The mechanical stability of epithelial cells, which protect organisms from harmful external factors, is maintained by hemidesmosomes via the interaction between plectin 1a (P1a) and integrin α6β4. Binding of calcium-calmodulin (Ca(2+)-CaM) to P1a together with phosphorylation of integrin β4 disrupts this complex, resulting in disassembly of hemidesmosomes. We present structures of the P1a actin binding domain either in complex with the N-ter lobe of Ca(2+)-CaM or with the first pair of integrin β4 fibronectin domains. Ca(2+)-CaM binds to the N-ter isoform-specific tail of P1a in a unique manner, via its N-ter lobe in an extended conformation. Structural, cell biology, and biochemical studies suggest the following model: binding of Ca(2+)-CaM to an intrinsically disordered N-ter segment of plectin converts it to an α helix, which repositions calmodulin to displace integrin β4 by steric repulsion. This model could serve as a blueprint for studies aimed at understanding how Ca(2+)-CaM or EF-hand motifs regulate F-actin-based cytoskeleton.

• MeSH
• hemidesmozomy chemie   MeSH
• hydrofobní a hydrofilní interakce MeSH
• integrin beta4 chemie   MeSH
• interakční proteinové domény a motivy MeSH
• kalmodulin chemie   MeSH
• krysa rodu Rattus MeSH
• krystalografie rentgenová MeSH
• lidé MeSH
• molekulární modely MeSH
• molekulární sekvence - údaje MeSH
• myši MeSH
• nádorové buněčné linie MeSH
• plektin chemie   MeSH
• sekvence aminokyselin MeSH
• terciární struktura proteinů MeSH
• vazba proteinů MeSH
• zvířata MeSH
• Check Tag
• krysa rodu Rattus MeSH
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• integrin beta4 MeSH
• kalmodulin MeSH
• Plec protein, mouse MeSH Prohlížeč
• plektin MeSH

Autophagy is a catabolic process that was described to play a critical role in advanced stages of cancer, wherein it maintains tumor cell homeostasis and growth by supplying nutrients. Autophagy is also described to support alternative cellular trafficking pathways, providing a non-canonical autophagy-dependent inflammatory cytokine secretion mechanism. Therefore, autophagy inhibitors have high potential in the treatment of cancer and acute inflammation. In our study, we identified compound 1 as an inhibitor of the ATG12-ATG3 protein-protein interaction. We focused on the systematic modification of the original hit 1, a casein kinase 2 (CK2) inhibitor, to find potent disruptors of ATG12-ATG3 protein-protein interaction. A systematic modification of the hit structure led us to a wide plethora of compounds that maintain its ATG12-ATG3 inhibitory activity, which could act as a viable starting point to design new compounds with diverse therapeutic applications.

• Klíčová slova
• Autophagy, Autophagy inhibition, Protein–protein interaction, Small molecule,
• MeSH
• autofagie účinky léků   MeSH
• kaseinkinasa II antagonisté a inhibitory   metabolismus   MeSH
• knihovny malých molekul * chemie   farmakologie   chemická syntéza   MeSH
• lidé MeSH
• molekulární struktura MeSH
• proteiny spojené s autofagií * metabolismus   antagonisté a inhibitory   MeSH
• vazba proteinů MeSH
• vztah mezi dávkou a účinkem léčiva MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• kaseinkinasa II MeSH
• knihovny malých molekul * MeSH
• proteiny spojené s autofagií * MeSH

Interaction of polycations with lipid membranes is a very important issue in many biological and medical applications such as gene delivery or antibacterial usage. In this work, we address the influence of hydrophobic substitution of strong polycations containing quaternary ammonium groups on the polymer-zwitterionic membrane interactions. In particular, we focus on the polymer tendency to adsorb on or/and incorporate into the membrane. We used complementary experimental and computational methods to enhance our understanding of the mechanism of the polycation-membrane interactions. Polycation adsorption on liposomes was assessed using dynamic light scattering (DLS) and zeta potential measurements. The ability of the polymers to form hydrophilic pores in the membrane was evaluated using a calcein-release method. The polymer-membrane interaction at the molecular scale was explored by performing atomistic molecular dynamics (MD) simulations. Our results show that the length of the alkyl side groups plays an essential role in the polycation adhesion on the zwitterionic surface, while the degree of substitution affects the polycation ability to incorporate into the membrane. Both the experimental and computational results show that the membrane permeability can be dramatically affected by the amount of alkyl side groups attached to the polycation main chain.

