In Silico Analysis of Protein Disulfide Isomerases in Soybean

Öz

Protein disulfide isomerases are molecular chaperones containing the thioredoxin domain that are involved in the correct formation of disulfide bonds during the protein folding process. There are many studies investigating the catalytic and chaperone roles of PDI proteins in animals. Studies on the diversity and function of PDI proteins in plants are limited. In this study, the presence of 12 PDI genes in the soybean genome was shown with reference to the Arabidopsis PDI gene. The properties of the proteins belonging to these genes were revealed by in silico approaches. It was found that the active site-WCXXC motif was not conserved in the GmPDI6c and GmPDI6d proteins, but this sequence was present in other proteins. As a result of protein modeling, the protein with the highest GMQE score among soy PDI proteins was taken into consideration and its interaction with the coat protein of Tobacco ringspot virus was revealed through docking. The in silico analysis results obtained from the study need to be verified by experimental approaches.

Anahtar Kelimeler

• Soybean
• Protein disulfide isomerase (PDI)
• in silico
• protein-protein docking

Soyada Protein Disülfit İzomeraz’ların İn Silico Analizi

Öz

Protein disülfit izomerazlar protein katlanma sürecinde disülfit bağlarının doğru bir şekilde oluşmasında görev alan thioredoxin domaini içeren moleküler şaperonlardır. Hayvanlarda PDI proteinlerinin katalitik ve şaperon rollerinin araştırıldığı birçok çalışma mevcuttur. Bitkilerde ise PDI proteinlerinin varyasyonu ve fonksiyonu ile ilgili çalışmalar sınırlıdır. Bu çalışmada Arabidopsis PDI geni referans alınarak soya genomunda 12 PDI geninin varlığı gösterilmiş ve bu genlere ait proteinlerin özellikleri in silico yaklaşımlar ile ortaya konmuştur. WCXXC aktif dizi motifinin GmPDI6c ve GmPDI6d proteinlerinde korunmadığı ve diğer proteinlerde bu dizinin mevcut olduğu tespit edilmiştir. Protein modellemesi sonucunda soya PDI proteinlerinden GMQE skoru en yüksek olanı ele alınarak Tobacco ringspot virus’e ait kılıf proteini arasındaki etkileşim docking ile ortaya konmuştur. Çalışma sonucunda elde edilen in silico analiz sonuçlarının deneysel yaklaşımlar ile doğrulanması gerekmektedir.

Anahtar Kelimeler

• Soya
• Protein disülfit izomeraz (PDI)
• in silico
• protein-protein docking

Kaynakça

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