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:
- 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.
- 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.
 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
 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
|Last modified:||20 June 2017 4.18 p.m.|