Chinese Journal of Tissue Engineering Research ›› 2018, Vol. 22 ›› Issue (16): 2549-2557.doi: 10.3969/j.issn.2095-4344.0237

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Variations of sodium chloride concentration affect conformational dynamics of human neuronal calcium sensor-1 protein: a molecular dynamics simulation study

Zhu Yu-zhen1, Li Yun-xiang1, Cai Hao1, Zhang Qing-wen2   

  1. 1Physical Education College, Shanghai Normal University, Shanghai 200234, China; 2Shanghai University of Sport, Shanghai 200438, China
  • Received:2018-03-12 Online:2018-06-08 Published:2018-06-08
  • Contact: Cai Hao, Professor, Physical Education College, Shanghai Normal University, Shanghai 200234, China
  • About author:Zhu Yu-zhen, Ph.D., Physical Education College, Shanghai Normal University, Shanghai 200234, China
  • Supported by:

    the Young Teacher Training Project of Shanghai Universities, No. A-9103-17-041331; the Postgraduate Education Innovative Research Project of Shanghai University of Sport, No. yjscx2015003

Abstract:

BACKGROUND: Human neuronal calcium sensor-1 (NCS-1) protein with a high charge is extremely sensitive to solution temperature, but whether the change of ion concentration in the solution can change the protein structure and affect the physiological function has not been reported.
OBJECTIVE: To investigate the molecular mechanism of variations of sodium chloride concentration altering conformational dynamics of human NCS-1.
METHODS: Through molecular dynamics simulation, the first two minimum energy models (PDB id: 2LCP) were utilized as the starting states of each independent molecular dynamics simulation of the human NCS-1 protein. After energy minimization, two different initial structures were used to conduct three independent 500 ns molecular dynamics simulations with explicit solvent for human NCS-1 protein at 0.1, 0.3 and 1 mol/L sodium chloride concentration.
RESULTS AND CONCLUSION: The slightly high concentration of sodium chloride increased the flexibility of loop L2, simultaneously expanded the global and local structure of NCS-1 protein. Increase in sodium chloride concentration induced loop L3 to adopt a collapsed state and reduced the connectivity between the starting and ending residues of loop L3. N-domain and C-domain interdomain correlation was weakened and the intradomain coupling strengthened. Formation number and the probability of the salt bridges were reduced dramatically, especially at 0.3 mol/L sodium chloride. These findings manifest that human NCS-1 protein is sensitive to the small variation of sodium chloride concentration, which may alter the key factors on protein conformation. Our study may provide the theoretical reference at the atomic structural insights for probing the conformational variations of human NCS-1 protein at the different aqueous solutions.

中国组织工程研究杂志出版内容重点:组织构建;骨细胞;软骨细胞;细胞培养;成纤维细胞;血管内皮细胞;骨质疏松组织工程

Key words: Neuronal Calcium-Sensor Proteins, Sodium Chloride, Protein Structure, Quaternary, Kinetics, Computer Simulation, Tissue Engineering

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