Comparative Bindings\nof Glycosaminoglycans with CXCL8\nMonomer and Dimer: Insights from Conformational Dynamics and Kinetics\nof Hydrogen Bonds

GAGs bind to both the monomeric and dimeric forms of\nCXCL8, helping\nto form a concentration gradient of the chemokine that facilitates\nthe recruitment of neutrophils to an injury site and supports other\nbiological functions. In this study, atomistic molecular dynamics\nsimulations were conducted to investigate the binding behavior of\ntwo hexameric GAGs sulfated at two different positions, chondroitin\nsulfate (CS) and heparan sulfate (HS), with the monomer (SIL8) and\ndimer (DIL8) forms of the CXCL8 protein. The results support that\nthe conformational diversity of CS and HS appeared to be more when\nbinding with monomer SIL8 than dimer DIL8. CS gained more configurational\nentropy from glycosidic linkage flexibility when bound to SIL8 than\nDIL8, with a higher energy barrier, whereas HS exhibited a lower energy\nbarrier for configurational entropy when bound to SIL8 and DIL8. The\nmonomer SIL8 exhibited more favorable and preferential binding with\nGAGs compared to DIL8. Formation of hydrogen bonds with the basic\namino acids of SIL8 and GAG was more rigid and required higher activation\nenergy to break than the other identified hydrogen bondings. Water\nmolecules involved in hydrogen bonding with GAGs, excluding those\nwith basic amino acids of DIL8, showed longer lifetimes and slower\nrelaxation compared to SIL8. This suggests that water-mediated interactions\nalso favor binding of DIL8 with GAGs. Despite having more basic amino\nacids, DIL8 did not display stronger binding than SIL8, indicating\nthe significant role of basic residues in stabilizing the GAG–protein\ninteractions in the monomers. The reason could be that the greater\nnumber of nonbasic amino acids in dimeric CXCL8 stabilizes the complex\nby forming water-mediated hydrogen bonds, reducing the conformational\npreferences for binding with GAGs. In contrast, the monomeric form\nof CXCL8 exhibits a higher conformational preference for protein–GAG\ninteractions.