Assessment of the potential allergenicity of ice structuring protein type III HPLC 12 using the FAO/WHO 2001 decision tree for novel foods

Protein Science Meets Artificial Intelligence: A Systematic Review and a Biochemical Meta-Analysis of an Inter-Field

Proteins are some of the most fascinating and challenging molecules in the universe, and they pose a big challenge for artificial intelligence. The implementation of machine learning/AI in protein science gives rise to a world of knowledge adventures in the workhorse of the cell and proteome homeostasis, which are essential for making life possible. This opens up epistemic horizons thanks to a coupling of human tacit–explicit knowledge with machine learning power, the benefits of which are already tangible, such as important advances in protein structure prediction. Moreover, the driving force behind the protein processes of self-organization, adjustment, and fitness requires a space corresponding to gigabytes of life data in its order of magnitude. There are many tasks such as novel protein design, protein folding pathways, and synthetic metabolic routes, as well as protein-aggregation mechanisms, pathogenesis of protein misfolding and disease, and proteostasis networks that are currently unexplored or unrevealed. In this systematic review and biochemical meta-analysis, we aim to contribute to bridging the gap between what we call binomial artificial intelligence (AI) and protein science (PS), a growing research enterprise with exciting and promising biotechnological and biomedical applications. We undertake our task by exploring “the state of the art” in AI and machine learning (ML) applications to protein science in the scientific literature to address some critical research questions in this domain, including What kind of tasks are already explored by ML approaches to protein sciences? What are the most common ML algorithms and databases used? What is the situational diagnostic of the AI–PS inter-field? What do ML processing steps have in common? We also formulate novel questions such as Is it possible to discover what the rules of protein evolution are with the binomial AI–PS? How do protein folding pathways evolve? What are the rules that dictate the folds? What are the minimal nuclear protein structures? How do protein aggregates form and why do they exhibit different toxicities? What are the structural properties of amyloid proteins? How can we design an effective proteostasis network to deal with misfolded proteins? We are a cross-functional group of scientists from several academic disciplines, and we have conducted the systematic review using a variant of the PICO and PRISMA approaches. The search was carried out in four databases (PubMed, Bireme, OVID, and EBSCO Web of Science), resulting in 144 research articles. After three rounds of quality screening, 93 articles were finally selected for further analysis. A summary of our findings is as follows: regarding AI applications, there are mainly four types: 1) genomics, 2) protein structure and function, 3) protein design and evolution, and 4) drug design. In terms of the ML algorithms and databases used, supervised learning was the most common approach (85%). As for the databases used for the ML models, PDB and UniprotKB/Swissprot were the most common ones (21 and 8%, respectively). Moreover, we identified that approximately 63% of the articles organized their results into three steps, which we labeled pre-process, process, and post-process. A few studies combined data from several databases or created their own databases after the pre-process. Our main finding is that, as of today, there are no research road maps serving as guides to address gaps in our knowledge of the AI–PS binomial. All research efforts to collect, integrate multidimensional data features, and then analyze and validate them are, so far, uncoordinated and scattered throughout the scientific literature without a clear epistemic goal or connection between the studies. Therefore, our main contribution to the scientific literature is to offer a road map to help solve problems in drug design, protein structures, design, and function prediction while also presenting the “state of the art” on research in the AI–PS binomial until February 2021. Thus, we pave the way toward future advances in the synthetic redesign of novel proteins and protein networks and artificial metabolic pathways, learning lessons from nature for the welfare of humankind. Many of the novel proteins and metabolic pathways are currently non-existent in nature, nor are they used in the chemical industry or biomedical field.

Structural diversity of marine anti-freezing proteins, properties and potential applications: a review

Cold-adapted organisms, such as fishes, insects, plants and bacteria produce a group of proteins known as antifreeze proteins (AFPs). The specific functions of AFPs, including thermal hysteresis (TH), ice recrystallization inhibition (IRI), dynamic ice shaping (DIS) and interaction with membranes, attracted significant interest for their incorporation into commercial products. AFPs represent their effects by lowering the water freezing point as well as preventing the growth of ice crystals and recrystallization during frozen storage. The potential of AFPs to modify ice growth results in ice crystal stabilizing over a defined temperature range and inhibiting ice recrystallization, which could minimize drip loss during thawing, improve the quality and increase the shelf-life of frozen products. Most cryopreservation studies using marine-derived AFPs have shown that the addition of AFPs can increase post-thaw viability. Nevertheless, the reduced availability of bulk proteins and the need of biotechnological techniques for industrial production, limit the possible usage in foods. Despite all these drawbacks, relatively small concentrations are enough to show activity, which suggests AFPs as potential food additives in the future. The present work aims to review the results of numerous investigations on marine-derived AFPs and discuss their structure, function, physicochemical properties, purification and potential applications.