• MeSH
• adsorpce MeSH
• amoniové sloučeniny chemie   MeSH
• dynamický rozptyl světla MeSH
• elektronová kryomikroskopie MeSH
• hydrofobní a hydrofilní interakce MeSH
• liposomy chemie   metabolismus   MeSH
• polyaminy chemie   metabolismus   MeSH
• polyelektrolyty MeSH
• simulace molekulární dynamiky MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• amoniové sloučeniny MeSH
• liposomy MeSH
• polyaminy MeSH
• polycations MeSH Prohlížeč
• polyelektrolyty MeSH

The retention and splicing (RES) complex is a conserved spliceosome-associated module that was shown to enhance splicing of a subset of transcripts and promote the nuclear retention of unspliced pre-mRNAs in yeast. The heterotrimeric RES complex is organized around the Snu17p protein that binds to both the Bud13p and Pml1p subunits. Snu17p exhibits an RRM domain that resembles a U2AF homology motif (UHM) and Bud13p harbors a Trp residue reminiscent of an UHM-ligand motif (ULM). It has therefore been proposed that the interaction between Snu17p and Bud13p resembles canonical UHM-ULM complexes. Here, we have used biochemical and NMR structural analysis to characterize the structure of the yeast Snu17p-Bud13p complex. Unlike known UHMs that sequester the Trp residue of the ULM ligand in a hydrophobic pocket, Snu17p and Bud13p utilize a large interaction surface formed around the two helices of the Snu17p domain. In total 18 residues of the Bud13p ligand wrap around the Snu17p helical surface in an U-turn-like arrangement. The invariant Trp(232) in Bud13p is located in the center of the turn, and contacts surface residues of Snu17p. The structural data are supported by mutational analysis and indicate that Snu17p provides an extended binding surface with Bud13p that is notably distinct from canonical UHM-ULM interactions. Our data highlight structural diversity in RRM-protein interactions, analogous to the one seen for nucleic acid interactions.

• Klíčová slova
• Gene Regulation, Protein Complex, Protein Structure, Protein-protein Interaction, RNA-binding Protein, Spliceosome, U2AF Homology Motif,
• MeSH
• Escherichia coli genetika   metabolismus   MeSH
• exprese genu MeSH
• fosforylace MeSH
• fungální RNA biosyntéza   genetika   MeSH
• hydrofobní a hydrofilní interakce MeSH
• interakční proteinové domény a motivy MeSH
• malý jaderný ribonukleoprotein U2 chemie   genetika   metabolismus   MeSH
• molekulární modely MeSH
• molekulární sekvence - údaje MeSH
• prekurzory RNA biosyntéza   genetika   MeSH
• rekombinantní proteiny chemie   genetika   metabolismus   MeSH
• Saccharomyces cerevisiae - proteiny chemie   genetika   metabolismus   MeSH
• Saccharomyces cerevisiae chemie   genetika   metabolismus   MeSH
• sekundární struktura proteinů MeSH
• sekvence aminokyselin MeSH
• sekvenční seřazení MeSH
• sestřih RNA MeSH
• spliceozomy chemie   metabolismus   MeSH
• transportní proteiny chemie   genetika   metabolismus   MeSH
• tryptofan chemie   metabolismus   MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• Bud13 protein, S cerevisiae MeSH Prohlížeč
• fungální RNA MeSH
• IST3 protein, S cerevisiae MeSH Prohlížeč
• malý jaderný ribonukleoprotein U2 MeSH
• prekurzory RNA MeSH
• rekombinantní proteiny MeSH
• Saccharomyces cerevisiae - proteiny MeSH
• transportní proteiny MeSH
• tryptofan MeSH

In order to predict interaction interface for proteins, it is crucial to identify their characteristic features controlling the interaction process. We present analysis of 69 crystal structures of dimer protein complexes that provides a basis for reasonable description of the phenomenon. Interaction interfaces of two proteins at amino acids level were localized and described in terms of their chemical composition, binding preferences, and residue interaction energies utilizing Amber empirical force field. The characteristic properties of the interaction interface were compared against set of corresponding intramolecular binding parameters for amino acids in proteins. It has been found that geometrically distinct clusters of large hydrophobic amino acids (leucine, valine, isoleucine, and phenylalanine) as well as polar tyrosines and charged arginines are signatures of the protein-protein interaction interface. At some extent, we can generalize that protein-protein interaction (seen through interaction between amino acids) is very similar to the intramolecular arrangement of amino acids, although intermolecular pairs have generally lower interaction energies with their neighbors. Interfaces, therefore, possess high degree of complementarity suggesting also high selectivity of the process. The utilization of our results can improve interface prediction algorithms and improve our understanding of protein-protein recognition.

