Many dynamic interactions within the cell microenvironment modulate cell behavior and cell fate. However, the pathways and mechanisms behind cell-cell or cell-extracellular matrix interactions remain understudied, as they occur at a nanoscale level. Recent progress in nanotechnology allows for mimicking of the microenvironment at nanoscale in vitro; electron-beam lithography (EBL) is currently the most promising technique. Although this nanopatterning technique can generate nanostructures of good quality and resolution, it has resulted, thus far, in the production of only simple shapes (e.g., rectangles) over a relatively small area (100 × 100 μm), leaving its potential in biological applications unfulfilled. Here, we used EBL for cell-interaction studies by coating cell-culture-relevant material with electron-conductive indium tin oxide, which formed nanopatterns of complex nanohexagonal structures over a large area (500 × 500 μm). We confirmed the potential of EBL for use in cell-interaction studies by analyzing specific cell responses toward differentially distributed nanohexagons spaced at 1000, 500, and 250 nm. We found that our optimized technique of EBL with HaloTags enabled the investigation of broad changes to a cell-culture-relevant surface and can provide an understanding of cellular signaling mechanisms at a single-molecule level.

• Klíčová slova
• biomimetic surface, cell adhesion and spreading, cell−cell interaction, electron-beam lithography, ligand clustering, nanopatterning, nanospacing,
• MeSH
• buněčná diferenciace MeSH
• buněčné kultury MeSH
• extracelulární matrix MeSH
• nanostruktury * chemie   MeSH
• nanotechnologie * metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Ice nanoparticles (H2O)N, N ≈ 450 generated in a molecular beam experiment pick up individual gas phase molecules of 2-hydroxypyridine and 2-pyridone (HP) evaporated in a pickup cell at temperatures between 298 and 343 K. The mass spectra of the doped nanoparticles show evidence for generation of clusters of adsorbed molecules (HP)n up to n = 8. The clusters are ionized either by 70 eV electrons or by two photons at 315 nm (3.94 eV). The two ionization methods yield different spectra, and their comparison provides an insight into the neutral cluster composition, ionization and intracluster ion-molecule reactions, and cluster fragmentation. Quite a few molecules were reported not to coagulate on ice nanoparticles previously. The (HP)n cluster generation on ice nanoparticles represents the first evidence for coagulating of molecules and cluster formation on free ice nanoparticles. For comparison, we investigate the coagulation of HP molecules picked up on large clusters ArN, N ≈ 205, and also (HP)n clusters generated in supersonic expansions with Ar buffer gas. This comparison points to a propensity for the (HP)2 dimer generation on ice nanoparticles. This shows the feasibility of base pairing for model of biological molecules on free ice nanoparticles. This result is important for hypotheses of the biomolecule synthesis on ice grains in the space. We support our findings by theoretical calculations that show, among others, the HP dimer structures on water clusters.

• Publikační typ
• časopisecké články MeSH

Solvent interactions, particularly hydration, are vital in chemical and biochemical systems. Model systems reveal microscopic details of such interactions. We uncover a specific hydrogen-bonding motif of the biomolecular building block indole (C8H7N), tryptophan's chromophore, in water: a strong localized N-H···OH2 hydrogen bond, alongside unstructured solvent interactions. This insight is revealed from a combined experimental and theoretical analysis of the electronic structure of indole in aqueous solution. We recorded the complete X-ray photoemission and Auger spectrum of aqueous-phase indole, quantitatively explaining all peaks through ab initio modeling. The efficient and accurate technique for modeling valence and core photoemission spectra involves the maximum-overlap method and the nonequilibrium polarizable-continuum model. A two-hole electron-population analysis quantitatively describes the Auger spectra. Core-electron binding energies for nitrogen and carbon highlight the specific interaction with a hydrogen-bonded water molecule at the N-H group and otherwise nonspecific solvent interactions.

