární sekvence - údaje MeSH
• myši inbrední C57BL MeSH
• myši MeSH
• sekvence aminokyselin MeSH
• sekvenční analýza proteinů MeSH
• serpiny genetika   imunologie   metabolismus   MeSH
• slinné proteiny a peptidy genetika   imunologie   metabolismus   MeSH
• zánět imunologie   metabolismus   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• chymasy MeSH
• hmyzí proteiny MeSH
• kathepsin G MeSH
• serpin-2 MeSH Prohlížeč
• serpiny MeSH
• slinné proteiny a peptidy MeSH

In this perspective we summarize current knowledge of the effect of monosialoganglioside GM1 on the membrane-mediated aggregation of the β-amyloid (Aβ) peptide. GM1 has been suggested to be actively involved in the development of Alzheimer's disease due to its ability to seed the aggregation of Aβ. However, GM1 is known to be neuroprotective against Aβ-induced toxicity. Here we suggest that the two scenarios are not mutually exclusive but rather complementary, and might depend on the organization of GM1 in membranes. Improving our understanding of the molecular details behind the role of gangliosides in neurodegenerative amyloidoses might help in developing disease-modifying treatments.

• MeSH
• amyloidní beta-protein chemie   metabolismus   MeSH
• G(M1) gangliosid chemie   metabolismus   MeSH
• lidé MeSH
• mozek metabolismus   MeSH
• patologická konformace proteinů metabolismus   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• amyloidní beta-protein MeSH
• G(M1) gangliosid MeSH

The abnormal deposition of Aβ amyloid deposits in the brain is a hallmark of Alzheimer's disease (AD). Based on this evidence, many current therapeutic approaches focus on the development of small molecules halting Aβ aggregation. However, due to the temporary and elusive structures of amyloid assemblies, the rational design of aggregation inhibitors remains a challenging task. Here we combine ThT assays and MD simulations to study Aβ aggregation in the presence of the natural compounds tyrosol (TY), 3-hydroxytyrosol (HDT), and 3-methoxytyrosol (homovanillyl alcohol - HVA). We show that albeit HDT is a potent inhibitor of amyloid growth, TY and HVA catalyze fibril formation. An inspection of MD simulations trajectories revealed that the different effects of these three molecules on Aβ1-40 aggregation are ascribable to their capacity to arrange H-bonds network between the ligand (position C-3) and the peptide (Glu22). We believe that our results may contribute to the design of more effective and safe small molecules able to contrast pathogenic amyloid aggregation.

• Klíčová slova
• Alzheimer's disease, Aβ anti-aggregation, Homovanillyl alcohol, Hydroxytyrosol, Tyrosol,
• MeSH
• amyloidní beta-protein antagonisté a inhibitory   chemie   metabolismus   MeSH
• fenethylalkohol analogy a deriváty   chemie   farmakologie   MeSH
• katalýza MeSH
• katecholy metabolismus   MeSH
• kyselina homovanilová farmakologie   MeSH
• lidé MeSH
• ligandy MeSH
• peptidové fragmenty antagonisté a inhibitory   chemie   metabolismus   MeSH
• simulace molekulární dynamiky MeSH
• vazba proteinů MeSH
• vodíková vazba MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• 4-hydroxyphenylethanol MeSH Prohlížeč
• amyloid beta-protein (1-40) MeSH Prohlížeč
• amyloid beta-protein (1-42) MeSH Prohlížeč
• amyloidní beta-protein MeSH
• catechol MeSH Prohlížeč
• fenethylalkohol MeSH
• homovanillic alcohol MeSH Prohlížeč
• katecholy MeSH
• kyselina homovanilová MeSH
• ligandy MeSH
• peptidové fragmenty MeSH