Effect of the hydrolysis method on the determination of the amino acid composition of proteins

An MCDM approach for Reverse vaccinology model to predict bacterial protective antigens

Reverse vaccinology (RV) is a significant step in sensible vaccine design. In recent years, many machine learning (ML) methods have been used to improve RV prediction accuracy. However, there are still issues with prediction accuracy and programme accessibility in ML-based RV. This paper presents a supervised ML-based method to classify bacterial protective antigens (BPAgs) and identify the model(s) that consistently perform well for the training dataset. Six ML classifiers are used for testing with physiochemical features extracted from a comprehensive training dataset. Selecting the best performing model from different performance metrics (accuracy, precision, recall, F1-score, and AUC-ROC) has not been easy, because all the metrics has the same importance to predict BPAgs. To fix this issue, we propose a soft and hard ranking model based on multi-criteria decision-making (MCDM) approach for selecting the best performing ML method that classifies BPAgs. First, our proposed model uses homologous proteins (positive and negative samples) from Protegen and Uniprot databases. Second, we applied four strategies of Synthetic Minority Oversampling Technique and Edited Nearest Neighbour (SMOTE-ENN) to handle the data imbalance problem and train the model using ML methods. Third, we consider MCDM-based technique for order preference by similarity to the ideal solution (TOPSIS) method integrated with soft and hard ranking model. The entropy is used to obtain weighted evaluation criteria for ranking the models. Our experimental evaluations show that the proposed method with best performing models (Random Forest and Extreme Gradient Boosting) outperforms compared to existing open-source RV methods using benchmark datasets.

Optimization of hydrolysis conditions of amino acid analysis for UHPLC-UV antigens content determination: Bexsero vaccine a case study

In the present study the compositional analysis of the amino acids released by the acidic hydrolysis of the vaccine antigens was approached as an alternative to the dye-binding methods, for improvement of the quality control. In particular, the Analytical Quality by Design principles were undertaken in optimizing the hydrolysis conditions of the antigens to be applied prior to the quantitation by UHPLC-UV. Bexsero was used as a case study; it is a recombinant meningococcal B vaccine and one of its critical quality attributes is the content of the three core protein antigens, namely Neisseria Heparin Binding Antigen, factor H binding protein and Neisseria adhesin A, in the final formulation. Conventionally, the proteins quantitation is carried out by dye-binding assays. Analytical Target Profile was defined as the accurate determination of amounts of the Bexsero antigens. The Critical Method Parameters were chosen by means of the cause-effect matrix. A Face Centered Design was used to select the experiments to investigate the process and finally a Method Operable Design Region with a risk of failure of 5% was defined. The selected working point for routine use was: hydrolysis time, 17 hrs; temperature, 112 °C; 6 M HCl volume, 300 µl; antioxidant 90% phenol volume, 5 µl.

Evaluation of different isotope dilution mass spectrometry strategies for the characterization of naturally abundant and isotopically labelled peptide standards

Natural abundance and isotopically labelled tryptic peptides are routinely employed as standards in quantitative proteomics. The certification of the peptide content is usually carried out by amino acid analysis using isotope dilution mass spectrometry (IDMS) after the acid hydrolysis of the peptide. For the validation and traceability of the amino acid analysis procedure, expensive certified peptides must be employed. In this work we evaluate different IDMS alternatives which will reduce the amount of certified peptide required for validation of the amino acid analysis procedure. In this context, the characterization of both natural and isotopically labelled synthetic angiotensin I peptides was carried out. First, we applied a fast procedure for peptide hydrolysis based on microwave-assisted digestion and employed two certified peptide reference materials SRM 998 angiotensin I and CRM 6901-b C-peptide for validation of the hydrolysis procedure. The amino acids proline, leucine, isoleucine, valine, tyrosine, arginine and phenylalanine were evaluated for their suitability for peptide certification by IDMS by both liquid chromatography with tandem mass spectrometry (LC-MS/MS) and gas chromatography with mass spectrometry (GC)-MS/MS. Then, natural angiotensin I and 13C1-labelled angiotensin I were synthesized in-house and purified by preparative liquid chromatography. The concentration of the 13C1-labelled angiotensin I peptide was established by reverse IDMS in its native form using SRM 998 angiotensin I as reference. The concentration of the natural synthesized peptide was determined by IDMS both using the 13C1-labelled peptide in its native form and by amino acid analysis showing comparable results. Finally, the synthetic naturally abundant angiotensin I peptide was employed as "in-house" standard for the validation of subsequent peptide characterization procedures. Therefore, the novelty of this work relies on, first, the development of a faster hydrolysis procedure assisted by focused microwaves, providing complete hydrolysis in 150 min, and secondly, a validation strategy combining GC-MS and LC-MS/MS that allowed us to certify the purity of an in-house-synthesized peptide standard that can be employed as quality control in further experiments.