Common Amino Acid Subsequences in a Universal Proteome--Relevance for Food Science

A common subsequence is a fragment of the amino acid chain that occurs in more than one protein. Common subsequences may be an object of interest for food scientists as biologically active peptides, epitopes, and/or protein markers that are used in comparative proteomics. An individual bioactive fragment, in particular the shortest fragment containing two or three amino acid residues, may occur in many protein sequences. An individual linear epitope may also be present in multiple sequences of precursor proteins. Although recent recommendations for prediction of allergenicity and cross-reactivity include not only sequence identity, but also similarities in secondary and tertiary structures surrounding the common fragment, local sequence identity may be used to screen protein sequence databases for potential allergens in silico. The main weakness of the screening process is that it overlooks allergens and cross-reactivity cases without identical fragments corresponding to linear epitopes. A single peptide may also serve as a marker of a group of allergens that belong to the same family and, possibly, reveal cross-reactivity. This review article discusses the benefits for food scientists that follow from the common subsequences concept.

Characterization of the allergenic potential of proteins: an assessment of the kiwifruit allergen actinidin

Assessment of the potential allergenicity (IgE-inducing properties) of novel proteins is an important challenge in the overall safety assessment of foods. Resistance to digestion with pepsin is commonly measured to characterize allergenicity, although the association is not absolute. We have previously shown that specific IgE antibody production induced by systemic [intraperitoneal (i.p.)] exposure of BALB/c strain mice to a range of proteins correlates with allergenic potential for known allergens. The purpose of the present study was to explore further the utility of these approaches using the food allergen, actinidin. Recently, kiwifruit has become an important allergenic foodstuff, coincident with its increased consumption, particularly as a weaning food. The ability of the kiwifruit allergen actinidin to stimulate antibody responses has been compared with the reference allergen ovalbumin, and with the non-allergen bovine haemoglobin. Haemoglobin was rapidly digested by pepsin whereas actinidin was resistant unless subjected to prior chemical reduction (reflecting intracellular digestion conditions). Haemoglobin stimulated detectable IgG antibody production at relatively high doses (10%), but failed to provoke detectable IgE. In contrast, actinidin was both immunogenic and allergenic at relatively low doses (0.25% to 1%). Vigorous IgG and IgG1 antibody and high titre IgE antibody responses were recorded, similar to those provoked by ovalbumin. Thus, actinidin displays a marked ability to provoke IgE, consistent with allergenic potential. These data provide further encouragement that in tandem with analysis of pepsin stability, the induction of IgE after systemic exposure of BALB/c strain mice provides a useful approach for the prospective identification of protein allergens.

Epitopic hexapeptide sequences from Baltic cod parvalbumin beta (allergen Gad c 1) are common in the universal proteome

The aim of this study was to analyze the distribution of hexapeptide fragments considered as epitopes of Baltic cod parvalbumin beta (allergen Gad c 1) in the universal proteome. Cod (Gadus morhua subsp. callarias) parvalbumin hexapeptides cataloged in the Immune Epitope Database were used as query sequences. The UniProt database was screened using the WU-BLAST 2 program. The distribution of hexapeptide fragments was investigated in various protein families, classified according to the presence of the appropriate domains, and in proteins of plant, animal and microbial species. Hexapeptides from cod parvalbumin were found in the proteins of plants and animals which are food sources, microorganisms with various applications in food technology and biotechnology, microorganisms which are human symbionts and commensals as well as human pathogens. In the last case possible coverage between epitopes from pathogens and allergens should be avoided during vaccine design.

An Allergen Portrait Gallery: Representative Structures and an Overview of IgE Binding Surfaces

Recent progress in the biochemical classification and structural determination of allergens and allergen-antibody complexes has enhanced our understanding of the molecular determinants of allergenicity. Databases of allergens and their epitopes have facilitated the clustering of allergens according to their sequences and, more recently, their structures. Groups of similar sequences are identified for allergenic proteins from diverse sources, and all allergens are classified into a limited number of protein structural families. A gallery of experimental structures selected from the protein classes with the largest number of allergens demonstrate the structural diversity of the allergen universe. Further comparison of these structures and identification of areas that are different from innocuous proteins within the same protein family can be used to identify features specific to known allergens. Experimental and computational results related to the determination of IgE binding surfaces and methods to define allergen-specific motifs are highlighted.

