BIOQUANT

Theoretical approaches, Simulation and Modelling

Nucleosome simulations at all-atom resolution with Molecular Dynamics (MD)

The nucleosome is the first stage of packing the DNA into chromatin. It contains eight histone proteins (two of each H2A, H2B, H3 and H4) forming a disc shaped complex. The DNA molecule wraps in a 1.67 fold turn around this protein core and forms stable electrostatic interactions between its phosphate-sugar backbone and the positively charged histone proteins. By sharply bending the DNA and thereby preventing other DNA interacting proteins to bind at DNA binding sites, nucleosomes regulate the access to the DNA sequence. The position of nucleosomes along the DNA is therefore important and has to be well defined.

 

figure of the nucleosome

Fig.1 Nucleosome structure in front (left) and side view (right). The different histone proteins (depicted in cartoon representation) are drawn in yellow: H3, green: H4, red: H2A and gray: H2B. The backbone of DNA is highlighted in blue.

 

In the cell a whole family of ATP-consuming proteins named remodeling complexes are in duty to provide the appropriate pattern and position of the nucleosomes. Remodeling complexes are able to move the nucleosomes along the DNA opening or closing important binding sites. So far the physical mechanism by which this is accomplished as well as the rules that direct the remodeling complexes are not well understood.

In this project we investigate the dynamics of single nucleosomes and related structures, e.g. the chromatosome (complex of the nucleosome and a H1 Histone protein) and pure DNA fragments. Molecular Dynamics simulations enable to observe the behavior of a particle in a well-defined environment (in explicit water with Na+ and Cl- ions, at temperature T, pressure p etc.). By calculating Newtons equation for every atom in the system the motion of the entire complex can be achieved for small time scales (up to ~100 ns). Since the parameters of the system can be varied over wide ranges, rare or unrealistic situations can also be calculated as scenarios of single molecule experiments.

In our lab we focus on the interaction of DNA and histone proteins in the nucleosome in order to learn how the DNA can move along the histone proteins on the one hand side while on the other side the complex of DNA and histone proteins is very stable. We perform different simulations with and without additional applied external forces to simulate single molecule stretch experiments and analyze the interaction sites.

 

Simulation and Modeling of Chromatin Fibers

In eukaryotes, the DNA inside the nucleus is organized by histone proteins into a nucleoprotein complex referred to as chromatin. The dynamic organization of chromatin has been identified as a major regulatory factor for molecular biological processes such as replication, transcription, repair, and recombination, as it controls the accessibility of chromatin for DNA binding factors. Based on nucleosome model structures with atomic resolution, a coarse-grained model for the nucleosome geometry was developed. In collaboration with Gero Wedemann this was included into a Monte-Carlo simulation package for chromatin fibers.

 

Chromatin fiber compaction

Fig. 2 Model for chromatin fiber compaction induced by binding of linker histone H1. The crossed linker (CL) fiber (left), without linker histone, represents an open conformation with straight linker DNA, in which DNA access is facilitated for other proteins. The binding of linker histone H1 changes the local nucleosome geometry to a structure with partial DNA charge neutralization (right). This induces a transition to an interdigitated (ID) fiber conformation. The structures shown have an NRL of 188 bp in both the crossed linked fiber (left side) and the interdigitated conformation (right side), and are taken from Monte-Carlo simulations simulations.

 

In this project we investigate different structures in the chromatin fiber. The dependence of the chromatin fiber conformation on the spatial orientation of nucleosomes and the path and length of the linker DNA was systematically explored by Monte Carlo simulations. Two fiber types were analyzed in detail that represent nucleosome chains without and with linker histones, respectively: two-start helices with crossed-linker DNA (CL conformation) and interdigitated one-start helices (ID conformation) with different nucleosome tilt angles.

With the help of the monte carlo simulation of chromatin fibers, we reproduce experiments in situ to identify local changes in the chromatin fiber, based on experimental measurements, where global changes are observed. Also influences of local changes, for example in the nucleosome geometry, are investigated.

References

  • Kepper, N., Ettig, R., Stehr, R., Wedemann, G. & Rippe, K. (2010) Force spectroscopy of chromatin fibers: extracting energetics and structural information from Monte Carlo simulations, submitted.
  • Stehr, R., Schöpflin, R., Ettig, R., Kepper, N., Rippe, K. & Wedemann, G. (2010) Exploring the conformational space of chromatin fibers and their stability by numerical dynamic phase diagrams. Biophys. J. 98, 1028–1037.
  • Kepper, N., Foethke, D., Stehr, R., Wedemann, G. & Rippe, K. (2008). Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation. Biophys. J. 95, 3692–3705.
  • Stehr, R., Kepper, N., Rippe, K. & Wedemann, G. (2008). The effect of the internucleosomal interaction potential on the folding of the chromatin fiber. Biophys. J. 95, 3677–3691.
  • People working on modeling projects

  • Nick Kepper
  • Vladimir Teif
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    Related research projects

    Chromatin Fibers

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