Recent research has demonstrated the significance of incorporating invariance into neural networks. However, existing methods require direct sampling over the entire transformation set, notably computationally taxing for large groups like the affine group. In this study, we propose a more efficient approach by addressing the invariances of the subgroups within a larger group. For tackling affine invariance, we split it into the Euclidean group E(n) and uni-axial scaling group US(n), handling invariance individually. We employ an E(n)-invariant model for E(n)-invariance and average model outputs over data augmented from a US(n) distribution for US(n)-invariance. Our method maintains a favorable computational complexity of O(N2) in 2D and O(N4) in 3D scenarios, in contrast to the O(N6) (2D) and O(N12) (3D) complexities of averaged models. Crucially, the scale range for augmentation adapts during training to avoid excessive scale invariance. This is the first time nearly exact affine invariance is incorporated into neural networks without directly sampling the entire group. Extensive experiments unequivocally confirm its superiority, achieving new state-of-the-art results in affNIST and SIM2MNIST classifications while consuming less than 15% of inference time and fewer computational resources and model parameters compared to averaged models.

• MeSH
• neuronové sítě * MeSH
• učení * MeSH
• Publikační typ
• časopisecké články MeSH

N-Acetyl-D-glucosamine-coated polyamidoamine dendrimer (GlcNAc8) was shown previously to exhibit binding affinity to the rat recombinant NKR-P1 molecule (known in mice also as NK1.1) and to induce NK cell-mediated cytotoxicity. In this study, we investigated whether GlcNAc8 modulates antibody formation as activated NK cells were reported to participate in its regulation. C57BL/6 mice treated with GlcNAc8 and intact controls were immunized either with sheep red blood cells (SRBCs), 2,4-dinitrophenylated-lipopolysaccharide (DNP-LPS) or keyhole limpet hemocyanin (KLH) for evaluation of splenic antibody forming cell counts and serum immunoglobulin (Ig) levels. In vitro Ig formation was determined using supernatants of spleen mononuclear cells (SMCs) and CD49b or NK1.1-depleted SMC subpopulations. Serum antigen-specific IgG2a levels were also measured in DBA/2 and BALB/c mice (NK1.1-negative mouse strains on the basis of flow cytometric analysis) which possess different Nkr-p1c gene form than C57BL/6 ones. A significant increase in anti-SRBC IgG forming cells, serum levels of anti-KLH as well as anti-DNP IgG and IgG2a was observed after GlcNAc8 administration in C57BL/6 mice. IgM levels in supernatants of SMCs stimulated in vitro simultaneously with DNP-LPS and GlcNAc8 were significantly mounted compared with supernatants of SMCs primed with the antigen alone, but this enhancement was blocked after depletion of CD49b-positive or NK1.1-positive cells. In DBA/2 and BALB/c mice, GlcNAc8 influenced neither serum levels of anti-KLH nor anti-DNP IgG2a. These results indicate that GlcNAc8-induced upregulation of antibody formation is triggered by NK cell stimulation and depends on expressed NKR-P1 isoforms, particularly NKR-P1C.

• MeSH
• acetylglukosamin analogy a deriváty   farmakologie   chemie   MeSH
• antigeny Ly imunologie   metabolismus   MeSH
• B-lymfocyty imunologie   účinky léků   MeSH
• buňky NK imunologie   účinky léků   MeSH
• buňky produkující protilátky imunologie   účinky léků   MeSH
• dendrimery farmakologie   chemie   MeSH
• hemokyanin imunologie   MeSH
• imunoglobuliny krev   MeSH
• imunologické faktory farmakologie   chemie   MeSH
• krysa rodu rattus MeSH
• lektinové receptory NK-buněk - podrodina B imunologie   metabolismus   MeSH
• myši inbrední BALB C MeSH
• myši inbrední C57BL MeSH
• myši inbrední DBA MeSH
• myši MeSH
• NKT buňky imunologie   účinky léků   MeSH
• tvorba protilátek účinky léků   MeSH
• zvířata MeSH
• Check Tag
• krysa rodu rattus MeSH
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• práce podpořená grantem MeSH

Recognition of glycosylation patterns is one of the basic features of innate immunity. Ability of C-type lectin-like receptors such as NKR-P1 to bind saccharide moieties has become recently a controversial issue. In the present study, binding assay with soluble fluorescently labeled recombinant rat NKR-P1A and mouse NKR-P1C proteins revealed apparently no affinity to the various neoglycoproteins. Lack of functional linkage between NKR-P1 and previously described saccharide binder was supported by the fact, that synthetic N-acetyl-D-glucosamine octabranched dendrimer on polyamidoamine scaffold (GN8P) did not change gene expression of NKR-P1 isoforms in C57BL/6 and BALB/c mice divergent in the NK gene complex (both in vitro and in vivo). Surprisingly, N-acetyl-D-glucosamine-coated tetrabranched polyamido-amine dendrimer specifically binds to NKT cells and macrophages but not to NK cells (consistently with changes in cytokine patterns). Despite the fact that GN8P has been tested as an immunomodulator in anti-cancer treatment animal models for many years, surprisingly no changes in cytokine profiles in serum relevant to anti-cancer responses using B16F10 and CT26 harboring mouse strains C57BL/6 and BALB/c are observed. Our results indicate possible indirect involvement of NK cells in GN8P mediated immune responses.

