Monday, October 21, 2019
Identification Of Homologous Of Known Food Allergens Biology Essay Essay Example
Identification Of Homologous Of Known Food Allergens Biology Essay Essay Example Identification Of Homologous Of Known Food Allergens Biology Essay Essay Identification Of Homologous Of Known Food Allergens Biology Essay Essay The cause of immune response in worlds is protein which is a nutrient allergen. The aim of this study is to find the utility of bioinformatics in designation of homologues of known nutrient allergens, such as major peanut allergen Ara h1. The allergen informations was identified from published diaries and from Medline and Embase databases. Those databases were combined with text word and MeSH header scheme. The study focussed on assorted, nutrient allergen databases and bioinformatics tools which are utile in the designation of possible nutrient allergens. The usage of bioinformatics tools is to compare the protein structures which are going more of import because more structural information is available in each twenty-four hours. The bioinformatics are used to look into the structural and functional relation between known nutrient allergens and those relationships can be used to place fresh nutrient allergens. Bioinformatics does non 100 % accurate on happening fresh allergens. Howe ver, with the usage of bioinformatics, cross-reaction between proteins analyzed and immunotherapy could be developed. The allergens are proteins which are immune to heat during cookery, acid in tummy and digestive enzymes. The allergen proteins can come in the blood stream and causes an immune response. Food allergic reaction is a hypersensitivity province. Contact with a nutrient allergen activates the plasma cell ( lymph cells ) which produces the allergen specific immunoglobin E ( IgE ) antibody. IgE molecules so attach to the surface of the mast cells. Mast cells are specialised which contains histamine and heparine. The binding of IgE to mast cells causes an immunological memory and when individual is exposed to the same allergen 2nd clip, the IgE antibodies presented on the surface of mast cells become activated releasing histamine which is responsible for the symptoms related to the nutrient allergic reaction ( Kindt, T.J. et Al, 2007 ) . The symptoms of allergic reaction occurred due to exposure with nutrient allergens are: itchiness, swelling of lips, coughing, runny nose besides the allerg ens can do asthma and can ensue in anaphylaxis which is a sudden bead in the blood force per unit area ( Bupa, 2008 ) . Food allergic reaction is one of the major increasing wellness jobs both in kids and in grownup. Some of the nutrient allergens are derived from ; peanuts, wheat, milk, eggs and soy. These allergens affect 8 % of babies and immature kids ( Samson, H. , 2005 ) . Harmonizing to the surveies of Jenkins et Al. ( 2005 ) ; Ferreira et Al. ( 2004 ) and Mari, A. ( 2001 ) , common antigenic determinants of different beginnings may ensue in clinical nutrient allergic reactions. For illustration ; Ara h1 is a major peanut allergen protein where its IgE reactive antigenic determinants from its peptide sequence was identified by Burks et Al. in 1997. Subsequently, comparing the IgE antigenic determinants of Ara h1 helped to place similar allergen antigenic determinants in other nutrients like tree nuts and leguminous plants ( Lopez-Torrejen, 2003 ) . Designation of similar allergenic antigenic determinants by comparing the possible allegens with known nutrient allergens is really of import beca use the allergens have conserved sequences within the antigenic determinants. For this ground, after the designation of reactive antigenic determinants, bioinformatics tools can be used to place other related proteins associated with similar reactive allergic reaction and to specify more specific interventions. For illustration, in the survey Bolhaar ( 2004 ) the patients with allergic syndrome to apples are besides sensitive to birch pollen. This is due to the similarity between Bet v1 allergen and the Mal d1 protein from apple. The specific immunotherapy incorporating Bet v1 infusions is able to diminish the sensitiveness of apple protein Mal d1. The purpose of this study is to place the allergenic nutrient homologues of allergenic proteins and comparing the protein sequences, antigenic determinants and construction