Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology Rourkela, Rourkela 769008, India.
J Phys Chem B. 2024 Oct 24;128(42):10348-10362. doi: 10.1021/acs.jpcb.4c03670. Epub 2024 Oct 15.
GAGs bind to both the monomeric and dimeric forms of CXCL8, helping to form a concentration gradient of the chemokine that facilitates the recruitment of neutrophils to an injury site and supports other biological functions. In this study, atomistic molecular dynamics simulations were conducted to investigate the binding behavior of two hexameric GAGs sulfated at two different positions, chondroitin sulfate (CS) and heparan sulfate (HS), with the monomer (SIL8) and dimer (DIL8) forms of the CXCL8 protein. The results support that the conformational diversity of CS and HS appeared to be more when binding with monomer SIL8 than dimer DIL8. CS gained more configurational entropy from glycosidic linkage flexibility when bound to SIL8 than DIL8, with a higher energy barrier, whereas HS exhibited a lower energy barrier for configurational entropy when bound to SIL8 and DIL8. The monomer SIL8 exhibited more favorable and preferential binding with GAGs compared to DIL8. Formation of hydrogen bonds with the basic amino acids of SIL8 and GAG was more rigid and required higher activation energy to break than the other identified hydrogen bondings. Water molecules involved in hydrogen bonding with GAGs, excluding those with basic amino acids of DIL8, showed longer lifetimes and slower relaxation compared to SIL8. This suggests that water-mediated interactions also favor binding of DIL8 with GAGs. Despite having more basic amino acids, DIL8 did not display stronger binding than SIL8, indicating the significant role of basic residues in stabilizing the GAG-protein interactions in the monomers. The reason could be that the greater number of nonbasic amino acids in dimeric CXCL8 stabilizes the complex by forming water-mediated hydrogen bonds, reducing the conformational preferences for binding with GAGs. In contrast, the monomeric form of CXCL8 exhibits a higher conformational preference for protein-GAG interactions.
GAGs 与 CXCL8 的单体和二聚体形式都结合，帮助形成趋化因子的浓度梯度，促进中性粒细胞向损伤部位募集，并支持其他生物学功能。在这项研究中，进行了原子分子动力学模拟，以研究两种在不同位置硫酸化的六聚体 GAG（硫酸软骨素 (CS) 和硫酸乙酰肝素 (HS)）与 CXCL8 蛋白的单体（SIL8）和二聚体（DIL8）形式的结合行为。结果表明，CS 和 HS 与单体 SIL8 结合时的构象多样性似乎比与二聚体 DIL8 结合时更多。CS 在与 SIL8 结合时比与 DIL8 结合时从糖苷键灵活性获得更多的构象熵，具有更高的能量势垒，而 HS 在与 SIL8 和 DIL8 结合时具有更低的构象熵能量势垒。与 DIL8 相比，单体 SIL8 表现出与 GAG 更有利和更优先的结合。与 SIL8 和 GAG 的碱性氨基酸形成氢键比其他鉴定的氢键更刚性，需要更高的活化能才能断裂。与 GAG 形成氢键的水分子，不包括 DIL8 的碱性氨基酸的水分子，与 SIL8 相比表现出更长的寿命和更慢的弛豫。这表明水介导的相互作用也有利于 DIL8 与 GAG 的结合。尽管 DIL8 具有更多的碱性氨基酸，但它的结合强度并不比 SIL8 强，这表明碱性残基在稳定单体中 GAG-蛋白相互作用方面发挥了重要作用。原因可能是二聚体 CXCL8 中更多的非碱性氨基酸通过形成水介导的氢键稳定了复合物，减少了与 GAG 结合的构象偏好。相比之下，单体形式的 CXCL8 表现出更高的蛋白质-GAG 相互作用构象偏好。
