ArticleBiophysical journal2005
Molecular dynamics of a protein surface: ion-residues interactions.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 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
28 citing papers in PubMed.
- Computational optimization of DEK1 calpain domain solubility through integrated structural modelling and data-driven targeted mutagenesis.Scientific reports · 2026Article
- Hofmeister-Driven Ion Pairing in Monovalent Salts Directs Fibrinogen Nanofiber Assembly during Drying.Biomacromolecules · 2025Article
- Host-Gated Enzymatic Release (H-GER) Enables Colorimetric Transduction for Enzyme Measurement.ACS applied materials & interfaces · 2025Article
- Designing of a novel chimeric antimicrobial peptide againstResearch in pharmaceutical sciences · 2025Article
- Balancing Group 1 Monoatomic Ion-Polar Compound Interactions in the Polarizable Drude Force Field: Application in Protein and Nucleic Acid Systems.The journal of physical chemistry. B · 2024Article
- Site Identification by Ligand Competitive Saturation-Biologics Approach for Structure-Based Protein Charge Prediction.Molecular pharmaceutics · 2023Article
- Article
- Preferential Binding of Lanthanides to Methanol Dehydrogenase Evaluated with Density Functional Theory.The journal of physical chemistry. B · 2021Article
- Aqueous ionic liquids redistribute local enzyme stability via long-range perturbation pathways.Computational and structural biotechnology journal · 2021Article
- Bioengineering of non-pathogenic Escherichia coli to enrich for accumulation of environmental copper.Scientific reports · 2020Article
- CAIX forms a transport metabolon with monocarboxylate transporters in human breast cancer cells.Oncogene · 2020Article
- Article
- Construction and characterization of metal ion-containing DNA nanowires for synthetic biology and nanotechnology.Scientific reports · 2019Article
- Membrane-anchored carbonic anhydrase IV interacts with monocarboxylate transporters via their chaperones CD147 and GP70.The Journal of biological chemistry · 2019Article
- The proteoglycan-like domain of carbonic anhydrase IX mediates non-catalytic facilitation of lactate transport in cancer cells.Oncotarget · 2018Article
- Membrane-Ion Interactions.The Journal of membrane biology · 2018Article
- A surface proton antenna in carbonic anhydrase II supports lactate transport in cancer cells.eLife · 2018Article
- Ion-induced alterations of the local hydration environment elucidate Hofmeister effect in a simple classical model of Trp-cage miniprotein.Journal of molecular modeling · 2017Article
- A theoretical and experimental study of calcium, iron, zinc, cadmium, and sodium ions absorption by aspartame.Journal of biological physics · 2017Article
- Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations.Journal of computational chemistry · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Time-resolved measurements indicated that protons could propagate on the surface of a protein or a membrane by a special mechanism that enhanced the shuttle of the proton toward a specific site. It was proposed that a suitable location of residues on the surface contributes to the proton shuttling function. In this study, this notion was further investigated by the use of molecular dynamics simulations, where Na(+) and Cl(-) are the ions under study, thus avoiding the necessity for quantum mechanical calculations. Molecular dynamics simulations were carried out using as a model a few Na(+) and Cl(-) ions enclosed in a fully hydrated simulation box with a small globular protein (the S6 of the bacterial ribosome). Three independent 10-ns-long simulations indicated that the ions and the protein's surface were in equilibrium, with rapid passage of the ions between the protein's surface and the bulk. However, it was noted that close to some domains the ions extended their duration near the surface, thus suggesting that the local electrostatic potential hindered their diffusion to the bulk. During the time frame in which the ions were detained next to the surface, they could rapidly shuttle between various attractor sites located under the electrostatic umbrella. Statistical analysis of the molecular dynamics and electrostatic potential/entropy consideration indicated that the detainment state is an energetic compromise between attractive forces and entropy of dilution. The similarity between the motion of free ions next to a protein and the proton transfer on the protein's surface are discussed.
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.