ArticleJournal of molecular modeling2011
Molecular dynamics studies of the 3D structure and planar ligand binding of a quadruplex dimer.
Article in Journal of molecular modeling, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Article
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- Review
- Identification of FDA-approved drugs with triple targeting mode of action for the treatment of monkeypox: a high throughput virtual screening study.Molecular diversity · 2024Article
- Comprehensive Molecular Interaction Studies to Construe the Repellent/Kill Activity of Geraniol During Binding Event Against Aedes aegypti Proteins.Molecular biotechnology · 2023Article
- Translational vaccinomics and structural filtration algorithm to device multiepitope vaccine for catastrophic monkeypox virus.Computers in biology and medicine · 2023Article
- Comparative Dynamic Features of Apo and Bound MDM2 Protein Reveal the Mechanism of Inhibitor Recognition for Anti-Cancer Activity.Current medicinal chemistry · 2023Article
- Functional metagenomics uncovers nitrile-hydrolysing enzymes in a coal metagenome.Frontiers in molecular biosciences · 2023Article
- In Silico Studies on Zinc Oxide Based Nanostructured Oil Carriers with Seed Extracts ofMolecules (Basel, Switzerland) · 2022Article
- Investigating Structural Dynamics of KCNE3 in Different Membrane Environments Using Molecular Dynamics Simulations.Membranes · 2022Article
- Kidney injury molecule-1 is a potential receptor for SARS-CoV-2.Journal of molecular cell biology · 2021Article
- Enhanced Rigidity Changes Ultraviolet Absorption: Effect of a Merocyanine Binder on G-Quadruplex Photophysics.The journal of physical chemistry letters · 2020Article
- Computational Approaches to Prioritize Cancer Driver Missense Mutations.International journal of molecular sciences · 2018Review
- Probing the Limits of Supramolecular G-Quadruplexes Using Atomistic Molecular Dynamics Simulations.Inorganica chimica acta · 2017Article
- Molecular modeling of methyl-α-Neu5Ac analogues docked against cholera toxin--a molecular dynamics study.Glycoconjugate journal · 2015Article
- Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures.Methods (San Diego, Calif.) · 2012Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
G-rich sequences can fold into a four-stranded structure called a G-quadruplex, and sequences with short loops are able to aggregate to form stable quadruplex multimers. Few studies have characterized the properties of this variety of quadruplex multimers. Using molecular modeling and molecular dynamics simulations, the present study investigated a dimeric G-quadruplex structure formed from a simple sequence of d(GGGTGGGTGGGTGGGT) (G1), and its interactions with a planar ligand of a perylene derivative (Tel03). A series of analytical methods, including free energy calculations and principal components analysis (PCA), was used. The results show that a dimer structure with stacked parallel monomer structures is maintained well during the entire simulation. Tel03 can bind to the dimer efficiently through end stacking, and the binding mode of the ligand stacked with the 3'-terminal thymine base is most favorable. PCA showed that the dominant motions in the free dimer occur on the loop regions, and the presence of the ligand reduces the flexibility of the loops. Our investigation will assist in understanding the geometric structure of stacked G-quadruplex multimers and may be helpful as a platform for rational drug design.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.