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Activity 1

This document provides a step-by-step guide for understanding protein structures using the Protein Data Bank (PDB) and PyMOL software. It outlines objectives, methods for accessing protein data, and instructions for analyzing primary, secondary, tertiary, and quaternary structures. Additionally, it includes details on saving and exporting visualizations for presentations.

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8 views5 pages

Activity 1

This document provides a step-by-step guide for understanding protein structures using the Protein Data Bank (PDB) and PyMOL software. It outlines objectives, methods for accessing protein data, and instructions for analyzing primary, secondary, tertiary, and quaternary structures. Additionally, it includes details on saving and exporting visualizations for presentations.

Uploaded by

tanyotanaka
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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Take screenshots of each step, paste the screenshots in PowerPoint slides and upload in this

folder: https://mahindraecolecentrale-
my.sharepoint.com/:f:/g/personal/mrittika_sengupta_mahindrauniversity_edu_in/EmFM-
v8iIH9AlSzYz1nnfD8BxrSGSP252bHkUw92h325Vw?e=hRt2h6

I will match the folder submissions with attendance.

Activity 1
sharepoint.com
Understanding Protein Structure Using the Protein Data Bank (PDB)

Objective:
This guide will help you to explore the primary, secondary, tertiary, and quaternary structures of
proteins using the Protein Data Bank (PDB) (www.rcsb.org).

Step 1: Accessing the Protein Data Bank (PDB)

1. Open a web browser and go to https://www.rcsb.org/.

2. Use the search bar to enter the name or PDB ID of a protein (e.g., Hemoglobin: 1HHO,
Insulin: 4INS, Lysozyme: 1LYZ).

3. Click on the relevant search result to open the protein’s structural page.

Step 2: Understanding Protein Structures

4. Primary Structure (Amino Acid Sequence)

• Scroll down to the “Sequence” section on the PDB entry page.

• The amino acid sequence is displayed in single-letter codes.


• Click on “FASTA” to download the sequence.

• Observe the linear arrangement of amino acids, which defines the primary structure.
2. Secondary Structure (Alpha Helices & Beta Sheets)

• Locate the “3D View” section and open the “Structure Viewer” (e.g., Mol or Jsmol*).

• Identify regions of alpha-helices (coils/spirals) and beta-sheets (flat arrows).

• Some PDB entries also provide secondary structure annotations in a tabular form.

5. Tertiary Structure (3D Folding of a Single Polypeptide)


• Use the interactive 3D viewer to rotate and zoom in on the protein.
• Observe how the helices, sheets, and loops fold into a three-dimensional shape.

• Look for key features such as disulfide bonds, active sites, and binding pockets.

• Use the coloring options (cartoon, surface, space-filling) to enhance visualization.

6. Quaternary Structure (Multiple Polypeptide Chains)

• Check if the protein consists of multiple chains under the “Macromolecules” section.

• If the protein is multimeric (like Hemoglobin), distinguish between different subunits


using chain coloring.

• Rotate the structure to understand how different polypeptide chains interact.

Step 3: Analyzing and Interpreting the Structure

• Use the Ligand Viewer to see how small molecules interact with the protein.

• Check the Experimental Data tab for resolution and method used (X-ray, NMR, Cryo-
EM).

• Explore the Protein Feature View to see functional domains.

Activity 2

Objective

To use PyMOL, a molecular visualization software, along with Protein Data Bank (PDB)
files to understand the primary, secondary, tertiary, and quaternary structures of proteins.

Step 1: Install PyMOL


1. Download PyMOL from https://pymol.org or PyMOL Open-
Source from https://github.com/schrodinger/pymol-open-source

Step 2: Download a Protein Structure from PDB

1. Visit www.rcsb.org

2. Use the Search bar to enter the name or PDB ID of a protein (Hemoglobin = 1A3N, GFP
= 1GFL, Lysozyme = 1LYZ).

3. Click on the structure page and go to the Download Files section.


4. Select PDB format (.pdb) and save the file.
Step 3: Open the PDB File in PyMOL

1. Open PyMOL.

2. Click File → Open → Select the PDB file you downloaded.

3. The 3D structure of the protein will appear.

Step 4: Analyze Different Levels of Protein Structure

1. Primary Structure (Amino Acid Sequence)

• Type the command:


lua

show lines

This displays the backbone connections between atoms.

• To label amino acids:

perl

show sticks

label resn+resi, "%s-%s" % (resn, resi)

This shows residue names and positions.

2. Secondary Structure (α-Helices and β-Sheets)

Use the cartoon representation to view helices and sheets:

sql
show cartoon

To color-code different secondary structures:

nginx

color red, ss h # Helices in red


color yellow, ss s # Sheets in yellow

color blue, ss l+'' # Loops in blue

To isolate only helices or sheets:

sql
hide everything

show cartoon, ss h # Shows only helices

show cartoon, ss s # Shows only sheets

3. Tertiary Structure (3D Folding of a Single Polypeptide Chain)

To visualize the surface of the protein:

sql

show surface
To color by hydrophobicity (useful for understanding protein folding):

nginx

spectrum hydrophobicity

To show interactions between amino acids:

sql

show sticks, byres (within 5 of resn HIS)

This highlights residues within 5 Å of histidine.

4. Quaternary Structure (Multiple Subunits in a Protein Complex)

If the protein has multiple chains, color each one differently:

css
color red, chain A

color blue, chain B

color green, chain C

To display interfaces between subunits:


css

show sticks, byres (chain A within 5 of chain B)

To highlight the entire complex:


css

show cartoon

color bychain

Step 5: Save and Export

Save your PyMOL session for later:

nginx

save my_protein.pse
Export images for presentations:

nginx

ray

png my_protein.png, dpi=300

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