Paper Citing NAMD - Abstract
Materese, Christopher K.; Savelyev, Alexey; Papoian, Garegin A.
Counterion Atmosphere and Hydration Patterns near a Nucleosome Core Particle
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:15005-15013, OCT 21 2009
The chromatin folding problem is an exciting and rich field for modern research. On the most basic level, chromatin fiber consists of a collection of protein-nucleic acid complexes, known as nucleosomes, joined together by segments of linker DNA Understanding how the cell successfully compacts meters of highly charged DNA into a micrometer size nucleus while still enabling rapid access to the genetic code for transcriptional processes is a challenging goal In this work we shed light on the way mobile ions condense around the nucleosome core particle, as revealed by an extensive all-atom molecular dynamics simulation On a hundred nanosecond time scale, the nucleosome exhibited only small conformational fluctuations. We found that nucleosomal DNA is better neutralized by the combination of histone charges and mobile ions compared with free DNA. We provide a detailed physical explanation of this effect using ideas from electrostatics in continuous media We also discovered that sodium condensation around the histone core is dominated by an experimentally characterized acidic patch, which is thought to play a significant role in chromatin compaction by binding with basic histone tails Finally, we found that the nucleosome is extensively permeated by over a thousand water molecules, which in turn allows mobile ions to penetrate deeply into the complex Overall, our work sheds light on the way ionic and hydration interactions within a nucleosome may affect internucleosomal interactions in higher order chromatin fibers
