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  Structural Flexibility of Cyclosporine A Is Mediated by Amide Cis–Trans Isomerization and the Chameleonic Roles of Calcium

Gray, A. L. H., Steren, C. A., Haynes, I. W., Bermejo, G. A., Favretto, F., Zweckstetter, M., et al. (2021). Structural Flexibility of Cyclosporine A Is Mediated by Amide Cis–Trans Isomerization and the Chameleonic Roles of Calcium. Journal of Physical Chemistry B, 125(5), 1378-1391. doi:10.1021/acs.jpcb.0c11152.

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Gray, Amber L. H., Author
Steren, Carlos A., Author
Haynes, Isaac W., Author
Bermejo, Guillermo A., Author
Favretto, Filippo, Author
Zweckstetter, M.1, Author              
Do, Thanh D., Author
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1Research Group of Protein Structure Determination using NMR, MPI for biophysical chemistry, Max Planck Society, ou_578571              

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 Abstract: Falling outside of Lipinski’s rule of five, macrocyclic drugs have accessed unique binding sites of their target receptors unreachable by traditional small molecules. Cyclosporin(e) A (CycA), an extensively studied macrocyclic natural product, is an immunosuppressant with undesirable side effects such as electrolytic imbalances. In this work, a comprehensive view on the conformational landscape of CycA, its interactions with Ca2+, and host–guest interactions with cyclophilin A (CypA) is reported through exhaustive analyses that combine ion-mobility spectrometry–mass spectrometry (IMS–MS), nuclear magnetic resonance (NMR) spectroscopy, distance-geometry modeling, and NMR-driven molecular dynamics. Our IMS–MS data show that CycA can adopt extremely compact conformations with significantly smaller collisional cross sections than the closed conformation observed in CDCl3. To adopt these conformations, the macrocyclic ring has to twist and bend via cis–trans isomerization of backbone amides, and thus, we termed this family of structures the “bent” conformation. Furthermore, NMR measurements indicate that the closed conformation exists at 19% in CD3OD/H2O and 55% in CD3CN. However, upon interacting with Ca2+, in addition to the bent and previously reported closed conformations of free CycA, the CycA:Ca2+ complex is open and has all-trans peptide bonds. Previous NMR studies using calcium perchlorate reported only the closed conformation of CycA (which contains one cis peptide bond). Here, calcium chloride, a more biologically relevant salt, was used, and interestingly, it helps converting the cis-MeLeu9–MeLeu10 peptide bond into a trans bond. Last, we were able to capture the native binding of CycA and CypA to give forth evidence that IMS–MS is able to probe the solution-phase structures of the complexes and that the Ca2+:CycA complex may play an essential role in the binding of CycA to CypA.

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Language(s): eng - English
 Dates: 2021-02-012021-02-11
 Publication Status: Published in print
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 Rev. Type: Peer
 Identifiers: DOI: 10.1021/acs.jpcb.0c11152
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Title: Journal of Physical Chemistry B
Source Genre: Journal
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Pages: - Volume / Issue: 125 (5) Sequence Number: - Start / End Page: 1378 - 1391 Identifier: -