Bora Karasulu, Computational Science and Engineering

bkarasulu@ku.edu.tr

 

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.