PROJECT SUMMARY
Epigenetic regulation is one of eukaryotic cells' most central and complex processes. Enzymatic
demethylation of N-methylated lysine residues in histone proteins is performed almost
exclusively by non-heme Fe(II) and 2-oxoglutarate (2OG) - dependent histone demethylases
(KDMs). KDMs are divided into six classes (KDM2-8), which differ in their specificity towards the
methylation state of the lysine residues and the position of the lysine residue in the sequence of
the histone proteins. Importantly, KDMs from different classes are involved in diverse steps of
epigenetic regulation and are linked to various pathologic processes, including cancers and other
genetic disorders. The catalytic mechanisms of KDMs with standard histone substrates containing
methyl groups (HSCMGs), including the dioxygen (O2) binding, activation, and substrate
oxidation, have been comprehensively explored by us during the previous award period; however,
the diverse catalytic mechanisms of KDMs with histone substrates containing lysine residues
with large alkyl groups (HSCLAGs) are entirely unexplored. Experimental studies show that
human KDMs such as KDM2A, KDM4E, KDM6B, and KDM7B can catalyze diverse
transformations with a variety of HSCLAGs implementing different chemical mechanisms such
as hydroxylations, hydroxylations followed by dealkylations, and sequential hydroxylations,
however, the catalytic mechanisms of these transformations remain unknown.
Therefore, this proposal's overarching goal is to elucidate how KDMs perform catalysis of
HSCLAGs compared to HSCMGs regarding the primary substrate binding, dioxygen transport
and binding, and their diverse reaction mechanisms. Subjects of our study are four human
KDMs from four different classes (2, 4, 6, and 7), which differ in their structure and substrate
specificities, namely KDM2A, KDM4E, KDM6B, and KDM7B.
An exciting aspect of the research plan is that it will provide motivated undergraduate students
with a unique opportunity to engage in top class research using modern computational and
experimental methods in line with the mission of the Academic Research Enhancement Award.
