G4IPDB: A database for G-quadruplex structure forming nucleic acid interacting proteins

Abstract

Nucleic acid G-quadruplex structure (G4) Interacting Proteins DataBase (G4IPDB) is an important database that contains detailed information about proteins interacting with nucleic acids that forms G-quadruplex structures. G4IPDB is the first database that provides comprehensive information about this interaction at a single platform. This database contains more than 200 entries with details of interaction such as interacting protein name and their synonyms, their UniProt-ID, source organism, target name and its sequences, ∆Tm, binding/dissociation constants, protein gene name, protein FASTA sequence, interacting residue in protein, related PDB entries, interaction ID, graphical view, PMID, author’s name and techniques that were used to detect their interactions. G4IPDB also provides an efficient web-based “G-quadruplex predictor tool” that searches putative G-quadruplex forming sequences simultaneously in both sense and anti-sense strands of the query nucleotide sequence and provides the predicted G score. Studying the interaction between proteins and nucleic acids forming G-quadruplex structures could be of therapeutic significance for various diseases including cancer and neurological disease, therefore, having detail information about their interactions on a single platform would be helpful for the discovery and development of novel therapeutics. G4IPDB can be routinely updated (twice in year) and freely available on http://bsbe.iiti.ac.in/bsbe/ipdb/index.php.

DNA G‐Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling

“…Over the last several years, progress in profiling technologies has enabled the large‐scale investigation of nucleosome–protein and DNA–protein interactions, and among the newly revealed G4‐binding partners, chromatin remodelers/modulators appear to be enriched (the majority of previously identified G4‐binding partners are reviewed in works published in 2014–2016). In 2018, microarray technology was applied to test several thousand human proteins for interactions with G4s.…”

G-quadruplex stabilization in the ions and maltose transporters inhibitSalmonella entericagrowth and virulence

“…Completely sequenced strains of S. enterica (S1 Table) were downloaded from National Center for Biotechnology Information (NCBI). These strains were then extensively mined for the potential Gquadruplex motifs in both sense and antisense strand using our previously developed G-quadruplex predictor tool [63]. This prediction tools used the following regular expression.…”

“…For our prediction, we used G-tracts -3 or 4 and loop length 1-20 nucleotide [63]. The results were further cross verified by using QGRS Mapper [64] and PGSFinder [65] tools.…”

G-quadruplex–forming promoter sequences enable transcriptional activation in response to oxidative stress

“…Non-Watson-Crick secondary structures of nucleic acids, and in particular, G4 structures in DNA is an area of extremely active research (12)(13)(14)(15)(16). Although G4 structures were initially described in the context of telomeres, recent genomic data revealed tens of thousands of sequences throughout the genome (14,17) that, in principle, could form G4 structures, called potential G-quadruplex-forming sequences (PQS).…”

“…Although G4 structures were initially described in the context of telomeres, recent genomic data revealed tens of thousands of sequences throughout the genome (14,17) that, in principle, could form G4 structures, called potential G-quadruplex-forming sequences (PQS). Many of these sequences, when folded as G4s, can bind with high-affinity cellular proteins or transcription factors (16), but the relevance and physiological role of such interactions are still actively investigated. In PNAS, Fleming et al advance the hypothesis that a subset of these PQS can function as sensors of oxidative stress (8).…”