Molecular Hydrogen Improves Rice Storage Quality via Alleviating Lipid Deterioration and Maintaining Nutritional Values

Improvement of the storage quality of rice is a critical challenge for the scientific community. This study assesses the effects of the irrigation with hydrogen nanobubble water (HNW) on the storage quality of rice (Oryza sativa 'Huruan1212'). Compared with ditch water control, after one year of storage at 25 °C and 70% RH, the HNW-irrigated rice had higher contents of essential amino acids, especially lysine. Importantly, the generation of off-flavors in the stored rice was significantly decreased, which was confirmed by the lower levels of volatile substances, including pentanal, hexanal, heptanal, octanal, 1-octen-3-ol, and 2-heptanone. The subsequent results showed that the HNW-irrigated rice not only retained lower levels of free fatty acid values, but also had increased antioxidant capacity and decreased lipoxygenase activity and transcripts, thus resulting in decreased lipid peroxidation. This study opens a new window for the practical application of HNW irrigation in the production and subsequent storage of crops.

Determination of amino acids in food and feed by microwave hydrolysis and UHPLC-MS/MS

The determination of amino acids in food and feed by chromatography has a long history and is described in several official methods, including standards from ISO, AOAC, and the European Commission (EC) regulation 152/2009. The procedure usually consists of labor- and time-consuming preparation techniques and ion-exchange chromatography with challenging chromatographic conditions. Consequently, several approaches have been published to overcome these drawbacks but the knowledge about their suitability for complex matrices such as food and feed is limited. In this paper, we describe the development of two new methods to determine amino acids in food and feed. These methods involve microwave hydrolysis and reversed-phase UHPLC-MS/MS with pre-column derivatization using 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC). Both methods provide streamlined sample preparations and a dramatic reduction in analysis time while offering a high degree of specificity and selectivity. Selectivity also enabled the simultaneous determination of the more uncommon substances hydroxyproline, hydroxylysine, taurine, ornithine, and γ-amino butyric acid (GABA) along with amino acids typically present in food and feed. The results were all satisfactory with regards to sensitivity, accuracy, precision, and comparability with laboratories that use other methods, for example from ISO, AOAC, or regulation (EC) 152/2009. We therefore concluded that both methods provide a reliable and modern approach to overcome many of the drawbacks that occur with the conventional standard methods.

In silico comparative structural and compositional analysis of glycoproteins of RSV to study the nature of stability and transmissibility of RSV A

The current scenario of COVID-19 makes us to think about the devastating diseases that kill so many people every year. Analysis of viral proteins contributes many things that are utterly useful in the evolution of therapeutic drugs and vaccines. In this study, sequence and structure of fusion glycoproteins and major surface glycoproteins of respiratory syncytial virus (RSV) were analysed to reveal the stability and transmission rate. RSV A has the highest abundance of aromatic residues. The Kyte-Doolittle scale indicates the hydrophilic nature of RSV A protein which leads to the higher transmission rate of this virus. Intra-protein interactions such as carbonyl interactions, cation-pi, and salt bridges were shown to be greater in RSV A compared to RSV B, which might lead to improved stability. This study discovered the presence of a network aromatic-sulphur interaction in viral proteins. Analysis of ligand binding pocket of RSV proteins indicated that drugs are performing better on RSV B than RSV A. It was also shown that increasing the number of tunnels in RSV A proteins boosts catalytic activity. This study will be helpful in drug discovery and vaccine development.

Quail (Coturnix japonica) egg attenuated 2-butoxyethanol-induced enzymatic dysregulation, disseminated thrombosis and hemolytic impairment in female wistar rats

Influence of quail egg on pathologies has increased research interests and series of investigations are currently being done on its influence against these pathologies. The influence of quail egg against 2-butoxyethanol induced hemolysis and disseminated thrombosis was investigated to determine the enzymatic regulations that ensue in the amelioration of deleterious hemolytic and disseminated thrombosis displayed in female Wistar rats. Quail egg was separated into three (3) components (extracts)-quail egg yolk water soluble (QYWS) and fat soluble (QYFS), and albumen extract (QA) and the inorganic and organic compositions were characterized. Depranocytotic assaults was achieved by 250 mg/kg of 2-Butoxyethanol administered for 4 days, the clinical observation revealed a dark purple-red discoloration on the distal tails of the rats and therapeutic applications followed with 1000 mg/kg BWT of QYWS, QYFS and QA, and 15 mg/kg BWT of hydroxyurea. Morphological evaluation, haematological estimations and biochemical evaluations of the influence on the activities of sphingosine kinase-1, RNase, red cell carbonic anhydrase, lactate dehydrogenase, glutathione peroxidase and caspase-3, vis a vis the concentrations of sphingosine-1 phosphate, selenium and zinc (plasma and urine). In vitro anti-inflammatory influence of quail egg components were investigated against hemolysis and key enzymes of inflammation-cycloxygenase, lipoxygenase and β-glucuronidase. The in vitro anti-inflammatory effects of QYWS, QYFS and QA were concentration dependent from 200 to 800 μg/ml against hemolysis and the key enzymes of inflammation. The characterization of inorganic and organic bioactive composition of the yolk and albumen revealed the presence of folic acid, cobalamin, pyridine, riboflavin, ascorbic acid as well as vitamins D and E, selenium, zinc, iron and calcium. These had reflected in the attenuation of the induced hemolytic and disseminated thrombosis by regulations of enzymes linked to the infarction, apoptosis and oxidative stress characterized in sickle cell index.

