Ligand-induced CaMKIIα hub Trp403 flip, hub domain stacking and kinase inhibition

Narayanan, D.; Larsen, A. S. G.; Gauger, S. J.; Adafia, R.; Hammershoi, R. B.; Hamborg, L.; Bruus-Jensen, J.; Griem-Krey, N.; Gee, C. L.; Frolund, B.; Stratton, M. M.; Kuriyan, J.; Kastrup, J. S.; Langkilde, A. E.; Wellendorph, P.; Solbak, S. M. O.

doi:10.1101/2024.03.26.586665

bioRxiv · 10.1101/2024.03.26.586665

Ligand-induced CaMKIIα hub Trp403 flip, hub domain stacking and kinase inhibition

Narayanan, D.·Larsen, A. S. G.·Gauger, S. J.·Adafia, R.·Hammershoi, R. B.·Hamborg, L.·Bruus-Jensen, J.·Griem-Krey, N.·Gee, C. L.·Frolund, B.·Stratton, M. M.·Kuriyan, J.·Kastrup, J. S.·Langkilde, A. E.·Wellendorph, P.·Solbak, S. M. O.

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Abstract

{gamma}-Hydroxybutyric acid (GHB) analogs are small molecules that bind competitively to a specific cavity in the oligomeric CaMKII hub domain. Binding affects conformation and stability of the hub domain, which may explain the neuroprotective action of some of these compounds. Here, we describe molecular details of interaction of the larger-type GHB analog 2-(6-(4-chlorophenyl)imidazo[1,2-b]pyridazine-2-yl)acetic acid (PIPA). Like smaller-type analogs, PIPA binding to the CaMKII hub domain promoted thermal stability. PIPA additionally inhibited CaMKII kinase activity by reducing CaM sensitivity. A high-resolution X-ray crystal structure of a stabilized CaMKII (6x mutant) hub construct revealed details of the binding mode of PIPA, which involved outward placement of tryptophan 403 (Trp403), a central residue in a flexible loop close to the upper hub cavity. Small-angle X-ray scattering (SAXS) solution structures and mass photometry of the CaMKII wildtype hub domain in the presence of PIPA revealed a high degree of ordered self-association (stacks of CaMKII hub domains). This stacking neither occurred with the smaller compound 3-hydroxycyclopent-1-enecarboxylic acid (HOCPCA), nor when Trp403 was replaced with leucine (W403L). Additionally, CaMKII W403L hub was stabilized to a larger extent by PIPA compared to CaMKII hub wildtype, indicating that loop flexibility is important for holoenzyme stability. Thus, we propose that ligand-induced outward placement of Trp403 by PIPA, which promotes an unforeseen mechanism of hub domain stacking, may be involved in the observed reduction in CaMKII kinase activity. Altogether, this sheds new light on allosteric regulation of CaMKII activity via the hub domain.

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Narayanan, D., Larsen, A. S. G., Gauger, S. J., Adafia, R., Hammershoi, R. B., Hamborg, L., Bruus-Jensen, J., Griem-Krey, N., Gee, C. L., Frolund, B., Stratton, M. M., Kuriyan, J., Kastrup, J. S., Langkilde, A. E., Wellendorph, P., Solbak, S. M. O.. 2024-03-27. Ligand-induced CaMKIIα hub Trp403 flip, hub domain stacking and kinase inhibition. https://doi.org/10.1101/2024.03.26.586665

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