Conformational Preferences for N‑Glycans at the Surface of CEACAM1-Ig1

TL;DR

This study uses NMR and simulations to explore how glycans on a protein's surface adopt specific shapes that may help stabilize the protein.

Contribution

The study demonstrates the successful application of Pep-GaMD to glycan conformations using NMR data for validation.

Findings

NMR data confirmed preferred glycan conformations at the CEACAM1-Ig1 surface.

Hydrophobic interactions between glycans and protein residues contribute to stability.

Pep-GaMD simulations effectively sampled glycan conformations relevant to protein function.

Abstract

Glycans on glycoproteins
play roles that range from quality control
in protein folding, to mediation of interactions with other proteins,
to stabilization of the protein to which they are attached. Computation
can suggest structures that underlie these roles, but confidence is
limited by the accuracy of energetic calculations and their applicability
to the aqueous environment in which proteins function. Experimental
validation of suggested structures is therefore of primary importance.
Here we use NMR data, including long-range pseudocontact shifts (PCSs)
and residual dipolar couplings (RDCs), to screen structures produced
by a version of accelerated molecular dynamics (Pep-GaMD). This version
was designed to improve the search for peptide–protein interactions,
but here it is successfully applied to glycans attached to a target
protein. The target protein, the N-terminal domain of human CEACAM1,
is expressed with homogeneous GlcNAc2Man5 glycans
at its three N-glycosylation sites. One site (N104) is found to have
preferred conformations that exploit hydrophobic interactions between
its glycans and protein hydrophobic residues, potentially adding to
protein stability and protection from adverse interactions.

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