Atomic visualization of flipped‐back conformations of high mannose glycans interacting with cargo lectins: An MD simulation perspective

Abstract

Protein–carbohydrate interactions play a crucial role in mediating several biomolecular recognition events. We attempt to unravel its intricacies by understanding how carbohydrate‐binding proteins interpret the glycan code. We aim to decipher lectin‐mediated recognition in the endoplasmic reticulum (ER), which plays a crucial role in ER‐mediated quality control (ER‐QC). The ER‐QC functions in three phases—protein folding, transport, and degradation. Altered protein QC leads to ER‐related storage disorders. Cargo transport proteins—Ergic53 and Vip36—necessary for maintaining cellular homeostasis—are our primary focus. They recognize monoglucosylated/high mannose N‐glycans on the folded glycoproteins. This article reports on the first dynamic investigation of the ER cargo lectins in complex with the high mannose glycans using an advanced sampling technique—replica exchange molecular dynamics to decipher the inherent conformational heterogeneity and the binding mechanism. The study involves simulations for the proteins complexed with three high mannose glycans—Man8B, Man9, and mono‐glucosylated glycan. The recognition process is captured using MD simulations to achieve mechanistic insights and characterize the dynamics of glycans in their native and bound states via dihedral angle analysis. Results indicate that the flipped conformation of the glycans was crucial in differentiating their interaction with the proteins. Similar conformers of the glycans are preferred for Ergic53 and Vip36 in their glycan recognition events. Ergic53 preferred Man8B while it was Man9 for Vip36, in coherence with the previous experimental reports. These simulations provide a computational microscopic purview of the mechanism at both spatial and temporal scales. The results correlate with the published experimental data on the specificities of these lectins.