ASM Variants in the Spotlight: A Structure-Based Atlas for Unraveling Pathogenic Mechanisms in Lysosomal Acid Sphingomyelinase

Abstract

Lysosomal acid sphingomyelinase (ASM), a critical enzyme in lipid metabolism encoded by the SMPD1 gene, plays a crucial role in sphingomyelin hydrolysis in lysosomes. ASM deficiency leads to acid sphingomyelinase deficiency, a rare genetic disorder with diverse clinical manifestations, and the protein can be found mutated in other diseases. We employed a structure-based framework to comprehensively understand the functional implications of ASM variants, integrating pathogenicity predictions with molecular insights derived from molecular dynamics simulations in a lysosomal membrane environment. Our analysis, encompassing over 400 variants, establishes a structural atlas of missense variants of lysosomal ASM, associating mechanistic indicators with pathogenic potential. Our study highlights variants that influence structural stability or exert local and long-range effects at functional sites. To validate our predictions, we compared them to available experimental data on residual catalytic activity in 135 ASM variants. Notably, our findings also suggest applications of the resulting data for identifying cases suited for enzyme replacement therapy. This comprehensive approach enhances the understanding of ASM variants and provides valuable insights for potential therapeutic interventions.

Acidic Sphingomyelinase Interactions with Lysosomal Membranes and Cation Amphiphilic Drugs: a Molecular Dynamics Investigation

“…To characterize the interaction between ASM and the lysosomal membrane, we collected four one-μs all-atom MD simulations of the protein with the lipid bilayer (Table1) , employing two strategies to predict how they associate (Figure2B) . A model and its first MD simulation (i.e., replicate 1 of model 1) are taken from ref 37 . This initial system for MD simulations had ASM positioned on the bilayer surface and interacting with the lipids.…”

“…We designed two systems with different starting orientations of ASM to the lipid bilayer. In the first system, we modeled ASM as already localized on top of the lipid bilayer by using the initial configuration previously published 37 . In the second system, we avoided imposing extensive starting contacts between ASM and the lipids using an approach similar to the one used for other peripheral membrane proteins 38 .…”

“…We used the MD simulation of model 1 previously published 37 and performed two additional all-atom MD simulations of one-μs each for ASM embedded in a lipid bilayer with a mammalian “lysosomal-like” composition 35 with the CHARMM36m force field 39 . Moreover, we carried out one additional simulation using model 2 ( Table 1 ).…”

“…In addition, we accounted for the N-glycosylations of ASM in the interaction with the membrane. Hence, we modeled a fully Man5-glycosylated variant of ASM (i.e., at the sites N88, N177, N337, N397, N505, and N522), as previously described 37 . We investigated the structural properties of the lipid bilayer and the effects induced by the association with ASM.…”

“…Moreover, ebastine did not have effects on the curvature induced by ASM itself on the bilayer in the EBAH-ASM systems compared to what observed with the ASM model 1 replicates (Figure S8). We evaluated the binding modes of ebastine into the ASM structure using a contact-based analysis combined with the analysis of solvent-exposed pockets of ASM (Figures 7C-D and 8) taken from our previous study 37 . According to the previous analysis, pockets 1, 3, 6, 7, 15, and 22 matched with regions for ASM-membrane interactions, whereas pockets 5 and 12 included residues near the catalytic site.…”