Protein Analysis

1. Lab#9: Protein Analysis
Asian University For Women
BINF 2000: Introduction to Bioinformatics
(Lab - Fall 2022)
Syed Mohammad Lokman
Instructor
Asian University for Women

2. The DataBase
● UniProtKB (https://www.uniprot.org/ )
○ Protein Information with Sequence
● RCSB PDB (https://www.rcsb.org/ )
○ Protein Structure Database

3. 1. Visit UniProtKB (https://www.uniprot.org/ )
2. Search for a Protein (e.g., human Transmembrane protein 218)
3. Click on the “Entry” ID for the best match (A2RU14)
○ Take note of the “Entry ID”
4. In the left panel, click on the “Sequence” option.
○ What is the Length and Mass (Da) of the protein?
5. Click on the “Download” and save the sequence.
Exercise:
Retrieve the sequence of following proteins:
1. Human Clarin-2
2. Human Interferon-induced transmembrane protein 5
3. Human Espin
4. Human Rho GTPase-activating protein 10
Retrieve Protein Sequence from UniProtKB

4. Exercise:
Retrieve the structure of following proteins:
1. Insulin of Human
2. Amylase from Bacillus
3. HUMAN ANTITHROMBIN-III
1. Visit RCSB PDB (https://www.rcsb.org/)
2. Search for a Protein (e.g., human serum albumin)
3. Click on the best match result (e.g., 4LA0)
○ What is the “PDB ID” of the first hit?
4. Click on the “Download Files” from the right section of
the page.
○ How many Macromolecules are present in the
structure?
○ How many Small Molecules are present in the
structure?
5. Click on “PDB Format” and Save it.
Retrieve Protein Structure from RCSB PDB

5. 1. Visit MolStar Viewer (https://molstar.org/viewer/ )
2. Click on “Open Files”, then “Select Files”, and select the
protein structure file.
3. Click on Apply
Protein Visualization: MolStar Viewer

6. Protein Modeling: Homology Modeling of Protein

7. Experimental Method
● X-Ray
● NMR
● Cryo-EM
Prediction Method
1. Knowledge Based Method
a. Homology (Comparative) Modeling
b. Threading/ Fold Recognition
2. Ab Initio Method
a. Deep Learning Based
b. Physico-chemical Properties Based

8. Some Common Tools for Prediction Method:
1. Knowledge Based Method
a. Homology (Comparative) Modeling:
i. SWISS-MODEL; MODELLER
b. Threading/ Fold Recognition
i. I-TASSER; Rosetta
2. Ab Initio Method
a. Deep Learning Based
i. RoseTTAFold; AlphaFold
b. Physico-chemical Properties Based
i. CABS-flex

9. ➔ ≥ 30% Sequence Identity is Required for a Decent Model Prediction.

10. Protein Modeling: Swiss-Model
1. Visit SWISS-Model (https://swissmodel.expasy.org/interactive );
2. Upload the sequence of “human Transmembrane protein 218”
protein retrieved from UniProtKB.
3. Click on “Build Model”
4. Click on “Model 01” and Download model as PDB format.

11. Protein Modeling: Swiss-Model
Exercise:
Build Model of following Proteins using Swiss-Model:
1. Human Clarin-2
2. Human Interferon-induced transmembrane protein 5
3. Human Espin
4. Human Rho GTPase-activating protein 10
● Download the Models in PDB Format.
● Visualize the Models in MolStar Visualizer and Take Screenshot