Insights into the effect of molecular crowding on the structure, interactions and functions of siRNA–PAZ complex through molecular dynamics studies

Abstract

siRNA molecules are well known to be involved in the post-transcriptional regulation of gene expression and play a key role in understanding the intricacies of eukaryotic gene regulation. While it is widely known that 3′ end of siRNA binds to the PAZ domain of Argonaute proteins, it remains unclear whether the molecular crowding facilitates or hinders the overall siRNA-protein interactions during RNA interference. The biological interaction networks controlling the cellular functions of any biological cell may behave very differently in crowded environment as compared to the dilute conditions. Therefore, it is of interest to study the siRNA–protein interactions under more physiologically relevant conditions. In our previous work, we studied the role of hydrogen bond interactions and water network interactions towards the structural integrity of siRNA–PAZ complex. We also described the motions relevant for the functioning of the complex and analyzed the biphasic interaction of the 3′ end of siRNA within the PAZ domain under aqueous condition. In the present work, we studied the dynamics of siRNA–PAZ complex in the presence of water-soluble crowding agent. We observed significant changes in interactions and dynamics of siRNA–PAZ complex in the presence of crowder. The conserved H-bond interactions were destabilized by ≈12%, while interfacial water networks were stabilized in the presence of crowder. The analysis of siRNA–PAZ dynamics revealed the stabilizing role of ARG52, ARG172, LYS53 and LYS173 in siRNA–PAZ complex. Interestingly, despite increase in flexibility as measured by RMSD, crowding stabilized top modes.

Communicated by Ramaswamy H. Sarma

Keywords:

• molecular crowding
• molecular dynamics simulation
• hydration analysis
• water networks and essential dynamics

Acknowledgements

We are thankful to the Indian Institute of Information Technology, Allahabad, for providing us research environment to carry out this research work. We would also like to acknowledge Professor David A. Case (Rutgers University) for providing us the license of AMBER 12.

Disclosure statement

No potential conflict of interest was reported by the authors.

Supplemental Data

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