Conformational Features and Hydrogen Bonding Properties of Glycosaminoglycan-Interleukin8 Complexes in Aqueous Medium: An Insight from Computer Simulation Study

Abstract

Glycosaminoglycans (GAGs) are an important class of unbranched, negatively charged hetero-polysaccharides. They are the structural components of connective tissue and the extracellular matrix of higher organisms. GAGs are crucial in physiological, pathological, and cell signaling processes. [1] The structural diversity, highly anionic charged surface and their typical location in extracellular matrices make the GAGs molecules biologically important. The protein targets of GAGs are chemokines and growth factors. [2] GAGs bind with their protein targets in the extracellular matrix and participate in biological processes like angiogenesis and cancer, inflammation, neural development etc. [1] Due to the highly flexible nature of GAGs, the molecules can adopt many energetically alike conformational states, making the molecules more challenging for researchers. [3] Controlling GAG sulphation patterns is an important task that can be taken care of during molecular modeling to understand the behavior of different sulphated GAGs towards protein binding with varying sulphation positions. In this work, we tried to identify different binding modes of GAGs to chemokine; Interleukin8 (IL8) by performing molecular docking experiments and extensive atomistic molecular dynamics (MD) simulations. Emphasis was given to investigating the conformational features, binding affinities, and hydrogen bonding properties of sulphated and non-sulphated GAGs in their free and bound form. [4, 5] The GAG molecules exhibit higher flexibility in the bound forms than the corresponding free forms, irrespective of their chemical structure. Estimation of Cremer–Pople Puckering Parameters (Θ, Φ) inferred that the GAG conformations primarily lie in chair form with occasional appearances of equatorial and tropical conformations in both free and bound states. Our study showed that the flexibility of the GAGs is mainly due to the flexibility in glycosidic linkages and the ω rotation. The free landscape was generated with the help of two reaction coordinates, φ, and ψ, to understand the conformational pattern of the GAGs through the different glycosidic linkage (1→3 and 1→4). The appearance of multiple minima separated by the energy barriers depends on the disaccharide linkage involved in the GAGs. Our study further reveals the role of hydrogen bonds and conserved water in the binding process. The average lifetime of the IL8-GAG direct HB pairs was ~ ten times less than the IL8-GAG-shared water HBs. We find that despite the highly negatively charged surface of GAGs, the IL8 surface populated by non-cationic amino acids could serve as a promising binding site in addition to the cationic surface of the protein. [5]