SoyProDB: A database for the identification of soybean seed proteins

Soybean continues to serve as a rich and inexpensive source of protein for humans and animals. A substantial amount of information has been reported on the genotypic variation and beneficial genetic manipulation of soybeans. For better understanding of the consequences of genetic manipulation, elucidation of soybean protein composition is necessary, because of its direct relationship to phenotype. We have conducted studies to determine the composition of storage, allergen and anti-nutritional proteins in cultivated soybean using a combined proteomics approach. Two-dimensional polyacrylamide gel electrophoresis (2DPAGE) was implemented for the separation of proteins along with matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and liquid chromatography mass spectrometry (LC-MS/MS) for the identification of proteins. Our analysis resulted in the identification of several proteins, and a web based database named soybean protein database (SoyProDB) was subsequently built to house and allow scientists to search the data. This database will be useful to scientists who wish to genetically alter soybean with higher quality storage proteins, and also helpful for consumers to get a greater understanding about proteins that compose soy products available in the market. The database is freely accessible.

Availability

http://bioinformatics.towson.edu/Soybean_Seed_Proteins_2D_Gel_DB/Home.aspx     

Purification of the two major proteins from whey concentrate using a cation‐exchange selective adsorption process

The packed‐bed adsorption and elution of aqueous solutions of whey concentrate powders were investigated at pH 3.7 using a 5‐mL SP Sepharose FF column to separate and isolate two major proteins namely, α‐lactalbumin (ALA) and β‐lactoglobulin (BLG) from these solutions. ALA displaced and eluted BLG from the column in a pure form. Pure ALA could then be eluted with good recovery. A novel consecutive two‐stage separation process was developed to separate ALA and BLG from whey concentrate mixtures. Almost all of the BLG in the feed was recovered, with 78% being recovered at 95% purity and a further 20% at 86% purity. In addition, 67% of ALA was recovered, 48% at 54% purity and 19% at 60% purity. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Improvement of covalent immobilization procedure of β‐galactosidase from Kluyveromyces lactis for galactooligosaccharides production: Modeling and kinetic study

Galactooligosaccharides (GOS) are prebiotics produced from lactose through an enzymatic reaction. Employing an immobilized enzyme may result in cost reductions; however, the changes in its kinetics due to immobilization has not been studied. This study experimentally determined the optimal reaction conditions for the production of GOS from lactose by β‐galactosidase (EC 3.2.1.23) from Kluyveromyces lactis covalently immobilized to a polysiloxane‐polyvinyl alcohol (POS‐PVA) polymer activated with glutaraldehyde (GA), and to study the transgalactosylation kinetics. Yield immobilization was 99 ± 1.1% with 78.5 ± 2.4% enzyme activity recovery. An experimental design 24 with 1 center point and 2 replicates was used. Factors were lactose [L], enzyme concentration [E], pH and temperature (T). Response variables were glucose and galactose as monosaccharides [G1], residual lactose [Lac]r and GOS as disaccharides [G2] and trisaccharides [G3]. Best conditions were pH 7.1, 40 °C, 270 gL^?1 initial lactose concentration and 6 U mL^?1 enzyme concentration, obtaining 25.46 ± 0.01 gL^?1 yield of trisaccharides. Although below the HPLC‐IR detection limit, tetrasaccharides were also identified after 115 min of reaction. The immobilization protocol was then optimized by diminishing total reactant volumes : support ratio, resulting in improved enzyme activity synthesizing 43.53 ± 0.02 gL^?1 of trisaccharides and 13.79 ± 0.21 gL^?1 of tetrasaccharides, and after four cycles remaining relative activity was 94%. A reaction mechanism was proposed through which a mathematical model was developed and rate constants were estimated, considering a pseudo steady‐state hypothesis for two concomitant reactions, and from this simplified analysis, the reaction yield could eventually be improved. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1568–1578, 2017     

Selection and structural analysis of de novo proteins from an α3β3 genetic library

