分子動力学計算によるRNAアプタマーとヒト抗体の複合体形成におけるCa2+の役割の解析 [Published online J. Comput. Chem. Jpn., 18, 208-210, by J-STAGE]

[Published online Journal of Computer Chemistry, Japan Vol.18, 208-210, by J-STAGE]
<Title:> 分子動力学計算によるRNAアプタマーとヒト抗体の複合体形成におけるCa²⁺の役割の解析
<Author(s):> 石井　清一郎, 関口　真裕, 吉田　尚恵, 増川　恵介, 石川　岳志, 坂本　泰一, 山岸　賢司
<Corresponding author E-Mill:> yamagishi.kenji(at)nihon-u.ac.jp
<Abstract:> An RNA aptamer that binds with high affinity and specificity to human immunoglobulin G (IgG) is a 24-mer single-stranded oligonucleotide containing 2′-fluoro pyrimidine nucleotides. Using X-ray crystallographic analysis, a Ca²⁺ ion was reported as being located near the G7 phosphate of the RNA aptamer. Surface plasmon resonance analysis showed that the RNA aptamer could not bind to IgG in a buffer without Ca²⁺ ions. To elucidate the role of Ca²⁺ ions in the binding of the RNA aptamer to IgG, we performed molecular dynamics simulation for the RNA aptamer/IgG complex with and without Ca²⁺ ions in a solvent. In the presence of Ca²⁺ ions, the RMSD of the RNA aptamer backbone remained below approximately 3.0 from the crystal structure during a 1,500-ns simulation. The distance between the centroids of the RNA aptamer and IgG was maintained between the centroids in the crystal structure. However, in the absence of Ca²⁺ ions, the RMSD increased and the structure of the RNA aptamer changed from the initial structure. These results indicate that Ca²⁺ ions play a role in maintaining the conformation of the RNA aptamer to the binding form.
<Keywords:> RNA aptamer, Human immunoglobulin G, Calcium ion, Molecular dynamics, Structural analysis
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0051/_article/-char/ja/