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Effect of monovalent ion binding on molecular dynamics of the S100‐family calcium‐binding protein calbindin D 9k
Author(s) -
Thapa Mahendra,
Johnson Eric,
Rance Mark
Publication year - 2019
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.25839
Subject(s) - molecular dynamics , chemistry , calcium binding protein , calbindin , calcium , ion , binding site , crystallography , subfamily , dynamics (music) , biophysics , computational chemistry , physics , biochemistry , biology , organic chemistry , gene , acoustics
Calbindin D 9k 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.