scientificomputing/NCOMMS-25-06286-T-MUC1-in-vitro-Synthesis-

Supporting raw data for "An in vitro one-pot synthetic biology approach to simulating diverging Golgi O-glycosylation of tumor-associated MUC1 from normal tissue MUC1." https://doi.org/10.21203/rs.3.rs-5783651/v1 This repository contains: PDB files of the final and initial coordinates from which QM/MM reaction dynamic simulations were run. Each system comprises a fully glycosylated MUC1 peptide (5 GalNac sugars) bound to the ST6GALNAC1 enzyme with different GalNac-bearing Thr residues orientated in the catalytic pocket (i.e. T8, T13 or T20) solvated in a water sphere with a radius of 33 Å. Hydrogen link atoms are added to isolate the QM region which comprises, His552, His567, the phosphate and Neu5Ac moieties of CMP-Neu5Ac and the acceptor GalNAc sugar.MP4 movies of product forming trajectories for each system illustrating the generalized reaction mechanism of ST6GALNAC1. In each exported MP4, the ST6GALNAC1 protein in represented in a translucent ribbon structure with the QM region under investigation shown in tube form. The bonds are treated as dynamic to illustrate bond breaking and bond forming during the reaction. The QM region comprises His552, His567, the phosphate and Neu5Ac moieties of CMP-Neu5Ac and the acceptor GalNAc sugar. The trajectories are extracted directly from QM/MM reaction dynamics simulation run with FEARCF. The trajectories shown in a single instance of a product forming trajectory for each system. These do not necessarily represent the minimum energy pathway and are provided solely as evidence of the reaction dynamics simulation work done. Full trajectories and additional data may be made available upon request.