ArticleThe journal of physical chemistry. B2011
New method for calculating the absolute free energy of binding: the effect of a mobile loop on the avidin/biotin complex.
Article in The journal of physical chemistry. B, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 18 citations in OpenAlex.
- Heterogeneous and Allosteric Role of Surface Hydration for Protein-Ligand Binding.Journal of chemical theory and computation · 2023Article
- Standard binding free energies from computer simulations: What is the best strategy?Journal of chemical theory and computation · 2013Article
- Current progress in Structure-Based Rational Drug Design marks a new mindset in drug discovery.Computational and structural biotechnology journal · 2013Review
- Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation.Journal of computer-aided molecular design · 2012Article
- Absolute free energy of binding of avidin/biotin, revisited.The journal of physical chemistry. B · 2012Article
- 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
- Entropy and Free Energy of a Mobile Loop Based on the Crystal Structures of the Free and Bound Proteins.Entropy (Basel, Switzerland) · 2010Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Hypothetical scanning molecular dynamics (HSMD) is a relatively new method for calculating the absolute free energy and entropy. HSMD is extended here for the first time for calculating the absolute free energy of binding, ΔA(0), as applied to the avidin-biotin complex. With HSMD the ligand is built (more accurately reconstructed) from nothing in solvent and in the protein, in contrast to the commonly used methods where the ligand is annihilated (by thermodynamic integration) in these environments. Therefore, the end-point problem encountered with the latter methods does not exist with HSMD and the need for restraints is avoided. Also, the entropy of the ligand and water in both environments is obtained directly as a byproduct of the simulation. The binding mechanism of biotin to avidin involves a mobile loop that is expected to be in an open conformation in unbound avidin, which is changed to a closed one upon binding, that is, the loop moves to cover biotin in the active site. The contribution of the loop's conformational change to the total free energy of binding is calculated here for the first time. Our result, ΔA(0) = -24.9 ± 7 covers the experimental value -20.7 kcal/mol within the error bars.
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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.