Molecular dynamics simulations reveal molecular mechanisms for the gain and loss of function effects of four SCN2A variants

Genetic variants in the SCN2A gene cause a wide spectrum of neurodevelopmental disorders. The current binary classification of pathogenic missense variants as either gain or loss of function does not correlate with the diverse clinical presentations observed in affected individuals. We hypothesize that missense variants lead to a spectrum of disease mechanisms and that computational extensive molecular dynamics (MD) simulations can uncover these. We have selected four variants within the SCN2A gene based on their high prevalence among SCN2A patients and distinct molecular read-outs, classified as either gain or loss of function based upon in vitro demonstrated increase or decrease in ion flux. We designed five systems, employed 500ns MD simulations with 3 replicas each, to investigate a comprehensive range of biophysical properties exhibited by disease-causing variants at the atomic level. All patient variant structure models were less tightly packed and exhibited a greater range of conformations compared to the wild type, suggesting that all mutants undergo structural changes. In addition, we also studied the possible variant specific disease mechanisms responsible for all four variants. These findings go beyond the binary classification of gain and loss of function obtained from electrophysiological studies. We identified two different mechanisms resulting in a loss of function and two different mechanisms resulting in a gain of function, therefore providing greater detail and understanding of the variant effect, which also suggests that categorization of a variant solely as a gain or loss of function oversimplifies the complex nature of these mechanisms. These molecular dynamics (MD) studies serve as the initial step in examining numerous variants in sodium ion channel genes, and with adequate computing resources, this approach could be applied to analyze all missense variants.