ArticleBiophysical journal2009
Mechanism and energetics of charybdotoxin unbinding from a potassium channel from molecular dynamics simulations.
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 19 papers.
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Who cites it
19 citing papers in PubMed.
- Complexes of Peptide Blockers with Kv1.6 Pore Domain: Molecular Modeling and Studies with KcsA-Kv1.6 Channel.Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2017Article
- Opposing Intermolecular Tuning of CaBiophysical journal · 2017Article
- Molecular Simulations of Disulfide-Rich Venom Peptides with Ion Channels and Membranes.Molecules (Basel, Switzerland) · 2017Review
- Biobetters From an Integrated Computational/Experimental Approach.Computational and structural biotechnology journal · 2017Review
- 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
- Computational methods of studying the binding of toxins from venomous animals to biological ion channels: theory and applications.Physiological reviews · 2013Review
- Computational studies of marine toxins targeting ion channels.Marine drugs · 2013Review
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- Absolute free energy of binding of avidin/biotin, revisited.The journal of physical chemistry. B · 2012Article
- Article
- Permeation and block of the Kv1.2 channel examined using brownian and molecular dynamics.Biophysical journal · 2011Article
- Modeling the binding of three toxins to the voltage-gated potassium channel (Kv1.3).Biophysical journal · 2011Article
- Calculation of the Absolute Free Energy of Binding and Related Entropies with the HSMD-TI Method: The FKBP12-L8 Complex.Journal of chemical theory and computation · 2011Article
- Accurate determination of the binding free energy for KcsA-charybdotoxin complex from the potential of mean force calculations with restraints.Biophysical journal · 2011Article
- New method for calculating the absolute free energy of binding: the effect of a mobile loop on the avidin/biotin complex.The journal of physical chemistry. B · 2011Article
- Modeling of the Binding of Peptide Blockers to Voltage-Gated Potassium Channels: Approaches and Evidence.Acta naturaeArticle
- Anti-inflammatory effects of FS48, the first potassium channel inhibitor from the salivary glands of the flea Xenopsylla cheopis.The Journal of biological chemistryArticle
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2 authors.
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Abstract
Ion channel-toxin complexes are ideal systems for computational studies of protein-ligand interactions, because, in most cases, the channel axis provides a natural reaction coordinate for unbinding of a ligand and a wealth of physiological data is available to check the computational results. We use a recently determined structure of a potassium channel-charybdotoxin complex in molecular dynamics simulations to investigate the mechanism and energetics of unbinding. Pairs of residues on the channel protein and charybdotoxin that are involved in the binding are identified, and their behavior is traced during umbrella-sampling simulations as charybdotoxin is moved away from the binding site. The potential of mean force for the unbinding of charybdotoxin is constructed from the umbrella sampling simulations using the weighted histogram analysis method, and barriers observed are correlated with specific breaking of interactions and influx of water molecules into the binding site. Charybdotoxin is found to undergo conformational changes as a result of the reaction coordinate choice--a nontrivial decision for larger ligands--which we explore in detail, and for which we propose solutions. Agreement between the calculated and the experimental binding energies is obtained once the energetic consequences of these conformational changes are included in the calculations.
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