Scientists have uncovered a crucial mechanism driving an enzyme linked to aging and cancer, offering new insights into potential therapeutic applications.
The enzyme Sir2, a member of the sirtuin family, plays a vital role in deacetylation of proteins. Researchers from the Institute of Science Tokyo have revealed that a unique tandem allosteric effect of reactants and products is responsible for the efficient deacetylation cycle of the Sir2 enzyme.
This discovery opens up a new avenue for modulating Sir2, an enzyme essential for various biological processes, including aging, metabolic regulation, and cancer suppression. The study, published in the Journal of Chemical Information and Modeling, suggests potential therapeutic applications, particularly in cancer treatment.
Sirtuins, including SIRT1 and Sir2, are a family of enzymes with broad roles in aging, stress resistance, metabolic regulation, and cancer suppression across various organisms. These enzymes trigger deacetylation, a post-translational modification, which is a chemical alteration to proteins after synthesis. Sir2, found in yeast, deacetylates proteins like histones and the tumor suppressor p53.
The acetylation and deacetylation of p53 are crucial for its function. Previous studies have shown that Sir2 relies on the co-substrate nicotinamide adenine dinucleotide (NAD+) for deacetylation reactions. Structural studies have identified a flexible region within Sir2, known as the cofactor binding loop (CBL), as essential for NAD+ binding. However, the exact role and mechanisms of CBL in NAD+ binding and deacetylation remained unclear.
To address this, a research team led by Professor Akio Kitao, along with doctoral student Zhen Bai and Assistant Professor Tran Phuoc Duy, all from the School of Life Science and Technology at the Institute of Science Tokyo, Japan, uncovered the key mechanisms behind Sir2's efficient protein deacetylation.
Professor Kitao explains, "A detailed understanding of the Sir2 deacetylation process can significantly advance our knowledge of aging suppression, carbohydrate and lipid metabolism, DNA repair, and support rational drug design. Using large-scale computational simulations, we investigated the conformational changes in CBL induced by p53 binding, revealing a 'tandem allosteric effect'—two successive allosteric steps acting in concert."
The researchers employed molecular dynamics (MD) simulations, combined with parallel cascade selection MD (PaCS-MD), to simulate three states of Sir2: a form bound to acetylated p53, a form bound to nonacetylated p53, and the apo state. These simulations revealed the key mechanisms enabling efficient deacetylation.
In its apo state, Sir2 exists in a closed form, allowing only weak NAD+ binding. When an acetylated protein substrate like p53 binds, an allosteric change in CBL occurs, transforming Sir2 into an open state that promotes NAD+ entry and tighter binding, leading to deacetylation.
This deacetylation process results in the breakdown of NAD+ into nicotinamide and 2′-O-acetyl-ADP-ribose, both quickly released. After deacetylation, a reverse allosteric effect facilitates the efficient release of the deacetylated protein, resetting Sir2 for the next reaction cycle. The tandem allosteric effects of the reactant (acetylated p53) and the product (deacetylated p53) accelerate the entire deacetylation process.
Furthermore, the researchers demonstrated that the CBL region involved in the tandem allosteric effect is present in sirtuins of many species, including humans. This suggests that the tandem allosteric mechanism is an evolutionarily conserved strategy among sirtuins.
The study's implications for drug development are significant. Professor Kitao notes, "Our study introduces a potential new approach for cancer therapy, targeting NAD+ binding mechanisms in sirtuins. Moreover, the PaCS-MD technique employed in this study holds promise for studying other biological systems with similar mechanisms."
In summary, this research enhances our understanding of the crucial sirtuin deacetylation mechanism, paving the way for new therapeutic strategies for aging-related and metabolic diseases.
For more information, see: Zhen Bai et al, Tandem Allosteric Effects of Reactant and Product that Promote Deacetylation Cycles in Sir2, Journal of Chemical Information and Modeling (2025). DOI: 10.1021/acs.jcim.5c01755 (https://dx.doi.org/10.1021/acs.jcim.5c01755)
