Molecular dynamics (MD) simulations using a graphics processing unit (GPU) has been employed in order to determine the conformational space of the methane-thiosulfonate spin label (MTSL) attached to the activation loop of the Aurora-A kinase protein and compared with quantum mechanical (QM) methods rooted on density functional theory (DFT). MD provided a wealth of information about interactions between the MTSL and the residues of the protein and  on the different motional contributions to the overall dynamics of the MTSL . Data obtained from MD were seen to be in good agreement with those obtained from QM but the dynamics of the system revealed more interactions than those observed from QMmethods . A strong correlation between the tumbling of the protein and the transitions of the X4 and X5 dihedral angles of the MTSL , was observed with a consequent effect also the distribution of the nitroxide (NO) group in the space . Theoretical EPR spectra calculated from opportunely selected MD frames showing interactions between the MTSL and residues of the protein were seen to be in good agreement with the experimental EPR spectrum , indicating a predominance of some conformational states of the full spin-labelled system. 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 overall tumbling and biological activity.
Classical molecular dynamics (MD) simulations , within the AMBER program package that runs entirely on a CUDA-enabled NVIDIA graphic processing unit (GPU) , were employed to study the dynamics of the methane-thiosulfonate spin labelled (MTSL) Aurora-A kinase activation loop in a very short time and with good quality of the sampling. The MD simulation provided a wealth of information on the interactions between MTSL and protein residues, and on the different motional contributions to the overall dynamics of the MTSL that were validated using a multifrequency electron paramagnetic resonance (EPR) approach. The latter relayed on the frequency dependence of the resolution of the fast and slow motions of the spin probe and was used to distinguish the fast internal motion of the spin label from the slow protein tumbling. Data obtained from MD were in good agreement with those obtained from quantum mechanical (QM) methods, but more interactions within the dynamics of the system were revealed than from QM . A strong correlation between the tumbling of the protein and the transitions of the X4 dihedral angle of the MTSL was observed with a consequent effect on the distribution of the nitroxide (NO) group in space and time. The theoretical EPR spectra were calculated using selected configurations of MTSL probing different micro-environments of the protein characterized by different polarity. The comparison between the theoretical and experimental 9 GHz and 94 GHz EPR spectra revealed that some fits were in good agreement with the experimental EPR spectra , indicating a predominance of some conformational states of the full spin-labelled system. This work is a starting point for deeper experimental and theoretical studies of the diffusion properties of the Aurora-A kinase protein related to its overall tumbling and biological activity.
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