ArticlePLoS computational biology2010
Non-bulk-like solvent behavior in the ribosome exit tunnel.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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Who cites it
22 citing papers in PubMed, 47 citations in OpenAlex.
- Evolution of the ribosomal exit tunnel through the eyes of the nascent chain.Nucleic acids research · 2026Article
- Disease-associated Kv1.3 Variants are Energy Compromised with Impaired Nascent Chain Folding.Journal of molecular biology · 2025Article
- Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding.Journal of chemical information and modeling · 2024Article
- Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel.Nucleic acids research · 2022Article
- Hydrophobic and electrostatic interactions modulate protein escape at the ribosomal exit tunnel.Biophysical journal · 2021Article
- An intrinsically disordered nascent protein interacts with specific regions of the ribosomal surface near the exit tunnel.Communications biology · 2021Article
- The driving force for co-translational protein folding is weaker in the ribosome vestibule due to greater water ordering.Chemical science · 2021Article
- A noncanonical binding site of linezolid revealed via molecular dynamics simulations.Journal of computer-aided molecular design · 2020Article
- Cotranslational Folding of Proteins on the Ribosome.Biomolecules · 2020Review
- Differences in the path to exit the ribosome across the three domains of life.Nucleic acids research · 2019Article
- Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR.Current opinion in structural biology · 2019Review
- The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation.PLoS genetics · 2018Article
- Effect of Nascent Peptide Steric Bulk on Elongation Kinetics in the Ribosome Exit Tunnel.Journal of molecular biology · 2017Article
- Determinants of Helix Formation for a Kv1.3 Transmembrane Segment inside the Ribosome Exit Tunnel.Journal of molecular biology · 2017Article
- Chemistry in nanoconfined water.Chemical science · 2017Article
- Using simulations to provide the framework for experimental protein folding studies.Archives of biochemistry and biophysics · 2013Review
- Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding.Nature structural & molecular biology · 2013Article
- Computational studies of molecular machines: the ribosome.Current opinion in structural biology · 2012Review
- Nascent peptide side chains induce rearrangements in distinct locations of the ribosomal tunnel.Journal of molecular biology · 2011Article
- Free energy of nascent-chain folding in the translocon.Journal of the American Chemical Society · 2011Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
As nascent proteins are synthesized by the ribosome, they depart via an exit tunnel running through the center of the large subunit. The exit tunnel likely plays an important part in various aspects of translation. Although water plays a key role in many bio-molecular processes, the nature of water confined to the exit tunnel has remained unknown. Furthermore, solvent in biological cavities has traditionally been characterized as either a continuous dielectric fluid, or a discrete tightly bound molecule. Using atomistic molecular dynamics simulations, we predict that the thermodynamic and kinetic properties of water confined within the ribosome exit tunnel are quite different from this simple two-state model. We find that the tunnel creates a complex microenvironment for the solvent resulting in perturbed rotational dynamics and heterogenous dielectric behavior. This gives rise to a very rugged solvation landscape and significantly retarded solvent diffusion. We discuss how this non-bulk-like solvent is likely to affect important biophysical processes such as sequence dependent stalling, co-translational folding, and antibiotic binding. We conclude with a discussion of the general applicability of these results to other biological cavities.
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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.