Skip to content

Week 10 - Protein Structure Prediction with Homology Modeling

Homology modeling, also known as comparative modeling, predicts the 3D structure of a protein using the 3D structure of its homolog as a template.

A condition for homology modeling is at least 25% homology between the protein of interest and the template protein. The first step is to find a homolog PDB structure for the protein to be predicted.

Example 1: Predict 3D structure of dopamine D2 receptor (Homo sapiens) using Modeller

  1. Run PSI-BLAST for the D2 receptor from Homo sapiens using NCBI’s BLAST (as learned in Week 8).
  2. Search only the PDB database.
  3. You will find 3PBL (dopamine D3 receptor) as one of the homolog structures.
  4. Download the PDB file for 3PBL and get the FASTA sequence of D2 dopamine receptor.
  5. Open EasyModeller (if you use Mac, try using Chimera).
  6. Enter D2R sequence in FASTA format into the specified box.

Protein sequence input

  1. Load the 1st template after browsing and finding its location on your computer.

Browse template

  1. Click SALIGN to structurally align the two proteins.
  2. After SALIGN process is complete, click Perform Alignment (may take several minutes).
  3. Next, click Generate Model.
  4. The homology-modeled PDB file for your protein will appear on the screen.
  5. Open this file in UCSF Chimera together with the template 3PBL.
  6. After deleting chain B of 3PBL, structurally compare and contrast the two structures.
    • Create a chimeric structure using MatchMaker.
  7. You can perform alignment with UCSF Chimera as well:
    • Tools → Sequence → Match → Align → Apply
  8. Display the alignment of two proteins in this way.

Example 2: Model an already known structure to test modeling accuracy

We can model dopamine D3 receptor from Homo sapiens using another GPCR as a template:

  • Adenosine A2A receptor
  • PDB ID: 3EML

Steps:

  1. Align two sequences (dopamine D3 receptor and adenosine A2A receptor) using NCBI’s BLAST.
  2. Check if there is more than 25% homology.
  3. Open EasyModeller.
  4. Enter FASTA sequence of D3 receptor into the box provided.
  5. Load 3EML.pdb as the 1st template.
  6. Run the program as in Example 1.
  7. Open the modeled PDB structure in UCSF Chimera together with 3PBL (real PDB structure of D3 receptor).
  8. Do MatchMaker analysis and perform alignment.
  9. In the alignment window, use:
  10. Structure → Secondary Structure → show actual
  11. Examine secondary structure to test the success of homology modeling.
  12. Detect the region badly predicted.

Homology modeling using more than one template

Example 3: Model Abl kinase from Abelson murine leukemia virus

  1. Run BLAST for Abl kinase and find 3 PDB structures for it.
  2. Open EasyModeller.
  3. Enter FASTA sequence into the provided box.
  4. Load the 3 templates you found.
  5. Click SALIGN.
  6. Click Perform Alignment.
  7. Click Generate Model.
  8. Examine the model and comment on what can be done to refine this model.