Analysis of the movements of helices in EF-hands.
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.
Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, Tsurumi-ku, Yokohama 230-0045, Japan. kawasaki@yokohama-cu.ac.jp
Hiroshi
H
Kawasaki
Robert H
RH
Kretsinger
D000818:Animals; D002118:Calcium / Q000378:metabolism; D002147:Calmodulin / Q000737:chemistry* / Q000378:metabolism; D030562:Databases, Protein; D020832:EF Hand Motifs; D006801:Humans; D008958:Models, Molecular; D018994:Myosin Light Chains / Q000737:chemistry* / Q000378:metabolism; D017434:Protein Structure, Tertiary; D019209:Troponin C / Q000737:chemistry* / Q000378:metabolism
D002147:Calmodulin; D018994:Myosin Light Chains; D019209:Troponin C; D002118:Calcium