ArticleEuropean biophysics journal : EBJ2005
Influence of protein flexibility on the electrostatic energy landscape in gramicidin A.
Article in European biophysics journal : EBJ, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 18 citations in OpenAlex.
- Site-specific ion occupation in the selectivity filter causes voltage-dependent gating in a viral KScientific reports · 2018Article
- Dual mechanism of ion permeation through VDAC revealed with inorganic phosphate ions and phosphate metabolites.PloS one · 2015Article
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- Multiple Scales in the Simulation of Ion Channels and Proteins.The journal of physical chemistry. C, Nanomaterials and interfaces · 2010Article
- Conduction properties of KcsA measured using brownian dynamics with flexible carbonyl groups in the selectivity filter.Biophysical journal · 2007Article
- Ion permeation through a narrow channel: using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields.Biophysical journal · 2006Article
- Role of protein flexibility in ion permeation: a case study in gramicidin A.Biophysical journal · 2006Article
- Molecular dynamics simulations of proteins in lipid bilayers.Current opinion in structural biology · 2005Review
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We describe an electrostatic model of the gramicidin A channel that allows protein atoms to move in response to the presence of a permeating ion. To do this, molecular dynamics simulations are carried out with a permeating ion at various positions within the channel. Then an ensemble of atomic coordinates taken from the simulations are used to construct energy profiles using macroscopic electrostatic calculations. The energy profiles constructed are compared to experimentally-determined conductance data by inserting them into Brownian dynamics simulations. We find that the energy landscape seen by a permeating ion changes significantly when we allow the protein atoms to move rather than using a rigid protein structure. However, the model developed cannot satisfactorily reproduce all of the experimental data. Thus, even when protein atoms are allowed to move, the dielectric model used in our electrostatic calculations breaks down when modeling the gramicidin channel.
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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.