3D structure prediction of histone acetyltransferase proteins of the MYST family and their interactome in Arabidopsis thaliana

• Published in: Journal of molecular modeling 2016-11, Vol.22 (11), p.256-9, Article 256
• Main Authors: Raevsky, A. V., Sharifi, M., Samofalova, D. A., Karpov, P. A., Blume, Y. B.
• Format: Article
• Language: English
• Subjects: Acetyl Coenzyme A - chemistry; Acetylation; Apoptosis; Arabidopsis - enzymology; Arabidopsis - genetics; Arabidopsis Proteins - chemistry; Arabidopsis Proteins - genetics; Bioinformatics; Characterization and Evaluation of Materials; Chemistry; Chemistry and Materials Science; Chromatin; Computer Appl. in Life Sciences; Computer Applications in Chemistry; Deoxyribonucleic acid; Deregulation; DNA; Docking; Enzymes; Gene sequencing; Histone Acetyltransferases - chemistry; Histone Acetyltransferases - genetics; Homology; Identification methods; Lysine; Molecular Medicine; Original Paper; Predictions; Probabilistic methods; Protein Domains; Proteins; Sequence Analysis, Protein; Theoretical and Computational Chemistry
• ISSN: 1610-2940; 0948-5023
• DOI: 10.1007/s00894-016-3103-0

Histone lysine acetylation is a reversible post-translational modification that does not involve changes in DNA sequences. Enzymes play an important role in developmental processes and their deregulation has been linked to the progression of diverse disorders. The HAT enzyme family fulfills an important role in various developmental processes mediated by the state of chromatin, and have been attributed to its deregulation. To understand acetylation mechanisms and their role in cell signaling, transcriptional regulation, and apoptosis, it is crucial to identify and analyze acetylation sites. Bioinformatics methods can be used to generate relatively precise predictions. Here we applied classical bioinformatics methods—sequence alignment, homology modeling, and docking—to compare approved and predicted lysine acetylation processes in different organisms. HAM1 and HAM2 are analogs of KAT8 and KAT7 (MYST1 and MYST2), members of the MYST histone acetyltransferase family, and our results show that HAM1 and HAM2 have much in common with other representatives of MYST families from various organisms. One function of acetyl-CoA binding was predicted with a high level of probability by computational methods. Based on our data, we conclude that, despite huge genetic distances and some structural differences between animal and plant species, a closer look at acetylation mechanism shows that they have much in common.