of known allergens by utilizing bioinformatics tools. Methods The relevant nutrient allergic reaction surveies and nutrient allergen databases identified from Medline and Embase databases. Medline and Embase are bibliographic databases which contains over 16 million and 20 million diary articles severally. The database was combined with text word and MeSH heading hunt scheme. ( hypertext transfer protocol: //www.ncbi.nlm.nih.gov/sites/entrez? db=mesh ) The text words were allergens , nutrient allergens and nutrient allergens databases . Besides, the hunt was supplemented by analyzing specific reappraisal articles and bibliographies. Further articles identified by utilizing retrieved articles. Table 1 shows the flow chart of the hunt scheme. Using this scheme, a entire figure of 34226 hits were obtained from allergens hunt standards. By seeking Food allergens 6085 hits were obtained when Allergen database was searched 196 hits were obtained. Food allergen database hunt standards produced 66 hits. The consequences were searched once more by excepting non-bioinformatics stuffs which was ended up with 14 relevant databases and 22 relevant articles. Table: 1 Flow chart of hunt scheme. Allergens: Entire hits 34226 Food allergens: Entire hits 6085 Allergens databases: Entire hits 196 Food allergens databases: Hits 66 Databases with relevant result: 14 Articles with relevant informations: 22 Consequences Allergen Databases There were14 databases identified which contains sequences and information about the allergenic proteins. Table 2 shows these databases. Table: 2 Website name Web-site nexus Information available All Allergy hypertext transfer protocol: //allallergy.net/ Genbank accession Numberss of allergens IUIS hypertext transfer protocol: //www.allergen.org Genbank accession Numberss of allergens Allergome hypertext transfer protocol: //www.allergome.org Name callings of allergens, and links to PubMed A ; sequence databases CSL hypertext transfer protocol: //www.csl.gov.uk/allergen/ index.htm Name callings of nutrient allergens with links to Genbank NCF hypertext transfer protocol: //www.iit.edu/~sgendel/fa.htm Name callings of nutrient allergens with links to Genbank S.t.p. hypertext transfer protocol: //www.ifrn.bbsrc.ac.uk/protall/ Biochemical, structural, and clinical informations InformAll hypertext transfer protocol: //foodallergens.ifr.ac.uk/ Food allergens, antigenic determinants, sequences, links to literature FARRP hypertext transfer protocol: //allergenonline.com/asp/public/login.asp Allergens, sequence links to Genbank, and a FASTA hunt ADFS hypertext transfer protocol: //allergen.nihs.go.jp/ADFS/ Allergen sequences, WHO allergenicity regulations utilizing FASTA SDAP hypertext transfer protocol: //fermi.utmb.edu/SDAP Allergens sequences, protein type, IgE epitopes aggregation, tools for sequence and antigenic determinant comparing ALLERDB hypertext transfer protocol: //sdmc.i2r.a-star.edu.sg/Templar/ DB/Allergen Allergens, a BLAST hunt, and implements the WHO allergenicity regulations WebAllergen hypertext transfer protocol: //weballergen.bii.a-star.edu.sg/ Potential allergenicity of proteins utilizing motives found by a ripple algorithm AlgPred hypertext transfer protocol: //www.imtech.res.in/raghava/algpred Predicts allergenicity with MEME/MAST motives Allermatch www.allermatch.org/ WHO allergenicity regulations utilizing FASTA Table 2 shows the name and nexus of allergen databases besides, bioinformatics tools to find allergenicity. These databases give indicant of allergenic protein. For illustration International Union of Immunological Societies ( IUIS ) contains the names, genbank accession figure and information of allergens. Most of these databases do non hold cross database for cross indexing could be Allergome. It contains allergenic, clinical, biological and structural informations. The Allergome database has no bioinformatics tool but contains allergen MEME sequence motives which are strongly related with allergen. Swiss Prot, PIR, and Genbank contain protein sequences where CSL and Biotechnology Information for Food Safety databases use those sequences to supply list of allergens. Some databases provides direct comparing of allergen sequences by bioinformatics tools and permit the usage of WHO guidelines for foretelling allerginity ( WHO 2001 ) .On the other manus some databases such as FARRP