Structural dynamics and conformational behavior of aptamer binding to AML1 protein
Ryusei KUMATANI *1, Sato HIDEMI2, Atsushi TANAKA1, Taiichi SAKAMOTO2, Kenji YAMAGISHI1
1Nihon University
2Chiba Institute of Technology
Aptamers are short single-stranded nucleic acids with high affinity and specificity for their target molecules, which can be nucleic acids, proteins, or small organic compounds. Aptamers, therefore, have many potential applications in medicine and technology.
The AML1 aptamer specifically binds to the Runt domain (RD) of the AML1 protein and prevents its binding to DNA. The AML1 protein contains a DNA-binding domain, known as the RD, which recognizes a specific DNA element. One of authors has already obtained several AML1 aptamers (Apt S4-S and Apt S4-SS) that exhibit higher affinity (Kd = 0.034 ± 0.004 nM and 0.289 ± 0.006 nM, respectively) than the Runt-binding double-stranded DNA element (Kd = 9.6 ± 0.2 nM)[1,2].
In this study, with the aim of elucidating the specific binding mechanism, we performed molecular dynamics (MD) simulations on several AML1 aptamers to investigate their structural dynamics and conformational behavior. The MD calculations for the Apt S4-SS aptamer revealed that stem1 at the terminal region maintained an A-form helical structure throughout the trajectory, indicating the formation of a stable stem structure. The DNA-mimicking region, Stem 2, preserved the DNA-like conformation over the course of the simulation. Continuous base stacking was observed from Stem 3 to the multibranched loop, suggesting a contribution to the stabilization of the loop.
Furthermore, by comparing the MD simulation results with the surface plasmon resonance (SPR) experimental results for the mutant AML1 aptamers, we conducted molecular-level analyses of the changes in binding activity.
Reference
[1] R.Amano, T. Sakamoto et al., Biochemistry, 55, 6221, 2016
[2] K.Takada, T.Sakamoto et al., FEBS Open Bio, 8, 264, 2018