Mechanistic and evolutionary insights into isoform-specific ‘supercharging’ in DCLK family kinases


Venkat, Aarya ORCID: 0000-0002-8793-4097, Watterson, Grace, Byrne, Dominic P, O'Boyle, Brady, Shrestha, Safal, Gravel, Nathan, Fairweather, Emma E, Daly, Leonard A ORCID: 0000-0001-9712-9676, Bunn, Claire, Yeung, Wayland et al (show 5 more authors) (2023) Mechanistic and evolutionary insights into isoform-specific ‘supercharging’ in DCLK family kinases. eLife, 12.

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Abstract

<jats:p>Catalytic signaling outputs of protein kinases are dynamically regulated by an array of structural mechanisms, including allosteric interactions mediated by intrinsically disordered segments flanking the conserved catalytic domain. The doublecortin-like kinases (DCLKs) are a family of microtubule-associated proteins characterized by a flexible C-terminal autoregulatory ‘tail’ segment that varies in length across the various human DCLK isoforms. However, the mechanism whereby these isoform-specific variations contribute to unique modes of autoregulation is not well understood. Here, we employ a combination of statistical sequence analysis, molecular dynamics simulations, and in vitro mutational analysis to define hallmarks of DCLK family evolutionary divergence, including analysis of splice variants within the DCLK1 sub-family, which arise through alternative codon usage and serve to ‘supercharge’ the inhibitory potential of the DCLK1 C-tail. We identify co-conserved motifs that readily distinguish DCLKs from all other calcium calmodulin kinases (CAMKs), and a ‘Swiss Army’ assembly of distinct motifs that tether the C-terminal tail to conserved ATP and substrate-binding regions of the catalytic domain to generate a scaffold for autoregulation through C-tail dynamics. Consistently, deletions and mutations that alter C-terminal tail length or interfere with co-conserved interactions within the catalytic domain alter intrinsic protein stability, nucleotide/inhibitor binding, and catalytic activity, suggesting isoform-specific regulation of activity through alternative splicing. Our studies provide a detailed framework for investigating kinome-wide regulation of catalytic output through cis-regulatory events mediated by intrinsically disordered segments, opening new avenues for the design of mechanistically divergent DCLK1 modulators, stabilizers, or degraders.</jats:p>

Item Type: Article
Uncontrolled Keywords: Genetics, 1.1 Normal biological development and functioning, 1 Underpinning research, Generic health relevance
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology
Depositing User: Symplectic Admin
Date Deposited: 25 Mar 2024 08:48
Last Modified: 25 Mar 2024 08:48
DOI: 10.7554/elife.87958.3
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3179835
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