期刊
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
卷 528, 期 2, 页码 389-397出版社
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.bbrc.2019.12.076
关键词
Chemokine; G protein-coupled receptor; Chemokine receptor; Rosetta; Homology modeling; GPCR interface
资金
- National Institutes of Health [R01 Al058072, R01 GM080403, R01 GM073151]
Chemokine receptors are a subset of G protein-coupled receptors defined by the distinct property of binding small protein ligands in the chemokine family. Chemokine receptors recognize their ligands by a mechanism that is distinct from other class A GPCRs that bind peptides or small molecules. For this reason, structural information on other ligand-GPCR interactions are only indirectly relevant to understanding the chemokine receptor interface. Additionally, the experimentally determined structures of chemokine-GPCR complexes represent less than 3% of the known interactions of this complex, multi-ligand/multi-receptor network. To enable predictive modeling of the remaining 97% of interactions, a general in silico protocol was designed to utilize existing chemokine receptor crystal structures, co-crystal structures, and NMR ensembles of chemokines bound to receptor fragments. This protocol was benchmarked on the ability to predict each of the three published co-crystal structures, while being blinded to the target structure. Averaging ensembles selected from the top-ranking models reproduced up to 84% of the intermolecular contacts found in the crystal structure, with the lowest C alpha-RMSD of the complex at 3.3 angstrom. The chemokine receptor N-terminus, unresolved in crystal structures, was included in the modeling and recapitulates contacts with known sulfotyrosine binding pockets seen in structures derived from experimental NMR data. This benchmarking experiment suggests that realistic homology models of chemokine-GPCR complexes can be generated by leveraging current structural data. (C) 2019 Elsevier Inc. All rights reserved.
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