The construction of novel functional proteins has been a key area of protein engineering. However, there are few reports of functional proteins constructed from artificial scaffolds. Here, we have constructed a genetic library encoding α3β3 de novo proteins to generate novel scaffolds in smaller size using a binary combination of simplified hydrophobic and hydrophilic amino acid sets. To screen for folded de novo proteins, we used a GFP‐based screening system and successfully obtained the proteins from the colonies emitting the very bright fluorescence as a similar intensity of GFP. Proteins isolated from the very bright colonies (vTAJ) and bright colonies (wTAJ) were analyzed by circular dichroism (CD), 8‐anilino‐1‐naphthalenesulfonate (ANS) binding assay, and analytical size‐exclusion chromatography (SEC). CD studies revealed that vTAJ and wTAJ proteins had both α‐helix and β‐sheet structures with thermal stabilities. Moreover, the selected proteins demonstrated a variety of association states existing as monomer, dimer, and oligomer formation. The SEC and ANS binding assays revealed that vTAJ proteins tend to be a characteristic of the folded protein, but not in a molten‐globule state. A vTAJ protein, vTAJ13, which has a packed globular structure and exists as a monomer, was further analyzed by nuclear magnetic resonance. NOE connectivities between backbone signals of vTAJ13 suggested that the protein contains three α‐helices and three β‐strands as intended by its design. Thus, it would appear that artificially generated α3β3 de novo proteins isolated from very bright colonies using the GFP fusion system exhibit excellent properties similar to folded proteins and would be available as artificial scaffolds to generate functional proteins with catalytic and ligand binding properties.     

Ecological immunity of human milk: Life history perspectives from the United States and Kenya

Objectives

Previous research has established population variation in anti‐inflammatory immunological biomarkers in human milk. This immunity is potentially ecology‐dependent and may alter the life history trade‐off between growth and maintenance in infants. The current study has two aims: (1) to assess the ecological differences in milk immunity in two populations, one from the urban U.S. and one from rural Kenya; and (2) to test the hypothesis that milk immunity can affect infant growth indicators.

Materials and Methods

Kenyan Ariaal (n = 233) and U.S. (n = 75) breastfeeding mother‐infant pairs participated in a cross‐sectional study at two separate field sites. Laboratory analysis was performed on milk for the anti‐inflammatory biomarkers TGF‐β2, sTNF‐αRI, sTNF‐αRII, and IL‐1ra using ELISA. Multiple imputation was used to extrapolate data below the limit of detection before multivariate analysis.

Results

There were significant differences between U.S. and Kenyan mothers on all four milk biomarkers, with Kenyan mothers having significantly higher sTNF‐αRI and sTNF‐αRII and lower TGF‐β2 and IL‐1ra than U.S. mothers. U.S. mothers with higher milk TGF‐β2 and IL‐1ra have infants that are significantly longer and heavier for their age, while Kenyan mothers with higher sTNF‐αRI have significantly longer and heavier infants for their age, and those with higher TGF‐β2 have marginally significantly longer infants.

Discussion

There were significant differences in ecological milk immunity between U.S. and Kenyan mothers. These differences potentially play a role in the growth of their infants. Further research in milk immunity should consider the possibility of shared maternal–infant life histories.

     

Redesigning the type II' β‐turn in green fluorescent protein to type I': Implications for folding kinetics and stability

Both Type I' and Type II' β‐turns have the same sense of the β‐turn twist that is compatible with the β‐sheet twist. They occur predominantly in two residue β‐hairpins, but the occurrence of Type I' β‐turns is two times higher than Type II' β‐turns. This suggests that Type I' β‐turns may be more stable than Type II' β‐turns, and Type I' β‐turn sequence and structure can be more favorable for protein folding than Type II' β‐turns. Here, we redesigned the native Type II' β‐turn in GFP to Type I' β‐turn, and investigated its effect on protein folding and stability. The Type I' β‐turns were designed based on the statistical analysis of residues in natural Type I' β‐turns. The substitution of the native “GD” sequence of i+1 and i+2 residues with Type I' preferred “(N/D)G” sequence motif increased the folding rate by 50% and slightly improved the thermodynamic stability. Despite the enhancement of in vitro refolding kinetics and stability of the redesigned mutants, they showed poor soluble expression level compared to wild type. To overcome this problem, i and i + 3 residues of the designed Type I' β‐turn were further engineered. The mutation of Thr to Lys at i + 3 could restore the in vivo soluble expression of the Type I' mutant. This study indicates that Type II' β‐turns in natural β‐hairpins can be further optimized by converting the sequence to Type I'. Proteins 2014; 82:2812–2822. © 2014 Wiley Periodicals, Inc.     

Development and application of a simple,rapid and sensitive method for detecting moderately carbendazim‐resistant isolates in Botrytis cinerea

Sustainable disease management depends on the ability to monitor the development of fungicide resistance in pathogen populations. A point mutation resulting in an alteration (F200Y) at codon 200 of the target protein β‐tubulin leads to a moderate level of resistance to carbendazim in Botrytis cinerea. Although traditional methods remain a cornerstone in detection of fungicide resistance, molecular methods that do not require the isolation of pathogens, can detect the presence of resistance alleles at low frequencies, and require less time and labour than traditional methods. In this study, we present an efficient, rapid, and highly specific method for detecting the moderately carbendazim‐resistant isolates in B. cinerea based on loop‐mediated isothermal amplification (LAMP). By using specific LAMP primers, we detected the resistance‐conferring mutation underlying β‐tubulin F200Y. The concentrations of LAMP components and LAMP parameters were optimised, resulting in reaction temperatures and times of 61–65°C and 45 min, respectively. The feasibility of the LAMP assay was verified by assaying the diseased samples with artificial inoculation in the different hosts. The LAMP assay developed in the current study was specific, stable, repeatable and sensitive, and was successfully applied for detection of moderately carbendazim‐resistant isolates of B. cinerea in plant samples.     

