PREDIKSI STRUKTUR TIGA DIMENSI PROTEIN ALERGEN PANGAN DENGAN METODE HOMOLOGI MENGGUNAKAN PROGRAM SWISS-MODEL - (Prediction of Three-Dimensional Structure from Food Allergen Protein Through Homology Method Using SWISS-MODEL Program)

Hendra Wijaya, Fitri Hasanah

Abstract


Information about three-dimensional structure of protein is important to clearly understand its character and function in molecular level. Protein structure determination through laboratory testing needs highly cost of steps and instrument. Three dimensional structure of protein can be scientifically predicted using several in silico methods. The structure of allergen protein was predicted using SWISS-MODEL as homology method in this research. The result showed that structure prediction of allergen protein B7TWE7 (UniProt ID) from Fagus sylfatica (beechnut) have three-dimensional structure with identity value 72% and e-value = 3,4x10-58. This study used the 1e09A (PDB ID) of Prunus avinus (cherry) as a template.

Keywords: allergen, homology method, protein structure, swiss-model

 

ABSTRAK

Informasi struktur tiga dimensi protein penting untuk memahami sifat dan fungsi protein ditingkat molekular secara detil. Penentuan struktur protein dengan cara pengujian di laboratorium memerlukan tahapan dan instrumentasi dengan biaya tinggi. Struktur tiga dimensi protein dapat diprediksi secara ilmiah dengan menggunakan beberapa metode secara in silico. Metode yang digunakan pada penelitian ini adalah metode homologi menggunakan program SWISS-MODEL. Protein yang akan diprediksi struktur tiga dimensinya adalah protein alergen pangan. Hasil penelitian menunjukkan bahwa prediksi struktur protein alergen B7TWE7 (UniProt ID) dari Fagus sylfatica (beechnut) dengan metode homologi menggunakan program SWISS-MODEL menghasilkan model struktur tiga dimensi protein dengan nilai identity 72% dan e-value = 3,4x10-58. Template protein yang digunakan adalah 1e09A (PDB ID) dari Prunus avinus (cherry).

Kata kunci: alergen, metode homologi, struktur protein,  swiss-model



Keywords


allergen; homology method; protein structure; swiss-model

Full Text:

PDF

References


Baker, D. & Sali, A. (2001). Protein structure prediction and structural genomics. Science (New York, N.Y.), 294(5540), 93–6. doi:10.1126/science.1065659.

Berman, H., Henrick, K., Nakamura, H. & Markley, J. L. (2007). The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Research, 35(Database issue), D301–3. doi:10.1093/nar/gkl971.

Bordoli, L., Kiefer, F., Arnold, K., Benkert, P., Battey, J. & Schwede, T. (2009). Protein structure homology modeling using SWISS-MODEL workspace. Nature Protocols, 4(1), 1–13. doi:10.1038/ nprot.2008.197.

Chothia, C. (1992). Proteins. One thousand families for the molecular biologist. Nature, 357(6379), 543–4. doi:10.1038/ 357543a0.

Hardin, C., Pogorelov, T.V. & Luthey-Schulten, Z. (2002). Ab initio protein structure prediction. Current Opinion in Structural Biology, 12(2), 176-81. Retrieved from http://www.ncbi.nlm. nih.gov/pubmed/11959494.

Hauser, M., Wallner, M., Erler, A., Briza P. & Ferreira, F. (2008). Cloning and characterization of Fags 1, a Bet v 1 homologous pollen alergen from beech. EMBL/GenBank/DDBJ databases.

Hillisch, A., Pineda, L. F., & Hilgenfeld, R. (2004). Utility of homology models in the drug discovery process. Drug Discovery Today, 9(15), 659–69. doi:10.1016/S1359-6446(04)03196-4.

Hung, L-H. & Samudrala, R. (2003). PROTINFO: Secondary and tertiary protein structure prediction. Nucleic Acids Research, 3(13), 3296-9. Retrieved from http://www.ncbi.nlm.nih.gov/ pubmed/12824311.

Kopp, J. & Schwede, T. (2004). Automated protein structure homology modeling: a progress report. Pharmacogenomics, 5(4), 405-16. doi:10.1517/14622416.5.4. 405.

Kopp, J., Bordoli, L., Battey, J. N. D., Kiefer, F. & Schwede, T. (2007). Assessment of CASP7 predictions for template-based modeling targets. Proteins, 69 Suppl., 8, 38-46. doi:10.1002/prot.21753.

Mulder, N. & Apweiler, R. (2007). InterPro and InterProScan. Comparative Genomics, 396, 59-70. doi:10.1007/978-1-59745-515-2 5.

Murray (2006). Harper’s illustrated biochemistry. Boston, Mass.: McGraw-Hill.

Nelson, D.L., Cox, M.M. & Lahninger, A.L. (2005). Lehninger: Principles of biochemistry. New York: W.H. Freeman and Company.

Neudecker, P., Schweimer, K., Nerkamp, J., Scheurer, S., Vieths, S., Sticht, H. & Rösch, P. (2001). Allergic cross-reactivity made visible: solution structure of the major cherry allergen Pru av 1. The Journal of Biological Chemistry, 276(25), 22756-63. doi:10.1074/jbc. M101657200.

RCSB Protein Data Bank (RCSB PDB) Web site. (2016). PDB Current Holdings Breakdown. Retrieved January 19, 2016, from http://www.rcsb.org/pdb/statistics /holdings.do.

Rouvinen, J., Rautiainen, J, Virtanen, T., Zeiler, T., Kauppinen, J., Taivainen, A. & Mäntyjärvi, R. (1999). Probing the molecular basis of allergy. three-dimensional structure of the bovine lipocalin allergen Bos d 2. The Journal of Biological Chemistry, 274(4), 2337-43. Retrieved from http://www.ncbi.nlm. nih.gov/ pubmed/9891000.

Sali, A. & Blundell, Tzaki. L. (1993). Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology, 234(3), 779-815. doi:10.1006/jmbi.1993.1626.

Taylor, W.R., Alex, C.W., May, Nigel, P. Browny & Andras Aszodi. (2001). Protein Structure: Geometry, Topology and Classification. London: The Ridgeway.

Uniprot Web site. (2016). Sequence archive. Retrieved January 19, 2016, from http://www.uniprot.org/uniparc/.

Zaki, M. J. & Bystroff, C. (2008). Protein Structure Prediction, 2nd ed. USA: Humana Press/Springer.




DOI: http://dx.doi.org/10.36974/jbi.v7i2.692

Refbacks



BIOPROPAL Industri

Published by :

Institute for Industrial Research and Standardization (Baristand Industri) in Pontianak

Agency for Industrial Research and Development, Ministry of Industry 

Jl. Budi Utomo No. 41 Pontianak, West Kalimantan, Indonesia

Tel / Fax : +62 561 881393, 881533

email      : biopropal.industri@gmail.com

 

BIOPROPAL Industri indexed in: 

Hasil gambar untuk gambar doajHasil gambar untuk gambar google scholar