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

Zhu Yu-zhen; Li Yun-xiang; Cai Hao; Zhang Qing-wen

doi:10.3969/j.issn.2095-4344.0237

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.