{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,25]],"date-time":"2026-07-25T05:28:15Z","timestamp":1784957295528,"version":"3.55.0"},"reference-count":44,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2004,2,6]],"date-time":"2004-02-06T00:00:00Z","timestamp":1076025600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Proteins"],"published-print":{"date-parts":[[2004,4]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Antiestradiol antibody 57\u20102 binds 17\u03b2\u2010estradiol (E2) with moderately high affinity (<jats:italic>K<\/jats:italic><jats:sub>a<\/jats:sub> = 5 \u00d7 10<jats:sup>8<\/jats:sup> M<jats:sup>\u22121<\/jats:sup>). The structurally related natural estrogens estrone and estriol as well synthetic 17\u2010deoxy\u2010estradiol and 17\u03b1\u2010estradiol are bound to the antibody with 3.7\u20134.9 kcal mol<jats:sup>\u22121<\/jats:sup> lower binding free energies than E2. Free energy perturbation (FEP) simulations and the molecular mechanics\u2013Poisson\u2013Boltzmann surface area (MM\u2013PBSA) method were applied to investigate the factors responsible for the relatively low cross\u2010reactivity of the antibody with these four steroids, differing from E2 by the substituents of the steroid D\u2010ring. In addition, computational alanine scanning of the binding site residues was carried out with the MM\u2013PBSA method. Both the FEP and MM\u2013PBSA 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\u2013antibody interaction free energies. One hydrogen bond was calculated to contribute about 3 kcal mol<jats:sup>\u22121<\/jats:sup> to the interaction energy. Because the relative binding free energies of estrone (two antibody\u2010steroid hydrogen bonds), estriol (three hydrogen bonds), 17\u2010deoxy\u2010estradiol (no hydrogen bonds), and 17\u03b1\u2010estradiol (two hydrogen bonds) are close to each other and clearly lower than that of E2 (three hydrogen bonds), the water\u2013steroid interactions lost upon binding to the antibody make an important contribution to the binding free energies. The MM\u2013PBSA 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\u20102 was compared to the binding to the antiprogesterone antibody DB3 and antitestosterone antibody 3\u2010C<jats:sub>4<\/jats:sub>F<jats:sub>5<\/jats:sub>, studied earlier with the MM\u2013PBSA method. Proteins 2004. \u00a9 2004 Wiley\u2010Liss, Inc.<\/jats:p>","DOI":"10.1002\/prot.10399","type":"journal-article","created":{"date-parts":[[2004,2,26]],"date-time":"2004-02-26T20:40:10Z","timestamp":1077828010000},"page":"34-43","source":"Crossref","is-referenced-by-count":30,"title":["Free energy simulations and MM\u2013PBSA analyses on the affinity and specificity of steroid binding to antiestradiol antibody"],"prefix":"10.1002","volume":"55","author":[{"given":"Tuomo","family":"Laitinen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jussi A.","family":"Kankare","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mikael","family":"Per\u00e4kyl\u00e4","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2004,2,20]]},"reference":[{"key":"e_1_2_7_2_2","doi-asserted-by":"publisher","DOI":"10.1210\/endo.138.3.4979"},{"key":"e_1_2_7_3_2","volume-title":"Clinical Laboratory Diagnostics. 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