Structural analysis of linear and conformational epitopes of allergens

In many countries regulatory agencies have adopted safety guidelines, based on bioinformatics rules from the WHO/FAO and EFSA recommendations, to prevent potentially allergenic novel foods or agricultural products from reaching consumers. We created the Structural Database of Allergenic Proteins (SDAP, http://fermi.utmb.edu/SDAP/) to combine data that had previously been available only as flat files on Web pages or in the literature. SDAP was designed to be user friendly, to be of maximum use to regulatory agencies, clinicians, as well as to scientists interested in assessing the potential allergenic risk of a protein. We developed methods, unique to SDAP, to compare the physicochemical properties of discrete areas of allergenic proteins to known IgE epitopes. We developed a new similarity measure, the property distance (PD) value that can be used to detect related segments in allergens with clinical observed cross-reactivity. We have now expanded this work to obtain experimental validation of the PD index as a quantitative predictor of IgE cross-reactivity, by designing peptide variants with predetermined PD scores relative to known IgE epitopes. In complementary work we show how sequence motifs characteristic of allergenic proteins in protein families can be used as fingerprints for allergenicity.

Assessment of the potential allergenicity of a Milk Basic Protein fraction

BACKGROUND

A specific basic fraction of bovine milk, termed Milk Basic Protein (MBP), has the potential to provide nutritionally important benefits if used as a food ingredient. Although derived from milk, MBP is intended for use as an ingredient in other foods. Cows' milk is a well studied, commonly allergenic food. Although the proteins in MBP are not identified as milk allergens, food products containing MBP will be labelled as containing milk as a caution to milk allergic consumers under food labelling guidelines in the US and the European Union as MBP has not been demonstrated to be free of milk allergens. However, as part of an overall safety evaluation of MBP, the developers sought to evaluate the potential allergenicity of the primary protein components for characteristics of allergenic food proteins and to assess whether intake of these proteins at intended use levels could present a significant new allergenic risk for consumers.

OBJECTIVE

To evaluate the potential allergenicity of the five identified proteins in MBP. While extensive studies have not demonstrated allergenicity of lactoferrin, the four other proteins are less studied. The four were tested here by sequence identity comparison to known allergens, and for stability of these proteins in acidic pepsin as a characteristic common to many food allergens.

METHODS

Sequences of the proteins were compared to those listed in AllergenOnline.com, by methods recommended for the evaluation of proteins introduced in crops through genetic engineering. Pepsin stability was assessed by incubating the various proteins in simulated gastric fluid at pH 1.2 with porcine pepsin for up to 60 min at 37 degrees C, with samples withdrawn and analyzed at specific times.

RESULTS

No significant sequence similarities were identified for the MBP proteins compared to known allergens. All but one of the protein components of MBP were digested relatively quickly by pepsin. The more stable protein will be of low abundance as consumed in contrast to most pepsin-stable food allergens.

CONCLUSIONS

Based on molecular characteristics and expected exposure, the protein components in MBP are unlikely to present any increased risk of allergy for milk allergic subjects or of cross-reactivity for other allergic subjects. However, since the proteins are derived from milk, products containing MBP will need to be labelled as containing milk proteins to warn milk allergic subjects of the potential risk of allergic reactions.

Bioinformatics approaches to classifying allergens and predicting cross-reactivity

Allergenic proteins from very different environmental sources have similar sequences and structures. This fact may account for multiple allergen syndromes, whereby a myriad of diverse plants and foods may induce a similar IgE-based reaction in certain patients. Identifying the common triggering protein in these sources, in silico, can aid designing individualized therapy for allergen sufferers. This article provides an overview of databases on allergenic proteins, and ways to identify common proteins that may be the cause of multiple allergy syndromes. The major emphasis is on the relational Structural Database of Allergenic Proteins (SDAP []), which includes cross-referenced data on the sequence, structure, and IgE epitopes of over 800 allergenic proteins, coupled with specially developed bioinformatics tools to group all allergens and identify discrete areas that may account for cross-reactivity. SDAP is freely available on the Web to clinicians and patients.

