Unravelling Over-Represented Amino Acids in Protein Structure of Allergen Proteins; A Large-Scale Study

Journal of Cell and Molecular Research

مقاله 6، دوره 8، شماره 2 - شماره پیاپی 16، اسفند 2016، صفحه 65-70   

نوع مقاله: Research Articles

شناسه دیجیتال (DOI): 10.22067/jcmr.v0i0.60190

نویسندگان

Nassim Rahmani¹؛ Esmaeil Ebrahimie^{* 1}؛ Ali Niazi¹؛ Najaf Allahyari Fard²؛ Bijan Bambai²؛ Zarrin Minuchehr²؛ Mansour Ebrahimi³

¹Shiraz University

²National Institute of Genetic Engineering and Biotechnology (NIGEB)

³University of Qom

چکیده

Allergens are proteins or glycoproteins which make widespread disorders that can lead to a systemic anaphylactic shock and even death within a short period of time. Understanding the protein features that are involved in allergenicity is important in developing future treatments as well as engineering proteins in genetic transformation projects. A big dataset of 1439 protein features from 761 plant allergens and 7815 non-allergen proteins was constructed. Thereafter, 10 different attribute weighting algorithms were utilized to find the key characteristics differentiating allergens and non-allergen proteins. The frequency of Leu, Arg and Gln selected by different attribute weighting algorithms with more than 50% confidence, including attribute weighting by Weight_Info Gain, Weight Chi Squared, Weight_Gini Index and Weight_Relief. High amount of Gln and low percentage of Leu and Arg discriminate plant allergens from non-allergens

کلیدواژه‌ها

Plant allergens؛ Attribute weighting algorithms؛ Amino acid

مراجع

Baumgartner C., Lewis G. D., Netzer M., Pfeifer B. and Gerszten R. E. (2010) A new data mining approach for profiling and categorizing kinetic patterns of metabolic biomarkers after myocardial injury. Bioinformatics 26:1745–1751.

2. Bijanzadeh E., Emam Y. and Ebrahimie E. (2010) Determining the most important features contributing to wheat grain yield using supervised feature selection mode. Australian Journal of Crop Science 4:402-407.

3. Breiteneder H. and Mills C. (2005) Plant food allergens—structural and functional aspects of allergenicity. Biotechnology Advances 23:395-399.

4. Ebrahimi M., Aghagolzadeh P., Shamabadi N., Tahmasebi A., Alsharifi M., Adelson D. L., Hemmatzadeh F. and Ebrahimie E. (2014) Understanding the underlying mechanism of HA subtyping in the level of physic-chemical characteristics of Protein. PLOS ONE 9.

5. Ebrahimi M. and Ebrahimie E. (2010) Sequence-based prediction of enzyme thermostability through bioinformatics algorithms. Current Bioinformatics 5.

6. Ebrahimi M., Lakizadeh A., AghaGolzadeh P., Ebrahimie E. and Ebrahimi M. (2011) Prediction of thermostability from amino acid attributes by combination of clustering with attribute weighting: a new vista in engineering enzymes. PLoS One 6.

7. Ebrahimie E., Ebrahimi M. and Sarvestani N. R. (2011) Protein attributes contribute to halo _ stability, bioinformatics approach. Saline Systems 7.

8. Hosseinzadeh F., Ebrahimi M., Goliaei B. and Shamabadi N. (2012) Classification of lung cancer tumors based on structural and physicochemical properties of proteins by bioinformatics models. PLoS One 7.

9. Kumar M., Gromiha M. M. and Raghava G. P. (2011) SVM based prediction of RNA binding proteins using binding residues and evolutionary information. Journal of Molecular Recognition 24:303-313.

10. Mondal A. K., Parui S. and Mandal S. (1998) Analysis of the free amino acid content in pollen of nine Asteraceae species of known allergenic activity. Annals of Agricultural and Environmental Medicine 5:17-20.

11. Pawankar R., Canonica G. W., Holgate S. T., Lockey R. F. and Blaiss M. (2013) The WAO White Book on Allergy.

12. Ross S. M. and Montoya M. I. (2015) Allergic reactions. In Basic Clinical Anesthesia. Springer. 197-202.

13. Shewry P. R., Beaudoin F., Jenkins J., Griffiths S. and Mills E. (2002) Plant protein families and their relationships to food allergy. Biochemical Society Transactions 30:906-910.

14. Tanabe S. (2001) Identification of wheat allergens. Internet Symposium on Food Allergens 3:163_170.

15. Taylor S. L. and Hefle S. L. (2006) Food allergen labeling in the USA and Europe. Current Opinion in Allergy and Clinical Immunology 6:186–190.

16. Van Gasse A., Mangodt E., Faber M., Sabato V., Bridts C. and Ebo D. (2015) Molecular allergy diagnosis: Status anno 2015. Clinica Chimica Acta 444:54-61.

17. Youngshin H., Jing L., Ludmilla B., Galina A. G., Chaeyoon L., Won H. S. and Hugh A. S. (2016) What characteristics confer proteins the ability to induce allergic responses? IgE epitope mapping and comparison of the structure of soybean 2S albumins and ara h 2. Molecules 21.

18. Zinati Z., Zamansani F., KayvanJoo A., Ebrahimi M., Ebrahimi M., Ebrahimie E. and MohammadiDehcheshmeh M. (2014) New layers in understanding and predicting α-linolenic acid content in plants using amino acid characteristics of omega-3 fatty acid desaturase. Computers in Biology and Medicine 54:14-23.