The virulence of the Candida pathogens is enhanced by the production of secreted aspartic proteases, which therefore represent possible targets for drug design. Here, the crystal structure of the secreted aspartic protease Sapp2p from Candida parapsilosis was determined. Sapp2p was isolated from its natural source and crystallized in complex with pepstatin A, a classical aspartic protease inhibitor. The atomic resolution of 0.83 Å allowed the protonation states of the active-site residues to be inferred. A detailed comparison of the structure of Sapp2p with the structure of Sapp1p, the most abundant C. parapsilosis secreted aspartic protease, was performed. The analysis, which included advanced quantum-chemical interaction-energy calculations, uncovered molecular details that allowed the experimentally observed equipotent inhibition of both isoenzymes by pepstatin A to be rationalized.

• Klíčová slova
• Candida parapsilosis, Sapp2p, aspartic protease, crystal structure, interaction energy, quantum mechanics, ultrahigh resolution,
• MeSH
• aspartátové proteasy chemie   genetika   izolace a purifikace   metabolismus   MeSH
• Candida chemie   enzymologie   genetika   MeSH
• exprese genu MeSH
• fungální proteiny chemie   genetika   izolace a purifikace   metabolismus   MeSH
• inhibitory proteas chemie   MeSH
• izoenzymy chemie   genetika   izolace a purifikace   metabolismus   MeSH
• katalytická doména MeSH
• kinetika MeSH
• krystalografie rentgenová MeSH
• kvantová teorie MeSH
• molekulární modely MeSH
• molekulární sekvence - údaje MeSH
• pepstatiny chemie   MeSH
• sekundární struktura proteinů MeSH
• sekvence aminokyselin MeSH
• sekvenční seřazení MeSH
• strukturní homologie proteinů MeSH
• substrátová specifita MeSH
• termodynamika MeSH
• vazba proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• aspartátové proteasy MeSH
• fungální proteiny MeSH
• inhibitory proteas MeSH
• izoenzymy MeSH
• pepstatin MeSH Prohlížeč
• pepstatiny MeSH

Submolecular imaging by atomic force microscopy (AFM) has recently been established as a stunning technique to reveal the chemical structure of unknown molecules, to characterize intramolecular charge distributions and bond ordering, as well as to study chemical transformations and intermolecular interactions. So far, most of these feats were achieved on planar molecular systems because high-resolution imaging of three-dimensional (3D) surface structures with AFM remains challenging. Here we present a method for high-resolution imaging of nonplanar molecules and 3D surface systems using AFM with silicon cantilevers as force sensors. We demonstrate this method by resolving the step-edges of the (101) anatase surface at the atomic scale by simultaneously visualizing the structure of a pentacene molecule together with the atomic positions of the substrate and by resolving the contour and probe-surface force field on a C60 molecule with intramolecular resolution. The method reported here holds substantial promise for the study of 3D surface systems such as nanotubes, clusters, nanoparticles, polymers, and biomolecules using AFM with high resolution.

• Klíčová slova
• Noncontact atomic force microscopy (NC-AFM), high-resolution imaging, submolecular resolution, three-dimensional dynamic force spectroscopy,
• MeSH
• analýza selhání vybavení MeSH
• design vybavení MeSH
• fullereny chemie   MeSH
• krystalografie metody   MeSH
• mikroskopie atomárních sil přístrojové vybavení   MeSH
• molekulární konformace MeSH
• molekulární sondy - techniky přístrojové vybavení   MeSH
• molekulární zobrazování přístrojové vybavení   MeSH
• reprodukovatelnost výsledků MeSH
• senzitivita a specificita MeSH
• vylepšení obrazu přístrojové vybavení   MeSH
• zobrazování trojrozměrné přístrojové vybavení   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• fullerene C60 MeSH Prohlížeč
• fullereny MeSH

The determination of trace metal contents directly from a solid sample is a trend in modern atomic spectrometry. The aim of this study was to develop an analytical method for the routine determination of Cd in lichens using solid sampling graphite furnace atomic absorption spectrometry (SS-GF-AAS). For the determination of Cd, the temperature program of the graphite furnace was optimized using a mixed matrix modifier (Pd + Mg (NO3)2 + Triton X-100). The limit of detection and the limit of quantification were 0.9 μg/kg and 3 μg/kg, respectively. The analytical method for Cd determination in the plant matrix was verified by the analysis of certified reference materials of lichens, seaweed, and rye grass. The developed procedure was applied to the study of Cd distribution in thalli of Usnea antarctica lichen from James Ross Island, Antarctica. The SS-GF-AAS analytical method is particularly suited for use in environmental studies and plant physiology (the microanalysis of anatomical structures).

