Prediction of Three Dimensional Structure of Calmodulin |
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Authors: | Ke Chen Jishou Ruan Lukasz A Kurgan |
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Institution: | (1) College of Mathematical Sciences and LPMC, Chern Institute of Mathematics and Liuhui Center for Applied Mathematics, Nankai University, Tianjin, 300071, Peoples Republic of China;(2) Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada |
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Abstract: | Calmodulin (CaM) is an important human protein, which has multiple structures. Numerous researchers studied the CaM structures
in the past, and about 50 different structures in complex with fragments derived from CaM-regulated proteins have been discovered.
Discovery and analysis of existing and new CaM structures is difficult due to the inherent complexity, i.e. flexibility of
6 loops and a central linker that constitute part of the CaM structure. The extensive interest in CaM structure analysis and
discovery calls for a comprehensive study, which based on the accumulated expertise would design a method for prediction and
analysis of future and existing CaM structures. It is also important to find the mechanisms by which the protein adjusts its
structure with respect to various factors. To this end, this paper analyzes the known CaM structures and finds four factors
that influence CaM structure, which include existence of Ca2+ binding, different binding segments, measuring surroundings, and sequence mutation. The degree of influence of specific factors
on different structural regions is also investigated. Based on the analysis of the relation between the four factors and the
corresponding CaM structure a novel method for prediction of the CaM structure in complex with novel segments, given that
the surroundings of the complex, is developed. The developed prediction method is tested on a set aside, newest CaM structure.
The prediction results provide useful and accurate information about the structure verifying high quality of the proposed
prediction method and performed structural analysis. |
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Keywords: | Calmodulin Ca2+-binding protein protein structure binding segment |
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