Intrinsically disordered proteins lack stable three-dimensional structures under physiological conditions and are known to perform important roles in several processes including signaling, regulation, interactions with proteins/nucleic acids and binding multiple partners. Residues, which are missing in a free protein (disordered residues) and attain stable three-dimensional structures upon complex formation, are known as disorder-to-order transition (DOT) residues. In this work, we have mainly focused on understanding the recognition mechanism of RNA binding proteins and the influence of DOT regions protein-RNA complexes.
We have studied the role of residues, which are involved in both stabilizing and binding in protein-RNA complexes, also termed as key residues (KRs). We observed that 5% of stabilizing, 3% of binding residues serve as key residues. In addition, residues with similar chemical behavior have different preferences to be KRs, such that Arg, Tyr, Val and Thr are preferred over Lys, Trp, Ile and Ser, respectively.
We have analyzed a dataset of protein–RNA complexes, which undergo disorder-to-order transition upon binding. The DOT regions are enriched with positively charged residues, which are found to interact with RNA molecules indicating the dominance of electrostatic and cation-π interactions. We have computed the interaction energy for amino acids–nucleotide pairs, which showed the preference of His–G; Asn–U and Ser–U at the interface of DOT regions.
Further, we have performed molecular dynamics simulations for a set of protein-RNA complexes to understand the importance of disorder-to-order transition regions towards protein-RNA recognition. The simulation results showed that most of the disordered regions are important for RNA-binding and have a transition from disorder-to-order conformation upon binding, which often contribute significantly towards the binding affinity. The DOT regions are overlapped or flanked with experimentally reported functionally important residues for the recognition of protein-RNA complexes.
Specifically, we explored the role of DOT regions in tyrosine tRNA synthetase and tRNA methyltransferase complexes. In tyrosine tRNA synthetase, one of the disordered regions undergoes disorder-to-order transition (DOT) upon complex formation with tRNA whereas the other remains disordered (DR). We observed that the DOT and DR regions of the first subunit acts as a flap and interact with the acceptor arm of the tRNA. The DOT-DR flap closes when tyrosine (TyrRSTyr) is present at the active site of the complex and opens in the presence of tyrosine monophosphate (TyrRSYMP). In methyltransferase complex, the energetic contribution shows that DOT residues are important for stabilizing the complex. Specifically, DOT1 and DOT2 are mainly observed to be important for stabilization while DOT3 is present near the active site to coordinate the interactions between methyl donating ligand and acceptor G37 nucleotide. The study provides additional insights for understanding the role of disordered regions and recognition mechanism in protein–RNA complexes.
Publications:
[1] Srivastava, A., Yesudhas, D., Ahmad, S. and Gromiha, M.M., (2021). Understanding disorder-to-order transitions in protein–RNA complexes using molecular dynamics simulations. J Biomol Struct Dyn. (in press).
[2] Srivastava, A., Yesudhas, D., Ahmad, S. and Gromiha, M.M., (2021). Deciphering the Role of Residues Involved in Disorder-To-Order Transition Regions in Archaeal tRNA Methyltransferase 5. Genes. 12(3), 399.
[3] Srivastava, A., Yesudhas, D., Ramakrishnan, C., Ahmad, S. and Gromiha, M.M., (2020). Role of disordered regions in transferring tyrosine to its cognate tRNA. Int J Biol Macromol. 150, 705-713.
[4] Srivastava, A., Ahmad, S. and Gromiha, M.M., (2018). Deciphering RNA-recognition patterns of intrinsically disordered proteins. Int J Mol Sci., 19, 1595.
[5] Kulandaisamy, A., Srivastava, A., Kumar, P., Nagarajan, R., Priya, S.B. and Gromiha, M.M., (2018). Identification and Analysis of Key Residues in Protein–RNA Complexes. IEEE/ACM Trans Comput Biol Bioinform., 15, 1436-1444.
[6] Kulandaisamy, A., Srivastava, A., Nagarajan, R. and Gromiha, M.M., (2018). Dissecting and analyzing key residues in protein‐DNA complexes. J Mol Recognit., 31, e2692.