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Important fluctuation dynamics of large protein structures are preserved upon coarse-grained renormalization

Abstract : The fluctuations and important motions of three large proteins--hemaglutinin, xanthine dehydrogenase, and β-galactosidase--have been considered with a range of models having various levels of detail to represent the structures. Because the slowest modes of motion are the largest contributors to the total motions, and because these motions depend mainly on the shapes of the structures rather than their details, it is possible to replace the real structures with significantly fewer points and still retain the essential features of the structure for these modes of motion. We obtain excellent results, both for the magnitudes of the individual motions as well as for the molecular changes occurring during these motions. Similar results are obtained with another completely different approach where the coarse graining is based on invariant regions of structure found by comparing two structures of the same protein, given as an example here for myosin. Results confirm the important coupling of local functional motions with the large-scale motions, implying important functional roles for the entire protein structure.
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https://hal-upec-upem.archives-ouvertes.fr/hal-00750112
Contributor : Isabelle Navizet <>
Submitted on : Friday, November 9, 2012 - 8:29:48 AM
Last modification on : Monday, March 30, 2020 - 1:50:03 PM

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P. Doruker, Isabelle Navizet, R. Jernigan, R. Hernandez. Important fluctuation dynamics of large protein structures are preserved upon coarse-grained renormalization. International Journal of Quantum Chemistry, Wiley, 2002, 90 (2), pp.822-837. ⟨10.1002/qua.955⟩. ⟨hal-00750112⟩

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