• Publikační typ
• časopisecké články MeSH

In this work, a simple method for alcohol synthesis with high enantiomeric purity was proposed. For this, colloidal gold and silver surface modifications with 3-mercaptopropanoic acid and cysteamine were used to generate carboxyl and amine functionalized gold and silver nanoparticles of 15 and 45 nm, respectively. Alcohol dehydrogenase from Thermoanaerobium brockii (TbADH) and its cofactor (NADPH) were physical and covalent (through direct adsorption and using cross-linker) immobilized on nanoparticles' surface. In contrast to the physical and covalent immobilizations that led to a loss of 90% of the initial enzyme activity and 98% immobilization, the use of a cross-linker in immobilization process promoted a loss to 30% of the initial enzyme activity and >92% immobilization. The yield of NADPH immobilization was about 80%. The best results in terms of activity were obtained with Ag-citr nanoparticle functionalized with carboxyl groups (Ag-COOH), Au-COOH(CTAB), and Au-citr functionalized with amine groups and stabilized with CTAB (Au-NH2(CTAB)) nanoparticles treated with 0.7% and 1.0% glutaraldehyde. Enzyme conformation upon immobilization was studied using fluorescence and circular dichroism spectroscopies. Shift in ellipticity at 222 nm with about 4 to 7 nm and significant decreasing in fluorescence emission for all bioconjugates were observed by binding of TbADH to silver/gold nanoparticles. Emission redshifting of 5 nm only for Ag-COOH-TbADH bioconjugate demonstrated change in the microenvironment of TbADH. Enzyme immobilization on glutaraldehyde-treated Au-NH2(CTAB) nanoparticles promotes an additional stabilization preserving about 50% of enzyme activity after 15 days storage. Nanoparticles attached-TbADH-NADPH systems were used for enantioselective (ee > 99%) synthesis of (S)-7-hydroxy-2-tetralol.

• Publikační typ
• časopisecké články MeSH

The use of polymers in all aspects of daily life is increasing considerably, so there is high demand for polymers with specific properties. Polymers with antibacterial properties are highly needed in the food and medical industries. Low-density polyethylene (LDPE) is widely used in various industries, especially in food packaging, because it has suitable mechanical and safety properties. Nevertheless, the hydrophobicity of its surface makes it vulnerable to microbial attack and culturing. To enhance antimicrobial activity, a progressive surface modification of LDPE using the antimicrobial agent grafting process was applied. LDPE was first exposed to nonthermal radio-frequency (RF) plasma treatment to activate its surface. This led to the creation of reactive species on the LDPE surface, resulting in the ability to graft antibacterial agents, such as ascorbic acid (ASA), commonly known as vitamin C. ASA is a well-known antioxidant that is used as a food preservative, is essential to biological systems, and is found to be reactive against a number of microorganisms and bacteria. The antimicrobial effect of grafted LDPE with ASA was tested against two strong kinds of bacteria, namely, Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli), with positive results. Surface analyses were performed thoroughly using contact angle measurements and peel tests to measure the wettability or surface free energy and adhesion properties after each modification step. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) were used to analyze the surface morphology or topography changes of LDPE caused by plasma treatment and ASA grafting. Surface chemistry was studied by measuring the functional groups and elements introduced to the surface after plasma treatment and ASA grafting, using Fourier transform infrared (FTIR) spectroscopy and X-ray photoelectron spectroscopy (XPS). These results showed wettability, adhesion, and roughness changes in the LDPE surface after plasma treatment, as well as after ASA grafting. This is a positive indicator of the ability of ASA to be grafted onto polymeric materials using plasma pretreatment, resulting in enhanced antibacterial activity.