Charged cyclodextrin-mediated sample stacking in micellar capillary electrophoresis: A simple method for enhancing the detection sensitivity of hydrophobic compounds

The development of on-line sample stacking techniques for enhancing limits of detection of neutral analytes in micellar capillary electrophoresis (MCE) has recently gained much attention. Utilizing high-conductivity sample matrices to invoke sample stacking is promising, but requires the limited use of sample solubilizing agents such as alcohols in the sample matrix. In this study, we show how simple replacement of the sample solvent (methanol) with a solution of sulfated β-cyclodextrin (sβ-CD) allows a significant increase in the sensitivity of detection of model hydrophobic analytes. This increase in sensitivity is accompanied by significant peak sharpening. Sulfated CDs in the sample matrix allow for effective solubilization of hydrophobic analytes without the use of organic solvents such as methanol. The testing of various sample matrix sβ-CD concentrations for their effect on peak sharpening identified 3 to 5% as optimal for the estrogen standards. The use of a sβ-CD sample matrix allowed for hydrostatic injections (3.5 kPa) of 297 s, compared with 4 s when the analytes were dissolved in methanol. A mechanism explaining the sβ-CD-induced effect involves an analyte transfer mechanism where the sβ-CDs, despite providing anodic mobility to analytes in the sample zone, are able to transfer analytes to trailing separation buffer micelles for “recycling” back into the sample zone without compromising the stacking process. The overall improvement in sensitivity allows detection of estrogens in the parts-per-billion range and stands to improve the utility of MCE as a bioanalytical technique.     

The role of proline‐containing peptide triads in β‐sheet formation: A kinetic study

The design of biomimetic materials through molecular self‐assembly is a growing area of modern nanotechnology. With problems of protein folding, self‐assembly, and sequence–structure relationships as essential in nanotechnology as in biology, the effect of the nucleation of β‐hairpin formation by proline on the folding process has been investigated in model studies. Previously such studies were limited to investigations of the influence of proline on the formation of turns in short peptide sequences. The effect of proline‐based triads on the folding of an 11‐kDa amyloidogenic peptide GH₆[(GA)₃GY(GA)₃GE]₈GAH₆ ( YE8 ) was investigated by selective substitution of the proline‐substituted triads at the γ‐turn sites. The folding and fibrillation of the singly proline‐substituted polypeptides, e.g., GH6? [(GA)3GY(GA)3GE]7(GA)3GY(GA)3PD? GAH6 ( 8PD ), and doubly proline‐substituted polypeptides, e.g., GH6? [(GA)3GY(GA)3GE]3(GA)3GY(GA)3PD[(GA)3GY(GA)3GE]3(GA)3GY(GA)3PD? GAH6 ( 4,8PD ), were directly monitored by circular dichroism and deep UV resonance Raman and fluorescence spectroscopies. These findings were used to identify the essential folding domains, i.e., the minimum number of β‐strands necessary for stable folding. These experimental findings may be especially useful in the design and construction of peptidic materials for a wide range of applications as well as in understanding the mechanisms of folding critical to fibril formation. © 2015 Wiley Periodicals, Inc. Biopolymers 103: 339–350, 2015.     

Isolation of alpha-lactalbumin,beta-lactoglobulin,and bovine serum albumin from cow's milk using gel filtration and anion-exchange chromatography including evaluation of their antigenicity

The aim of this study was to introduce a simple, reproducible, and less expensive method for isolation of alpha-lactalbumin, beta-lactoglobulin, and bovine serum albumin from cow's milk while retaining their antigenicity. Whey (lactoserum) was obtained by isolating casein from defatted milk using hydrochloric acid. Globulins were then precipitated from whey by half-saturated ammonium sulfate and beta-lactoglobulin was purified further using Sephadex G-50 gel filtration. The proteins in the supernatant were also fractionated using diethylaminoethyl cellulose chromatography in which beta-lactoglobulin was separated from alpha-lactalbumin and bovine serum albumin. The latter two proteins that co-eluted in anion-exchange chromatography were then gently isolated from each other by Sephadex G-50 gel filtration. Pure beta-lactoglobulin was also obtained by anion-exchange chromatography of the ammonium sulfate-precipitated globulins. Using enzyme-linked immunosorbent assay (ELISA), Western blotting, and ELISA inhibition assay, antigenicity of the purified proteins was evaluated. Our results showed high purity and well-preserved antigenicity of alpha-lactalbumin, beta-lactoglobulin, and bovine serum albumin thus purified.     

