Absolute free energy of binding of avidin/biotin, revisited.
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.
Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, 3059 BST3, Pittsburgh, Pennsylvania 15260, USA.
Ignacio J
IJ
General
Ralitsa
R
Dragomirova
Hagai
H
Meirovitch
D001360:Avidin / Q000737:chemistry*; D001710:Biotin / Q000737:chemistry*; D019277:Entropy; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation
D001360:Avidin; D001710:Biotin