ArticleThe journal of physical chemistry. B2012
Absolute free energy of binding of avidin/biotin, revisited.
Article in The journal of physical chemistry. B, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A quantum-mechanical framework for million-atom scale biological systems.Communications chemistry · 2026Article
- Live-cell decoding of labile post-translational modifications in APE1 with a rationally engineered nano-catcher.Nucleic acids research · 2026Article
- Application of electrospun chitosan-based nanofibers as immobilization matrix for biomolecules.Applied microbiology and biotechnology · 2023Article
- Microtubule assembly and disassembly dynamics model: Exploring dynamic instability and identifying features of Microtubules' Growth, Catastrophe, Shortening, and Rescue.Computational and structural biotechnology journal · 2022Article
- Thermodynamic Integration in 3n Dimensions without Biases or Alchemy for Protein Interactions.Frontiers in physics · 2020Article
- Detection of streptavidin-biotin intermediate metastable states at the single-molecule level using high temporal-resolution atomic force microscopy.RSC advances · 2019Article
- Detailed characterization of the solution kinetics and thermodynamics of biotin, biocytin and HABA binding to avidin and streptavidin.PloS one · 2019Article
- Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics.Biochemical and biophysical research communications · 2017Article
- Computing Protein-Protein Association Affinity with Hybrid Steered Molecular Dynamics.Journal of chemical theory and computation · 2015Article
- Hybrid Steered Molecular Dynamics Approach to Computing Absolute Binding Free Energy of Ligand-Protein Complexes: A Brute Force Approach That Is Fast and Accurate.Journal of chemical theory and computation · 2015Article
- Experimental and theoretical investigations in stimuli responsive dendrimer-based assemblies.Nanoscale · 2015Review
- Computing membrane-AQP5-phosphatidylserine binding affinities with hybrid steered molecular dynamics approach.Molecular membrane biology · 2015Article
- Protein-triggered supramolecular disassembly: insights based on variations in ligand location in amphiphilic dendrons.Journal of the American Chemical Society · 2014Article
- Integrin-generated forces lead to streptavidin-biotin unbinding in cellular adhesions.Biophysical journal · 2014Article
- Standard binding free energies from computer simulations: What is the best strategy?Journal of chemical theory and computation · 2013Article
- Relative stability of the open and closed conformations of the active site loop of streptavidin.The Journal of chemical physics · 2011Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The binding of biotin to avidin is one of the strongest in nature with absolute free energy of binding, ΔA(0) = -20.4 kcal/mol. Therefore, this complex became a target for a large number of computational studies, which all, however, are based on approximate techniques or simplified models and have led to a wide range of results Therefore, ΔA(0) is calculated here by rigorous statistical mechanical methods and models that consider long-range electrostatics. (1) We apply our method, "hypothetical scanning molecular dynamics with thermodynamic integration" (HSMD-TI) to avidin-biotin modeled by periodic boundary conditions with particle mesh ewald (PME). (2) We apply the double decoupling method (DDM) to this system modeled by the spherical solvent boundary potential (SSBP) and the generalized solvent boundary potential (GSBP). The corresponding results for neutral biotin, ΔA(0) = -29.1 ± 0.8 and -25.2 ± 0.5 kcal/mol are significantly lower than the experimental value; we also provide the result for a charged biotin, ΔA(0) = -33.3 ± 0.8 kcal/mol. It is plausible to suggest that this disagreement with the experiment may stem from ignoring the (positive) contribution of a mobile loop that changes its structure upon ligand binding.
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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.