Glycine betaine: A widely reported osmolyte induces differential and selective conformational stability and enhances aggregation in some proteins in the presence of surfactants

In this study, we extensively report the effect of glycine betaine during the refolding of partially folded bovine α‐lactalbumin (α‐LA) in presence of hexadecyl trimethyl ammonium bromide (HTAB), and Ribonuclease A (RNAse A) in presence of sodium dodecyl sulfate (SDS) by different complementary biophysical, light scattering, and microscopic techniques. Though a substantial refolding/compaction was observed in both the studied proteins, the fluorescence studies contradicted the finding obtained from circular dichroism spectroscopy (CD) in case of α‐LA. CD stopped flow showed extensive presence of intermediates during the refolding of proteins which could potentially lead to aggregation. The aggregates as observed in dynamic light scattering (DLS), in α‐LA were massive as compared to RNAse A and was directly proportional to betaine concentration. The zeta potential confirmed that the aggregates are a direct manifestation of strong aggregating and/or immense preferential excluding tendency of GB and not because of charge neutralization; however a possible role of conformational change as observed in FTIR spectroscopy cannot be completely ruled out. In contrary though RNAse A showed a substantial refolding, the final state of the folded protein was significantly different from the native state. These findings for α‐LA and RNAse A were further supported by electron microscopic and thermodynamic studies. We thus propose that betaine has a strong macromolecular excluding tendency, primarily directed to shield the hydrophobic exposure either by refolding or aggregation, and depending on the hydrophobicity of the proteins, the functional restoration of the protein is manifested. © 2012 Wiley Periodicals, Inc. Biopolymers 97:933–949, 2012.     

Structure prediction and fold recognition for the ferrochelatase family of proteins

An α/β barrel is predicted for the three-dimensional (3D) structure of Bacillus subtilis ferrochelatase. To arrive at this structure, the THREADER program was used to find possible homologous 3D structures and to predict the secondary structure for the ferrochelatase sequence. The secondary structure was fit by hand to the selected homologous 3D structure then the MODELLER program was used to predict the fold of ferrochelatase. Molecular biological information about the conserved residues of ferrochelatase was used as the criteria to help select the homologous 3D structure used to predict the fold of ferrochelatase. Based on the predicted structure possible, ligands binding to the iron and protoporphyrin IX are discussed. The structure has been deposited in the Brookhaven database as ID 1FJI. © 1997 Wiley-Liss Inc.     

A novel β-thymosin from the sea urchin: extending the phylogenetic distribution of β-thymosins from mammals to echinoderms

The study of the phylogenetic distribution of the β-thymosin family is important to elucidate its biological function further. A new thymosin, designated as thymosin β₁₄, consisting of 40 amino acid residues and with a molecular weight of 4537 Da as determined by ion spray mass spectrometry, was isolated from the sea urchin. The N-terminus of this polypeptide is blocked by an acetyl group as found by matrix-assisted laser desorption mass spectrometric and amino acid analysis. The primary structure was elucidatd by Edman degradation of the HPLC-purified thymosin β₁₄ fragments produced by digestion with endoproteinase Asp-N and trypsin. Sequence comparison reveals that thymosin β₁₄ is 73% homologous to thymosin β₄, obtained from calf thymus. By isolating and characterising the structure of thymosin β₁₄ from the sea urchin, an invertebrate, substantial knowledge about the phylogenetic distribution and evolution of β-thymosins is gained. © 1997 European Peptide Society and John Wiley & Sons Ltd.     

