Molecular Insights Into the Differential Binding Affinity of Human Katanin Hexamer for C‐Terminal Tails of β‐Tubulin Isotypes

ABSTRACT Katanin is a microtubule‐severing enzyme critical for cellular processes such as cell division, migration, signaling, and cellular homeostasis. Katanin, a heterodimeric protein composed of p60 and p80, exhibits ATPase activity that is stimulated by microtubules and is responsible for removing tubulin subunits during severing. This severing function requires the assembly of katanin into a hexameric complex. Previous studies have demonstrated that katanin has a differential binding affinity towards C‐terminal tails (CTTs) of β‐tubulin isotypes. However, the interaction dynamics of human katanin hexamer with different β‐tubulin isotypes—especially those overexpressed in various carcinomas—remain poorly understood at the atomic level. In this study, we employed homology modeling, docking, and molecular dynamics simulations to examine the binding behavior of the human katanin hexamer with the CTTs of five β‐tubulin isotypes, which include βI, βIIa, βIII, βIVb, and βV. Our findings reveal that the katanin hexamer exhibits distinct interaction patterns with each isotype, attributed to their sequence‐specific variations in the CTTs. Detailed MD analyses, including radius of gyration, solvent‐accessible surface area, hydrogen bonding, principal component analysis, and free energy landscape profiling, further support these isoform‐specific differences in the interaction dynamics. Moreover, binding free energy calculations indicate that the hexamer shows the highest affinity for βIIa, followed by βIII, βIVb, and βV, with the weakest interaction observed for βI. These computational insights underscore the mechanism of isoform‐specific binding preferences of the human katanin hexamer toward β‐tubulin CTTs, highlighting their potential implications for therapeutic targeting in cancer contexts where specific β‐tubulin isotypes are upregulated.