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Title
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An efficient computational method for predicting rotational diffusion tensors of globular proteins using an ellipsoid representation.
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Authors
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Y.E.Ryabov,
C.Geraghty,
A.Varshney,
D.Fushman.
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Ref.
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J Am Chem Soc, 2006,
128,
15432-15444.
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PubMed id
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Abstract
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We propose a new computational method for predicting rotational diffusion
properties of proteins in solution. The method is based on the idea of
representing protein surface as an ellipsoid shell. In contrast to other
existing approaches this method uses principal component analysis of protein
surface coordinates, which results in a substantial increase in the
computational efficiency of the method. Direct comparison with the experimental
data as well as with the recent computational approach (Garcia de la Torre; et
al. J. Magn. Reson. 2000, B147, 138-146), based on representation of protein
surface as a set of small spherical friction elements, shows that the method
proposed here reproduces experimental data with at least the same level of
accuracy and precision as the other approach, while being approximately 500
times faster. Using the new method we investigated the effect of hydration layer
and protein surface topography on the rotational diffusion properties of a
protein. We found that a hydration layer constructed of approximately one
monolayer of water molecules smoothens the protein surface and effectively
doubles the overall tumbling time. We also calculated the rotational diffusion
tensors for a set of 841 protein structures representing the known protein
folds. Our analysis suggests that an anisotropic rotational diffusion model is
generally required for NMR relaxation data analysis in single-domain proteins,
and that the axially symmetric model could be sufficient for these purposes in
approximately half of the proteins.
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