ArticleNucleic acids research2014
Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 88 citations in OpenAlex.
- C-MET tyrosine kinase receptor: mechanisms, clinical applications and future perspectives in cancer therapy.Signal transduction and targeted therapy · 2026Review
- A truncated aptamer-based electrochemical sensor for sensitive Ara h 1 determination on gold nanoparticle-modified screen-printed electrodes.Mikrochimica acta · 2026Article
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- Elucidating the solution structure of the monomolecularChemical science · 2025Article
- DNA-based hydrogels for bone regeneration: A promising tool for bone organoids.Materials today. Bio · 2025Review
- Recent Advances and Prospects of Nucleic Acid Therapeutics for Anti-Cancer Therapy.Molecules (Basel, Switzerland) · 2024Review
- Application of a dual-modality colorimetric analysis method to inkjet printing lateral flow detection of Salmonella typhimurium.Mikrochimica acta · 2024Article
- Role of Natural Binding Proteins in Therapy and Diagnostics.Life (Basel, Switzerland) · 2024Article
- Comprehensive analysis of intramolecular G-quadruplex structures: furthering the understanding of their formalism.Nucleic acids research · 2024Article
- Aptamers as an approach to targeted cancer therapy.Cancer cell international · 2024Review
- Improving the accuracy of the FMO binding affinity prediction of ligand-receptor complexes containing metals.Journal of computer-aided molecular design · 2023Article
- Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies.International journal of molecular sciences · 2023Review
- Exploring the Potential of Aptamers in Targeting Neuroinflammation and Neurodegenerative Disorders: Opportunities and Challenges.International journal of molecular sciences · 2023Review
- Functional regulation of an intrinsically disordered protein via a conformationally excited state.Science advances · 2023Article
- Analysis of aptamer-target binding and molecular mechanisms by thermofluorimetric analysis and molecular dynamics simulation.Frontiers in chemistry · 2023Article
- Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field.Nucleic acids research · 2022Article
- Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets.Biosensors · 2022Review
- Deep structural insights into RNA-binding disordered protein regions.Wiley interdisciplinary reviews. RNA · 2022Review
- Unraveling the binding mode of a methamphetamine aptamer: A spectroscopic and calorimetric study.Biophysical journal · 2022Article
- Non-canonical DNA structures: Diversity and disease association.Frontiers in genetics · 2022Review
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6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is a central issue to elucidate the new type of molecular recognition accompanied by a global structural change of a molecule upon binding to its targets. Here we investigate the driving force for the binding of R12 (a ribonucleic acid aptamer) and P16 (a partial peptide of a prion protein) during which P16 exhibits the global structural change. We calculate changes in thermodynamic quantities upon the R12-P16 binding using a statistical-mechanical approach combined with molecular models for water which is currently best suited to studies on hydration of biomolecules. The binding is driven by a water-entropy gain originating primarily from an increase in the total volume available to the translational displacement of water molecules in the system. The energy decrease due to the gain of R12-P16 attractive (van der Waals and electrostatic) interactions is almost canceled out by the energy increase related to the loss of R12-water and P16-water attractive interactions. We can explain the general experimental result that stacking of flat moieties, hydrogen bonding and molecular-shape and electrostatic complementarities are frequently observed in the complexes. It is argued that the water-entropy gain is largely influenced by the geometric characteristics (overall shapes, sizes and detailed polyatomic structures) of the biomolecules.
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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.