Structural Dynamics of LDL Receptor Interactions with E498A and R499G Variants of PCSK9

Abstract The low-density lipoprotein receptor (LDLR) plays an integral role in cellular cholesterol uptake and lipid metabolism by primarily regulating hepatic clearance of plasma low-density lipoprotein cholesterol (LDL-C). Physiologically, proprotein convertase subtilisin/kexin type-9 (PCSK9) attenuates LDLR function by binding to the LDLR extracellular domain, leading to its lysosomal degradation and thereby preventing the total depletion of circulating LDL-C. However, pathogenic variants of PCSK9 are able to reduce the availability of LDLR, thus significantly increasing plasma LDL-C levels. Despite this understanding, the detailed molecular mechanism of LDLR-PCSK9 interaction remains elusive due to the lack of a full atomistic structure of LDLR. In this study, molecular dynamics (MD) simulations were employed to predict LDLR structural dynamics upon binding to PCSK9. Furthermore, two PCSK9 variants, E498A and R499G that were identified in clinically diagnosed Malaysian FH patients were investigated for their mutational effects. The simulations, spanning 500 ns, were conducted for three LDLR-PCSK9 complexes: LDLR-PCSK9 wild-type (WT), LDLR-PCSK9 (E498A), and LDLR-PCSK9 (R499G). Throughout the simulations, PCSK9 structure remained highly stable, in contrast to the LDLR structure that sampled large conformational space. The WT complex exhibited the least change, whereas the R499G complex displayed the most pronounced conformational rearrangement. During the simulations of WT and E498A complexes, the β-propeller domain of LDLR formed interactions with the prodomain of PCSK9. Aligned with the observation, the MM/GBSA analysis revealed that the E498A complex exhibited the highest LDLR-PCSK9 binding affinity (−63.81 kcal/mol), followed by the WT complex (−33.07 kcal/mol), and the R499G complex (−24.21 kcal/mol). These findings provide novel insights into the dynamic interactions between LDLR and PCSK9, highlighting the importance of structural flexibility in mediating their functional relationship. Further studies with complete LDLR structures are required to fully elucidate the molecular mechanisms underlying LDLR-PCSK9-mediated cholesterol homeostasis.