Allergen-specific IgE testing in the diagnosis of food allergy and the event of a positive match in the bioinformatics search

Current documents on risk assessment of genetically modified foods recommend including IgE-binding tests on sera from allergic patients. However, there is no generally accepted recommendation on technical aspects of the testing procedures or on the interpretation of the results, despite that fact that both false positive and false-negative results may be caused by variability of the test procedures. The present article discusses the state-of-the-art of serological test procedures for qualitative and quantitative determination of specific IgE and interpretation of test results. It is emphasized that the use of sera from clinically well-characterized subjects is of high importance. In the case of a positive test result, the biological activity of the detected IgE antibodies, i. e., the potential to trigger mediator release from basophils or mast cells in an allergen-specific manner, should be taken into account. However, present data also indicate that validation of such mediator release tests is required, both in terms of experimental protocols and with respect to correlation of the test results with the clinical situation. Further studies are also required to prove the usefulness of targeted serum screening, i. e., the testing of gene products from organisms not known to be allergenic with sera from subjects allergic to related species.

Lack of immunogenicity of ice structuring protein type III HPLC12 preparation administered by the oral route to human volunteers

Before a novel protein can be used in foods, its potential allergenicity must be assessed. In this study, healthy volunteers consumed ice structuring protein (ISP) Type III preparation or a control material 5 days a week for a total of 8 weeks. General measures of health were recorded during the study, and the immunogenicity of the protein was assessed by monitoring the levels of IgG and IgE antibodies specific for ISP Type III. The participants remained in good health throughout the study and during the 4 week follow-up period. No IgG or IgE antibodies specific for ISP Type III were detected in the blood of the participants. Investigations of immunogenicity in man have not been previously applied in the context of safety evaluation and they do not form part of the regimens proposed for the evaluation of protein allergenicity. Consequently no standardised protocols exist for such studies, nor any background against which to interpret the results. Nevertheless, the absence of an immune response using a protocol which could have been expected to result in a response with a strongly immunogenic protein, confirms the conclusions of earlier published work, and attests to the lack of allergenicity of ISP Type III preparation.

Digestion assays in allergenicity assessment of transgenic proteins

The food-allergy risk assessment for transgenic proteins expressed in crops is currently based on a weight-of-evidence approach that holistically considers multiple lines of evidence. This approach recognizes that no single test or property is known to distinguish allergens from nonallergens. The stability of a protein to digestion, as predicted by an in vitro simulated gastric fluid assay, currently is used as one element in the risk assessment process. A review of the literature on the use of the simulated gastric fluid assay to predict the allergenic status of proteins suggests that more extensive kinetic studies with well-characterized reference proteins are required before the predictive value of this assay can be adequately judged.

Investigation on possible allergenicity of 19 different commercial enzymes used in the food industry

The aim of the study was to investigate the safety to allergic patients of 19 commercially available and authority-approved enzymes used in the food industry. Enzymes produced by genetically modified organisms were included. Four hundred consecutive adult patients with a diagnosed allergy to inhalation allergens, food allergens, bee or wasp were included. All had at least one positive skin prick test to the above allergens. Skin prick testing with the 19 enzymes was performed on the forearm and if positive (in 13 patients), in vitro histamine release from blood basophils were performed. Patients with positive results in skin prick test were subsequently reinvestigated with further purified enzymes and finally challenged orally with the enzymes in a double-blind, placebo-controlled protocol. Only one reaction to a placebo challenge was seen. In some instances a positive skin prick test result or a positive histamine release was seen elicited by the enzymes, but since none of the patients were positive to any of the commercial enzymes in the subsequent oral challenges using exaggerated dosages of the enzymes compared to normal daily intake, the findings are without clinical relevance. A wide variety of enzyme classes and origins was included in the study. Because there were no allergenic findings of clinical relevance it is concluded that ingestion of food enzymes in general is not considered to be a concern with regard to food allergy.

Need for an "integrated safety assessment" of GMOs, linking food safety and environmental considerations

Evidence for substantial environmental influences on health and food safety comes from work with environmental health indicators which show that agroenvironmental practices have direct and indirect effects on human health, concluding that "the quality of the environment influences the quality and safety of foods" [Fennema, O. Environ. Health Perspect. 1990, 86, 229-232). In the field of genetically modified organisms (GMOs), Codex principles have been established for the assessment of GM food safety and the Cartagena Protocol on Biosafety outlines international principles for an environmental assessment of living modified organisms. Both concepts also contain starting points for an assessment of health/food safety effects of GMOs in cases when the environment is involved in the chain of events that could lead to hazards. The environment can act as a route of unintentional entry of GMOs into the food supply, such as in the case of gene flow via pollen or seeds from GM crops, but the environment can also be involved in changes of GMO-induced agricultural practices with relevance for health/food safety. Examples for this include potential regional changes of pesticide uses and reduction in pesticide poisonings resulting from the use of Bt crops or influences on immune responses via cross-reactivity. Clearly, modern methods of biotechnology in breeding are involved in the reasons behind the rapid reduction of local varieties in agrodiversity, which constitute an identified hazard for food safety and food security. The health/food safety assessment of GM foods in cases when the environment is involved needs to be informed by data from environmental assessment. Such data might be especially important for hazard identification and exposure assessment. International organizations working in these areas will very likely be needed to initiate and enable cooperation between those institutions responsible for the different assessments, as well as for exchange and analysis of information. An integrated assessment might help to focus and save capacities in highly technical areas such as molecular characterization or profiling, which are often necessary for both assessments. In the area of establishing international standards for traded foods, such as for the newly created Standards in Trade and Development Facility (STDF), an integrated assessment might help in the consideration of important environmental aspects involved in health and food safety. Furthermore, an established integrated view on GMOs may create greater consumer confidence in the technology.

