Dataset Information

Structural basis for differential binding of the interleukin-8 monomer and dimer to the CXCR1 N-domain: role of coupled interactions and dynamics.

ABSTRACT: Interleukin-8 (IL-8 or CXCL8) plays a critical role in orchestrating the immune response by binding and activating the receptor CXCR1 that belongs to the GPCR class. IL-8 exists as both monomers and dimers, and both bind CXCR1 but with differential affinities. It is well established that the monomer is the high-affinity ligand and that the interactions between the ligand N-loop and receptor N-domain play a critical role in determining binding affinity. In order to characterize the structural basis of differential binding of the IL-8 monomer and dimer to the CXCR1 N-domain, we analyzed binding-induced NMR chemical shift and peak intensity changes and show that they are exquisitely sensitive and can provide detailed insights into the binding process. We used three IL-8 variants, a designed monomer, a trapped disulfide-linked dimer, and WT at dimeric concentrations. NMR data for the monomer show that nonsequential residues that span the entire N-loop are involved in the binding process and that the binding is mediated by a network of extensive direct and indirect coupled interactions. Interestingly, in the case of WT, binding induces dissociation of the dimer-receptor complex to the monomer-receptor complex, and in the case of the trapped dimer, binding results in increased global conformational flexibility. Increased dynamics is evidence of unfavorable interactions, indicating that binding of the WT dimer triggers conformational changes that disrupt dimer-interface interactions, resulting in its dissociation. These results together provide evidence that binding is not a localized event but results in extensive coupled interactions within the monomer and across the dimer interface and that these interactions play a fundamental role in determining binding affinity.

SUBMITTER: Ravindran A

PROVIDER: S-EPMC2858980 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature

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Structural basis for differential binding of the interleukin-8 monomer and dimer to the CXCR1 N-domain: role of coupled interactions and dynamics.

Ravindran Aishwarya A Joseph Prem Raj B PR Rajarathnam Krishna K

Biochemistry 20090901 37

Interleukin-8 (IL-8 or CXCL8) plays a critical role in orchestrating the immune response by binding and activating the receptor CXCR1 that belongs to the GPCR class. IL-8 exists as both monomers and dimers, and both bind CXCR1 but with differential affinities. It is well established that the monomer is the high-affinity ligand and that the interactions between the ligand N-loop and receptor N-domain play a critical role in determining binding affinity. In order to characterize the structural bas ...[more]

PMID: 19681642

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Project description:Plexin-B1 is a single-pass transmembrane receptor. Its Rho GTPase binding domain (RBD) can associate with small Rho GTPases and can also self-bind to form a dimer. In total, more than 400 ns of NAMD molecular dynamics simulations were performed on RBD monomer and dimer. Different analysis methods, such as root mean squared fluctuation (RMSF), order parameters (S(2)), dihedral angle correlation, transfer entropy, principal component analysis, and dynamical network analysis, were carried out to characterize the motions seen in the trajectories. RMSF results show that after binding, the L4 loop becomes more rigid, but the L2 loop and a number of residues in other regions become slightly more flexible. Calculating order parameters (S(2)) for CH, NH, and CO bonds on both backbone and side chain shows that the L4 loop becomes essentially rigid after binding, but part of the L1 loop becomes slightly more flexible. Backbone dihedral angle cross-correlation results show that loop regions such as the L1 loop including residues Q25 and G26, the L2 loop including residue R61, and the L4 loop including residues L89-R91, are highly correlated compared to other regions in the monomer form. Analysis of the correlated motions at these residues, such as Q25 and R61, indicate two signal pathways. Transfer entropy calculations on the RBD monomer and dimer forms suggest that the binding process should be driven by the L4 loop and C-terminal. However, after binding, the L4 loop functions as the motion responder. The signal pathways in RBD were predicted based on a dynamical network analysis method using the pathways predicted from the dihedral angle cross-correlation calculations as input. It is found that the shortest pathways predicted from both inputs can overlap, but signal pathway 2 (from F90 to R61) is more dominant and overlaps all of the routes of pathway 1 (from F90 to P111). This project confirms the allosteric mechanism in signal transmission inside the RBD network, which was in part proposed in the previous experimental study.

Dataset Information

Structural basis for differential binding of the interleukin-8 monomer and dimer to the CXCR1 N-domain: role of coupled interactions and dynamics.

Publications

Structural basis for differential binding of the interleukin-8 monomer and dimer to the CXCR1 N-domain: role of coupled interactions and dynamics.

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