Conformational Preferences for N-Glycans at the Surface of CEACAM1-Ig1 (Trajectories)

Supplementary Information for CEACAM-Ig1 Gaussian Accelerated MD Trajectories Three 1 us MD trajectories were prepared to allow glycan structures to be screened for consistency with NMR data. They were generated using Pep-GaMD in AMBER22. The starting point for MD calculations was a minimum energy structure for the glycosylated protein selected from MD trajectories used in our previous work. The system was solvated in TIP5P water in a rectangular box with a minimum distance between the glycans and the edge of the box of 10 Å. The ff14SB forcefield was used for amino acids and the GLYCAM_06j-1 forcefield was used for glycans. After minimization, the system was heated to 300 K and allowed to equilibrate. The potential energy for each of three N-glycans (beginning with GlcNac residues 125, 132 and 139) were boosted along with the remaining system potential energy in a dual-boost Pep-GaMD simulation, which began with a 4 ns conventional MD run and then 16 ns Pep-GaMD equilibration. In each of three 1000 ns Pep-GaMD production runs, simulation frames and energies were saved every 2 ps, resulting in 500,000 frames. The standard deviation of the boosts was set to 8.0 kcal/mol for all systems. It is important to note that probabilities assigned to these structures are ultimately dependent on the accuracy of forcefields for glycans, protein and the particular water model used.