Developing and\nBenchmarking Sulfate and Sulfamate\nForce Field Parameters via Ab Initio Molecular Dynamics Simulations\nTo Accurately Model Glycosaminoglycan Electrostatic Interactions

Glycosaminoglycans (GAGs) are negatively charged polysaccharides\nfound on cell surfaces, where they regulate transport pathways of\nforeign molecules toward the cell. The structural and functional diversity\nof GAGs is largely attributed to varied sulfation patterns along the\npolymer chains, which makes understanding their molecular recognition\nmechanisms crucial. Molecular dynamics (MD) simulations, thanks to\ntheir unmatched microscopic resolution, have the potential to be a\nreference tool for exploring the patterns responsible for biologically\nrelevant interactions. However, the capability of molecular dynamics\nforce fields used in biosimulations to accurately capture sulfation-specific\ninteractions is not well established, partly due to the intrinsic\nproperties of GAGs that pose challenges for most experimental techniques.\nIn this work, we evaluate the performance of molecular dynamics force\nfields for sulfated GAGs by studying ion pairing of Ca<sup>2+</sup> to sulfated moieties<i>N</i>-methylsulfamate and\nmethylsulfatethat resemble N- and O-sulfation found in GAGs,\nrespectively. We tested available nonpolarizable (CHARMM36 and GLYCAM06)\nand explicitly polarizable (Drude and AMOEBA) force fields, and derived\nnew implicitly polarizable models through charge scaling (prosECCo75\nand GLYCAM-ECC75) that are consistent with our developed “charge-scaling”\nframework. The calcium–sulfamate/sulfate interaction free energy\nprofiles obtained with the tested force fields were compared against\nreference ab initio molecular dynamics (AIMD) simulations, which serve\nas a robust alternative to experiments. AIMD simulations indicate\nthat the preferential Ca<sup>2+</sup> binding mode to sulfated GAG\ngroups is solvent-shared pairing. Only our scaled-charge models agree\nsatisfactorily with the AIMD data, while all other force fields exhibit\npoorer agreement, sometimes even qualitatively. Surprisingly, even\nexplicitly polarizable force fields display a notable disagreement\nwith the AIMD data, likely attributed to difficulties in their optimization\nand possible inherent limitations in depicting high-charge-density\nion interactions accurately. Finally, the underperforming force fields\nlead to unrealistic aggregation of sulfated saccharides, which qualitatively\ndisagrees with our understanding of the soft glycocalyx environment.\nOur results highlight the importance of accurately treating electronic\npolarization in MD simulations of sulfated GAGs and caution against\nover-reliance on currently available models without thorough validation\nand optimization.