Investigation of the Acetylation Mechanism by GCN5 Histone Acetyltransferase

Junfeng Jiang,Sisheng Ouyang,Zhongjie Liang,Lianchun Li,Dan Lu,Bairong Shen,Hualiang Jiang,Junyan Lu,Xiangqian Kong,Cheng Luo

doi:10.1371/journal.pone.0036660

Abstract

The histone acetylation of post-translational modification can be highly dynamic and play a crucial role in regulating cellular proliferation, survival, differentiation and motility. Of the enzymes that mediate post-translation modifications, the GCN5 of the histone acetyltransferase (HAT) proteins family that add acetyl groups to target lysine residues within histones, has been most extensively studied. According to the mechanism studies of GCN5 related proteins, two key processes, deprotonation and acetylation, must be involved. However, as a fundamental issue, the structure of hGCN5/AcCoA/pH3 remains elusive. Although biological experiments have proved that GCN5 mediates the acetylation process through the sequential mechanism pathway, a dynamic view of the catalytic process and the molecular basis for hGCN5/AcCoA/pH3 are still not available and none of theoretical studies has been reported to other related enzymes in HAT family. To explore the molecular basis for the catalytic mechanism, computational approaches including molecular modeling, molecular dynamic (MD) simulation and quantum mechanics/molecular mechanics (QM/MM) simulation were carried out. The initial hGCN5/AcCoA/pH3 complex structure was modeled and a reasonable snapshot was extracted from the trajectory of a 20 ns MD simulation, with considering post-MD analysis and reported experimental results. Those residues playing crucial roles in binding affinity and acetylation reaction were comprehensively investigated. It demonstrated Glu80 acted as the general base for deprotonation of Lys171 from H3. Furthermore, the two-dimensional QM/MM potential energy surface was employed to study the sequential pathway acetylation mechanism. Energy barriers of addition-elimination reaction in acetylation obtained from QM/MM calculation indicated the point of the intermediate ternary complex. Our study may provide insights into the detailed mechanism for acetylation reaction of GCN5, and has important implications for the discovery of regulators against GCN5 enzymes and related HAT family enzymes.

Highlights

The post-translational modification of histones has been reported playing crucial roles in chromatin regulation
Prior to investigate the mechanism of catalytic process of GCN5 through computational method, it is of vital importance to obtain an accurate model of the enzyme-substrate complex
Hydrophobic interactions and key residues involved in catalytic reactions based on experimental data and homology crystal structures were used as the validation sources

Summary

Introduction

The post-translational modification of histones has been reported playing crucial roles in chromatin regulation It insures the fidelity of opened chromatin structure, increased gene expression and other DNA transactions [1,2]. Involved in DNA recognition by transcription factors and access of genetic information, histone modification is one of the most important processes to obtain an open chromatin structure and/or to recruit specific proteins and influence gene expression, DNA replication and repair, and chromosome condensation and segregation. These ‘‘epigenetic’’ changes can be highly dynamic and play a crucial role in regulating cell proliferation, survival, differentiation and motility. Since altered epigenetic modifications play key roles in kinds of diseases, an intense attention should be paid for the players that adding or removing of these epigenetic markers because of their roles as potential ‘‘druggable’’ therapeutic targets

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Conclusion