Vestibular schwannoma is the most common benign neoplasm of the cerebellopontine angle. Its first symptoms include hearing loss, tinnitus, and vestibular symptoms, followed by cerebellar and brainstem symptoms, along with palsy of the adjacent cranial nerves. However, the clinical picture has unpredictable dynamics and currently, there are no reliable predictors of tumor behavior. Hence, it is desirable to have a fast routine method for analysis of vestibular schwannoma tissues at the molecular level. The major objective of this study was to verify whether a technique using in-sample specific protein digestion with trypsin would have the potential to provide a proteomic characterization of these pathological tissues. The achieved results showed that the use of this approach with subsequent liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of released peptides allowed a fast identification of a considerable number of proteins in two differential parts of vestibular schwannoma tissue as well as in tissues of control healthy samples. Furthermore, mathematical analysis of MS data was able to discriminate between pathological vestibular schwannoma tissues and healthy tissues. Thus, in-sample protein digestion combined with LC-MS/MS separation and identification of released specific peptides followed by mathematical analysis appears to have the potential for routine characterization of vestibular schwannomas at the molecular level. Data are available via ProteomeXchange with identifier PXD045261.

• Klíčová slova
• In-sample protein digestion, liquid chromatography, principal component analysis, tandem mass spectrometry, vestibular schwannomas,
• MeSH
• chromatografie kapalinová metody   MeSH
• lidé MeSH
• peptidové fragmenty * analýza   chemie   metabolismus   MeSH
• peptidy metabolismus   MeSH
• proteolýza MeSH
• proteomika metody   MeSH
• tandemová hmotnostní spektrometrie metody   MeSH
• trypsin chemie   MeSH
• vestibulární schwannom * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• peptidové fragmenty * MeSH
• peptidy MeSH
• trypsin MeSH

Atomic characterization of large nonfibrillar aggregates of amyloid polypeptides cannot be determined by experimental means. Starting from β-rich aggregates of Y and elongated topologies predicted by coarse-grained simulations and consisting of more than 100 Aβ16-22 peptides, we performed atomistic molecular dynamics (MD), replica exchange with solute scaling (REST2), and umbrella sampling simulations using the CHARMM36m force field in explicit solvent. Here, we explored the dynamics within 3 μs, the free energy landscape, and the potential of mean force associated with either the unbinding of one single peptide in different configurations within the aggregate or fragmentation events of a large number of peptides. Within the time scale of MD and REST2, we find that the aggregates experience slow global conformational plasticity, and remain essentially random coil though we observe slow beta-strand structuring with a dominance of antiparallel beta-sheets over parallel beta-sheets. Enhanced REST2 simulation is able to capture fragmentation events, and the free energy of fragmentation of a large block of peptides is found to be similar to the free energy associated with fibril depolymerization by one chain for longer Aβ sequences.

• Klíčová slova
• amyloid, free energy, molecular dynamics, proto-fibrils,
• MeSH
• amyloid chemie   MeSH
• amyloidní beta-protein * chemie   MeSH
• konformace proteinů, beta-řetězec MeSH
• peptidové fragmenty chemie   MeSH
• rozpouštědla chemie   MeSH
• simulace molekulární dynamiky * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• amyloid MeSH
• amyloidní beta-protein * MeSH
• peptidové fragmenty MeSH
• rozpouštědla MeSH

The physical stability of peptide-based drugs is of great interest to the pharmaceutical industry. Glucagon-like peptide 1 (GLP-1) is a 31-amino acid peptide hormone, the analogs of which are frequently used in the treatment of type 2 diabetes. We investigated the physical stability of GLP-1 and its C-terminal amide derivative, GLP-1-Am, both of which aggregate into amyloid fibrils. While off-pathway oligomers have been proposed to explain the unusual aggregation kinetics observed previously for GLP-1 under specific conditions, these oligomers have not been studied in any detail. Such states are important as they may represent potential sources of cytotoxicity and immunogenicity. Here, we identified and isolated stable, low-molecular-weight oligomers of GLP-1 and GLP-1-Am, using size-exclusion chromatography. Under the conditions studied, isolated oligomers were shown to be resistant to fibrillation or dissociation. These oligomers contain between two and five polypeptide chains and they have a highly disordered structure as indicated by a variety of spectroscopic techniques. They are highly stable with respect to time, temperature, or agitation despite their noncovalent character, which was established using liquid chromatography-mass spectrometry and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. These results provide evidence of stable, low-molecular-weight oligomers that are formed by an off-pathway mechanism which competes with amyloid fibril formation.