and ADFS enable to seek lists of allergens, protein sequences and a FASTA hunt for related sequences. ALLERDB database contains allergen sequences and BLAST hunt can place the sequence similarities. SDAP Database SDAP ( Structural Database of Allergenic Proteins ) ( hypertext transfer protocol: //fermi.utmb.edu/SDAP ) is one of the biggest nutrient allergen databases. The difference of SDAP database from other databases is, it uses bioinformatics tools to compare allergenic proteins. Some bioinformatics tools enable to compare protein sequences to place allergens due to similar IgE antigenic determinants of the known allergen and proteins ( Schein, 2005 ) . By utilizing SDAP hunt in allergenic proteins, fresh allergenic proteins could be identified. The hunt is rapid and it depends on the sequence similarities, 3D construction and known allergenic antigenic determinants. SDAP database compare the allergen sequences in different methods. The in-house bioinformatics method provides designation of the sequence similarities and links to other big databases ( Swiss Prot and Gen bank ) . By utilizing BLAST and FASTA protein hunt tools, resemblances of the amino acerb sequences of the allergens could was determined. Besides, Pfam grouping is available for the allergens in SDAP which identifies the protein similarities. Bioinformatics tools identify the related IgE antigenic determinants, in this manner the user map the IgE incorporating peptides onto 3D theoretical accounts of allergens. SDAP besides contains IgE adhering antigenic determinants of the allergenic proteins. The antigenic determinant sequences identified by in vivo binding experiments which is adhering of the short peptide sequences to solid stage. The edge peptides assumed to be antigenic determinants ( Li,2003 ) . SDAP database includes information about IgE antigenic determinants of some allergens such as ; peanut ( Ara h1, Ara h 2, Ara h 3 ) , hen egg ( Gal d 1 ) , Polygonum fagopyrum ( Fag e 1 ) , English walnut ( Jug r 1 ) , soya bean ( Glym glycinin G1 and G2 ) , shrimp ( write a 1, pen i 1 ) etc. Comparing Allergenic Protein Sequences Using FASTA Tool The similarity between protein sequences and other allergen sequences might do cross-reacting. This similarity can be identified by the usage of the bioinformatics tool FASTA ( Pearson, 1990 ) . A FASTA tally for sequences consequence in an end product which shows the similar allergens in SDAP including their E-value . Table 3 shows the FASTA hunt in SDAP database Jun a 3 allergenic protein sequence was used. E-value is the statistical significance of the lucifer hit and it shows how many lucifers expected to happen indiscriminately utilizing the same sequence in a database of a given size. Lower the E-value, higher the lucifer. Harmonizing to the tabular array 3, Cup a 3 is the most similar allergen to Jun a 3. Cup a 3 is cypress tree allergen. The tabular array 3 besides shows several vegetable and fruit allergens. Based on the FASTA alliance, individual with a cedar pollen allergic reaction may develop allergenic symptoms due to ingestion of apples or cherries ( Breiteneder and Millis, 2005 ) . Table:3 FASTA hunt utilizing the Jun a 3 protein Number Allergen Sequence Beginning Sequence Length spot mark Tocopherol mark 1 Jun a 3 P81295 cedar pollen 225 311.0 1.0e-86 2 Cup a 3 CAC05258 cypress 199 272.9 2.7e-75 3 Cap a 1w CAC34055 bell Piper nigrum 246 167.5 1.7e-43 4 Lyc vitamin E NP24 P12670 tomato 247 161.2 1.4e-41 5 Cap a 1 AAG34078 bll Piper nigrum 180 136.2 3.4e-34 6 Mal d 2 CAC10270 apple 246 77.0 3.0e-16 7 Pru av 2 P50694 cherry 245 75.1 1.2e-15 8 Act c 2 P81370 Chinese gooseberry 29 36.0 7.9e-05 Table 3 shows FASTA end product in SDAP. Jun a 3 used as an allergen. The consequences show Jun a 3 proteins. They are aligned harmonizing to low E-scores . Pfam Families Pfam is a protein database ( hypertext transfer protocol: //pfam.sanger.ac.uk ) . Protein households are represented harmonizing to multiple sequence alliances and Hidden Markov Models ( HMMs ) . The protein map is identified by active spheres and the interaction of spheres. Active spheres are in the protein that means by placing the active domains the maps of the protein can be understood. The Pfam database is held at: Wellcome Trust Sanger in UK, Howard Hughes Janelia Farm Research Campus in USA and Stockholm Bioinformatics Centre in