Structural Impact Assessment of DogCatcher Fusion Using AlphaFold and ChimeraX
To assess whether fusing the DogCatcher domain to our protein of interest would disrupt its native structure, we used a two-step structural modeling and comparison approach:
AlphaFold Modeling
We used AlphaFold to predict the 3D structure of our protein with the DogCatcher domain fused to it. This allowed us to visualize the potential folding of the entire fusion protein and check for major structural disturbances.
- Retrieved structures from AlphaFold database
- Identified reliable structural regions
- Downloaded structures in PDB format
Structural Alignment with Native Protein
To validate the structural integrity of the core protein, we performed a structural alignment (matchmaking analysis) using ChimeraX. We compared the AlphaFold model of the fusion protein to the experimentally resolved structure of the native protein (from the Protein Data Bank).
- 3D molecular visualization and rendering
- Structural alignment and comparison
- Surface analysis and binding site identification
- Publication-quality figure generation
Modelling Workflow
1. Structure Acquisition
Import our protein sequences in the AlphaFold 3 server.
2. Structure Preparation
Import structures from PDB into ChimeraX.
3. Structural Analysis
Compare visualy the prediction with the original protein with the matchmaking option from ChimeraX.
Figure 1: Computational workflow showing AlphaFold 3 prediction of the protein of interest fused with DogCatcher, followed by ChimeraX structural alignment with the corresponding PDB structure for validation. Created in https://BioRender.com
Results & Analysis
Our structural modeling revealed important insights about the fusion protein's stability and functionality.
Structural Integrity
Native protein structure maintained
Binding Sites
All critical binding sites preserved in fusion protein
Results & Structural Analysis
Our ChimeraX matchmaking analysis between AlphaFold 3 predictions and PDB experimental structures reveals the structural integrity of our fusion proteins:
Figure 2: 8FNR protein binding Dysprosium
Figure 3: 8DQ2 protein binding Lanthanum and Cerium
Figure 4: 8FNS protein binding Neodymium
Figure 5: GLAM (3WLC) binding Gadolinium
Figure 6: 6ZCW binding Praseodynmium
Matchmaking Gallery: ChimeraX structural alignment visualizations showing superposition between AlphaFold 3 predicted structures (blue/light green) and experimental PDB structures (light-brown) of DogCatcher fusion proteins. Hover over images to enlarge.
Software & Tools
Our computational pipeline leverages state-of-the-art software for structural analysis:
AlphaFold 3
AI-powered protein structure prediction with unprecedented accuracy.
ChimeraX
Advanced molecular visualization and analysis platform.