Modeling and molecular dynamics simulation of nucleic acid complexes

Prof. Yuichi Togashi, Ritsumeikan University, Japan

DNA is generally assumed to be an information medium like a data tape, which stores genetic information using nucleic acid (A, T, G, C) sequences. However, recent experiments have shown that DNA or chromatin (DNA-protein complex in the nucleus) drastically changes structure and distribution depending on the state, such as the cell cycle and differentiation, which serve as part of the information processing machinery. RNA also functions as a molecular machine in gene regulation and translation. To elucidate the operation principles of protein machines, molecular dynamics (MD) simulations have been broadly used to track structural changes. With improvements in modeling, the same method is also applied to nucleic acids and their complexes. Still, there remain difficulties intrinsic to nucleic acids and chromatin. In this seminar, I will introduce our recent MD-based results on nucleic acids and their complexes:
- Bare DNA: effects of modification on the mechanical property
- Nucleosomes: partial disassembly (histone removal) and DNA dynamics
- Chromatin: bead-spring polymer modeling and data assimilation for Hi-C experiments
- Ribosome: probing codon-anticodon interactions in translation initiation
I will also discuss the difficulties and possible workarounds in collaboration with experimentalists.