Allergy assessment of foods or ingredients derived from biotechnology, gene-modified organisms, or novel foods

The introduction of novel proteins into foods carries a risk of eliciting allergic reactions in individuals sensitive to the introduced protein and a risk of sensitizing susceptible individuals. No single predictive test exists to perform a hazard assessment in relation to allergenic properties of newly expressed proteins in gene-modified organisms (GMOs). Instead, performance of a weighted risk analysis based on the decision tree approach has been suggested. The individual steps of this analysis comprise sequence homology to known allergens, specific or targeted serum screens for immunoglobulin E (IgE) cross-reactions to known allergens, digestability studies of the proteins in simulated gastric and/or intestinal fluids, and animal studies. These steps are discussed and five examples of risk evaluation of GMOs or novel foods are presented. These include ice-structuring protein derived from fish, microbial transglutaminase, GMO-soybeans, amylase and the Nangai nut.

Evaluation of the potential allergenicity of the enzyme microbial transglutaminase using the 2001 FAO/WHO Decision Tree

All novel proteins must be assessed for their potential allergenicity before they are introduced into the food market. One method to achieve this is the 2001 FAO/WHO Decision Tree recommended for evaluation of proteins from genetically modified organisms (GMOs). It was the aim of this study to investigate the allergenicity of microbial transglutaminase (m-TG) from Streptoverticillium mobaraense. Amino acid sequence similarity to known allergens, pepsin resistance, and detection of protein binding to specific serum immunoglobulin E (IgE) (RAST) have been evaluated as recommended by the decision tree. Allergenicity in the source material was thought unlikely, since no IgE-mediated allergy to any bacteria has been reported. m-TG is fully degraded after 5 min of pepsin treatment. A database search showed that the enzyme has no homology with known allergens, down to a match of six contiguous amino acids, which meets the requirements of the decision tree. However, there is a match at the five contiguous amino acid level to the major codfish allergen Gad c1. The potential cross reactivity between m-TG and Gad c1 was investigated in RAST using sera from 25 documented cod-allergic patients and an extract of raw codfish. No binding between patient IgE and m-TG was observed. It can be concluded that no safety concerns with regard to the allergenic potential of m-TG were identified.

Sequence analysis and resistance to pepsin hydrolysis as part of an assessment of the potential allergenicity of ice structuring protein type III HPLC 12

The recently published WHO/FAO guidelines on the assessment of allergenicity of novel food proteins provide a strategy with which to approach the determination of the potential of novel proteins in foods to be allergens. Key to this strategy are the assessment of sequence similarity to known allergens and the assessment of the resistance to pepsin hydrolysis. Ice structuring proteins (also commonly referred to as anti-freeze or thermal hysteresis proteins) are a group of naturally occurring proteins that bind to ice and structure ice crystal formation. The amino acid sequence of the ice structuring protein (ISP) type III HPLC 12 (ISP type III) was compared in silico with the sequences of known allergens. Secondly, the resistance to pepsin hydrolysis of ISP type III and its glycoconjugates (produced in recombinant baker's yeast) was assessed. The results indicate that ISP type III has no sequence similarity with known allergenic proteins. Both ISP type III and ISP type III glycoconjugates contained within the fermentation product were hydrolysed readily by pepsin (50% loss in <10 min at pH 1.5) to give peptide fragments that were too small to be allergenic or to trigger cross-linking to IgE. In an accompanying study, we demonstrated that IgE from fish-allergic individuals did not bind ISP Type III. Therefore, in accordance with the WHO/FAO strategy, the assessment of ISP type III and ISP type III glycoconjugates by sequence analysis together with lack of resistance to pepsin hydrolysis and the absence of IgE binding supports the conclusion that both are unlikely to present a potential sensitisation hazard.