• Klíčová slova
• antibacterial, biointerface, grafting modification, plasma treatment, polyethylene,
• Publikační typ
• časopisecké články MeSH

In this paper, we report on the synthesis of FeCo/Cu multisegmented nanowires by means of pulse electrodeposition in nanoporous anodic aluminum oxide arrays supported on silicon chips. By adjustment of the electrodeposition conditions, such as the pulse scheme and the electrolyte, alternating segments of Cu and ferromagnetic FeCo alloy can be fabricated. The segments can be built with a wide range of lengths (15-150 nm) and exhibit a close-to-pure composition (Cu or FeCo alloy) as suggested by energy-dispersive X-ray mapping results. The morphology and the crystallographic structure of different nanowire configurations have been assessed thoroughly, concluding that Fe, Co, and Cu form solid solution. Magnetic characterization using vibrating sample magnetometry and magnetic force microscopy reveals that by introduction of nonmagnetic Cu segments within the nanowire architecture, the magnetic easy axis can be modified and the reduced remanence can be tuned to the desired values. The experimental results are in agreement with the provided simulations. Furthermore, the influence of nanowire magnetic architecture on the magnetically triggered protein desorption is evaluated for three types of nanowires: Cu, FeCo, and multisegmented FeCo15nm/Cu15nm. The application of an external magnetic field can be used to enhance the release of proteins on demand. For fully magnetic FeCo nanowires the applied oscillating field increased protein release by 83%, whereas this was found to be 45% for multisegmented FeCo15nm/Cu15nm nanowires. Our work suggests that a combination of arrays of nanowires with different magnetic configurations could be used to generate complex substance concentration gradients or control delivery of multiple drugs and macromolecules.

• Klíčová slova
• magnetically triggered release, multisegmented nanowires, template-assisted electrodeposition, tunable magnetic properties,
• MeSH
• adsorpce účinky záření   MeSH
• fyzikální absorpce účinky záření   MeSH
• kobalt chemie   MeSH
• kovové nanočástice chemie   účinky záření   ultrastruktura   MeSH
• krystalizace metody   MeSH
• magnetické pole MeSH
• měď chemie   MeSH
• nanodráty chemie   účinky záření   ultrastruktura   MeSH
• pokovování galvanické metody   MeSH
• proteiny chemie   účinky záření   MeSH
• testování materiálů MeSH
• vazba proteinů účinky záření   MeSH
• železo chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• kobalt MeSH
• měď MeSH
• proteiny MeSH
• železo MeSH

Para-coumaric acid (p-CA) is a plant derived secondary metabolite belonging to the phenolic compounds. It is widely distributed in the plant kingdom and found mainly in fruits, vegetables, and cereals. Various in vivo and in vitro studies have revealed its scavenging and antioxidative properties in the reduction of oxidative stress and inflammatory reactions. This evidence-based review focuses on the protective role of p-CA including its therapeutic potential. p-CA and its conjugates possesses various bioactivities such as antioxidant, anti-inflammatory, anti-cancer, anti-diabetic, and anti-melanogenic properties. Due to its potent free radical scavenging activity, it can mitigate the ill effects of various diseases including arthritis, neurological disorders, and cardio-vascular diseases. Recent studies have revealed that p-CA can ameliorate the harmful effects associated with oxidative stress in the reproductive system, also by inhibiting enzymes linked with erectile function.

• Klíčová slova
• ROS, anti-cancer, anti-diabetic, anti-inflammatory, anti-melanogenic, antioxidant, disease, oxidative stress, para-coumaric acid,
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

In the 21st century, nanomaterials play an increasingly important role in our lives with applications in many sectors, including agriculture, biomedicine, and biosensors. Over the last two decades, extensive research has been conducted to find ways to synthesise nanoparticles (NPs) via mediation with fungi or fungal extracts. Mycosynthesis can potentially be an energy-efficient, highly adjustable, environmentally benign alternative to conventional physico-chemical procedures. This review investigates the role of metal toxicity in fungi on cell growth and biochemical levels, and how their strategies of resistance, i.e., metal chelation, biomineral formation, biosorption, bioaccumulation, compartmentalisation, and efflux of metals from cells, contribute to the synthesis of metal-containing NPs used in different applications, e.g., biomedical, antimicrobial, catalytic, biosensing, and precision agriculture. The role of different synthesis conditions, including that of fungal biomolecules serving as nucleation centres or templates for NP synthesis, reducing agents, or capping agents in the synthesis process, is also discussed. The authors believe that future studies need to focus on the mechanism of NP synthesis, as well as on the influence of such conditions as pH, temperature, biomass, the concentration of the precursors, and volume of the fungal extracts on the efficiency of the mycosynthesis of NPs.

