Vitamin D receptor agonists specifically modulate the volume of the ligand-binding pocket.
Existing crystal structure data has indicated that 1alpha,25-dihydroxyvitamin D(3) (1alpha,25(OH)(2) D(3)) and its analogues bind the ligand-binding pocket (LBP) of the human vitamin D receptor in a very similar fashion. Because docking of a ligand into the LBP is a more flexible process than crystallography can monitor, we analyzed 1alpha,25(OH)(2)D(3), its 20-epi derivative MC1288, the two side-chain analogues Gemini and Ro43-83582 (a hexafluoro-derivative) by molecular dynamics simulations in a complex with the vitamin D receptor ligand-binding domain and a co-activator peptide. Superimposition of the structures showed that the side chain of MC1288, the first side chain of the conformation II of Gemini, the second side chain of Ro43-83582 in conformation I and the first side chain of Ro43-83582 in conformation II take the same agonistic position as the side chain of 1alpha,25(OH)(2)D(3). Compared with the LBP of the natural hormone MC1288 reduced the volume by 17%, and Gemini expanded it by 19%. The shrinking of the LBP of MC1288 and its expansion to accommodate the second side chain of Gemini or Ro43-83582 is the combined result of minor movements of more than 30 residues and major movements of a few critical amino acids. The agonist-selective recognition of anchoring OH groups by the conformational flexible residues Ala-303, Leu-309, and His-397 was confirmed by in vitro assays. In summary, variations in the volume of agonists lead to adaptations in the volume of the LBP and alternative contacts of anchoring OH-groups.
Department of Biochemistry, University of Kuopio, FIN-70211 Kuopio, Finland.
Ferdinand
F
Molnár
Mikael
M
Peräkylä
Carsten
C
Carlberg
D000596:Amino Acids / Q000737:chemistry; D002117:Calcitriol / Q000031:analogs & derivatives* / Q000737:chemistry / Q000494:pharmacology; D045744:Cell Line, Tumor; D003198:Computer Simulation; D004252:DNA Mutational Analysis; D018076:DNA, Complementary / Q000378:metabolism; D017930:Genes, Reporter; D005822:Genetic Vectors; D006801:Humans; D008024:Ligands; D008156:Luciferases / Q000378:metabolism; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D010447:Peptide Hydrolases / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D018167:Receptors, Calcitriol / Q000819:agonists* / Q000378:metabolism; D014162:Transfection
D000596:Amino Acids; D018076:DNA, Complementary; D008024:Ligands; D018167:Receptors, Calcitriol; C510609:Ro43 83582; D008156:Luciferases; D010447:Peptide Hydrolases; D002117:Calcitriol