Cryo-EM reveals the architecture of placental malaria VAR2CSA and provides molecular insight into chondroitin sulfate binding

Thomas Lavstsen,Kresten Lindorff-Larsen,Charlotte B Spliid,Yong Wang,Thor G Theander,Tobias Gustavsson,Thomas Mandel Clausen,Mette Ø Agerbaek,Swati Choudhary,Elena Ethel Vidal-Calvo,Kaituo Wang,Daniel R Sandoval,Pontus Gourdon,Morten A Nielsen,Ali Salanti,Sandeep K Misra,Robert Dagil,Joshua S Sharp

doi:10.1038/s41467-021-23254-1

Abstract

Placental malaria can have severe consequences for both mother and child and effective vaccines are lacking. Parasite-infected red blood cells sequester in the placenta through interaction between parasite-expressed protein VAR2CSA and the glycosaminoglycan chondroitin sulfate A (CS) abundantly present in the intervillous space. Here, we report cryo-EM structures of the VAR2CSA ectodomain at up to 3.1 Å resolution revealing an overall V-shaped architecture and a complex domain organization. Notably, the surface displays a single significantly electropositive patch, compatible with binding of negatively charged CS. Using molecular docking and molecular dynamics simulations as well as comparative hydroxyl radical protein foot-printing of VAR2CSA in complex with placental CS, we identify the CS-binding groove, intersecting with the positively charged patch of the central VAR2CSA structure. We identify distinctive conserved structural features upholding the macro-molecular domain complex and CS binding capacity of VAR2CSA as well as divergent elements possibly allowing immune escape at or near the CS binding site. These observations will support rational design of second-generation placental malaria vaccines.

Highlights

Placental malaria can have severe consequences for both mother and child and effective vaccines are lacking
It was identified that infected erythrocytes binding to placental chondroitin sulfate A expressed a Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) gene named var2csa[5]
Several of the Duffy Binding-Like (DBL) domains are linked by complex inter-domain (ID1-3) regions with limited or no homology among PfEMP1s yielding a DBL1-ID1-DBL2ID2-DBL3-DBL4-ID3-DBL5-ID4-DBL6 structure[10]

Summary

Introduction

Placental malaria can have severe consequences for both mother and child and effective vaccines are lacking. Using molecular docking of CS oligosaccharides, we show that atypical DBL features of VAR2CSA DBL2 domains form the structural basis for CS binding. By fast photochemical oxidation of proteins (FPOP) analyses of VAR2CSA in complex with placental CS and mutational analyses, we validate the structural and surface exposed regions involved in CS binding and demonstrate that the groove can encompass a CS oligo of around 13 saccharides.

Results

Conclusion