ArticleThe journal of physical chemistry. B2017
Role of Electrostatics in Protein-RNA Binding: The Global vs the Local Energy Landscape.
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 28 citations in OpenAlex.
- AMPK modulates a DEAH box RNA-helicase to attenuate TOR signaling and establish developmental quiescence in Caenorhabditis elegans.PLoS biology · 2025Article
- Noncanonical RNA binding of human La-related protein 6.Nucleic acids research · 2025Article
- RNAproDB: A Webserver and Interactive Database for Analyzing Protein-RNA Interactions.Journal of molecular biology · 2025Article
- Functionality of IAV packaging signals depends on site-specific charges within the viral nucleoprotein.Journal of virology · 2024Article
- Electrostatic complementarity at the interface drives transient protein-protein interactions.Scientific reports · 2023Article
- Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids.Journal of molecular biology · 2022Review
- Spliceosomal SL1 RNA binding to U1-70K: the role of the extended RRM.Nucleic acids research · 2022Article
- Unraveling the Role of Charge Patterning in the Micellar Structure of Sequence-Defined Amphiphilic Peptoid Oligomers by Molecular Dynamics Simulations.Macromolecules · 2022Article
- Article
- Protein electrostatics: From computational and structural analysis to discovery of functional fingerprints and biotechnological design.Computational and structural biotechnology journal · 2020Review
- Computational approaches to macromolecular interactions in the cell.Current opinion in structural biology · 2019Review
- Crimean-Congo hemorrhagic fever virus nucleocapsid protein harbors distinct RNA-binding sites in the stalk and head domains.The Journal of biological chemistry · 2019Article
- Modeling Electrostatic Force in Protein-Protein Recognition.Frontiers in molecular biosciences · 2019Article
- A structural dissection of protein-RNA interactions based on different RNA base areas of interfaces.RSC advances · 2018Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
U1A protein-stem loop 2 RNA association is a basic step in the assembly of the spliceosomal U1 small nuclear ribonucleoprotein. Long-range electrostatic interactions due to the positive charge of U1A are thought to provide high binding affinity for the negatively charged RNA. Short range interactions, such as hydrogen bonds and contacts between RNA bases and protein side chains, favor a specific binding site. Here, we propose that electrostatic interactions are as important as local contacts in biasing the protein-RNA energy landscape toward a specific binding site. We show by using molecular dynamics simulations that deletion of two long-range electrostatic interactions (K22Q and K50Q) leads to mutant-specific alternative RNA bound states. One of these states preserves short-range interactions with aromatic residues in the original binding site, while the other one does not. We test the computational prediction with experimental temperature-jump kinetics using a tryptophan probe in the U1A-RNA binding site. The two mutants show the distinct predicted kinetic behaviors. Thus, the stem loop 2 RNA has multiple binding sites on a rough RNA-protein binding landscape. We speculate that the rough protein-RNA binding landscape, when biased to different local minima by electrostatics, could be one way that protein-RNA interactions evolve toward new binding sites and novel function.
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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.