Fig. 4: Docking model of VAR2CSA in complex with a CS 20-mer. | Nature Communications

Fig. 4: Docking model of VAR2CSA in complex with a CS 20-mer.

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

Fig. 4

a The docking structure of VAR2CSA in complex with CS 20-mer. The electrostatic potential surfaces of VAR2CSA with the minimal binding region and binding groove, which is highlighted by a black box. A surface potential (kT/e) color bar is shown. The CS molecule is represented by sticks in red. The DBL5/6 domains are shown in white cartoon. The right panel shows the structure turned 90°. b Docking structure of VAR2CSA shown as cartoon with domains colored as in Fig. 1d. The CS molecule is shown as sticks in magenta. c Conformational flexibility of CS ligand in the binding groove of VAR2CSA. Boxed area shows the core part of the CS chain with relatively low RMSF values, corresponding to roughly seven disaccharide units. d Binding groove of VAR2CSA with an ensemble of CS 20-mer with 70 conformers sampled in a 70 ns MD simulation with an interval of 1 ns. CS interacting residues from VAR2CSA are labeled with residue numbers.

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