ArticleThe Journal of general physiology2004
On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation.
Article in The Journal of general physiology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed.
- Molecular basis of trypsin's autolysis resistance acetylation for sustained enzymatic activity.Food chemistry: X · 2026Article
- Identification of potential PIM-2 inhibitors via ligand-based generative models, molecular docking and molecular dynamics simulations.Molecular diversity · 2024Article
- Scaling of ionic conductance in a fluctuating single-layer nanoporous membrane.Scientific reports · 2023Article
- Antithetic effects of agonists and antagonists on the structural fluctuations of TRPV1 channel.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Synthesis and biological evaluation of substituted acetamide derivatives as potential butyrylcholinestrase inhibitors.Scientific reports · 2023Article
- Fluids and Electrolytes under Confinement in Single-Digit Nanopores.Chemical reviews · 2023Review
- Probing Structural Perturbation of Biomolecules by Extracting Cryo-EM Data Heterogeneity.Biomolecules · 2022Review
- Article
- Determinants of ion selectivity in ASIC1a- and ASIC2a-containing acid-sensing ion channels.The Journal of general physiology · 2020Article
- Picket-fences in the plasma membrane: functions in immune cells and phagocytosis.Seminars in immunopathology · 2018Review
- Site-specific ion occupation in the selectivity filter causes voltage-dependent gating in a viral KScientific reports · 2018Article
- Time-resolved measurements of an ion channel conformational change driven by a membrane phase transition.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- A glimpse into the C-type-inactivated state for a Potassium Channel.Nature structural & molecular biology · 2017Article
- Ion channels and ion selectivity.Essays in biochemistry · 2017Review
- Pore size matters for potassium channel conductance.The Journal of general physiology · 2016Review
- Computational investigation of dynamical transitions in Trp-cage miniprotein powders.Scientific reports · 2016Article
- Understanding Sodium Channel Function and Modulation Using Atomistic Simulations of Bacterial Channel Structures.Current topics in membranes · 2016Article
- Fe(2+) substrate transport through ferritin protein cage ion channels influences enzyme activity and biomineralization.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2015Article
- Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.The Journal of membrane biology · 2015Review
- Theoretical and simulation studies on voltage-gated sodium channels.Protein & cell · 2015Review
7 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Proteins, including ion channels, often are described in terms of some average structure and pictured as rigid entities immersed in a featureless solvent continuum. This simplified view, which provides for a convenient representation of the protein's overall structure, incurs the risk of deemphasizing important features underlying protein function, such as thermal fluctuations in the atom positions and the discreteness of the solvent molecules. These factors become particularly important in the case of ion movement through narrow pores, where the magnitude of the thermal fluctuations may be comparable to the ion pore atom separations, such that the strength of the ion channel interactions may vary dramatically as a function of the instantaneous configuration of the ion and the surrounding protein and pore water. Descriptions of ion permeation through narrow pores, which employ static protein structures and a macroscopic continuum dielectric solvent, thus face fundamental difficulties. We illustrate this using simple model calculations based on the gramicidin A and KcsA potassium channels, which show that thermal atomic fluctuations lead to energy profiles that vary by tens of kcal/mol. Consequently, within the framework of a rigid pore model, ion-channel energetics is extremely sensitive to the choice of experimental structure and how the space-dependent dielectric constant is assigned. Given these observations, the significance of any description based on a rigid structure appears limited. Creating a conducting channel model from one single structure requires substantial and arbitrary engineering of the model parameters, making it difficult for such approaches to contribute to our understanding of ion permeation at a microscopic level.
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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.