• MeSH
• aminokyseliny chemie   MeSH
• databáze proteinů MeSH
• houby chemie   MeSH
• interakční proteinové domény a motivy MeSH
• kinetika MeSH
• krystalografie rentgenová MeSH
• lidé MeSH
• mapování interakce mezi proteiny * MeSH
• prokaryotické buňky chemie   MeSH
• proteiny chemie   MeSH
• rostliny chemie   MeSH
• sekundární struktura proteinů MeSH
• statická elektřina MeSH
• termodynamika MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• viry chemie   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• aminokyseliny MeSH
• proteiny MeSH

The effect of non-denaturing concentrations of three different organic solvents, formamide, acetone and isopropanol, on the structure of haloalkane dehalogenases DhaA, LinB, and DbjA at the protein-solvent interface was studied using molecular dynamics simulations. Analysis of B-factors revealed that the presence of a given organic solvent mainly affects the dynamical behavior of the specificity-determining cap domain, with the exception of DbjA in acetone. Orientation of organic solvent molecules on the protein surface during the simulations was clearly dependent on their interaction with hydrophobic or hydrophilic surface patches, and the simulations suggest that the behavior of studied organic solvents in the vicinity of hyrophobic patches on the surface is similar to the air/water interface. DbjA was the only dimeric enzyme among studied haloalkane dehalogenases and provided an opportunity to explore effects of organic solvents on the quaternary structure. Penetration and trapping of organic solvents in the network of interactions between both monomers depends on the physico-chemical properties of the organic solvents. Consequently, both monomers of this enzyme oscillate differently in different organic solvents. With the exception of LinB in acetone, the structures of studied enzymes were stabilized in water-miscible organic solvents.

• MeSH
• 2-propanol chemie   farmakologie   MeSH
• aceton chemie   farmakologie   MeSH
• formamidy chemie   farmakologie   MeSH
• hydrofobní a hydrofilní interakce MeSH
• hydrolasy chemie   MeSH
• krystalografie rentgenová MeSH
• kvarterní struktura proteinů účinky léků   MeSH
• molekulární modely MeSH
• rozpouštědla chemie   MeSH
• simulace molekulární dynamiky MeSH
• terciární struktura proteinů účinky léků   MeSH
• voda chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• 2-propanol MeSH
• aceton MeSH
• formamide MeSH Prohlížeč
• formamidy MeSH
• haloalkane dehalogenase MeSH Prohlížeč
• hydrolasy MeSH
• rozpouštědla MeSH
• voda MeSH

Cyanidin and its O-glycosides have many important physiological functions in plants and beneficial effects on human health. Their biological activity is not entirely clear and depends on the structure of the molecule, in particular, on the number and type of sugar substituents. Therefore, in this study the detailed structure-activity relationship (SARs) of the anthocyanins/anthocyanidins in relation to their interactions with lipid bilayer was determined. On the basis of their antioxidant activity and the changes induced by them in size and Zeta potential of lipid vesicles, and mobility and order of lipid acyl chains, the impact of the number and type of sugar substituents on the biological activity of the compounds was evaluated. The obtained results have shown, that 3-O-glycosylation changes the interaction of cyanidin with lipid bilayer entirely. The 3-O-glycosides containing a monosaccharide induces greater changes in physical properties of the lipid membrane than those containing disaccharides. The presence of additional sugar significantly reduces glycoside interaction with model lipid membrane. Furthermore, O-glycosylation alters the ability of cyanidin to scavenge free radicals. This alteration depends on the type of free radicals and the sensitivity of the method used for their determination.

• Klíčová slova
• anthocyanin, fluorescence dyes, hydrogen peroxide, lipid peroxidation, membrane fluidity, phospholipid membrane, structure-activity relationships,
• MeSH
• anthokyaniny metabolismus   MeSH
• fosfatidylcholiny metabolismus   MeSH
• glykosylace MeSH
• peroxid vodíku metabolismus   MeSH
• peroxidace lipidů MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• 1-palmitoyl-2-oleoylphosphatidylcholine MeSH Prohlížeč
• anthokyaniny MeSH
• cyanidin MeSH Prohlížeč
• fosfatidylcholiny MeSH
• peroxid vodíku MeSH

The synergistic functioning of redox-active components that emerges from prototypical 2,2'-di(N-methylpyrid-4-ylium)-1,1'-biphenyl is described. Interestingly, even if a trans conformation of the native assembly is expected, due to electrostatic repulsion between cationic pyridinium units, we demonstrate that cis conformation is equally energy-stabilized on account of a peculiar LUMO (SupLUMO) that develops through space, encompassing the two pyridiniums in a single, made-in-one-piece, electronic entity (superelectrophoric behavior). This SupLUMO emergence, with the cis species as superelectrophore embodiment, originates in a sudden change of electronic structure. This finding is substantiated by insights from solid state (single-crystal X-ray diffraction) and solution (NOE NMR and UV-vis-NIR spectroelectrochemistry) studies, combined with electronic structure computations. Electrochemistry shows that electron transfers are so strongly correlated that two-electron reduction manifests itself as a single-step process with a large potential inversion consistent with inner creation of a carbon-carbon bond (digital simulation). Besides, absence of reductive formation of dimers is a further indication of a preferential intramolecular reactivity determined by the SupLUMO interaction (cis isomer pre-organization). The redox-gated covalent bond, serving as electron reservoir, was studied via atropisomerism of the reduction product (VT NMR study). The overall picture derived from this in-depth study of 2,2'-di(N-methylpyrid-4-ylium)-1,1'-biphenyl proves that trans and cis species are worth considered as intrinsically sharply different, that is, as doubly-electrophoric and singly-superelectrophoric switchable assemblies, beyond conformational isomerism. Most importantly, the through-space-mediated SupLUMO may come in complement of other weak interactions encountered in Supramolecular Chemistry as a tool for the design of electroactive architectures.

