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

William R Martin,Feixiong Cheng,Felice C Lightstone

doi:10.3390/ijms21051550

Abstract

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.

Highlights

Cardiovascular disease is the number one killer in the United States; according to the Center for Disease Control and Prevention, nearly 650,000 people died of heart disease in 2017, accounting for roughly 1 in 4 deaths [1]
Autosomal dominant familial hypercholesterolemia (FH), defined by elevated LDL levels in which 70–95% of cases result from mutations in one of three genes [2], is associated with a substantial increase in coronary heart disease and atherosclerotic cardiovascular disease [3] and affects roughly 1 in 250 U.S adults [4]
We have proposed a plausible mechanism behind the disease-causing protein–protein interaction (PPI) disruptive mutations Ser127Arg and Asp374Tyr on proprotein convertase subtilisin/kexin type 9 (PCSK9) and LDL receptor (LDLR) complex

Summary

Introduction

Cardiovascular disease is the number one killer in the United States; according to the Center for Disease Control and Prevention, nearly 650,000 people died of heart disease in 2017, accounting for roughly 1 in 4 deaths [1]. WWhhiliele inin tthhee AArrgg449966TTrp mutant simulation the LDLR remains in an extended conformation (Supplemental Figure S2), a replicate of the Asp374Tyr mutant results in the β-propeller curling back into the EGF domains (Supplemental Figure S3), which would be an unlikely result in the presence of a membrane surface This does provide some evidence that it is possible for PCSK9 to bind LDLR without preventing a closed conformation. A mapping of the crystal structure of LDLR in its closed conformation (PDB ID: 1N7D simulation the LDLR remains in an extended conformation (Supplemental Figure S2), a replicate of the Asp374Tyr mutant results in the β-propeller curling back into the EGF domains (Supplemental Figure S3), which would be an unlikely result in the presence of a membrane surface A mapping of the crystal structure of LDLR in its closed conformation (PDB ID: 1N7D [10]) indicates that the interaction between the β-propeller and the ligand binding domains is not sterically inhibited in this conformation, though a rotation in EGF(B) would be required

Discussion

Selection of Disease-Causing Mutations

System Construction

Simulation Parameters

Findings

System Analysis