Preparative isolation and purification of four flavonoids from the petals of nelumbo nucifera by high‐speed counter‐current chromatography

Introduction – Flavonoids, the primary constituents of the petals of Nelumbo nucifera, are known to have antioxidant properties and antibacterial bioactivities. However, efficient methods for the preparative isolation and purification of flavonoids from this plant are not currently available. Objective – To develop an efficient method for the preparative isolation and purification of flavonoids from the petals of N. nucifera by high‐speed counter‐current chromatography (HSCCC). Methodology – Following an initial clean‐up step on a polyamide column, HSCCC was utilised to separate and purify flavonoids. Purities and identities of the isolated compounds were established by HPLC‐PAD, ESI‐MS, ¹H‐NMR and ¹³C‐NMR. Results – The separation was performed using a two‐phase solvent system composed of ethyl acetate–methanol–water–acetic acid (4 : 1 : 5 : 0.1, by volume), in which the upper phase was used as the stationary phase and the lower phase was used as the mobile phase at a flow‐rate of 1.0 mL/min in the head‐to‐tail elution mode. Ultimately, 5.0 mg syringetin‐3‐O‐β‐d‐glucoside, 6.5 mg quercetin‐3‐O‐β‐d‐glucoside, 12.8 mg isorhamnetin‐3‐O‐β‐d‐glucoside and 32.5 mg kaempferol‐3‐O‐β‐d‐glucoside were obtained from 125 mg crude sample. Conclusion – The combination of HSCCC with a polyamide column is an efficient method for the preparative separation and purification of flavonoids from the petals of N. nucifera. Copyright © 2009 John Wiley & Sons, Ltd.     

Production and comprehensive quality control of recombinant human Interleukin-1beta: a case study for a process development strategy

We describe an efficient strategy to produce high-quality proteins by using a single large IMAC chromatography column and enzymatic His-tag removal via the TAGZyme system in pilot scale. Numerous quality assays demonstrated a high purity of the final product, the human cytokine Interleukin-1beta (IL-1beta). The protein preparation was apparently free of host cell proteins, endotoxins, protease, and aggregates. The N-terminal amino acid sequence of IL-1beta was in full agreement with the natural mature form of IL-1beta. The homogeneity of the product was further shown by X-ray structure determination which confirmed the previously solved structure of the protein. We propose the applied workflow as a strategy for industrial production of protein-based biopharmaceuticals.     

Rings and ribbons in protein structures: Characterization using helical parameters and Ramachandran plots for repeating dipeptides

Helical parameters displayed on a Ramachandran plot allow peptide structures with successive residues having identical main chain conformations to be studied. We investigate repeating dipeptide main chain conformations and present Ramachandran plots encompassing the range of possible structures. Repeating dipeptides fall into the categories: rings, ribbons, and helices. Partial rings occur in the form of “nests” and “catgrips”; many nests are bridged by an oxygen atom hydrogen bonding to the main chain NH groups of alternate residues, an interaction optimized by the ring structure of the nest. A novel recurring feature is identified that we name unpleated β, often situated at the ends of a β‐sheet strand. Some are partial rings causing the polypeptide to curve gently away from the sheet; some are straight. They lack β‐pleat and almost all incorporate a glycine. An example is the first glycine in the GxxxxGK motif of P‐loop proteins. Ribbons in repeating dipeptides can be either flat, as seen in repeated type II and type II′ β‐turns, or twisted, as in multiple type I and type I′ β‐turns. Hexa‐ and octa‐peptides in such twisted ribbons occur frequently in proteins, predominantly with type I β‐turns, and are the same as the “β‐bend ribbons” hitherto identified only in short peptides. One is seen in the GTPase‐activating protein for Rho in the active, but not the inactive, form of the enzyme. It forms a β‐bend ribbon, which incorporates the catalytic arginine, allowing its side chain guanidino group to approach the active site and enhance enzyme activity. Proteins 2014; 82:230–239. © 2013 Wiley Periodicals, Inc.     

Screening of Commercial Enzymes for Transfructosylation of Tyrosol: Effect of Process Conditions and Reaction Network

Enzymatic fructosylation of organic acceptors other than saccharides brings new possibilities to synthesize molecules that do not exist in nature. The introduction of fructosyl moiety may lead to glycosides possessing enhanced physicochemical and bioactive properties which could be useful in the pharmaceutical and cosmetic industry. In this work, the regioselective synthesis of tyrosol β‐d ‐fructofuranoside (TF) catalyzed by β‐fructofuranosidase is investigated. In the first step, 32 commercial enzyme preparations are screened for fructoside‐hydrolyzing activity. The most active preparations are subsequently examined for fructofuranosyl transfer from sucrose to tyrosol. The best candidate, Novozym 188, is chosen to study the effect of reaction conditions on the product formation in a batch reactor. The effects of substrate concentration, temperature, pH, time, and enzyme dosage on the concentration of TF produced are studied using the design of experiments methodology. The maximal product concentration of 3.8 g L^?1 is achieved for the sucrose concentration of 1.5 m , tyrosol concentration of 29 g L^?1, temperature of 41 °C, and pH 5.1. Besides the main transfructosylation reaction between sucrose and tyrosol, several side reactions take place. A reaction network includes also the formation of fructooligosaccharides and the hydrolysis of sucrose and all reaction products.