Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus?

The determination of a protein''s folding nucleus, i.e. a set of native contacts playing an important role during its folding process, remains an elusive yet essential problem in biochemistry. In this work, we investigate the mechanical properties of 70 protein structures belonging to 14 protein families presenting various folds using coarse-grain Brownian dynamics simulations. The resulting rigidity profiles combined with multiple sequence alignments show that a limited set of rigid residues, which we call the consensus nucleus, occupy conserved positions along the protein sequence. These residues'' side chains form a tight interaction network within the protein''s core, thus making our consensus nuclei potential folding nuclei. A review of experimental and theoretical literature shows that most (above 80%) of these residues were indeed identified as folding nucleus member in earlier studies.     

Physical Stability of Octenyl Succinate–Modified Polysaccharides and Whey Proteins for Potential Use as Bioactive Carriers in Food Systems

The high cost and potential toxicity of biodegradable polymers like poly(lactic‐co‐glycolic)acid (PLGA) has increased the interest in natural and modified biopolymers as bioactive carriers. This study characterized the physical stability (water sorption and state transition behavior) of selected starch and proteins: octenyl succinate–modified depolymerized waxy corn starch (DWxCn), waxy rice starch (DWxRc), phytoglycogen, whey protein concentrate (80%, WPC), whey protein isolate (WPI), and α‐lactalbumin (α‐L) to determine their potential as carriers of bioactive compounds under different environmental conditions. After enzyme modification and particle size characterization, glass transition temperature and moisture isotherms were used to characterize the systems. DWxCn and DWxRc had increased water sorption compared to native starch. The level of octenyl succinate anhydrate (OSA) modification (3% and 7%) did not reduce the water sorption of the DWxCn and phytoglycogen samples. The Guggenheim–Andersen–de Boer model indicated that native waxy corn had significantly (P < 0.05) higher water monolayer capacity followed by 3%‐OSA‐modified DWxCn, WPI, 3%‐OSA‐modified DWxRc, α‐L, and native phytoglycogen. WPC had significantly lower water monolayer capacity. All Tg values matched with the solid‐like appearance of the biopolymers. Native polysaccharides and whey proteins had higher glass transition temperature (Tg) values. On the other hand, depolymerized waxy starches at 7%‐OSA modification had a “melted” appearance when exposed to environments with high relative humidity (above 70%) after 10 days at 23 °C. The use of depolymerized and OSA‐modified polysaccharides blended with proteins created more stable blends of biopolymers. Hence, this biopolymer would be suitable for materials exposed to high humidity environments in food applications.     

Effect of select parameters on the properties of edible film from water-soluble fish proteins in surimi wash-water

Edible film from water-soluble fish proteins were developed by casting film solution on leveled trays and effects of pH (9.5, 10.0 and 10.5), heating temperature (60, 70 and 80 °C), and heating time (10, 20 and 30 min) of the film solution on various film properties were determined using Response Surface Methodology (RSM). The impact of pH and heating temperature of film solution was more significant, overall, on the film's properties than heating time. Contour plots of tensile strength and elongation at break was highest at pH of 10.0 at 70 °C (2.75-3.02 MPa) but low in elongation at break (6.35-9.16%), while water vapor permeability and oxygen permeability were at their lowest (58.55-65.96 g mm/m² d kPa and 351.33-624.18 cm³ μm/m² d kPa). There was a direct correlation between the films’ and proteins’ solubility on one hand, and heating temperature of film solution on the other, which reversed with change in pH of film solution. Film color was darker and more yellowish with increase in the pH of film solution.     

Effects of genotype and treatment on the antioxidant activity of sweet potato in Taiwan

Six genotypes of sweet potato commercially available in Taiwan, including TNG57, TNG66, TNG68, TYY1, RP and WP, were used as samples in this study of the effects of steaming and kneading with pre-steaming treatments on the antioxidant components and antioxidant properties of methanolic extracts. Steam treatment increased the total phenols contents of all genotypes (2–13 times), flavonoids content of RP (1.3 times) and anthocyanins contents of RP and WP (5–6 times). Steam treatment also increased the reducing power and scavenging DPPH radical effect of sweet potato flours. For the methanolic extracts of steamed and kneaded flours, reducing powers were 0.02–1.70 at 5.0 mg ml⁻¹ and the scavenging effects on DPPH radicals were 19–92% at 2.5 mg ml⁻¹. Both showed the order of RP > WP > TYY1 and TNG66 > TNG57 and TNG68. However, the chelating effect of the six genotypes at 1.0 mg ml⁻¹ ranged from 50% to 73%. Contents of total phenols, flavonoids, and anthocyanins of sweet potato flours were significantly positively correlated with the reducing power and scavenging DPPH radical effects. After steaming and kneading treatments, RP showed the highest increase in the contents of total phenols, flavonoids and anthocyanins among the six genotypes studied.     

