Molecular modelling for investigating structure–function relationships of soy glycinin

Molecular dynamic (in silico) modeling of structure-function of glutelin type-B 5-like from proso millet storage protein: effects of temperature and pressure

Molecular dynamic (MD) simulation provides an insight into the behavior of a protein under applied processing at the molecular level. The behavior of glutelin type-B 5-like protein, a type of glutelin protein from proso millet was studied, in solution under different temperatures (300, 350, and 400 K) and pressure (1 bar, 3 kbar, and 6 kbar) levels using a molecular dynamics simulation approach. The combined treatment effect (400 K, 6 kbar) increased the compaction of the protein compared to the level at (300 K, 1 bar) as shown by the decreased radius of gyration values from 3.26 to 2.92 nm, decreased solvent accessibility surface area from 327.47 to 311.06 nm2 and decreased volume from 108.35 to 105.04 nm3. The root means square deviation increased with increasing temperature but decreased with increasing pressure while the root means square fluctuations increased significantly with increased in temperature and pressure. A snapshot of the three-dimensional structure of the protein revealed compression of its occluded cavities at higher pressure levels but no obvious disruption to the secondary structure elements of the protein was observed, except for the loss of a few amino acid residues that comprise the secondary structure element.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-022-05594-y.

Influence of mild oxidation induced through DBD-plasma treatment on the structure and gelling properties of glycinin

The effects of dielectric-barrier discharge (DBD) plasma treatment (20 s to 120 s treatment time with 40 kV, 12 kHz) induced mild oxidation on the gelling properties, and related structural changes of glycinin were investigated. The gelling ability of glycinin was improved by the mild oxidation induced by the plasma treatment. Treated glycinin gels exhibited a continuous and uniform network microstructure. Samples treated for 120 s had a 2.07-, 3.99- and 2.03-fold increase in hardness, chewiness, and resilience compared to the 20 s treated samples. Structural analyses showed that primary and secondary structures of glycinin were unaffected. The tertiary structure was shifted, accompanied by a decrease in free sulfhydryl (-SH) content. At the same time, carbonyl content and average particle diameter were increased by DBD treatment. The DBD treatment facilitated the generation/exchange of intermolecular disulfide bonds and enhanced gelling properties of glycinin. It is concluded that controlled plasma-induced protein oxidation can improve protein functionality.

Evaluation of Vegetation Restoration along an Expressway in a Cold, Arid, and Desertified Area of China

Vegetation restoration plays a significant role in the restoration of expressways in the arid zone of China, but we still do not know which soil and vegetation types are most effective. We investigated soil particle size (SPZ), volume weight of the soil (VWS), soil water content (SWC), total porosity of soil (TP), soil organic matter (SOM), water erosion (WrE), and wind erosion (WdE) of eight sites (S1–S8) and evaluated them using the gray correlation method (GCM). Based on our results, the average SWC of the treatments ranged from 9.6% to 18.8%, following the order S4 > S5 > S8 > S6 > S3 > S7 > S1 > S2. The average SPZ of soils in S1, S2, S4, S5, S6, and S8 was larger, ranging from 0.23 to 0.68 mm, while that of soils in S3 and S7 was smaller, ranging from 0.01 to 0.09 mm. The TP in different treatment areas ranged from 50% to 60%, which is not conducive to soil and water conservation. The SOM levels varied widely among the different soils and were always below the threshold levels established by the second National Soil Census, rendering the soils not suitable for plant growth. The WrE (36–80 t/ha) was greater than the WdE (7–24 t/ha). In general, to achieve high soil and water conservation outcomes in this area, S1 and S7 offered the best protection benefits in terms of soil and water conservation.

Protein analysis reveals differential accumulation of late embryogenesis abundant and storage proteins in seeds of wild and cultivated amaranth species

BACKGROUND

Amaranth is a plant naturally resistant to various types of stresses that produces seeds of excellent nutritional quality, so amaranth is a promising system for food production. Amaranth wild relatives have survived climate changes and grow under harsh conditions, however no studies about morphological and molecular characteristics of their seeds are known. Therefore, we carried out a detailed morphological and molecular characterization of wild species A. powellii and A. hybridus, and compared them with the cultivated amaranth species A. hypochondriacus (waxy and non-waxy seeds) and A. cruentus.

RESULTS

Seed proteins were fractionated according to their polarity properties and were analysed in one-dimensional gel electrophoresis (1-DE) followed by nano-liquid chromatography coupled to tandem mass spectrometry (nLC-MS/MS). A total of 34 differentially accumulated protein bands were detected and 105 proteins were successfully identified. Late embryogenesis abundant proteins were detected as species-specific. Oleosins and oil bodies associated proteins were observed preferentially in A. cruentus. Different isoforms of the granule-bound starch synthase I, and several paralogs of 7S and 11S globulins were also identified. The in silico structural analysis from different isoforms of 11S globulins was carried out, including new types of 11S globulin not reported so far.

CONCLUSIONS

The results provide novel information about 11S globulins and proteins related in seed protection, which could play important roles in the nutritional value and adaptive tolerance to stress in amaranth species.

Crystal structure determination and analysis of 11S coconut allergen: Cocosin

Allergy is an abnormal immune response against an innocuous target. Food allergy is an adverse reaction caused by common foods most well-known being those involving peanuts. Apart from mono sensitized food allergy, cross-reactivity with other food allergens is also commonly observed. To understand the phenomenon of cross-reactivity related to immune response, three dimensional structures of the allergens and their antigenic epitopes has to be analysed in detail. The X-ray crystal structure of Cocosin, a common 11S food allergen from coconut, has been determined at 2.2Å resolution using molecular replacement technique. The monomer of 52kDa is composed of two β-jelly roll domains, one with acidic and the other with basic character. The structure shows hexameric association with two trimers facing each other. Though the overall structure of Cocosin is similar to other 11S allergens, the occurrence of experimentally determined epitopes of the peanut allergen Ara h 3 at flexible as well as variable regions could be the reason for the clinically reported result of cross-reactivity that the peanut allergic patients are not sensitized with coconut allergen.

Modification of solubility and heat-induced gelation of amaranth 11S globulin by protein engineering

The primary structure of amaranth 11S globulin (Ah11S) was engineered with the aim to improve its functional properties. Four continuous methionines were inserted in variable region V, obtaining the Ah11Sr+4M construction. Changes on protein structure and surface characteristics were analyzed in silico. Solubility and heat-induced gelation of recombinant amaranth 11S proglobulin (Ah11Sr and Ah11Sr+4M) were compared with the native protein (Ah11Sn) purified from amaranth seed flour. The Ah11Sr+4 M showed the highest surface hydrophobicity, but as consequence the solubility was reduced. At low ionic strength (μ = 0.2) and acidic pH (<4.1), the recombinant proteins Ah11Sr and Ah11Sr+4 M had the highest and lowest solubility values, respectively. All globulins samples formed gels at 90 °C and low ionic strength, but Ah11Sn produced the weakest and Ah11Sr the strongest gels. Differential scanning calorimetry analysis under gel forming conditions revealed only exothermic transitions for all amaranth 11S globulins analyzed. In conclusion, the 3D structure analysis has revealed interesting molecular features that could explain the thermal resistance and gel forming ability of amaranth 11S globulins. The incorporation of four continuous methionines in amaranth increased the hydrophobicity, and self-supporting gels formed had intermediate hardness between Ah11Sn and Ah11Sr. These functional properties could be used in the food industry for the development of new products based on amaranth proteins.