Understanding the unfolding mechanism of human telomeric G-quadruplex using steered molecular dynamics simulation


 

Samanta, Pralok Kumar; Pati, Swapan K.

Abstract

The unfolding pathway of human telomeric G-quadruplex with three G-tetrads in presence of K+ and Na+ ions, separately using steered molecular dynamics (SMD) simulation is reported. The isothermal-isobaric all-atoms classical molecular dynamics simulation results show that three K+ and three Na+ ions are required within the central channel of the G-quadruplex (PDB ID: 143D and 2HY9, respectively) to stabilize the respective overall structure. To obtain the unfolded G-quadruplex which is ~5-6 times of its initial contour length, SMD simulation has been carried out by fixing one end of the G-quadruplex and constraining the other end to move only along the long axis (z-axis). The SMD results suggest that the unfolding of G-quadruplex occurs via G-triplex intermediates independent of the presence of cations (K+, Na+).


 


Keyword(s)

Molecular dynamics, Steered molecular dynamics, Unfolding kinetics, H-bonding, G-Quadruplex, DNA, Triplex DNA, Telomeres, Guanine


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