• MeSH
• acetylglukosamin imunologie   metabolismus   MeSH
• buňky NK imunologie   metabolismus   MeSH
• dendrimery metabolismus   MeSH
• experimentální nádory farmakoterapie   genetika   imunologie   MeSH
• exprese genu účinky léků   imunologie   MeSH
• glykokonjugáty imunologie   metabolismus   farmakologie   MeSH
• interferon gama krev   genetika   imunologie   MeSH
• krysa rodu rattus MeSH
• kultivované buňky MeSH
• lektinové receptory NK-buněk - podrodina B genetika   imunologie   metabolismus   MeSH
• lektiny typu C genetika   imunologie   metabolismus   MeSH
• makrofágy imunologie   metabolismus   MeSH
• myši inbrední BALB C MeSH
• myši inbrední C57BL MeSH
• myši MeSH
• nádorové buněčné linie MeSH
• NKT buňky imunologie   metabolismus   MeSH
• oligosacharidy imunologie   metabolismus   MeSH
• polyaminy imunologie   metabolismus   MeSH
• polymerázová řetězová reakce s reverzní transkripcí MeSH
• protein - isoformy genetika   imunologie   metabolismus   MeSH
• průtoková cytometrie MeSH
• slezina cytologie   imunologie   metabolismus   MeSH
• TNF-alfa krev   genetika   imunologie   MeSH
• zvířata MeSH
• Check Tag
• krysa rodu rattus MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Protein-ligand affinities can be significantly influenced not only by the interaction itself but also by conformational equilibrium of both binding partners, free ligand and free protein. Identification of important conformational families of a ligand and prediction of their thermodynamics is important for efficient ligand design. Here we report conformational free energy modeling of nine small-molecule drugs in explicitly modeled water by metadynamics with a bias potential applied in the space of weighted holistic invariant molecular (WHIM) descriptors. Application of metadynamics enhances conformational sampling compared to unbiased molecular dynamics simulation and allows to predict relative free energies of key conformations. Selected free energy minima and one example of transition state were tested by a series of unbiased molecular dynamics simulation. Comparison of free energy surfaces of free and target-bound Imatinib provides an estimate of free energy penalty of conformational change induced by its binding to the target.

• MeSH
• katalytická doména MeSH
• léčivé přípravky chemie   MeSH
• molekulární konformace MeSH
• simulace molekulární dynamiky MeSH
• termodynamika MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

UNLABELLED: Inhibitors targeting human glutamate carboxypeptidase II (GCPII) typically consist of a P1' glutamate-derived binding module, which warrants the high affinity and specificity, linked to an effector function that is positioned within the entrance funnel of the enzyme. Here we present a comprehensive structural and computational study aimed at dissecting the importance of the effector function for GCPII binding and affinity. To this end we determined crystal structures of human GCPII in complex with a series of phosphoramidate-based inhibitors harboring effector functions of diverse physicochemical characteristics. Our data show that higher binding affinities of phosphoramidates, compared to matching phosphonates, are linked to the presence of additional hydrogen bonds between Glu424 and Gly518 of the enzyme and the amide group of the phosphoramidate. While the positioning of the P1' glutamate-derived module within the S1' pocket of GCPII is invariant, interaction interfaces between effector functions and residues lining the entrance funnel are highly varied, with the positively charged arginine patch defined by Arg463, Arg534 and Arg536 being the only 'hot-spot' common to several studied complexes. This variability stems in part from the fact that the effector/GCPII interfaces generally encompass isolated areas of nonpolar residues within the entrance funnel and resulting van der Waals contacts lack the directionality typical for hydrogen bonding interactions. The presented data unravel a complexity of binding modes of inhibitors within non-prime site(s) of GCPII and can be exploited for the design of novel GCPII-specific compounds. PDB ID CODES: Atomic coordinates of the present structures together with the experimental structure factor amplitudes were deposited at the RCSB Protein Data Bank under accession codes 4P44 (complex with JRB-4-81), 4P45 (complex with JRB-4-73), 4P4B (complex with CTT54), 4P4D (complex with MP1C), 4P4E (complex with MP1D), 4P4F (complex with NC-2-40), 4P4I (complex with T33) and 4P4J (complex with T33D).

