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Scientific reports 12(1), 14077 (2022). doi:10.1038/s41598-022-17929-y, In recent years silver nanoparticles (Ag NPs) gained increased and widespread applications in various fields of industry, technology, and medicine. This study describes the green synthesis of silver nanoparticles (Ag NPs) applying a low-molecular-weight fraction (LMF) of Royal Jelly, the nanoparticle characterization, and particularly their antibacterial activity. The optical properties of NPs, characterized by UV–Vis absorption spectroscopy, showed a peak at ~ 430 nm. The hydrodynamic radius and concentration were determined by complementary dynamic light scattering (DLS) and nanoparticle tracking analysis (NTA). The particle morphology was investigated using transmission electron microscopy (TEM), and the crystallinity of the silver was confirmed by X-ray diffraction (XRD). The antibacterial activities were evaluated utilizing Gram-negative and Gram-positive bacteria and colony counting assays. The growth inhibition curve method was applied to obtain information about the corresponding minimum inhibitory concentrations (MIC) and the minimum bactericidal concentrations (MBC) required. Obtained results showed that (i) the sizes of Ag NPs are increasing within the increase of silver ion precursor concentration, (ii) DLS, in agreement with NTA, showed that most particles have dimensions in the range of 50–100 nm; (iii) E. coli was more susceptible to all Ag NP samples compared to B. subtilis., Published by Macmillan Publishers Limited, part of Springer Nature, [London]

Scientific reports 11(1), 24066 (2021). doi:10.1038/s41598-021-02174-6, A potent napin protein has been thoroughly characterized from seeds of rocket salad (Eruca sativa). Eruca sativa napin (EsNap) was purified by ammonium sulfate precipitation (70%) and size-exclusion chromatography. Single intact 16 kDa EsNap band was reduced to 11 and 5 kDa bands respectively on SDS-PAGE. Nano LC���MS/MS yielded two fragments comprising of 26 residues which showed 100% sequence identity with napin-3 of Brassica napus. CD spectroscopy indicated a dominant ��-helical structure of EsNap. Monodispersity of EsNap was verified by dynamic light scattering, which also confirmed the monomeric status with a corresponding hydrodynamic radius of 2.4 �� 0.2 nm. An elongated ab initio shape of EsNap was calculated based on SAXS data, with an R$_g$ of 1.96 �� 0.1 nm. The ab initio model calculated by DAMMIF with P1 symmetry and a volume of approx. 31,100 nm$^3$, which corresponded to a molecular weight of approximately 15.5 kDa. The comparison of the SAXS and ab initio modeling showed a minimized ��$^2$-value of 1.87, confirming a similar molecular structure. A homology model was predicted using the coordinate information of Brassica napus rproBnIb (PDB ID: 1SM7). EsNap exhibited strong antifungal activity by significantly inhibiting the growth of Fusarium graminearum. EsNap also showed cytotoxicity against the hepatic cell line Huh7 and the obtained IC50 value was 20.49 ��M. Further, strong entomotoxic activity was experienced against different life stages of stored grain insect pest T. castaneum. The result of this study shows insights that can be used in developing potential antifungal, anti-cancerous and insect resistance agents in the future using EsNap from E. sativa., Published by Macmillan Publishers Limited, part of Springer Nature, [London]

The formation of stable and functional surface layers (S-layers) via self-assembly of surface-layer proteins on the cell surface is a dynamic and complex process. S-layers facilitate a number of important biological functions, e.g., providing protection and mediating selective exchange of molecules and thereby functioning as molecular sieves. Furthermore, S-layers selectively bind several metal ions including uranium, palladium, gold, and europium, some of them with high affinity. Most current research on surface layers focuses on investigating crystalline arrays of protein subunits in Archaea and bacteria. In this work, several complementary analytical techniques and methods have been applied to examine structure-function relationships and dynamics for assembly of S-layer protein slp-B53 from Lysinibacillus sphaericus: (1) The secondary structure of the S-layer protein was analyzed by circular dichroism spectroscopy; (2) Small-angle X-ray scattering was applied to gain insights into the three-dimensional structure in solution; (3) The interaction with bivalent cations was followed by differential scanning calorimetry; (4) The dynamics and time-dependent assembly of S-layers were followed by applying dynamic light scattering; (5) The two-dimensional structure of the paracrystalline S-layer lattice was examined by atomic force microscopy. The data obtained provide essential structural insights into the mechanism of S-layer self-assembly, particularly with respect to binding of bivalent cations, i.e., Mg2+ and Ca2+. Furthermore, the results obtained highlight potential applications of S-layers in the fields of micromaterials and nanobiotechnology by providing engineered or individual symmetric thin protein layers, e.g., for protective, antimicrobial, or otherwise functionalized surfaces.

Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo-grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.