• Klíčová slova
• aggregation, amyloid, glucagon-like peptide 1, oligomers, self-assembly,
• MeSH
• amyloid chemie   MeSH
• amyloidní beta-protein chemie   MeSH
• diabetes mellitus 2. typu * MeSH
• gelová chromatografie MeSH
• glukagonu podobný peptid 1 * MeSH
• lidé MeSH
• peptidové fragmenty chemie   MeSH
• peptidy MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• amyloid MeSH
• amyloidní beta-protein MeSH
• glukagonu podobný peptid 1 * MeSH
• peptidové fragmenty MeSH
• peptidy MeSH

Preptin is a 34-amino-acid-long peptide derived from the E-domain of a precursor of insulin-like growth factor 2 (pro-IGF2) with bone-anabolic and insulin secretion amplifying properties. Here, we describe the synthesis, structures, and biological activities of six shortened analogues of human preptin. Eight- and nine-amino-acid-long peptide amides corresponding to the C-terminal part of human preptin were stabilised by two types of staples to induce a higher proportion of helicity in their secondary structure. We monitored the secondary structure of the stapled peptides using circular dichroism. The biological effect of the structural changes was determined afterwards by the ability of peptides to stimulate the release of intracellular calcium ions. We confirmed the previous observation that the stabilisation of the disordered conformation of human preptin has a deleterious effect on biological potency. However, surprisingly, one of our preptin analogues, a nonapeptide stabilised by olefin metathesis between positions 3 and 7 of the amino acid chain, had a similar ability to stimulate calcium ions' release to the full-length human preptin. Our findings could open up new ways to design new preptin analogues, which may have potential as drugs for the treatment of diabetes and osteoporosis.

• MeSH
• insulinu podobný růstový faktor II * chemie   MeSH
• kosti a kostní tkáň MeSH
• lidé MeSH
• peptidové fragmenty chemie   MeSH
• peptidy MeSH
• vápník * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• insulinu podobný růstový faktor II * MeSH
• peptidové fragmenty MeSH
• peptidy MeSH
• preptin MeSH Prohlížeč
• vápník * MeSH

Tumor-specific neoantigens can be highly immunogenic, but their identification for each patient and the production of personalized cancer vaccines can be time-consuming and prohibitively expensive. In contrast, tumor-associated antigens are widely expressed and suitable as an off the shelf immunotherapy. Here, we developed a PLGA-based nanoparticle vaccine that contains both the immunogenic cancer germline antigen NY-ESO-1 and an α-GalCer analog IMM60, as a novel iNKT cell agonist and dendritic cell transactivator. Three peptide sequences (85-111, 117-143, and 157-165) derived from immunodominant regions of NY-ESO-1 were selected. These peptides have a wide HLA coverage and were efficiently processed and presented by dendritic cells via various HLA subtypes. Co-delivery of IMM60 enhanced CD4 and CD8 T cell responses and antibody levels against NY-ESO-1 in vivo. Moreover, the nanoparticles have negligible systemic toxicity in high doses, and they could be produced according to GMP guidelines. Together, we demonstrated the feasibility of producing a PLGA-based nanovaccine containing immunogenic peptides and an iNKT cell agonist, that is activating DCs to induce antigen-specific T cell responses.

• Klíčová slova
• B cell epitope, CD4 T cell, CD8 T cell, IMM60, NY-ESO-1, PLGA nanoparticle, iNKT cell, peptide vaccine,
• MeSH
• B-lymfocyty imunologie   MeSH
• CD4-pozitivní T-lymfocyty imunologie   MeSH
• CD8-pozitivní T-lymfocyty imunologie   MeSH
• kopolymer kyseliny glykolové a mléčné chemie   farmakologie   MeSH
• lidé MeSH
• nádorové proteiny chemie   farmakologie   MeSH
• nanočástice chemie   terapeutické užití   MeSH
• nosiče léků chemie   farmakologie   MeSH
• peptidové fragmenty chemie   farmakologie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• kopolymer kyseliny glykolové a mléčné MeSH
• nádorové proteiny MeSH
• nosiče léků MeSH
• peptide NY-ESO-1 157-165 MeSH Prohlížeč
• peptidové fragmenty MeSH

