Unravelling the conformational dynamics of pathogenic mutations of apolipoprotein M: an integrative computational and molecular dynamics simulation approach

Apolipoprotein M (ApoM), a sphingosine-1-phosphate (S1P) binding protein, is primarily synthesized in the liver and kidney. It is a key component of high-density lipoprotein (HDL) and plays a pivotal role in reverse cholesterol transport, vascular homeostasis and anti-inflammatory responses via the ApoM-S1P axis. Dysregulation of ApoM expression or S1P metabolism is associated with cardiovascular, metabolic and inflammatory disorders, highlighting the importance of understanding its structural and functional dynamics. Despite extensive knowledge of individual transcriptional and post-transcriptional changes in ApoM, the coordinated mechanisms integrating these signals and the impact of naturally occurring non-synonymous single-nucleotide polymorphisms (nsSNPs) remain poorly understood. This study systematically investigated the structural and functional impact of nsSNPs in ApoM using an integrated in silico approach. From 4097 variants, 162 nsSNPs were prioritized, with A51S, F63V and R89S identified as highly deleterious. A51S disrupts a conserved hydrophobic core, resulting in a compact and less dynamic structure with reduced flexibility. F63V induces severe destabilization by altering β-turn integrity and binding pocket architecture, leading to increased solvent exposure and conformational heterogeneity. In contrast, R89S enhances hydrogen bonding and maintains a more stable conformation. These mutation-oriented effects are predicted to influence S1P binding and HDL function. Overall, the findings provide mechanistic insight into ApoM variant-induced dysfunction and establish a framework for prioritizing functionally significant mutations.