We have noticed that during a long storage and handling, the plant methionine initiator tRNA is spontaneously hydrolyzed within the anticodon loop at the C34-A35 phosphodiester bond. A literature search indicated that there is also the case for human initiator tRNA(Met) but not for yeast tRNA(i)Met or E. coli tRNA(f)Met. All these tRNAs have an identical nucleotide sequence of the anticodon stems and loops with only one difference at position 33 within the loop. It means that cytosine 33 (C33) makes the anticodon loop of plant and human tRNA(i)Met susceptible to the specific cleavage reaction. Using crystallographic data of tRNA(f)Met of E. coli with U33, we modeled the anticodon loop of this tRNA with C33. We found that C33 within the anticodon loop creates a pocket that can accomodate a hydrogen bonded water molecule that acts as a general base and catalyzes a hydrolysis of C-A bond. We conclude that a single nucleotide change in the primary structure of tRNA(i)Met made changes in hydration pattern and readjustment in hydrogen bonding which lead to a cleavage of the phosphodiester bond.

Structural and functional characteristics were compared for wild-type nuclease from Serratia marcescens, which belongs to the family of DNA/RNA nonspecific endonucleases, its mutational forms, and the nuclease I-PpoI from Physarum polycephalum, which is a representative of the Cys-His box-containing subgroup of the superfamily of extremely specific intron-encoded homing DNases. Despite the lack of sequence homology and the overall different topology of the Serratia marcescens and I-PpoI nucleases, their active sites have a remarkable structural similarity. Both of them have a unique magnesium atom in the active site, which is a part of the coordinatively bonded water-magnesium complex involved in their catalytic acts. In the enzyme-substrate complexes, the Mg2+ ion is chelated by an Asp residue, coordinates two oxygen atoms of DNA, and stabilizes the transition state of the phosphate anion and 3'-OH group of the leaving nucleotide. A new mechanism of the phosphodiester bond cleavage, which is common for the Serratia marcescens and I-PpoI nucleases and differs from the known functioning mechanism of the restriction and homing endonucleases, was proposed. It presumes a His residue as a general base for the activation of a non-cluster water molecule at the nucleophilic in line displacement of the 3'-leaving group. A strained metalloenzyme-substrate complex is formed during hydrolysis and relaxes to the initial state after the reaction. The English version of the paper.

The structure of native yeast tRNAPhe and wheat germ ribosomal 5S RNA induced by different magnesium ion concentrations was studied in solution with a synchrotron mediated hydroxyl radical RNA cleavage reaction. We showed that very small amounts of Mg+2 can induce significant changes in the hydroxyl radical cleavage pattern of tRNAPhe. It also turned out that a reactivity of tRNAPhe towards •OH coincides with the strong metal binding sites. Because of the Mg ions are heavily hydrated one can suggest the strong correlation of the observed nucleosides reactivity in vicinity of Mg2+ binding sites with availability of water molecules as a source of hydroxyl radical. On the other hand the structure of wheat germ 5S rRNA is less sensitive to the hydroxyl radical reaction than tRNAPhe although some changes are visible at 4 mM Mg ions. It is probably due to the lack of strong Mg+2 binding sites in that molecule. The reactivity of nucleotides in loops C and D of 5S rRNA is not effected, what suggests their flexibility or involvement in higher order structure formation. There is different effect of magnesium on tRNA and 5S rRNA folding. We found that nucleotides forming strong binding sites for magnesium are very sensitive to X-ray generated hydroxyl radical and can be mapped with •OH. The results show, that guanine nucleotides are preferentially hydrated. X-ray footprinting mediated hydroxyl radical RNA cleavage is a very powerful method and has been applied to studies of stable RNAs for the first time.

X-ray structure analysis shows that the monomer of trimeric photosystem I (PS I) of Synechococcus sp. consists of a catalytic domain and a smaller domain that connects the monomers. The 4Fe–4S clusters FX,FA and FB, 28 α-helices and 45 chlorophyll a molecules were located. The two large subunits of PS I are represented by nine a-helices each; they are related by a local 2-fold rotation axis passing through Fx. Electron densities close to this axis are interpreted as carriers of the electron transfer chain.

α-Cyclodextrin, a torus shaped molecule with a 5 A wide central cavity, forms a number of deep green, blue and black crystals when complexed with iodine/metal iodide. In contrast, β-cyclodextrin, having a 6 A cavity produces only one type of reddish-brown crystal, no matter what metal iodide is used. The complex (β-cyclodextrin)2 ·KI7·9H2O displays space groupP21 (pseudo-C2) with cell constantsa=19.609(5),b=24.513(7),c=15.795(6)A, β=109.50(2)°,Z=4. The crystal structure was solved inC2 on the basis of 3022 absorption corrected CuKα (Ni-filter) X-ray intensities and refined by full matrix least squares toR=17%. This relatively highR-factor is due to many weak reflections (pseudo-C2) and considerable disorder exhibited by water and iodine. In the complex, β-cyclodextrin adopts a ‘round’ shape with O(2)...O(3) interglucose hydrogen bonds formed and all O(6) hydroxyls pointing away from the cavity. Two molecules are arranged head-to-head to produce a dimer, and dimers are stacked such that a slightly zigzagged cylinder with a 6 A-wide cavity is formed. In the cavity described by each dimer, an I 7 − ion composed of I2·I 3 − ·I2 units is located, with I2 and I 3 − perpendicular to each other. K+ ions and 9 H2O molecules are found in interstices between the β-cyclodextrin cylinders. This zigzag polyiodide contrasts with the linear form observed in the 5 A wide α-cyclodextrin channels. It explains differences in color of the crystals and suggests that β-cyclodextrin polyiodide is not a good model for blue starch-iodine.