Conformational Insights into Glycosaminoglycan Binding with CXCL8 Monomer and Dimer: Dynamics and Hydrogen Bond Kinetics

Abstract

Glycosaminoglycans (GAGs) interact with both monomeric and dimeric forms of the chemokine CXCL8, contributing to the formation of concentration gradients that aid neutrophil recruitment to sites of injury and support other physiological functions.1,2 In this study molecular dynamics simulations were perfomed to explore how two hexameric GAGs chondroitin sulfate (CS), and heparan sulfate (HS), each sulfated at distinct positions bind to the monomeric (SIL8) and dimeric (DIL8) forms of CXCL8.3 The results indicate that both CS and HS adopt a wider range of conformations when interacting with the monomer (SIL8) compared to the dimer (DIL8). CS, in particular, demonstrated greater configurational entropy due to flexible glycosidic linkages when bound to SIL8, along with a high energy barrier. In contrast, HS exhibited a less energy barrier for the configurational changes when bound to either form. SIL8 showed stronger and more favourable binding to GAGs than DIL8. Hydrogen bonds formed between SIL8 and GAGs especially those involving basic amino acids were more rigid and required higher energy to break. Additionally, water molecules forming hydrogen bonds with GAGs, excluding those bonded to DIL8’s basic residues had longer lifetimes and slower relaxation in the DIL8 complex, suggesting that water-mediated interactions stabilize GAG binding in the dimer. Interestingly, despite having higher basic residues, DIL8 did not exhibit stronger GAG binding than SIL8. This suggests that in the monomeric form, basic residues play a more direct and stabilizing role in GAG binding. In contrast, the dimer's increased number of non-basic residues likely stabilizes the complex through water-mediated hydrogen bonding, reducing its conformational specificity for GAG interaction. As a result, the monomeric CXCL8 shows a higher structural preference for interacting with GAGs compared to the dimeric form.