A chiral GC-MS method for analysis of secondary amino acids after heptafluorobutyl chloroformate & methylamine derivatization

L-amino acids (L-AAs) play different important roles in the physiology of all living organisms. Their chiral counterparts, D-amino acids (D-AAs) are increasingly being recognized as essential molecules in many biological systems. Secondary amino acids with cyclic structures, such as prolines, exhibit conformational rigidity and thus unique properties in the structural and protein folding. Despite their widespread occurrence, much less attention was paid to their chiral analysis, particularly when the minor, typically D-enantiomer, is present in low amounts in a complex biological matrix. In this paper, a cost-effective, chiral GC-MS method is described for capillary Chirasil-L-Val separation of nine cyclic secondary amino acid enantiomers with four-, five-, and six-membered rings, involving azetidine-2-carboxylic acid, pipecolic acid, nipecotic acid, proline, isomeric cis/trans 3-hydroxy, 4-hydroxyproline, and cis/trans-5-hydroxy-L-pipecolic acid in the excess of its enantiomeric antipode. The sample preparation involves in-situ derivatization with heptafluorobutyl chloroformate, simultaneous liquid-liquid micro-extraction into isooctane followed by amidation of the arising low-polar derivatives with methylamine, an evaporation step, re-dissolution, and final GC-MS analysis. The developed method was used for analyses of human biofluids, biologically active peptides containing chiral proline constituents, and collagen.

Robust Analytical Methods for the Accurate Quantification of the Total Biomass Composition of Mammalian Cells

Biomass composition is an important input for genome-scale metabolic models and has a big impact on their predictive capabilities. However, researchers often rely on generic data for biomass composition, e.g. collected from similar organisms. This leads to inaccurate predictions, because biomass composition varies between different cell lines, conditions, and growth phases. In this chapter we present protocols for the determination of the biomass composition of Chinese Hamster Ovary (CHO) cells. These methods can easily be adapted to other types of mammalian cells. The protocols include the quantification of cell dry mass and of the main biomass components, namely protein, lipid, DNA, RNA, and carbohydrates. Cell dry mass is determined gravimetrically by weighing a defined number of cells. Amino acid composition and protein content are measured by gas chromatography mass spectrometry. Lipids are quantified by shotgun mass spectrometry, which provides quantities for the different lipid classes and also the distribution of fatty acids. RNA is purified and then quantified spectrophotometrically. The methods for DNA and carbohydrates are simple fluorometric and colorimetric assays adapted to a 96-well plate format. To ensure quantitative results, internal standards or spike-in controls are used in all methods, e.g. to account for possible matrix effects or loss of material. Finally, the last section provides a guide on how to convert the measured data into biomass equations, which can then be integrated into a metabolic model.

Accurate and efficient amino acid analysis for protein quantification using hydrophilic interaction chromatography coupled tandem mass spectrometry

BACKGROUND

Methods used to quantify protein from biological samples are often inaccurate with significant variability that requires care to minimize. The errors result from losses during protein preparation and purification and false detection of interfering compounds or elements. Amino acid analysis (AAA) involves a series of chromatographic techniques that can be used to measure protein levels, avoiding some difficulties and providing specific compositional information. However, unstable derivatives, that are toxic and can be costly, incomplete reactions, inadequate chromatographic separations, and the lack of a single hydrolysis method with sufficient recovery of all amino acids hinder precise protein quantitation using AAA.

RESULTS

In this study, a hydrophilic interaction chromatography based method was used to separate all proteinogenic amino acids, including isobaric compounds leucine and isoleucine, prior to detection by multiple reaction monitoring with LC-MS/MS. Through inclusion of commercially available isotopically labeled (13C, 15N) amino acids as internal standards we adapted an isotopic dilution strategy for amino acid-based quantification of proteins. Three hydrolysis methods were tested with ubiquitin, bovine serum albumin, (BSA), and a soy protein biological reference material (SRM 3234; NIST) resulting in protein estimates that were 86-103%, 82-94%, and 90-99% accurate for the three protein samples respectively. The methane sulfonic acid hydrolysis approach provided the best recovery of labile amino acids including: cysteine, methionine and tryptophan that are challenging to accurately quantify.

CONCLUSIONS

Accurate determination of protein quantity and amino acid composition in heterogeneous biological samples is non-trivial. Recent advances in chromatographic phases and LC-MS/MS based methods, along with the availability of isotopic standards can minimize difficulties in analysis and improve protein quantitation. A robust method is described for high-throughput protein quantification and amino acid compositional analysis. Since accurate measurement of protein quality and quantity are a requirement for many biological studies that relate to crop improvement or more generally, our understanding of metabolism in living systems, we envision this method will have broad applicability.

