Bora Karasulu,
Computational Science and Engineering
Histone Methylation and Demethylation Using
QM/MM and IRC
Calculation Techniques
Implemented in Gaussian03 and Charmm
Bora Karasulu
is in the first year of his Computational Science and Engineering MSc. study
after
his undergraduate study in chemistry. He
is mainly conducting research for the reaction mechanisms
of methylation
and demethylation of histone proteins. Histone proteins are one of the
indispensable
proteins that are involved in cell
regulatory processes, such as chromatin regulation, gene silencing
and transcription, cell cycle control,
and epigenetics. These regulatory processes are controlled via
post-transcriptional modifications of histone protein
tails, which are mainly grouped into
methylation, acetylation, ubiquitination, and
phosphorylation. From these four types of
modifications, methylation
has been very recently proven to be reversible with thediscovery
of histone
demethylase proteins. On the other hand, it has
been shown that the abnormal methylation rates
cause the excess proliferation of the
cell and lead to cancer. Therefore, understanding the details
of reaction mechanisms of histone methylation and demethylation
processes provide the required knowledge
basis for preventing the abnormal methylation rates by designing proper inhibitor (drug)
molecules.
At this point, Bora Karasulu tries
to understand the details of reaction mechanisms of methylation and
demethylation processes, propose new possible
mechanisms and inhibitor molecules suitable for the
mechanism. For this purpose, he uses QM/MM
and IRC calculation techniques implemented
in Gaussian03 and Charmm and he also
uses other molecular design and MD tools.