The formation of intra- and intermolecular double oligo(A)-helices of different stability is considered as a possible physical mechanism of mRNA poly(A) tail functioning in a number of biological processes. The formation of double helices is induced by intermolecular proton transfer from proteins specifically interacting with Poly(A) to the N1 nitrogen atom of adenine residues. The main purpose of this research was to study the structure of double-stranded and single-stranded Poly(rA) using computational methods. Molecular Dynamics (MD) simulation was used to study complexes on atomistic level under different conditions: ionic strength, temperature and protonation level. It is known that Poly(rA) can exist in two forms and their formation depends on those conditions. From A (stands for acidic) – is formed in a more acidic environment; form B (basic) is formed when pH becomes more basic. Calculations have been done with NAMD2.11 program package and two force field parameters: CHARMM36 and Amber. Following levels of protonation were considered: fully protonated complex; unprotonated; 60% protonation; 40% protonation; 30% protonation and 25% protonation. Calculations for double-strand Poly(rA) were performed in two stages. Stage I. 100 ns trajectories were calculated for three complexes made of 30 adenine pairs. Fully protonated complex shows good stability during the whole time of the simulation when unprotonated complex starts to lose its initial structure just after 5 ns of the trajectory. 60 % protonation complex underwent less changes than unprotonated complex and we were able to observe two A and B forms. Analysis of geometrical parameters have been done for each system. Stage II. Complexes with 30 pairs might require much longer simulation before it reaches equilibrium, therefore for further studies the system was reduced to 15 pairs per each complex. Simulations were performed at a temperature of 10 C and ion concentration 50 mM/L. Simulations were carried out for 5 complexes with trajectory length 100ns. Results for fully protonated and unprotonated complexes were similar to the one obtained for 30 pairs poly(rA). However, analysis of the geometry for 40%, 30% and 25% protonation levels revealed that the presence of protonation adenine helps stabilize complexes. Comparison of the two force fields on the example of unprotonated duplex has shown that structure estimated with Amber is similar to the structure obtained with CHARMM.

Double-stranded protonated Poly(rA) RNA complex – computational studies

255th National Meeting (2018)

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