• MeSH
• amidy chemická syntéza   chemie   farmakologie   MeSH
• antigeny povrchové metabolismus   MeSH
• glutamátkarboxypeptidasa II antagonisté a inhibitory   metabolismus   MeSH
• inhibitory enzymů chemická syntéza   chemie   farmakologie   MeSH
• krystalografie rentgenová MeSH
• kyseliny fosforečné chemická syntéza   chemie   farmakologie   MeSH
• lidé MeSH
• molekulární modely MeSH
• molekulární struktura MeSH
• racionální návrh léčiv * MeSH
• vodíková vazba MeSH
• vztah mezi dávkou a účinkem léčiva MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The human lectin galectin-3 is a multifunctional effector with special functions in regulation of adhesion and apoptosis. Its unique trimodular organization includes the 12-residue N-terminal sequence, a substrate for protein kinase CK1-dependent phosphorylation. As a step towards elucidating its significance, we prepared phosphorylated galectin-3, labelled it and used it as a tool in histochemistry. We monitored normal and malignant squamous epithelia. Binding was suprabasal with obvious positive correlation to the degree of differentiation and negative correlation to proliferation. The staining pattern resembled that obtained with the unmodified lectin. Basal cell carcinomas were invariably negative. The epidermal positivity profile was akin to distribution of the desmosomal protein desmoglein, as also seen with keratinocytes in vitro. In all cases, binding was inhibitable by the presence of lactose, prompting further investigation of the activity of the lectin site by a sensitive biochemical method, i.e. isothermal titration calorimetry. The overall affinity and the individual enthalpic and entropic contributions were determined. No effect of phosphorylation was revealed. This strategic combination of histo- and biochemical techniques applied to an endogenous effector after its processing by a protein kinase thus enabled a detailed monitoring of the binding properties of the post-translationally modified lectin. It underscores the value of using endogenous lectins as a histochemical tool. The documented approach has merit for applications beyond lectinology.

• MeSH
• barvení a značení MeSH
• epitel chemie   metabolismus   patologie   MeSH
• epitelové buňky cytologie   chemie   MeSH
• financování organizované MeSH
• fosforylace MeSH
• galektin 3 metabolismus   MeSH
• imunohistochemie MeSH
• kalorimetrie MeSH
• lidé MeSH
• posttranslační úpravy proteinů MeSH
• skvamocelulární nádory chemie   mikrobiologie   patologie   MeSH
• vazebná místa MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH

To ensure successful feeding tick saliva contains a number of inhibitory proteins that interfere with the host immune response and help to create a permissive environment for pathogen transmission. Among the potential targets of the salivary cystatins are two host cysteine proteases, cathepsin S, which is essential for antigen- and invariant chain-processing, and cathepsin C (dipeptidyl peptidase 1, DPP1), which plays a critical role in processing and activation of the granule serine proteases. Here, the effect of salivary cystatin OmC2 fromOrnithodoros moubatawas studied using differentiated MUTZ-3 cells as a model of immature dendritic cells of the host skin. Following internalization, cystatin OmC2 was initially found to inhibit the activity of several cysteine cathepsins, as indicated by the decreased rates of degradation of fluorogenic peptide substrates. To identify targets, affinity chromatography was used to isolate His-tagged cystatin OmC2 together with the bound proteins from MUTZ-3 cells. Cathepsins S and C were identified in these complexes by mass spectrometry and confirmed by immunoblotting. Furthermore, reduced increase in the surface expression of MHC II and CD86, which are associated with the maturation of dendritic cells, was observed. In contrast, human inhibitor cystatin C, which is normally expressed and secreted by dendritic cells, did not affect the expression of CD86. It is proposed that internalization of salivary cystatin OmC2 by the host dendritic cells targets cathepsins S and C, thereby affecting their maturation.

• MeSH
• antigeny CD86 MeSH
• antigeny diferenciační B-lymfocytární MeSH
• buněčné linie MeSH
• cystatiny metabolismus   MeSH
• dendritické buňky imunologie   metabolismus   MeSH
• epoxidové sloučeniny imunologie   metabolismus   MeSH
• geny MHC třídy II imunologie   MeSH
• kathepsin C metabolismus   MeSH
• kathepsiny chemie   imunologie   metabolismus   MeSH
• klíšťata enzymologie   MeSH
• lidé MeSH
• lyzozomy enzymologie   MeSH
• MHC antigeny II. třídy MeSH
• Ornithodoros enzymologie   MeSH
• rekombinantní proteiny MeSH
• sliny enzymologie   MeSH
• tyrosin analogy a deriváty   imunologie   metabolismus   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• MeSH
• imunita MeSH
• imunitní systém fyziologie   patofyziologie   MeSH
• imunoterapie MeSH

• Konspekt
• Patologie. Klinická medicína
• NLK Obory
• alergologie a imunologie
• biologie
• fyziologie
• NLK Publikační typ
• kolektivní monografie

• MeSH
• imunita MeSH
• imunitní systém MeSH
• imunoterapie MeSH
• Publikační typ
• monografie MeSH

• Konspekt
• Patologie. Klinická medicína
• NLK Obory
• alergologie a imunologie
• biologie