MD and EPR studies of the structure and dynamics of the MTSL spin-labelled activation loop of the Aurora-A kinase

TL;DR

This study combines molecular dynamics simulations and EPR spectroscopy to explore the conformational dynamics of the Aurora-A kinase activation loop in solution, providing insights beyond static crystal structures.

Contribution

It demonstrates exhaustive MD sampling of the kinase activation loop and spin label, linking simulations with experimental EPR data to understand protein motion in solution.

Findings

MD simulations sampled all conformations of the activation loop and spin label

Simulated and experimental EPR data showed similar timescales of motion

Results support further studies on kinase dynamics related to biological activity

Abstract

The understanding of kinase structure is mostly based on protein crystallography, which is limited by the requirement to trap molecules within a crystal lattice. Therefore, characterisations of the conformational dynamics of the activation loop in solution are important to enhance the understanding of molecular processes related to diseases and to support the discovery of small molecule kinase inhibitors. In this work, we demonstrated that long molecular dynamics simulations exhaustively sampled all the conformational space of the activation loop of the Aurora-A kinase and of the methane-thiosulfonate spin label, introduced into the activation loop for the electron paramagnetic measurements. MD was used to determine structural fluctuations, order parameters and rotational correlation times of the motion of the activation loop and of the MTSL. Theoretical data obtained were used as input for the calculation of the room temperature 9 GHz continuous wave EPR of the Aurora-A kinase in solution and the comparison between simulated and experimental date revealed that the motion of the protein and spin label occurred on comparable timescales. This work is a starting point for deeper experimental and theoretical studies of the rotational and translational diffusion properties of the Aurora-A kinase protein related to its biological activity.