Ligand- and mutation-induced conformational selection in the CCR5 chemokine G protein-coupled receptor
Abstract
We predicted the structural basis for pleiotropic signaling of the C-C chemokine type 5 (CCR5) G protein-coupled receptor (GPCR) by predicting the binding of several ligands to the lower-energy conformations of the CCR5 receptor and 11 mutants. For each case, we predicted the ∼20 most stable conformations for the receptor along with the binding sites for four anti-HIV ligands. We found that none of the ligands bind to the lowest-energy apo-receptor conformation. The three ligands with a similar pharmacophore (Maraviroc, PF-232798, and Aplaviroc) bind to a specific higher-energy receptor conformation whereas TAK-779 (with a different pharmacophore) binds to a different high-energy conformation. This result is in agreement with the very different binding-site profiles for these ligands obtained by us and others. The predicted Maraviroc binding site agrees with the recent structure of CCR5 receptor cocrystallized with Maraviroc. We performed 11 site-directed mutagenesis experiments to validate the predicted binding sites. Here, we independently predicted the lowest 10 mutant protein conformations for each of the 11 mutants and then docked the ligands to these lowest conformations. We found the predicted binding energies to be in excellent agreement with our mutagenesis experiments. These results show that, for GPCRs, each ligand can stabilize a different protein conformation, complicating the use of cocrystallized structures for ligand screening. Moreover, these results show that a single-point mutation in a GPCR can dramatically alter the available low-energy conformations, which in turn alters the binding site, potentially altering downstream signaling events. These studies validate the conformational selection paradigm for the pleiotropic function and structural plasticity of GPCRs.
Additional Information
Copyright © 2014 National Academy of Sciences. Contributed by William A. Goddard III, July 27, 2014 (sent for review January 25, 2014). Published online before print August 25, 2014, doi: 10.1073/pnas.1413216111. We thank Soo-Kyung Kim and Andrea Kirkpatrick for useful discussions. A portion of this research was funded by a gift from Accelerator/PharmSelex. The balance was from gifts to the Materials and Process Simulation Center. R.A., B.T., and W.A.G. contributed equally to this work. Author contributions: R.A. and W.A.G. designed research; R.A., B.T., W.A.G., A.N., I.O., and C.I. performed research; R.A., B.T., W.A.G., A.N., I.O., and C.I. analyzed data; and R.A., B.T., and W.A.G. wrote the paper. The authors declare no conflict of interest. This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1413216111/-/DCSupplemental.Attached Files
Published - 13040.full.pdf
Supplemental Material - pnas.201413216SI.pdf
Files
Name | Size | Download all |
---|---|---|
md5:4a8af3a268bdb68ce81508e1d414dacd
|
792.8 kB | Preview Download |
md5:7d148169c0b75b5beb8d86fdd6f8ccf2
|
1.1 MB | Preview Download |
Additional details
- PMCID
- PMC4246978
- Eprint ID
- 48878
- Resolver ID
- CaltechAUTHORS:20140825-223735998
- Accelerator/PharmSelex
- Created
-
2014-08-26Created from EPrint's datestamp field
- Updated
-
2021-11-10Created from EPrint's last_modified field