ArticleComputational and structural biotechnology journal2020
Structural insights into the mechanism of RNA recognition by the N-terminal RNA-binding domain of the SARS-CoV-2 nucleocapsid phosphoprotein.
Article in Computational and structural biotechnology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers, 1 of them a synthesis that pooled it.
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Who cites it
58 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A systematic review on impact of SARS-CoV-2 infection.Microbiological research · 2023Pooled it
- Characterization of the binding features between SARS-CoV-2 5'-proximal transcripts of genomic RNA and nucleocapsid proteins.RNA biology · 2025Review
- Article
- Structural Modelling of Krüppel-Like Factor 15 Zinc Finger Binding Domain to DNA Using AlphaFold 3.0: Potential Therapeutic Target for Type 2 Diabetes.Journal of cellular and molecular medicine · 2025Article
- Coupling of SARS-CoV-2 to Amyloid Fibrils and Liquid-Liquid Phase Separation.Current protein & peptide science · 2025Review
- Coordinated subdomain movements of MlaC regulate ligand binding and transport.Computational and structural biotechnology journal · 2025Article
- A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.Nature communications · 2024Article
- Comparative Atlas of SARS-CoV-2 Substitution Mutations: A Focus on Iranian Strains Amidst Global Trends.Viruses · 2024Article
- Impact of mutations on the stability of SARS-CoV-2 nucleocapsid protein structure.Scientific reports · 2024Article
- WGX50 mitigates doxorubicin-induced cardiotoxicity through inhibition of mitochondrial ROS and ferroptosis.Journal of translational medicine · 2023Article
- Structural and pKa Estimation of the Amphipathic HR1 in SARS-CoV-2: Insights from Constant pH MD, Linear vs. Nonlinear Normal Mode Analysis.International journal of molecular sciences · 2023Article
- Phytocompound screening, antioxidant activity and molecular docking studies of pomegranate seed: a preventive approach for SARS-CoV-2 pathogenesis.Scientific reports · 2023Article
- RETRACTED: Delineating Conformational Variability in Small Protein Structures Using Combinatorial Refinement StrategiesMicromachines · 2023Article
- Article
- Identification of a novel linear B-cell epitope in porcine deltacoronavirus nucleocapsid protein.Applied microbiology and biotechnology · 2023Article
- Liquid-liquid phase separation of nucleocapsid proteins during SARS-CoV-2 and HIV-1 replication.Cell reports · 2023Review
- Synthesis, Biological Evaluation, and Molecular Dynamics of Carbothioamides Derivatives as Carbonic Anhydrase II and 15-Lipoxygenase Inhibitors.Molecules (Basel, Switzerland) · 2022Article
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
- Investigation of the binding and dynamic features of A.30 variant revealed higher binding of RBD for hACE2 and escapes the neutralizing antibody: A molecular simulation approach.Computers in biology and medicine · 2022Article
- Computational Investigations of Traditional Chinese Medicinal Compounds against the Omicron Variant of SARS-CoV-2 to Rescue the Host Immune System.Pharmaceuticals (Basel, Switzerland) · 2022Article
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8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The emergence of recent SARS-CoV-2 has become a global health issue. This single-stranded positive-sense RNA virus is continuously spreading with increasing morbidities and mortalities. The proteome of this virus contains four structural and sixteen nonstructural proteins that ensure the replication of the virus in the host cell. However, the role of phosphoprotein (N) in RNA recognition, replicating, transcribing the viral genome, and modulating the host immune response is indispensable. Recently, the NMR structure of the N-terminal domain of the Nucleocapsid Phosphoprotein has been reported, but its precise structural mechanism of how the ssRNA interacts with it is not reported yet. Therefore, here, we have used an integrated computational pipeline to identify the key residues, which play an essential role in RNA recognition. We generated multiple variants by using an alanine scanning strategy and performed an extensive simulation for each system to signify the role of each interfacial residue. Our analyses suggest that residues T57A, H59A, S105A, R107A, F171A, and Y172A significantly affected the dynamics and binding of RNA. Furthermore, per-residue energy decomposition analysis suggests that residues T57, H59, S105 and R107 are the key hotspots for drug discovery. Thus, these residues may be useful as potential pharmacophores in drug designing.
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