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Computational Enzymology in Neurobiology

Epigenetic modifications are crucial for the regulation of life and health. These modifications consist in inheritable changes of DNA, which are promoted by specific enzymes. Epigenetics has remarkable consequences on the gene activity and expression. For these reasons, the altered activity of enzymes that control epigenetic traits show, at times, a strong correlation with the development of human diseases.

In this context, over the last decades, increasing attention has been given to the emerging field of neuroepigenetics [1-2], which involves the study of neurological and neurodegenerative pathologies. 

In this regard, we exploit our extensive experience in the study of protein-DNA interactions to understand the physical and chemical steps at the roots of the enzymatic reactions involved in epigenetic mechanisms. In fact, our primary interest is to obtain molecular insights on the functioning of epigenetic modification enzymes and to use this knowledge to initiate drug discovery for neurodegenerative diseases.

Toward this goal, the group employs a wide set of computational tools, including classical molecular dynamics, enhanced sampling methods, and QM/MM simulations. Our investigations build on recent successful multiscale simulation studies on nucleic acids processing by enzymes such as DNA polymerases [3].


References

[1] J. D. Sweatt, "The Emerging Field of Neuroepigenetics". Neuron 80, 624–632 (2013).

[2] J. Landgrave-Gómez, O. Mercado-Gómez, R. Guevara-Guzmán, "Epigenetic mechanisms in neurological and neurodegenerative diseases". Front. Cell. Neurosci. 9, 58 (2015).

[3] V. Genna, P. Vidossich, E. Ippoliti, P. Carloni, M. De Vivo, "A self-activated mechanism for nucleic acid polymerization catalyzed by DNA/RNA polymerases". J. Am. Chem. Soc. 138, 14592-14598 (2016).


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