Impact of intrinsically disordered regions and functional disorder hotspots in the human kinome.

Abstract

A ubiquitous and reversible phosphorylation is important for molecular signaling cascades, regulated by the transient interaction of protein kinases. The coupled folding and phosphorylation determining substrate specificity re-calibrates the interactive environment of intrinsically disordered regions (IDRs). There are over 50 computational methods for predicting IDRs in the proteome, yet achieving an accurate depiction remains an ongoing challenge. In this study, we present a standardized and kinase-centric approach for IDR prediction within the human kinome, employing a long short-term memory deep learning framework that achieves a high predictive performance (AUC = 0.97). The web server is now publicly accessible at: https://ciods.in/kindisorder. Our workflow begins with proteome-wide IDR prediction and proceeds with the categorization of short and long IDR segments, followed by an in-depth analysis of their distribution relative to the kinase domain regulatory core. We evaluated the conservation of these IDRs across all 137 human kinase families, computing a trend-setting conservation index to identify both conserved and variable disorder patterns. Through this framework, we uncovered 1039 functional disorder region hotspots that correlate with dynamic conformational shifts, phosphorylation sites, functional motif enrichment, and mutation impact embedded within IDRs. To further validate their regulatory significance, we conducted biophysical profiling of conserved and variable IDRs. Finally, we developed a structural integrity framework to link these IDRs to their influence on intrinsic signaling cascades and substrate specificity. This study offers a comprehensive functional characterization of IDRs in the human kinome, providing a valuable resource for exploring kinase regulation and opportunities in drug repurposing.