Understanding disorder-to-order transitions in protein–RNA complexes using molecular dynamics simulations

Abstract

Intrinsically disordered regions (IDRs) in proteins are characterized by their flexibilities and low complexity regions, which lack unique 3 D structures in solution. IDRs play a significant role in signaling, regulation, and binding multiple partners, including DNA, RNA, and proteins. Although various experiments have shown the role of disordered regions in binding with RNA, a detailed computational analysis is required to understand their binding and recognition mechanism. In this work, we performed molecular dynamics simulations of 10 protein–RNA complexes to understand the binding governed by intrinsically disordered regions. The simulation results show that most of the disordered regions are important for RNA-binding and have a transition from disordered-to-ordered conformation upon binding, which often contribute significantly towards the binding affinity. Interestingly, most of the disordered residues are present at the interface or located as a linker between two regions having similar movements. The DOT regions are overlaped or flanked with experimentally reported functionally important residues in the recognition of protein-RNA complexes. This study provides additional insights for understanding the role and recognition mechanism of disordered regions in protein–RNA complexes.

Communicated by Ramaswamy H. Sarma

Keywords:

• Intrinsically disordered proteins
• disorder-to-order transition
• protein–RNA complex
• molecular dynamics simulation
• flexible

Acknowledgement

We thank the Department of Biotechnology, Indian Institute of Technology Madras for computational facilities. A.S. thank the Ministry of Human Resource and Development (MHRD) for the fellowship.

Authors contribution

M.M.G. conceived the hypothesis of the work. M.M.G. and S.A. have refined the hypothesis. A.S. and M.M.G. have designed the experiments. A.S. and D.Y. have performed the experiments and data analysis. A.S. and D.Y. wrote the manuscript which is refined by S.A. and M.M.G.

Disclosure statement

Authors declare no conflicts of interest.

Additional information

Funding

This project is partially supported by the Council of Scientific & Industrial Research (CSIR), Government of India to M.M.G. and S.A. (grant numbers: 37(1694)/17/EMR-II) and 37(1695)/17/EMRII, respectively).