DOI: 10.5281/zenodo.17870795
title: Molecular Dynamics Simulation Data: Core Fucosylation Effects on α4-Integrin

description:  



This repository contains molecular dynamics (MD) simulation data and analysis scripts accompanying the publication:


 



Discovering Glycosylation-Dependent Protein Function by Thermal Proteome Profiling


Johannes F. Hevler, Mirat Soijtra, Tomislav Caval, Michael Schoof, André Mateus and Carolyn R. Bertozzi - Hevler et al. (2025), bioRxiv

 

The simulations investigate how core fucosylation at the N138 glycosylation site regulates α4-integrin (ITGA4) function at the molecular level. We compare two glycoproteoforms:





N4H5F1A1: Core fucosylated complex glycan (abundant in vehicle-treated cells)







N4H5A1: Afucosylated complex glycan (present in 2FF-treated cells)



Key Findings

Our MD simulations reveal that:





Core fucosylation rigidifies the glycan backbone, restricting its conformational space

Afucosylated glycans show increased flexibility* enabling them to shield the Ca²⁺-binding site

Loss of core fucose eliminates stabilizing hydrogen bonds with residues near N138 (particularly S140)

Afucosylated glycans form extended contacts with the Ca²⁺-binding loop (Gal10-N442) and Thigh domain (Sia7-R554)

A conformational paradox emerges: increased glycan flexibility restricts protein dynamics through frequent glycan-protein contacts





System Details



Protein: ITGA4 (residues 34-620), encompassing the β-propeller, Thigh, and Ca²⁺-binding domains

Glycan variants:



N4H5F1A1 (fucosylated): Complex glycan with core fucosylation and terminal sialic acid

N4H5A1 (afucosylated): Complex glycan lacking core fucosylation



Simulation software: GROMACS (version 2023.1)

Analysis tools: MDAnalysis, custom Python scripts





Analyses Included



Glycan conformational clustering: Torsion angle-based clustering to characterize glycan flexibility

SASA analysis: Solvent accessible surface area calculations for glycoforms

Volmap analysis: Occupancy analysis for glycoforms

RMSF/RMSD analysis: Backbone and Per-residue flexibility comparison between glycoforms

Contact analysis: Protein-glycan interaction mapping

Hydrogen bond analysis: Identification of key stabilizing interactions







Citation
If you use this data, please cite:



```bibtex

@article {Hevler et al. (2025),

author = {Hevler, Johannes Florian and Sojitra, Mirat and Caval, Tomislav and Schoof, Michael Lewis and Mateus, Andre and Bertozzi, Carolyn},

title = {Discovering Glycosylation-Dependent Protein Function by Thermal Proteome Profiling},

year = {2025},

doi = {10.64898/2025.12.06.692499},

publisher = {Cold Spring Harbor Laboratory},

URL = {https://www.biorxiv.org/content/early/2025/12/07/2025.12.06.692499},

journal = {bioRxiv}

}

```


License
CC BY 4.0

Contact
For questions regarding the data or analysis, please contact:







Johannes F. Hevler - jfhevler@stanford.edu




Acknowledgments
This work was supported in part by National Institutes of Health grant CA200423 (C.R.B.), EMBO Postdoctoral Fellowship (ALTF 904-2023; J.F.H.), Howard Hughes Medical Institute Fellowship of the Life Sciences Research Foundation (J.F.H), the Cancer Research Institute Irvington Fellowship (#CRI5766; M.So.) and Schmidt Science Fellowship, an initiative of Schmidt Futures and the Rhodes Trust (M.Sc.). Some of the computing for this project was performed on the Sherlock cluster. We would like to thank Stanford University and the Stanford Research Computing Center for providing computational resources and support that contributed to these research results.