Dynamic Play between Human N-α-acetyltransferase D and H4-mutant
Histones: Molecular Dynamics Study
Authors: Rathod Shravan B. , Srivastava Kinshuk Raj 
Published: March 2023

Background:

Many N-terminal acetyltransferases (NATs) play important role in the posttranslational
modifications of histone tails. Research showed that these enzymes have been reported upregulated
in many cancers. NatD is known to acetylate H4/H2A at the N-terminal. During lung cancer, this enzyme
competes with the protein kinase CK2α and blocks the phosphorylation of H4 and, acetylates. It also,
we observed that H4 has various mutations at the N-terminal and we considered only four mutations (S1C,
R3C, G4D and G4S) to study the impacts of these mutations on H4 binding with NatD using MD simulation.

Objective:

Our main objective in this study was to understand the structure and dynamics of hNatD under
the influence of WT and MT H4 histones bindings. The previous experimental study reported that mutations
on H4 N-terminus reduce the catalytic efficiency of N-Terminal acetylation. But here, we performed a molecular-
level study thus, we can understand how these mutations (S1C, R3C, G4D and G4S) cause significant
depletion in catalytic efficiency of hNatD.

Methods:

Purely computational approaches were employed to investigate the impacts of four mutations in
human histone H4 on its binding with the N-α-acetyltransferase D. Initially, molecular docking was used to
dock the histone H4 peptide with the N-α-acetyltransferase. Next, all-atom molecular dynamics simulation
was performed to probe the structural deviation and dynamics of N-α-acetyltransferase D under the binding
of WT and MT H4 histones.

Result:

Our results show that R3C stabilizes the NatD whereas the remaining mutations destabilize the
NatD. Thus, mutations have significant impacts on NatD structure. Our finding supports the previous analysis
also. Another interesting observation is that the enzymatic activity of hNatD is altered due to the considerably
large deviation of acetyl-CoA from its original position (G4D). Further, simulation and correlation
data suggest which regions of the hNatD are highly flexible and rigid and, which domains or residues have
the correlation and anticorrelation. As hNatD is overexpressed in lung cancer, it is an important drug target
for cancer hence, our study provides structural information to target hNatD.

Conclusion:

In this study, we examined the impacts of WT and MTs (S1C, R3C, G4D and G4S) histone H4
decapeptides on their bindings with hNatD by using 100 ns all-atom MD simulation. Our results support the
previous finding that the mutant H4 histones reduce the catalytic efficiency of hNatD. The MD posttrajectory
analyses revealed that S1C, G4S and G4D mutants remarkably alter the residue network in
hNatD. The intramolecular hydrogen bond analysis suggested that there is a considerable number of loss of
hydrogen bonds in hNatD of hNatD-H4_G4D and hNatD-H4_G4S complexes whereas a large number of
hydrogen bonds were increased in hNatD of hNatD-H4_R3C complex during the entire simulations. This
implies that R3C mutant binding to hNatD brings stability in hNatD in comparison with WT and other MTs
complexes. The linear mutual information (LMI) and Betweenness centrality (BC) suggest that S1C, G4D
and G4S significantly disrupt the catalytic site residue network as compared to R3C mutation in H4 histone.
Thus, this might be the cause of a notable reduction in the catalytic efficiency of hNatD in these three mutant
complexes. Further, interaction analysis supports that E126 is the important residue for the acetyltransferase
mechanisms as it is dominantly found to have interactions with numerous residues of MTs histones in
MD frames. Additionally, intermolecular hydrogen bond and RMSD analyses of acetyl-CoA predict the
higher stability of acetyl-CoA inside the WT complex of hNatD and R3C complex. Also, we report here the
structural and dynamic aspects and residue interactions network (RIN) of hNatD to target it to control cell
proliferation in lung cancer conditions.