ArticleJournal of the American Chemical Society2006
Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain.
Article in Journal of the American Chemical Society, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 87 citations in OpenAlex.
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- Nicotinic receptor pharmacology in silico: Insights and challenges.Neuropharmacology · 2020Review
- In Silico Modeling of the α7 Nicotinic Acetylcholine Receptor: New Pharmacological Challenges Associated with Multiple Modes of Signaling.Mini reviews in medicinal chemistry · 2020Review
- Catalytic transport of molecular cargo using diffusive binding along a polymer track.Nature chemistry · 2019Article
- Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge.Journal of computer-aided molecular design · 2018Article
- Theoretical and Experimental Studies on Inclusion Complexes of Pinostrobin and β-Cyclodextrins.Scientia pharmaceutica · 2018Article
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- Key Residues and Phosphate Release Routes in the Saccharomyces cerevisiae Pho84 Transceptor: THE ROLE OF TYR179 IN FUNCTIONAL REGULATION.The Journal of biological chemistry · 2016Article
- A Self-Adaptive Steered Molecular Dynamics Method Based on Minimization of Stretching Force Reveals the Binding Affinity of Protein-Ligand Complexes.Molecules (Basel, Switzerland) · 2015Article
- Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics.PloS one · 2014Article
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- Investigation of indazole unbinding pathways in CYP2E1 by molecular dynamics simulations.PloS one · 2012Article
- Slow dissociation of a charged ligand: analysis of the primary quinone Q(A) site of photosynthetic bacterial reaction centers.Journal of the American Chemical Society · 2011Article
- Biophysical and computational studies of membrane penetration by the GRP1 pleckstrin homology domain.Structure (London, England : 1993) · 2011Article
- Probing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods.The Journal of biological chemistry · 2011Article
- Accurate determination of the binding free energy for KcsA-charybdotoxin complex from the potential of mean force calculations with restraints.Biophysical journal · 2011Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 3 institutions in 1 country.
Funding
Abstract
The nicotinic acetylcholine receptor is a prototype ligand-gated ion channel that mediates signal transduction in the neuromuscular junctions and other cholinergic synapses. The molecular basis for the energetics of ligand binding and unbinding is critical to our understanding of the pharmacology of this class of receptors. Here, we used steered molecular dynamics to investigate the unbinding of acetylcholine from the ligand-binding domain of human alpha7 nicotinic acetylcholine receptor along four different predetermined pathways. Pulling forces were found to correlate well with interactions between acetylcholine and residues in the binding site during the unbinding process. From multiple trajectories along these unbinding pathways, we calculated the potentials of mean force for acetylcholine unbinding. Four available methods based on Jarzynski's equality were used and compared for their efficiencies. The most probable pathway was identified to be along a direction approximately parallel to the membrane. The derived binding energy for acetylcholine was in good agreement with that derived from the experimental binding constant for acetylcholine binding protein, but significantly higher than that for the complete human alpha7 nicotinic acetylcholine receptor. In addition, it is likely that several intermediate states exist along the unbinding pathways.
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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.