Sweden. Two entries of Pfam are ; Pfam-A and Pfam-B. Pfam-A contains protein households and Pfam-B contains extra database which can be used in the designation of conserved parts when no lucifer observed from Pfam-A. Consorting different types of allergens into Pfam group is of import because in this manner the individuality of similar proteins with different names can be determined. Besides, Pfam information specifies the functional similarities of the proteins ( Schein et al. , 2006 ) . Entries into SDAP database are assorted into suited Pfam group and the similar allergens to other proteins identified in the Pfam mixture. Table 4 shows 18 common allergenic Pfam households. The widest allergen household is PF00234 which is protease inhibitor/ seed storage/ LTP household incorporating 34 allergens. Novel allergens might be introduced to an bing Pfam household or they might be introduced into a new Pfam household harmonizing to their multiple sequence alliance and HMM profile. Family name Pfam codification Number of Allergens LTP family/Protease inhibitor/seed storage PF00234 34 Profilin PF00235 27 EF manus PF00036 23 Pollen allergen PF01357 20 SCP-like extracellular protein PF00188 19 Bet V I household ( Pathogenesis-related protein ) PF00407 16 Cupin PF00190 15 Tropomyosin PF00261 15 Lipocalin /cytosolic fatty-acid binding protein household PF00061 12 Rare lipoprotein A ( RlpA ) -like double-psi beta-barrel PF03330 12 Globin PF00042 9 Pectate lyase PF00544 9 Papain household cysteine peptidase PF00112 8 60s Acidic ribosomal protein PF00428 8 Subtilase household PF00082 7 Thaumatin household PF00314 7 Pollen proteins Ole vitamin E I household PF01190 7 Ribonuclease ( pollen allergen ) PF01620 7 Table 4 shows Pfam-A allergen households from SDAP. Discussion The cross-reactive proteins have similar sequence and construction but they differ in their beginning. Pfam group has a restriction because it contains both allergenic and non-allergenic proteins together therefore it is hard to choose allergenic proteins from the others. The cross-reactive allergens in the WHO counsel shows deficient sequence individuality ( 35 % ) ( WHO guidelines ) . On the other manus, the IgE binding belongingss reduced due to protein mutants ( de Leon et al. , 2003 ) . For illustration Bet v 1 protein which has 98 % sequence individuality do non cross-react ( Hartl et al. , 1999 ) . Some bioinformatics tools recognise whether the protein is allergenic or non due to allergenic motives. For illustration Web Allergen determines the poteintial allergenic motives ( Riaz et al. , 2005 ) . The IgE binding sites of the possible allergenic motive must be proved to verify the allergen. AlgPred ( hypertext transfer protocol: //www.imtech.res.in/raghava/algpred/ ) gets aid of BLAST hunt and support vector machines ( SVM ) to place the allergenic antigenic determinant motives. Besides, it permits MEME/MAST allergenic motives hunt. The MAST has ability to turn up the IgE binding sites on the protein. AlgPred gives chance to find allergens utilizing combination of SVM, BLAST, MAST and IgE antigenic determinant. Harmonizing to the Schein et Al. ( 2006 ) there are some jobs in separating whether the tropomyosins are allergenic or non-allergenic because of their similar sequences. Some studies have evidenced the protein allergenicity by utilizing bioinformatics and experimental processs. Motifs are sequences where the sequences are conserved in related proteins. IgE binding is characterized by conserved sequence motive in allergenic proteins ( Brusic and Petrovsky, 2003 ) . Decision The nutrient allergens cause an immune response in worlds. Some isoforms of the nutrient allergens where point mutant occurred does non demo allergenic belongingss. The usage of bioinformatics tools is to compare the protein structures which are going more of import because more structural information is available in each twenty-four hours. The study focused on some of the hunt tools used in bioinformatics which can be used to look into the structural and functional relationship between known allergens. Those relationships can be used to place possible novel allergens. Bioinformatics does non 100 % accurate on happening fresh allergens. However, with the usage of bioinformatics, cross-reaction between proteins analyzed and immunotherapy could be developed ( Shein et al. , 2006 ) .