Reduction of β-ODAP and IP6 contents in Lathyrus sativus L. seed by high hydrostatic pressure

Grass pea (Lathyrus sativus L.) seeds contain an endogenous neurotoxic non-proteinogenic amino acid, β-N-oxalyl-l-α,β-diaminopropionic acid (β-ODAP), a major limiting factor-for their human consumption. Furthermore, phytate (IP₆), a well-known antinutrient is present in concentration capable of hindering bioavailability of iron (Fe), zinc (Zn), calcium (Ca), phosphorus (P) and other micronutrients from the seeds. Due to the reported capability of high hydrostatic pressure (HHP) to reduce the content of certain antinutritional/toxic agents in seeds and grains, the impact of HHP on the reduction of β-ODAP and IP₆ were investigated. The contents of β-ODAP of accessions from different regions in Ethiopia were found to be in the range of 51.94 to 806.52 mg/100 g. Accession (GF₁- Alemu, AK) exhibiting the highest β-ODAP content was selected for HHP treatment in soaked and batter forms using Central Composite Face Centered Design of experiments. The best HHP conditions in respect to β-ODAP reduction were also applied to the accession (GP-240038) with the lowest β-ODAP-content, a genetically improved variety (Wassie) and a variety from Germany (GR). The HHP treatment at 600 MPa for 25 min of seeds soaked for 6 h and 12 h exhibited the maximum reduction of β-ODAP (232.11 mg/100 g) and IP₆ (21.11 mg/100 g) respectively. The combined incremental effect of pressure and soaking time resulted in a more significant (p ≤ .001) reduction in both compounds than the interaction of pressure with holding time (p ≤ .05). A reduction of β-ODAP from 36.00 to 71.22% by soaked-HHP treatment was observed. β-ODAP reductions were always higher for soaked compared to batter grass pea seeds. IP₆ contents after HHP treatment ranged from 33.65 mg/100 g to nill. It can be concluded that pressure, soaking and holding time as well as the grass pea seed accession/variety had great impact on molecular structure changes, enhancement of enzyme activity and reduction in β-ODAP and IP₆ content.

The influence of hydrolysis and derivatization on the determination of amino acid content and isotopic ratios in dual-labeled (13 C, 15 N) white clover

RATIONALE

The cycling of peptide- and protein-bound amino acids (AAs) is important for studying the rate-limiting steps in soil nitrogen (N) turnover. A strong tool is stable C and N isotopes used in combination with compound-specific isotope analysis (CSIA), where a prerequisite for analysis is appropriate methods for peptide and protein hydrolysis and appropriate methods for derivatization of AAs for analysis by gas chromatography (GC).

METHODS

We examined the efficiency of a standard acidic hydrolysis (6 M HCl, 20 h at 110°C) and a fast acidic hydrolysis (6 M HCl, 70 min at 150°C) on the recovery of AAs from a protein standard (bovine serum albumin). The best methods were used on dual-labeled (¹³ C and ¹⁵ N) clover shoot and root juice, divided into four molecular weight (Mw) size fractions. We used NAIP (N-acetyl isopropyl esterification) derivatization for GC/combustion-isotope ratio mass spectrometry (C-IRMS) analysis of AA standards.

RESULTS

The NAIP derivatization gave very low limits of detection (LODs) (< 2 pmol) and limits of quantification (LOQs) ranging from 0.55 to 4.89 pmol. Comparing the concentrations of individual AAs in hydrolyzed versus unhydrolyzed clover juice samples of the low Mw size fraction (<1 kDa) showed a significant decline in concentration (p <0.03) for seven AAs after hydrolysis. Despite the decline in AA concentration, we found a linear connection between the obtained atomic fraction (¹³ C/total carbon and ¹⁵ N/total nitrogen) for individual AAs of hydrolyzed versus unhydrolyzed samples.

CONCLUSIONS

The methodology distinguished differences in atomic fractions across AAs, in individual AAs in Mw size fractions, and between shoot and root samples of experimentally labeled white clover. Specifically, the method separated L-glutamate (Glu) and glutamine (Gln). Thus, for a broader use in plant and soil ecology, we present an optimized methodology for GC/C-IRMS analysis of AAs from organic nitrogen samples enriched with ¹³ C and ¹⁵ N - AA stable isotope probing (SIP).

The concentrations of bioelements in the hair samples of Jordanian children who stutter

OBJECTIVES

This study investigates the levels of 15 bioelements (calcium, copper, chromium, sodium, iron, magnesium, manganese, zinc, cobalt, selenium, molybdenum, vanadium, potassium, boron, and lithium) in the hair species of Jordanian stutterer.

METHODS

The subjects of the study included 25 cases of stuttering, and 25 normal children (age and sex matched). The severity of stuttering (low, moderate, and severe) were assessed using Stuttering Severity Instrument, Fourth edition (SSI-4). Hair samples of subjects were cut, washed, dried, physically degraded, hydrolyzed, and analyzed by Inductively Coupled Plasma Mass Spectrometry (ICP-MS).

RESULTS

Results indicated that the levels of bioelements (Calcium, Copper, Chromium, Magnesium, Manganese, Cobalt, Selenium, Molybdenum, Vanadium, Boron, and Lithium) were significantly lesser in the hair samples of stuttering group than the control group.

CONCLUSION

The findings of the current study could support the use of biochemical analyses as diagnostic biomarker for stuttering.