• Klíčová slova
• AAS, Cadmium, Lichen, Solid sampling,
• MeSH
• grafit * MeSH
• kadmium * analýza   MeSH
• látky znečišťující životní prostředí * analýza   MeSH
• lišejníky * chemie   MeSH
• monitorování životního prostředí MeSH
• ostrovy MeSH
• spektrofotometrie atomová MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Antarktida MeSH
• ostrovy MeSH
• Názvy látek
• grafit * MeSH
• kadmium * MeSH
• látky znečišťující životní prostředí * MeSH

A Si adatom on a Si(111)-(7 × 7) reconstructed surface is a typical atomic feature that can rather easily be imaged by a non-contact atomic force microscope (nc-AFM) and can be thus used to test the atomic resolution of the microscope. Based on our first principles density functional theory (DFT) calculations, we demonstrate that the structure of the termination of the AFM tip plays a decisive role in determining the appearance of the adatom image. We show how the AFM image changes depending on the tip-surface distance and the composition of the atomic apex at the end of the tip. We also demonstrate that contaminated tips may give rise to image patterns displaying so-called 'sub-atomic' features even in the attractive force regime.

• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Butterfly wings have complex structure lending it several interesting properties. Coloration of the wing is one of the first things to encounter and the overall visual effect is in fact influenced by several factors. Chemical pigments set the base color of the wing, topographical structures on the wing scales cause color shift by interference and their arrangement into diffraction grating causes iridescence. The thin film interference can be attributed to microscopic ridges covering wing scales. Observation and calculation of the color shift on wings of Euploea mulciber species using Fourier transform of images obtained by atomic force microscopy is the focus of this article.

• Klíčová slova
• AFM, FTIR, Fourier transform, butterfly wing,
• MeSH
• Fourierova analýza MeSH
• křídla zvířecí ultrastruktura   MeSH
• mikroskopie atomárních sil MeSH
• motýli fyziologie   ultrastruktura   MeSH
• pigmentace fyziologie   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Atomic force microscopy is capable of resolving the chemical structure of a single molecule on a surface. In previous research, such high resolution has only been obtained at low temperatures. Here we demonstrate that the chemical structure of a single molecule can be clearly revealed even at room temperature. 3,4,9,10-perylene tetracarboxylic dianhydride, which is strongly adsorbed onto a corner-hole site of a Si(111)-(7 × 7) surface in a bridge-like configuration is used for demonstration. Force spectroscopy combined with first-principle calculations clarifies that chemical structures can be resolved independent of tip reactivity. We show that the submolecular contrast over a central part of the molecule is achieved in the repulsive regime due to differences in the attractive van der Waals interaction and the Pauli repulsive interaction between different sites of the molecule.

• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

This paper aimed to investigate the structure and physicochemical and tribological properties of ZnO coatings deposited by ALD on 316L stainless steel for biomedical applications. To obtain ZnO films, diethylzinc (DEZ) and water were used as ALD precursors. Zinc oxide layers were deposited at the same temperature of 200 °C using three types of ALD cycles: 500, 1000 and 1500. The structure and morphology of ZnO coatings were examined using SEM and AFM microscopes. The XRD and GIXRD methods were used for the phase analysis of the obtained coatings. To determine the resistance to pitting corrosion, potentiodynamic investigations and impedance spectroscopy were conducted in a Ringer solution at a temperature of 37 °C. The obtained results showed that the number of ALD cycles had a significant impact on the structure, morphology and corrosion resistance of the ZnO layers. It was found that after increasing the coating thickness of the ZnO on the material, its electrochemical properties determining the corrosion resistance also increased. Moreover, on the basis of the ball-on-plate tribological investigations, we found a significant reduction in the friction coefficient of the samples with the investigated coatings in relation to the noncoated substrates.

• Klíčová slova
• 316L stainless steel, ALD, ZnO, atomic layer deposition, corrosion resistance, mechanical properties, nanostructured, zinc oxide,
• Publikační typ
• časopisecké články MeSH

Atomically flat mica surfaces were chemically modified with an alkyl trifluoromethyl ketone, a covalent inhibitor of esterase 2 from Alicyclobacillus acidocaldarius, which served as a tag for ligand-directed immobilization of esterase-linked proteins. Purified NADH oxidase from Thermus thermophilus and human exportin-t from cell lysates were anchored on the modified surfaces. The immobilization effectiveness of the proteins was studied by atomic force microscopy (AFM). It was shown that ligand-esterase interaction allowed specific attachment of exportin-t and resulted in high-resolution images and coverage patterns that were comparable with immobilized purified protein. Moreover, the biological functionality of immobilized human exportin-t in forming a quaternary complex with tRNA and the GTPase Ran-GTP, and the dimension changes before and after complex formation were also determined by AFM.

