ArticleBiophysical journal2011
Accurate determination of the binding free energy for KcsA-charybdotoxin complex from the potential of mean force calculations with restraints.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed.
- Molecular Mechanisms Underlying Medium-Chain Free Fatty Acid-Regulated Activity of the Phospholipase PlaF fromJACS Au · 2024Article
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- Tetracycline as an inhibitor to the SARS-CoV-2.Journal of cellular biochemistry · 2021Article
- On Restraints in End-Point Protein-Ligand Binding Free Energy Calculations.Journal of computational chemistry · 2020Article
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- 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
- Sulfonanilide Derivatives in Identifying Novel Aromatase Inhibitors by Applying Docking, Virtual Screening, and MD Simulations Studies.BioMed research international · 2017Article
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- Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions.International journal of molecular sciences · 2016Article
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- Computational approaches for designing potent and selective analogs of peptide toxins as novel therapeutics.Future medicinal chemistry · 2014Review
- A potent and Kv1.3-selective analogue of the scorpion toxin HsTX1 as a potential therapeutic for autoimmune diseases.Scientific reports · 2014Article
- Molecular dynamics study of binding of µ-conotoxin GIIIA to the voltage-gated sodium channel Na(v)1.4.PloS one · 2014Article
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- Molecular dynamics simulations of scorpion toxin recognition by the Ca(2+)-activated potassium channel KCa3.1.Biophysical journal · 2013Article
- 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
- A potent and selective peptide blocker of the Kv1.3 channel: prediction from free-energy simulations and experimental confirmation.PloS one · 2013Article
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Abstract
Free energy calculations for protein-ligand dissociation have been tested and validated for small ligands (50 atoms or less), but there has been a paucity of studies for larger, peptide-size ligands due to computational limitations. Previously we have studied the energetics of dissociation in a potassium channel-charybdotoxin complex by using umbrella sampling molecular-dynamics simulations, and established the need for carefully chosen coordinates and restraints to maintain the physiological ligand conformation. Here we address the ligand integrity problem further by constructing additional potential of mean forces for dissociation of charybdotoxin using restraints. We show that the large discrepancies in binding free energy arising from simulation artifacts can be avoided by using appropriate restraints on the ligand, which enables determination of the binding free energy within the chemical accuracy. We make several suggestions for optimal choices of harmonic potential parameters and restraints to be used in binding studies of large ligands.
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