Effects of the incorporation of cantaloupe pulp in yogurt: Physicochemical, phytochemical and rheological properties

The therapeutic effects of cantaloupe are of great interest for the development of functional foods such as yogurt. In this study a new dairy product has been formulated by enriching natural yogurt with fruit cantaloupe (yogurt with cantaloupe puree, yogurt with dry cantaloupe and yogurt with dry cantaloupe and cantaloupe puree). Thus, composition (moisture, ash, lipids, proteins), including amino acid contents, lactic flora as well as rheological (viscoelasticity, viscosity) property of cantaloupe yogurt and natural yogurt is assessed. In addition, pH value, water holding capacity and antioxidant activity (reducing power) are measured over refrigerated storage time. There are significant differences between natural yogurt and cantaloupe yogurt in almost all parameters. The results show that the pH decreases during the storage period and the antioxidant activity as well as the water holding capacity are more remarkable in the yogurt with dry cantaloupe at the 14th and the 28th day of storage, respectively. The addition of cantaloupe in natural yogurt ameliorates the load of lactic flora and modifies the rheological property of the new products. The results of the current study show that the addition of cantaloupe to yogurt significantly improved its quality.

Identification of edible Bird’s nest with amino acid and monosaccharide analysis

This study describes the approach of amino acid and monosaccharide combined with Hotelling T2 range plot to identify edible bird nests (EBN) and non-EBN. Prior to the approach, an analytical method was developed and validated to quantify monosaccharides in EBN. Hotelling T2 range plots of both compounds were successful in predicting the different types of EBN and differentiating EBN and non-EBN. This outcome suggests EBN contains a group of glycoproteins which is not affected by the EBN’s coloration, country of origin, and/or the processing method of the food item. In addition, the glycoproteins were shown to be unique to EBN. EBN were revealed to be rich in protein and essential amino acids as well as contain a wider variety of monosaccharides than most food items. The overall findings suggest that amino acid and monosaccharide provide information not only on the detected compounds and also insights into the glycoproteins of EBN.

Analytical methods for soluble microbial products (SMP) and extracellular polymers (ECP) in wastewater treatment systems: a review

Effluents from biological processes contain a wide range of complex organic compounds, including soluble microbial products (SMP) and extracellular polymers (ECP), released during bacteria metabolism in mixed culture in bioreactors. It is important to clearly identify the primary components of SMPs and ECPs in order to understand the fundamental mechanisms of biological activity that create these compounds, and how to reduce these compounds in the effluent. In addition, these compounds constitute the main foulants in membrane bioreactors which are being used more widely around the world. A review on the extraction of ECP, characterization, and identification of SMPs and ECPs is presented, and we summarize up-to-date pretreatments and analytical methods for SMPs. Most researchers have focused more on the overall properties of SMPs and ECPs such as their concentrations, molecular weight distribution, aromaticity, hydrophobic and hydrophilic properties, biodegradability, and toxicity characteristics. Many studies on the identification of effluent SMPs show that most of these compounds were not present in the influent, such as humic acids, polysaccharides, proteins, nucleic acids, organic acids, amino acids, exocellular enzymes, structural components of cells and products of energy metabolism. A few groups of researchers have been working on the identification of compounds in SMPs using advanced analytical techniques such as GC-MS, LC-IT-TOF-MS and MALDI-TOF-MS. However, there is still considerably more work needed to be done analytically to fully understand the chemical characteristics of SMPs and ECPs.

Analysis of amino acid composition in proteins of animal tissues and foods as pre-column o-phthaldialdehyde derivatives by HPLC with fluorescence detection

Studies of protein nutrition and biochemistry require reliable methods for analysis of amino acid (AA) composition in polypeptides of animal tissues and foods. Proteins are hydrolyzed by 6M HCl (110°C for 24h), 4.2M NaOH (105°C for 20 h), or proteases. Analytical techniques that require high-performance liquid chromatography (HPLC) include pre-column derivatization with 4-chloro-7-nitrobenzofurazan, 9-fluorenyl methylchloroformate, phenylisothiocyanate, naphthalene-2,3-dicarboxaldehyde, 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate, and o-phthaldialdehyde (OPA). OPA reacts with primary AA (except cysteine or cystine) in the presence of 2-mercaptoethanol or 3-mercaptopropionic acid to form a highly fluorescent adduct. OPA also reacts with 4-amino-1-butanol and 4-aminobutane-1,3-diol produced from oxidation of proline and 4-hydroxyproline, respectively, in the presence of chloramine-T plus sodium borohydride at 60°C, or with S-carboxymethyl-cysteine formed from cysteine and iodoacetic acid at 25°C. Fluorescence of OPA derivatives is monitored at excitation and emission wavelengths of 340 and 455 nm, respectively. Detection limits are 50 fmol for AA. This technique offers the following advantages: simple procedures for preparation of samples, reagents, and mobile-phase solutions; rapid pre-column formation of OPA-AA derivatives and their efficient separation at room temperature (e.g., 20-25°C); high sensitivity of detection; easy automation on the HPLC apparatus; few interfering side reactions; a stable chromatography baseline for accurate integration of peak areas; and rapid regeneration of guard and analytical columns. Thus, the OPA method provides a useful tool to determine AA composition in proteins of animal tissues (e.g., skeletal muscle, liver, intestine, placenta, brain, and body homogenates) and foods (e.g., milk, corn grain, meat, and soybean meal).

