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Open AccessArticle

Deciphering RNA-Recognition Patterns of Intrinsically Disordered Proteins

1
Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India
2
School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110 067, India
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2018, 19(6), 1595; https://doi.org/10.3390/ijms19061595
Received: 12 April 2018 / Revised: 10 May 2018 / Accepted: 16 May 2018 / Published: 29 May 2018
Intrinsically disordered regions (IDRs) and protein (IDPs) are highly flexible owing to their lack of well-defined structures. A subset of such proteins interacts with various substrates; including RNA; frequently adopting regular structures in the final complex. In this work; we have analysed a dataset of protein–RNA complexes undergoing disorder-to-order transition (DOT) upon binding. We found that DOT regions are generally small in size (less than 3 residues) for RNA binding proteins. Like structured proteins; positively charged residues are found to interact with RNA molecules; indicating the dominance of electrostatic and cation-π interactions. However, a comparison of binding frequency shows that interface hydrophobic and aromatic residues have more interactions in only DOT regions than in a protein. Further; DOT regions have significantly higher exposure to water than their structured counterparts. Interactions of DOT regions with RNA increase the sheet formation with minor changes in helix forming residues. We have computed the interaction energy for amino acids–nucleotide pairs; which showed the preference of His–G; Asn–U and Ser–U at for the interface of DOT regions. This study provides insights to understand protein–RNA interactions and the results could also be used for developing a tool for identifying DOT regions in RNA binding proteins. View Full-Text
Keywords: intrinsically disorder proteins; disorder-to-order regions; protein–RNA interactions; unstructured proteins intrinsically disorder proteins; disorder-to-order regions; protein–RNA interactions; unstructured proteins
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Srivastava, A.; Ahmad, S.; Gromiha, M.M. Deciphering RNA-Recognition Patterns of Intrinsically Disordered Proteins. Int. J. Mol. Sci. 2018, 19, 1595.

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