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Effect of monovalent ion binding on molecular dynamics of the S100-family calcium-binding protein calbindin D.

08:00 EDT 12th April 2019 | BioPortfolio

Summary of "Effect of monovalent ion binding on molecular dynamics of the S100-family calcium-binding protein calbindin D."

Calbindin D is a member of the S100 subfamily of EF-hand calcium binding proteins, and has served as an important model system for biophysical studies. The fast timescale dynamics of the calcium-free (apo) state is characterized using molecular dynamics simulations. Order parameters for the backbone NH bond vectors are determined from the simulations and compared with experimentally derived values, with a focus on the dynamics of calcium-binding site I. There is a significant discrepancy between simulated and experimental order parameters for site I residues in the case of no ion bound in site I. However, it was found in the simulations that a Na ion can bind in site I, and the resulting order parameters determined from the simulations are in excellent agreement with experiment. Comparisons are made to X-ray structures of other S100 family members in which Na ions were observed or suggested to be bound in site I. © 2019 Wiley Periodicals, Inc.

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This article was published in the following journal.

Name: Journal of computational chemistry
ISSN: 1096-987X
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