抗真菌蛋白Rs-AFP2基因定点突变及其对大肠杆菌中表达的影响

为了研究遗传密码子对表达调控的影响,利用PCR重叠延伸法,对萝卜抗真菌蛋白Rs-AFP2基因编码序列区的部分核苷酸进行沉默突变,构建突变体Rs-AFPm.序列分析表明,PCR产物全长240bp,有一个阅读框,编码的蛋白由29个氨基酸的信号肽和51个氨基酸的抗真菌蛋白组成.突变体与突变前的Rs-AFP2基因相比,在编码区第3号氨基酸Lys相差一个碱基(TTG→TTA),第5号氨基酸Gln相差一个碱基(CAG→CAA),第6号稀有密码子Arg相差两个碱基(CAG→CGA).重新合成引物,将切除信号肽的Rs-AFP2基因和Rs-AFPm基因与原核表达载体pET-21b(+)分别重组到大肠杆菌BL21菌株.IPTG诱导后,二者均得到了表达.软件分析显示,突变前pETAFPo表达产物占全菌蛋白的3%,突变后pETAFPm的表达产物占全菌蛋白含量的8%;表达蛋白主要以包涵体的形式存在,包涵体经超声波破碎后,蛋白质复性,抑菌结果表明,pETAFPm表达产物的抑菌半径大于pETAFP2表达产物的抑菌半径.这些都说明改造后的Rs-AFPm基因与Rs-AFP2基因相比,已有效地提高表达量.     

Insertional re-activation of a chloramphenicol acetyltransferase misfolding mutant protein

The deletion of nine residues from the C-terminus of the bacterialchloramphenicol acetyltransferase (CAT) results in depositionof the mutant protein in cytoplasmic inclusion bodies and lossof chloramphenicol resistance in Escherichia coli. This foldingdefect is relieved by C-terminal fusion of the polypeptide withas few as two residues. Based on these observations, efficientpositive selection for the cloning of DNA fragments has beendemonstrated. The cloning vector encodes a C-terminally truncatedCAT protein. Restriction sites in front of the stop codon allowthe insertion of target DNA, resulting in the production ofproperly folded CAT fusion proteins and regained chloramphenicolresistance. The positive selection of recombinants is accomplishedby growth of transformants on chloramphenicol-containing agarplates. The method appears particularly convenient for the cloningof DNA fragments amplified by the PCR because minimal informationto restore CAT folding can be included in the primers. The cloningof random sequences shows that the folding defect can be relievedby fusion to a wide variety of peptides, providing great flexibilityto the positive selection system. This vector may also contributeto the determination of the role of the C-terminus in CAT folding.     

Investigation of the use of ram horn hydrolysate for fungal protein production

Production of the fungus Aspergillus niger NRRL 330 was studied in submerged fermentation with ram horn hydrolysate (RHH) as substrate. The characteristics of RHH have been reported previously. The RHH was enriched by addition of glucose and KH₂PO₄. The effects of kinetic parameters on the biomass yield of the fungus were investigated. The optimal conditions for growth of A niger on RHH were initial pH 6.5, temperature 30 °C, fermentation time 96 h and agitation speed 150 rpm. Under these optimal conditions the initial carbohydrate content of RHH was reduced from 1.52 to 0.2% and the biomass yield was 8.9 g l^?1. The biomass contained about 48.1% protein, 5.2% fat and 9.4% ash (on a dry weight basis). The amino acid content of the biomass was compared with Food and Agricultural Organisation (FAO) and animal feed standards. The protein produced contained all the essential amino acids for animal feed, but the amounts of these amino acids were somewhat lower than those of FAO and soybean reference protein. However, the amino acid composition of the biomass was better than that of animal feed. The results with RHH were also compared with previously reported data on fungal mycelium grown on waste liquor substrate. In conclusion, it was found that RHH could be used as a substrate in the production of fungal protein for use as animal feed. Copyright © 2003 Society of Chemical Industry     

Protein Extraction from Heat-stabilized Defatted Rice Bran: II. The Role of Amylase, Celluclast, and Viscozyme

ABSTRACT: The effectiveness of 3 carbohydrases for protein extraction from heat-stabilized defatted rice bran (HDRB) was evaluated. Amylase, viscozyme and celluclast extracted a maximum of 45.4, 12.1, and 28.5% protein, respectively. Further study showed that extracted protein ranged from 9.5 to 58.4% under conditions of water to bran ratio (5:1 to 20:1), α-amylase (0 to 110000 units/10 g rice bran), temperature (35 to 55 °C), and time (1 to 8 h). The maximum protein extracted was 58.4% with a water to bran ratio of 17:1, 87637 units amylase, and 50.9 °C. These results suggest that impure food-grade amylase containing protease is more effective than celluclast and viscozyme in protein extraction from HDRB.