DNA/RNA - protein interactions

With the release of DNA and RNA coarse grain parameters (Uusitalo et al., submitted), the Groningen MD group has entered in a new field. The study of protein-DNA/RNA complexes such as transcription factors or the role of architectural proteins such as histones in chromatin organization is now possible using coarse-grained MARTINI models.

Our efforts are currently focused in two major topics:

1. The study of protein-DNA or protein-RNA interactions, e.g. those involved in the ribozyme or the self-assembly of complexes involved in the transcription control.
2. Cooperativity between protein complexes in DNA compaction.

Moreover, we also develop tools to analyze the DNA and RNA structure (helical parameters, bending fluctuations) and protein-DNA interactions.

[1] J.J. Uusitalo, H. I. Ingólfsson, P. Akhshi, D. P. Tieleman, S. J. Marrink. Martini coarse-grained force field: extension to DNA. JCTC, http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00286

[2] J.J. Uusitalo, H.I. Ingólfsson, S.J. Marrink, I. Faustino. MARTINI coarse -grained force field: extension to RNA. Biophys. J., http://www.cell.com/biophysj/abstract/S0006-3495(17)30612-4