Effect of sample preparation methods on the D,L-enantiomer ratio of extracted selenomethionine

Effects of the two most widespread sample preparation techniques on the D,L-enantiomer ratio of extracted selenomethionine were monitored through the analysis of the certified reference material selenium-enriched yeast and the isolated protein fraction of high selenium monkeypot nut. The extracted selenomethionine (SeMet) fractions were orthogonally cleaned up with anion exchange chromatography before carrying out the enantiomer-specific detection to increase the robustness and the efficiency of the subsequent o-phthal-aldehyde and n-isobutyril-cysteine-based derivatisation process and reversed phase-high-performance liquid chromatography-inductively coupled plasma mass spectroscopy (ICP-MS) detection. The two techniques, namely methanesulphonic acid (MSA) based digestion and proteolytic digestion with protease XIV, resulted in significantly different ratio of D,L-selenomethionine with the final results of 2.2-2.7% and 0.5-0.6% of D-SeMet, respectively. The study revealed significant differences in the ICP-MS-related sensitivity of the derivatised selenomethionine enantiomers, which calls attention to the quantification of this selenoamino acid after MSA hydrolysis.

Seaweed proteins and amino acids as nutraceuticals

Seaweeds demonstrate original and interesting nutritional characteristics. Protein concentration ranges from 5% to 47% of dry basic. Its value depends particularly on species and the environmental conditions. Seaweed protein is a source of all amino acids, especially glycine, alanine, arginine, proline, glutamic, and aspartic acids. In algae, essential amino acids (EAAs) represent almost a half of total amino acids and their protein profile is close to the profile of egg protein. In case of non-EAAs, all three groups (green, brown, and red seaweeds) contain the similar amount. Red seaweed seems to be a good source of protein because its value reaches 47%. The issue of protein malnutrition supports the trend to find a new and cheap alternative source of protein. Algae could play an important role in the above-mentioned challenge because of relatively high content of nitrogen compounds. Algae may be used in the industry as a source of ingredients with high nutritional quality.

Microwave-assisted high-throughput acid hydrolysis in silicon carbide microtiter platforms--a rapid and low volume sample preparation technique for total amino acid analysis in proteins and peptides

An efficient microwave-assisted high-throughput protein hydrolysis protocol was developed utilizing strongly microwave absorbing silicon carbide-based microtiter platforms. The plates are equipped with 20 bore holes having the proper dimensions for holding standard screw-capped HPLC/GC vials. Due to the possibility of heating up to four heating platforms simultaneously (80 vials), parallel microwave-assisted acid hydrolyses can be performed under carefully controlled conditions significantly reducing the overall time required for protein hydrolysis and the subsequent evaporation step required for larger volumes of acid. An extensive optimization of the hydrolysis conditions has demonstrated that 5min irradiation at 160°C with 6N HCl leads to comparable results in terms of total and individual amino acid recovery as the traditional method requiring 24h heating at 110°C. Complete hydrolysis of several proteins and synthetic peptides was performed using 25μg of sample material and 100μL of 6N HCl in a dedicated low-volume HPLC/GC vial. Since the hydrolysis and subsequent analysis can be performed from the same vial, errors caused by sample transfer can be minimized. Control experiments have demonstrated that the observed rate enhancements are the result of a purely thermal/kinetic effect as a consequence of the considerable higher reaction temperatures.

Automated protein hydrolysis delivering sample to a solid acid catalyst for amino acid analysis

In this study, we developed an automatic protein hydrolysis system using strong cation-exchange resins as solid acid catalysts. Examining several kinds of inorganic solid acids and cation-exchange resins, we found that a few cation-exchange resins worked as acid catalysts for protein hydrolysis when heated in the presence of water. The most efficient resin yielded amounts of amino acids that were over 70% of those recovered after conventional hydrolysis with hydrochloric acid and resulted in amino acid compositions matching the theoretical values. The solid-acid hydrolysis was automated by packing the resin into columns, combining the columns with a high-performance liquid chromatography system, and heating them. The amino acids that constitute a protein can thereby be determined, minimizing contamination from the environment.

Unintended compositional changes in transgenic rice seeds ( Oryza sativa L.) studied by spectral and chromatographic analysis coupled with chemometrics methods

Unintended compositional changes in transgenic rice seeds were studied by near-infrared reflectance, GC-MS, HPLC, and ICP-AES coupled with chemometrics strategies. Three kinds of transgenic rice with resistance to fungal diseases or insect pests were comparatively studied with the nontransgenic counterparts in terms of key nutrients such as protein, amino acids, fatty acids, vitamins, elements, and antinutrient phytic acid recommended by the Organization for Economic Co-operation and Development (OECD). The compositional profiles were discriminated by chemometrics methods, and the discriminatory compounds were protein, three amino acids, two fatty acids, two vitamins, and several elements. Significance of differences for these compounds was proved by analysis of variance, and the variation extent ranged from 20 to 74% for amino acids, from 19 to 38% for fatty acids, from 25 to 57% for vitamins, from 20 to 50% for elements, and 25% for protein, whereas phytic acid content did not change significantly. The unintended compositional alterations as well as unintended change of physical characteristic in transgenic rice compared with nontransgenic rice might be related to the genetic transformation, the effect of which needs to be elucidated by additional studies.

