The three-dimensional structure of recombinant nicking endonuclease S11C Cys-free Nt.BspD6I was determined at 1.85 Å resolution. Nickase S11C Cys-free Nt.BspD6I was produced by the reversion back to Cys11 in Cys-free Nt.BspD6I using site-directed mutagenesis. An analysis of the crystal structure of nickase S11C Cys-free Nt.BspD6I demonstrated that the reversion back to Cys11 induces significant conformational changes in the recognition domain of nickase, which are accompanied by changes in its functions, such as a decrease in the affinity to DNA, the loss of the ability to undergo oligomerization, and high activity of restriction endonuclease S11C Cys-free R.BspD6I.

Nicking endonuclease Nt.BspD6I (Nt.BspD6I) is the large subunit of the heterodimeric restriction endonuclease R.BspD6I. It recognizes the short specific DNA sequence 5'-GAGTC and cleaves only the top strand in dsDNA at a distance of four nucleotides downstream the recognition site toward the 3'-terminus. A mechanism of interaction of this protein with DNA is still unknown. Here we report the crystal structure of Cysteine-free Nt.BspD6I, with four cysteine residues (11, 160, 508, 578) substituted by serine, which was determined with a resolution of 1.93 angstrom. A comparative structural analysis showed that the substitution of cysteine residues induced marked conformational changes in the N-terminal recognition and the C-terminal cleavage domains. As a result of this changes were formed three new hydrogen bonds and the electrostatic field in these regions changed compared with wild type Nt.BspD6I. The substitution of cysteine residues did not alter the nicking function of Cysteine-free Nt.BspD6I but caused change in the activity of Cysteine-free heterodimeric restriction endonuclease R.BspD6I due to a change in the interaction between its large and small subunits. The results obtained contribute to the identification of factors influencing the interactions of subunits in the heterodimeric restriction enzyme R.BspD6I.

The mutated nickase Nt.BspD6I E418A has been obtained by site-directed mutagenesis. The purified protein has been crystallized, and its spatial structure has been determined at 2.45 Å resolution. An analysis of the crystal structures of the wild-type and mutated nickase have shown that the elimination of a carboxyl group due to the E418A mutation initiates marked conformational changes in both the N-terminal recognition domain and the C-terminal catalytic domain of nickase and insignificantly affects its linker domain. This is supported by changes in the functional properties of mutated nickase: an increase in the oligomerization capacity in the presence of a substrate, a reduction in the capacity to bind a substrate, and complete loss of catalytic activity.

The L232H mutant of the enhanced green fluorescent protein (EGFP) was expressed and crystallized. An X-ray diffraction data set was collected from the crystals to 1.53 Å resolution. An analysis of the three-dimensional structure revealed a stacking interaction between the amino-acid residues Н78 and Н232, which contributes to the fastening of the C-terminal region of the protein in the vicinity of the chromophore and influences chromophore maturation of hybrid fluorescent proteins produced by fusion of the target proteins with the C-terminus of EGFP. This hypothesis was experimentally confirmed by investigating chromophore maturation of the hybrid proteins fused to the N- and C-termini of EGFP and EGFP-L232H.

The physicochemical characteristics and functional properties of pumpkin (Cucurbita maxima D. var. Cabello de Ángel) pectin obtained by cavitation facilitated extraction from pumpkin pulp have been evaluated and compared with commercial citrus and apple pectins. C. maxima pectin had an Mw value of 90 kDa and a high degree (72%) of esterification. The cytoprotective and antioxidant effects of citrus, apple and pumpkin pectin samples with different concentrations were studied in vitro in cell lines HT-29 (human colon adenocarcinoma) and MDCK1 (canine kidney epithelium). All pectin samples exhibited cytoprotective effect in HT-29 and MDCK1 cells after incubation with toxic concentrations of cadmium and mercury for 4 h. Pumpkin pectin increased the proliferation of cadmium-treated MDCK1 cells by 210%. The studied pectins also inhibited oxidative stress induced by 2,2'-azobis(2-methylpropionamidine) dihydrochloride (AAPH) in cell cultures, as determined by measuring the production of intracellular reactive species using dihydrochlorofluorescein diacetate (DCFH-DA). Pectin from pumpkin pomace had the highest (p < 0.05) protective effect against reactive oxygen species generation in MDCK1 cells induced by AAPH. Distinctive features of pumpkin pectin were highly branched RG-I regions, the presence of RG-II regions and the highest galacturonic acid content among the studied samples of pectins. This correlates with a considerable protective effect of C. maxima pectin against oxidative stress and cytotoxicity induced by heavy metal ions. Thus, C. maxima pectin can be considered as a source of new functional foods of agricultural origin.

The spatial organization of the genome is controlled by a special class of architectural proteins, including proteins containing BTB domains that are able to dimerize or multimerize. The centrosomal protein 190 is one of such architectural proteins. The purification, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 are reported. The crystallization conditions were found by the vapor-diffusion technique. The crystals diffracted to 1.5 Å resolution and belonged to sp. gr. P3221. The structure was solved by the molecular replacement method. The structure refinement is currently underway.

The three-dimensional structure of the D456A mutant of the nicking endonuclease Nt.BspD6I was determined. According to the concept of the cleavage scaffold, the replacement of D456 by A456, which resulted in complete (100%) loss of nickase activity, was shown to be a trigger of structural changes in the cleavage-scaffold region. Besides, the displacement of Е482 and the rotation of Н449 toward the N-terminal domain initiate conformational changes in the D1 recognition subdomain of the N-terminal domain with the result that the centers of mass of the С- and N-terminal domains are brought into close proximity to each other. Electrostatic calculations showed that changes in the free energy and electrostatic interactions for the mutant nickase are distributed predominantly in the N-terminal domain and that these changes are not attenuated in a radial fashion away from the mutation site but have a distinct direction.

The Drosophila genome has several dozens of transcription factors (TTK group) containing ВТВ domains assembled into octamers. The LOLA protein belongs to this family. The purification, crystallization, and preliminary X-ray diffraction and small-angle X-ray scattering (SAXS) studies of the BTB domain of this protein are reported. The crystallization conditions were found by the vapor-diffusion technique. A very low diffraction resolution (8.7 Å resolution) of the crystals was insufficient for the determination of the threedimensional structure of the BTB domain. The SAXS study demonstrated that the BTB domain of the LOLA protein exists as an octamer in solution.