Analyzing protein structure and topology

Use VMD to learn more about a protein. The example we use is adenylate kinase (“AdK”).

For background on using VMD, look at [Hsin2008] and the VMD tutorial.

Topology and 2ndary structure

• get adk_open.pdb from http://becksteinlab.physics.asu.edu/pages/courses/2013/SimBioNano/09/
• settings in VMD:
  • Display -> Orthographic
  • Display -> Rendermode: GLSL
  • Graphics -> Color: Display: Background: White
• select protein
• new cartoon representation, color by secondary structure

Exercises

• Identify secondary structure and topology
• Identify domains (tertiary structure)
• Ligands
• Summary