Free energy simulations and MM-PBSA analyses on the affinity and specificity of steroid binding to antiestradiol antibody

• Published in: Proteins, structure, function, and bioinformatics Vol. 55; no. 1; pp. 34 - 43
• Main Authors: Laitinen, Tuomo, Kankare, Jussi A., Peräkylä, Mikael
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01.04.2004
• Subjects: Antibodies, Monoclonal - chemistry; Antibodies, Monoclonal - genetics; Antibody Affinity; antibody fab fragment; Antibody Specificity; Binding Sites, Antibody; Computer Simulation; Estradiol - analogs & derivatives; Estradiol - chemistry; Estradiol - immunology; Estrogens - chemistry; Estrogens - immunology; free energy perturbation simulation; Hydrogen Bonding; Models, Molecular; molecular dynamics simulation; molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method; Mutagenesis; Progesterone - chemistry; Progesterone - immunology; Protein Binding; steroid; Testosterone - chemistry; Testosterone - immunology
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.10399

Antiestradiol antibody 57‐2 binds 17β‐estradiol (E2) with moderately high affinity (Ka = 5 × 108 M−1). The structurally related natural estrogens estrone and estriol as well synthetic 17‐deoxy‐estradiol and 17α‐estradiol are bound to the antibody with 3.7–4.9 kcal mol−1 lower binding free energies than E2. Free energy perturbation (FEP) simulations and the molecular mechanics–Poisson–Boltzmann surface area (MM–PBSA) method were applied to investigate the factors responsible for the relatively low cross‐reactivity of the antibody with these four steroids, differing from E2 by the substituents of the steroid D‐ring. In addition, computational alanine scanning of the binding site residues was carried out with the MM–PBSA method. Both the FEP and MM–PBSA methods reproduced the experimental relative affinities of the five steroids in good agreement with experiment. On the basis of FEP simulations, the number of hydrogen bonds formed between the antibody and steroids, which varied from 0 to 3 in the steroids studied, determined directly the magnitude of the steroid–antibody interaction free energies. One hydrogen bond was calculated to contribute about 3 kcal mol−1 to the interaction energy. Because the relative binding free energies of estrone (two antibody‐steroid hydrogen bonds), estriol (three hydrogen bonds), 17‐deoxy‐estradiol (no hydrogen bonds), and 17α‐estradiol (two hydrogen bonds) are close to each other and clearly lower than that of E2 (three hydrogen bonds), the water–steroid interactions lost upon binding to the antibody make an important contribution to the binding free energies. The MM–PBSA calculations showed that the binding of steroids to the antiestradiol antibody is driven by van der Waals interactions, whereas specificity is solely due to electrostatic interactions. In addition, binding of steroids to the antiestradiol antibody 57‐2 was compared to the binding to the antiprogesterone antibody DB3 and antitestosterone antibody 3‐C4F5, studied earlier with the MM–PBSA method. Proteins 2004. © 2004 Wiley‐Liss, Inc.