• Klíčová slova
• electronic structure, electrostatic interactions, pyridinium, structure-activity relationships, supramolecular electrochemistry,
• MeSH
• elektrochemie MeSH
• elektronika * MeSH
• krystalografie rentgenová MeSH
• magnetická rezonanční spektroskopie MeSH
• molekulární konformace MeSH
• Publikační typ
• časopisecké články MeSH

The analysis of intact glycopeptides is a challenge because of the structural variety of the complex conjugates. In this work, we used separation involving hydrophilic interaction liquid chromatography using a superficially porous particle HALO® penta-HILIC column with tandem mass spectrometric detection for the analysis of N-glycopeptides of hemopexin. We tested the effect of the mobile phase composition on retention and separation of the glycopeptides. The results indicated that the retention of the glycopeptides was the combination of partitioning and adsorption processes. Under the optimized conditions, our HILIC method showed the ability to efficiently separate the glycoforms of the same peptide backbone including separation of the isobaric glycoforms. We achieved efficient separation of core and outer arm linked fucose of bi-antennary and tri-antennary glycoforms of the SWPAVGNCSSALR peptide and bi-antennary glycoform of the ALPQPQNVTSLLGCTH peptide, respectively. Moreover, we demonstrated the separation of antennary position of sialic acid linked via α2-6 linkage of the monosialylated glycopeptides. Glycopeptide isomers are often differentially associated with various biological processes. Therefore, chromatographic separation of the species without the need for an extensive sample preparation appears attractive for their identification, characterization, and reliable quantification.

• Klíčová slova
• Glycopeptides, Glycoproteomics, Hemopexin, Hydrophilic interaction liquid chromatography, LC-MS/MS,
• MeSH
• chromatografie kapalinová metody   MeSH
• glykopeptidy analýza   izolace a purifikace   MeSH
• hemopexin chemie   MeSH
• hydrofobní a hydrofilní interakce MeSH
• isomerie MeSH
• lidé MeSH
• proteomika metody   MeSH
• sekvence aminokyselin MeSH
• tandemová hmotnostní spektrometrie metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• glykopeptidy MeSH
• hemopexin MeSH

BACKGROUND AND OBJECTIVE: Geometry of aorto-iliac bifurcation may affect pressure and wall stress in aorta and thus potentially serve as a predictor of abdominal aortic aneurysm (AAA), similarly to hypertension. METHODS: Effect of aorto-iliac bifurcation geometry was investigated via parametric analysis based on two-way weakly coupled fluid-structure interaction simulations. The arterial wall was modelled as isotropic hyperelastic monolayer, and non-Newtonian behaviour was introduced for the fluid. Realistic boundary conditions of the pulsatile blood flow were used on the basis of experiments in literature and their time shift was tailored to the pulse wave velocity in the model to obtain physiological wave shapes. Eighteen idealized and one patient-specific geometries of human aortic tree with common iliac and renal arteries were considered with different angles between abdominal aorta (AA) and both iliac arteries and different area ratios (AR) of iliac and aortic luminal cross sections. RESULTS: Peak wall stress (PWS) and systolic blood pressure (SBP) were insensitive to the aorto-iliac angles but sensitive to the AR: when AR decreased by 50%, the PWS and SBP increased by up to 18.4% and 18.8%, respectively. CONCLUSIONS: Lower AR (as a result of the iliac stenosis or aging), rather than the aorto-iliac angles increases the BP in the AA and may be thus a risk factor for the AAA development.

• Klíčová slova
• Abdominal aortic aneurysm, Aortic bifurcation, Aorto-iliac angles, Aorto-iliac ratio, Atherosclerosis, Fluid-structure interaction,
• MeSH
• analýza pulzové vlny MeSH
• aneurysma břišní aorty * MeSH
• aorta abdominalis * MeSH
• arteria iliaca fyziologie   MeSH
• hemodynamika MeSH
• lidé MeSH
• modely kardiovaskulární MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH