In Silico Insights into Protein-protein Interaction Disruptive Mutations in the PCSK9-LDLR complex

Int J Mol Sci. 2020 Feb 25;21(5):1550. doi: 10.3390/ijms21051550.


Gain-of-function mutations in PCSK9 (proprotein convertase subtilisin/kexin type 9) lead to reduced uptake of LDL (low density lipoprotein) cholesterol and, therefore, increased plasma LDL levels. However, the mechanism by which these mutants reduce LDL reuptake is not fully understood. Here, we have used molecular dynamics simulations, MM/PBSA (Molecular Mechanics/Poisson-Boltzmann Surface Area) binding affinity calculations, and residue interaction networks, to investigate the protein-protein interaction (PPI) disruptive effects of two of PCSK9's gain-of-function mutations, Ser127Arg and Asp374Tyr on the PCSK9 and LDL receptor complex. In addition to these PPI disruptive mutants, a third, non-interface mutation (Arg496Trp) is included as a positive control. Our results indicate that Ser127Arg and Asp374Tyr confer significantly improved binding affinity, as well as different binding modes, when compared to the wild-type. These PPI disruptive mutations lie between the EGF(A) (epidermal growth factor precursor homology domain A) of the LDL receptor and the catalytic domain of PCSK9 (Asp374Tyr) and between the prodomain of PCSK9 and the β-propeller of the LDL receptor (Ser127Arg). The interactions involved in these two interfaces result in an LDL receptor that is sterically inhibited from entering its closed conformation. This could potentially implicate the prodomain as a target for small molecule inhibitors.

Keywords: LDLR; MM/PBSA; Molecular Dynamics; PCSK9; PPI disruptive mutation; protein–protein interaction (PPI); residue interaction network.

MeSH terms

  • Catalytic Domain
  • Humans
  • Molecular Dynamics Simulation
  • Mutation
  • Proprotein Convertase 9 / chemistry*
  • Proprotein Convertase 9 / genetics
  • Proprotein Convertase 9 / metabolism
  • Protein Binding
  • Receptors, LDL / chemistry*
  • Receptors, LDL / genetics
  • Receptors, LDL / metabolism


  • LDLR protein, human
  • Receptors, LDL
  • PCSK9 protein, human
  • Proprotein Convertase 9