ArticleNucleic acids research2015
Absolute binding-free energies between standard RNA/DNA nucleobases and amino-acid sidechain analogs in different environments.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- RNA-binding protein transcripts reflect composition of target mRNAs.Nucleic acids research · 2026Article
- Decoding nucleic acid contributions to phase separation and ordering in biomolecular condensates.Nucleic acids research · 2026Article
- To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era.Briefings in bioinformatics · 2025Article
- NMolecular cell · 2024Article
- Multiscale Modeling of Protein-RNA Condensation in and Out of Equilibrium.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Widespread autogenous mRNA-protein interactions detected by CLIP-seq.Nucleic acids research · 2022Article
- Compositional complementarity between genomic RNA and coat proteins in positive-sense single-stranded RNA viruses.Nucleic acids research · 2022Article
- Programmable viscoelasticity in protein-RNA condensates with disordered sticker-spacer polypeptides.Nature communications · 2021Article
- Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA-protein complexes.Nucleic acids research · 2021Article
- RNA polymerase II-binding aptamers in human ACRO1 satellites disrupt transcriptionTranscription · 2020Article
- Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces.Life (Basel, Switzerland) · 2020Article
- A Mutation inJournal of clinical medicine · 2019Article
- Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins.PLoS computational biology · 2019Article
- Chimeric Translation for Mitochondrial Peptides: Regular and Expanded Codons.Computational and structural biotechnology journal · 2019Article
- Amino Acid Stabilization of Nucleic Acid Secondary Structure: Kinetic Insights from Single-Molecule Studies.The journal of physical chemistry. B · 2018Article
- RNA-protein interactions in an unstructured context.FEBS letters · 2018Review
- Mechanism of premature translation termination on a sense codon.The Journal of biological chemistry · 2018Article
- Quantifying Interactions of Nucleobase Atoms with Model Compounds for the Peptide Backbone and Glutamine and Asparagine Side Chains in Water.Biochemistry · 2018Article
- Inevitability of the emergence and persistence of genetic parasites caused by evolutionary instability of parasite-free states.Biology direct · 2017Article
- mRNA/protein sequence complementarity and its determinants: The impact of affinity scales.PLoS computational biology · 2017Article
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2 authors.
Funding
Abstract
Despite the great importance of nucleic acid-protein interactions in the cell, our understanding of their physico-chemical basis remains incomplete. In order to address this challenge, we have for the first time determined potentials of mean force and the associated absolute binding free energies between all standard RNA/DNA nucleobases and amino-acid sidechain analogs in high- and low-dielectric environments using molecular dynamics simulations and umbrella sampling. A comparison against a limited set of available experimental values for analogous systems attests to the quality of the computational approach and the force field used. Overall, our analysis provides a microscopic picture behind nucleobase/sidechain interaction preferences and creates a unified framework for understanding and sculpting nucleic acid-protein interactions in different contexts. Here, we use this framework to demonstrate a strong relationship between nucleobase density profiles of mRNAs and nucleobase affinity profiles of their cognate proteins and critically analyze a recent hypothesis that the two may be capable of direct, complementary interactions.
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