Amino acid analysis

Amino acid analysis is used to determine the amino acid content of amino acid-, peptide- and protein-containing samples. With minor exceptions, proteins are long linear polymers of amino acids connected to each other via peptide bonds. The first step of amino acid analysis involves hydrolyzing these peptide bonds. The liberated amino acids are then separated, detected, and quantified. The method was first developed by Moore, Stein and coworkers in the 1950s using HCl acid hydrolysis, and, despite considerable effort by many workers, the basic methodology remains relatively unchanged. This unit provides an overview and strategic planning for amino acid analysis, discussing a range of methodologies and issues. In addition, several common methods used for analysis of L-amino acids are described in detail, including: HCl acid hydrolysis, performic acid oxidation for methionine and cysteine analysis, base hydrolysis for tryptophan analysis, analysis of free amino acids, and analysis of reactive lysine.

Wheat gluten amino acid composition analysis by high-performance anion-exchange chromatography with integrated pulsed amperometric detection

A simple accurate method for determining amino acid composition of wheat gluten proteins and their gliadin and glutenin fractions using high-performance anion-exchange chromatography with integrated pulsed amperometric detection is described. In contrast to most conventional methods, the analysis requires neither pre- or post-column derivatization, nor oxidation of the sample. It consists of hydrolysis (6.0M hydrochloric acid solution at 110 degrees C for 24h), evaporation of hydrolyzates (110 degrees C), and chromatographic separation of the liberated amino acids. Correction factors (f) accounted for incomplete cleavage of peptide bonds involving Val (f=1.07) and Ile (f=1.13) after hydrolysis for 24h and for Ser (f=1.32) losses during evaporation. Gradient conditions including an extra eluent (0.1M acetic acid solution) allowed multiple sequential sample analyses without risk of Glu contamination on the anion-exchange column. While gluten amino acid compositions by the present method were mostly comparable to those obtained by a conventional method involving oxidation, acid hydrolysis and post-column ninhydrin derivatization, the latter method underestimated Tyr, Val and Ile levels. Results for the other amino acids obtained by the different methods were linearly correlated (r>0.99, slope=1.03).

Direct determination of methionine sulfoxide in milk proteins by enzyme hydrolysis/high-performance liquid chromatography

A direct and simultaneous HPLC/UV determination of methionine and methionine sulfoxide in enzyme-hydrolyzed milk proteins is described. Protein hydrolysis is accomplished by a three-enzyme (pronase, leucine aminopeptidase, prolidase) 20-h/37 degrees C digestion. A gradient elution reversed-phase HPLC system with UV detection at 214 nm and 280 nm is then used to determine the quantitative releases of methionine sulfoxide, methionine, tyrosine, and tryptophan. The ease of methionine oxidation by a wide variety of oxidants, coupled with the quantitative release of both methionine and its sulfoxide by the three-enzyme hydrolysis, renders the approach valuable for identifying oxidized milk proteins. The relatively simple method proved accurate and precise in its application to commercial milk products, finding methionine sulfoxide levels as high as 74% of the total methionine.

Analysis of hydroxyproline isomers and hydroxylysine by reversed-phase HPLC and mass spectrometry

Collagens, the most abundant mammalian proteins, contain a high content of hydroxylated amino acids, such as, 3- and 4-cis-/trans-hydroxyproline (Hyp) and 5-hydroxylysine (Hyl). Whereas the global content of 4-Hyp was studied by amino acid analysis, no technique to determine all five hydroxyamino acids simultaneously in collagens has been reported. Here, we report the separation of all five hydroxyamino acids as well as two Hyp epimers from all other proteinogenic amino acids after derivatization with N(2)-(5-fluoro-2,4-dinitrophenyl)-l-valine amide (l-FDVA) by RPC-UV-ESI-MS. The general applicability of this method is shown for three Hyp-containing peptides as well as collagen type I.

Determination of the structure of the fatty acid chain in a cyclic lipopeptide using GC-MS

A GC-EIMS method to determine the structure of the fatty acid chains in cyclic lipopeptides is described. The structure of the fatty acid chains can be determined by the characteristic peaks of the MS spectrogram according to the fact that the alpha cleavage predominates the MS of a fatty acid with amino and hydroxy groups, while the McLafferty rearrangement predominates the MS of one without amino or hydroxy group. The characteristics of the strongest peaks of 103 and 102 in MS spectrograms due to alpha cleavage represent the beta-hydroxy-fatty acid and the beta-amino fatty acid, respectively; the strongest peak of 117 due to alpha cleavage and the relatively weak peak of 88 due to McLafferty rearrangement indicate the beta-hydroxy-fatty acid with a branched methyl group at its alpha position. The strongest peak of 74 due to McLafferty suggests the fatty acid without hydroxy or amino group. The ratio of relative intensity (I(43)/I(57)) characterizes the branches of alkyl chains. The greater I(43)/I(57) corresponds to an iso alkyl, and the smaller I(43)/I(57) corresponds to an anteiso alkyl. This method can be used to determine the full structure of the fatty acid chains in lipopeptides.

