Related Experiment Video
Updated: May 29, 2026
09:17
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.
Journal of Biomolecular Structure & Dynamics
|August 31, 2011
Summary
This study models the Delta-Notch complex structure using computational methods. The proposed structure provides insights into the molecular interactions between these key signaling proteins.
Area of Science:
- Biochemistry
- Structural Biology
- Computational Biology
Background:
- Notch receptors and Delta ligands are crucial single-pass transmembrane proteins involved in cell signaling.
- Specific EGF repeats (11th and 12th) on Notch mediate interactions with Delta.
- The extracellular domain (ECD) of Notch binds to ligands like Delta.
Purpose of the Study:
- To model the three-dimensional structure of the Delta-Notch complex.
- To investigate the interaction interface between Drosophila Delta and the Notch ECD.
- To propose a stable structural model for the Delta-Notch complex.
Main Methods:
- Homology modeling was used to construct the structure of the Drosophila Delta protein portion.
- Protein docking using GRAMM was employed to model the Delta-Notch complex.
- Molecular Dynamics (MD) simulations were performed on the modeled structures.
- Interaction energy and planarity studies were conducted to validate the proposed complex structure.
Main Results:
- A homology model for the relevant portion of the Drosophila Delta protein was generated.
- The Delta-Notch complex structure was modeled using computational docking.
- MD simulations provided dynamic insights into the complex.
- A proposed structure for the Delta-Notch complex was determined based on energy and planarity analyses.
Conclusions:
- The study successfully modeled the Delta-Notch complex structure.
- The findings offer a structural basis for understanding Delta-Notch interactions.
- The proposed model can guide further experimental investigations into Notch signaling.
Related Concept Videos
02:00Molecular Models
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
03:14Notch Signaling Pathway
The Notch signaling pathway is a major intracellular signaling pathway that is highly conserved over a broad spectrum of metazoan species. It stands unique from other intracellular signaling mechanisms in animals because notch protein itself acts as the receptor as well as the primary signaling molecule.
The Notch gene came into the limelight in 1914 after the discovery that its mutation in Drosophila melanogaster leads to a serrated (or "notched") wing margin phenotype. It was not until 1985...
The Notch gene came into the limelight in 1914 after the discovery that its mutation in Drosophila melanogaster leads to a serrated (or "notched") wing margin phenotype. It was not until 1985...
02:06Newman Projections
Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.