• Klíčová slova
• biomolecule, biosynthesis, fungus, green synthesis, metal oxide nanoparticle, metallic nanoparticle, nanomaterial,
• MeSH
• bioakumulace MeSH
• biologický transport MeSH
• katalýza MeSH
• kovové nanočástice * MeSH
• redukční činidla MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• redukční činidla MeSH

Bioorthogonal chemistry has emerged as a new powerful tool that facilitates the study of structure and function of biomolecules in their native environment. A wide variety of bioorthogonal reactions that can proceed selectively and efficiently under physiologically relevant conditions are now available. The common features of these chemical reactions include: fast kinetics, tolerance to aqueous environment, high selectivity and compatibility with naturally occurring functional groups. The design and development of new chemical transformations in this direction is an important step to meet the growing demands of chemical biology. This chapter aims to introduce the reader to the field by providing an overview on general principles and strategies used in bioorthogonal chemistry. Special emphasis is given to cycloaddition reactions, namely to 1,3-dipolar cycloadditions and Diels-Alder reactions, as chemical transformations that play a predominant role in modern bioconjugation chemistry. The recent advances have established these reactions as an invaluable tool in modern bioorthogonal chemistry. The key aspects of the methodology as well as future outlooks in the field are discussed.

• Klíčová slova
• 1,3-dipolar cycloaddition, Biomolecule labeling, Bioorthogonal reactions, Click chemistry, Diels–Alder reaction,
• MeSH
• alkyny chemie   MeSH
• azidy chemie   MeSH
• cykloadiční reakce * MeSH
• katalýza MeSH
• kvantová teorie MeSH
• měď chemie   MeSH
• nitrily chemie   MeSH
• oxidy dusíku chemie   MeSH
• zelené fluorescenční proteiny chemie   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• alkyny MeSH
• azidy MeSH
• měď MeSH
• nitrily MeSH
• nitrones MeSH Prohlížeč
• oxidy dusíku MeSH
• zelené fluorescenční proteiny MeSH

Computational study of the effect of drug candidates on intrinsically disordered biomolecules is challenging due to their vast and complex conformational space. Here, we developed a comparative Markov state analysis (CoVAMPnet) framework to quantify changes in the conformational distribution and dynamics of a disordered biomolecule in the presence and absence of small organic drug candidate molecules. First, molecular dynamics trajectories are generated using enhanced sampling, in the presence and absence of small molecule drug candidates, and ensembles of soft Markov state models (MSMs) are learned for each system using unsupervised machine learning. Second, these ensembles of learned MSMs are aligned across different systems based on a solution to an optimal transport problem. Third, the directional importance of inter-residue distances for the assignment to different conformational states is assessed by a discriminative analysis of aggregated neural network gradients. This final step provides interpretability and biophysical context to the learned MSMs. We applied this novel computational framework to assess the effects of ongoing phase 3 therapeutics tramiprosate (TMP) and its metabolite 3-sulfopropanoic acid (SPA) on the disordered Aβ42 peptide involved in Alzheimer's disease. Based on adaptive sampling molecular dynamics and CoVAMPnet analysis, we observed that both TMP and SPA preserved more structured conformations of Aβ42 by interacting nonspecifically with charged residues. SPA impacted Aβ42 more than TMP, protecting α-helices and suppressing the formation of aggregation-prone β-strands. Experimental biophysical analyses showed only mild effects of TMP/SPA on Aβ42 and activity enhancement by the endogenous metabolization of TMP into SPA. Our data suggest that TMP/SPA may also target biomolecules other than Aβ peptides. The CoVAMPnet method is broadly applicable to study the effects of drug candidates on the conformational behavior of intrinsically disordered biomolecules.

• Publikační typ
• časopisecké články MeSH