In early stages of Alzheimer's disease (AD), amyloid beta (Aβ) accumulates in the mitochondrial matrix and interacts with mitochondrial proteins, such as cyclophilin D (cypD) and 17β-hydroxysteroid dehydrogenase 10 (17β-HSD10). Multiple processes associated with AD such as increased production or oligomerization of Aβ affect these interactions and disbalance the equilibrium between the biomolecules, which contributes to mitochondrial dysfunction. Here, we investigate the effect of the ionic environment on the interactions of Aβ (Aβ1-40, Aβ1-42) with cypD and 17β-HSD10 using a surface plasmon resonance (SPR) biosensor. We show that changes in concentrations of K+ and Mg2+ significantly affect the interactions and may increase the binding efficiency between the biomolecules by up to 35% and 65% for the interactions with Aβ1-40 and Aβ1-42, respectively, in comparison with the physiological state. We also demonstrate that while the binding of Aβ1-40 to cypD and 17β-HSD10 takes place preferentially around the physiological concentrations of ions, decreased concentrations of K+ and increased concentrations of Mg2+ promote the interaction of both mitochondrial proteins with Aβ1-42. These results suggest that the ionic environment represents an important factor that should be considered in the investigation of biomolecular interactions taking place in the mitochondrial matrix under physiological as well as AD-associated conditions.

• Klíčová slova
• 17β-hydroxysteroid dehydrogenase 10 (17β-HSD10), amyloid beta (Aβ), biomolecular interactions, cyclophilin D (cypD), ionic environment, mitochondrial matrix, surface plasmon resonance (SPR),
• MeSH
• 17-hydroxysteroidní dehydrogenasy chemie   genetika   MeSH
• Alzheimerova nemoc diagnóza   genetika   patologie   MeSH
• amyloidní beta-protein chemie   MeSH
• biosenzitivní techniky metody   MeSH
• ionty chemie   MeSH
• lidé MeSH
• mitochondriální proteiny chemie   MeSH
• mitochondrie chemie   MeSH
• peptidové fragmenty chemie   genetika   MeSH
• peptidylprolylisomerasa F chemie   genetika   MeSH
• povrchová plasmonová rezonance metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• 17-hydroxysteroidní dehydrogenasy MeSH
• 3 (or 17)-beta-hydroxysteroid dehydrogenase MeSH Prohlížeč
• amyloidní beta-protein MeSH
• ionty MeSH
• mitochondriální proteiny MeSH
• peptidové fragmenty MeSH
• peptidylprolylisomerasa F 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

In order to study the effects of peptide exposure to oxidative attack, we chose a model reaction in which the hydroxyl radical discretely abstracts a hydrogen atom from the α-carbon of each residue of a highly amyloidogenic region in the human calcitonin hormone, hCT15-19. Based on a combined Molecular Mechanics / Quantum Mechanics approach, the extended and folded L- and D-configuration and radical intermediate hCT15-19 peptides were optimized to obtain their compactness, secondary structure and relative thermodynamic data. The results suggest that the epimerization of residues is generally an exergonic process that can explain the cumulative nature of molecular aging. Moreover, the configurational inversion induced conformational changes can cause protein dysfunction. The epimerization of the central residue to the D-configuration induced a hairpin structure in hCT15-19, concomitant with a possible oligomerization of human calcitonin into Aβ(1-42)-like amyloid fibrils present in patients suffering from Alzheimer's disease.

• Klíčová slova
• Aggregation, Amyloidosis, DFNKF, Molecular ageing, Oxidative-stress, Peptide,
• MeSH
• amyloidní beta-protein chemie   MeSH
• amyloidogenní proteiny chemie   MeSH
• chemické modely MeSH
• kalcitonin chemie   MeSH
• lidé MeSH
• oxidace-redukce MeSH
• peptidové fragmenty chemie   MeSH
• sekundární struktura proteinů MeSH
• simulace molekulární dynamiky MeSH
• stereoizomerie MeSH
• teorie funkcionálu hustoty MeSH
• termodynamika MeSH
• vodíková vazba MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• amyloid beta-protein (1-42) MeSH Prohlížeč
• amyloidní beta-protein MeSH
• amyloidogenní proteiny MeSH
• calcitionin(15-19) peptide, human MeSH Prohlížeč
• kalcitonin MeSH
• peptidové fragmenty MeSH