Capillary electrophoresis analysis of hydrolysis, isomerization and enantiomerization of aspartyl model tripeptides in acidic and alkaline solution

In order to investigate the degradation of two aspartyl tripeptides, Gly-Asp-PheNH2 and Phe-Asp-GlyNH2 in solution capillary, electrophoresis methods were developed and validated. Separation of most degradation products including those arising from isomerization and enantiomerization of the Asp residues was achieved in a 50 mM sodium phosphate buffer, pH 3.0. Resolution of comigrating compounds could be achieved by addition of cyclodextrins to the background electrolyte. For tripeptide derivatives the assays were linear in the range of 0.015-3.0 mmol/l. Some dipeptides and amino acids exhibited a narrower linear range due to low UV absorbance. The limits of detection were in the range of 0.005-0.1 mmol/l. Incubation of the model peptides was carried out at pH 2 and 10. At pH 2, degradation of the peptides proceeded via C-terminal deamidation and peptide backbone hydrolysis. In contrast, isomerization and enantiomerization were observed in combination with deamidation at pH 10. Generally, degradation of Phe-Asp-GlyNH2 proceeded faster compared to Gly-Asp-PheNH2 due to steric hindrance by the phenyl side chain.

Optimum conditions of autoclaving for hydrolysis of proteins and urinary peptides of prolyl and hydroxyprolyl residues and HPLC analysis

A method for urinary peptide(s) and protein hydrolysis, involving autoclaving at 15psi (121 degrees C) for 60min, is described. Using three candidate proteins (bovine serum albumin, casein and gelatin) and urine specimens, the effect of autoclaving with respect to the optimum time required for hydrolysis under both acidic (6N HCl) and alkaline (6N KOH) conditions was studied. Recoveries of total amino acids from proteins and urine hydrolysate(s) suggest that complete hydrolysis of proteins and urinary peptides could be achieved by autoclaving for 30-60min instead of 16h of incubation at 110 degrees C. Further, stability of some of the individual amino acids was also studied. The observed differential stability of amino acids under acidic and alkaline conditions, as demonstrated in this study by HPLC analysis, makes it imperative to choose the appropriate hydrolytic condition while studying the composition of any given amino acids in urinary peptide(s)/protein hydrolysates. Further, the finding that both Pro and Hyp were stable under alkaline conditions of hydrolysis by autoclaving renders this method suitable for assaying these two amino acids from urine hydrolysates, hence its utility in the study of urinary peptide derived Hyp and Pro in bone/cartilage disorders.

LC determination of leuprolide component amino acids in injectable solution by phanquinone pre-column derivatization labelling procedure

A sensitive LC method for the determination of leuprolide acetate component amino acids in injectable solution with fluorogenic pre-column derivatization has been developed. The derivatization reaction with phanquinone was optimised by a series of experiments. Histidine, arginine, serine, tryptophan, glutamic acid, tyrosine, methionine, isoleucine, leucine and phenylalanine were separated on a reversed-phase ODS column using as eluent a binary mixture of triethylammonium phosphate buffer-methanol, under gradient elution conditions. The derivatives were eluted in 30 min with good reproducibility. The hydrolysis reaction of the peptide was carried out at reflux with 12 N hydrochloric acid for 2 h 30 min. The intra-day accuracy of the entire procedure (hydrolysis, derivatization, LC separation) ranged from 80.5 to 109.5% of the nominal concentration of leuprolide acetate and the precision (%R.S.D.) was less than 5.8%; the inter-day accuracy was in the range 81.5-107.2% and corresponding R.S.D. values were less than 4.6%. The detection limits (signal-to-noise ratio=3) for the adducts are 30-800 fmol.

Application of proteomics technologies in the investigation of the brain

Approximately 30-50% of the genes in mammals are expressed in the nervous system. A differential expression of genes in distinct patterns is necessary for the generation of the large variety of neuronal phenotypes. Proteomic analysis of brain compartments may be useful to understand the complexity, to investigate disorders of the central nervous system, and to search for corresponding early markers. Up to now, proteomics has mainly studied the identity and levels of the abundant human, rat, and mouse brain proteins as well as changes of their levels and the modifications that result from various neurological disorders, like Alzheimer's disease and Down's syndrome in humans and in animal models of those diseases. The proteins, for which altered levels in these disorders have been observed, exert mainly neurotransmission, guidance, and signal-transduction functions, or are involved in detoxification, metabolism, and conformational changes. Some of those proteins may be potential drug targets. Further improvement of proteomics technologies to increase sensitivity and efficiency of detection of certain protein classes is necessary for a more detailed analysis of the brain proteome. In this review, a description of the proteomics technologies applied in the investigation of the brain, the major findings that resulted from their application, and the potential and limitations of the current technologies are discussed.