Molecular Dynamics Simulation Reveals Exposed Residues in the Ligand-Binding Domain of the Low-Density Lipoprotein Receptor that Interacts with Vesicular Stomatitis Virus-G Envelope
Abstract
:1. Introduction
2. Material and Methods
2.1. Construction of a 5′-LDLReGFP-3′ Fusion Cassette and Packaging of a Lentiviral Vector (LVV)
2.2. Transfection of 293T Cells Using Lipofectamine
2.3. Packaging and Transduction of 293T/HepG2 Cells with Supernatant
2.4. PCR using RNA from Viral Supernatant
2.5. Target Sequence, Template Identification, and Sequence Alignment
2.6. Protein Structure Modeling and Binding Site Prediction
2.7. Molecular Docking and Molecular Dynamics (MD) Simulation
2.8. Constructs with Mutations and Sequential Deletions at 3′ and 5′ Ends of the LDLR cDNA or Liver-Specific Promoter
2.9. Data Availability Statement
3. Results
3.1. Transduction of 293T Cells with eGFP or pLDLR–eGFP
3.2. Docking Calculation and Protein–Protein Interaction Determination through MD Simulation
3.3. Functional Effect of Mutations and Sequential Deletions at the 3′ End of LDLR cDNA
3.4. Effect of a Liver-Specific Promoter and Sequential Deletions at the 5′ End of the LDLR cDNA on the Packaging of LDLR–eGFP
3.5. Interaction between VSV-G Protein and LDLR
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Al-Allaf, F.A.; Abduljaleel, Z.; Taher, M.M.; Abdellatif, A.A.H.; Athar, M.; Bogari, N.M.; Al-Ahdal, M.N.; Al-Mohanna, F.; Al-Hassnan, Z.N.; Alzabeedi, K.H.Y.; et al. Molecular Dynamics Simulation Reveals Exposed Residues in the Ligand-Binding Domain of the Low-Density Lipoprotein Receptor that Interacts with Vesicular Stomatitis Virus-G Envelope. Viruses 2019, 11, 1063. https://doi.org/10.3390/v11111063
Al-Allaf FA, Abduljaleel Z, Taher MM, Abdellatif AAH, Athar M, Bogari NM, Al-Ahdal MN, Al-Mohanna F, Al-Hassnan ZN, Alzabeedi KHY, et al. Molecular Dynamics Simulation Reveals Exposed Residues in the Ligand-Binding Domain of the Low-Density Lipoprotein Receptor that Interacts with Vesicular Stomatitis Virus-G Envelope. Viruses. 2019; 11(11):1063. https://doi.org/10.3390/v11111063
Chicago/Turabian StyleAl-Allaf, Faisal A., Zainularifeen Abduljaleel, Mohiuddin M. Taher, Ahmed A. H. Abdellatif, Mohammad Athar, Neda M. Bogari, Mohammed N. Al-Ahdal, Futwan Al-Mohanna, Zuhair N. Al-Hassnan, Kamal H. Y. Alzabeedi, and et al. 2019. "Molecular Dynamics Simulation Reveals Exposed Residues in the Ligand-Binding Domain of the Low-Density Lipoprotein Receptor that Interacts with Vesicular Stomatitis Virus-G Envelope" Viruses 11, no. 11: 1063. https://doi.org/10.3390/v11111063