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 with low computational cost the dynamics of the methane-thiosulfonate spin label (MTSL) attached to the activation loop of  Aurora-A kinase. MD provided information about the conformational space of MTSL in the protein environment; an isotropic and uniform distribution of orientations of the spin label in space was found due to the large exposure of the activation loop to the solvent water. A hydrodynamic approach was employed to determine the rotational protein tumbling, while the internal motion of the spin probe was determined from 94 GHz measurements that reflect the fast motions. The theoretical 9 GHz EPR spectra were calculated using configurations representing interactions between MTSL and water and the tyrosine residue 208 in the C-lobe and the comparison with experimental EPR spectra produced fits that successfully reproduced the experimental spectra in agreement with the average structures obtained from the MD trajectories showing the MTSL exposed to the solvent and probing the C-lobe of the protein .
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 .
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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 with low computational cost the
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
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methane-thiosulfonate spin label (MTSL) attached to the
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the
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MD provided information about the conformational space of MTSL in the protein environment; an isotropic and uniform distribution of orientations of the spin label in space was found due to the large exposure of
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
R
to the solvent water. A hydrodynamic approach was employed to determine the rotational protein tumbling, while the internal motion of the spin probe was determined from 94 GHz measurements that reflect the fast motions. The theoretical
. The
R
GHz EPR spectra were calculated using configurations representing interactions between MTSL and water and the tyrosine residue 208 in the C-lobe and the comparison with experimental EPR spectra produced fits that successfully reproduced the experimental spectra in agreement with the average structures obtained from
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
R
MD trajectories showing the MTSL exposed to the solvent and probing the C-lobe of the protein
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