Conformational Motions and Functionally Key Residues for Vitamin B12 Transporter BtuCD–BtuF Revealed by Elastic Network Model with a Function-Related Internal Coordinate
Abstract
:1. Introduction
2. Results and Discussion
2.1. The Contribution of Each Motion Modes to the Channel-Gating Function of BtuCD–BtuF
2.2. The Motions of BtuCD–BtuF Relevant to the Channel-Gating Function
2.3. The Key Residue Interactions that Control the Channel-Gating Motion of BtuCD–BtuF
3. Experimental Section
3.1. Anisotropic Network Model (ANM)
3.2. The Internal Coordinate Related to the Channel-Gating Function of BtuCD-F
3.3. Methods to Analyze the Function-Related Motions and Identify the Functionally Important Residue Interactions
3.3.1. The Mean-Square Fluctuation of the Internal Coordinate for Each Normal Mode
3.3.2. The Cross-Correlation between the Displacement of the Inter-Distance and the Movement of Each Residue in the Transporter
3.3.3. The Perturbation Method to Identify Functionally Key Residue Interactions
4. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Su, J.-G.; Zhang, X.; Zhao, S.-X.; Li, X.-Y.; Hou, Y.-X.; Wu, Y.-D.; Zhu, J.-Z.; An, H.-L. Conformational Motions and Functionally Key Residues for Vitamin B12 Transporter BtuCD–BtuF Revealed by Elastic Network Model with a Function-Related Internal Coordinate. Int. J. Mol. Sci. 2015, 16, 17933-17951. https://doi.org/10.3390/ijms160817933
Su J-G, Zhang X, Zhao S-X, Li X-Y, Hou Y-X, Wu Y-D, Zhu J-Z, An H-L. Conformational Motions and Functionally Key Residues for Vitamin B12 Transporter BtuCD–BtuF Revealed by Elastic Network Model with a Function-Related Internal Coordinate. International Journal of Molecular Sciences. 2015; 16(8):17933-17951. https://doi.org/10.3390/ijms160817933
Chicago/Turabian StyleSu, Ji-Guo, Xiao Zhang, Shu-Xin Zhao, Xing-Yuan Li, Yan-Xue Hou, Yi-Dong Wu, Jian-Zhuo Zhu, and Hai-Long An. 2015. "Conformational Motions and Functionally Key Residues for Vitamin B12 Transporter BtuCD–BtuF Revealed by Elastic Network Model with a Function-Related Internal Coordinate" International Journal of Molecular Sciences 16, no. 8: 17933-17951. https://doi.org/10.3390/ijms160817933