ArticleBiophysical journal2009
Importance of the peptide backbone description in modeling the selectivity filter in potassium channels.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 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
12 citing papers in PubMed, 23 citations in OpenAlex.
- Biobetters From an Integrated Computational/Experimental Approach.Computational and structural biotechnology journal · 2017Review
- Article
- Article
- Computational approaches for designing potent and selective analogs of peptide toxins as novel therapeutics.Future medicinal chemistry · 2014Review
- Molecular dynamics study of binding of µ-conotoxin GIIIA to the voltage-gated sodium channel Na(v)1.4.PloS one · 2014Article
- Energetics of Multi-Ion Conduction Pathways in Potassium Ion Channels.Journal of chemical theory and computation · 2013Article
- The mechanism of Na⁺/K⁺ selectivity in mammalian voltage-gated sodium channels based on molecular dynamics simulation.Biophysical journal · 2013Article
- Computational studies of marine toxins targeting ion channels.Marine drugs · 2013Review
- High-risk long QT syndrome mutations in the Kv7.1 (KCNQ1) pore disrupt the molecular basis for rapid K(+) permeation.Biochemistry · 2012Article
- Molecular dynamics simulations of membrane proteins.Biophysical reviews · 2012Review
- Comparative study of the energetics of ion permeation in Kv1.2 and KcsA potassium channels.Biophysical journal · 2011Article
- Selective complexation of K+ and Na+ in simple polarizable ion-ligating systems.Journal of the American Chemical Society · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A dihedral energy correction (CMAP) term has been recently included in the CHARMM force field to obtain a more accurate description of the peptide backbone. Its importance in improving dynamical properties of proteins and preserving their stability in long molecular-dynamics simulations has been established for several globular proteins. Here we investigate its role in maintaining the structure and function of two potassium channels, Shaker K(v)1.2 and KcsA, by performing molecular-dynamics simulations with and without the CMAP correction in otherwise identical systems. We show that without CMAP, it is not possible to maintain the experimentally observed orientations of the carbonyl groups in the selectivity filter in Shaker, and the channel loses its selectivity property. In the case of KcsA, the channel retains some selectivity even without CMAP because the carbonyl orientations are relatively better preserved compared to Shaker.
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.