Interactions between 1alpha,25(OH)2D3 and residues in the ligand-binding pocket of the vitamin D receptor: a correlated fragment molecular orbital study.
To provide physicochemical insight into the role of each residue in the ligand-binding pocket (LBP) of the vitamin D receptor (VDR), we evaluated the energies of the interactions between the LBP residues and 1alpha,25(OH)2D3 by using an ab initio fragment molecular orbital (FMO) method at the Møller-Plesset second-order perturbation (MP2) level. This FMO-MP2 method can be used to correctly evaluate both electrostatic and van der Waals dispersion interactions, and it affords these interaction energies separately. We deduced the nature of each interaction and determined the importance of all the LBP residues involved in ligand recognition by the VDR. We previously reported the results of alanine-scanning mutational analysis (ASMA) of all 34 non-alanine residues lining the LBP of the human VDR. The theoretical results in combination with the ASMA results enabled us to assign the role of each LBP residue. We concluded that electrostatic interactions are the major determinant of the ligand-binding activity and ligand recognition specificity and that van der Waals interactions are important for protein folding and, in turn, for cofactor binding.
Yamagishi
Kenji
K
Research Information Center for Extremophile, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
Tokiwa
Hiroaki
H
Makishima
Makoto
M
Yamada
Sachiko
S
D000409:Alanine / Q000737:chemistry; D000495:Allosteric Site; D002117:Calcitriol / Q000737:chemistry*; D004252:DNA Mutational Analysis; D015195:Drug Design; D006801:Humans; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D017510:Protein Folding; D018167:Receptors, Calcitriol / Q000737:chemistry*; D047488:Retinoid X Receptors / Q000737:chemistry; D055672:Static Electricity
D008024:Ligands; D018167:Receptors, Calcitriol; D047488:Retinoid X Receptors; D002117:Calcitriol; D000409:Alanine