Tandem Allosteric Effects of Reactant and Product that Promote Deacetylation Cycles in Sir2

Post-translational modifications play important roles in the regulation of protein function, with N^ε acetylation being a key reversible modification affecting processes such as transcription, metabolism, and stress responses. Sirtuins, particularly SIRT1 and its ortholog, Sir2, are NAD+-dependent deacetylases that target both histone and non-histone proteins, such as the tumor suppressor p53. Acetylation of p53 on K382 influences its degradation and transcriptional activity. Despite structural studies of the Sir2/p53 complex, the role of the conserved cofactor-binding loop (CBL) in regulating NAD+ binding and deacetylation remains unclear. Using both conventional molecular dynamics (MD) and parallel cascade selection MD (PaCS-MD) simulations, we explored the conformational changes in the CBL of Sir2 in response to p53 acetylation. We identified open and closed states of the NAD+ binding pocket, which are caused by a CBL conformational change, suggesting the mechanism involves acetylation-driven NAD+ binding pocket opening. Combining these simulations with entropy transfer analysis, we mapped allosteric pathways that highlight the role of CBL in deacetylating p53. Our findings offer insights into broader roles of Sir2 in aging, metabolism, and various diseases, including cancer.