Medizinische Universität Graz Austria/Österreich - Forschungsportal - Medical University of Graz
Gewählte Publikation:
SHR Neuro Krebs Kardio Lipid Stoffw Microb
Esfandiari, N; Sefidbakht, Y.
An isolate of Potato Virus X capsid protein from N. benthamiana: Insights from homology modeling and molecular dynamics simulation.
Int J Biol Macromol. 2018; 116: 939-946.
Doi: 10.1016/j.ijbiomac.2018.05.042
Web of Science
PubMed
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- Esfandiari Neda
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- Abstract:
- Since Potato Virus X (PVX) is easily transmitted mechanically between their hosts, its control is difficult. We have previously reported new isolate of this virus (PVX-Iran, GenBank Accession number FJ461343). However, the molecular basis of resistance breaking activity and its relation to capsid protein structure are still not well-understood. SDS-PAGE, ELISA, Western blot and RT-PCR molecular examinations were performed on the inoculated plants Nicotiana benthamiana. The pathological symptoms were related to the PVX isolate. The capsid protein (CP) structure were modeled based on homology and subjected to three independent 80 ns molecular dynamics minimization (GROMACS, OPLS force field) in the SPC water box. The RMSD, RMSF, SASA, and electrostatic properties were retrieved from the trajectories. Flexibility and hydrophilic nature of the N-terminal residues (1-34) of solvated CP could be observed in conformational changes upon minimization. The obtained structure was then docked with NbPCIP1 using ClusPro 2.0. The strong binding affinity of these two proteins (≈-16.0 Kcal mol-1) represents the formation of inclusion body and hence appearance of the symptoms.
- Find related publications in this database (using NLM MeSH Indexing)
- Capsid Proteins - chemistry, metabolism
- Molecular Docking Simulation - administration & dosage
- Molecular Dynamics Simulation - administration & dosage
- Potexvirus - chemistry, metabolism
- Nicotiana - chemistry, metabolism, virology
- Find related publications in this database (Keywords)
- Potato Virus X
- Capsid protein
- Pathology
- Molecular dynamics