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Vinculin Motion Modes Analysis with Elastic Network Model
Institute of Applied Mechanics and Biomedical Engineering, Taiyuan University of Technology, Taiyuan 030024, China
College of Informatics, South China Agricultural University, Guangzhou 510642, China
College of Computer Science and Technology, College of Software, Taiyuan University of Technology, Taiyuan 030024, China
* Author to whom correspondence should be addressed.
Received: 14 October 2011; in revised form: 11 December 2011 / Accepted: 12 December 2011 / Published: 27 December 2011
Abstract: Vinculin is an important protein for the linkage between adhesion molecules and the actin cytoskeleton. The activation mechanism of vinculin is still controversial. In order to provide useful information for a better understanding of its activation, we analyze the motion mode of vinculin with elastic network model in this work. The results show that, to some extent, the five domains will present structural rigidity in the motion process. The differences between the structure fluctuations of these domains are significant. When vinculin interacted with other partners, the central long alpha-helix of the first domain becomes bent. This bending deformation can weaken the interaction between the first domain and the tail domain. This motion mode of the first domain is in good agreement with the information extracted from some realistic complex structures. With the aid of the anisotropy elastic network mode, we analyze the motion directions of these domains. The fourth domain has a rotational motion. This rotation is favorable for the releasing of the tail domain from the pincer-like clamp, which is formed by the first and the third domain. All these motion modes are an inherent feature of the structure, and these modes mainly depend on the topology character of the structure.
Keywords: vinculin; motion mode; elastic network model; activation mechanism
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MDPI and ACS Style
Jiao, X.; Chang, S.; Yang, L.; An, M.; Chen, W. Vinculin Motion Modes Analysis with Elastic Network Model. Int. J. Mol. Sci. 2012, 13, 208-220.
Jiao X, Chang S, Yang L, An M, Chen W. Vinculin Motion Modes Analysis with Elastic Network Model. International Journal of Molecular Sciences. 2012; 13(1):208-220.
Jiao, Xiong; Chang, Shan; Yang, Lifeng; An, Meiwen; Chen, Weiyi. 2012. "Vinculin Motion Modes Analysis with Elastic Network Model." Int. J. Mol. Sci. 13, no. 1: 208-220.