Analysis of the movements of helices in EF-hands

Authors

  • Hiroshi Kawasaki,

    Corresponding author
    1. Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, Tsurumi-ku, Yokohama 230-0045, Japan
    • Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, Suehiro-cho 1-7-23, Tsurumi-ku, Yokohama 230-0045, Japan
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  • Robert H. Kretsinger

    1. Department of Biology, University of Virginia, Charlottesville, Virginia 22903-2477
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Abstract

We have developed a method to place an EF-lobe in a coordinate system that recognizes the similarity of its two EF-hand domains as well as their relationship by a pseudo-two fold axis, z. The x-axis connects the center of mass, calculated from α-carbons of helices E1 and F1, with the center of mass of E2 and F2. The resulting coordinate system is intrinsic to each EF-lobe and requires no comparison with other EF-lobes. It has provided an intuitive and informative way to compare EF-lobes and especially those changes associated with calcium and/or target binding. We analyzed the EF-lobes of calmodulin and of other subfamilies with four EF-hands. We have rationalized a complex pattern of changes of conformation associated with calcium coordination and effector binding as observed in different subfamilies of EF-hand proteins. Proteins 2012. © 2012 Wiley Periodicals, Inc.

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