Lab Activity 1: Modeling Antibody-Antigen Binding

Objective

Students will build 3D models to understand antibody-antigen interactions and analyze how microgravity might affect binding efficiency.

Time Required

90 minutes

Materials Per Group (4 students)

• Molecular model kit (ball-and-stick or space-filling)
• Pipe cleaners (various colors)
• Clay or Play-Doh (multiple colors)
• Antibody structure templates
• Computer with PyMOL or Jmol software
• Lab notebooks
• Measuring tools

Safety Considerations

• Standard laboratory safety protocols
• Proper handling of materials
• Computer lab safety

Background

Antibodies recognize and bind to specific antigens through complementary structural regions. The binding site consists of six hypervariable loops called Complementarity Determining Regions (CDRs) - three from the heavy chain and three from the light chain.

Key Concepts:
- Lock-and-key model
- Induced fit mechanism
- Non-covalent interactions (hydrogen bonds, van der Waals, electrostatic)
- Specificity vs. affinity

Pre-Lab Questions

1. What makes antibody-antigen binding specific?
2. What types of molecular interactions hold antibodies and antigens together?
3. How might microgravity affect protein-protein interactions?

Procedure

Part 1: Build Antibody Fab Fragment (30 minutes)

1. Identify Components:
2. Heavy chain variable region (VH)
3. Light chain variable region (VL)

4. CDR loops (CDR-H1, CDR-H2, CDR-H3, CDR-L1, CDR-L2, CDR-L3)

5. Construction:

6. Use pipe cleaners for backbone structure
7. Create Y-shaped antibody basic form
8. Focus on Fab region (one arm of the Y)
9. Use different colors for heavy vs. light chains

10. Mark CDR regions with clay pieces

11. Add Binding Site:

12. Form binding pocket with CDRs
13. Ensure complementary shape for antigen

Part 2: Build Antigen (15 minutes)

1. Design:
2. Create epitope (binding region) on antigen surface
3. Must be complementary to antibody binding site

4. Use contrasting colors

5. Features:

6. Represent key amino acids
7. Show charged regions
8. Indicate hydrophobic patches

Part 3: Model Binding Event (20 minutes)

1. Demonstrate Binding:
2. Bring antibody and antigen together
3. Show complementary fit

4. Illustrate conformational changes (induced fit)

5. Identify Interactions:

6. Mark hydrogen bond locations (use toothpicks)
7. Indicate electrostatic interactions

8. Show hydrophobic regions

9. Measure:

10. Binding site surface area
11. Number of interaction points
12. Burial of surface area

Part 4: Computer Visualization (20 minutes)

1. Open Antibody-Antigen Complex:
2. Use PDB file (e.g., 1IGT - antibody-lysozyme complex)

3. Load into PyMOL or Jmol

4. Analysis:

5. Identify CDR regions
6. Locate interface residues
7. Measure distances between key atoms

8. Visualize hydrogen bonds

9. Compare:

10. How does your model compare to real structure?
11. Identify accuracy and limitations

Part 5: Microgravity Analysis (15 minutes)

Discussion and Hypothesis:
1. How might microgravity affect:
- Protein folding?
- Binding kinetics?
- Complex stability?

1. Design experiment to test effects

Data Collection

Table 1: Physical Model Measurements

Table 2: Computer Model Analysis

Analysis Questions

1. How well did your physical model represent the actual molecular structure?

2. What types of interactions are most important for antibody-antigen binding?

3. Calculate the approximate binding surface area. How does this compare to the total antibody surface?

4. Based on your models, predict how the following might affect binding:

5. Temperature increase
6. pH change
7. Presence of other proteins (crowding)

8. Microgravity environment

9. Why is the complementary fit between antibody and antigen so specific?

Post-Lab Questions

1. Application to Space Medicine:
   How might changes in antibody-antigen binding affect astronaut health?

2. Therapeutic Development:
   How could understanding binding interactions help design better antibody drugs for space?

3. Design Challenge:
   Propose modifications to an antibody that might improve its stability in space conditions.

Lab Report Requirements

Format

• Title page
• Introduction (background on antibody structure)
• Materials and Methods (brief)
• Results (data tables, photos of models, computer screenshots)
• Discussion (answer analysis questions)
• Conclusions
• References

Due Date

One week from lab completion

Grading Rubric (100 points)

• Physical model quality and accuracy (20 points)
• Computer analysis completion (20 points)
• Data tables (15 points)
• Analysis questions (25 points)
• Discussion and conclusions (15 points)
• Overall presentation (5 points)

Extensions

Advanced Students

• Model antibody engineering for improved binding
• Analyze multiple antibody-antigen complexes
• Research computational docking methods
• Explore CAR-T cell receptor engineering

Integration with Lesson Content

This lab directly supports:
- Lesson 2 (Antibody Structure and Function)
- Lesson 3 (Biomanufacturing - protein production)
- Lesson 4 (Drug Formulation - stability considerations)

Resources

PDB Files for Analysis

• 1IGT: Anti-lysozyme antibody complex
• 1FBI: Influenza hemagglutinin-antibody complex
• 1AHW: HIV gp120-antibody complex

Software

• PyMOL: https://pymol.org/
• Jmol: http://jmol.sourceforge.net/
• Protein Data Bank: https://www.rcsb.org/

Videos

• "Antibody Structure and Function" (YouTube/Khan Academy)
• "Protein-Protein Interactions" (iBiology)
• NASA research on protein crystallization in space

Teacher Notes

Preparation:
- Pre-make one complete antibody-antigen model as example
- Test software on all computers
- Download PDB files in advance
- Prepare data sheets

Time Management:
- Physical modeling: 45 minutes
- Computer work: 25 minutes
- Analysis and cleanup: 20 minutes

Common Issues:
- Students struggle with 3D thinking - use pre-made models as guides
- Scale issues - emphasize this is representational
- Software learning curve - have tutorial ready

Assessment Tips:
- Circulate during lab to assess understanding
- Take photos of student models for grading reference
- Check data tables for completion and accuracy

Part of the Space Medicine Antibody Drug Development Curriculum
Supports NGSS Standards: HS-LS1-1, HS-LS3-1