• MeSH
• bakteriální proteiny MeSH
• esterasy antagonisté a inhibitory   chemie   genetika   ultrastruktura   MeSH
• exprese genu MeSH
• ketony chemie   farmakologie   MeSH
• lidé MeSH
• ligandy MeSH
• mikroskopie atomárních sil * MeSH
• multienzymové komplexy chemie   genetika   MeSH
• NADH, NADPH oxidoreduktasy chemie   genetika   MeSH
• nukleocytoplazmatické transportní proteiny chemie   genetika   MeSH
• rekombinantní fúzní proteiny chemie   genetika   ultrastruktura   MeSH
• silikáty hliníku chemie   MeSH
• terciární struktura proteinů MeSH
• Thermus thermophilus enzymologie   MeSH
• vazebná místa MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny MeSH
• esterasy MeSH
• ketony MeSH
• ligandy MeSH
• mica MeSH Prohlížeč
• multienzymové komplexy MeSH
• NADH oxidase MeSH Prohlížeč
• NADH, NADPH oxidoreduktasy MeSH
• nukleocytoplazmatické transportní proteiny MeSH
• rekombinantní fúzní proteiny MeSH
• silikáty hliníku MeSH

Although lead-free halide double perovskites are considered as promising alternatives to lead halide perovskites for optoelectronic applications, state-of-the-art double perovskites are limited by their large bandgap. The doping/alloying strategy, key to bandgap engineering in traditional semiconductors, has also been employed to tune the bandgap of halide double perovskites. However, this strategy has yet to generate new double perovskites with suitable bandgaps for practical applications, partially due to the lack of fundamental understanding of how the doping/alloying affects the atomic-level structure. Here, we take the benchmark double perovskite Cs2AgInCl6 as an example to reveal the atomic-level structure of double perovskite alloys (DPAs) Cs2AgIn1-x Fe x Cl6 (x = 0-1) by employing solid-state nuclear magnetic resonance (ssNMR). The presence of paramagnetic alloying ions (e.g. Fe3+ in this case) in double perovskites makes it possible to investigate the nuclear relaxation times, providing a straightforward approach to understand the distribution of paramagnetic alloying ions. Our results indicate that paramagnetic Fe3+ replaces diamagnetic In3+ in the Cs2AgInCl6 lattice with the formation of [FeCl6]3-·[AgCl6]5- domains, which show different sizes and distribution modes in different alloying ratios. This work provides new insights into the atomic-level structure of bandgap engineered DPAs, which is of critical significance in developing efficient optoelectronic/spintronic devices.

• Publikační typ
• časopisecké články MeSH

Partial atomic charges serve as a simple model for the electrostatic distribution of a molecule that drives its interactions with its surroundings. Since partial atomic charges are frequently used in computational chemistry, chemoinformatics and bioinformatics, many computational approaches for calculating them have been introduced. The most applicable are fast and reasonably accurate empirical charge calculation approaches. Here, we introduce Atomic Charge Calculator II (ACC II), a web application that enables the calculation of partial atomic charges via all the main empirical approaches and for all types of molecules. ACC II implements 17 empirical charge calculation methods, including the highly cited (QEq, EEM), the recently published (EQeq, EQeq+C), and the old but still often used (PEOE). ACC II enables the fast calculation of charges even for large macromolecular structures. The web server also offers charge visualization, courtesy of the powerful LiteMol viewer. The calculation setup of ACC II is very straightforward and enables the quick calculation of high-quality partial charges. The application is available at https://acc2.ncbr.muni.cz.

• MeSH
• fenoly chemie   MeSH
• internet MeSH
• molekulární modely * MeSH
• molekulární struktura MeSH
• nikotinové receptory chemie   MeSH
• protein X asociovaný s bcl-2 chemie   MeSH
• software * MeSH
• statická elektřina MeSH
• vodík chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• fenoly MeSH
• nikotinové receptory MeSH
• protein X asociovaný s bcl-2 MeSH
• vodík MeSH