Carba-NAD binding activates SIR2 by reshaping conformational plasticity and rewiring long-range allosteric networks

Abstract

Allosteric regulation enables proteins to couple local structural changes to distal functional outcomes, yet the underlying mechanisms often remain difficult to fully decipher. Using yeast SIR2, an NAD ⁺ -dependent deacetylase, as a model system, this study systematically elucidates how cofactor binding reshapes its conformational dynamics and internal communication network. Through multiple 3-μs molecular dynamics simulations combined with a graph-based deep learning model (Neural Relational Inference), we identify a highly reproducible characteristic response across independent replicates: the β1-α2 loop near the active site undergoes pronounced rigidification, whereas several distal structural modules exhibit concomitant increases in flexibility, together forming a "core-locking with peripheral-release" dynamic mode. Further signal-pathway analysis reveals that the local and distal conformational changes are not independent; instead, they are interconnected through newly identified "relay-type" residues such as Pro214 and Thr224. These residues act as bridges, converting the previously β1-α2-centered centralized network into a relay-style network coordinated by multiple nodes, thereby establishing a continuous and directionally coherent allosteric cascade. Beyond mechanistic insights, we also identify a distal cavity spatially overlapping with key relay residues, whose physicochemical properties meet the criteria of druggable pockets. This structural convergence suggests that future small-molecule allosteric activators may exploit this intrinsic communication pathway to mimic or amplify the regulatory effects of the cofactor NAD ⁺. Given that NAD⁺ levels decline with aging, this cavity provides a rational target for designing longevity-promoting allosteric activators.