Molecular Dynamic Simulation Of IL-8 With Chemokine Receptor CXCR1

Interleukin 8(a.k.a. chemokine CXCL8) binds and activates its specific receptor C XCR1(Class A G-protein coupled receptor family), plays an essential role in human immune response.The combination of IL-8 and CXC R1 is not one step, but dynamic.Therefore, investigating the IL-8/CXCR1 dynamic binding p rocess and receptor- ligand interactions are critical for understanding the molecular mechanisms of chemokine-receptor function and designing targeted drugs.Based on "Multistep" binding mechanism[1],three models(Step0,Step1 and Step2) are built to represent different binding states of IL-8 and CXCR1.Step0,namly the unliganded wide type C XCR1.Step1 is the complex structure of IL-8 and the N-terminal loop of C XCR1. Step2 is the predicted complex structure by protein-protein docking, because the native complex of IL-8 and CXCR1-ECLs are absent. The above three models are used in 50 ns MD simulations independently. Although Step2 is a predicted structure, the complex is in accord with experimental data, because the key residues, which were verified by mutant studies, are defined to be inside the binding interface. Analysis of Step2 reveals that electrostatic,H-bond, saltbridge and Hydrophobic interactions exist in the receptor- ligand binding surface, and finds out a series of residues,which are invovled in receptor- ligand interactions.Some of these residues were verified by previous studies,such as C ys110,Arg199,Glu275 and Arg280 in CXCR1, as well as Glu4, Arg6 in IL-8. Other residues,such as Glu24,Asp45 and Glu48 in IL-8 are found to be involved in both electrostatic interaction and H-bond, and play important roles in receptor-ligand interactions, even though they have not verified by experiment yet.Analysis of MD simulation trajectories of three models reveals the conformational differences of CXCR1 in different binding states. After IL-8 coupled to CXC R1 N-terminus(Step1), three extracellular loops(ECLs) of CXC R1 become more flexible and the binding sites in C XCR1-EC Ls are exposed, those changes make it convenient for IL-8 to bind the ECLs of CXCR1(Step2). Besides, the trend that IL-8 in Step1 moves towards the EC Ls domain of CXCR1 are also found in our simulations. As we know, ligand binds and activates GPCR, then conformatio nal changes occur in TM and ICL domains, αunit of G protein binds to IC Ls of GPCR and triggers signal tranduction. Our 50 ns simulations are too short to observe obvious conformational changes in TM and IC L domains, but we can still find out the flexibility and exposure differences of the key residues(Tyr136, Leu137, Ile139,Val140 and Met241) in CXCR1-ICLs, which are considered as G-protein binding sites of CXCR1. Compared to Step0 and Step1, the five residues in Step2 have the maximum flexibility and the maximum exposure, we have reasons to believe it is a sign of C XCR1 activation.We believe that our study provides a more indepth understanding of IL-8/CXCR1 interaction mechanism and a reference for subsequent drug design experiments.