The understanding of kinase structure is mostly based on protein crystallography, which is limited by the requirement to trap molecules within a crystal lattice. Characterisation of the conformations 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,  molecular dynamics simulations have been employed in order to study structure and dynamics of the activation loop of the Aurora-A kinase . The main conformational states were determined using a clustering analysis routine within the AMBER software and the predominant modes of motion of the activation were determined performing a principal component analysis that revealed different degree of flexibility within the  activation loop . The 9 GHz EPR spectrum of the Aurora-A kinase was measured in order to study the dynamics of the MTSL spin label attached within the activation loop , MD provided information about the different motional contributions to the overall dynamics of the MTSL and about interactions between the MTSL and the residues of the protein . Data obtained from MD were seen to be in good agreement with those obtained from QM performed in previous work and with the experimental EPR data . 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.
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.
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Characterisation of the conformations
Therefore, characterisations of the conformational dynamics
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,
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we demonstrated that long
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have been employed in order to study structure and dynamics
exhaustively sampled all the conformational space
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. The main conformational states were determined using a clustering analysis routine within the AMBER software and the predominant modes of motion of the activation were determined performing a principal component analysis that revealed different degree of flexibility within
and of
A
methane-thiosulfonate spin label, introduced into the
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. The
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
R
GHz EPR spectrum of the
GHz continuous wave EPR of the
R
kinase was measured in order to study the dynamics of the MTSL spin label attached within the activation loop , MD provided information about the different motional contributions to the overall dynamics of the MTSL and about interactions between the MTSL and
kinase in solution and
R
residues
comparison between simulated and experimental date revealed that the motion
R
. Data obtained from MD were seen to be in good agreement with those obtained from QM performed in previous work and with the experimental EPR data
and spin label occurred on comparable timescales
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overall tumbling and