ArticleNucleic acids research2019
Understanding the binding specificities of mRNA targets by the mammalian Quaking protein.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Interaction of circular RNAs with splicing factors in cervical cancer: Modulation, interplay and theranostics (Review).Molecular medicine reports · 2026Review
- Ubiquitin's code: UPS orchestrating DNA repair and genomic stability under genotoxic stress.Molecular and cellular biochemistry · 2026Review
- Exploring the impact of deleterious missense nonsynonymous single nucleotide polymorphisms in the DRD4 gene using computational approaches.Scientific reports · 2025Article
- Exosome miRNA sorting controlled by RNA-binding protein-motif interactions.Extracellular vesicles and circulating nucleic acids · 2025Review
- ABCB1 Polymorphism in HIV-Infected Individuals Taking Antiretroviral Drugs.AIDS research and treatment · 2025Article
- Bioinformatics and computational studies of chabamide F and chabamide G for breast cancer and their probable mechanisms of action.Scientific reports · 2024Article
- Mutant KRAS Mediates circARFGEF2 Biogenesis to Promote Lymphatic Metastasis of Pancreatic Ductal Adenocarcinoma.Cancer research · 2023Article
- Emerging Roles of RNA-Binding Proteins in Neurodevelopment.Journal of developmental biology · 2022Review
- Regulation of the Proliferation of Diabetic Vascular Endothelial Cells by Degrading Endothelial Cell Functional Genes with QKI-7.Contrast media & molecular imaging · 2022Article
- Qki activates Srebp2-mediated cholesterol biosynthesis for maintenance of eye lens transparency.Nature communications · 2021Article
- MD simulations reveal the basis for dynamic assembly of Hfq-RNA complexes.The Journal of biological chemistryArticle
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Authors and funding
3 authors.
Funding
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Abstract
Mammalian Quaking (QKI) protein, a member of STAR family of proteins is a mRNA-binding protein, which post-transcriptionally modulates the target RNA. QKI protein possesses a maxi-KH domain composed of single heterogeneous nuclear ribonucleoprotein K homology (KH) domain and C-terminal QUA2 domain, that binds a sequence-specific QKI RNA recognition element (QRE), CUAAC. To understand the binding specificities for different mRNA sequences of the KH-QUA2 domain of QKI protein, we introduced point mutations at different positions in the QRE resulting in twelve different mRNA sequences with single nucleotide change. We carried out long unbiased molecular dynamics simulations using two different sets of recently updated forcefield parameters: AMBERff14SB+RNAχOL3 and CHARMM36 (with CMAP correction). We analyzed the changes in intermolecular dynamics as a result of mutation. Our results show that AMBER forcefields performed better to model the interactions between mRNA and protein. We also calculated the binding affinities of different mRNA sequences and found that the relative order correlates to the reported experimental studies. Our study shows that the favorable binding with the formation of stable complex will occur when there is an increase of the total intermolecular contacts between mRNA and protein, but without the loss of native contacts within the KH-QUA domain.
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