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Updated: May 29, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
Published on: March 1, 2022
Molecular modeling and molecular dynamics simulation studies of Delta-Notch complex
Riddhi Majumder1, Sujata Roy, Ashoke Ranjan Thakur
1West Bengal State University, Berunanpukuria, P.O. Malikapur, Barasat, Kolkata-700126, India.
Abstract:
Notch is a single-pass transmembrane receptor protein which is composed of a short extracellular region, a single-pass transmembrane domain and a small intracellular region. Notch ligand like Delta, member of the DSL protein family, is also single-pass transmembrane protein. It has been demonstrated that of the 36 EGF repeats of Notch, 11th and 12th are sufficient to mediate interactions with Delta. Crystal structure of mammalian Notch extracellular ligand binding domain contains 11 and 12 EGF-like repeats. Here a portion of the Delta protein of Drosophila, known to interact with Notch extracellular domain (ECD) has been modeled using homology modeling. The structure of the Delta-Notch complex was subsequently modeled by protein docking method using GRAMM. MD simulations of the modeled structures were performed. The structure for Delta-Notch complex has been proposed based on interaction energy parameter and planarity studies.
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