| 研究実績の概要 |
Over the past year, we run extensive (microsecond-long) all-atom molecular dynamics simulations of histones in complex with DNA. By comparing the effect of DNA sequence and base-pair mismatches, our simulations highlighted very interesting changes in nucleosomal DNA structure and dynamics, which show how such features may impact the activity of chromatin remodelers, as found in past experimental observations. Furthermore, coarse-grained molecular dynamics simulations of full nucleosomes allowed us to explore longer time scales for a wide variety of DNA sequences, and further complement the insights obtained from the all-atom simulations.
These unbiased simulations turned out to be unsuitable for Markov state modeling due to the slow timescales of the process investigated. However, we now optimized a series of collective variables that should allow us to reconstruct the free energy landscape of nucleosome sliding using the string method implemented in the software Genesis, as originally planned. Preliminary results in this direction were presented at the last Annual Meeting of the Biophysical Society of Japan in 2021.
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| 次年度使用額が生じた理由 |
The incurring amount will be mainly used to buy computational resources from the Kyoto University supercomputer center and expand the local cpu cluster in our laboratory. Also, we will present our results at at least one conference within Japan or abroad. Using these supercomputer resources, we will run unbiased and string method molecular dynamics simulations to characterize the nucleosome repositioning process.
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