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PIM-1L kinase binds to and inactivates SRPK1: A Biochemical and Molecular Dynamics Study
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  • Nastazia Lesgidou,
  • Anastasia Koukiali,
  • Eleni Nikolakaki,
  • Thomas Giannakouros,
  • Metaxia Vlassi
Nastazia Lesgidou
Ethniko Kentro Ereunas Physikon Epistemon Demokritos
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Anastasia Koukiali
Aristoteleio Panepistemio Thessalonikes
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Eleni Nikolakaki
Aristoteleio Panepistemio Thessalonikes
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Thomas Giannakouros
Aristoteleio Panepistemio Thessalonikes
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Metaxia Vlassi
Ethniko Kentro Ereunas Physikon Epistemon Demokritos

Corresponding Author:meta@bio.demokritos.gr

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Abstract

SR/RS dipeptide repeats vary in both length and position and are phosphorylated by SR protein kinases (SRPKs). PIM-1L, the long isoform of PIM-1 kinase, the splicing of which has been implicated in acute myeloid leukemia, contains a domain which consists largely of repeating SR/RS and SH/HS dipeptides (SR/SH-rich). In order to extend our knowledge on the specificity and cellular functions of SRPK1, here we investigate whether PIM-1L could act as substrate of SRPK1 by a combination of biochemical and computational approaches. Our biochemical data showed that the SR/SH-rich domain of PIM-1L was able to associate with SRPK1, yet it could not act as a substrate but, instead, inactivated the kinase. In line with our biochemical data, molecular modeling followed by a microsecond-scale all-atom molecular dynamics (MD) simulation suggests that the SR/SH-rich domain acts as a pseudo-docking peptide that binds to the same acidic docking-groove used in other SRPK1 interactions and induces inactive SRPK1 conformations. Comparative community network analysis of the MD trajectories, unraveled the dynamic architecture of apo SRPK1 and notable alterations of allosteric communications upon PIM-1L peptide binding. This analysis also allowed us to identify key SRPK1 residues, including unique ones, with a pivotal role in mediating allosteric signal propagation within the kinase core. Interestingly, most of the identified amino acids correspond to cancer-associated amino acid changes, validating our results. In total, this work provides insights not only on the details of SRPK1 inhibition by the PIM-1L SR/SH-domain, but also contributes to an in-depth understanding of SRPK1 regulation.
31 Jul 2024Submitted to PROTEINS: Structure, Function, and Bioinformatics
01 Aug 2024Submission Checks Completed
01 Aug 2024Assigned to Editor
01 Aug 2024Review(s) Completed, Editorial Evaluation Pending
05 Aug 2024Reviewer(s) Assigned
26 Aug 2024Editorial Decision: Revise Major
04 Oct 20241st Revision Received
07 Oct 2024Submission Checks Completed
07 Oct 2024Assigned to Editor
07 Oct 2024Review(s) Completed, Editorial Evaluation Pending
07 Oct 2024Reviewer(s) Assigned
08 Oct 2024Editorial Decision: Accept