Related Experiment Video
Updated: Jun 13, 2025

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo
Published on: January 14, 2016
Computational exploration of Arabidopsis thaliana N-Myc downregulated-like-1 for protein-protein interaction and
Abhishek Kanojia1, Asani Bhaduri, Soumya Nayak
1Department of Botany, University of Delhi, New Delhi 110007, India.
Abstract:
N-Myc downregulated-like (NDL) proteins belong to the α/ꞵ-hydrolase-fold-containing protein family. NDLs are interacting partners of G-protein subunits which are involved in abiotic and biotic stress signaling mechanisms in plants. Three NDLs (NDL1, NDL2, and NDL3) have been identified in Arabidopsis thaliana. The NDL1 interactome reveals its interaction with numerous proteins involved in diverse plant functions, suggesting its role in various signaling mechanisms. The current study was designed to explore the level of conservation of NDL proteins across the plant kingdom to analyze protein structure for the conserved sites involved in protein-protein interactions. We analyzed NDL proteins from different plant groups for sequence conservation patterns through phylogenetic and motif analyses. Subsequently, homology-based models were built for NDLs and their selected interactors using MODELLER, and interaction sites were also analyzed using molecular docking. Overall, our study revealed sequence conservation within the NDL family and the presence of several conserved motifs across diverse plant groups. Additionally, docking analysis suggests that two specific regions, spanning positions 40-50 and 135-170 in the NDL1 structure, may serve as hotspots for various protein-protein interactions.
Related Concept Videos
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-protein Interfaces
Cell Signaling in Plants
Conservation of Protein Domains Over Different Proteins
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

