Structural exploration of acid sphingomyelinase at different physiological pH through molecular dynamics and docking studies

Abstract

Acid sphingomyelinase (ASM) is an enzyme involved in the hydrolysis of sphingomyelin leading to the production of ceramide. It is responsible for the stimulation of apoptosis and has a pH dependent efficacy for its substrate binding. Deficiency of this enzyme causes an autosomal recessive lysosomal storage disorder called Niemann–Pick disease. To understand the full length structure of ASM at different physiological pH, the protein was modeled based on its structure homologue purple acid phosphatase (PAP) and topological folding matching through ab initio calculations. Results from molecular dynamics simulations at different physiological pH, PCA and FEL analysis clearly depict the folding mechanism of the loop region (D206–L248) towards the catalytic domain. The ASM structure at neutral pH and pH 3.0 adopts a conformational fold that subsequently either closes or partially opens the catalytic domain making it inaccessible for the binding of substrate, whereas the ASM structure at pH 5.0 maintains a completely open conformation of the loop that creates a tunnel in the catalytic domain for the accessibility of substrate. This observation was also confirmed through molecular docking studies, showing that sphingomyelin binds at a different site which is away from the catalytic domain of neutral ASM. Though the substrate binds near the catalytic domain in the pH 3.0 ASM structure, it is unable to form a proper mode of interaction which is essential for its hydrolysis process. Only in the pH 5.0 ASM structure, a proper mode of interaction formulated by the phosphate ion that is posing towards the two catalytic zinc ions confirmed their ability to effectively engage the substrate for its hydrolysis. The structural insights of ASM at different physiological pH and subsequent substrate interactions provide an indispensable understanding of their catalytic mechanism which can lead to the enhancement of apoptosis and control of Niemann–Pick disease.