Histone deacetylase 6 (HDAC6) is a multidomain cytosolic hydrolase acting mostly on nonhistone protein substrates. Investigations of the substrate specificity of HDAC6 are confounded by the presence of 2 catalytically active deacetylase domains (DD1 and DD2). In this study, acetylome peptide microarrays and peptide libraries were used to map the substrate specificity of DD1 and DD2 of human HDAC6. The results show that DD1 is solely responsible for the deacetylation of substrates harboring the acetyllysine at their C terminus, whereas DD2 exclusively deacetylates peptides with an internal acetyllysine residue. Also, statistical analysis of the deacetylation data revealed amino acid preferences at individual positions flanking the acetyllysine, where glycine and arginine residues are favored at positions N-terminal to the central acetyllysine; negatively charged glutamate is strongly disfavored throughout the sequence. Finally, the deacylation activity of HDAC6 was profiled by using a panel of acyl derivatives of the optimized peptide substrate and showed that HDAC6 acts as a proficient deformylase. Our data thus offer a detailed insight into the substrate preferences of the individual HDAC6 domains at the peptide level, and these findings can in turn help in elucidating the biologic roles of the enzyme and facilitate the development of new domain-specific inhibitors as research tools or therapeutic agents.-Kutil, Z., Skultetyova, L., Rauh, D., Meleshin, M., Snajdr, I., Novakova, Z., Mikesova, J., Pavlicek, J., Hadzima, M., Baranova, P., Havlinova, B., Majer, P., Schutkowski, M., Barinka, C. The unraveling of substrate specificity of histone deacetylase 6 domains using acetylome peptide microarrays and peptide libraries.

• Klíčová slova
• deacylation, deformylation, human acetylome, logo,
• MeSH
• HEK293 buňky MeSH
• histondeacetylasa 6 chemie   metabolismus   MeSH
• katalytická doména * MeSH
• lidé MeSH
• lysin chemie   metabolismus   MeSH
• peptidové fragmenty chemie   metabolismus   MeSH
• statická elektřina MeSH
• substrátová specifita MeSH
• vazba proteinů MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• HDAC6 protein, human MeSH Prohlížeč
• histondeacetylasa 6 MeSH
• lysin MeSH
• peptidové fragmenty MeSH

The transient receptor potential channel of melastatin 4 (TRPM4) belongs to a group of large ion receptors that are involved in countless cell signalling cascades. This unique member is ubiquitously expressed in many human tissues, especially in cardiomyocytes, where it plays an important role in cardiovascular processes. Transient receptor potential channels (TRPs) are usually constituted by intracellular N- and C- termini, which serve as mediators affecting allosteric modulation of channels, resulting in the regulation of the channel function. The TRPs tails contain a number of conserved epitopes that specifically bind the intracellular modulators. Here, we identify new binding sites for the calmodulin (CaM) and S100 calcium-binding protein A1 (S100A1), located in the very distal part of the TRPM4 N terminus. We have used chemically synthesized peptides of the TRPM4, mimicking the binding epitopes, along with fluorescence methods to determine and specify CaM- and S100A1-binding sites. We have found that the ligands binding epitopes at the TRPM4 N terminus overlap, but the interacting mechanism of both complexes is probably different. The molecular models supported by data from the fluorescence method confirmed that the complexes formations are mediated by the positively charged (R139, R140, R144) and hydrophobic (L134, L138, V143) residues present at the TRPM4 N terminus-binding epitopes. The data suggest that the molecular complexes of TRPM4/CaM and TRPM4/S100A1 would lead to the modulation of the channel functions.

• Klíčová slova
• S100A1, TRPM4 channel, calmodulin, fluorescence anisotropy, ligand-binding domains,
• MeSH
• databáze proteinů MeSH
• epitopy MeSH
• expertní systémy MeSH
• fluorescenční polarizace MeSH
• interakční proteinové domény a motivy MeSH
• kalmodulin chemie   genetika   metabolismus   MeSH
• kationtové kanály TRPM chemie   genetika   metabolismus   MeSH
• kinetika MeSH
• konformace proteinů MeSH
• konzervovaná sekvence MeSH
• lidé MeSH
• ligandy MeSH
• molekulární modely * MeSH
• mutace MeSH
• peptidové fragmenty chemická syntéza   chemie   genetika   metabolismus   MeSH
• proteiny S100 chemie   genetika   metabolismus   MeSH
• rekombinantní proteiny chemie   metabolismus   MeSH
• sekvence aminokyselin MeSH
• simulace molekulového dockingu MeSH
• substituce aminokyselin MeSH
• vazebná místa MeSH
• výpočetní biologie MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Názvy látek
• CALM1 protein, human MeSH Prohlížeč
• epitopy MeSH
• kalmodulin MeSH
• kationtové kanály TRPM MeSH
• ligandy MeSH
• peptidové fragmenty MeSH
• proteiny S100 MeSH
• rekombinantní proteiny MeSH
• S100A1 protein MeSH Prohlížeč
• TRPM4 protein, human MeSH Prohlížeč