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The perpetually changing cellular conditions, nucleotide sequence, and environmental effects including osmotic stress have multiple effects on DNA, leading to several conformational alternations and subsequently influencing their activity, too. In this work, single-molecule FRET microspectroscopy has been employed to monitor the breathing dynamics as an effect of molecular crowding in the stem region of Fork-DNA. The structural integrity greatly alters with the presence or absence of nucleotide overhangs and on the nature and concentration of the crowding agent, thus affecting the stability of the stem region and hence the forked DNA. The multiple hydrogen bonds and hydrophobic interactions between the polynucleotide strands appear to be altered with osmotic crowding. This induces increased flexibility in the double helix and allows DNA to breath. The conformational alternation of the DNA happens in nanometer resolution, that is been monitored by the change in the FRET efficiency between the dyes attached to two different strands of the DNA. The nature and molecular weight of crowding agents control the degree of spatial breathing in the stem of Fork-DNA. These constant fluctuations between the entropically favorable partially folded structures to an enthalpically favorable folded structure are not only valuable for elucidating nucleic acid structure but might play an important role in enzyme kinetics.The correlation of molecular function and protein intrinsic disorder is an important aspect of understanding the relationship between function, sequence and structure. This research was inspired by statistical correlation evaluation method described by Xie et al. (J Proteome Res 6 (2007) 1882-1898, reference study), where the authors analyzed the relationship between structure and function of proteins from Swiss-Prot database and where these functions were described with Swiss-Prot function keywords. In this research, we investigated whether the conclusions from the reference study stand for another dataset with richer functional annotation. We used CAFA3 challenge training dataset where the function was described with terms from Gene Ontology (GO terms). In order to compare the results with the previous work, we associated the GO terms with the corresponding Swiss-Prot function keywords. The results were compared with the reference study by first repeating the analysis with Swiss-Prot function keywords and ttated by different functions. Comparison with results from the reference study revealed prevalence of binding related functions (disorder related) in the current dataset even though the same functions were not present in previous results.Spinal cord injury (SCI) often causes neuronal death and axonal degeneration. In this study, we report a new strategy for preparing injectable and conductive polysaccharides-based hydrogels that could sustainably deliver brain-derived neurotrophic factor (BDNF) for SCI repair. We used poly(lactic-co-glycolic acid) (PLGA) as a carrier to encapsulate BDNF. The resulting microspheres were then modified with tannic acid (TA). The polysaccharides-based hydrogel composed of oxidized dextran (Dex) and hyaluronic acid-hydrazide (HA) was mixed with TA-modified microspheres to form the ultimate BDNF@TA-PLGA/Dex-HA hydrogel. Our results showed that the hydrogel had properties similar to natural spinal cords. check details Specifically, the hydrogel had soft mechanical properties and high electrical conductivity. The cross-sectional morphology of the hydrogel exhibited a continuous and porous structure. The swelling and degradation behaviors of the Dex-HA hydrogel in vitro indicated the incorporation of TA into hydrogel matrix could improve the stability of the hydrogel matrix as well as extend the release time of BDNF from the matrix. Furthermore, results from immunostaining and real-time PCR demonstrated that BDNF@TA-PLGA/Dex-HA hydrogel could promote the differentiation of neural stem cells (NSCs) into neurons and inhibit astrocyte differentiation in vitro. These results show the great potential of this hydrogel as a biomimetic material in SCI regeneration.Foodborne nanoparticles have attracted considerable interest due to their distinctive fluorescence and physicochemical properties. The discovery of vinegar carbon dots (VCDs) has drawn our attention to study their effect on human plasma protein. Herein, spectral, constructional, morphological, and enzymatic activity assessments were carried out to investigate the interaction of VCDs with human hemoglobin (HHb). The intrinsic fluorescence of HHb was quenched significantly by the VCDs through a static quenching process. Furthermore, binding constants and important thermodynamic parameters were calculated, the negative enthalpy and entropy changes were accompanied by a negative Gibbs energy, which proposed the binding between VCDs with HHb was spontaneous. Moreover, negative enthalpy and entropy change corroborated the involvement of van der Waals force and hydrogen bonds in the binding process. Results from FTIR, atomic force microscopy and circular dichroism revealed change of HHB after binding with VCDs although their essential morphological features were unaffected. The esterase activity of HHb decreased after VCDs treatment in a dose-dependent manner, which further confirmed the effect of VCDs on HHb. The results offered detailed information about the interaction between VCDs and HHb.Feasible and easily accessible methods for the rational design of enzyme engineering strategies remain to be established. Thus, a new rationally combined strategy based on disulfide bond engineering and HotSpot Wizard 3.0 was proposed and experimentally demonstrated to be effective using a hyperthermostable β-mannanase. Ten of 42 mutants showed prominent enhancement of kinetic stability with 26.4%-39.9% increases in t1/2 (75 °C) compared with the parent enzyme ManAKH. The best mutant, D273-V308, showed apparent increases in both optimal temperature (5 °C) and T50 (6.8 °C), as well as advanced catalytic efficiency. The low rate of inactive mutants and the high rate of positive mutants indicated that newly introduced screening factors (distance from catalytic residues, Gibbs free energy term, molecular simulation, and visual inspections) greatly enhance the design of thermostable β-mannanase. Moreover, these findings further advance the industrial application of β-mannanase (ManAK) in food and food-related applications.
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