Molecular dynamics simulation of telomeric single-stranded DNA and POT1

Abstract

Telomeres, which consist of single-, double-and four-stranded DNA, shorten after each round of cell division. The repeated telomeric DNA sequence 5′-TTAGGG-3′ does not encode genetic information and is not replicated completely. We performed molecular dynamics (MD) simulations of telomeric single-stranded DNA (ssDNA) and protection of telomere 1 (POT1) for 100 ns. We calculated the distance between C α (POT1) and O5' (telomeric ssDNA) to verify the binding system for 100 ns MD. We then calculated the distance between the bases of the telomeric DNA ends and the root-mean-square deviation and gyration radius in the single and binding states. Moreover, we compared the root-mean-square fluctuations (RMSFs) between the single and binding states and calculated the number of hydrogen bonds between POT1 and telomeric DNA. There are many hydrogen bonds between Gln94 and the first guanine of the closest 5′-TTAGGG-3′ sequence in telomeric single-stranded DNA, and the RMSF between the single and binding states has a large difference between Gln94 and guanine. Overall, we found that Gln94 and guanine are important components of the binding system and are related to the stability of this system.

Understanding The Role of Reline, a Natural DES, on Temperature-Induced Conformational Changes of C-Kit G-Quadruplex DNA: A Molecular Dynamics Study

“…Radius of gyration is an essential method for checking the compactness of biomacromolecules. , The radius of gyration ( R g ) is the root-mean-square distance of various atoms of a molecule from the axis of rotation. In Figure S6b (of Supporting Information), we have shown the estimated R g of the G-quadruplex c-kit DNA considering the O6 atom of guanine residue of tetrads region.…”

Mutual effects between single-stranded DNA conformation and Na+–Mg2+ion competition in mixed salt solutions

“…23 Parallel to experimental investigations is the development of promising computational approaches for the modeling of ssDNA conformations and ion effects. 24 All-atom molecular dynamics (MD) simulations, [25][26][27][28] which include all the components (such as ssDNA, ions, and water molecules) in the ssDNAion system, can describe the ssDNA conformations [29][30][31] and ion atmosphere [32][33][34] at the atomic level. However, all-atom descriptions usually require exceedingly long computational times, 35 and the simulation results are strongly sensitive to the applied force fields.…”

Structural investigations on mechanism of lapatinib resistance caused by HER-2 mutants

“…To study change in molecular size over MD simulation time, the gyration radius (Rg) of the studied HER-2 mutants in lapatinib binding state was calculated. The Rg value represents the mean squared distance of the atoms from the centre of mass of the molecule [ 31 ]. To determine which parts of HER-2 mutants in lapatinib binding state are influenced by lapatinib, we compared the fluctuation of residues of studied HER-2 mutants in the binding state.…”