Potato virus S (PVS)-Bitlis izolatının Kılıf Proteinin in silico Karakterizasyonu ve Konak Proteini ile Docking Analizi

Abstract

Patates virus S (PVS) dünya çapında yaygın olan virüslerden biridir ve patates bitkilerinde genellikle orta düzeyde simptomlar oluşturur. Viral proteinlerin konakçılarıyla etkileşimleri başarılı bir enfeksiyon oluşturmada ve sistemik yayılmayı sağlamada oldukça önemlidir. Bu çalışmada PVS’nün kılıf proteini (CP) ve patates bitkisi tarafından kodlanan savunma sisteminde yer alan PSH-RGH6 proteini arasındaki interaksiyon homoloji modelleme ve protein-protein docking yaklaşımı kullanılarak araştırılmıştır. PVS-Bitlis izolatının CP geni gen spesifik primerler kullanılarak RT-PCR ile çoğaltıldı. İlgili gen pGEM-T Easy vektöre klonlandı ve PVS-Bitlis CP genini taşıyan plazmid sekanslandı. Elde edilen sekansa ait amino ait dizisi kullanılarak I-TASSER programı ile homolojiye ait protein modeli oluşturuldu. PSH-RGH6 proteini için Swiss-model programı kullanılarak proteine ait model oluşturuldu. Her iki proteine ait modeller arasında interaksiyon Chimera 1.15 programında AutoDock yaklaşımı ile araştırıldı. Docking sonucuna göre PVS-Bitlis CP ve PSH-RGH6 proteinleri arasında interaksiyon varlığı belirlenmiş olup bu interaksiyonun ayrıntılı analizler ile doğrulanması gerekmektedir.

Keywords

• PVS
• Patates
• Protein-protein interaksiyonu
• Docking

In Silico Characterization of Coat Protein of PVS-Bitlis Isolate and Docking Analysis with Host Protein

Abstract

Potato virus S (PVS) is one of the common viruses worldwide and usually produces moderate symptoms in potato plants. The interactions of viral proteins with their hosts are very important in establishing a successful infection and ensuring systemic spread. In this study, the interaction between the PVS coat protein (CP) and the PSH-RGH6 protein in the defense system encoded by the potato plant was investigated using homology modeling and protein-protein docking approach. The CP gene of the PVS-Bitlis isolate was amplified by RT-PCR using gene-specific primers. The gene of interest was cloned into the pGEM-T Easy vector and the plasmid carrying the PVS-Bitlis CP gene was sequenced. By using the amino subsequence of the obtained sequence, I-TASSER program created a protein model based on homology. For the PSH-RGH6 protein, a model of the protein was created using the Swiss-model program. The interaction among both proteins was investigated with the AutoDock approach in Chimera 1.15 program. According to the docking results, the existence of interaction between PVS-Bitlis CP and PSH-RGH6 proteins has been determined and this interaction needs to be confirmed with further analysis.

Keywords

• PVS
• Potato
• Protein-protein interaction
• Docking

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