Model of three‐dimensional structure of vitamin D receptor and its binding mechanism with 1α,25‐dihydroxyvitamin D 3

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2001-08, Vol.44 (3), p.188-199
• Main Authors: Rotkiewicz, Piotr, Sicinska, Wanda, Kolinski, Andrzej, DeLuca, Hector F.
• Format: Article
• Language: English
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.1084

Comparative modeling of the vitamin D receptor three‐dimensional structure and computational docking of 1α,25‐dihydroxyvitamin D 3 into the putative binding pocket of the two deletion mutant receptors: (207–423) and (120–422, Δ [164–207]) are reported and evaluated in the context of extensive mutagenic analysis and crystal structure of holo hVDR deletion protein published recently. The obtained molecular model agrees well with the experimentally determined structure. Six different conformers of 1α,25‐dihydroxyvitamin D 3 were used to study flexible docking to the receptor. On the basis of values of conformational energy of various complexes and their consistency with functional activity, it appears that 1α,25‐dihydroxyvitamin D 3 binds the receptor in its 6‐s‐ trans form. The two lowest energy complexes obtained from docking the hormone into the deletion protein (207–423) differ in conformation of ring A and orientation of the ligand molecule in the VDR pocket. 1α,25‐Dihydroxyvitamin D 3 possessing the A‐ring conformation with axially oriented 1α‐hydroxy group binds receptor with its 25‐hydroxy substituent oriented toward the center of the receptor cavity, whereas ligand possessing equatorial conformation of 1α‐hydroxy enters the pocket with A ring directed inward. The latter conformation and orientation of the ligand is consistent with the crystal structure of hVDR deletion mutant (118–425, Δ [165–215]). The lattice model of rVDR (120–422, Δ [164–207]) shows excellent agreement with the crystal structure of the hVDR mutant. The complex obtained from docking the hormone into the receptor has lower energy than complexes for which homology modeling was used. Thus, a simple model of vitamin D receptor with the first two helices deleted can be potentially useful for designing a general structure of ligand, whereas the advanced lattice model is suitable for examining binding sites in the pocket. Proteins 2001;44:188–199. © 2001 Wiley‐Liss, Inc.