Computer simulation reveals the effect of severing enzymes on dynamic and stabilized microtubules

Abstract

Microtubule severing enzymes Katanin and Spastin cut the microtubule (MT) into smaller fragments and are being studied extensively using in-vitro experiments due to their crucial role in different cancers and
neurodevelopmental disorders. It has been reported that the severing enzymes are either involved in increasing or decreasing the tubulin mass. Currently, there are a few analytical and computational models for MT amplification and severing. However, these models do not capture the action of microtubule severing explicitly, as these are based on partial differential equations in one dimension. On the other hand, a few discrete lattice-based models were used earlier to understand the activity of severing enzymes only on stabilized MTs. Hence, in this study, discrete lattice-based Monte Carlo models that included microtubule dynamics and severing enzyme activity have been developed to understand the effect of severing enzymes on tubulin mass, MT number, and MT length. It was found that the action of severing enzyme reduces average MT length while increasing their number; however, the total tubulin mass can decrease or increase depending on the concentration of GMPCPP (Guanylyl-(α, β)-methylene-diphosphonate) - which is a slowly hydrolyzable analogue of GTP (Guanosine triphosphate). Further, relative tubulin mass also depends on the detachment ratio of GTP/GMPCPP and GDP (Guanosine diphosphate) tubulin dimers and the binding energies of
tubulin dimers covered by the severing enzyme.

Ultrasensitivity of microtubule severing due to damage repair

“…We also note that although our study here is focused on tubulin-induced repair at damages created by severing proteins on microtubules, our model of damage spreading may be useful for analyzing other situations where reincorporation of new tubulin on a microtubule shaft has been observed, such as at sites of defects created by mechanical stress 46 , 56 or motor protein-induced damage 49 , 50 on microtubules.…”

“… 45 Further, in-vitro studies and computational studies have reported that severing proteins promote the regrowth of severed microtubules by enhancing the rate of rescue in microtubules 46 , 47 and lead to a net increase in microtubule number and mass. 20 , 28 , 29 , 48 , 49 It is unknown whether severing proteins have the same effect in vivo where they interact with other microtubule-associated proteins. Interestingly, incorporation of new tubulin dimers into microtubule lattice has also been reported at defects arising from mechanical stress, 46 , 47 or damages created by molecular motors.…”

“…This results in negative feedback of filament length on a growing filament and leads to control of length of cytoskeletal filaments. This property of severing proteins has been explored by a number of theoretical and experimental studies, 28 , 46 , 47 , 48 , 49 , 53 , 54 , 55 , 56 however, how these proteins work with other proteins to control the sizes of filamentous structures in vivo is not well understood.…”

Exploring Purine Analogues as Inhibitors against Katanin, a Microtubule Severing Enzyme using Molecular Modeling Approach

“…The ATP hydrolysis-driven conformational changes of the hexameric ring enable it to exert force or produce motion that helps to remove the tubulin subunit from the MT 13 . Recently, discrete lattice-based Monte Carlo models incorporating microtubule (MT) dynamics and severing enzyme activity have been developed to elucidate the effects of severing enzymes on tubulin mass, MT quantity, and MT length 14 . However, the breaking and reorganization of MTs by the katanin play a crucial role in ciliogenesis 15 , cell size regulation 4 , plant cell wall biosynthesis and phototropism 16,17 .…”