ArticleBiophysical journal2008
Conformational sampling of peptides in cellular environments.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed.
- Energetic and durable all-polymer aqueous battery for sustainable, flexible power.Nature communications · 2024Article
- BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation.Journal of chemical information and modeling · 2024Article
- Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding.Journal of chemical information and modeling · 2024Article
- What determines sub-diffusive behavior in crowded protein solutions?Biophysical journal · 2024Article
- Modeling Crowded Environment in Molecular Simulations.Frontiers in molecular biosciences · 2019Review
- Definition of the Minimal Contents for the Molecular Simulation of the Yeast Cytoplasm.Frontiers in molecular biosciences · 2019Article
- Co-translational folding of α-helical proteins: structural studies of intermediate-length variants of the λ repressor.FEBS open bio · 2018Article
- Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments.BMC biophysics · 2018Article
- Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.The journal of physical chemistry. B · 2017Article
- Article
- Structural studies of the N-terminal fragments of the WW domain: Insights into co-translational folding of a beta-sheet protein.Scientific reports · 2016Article
- Thermal Stability of RNA Structures with Bulky Cations in Mixed Aqueous Solutions.Biophysical journal · 2016Article
- The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents.Biophysical reviews · 2016Review
- Characterizing the Conformational Landscape of Flavivirus Fusion Peptides via Simulation and Experiment.Scientific reports · 2016Article
- Effects of background anionic compounds on the activity of the hammerhead ribozyme in Mg(2+)-unsaturated solutions.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2015Article
- Conformational preferences of DNA in reduced dielectric environments.The journal of physical chemistry. B · 2014Article
- Article
- Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds.FEBS open bio · 2014Article
- Equilibrium and folding simulations of NS4B H2 in pure water and water/2,2,2-trifluoroethanol mixed solvent: examination of solvation models.Journal of molecular modeling · 2013Article
- Reaching new levels of realism in modeling biological macromolecules in cellular environments.Journal of molecular graphics & modelling · 2013Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Biological systems provide a complex environment that can be understood in terms of its dielectric properties. High concentrations of macromolecules and cosolvents effectively reduce the dielectric constant of cellular environments, thereby affecting the conformational sampling of biomolecules. To examine this effect in more detail, the conformational preference of alanine dipeptide, poly-alanine, and melittin in different dielectric environments is studied with computer simulations based on recently developed generalized Born methodology. Results from these simulations suggest that extended conformations are favored over alpha-helical conformations at the dipeptide level at and below dielectric constants of 5-10. Furthermore, lower-dielectric environments begin to significantly stabilize helical structures in poly-alanine at epsilon = 20. In the more complex peptide melittin, different dielectric environments shift the equilibrium between two main conformations: a nearly fully extended helix that is most stable in low dielectrics and a compact, V-shaped conformation consisting of two helices that is preferred in higher dielectric environments. An additional conformation is only found to be significantly populated at intermediate dielectric constants. Good agreement with previous studies of different peptides in specific, less-polar solvent environments, suggest that helix stabilization and shifts in conformational preferences in such environments are primarily due to a reduced dielectric environment rather than specific molecular details. The findings presented here make predictions of how peptide sampling may be altered in dense cellular environments with reduced dielectric response.
Indexed as
Identifiers
What OpenQuestion holds
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.