MOLECULAR DOCKING STUDIES ON DNA-BINDING PROCESS OF LEC2 SYNTHETIC TRANSCRIPTION FACTORS
Authors: Rahman M. Z. A., Jainuddin H., Mohammed A. and Kasran R.
Journal Issue: Malaysian Cocoa Journal, Volume 14/2022
Keywords: LEAFY COTYLEDON 2, artificial transcription factor, molecular dynamics simulation, protein modelling
Published On: 10/05/2022
Abstract
Transcription factors (TFs) are essential for the expression of all proteins, including those involved in the plant regeneration and totipotency. LEAFY COTYLEDON 2 (LEC2) exerts significant impacts on determining embryogenic potential and various metabolic processes through a complicated genetic regulatory network and is sufficient to induce somatic embryo development in vegetative cells. Previously, electrophoretic mobility shift assay (EMSA) was conducted for five TcLEC2 artificial transcription factors (ATFs) constructs namely L1, L2, L6, L7 and L8 and the assay results showed that only L1, L2 and L7 ATFs have shifted DNA bands. Based on EMSA principle, the shifted DNA band indicates that there is DNA-protein interaction present, thus effecting the mobility of the detected DNA on the gel. In order to validate further the DNA-protein interactions between corresponding ATFs, molecular dynamics studies were conducted to investigate the interaction of the ATFs with the targeted DNA sequence. The protein structure of ATFs models were built using either comparative modeling approach (L1) or de novo approach via PEP-FOLD server (L7) Molecular docking experiments were conducted to depict the protein-DNA interaction and to delineate the mechanism of DNA binding for TcLEC2 ATFs. The details of DNA binding activity of the ATFs provided here will be helpful to better understand the regulation of LEC2 in plants.