IIIT Hyderabad Publications |
|||||||||
|
Effect of post-transcriptional modifications on geometry and stability of base pairs and triplets in functional RNAs: A Quantum chemical studyAuthors: Preethi S P,Purshotam Sharma,Dhananjay Bhattacharyya,Abhijit Mitra Conference: The 3rd Indo-German Conference on Modeling Chemical & Biological Reactivity (MCBR3, February 2013 2013) Location NIPER, Mohali Date: 2013-02-26 Report no: IIIT/TR/2013/15 AbstractSingle stranded RNA molecules are known to fold into complex protein like functional structures, consisting of stems and loops, which are further stabilized through tertiary interactions. While it is remarkable that RNA molecules are able to exhibit such structural complexity and functional specificity, with only an alphabet of four bases, one of the strategies employed for creating variety is through post-transcriptional modifications such as methylation, pseudouridylation, thiolation and isomerization. In fact, modified bases are known to play major role in providing chemical and biological diversity to RNA and contribute to overall fitness of the cell1. Base modifications are also known to help RNA molecules to exhibit alternate conformations2. The objectives of this study are: To understand (1) how these modifications affect the base pairing properties of RNA bases and (2) why nature have adopted mechanism to modified these bases. These objectives are studied through quantum chemical methods. We extracted the coordinates of 32 modified base pairs and 11 base triplets from a total of 208 RNA crystal structures from the PDB database. Of these 208 files, 128 were directly taken from HD-RNAS’s non redundant dataset3 and searched for modified bases using BPFind software4. The remaining 77 PDB files were included in the dataset based on information from HET group information from PDBSum5. We have optimized the initial geometries at B3LYP/6-31G (d,p) level and have evaluated the complete basis set (CBS) extrapolated interaction energies using RIMP2 calculation with aug-cc-pVDZ and aug-cc-pVTZ basis sets. Molecular electrostatic surface potential maps were also generated for modified base pairs. This study provides insights into the characteristics of modified base pairs and triples in complex RNA structure. Full paper: pdf Centre for Computational Natural Sciences and Bioinformatics |
||||||||
Copyright © 2009 - IIIT Hyderabad. All Rights Reserved. |