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1 TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

1 2014

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Molecular dynamics simulation of histone H3 and H4 N-terminal tail conformation in the presence and absence of nucleosome core

Zhang R., Erler J., Langowski J.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

2014

Vol. 18, No 3

281--288

Histone N ( C )-terminal tails play an important role in chromatin remodeling and gene regulation. Posttranslational modifications ( PTM s) of histone tails are known to be correlated to distinct states of gene activity, but the molecular mechanism of these processes is largely unknown. PTM s alter the electrostatic environment and conformation of histone tails, as w ell as their interaction with other components. Here we performed extensiv e Replica Exchange Molecular Dynamics ( REMD ) simulations for the H 4 and H 3 tails, isolated and with inclusion of a nucleosome. Our results agree with the predictions of previous the oretical studies for the secondary structure of isolated tails, but show strong dependence on the force field used. In the presence of the nucleosome, the secondary structure of histone tails i s destabilized. Furthermore, H 4 K 16 is found to insert into the DNA minor groove, whereas the acetylated H 4 K 16 stays on the surface of DNA .