Deciphering RNA-Recognition Patterns of Intrinsically Disordered Proteins

International Journal of Molecular Sciences
Ambuj SrivastavaM Michael Gromiha

Abstract

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⁻...Continue Reading

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Citations

Jan 17, 2020·International Journal of Molecular Sciences·István Simon
May 16, 2019·Biochemical Society Transactions·Giulia RossettiPaolo Carloni
Dec 6, 2019·Frontiers in Genetics·Sina GhadermarziLukasz Kurgan
Apr 16, 2020·Biomolecules·Daria MordovkinaIrina Eliseeva
Jul 28, 2020·International Journal of Molecular Sciences·Katarzyna Taylor, Krzysztof Sobczak
Mar 12, 2021·Biophysical Journal·Sushmita BasuRanjit Prasad Bahadur
Jul 19, 2020·Experimental Hematology·Stefania BottardiEric Milot
Mar 30, 2021·Journal of Biomolecular Structure & Dynamics·Ambuj SrivastavaM Michael Gromiha

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Methods Mentioned

BETA
NMR
X-ray
pull-down

Software Mentioned

CD
NACCESS
- Hit suite
DSSP
RASA
AMBER
DOT
BLAST
DSSR

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