Loops, Turns, Motifs - Feb 26

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

3) From EXPASY text Chp 1- The image of type I and II turns nicely compliment table I of Chou

  • You do not have to focus on history of development of b-turns

4) From EXPASY text Chp 2 - The image of type I' and type II' turns compliments table I nicely

5) Voet

  • B. Tertiary Structure, a through i, p245-p256
  • Focus of this reading is on Motifs (supersecondary structure) 

6) Loops and Turns Pre-Assignment Worksheet

In Class Activities

  • Discussion of Chou and Voet readings
  • Turns and loops as secondary structure analyzed - using molecular modeling software get worksheet
    • Inspect the structures of 1HEW, 1TNF, or 1RCP
      • Identify two β-turns (according to the nomenclature of Chou), identify the residues in the turn, and discuss an stabilizing interactions in the turn.

Problems
1)
Topology and Turns

2) 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

3) PDBsum. Please try out this tool and compare to the answers you assigned for 4CHA and other proteins. Help with the Codes in PDBsum, ProMotif.

4) Due Friday (see assignment in Worksheet)