Exploring a Protein Structure in the rcsb pdb: Insulin Learning Goals

Level: Advanced

Teaching Notes

Exploring a Protein Structure in the RCSB PDB: Insulin
Learning Goals:

1. 
   Visualize the structure of a given molecule using RCSB PDB resources.
   
2. 
   Explore the structure to understand its structure function relationships
   

Educational Standards

1. 
   Common Core
   
   1. 
      Craft and Structure
      
      1. 
         RI.9-10.4
         
      2. 
         RI.11-12.4
         
   2. 
      Integration of Knowledge and Ideas
      
      1. 
         RI.9-10.7
         
      2. 
         RI.11-12.7
         
2. 
   Next Generation Science Standards
   
   1. 
      Practices
      
      1. 
         8. Obtaining, Evaluating and Communicating Information
         
   2. 
      Crosscutting Concepts
      
      1. 
         3. Scale, proportion and quantity
         
      2. 
         4. Systems and system models
         
      3. 
         6. Structure and function
         
   3. 
      Disciplinary Core Ideas
      
      1. 
         LS1.A: Structure and Function
         
      2. 
         PS2.B: Types of Interactions
         
3. 
   Advanced Placement Biology - Essential Knowledge (EK), Learning Objectives (LO), Science Practices (SP)
   
   1. 
      EK 4.A.1
      
      1. 
         LO 4.2, SP 1.3
         
      2. 
         LO 4.3, SP 6.1, 6.4
         

Teaching Notes:
About Insulin Biosynthesis:

The insulin protein is composed of 2 protein polymer chains. Although synthesized as a single large protein polymer, the central region of the polymer is cleaved off (see figure below) while the two terminal portions (Chain A, 21 residues long and Chain B, 30 residues long) form the insulin molecule and are held together by disulfide bonds.

Insulin Biosynthesis from http://www.ncbi.nlm.nih.gov/books/NBK30/bin/ch2fb15.jpg

The function of the C-peptide is not known but it is used as a diagnostic to determine if an individual is producing insulin.
Answers to questions asked in the Exercise:
Q1. What is the predominant secondary structural element seen in the insulin structure?

A1: Alpha helix. Both chains A and B have alpha helices while chain B has a single beta strand.

Q2. What do you think the grey spheres shown in the above images are? What is their function?

A2: These are zinc atoms that interact with and stabilize the insulin protein molecules.

Q3. How are these grey atoms interacting with the insulin protein?

A3: His residues from the insulin covalently coordinate the Zinc atoms/ions through the NE2 atoms in the residue.

Q4. Where are these (Cys) residues located? Can you explain the role that these residues play in the stability of the insulin structure?

A4: There are 3 Cys residues on chain A and 2 on chain B. These Cys residues form 3 disulfide bridges – two inter-chain and 1 intra-chain. All these help stabilize the structure of insulin and hold the two protein chains of insulin together.

Q5. How many insulin molecules are shown in the above image? What does this structure tell you about a functional assembly of insulin?

A5: There are 6 insulin molecules – each with two protein chains. This structure shows that insulin can form a large oligomeric assembly such as the hexamer structure seen here – perhaps for storage and transport.

Q6. Based on the structure seen here, what do you think the role of Zinc is?

A6: Zinc facilitates the storage of insulin molecules by forming a stable complex.

Developed as part of the RCSB Collaborative Curriculum Development Program 2015