Reading (to be completed before class!)

Reading on Loops and Turns

  1. Whitford
    • This first reading is very short but provides a nice introduction to the topic.
  2. Chou Analytical Biochemistry 2000
    • Read just through beta-turns
      • Note there is a mistake in the phi and psi angles for residue i+1 in the type II' turn in table I. They should be phi = 60o psi = -120o
      • You do not have to focus on history of development of b-turns
  3. Voet
    • B. Tertiary Structure, a through i, p245-p256
    • Focus of this reading is on Motifs (supersecondary structure)

Problems

Topology and Turns

You can practice looking at turns and loops using the identified structures from this paper
Protein Structure 1973 Lewis
Go to table II. Find some of the identified β-turns and then confirm in DeepView using the PDB structures of those enzymes

In Class Activities

  • In Class QUIZ (on material from week 1 and last Mon)
  • Discussion of Chou and Voet readings
  • Turns and loops as secondary structure analyzed - using molecular modeling software
    • Inspect the structures of the following protein.
      • 1TNF (Note: we actually did 1HEW in class)

Identify two β-turns (according to the nomenclature of Chou), identify the residues in the turn, and discuss an stabilizing interactions in the turn.

This material will be addressed later ...